From 9469722d7848c0b57a5d7e022c28d74c4aaf059a Mon Sep 17 00:00:00 2001 From: scorreard <54953390+scorreard@users.noreply.github.com> Date: Wed, 1 Jul 2026 14:08:06 +0000 Subject: [PATCH] microgalaxy community resources update --- .../lab/sections/2_microbial_isolates.yml | 72 +- .../microgalaxy/lab/sections/3_microbiome.yml | 82 +- .../microgalaxy/lab/sections/4_tools.yml | 32 +- .../microgalaxy/lab/sections/5_workflows.yml | 758 +- .../microgalaxy/lab/sections/8_tutorials.yml | 46 +- .../microgalaxy/lab/tools/all/APOSTL.yaml | 518 +- .../microgalaxy/lab/tools/all/CIRM-CFBP.yaml | 518 +- .../microgalaxy/lab/tools/all/ChemFlow.yaml | 518 +- .../lab/tools/all/Coloc-stats.yaml | 518 +- .../microgalaxy/lab/tools/all/GASLINI.yaml | 518 +- .../lab/tools/all/Galaxy@AuBi.yaml | 389 +- .../lab/tools/all/Galaxy@Pasteur.yaml | 518 +- .../lab/tools/all/GalaxyTrakr.yaml | 511 +- .../lab/tools/all/HyPhy_HIV_NGS_Tools.yaml | 518 +- .../lab/tools/all/IPK_Galaxy_Blast_Suite.yaml | 518 +- .../lab/tools/all/ImmPort_Galaxy.yaml | 518 +- .../lab/tools/all/InteractoMIX.yaml | 518 +- .../tools/all/Lebanese_University_Galaxy.yaml | 518 +- .../lab/tools/all/Local_Galaxy.yaml | 518 +- .../lab/tools/all/MISSISSIPPI.yaml | 518 +- .../lab/tools/all/Mandoiu_Lab.yaml | 518 +- .../microgalaxy/lab/tools/all/Oqtans.yaml | 518 +- .../microgalaxy/lab/tools/all/Palfinder.yaml | 518 +- .../lab/tools/all/PhagePromotor.yaml | 530 +- .../lab/tools/all/UseGalaxy_be.yaml | 524 +- .../lab/tools/all/UseGalaxy_cz.yaml | 394 +- .../lab/tools/all/UseGalaxy_eu.yaml | 290 +- .../lab/tools/all/UseGalaxy_fr.yaml | 389 +- .../lab/tools/all/UseGalaxy_no.yaml | 515 +- .../lab/tools/all/UseGalaxy_org_Main.yaml | 392 +- .../lab/tools/all/UseGalaxy_org_au.yaml | 393 +- .../all/Viral_Variant_Visualizer_VVV.yaml | 518 +- .../microgalaxy/lab/tools/top/APOSTL.yaml | 448 +- .../microgalaxy/lab/tools/top/CIRM-CFBP.yaml | 448 +- .../microgalaxy/lab/tools/top/ChemFlow.yaml | 448 +- .../lab/tools/top/Coloc-stats.yaml | 448 +- .../microgalaxy/lab/tools/top/GASLINI.yaml | 448 +- .../lab/tools/top/Galaxy@AuBi.yaml | 319 +- .../lab/tools/top/Galaxy@Pasteur.yaml | 448 +- .../lab/tools/top/GalaxyTrakr.yaml | 445 +- .../lab/tools/top/HyPhy_HIV_NGS_Tools.yaml | 448 +- .../lab/tools/top/IPK_Galaxy_Blast_Suite.yaml | 448 +- .../lab/tools/top/ImmPort_Galaxy.yaml | 448 +- .../lab/tools/top/InteractoMIX.yaml | 448 +- .../tools/top/Lebanese_University_Galaxy.yaml | 448 +- .../lab/tools/top/Local_Galaxy.yaml | 448 +- .../lab/tools/top/MISSISSIPPI.yaml | 448 +- .../lab/tools/top/Mandoiu_Lab.yaml | 448 +- .../microgalaxy/lab/tools/top/Oqtans.yaml | 448 +- .../microgalaxy/lab/tools/top/Palfinder.yaml | 448 +- .../lab/tools/top/PhagePromotor.yaml | 454 +- .../lab/tools/top/UseGalaxy_be.yaml | 451 +- .../lab/tools/top/UseGalaxy_cz.yaml | 319 +- .../lab/tools/top/UseGalaxy_eu.yaml | 290 +- .../lab/tools/top/UseGalaxy_fr.yaml | 319 +- .../lab/tools/top/UseGalaxy_no.yaml | 445 +- .../lab/tools/top/UseGalaxy_org_Main.yaml | 322 +- .../lab/tools/top/UseGalaxy_org_au.yaml | 318 +- .../top/Viral_Variant_Visualizer_VVV.yaml | 448 +- .../microgalaxy/metadata/tool_status.tsv | 58 +- .../microgalaxy/metadata/workflow_status.tsv | 5 +- .../microgalaxy/resources/curated_tools.tsv | 748 +- .../microgalaxy/resources/curated_tools.yml | 3012 +- .../resources/curated_tools_w_biotools.tsv | 5 +- .../resources/curated_tools_wo_biotools.tsv | 7 + .../resources/curated_workflows.json | 2766 +- .../resources/curated_workflows.tsv | 293 +- .../resources/curated_workflows.yml | 2508 +- .../resources/tag_filtered_workflows.json | 4656 +- .../resources/tag_filtered_workflows.tsv | 471 +- communities/microgalaxy/resources/tools.html | 5588 +- .../tools_filtered_by_ts_categories.json | 13010 +- .../microgalaxy/resources/tools_wordcloud.png | Bin 358250 -> 360996 bytes .../microgalaxy/resources/tutorials.html | 748 +- .../microgalaxy/resources/tutorials.tsv | 84 +- .../microgalaxy/resources/tutorials.yml | 103782 +++++++-------- .../microgalaxy/resources/workflows.html | 560 +- 77 files changed, 82498 insertions(+), 81224 deletions(-) diff --git a/communities/microgalaxy/lab/sections/2_microbial_isolates.yml b/communities/microgalaxy/lab/sections/2_microbial_isolates.yml index 925bad6f3..2a7b8ebc4 100644 --- a/communities/microgalaxy/lab/sections/2_microbial_isolates.yml +++ b/communities/microgalaxy/lab/sections/2_microbial_isolates.yml @@ -503,6 +503,16 @@ tabs: title: Tutorials heading_md: Tutorials to train you to perform microbial data analysis content: + - title_md: Genome Assembly of MRSA from Oxford Nanopore MinION data (and + optionally Illumina data) + description_md: Tutorial stored in Assembly topic on the Galaxy Training + Network and covering topics related to Sequence assembly, Whole genome + sequencing, Public health and epidemiology, Genomics, Microbiology, + Antimicrobial resistance + button_link: + https://training.galaxyproject.org//topics/assembly/tutorials/mrsa-nanopore/tutorial.html + button_tip: View tutorial + button_icon: tutorial - title_md: Making sense of a newly assembled genome description_md: Tutorial stored in Assembly topic on the Galaxy Training Network and covering topics related to Sequence assembly, Genomics, @@ -519,15 +529,6 @@ tabs: https://training.galaxyproject.org//topics/assembly/tutorials/unicycler-assembly/tutorial.html button_tip: View tutorial button_icon: tutorial - - title_md: Genome Assembly of a bacterial genome (MRSA) sequenced using - Illumina MiSeq Data - description_md: Tutorial stored in Assembly topic on the Galaxy Training - Network and covering topics related to Sequence assembly, Whole genome - sequencing, Public health and epidemiology, Genomics, Microbiology - button_link: - https://training.galaxyproject.org//topics/assembly/tutorials/mrsa-illumina/tutorial.html - button_tip: View tutorial - button_icon: tutorial - title_md: Assembly of metagenomic sequencing data description_md: Tutorial stored in Assembly topic on the Galaxy Training Network and covering topics related to Metagenomics, Sequence assembly @@ -535,14 +536,13 @@ tabs: https://training.galaxyproject.org//topics/assembly/tutorials/metagenomics-assembly/tutorial.html button_tip: View tutorial button_icon: tutorial - - title_md: Genome Assembly of MRSA from Oxford Nanopore MinION data (and - optionally Illumina data) + - title_md: Genome Assembly of a bacterial genome (MRSA) sequenced using + Illumina MiSeq Data description_md: Tutorial stored in Assembly topic on the Galaxy Training Network and covering topics related to Sequence assembly, Whole genome - sequencing, Public health and epidemiology, Genomics, Microbiology, - Antimicrobial resistance + sequencing, Public health and epidemiology, Genomics, Microbiology button_link: - https://training.galaxyproject.org//topics/assembly/tutorials/mrsa-nanopore/tutorial.html + https://training.galaxyproject.org//topics/assembly/tutorials/mrsa-illumina/tutorial.html button_tip: View tutorial button_icon: tutorial - title_md: Checking expected species and contamination in bacterial isolate @@ -585,21 +585,21 @@ tabs: https://training.galaxyproject.org//topics/genome-annotation/tutorials/annotation-with-prokka/tutorial.html button_tip: View tutorial button_icon: tutorial - - title_md: Refining Genome Annotations with Apollo (prokaryotes) + - title_md: Bacterial Genome Annotation description_md: Tutorial stored in Genome Annotation topic on the Galaxy Training Network and covering topics related to Genomics, Microbiology, - Gene and protein families, Sequence analysis + Gene and protein families, Sequence analysis, Whole genome sequencing, + Functional genomics, Mobile genetic elements button_link: - https://training.galaxyproject.org//topics/genome-annotation/tutorials/apollo/tutorial.html + https://training.galaxyproject.org//topics/genome-annotation/tutorials/bacterial-genome-annotation/tutorial.html button_tip: View tutorial button_icon: tutorial - - title_md: Bacterial Genome Annotation + - title_md: Refining Genome Annotations with Apollo (prokaryotes) description_md: Tutorial stored in Genome Annotation topic on the Galaxy Training Network and covering topics related to Genomics, Microbiology, - Gene and protein families, Sequence analysis, Whole genome sequencing, - Functional genomics, Mobile genetic elements + Gene and protein families, Sequence analysis button_link: - https://training.galaxyproject.org//topics/genome-annotation/tutorials/bacterial-genome-annotation/tutorial.html + https://training.galaxyproject.org//topics/genome-annotation/tutorials/apollo/tutorial.html button_tip: View tutorial button_icon: tutorial - title_md: Identification of AMR genes in an assembled bacterial genome @@ -611,18 +611,18 @@ tabs: https://training.galaxyproject.org//topics/genome-annotation/tutorials/amr-gene-detection/tutorial.html button_tip: View tutorial button_icon: tutorial - - title_md: Bacterial genome quality control + - title_md: Dataset construction for bacterial comparative genomics description_md: Tutorial stored in Genome Annotation topic on the Galaxy Training Network and covering topics related to Genomics, Microbiology button_link: - https://training.galaxyproject.org//topics/genome-annotation/tutorials/bacterial-genome-quality-control/tutorial.html + https://training.galaxyproject.org//topics/genome-annotation/tutorials/bacterial-comparative-genomics-dataset-construction/tutorial.html button_tip: View tutorial button_icon: tutorial - - title_md: Dataset construction for bacterial comparative genomics + - title_md: Bacterial genome quality control description_md: Tutorial stored in Genome Annotation topic on the Galaxy Training Network and covering topics related to Genomics, Microbiology button_link: - https://training.galaxyproject.org//topics/genome-annotation/tutorials/bacterial-comparative-genomics-dataset-construction/tutorial.html + https://training.galaxyproject.org//topics/genome-annotation/tutorials/bacterial-genome-quality-control/tutorial.html button_tip: View tutorial button_icon: tutorial - title_md: Comparative gene analysis in unannotated genomes @@ -659,36 +659,36 @@ tabs: https://training.galaxyproject.org//topics/variant-analysis/tutorials/tb-variant-analysis/tutorial.html button_tip: View tutorial button_icon: tutorial - - title_md: 'metaQuantome 1: Data creation' + - title_md: 'metaQuantome 3: Taxonomy' description_md: Tutorial stored in Proteomics topic on the Galaxy Training Network and covering topics related to Proteomics, Proteogenomics, - Biodiversity, Taxonomy + Metatranscriptomics, Microbial ecology, Metagenomics, Taxonomy button_link: - https://training.galaxyproject.org//topics/proteomics/tutorials/metaquantome-data-creation/tutorial.html + https://training.galaxyproject.org//topics/proteomics/tutorials/metaquantome-taxonomy/tutorial.html button_tip: View tutorial button_icon: tutorial - - title_md: Metaproteomics tutorial + - title_md: 'metaQuantome 1: Data creation' description_md: Tutorial stored in Proteomics topic on the Galaxy Training Network and covering topics related to Proteomics, Proteogenomics, Biodiversity, Taxonomy button_link: - https://training.galaxyproject.org//topics/proteomics/tutorials/metaproteomics/tutorial.html + https://training.galaxyproject.org//topics/proteomics/tutorials/metaquantome-data-creation/tutorial.html button_tip: View tutorial button_icon: tutorial - - title_md: 'metaQuantome 3: Taxonomy' + - title_md: 'metaQuantome 2: Function' description_md: Tutorial stored in Proteomics topic on the Galaxy Training Network and covering topics related to Proteomics, Proteogenomics, - Metatranscriptomics, Microbial ecology, Metagenomics, Taxonomy + Metatranscriptomics, Microbial ecology, Metagenomics button_link: - https://training.galaxyproject.org//topics/proteomics/tutorials/metaquantome-taxonomy/tutorial.html + https://training.galaxyproject.org//topics/proteomics/tutorials/metaquantome-function/tutorial.html button_tip: View tutorial button_icon: tutorial - - title_md: 'metaQuantome 2: Function' + - title_md: Metaproteomics tutorial description_md: Tutorial stored in Proteomics topic on the Galaxy Training Network and covering topics related to Proteomics, Proteogenomics, - Metatranscriptomics, Microbial ecology, Metagenomics + Biodiversity, Taxonomy button_link: - https://training.galaxyproject.org//topics/proteomics/tutorials/metaquantome-function/tutorial.html + https://training.galaxyproject.org//topics/proteomics/tutorials/metaproteomics/tutorial.html button_tip: View tutorial button_icon: tutorial - title_md: Quality and contamination control in bacterial isolate using diff --git a/communities/microgalaxy/lab/sections/3_microbiome.yml b/communities/microgalaxy/lab/sections/3_microbiome.yml index e38ba30a4..4aff2a426 100644 --- a/communities/microgalaxy/lab/sections/3_microbiome.yml +++ b/communities/microgalaxy/lab/sections/3_microbiome.yml @@ -562,12 +562,13 @@ tabs: https://training.galaxyproject.org//topics/microbiome/tutorials/general-tutorial/tutorial.html button_tip: View tutorial button_icon: tutorial - - title_md: Metatranscriptomics analysis using microbiome RNA-seq data (short) + - title_md: Pathogen detection from (direct Nanopore) sequencing data using + Galaxy - Foodborne Edition description_md: Tutorial stored in Microbiome topic on the Galaxy Training - Network and covering topics related to Metatranscriptomics, Microbial - ecology, Taxonomy, Function analysis, Sequence analysis + Network and covering topics related to Metagenomics, Public health and + epidemiology, Taxonomy, Sequence assembly, Pathology, Sequence analysis button_link: - https://training.galaxyproject.org//topics/microbiome/tutorials/metatranscriptomics-short/tutorial.html + https://training.galaxyproject.org//topics/microbiome/tutorials/pathogen-detection-from-nanopore-foodborne-data/tutorial.html button_tip: View tutorial button_icon: tutorial - title_md: Taxonomic Profiling and Visualization of Metagenomic Data @@ -578,6 +579,14 @@ tabs: https://training.galaxyproject.org//topics/microbiome/tutorials/taxonomic-profiling/tutorial.html button_tip: View tutorial button_icon: tutorial + - title_md: Metatranscriptomics analysis using microbiome RNA-seq data + description_md: Tutorial stored in Microbiome topic on the Galaxy Training + Network and covering topics related to Metatranscriptomics, Microbial + ecology, Taxonomy, Function analysis, Sequence analysis + button_link: + https://training.galaxyproject.org//topics/microbiome/tutorials/metatranscriptomics/tutorial.html + button_tip: View tutorial + button_icon: tutorial - title_md: Antibiotic resistance detection description_md: Tutorial stored in Microbiome topic on the Galaxy Training Network and covering topics related to Metagenomic sequencing, Public @@ -595,68 +604,59 @@ tabs: https://training.galaxyproject.org//topics/microbiome/tutorials/nanopore-16S-metagenomics/tutorial.html button_tip: View tutorial button_icon: tutorial - - title_md: Binning of metagenomic sequencing data - description_md: Tutorial stored in Microbiome topic on the Galaxy Training - Network and covering topics related to Metagenomics, Sequence assembly - button_link: - https://training.galaxyproject.org//topics/microbiome/tutorials/metagenomics-binning/tutorial.html - button_tip: View tutorial - button_icon: tutorial - - title_md: Remove contamination and host reads + - title_md: Identification of the micro-organisms in a beer using Nanopore + sequencing description_md: Tutorial stored in Microbiome topic on the Galaxy Training - Network and covering topics related to nan + Network and covering topics related to Metagenomics, Microbial ecology, + Taxonomy, Sequence analysis button_link: - https://training.galaxyproject.org//topics/microbiome/tutorials/host-removal/tutorial.html + https://training.galaxyproject.org//topics/microbiome/tutorials/beer-data-analysis/tutorial.html button_tip: View tutorial button_icon: tutorial - - title_md: Metatranscriptomics analysis using microbiome RNA-seq data + - title_md: Metatranscriptomics analysis using microbiome RNA-seq data (short) description_md: Tutorial stored in Microbiome topic on the Galaxy Training Network and covering topics related to Metatranscriptomics, Microbial ecology, Taxonomy, Function analysis, Sequence analysis button_link: - https://training.galaxyproject.org//topics/microbiome/tutorials/metatranscriptomics/tutorial.html + https://training.galaxyproject.org//topics/microbiome/tutorials/metatranscriptomics-short/tutorial.html button_tip: View tutorial button_icon: tutorial - - title_md: Building an amplicon sequence variant (ASV) table from 16S data - using DADA2 + - title_md: Remove contamination and host reads description_md: Tutorial stored in Microbiome topic on the Galaxy Training - Network and covering topics related to Microbial ecology, Taxonomy, - Sequence analysis, Metabarcoding + Network and covering topics related to nan button_link: - https://training.galaxyproject.org//topics/microbiome/tutorials/dada-16S/tutorial.html + https://training.galaxyproject.org//topics/microbiome/tutorials/host-removal/tutorial.html button_tip: View tutorial button_icon: tutorial - - title_md: Assembly of metagenomic sequencing data + - title_md: Binning of metagenomic sequencing data description_md: Tutorial stored in Microbiome topic on the Galaxy Training Network and covering topics related to Metagenomics, Sequence assembly button_link: - https://training.galaxyproject.org//topics/microbiome/tutorials/metagenomics-assembly/tutorial.html + https://training.galaxyproject.org//topics/microbiome/tutorials/metagenomics-binning/tutorial.html button_tip: View tutorial button_icon: tutorial - - title_md: Identification of the micro-organisms in a beer using Nanopore - sequencing + - title_md: Assembly of metagenomic sequencing data description_md: Tutorial stored in Microbiome topic on the Galaxy Training - Network and covering topics related to Metagenomics, Microbial ecology, - Taxonomy, Sequence analysis + Network and covering topics related to Metagenomics, Sequence assembly button_link: - https://training.galaxyproject.org//topics/microbiome/tutorials/beer-data-analysis/tutorial.html + https://training.galaxyproject.org//topics/microbiome/tutorials/metagenomics-assembly/tutorial.html button_tip: View tutorial button_icon: tutorial - - title_md: Pathogen detection from (direct Nanopore) sequencing data using - Galaxy - Foodborne Edition + - title_md: Building an amplicon sequence variant (ASV) table from 16S data + using DADA2 description_md: Tutorial stored in Microbiome topic on the Galaxy Training - Network and covering topics related to Metagenomics, Public health and - epidemiology, Taxonomy, Sequence assembly, Pathology, Sequence analysis + Network and covering topics related to Microbial ecology, Taxonomy, + Sequence analysis, Metabarcoding button_link: - https://training.galaxyproject.org//topics/microbiome/tutorials/pathogen-detection-from-nanopore-foodborne-data/tutorial.html + https://training.galaxyproject.org//topics/microbiome/tutorials/dada-16S/tutorial.html button_tip: View tutorial button_icon: tutorial - - title_md: Building and Annotating Metagenome-Assembled Genomes (MAGs) from - Short Metagenomics Paired Reads + - title_md: QIIME 2 Moving Pictures description_md: Tutorial stored in Microbiome topic on the Galaxy Training - Network and covering topics related to Metagenomics, Sequence assembly + Network and covering topics related to Microbial ecology, Taxonomy, + Sequence analysis, Metabarcoding button_link: - https://training.galaxyproject.org//topics/microbiome/tutorials/mags-building/tutorial.html + https://training.galaxyproject.org//topics/microbiome/tutorials/qiime2-moving-pictures/tutorial.html button_tip: View tutorial button_icon: tutorial - title_md: QIIME 2 Cancer Microbiome Intervention @@ -667,12 +667,12 @@ tabs: https://training.galaxyproject.org//topics/microbiome/tutorials/qiime2-cancer-microbiome-intervention/tutorial.html button_tip: View tutorial button_icon: tutorial - - title_md: QIIME 2 Moving Pictures + - title_md: Building and Annotating Metagenome-Assembled Genomes (MAGs) from + Short Metagenomics Paired Reads description_md: Tutorial stored in Microbiome topic on the Galaxy Training - Network and covering topics related to Microbial ecology, Taxonomy, - Sequence analysis, Metabarcoding + Network and covering topics related to Metagenomics, Sequence assembly button_link: - https://training.galaxyproject.org//topics/microbiome/tutorials/qiime2-moving-pictures/tutorial.html + https://training.galaxyproject.org//topics/microbiome/tutorials/mags-building/tutorial.html button_tip: View tutorial button_icon: tutorial - title_md: 16S Microbial Analysis with mothur (extended) diff --git a/communities/microgalaxy/lab/sections/4_tools.yml b/communities/microgalaxy/lab/sections/4_tools.yml index 6e3b8d796..8036ee3c4 100644 --- a/communities/microgalaxy/lab/sections/4_tools.yml +++ b/communities/microgalaxy/lab/sections/4_tools.yml @@ -552,10 +552,15 @@ tabs: - title_md: peptideshaker @@ -732,6 +737,13 @@ tabs: + - title_md: prinseq + description_md: |- + PRINSEQ is a tool for easy and rapid quality control and data processing of metagenomic and metatranscriptomic datasets + (Tool usage: 29142) + - title_md: smallgenomeutilities description_md: |- Set of utilities for manipulating small viral genome data. @@ -914,15 +926,6 @@ tabs:
  • kraken-translate
  • kraken
    • - - title_md: qiime2 - description_md: |- - nan - (Tool usage: 131678) - - title_md: metaphlan description_md: |- MetaPhlAn for Metagenomic Phylogenetic Analysis @@ -979,6 +982,17 @@ tabs:
  • megan_read_extractor
  • megan_sam2rma
    • + - title_md: qiime2 + description_md: |- + nan + (Tool usage: 4925) + - title_md: genomad description_md: |- Identify virus and plasmid genomes from nucleotide sequences diff --git a/communities/microgalaxy/lab/sections/5_workflows.yml b/communities/microgalaxy/lab/sections/5_workflows.yml index 31dc00422..c078b18dd 100644 --- a/communities/microgalaxy/lab/sections/5_workflows.yml +++ b/communities/microgalaxy/lab/sections/5_workflows.yml @@ -65,68 +65,67 @@ tabs: button_link: https://training.galaxyproject.org/training-material/faqs/galaxy/workflows_import.html - title_md: metagenomic-raw-reads-amr-analysis/main - description_md: Workflow covering operations related to Data parsing,Gene - functional annotation,Validation,Taxonomic classification,Sequencing - quality control,Antimicrobial resistance prediction + description_md: Workflow covering operations related to Data + parsing,Taxonomic classification,Gene functional annotation,Sequencing + quality control,Antimicrobial resistance prediction,Validation button_link: '{{ galaxy_base_url }}/workflows/trs_import?trs_server=workflowhub.eu&run_form=true&trs_id=2068' button_tip: View workflow button_icon: view - title_md: cgmlst-bacterial-genome/main - description_md: Workflow covering operations related to Multilocus sequence - typing,Data parsing + description_md: Workflow covering operations related to Data + parsing,Multilocus sequence typing button_link: '{{ galaxy_base_url }}/workflows/trs_import?trs_server=workflowhub.eu&run_form=true&trs_id=2055' button_tip: View workflow button_icon: view - title_md: bacterial-quality-and-contamination-control-post-assembly/main - description_md: Workflow covering operations related to - Visualisation,Sequence composition calculation,Sequence assembly - validation,Statistical calculation,Validation,Cross-assembly,Data - parsing,Expression analysis,Taxonomic classification,Sequencing quality - control + description_md: Workflow covering operations related to Statistical + calculation,Taxonomic classification,Expression analysis,Sequence assembly + validation,Data parsing,Sequencing quality control,Validation,Sequence + composition calculation,Visualisation,Cross-assembly button_link: '{{ galaxy_base_url }}/workflows/trs_import?trs_server=workflowhub.eu&run_form=true&trs_id=1882' button_tip: View workflow button_icon: view - title_md: sars-cov-2-pe-illumina-artic-ivar-analysis/SARS-COV-2-ILLUMINA-AMPLICON-IVAR-PANGOLIN-NEXTCLADE - description_md: Workflow covering operations related to Methylation - analysis,Sequence alignment,Genome indexing,SNP detection,Validation,Read - mapping,Variant calling,Primer removal,Sequence contamination - filtering,Generation,Tree-based sequence alignment,Variant - classification,Sequencing quality control + description_md: Workflow covering operations related to Read + mapping,Generation,Variant classification,Variant calling,Tree-based + sequence alignment,Sequence alignment,Genome indexing,Sequencing quality + control,Sequence contamination filtering,Validation,Methylation + analysis,Primer removal,SNP detection button_link: '{{ galaxy_base_url }}/workflows/trs_import?trs_server=workflowhub.eu&run_form=true&trs_id=155' button_tip: View workflow button_icon: view - title_md: sars-cov-2-pe-illumina-wgs-variant-calling/COVID-19-PE-WGS-ILLUMINA - description_md: Workflow covering operations related to Formatting,Sequence - alignment,Genome indexing,SNP detection,Validation,Read mapping,Sequence - contamination filtering,Generation,Sequencing quality control + description_md: Workflow covering operations related to + Formatting,Generation,Sequence alignment,Genome indexing,Sequencing + quality control,Sequence contamination filtering,Validation,Read + mapping,SNP detection button_link: '{{ galaxy_base_url }}/workflows/trs_import?trs_server=workflowhub.eu&run_form=true&trs_id=113' button_tip: View workflow button_icon: view - title_md: generic-non-segmented-viral-variant-calling/main - description_md: Workflow covering operations related to Sequence - alignment,Genome indexing,Validation,Read mapping,Primer removal,Sequence - contamination filtering,Generation,Sequencing quality control + description_md: Workflow covering operations related to Sequencing quality + control,Sequence contamination filtering,Generation,Validation,Read + mapping,Sequence alignment,Primer removal,Genome indexing button_link: '{{ galaxy_base_url }}/workflows/trs_import?trs_server=workflowhub.eu&run_form=true&trs_id=1876' button_tip: View workflow button_icon: view - title_md: influenza-isolates-consensus-and-subtyping/main - description_md: Workflow covering operations related to Multiple sequence - alignment,Sequence alignment,Genome indexing,Sequence file - editing,Phylogenetic analysis,Read mapping,Sequence analysis,Primer - removal,Base position variability plotting,Sequence contamination - filtering,Data retrieval,Sequence alignment analysis,Data - handling,Generation,Sequencing quality control,De-novo assembly + description_md: Workflow covering operations related to Data + retrieval,Generation,Multiple sequence alignment,Data handling,De-novo + assembly,Sequence file editing,Sequence alignment,Base position + variability plotting,Genome indexing,Sequencing quality control,Sequence + contamination filtering,Sequence alignment analysis,Sequence analysis,Read + mapping,Primer removal,Phylogenetic analysis button_link: '{{ galaxy_base_url }}/workflows/trs_import?trs_server=workflowhub.eu&run_form=true&trs_id=1260' button_tip: View workflow button_icon: view - title_md: pox-virus-amplicon/main - description_md: Workflow covering operations related to Sequence - alignment,Genome indexing,Validation,Read mapping,Sequence analysis,Primer - removal,Local alignment,Sequence contamination filtering,Global - alignment,Sequence alignment analysis,Generation,Sequencing quality - control + description_md: Workflow covering operations related to Generation,Sequence + alignment,Genome indexing,Sequencing quality control,Sequence + contamination filtering,Sequence alignment analysis,Validation,Global + alignment,Sequence analysis,Read mapping,Primer removal,Local alignment button_link: '{{ galaxy_base_url }}/workflows/trs_import?trs_server=workflowhub.eu&run_form=true&trs_id=439' button_tip: View workflow button_icon: view @@ -143,30 +142,29 @@ tabs: button_icon: view - title_md: mgnify-amplicon-pipeline-v5-its/main description_md: Workflow covering operations related to k-mer - counting,Visualisation,Formatting,Mapping + counting,Formatting,Visualisation,Mapping button_link: '{{ galaxy_base_url }}/workflows/trs_import?trs_server=workflowhub.eu&run_form=true&trs_id=1273' button_tip: View workflow button_icon: view - title_md: mgnify-amplicon-pipeline-v5-quality-control-paired-end/main - description_md: Workflow covering operations related to Sequence - trimming,Sequence composition calculation,Nucleic acid design,Statistical - calculation,Validation,Read pre-processing,Sequence contamination - filtering,Sequencing quality control + description_md: Workflow covering operations related to Statistical + calculation,Sequencing quality control,Sequence contamination + filtering,Sequence trimming,Validation,Nucleic acid design,Read + pre-processing,Sequence composition calculation button_link: '{{ galaxy_base_url }}/workflows/trs_import?trs_server=workflowhub.eu&run_form=true&trs_id=1272' button_tip: View workflow button_icon: view - title_md: mgnify-amplicon-pipeline-v5-quality-control-single-end/main - description_md: Workflow covering operations related to Sequence - trimming,Read pre-processing,Sequence composition calculation,Sequence - contamination filtering,Statistical calculation,Validation,Sequencing - quality control + description_md: Workflow covering operations related to Sequencing quality + control,Statistical calculation,Sequence contamination filtering,Sequence + trimming,Validation,Read pre-processing,Sequence composition calculation button_link: '{{ galaxy_base_url }}/workflows/trs_import?trs_server=workflowhub.eu&run_form=true&trs_id=1271' button_tip: View workflow button_icon: view - title_md: mgnify-amplicon-pipeline-v5-rrna-prediction/main - description_md: Workflow covering operations related to - Visualisation,Alignment,Formatting,Mapping,k-mer - counting,Comparison,Nucleic acid feature detection + description_md: Workflow covering operations related to k-mer + counting,Formatting,Comparison,Mapping,Alignment,Nucleic acid feature + detection,Visualisation button_link: '{{ galaxy_base_url }}/workflows/trs_import?trs_server=workflowhub.eu&run_form=true&trs_id=1270' button_tip: View workflow button_icon: view @@ -176,16 +174,16 @@ tabs: button_tip: View workflow button_icon: view - title_md: clinicalmp-discovery/main - description_md: Workflow covering operations related to - Visualisation,Filtering,Formatting,Statistical - calculation,Imputation,Standardisation and normalisation,Heat map - generation,Protein quantification,Principal component plotting,Clustering + description_md: Workflow covering operations related to Statistical + calculation,Imputation,Formatting,Heat map + generation,Filtering,Standardisation and normalisation,Protein + quantification,Clustering,Principal component plotting,Visualisation button_link: '{{ galaxy_base_url }}/workflows/trs_import?trs_server=workflowhub.eu&run_form=true&trs_id=1225' button_tip: View workflow button_icon: view - title_md: clinicalmp-data-interpretation/main - description_md: Workflow covering operations related to - Visualisation,Prediction and recognition + description_md: Workflow covering operations related to Prediction and + recognition,Visualisation button_link: '{{ galaxy_base_url }}/workflows/trs_import?trs_server=workflowhub.eu&run_form=true&trs_id=1219' button_tip: View workflow button_icon: view @@ -195,30 +193,30 @@ tabs: button_tip: View workflow button_icon: view - title_md: clinicalmp-database-generation/main - description_md: Workflow covering operations related to Expression - analysis,Protein identification,Tag-based peptide identification,de Novo - sequencing,Target-Decoy + description_md: Workflow covering operations related to de Novo + sequencing,Target-Decoy,Expression analysis,Tag-based peptide + identification,Protein identification button_link: '{{ galaxy_base_url }}/workflows/trs_import?trs_server=workflowhub.eu&run_form=true&trs_id=1216' button_tip: View workflow button_icon: view - title_md: clinicalmp-quantitation/main - description_md: Workflow covering operations related to - Visualisation,Statistical calculation,Imputation,Standardisation and - normalisation,Heat map generation,Protein quantification,Principal - component plotting,Clustering + description_md: Workflow covering operations related to Statistical + calculation,Imputation,Heat map generation,Standardisation and + normalisation,Protein quantification,Clustering,Principal component + plotting,Visualisation button_link: '{{ galaxy_base_url }}/workflows/trs_import?trs_server=workflowhub.eu&run_form=true&trs_id=1177' button_tip: View workflow button_icon: view - title_md: bacterial-genome-assembly/main - description_md: Workflow covering operations related to Data parsing,Genome - assembly,Sequence assembly visualisation + description_md: Workflow covering operations related to Data + parsing,Sequence assembly visualisation,Genome assembly button_link: '{{ galaxy_base_url }}/workflows/trs_import?trs_server=workflowhub.eu&run_form=true&trs_id=1043' button_tip: View workflow button_icon: view - title_md: quality-and-contamination-control/main - description_md: Workflow covering operations related to Cross-assembly,Data - parsing,Sequence contamination filtering,Expression analysis,Statistical - calculation,Taxonomic classification,Sequencing quality control + description_md: Workflow covering operations related to Sequencing quality + control,Sequence contamination filtering,Data parsing,Taxonomic + classification,Expression analysis,Statistical calculation,Cross-assembly button_link: '{{ galaxy_base_url }}/workflows/trs_import?trs_server=workflowhub.eu&run_form=true&trs_id=1052' button_tip: View workflow button_icon: view @@ -229,34 +227,32 @@ tabs: button_tip: View workflow button_icon: view - title_md: gene-based-pathogen-identification/main - description_md: Workflow covering operations related to Antimicrobial - resistance prediction,Base-calling,Variant calling,Cross-assembly,Mapping - assembly,Sequence assembly,Genome assembly,Sequence assembly - visualisation,De-novo assembly + description_md: Workflow covering operations related to + Base-calling,Antimicrobial resistance prediction,De-novo assembly,Variant + calling,Sequence assembly visualisation,Sequence + assembly,Cross-assembly,Mapping assembly,Genome assembly button_link: '{{ galaxy_base_url }}/workflows/trs_import?trs_server=workflowhub.eu&run_form=true&trs_id=1062' button_tip: View workflow button_icon: view - title_md: pathogen-detection-pathogfair-samples-aggregation-and-visualisation/main description_md: Workflow covering operations related to Phylogenetic tree - generation (from molecular sequences),Visualisation,Phylogenetic tree - generation (maximum likelihood and Bayesian methods),Multiple sequence - alignment,Mapping,Phylogenetic tree reconstruction,Phylogenetic tree - analysis,Phylogenetic tree generation + generation,Visualisation,Multiple sequence alignment,Phylogenetic tree + reconstruction,Phylogenetic tree analysis,Mapping button_link: '{{ galaxy_base_url }}/workflows/trs_import?trs_server=workflowhub.eu&run_form=true&trs_id=1060' button_tip: View workflow button_icon: view - title_md: taxonomy-profiling-and-visualization-with-krona/main - description_md: Workflow covering operations related to - Visualisation,Taxonomic classification,Aggregation + description_md: Workflow covering operations related to Taxonomic + classification,Aggregation,Visualisation button_link: '{{ galaxy_base_url }}/workflows/trs_import?trs_server=workflowhub.eu&run_form=true&trs_id=1059' button_tip: View workflow button_icon: view - title_md: bacterial_genome_annotation/main - description_md: Workflow covering operations related to - Scaffolding,Multilocus sequence typing,Structural variation - detection,Sequence motif recognition,Genome annotation,Data parsing,Genome - assembly,Protein feature detection,Nucleic acid feature detection + description_md: Workflow covering operations related to Scaffolding,Genome + annotation,Nucleic acid feature detection,Data parsing,Protein feature + detection,Structural variation detection,Sequence motif + recognition,Multilocus sequence typing,Genome assembly button_link: '{{ galaxy_base_url }}/workflows/trs_import?trs_server=workflowhub.eu&run_form=true&trs_id=1050' button_tip: View workflow button_icon: view @@ -286,33 +282,47 @@ tabs: button_icon: tutorial button_link: https://training.galaxyproject.org/training-material/faqs/galaxy/workflows_import.html + - title_md: MPXV (Mpox) Phylogenetic Analysis with Squirrel + description_md: Workflow covering operations related to Sequencing quality + control,Phylogenetic analysison topics related to + Bioinformatics,Biomedical science,Genomics,Virology + button_link: '{{ galaxy_base_url }}/workflows/trs_import?trs_server=workflowhub.eu&run_form=true&trs_id=2196' + button_tip: View workflow + button_icon: view + - title_md: Viral Amplicon Analysis Pipeline for ONT Data + description_md: Workflow covering operations related to Sequencing quality + control,Sequence alignment,Validation,Mappingon topics related to + Bioinformatics,Biomedical science,Genomics,Virology + button_link: '{{ galaxy_base_url }}/workflows/trs_import?trs_server=workflowhub.eu&run_form=true&trs_id=2195' + button_tip: View workflow + button_icon: view - title_md: Taxonomy Assignment with QIIME2 - description_md: Workflow covering operations related to - Visualisation,Formatting,Demultiplexing,Taxonomic classificationon topics - related to Taxonomy + description_md: Workflow covering operations related to Taxonomic + classification,Formatting,Demultiplexing,Visualisationon topics related to + Taxonomy button_link: '{{ galaxy_base_url }}/workflows/trs_import?trs_server=workflowhub.eu&run_form=true&trs_id=2098' button_tip: View workflow button_icon: view - title_md: Taxonomy classification using Kraken2 and Bracken - description_md: Workflow covering operations related to - Visualisation,Statistical calculation,Taxonomic - classification,Aggregationon topics related to Metagenomics,Taxonomy + description_md: Workflow covering operations related to Statistical + calculation,Taxonomic classification,Aggregation,Visualisationon topics + related to Metagenomics,Taxonomy button_link: '{{ galaxy_base_url }}/workflows/trs_import?trs_server=workflowhub.eu&run_form=true&trs_id=1199' button_tip: View workflow button_icon: view - title_md: AMR-Pathfinder - description_md: Workflow covering operations related to Parsing,Data - handling,Genome assembly,Antimicrobial resistance prediction + description_md: Workflow covering operations related to Antimicrobial + resistance prediction,Data handling,Parsing,Genome assembly button_link: '{{ galaxy_base_url }}/workflows/trs_import?trs_server=workflowhub.eu&run_form=true&trs_id=1189' button_tip: View workflow button_icon: view - title_md: 'Workflow 3: AMR - SeqSero2/SISTR' - description_md: Workflow covering operations related to - Visualisation,Multilocus sequence typing,Sequence alignment,Genome - indexing,Read mapping,Sequence contamination filtering,Clustering,Genome - alignment,Parsing,Data handling,Genome assembly,RNA-Seq analysis,Sequence - trimming,Antimicrobial resistance prediction,Read binning,Sequence - analysis + description_md: Workflow covering operations related to Genome + alignment,Read binning,Sequence contamination + filtering,Clustering,Antimicrobial resistance prediction,Data + handling,Sequence alignment,Parsing,Genome indexing,RNA-Seq + analysis,Sequence trimming,Sequence analysis,Read mapping,Multilocus + sequence typing,Visualisation,Genome assembly button_link: '{{ galaxy_base_url }}/workflows/trs_import?trs_server=workflowhub.eu&run_form=true&trs_id=407' button_tip: View workflow button_icon: view @@ -322,8 +332,8 @@ tabs: button_tip: View workflow button_icon: view - title_md: 'Workflow 4: Staramr' - description_md: Workflow covering operations related to Parsing,Data - handling,Genome assembly,Antimicrobial resistance prediction + description_md: Workflow covering operations related to Antimicrobial + resistance prediction,Data handling,Parsing,Genome assembly button_link: '{{ galaxy_base_url }}/workflows/trs_import?trs_server=workflowhub.eu&run_form=true&trs_id=470' button_tip: View workflow button_icon: view @@ -334,12 +344,12 @@ tabs: button_tip: View workflow button_icon: view - title_md: TB Variant Analysis v1.0 - description_md: Workflow covering operations related to Phylogenetic tree - visualisation,Sequence alignment,Validation,Antimicrobial resistance - prediction,Phylogenetic tree generation,Variant calling,Sequence - analysis,Local alignment,Sequence contamination filtering,Global - alignment,Sequence alignment analysis,Taxonomic classification,Sequencing - quality controlon topics related to Genetic variation,Infectious + description_md: Workflow covering operations related to Taxonomic + classification,Antimicrobial resistance prediction,Variant + calling,Sequence alignment,Phylogenetic tree visualisation,Sequencing + quality control,Sequence contamination filtering,Sequence alignment + analysis,Phylogenetic tree generation,Validation,Global alignment,Sequence + analysis,Local alignmenton topics related to Genetic variation,Infectious disease,Microbiology,Public health and epidemiology,Sequence assembly button_link: '{{ galaxy_base_url }}/workflows/trs_import?trs_server=workflowhub.eu&run_form=true&trs_id=1035' button_tip: View workflow @@ -350,86 +360,80 @@ tabs: button_tip: View workflow button_icon: view - title_md: Analyses of shotgun metagenomics data with MetaPhlAn2 - description_md: Workflow covering operations related to - Visualisation,Taxonomic classificationon topics related to Metagenomic + description_md: Workflow covering operations related to Taxonomic + classification,Visualisationon topics related to Metagenomic sequencing,Metagenomics button_link: '{{ galaxy_base_url }}/workflows/trs_import?trs_server=workflowhub.eu&run_form=true&trs_id=624' button_tip: View workflow button_icon: view - title_md: 'Workflow 7 : Beta Diversity [16S Microbial Analysis With Mothur]' - description_md: Workflow covering operations related to - Visualisation,Phylogenetic tree reconstruction,Sequence - clustering,Phylogenetic tree generation,DNA barcoding,Phylogenetic tree - analysis,Taxonomic classification,Sequence read processing,Sequencing - quality control,Phylogenetic analysis + description_md: Workflow covering operations related to Taxonomic + classification,DNA barcoding,Sequence read processing,Sequencing quality + control,Phylogenetic tree generation,Phylogenetic tree + reconstruction,Sequence clustering,Phylogenetic tree analysis,Phylogenetic + analysis,Visualisation button_link: '{{ galaxy_base_url }}/workflows/trs_import?trs_server=workflowhub.eu&run_form=true&trs_id=653' button_tip: View workflow button_icon: view - title_md: 'Workflow 6: Alpha Diversity [16S Microbial Analysis With Mothur]' - description_md: Workflow covering operations related to - Visualisation,Sequence clustering,DNA barcoding,Taxonomic - classification,Sequence read processing,Sequencing quality - control,Phylogenetic analysis + description_md: Workflow covering operations related to Taxonomic + classification,DNA barcoding,Sequence read processing,Sequencing quality + control,Sequence clustering,Phylogenetic analysis,Visualisation button_link: '{{ galaxy_base_url }}/workflows/trs_import?trs_server=workflowhub.eu&run_form=true&trs_id=652' button_tip: View workflow button_icon: view - title_md: 'Workflow 5: OTU Clustering [16S Microbial Analysis With Mothur]' - description_md: Workflow covering operations related to - Visualisation,Sequence clustering,DNA barcoding,Taxonomic - classification,Sequence read processing,Sequencing quality - control,Phylogenetic analysis + description_md: Workflow covering operations related to Taxonomic + classification,DNA barcoding,Sequence read processing,Sequencing quality + control,Sequence clustering,Phylogenetic analysis,Visualisation button_link: '{{ galaxy_base_url }}/workflows/trs_import?trs_server=workflowhub.eu&run_form=true&trs_id=651' button_tip: View workflow button_icon: view - title_md: 'Workflow 3: Classification [Galaxy Training: 16S Microbial Analysis With Mothur]' - description_md: Workflow covering operations related to - Visualisation,Sequence clustering,DNA barcoding,Taxonomic - classification,Sequence read processing,Sequencing quality - control,Phylogenetic analysis + description_md: Workflow covering operations related to Taxonomic + classification,DNA barcoding,Sequence read processing,Sequencing quality + control,Sequence clustering,Phylogenetic analysis,Visualisation button_link: '{{ galaxy_base_url }}/workflows/trs_import?trs_server=workflowhub.eu&run_form=true&trs_id=650' button_tip: View workflow button_icon: view - title_md: 'Workflow 1: Further Quality Control [16S Microbial Analysis With Mothur]' - description_md: Workflow covering operations related to - Visualisation,Sequence clustering,DNA barcoding,Taxonomic - classification,Sequence read processing,Sequencing quality - control,Phylogenetic analysis + description_md: Workflow covering operations related to Taxonomic + classification,DNA barcoding,Sequence read processing,Sequencing quality + control,Sequence clustering,Phylogenetic analysis,Visualisation button_link: '{{ galaxy_base_url }}/workflows/trs_import?trs_server=workflowhub.eu&run_form=true&trs_id=648' button_tip: View workflow button_icon: view - title_md: 'Workflow 2: Data Cleaning And Chimera Removal [16S Microbial Analysis With Mothur]' - description_md: Workflow covering operations related to - Visualisation,Sequence clustering,DNA barcoding,Taxonomic - classification,Sequence read processing,Sequencing quality - control,Phylogenetic analysis + description_md: Workflow covering operations related to Taxonomic + classification,DNA barcoding,Sequence read processing,Sequencing quality + control,Sequence clustering,Phylogenetic analysis,Visualisation button_link: '{{ galaxy_base_url }}/workflows/trs_import?trs_server=workflowhub.eu&run_form=true&trs_id=649' button_tip: View workflow button_icon: view - title_md: '3: Plant virus exploration' - description_md: Workflow covering operations related to Genome - assembly,Sequence contamination filtering,Sequencing quality control + description_md: Workflow covering operations related to Sequencing quality + control,Sequence contamination filtering,Genome assembly button_link: '{{ galaxy_base_url }}/workflows/trs_import?trs_server=workflowhub.eu&run_form=true&trs_id=103' button_tip: View workflow button_icon: view - title_md: '2: Plant virus confirmation' - description_md: Workflow covering operations related to Read - pre-processing,Sequence contamination filtering,Formatting,Pairwise - sequence alignment,Genome assembly,Sequencing quality control,Variant - calling + description_md: Workflow covering operations related to Sequencing quality + control,Formatting,Sequence contamination filtering,Pairwise sequence + alignment,Variant calling,Read pre-processing,Genome assembly button_link: '{{ galaxy_base_url }}/workflows/trs_import?trs_server=workflowhub.eu&run_form=true&trs_id=102' button_tip: View workflow button_icon: view - title_md: '1: Plant virus detection with kraken2 (SE)' - description_md: Workflow covering operations related to - Visualisation,Taxonomic classification + description_md: Workflow covering operations related to Taxonomic + classification,Visualisation button_link: '{{ galaxy_base_url }}/workflows/trs_import?trs_server=workflowhub.eu&run_form=true&trs_id=124' button_tip: View workflow button_icon: view - title_md: '1: Plant virus detection with kraken2 (PE)' - description_md: Workflow covering operations related to - Visualisation,Taxonomic classification + description_md: Workflow covering operations related to Taxonomic + classification,Visualisation button_link: '{{ galaxy_base_url }}/workflows/trs_import?trs_server=workflowhub.eu&run_form=true&trs_id=101' button_tip: View workflow button_icon: view @@ -448,61 +452,60 @@ tabs: button_link: https://training.galaxyproject.org/training-material/faqs/galaxy/workflows_import.html - title_md: TB Variant Analysis v1.0 - description_md: Workflow covering operations related to Phylogenetic tree - visualisation,Sequence alignment,Validation,Antimicrobial resistance - prediction,Phylogenetic tree generation,Variant calling,Sequence - analysis,Local alignment,Sequence contamination filtering,Global - alignment,Sequence alignment analysis,Taxonomic classification,Sequencing - quality control + description_md: Workflow covering operations related to Taxonomic + classification,Antimicrobial resistance prediction,Variant + calling,Sequence alignment,Phylogenetic tree visualisation,Sequencing + quality control,Sequence contamination filtering,Sequence alignment + analysis,Phylogenetic tree generation,Validation,Global alignment,Sequence + analysis,Local alignment button_link: '{{ galaxy_base_url }}/workflows/trs_import?trs_server=workflowhub.eu&run_form=true&trs_id=1647' button_tip: View workflow button_icon: view - title_md: Quality and contamination control in bacterial isolate using Illumina MiSeq Data - description_md: Workflow covering operations related to - Visualisation,Statistical calculation,Read mapping,Cross-assembly,Sequence - contamination filtering,Expression analysis,Taxonomic - classification,Sequencing quality control + description_md: Workflow covering operations related to Statistical + calculation,Taxonomic classification,Expression analysis,Sequencing + quality control,Sequence contamination filtering,Read + mapping,Visualisation,Cross-assembly button_link: '{{ galaxy_base_url }}/workflows/trs_import?trs_server=workflowhub.eu&run_form=true&trs_id=2043' button_tip: View workflow button_icon: view - title_md: Taxonomic Profiling and Visualization of Metagenomic Data - description_md: Workflow covering operations related to - Visualisation,Statistical calculation,Taxonomic classification,Genome - annotation,Aggregation + description_md: Workflow covering operations related to Statistical + calculation,Taxonomic classification,Aggregation,Genome + annotation,Visualisation button_link: '{{ galaxy_base_url }}/workflows/trs_import?trs_server=workflowhub.eu&run_form=true&trs_id=1470' button_tip: View workflow button_icon: view - title_md: Checking expected species and contamination in bacterial isolate - description_md: Workflow covering operations related to - Cross-assembly,Statistical calculation,Taxonomic classification,Expression - analysis + description_md: Workflow covering operations related to Statistical + calculation,Taxonomic classification,Expression analysis,Cross-assembly button_link: '{{ galaxy_base_url }}/workflows/trs_import?trs_server=workflowhub.eu&run_form=true&trs_id=1674' button_tip: View workflow button_icon: view - title_md: Metagenomic Binning description_md: Workflow covering operations related to Sequence - assembly,Read mapping,Genome annotation,Sequence clustering,Read binning + assembly,Read mapping,Sequence clustering,Genome annotation,Read binning button_link: '{{ galaxy_base_url }}/workflows/trs_import?trs_server=workflowhub.eu&run_form=true&trs_id=2028' button_tip: View workflow button_icon: view - title_md: MGnify's amplicon pipeline v5.0 - ITS description_md: Workflow covering operations related to k-mer - counting,Visualisation,Formatting,Mapping + counting,Formatting,Visualisation,Mapping button_link: '{{ galaxy_base_url }}/workflows/trs_import?trs_server=workflowhub.eu&run_form=true&trs_id=1856' button_tip: View workflow button_icon: view - title_md: MAPseq to ampvis2 description_md: Workflow covering operations related to - Visualisation,Analysis + Analysis,Visualisation button_link: '{{ galaxy_base_url }}/workflows/trs_import?trs_server=workflowhub.eu&run_form=true&trs_id=1855' button_tip: View workflow button_icon: view - title_md: MGnify's amplicon pipeline v5.0 - Quality control PE - description_md: Workflow covering operations related to Sequence - trimming,Sequence composition calculation,Nucleic acid design,Statistical - calculation,Validation,Read pre-processing,Sequence contamination - filtering,Sequencing quality control + description_md: Workflow covering operations related to Statistical + calculation,Sequencing quality control,Sequence contamination + filtering,Sequence trimming,Validation,Nucleic acid design,Read + pre-processing,Sequence composition calculation button_link: '{{ galaxy_base_url }}/workflows/trs_import?trs_server=workflowhub.eu&run_form=true&trs_id=1854' button_tip: View workflow button_icon: view @@ -517,119 +520,117 @@ tabs: button_tip: View workflow button_icon: view - title_md: MGnify's amplicon pipeline v5.0 - Quality control SE - description_md: Workflow covering operations related to Sequence - trimming,Read pre-processing,Sequence composition calculation,Sequence - contamination filtering,Statistical calculation,Validation,Sequencing - quality control + description_md: Workflow covering operations related to Sequencing quality + control,Statistical calculation,Sequence contamination filtering,Sequence + trimming,Validation,Read pre-processing,Sequence composition calculation button_link: '{{ galaxy_base_url }}/workflows/trs_import?trs_server=workflowhub.eu&run_form=true&trs_id=1850' button_tip: View workflow button_icon: view - title_md: MGnify's amplicon pipeline v5.0 - rRNA prediction - description_md: Workflow covering operations related to - Visualisation,Alignment,Formatting,Mapping,k-mer - counting,Comparison,Nucleic acid feature detection + description_md: Workflow covering operations related to k-mer + counting,Formatting,Comparison,Mapping,Alignment,Nucleic acid feature + detection,Visualisation button_link: '{{ galaxy_base_url }}/workflows/trs_import?trs_server=workflowhub.eu&run_form=true&trs_id=1842' button_tip: View workflow button_icon: view - title_md: 'Workflow 3: Functional Information (quick)' - description_md: Workflow covering operations related to Species frequency - estimation,Taxonomic classification,Phylogenetic analysis + description_md: Workflow covering operations related to Taxonomic + classification,Species frequency estimation,Phylogenetic analysis button_link: '{{ galaxy_base_url }}/workflows/trs_import?trs_server=workflowhub.eu&run_form=true&trs_id=1447' button_tip: View workflow button_icon: view - title_md: Building an amplicon sequence variant (ASV) table from 16S data using DADA2 - description_md: Workflow covering operations related to Visualisation,DNA - barcoding,Deposition,Analysis,Variant calling + description_md: Workflow covering operations related to DNA + barcoding,Analysis,Variant calling,Deposition,Visualisation button_link: '{{ galaxy_base_url }}/workflows/trs_import?trs_server=workflowhub.eu&run_form=true&trs_id=1395' button_tip: View workflow button_icon: view - title_md: Metatranscriptomics analysis using microbiome RNA-seq data - description_md: Workflow covering operations related to Sequence - comparison,Phylogenetic tree visualisation,Visualisation,Sequence - composition calculation,Statistical calculation,Phylogenetic - inference,Validation,Primer removal,Sequence alignment analysis,Sequencing - quality control,Phylogenetic analysis,Sequence trimming,Phylogenetic tree - editing,Read pre-processing,Species frequency estimation,Taxonomic - classification,Sequence similarity search,Conversion,Aggregation + description_md: Workflow covering operations related to Statistical + calculation,Phylogenetic inference,Conversion,Sequencing quality + control,Sequence alignment analysis,Sequence comparison,Sequence + composition calculation,Phylogenetic analysis,Taxonomic + classification,Aggregation,Species frequency estimation,Phylogenetic tree + visualisation,Sequence similarity search,Phylogenetic tree + editing,Sequence trimming,Validation,Read pre-processing,Primer + removal,Visualisation button_link: '{{ galaxy_base_url }}/workflows/trs_import?trs_server=workflowhub.eu&run_form=true&trs_id=1466' button_tip: View workflow button_icon: view - title_md: 'Metatranscriptomics analysis using microbiome RNA-seq data - Workflow 2: Community profile' - description_md: Workflow covering operations related to Phylogenetic tree - visualisation,Visualisation,Phylogenetic inference,Phylogenetic tree - editing,Taxonomic classification,Conversion + description_md: Workflow covering operations related to Taxonomic + classification,Phylogenetic inference,Conversion,Phylogenetic tree + visualisation,Phylogenetic tree editing,Visualisation button_link: '{{ galaxy_base_url }}/workflows/trs_import?trs_server=workflowhub.eu&run_form=true&trs_id=1451' button_tip: View workflow button_icon: view - title_md: 'Metatranscriptomics analysis using microbiome RNA-seq data - Workflow 1: Preprocessing' - description_md: Workflow covering operations related to Sequence - trimming,Sequence composition calculation,Statistical - calculation,Validation,Primer removal,Read pre-processing,Sequence - similarity search,Sequence alignment analysis,Sequence - comparison,Sequencing quality control + description_md: Workflow covering operations related to Statistical + calculation,Sequence similarity search,Primer removal,Sequencing quality + control,Sequence trimming,Sequence alignment analysis,Sequence + comparison,Validation,Read pre-processing,Sequence composition calculation button_link: '{{ galaxy_base_url }}/workflows/trs_import?trs_server=workflowhub.eu&run_form=true&trs_id=1444' button_tip: View workflow button_icon: view - title_md: 'Metatranscriptomics analysis using microbiome RNA-seq data - Workflow 3: Functional Information' - description_md: Workflow covering operations related to Species frequency - estimation,Taxonomic classification,Phylogenetic analysis + description_md: Workflow covering operations related to Taxonomic + classification,Species frequency estimation,Phylogenetic analysis button_link: '{{ galaxy_base_url }}/workflows/trs_import?trs_server=workflowhub.eu&run_form=true&trs_id=1456' button_tip: View workflow button_icon: view - title_md: Assembly of metagenomic sequencing data - description_md: Workflow covering operations related to Visualisation,Local - alignment,Sequence assembly validation,Read mapping,Genome - assembly,Sequence assembly visualisation + description_md: Workflow covering operations related to Visualisation,Read + mapping,Sequence assembly validation,Sequence assembly visualisation,Local + alignment,Genome assembly button_link: '{{ galaxy_base_url }}/workflows/trs_import?trs_server=workflowhub.eu&run_form=true&trs_id=1390' button_tip: View workflow button_icon: view - title_md: Taxonomic Analysis of eDNA - description_md: Workflow covering operations related to Sequence - contamination filtering,Sequencing quality control + description_md: Workflow covering operations related to Sequencing quality + control,Sequence contamination filtering button_link: '{{ galaxy_base_url }}/workflows/trs_import?trs_server=workflowhub.eu&run_form=true&trs_id=1723' button_tip: View workflow button_icon: view - title_md: Quality and contamination control in bacterial isolate using Illumina MiSeq Data - description_md: Workflow covering operations related to - Visualisation,Statistical calculation,Read mapping,Cross-assembly,Sequence - contamination filtering,Expression analysis,Taxonomic - classification,Sequencing quality control + description_md: Workflow covering operations related to Statistical + calculation,Taxonomic classification,Expression analysis,Sequencing + quality control,Sequence contamination filtering,Read + mapping,Visualisation,Cross-assembly button_link: '{{ galaxy_base_url }}/workflows/trs_import?trs_server=workflowhub.eu&run_form=true&trs_id=1644' button_tip: View workflow button_icon: view - title_md: pox-virus-tiled-amplicon-ref-masking - description_md: Workflow covering operations related to Local - alignment,Sequence alignment,Global alignment,Sequence alignment - analysis,Sequence analysis + description_md: Workflow covering operations related to Sequence alignment + analysis,Global alignment,Sequence analysis,Sequence alignment,Local + alignment button_link: '{{ galaxy_base_url }}/workflows/trs_import?trs_server=workflowhub.eu&run_form=true&trs_id=1632' button_tip: View workflow button_icon: view - title_md: Copy Of GTN Training - Antibiotic Resistance Detection - description_md: Workflow covering operations related to Aggregation,Mapping - assembly,Antimicrobial resistance prediction,Sequence analysis,Box-Whisker - plot plotting,Pairwise sequence alignment,Genome assembly,Sequence - assembly visualisation,Scatter plot plotting,De-novo assembly + description_md: Workflow covering operations related to Pairwise sequence + alignment,Aggregation,Antimicrobial resistance prediction,Box-Whisker plot + plotting,De-novo assembly,Scatter plot plotting,Sequence assembly + visualisation,Sequence analysis,Mapping assembly,Genome assembly button_link: '{{ galaxy_base_url }}/workflows/trs_import?trs_server=workflowhub.eu&run_form=true&trs_id=1477' button_tip: View workflow button_icon: view - title_md: Amplicon Tutorial - description_md: Workflow covering operations related to - Visualisation,Sequence clustering,DNA barcoding,Taxonomic - classification,Sequence read processing,Sequencing quality - control,Phylogenetic analysis + description_md: Workflow covering operations related to Taxonomic + classification,DNA barcoding,Sequence read processing,Sequencing quality + control,Sequence clustering,Phylogenetic analysis,Visualisation button_link: '{{ galaxy_base_url }}/workflows/trs_import?trs_server=workflowhub.eu&run_form=true&trs_id=1476' button_tip: View workflow button_icon: view - title_md: 'Training: 16S rRNA Analysis with Nanopore Sequencing Reads' - description_md: Workflow covering operations related to - Visualisation,Sequence composition calculation,Sequence contamination - filtering,Statistical calculation,Validation,Taxonomic - classification,Sequencing quality control + description_md: Workflow covering operations related to Sequencing quality + control,Sequence contamination filtering,Taxonomic + classification,Statistical calculation,Validation,Sequence composition + calculation,Visualisation button_link: '{{ galaxy_base_url }}/workflows/trs_import?trs_server=workflowhub.eu&run_form=true&trs_id=1473' button_tip: View workflow button_icon: view @@ -640,111 +641,105 @@ tabs: button_icon: view - title_md: Query a metaplasmidome database to identify and annotate plasmids in metagenomes - description_md: Workflow covering operations related to - Visualisation,Pairwise sequence alignment + description_md: Workflow covering operations related to Pairwise sequence + alignment,Visualisation button_link: '{{ galaxy_base_url }}/workflows/trs_import?trs_server=workflowhub.eu&run_form=true&trs_id=1469' button_tip: View workflow button_icon: view - title_md: 'Training: 16S rRNA Sequencing With Mothur: Main Tutorial' - description_md: Workflow covering operations related to - Visualisation,Phylogenetic tree reconstruction,Sequence - clustering,Phylogenetic tree generation,DNA barcoding,Phylogenetic tree - analysis,Taxonomic classification,Sequence read processing,Sequencing - quality control,Phylogenetic analysis + description_md: Workflow covering operations related to Taxonomic + classification,DNA barcoding,Sequence read processing,Sequencing quality + control,Phylogenetic tree generation,Phylogenetic tree + reconstruction,Sequence clustering,Phylogenetic tree analysis,Phylogenetic + analysis,Visualisation button_link: '{{ galaxy_base_url }}/workflows/trs_import?trs_server=workflowhub.eu&run_form=true&trs_id=1465' button_tip: View workflow button_icon: view - title_md: Workflow for Identifying MF from ITS2 sequencing using LotuS2 - tutorial example run' - description_md: Workflow covering operations related to Sequence feature - detection,DNA barcoding + description_md: Workflow covering operations related to DNA + barcoding,Sequence feature detection button_link: '{{ galaxy_base_url }}/workflows/trs_import?trs_server=workflowhub.eu&run_form=true&trs_id=1460' button_tip: View workflow button_icon: view - title_md: Identification of the micro-organisms in a beer using Nanopore sequencing - description_md: Workflow covering operations related to - Visualisation,Sequence composition calculation,Sequence contamination - filtering,Statistical calculation,Taxonomic - classification,Aggregation,Sequencing quality control + description_md: Workflow covering operations related to Sequencing quality + control,Sequence contamination filtering,Taxonomic + classification,Statistical calculation,Aggregation,Sequence composition + calculation,Visualisation button_link: '{{ galaxy_base_url }}/workflows/trs_import?trs_server=workflowhub.eu&run_form=true&trs_id=1439' button_tip: View workflow button_icon: view - title_md: Calculating diversity from microbiome taxonomic data description_md: Workflow covering operations related to - Visualisation,Aggregation + Aggregation,Visualisation button_link: '{{ galaxy_base_url }}/workflows/trs_import?trs_server=workflowhub.eu&run_form=true&trs_id=1431' button_tip: View workflow button_icon: view - title_md: 'Workflow 3: Classification [Galaxy Training: 16S Microbial Analysis With Mothur]' - description_md: Workflow covering operations related to - Visualisation,Sequence clustering,DNA barcoding,Taxonomic - classification,Sequence read processing,Sequencing quality - control,Phylogenetic analysis + description_md: Workflow covering operations related to Taxonomic + classification,DNA barcoding,Sequence read processing,Sequencing quality + control,Sequence clustering,Phylogenetic analysis,Visualisation button_link: '{{ galaxy_base_url }}/workflows/trs_import?trs_server=workflowhub.eu&run_form=true&trs_id=1428' button_tip: View workflow button_icon: view - title_md: 'Workflow 1: Quality Control [Galaxy Training: 16S Microbial Analysis With Mothur]' - description_md: Workflow covering operations related to - Visualisation,Sequence clustering,DNA barcoding,Taxonomic - classification,Sequence read processing,Sequencing quality - control,Phylogenetic analysis + description_md: Workflow covering operations related to Taxonomic + classification,DNA barcoding,Sequence read processing,Sequencing quality + control,Sequence clustering,Phylogenetic analysis,Visualisation button_link: '{{ galaxy_base_url }}/workflows/trs_import?trs_server=workflowhub.eu&run_form=true&trs_id=1422' button_tip: View workflow button_icon: view - title_md: 'Workflow7: Beta Diversity [Galaxy Training: 16S Microbial Analysis With Mothur]' - description_md: Workflow covering operations related to - Visualisation,Phylogenetic tree reconstruction,Sequence - clustering,Phylogenetic tree generation,DNA barcoding,Phylogenetic tree - analysis,Taxonomic classification,Sequence read processing,Sequencing - quality control,Phylogenetic analysis + description_md: Workflow covering operations related to Taxonomic + classification,DNA barcoding,Sequence read processing,Sequencing quality + control,Phylogenetic tree generation,Phylogenetic tree + reconstruction,Sequence clustering,Phylogenetic tree analysis,Phylogenetic + analysis,Visualisation button_link: '{{ galaxy_base_url }}/workflows/trs_import?trs_server=workflowhub.eu&run_form=true&trs_id=1418' button_tip: View workflow button_icon: view - title_md: 'Workflow 6: Alpha Diversity [Galaxy Training: 16S Microbial Analysis With Mothur]' - description_md: Workflow covering operations related to - Visualisation,Sequence clustering,DNA barcoding,Taxonomic - classification,Sequence read processing,Sequencing quality - control,Phylogenetic analysis + description_md: Workflow covering operations related to Taxonomic + classification,DNA barcoding,Sequence read processing,Sequencing quality + control,Sequence clustering,Phylogenetic analysis,Visualisation button_link: '{{ galaxy_base_url }}/workflows/trs_import?trs_server=workflowhub.eu&run_form=true&trs_id=1412' button_tip: View workflow button_icon: view - title_md: 'Workflow 4: Mock OTU Clustering [Galaxy Training: 16S Microbial Analysis With Mothur]' - description_md: Workflow covering operations related to - Visualisation,Sequence clustering,DNA barcoding,Taxonomic - classification,Sequence read processing,Sequencing quality - control,Phylogenetic analysis + description_md: Workflow covering operations related to Taxonomic + classification,DNA barcoding,Sequence read processing,Sequencing quality + control,Sequence clustering,Phylogenetic analysis,Visualisation button_link: '{{ galaxy_base_url }}/workflows/trs_import?trs_server=workflowhub.eu&run_form=true&trs_id=1408' button_tip: View workflow button_icon: view - title_md: 'Workflow 5: OTU Clustering [Galaxy Training: 16S Microbial Analysis With Mothur]' - description_md: Workflow covering operations related to - Visualisation,Sequence clustering,DNA barcoding,Taxonomic - classification,Sequence read processing,Sequencing quality - control,Phylogenetic analysis + description_md: Workflow covering operations related to Taxonomic + classification,DNA barcoding,Sequence read processing,Sequencing quality + control,Sequence clustering,Phylogenetic analysis,Visualisation button_link: '{{ galaxy_base_url }}/workflows/trs_import?trs_server=workflowhub.eu&run_form=true&trs_id=1404' button_tip: View workflow button_icon: view - title_md: 'Workflow 2: Data Cleaning And Chimera Removal [Galaxy Training: 16S Microbial Analysis With Mothur]' - description_md: Workflow covering operations related to - Visualisation,Sequence clustering,DNA barcoding,Taxonomic - classification,Sequence read processing,Sequencing quality - control,Phylogenetic analysis + description_md: Workflow covering operations related to Taxonomic + classification,DNA barcoding,Sequence read processing,Sequencing quality + control,Sequence clustering,Phylogenetic analysis,Visualisation button_link: '{{ galaxy_base_url }}/workflows/trs_import?trs_server=workflowhub.eu&run_form=true&trs_id=1400' button_tip: View workflow button_icon: view - title_md: GTN Training - Antibiotic Resistance Detection - description_md: Workflow covering operations related to Aggregation,Mapping - assembly,Antimicrobial resistance prediction,Sequence analysis,Box-Whisker - plot plotting,Pairwise sequence alignment,Genome assembly,Sequence - assembly visualisation,Scatter plot plotting,De-novo assemblyon topics + description_md: Workflow covering operations related to Pairwise sequence + alignment,Aggregation,Antimicrobial resistance prediction,Box-Whisker plot + plotting,De-novo assembly,Scatter plot plotting,Sequence assembly + visualisation,Sequence analysis,Mapping assembly,Genome assemblyon topics related to Microbiology button_link: '{{ galaxy_base_url }}/workflows/trs_import?trs_server=workflowhub.eu&run_form=true&trs_id=406' button_tip: View workflow @@ -769,123 +764,132 @@ tabs: https://training.galaxyproject.org/training-material/faqs/galaxy/workflows_import.html - title_md: Quality control of bins generated by MetaBAT2, MaxBin2, SemiBin, and CONCOCT - description_md: Workflow covering operations related to Sequence composition - calculation,Sequence assembly validation,Statistical - calculation,Validation,Sequencing quality control + description_md: Workflow covering operations related to Statistical + calculation,Sequencing quality control,Validation,Sequence composition + calculation,Sequence assembly validation button_link: https://usegalaxy.fr/published/workflow?id=f0776f7a890b523a button_tip: View workflow button_icon: view - - title_md: Copy of Metaproteomics_GTN shared by user engy.nasr - description_md: Workflow covering operations related to - Visualisation,Prediction and recognition - button_link: https://usegalaxy.eu/published/workflow?id=6ca1b4fe047a03d2 - button_tip: View workflow - button_icon: view - title_md: 'Training: 16S rRNA Analysis with Nanopore Sequencing Reads' - description_md: Workflow covering operations related to - Visualisation,Sequence composition calculation,Sequence contamination - filtering,Statistical calculation,Validation,Taxonomic - classification,Sequencing quality control + description_md: Workflow covering operations related to Sequencing quality + control,Sequence contamination filtering,Taxonomic + classification,Statistical calculation,Validation,Sequence composition + calculation,Visualisation button_link: https://usegalaxy.eu/published/workflow?id=2a093e63ebf6876b button_tip: View workflow button_icon: view + - title_md: Sadowsky_MetaG-DBgen_02102026 + description_md: Workflow covering operations related to Statistical + calculation,Taxonomic classification,Genome annotation,Sequencing quality + control,Sequence trimming,Sequence assembly,Fold recognition,Information + extraction,Homology-based gene prediction,Gene prediction,Read + pre-processing,Coding region prediction,Primer removal,Query and + retrieval,Sequence composition calculation + button_link: https://usegalaxy.eu/published/workflow?id=7be08f99f83c927e + button_tip: View workflow + button_icon: view + - title_md: Copy of Metaproteomics_GTN shared by user engy.nasr + description_md: Workflow covering operations related to Prediction and + recognition,Visualisation + button_link: https://usegalaxy.eu/published/workflow?id=6ca1b4fe047a03d2 + button_tip: View workflow + button_icon: view - title_md: MetaG_extended - description_md: Workflow covering operations related to - Visualisation,Sequence composition calculation,Formatting,Statistical - calculation,Validation,Sequence database search,Format validation,Primer - removal,Coding region prediction,Local alignment,Sequence - assembly,Database search,Sequence profile generation,Sequencing quality - control,Protein feature detection,Sequence trimming,Multiple sequence - alignment,Sequence assembly validation,Sequence motif recognition,Sequence - generation,Read pre-processing,Data retrieval,Gene prediction,Taxonomic - classification,Conversion,Probabilistic sequence generation + description_md: Workflow covering operations related to Statistical + calculation,Formatting,Visualisation,Format + validation,Conversion,Probabilistic sequence generation,Sequencing quality + control,Sequence assembly,Protein feature detection,Gene + prediction,Sequence motif recognition,Coding region prediction,Sequence + composition calculation,Sequence generation,Database search,Sequence + database search,Data retrieval,Taxonomic classification,Multiple sequence + alignment,Sequence assembly validation,Sequence trimming,Sequence profile + generation,Validation,Read pre-processing,Primer removal,Local alignment button_link: https://usegalaxy.eu/published/workflow?id=8c91345ed468e22d button_tip: View workflow button_icon: view - title_md: 'Metagenomic Taxonomy Analysis ' - description_md: Workflow covering operations related to - Visualisation,Formatting,Statistical calculation,Taxonomic - classification,Conversion,Aggregation,Standardisation and normalisation + description_md: Workflow covering operations related to Statistical + calculation,Taxonomic classification,Standardisation and + normalisation,Formatting,Aggregation,Conversion,Visualisation button_link: https://usegalaxy.eu/published/workflow?id=7491883694fff308 button_tip: View workflow button_icon: view - title_md: Quality control of bins generated by MetaBAT2, MaxBin2, SemiBin, and CONCOCT - description_md: Workflow covering operations related to Sequence composition - calculation,Sequence assembly validation,Statistical - calculation,Validation,Sequencing quality control + description_md: Workflow covering operations related to Statistical + calculation,Sequencing quality control,Validation,Sequence composition + calculation,Sequence assembly validation button_link: https://usegalaxy.eu/published/workflow?id=7371b6918e895e0c button_tip: View workflow button_icon: view - title_md: pAllori Amplicon 16S Pre-Processing and Taxonomy Classification - description_md: Workflow covering operations related to - Visualisation,Sequence feature detection,Sequence composition - calculation,Filtering,Formatting,Statistical - calculation,Deposition,Validation,Analysis,Standardisation and - normalisation,Classification,DNA barcoding,Sequencing quality control + description_md: Workflow covering operations related to Statistical + calculation,Formatting,DNA barcoding,Filtering,Sequence feature + detection,Sequencing quality control,Standardisation and + normalisation,Analysis,Validation,Deposition,Sequence composition + calculation,Visualisation,Classification button_link: https://usegalaxy.eu/published/workflow?id=466bdd8ba7b67264 button_tip: View workflow button_icon: view - title_md: Metagenomic Taxonomy and Functional Analysis - description_md: Workflow covering operations related to - Visualisation,Formatting,Statistical calculation,Standardisation and - normalisation,Species frequency estimation,Taxonomic - classification,Conversion,Aggregation,Phylogenetic analysis + description_md: Workflow covering operations related to Statistical + calculation,Taxonomic classification,Formatting,Aggregation,Species + frequency estimation,Conversion,Standardisation and + normalisation,Phylogenetic analysis,Visualisation button_link: https://usegalaxy.eu/published/workflow?id=cb2df493f5e334f7 button_tip: View workflow button_icon: view - title_md: pAllori Blood RNA - description_md: Workflow covering operations related to Read - summarisation,Sequence composition calculation,RNA-Seq - quantification,Statistical calculation,Sequence - alignment,Validation,Sequencing quality control + description_md: Workflow covering operations related to Sequencing quality + control,Statistical calculation,Validation,Read summarisation,Sequence + alignment,Sequence composition calculation,RNA-Seq quantification button_link: https://usegalaxy.eu/published/workflow?id=ca9d3233b0912765 button_tip: View workflow button_icon: view - title_md: 'MetaG: Preparation, Building and Annotation of Metagenomics Assembled Genomes ' - description_md: Workflow covering operations related to - Visualisation,Sequence composition calculation,Formatting,Statistical - calculation,Gene functional annotation,Validation,Sequence database - search,Format validation,Primer removal,Coding region prediction,Local - alignment,Sequence assembly,Database search,Sequence profile - generation,Sequencing quality control,Protein feature detection,Sequence - trimming,Multiple sequence alignment,Sequence assembly validation,Sequence - motif recognition,Sequence generation,Sequence analysis,Read - pre-processing,Data retrieval,Gene prediction,Taxonomic - classification,Conversion,Probabilistic sequence generation + description_md: Workflow covering operations related to Statistical + calculation,Formatting,Gene functional annotation,Visualisation,Format + validation,Conversion,Probabilistic sequence generation,Sequencing quality + control,Sequence assembly,Protein feature detection,Gene + prediction,Sequence motif recognition,Coding region prediction,Sequence + composition calculation,Sequence generation,Database search,Sequence + database search,Data retrieval,Taxonomic classification,Multiple sequence + alignment,Sequence assembly validation,Sequence trimming,Sequence profile + generation,Validation,Sequence analysis,Read pre-processing,Primer + removal,Local alignment button_link: https://usegalaxy.eu/published/workflow?id=667bac8d7453e5f1 button_tip: View workflow button_icon: view - title_md: 'ASaiM-MT: Metatranscriptomics Analysis of Microbes' - description_md: Workflow covering operations related to Sequence - comparison,Phylogenetic tree visualisation,Visualisation,Sequence - composition calculation,Formatting,Statistical calculation,Phylogenetic - inference,Validation,Primer removal,Sequence alignment analysis,Sequencing - quality control,Sequence trimming,Phylogenetic tree editing,Read - pre-processing,Taxonomic classification,Sequence similarity - search,Conversion + description_md: Workflow covering operations related to Statistical + calculation,Phylogenetic inference,Taxonomic + classification,Formatting,Conversion,Phylogenetic tree + visualisation,Sequence similarity search,Sequence composition + calculation,Phylogenetic tree editing,Sequencing quality control,Sequence + trimming,Sequence alignment analysis,Sequence comparison,Validation,Read + pre-processing,Primer removal,Visualisation button_link: https://usegalaxy.eu/published/workflow?id=096b75501c8e0888 button_tip: View workflow button_icon: view - title_md: 'MetaT: Metatranscriptomics data analysis' - description_md: Workflow covering operations related to Sequence - trimming,Sequence composition calculation,Statistical calculation,Gene - expression profiling,Primer removal,Read pre-processing,Sequence - similarity search,Sequence alignment analysis,Sequence - comparison,Sequencing quality control + description_md: Workflow covering operations related to Statistical + calculation,Sequence similarity search,Sequencing quality control,Gene + expression profiling,Sequence trimming,Sequence alignment + analysis,Sequence comparison,Read pre-processing,Primer removal,Sequence + composition calculation button_link: https://usegalaxy.eu/published/workflow?id=fd90652d475ed739 button_tip: View workflow button_icon: view - title_md: Halophiles workup of Comparative gene analysis description_md: Workflow covering operations related to Sequence alignment - analysis,Multiple sequence alignment,Phylogenetic tree generation + analysis,Phylogenetic tree generation,Multiple sequence alignment button_link: https://usegalaxy.eu/published/workflow?id=a2c46deea34d9d80 button_tip: View workflow button_icon: view - title_md: Metaproteomics workflow - description_md: Workflow covering operations related to - Visualisation,Prediction and recognition + description_md: Workflow covering operations related to Prediction and + recognition,Visualisation button_link: https://usegalaxy.eu/published/workflow?id=cefc49c13ff73231 button_tip: View workflow button_icon: view @@ -896,35 +900,36 @@ tabs: button_icon: view - title_md: metaQuantome_datacreation_workflow description_md: Workflow covering operations related to - Visualisation,Label-free quantification,Prediction and - recognition,Filtering,Formatting + Formatting,Prediction and recognition,Filtering,Visualisation,Label-free + quantification button_link: https://usegalaxy.eu/published/workflow?id=cd675ab32d3e7833 button_tip: View workflow button_icon: view - title_md: metaquantome-function-worklow description_md: Workflow covering operations related to - Visualisation,Statistical inference,Quantification,Heat map - generation,Query and retrieval,Indexing,Differential protein expression - analysis,Principal component visualisation,Filtering,Functional clustering + Quantification,Differential protein expression analysis,Query and + retrieval,Principal component visualisation,Indexing,Heat map + generation,Filtering,Functional clustering,Statistical + inference,Visualisation button_link: https://usegalaxy.eu/published/workflow?id=e5a89ef7b5f1c1d9 button_tip: View workflow button_icon: view - title_md: Cloud Aerosol MT-MG Contamination Filtering - description_md: Workflow covering operations related to - Cross-assembly,Taxonomic classification,Read mapping,Expression analysis + description_md: Workflow covering operations related to Taxonomic + classification,Expression analysis,Read mapping,Cross-assembly button_link: https://usegalaxy.eu/published/workflow?id=c09159d7aad0f264 button_tip: View workflow button_icon: view - title_md: ' Cloud-Aerosole MT-MG Functional Profiling' - description_md: Workflow covering operations related to Read - summarisation,RNA-Seq quantification,Validation,Read mapping,Sequencing - quality control + description_md: Workflow covering operations related to Sequencing quality + control,Validation,Read summarisation,Read mapping,RNA-Seq quantification button_link: https://usegalaxy.eu/published/workflow?id=63478edcea3f449a button_tip: View workflow button_icon: view - title_md: Cloud-Aerosole MT-MG Pre-Processing - description_md: Workflow covering operations related to Sequence composition - calculation,Statistical calculation,Validation,Sequencing quality control + description_md: Workflow covering operations related to Sequencing quality + control,Statistical calculation,Validation,Sequence composition + calculation button_link: https://usegalaxy.eu/published/workflow?id=1ef76b7b86e15792 button_tip: View workflow button_icon: view @@ -941,7 +946,7 @@ tabs: button_icon: view - title_md: Comparative gene analysis description_md: Workflow covering operations related to Sequence alignment - analysis,Multiple sequence alignment,Phylogenetic tree generation + analysis,Phylogenetic tree generation,Multiple sequence alignment button_link: https://usegalaxy.eu/published/workflow?id=86900be4282d4b1d button_tip: View workflow button_icon: view @@ -951,13 +956,13 @@ tabs: button_tip: View workflow button_icon: view - title_md: Flye-AMR workflow EMC/WMDI - v3.5 (imported from URL) - description_md: Workflow covering operations related to Genome - assembly,Sequence visualisation,Gene prediction,Genome annotation,Sequence - analysis,Variant calling,Base-calling,Antimicrobial resistance - prediction,Coding region prediction,Cross-assembly,Mapping - assembly,Sequence assembly,Box-Whisker plot plotting,Genome - visualisation,Pairwise sequence alignment,Sequence assembly - visualisation,Scatter plot plotting,De-novo assembly + description_md: Workflow covering operations related to + Base-calling,Pairwise sequence alignment,Sequence visualisation,De-novo + assembly,Variant calling,Scatter plot plotting,Genome annotation,Sequence + assembly,Gene prediction,Genome visualisation,Mapping assembly,Coding + region prediction,Cross-assembly,Antimicrobial resistance + prediction,Box-Whisker plot plotting,Sequence assembly + visualisation,Sequence analysis,Genome assembly button_link: https://usegalaxy.eu/published/workflow?id=152223c8aed27357 button_tip: View workflow button_icon: view @@ -968,7 +973,7 @@ tabs: button_icon: view - title_md: From Fastqs to VCFs and BAMs description_md: Workflow covering operations related to Phylogenetic tree - visualisation,Variant calling,Phylogenetic tree generation + visualisation,Phylogenetic tree generation,Variant calling button_link: https://usegalaxy.eu/published/workflow?id=3a8fde248a4d0383 button_tip: View workflow button_icon: view @@ -992,9 +997,9 @@ tabs: button_icon: view - title_md: Quality control of bins generated by MetaBAT2, MaxBin2, SemiBin, and CONCOCT - description_md: Workflow covering operations related to Sequence composition - calculation,Sequence assembly validation,Statistical - calculation,Validation,Sequencing quality control + description_md: Workflow covering operations related to Statistical + calculation,Sequencing quality control,Validation,Sequence composition + calculation,Sequence assembly validation button_link: https://usegalaxy.org/published/workflow?id=a8aee61c2cbaf6ea button_tip: View workflow button_icon: view @@ -1005,25 +1010,24 @@ tabs: button_icon: view - title_md: MGnify's amplicon pipeline v5.0 - ITS (release v0.1) description_md: Workflow covering operations related to k-mer - counting,Visualisation,Formatting,Mapping + counting,Formatting,Visualisation,Mapping button_link: https://usegalaxy.org/published/workflow?id=45f959d5bf505b15 button_tip: View workflow button_icon: view - title_md: MGnify's amplicon pipeline v5.0 - Quality control PE (release v0.1) - description_md: Workflow covering operations related to Sequence - trimming,Sequence composition calculation,Nucleic acid design,Statistical - calculation,Validation,Read pre-processing,Sequence contamination - filtering,Sequencing quality control + description_md: Workflow covering operations related to Statistical + calculation,Sequencing quality control,Sequence contamination + filtering,Sequence trimming,Validation,Nucleic acid design,Read + pre-processing,Sequence composition calculation button_link: https://usegalaxy.org/published/workflow?id=a71fcbc60caae8b6 button_tip: View workflow button_icon: view - title_md: MGnify's amplicon pipeline v5.0 - Quality control SE (release v0.1) - description_md: Workflow covering operations related to Sequence - trimming,Read pre-processing,Sequence composition calculation,Sequence - contamination filtering,Statistical calculation,Validation,Sequencing - quality control + description_md: Workflow covering operations related to Sequencing quality + control,Statistical calculation,Sequence contamination filtering,Sequence + trimming,Validation,Read pre-processing,Sequence composition calculation button_link: https://usegalaxy.org/published/workflow?id=5f878c4cc3bff68c button_tip: View workflow button_icon: view @@ -1035,10 +1039,9 @@ tabs: button_icon: view - title_md: MGnify's amplicon pipeline v5.0 - Quality control SE (release v0.2) - description_md: Workflow covering operations related to Sequence - trimming,Read pre-processing,Sequence composition calculation,Sequence - contamination filtering,Statistical calculation,Validation,Sequencing - quality control + description_md: Workflow covering operations related to Sequencing quality + control,Statistical calculation,Sequence contamination filtering,Sequence + trimming,Validation,Read pre-processing,Sequence composition calculation button_link: https://usegalaxy.org/published/workflow?id=afb67b4b9952f57d button_tip: View workflow button_icon: view @@ -1055,43 +1058,42 @@ tabs: button_icon: view - title_md: MGnify's amplicon pipeline v5.0 - ITS (release v0.2) description_md: Workflow covering operations related to k-mer - counting,Visualisation,Formatting,Mapping + counting,Formatting,Visualisation,Mapping button_link: https://usegalaxy.org/published/workflow?id=8151be18aab3a3c6 button_tip: View workflow button_icon: view - title_md: MGnify's amplicon pipeline v5.0 - Quality control PE (release v0.2) - description_md: Workflow covering operations related to Sequence - trimming,Sequence composition calculation,Nucleic acid design,Statistical - calculation,Validation,Read pre-processing,Sequence contamination - filtering,Sequencing quality control + description_md: Workflow covering operations related to Statistical + calculation,Sequencing quality control,Sequence contamination + filtering,Sequence trimming,Validation,Nucleic acid design,Read + pre-processing,Sequence composition calculation button_link: https://usegalaxy.org/published/workflow?id=20b7ae4b517a80fd button_tip: View workflow button_icon: view - title_md: MGnify's amplicon pipeline v5.0 - Quality control SE (release v0.3) - description_md: Workflow covering operations related to Sequence - trimming,Read pre-processing,Sequence composition calculation,Sequence - contamination filtering,Statistical calculation,Validation,Sequencing - quality control + description_md: Workflow covering operations related to Sequencing quality + control,Statistical calculation,Sequence contamination filtering,Sequence + trimming,Validation,Read pre-processing,Sequence composition calculation button_link: https://usegalaxy.org/published/workflow?id=46f184a0e95f3c1c button_tip: View workflow button_icon: view - title_md: Nanopore Preprocessing (release v0.1) - description_md: Workflow covering operations related to - Visualisation,Sequence composition calculation,Statistical - calculation,Validation,Sequence contamination filtering,Box-Whisker plot - plotting,Sequence alignment analysis,Taxonomic classification,Data - handling,Pairwise sequence alignment,Aggregation,Scatter plot - plotting,Sequencing quality control + description_md: Workflow covering operations related to Statistical + calculation,Taxonomic classification,Pairwise sequence + alignment,Box-Whisker plot plotting,Aggregation,Data handling,Scatter plot + plotting,Sequencing quality control,Sequence contamination + filtering,Sequence alignment analysis,Validation,Sequence composition + calculation,Visualisation button_link: https://usegalaxy.org/published/workflow?id=a8b9252fad5fe06a button_tip: View workflow button_icon: view - title_md: Quality control of bins generated by MetaBAT2, MaxBin2, SemiBin, and CONCOCT - description_md: Workflow covering operations related to Sequence composition - calculation,Sequence assembly validation,Statistical - calculation,Validation,Sequencing quality control + description_md: Workflow covering operations related to Statistical + calculation,Sequencing quality control,Validation,Sequence composition + calculation,Sequence assembly validation button_link: https://usegalaxy.org.au/published/workflow?id=f05ed1e5c5dfffa9 button_tip: View workflow button_icon: view diff --git a/communities/microgalaxy/lab/sections/8_tutorials.yml b/communities/microgalaxy/lab/sections/8_tutorials.yml index 6cc7ef846..1544a1b52 100644 --- a/communities/microgalaxy/lab/sections/8_tutorials.yml +++ b/communities/microgalaxy/lab/sections/8_tutorials.yml @@ -5,7 +5,7 @@ tabs: title: Assembly heading_md: 'Top 10 most visited tutorials for the Topic : Assembly' content: - - title_md: "Unicycler Assembly\n (Visitors: 3823772)" + - title_md: "Unicycler Assembly\n (Visitors: 3931702)" description_md: Tutorial stored in Assembly topic on the Galaxy Training Network and covering topics related to Sequence assembly, Genomics, Microbiology @@ -14,7 +14,7 @@ tabs: button_tip: View tutorial button_icon: tutorial - title_md: "Genome Assembly of a bacterial genome (MRSA) sequenced using Illumina - MiSeq Data\n (Visitors: 11568)" + MiSeq Data\n (Visitors: 11970)" description_md: Tutorial stored in Assembly topic on the Galaxy Training Network and covering topics related to Sequence assembly, Whole genome sequencing, Public health and epidemiology, Genomics, Microbiology @@ -23,7 +23,7 @@ tabs: button_tip: View tutorial button_icon: tutorial - title_md: "Genome Assembly of MRSA from Oxford Nanopore MinION data (and optionally - Illumina data)\n (Visitors: 11438)" + Illumina data)\n (Visitors: 11648)" description_md: Tutorial stored in Assembly topic on the Galaxy Training Network and covering topics related to Sequence assembly, Whole genome sequencing, Public health and epidemiology, Genomics, Microbiology, @@ -32,7 +32,7 @@ tabs: https://training.galaxyproject.org//topics/assembly/tutorials/mrsa-nanopore/tutorial.html button_tip: View tutorial button_icon: tutorial - - title_md: "Making sense of a newly assembled genome\n (Visitors: 6969)" + - title_md: "Making sense of a newly assembled genome\n (Visitors: 7029)" description_md: Tutorial stored in Assembly topic on the Galaxy Training Network and covering topics related to Sequence assembly, Genomics, Microbiology @@ -40,7 +40,7 @@ tabs: https://training.galaxyproject.org//topics/assembly/tutorials/ecoli_comparison/tutorial.html button_tip: View tutorial button_icon: tutorial - - title_md: "Assembly of metagenomic sequencing data\n (Visitors: 6)" + - title_md: "Assembly of metagenomic sequencing data\n (Visitors: 3)" description_md: Tutorial stored in Assembly topic on the Galaxy Training Network and covering topics related to Metagenomics, Sequence assembly button_link: @@ -51,7 +51,7 @@ tabs: title: Genome Annotation heading_md: 'Top 10 most visited tutorials for the Topic : Genome Annotation' content: - - title_md: "Genome annotation with Prokka\n (Visitors: 3829962)" + - title_md: "Genome annotation with Prokka\n (Visitors: 3937916)" description_md: Tutorial stored in Genome Annotation topic on the Galaxy Training Network and covering topics related to Genomics, Microbiology, Gene and protein families, Sequence analysis @@ -60,7 +60,7 @@ tabs: button_tip: View tutorial button_icon: tutorial - title_md: "Essential genes detection with Transposon insertion sequencing\n (Visitors: - 3819196)" + 3926930)" description_md: Tutorial stored in Genome Annotation topic on the Galaxy Training Network and covering topics related to Genomics, Microbiology, Sequence analysis, Mobile genetic elements @@ -69,7 +69,7 @@ tabs: button_tip: View tutorial button_icon: tutorial - title_md: "Refining Genome Annotations with Apollo (prokaryotes)\n (Visitors: - 3585787)" + 3693456)" description_md: Tutorial stored in Genome Annotation topic on the Galaxy Training Network and covering topics related to Genomics, Microbiology, Gene and protein families, Sequence analysis @@ -77,7 +77,7 @@ tabs: https://training.galaxyproject.org//topics/genome-annotation/tutorials/apollo/tutorial.html button_tip: View tutorial button_icon: tutorial - - title_md: "Bacterial Genome Annotation\n (Visitors: 8485)" + - title_md: "Bacterial Genome Annotation\n (Visitors: 8849)" description_md: Tutorial stored in Genome Annotation topic on the Galaxy Training Network and covering topics related to Genomics, Microbiology, Gene and protein families, Sequence analysis, Whole genome sequencing, @@ -87,7 +87,7 @@ tabs: button_tip: View tutorial button_icon: tutorial - title_md: "Identification of AMR genes in an assembled bacterial genome\n (Visitors: - 4294)" + 4562)" description_md: Tutorial stored in Genome Annotation topic on the Galaxy Training Network and covering topics related to Whole genome sequencing, Public health and epidemiology, Genomics, Microbiology, Sequence analysis, @@ -96,7 +96,7 @@ tabs: https://training.galaxyproject.org//topics/genome-annotation/tutorials/amr-gene-detection/tutorial.html button_tip: View tutorial button_icon: tutorial - - title_md: "Comparative gene analysis in unannotated genomes\n (Visitors: 2056)" + - title_md: "Comparative gene analysis in unannotated genomes\n (Visitors: 2094)" description_md: Tutorial stored in Genome Annotation topic on the Galaxy Training Network and covering topics related to Genomics, Gene and protein families, Sequence analysis, Phylogeny, Comparative genomics @@ -104,7 +104,7 @@ tabs: https://training.galaxyproject.org//topics/genome-annotation/tutorials/gene-centric/tutorial.html button_tip: View tutorial button_icon: tutorial - - title_md: "Bacterial genome quality control\n (Visitors: 195)" + - title_md: "Bacterial genome quality control\n (Visitors: 223)" description_md: Tutorial stored in Genome Annotation topic on the Galaxy Training Network and covering topics related to Genomics, Microbiology button_link: @@ -112,7 +112,7 @@ tabs: button_tip: View tutorial button_icon: tutorial - title_md: "Dataset construction for bacterial comparative genomics\n (Visitors: - 115)" + 134)" description_md: Tutorial stored in Genome Annotation topic on the Galaxy Training Network and covering topics related to Genomics, Microbiology button_link: @@ -124,7 +124,7 @@ tabs: heading_md: 'Top 10 most visited tutorials for the Topic : Microbiome' content: - title_md: "Metatranscriptomics analysis using microbiome RNA-seq data\n (Visitors: - 3818338)" + 3926230)" description_md: Tutorial stored in Microbiome topic on the Galaxy Training Network and covering topics related to Metatranscriptomics, Microbial ecology, Taxonomy, Function analysis, Sequence analysis @@ -133,7 +133,7 @@ tabs: button_tip: View tutorial button_icon: tutorial - title_md: "Taxonomic Profiling and Visualization of Metagenomic Data\n (Visitors: - 14694)" + 15278)" description_md: Tutorial stored in Microbiome topic on the Galaxy Training Network and covering topics related to Metagenomics, Microbial ecology, Taxonomy, Sequence analysis @@ -141,7 +141,7 @@ tabs: https://training.galaxyproject.org//topics/microbiome/tutorials/taxonomic-profiling/tutorial.html button_tip: View tutorial button_icon: tutorial - - title_md: "16S Microbial Analysis with mothur (extended)\n (Visitors: 14146)" + - title_md: "16S Microbial Analysis with mothur (extended)\n (Visitors: 14424)" description_md: Tutorial stored in Microbiome topic on the Galaxy Training Network and covering topics related to Microbial ecology, Taxonomy, Sequence analysis, Metabarcoding @@ -149,7 +149,7 @@ tabs: https://training.galaxyproject.org//topics/microbiome/tutorials/mothur-miseq-sop/tutorial.html button_tip: View tutorial button_icon: tutorial - - title_md: "Analyses of metagenomics data - The global picture\n (Visitors: 11137)" + - title_md: "Analyses of metagenomics data - The global picture\n (Visitors: 11493)" description_md: Tutorial stored in Microbiome topic on the Galaxy Training Network and covering topics related to Metagenomics, Microbial ecology, Taxonomy, Sequence analysis, Metabarcoding @@ -157,7 +157,7 @@ tabs: https://training.galaxyproject.org//topics/microbiome/tutorials/general-tutorial/tutorial.html button_tip: View tutorial button_icon: tutorial - - title_md: "16S Microbial analysis with Nanopore data\n (Visitors: 10045)" + - title_md: "16S Microbial analysis with Nanopore data\n (Visitors: 10366)" description_md: Tutorial stored in Microbiome topic on the Galaxy Training Network and covering topics related to Microbial ecology, Taxonomy, Sequence analysis, Metabarcoding @@ -166,7 +166,7 @@ tabs: button_tip: View tutorial button_icon: tutorial - title_md: "Building an amplicon sequence variant (ASV) table from 16S data using - DADA2\n (Visitors: 9282)" + DADA2\n (Visitors: 9857)" description_md: Tutorial stored in Microbiome topic on the Galaxy Training Network and covering topics related to Microbial ecology, Taxonomy, Sequence analysis, Metabarcoding @@ -174,14 +174,14 @@ tabs: https://training.galaxyproject.org//topics/microbiome/tutorials/dada-16S/tutorial.html button_tip: View tutorial button_icon: tutorial - - title_md: "Binning of metagenomic sequencing data\n (Visitors: 7203)" + - title_md: "Binning of metagenomic sequencing data\n (Visitors: 7493)" description_md: Tutorial stored in Microbiome topic on the Galaxy Training Network and covering topics related to Metagenomics, Sequence assembly button_link: https://training.galaxyproject.org//topics/microbiome/tutorials/metagenomics-binning/tutorial.html button_tip: View tutorial button_icon: tutorial - - title_md: "16S Microbial Analysis with mothur (short)\n (Visitors: 6699)" + - title_md: "16S Microbial Analysis with mothur (short)\n (Visitors: 6785)" description_md: Tutorial stored in Microbiome topic on the Galaxy Training Network and covering topics related to Microbial ecology, Taxonomy, Sequence analysis, Metabarcoding @@ -190,7 +190,7 @@ tabs: button_tip: View tutorial button_icon: tutorial - title_md: "Pathogen detection from (direct Nanopore) sequencing data using Galaxy - - Foodborne Edition\n (Visitors: 5672)" + - Foodborne Edition\n (Visitors: 5895)" description_md: Tutorial stored in Microbiome topic on the Galaxy Training Network and covering topics related to Metagenomics, Public health and epidemiology, Taxonomy, Sequence assembly, Pathology, Sequence analysis @@ -198,7 +198,7 @@ tabs: https://training.galaxyproject.org//topics/microbiome/tutorials/pathogen-detection-from-nanopore-foodborne-data/tutorial.html button_tip: View tutorial button_icon: tutorial - - title_md: "Assembly of metagenomic sequencing data\n (Visitors: 5414)" + - title_md: "Assembly of metagenomic sequencing data\n (Visitors: 5645)" description_md: Tutorial stored in Microbiome topic on the Galaxy Training Network and covering topics related to Metagenomics, Sequence assembly button_link: diff --git a/communities/microgalaxy/lab/tools/all/APOSTL.yaml b/communities/microgalaxy/lab/tools/all/APOSTL.yaml index a8c67bb3f..47a750f2c 100644 --- a/communities/microgalaxy/lab/tools/all/APOSTL.yaml +++ b/communities/microgalaxy/lab/tools/all/APOSTL.yaml @@ -1229,6 +1229,9 @@ tools: - name: kmindex_query owner: iuc tool_panel_section_id: '' +- name: kneaddata + owner: iuc + tool_panel_section_id: '' - name: kofamscan owner: iuc tool_panel_section_id: '' @@ -1286,6 +1289,9 @@ tools: - name: legsta owner: iuc tool_panel_section_id: '' +- name: liftoff + owner: iuc + tool_panel_section_id: '' - name: lighter owner: bgruening tool_panel_section_id: '' @@ -1505,6 +1511,27 @@ tools: - name: mg_toolkit_original_metadata owner: iuc tool_panel_section_id: '' +- name: mgnify_genome_search + owner: iuc + tool_panel_section_id: '' +- name: mgnify_pipelines_toolkit_classify_var_regions + owner: iuc + tool_panel_section_id: '' +- name: mgnify_pipelines_toolkit_make_asv_count_table + owner: iuc + tool_panel_section_id: '' +- name: mgnify_pipelines_toolkit_mapseq_to_asv_table + owner: iuc + tool_panel_section_id: '' +- name: mgnify_pipelines_toolkit_permute_primers + owner: iuc + tool_panel_section_id: '' +- name: mgnify_pipelines_toolkit_primer_val_classification + owner: iuc + tool_panel_section_id: '' +- name: mgnify_pipelines_toolkit_rev_comp_se_primers + owner: iuc + tool_panel_section_id: '' - name: mgnify_seqprep owner: bgruening tool_panel_section_id: '' @@ -1526,6 +1553,12 @@ tools: - name: miniprot_index owner: iuc tool_panel_section_id: '' +- name: mist_call + owner: iuc + tool_panel_section_id: '' +- name: mist_dists + owner: iuc + tool_panel_section_id: '' - name: mitos owner: iuc tool_panel_section_id: '' @@ -1976,6 +2009,9 @@ tools: - name: msstats owner: galaxyp tool_panel_section_id: '' +- name: mtnucratio + owner: iuc + tool_panel_section_id: '' - name: multigsea owner: iuc tool_panel_section_id: '' @@ -2093,6 +2129,9 @@ tools: - name: obi_clean owner: iuc tool_panel_section_id: '' +- name: obi_complement + owner: iuc + tool_panel_section_id: '' - name: obi_convert owner: iuc tool_panel_section_id: '' @@ -2105,6 +2144,18 @@ tools: - name: obi_pairing owner: iuc tool_panel_section_id: '' +- name: obi_pcr + owner: iuc + tool_panel_section_id: '' +- name: obi_refidx + owner: iuc + tool_panel_section_id: '' +- name: obi_tag + owner: iuc + tool_panel_section_id: '' +- name: obi_taxonomy + owner: iuc + tool_panel_section_id: '' - name: obi_uniq owner: iuc tool_panel_section_id: '' @@ -2726,6 +2777,9 @@ tools: - name: ppanggolin_rarefaction owner: iuc tool_panel_section_id: '' +- name: prinseq + owner: iuc + tool_panel_section_id: '' - name: prodigal owner: iuc tool_panel_section_id: '' @@ -2747,6 +2801,9 @@ tools: - name: proteinortho_summary owner: iuc tool_panel_section_id: '' +- name: psauron + owner: iuc + tool_panel_section_id: '' - name: pycoqc owner: iuc tool_panel_section_id: '' @@ -2855,262 +2912,241 @@ tools: - name: qiime_make_otu_table owner: iuc tool_panel_section_id: '' -- name: qiime2_core__tools__export - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2_core__tools__import - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2_core__tools__import_fastq - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__quality_filter__q_score - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__cull_seqs - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__degap_seqs - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__dereplicate - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__edit_taxonomy +- name: qiime2__dada2__denoise_ccs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_classifications +- name: qiime2__dada2__denoise_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_cross_validate +- name: qiime2__dada2__denoise_pyro owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_fit_classifier +- name: qiime2__dada2__denoise_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_seqs +- name: qiime2__dada2__plot_base_transitions owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_taxonomy +- name: qiime2__cutadapt__demux_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__extract_seq_segments +- name: qiime2__cutadapt__demux_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__filter_seqs_length +- name: qiime2__cutadapt__trim_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__filter_seqs_length_by_taxon +- name: qiime2__cutadapt__trim_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__filter_taxa +- name: qiime2__composition__add_pseudocount owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_bv_brc_genome_features +- name: qiime2__composition__ancom owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_bv_brc_genomes +- name: qiime2__composition__ancombc owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_bv_brc_metadata +- name: qiime2__composition__ancombc2 owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_eukaryome_data +- name: qiime2__composition__ancombc2_visualizer owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_gtdb_data +- name: qiime2__composition__da_barplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_midori2_data +- name: qiime2__composition__tabulate owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_ncbi_data +- name: qiime2__boots__alpha owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_ncbi_data_protein +- name: qiime2__boots__alpha_average owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_ncbi_genomes +- name: qiime2__boots__alpha_collection owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_pr2_data +- name: qiime2__boots__beta owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_silva_data +- name: qiime2__boots__beta_average owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_unite_data +- name: qiime2__boots__beta_collection owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__merge_taxa +- name: qiime2__boots__core_metrics owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__orient_reads +- name: qiime2__boots__kmer_diversity owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__orient_seqs +- name: qiime2__boots__resample owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__parse_silva_taxonomy +- name: qiime2__vsearch__cluster_features_closed_reference owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__reverse_transcribe +- name: qiime2__vsearch__cluster_features_de_novo owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__subsample_fasta +- name: qiime2__vsearch__cluster_features_open_reference owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__trim_alignment +- name: qiime2__vsearch__dereplicate_sequences owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__classify_samples +- name: qiime2__vsearch__fastq_stats owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__classify_samples_from_dist +- name: qiime2__vsearch__merge_pairs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__classify_samples_ncv +- name: qiime2__vsearch__uchime_denovo owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__confusion_matrix +- name: qiime2__vsearch__uchime_ref owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__fit_classifier +- name: qiime2__demux__emp_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__fit_regressor +- name: qiime2__demux__emp_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__heatmap +- name: qiime2__demux__filter_samples owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__metatable +- name: qiime2__demux__partition_samples_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__predict_classification +- name: qiime2__demux__partition_samples_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__predict_regression +- name: qiime2__demux__subsample_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__regress_samples +- name: qiime2__demux__subsample_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__regress_samples_ncv +- name: qiime2__demux__summarize owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__scatterplot +- name: qiime2__demux__tabulate_read_counts owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__split_table +- name: qiime2__deblur__denoise_16S owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__summarize +- name: qiime2__deblur__denoise_other owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__align_to_tree_mafft_fasttree +- name: qiime2__deblur__visualize_stats owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__align_to_tree_mafft_iqtree +- name: qiime2__diversity__adonis owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__align_to_tree_mafft_raxml +- name: qiime2__diversity__alpha owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__fasttree +- name: qiime2__diversity__alpha_correlation owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__filter_table +- name: qiime2__diversity__alpha_group_significance owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__filter_tree +- name: qiime2__diversity__alpha_phylogenetic owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__iqtree +- name: qiime2__diversity__alpha_rarefaction owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__iqtree_ultrafast_bootstrap +- name: qiime2__diversity__beta owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__midpoint_root +- name: qiime2__diversity__beta_correlation owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__raxml +- name: qiime2__diversity__beta_group_significance owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__raxml_rapid_bootstrap +- name: qiime2__diversity__beta_phylogenetic owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__robinson_foulds +- name: qiime2__diversity__beta_rarefaction owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__distance_matrix +- name: qiime2__diversity__bioenv owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__merge +- name: qiime2__diversity__core_metrics owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__shuffle_groups +- name: qiime2__diversity__core_metrics_phylogenetic owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__tabulate +- name: qiime2__diversity__filter_alpha_diversity owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__alpha_group_significance +- name: qiime2__diversity__filter_distance_matrix owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__collate_stats +- name: qiime2__diversity__mantel owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__facet_across +- name: qiime2__diversity__partial_procrustes owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__facet_within +- name: qiime2__diversity__pcoa owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__mann_whitney_u +- name: qiime2__diversity__pcoa_biplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__mann_whitney_u_facet +- name: qiime2__diversity__procrustes_analysis owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__plot_rainclouds +- name: qiime2__diversity__tsne owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__prep_alpha_distribution +- name: qiime2__diversity__umap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__wilcoxon_srt +- name: qiime2__emperor__biplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__wilcoxon_srt_facet +- name: qiime2__emperor__plot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__bowtie2_build +- name: qiime2__emperor__procrustes_plot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__decontam_identify +- name: qiime2_core__tools__export owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__decontam_identify_batches +- name: qiime2_core__tools__import owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__decontam_score_viz +- name: qiime2_core__tools__import_fastq owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__evaluate_composition +- name: qiime2__taxa__barplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__evaluate_seqs +- name: qiime2__taxa__barplot2 owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__evaluate_taxonomy +- name: qiime2__taxa__collapse owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__exclude_seqs +- name: qiime2__taxa__filter_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__filter_reads +- name: qiime2__taxa__filter_table owner: q2d2 tool_panel_section_id: '' - name: qiime2__diversity_lib__alpha_passthrough @@ -3149,253 +3185,244 @@ tools: - name: qiime2__diversity_lib__weighted_unifrac owner: q2d2 tool_panel_section_id: '' -- name: qiime2__alignment__mafft - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__alignment__mafft_add - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__alignment__mask - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__vizard__boxplot +- name: qiime2__stats__alpha_group_significance owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vizard__heatmap +- name: qiime2__stats__collate_stats owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vizard__lineplot +- name: qiime2__stats__facet_across owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vizard__scatterplot_2d +- name: qiime2__stats__facet_within owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__adonis +- name: qiime2__stats__mann_whitney_u owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha +- name: qiime2__stats__mann_whitney_u_facet owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_correlation +- name: qiime2__stats__plot_rainclouds owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_group_significance +- name: qiime2__stats__prep_alpha_distribution owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_phylogenetic +- name: qiime2__stats__wilcoxon_srt owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_rarefaction +- name: qiime2__stats__wilcoxon_srt_facet owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta +- name: qiime2__sample_classifier__classify_samples owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_correlation +- name: qiime2__sample_classifier__classify_samples_from_dist owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_group_significance +- name: qiime2__sample_classifier__classify_samples_ncv owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_phylogenetic +- name: qiime2__sample_classifier__confusion_matrix owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_rarefaction +- name: qiime2__sample_classifier__fit_classifier owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__bioenv +- name: qiime2__sample_classifier__fit_regressor owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__core_metrics +- name: qiime2__sample_classifier__heatmap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__core_metrics_phylogenetic +- name: qiime2__sample_classifier__metatable owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__filter_alpha_diversity +- name: qiime2__sample_classifier__predict_classification owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__filter_distance_matrix +- name: qiime2__sample_classifier__predict_regression owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__mantel +- name: qiime2__sample_classifier__regress_samples owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__partial_procrustes +- name: qiime2__sample_classifier__regress_samples_ncv owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__pcoa +- name: qiime2__sample_classifier__scatterplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__pcoa_biplot +- name: qiime2__sample_classifier__split_table owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__procrustes_analysis +- name: qiime2__sample_classifier__summarize owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__tsne +- name: qiime2__rescript__cull_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__umap +- name: qiime2__rescript__degap_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__emp_paired +- name: qiime2__rescript__dereplicate owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__emp_single +- name: qiime2__rescript__edit_taxonomy owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__filter_samples +- name: qiime2__rescript__evaluate_classifications owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__partition_samples_paired +- name: qiime2__rescript__evaluate_cross_validate owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__partition_samples_single +- name: qiime2__rescript__evaluate_fit_classifier owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__subsample_paired +- name: qiime2__rescript__evaluate_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__subsample_single +- name: qiime2__rescript__evaluate_taxonomy owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__summarize +- name: qiime2__rescript__extract_seq_segments owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__tabulate_read_counts +- name: qiime2__rescript__filter_seqs_length owner: q2d2 tool_panel_section_id: '' -- name: qiime2__deblur__denoise_16S +- name: qiime2__rescript__filter_seqs_length_by_taxon owner: q2d2 tool_panel_section_id: '' -- name: qiime2__deblur__denoise_other +- name: qiime2__rescript__filter_taxa owner: q2d2 tool_panel_section_id: '' -- name: qiime2__deblur__visualize_stats +- name: qiime2__rescript__get_bv_brc_genome_features owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_ccs +- name: qiime2__rescript__get_bv_brc_genomes owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_paired +- name: qiime2__rescript__get_bv_brc_metadata owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_pyro +- name: qiime2__rescript__get_eukaryome_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_single +- name: qiime2__rescript__get_gtdb_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__plot_base_transitions +- name: qiime2__rescript__get_midori2_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__cutadapt__demux_paired +- name: qiime2__rescript__get_ncbi_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__cutadapt__demux_single +- name: qiime2__rescript__get_ncbi_data_protein owner: q2d2 tool_panel_section_id: '' -- name: qiime2__cutadapt__trim_paired +- name: qiime2__rescript__get_ncbi_genomes owner: q2d2 tool_panel_section_id: '' -- name: qiime2__cutadapt__trim_single +- name: qiime2__rescript__get_pr2_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__add_pseudocount +- name: qiime2__rescript__get_silva_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancom +- name: qiime2__rescript__get_unite_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancombc +- name: qiime2__rescript__merge_taxa owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancombc2 +- name: qiime2__rescript__orient_reads owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancombc2_visualizer +- name: qiime2__rescript__orient_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__da_barplot +- name: qiime2__rescript__parse_silva_taxonomy owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__tabulate +- name: qiime2__rescript__reverse_transcribe owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__barplot +- name: qiime2__rescript__subsample_fasta owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__barplot2 +- name: qiime2__rescript__trim_alignment owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__collapse +- name: qiime2__quality_filter__q_score owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__filter_seqs +- name: qiime2__vizard__boxplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__filter_table +- name: qiime2__vizard__heatmap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__alpha +- name: qiime2__vizard__lineplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__alpha_average +- name: qiime2__vizard__scatterplot_2d owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__alpha_collection +- name: qiime2__alignment__mafft owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__beta +- name: qiime2__alignment__mafft_add owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__beta_average +- name: qiime2__alignment__mask owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__beta_collection +- name: qiime2__phylogeny__align_to_tree_mafft_fasttree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__core_metrics +- name: qiime2__phylogeny__align_to_tree_mafft_iqtree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__kmer_diversity +- name: qiime2__phylogeny__align_to_tree_mafft_raxml owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__resample +- name: qiime2__phylogeny__fasttree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__cluster_features_closed_reference +- name: qiime2__phylogeny__filter_table owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__cluster_features_de_novo +- name: qiime2__phylogeny__filter_tree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__cluster_features_open_reference +- name: qiime2__phylogeny__iqtree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__dereplicate_sequences +- name: qiime2__phylogeny__iqtree_ultrafast_bootstrap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__fastq_stats +- name: qiime2__phylogeny__midpoint_root owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__merge_pairs +- name: qiime2__phylogeny__raxml owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__uchime_denovo +- name: qiime2__phylogeny__raxml_rapid_bootstrap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__uchime_ref +- name: qiime2__phylogeny__robinson_foulds owner: q2d2 tool_panel_section_id: '' -- name: qiime2__emperor__biplot +- name: qiime2__fragment_insertion__classify_otus_experimental owner: q2d2 tool_panel_section_id: '' -- name: qiime2__emperor__plot +- name: qiime2__fragment_insertion__filter_features owner: q2d2 tool_panel_section_id: '' -- name: qiime2__emperor__procrustes_plot +- name: qiime2__fragment_insertion__sepp owner: q2d2 tool_panel_section_id: '' - name: qiime2__feature_classifier__blast @@ -3431,6 +3458,39 @@ tools: - name: qiime2__feature_classifier__vsearch_global owner: q2d2 tool_panel_section_id: '' +- name: qiime2__longitudinal__anova + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__feature_volatility + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__first_differences + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__first_distances + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__linear_mixed_effects + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__maturity_index + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__nmit + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__pairwise_differences + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__pairwise_distances + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__plot_feature_volatility + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__volatility + owner: q2d2 + tool_panel_section_id: '' - name: qiime2__feature_table___summarize owner: q2d2 tool_panel_section_id: '' @@ -3500,76 +3560,73 @@ tools: - name: qiime2__feature_table__transpose owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue___get_sequences - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__fondue__combine_seqs +- name: qiime2__quality_control__bowtie2_build owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__get_all +- name: qiime2__quality_control__decontam_identify owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__get_ids_from_query +- name: qiime2__quality_control__decontam_identify_batches owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__get_metadata +- name: qiime2__quality_control__decontam_score_viz owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__get_sequences +- name: qiime2__quality_control__evaluate_composition owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__merge_metadata +- name: qiime2__quality_control__evaluate_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__scrape_collection +- name: qiime2__quality_control__evaluate_taxonomy owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fragment_insertion__classify_otus_experimental +- name: qiime2__quality_control__exclude_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fragment_insertion__filter_features +- name: qiime2__quality_control__filter_reads owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fragment_insertion__sepp +- name: qiime2__metadata__distance_matrix owner: q2d2 tool_panel_section_id: '' -- name: qiime2__kmerizer__core_metrics +- name: qiime2__metadata__merge owner: q2d2 tool_panel_section_id: '' -- name: qiime2__kmerizer__seqs_to_kmers +- name: qiime2__metadata__shuffle_groups owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__anova +- name: qiime2__metadata__tabulate owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__feature_volatility +- name: qiime2__kmerizer__core_metrics owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__first_differences +- name: qiime2__kmerizer__seqs_to_kmers owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__first_distances +- name: qiime2__fondue___get_sequences owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__linear_mixed_effects +- name: qiime2__fondue__combine_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__maturity_index +- name: qiime2__fondue__get_all owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__nmit +- name: qiime2__fondue__get_ids_from_query owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__pairwise_differences +- name: qiime2__fondue__get_metadata owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__pairwise_distances +- name: qiime2__fondue__get_sequences owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__plot_feature_volatility +- name: qiime2__fondue__merge_metadata owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__volatility +- name: qiime2__fondue__scrape_collection owner: q2d2 tool_panel_section_id: '' - name: qiime2_dbotu_q2 @@ -3698,6 +3755,27 @@ tools: - name: rseqc_tin owner: nilesh tool_panel_section_id: '' +- name: samestr_compare + owner: iuc + tool_panel_section_id: '' +- name: samestr_convert + owner: iuc + tool_panel_section_id: '' +- name: samestr_extract + owner: iuc + tool_panel_section_id: '' +- name: samestr_filter + owner: iuc + tool_panel_section_id: '' +- name: samestr_merge + owner: iuc + tool_panel_section_id: '' +- name: samestr_stats + owner: iuc + tool_panel_section_id: '' +- name: samestr_summarize + owner: iuc + tool_panel_section_id: '' - name: scoary owner: iuc tool_panel_section_id: '' @@ -3822,10 +3900,10 @@ tools: owner: artbio tool_panel_section_id: '' - name: srst2 - owner: iuc + owner: nml tool_panel_section_id: '' - name: srst2 - owner: nml + owner: iuc tool_panel_section_id: '' - name: staramr_search owner: iuc @@ -3938,6 +4016,12 @@ tools: - name: varvamp owner: iuc tool_panel_section_id: '' +- name: vcontact2 + owner: iuc + tool_panel_section_id: '' +- name: vcontact2_gene2genome + owner: iuc + tool_panel_section_id: '' - name: vegan_diversity owner: iuc tool_panel_section_id: '' diff --git a/communities/microgalaxy/lab/tools/all/CIRM-CFBP.yaml b/communities/microgalaxy/lab/tools/all/CIRM-CFBP.yaml index a8c67bb3f..47a750f2c 100644 --- a/communities/microgalaxy/lab/tools/all/CIRM-CFBP.yaml +++ b/communities/microgalaxy/lab/tools/all/CIRM-CFBP.yaml @@ -1229,6 +1229,9 @@ tools: - name: kmindex_query owner: iuc tool_panel_section_id: '' +- name: kneaddata + owner: iuc + tool_panel_section_id: '' - name: kofamscan owner: iuc tool_panel_section_id: '' @@ -1286,6 +1289,9 @@ tools: - name: legsta owner: iuc tool_panel_section_id: '' +- name: liftoff + owner: iuc + tool_panel_section_id: '' - name: lighter owner: bgruening tool_panel_section_id: '' @@ -1505,6 +1511,27 @@ tools: - name: mg_toolkit_original_metadata owner: iuc tool_panel_section_id: '' +- name: mgnify_genome_search + owner: iuc + tool_panel_section_id: '' +- name: mgnify_pipelines_toolkit_classify_var_regions + owner: iuc + tool_panel_section_id: '' +- name: mgnify_pipelines_toolkit_make_asv_count_table + owner: iuc + tool_panel_section_id: '' +- name: mgnify_pipelines_toolkit_mapseq_to_asv_table + owner: iuc + tool_panel_section_id: '' +- name: mgnify_pipelines_toolkit_permute_primers + owner: iuc + tool_panel_section_id: '' +- name: mgnify_pipelines_toolkit_primer_val_classification + owner: iuc + tool_panel_section_id: '' +- name: mgnify_pipelines_toolkit_rev_comp_se_primers + owner: iuc + tool_panel_section_id: '' - name: mgnify_seqprep owner: bgruening tool_panel_section_id: '' @@ -1526,6 +1553,12 @@ tools: - name: miniprot_index owner: iuc tool_panel_section_id: '' +- name: mist_call + owner: iuc + tool_panel_section_id: '' +- name: mist_dists + owner: iuc + tool_panel_section_id: '' - name: mitos owner: iuc tool_panel_section_id: '' @@ -1976,6 +2009,9 @@ tools: - name: msstats owner: galaxyp tool_panel_section_id: '' +- name: mtnucratio + owner: iuc + tool_panel_section_id: '' - name: multigsea owner: iuc tool_panel_section_id: '' @@ -2093,6 +2129,9 @@ tools: - name: obi_clean owner: iuc tool_panel_section_id: '' +- name: obi_complement + owner: iuc + tool_panel_section_id: '' - name: obi_convert owner: iuc tool_panel_section_id: '' @@ -2105,6 +2144,18 @@ tools: - name: obi_pairing owner: iuc tool_panel_section_id: '' +- name: obi_pcr + owner: iuc + tool_panel_section_id: '' +- name: obi_refidx + owner: iuc + tool_panel_section_id: '' +- name: obi_tag + owner: iuc + tool_panel_section_id: '' +- name: obi_taxonomy + owner: iuc + tool_panel_section_id: '' - name: obi_uniq owner: iuc tool_panel_section_id: '' @@ -2726,6 +2777,9 @@ tools: - name: ppanggolin_rarefaction owner: iuc tool_panel_section_id: '' +- name: prinseq + owner: iuc + tool_panel_section_id: '' - name: prodigal owner: iuc tool_panel_section_id: '' @@ -2747,6 +2801,9 @@ tools: - name: proteinortho_summary owner: iuc tool_panel_section_id: '' +- name: psauron + owner: iuc + tool_panel_section_id: '' - name: pycoqc owner: iuc tool_panel_section_id: '' @@ -2855,262 +2912,241 @@ tools: - name: qiime_make_otu_table owner: iuc tool_panel_section_id: '' -- name: qiime2_core__tools__export - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2_core__tools__import - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2_core__tools__import_fastq - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__quality_filter__q_score - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__cull_seqs - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__degap_seqs - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__dereplicate - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__edit_taxonomy +- name: qiime2__dada2__denoise_ccs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_classifications +- name: qiime2__dada2__denoise_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_cross_validate +- name: qiime2__dada2__denoise_pyro owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_fit_classifier +- name: qiime2__dada2__denoise_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_seqs +- name: qiime2__dada2__plot_base_transitions owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_taxonomy +- name: qiime2__cutadapt__demux_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__extract_seq_segments +- name: qiime2__cutadapt__demux_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__filter_seqs_length +- name: qiime2__cutadapt__trim_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__filter_seqs_length_by_taxon +- name: qiime2__cutadapt__trim_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__filter_taxa +- name: qiime2__composition__add_pseudocount owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_bv_brc_genome_features +- name: qiime2__composition__ancom owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_bv_brc_genomes +- name: qiime2__composition__ancombc owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_bv_brc_metadata +- name: qiime2__composition__ancombc2 owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_eukaryome_data +- name: qiime2__composition__ancombc2_visualizer owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_gtdb_data +- name: qiime2__composition__da_barplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_midori2_data +- name: qiime2__composition__tabulate owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_ncbi_data +- name: qiime2__boots__alpha owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_ncbi_data_protein +- name: qiime2__boots__alpha_average owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_ncbi_genomes +- name: qiime2__boots__alpha_collection owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_pr2_data +- name: qiime2__boots__beta owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_silva_data +- name: qiime2__boots__beta_average owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_unite_data +- name: qiime2__boots__beta_collection owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__merge_taxa +- name: qiime2__boots__core_metrics owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__orient_reads +- name: qiime2__boots__kmer_diversity owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__orient_seqs +- name: qiime2__boots__resample owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__parse_silva_taxonomy +- name: qiime2__vsearch__cluster_features_closed_reference owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__reverse_transcribe +- name: qiime2__vsearch__cluster_features_de_novo owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__subsample_fasta +- name: qiime2__vsearch__cluster_features_open_reference owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__trim_alignment +- name: qiime2__vsearch__dereplicate_sequences owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__classify_samples +- name: qiime2__vsearch__fastq_stats owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__classify_samples_from_dist +- name: qiime2__vsearch__merge_pairs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__classify_samples_ncv +- name: qiime2__vsearch__uchime_denovo owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__confusion_matrix +- name: qiime2__vsearch__uchime_ref owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__fit_classifier +- name: qiime2__demux__emp_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__fit_regressor +- name: qiime2__demux__emp_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__heatmap +- name: qiime2__demux__filter_samples owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__metatable +- name: qiime2__demux__partition_samples_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__predict_classification +- name: qiime2__demux__partition_samples_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__predict_regression +- name: qiime2__demux__subsample_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__regress_samples +- name: qiime2__demux__subsample_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__regress_samples_ncv +- name: qiime2__demux__summarize owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__scatterplot +- name: qiime2__demux__tabulate_read_counts owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__split_table +- name: qiime2__deblur__denoise_16S owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__summarize +- name: qiime2__deblur__denoise_other owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__align_to_tree_mafft_fasttree +- name: qiime2__deblur__visualize_stats owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__align_to_tree_mafft_iqtree +- name: qiime2__diversity__adonis owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__align_to_tree_mafft_raxml +- name: qiime2__diversity__alpha owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__fasttree +- name: qiime2__diversity__alpha_correlation owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__filter_table +- name: qiime2__diversity__alpha_group_significance owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__filter_tree +- name: qiime2__diversity__alpha_phylogenetic owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__iqtree +- name: qiime2__diversity__alpha_rarefaction owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__iqtree_ultrafast_bootstrap +- name: qiime2__diversity__beta owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__midpoint_root +- name: qiime2__diversity__beta_correlation owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__raxml +- name: qiime2__diversity__beta_group_significance owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__raxml_rapid_bootstrap +- name: qiime2__diversity__beta_phylogenetic owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__robinson_foulds +- name: qiime2__diversity__beta_rarefaction owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__distance_matrix +- name: qiime2__diversity__bioenv owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__merge +- name: qiime2__diversity__core_metrics owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__shuffle_groups +- name: qiime2__diversity__core_metrics_phylogenetic owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__tabulate +- name: qiime2__diversity__filter_alpha_diversity owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__alpha_group_significance +- name: qiime2__diversity__filter_distance_matrix owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__collate_stats +- name: qiime2__diversity__mantel owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__facet_across +- name: qiime2__diversity__partial_procrustes owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__facet_within +- name: qiime2__diversity__pcoa owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__mann_whitney_u +- name: qiime2__diversity__pcoa_biplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__mann_whitney_u_facet +- name: qiime2__diversity__procrustes_analysis owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__plot_rainclouds +- name: qiime2__diversity__tsne owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__prep_alpha_distribution +- name: qiime2__diversity__umap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__wilcoxon_srt +- name: qiime2__emperor__biplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__wilcoxon_srt_facet +- name: qiime2__emperor__plot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__bowtie2_build +- name: qiime2__emperor__procrustes_plot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__decontam_identify +- name: qiime2_core__tools__export owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__decontam_identify_batches +- name: qiime2_core__tools__import owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__decontam_score_viz +- name: qiime2_core__tools__import_fastq owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__evaluate_composition +- name: qiime2__taxa__barplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__evaluate_seqs +- name: qiime2__taxa__barplot2 owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__evaluate_taxonomy +- name: qiime2__taxa__collapse owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__exclude_seqs +- name: qiime2__taxa__filter_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__filter_reads +- name: qiime2__taxa__filter_table owner: q2d2 tool_panel_section_id: '' - name: qiime2__diversity_lib__alpha_passthrough @@ -3149,253 +3185,244 @@ tools: - name: qiime2__diversity_lib__weighted_unifrac owner: q2d2 tool_panel_section_id: '' -- name: qiime2__alignment__mafft - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__alignment__mafft_add - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__alignment__mask - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__vizard__boxplot +- name: qiime2__stats__alpha_group_significance owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vizard__heatmap +- name: qiime2__stats__collate_stats owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vizard__lineplot +- name: qiime2__stats__facet_across owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vizard__scatterplot_2d +- name: qiime2__stats__facet_within owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__adonis +- name: qiime2__stats__mann_whitney_u owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha +- name: qiime2__stats__mann_whitney_u_facet owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_correlation +- name: qiime2__stats__plot_rainclouds owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_group_significance +- name: qiime2__stats__prep_alpha_distribution owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_phylogenetic +- name: qiime2__stats__wilcoxon_srt owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_rarefaction +- name: qiime2__stats__wilcoxon_srt_facet owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta +- name: qiime2__sample_classifier__classify_samples owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_correlation +- name: qiime2__sample_classifier__classify_samples_from_dist owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_group_significance +- name: qiime2__sample_classifier__classify_samples_ncv owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_phylogenetic +- name: qiime2__sample_classifier__confusion_matrix owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_rarefaction +- name: qiime2__sample_classifier__fit_classifier owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__bioenv +- name: qiime2__sample_classifier__fit_regressor owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__core_metrics +- name: qiime2__sample_classifier__heatmap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__core_metrics_phylogenetic +- name: qiime2__sample_classifier__metatable owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__filter_alpha_diversity +- name: qiime2__sample_classifier__predict_classification owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__filter_distance_matrix +- name: qiime2__sample_classifier__predict_regression owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__mantel +- name: qiime2__sample_classifier__regress_samples owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__partial_procrustes +- name: qiime2__sample_classifier__regress_samples_ncv owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__pcoa +- name: qiime2__sample_classifier__scatterplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__pcoa_biplot +- name: qiime2__sample_classifier__split_table owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__procrustes_analysis +- name: qiime2__sample_classifier__summarize owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__tsne +- name: qiime2__rescript__cull_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__umap +- name: qiime2__rescript__degap_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__emp_paired +- name: qiime2__rescript__dereplicate owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__emp_single +- name: qiime2__rescript__edit_taxonomy owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__filter_samples +- name: qiime2__rescript__evaluate_classifications owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__partition_samples_paired +- name: qiime2__rescript__evaluate_cross_validate owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__partition_samples_single +- name: qiime2__rescript__evaluate_fit_classifier owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__subsample_paired +- name: qiime2__rescript__evaluate_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__subsample_single +- name: qiime2__rescript__evaluate_taxonomy owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__summarize +- name: qiime2__rescript__extract_seq_segments owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__tabulate_read_counts +- name: qiime2__rescript__filter_seqs_length owner: q2d2 tool_panel_section_id: '' -- name: qiime2__deblur__denoise_16S +- name: qiime2__rescript__filter_seqs_length_by_taxon owner: q2d2 tool_panel_section_id: '' -- name: qiime2__deblur__denoise_other +- name: qiime2__rescript__filter_taxa owner: q2d2 tool_panel_section_id: '' -- name: qiime2__deblur__visualize_stats +- name: qiime2__rescript__get_bv_brc_genome_features owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_ccs +- name: qiime2__rescript__get_bv_brc_genomes owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_paired +- name: qiime2__rescript__get_bv_brc_metadata owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_pyro +- name: qiime2__rescript__get_eukaryome_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_single +- name: qiime2__rescript__get_gtdb_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__plot_base_transitions +- name: qiime2__rescript__get_midori2_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__cutadapt__demux_paired +- name: qiime2__rescript__get_ncbi_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__cutadapt__demux_single +- name: qiime2__rescript__get_ncbi_data_protein owner: q2d2 tool_panel_section_id: '' -- name: qiime2__cutadapt__trim_paired +- name: qiime2__rescript__get_ncbi_genomes owner: q2d2 tool_panel_section_id: '' -- name: qiime2__cutadapt__trim_single +- name: qiime2__rescript__get_pr2_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__add_pseudocount +- name: qiime2__rescript__get_silva_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancom +- name: qiime2__rescript__get_unite_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancombc +- name: qiime2__rescript__merge_taxa owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancombc2 +- name: qiime2__rescript__orient_reads owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancombc2_visualizer +- name: qiime2__rescript__orient_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__da_barplot +- name: qiime2__rescript__parse_silva_taxonomy owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__tabulate +- name: qiime2__rescript__reverse_transcribe owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__barplot +- name: qiime2__rescript__subsample_fasta owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__barplot2 +- name: qiime2__rescript__trim_alignment owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__collapse +- name: qiime2__quality_filter__q_score owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__filter_seqs +- name: qiime2__vizard__boxplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__filter_table +- name: qiime2__vizard__heatmap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__alpha +- name: qiime2__vizard__lineplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__alpha_average +- name: qiime2__vizard__scatterplot_2d owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__alpha_collection +- name: qiime2__alignment__mafft owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__beta +- name: qiime2__alignment__mafft_add owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__beta_average +- name: qiime2__alignment__mask owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__beta_collection +- name: qiime2__phylogeny__align_to_tree_mafft_fasttree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__core_metrics +- name: qiime2__phylogeny__align_to_tree_mafft_iqtree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__kmer_diversity +- name: qiime2__phylogeny__align_to_tree_mafft_raxml owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__resample +- name: qiime2__phylogeny__fasttree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__cluster_features_closed_reference +- name: qiime2__phylogeny__filter_table owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__cluster_features_de_novo +- name: qiime2__phylogeny__filter_tree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__cluster_features_open_reference +- name: qiime2__phylogeny__iqtree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__dereplicate_sequences +- name: qiime2__phylogeny__iqtree_ultrafast_bootstrap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__fastq_stats +- name: qiime2__phylogeny__midpoint_root owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__merge_pairs +- name: qiime2__phylogeny__raxml owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__uchime_denovo +- name: qiime2__phylogeny__raxml_rapid_bootstrap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__uchime_ref +- name: qiime2__phylogeny__robinson_foulds owner: q2d2 tool_panel_section_id: '' -- name: qiime2__emperor__biplot +- name: qiime2__fragment_insertion__classify_otus_experimental owner: q2d2 tool_panel_section_id: '' -- name: qiime2__emperor__plot +- name: qiime2__fragment_insertion__filter_features owner: q2d2 tool_panel_section_id: '' -- name: qiime2__emperor__procrustes_plot +- name: qiime2__fragment_insertion__sepp owner: q2d2 tool_panel_section_id: '' - name: qiime2__feature_classifier__blast @@ -3431,6 +3458,39 @@ tools: - name: qiime2__feature_classifier__vsearch_global owner: q2d2 tool_panel_section_id: '' +- name: qiime2__longitudinal__anova + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__feature_volatility + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__first_differences + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__first_distances + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__linear_mixed_effects + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__maturity_index + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__nmit + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__pairwise_differences + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__pairwise_distances + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__plot_feature_volatility + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__volatility + owner: q2d2 + tool_panel_section_id: '' - name: qiime2__feature_table___summarize owner: q2d2 tool_panel_section_id: '' @@ -3500,76 +3560,73 @@ tools: - name: qiime2__feature_table__transpose owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue___get_sequences - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__fondue__combine_seqs +- name: qiime2__quality_control__bowtie2_build owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__get_all +- name: qiime2__quality_control__decontam_identify owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__get_ids_from_query +- name: qiime2__quality_control__decontam_identify_batches owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__get_metadata +- name: qiime2__quality_control__decontam_score_viz owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__get_sequences +- name: qiime2__quality_control__evaluate_composition owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__merge_metadata +- name: qiime2__quality_control__evaluate_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__scrape_collection +- name: qiime2__quality_control__evaluate_taxonomy owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fragment_insertion__classify_otus_experimental +- name: qiime2__quality_control__exclude_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fragment_insertion__filter_features +- name: qiime2__quality_control__filter_reads owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fragment_insertion__sepp +- name: qiime2__metadata__distance_matrix owner: q2d2 tool_panel_section_id: '' -- name: qiime2__kmerizer__core_metrics +- name: qiime2__metadata__merge owner: q2d2 tool_panel_section_id: '' -- name: qiime2__kmerizer__seqs_to_kmers +- name: qiime2__metadata__shuffle_groups owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__anova +- name: qiime2__metadata__tabulate owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__feature_volatility +- name: qiime2__kmerizer__core_metrics owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__first_differences +- name: qiime2__kmerizer__seqs_to_kmers owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__first_distances +- name: qiime2__fondue___get_sequences owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__linear_mixed_effects +- name: qiime2__fondue__combine_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__maturity_index +- name: qiime2__fondue__get_all owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__nmit +- name: qiime2__fondue__get_ids_from_query owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__pairwise_differences +- name: qiime2__fondue__get_metadata owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__pairwise_distances +- name: qiime2__fondue__get_sequences owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__plot_feature_volatility +- name: qiime2__fondue__merge_metadata owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__volatility +- name: qiime2__fondue__scrape_collection owner: q2d2 tool_panel_section_id: '' - name: qiime2_dbotu_q2 @@ -3698,6 +3755,27 @@ tools: - name: rseqc_tin owner: nilesh tool_panel_section_id: '' +- name: samestr_compare + owner: iuc + tool_panel_section_id: '' +- name: samestr_convert + owner: iuc + tool_panel_section_id: '' +- name: samestr_extract + owner: iuc + tool_panel_section_id: '' +- name: samestr_filter + owner: iuc + tool_panel_section_id: '' +- name: samestr_merge + owner: iuc + tool_panel_section_id: '' +- name: samestr_stats + owner: iuc + tool_panel_section_id: '' +- name: samestr_summarize + owner: iuc + tool_panel_section_id: '' - name: scoary owner: iuc tool_panel_section_id: '' @@ -3822,10 +3900,10 @@ tools: owner: artbio tool_panel_section_id: '' - name: srst2 - owner: iuc + owner: nml tool_panel_section_id: '' - name: srst2 - owner: nml + owner: iuc tool_panel_section_id: '' - name: staramr_search owner: iuc @@ -3938,6 +4016,12 @@ tools: - name: varvamp owner: iuc tool_panel_section_id: '' +- name: vcontact2 + owner: iuc + tool_panel_section_id: '' +- name: vcontact2_gene2genome + owner: iuc + tool_panel_section_id: '' - name: vegan_diversity owner: iuc tool_panel_section_id: '' diff --git a/communities/microgalaxy/lab/tools/all/ChemFlow.yaml b/communities/microgalaxy/lab/tools/all/ChemFlow.yaml index a8c67bb3f..47a750f2c 100644 --- a/communities/microgalaxy/lab/tools/all/ChemFlow.yaml +++ b/communities/microgalaxy/lab/tools/all/ChemFlow.yaml @@ -1229,6 +1229,9 @@ tools: - name: kmindex_query owner: iuc tool_panel_section_id: '' +- name: kneaddata + owner: iuc + tool_panel_section_id: '' - name: kofamscan owner: iuc tool_panel_section_id: '' @@ -1286,6 +1289,9 @@ tools: - name: legsta owner: iuc tool_panel_section_id: '' +- name: liftoff + owner: iuc + tool_panel_section_id: '' - name: lighter owner: bgruening tool_panel_section_id: '' @@ -1505,6 +1511,27 @@ tools: - name: mg_toolkit_original_metadata owner: iuc tool_panel_section_id: '' +- name: mgnify_genome_search + owner: iuc + tool_panel_section_id: '' +- name: mgnify_pipelines_toolkit_classify_var_regions + owner: iuc + tool_panel_section_id: '' +- name: mgnify_pipelines_toolkit_make_asv_count_table + owner: iuc + tool_panel_section_id: '' +- name: mgnify_pipelines_toolkit_mapseq_to_asv_table + owner: iuc + tool_panel_section_id: '' +- name: mgnify_pipelines_toolkit_permute_primers + owner: iuc + tool_panel_section_id: '' +- name: mgnify_pipelines_toolkit_primer_val_classification + owner: iuc + tool_panel_section_id: '' +- name: mgnify_pipelines_toolkit_rev_comp_se_primers + owner: iuc + tool_panel_section_id: '' - name: mgnify_seqprep owner: bgruening tool_panel_section_id: '' @@ -1526,6 +1553,12 @@ tools: - name: miniprot_index owner: iuc tool_panel_section_id: '' +- name: mist_call + owner: iuc + tool_panel_section_id: '' +- name: mist_dists + owner: iuc + tool_panel_section_id: '' - name: mitos owner: iuc tool_panel_section_id: '' @@ -1976,6 +2009,9 @@ tools: - name: msstats owner: galaxyp tool_panel_section_id: '' +- name: mtnucratio + owner: iuc + tool_panel_section_id: '' - name: multigsea owner: iuc tool_panel_section_id: '' @@ -2093,6 +2129,9 @@ tools: - name: obi_clean owner: iuc tool_panel_section_id: '' +- name: obi_complement + owner: iuc + tool_panel_section_id: '' - name: obi_convert owner: iuc tool_panel_section_id: '' @@ -2105,6 +2144,18 @@ tools: - name: obi_pairing owner: iuc tool_panel_section_id: '' +- name: obi_pcr + owner: iuc + tool_panel_section_id: '' +- name: obi_refidx + owner: iuc + tool_panel_section_id: '' +- name: obi_tag + owner: iuc + tool_panel_section_id: '' +- name: obi_taxonomy + owner: iuc + tool_panel_section_id: '' - name: obi_uniq owner: iuc tool_panel_section_id: '' @@ -2726,6 +2777,9 @@ tools: - name: ppanggolin_rarefaction owner: iuc tool_panel_section_id: '' +- name: prinseq + owner: iuc + tool_panel_section_id: '' - name: prodigal owner: iuc tool_panel_section_id: '' @@ -2747,6 +2801,9 @@ tools: - name: proteinortho_summary owner: iuc tool_panel_section_id: '' +- name: psauron + owner: iuc + tool_panel_section_id: '' - name: pycoqc owner: iuc tool_panel_section_id: '' @@ -2855,262 +2912,241 @@ tools: - name: qiime_make_otu_table owner: iuc tool_panel_section_id: '' -- name: qiime2_core__tools__export - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2_core__tools__import - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2_core__tools__import_fastq - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__quality_filter__q_score - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__cull_seqs - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__degap_seqs - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__dereplicate - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__edit_taxonomy +- name: qiime2__dada2__denoise_ccs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_classifications +- name: qiime2__dada2__denoise_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_cross_validate +- name: qiime2__dada2__denoise_pyro owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_fit_classifier +- name: qiime2__dada2__denoise_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_seqs +- name: qiime2__dada2__plot_base_transitions owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_taxonomy +- name: qiime2__cutadapt__demux_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__extract_seq_segments +- name: qiime2__cutadapt__demux_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__filter_seqs_length +- name: qiime2__cutadapt__trim_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__filter_seqs_length_by_taxon +- name: qiime2__cutadapt__trim_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__filter_taxa +- name: qiime2__composition__add_pseudocount owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_bv_brc_genome_features +- name: qiime2__composition__ancom owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_bv_brc_genomes +- name: qiime2__composition__ancombc owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_bv_brc_metadata +- name: qiime2__composition__ancombc2 owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_eukaryome_data +- name: qiime2__composition__ancombc2_visualizer owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_gtdb_data +- name: qiime2__composition__da_barplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_midori2_data +- name: qiime2__composition__tabulate owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_ncbi_data +- name: qiime2__boots__alpha owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_ncbi_data_protein +- name: qiime2__boots__alpha_average owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_ncbi_genomes +- name: qiime2__boots__alpha_collection owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_pr2_data +- name: qiime2__boots__beta owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_silva_data +- name: qiime2__boots__beta_average owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_unite_data +- name: qiime2__boots__beta_collection owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__merge_taxa +- name: qiime2__boots__core_metrics owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__orient_reads +- name: qiime2__boots__kmer_diversity owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__orient_seqs +- name: qiime2__boots__resample owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__parse_silva_taxonomy +- name: qiime2__vsearch__cluster_features_closed_reference owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__reverse_transcribe +- name: qiime2__vsearch__cluster_features_de_novo owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__subsample_fasta +- name: qiime2__vsearch__cluster_features_open_reference owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__trim_alignment +- name: qiime2__vsearch__dereplicate_sequences owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__classify_samples +- name: qiime2__vsearch__fastq_stats owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__classify_samples_from_dist +- name: qiime2__vsearch__merge_pairs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__classify_samples_ncv +- name: qiime2__vsearch__uchime_denovo owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__confusion_matrix +- name: qiime2__vsearch__uchime_ref owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__fit_classifier +- name: qiime2__demux__emp_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__fit_regressor +- name: qiime2__demux__emp_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__heatmap +- name: qiime2__demux__filter_samples owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__metatable +- name: qiime2__demux__partition_samples_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__predict_classification +- name: qiime2__demux__partition_samples_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__predict_regression +- name: qiime2__demux__subsample_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__regress_samples +- name: qiime2__demux__subsample_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__regress_samples_ncv +- name: qiime2__demux__summarize owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__scatterplot +- name: qiime2__demux__tabulate_read_counts owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__split_table +- name: qiime2__deblur__denoise_16S owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__summarize +- name: qiime2__deblur__denoise_other owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__align_to_tree_mafft_fasttree +- name: qiime2__deblur__visualize_stats owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__align_to_tree_mafft_iqtree +- name: qiime2__diversity__adonis owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__align_to_tree_mafft_raxml +- name: qiime2__diversity__alpha owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__fasttree +- name: qiime2__diversity__alpha_correlation owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__filter_table +- name: qiime2__diversity__alpha_group_significance owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__filter_tree +- name: qiime2__diversity__alpha_phylogenetic owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__iqtree +- name: qiime2__diversity__alpha_rarefaction owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__iqtree_ultrafast_bootstrap +- name: qiime2__diversity__beta owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__midpoint_root +- name: qiime2__diversity__beta_correlation owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__raxml +- name: qiime2__diversity__beta_group_significance owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__raxml_rapid_bootstrap +- name: qiime2__diversity__beta_phylogenetic owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__robinson_foulds +- name: qiime2__diversity__beta_rarefaction owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__distance_matrix +- name: qiime2__diversity__bioenv owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__merge +- name: qiime2__diversity__core_metrics owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__shuffle_groups +- name: qiime2__diversity__core_metrics_phylogenetic owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__tabulate +- name: qiime2__diversity__filter_alpha_diversity owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__alpha_group_significance +- name: qiime2__diversity__filter_distance_matrix owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__collate_stats +- name: qiime2__diversity__mantel owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__facet_across +- name: qiime2__diversity__partial_procrustes owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__facet_within +- name: qiime2__diversity__pcoa owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__mann_whitney_u +- name: qiime2__diversity__pcoa_biplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__mann_whitney_u_facet +- name: qiime2__diversity__procrustes_analysis owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__plot_rainclouds +- name: qiime2__diversity__tsne owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__prep_alpha_distribution +- name: qiime2__diversity__umap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__wilcoxon_srt +- name: qiime2__emperor__biplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__wilcoxon_srt_facet +- name: qiime2__emperor__plot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__bowtie2_build +- name: qiime2__emperor__procrustes_plot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__decontam_identify +- name: qiime2_core__tools__export owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__decontam_identify_batches +- name: qiime2_core__tools__import owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__decontam_score_viz +- name: qiime2_core__tools__import_fastq owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__evaluate_composition +- name: qiime2__taxa__barplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__evaluate_seqs +- name: qiime2__taxa__barplot2 owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__evaluate_taxonomy +- name: qiime2__taxa__collapse owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__exclude_seqs +- name: qiime2__taxa__filter_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__filter_reads +- name: qiime2__taxa__filter_table owner: q2d2 tool_panel_section_id: '' - name: qiime2__diversity_lib__alpha_passthrough @@ -3149,253 +3185,244 @@ tools: - name: qiime2__diversity_lib__weighted_unifrac owner: q2d2 tool_panel_section_id: '' -- name: qiime2__alignment__mafft - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__alignment__mafft_add - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__alignment__mask - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__vizard__boxplot +- name: qiime2__stats__alpha_group_significance owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vizard__heatmap +- name: qiime2__stats__collate_stats owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vizard__lineplot +- name: qiime2__stats__facet_across owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vizard__scatterplot_2d +- name: qiime2__stats__facet_within owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__adonis +- name: qiime2__stats__mann_whitney_u owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha +- name: qiime2__stats__mann_whitney_u_facet owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_correlation +- name: qiime2__stats__plot_rainclouds owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_group_significance +- name: qiime2__stats__prep_alpha_distribution owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_phylogenetic +- name: qiime2__stats__wilcoxon_srt owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_rarefaction +- name: qiime2__stats__wilcoxon_srt_facet owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta +- name: qiime2__sample_classifier__classify_samples owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_correlation +- name: qiime2__sample_classifier__classify_samples_from_dist owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_group_significance +- name: qiime2__sample_classifier__classify_samples_ncv owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_phylogenetic +- name: qiime2__sample_classifier__confusion_matrix owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_rarefaction +- name: qiime2__sample_classifier__fit_classifier owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__bioenv +- name: qiime2__sample_classifier__fit_regressor owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__core_metrics +- name: qiime2__sample_classifier__heatmap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__core_metrics_phylogenetic +- name: qiime2__sample_classifier__metatable owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__filter_alpha_diversity +- name: qiime2__sample_classifier__predict_classification owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__filter_distance_matrix +- name: qiime2__sample_classifier__predict_regression owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__mantel +- name: qiime2__sample_classifier__regress_samples owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__partial_procrustes +- name: qiime2__sample_classifier__regress_samples_ncv owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__pcoa +- name: qiime2__sample_classifier__scatterplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__pcoa_biplot +- name: qiime2__sample_classifier__split_table owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__procrustes_analysis +- name: qiime2__sample_classifier__summarize owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__tsne +- name: qiime2__rescript__cull_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__umap +- name: qiime2__rescript__degap_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__emp_paired +- name: qiime2__rescript__dereplicate owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__emp_single +- name: qiime2__rescript__edit_taxonomy owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__filter_samples +- name: qiime2__rescript__evaluate_classifications owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__partition_samples_paired +- name: qiime2__rescript__evaluate_cross_validate owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__partition_samples_single +- name: qiime2__rescript__evaluate_fit_classifier owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__subsample_paired +- name: qiime2__rescript__evaluate_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__subsample_single +- name: qiime2__rescript__evaluate_taxonomy owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__summarize +- name: qiime2__rescript__extract_seq_segments owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__tabulate_read_counts +- name: qiime2__rescript__filter_seqs_length owner: q2d2 tool_panel_section_id: '' -- name: qiime2__deblur__denoise_16S +- name: qiime2__rescript__filter_seqs_length_by_taxon owner: q2d2 tool_panel_section_id: '' -- name: qiime2__deblur__denoise_other +- name: qiime2__rescript__filter_taxa owner: q2d2 tool_panel_section_id: '' -- name: qiime2__deblur__visualize_stats +- name: qiime2__rescript__get_bv_brc_genome_features owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_ccs +- name: qiime2__rescript__get_bv_brc_genomes owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_paired +- name: qiime2__rescript__get_bv_brc_metadata owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_pyro +- name: qiime2__rescript__get_eukaryome_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_single +- name: qiime2__rescript__get_gtdb_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__plot_base_transitions +- name: qiime2__rescript__get_midori2_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__cutadapt__demux_paired +- name: qiime2__rescript__get_ncbi_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__cutadapt__demux_single +- name: qiime2__rescript__get_ncbi_data_protein owner: q2d2 tool_panel_section_id: '' -- name: qiime2__cutadapt__trim_paired +- name: qiime2__rescript__get_ncbi_genomes owner: q2d2 tool_panel_section_id: '' -- name: qiime2__cutadapt__trim_single +- name: qiime2__rescript__get_pr2_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__add_pseudocount +- name: qiime2__rescript__get_silva_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancom +- name: qiime2__rescript__get_unite_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancombc +- name: qiime2__rescript__merge_taxa owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancombc2 +- name: qiime2__rescript__orient_reads owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancombc2_visualizer +- name: qiime2__rescript__orient_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__da_barplot +- name: qiime2__rescript__parse_silva_taxonomy owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__tabulate +- name: qiime2__rescript__reverse_transcribe owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__barplot +- name: qiime2__rescript__subsample_fasta owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__barplot2 +- name: qiime2__rescript__trim_alignment owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__collapse +- name: qiime2__quality_filter__q_score owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__filter_seqs +- name: qiime2__vizard__boxplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__filter_table +- name: qiime2__vizard__heatmap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__alpha +- name: qiime2__vizard__lineplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__alpha_average +- name: qiime2__vizard__scatterplot_2d owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__alpha_collection +- name: qiime2__alignment__mafft owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__beta +- name: qiime2__alignment__mafft_add owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__beta_average +- name: qiime2__alignment__mask owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__beta_collection +- name: qiime2__phylogeny__align_to_tree_mafft_fasttree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__core_metrics +- name: qiime2__phylogeny__align_to_tree_mafft_iqtree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__kmer_diversity +- name: qiime2__phylogeny__align_to_tree_mafft_raxml owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__resample +- name: qiime2__phylogeny__fasttree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__cluster_features_closed_reference +- name: qiime2__phylogeny__filter_table owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__cluster_features_de_novo +- name: qiime2__phylogeny__filter_tree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__cluster_features_open_reference +- name: qiime2__phylogeny__iqtree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__dereplicate_sequences +- name: qiime2__phylogeny__iqtree_ultrafast_bootstrap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__fastq_stats +- name: qiime2__phylogeny__midpoint_root owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__merge_pairs +- name: qiime2__phylogeny__raxml owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__uchime_denovo +- name: qiime2__phylogeny__raxml_rapid_bootstrap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__uchime_ref +- name: qiime2__phylogeny__robinson_foulds owner: q2d2 tool_panel_section_id: '' -- name: qiime2__emperor__biplot +- name: qiime2__fragment_insertion__classify_otus_experimental owner: q2d2 tool_panel_section_id: '' -- name: qiime2__emperor__plot +- name: qiime2__fragment_insertion__filter_features owner: q2d2 tool_panel_section_id: '' -- name: qiime2__emperor__procrustes_plot +- name: qiime2__fragment_insertion__sepp owner: q2d2 tool_panel_section_id: '' - name: qiime2__feature_classifier__blast @@ -3431,6 +3458,39 @@ tools: - name: qiime2__feature_classifier__vsearch_global owner: q2d2 tool_panel_section_id: '' +- name: qiime2__longitudinal__anova + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__feature_volatility + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__first_differences + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__first_distances + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__linear_mixed_effects + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__maturity_index + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__nmit + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__pairwise_differences + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__pairwise_distances + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__plot_feature_volatility + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__volatility + owner: q2d2 + tool_panel_section_id: '' - name: qiime2__feature_table___summarize owner: q2d2 tool_panel_section_id: '' @@ -3500,76 +3560,73 @@ tools: - name: qiime2__feature_table__transpose owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue___get_sequences - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__fondue__combine_seqs +- name: qiime2__quality_control__bowtie2_build owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__get_all +- name: qiime2__quality_control__decontam_identify owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__get_ids_from_query +- name: qiime2__quality_control__decontam_identify_batches owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__get_metadata +- name: qiime2__quality_control__decontam_score_viz owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__get_sequences +- name: qiime2__quality_control__evaluate_composition owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__merge_metadata +- name: qiime2__quality_control__evaluate_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__scrape_collection +- name: qiime2__quality_control__evaluate_taxonomy owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fragment_insertion__classify_otus_experimental +- name: qiime2__quality_control__exclude_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fragment_insertion__filter_features +- name: qiime2__quality_control__filter_reads owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fragment_insertion__sepp +- name: qiime2__metadata__distance_matrix owner: q2d2 tool_panel_section_id: '' -- name: qiime2__kmerizer__core_metrics +- name: qiime2__metadata__merge owner: q2d2 tool_panel_section_id: '' -- name: qiime2__kmerizer__seqs_to_kmers +- name: qiime2__metadata__shuffle_groups owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__anova +- name: qiime2__metadata__tabulate owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__feature_volatility +- name: qiime2__kmerizer__core_metrics owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__first_differences +- name: qiime2__kmerizer__seqs_to_kmers owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__first_distances +- name: qiime2__fondue___get_sequences owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__linear_mixed_effects +- name: qiime2__fondue__combine_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__maturity_index +- name: qiime2__fondue__get_all owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__nmit +- name: qiime2__fondue__get_ids_from_query owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__pairwise_differences +- name: qiime2__fondue__get_metadata owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__pairwise_distances +- name: qiime2__fondue__get_sequences owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__plot_feature_volatility +- name: qiime2__fondue__merge_metadata owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__volatility +- name: qiime2__fondue__scrape_collection owner: q2d2 tool_panel_section_id: '' - name: qiime2_dbotu_q2 @@ -3698,6 +3755,27 @@ tools: - name: rseqc_tin owner: nilesh tool_panel_section_id: '' +- name: samestr_compare + owner: iuc + tool_panel_section_id: '' +- name: samestr_convert + owner: iuc + tool_panel_section_id: '' +- name: samestr_extract + owner: iuc + tool_panel_section_id: '' +- name: samestr_filter + owner: iuc + tool_panel_section_id: '' +- name: samestr_merge + owner: iuc + tool_panel_section_id: '' +- name: samestr_stats + owner: iuc + tool_panel_section_id: '' +- name: samestr_summarize + owner: iuc + tool_panel_section_id: '' - name: scoary owner: iuc tool_panel_section_id: '' @@ -3822,10 +3900,10 @@ tools: owner: artbio tool_panel_section_id: '' - name: srst2 - owner: iuc + owner: nml tool_panel_section_id: '' - name: srst2 - owner: nml + owner: iuc tool_panel_section_id: '' - name: staramr_search owner: iuc @@ -3938,6 +4016,12 @@ tools: - name: varvamp owner: iuc tool_panel_section_id: '' +- name: vcontact2 + owner: iuc + tool_panel_section_id: '' +- name: vcontact2_gene2genome + owner: iuc + tool_panel_section_id: '' - name: vegan_diversity owner: iuc tool_panel_section_id: '' diff --git a/communities/microgalaxy/lab/tools/all/Coloc-stats.yaml b/communities/microgalaxy/lab/tools/all/Coloc-stats.yaml index a8c67bb3f..47a750f2c 100644 --- a/communities/microgalaxy/lab/tools/all/Coloc-stats.yaml +++ b/communities/microgalaxy/lab/tools/all/Coloc-stats.yaml @@ -1229,6 +1229,9 @@ tools: - name: kmindex_query owner: iuc tool_panel_section_id: '' +- name: kneaddata + owner: iuc + tool_panel_section_id: '' - name: kofamscan owner: iuc tool_panel_section_id: '' @@ -1286,6 +1289,9 @@ tools: - name: legsta owner: iuc tool_panel_section_id: '' +- name: liftoff + owner: iuc + tool_panel_section_id: '' - name: lighter owner: bgruening tool_panel_section_id: '' @@ -1505,6 +1511,27 @@ tools: - name: mg_toolkit_original_metadata owner: iuc tool_panel_section_id: '' +- name: mgnify_genome_search + owner: iuc + tool_panel_section_id: '' +- name: mgnify_pipelines_toolkit_classify_var_regions + owner: iuc + tool_panel_section_id: '' +- name: mgnify_pipelines_toolkit_make_asv_count_table + owner: iuc + tool_panel_section_id: '' +- name: mgnify_pipelines_toolkit_mapseq_to_asv_table + owner: iuc + tool_panel_section_id: '' +- name: mgnify_pipelines_toolkit_permute_primers + owner: iuc + tool_panel_section_id: '' +- name: mgnify_pipelines_toolkit_primer_val_classification + owner: iuc + tool_panel_section_id: '' +- name: mgnify_pipelines_toolkit_rev_comp_se_primers + owner: iuc + tool_panel_section_id: '' - name: mgnify_seqprep owner: bgruening tool_panel_section_id: '' @@ -1526,6 +1553,12 @@ tools: - name: miniprot_index owner: iuc tool_panel_section_id: '' +- name: mist_call + owner: iuc + tool_panel_section_id: '' +- name: mist_dists + owner: iuc + tool_panel_section_id: '' - name: mitos owner: iuc tool_panel_section_id: '' @@ -1976,6 +2009,9 @@ tools: - name: msstats owner: galaxyp tool_panel_section_id: '' +- name: mtnucratio + owner: iuc + tool_panel_section_id: '' - name: multigsea owner: iuc tool_panel_section_id: '' @@ -2093,6 +2129,9 @@ tools: - name: obi_clean owner: iuc tool_panel_section_id: '' +- name: obi_complement + owner: iuc + tool_panel_section_id: '' - name: obi_convert owner: iuc tool_panel_section_id: '' @@ -2105,6 +2144,18 @@ tools: - name: obi_pairing owner: iuc tool_panel_section_id: '' +- name: obi_pcr + owner: iuc + tool_panel_section_id: '' +- name: obi_refidx + owner: iuc + tool_panel_section_id: '' +- name: obi_tag + owner: iuc + tool_panel_section_id: '' +- name: obi_taxonomy + owner: iuc + tool_panel_section_id: '' - name: obi_uniq owner: iuc tool_panel_section_id: '' @@ -2726,6 +2777,9 @@ tools: - name: ppanggolin_rarefaction owner: iuc tool_panel_section_id: '' +- name: prinseq + owner: iuc + tool_panel_section_id: '' - name: prodigal owner: iuc tool_panel_section_id: '' @@ -2747,6 +2801,9 @@ tools: - name: proteinortho_summary owner: iuc tool_panel_section_id: '' +- name: psauron + owner: iuc + tool_panel_section_id: '' - name: pycoqc owner: iuc tool_panel_section_id: '' @@ -2855,262 +2912,241 @@ tools: - name: qiime_make_otu_table owner: iuc tool_panel_section_id: '' -- name: qiime2_core__tools__export - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2_core__tools__import - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2_core__tools__import_fastq - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__quality_filter__q_score - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__cull_seqs - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__degap_seqs - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__dereplicate - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__edit_taxonomy +- name: qiime2__dada2__denoise_ccs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_classifications +- name: qiime2__dada2__denoise_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_cross_validate +- name: qiime2__dada2__denoise_pyro owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_fit_classifier +- name: qiime2__dada2__denoise_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_seqs +- name: qiime2__dada2__plot_base_transitions owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_taxonomy +- name: qiime2__cutadapt__demux_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__extract_seq_segments +- name: qiime2__cutadapt__demux_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__filter_seqs_length +- name: qiime2__cutadapt__trim_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__filter_seqs_length_by_taxon +- name: qiime2__cutadapt__trim_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__filter_taxa +- name: qiime2__composition__add_pseudocount owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_bv_brc_genome_features +- name: qiime2__composition__ancom owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_bv_brc_genomes +- name: qiime2__composition__ancombc owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_bv_brc_metadata +- name: qiime2__composition__ancombc2 owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_eukaryome_data +- name: qiime2__composition__ancombc2_visualizer owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_gtdb_data +- name: qiime2__composition__da_barplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_midori2_data +- name: qiime2__composition__tabulate owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_ncbi_data +- name: qiime2__boots__alpha owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_ncbi_data_protein +- name: qiime2__boots__alpha_average owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_ncbi_genomes +- name: qiime2__boots__alpha_collection owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_pr2_data +- name: qiime2__boots__beta owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_silva_data +- name: qiime2__boots__beta_average owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_unite_data +- name: qiime2__boots__beta_collection owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__merge_taxa +- name: qiime2__boots__core_metrics owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__orient_reads +- name: qiime2__boots__kmer_diversity owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__orient_seqs +- name: qiime2__boots__resample owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__parse_silva_taxonomy +- name: qiime2__vsearch__cluster_features_closed_reference owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__reverse_transcribe +- name: qiime2__vsearch__cluster_features_de_novo owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__subsample_fasta +- name: qiime2__vsearch__cluster_features_open_reference owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__trim_alignment +- name: qiime2__vsearch__dereplicate_sequences owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__classify_samples +- name: qiime2__vsearch__fastq_stats owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__classify_samples_from_dist +- name: qiime2__vsearch__merge_pairs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__classify_samples_ncv +- name: qiime2__vsearch__uchime_denovo owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__confusion_matrix +- name: qiime2__vsearch__uchime_ref owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__fit_classifier +- name: qiime2__demux__emp_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__fit_regressor +- name: qiime2__demux__emp_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__heatmap +- name: qiime2__demux__filter_samples owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__metatable +- name: qiime2__demux__partition_samples_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__predict_classification +- name: qiime2__demux__partition_samples_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__predict_regression +- name: qiime2__demux__subsample_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__regress_samples +- name: qiime2__demux__subsample_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__regress_samples_ncv +- name: qiime2__demux__summarize owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__scatterplot +- name: qiime2__demux__tabulate_read_counts owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__split_table +- name: qiime2__deblur__denoise_16S owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__summarize +- name: qiime2__deblur__denoise_other owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__align_to_tree_mafft_fasttree +- name: qiime2__deblur__visualize_stats owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__align_to_tree_mafft_iqtree +- name: qiime2__diversity__adonis owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__align_to_tree_mafft_raxml +- name: qiime2__diversity__alpha owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__fasttree +- name: qiime2__diversity__alpha_correlation owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__filter_table +- name: qiime2__diversity__alpha_group_significance owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__filter_tree +- name: qiime2__diversity__alpha_phylogenetic owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__iqtree +- name: qiime2__diversity__alpha_rarefaction owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__iqtree_ultrafast_bootstrap +- name: qiime2__diversity__beta owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__midpoint_root +- name: qiime2__diversity__beta_correlation owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__raxml +- name: qiime2__diversity__beta_group_significance owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__raxml_rapid_bootstrap +- name: qiime2__diversity__beta_phylogenetic owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__robinson_foulds +- name: qiime2__diversity__beta_rarefaction owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__distance_matrix +- name: qiime2__diversity__bioenv owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__merge +- name: qiime2__diversity__core_metrics owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__shuffle_groups +- name: qiime2__diversity__core_metrics_phylogenetic owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__tabulate +- name: qiime2__diversity__filter_alpha_diversity owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__alpha_group_significance +- name: qiime2__diversity__filter_distance_matrix owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__collate_stats +- name: qiime2__diversity__mantel owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__facet_across +- name: qiime2__diversity__partial_procrustes owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__facet_within +- name: qiime2__diversity__pcoa owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__mann_whitney_u +- name: qiime2__diversity__pcoa_biplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__mann_whitney_u_facet +- name: qiime2__diversity__procrustes_analysis owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__plot_rainclouds +- name: qiime2__diversity__tsne owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__prep_alpha_distribution +- name: qiime2__diversity__umap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__wilcoxon_srt +- name: qiime2__emperor__biplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__wilcoxon_srt_facet +- name: qiime2__emperor__plot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__bowtie2_build +- name: qiime2__emperor__procrustes_plot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__decontam_identify +- name: qiime2_core__tools__export owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__decontam_identify_batches +- name: qiime2_core__tools__import owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__decontam_score_viz +- name: qiime2_core__tools__import_fastq owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__evaluate_composition +- name: qiime2__taxa__barplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__evaluate_seqs +- name: qiime2__taxa__barplot2 owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__evaluate_taxonomy +- name: qiime2__taxa__collapse owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__exclude_seqs +- name: qiime2__taxa__filter_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__filter_reads +- name: qiime2__taxa__filter_table owner: q2d2 tool_panel_section_id: '' - name: qiime2__diversity_lib__alpha_passthrough @@ -3149,253 +3185,244 @@ tools: - name: qiime2__diversity_lib__weighted_unifrac owner: q2d2 tool_panel_section_id: '' -- name: qiime2__alignment__mafft - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__alignment__mafft_add - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__alignment__mask - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__vizard__boxplot +- name: qiime2__stats__alpha_group_significance owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vizard__heatmap +- name: qiime2__stats__collate_stats owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vizard__lineplot +- name: qiime2__stats__facet_across owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vizard__scatterplot_2d +- name: qiime2__stats__facet_within owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__adonis +- name: qiime2__stats__mann_whitney_u owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha +- name: qiime2__stats__mann_whitney_u_facet owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_correlation +- name: qiime2__stats__plot_rainclouds owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_group_significance +- name: qiime2__stats__prep_alpha_distribution owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_phylogenetic +- name: qiime2__stats__wilcoxon_srt owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_rarefaction +- name: qiime2__stats__wilcoxon_srt_facet owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta +- name: qiime2__sample_classifier__classify_samples owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_correlation +- name: qiime2__sample_classifier__classify_samples_from_dist owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_group_significance +- name: qiime2__sample_classifier__classify_samples_ncv owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_phylogenetic +- name: qiime2__sample_classifier__confusion_matrix owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_rarefaction +- name: qiime2__sample_classifier__fit_classifier owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__bioenv +- name: qiime2__sample_classifier__fit_regressor owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__core_metrics +- name: qiime2__sample_classifier__heatmap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__core_metrics_phylogenetic +- name: qiime2__sample_classifier__metatable owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__filter_alpha_diversity +- name: qiime2__sample_classifier__predict_classification owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__filter_distance_matrix +- name: qiime2__sample_classifier__predict_regression owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__mantel +- name: qiime2__sample_classifier__regress_samples owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__partial_procrustes +- name: qiime2__sample_classifier__regress_samples_ncv owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__pcoa +- name: qiime2__sample_classifier__scatterplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__pcoa_biplot +- name: qiime2__sample_classifier__split_table owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__procrustes_analysis +- name: qiime2__sample_classifier__summarize owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__tsne +- name: qiime2__rescript__cull_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__umap +- name: qiime2__rescript__degap_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__emp_paired +- name: qiime2__rescript__dereplicate owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__emp_single +- name: qiime2__rescript__edit_taxonomy owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__filter_samples +- name: qiime2__rescript__evaluate_classifications owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__partition_samples_paired +- name: qiime2__rescript__evaluate_cross_validate owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__partition_samples_single +- name: qiime2__rescript__evaluate_fit_classifier owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__subsample_paired +- name: qiime2__rescript__evaluate_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__subsample_single +- name: qiime2__rescript__evaluate_taxonomy owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__summarize +- name: qiime2__rescript__extract_seq_segments owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__tabulate_read_counts +- name: qiime2__rescript__filter_seqs_length owner: q2d2 tool_panel_section_id: '' -- name: qiime2__deblur__denoise_16S +- name: qiime2__rescript__filter_seqs_length_by_taxon owner: q2d2 tool_panel_section_id: '' -- name: qiime2__deblur__denoise_other +- name: qiime2__rescript__filter_taxa owner: q2d2 tool_panel_section_id: '' -- name: qiime2__deblur__visualize_stats +- name: qiime2__rescript__get_bv_brc_genome_features owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_ccs +- name: qiime2__rescript__get_bv_brc_genomes owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_paired +- name: qiime2__rescript__get_bv_brc_metadata owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_pyro +- name: qiime2__rescript__get_eukaryome_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_single +- name: qiime2__rescript__get_gtdb_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__plot_base_transitions +- name: qiime2__rescript__get_midori2_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__cutadapt__demux_paired +- name: qiime2__rescript__get_ncbi_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__cutadapt__demux_single +- name: qiime2__rescript__get_ncbi_data_protein owner: q2d2 tool_panel_section_id: '' -- name: qiime2__cutadapt__trim_paired +- name: qiime2__rescript__get_ncbi_genomes owner: q2d2 tool_panel_section_id: '' -- name: qiime2__cutadapt__trim_single +- name: qiime2__rescript__get_pr2_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__add_pseudocount +- name: qiime2__rescript__get_silva_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancom +- name: qiime2__rescript__get_unite_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancombc +- name: qiime2__rescript__merge_taxa owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancombc2 +- name: qiime2__rescript__orient_reads owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancombc2_visualizer +- name: qiime2__rescript__orient_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__da_barplot +- name: qiime2__rescript__parse_silva_taxonomy owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__tabulate +- name: qiime2__rescript__reverse_transcribe owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__barplot +- name: qiime2__rescript__subsample_fasta owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__barplot2 +- name: qiime2__rescript__trim_alignment owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__collapse +- name: qiime2__quality_filter__q_score owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__filter_seqs +- name: qiime2__vizard__boxplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__filter_table +- name: qiime2__vizard__heatmap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__alpha +- name: qiime2__vizard__lineplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__alpha_average +- name: qiime2__vizard__scatterplot_2d owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__alpha_collection +- name: qiime2__alignment__mafft owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__beta +- name: qiime2__alignment__mafft_add owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__beta_average +- name: qiime2__alignment__mask owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__beta_collection +- name: qiime2__phylogeny__align_to_tree_mafft_fasttree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__core_metrics +- name: qiime2__phylogeny__align_to_tree_mafft_iqtree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__kmer_diversity +- name: qiime2__phylogeny__align_to_tree_mafft_raxml owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__resample +- name: qiime2__phylogeny__fasttree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__cluster_features_closed_reference +- name: qiime2__phylogeny__filter_table owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__cluster_features_de_novo +- name: qiime2__phylogeny__filter_tree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__cluster_features_open_reference +- name: qiime2__phylogeny__iqtree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__dereplicate_sequences +- name: qiime2__phylogeny__iqtree_ultrafast_bootstrap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__fastq_stats +- name: qiime2__phylogeny__midpoint_root owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__merge_pairs +- name: qiime2__phylogeny__raxml owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__uchime_denovo +- name: qiime2__phylogeny__raxml_rapid_bootstrap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__uchime_ref +- name: qiime2__phylogeny__robinson_foulds owner: q2d2 tool_panel_section_id: '' -- name: qiime2__emperor__biplot +- name: qiime2__fragment_insertion__classify_otus_experimental owner: q2d2 tool_panel_section_id: '' -- name: qiime2__emperor__plot +- name: qiime2__fragment_insertion__filter_features owner: q2d2 tool_panel_section_id: '' -- name: qiime2__emperor__procrustes_plot +- name: qiime2__fragment_insertion__sepp owner: q2d2 tool_panel_section_id: '' - name: qiime2__feature_classifier__blast @@ -3431,6 +3458,39 @@ tools: - name: qiime2__feature_classifier__vsearch_global owner: q2d2 tool_panel_section_id: '' +- name: qiime2__longitudinal__anova + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__feature_volatility + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__first_differences + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__first_distances + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__linear_mixed_effects + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__maturity_index + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__nmit + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__pairwise_differences + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__pairwise_distances + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__plot_feature_volatility + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__volatility + owner: q2d2 + tool_panel_section_id: '' - name: qiime2__feature_table___summarize owner: q2d2 tool_panel_section_id: '' @@ -3500,76 +3560,73 @@ tools: - name: qiime2__feature_table__transpose owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue___get_sequences - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__fondue__combine_seqs +- name: qiime2__quality_control__bowtie2_build owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__get_all +- name: qiime2__quality_control__decontam_identify owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__get_ids_from_query +- name: qiime2__quality_control__decontam_identify_batches owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__get_metadata +- name: qiime2__quality_control__decontam_score_viz owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__get_sequences +- name: qiime2__quality_control__evaluate_composition owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__merge_metadata +- name: qiime2__quality_control__evaluate_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__scrape_collection +- name: qiime2__quality_control__evaluate_taxonomy owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fragment_insertion__classify_otus_experimental +- name: qiime2__quality_control__exclude_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fragment_insertion__filter_features +- name: qiime2__quality_control__filter_reads owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fragment_insertion__sepp +- name: qiime2__metadata__distance_matrix owner: q2d2 tool_panel_section_id: '' -- name: qiime2__kmerizer__core_metrics +- name: qiime2__metadata__merge owner: q2d2 tool_panel_section_id: '' -- name: qiime2__kmerizer__seqs_to_kmers +- name: qiime2__metadata__shuffle_groups owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__anova +- name: qiime2__metadata__tabulate owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__feature_volatility +- name: qiime2__kmerizer__core_metrics owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__first_differences +- name: qiime2__kmerizer__seqs_to_kmers owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__first_distances +- name: qiime2__fondue___get_sequences owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__linear_mixed_effects +- name: qiime2__fondue__combine_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__maturity_index +- name: qiime2__fondue__get_all owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__nmit +- name: qiime2__fondue__get_ids_from_query owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__pairwise_differences +- name: qiime2__fondue__get_metadata owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__pairwise_distances +- name: qiime2__fondue__get_sequences owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__plot_feature_volatility +- name: qiime2__fondue__merge_metadata owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__volatility +- name: qiime2__fondue__scrape_collection owner: q2d2 tool_panel_section_id: '' - name: qiime2_dbotu_q2 @@ -3698,6 +3755,27 @@ tools: - name: rseqc_tin owner: nilesh tool_panel_section_id: '' +- name: samestr_compare + owner: iuc + tool_panel_section_id: '' +- name: samestr_convert + owner: iuc + tool_panel_section_id: '' +- name: samestr_extract + owner: iuc + tool_panel_section_id: '' +- name: samestr_filter + owner: iuc + tool_panel_section_id: '' +- name: samestr_merge + owner: iuc + tool_panel_section_id: '' +- name: samestr_stats + owner: iuc + tool_panel_section_id: '' +- name: samestr_summarize + owner: iuc + tool_panel_section_id: '' - name: scoary owner: iuc tool_panel_section_id: '' @@ -3822,10 +3900,10 @@ tools: owner: artbio tool_panel_section_id: '' - name: srst2 - owner: iuc + owner: nml tool_panel_section_id: '' - name: srst2 - owner: nml + owner: iuc tool_panel_section_id: '' - name: staramr_search owner: iuc @@ -3938,6 +4016,12 @@ tools: - name: varvamp owner: iuc tool_panel_section_id: '' +- name: vcontact2 + owner: iuc + tool_panel_section_id: '' +- name: vcontact2_gene2genome + owner: iuc + tool_panel_section_id: '' - name: vegan_diversity owner: iuc tool_panel_section_id: '' diff --git a/communities/microgalaxy/lab/tools/all/GASLINI.yaml b/communities/microgalaxy/lab/tools/all/GASLINI.yaml index a8c67bb3f..47a750f2c 100644 --- a/communities/microgalaxy/lab/tools/all/GASLINI.yaml +++ b/communities/microgalaxy/lab/tools/all/GASLINI.yaml @@ -1229,6 +1229,9 @@ tools: - name: kmindex_query owner: iuc tool_panel_section_id: '' +- name: kneaddata + owner: iuc + tool_panel_section_id: '' - name: kofamscan owner: iuc tool_panel_section_id: '' @@ -1286,6 +1289,9 @@ tools: - name: legsta owner: iuc tool_panel_section_id: '' +- name: liftoff + owner: iuc + tool_panel_section_id: '' - name: lighter owner: bgruening tool_panel_section_id: '' @@ -1505,6 +1511,27 @@ tools: - name: mg_toolkit_original_metadata owner: iuc tool_panel_section_id: '' +- name: mgnify_genome_search + owner: iuc + tool_panel_section_id: '' +- name: mgnify_pipelines_toolkit_classify_var_regions + owner: iuc + tool_panel_section_id: '' +- name: mgnify_pipelines_toolkit_make_asv_count_table + owner: iuc + tool_panel_section_id: '' +- name: mgnify_pipelines_toolkit_mapseq_to_asv_table + owner: iuc + tool_panel_section_id: '' +- name: mgnify_pipelines_toolkit_permute_primers + owner: iuc + tool_panel_section_id: '' +- name: mgnify_pipelines_toolkit_primer_val_classification + owner: iuc + tool_panel_section_id: '' +- name: mgnify_pipelines_toolkit_rev_comp_se_primers + owner: iuc + tool_panel_section_id: '' - name: mgnify_seqprep owner: bgruening tool_panel_section_id: '' @@ -1526,6 +1553,12 @@ tools: - name: miniprot_index owner: iuc tool_panel_section_id: '' +- name: mist_call + owner: iuc + tool_panel_section_id: '' +- name: mist_dists + owner: iuc + tool_panel_section_id: '' - name: mitos owner: iuc tool_panel_section_id: '' @@ -1976,6 +2009,9 @@ tools: - name: msstats owner: galaxyp tool_panel_section_id: '' +- name: mtnucratio + owner: iuc + tool_panel_section_id: '' - name: multigsea owner: iuc tool_panel_section_id: '' @@ -2093,6 +2129,9 @@ tools: - name: obi_clean owner: iuc tool_panel_section_id: '' +- name: obi_complement + owner: iuc + tool_panel_section_id: '' - name: obi_convert owner: iuc tool_panel_section_id: '' @@ -2105,6 +2144,18 @@ tools: - name: obi_pairing owner: iuc tool_panel_section_id: '' +- name: obi_pcr + owner: iuc + tool_panel_section_id: '' +- name: obi_refidx + owner: iuc + tool_panel_section_id: '' +- name: obi_tag + owner: iuc + tool_panel_section_id: '' +- name: obi_taxonomy + owner: iuc + tool_panel_section_id: '' - name: obi_uniq owner: iuc tool_panel_section_id: '' @@ -2726,6 +2777,9 @@ tools: - name: ppanggolin_rarefaction owner: iuc tool_panel_section_id: '' +- name: prinseq + owner: iuc + tool_panel_section_id: '' - name: prodigal owner: iuc tool_panel_section_id: '' @@ -2747,6 +2801,9 @@ tools: - name: proteinortho_summary owner: iuc tool_panel_section_id: '' +- name: psauron + owner: iuc + tool_panel_section_id: '' - name: pycoqc owner: iuc tool_panel_section_id: '' @@ -2855,262 +2912,241 @@ tools: - name: qiime_make_otu_table owner: iuc tool_panel_section_id: '' -- name: qiime2_core__tools__export - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2_core__tools__import - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2_core__tools__import_fastq - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__quality_filter__q_score - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__cull_seqs - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__degap_seqs - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__dereplicate - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__edit_taxonomy +- name: qiime2__dada2__denoise_ccs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_classifications +- name: qiime2__dada2__denoise_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_cross_validate +- name: qiime2__dada2__denoise_pyro owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_fit_classifier +- name: qiime2__dada2__denoise_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_seqs +- name: qiime2__dada2__plot_base_transitions owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_taxonomy +- name: qiime2__cutadapt__demux_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__extract_seq_segments +- name: qiime2__cutadapt__demux_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__filter_seqs_length +- name: qiime2__cutadapt__trim_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__filter_seqs_length_by_taxon +- name: qiime2__cutadapt__trim_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__filter_taxa +- name: qiime2__composition__add_pseudocount owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_bv_brc_genome_features +- name: qiime2__composition__ancom owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_bv_brc_genomes +- name: qiime2__composition__ancombc owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_bv_brc_metadata +- name: qiime2__composition__ancombc2 owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_eukaryome_data +- name: qiime2__composition__ancombc2_visualizer owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_gtdb_data +- name: qiime2__composition__da_barplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_midori2_data +- name: qiime2__composition__tabulate owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_ncbi_data +- name: qiime2__boots__alpha owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_ncbi_data_protein +- name: qiime2__boots__alpha_average owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_ncbi_genomes +- name: qiime2__boots__alpha_collection owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_pr2_data +- name: qiime2__boots__beta owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_silva_data +- name: qiime2__boots__beta_average owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_unite_data +- name: qiime2__boots__beta_collection owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__merge_taxa +- name: qiime2__boots__core_metrics owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__orient_reads +- name: qiime2__boots__kmer_diversity owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__orient_seqs +- name: qiime2__boots__resample owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__parse_silva_taxonomy +- name: qiime2__vsearch__cluster_features_closed_reference owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__reverse_transcribe +- name: qiime2__vsearch__cluster_features_de_novo owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__subsample_fasta +- name: qiime2__vsearch__cluster_features_open_reference owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__trim_alignment +- name: qiime2__vsearch__dereplicate_sequences owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__classify_samples +- name: qiime2__vsearch__fastq_stats owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__classify_samples_from_dist +- name: qiime2__vsearch__merge_pairs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__classify_samples_ncv +- name: qiime2__vsearch__uchime_denovo owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__confusion_matrix +- name: qiime2__vsearch__uchime_ref owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__fit_classifier +- name: qiime2__demux__emp_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__fit_regressor +- name: qiime2__demux__emp_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__heatmap +- name: qiime2__demux__filter_samples owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__metatable +- name: qiime2__demux__partition_samples_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__predict_classification +- name: qiime2__demux__partition_samples_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__predict_regression +- name: qiime2__demux__subsample_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__regress_samples +- name: qiime2__demux__subsample_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__regress_samples_ncv +- name: qiime2__demux__summarize owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__scatterplot +- name: qiime2__demux__tabulate_read_counts owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__split_table +- name: qiime2__deblur__denoise_16S owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__summarize +- name: qiime2__deblur__denoise_other owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__align_to_tree_mafft_fasttree +- name: qiime2__deblur__visualize_stats owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__align_to_tree_mafft_iqtree +- name: qiime2__diversity__adonis owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__align_to_tree_mafft_raxml +- name: qiime2__diversity__alpha owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__fasttree +- name: qiime2__diversity__alpha_correlation owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__filter_table +- name: qiime2__diversity__alpha_group_significance owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__filter_tree +- name: qiime2__diversity__alpha_phylogenetic owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__iqtree +- name: qiime2__diversity__alpha_rarefaction owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__iqtree_ultrafast_bootstrap +- name: qiime2__diversity__beta owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__midpoint_root +- name: qiime2__diversity__beta_correlation owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__raxml +- name: qiime2__diversity__beta_group_significance owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__raxml_rapid_bootstrap +- name: qiime2__diversity__beta_phylogenetic owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__robinson_foulds +- name: qiime2__diversity__beta_rarefaction owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__distance_matrix +- name: qiime2__diversity__bioenv owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__merge +- name: qiime2__diversity__core_metrics owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__shuffle_groups +- name: qiime2__diversity__core_metrics_phylogenetic owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__tabulate +- name: qiime2__diversity__filter_alpha_diversity owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__alpha_group_significance +- name: qiime2__diversity__filter_distance_matrix owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__collate_stats +- name: qiime2__diversity__mantel owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__facet_across +- name: qiime2__diversity__partial_procrustes owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__facet_within +- name: qiime2__diversity__pcoa owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__mann_whitney_u +- name: qiime2__diversity__pcoa_biplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__mann_whitney_u_facet +- name: qiime2__diversity__procrustes_analysis owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__plot_rainclouds +- name: qiime2__diversity__tsne owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__prep_alpha_distribution +- name: qiime2__diversity__umap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__wilcoxon_srt +- name: qiime2__emperor__biplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__wilcoxon_srt_facet +- name: qiime2__emperor__plot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__bowtie2_build +- name: qiime2__emperor__procrustes_plot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__decontam_identify +- name: qiime2_core__tools__export owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__decontam_identify_batches +- name: qiime2_core__tools__import owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__decontam_score_viz +- name: qiime2_core__tools__import_fastq owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__evaluate_composition +- name: qiime2__taxa__barplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__evaluate_seqs +- name: qiime2__taxa__barplot2 owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__evaluate_taxonomy +- name: qiime2__taxa__collapse owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__exclude_seqs +- name: qiime2__taxa__filter_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__filter_reads +- name: qiime2__taxa__filter_table owner: q2d2 tool_panel_section_id: '' - name: qiime2__diversity_lib__alpha_passthrough @@ -3149,253 +3185,244 @@ tools: - name: qiime2__diversity_lib__weighted_unifrac owner: q2d2 tool_panel_section_id: '' -- name: qiime2__alignment__mafft - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__alignment__mafft_add - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__alignment__mask - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__vizard__boxplot +- name: qiime2__stats__alpha_group_significance owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vizard__heatmap +- name: qiime2__stats__collate_stats owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vizard__lineplot +- name: qiime2__stats__facet_across owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vizard__scatterplot_2d +- name: qiime2__stats__facet_within owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__adonis +- name: qiime2__stats__mann_whitney_u owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha +- name: qiime2__stats__mann_whitney_u_facet owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_correlation +- name: qiime2__stats__plot_rainclouds owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_group_significance +- name: qiime2__stats__prep_alpha_distribution owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_phylogenetic +- name: qiime2__stats__wilcoxon_srt owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_rarefaction +- name: qiime2__stats__wilcoxon_srt_facet owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta +- name: qiime2__sample_classifier__classify_samples owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_correlation +- name: qiime2__sample_classifier__classify_samples_from_dist owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_group_significance +- name: qiime2__sample_classifier__classify_samples_ncv owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_phylogenetic +- name: qiime2__sample_classifier__confusion_matrix owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_rarefaction +- name: qiime2__sample_classifier__fit_classifier owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__bioenv +- name: qiime2__sample_classifier__fit_regressor owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__core_metrics +- name: qiime2__sample_classifier__heatmap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__core_metrics_phylogenetic +- name: qiime2__sample_classifier__metatable owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__filter_alpha_diversity +- name: qiime2__sample_classifier__predict_classification owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__filter_distance_matrix +- name: qiime2__sample_classifier__predict_regression owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__mantel +- name: qiime2__sample_classifier__regress_samples owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__partial_procrustes +- name: qiime2__sample_classifier__regress_samples_ncv owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__pcoa +- name: qiime2__sample_classifier__scatterplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__pcoa_biplot +- name: qiime2__sample_classifier__split_table owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__procrustes_analysis +- name: qiime2__sample_classifier__summarize owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__tsne +- name: qiime2__rescript__cull_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__umap +- name: qiime2__rescript__degap_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__emp_paired +- name: qiime2__rescript__dereplicate owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__emp_single +- name: qiime2__rescript__edit_taxonomy owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__filter_samples +- name: qiime2__rescript__evaluate_classifications owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__partition_samples_paired +- name: qiime2__rescript__evaluate_cross_validate owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__partition_samples_single +- name: qiime2__rescript__evaluate_fit_classifier owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__subsample_paired +- name: qiime2__rescript__evaluate_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__subsample_single +- name: qiime2__rescript__evaluate_taxonomy owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__summarize +- name: qiime2__rescript__extract_seq_segments owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__tabulate_read_counts +- name: qiime2__rescript__filter_seqs_length owner: q2d2 tool_panel_section_id: '' -- name: qiime2__deblur__denoise_16S +- name: qiime2__rescript__filter_seqs_length_by_taxon owner: q2d2 tool_panel_section_id: '' -- name: qiime2__deblur__denoise_other +- name: qiime2__rescript__filter_taxa owner: q2d2 tool_panel_section_id: '' -- name: qiime2__deblur__visualize_stats +- name: qiime2__rescript__get_bv_brc_genome_features owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_ccs +- name: qiime2__rescript__get_bv_brc_genomes owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_paired +- name: qiime2__rescript__get_bv_brc_metadata owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_pyro +- name: qiime2__rescript__get_eukaryome_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_single +- name: qiime2__rescript__get_gtdb_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__plot_base_transitions +- name: qiime2__rescript__get_midori2_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__cutadapt__demux_paired +- name: qiime2__rescript__get_ncbi_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__cutadapt__demux_single +- name: qiime2__rescript__get_ncbi_data_protein owner: q2d2 tool_panel_section_id: '' -- name: qiime2__cutadapt__trim_paired +- name: qiime2__rescript__get_ncbi_genomes owner: q2d2 tool_panel_section_id: '' -- name: qiime2__cutadapt__trim_single +- name: qiime2__rescript__get_pr2_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__add_pseudocount +- name: qiime2__rescript__get_silva_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancom +- name: qiime2__rescript__get_unite_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancombc +- name: qiime2__rescript__merge_taxa owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancombc2 +- name: qiime2__rescript__orient_reads owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancombc2_visualizer +- name: qiime2__rescript__orient_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__da_barplot +- name: qiime2__rescript__parse_silva_taxonomy owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__tabulate +- name: qiime2__rescript__reverse_transcribe owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__barplot +- name: qiime2__rescript__subsample_fasta owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__barplot2 +- name: qiime2__rescript__trim_alignment owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__collapse +- name: qiime2__quality_filter__q_score owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__filter_seqs +- name: qiime2__vizard__boxplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__filter_table +- name: qiime2__vizard__heatmap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__alpha +- name: qiime2__vizard__lineplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__alpha_average +- name: qiime2__vizard__scatterplot_2d owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__alpha_collection +- name: qiime2__alignment__mafft owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__beta +- name: qiime2__alignment__mafft_add owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__beta_average +- name: qiime2__alignment__mask owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__beta_collection +- name: qiime2__phylogeny__align_to_tree_mafft_fasttree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__core_metrics +- name: qiime2__phylogeny__align_to_tree_mafft_iqtree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__kmer_diversity +- name: qiime2__phylogeny__align_to_tree_mafft_raxml owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__resample +- name: qiime2__phylogeny__fasttree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__cluster_features_closed_reference +- name: qiime2__phylogeny__filter_table owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__cluster_features_de_novo +- name: qiime2__phylogeny__filter_tree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__cluster_features_open_reference +- name: qiime2__phylogeny__iqtree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__dereplicate_sequences +- name: qiime2__phylogeny__iqtree_ultrafast_bootstrap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__fastq_stats +- name: qiime2__phylogeny__midpoint_root owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__merge_pairs +- name: qiime2__phylogeny__raxml owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__uchime_denovo +- name: qiime2__phylogeny__raxml_rapid_bootstrap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__uchime_ref +- name: qiime2__phylogeny__robinson_foulds owner: q2d2 tool_panel_section_id: '' -- name: qiime2__emperor__biplot +- name: qiime2__fragment_insertion__classify_otus_experimental owner: q2d2 tool_panel_section_id: '' -- name: qiime2__emperor__plot +- name: qiime2__fragment_insertion__filter_features owner: q2d2 tool_panel_section_id: '' -- name: qiime2__emperor__procrustes_plot +- name: qiime2__fragment_insertion__sepp owner: q2d2 tool_panel_section_id: '' - name: qiime2__feature_classifier__blast @@ -3431,6 +3458,39 @@ tools: - name: qiime2__feature_classifier__vsearch_global owner: q2d2 tool_panel_section_id: '' +- name: qiime2__longitudinal__anova + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__feature_volatility + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__first_differences + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__first_distances + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__linear_mixed_effects + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__maturity_index + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__nmit + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__pairwise_differences + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__pairwise_distances + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__plot_feature_volatility + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__volatility + owner: q2d2 + tool_panel_section_id: '' - name: qiime2__feature_table___summarize owner: q2d2 tool_panel_section_id: '' @@ -3500,76 +3560,73 @@ tools: - name: qiime2__feature_table__transpose owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue___get_sequences - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__fondue__combine_seqs +- name: qiime2__quality_control__bowtie2_build owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__get_all +- name: qiime2__quality_control__decontam_identify owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__get_ids_from_query +- name: qiime2__quality_control__decontam_identify_batches owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__get_metadata +- name: qiime2__quality_control__decontam_score_viz owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__get_sequences +- name: qiime2__quality_control__evaluate_composition owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__merge_metadata +- name: qiime2__quality_control__evaluate_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__scrape_collection +- name: qiime2__quality_control__evaluate_taxonomy owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fragment_insertion__classify_otus_experimental +- name: qiime2__quality_control__exclude_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fragment_insertion__filter_features +- name: qiime2__quality_control__filter_reads owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fragment_insertion__sepp +- name: qiime2__metadata__distance_matrix owner: q2d2 tool_panel_section_id: '' -- name: qiime2__kmerizer__core_metrics +- name: qiime2__metadata__merge owner: q2d2 tool_panel_section_id: '' -- name: qiime2__kmerizer__seqs_to_kmers +- name: qiime2__metadata__shuffle_groups owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__anova +- name: qiime2__metadata__tabulate owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__feature_volatility +- name: qiime2__kmerizer__core_metrics owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__first_differences +- name: qiime2__kmerizer__seqs_to_kmers owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__first_distances +- name: qiime2__fondue___get_sequences owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__linear_mixed_effects +- name: qiime2__fondue__combine_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__maturity_index +- name: qiime2__fondue__get_all owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__nmit +- name: qiime2__fondue__get_ids_from_query owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__pairwise_differences +- name: qiime2__fondue__get_metadata owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__pairwise_distances +- name: qiime2__fondue__get_sequences owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__plot_feature_volatility +- name: qiime2__fondue__merge_metadata owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__volatility +- name: qiime2__fondue__scrape_collection owner: q2d2 tool_panel_section_id: '' - name: qiime2_dbotu_q2 @@ -3698,6 +3755,27 @@ tools: - name: rseqc_tin owner: nilesh tool_panel_section_id: '' +- name: samestr_compare + owner: iuc + tool_panel_section_id: '' +- name: samestr_convert + owner: iuc + tool_panel_section_id: '' +- name: samestr_extract + owner: iuc + tool_panel_section_id: '' +- name: samestr_filter + owner: iuc + tool_panel_section_id: '' +- name: samestr_merge + owner: iuc + tool_panel_section_id: '' +- name: samestr_stats + owner: iuc + tool_panel_section_id: '' +- name: samestr_summarize + owner: iuc + tool_panel_section_id: '' - name: scoary owner: iuc tool_panel_section_id: '' @@ -3822,10 +3900,10 @@ tools: owner: artbio tool_panel_section_id: '' - name: srst2 - owner: iuc + owner: nml tool_panel_section_id: '' - name: srst2 - owner: nml + owner: iuc tool_panel_section_id: '' - name: staramr_search owner: iuc @@ -3938,6 +4016,12 @@ tools: - name: varvamp owner: iuc tool_panel_section_id: '' +- name: vcontact2 + owner: iuc + tool_panel_section_id: '' +- name: vcontact2_gene2genome + owner: iuc + tool_panel_section_id: '' - name: vegan_diversity owner: iuc tool_panel_section_id: '' diff --git a/communities/microgalaxy/lab/tools/all/Galaxy@AuBi.yaml b/communities/microgalaxy/lab/tools/all/Galaxy@AuBi.yaml index a6aa3165d..b78d9c189 100644 --- a/communities/microgalaxy/lab/tools/all/Galaxy@AuBi.yaml +++ b/communities/microgalaxy/lab/tools/all/Galaxy@AuBi.yaml @@ -1037,6 +1037,9 @@ tools: - name: kmindex_query owner: iuc tool_panel_section_id: '' +- name: kneaddata + owner: iuc + tool_panel_section_id: '' - name: kraken-filter owner: devteam tool_panel_section_id: '' @@ -1064,6 +1067,9 @@ tools: - name: legsta owner: iuc tool_panel_section_id: '' +- name: liftoff + owner: iuc + tool_panel_section_id: '' - name: lighter owner: bgruening tool_panel_section_id: '' @@ -1259,6 +1265,27 @@ tools: - name: mg_toolkit_original_metadata owner: iuc tool_panel_section_id: '' +- name: mgnify_genome_search + owner: iuc + tool_panel_section_id: '' +- name: mgnify_pipelines_toolkit_classify_var_regions + owner: iuc + tool_panel_section_id: '' +- name: mgnify_pipelines_toolkit_make_asv_count_table + owner: iuc + tool_panel_section_id: '' +- name: mgnify_pipelines_toolkit_mapseq_to_asv_table + owner: iuc + tool_panel_section_id: '' +- name: mgnify_pipelines_toolkit_permute_primers + owner: iuc + tool_panel_section_id: '' +- name: mgnify_pipelines_toolkit_primer_val_classification + owner: iuc + tool_panel_section_id: '' +- name: mgnify_pipelines_toolkit_rev_comp_se_primers + owner: iuc + tool_panel_section_id: '' - name: mgnify_seqprep owner: bgruening tool_panel_section_id: '' @@ -1277,6 +1304,12 @@ tools: - name: miniprot_index owner: iuc tool_panel_section_id: '' +- name: mist_call + owner: iuc + tool_panel_section_id: '' +- name: mist_dists + owner: iuc + tool_panel_section_id: '' - name: mitos owner: iuc tool_panel_section_id: '' @@ -1334,6 +1367,9 @@ tools: - name: msstatstmt owner: galaxyp tool_panel_section_id: '' +- name: mtnucratio + owner: iuc + tool_panel_section_id: '' - name: multigsea owner: iuc tool_panel_section_id: '' @@ -1442,6 +1478,9 @@ tools: - name: obi_clean owner: iuc tool_panel_section_id: '' +- name: obi_complement + owner: iuc + tool_panel_section_id: '' - name: obi_convert owner: iuc tool_panel_section_id: '' @@ -1454,6 +1493,18 @@ tools: - name: obi_pairing owner: iuc tool_panel_section_id: '' +- name: obi_pcr + owner: iuc + tool_panel_section_id: '' +- name: obi_refidx + owner: iuc + tool_panel_section_id: '' +- name: obi_tag + owner: iuc + tool_panel_section_id: '' +- name: obi_taxonomy + owner: iuc + tool_panel_section_id: '' - name: obi_uniq owner: iuc tool_panel_section_id: '' @@ -2063,370 +2114,334 @@ tools: - name: proteinortho_summary owner: iuc tool_panel_section_id: '' +- name: psauron + owner: iuc + tool_panel_section_id: '' - name: qiime_collapse_samples owner: iuc tool_panel_section_id: '' - name: qiime_make_otu_table owner: iuc tool_panel_section_id: '' -- name: qiime2__rescript__cull_seqs - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__degap_seqs - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__dereplicate - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__edit_taxonomy - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_classifications - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_cross_validate - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_fit_classifier - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_seqs - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_taxonomy - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__extract_seq_segments - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__filter_seqs_length - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__filter_seqs_length_by_taxon - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__filter_taxa - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__get_bv_brc_genome_features +- name: qiime2__dada2__denoise_ccs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_bv_brc_genomes +- name: qiime2__dada2__denoise_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_bv_brc_metadata +- name: qiime2__dada2__denoise_pyro owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_eukaryome_data +- name: qiime2__dada2__denoise_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_gtdb_data +- name: qiime2__dada2__plot_base_transitions owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_midori2_data +- name: qiime2__composition__add_pseudocount owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_ncbi_data +- name: qiime2__composition__ancom owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_ncbi_data_protein +- name: qiime2__composition__ancombc owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_ncbi_genomes +- name: qiime2__composition__ancombc2 owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_pr2_data +- name: qiime2__composition__ancombc2_visualizer owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_silva_data +- name: qiime2__composition__da_barplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_unite_data +- name: qiime2__composition__tabulate owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__merge_taxa +- name: qiime2__boots__alpha owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__orient_reads +- name: qiime2__boots__alpha_average owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__orient_seqs +- name: qiime2__boots__alpha_collection owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__parse_silva_taxonomy +- name: qiime2__boots__beta owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__reverse_transcribe +- name: qiime2__boots__beta_average owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__subsample_fasta +- name: qiime2__boots__beta_collection owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__trim_alignment +- name: qiime2__boots__core_metrics owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__distance_matrix +- name: qiime2__boots__kmer_diversity owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__merge +- name: qiime2__boots__resample owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__shuffle_groups +- name: qiime2__demux__emp_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__tabulate +- name: qiime2__demux__emp_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__alpha_group_significance +- name: qiime2__demux__filter_samples owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__collate_stats +- name: qiime2__demux__partition_samples_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__facet_across +- name: qiime2__demux__partition_samples_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__facet_within +- name: qiime2__demux__subsample_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__mann_whitney_u +- name: qiime2__demux__subsample_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__mann_whitney_u_facet +- name: qiime2__demux__summarize owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__plot_rainclouds +- name: qiime2__demux__tabulate_read_counts owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__prep_alpha_distribution +- name: qiime2__deblur__denoise_16S owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__wilcoxon_srt +- name: qiime2__deblur__denoise_other owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__wilcoxon_srt_facet +- name: qiime2__deblur__visualize_stats owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__bowtie2_build +- name: qiime2__diversity__adonis owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__decontam_identify +- name: qiime2__diversity__alpha owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__decontam_identify_batches +- name: qiime2__diversity__alpha_correlation owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__decontam_score_viz +- name: qiime2__diversity__alpha_group_significance owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__evaluate_composition +- name: qiime2__diversity__alpha_phylogenetic owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__evaluate_seqs +- name: qiime2__diversity__alpha_rarefaction owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__evaluate_taxonomy +- name: qiime2__diversity__beta owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__exclude_seqs +- name: qiime2__diversity__beta_correlation owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__filter_reads +- name: qiime2__diversity__beta_group_significance owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vizard__boxplot +- name: qiime2__diversity__beta_phylogenetic owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vizard__heatmap +- name: qiime2__diversity__beta_rarefaction owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vizard__lineplot +- name: qiime2__diversity__bioenv owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vizard__scatterplot_2d +- name: qiime2__diversity__core_metrics owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__adonis +- name: qiime2__diversity__core_metrics_phylogenetic owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha +- name: qiime2__diversity__filter_alpha_diversity owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_correlation +- name: qiime2__diversity__filter_distance_matrix owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_group_significance +- name: qiime2__diversity__mantel owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_phylogenetic +- name: qiime2__diversity__partial_procrustes owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_rarefaction +- name: qiime2__diversity__pcoa owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta +- name: qiime2__diversity__pcoa_biplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_correlation +- name: qiime2__diversity__procrustes_analysis owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_group_significance +- name: qiime2__diversity__tsne owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_phylogenetic +- name: qiime2__diversity__umap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_rarefaction +- name: qiime2__taxa__barplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__bioenv +- name: qiime2__taxa__barplot2 owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__core_metrics +- name: qiime2__taxa__collapse owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__core_metrics_phylogenetic +- name: qiime2__taxa__filter_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__filter_alpha_diversity +- name: qiime2__taxa__filter_table owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__filter_distance_matrix +- name: qiime2__stats__alpha_group_significance owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__mantel +- name: qiime2__stats__collate_stats owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__partial_procrustes +- name: qiime2__stats__facet_across owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__pcoa +- name: qiime2__stats__facet_within owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__pcoa_biplot +- name: qiime2__stats__mann_whitney_u owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__procrustes_analysis +- name: qiime2__stats__mann_whitney_u_facet owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__tsne +- name: qiime2__stats__plot_rainclouds owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__umap +- name: qiime2__stats__prep_alpha_distribution owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__emp_paired +- name: qiime2__stats__wilcoxon_srt owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__emp_single +- name: qiime2__stats__wilcoxon_srt_facet owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__filter_samples +- name: qiime2__rescript__cull_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__partition_samples_paired +- name: qiime2__rescript__degap_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__partition_samples_single +- name: qiime2__rescript__dereplicate owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__subsample_paired +- name: qiime2__rescript__edit_taxonomy owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__subsample_single +- name: qiime2__rescript__evaluate_classifications owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__summarize +- name: qiime2__rescript__evaluate_cross_validate owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__tabulate_read_counts +- name: qiime2__rescript__evaluate_fit_classifier owner: q2d2 tool_panel_section_id: '' -- name: qiime2__deblur__denoise_16S +- name: qiime2__rescript__evaluate_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__deblur__denoise_other +- name: qiime2__rescript__evaluate_taxonomy owner: q2d2 tool_panel_section_id: '' -- name: qiime2__deblur__visualize_stats +- name: qiime2__rescript__extract_seq_segments owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_ccs +- name: qiime2__rescript__filter_seqs_length owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_paired +- name: qiime2__rescript__filter_seqs_length_by_taxon owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_pyro +- name: qiime2__rescript__filter_taxa owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_single +- name: qiime2__rescript__get_bv_brc_genome_features owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__plot_base_transitions +- name: qiime2__rescript__get_bv_brc_genomes owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__add_pseudocount +- name: qiime2__rescript__get_bv_brc_metadata owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancom +- name: qiime2__rescript__get_eukaryome_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancombc +- name: qiime2__rescript__get_gtdb_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancombc2 +- name: qiime2__rescript__get_midori2_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancombc2_visualizer +- name: qiime2__rescript__get_ncbi_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__da_barplot +- name: qiime2__rescript__get_ncbi_data_protein owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__tabulate +- name: qiime2__rescript__get_ncbi_genomes owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__barplot +- name: qiime2__rescript__get_pr2_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__barplot2 +- name: qiime2__rescript__get_silva_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__collapse +- name: qiime2__rescript__get_unite_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__filter_seqs +- name: qiime2__rescript__merge_taxa owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__filter_table +- name: qiime2__rescript__orient_reads owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__alpha +- name: qiime2__rescript__orient_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__alpha_average +- name: qiime2__rescript__parse_silva_taxonomy owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__alpha_collection +- name: qiime2__rescript__reverse_transcribe owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__beta +- name: qiime2__rescript__subsample_fasta owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__beta_average +- name: qiime2__rescript__trim_alignment owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__beta_collection +- name: qiime2__vizard__boxplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__core_metrics +- name: qiime2__vizard__heatmap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__kmer_diversity +- name: qiime2__vizard__lineplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__resample +- name: qiime2__vizard__scatterplot_2d owner: q2d2 tool_panel_section_id: '' - name: qiime2__feature_classifier__blast @@ -2531,6 +2546,51 @@ tools: - name: qiime2__feature_table__transpose owner: q2d2 tool_panel_section_id: '' +- name: qiime2__quality_control__bowtie2_build + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__quality_control__decontam_identify + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__quality_control__decontam_identify_batches + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__quality_control__decontam_score_viz + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__quality_control__evaluate_composition + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__quality_control__evaluate_seqs + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__quality_control__evaluate_taxonomy + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__quality_control__exclude_seqs + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__quality_control__filter_reads + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__metadata__distance_matrix + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__metadata__merge + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__metadata__shuffle_groups + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__metadata__tabulate + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__kmerizer__core_metrics + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__kmerizer__seqs_to_kmers + owner: q2d2 + tool_panel_section_id: '' - name: qiime2__fondue___get_sequences owner: q2d2 tool_panel_section_id: '' @@ -2555,12 +2615,6 @@ tools: - name: qiime2__fondue__scrape_collection owner: q2d2 tool_panel_section_id: '' -- name: qiime2__kmerizer__core_metrics - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__kmerizer__seqs_to_kmers - owner: q2d2 - tool_panel_section_id: '' - name: qiime2_dbotu_q2 owner: bgruening tool_panel_section_id: '' @@ -2609,6 +2663,27 @@ tools: - name: repeatexplorer_clustering owner: gga tool_panel_section_id: '' +- name: samestr_compare + owner: iuc + tool_panel_section_id: '' +- name: samestr_convert + owner: iuc + tool_panel_section_id: '' +- name: samestr_extract + owner: iuc + tool_panel_section_id: '' +- name: samestr_filter + owner: iuc + tool_panel_section_id: '' +- name: samestr_merge + owner: iuc + tool_panel_section_id: '' +- name: samestr_stats + owner: iuc + tool_panel_section_id: '' +- name: samestr_summarize + owner: iuc + tool_panel_section_id: '' - name: scoary owner: iuc tool_panel_section_id: '' @@ -2727,10 +2802,10 @@ tools: owner: artbio tool_panel_section_id: '' - name: srst2 - owner: iuc + owner: nml tool_panel_section_id: '' - name: srst2 - owner: nml + owner: iuc tool_panel_section_id: '' - name: stringmlst owner: nml @@ -2801,6 +2876,12 @@ tools: - name: varvamp owner: iuc tool_panel_section_id: '' +- name: vcontact2 + owner: iuc + tool_panel_section_id: '' +- name: vcontact2_gene2genome + owner: iuc + tool_panel_section_id: '' - name: vegan_diversity owner: iuc tool_panel_section_id: '' diff --git a/communities/microgalaxy/lab/tools/all/Galaxy@Pasteur.yaml b/communities/microgalaxy/lab/tools/all/Galaxy@Pasteur.yaml index 4e8f4f6f1..36a89d220 100644 --- a/communities/microgalaxy/lab/tools/all/Galaxy@Pasteur.yaml +++ b/communities/microgalaxy/lab/tools/all/Galaxy@Pasteur.yaml @@ -1109,6 +1109,9 @@ tools: - name: kmindex_query owner: iuc tool_panel_section_id: '' +- name: kneaddata + owner: iuc + tool_panel_section_id: '' - name: kofamscan owner: iuc tool_panel_section_id: '' @@ -1145,6 +1148,9 @@ tools: - name: legsta owner: iuc tool_panel_section_id: '' +- name: liftoff + owner: iuc + tool_panel_section_id: '' - name: lighter owner: bgruening tool_panel_section_id: '' @@ -1355,6 +1361,27 @@ tools: - name: mg_toolkit_original_metadata owner: iuc tool_panel_section_id: '' +- name: mgnify_genome_search + owner: iuc + tool_panel_section_id: '' +- name: mgnify_pipelines_toolkit_classify_var_regions + owner: iuc + tool_panel_section_id: '' +- name: mgnify_pipelines_toolkit_make_asv_count_table + owner: iuc + tool_panel_section_id: '' +- name: mgnify_pipelines_toolkit_mapseq_to_asv_table + owner: iuc + tool_panel_section_id: '' +- name: mgnify_pipelines_toolkit_permute_primers + owner: iuc + tool_panel_section_id: '' +- name: mgnify_pipelines_toolkit_primer_val_classification + owner: iuc + tool_panel_section_id: '' +- name: mgnify_pipelines_toolkit_rev_comp_se_primers + owner: iuc + tool_panel_section_id: '' - name: mgnify_seqprep owner: bgruening tool_panel_section_id: '' @@ -1376,6 +1403,12 @@ tools: - name: miniprot_index owner: iuc tool_panel_section_id: '' +- name: mist_call + owner: iuc + tool_panel_section_id: '' +- name: mist_dists + owner: iuc + tool_panel_section_id: '' - name: mitos owner: iuc tool_panel_section_id: '' @@ -1823,6 +1856,9 @@ tools: - name: msstats owner: galaxyp tool_panel_section_id: '' +- name: mtnucratio + owner: iuc + tool_panel_section_id: '' - name: multigsea owner: iuc tool_panel_section_id: '' @@ -1934,6 +1970,9 @@ tools: - name: obi_clean owner: iuc tool_panel_section_id: '' +- name: obi_complement + owner: iuc + tool_panel_section_id: '' - name: obi_convert owner: iuc tool_panel_section_id: '' @@ -1946,6 +1985,18 @@ tools: - name: obi_pairing owner: iuc tool_panel_section_id: '' +- name: obi_pcr + owner: iuc + tool_panel_section_id: '' +- name: obi_refidx + owner: iuc + tool_panel_section_id: '' +- name: obi_tag + owner: iuc + tool_panel_section_id: '' +- name: obi_taxonomy + owner: iuc + tool_panel_section_id: '' - name: obi_uniq owner: iuc tool_panel_section_id: '' @@ -2561,6 +2612,9 @@ tools: - name: ppanggolin_rarefaction owner: iuc tool_panel_section_id: '' +- name: prinseq + owner: iuc + tool_panel_section_id: '' - name: prodigal owner: iuc tool_panel_section_id: '' @@ -2579,6 +2633,9 @@ tools: - name: proteinortho_summary owner: iuc tool_panel_section_id: '' +- name: psauron + owner: iuc + tool_panel_section_id: '' - name: pygenomeTracks owner: iuc tool_panel_section_id: '' @@ -2684,262 +2741,241 @@ tools: - name: qiime_make_otu_table owner: iuc tool_panel_section_id: '' -- name: qiime2_core__tools__export - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2_core__tools__import - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2_core__tools__import_fastq - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__quality_filter__q_score - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__cull_seqs - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__degap_seqs - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__dereplicate - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__edit_taxonomy +- name: qiime2__dada2__denoise_ccs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_classifications +- name: qiime2__dada2__denoise_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_cross_validate +- name: qiime2__dada2__denoise_pyro owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_fit_classifier +- name: qiime2__dada2__denoise_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_seqs +- name: qiime2__dada2__plot_base_transitions owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_taxonomy +- name: qiime2__cutadapt__demux_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__extract_seq_segments +- name: qiime2__cutadapt__demux_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__filter_seqs_length +- name: qiime2__cutadapt__trim_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__filter_seqs_length_by_taxon +- name: qiime2__cutadapt__trim_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__filter_taxa +- name: qiime2__composition__add_pseudocount owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_bv_brc_genome_features +- name: qiime2__composition__ancom owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_bv_brc_genomes +- name: qiime2__composition__ancombc owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_bv_brc_metadata +- name: qiime2__composition__ancombc2 owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_eukaryome_data +- name: qiime2__composition__ancombc2_visualizer owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_gtdb_data +- name: qiime2__composition__da_barplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_midori2_data +- name: qiime2__composition__tabulate owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_ncbi_data +- name: qiime2__boots__alpha owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_ncbi_data_protein +- name: qiime2__boots__alpha_average owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_ncbi_genomes +- name: qiime2__boots__alpha_collection owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_pr2_data +- name: qiime2__boots__beta owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_silva_data +- name: qiime2__boots__beta_average owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_unite_data +- name: qiime2__boots__beta_collection owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__merge_taxa +- name: qiime2__boots__core_metrics owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__orient_reads +- name: qiime2__boots__kmer_diversity owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__orient_seqs +- name: qiime2__boots__resample owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__parse_silva_taxonomy +- name: qiime2__vsearch__cluster_features_closed_reference owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__reverse_transcribe +- name: qiime2__vsearch__cluster_features_de_novo owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__subsample_fasta +- name: qiime2__vsearch__cluster_features_open_reference owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__trim_alignment +- name: qiime2__vsearch__dereplicate_sequences owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__classify_samples +- name: qiime2__vsearch__fastq_stats owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__classify_samples_from_dist +- name: qiime2__vsearch__merge_pairs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__classify_samples_ncv +- name: qiime2__vsearch__uchime_denovo owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__confusion_matrix +- name: qiime2__vsearch__uchime_ref owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__fit_classifier +- name: qiime2__demux__emp_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__fit_regressor +- name: qiime2__demux__emp_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__heatmap +- name: qiime2__demux__filter_samples owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__metatable +- name: qiime2__demux__partition_samples_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__predict_classification +- name: qiime2__demux__partition_samples_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__predict_regression +- name: qiime2__demux__subsample_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__regress_samples +- name: qiime2__demux__subsample_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__regress_samples_ncv +- name: qiime2__demux__summarize owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__scatterplot +- name: qiime2__demux__tabulate_read_counts owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__split_table +- name: qiime2__deblur__denoise_16S owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__summarize +- name: qiime2__deblur__denoise_other owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__align_to_tree_mafft_fasttree +- name: qiime2__deblur__visualize_stats owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__align_to_tree_mafft_iqtree +- name: qiime2__diversity__adonis owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__align_to_tree_mafft_raxml +- name: qiime2__diversity__alpha owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__fasttree +- name: qiime2__diversity__alpha_correlation owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__filter_table +- name: qiime2__diversity__alpha_group_significance owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__filter_tree +- name: qiime2__diversity__alpha_phylogenetic owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__iqtree +- name: qiime2__diversity__alpha_rarefaction owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__iqtree_ultrafast_bootstrap +- name: qiime2__diversity__beta owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__midpoint_root +- name: qiime2__diversity__beta_correlation owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__raxml +- name: qiime2__diversity__beta_group_significance owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__raxml_rapid_bootstrap +- name: qiime2__diversity__beta_phylogenetic owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__robinson_foulds +- name: qiime2__diversity__beta_rarefaction owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__distance_matrix +- name: qiime2__diversity__bioenv owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__merge +- name: qiime2__diversity__core_metrics owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__shuffle_groups +- name: qiime2__diversity__core_metrics_phylogenetic owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__tabulate +- name: qiime2__diversity__filter_alpha_diversity owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__alpha_group_significance +- name: qiime2__diversity__filter_distance_matrix owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__collate_stats +- name: qiime2__diversity__mantel owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__facet_across +- name: qiime2__diversity__partial_procrustes owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__facet_within +- name: qiime2__diversity__pcoa owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__mann_whitney_u +- name: qiime2__diversity__pcoa_biplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__mann_whitney_u_facet +- name: qiime2__diversity__procrustes_analysis owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__plot_rainclouds +- name: qiime2__diversity__tsne owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__prep_alpha_distribution +- name: qiime2__diversity__umap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__wilcoxon_srt +- name: qiime2__emperor__biplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__wilcoxon_srt_facet +- name: qiime2__emperor__plot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__bowtie2_build +- name: qiime2__emperor__procrustes_plot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__decontam_identify +- name: qiime2_core__tools__export owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__decontam_identify_batches +- name: qiime2_core__tools__import owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__decontam_score_viz +- name: qiime2_core__tools__import_fastq owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__evaluate_composition +- name: qiime2__taxa__barplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__evaluate_seqs +- name: qiime2__taxa__barplot2 owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__evaluate_taxonomy +- name: qiime2__taxa__collapse owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__exclude_seqs +- name: qiime2__taxa__filter_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__filter_reads +- name: qiime2__taxa__filter_table owner: q2d2 tool_panel_section_id: '' - name: qiime2__diversity_lib__alpha_passthrough @@ -2978,253 +3014,244 @@ tools: - name: qiime2__diversity_lib__weighted_unifrac owner: q2d2 tool_panel_section_id: '' -- name: qiime2__alignment__mafft - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__alignment__mafft_add - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__alignment__mask - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__vizard__boxplot +- name: qiime2__stats__alpha_group_significance owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vizard__heatmap +- name: qiime2__stats__collate_stats owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vizard__lineplot +- name: qiime2__stats__facet_across owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vizard__scatterplot_2d +- name: qiime2__stats__facet_within owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__adonis +- name: qiime2__stats__mann_whitney_u owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha +- name: qiime2__stats__mann_whitney_u_facet owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_correlation +- name: qiime2__stats__plot_rainclouds owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_group_significance +- name: qiime2__stats__prep_alpha_distribution owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_phylogenetic +- name: qiime2__stats__wilcoxon_srt owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_rarefaction +- name: qiime2__stats__wilcoxon_srt_facet owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta +- name: qiime2__sample_classifier__classify_samples owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_correlation +- name: qiime2__sample_classifier__classify_samples_from_dist owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_group_significance +- name: qiime2__sample_classifier__classify_samples_ncv owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_phylogenetic +- name: qiime2__sample_classifier__confusion_matrix owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_rarefaction +- name: qiime2__sample_classifier__fit_classifier owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__bioenv +- name: qiime2__sample_classifier__fit_regressor owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__core_metrics +- name: qiime2__sample_classifier__heatmap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__core_metrics_phylogenetic +- name: qiime2__sample_classifier__metatable owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__filter_alpha_diversity +- name: qiime2__sample_classifier__predict_classification owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__filter_distance_matrix +- name: qiime2__sample_classifier__predict_regression owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__mantel +- name: qiime2__sample_classifier__regress_samples owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__partial_procrustes +- name: qiime2__sample_classifier__regress_samples_ncv owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__pcoa +- name: qiime2__sample_classifier__scatterplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__pcoa_biplot +- name: qiime2__sample_classifier__split_table owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__procrustes_analysis +- name: qiime2__sample_classifier__summarize owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__tsne +- name: qiime2__rescript__cull_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__umap +- name: qiime2__rescript__degap_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__emp_paired +- name: qiime2__rescript__dereplicate owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__emp_single +- name: qiime2__rescript__edit_taxonomy owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__filter_samples +- name: qiime2__rescript__evaluate_classifications owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__partition_samples_paired +- name: qiime2__rescript__evaluate_cross_validate owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__partition_samples_single +- name: qiime2__rescript__evaluate_fit_classifier owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__subsample_paired +- name: qiime2__rescript__evaluate_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__subsample_single +- name: qiime2__rescript__evaluate_taxonomy owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__summarize +- name: qiime2__rescript__extract_seq_segments owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__tabulate_read_counts +- name: qiime2__rescript__filter_seqs_length owner: q2d2 tool_panel_section_id: '' -- name: qiime2__deblur__denoise_16S +- name: qiime2__rescript__filter_seqs_length_by_taxon owner: q2d2 tool_panel_section_id: '' -- name: qiime2__deblur__denoise_other +- name: qiime2__rescript__filter_taxa owner: q2d2 tool_panel_section_id: '' -- name: qiime2__deblur__visualize_stats +- name: qiime2__rescript__get_bv_brc_genome_features owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_ccs +- name: qiime2__rescript__get_bv_brc_genomes owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_paired +- name: qiime2__rescript__get_bv_brc_metadata owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_pyro +- name: qiime2__rescript__get_eukaryome_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_single +- name: qiime2__rescript__get_gtdb_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__plot_base_transitions +- name: qiime2__rescript__get_midori2_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__cutadapt__demux_paired +- name: qiime2__rescript__get_ncbi_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__cutadapt__demux_single +- name: qiime2__rescript__get_ncbi_data_protein owner: q2d2 tool_panel_section_id: '' -- name: qiime2__cutadapt__trim_paired +- name: qiime2__rescript__get_ncbi_genomes owner: q2d2 tool_panel_section_id: '' -- name: qiime2__cutadapt__trim_single +- name: qiime2__rescript__get_pr2_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__add_pseudocount +- name: qiime2__rescript__get_silva_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancom +- name: qiime2__rescript__get_unite_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancombc +- name: qiime2__rescript__merge_taxa owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancombc2 +- name: qiime2__rescript__orient_reads owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancombc2_visualizer +- name: qiime2__rescript__orient_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__da_barplot +- name: qiime2__rescript__parse_silva_taxonomy owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__tabulate +- name: qiime2__rescript__reverse_transcribe owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__barplot +- name: qiime2__rescript__subsample_fasta owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__barplot2 +- name: qiime2__rescript__trim_alignment owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__collapse +- name: qiime2__quality_filter__q_score owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__filter_seqs +- name: qiime2__vizard__boxplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__filter_table +- name: qiime2__vizard__heatmap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__alpha +- name: qiime2__vizard__lineplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__alpha_average +- name: qiime2__vizard__scatterplot_2d owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__alpha_collection +- name: qiime2__alignment__mafft owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__beta +- name: qiime2__alignment__mafft_add owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__beta_average +- name: qiime2__alignment__mask owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__beta_collection +- name: qiime2__phylogeny__align_to_tree_mafft_fasttree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__core_metrics +- name: qiime2__phylogeny__align_to_tree_mafft_iqtree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__kmer_diversity +- name: qiime2__phylogeny__align_to_tree_mafft_raxml owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__resample +- name: qiime2__phylogeny__fasttree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__cluster_features_closed_reference +- name: qiime2__phylogeny__filter_table owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__cluster_features_de_novo +- name: qiime2__phylogeny__filter_tree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__cluster_features_open_reference +- name: qiime2__phylogeny__iqtree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__dereplicate_sequences +- name: qiime2__phylogeny__iqtree_ultrafast_bootstrap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__fastq_stats +- name: qiime2__phylogeny__midpoint_root owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__merge_pairs +- name: qiime2__phylogeny__raxml owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__uchime_denovo +- name: qiime2__phylogeny__raxml_rapid_bootstrap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__uchime_ref +- name: qiime2__phylogeny__robinson_foulds owner: q2d2 tool_panel_section_id: '' -- name: qiime2__emperor__biplot +- name: qiime2__fragment_insertion__classify_otus_experimental owner: q2d2 tool_panel_section_id: '' -- name: qiime2__emperor__plot +- name: qiime2__fragment_insertion__filter_features owner: q2d2 tool_panel_section_id: '' -- name: qiime2__emperor__procrustes_plot +- name: qiime2__fragment_insertion__sepp owner: q2d2 tool_panel_section_id: '' - name: qiime2__feature_classifier__blast @@ -3260,6 +3287,39 @@ tools: - name: qiime2__feature_classifier__vsearch_global owner: q2d2 tool_panel_section_id: '' +- name: qiime2__longitudinal__anova + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__feature_volatility + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__first_differences + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__first_distances + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__linear_mixed_effects + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__maturity_index + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__nmit + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__pairwise_differences + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__pairwise_distances + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__plot_feature_volatility + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__volatility + owner: q2d2 + tool_panel_section_id: '' - name: qiime2__feature_table___summarize owner: q2d2 tool_panel_section_id: '' @@ -3329,76 +3389,73 @@ tools: - name: qiime2__feature_table__transpose owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue___get_sequences - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__fondue__combine_seqs +- name: qiime2__quality_control__bowtie2_build owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__get_all +- name: qiime2__quality_control__decontam_identify owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__get_ids_from_query +- name: qiime2__quality_control__decontam_identify_batches owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__get_metadata +- name: qiime2__quality_control__decontam_score_viz owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__get_sequences +- name: qiime2__quality_control__evaluate_composition owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__merge_metadata +- name: qiime2__quality_control__evaluate_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__scrape_collection +- name: qiime2__quality_control__evaluate_taxonomy owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fragment_insertion__classify_otus_experimental +- name: qiime2__quality_control__exclude_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fragment_insertion__filter_features +- name: qiime2__quality_control__filter_reads owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fragment_insertion__sepp +- name: qiime2__metadata__distance_matrix owner: q2d2 tool_panel_section_id: '' -- name: qiime2__kmerizer__core_metrics +- name: qiime2__metadata__merge owner: q2d2 tool_panel_section_id: '' -- name: qiime2__kmerizer__seqs_to_kmers +- name: qiime2__metadata__shuffle_groups owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__anova +- name: qiime2__metadata__tabulate owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__feature_volatility +- name: qiime2__kmerizer__core_metrics owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__first_differences +- name: qiime2__kmerizer__seqs_to_kmers owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__first_distances +- name: qiime2__fondue___get_sequences owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__linear_mixed_effects +- name: qiime2__fondue__combine_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__maturity_index +- name: qiime2__fondue__get_all owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__nmit +- name: qiime2__fondue__get_ids_from_query owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__pairwise_differences +- name: qiime2__fondue__get_metadata owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__pairwise_distances +- name: qiime2__fondue__get_sequences owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__plot_feature_volatility +- name: qiime2__fondue__merge_metadata owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__volatility +- name: qiime2__fondue__scrape_collection owner: q2d2 tool_panel_section_id: '' - name: qiime2_dbotu_q2 @@ -3512,6 +3569,27 @@ tools: - name: rseqc_tin owner: nilesh tool_panel_section_id: '' +- name: samestr_compare + owner: iuc + tool_panel_section_id: '' +- name: samestr_convert + owner: iuc + tool_panel_section_id: '' +- name: samestr_extract + owner: iuc + tool_panel_section_id: '' +- name: samestr_filter + owner: iuc + tool_panel_section_id: '' +- name: samestr_merge + owner: iuc + tool_panel_section_id: '' +- name: samestr_stats + owner: iuc + tool_panel_section_id: '' +- name: samestr_summarize + owner: iuc + tool_panel_section_id: '' - name: scoary owner: iuc tool_panel_section_id: '' @@ -3627,10 +3705,10 @@ tools: owner: iuc tool_panel_section_id: '' - name: srst2 - owner: iuc + owner: nml tool_panel_section_id: '' - name: srst2 - owner: nml + owner: iuc tool_panel_section_id: '' - name: stringmlst owner: nml @@ -3734,6 +3812,12 @@ tools: - name: varvamp owner: iuc tool_panel_section_id: '' +- name: vcontact2 + owner: iuc + tool_panel_section_id: '' +- name: vcontact2_gene2genome + owner: iuc + tool_panel_section_id: '' - name: vegan_diversity owner: iuc tool_panel_section_id: '' diff --git a/communities/microgalaxy/lab/tools/all/GalaxyTrakr.yaml b/communities/microgalaxy/lab/tools/all/GalaxyTrakr.yaml index e2551257a..c3dfb7f06 100644 --- a/communities/microgalaxy/lab/tools/all/GalaxyTrakr.yaml +++ b/communities/microgalaxy/lab/tools/all/GalaxyTrakr.yaml @@ -881,9 +881,6 @@ tools: - name: idba_ud owner: iuc tool_panel_section_id: '' -- name: interproscan - owner: bgruening - tool_panel_section_id: '' - name: iphop_predict owner: ufz tool_panel_section_id: '' @@ -992,6 +989,9 @@ tools: - name: legsta owner: iuc tool_panel_section_id: '' +- name: liftoff + owner: iuc + tool_panel_section_id: '' - name: lighter owner: bgruening tool_panel_section_id: '' @@ -1160,6 +1160,27 @@ tools: - name: mg_toolkit_original_metadata owner: iuc tool_panel_section_id: '' +- name: mgnify_genome_search + owner: iuc + tool_panel_section_id: '' +- name: mgnify_pipelines_toolkit_classify_var_regions + owner: iuc + tool_panel_section_id: '' +- name: mgnify_pipelines_toolkit_make_asv_count_table + owner: iuc + tool_panel_section_id: '' +- name: mgnify_pipelines_toolkit_mapseq_to_asv_table + owner: iuc + tool_panel_section_id: '' +- name: mgnify_pipelines_toolkit_permute_primers + owner: iuc + tool_panel_section_id: '' +- name: mgnify_pipelines_toolkit_primer_val_classification + owner: iuc + tool_panel_section_id: '' +- name: mgnify_pipelines_toolkit_rev_comp_se_primers + owner: iuc + tool_panel_section_id: '' - name: mgnify_seqprep owner: bgruening tool_panel_section_id: '' @@ -1172,6 +1193,12 @@ tools: - name: miniprot_index owner: iuc tool_panel_section_id: '' +- name: mist_call + owner: iuc + tool_panel_section_id: '' +- name: mist_dists + owner: iuc + tool_panel_section_id: '' - name: mitos owner: iuc tool_panel_section_id: '' @@ -1610,6 +1637,9 @@ tools: - name: msstats owner: galaxyp tool_panel_section_id: '' +- name: mtnucratio + owner: iuc + tool_panel_section_id: '' - name: multigsea owner: iuc tool_panel_section_id: '' @@ -1703,6 +1733,9 @@ tools: - name: obi_clean owner: iuc tool_panel_section_id: '' +- name: obi_complement + owner: iuc + tool_panel_section_id: '' - name: obi_convert owner: iuc tool_panel_section_id: '' @@ -1715,6 +1748,18 @@ tools: - name: obi_pairing owner: iuc tool_panel_section_id: '' +- name: obi_pcr + owner: iuc + tool_panel_section_id: '' +- name: obi_refidx + owner: iuc + tool_panel_section_id: '' +- name: obi_tag + owner: iuc + tool_panel_section_id: '' +- name: obi_taxonomy + owner: iuc + tool_panel_section_id: '' - name: obi_uniq owner: iuc tool_panel_section_id: '' @@ -2330,6 +2375,9 @@ tools: - name: proteinortho_summary owner: iuc tool_panel_section_id: '' +- name: psauron + owner: iuc + tool_panel_section_id: '' - name: pycoqc owner: iuc tool_panel_section_id: '' @@ -2438,262 +2486,241 @@ tools: - name: qiime_make_otu_table owner: iuc tool_panel_section_id: '' -- name: qiime2_core__tools__export - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2_core__tools__import - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2_core__tools__import_fastq - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__quality_filter__q_score - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__cull_seqs - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__degap_seqs - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__dereplicate - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__edit_taxonomy +- name: qiime2__dada2__denoise_ccs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_classifications +- name: qiime2__dada2__denoise_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_cross_validate +- name: qiime2__dada2__denoise_pyro owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_fit_classifier +- name: qiime2__dada2__denoise_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_seqs +- name: qiime2__dada2__plot_base_transitions owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_taxonomy +- name: qiime2__cutadapt__demux_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__extract_seq_segments +- name: qiime2__cutadapt__demux_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__filter_seqs_length +- name: qiime2__cutadapt__trim_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__filter_seqs_length_by_taxon +- name: qiime2__cutadapt__trim_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__filter_taxa +- name: qiime2__composition__add_pseudocount owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_bv_brc_genome_features +- name: qiime2__composition__ancom owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_bv_brc_genomes +- name: qiime2__composition__ancombc owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_bv_brc_metadata +- name: qiime2__composition__ancombc2 owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_eukaryome_data +- name: qiime2__composition__ancombc2_visualizer owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_gtdb_data +- name: qiime2__composition__da_barplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_midori2_data +- name: qiime2__composition__tabulate owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_ncbi_data +- name: qiime2__boots__alpha owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_ncbi_data_protein +- name: qiime2__boots__alpha_average owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_ncbi_genomes +- name: qiime2__boots__alpha_collection owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_pr2_data +- name: qiime2__boots__beta owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_silva_data +- name: qiime2__boots__beta_average owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_unite_data +- name: qiime2__boots__beta_collection owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__merge_taxa +- name: qiime2__boots__core_metrics owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__orient_reads +- name: qiime2__boots__kmer_diversity owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__orient_seqs +- name: qiime2__boots__resample owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__parse_silva_taxonomy +- name: qiime2__vsearch__cluster_features_closed_reference owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__reverse_transcribe +- name: qiime2__vsearch__cluster_features_de_novo owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__subsample_fasta +- name: qiime2__vsearch__cluster_features_open_reference owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__trim_alignment +- name: qiime2__vsearch__dereplicate_sequences owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__classify_samples +- name: qiime2__vsearch__fastq_stats owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__classify_samples_from_dist +- name: qiime2__vsearch__merge_pairs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__classify_samples_ncv +- name: qiime2__vsearch__uchime_denovo owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__confusion_matrix +- name: qiime2__vsearch__uchime_ref owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__fit_classifier +- name: qiime2__demux__emp_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__fit_regressor +- name: qiime2__demux__emp_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__heatmap +- name: qiime2__demux__filter_samples owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__metatable +- name: qiime2__demux__partition_samples_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__predict_classification +- name: qiime2__demux__partition_samples_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__predict_regression +- name: qiime2__demux__subsample_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__regress_samples +- name: qiime2__demux__subsample_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__regress_samples_ncv +- name: qiime2__demux__summarize owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__scatterplot +- name: qiime2__demux__tabulate_read_counts owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__split_table +- name: qiime2__deblur__denoise_16S owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__summarize +- name: qiime2__deblur__denoise_other owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__align_to_tree_mafft_fasttree +- name: qiime2__deblur__visualize_stats owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__align_to_tree_mafft_iqtree +- name: qiime2__diversity__adonis owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__align_to_tree_mafft_raxml +- name: qiime2__diversity__alpha owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__fasttree +- name: qiime2__diversity__alpha_correlation owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__filter_table +- name: qiime2__diversity__alpha_group_significance owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__filter_tree +- name: qiime2__diversity__alpha_phylogenetic owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__iqtree +- name: qiime2__diversity__alpha_rarefaction owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__iqtree_ultrafast_bootstrap +- name: qiime2__diversity__beta owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__midpoint_root +- name: qiime2__diversity__beta_correlation owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__raxml +- name: qiime2__diversity__beta_group_significance owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__raxml_rapid_bootstrap +- name: qiime2__diversity__beta_phylogenetic owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__robinson_foulds +- name: qiime2__diversity__beta_rarefaction owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__distance_matrix +- name: qiime2__diversity__bioenv owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__merge +- name: qiime2__diversity__core_metrics owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__shuffle_groups +- name: qiime2__diversity__core_metrics_phylogenetic owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__tabulate +- name: qiime2__diversity__filter_alpha_diversity owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__alpha_group_significance +- name: qiime2__diversity__filter_distance_matrix owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__collate_stats +- name: qiime2__diversity__mantel owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__facet_across +- name: qiime2__diversity__partial_procrustes owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__facet_within +- name: qiime2__diversity__pcoa owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__mann_whitney_u +- name: qiime2__diversity__pcoa_biplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__mann_whitney_u_facet +- name: qiime2__diversity__procrustes_analysis owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__plot_rainclouds +- name: qiime2__diversity__tsne owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__prep_alpha_distribution +- name: qiime2__diversity__umap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__wilcoxon_srt +- name: qiime2__emperor__biplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__wilcoxon_srt_facet +- name: qiime2__emperor__plot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__bowtie2_build +- name: qiime2__emperor__procrustes_plot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__decontam_identify +- name: qiime2_core__tools__export owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__decontam_identify_batches +- name: qiime2_core__tools__import owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__decontam_score_viz +- name: qiime2_core__tools__import_fastq owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__evaluate_composition +- name: qiime2__taxa__barplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__evaluate_seqs +- name: qiime2__taxa__barplot2 owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__evaluate_taxonomy +- name: qiime2__taxa__collapse owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__exclude_seqs +- name: qiime2__taxa__filter_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__filter_reads +- name: qiime2__taxa__filter_table owner: q2d2 tool_panel_section_id: '' - name: qiime2__diversity_lib__alpha_passthrough @@ -2732,253 +2759,244 @@ tools: - name: qiime2__diversity_lib__weighted_unifrac owner: q2d2 tool_panel_section_id: '' -- name: qiime2__alignment__mafft - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__alignment__mafft_add - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__alignment__mask - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__vizard__boxplot +- name: qiime2__stats__alpha_group_significance owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vizard__heatmap +- name: qiime2__stats__collate_stats owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vizard__lineplot +- name: qiime2__stats__facet_across owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vizard__scatterplot_2d +- name: qiime2__stats__facet_within owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__adonis +- name: qiime2__stats__mann_whitney_u owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha +- name: qiime2__stats__mann_whitney_u_facet owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_correlation +- name: qiime2__stats__plot_rainclouds owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_group_significance +- name: qiime2__stats__prep_alpha_distribution owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_phylogenetic +- name: qiime2__stats__wilcoxon_srt owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_rarefaction +- name: qiime2__stats__wilcoxon_srt_facet owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta +- name: qiime2__sample_classifier__classify_samples owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_correlation +- name: qiime2__sample_classifier__classify_samples_from_dist owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_group_significance +- name: qiime2__sample_classifier__classify_samples_ncv owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_phylogenetic +- name: qiime2__sample_classifier__confusion_matrix owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_rarefaction +- name: qiime2__sample_classifier__fit_classifier owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__bioenv +- name: qiime2__sample_classifier__fit_regressor owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__core_metrics +- name: qiime2__sample_classifier__heatmap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__core_metrics_phylogenetic +- name: qiime2__sample_classifier__metatable owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__filter_alpha_diversity +- name: qiime2__sample_classifier__predict_classification owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__filter_distance_matrix +- name: qiime2__sample_classifier__predict_regression owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__mantel +- name: qiime2__sample_classifier__regress_samples owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__partial_procrustes +- name: qiime2__sample_classifier__regress_samples_ncv owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__pcoa +- name: qiime2__sample_classifier__scatterplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__pcoa_biplot +- name: qiime2__sample_classifier__split_table owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__procrustes_analysis +- name: qiime2__sample_classifier__summarize owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__tsne +- name: qiime2__rescript__cull_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__umap +- name: qiime2__rescript__degap_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__emp_paired +- name: qiime2__rescript__dereplicate owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__emp_single +- name: qiime2__rescript__edit_taxonomy owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__filter_samples +- name: qiime2__rescript__evaluate_classifications owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__partition_samples_paired +- name: qiime2__rescript__evaluate_cross_validate owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__partition_samples_single +- name: qiime2__rescript__evaluate_fit_classifier owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__subsample_paired +- name: qiime2__rescript__evaluate_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__subsample_single +- name: qiime2__rescript__evaluate_taxonomy owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__summarize +- name: qiime2__rescript__extract_seq_segments owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__tabulate_read_counts +- name: qiime2__rescript__filter_seqs_length owner: q2d2 tool_panel_section_id: '' -- name: qiime2__deblur__denoise_16S +- name: qiime2__rescript__filter_seqs_length_by_taxon owner: q2d2 tool_panel_section_id: '' -- name: qiime2__deblur__denoise_other +- name: qiime2__rescript__filter_taxa owner: q2d2 tool_panel_section_id: '' -- name: qiime2__deblur__visualize_stats +- name: qiime2__rescript__get_bv_brc_genome_features owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_ccs +- name: qiime2__rescript__get_bv_brc_genomes owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_paired +- name: qiime2__rescript__get_bv_brc_metadata owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_pyro +- name: qiime2__rescript__get_eukaryome_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_single +- name: qiime2__rescript__get_gtdb_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__plot_base_transitions +- name: qiime2__rescript__get_midori2_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__cutadapt__demux_paired +- name: qiime2__rescript__get_ncbi_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__cutadapt__demux_single +- name: qiime2__rescript__get_ncbi_data_protein owner: q2d2 tool_panel_section_id: '' -- name: qiime2__cutadapt__trim_paired +- name: qiime2__rescript__get_ncbi_genomes owner: q2d2 tool_panel_section_id: '' -- name: qiime2__cutadapt__trim_single +- name: qiime2__rescript__get_pr2_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__add_pseudocount +- name: qiime2__rescript__get_silva_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancom +- name: qiime2__rescript__get_unite_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancombc +- name: qiime2__rescript__merge_taxa owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancombc2 +- name: qiime2__rescript__orient_reads owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancombc2_visualizer +- name: qiime2__rescript__orient_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__da_barplot +- name: qiime2__rescript__parse_silva_taxonomy owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__tabulate +- name: qiime2__rescript__reverse_transcribe owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__barplot +- name: qiime2__rescript__subsample_fasta owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__barplot2 +- name: qiime2__rescript__trim_alignment owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__collapse +- name: qiime2__quality_filter__q_score owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__filter_seqs +- name: qiime2__vizard__boxplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__filter_table +- name: qiime2__vizard__heatmap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__alpha +- name: qiime2__vizard__lineplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__alpha_average +- name: qiime2__vizard__scatterplot_2d owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__alpha_collection +- name: qiime2__alignment__mafft owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__beta +- name: qiime2__alignment__mafft_add owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__beta_average +- name: qiime2__alignment__mask owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__beta_collection +- name: qiime2__phylogeny__align_to_tree_mafft_fasttree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__core_metrics +- name: qiime2__phylogeny__align_to_tree_mafft_iqtree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__kmer_diversity +- name: qiime2__phylogeny__align_to_tree_mafft_raxml owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__resample +- name: qiime2__phylogeny__fasttree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__cluster_features_closed_reference +- name: qiime2__phylogeny__filter_table owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__cluster_features_de_novo +- name: qiime2__phylogeny__filter_tree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__cluster_features_open_reference +- name: qiime2__phylogeny__iqtree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__dereplicate_sequences +- name: qiime2__phylogeny__iqtree_ultrafast_bootstrap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__fastq_stats +- name: qiime2__phylogeny__midpoint_root owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__merge_pairs +- name: qiime2__phylogeny__raxml owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__uchime_denovo +- name: qiime2__phylogeny__raxml_rapid_bootstrap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__uchime_ref +- name: qiime2__phylogeny__robinson_foulds owner: q2d2 tool_panel_section_id: '' -- name: qiime2__emperor__biplot +- name: qiime2__fragment_insertion__classify_otus_experimental owner: q2d2 tool_panel_section_id: '' -- name: qiime2__emperor__plot +- name: qiime2__fragment_insertion__filter_features owner: q2d2 tool_panel_section_id: '' -- name: qiime2__emperor__procrustes_plot +- name: qiime2__fragment_insertion__sepp owner: q2d2 tool_panel_section_id: '' - name: qiime2__feature_classifier__blast @@ -3014,6 +3032,39 @@ tools: - name: qiime2__feature_classifier__vsearch_global owner: q2d2 tool_panel_section_id: '' +- name: qiime2__longitudinal__anova + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__feature_volatility + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__first_differences + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__first_distances + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__linear_mixed_effects + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__maturity_index + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__nmit + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__pairwise_differences + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__pairwise_distances + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__plot_feature_volatility + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__volatility + owner: q2d2 + tool_panel_section_id: '' - name: qiime2__feature_table___summarize owner: q2d2 tool_panel_section_id: '' @@ -3083,76 +3134,73 @@ tools: - name: qiime2__feature_table__transpose owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue___get_sequences - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__fondue__combine_seqs +- name: qiime2__quality_control__bowtie2_build owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__get_all +- name: qiime2__quality_control__decontam_identify owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__get_ids_from_query +- name: qiime2__quality_control__decontam_identify_batches owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__get_metadata +- name: qiime2__quality_control__decontam_score_viz owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__get_sequences +- name: qiime2__quality_control__evaluate_composition owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__merge_metadata +- name: qiime2__quality_control__evaluate_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__scrape_collection +- name: qiime2__quality_control__evaluate_taxonomy owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fragment_insertion__classify_otus_experimental +- name: qiime2__quality_control__exclude_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fragment_insertion__filter_features +- name: qiime2__quality_control__filter_reads owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fragment_insertion__sepp +- name: qiime2__metadata__distance_matrix owner: q2d2 tool_panel_section_id: '' -- name: qiime2__kmerizer__core_metrics +- name: qiime2__metadata__merge owner: q2d2 tool_panel_section_id: '' -- name: qiime2__kmerizer__seqs_to_kmers +- name: qiime2__metadata__shuffle_groups owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__anova +- name: qiime2__metadata__tabulate owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__feature_volatility +- name: qiime2__kmerizer__core_metrics owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__first_differences +- name: qiime2__kmerizer__seqs_to_kmers owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__first_distances +- name: qiime2__fondue___get_sequences owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__linear_mixed_effects +- name: qiime2__fondue__combine_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__maturity_index +- name: qiime2__fondue__get_all owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__nmit +- name: qiime2__fondue__get_ids_from_query owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__pairwise_differences +- name: qiime2__fondue__get_metadata owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__pairwise_distances +- name: qiime2__fondue__get_sequences owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__plot_feature_volatility +- name: qiime2__fondue__merge_metadata owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__volatility +- name: qiime2__fondue__scrape_collection owner: q2d2 tool_panel_section_id: '' - name: qiime2_dbotu_q2 @@ -3242,6 +3290,27 @@ tools: - name: rseqc_tin owner: nilesh tool_panel_section_id: '' +- name: samestr_compare + owner: iuc + tool_panel_section_id: '' +- name: samestr_convert + owner: iuc + tool_panel_section_id: '' +- name: samestr_extract + owner: iuc + tool_panel_section_id: '' +- name: samestr_filter + owner: iuc + tool_panel_section_id: '' +- name: samestr_merge + owner: iuc + tool_panel_section_id: '' +- name: samestr_stats + owner: iuc + tool_panel_section_id: '' +- name: samestr_summarize + owner: iuc + tool_panel_section_id: '' - name: scoary owner: iuc tool_panel_section_id: '' @@ -3410,6 +3479,12 @@ tools: - name: varvamp owner: iuc tool_panel_section_id: '' +- name: vcontact2 + owner: iuc + tool_panel_section_id: '' +- name: vcontact2_gene2genome + owner: iuc + tool_panel_section_id: '' - name: velvetg owner: devteam tool_panel_section_id: '' diff --git a/communities/microgalaxy/lab/tools/all/HyPhy_HIV_NGS_Tools.yaml b/communities/microgalaxy/lab/tools/all/HyPhy_HIV_NGS_Tools.yaml index b6371915b..9460f5425 100644 --- a/communities/microgalaxy/lab/tools/all/HyPhy_HIV_NGS_Tools.yaml +++ b/communities/microgalaxy/lab/tools/all/HyPhy_HIV_NGS_Tools.yaml @@ -1223,6 +1223,9 @@ tools: - name: kmindex_query owner: iuc tool_panel_section_id: '' +- name: kneaddata + owner: iuc + tool_panel_section_id: '' - name: kofamscan owner: iuc tool_panel_section_id: '' @@ -1280,6 +1283,9 @@ tools: - name: legsta owner: iuc tool_panel_section_id: '' +- name: liftoff + owner: iuc + tool_panel_section_id: '' - name: lighter owner: bgruening tool_panel_section_id: '' @@ -1499,6 +1505,27 @@ tools: - name: mg_toolkit_original_metadata owner: iuc tool_panel_section_id: '' +- name: mgnify_genome_search + owner: iuc + tool_panel_section_id: '' +- name: mgnify_pipelines_toolkit_classify_var_regions + owner: iuc + tool_panel_section_id: '' +- name: mgnify_pipelines_toolkit_make_asv_count_table + owner: iuc + tool_panel_section_id: '' +- name: mgnify_pipelines_toolkit_mapseq_to_asv_table + owner: iuc + tool_panel_section_id: '' +- name: mgnify_pipelines_toolkit_permute_primers + owner: iuc + tool_panel_section_id: '' +- name: mgnify_pipelines_toolkit_primer_val_classification + owner: iuc + tool_panel_section_id: '' +- name: mgnify_pipelines_toolkit_rev_comp_se_primers + owner: iuc + tool_panel_section_id: '' - name: mgnify_seqprep owner: bgruening tool_panel_section_id: '' @@ -1520,6 +1547,12 @@ tools: - name: miniprot_index owner: iuc tool_panel_section_id: '' +- name: mist_call + owner: iuc + tool_panel_section_id: '' +- name: mist_dists + owner: iuc + tool_panel_section_id: '' - name: mitos owner: iuc tool_panel_section_id: '' @@ -1970,6 +2003,9 @@ tools: - name: msstats owner: galaxyp tool_panel_section_id: '' +- name: mtnucratio + owner: iuc + tool_panel_section_id: '' - name: multigsea owner: iuc tool_panel_section_id: '' @@ -2087,6 +2123,9 @@ tools: - name: obi_clean owner: iuc tool_panel_section_id: '' +- name: obi_complement + owner: iuc + tool_panel_section_id: '' - name: obi_convert owner: iuc tool_panel_section_id: '' @@ -2099,6 +2138,18 @@ tools: - name: obi_pairing owner: iuc tool_panel_section_id: '' +- name: obi_pcr + owner: iuc + tool_panel_section_id: '' +- name: obi_refidx + owner: iuc + tool_panel_section_id: '' +- name: obi_tag + owner: iuc + tool_panel_section_id: '' +- name: obi_taxonomy + owner: iuc + tool_panel_section_id: '' - name: obi_uniq owner: iuc tool_panel_section_id: '' @@ -2717,6 +2768,9 @@ tools: - name: ppanggolin_rarefaction owner: iuc tool_panel_section_id: '' +- name: prinseq + owner: iuc + tool_panel_section_id: '' - name: prodigal owner: iuc tool_panel_section_id: '' @@ -2738,6 +2792,9 @@ tools: - name: proteinortho_summary owner: iuc tool_panel_section_id: '' +- name: psauron + owner: iuc + tool_panel_section_id: '' - name: pycoqc owner: iuc tool_panel_section_id: '' @@ -2846,262 +2903,241 @@ tools: - name: qiime_make_otu_table owner: iuc tool_panel_section_id: '' -- name: qiime2_core__tools__export - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2_core__tools__import - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2_core__tools__import_fastq - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__quality_filter__q_score - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__cull_seqs - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__degap_seqs - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__dereplicate - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__edit_taxonomy +- name: qiime2__dada2__denoise_ccs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_classifications +- name: qiime2__dada2__denoise_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_cross_validate +- name: qiime2__dada2__denoise_pyro owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_fit_classifier +- name: qiime2__dada2__denoise_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_seqs +- name: qiime2__dada2__plot_base_transitions owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_taxonomy +- name: qiime2__cutadapt__demux_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__extract_seq_segments +- name: qiime2__cutadapt__demux_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__filter_seqs_length +- name: qiime2__cutadapt__trim_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__filter_seqs_length_by_taxon +- name: qiime2__cutadapt__trim_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__filter_taxa +- name: qiime2__composition__add_pseudocount owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_bv_brc_genome_features +- name: qiime2__composition__ancom owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_bv_brc_genomes +- name: qiime2__composition__ancombc owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_bv_brc_metadata +- name: qiime2__composition__ancombc2 owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_eukaryome_data +- name: qiime2__composition__ancombc2_visualizer owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_gtdb_data +- name: qiime2__composition__da_barplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_midori2_data +- name: qiime2__composition__tabulate owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_ncbi_data +- name: qiime2__boots__alpha owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_ncbi_data_protein +- name: qiime2__boots__alpha_average owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_ncbi_genomes +- name: qiime2__boots__alpha_collection owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_pr2_data +- name: qiime2__boots__beta owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_silva_data +- name: qiime2__boots__beta_average owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_unite_data +- name: qiime2__boots__beta_collection owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__merge_taxa +- name: qiime2__boots__core_metrics owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__orient_reads +- name: qiime2__boots__kmer_diversity owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__orient_seqs +- name: qiime2__boots__resample owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__parse_silva_taxonomy +- name: qiime2__vsearch__cluster_features_closed_reference owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__reverse_transcribe +- name: qiime2__vsearch__cluster_features_de_novo owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__subsample_fasta +- name: qiime2__vsearch__cluster_features_open_reference owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__trim_alignment +- name: qiime2__vsearch__dereplicate_sequences owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__classify_samples +- name: qiime2__vsearch__fastq_stats owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__classify_samples_from_dist +- name: qiime2__vsearch__merge_pairs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__classify_samples_ncv +- name: qiime2__vsearch__uchime_denovo owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__confusion_matrix +- name: qiime2__vsearch__uchime_ref owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__fit_classifier +- name: qiime2__demux__emp_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__fit_regressor +- name: qiime2__demux__emp_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__heatmap +- name: qiime2__demux__filter_samples owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__metatable +- name: qiime2__demux__partition_samples_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__predict_classification +- name: qiime2__demux__partition_samples_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__predict_regression +- name: qiime2__demux__subsample_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__regress_samples +- name: qiime2__demux__subsample_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__regress_samples_ncv +- name: qiime2__demux__summarize owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__scatterplot +- name: qiime2__demux__tabulate_read_counts owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__split_table +- name: qiime2__deblur__denoise_16S owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__summarize +- name: qiime2__deblur__denoise_other owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__align_to_tree_mafft_fasttree +- name: qiime2__deblur__visualize_stats owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__align_to_tree_mafft_iqtree +- name: qiime2__diversity__adonis owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__align_to_tree_mafft_raxml +- name: qiime2__diversity__alpha owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__fasttree +- name: qiime2__diversity__alpha_correlation owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__filter_table +- name: qiime2__diversity__alpha_group_significance owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__filter_tree +- name: qiime2__diversity__alpha_phylogenetic owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__iqtree +- name: qiime2__diversity__alpha_rarefaction owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__iqtree_ultrafast_bootstrap +- name: qiime2__diversity__beta owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__midpoint_root +- name: qiime2__diversity__beta_correlation owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__raxml +- name: qiime2__diversity__beta_group_significance owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__raxml_rapid_bootstrap +- name: qiime2__diversity__beta_phylogenetic owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__robinson_foulds +- name: qiime2__diversity__beta_rarefaction owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__distance_matrix +- name: qiime2__diversity__bioenv owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__merge +- name: qiime2__diversity__core_metrics owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__shuffle_groups +- name: qiime2__diversity__core_metrics_phylogenetic owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__tabulate +- name: qiime2__diversity__filter_alpha_diversity owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__alpha_group_significance +- name: qiime2__diversity__filter_distance_matrix owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__collate_stats +- name: qiime2__diversity__mantel owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__facet_across +- name: qiime2__diversity__partial_procrustes owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__facet_within +- name: qiime2__diversity__pcoa owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__mann_whitney_u +- name: qiime2__diversity__pcoa_biplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__mann_whitney_u_facet +- name: qiime2__diversity__procrustes_analysis owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__plot_rainclouds +- name: qiime2__diversity__tsne owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__prep_alpha_distribution +- name: qiime2__diversity__umap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__wilcoxon_srt +- name: qiime2__emperor__biplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__wilcoxon_srt_facet +- name: qiime2__emperor__plot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__bowtie2_build +- name: qiime2__emperor__procrustes_plot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__decontam_identify +- name: qiime2_core__tools__export owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__decontam_identify_batches +- name: qiime2_core__tools__import owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__decontam_score_viz +- name: qiime2_core__tools__import_fastq owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__evaluate_composition +- name: qiime2__taxa__barplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__evaluate_seqs +- name: qiime2__taxa__barplot2 owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__evaluate_taxonomy +- name: qiime2__taxa__collapse owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__exclude_seqs +- name: qiime2__taxa__filter_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__filter_reads +- name: qiime2__taxa__filter_table owner: q2d2 tool_panel_section_id: '' - name: qiime2__diversity_lib__alpha_passthrough @@ -3140,253 +3176,244 @@ tools: - name: qiime2__diversity_lib__weighted_unifrac owner: q2d2 tool_panel_section_id: '' -- name: qiime2__alignment__mafft - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__alignment__mafft_add - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__alignment__mask - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__vizard__boxplot +- name: qiime2__stats__alpha_group_significance owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vizard__heatmap +- name: qiime2__stats__collate_stats owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vizard__lineplot +- name: qiime2__stats__facet_across owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vizard__scatterplot_2d +- name: qiime2__stats__facet_within owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__adonis +- name: qiime2__stats__mann_whitney_u owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha +- name: qiime2__stats__mann_whitney_u_facet owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_correlation +- name: qiime2__stats__plot_rainclouds owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_group_significance +- name: qiime2__stats__prep_alpha_distribution owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_phylogenetic +- name: qiime2__stats__wilcoxon_srt owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_rarefaction +- name: qiime2__stats__wilcoxon_srt_facet owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta +- name: qiime2__sample_classifier__classify_samples owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_correlation +- name: qiime2__sample_classifier__classify_samples_from_dist owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_group_significance +- name: qiime2__sample_classifier__classify_samples_ncv owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_phylogenetic +- name: qiime2__sample_classifier__confusion_matrix owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_rarefaction +- name: qiime2__sample_classifier__fit_classifier owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__bioenv +- name: qiime2__sample_classifier__fit_regressor owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__core_metrics +- name: qiime2__sample_classifier__heatmap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__core_metrics_phylogenetic +- name: qiime2__sample_classifier__metatable owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__filter_alpha_diversity +- name: qiime2__sample_classifier__predict_classification owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__filter_distance_matrix +- name: qiime2__sample_classifier__predict_regression owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__mantel +- name: qiime2__sample_classifier__regress_samples owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__partial_procrustes +- name: qiime2__sample_classifier__regress_samples_ncv owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__pcoa +- name: qiime2__sample_classifier__scatterplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__pcoa_biplot +- name: qiime2__sample_classifier__split_table owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__procrustes_analysis +- name: qiime2__sample_classifier__summarize owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__tsne +- name: qiime2__rescript__cull_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__umap +- name: qiime2__rescript__degap_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__emp_paired +- name: qiime2__rescript__dereplicate owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__emp_single +- name: qiime2__rescript__edit_taxonomy owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__filter_samples +- name: qiime2__rescript__evaluate_classifications owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__partition_samples_paired +- name: qiime2__rescript__evaluate_cross_validate owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__partition_samples_single +- name: qiime2__rescript__evaluate_fit_classifier owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__subsample_paired +- name: qiime2__rescript__evaluate_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__subsample_single +- name: qiime2__rescript__evaluate_taxonomy owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__summarize +- name: qiime2__rescript__extract_seq_segments owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__tabulate_read_counts +- name: qiime2__rescript__filter_seqs_length owner: q2d2 tool_panel_section_id: '' -- name: qiime2__deblur__denoise_16S +- name: qiime2__rescript__filter_seqs_length_by_taxon owner: q2d2 tool_panel_section_id: '' -- name: qiime2__deblur__denoise_other +- name: qiime2__rescript__filter_taxa owner: q2d2 tool_panel_section_id: '' -- name: qiime2__deblur__visualize_stats +- name: qiime2__rescript__get_bv_brc_genome_features owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_ccs +- name: qiime2__rescript__get_bv_brc_genomes owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_paired +- name: qiime2__rescript__get_bv_brc_metadata owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_pyro +- name: qiime2__rescript__get_eukaryome_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_single +- name: qiime2__rescript__get_gtdb_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__plot_base_transitions +- name: qiime2__rescript__get_midori2_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__cutadapt__demux_paired +- name: qiime2__rescript__get_ncbi_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__cutadapt__demux_single +- name: qiime2__rescript__get_ncbi_data_protein owner: q2d2 tool_panel_section_id: '' -- name: qiime2__cutadapt__trim_paired +- name: qiime2__rescript__get_ncbi_genomes owner: q2d2 tool_panel_section_id: '' -- name: qiime2__cutadapt__trim_single +- name: qiime2__rescript__get_pr2_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__add_pseudocount +- name: qiime2__rescript__get_silva_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancom +- name: qiime2__rescript__get_unite_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancombc +- name: qiime2__rescript__merge_taxa owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancombc2 +- name: qiime2__rescript__orient_reads owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancombc2_visualizer +- name: qiime2__rescript__orient_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__da_barplot +- name: qiime2__rescript__parse_silva_taxonomy owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__tabulate +- name: qiime2__rescript__reverse_transcribe owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__barplot +- name: qiime2__rescript__subsample_fasta owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__barplot2 +- name: qiime2__rescript__trim_alignment owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__collapse +- name: qiime2__quality_filter__q_score owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__filter_seqs +- name: qiime2__vizard__boxplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__filter_table +- name: qiime2__vizard__heatmap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__alpha +- name: qiime2__vizard__lineplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__alpha_average +- name: qiime2__vizard__scatterplot_2d owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__alpha_collection +- name: qiime2__alignment__mafft owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__beta +- name: qiime2__alignment__mafft_add owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__beta_average +- name: qiime2__alignment__mask owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__beta_collection +- name: qiime2__phylogeny__align_to_tree_mafft_fasttree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__core_metrics +- name: qiime2__phylogeny__align_to_tree_mafft_iqtree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__kmer_diversity +- name: qiime2__phylogeny__align_to_tree_mafft_raxml owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__resample +- name: qiime2__phylogeny__fasttree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__cluster_features_closed_reference +- name: qiime2__phylogeny__filter_table owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__cluster_features_de_novo +- name: qiime2__phylogeny__filter_tree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__cluster_features_open_reference +- name: qiime2__phylogeny__iqtree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__dereplicate_sequences +- name: qiime2__phylogeny__iqtree_ultrafast_bootstrap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__fastq_stats +- name: qiime2__phylogeny__midpoint_root owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__merge_pairs +- name: qiime2__phylogeny__raxml owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__uchime_denovo +- name: qiime2__phylogeny__raxml_rapid_bootstrap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__uchime_ref +- name: qiime2__phylogeny__robinson_foulds owner: q2d2 tool_panel_section_id: '' -- name: qiime2__emperor__biplot +- name: qiime2__fragment_insertion__classify_otus_experimental owner: q2d2 tool_panel_section_id: '' -- name: qiime2__emperor__plot +- name: qiime2__fragment_insertion__filter_features owner: q2d2 tool_panel_section_id: '' -- name: qiime2__emperor__procrustes_plot +- name: qiime2__fragment_insertion__sepp owner: q2d2 tool_panel_section_id: '' - name: qiime2__feature_classifier__blast @@ -3422,6 +3449,39 @@ tools: - name: qiime2__feature_classifier__vsearch_global owner: q2d2 tool_panel_section_id: '' +- name: qiime2__longitudinal__anova + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__feature_volatility + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__first_differences + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__first_distances + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__linear_mixed_effects + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__maturity_index + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__nmit + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__pairwise_differences + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__pairwise_distances + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__plot_feature_volatility + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__volatility + owner: q2d2 + tool_panel_section_id: '' - name: qiime2__feature_table___summarize owner: q2d2 tool_panel_section_id: '' @@ -3491,76 +3551,73 @@ tools: - name: qiime2__feature_table__transpose owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue___get_sequences - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__fondue__combine_seqs +- name: qiime2__quality_control__bowtie2_build owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__get_all +- name: qiime2__quality_control__decontam_identify owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__get_ids_from_query +- name: qiime2__quality_control__decontam_identify_batches owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__get_metadata +- name: qiime2__quality_control__decontam_score_viz owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__get_sequences +- name: qiime2__quality_control__evaluate_composition owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__merge_metadata +- name: qiime2__quality_control__evaluate_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__scrape_collection +- name: qiime2__quality_control__evaluate_taxonomy owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fragment_insertion__classify_otus_experimental +- name: qiime2__quality_control__exclude_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fragment_insertion__filter_features +- name: qiime2__quality_control__filter_reads owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fragment_insertion__sepp +- name: qiime2__metadata__distance_matrix owner: q2d2 tool_panel_section_id: '' -- name: qiime2__kmerizer__core_metrics +- name: qiime2__metadata__merge owner: q2d2 tool_panel_section_id: '' -- name: qiime2__kmerizer__seqs_to_kmers +- name: qiime2__metadata__shuffle_groups owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__anova +- name: qiime2__metadata__tabulate owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__feature_volatility +- name: qiime2__kmerizer__core_metrics owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__first_differences +- name: qiime2__kmerizer__seqs_to_kmers owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__first_distances +- name: qiime2__fondue___get_sequences owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__linear_mixed_effects +- name: qiime2__fondue__combine_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__maturity_index +- name: qiime2__fondue__get_all owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__nmit +- name: qiime2__fondue__get_ids_from_query owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__pairwise_differences +- name: qiime2__fondue__get_metadata owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__pairwise_distances +- name: qiime2__fondue__get_sequences owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__plot_feature_volatility +- name: qiime2__fondue__merge_metadata owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__volatility +- name: qiime2__fondue__scrape_collection owner: q2d2 tool_panel_section_id: '' - name: qiime2_dbotu_q2 @@ -3686,6 +3743,27 @@ tools: - name: rseqc_tin owner: nilesh tool_panel_section_id: '' +- name: samestr_compare + owner: iuc + tool_panel_section_id: '' +- name: samestr_convert + owner: iuc + tool_panel_section_id: '' +- name: samestr_extract + owner: iuc + tool_panel_section_id: '' +- name: samestr_filter + owner: iuc + tool_panel_section_id: '' +- name: samestr_merge + owner: iuc + tool_panel_section_id: '' +- name: samestr_stats + owner: iuc + tool_panel_section_id: '' +- name: samestr_summarize + owner: iuc + tool_panel_section_id: '' - name: scoary owner: iuc tool_panel_section_id: '' @@ -3810,10 +3888,10 @@ tools: owner: artbio tool_panel_section_id: '' - name: srst2 - owner: iuc + owner: nml tool_panel_section_id: '' - name: srst2 - owner: nml + owner: iuc tool_panel_section_id: '' - name: staramr_search owner: iuc @@ -3926,6 +4004,12 @@ tools: - name: varvamp owner: iuc tool_panel_section_id: '' +- name: vcontact2 + owner: iuc + tool_panel_section_id: '' +- name: vcontact2_gene2genome + owner: iuc + tool_panel_section_id: '' - name: vegan_diversity owner: iuc tool_panel_section_id: '' diff --git a/communities/microgalaxy/lab/tools/all/IPK_Galaxy_Blast_Suite.yaml b/communities/microgalaxy/lab/tools/all/IPK_Galaxy_Blast_Suite.yaml index a8c67bb3f..47a750f2c 100644 --- a/communities/microgalaxy/lab/tools/all/IPK_Galaxy_Blast_Suite.yaml +++ b/communities/microgalaxy/lab/tools/all/IPK_Galaxy_Blast_Suite.yaml @@ -1229,6 +1229,9 @@ tools: - name: kmindex_query owner: iuc tool_panel_section_id: '' +- name: kneaddata + owner: iuc + tool_panel_section_id: '' - name: kofamscan owner: iuc tool_panel_section_id: '' @@ -1286,6 +1289,9 @@ tools: - name: legsta owner: iuc tool_panel_section_id: '' +- name: liftoff + owner: iuc + tool_panel_section_id: '' - name: lighter owner: bgruening tool_panel_section_id: '' @@ -1505,6 +1511,27 @@ tools: - name: mg_toolkit_original_metadata owner: iuc tool_panel_section_id: '' +- name: mgnify_genome_search + owner: iuc + tool_panel_section_id: '' +- name: mgnify_pipelines_toolkit_classify_var_regions + owner: iuc + tool_panel_section_id: '' +- name: mgnify_pipelines_toolkit_make_asv_count_table + owner: iuc + tool_panel_section_id: '' +- name: mgnify_pipelines_toolkit_mapseq_to_asv_table + owner: iuc + tool_panel_section_id: '' +- name: mgnify_pipelines_toolkit_permute_primers + owner: iuc + tool_panel_section_id: '' +- name: mgnify_pipelines_toolkit_primer_val_classification + owner: iuc + tool_panel_section_id: '' +- name: mgnify_pipelines_toolkit_rev_comp_se_primers + owner: iuc + tool_panel_section_id: '' - name: mgnify_seqprep owner: bgruening tool_panel_section_id: '' @@ -1526,6 +1553,12 @@ tools: - name: miniprot_index owner: iuc tool_panel_section_id: '' +- name: mist_call + owner: iuc + tool_panel_section_id: '' +- name: mist_dists + owner: iuc + tool_panel_section_id: '' - name: mitos owner: iuc tool_panel_section_id: '' @@ -1976,6 +2009,9 @@ tools: - name: msstats owner: galaxyp tool_panel_section_id: '' +- name: mtnucratio + owner: iuc + tool_panel_section_id: '' - name: multigsea owner: iuc tool_panel_section_id: '' @@ -2093,6 +2129,9 @@ tools: - name: obi_clean owner: iuc tool_panel_section_id: '' +- name: obi_complement + owner: iuc + tool_panel_section_id: '' - name: obi_convert owner: iuc tool_panel_section_id: '' @@ -2105,6 +2144,18 @@ tools: - name: obi_pairing owner: iuc tool_panel_section_id: '' +- name: obi_pcr + owner: iuc + tool_panel_section_id: '' +- name: obi_refidx + owner: iuc + tool_panel_section_id: '' +- name: obi_tag + owner: iuc + tool_panel_section_id: '' +- name: obi_taxonomy + owner: iuc + tool_panel_section_id: '' - name: obi_uniq owner: iuc tool_panel_section_id: '' @@ -2726,6 +2777,9 @@ tools: - name: ppanggolin_rarefaction owner: iuc tool_panel_section_id: '' +- name: prinseq + owner: iuc + tool_panel_section_id: '' - name: prodigal owner: iuc tool_panel_section_id: '' @@ -2747,6 +2801,9 @@ tools: - name: proteinortho_summary owner: iuc tool_panel_section_id: '' +- name: psauron + owner: iuc + tool_panel_section_id: '' - name: pycoqc owner: iuc tool_panel_section_id: '' @@ -2855,262 +2912,241 @@ tools: - name: qiime_make_otu_table owner: iuc tool_panel_section_id: '' -- name: qiime2_core__tools__export - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2_core__tools__import - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2_core__tools__import_fastq - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__quality_filter__q_score - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__cull_seqs - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__degap_seqs - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__dereplicate - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__edit_taxonomy +- name: qiime2__dada2__denoise_ccs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_classifications +- name: qiime2__dada2__denoise_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_cross_validate +- name: qiime2__dada2__denoise_pyro owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_fit_classifier +- name: qiime2__dada2__denoise_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_seqs +- name: qiime2__dada2__plot_base_transitions owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_taxonomy +- name: qiime2__cutadapt__demux_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__extract_seq_segments +- name: qiime2__cutadapt__demux_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__filter_seqs_length +- name: qiime2__cutadapt__trim_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__filter_seqs_length_by_taxon +- name: qiime2__cutadapt__trim_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__filter_taxa +- name: qiime2__composition__add_pseudocount owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_bv_brc_genome_features +- name: qiime2__composition__ancom owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_bv_brc_genomes +- name: qiime2__composition__ancombc owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_bv_brc_metadata +- name: qiime2__composition__ancombc2 owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_eukaryome_data +- name: qiime2__composition__ancombc2_visualizer owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_gtdb_data +- name: qiime2__composition__da_barplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_midori2_data +- name: qiime2__composition__tabulate owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_ncbi_data +- name: qiime2__boots__alpha owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_ncbi_data_protein +- name: qiime2__boots__alpha_average owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_ncbi_genomes +- name: qiime2__boots__alpha_collection owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_pr2_data +- name: qiime2__boots__beta owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_silva_data +- name: qiime2__boots__beta_average owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_unite_data +- name: qiime2__boots__beta_collection owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__merge_taxa +- name: qiime2__boots__core_metrics owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__orient_reads +- name: qiime2__boots__kmer_diversity owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__orient_seqs +- name: qiime2__boots__resample owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__parse_silva_taxonomy +- name: qiime2__vsearch__cluster_features_closed_reference owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__reverse_transcribe +- name: qiime2__vsearch__cluster_features_de_novo owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__subsample_fasta +- name: qiime2__vsearch__cluster_features_open_reference owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__trim_alignment +- name: qiime2__vsearch__dereplicate_sequences owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__classify_samples +- name: qiime2__vsearch__fastq_stats owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__classify_samples_from_dist +- name: qiime2__vsearch__merge_pairs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__classify_samples_ncv +- name: qiime2__vsearch__uchime_denovo owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__confusion_matrix +- name: qiime2__vsearch__uchime_ref owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__fit_classifier +- name: qiime2__demux__emp_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__fit_regressor +- name: qiime2__demux__emp_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__heatmap +- name: qiime2__demux__filter_samples owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__metatable +- name: qiime2__demux__partition_samples_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__predict_classification +- name: qiime2__demux__partition_samples_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__predict_regression +- name: qiime2__demux__subsample_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__regress_samples +- name: qiime2__demux__subsample_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__regress_samples_ncv +- name: qiime2__demux__summarize owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__scatterplot +- name: qiime2__demux__tabulate_read_counts owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__split_table +- name: qiime2__deblur__denoise_16S owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__summarize +- name: qiime2__deblur__denoise_other owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__align_to_tree_mafft_fasttree +- name: qiime2__deblur__visualize_stats owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__align_to_tree_mafft_iqtree +- name: qiime2__diversity__adonis owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__align_to_tree_mafft_raxml +- name: qiime2__diversity__alpha owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__fasttree +- name: qiime2__diversity__alpha_correlation owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__filter_table +- name: qiime2__diversity__alpha_group_significance owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__filter_tree +- name: qiime2__diversity__alpha_phylogenetic owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__iqtree +- name: qiime2__diversity__alpha_rarefaction owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__iqtree_ultrafast_bootstrap +- name: qiime2__diversity__beta owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__midpoint_root +- name: qiime2__diversity__beta_correlation owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__raxml +- name: qiime2__diversity__beta_group_significance owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__raxml_rapid_bootstrap +- name: qiime2__diversity__beta_phylogenetic owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__robinson_foulds +- name: qiime2__diversity__beta_rarefaction owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__distance_matrix +- name: qiime2__diversity__bioenv owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__merge +- name: qiime2__diversity__core_metrics owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__shuffle_groups +- name: qiime2__diversity__core_metrics_phylogenetic owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__tabulate +- name: qiime2__diversity__filter_alpha_diversity owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__alpha_group_significance +- name: qiime2__diversity__filter_distance_matrix owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__collate_stats +- name: qiime2__diversity__mantel owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__facet_across +- name: qiime2__diversity__partial_procrustes owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__facet_within +- name: qiime2__diversity__pcoa owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__mann_whitney_u +- name: qiime2__diversity__pcoa_biplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__mann_whitney_u_facet +- name: qiime2__diversity__procrustes_analysis owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__plot_rainclouds +- name: qiime2__diversity__tsne owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__prep_alpha_distribution +- name: qiime2__diversity__umap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__wilcoxon_srt +- name: qiime2__emperor__biplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__wilcoxon_srt_facet +- name: qiime2__emperor__plot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__bowtie2_build +- name: qiime2__emperor__procrustes_plot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__decontam_identify +- name: qiime2_core__tools__export owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__decontam_identify_batches +- name: qiime2_core__tools__import owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__decontam_score_viz +- name: qiime2_core__tools__import_fastq owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__evaluate_composition +- name: qiime2__taxa__barplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__evaluate_seqs +- name: qiime2__taxa__barplot2 owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__evaluate_taxonomy +- name: qiime2__taxa__collapse owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__exclude_seqs +- name: qiime2__taxa__filter_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__filter_reads +- name: qiime2__taxa__filter_table owner: q2d2 tool_panel_section_id: '' - name: qiime2__diversity_lib__alpha_passthrough @@ -3149,253 +3185,244 @@ tools: - name: qiime2__diversity_lib__weighted_unifrac owner: q2d2 tool_panel_section_id: '' -- name: qiime2__alignment__mafft - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__alignment__mafft_add - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__alignment__mask - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__vizard__boxplot +- name: qiime2__stats__alpha_group_significance owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vizard__heatmap +- name: qiime2__stats__collate_stats owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vizard__lineplot +- name: qiime2__stats__facet_across owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vizard__scatterplot_2d +- name: qiime2__stats__facet_within owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__adonis +- name: qiime2__stats__mann_whitney_u owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha +- name: qiime2__stats__mann_whitney_u_facet owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_correlation +- name: qiime2__stats__plot_rainclouds owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_group_significance +- name: qiime2__stats__prep_alpha_distribution owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_phylogenetic +- name: qiime2__stats__wilcoxon_srt owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_rarefaction +- name: qiime2__stats__wilcoxon_srt_facet owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta +- name: qiime2__sample_classifier__classify_samples owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_correlation +- name: qiime2__sample_classifier__classify_samples_from_dist owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_group_significance +- name: qiime2__sample_classifier__classify_samples_ncv owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_phylogenetic +- name: qiime2__sample_classifier__confusion_matrix owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_rarefaction +- name: qiime2__sample_classifier__fit_classifier owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__bioenv +- name: qiime2__sample_classifier__fit_regressor owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__core_metrics +- name: qiime2__sample_classifier__heatmap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__core_metrics_phylogenetic +- name: qiime2__sample_classifier__metatable owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__filter_alpha_diversity +- name: qiime2__sample_classifier__predict_classification owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__filter_distance_matrix +- name: qiime2__sample_classifier__predict_regression owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__mantel +- name: qiime2__sample_classifier__regress_samples owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__partial_procrustes +- name: qiime2__sample_classifier__regress_samples_ncv owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__pcoa +- name: qiime2__sample_classifier__scatterplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__pcoa_biplot +- name: qiime2__sample_classifier__split_table owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__procrustes_analysis +- name: qiime2__sample_classifier__summarize owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__tsne +- name: qiime2__rescript__cull_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__umap +- name: qiime2__rescript__degap_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__emp_paired +- name: qiime2__rescript__dereplicate owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__emp_single +- name: qiime2__rescript__edit_taxonomy owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__filter_samples +- name: qiime2__rescript__evaluate_classifications owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__partition_samples_paired +- name: qiime2__rescript__evaluate_cross_validate owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__partition_samples_single +- name: qiime2__rescript__evaluate_fit_classifier owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__subsample_paired +- name: qiime2__rescript__evaluate_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__subsample_single +- name: qiime2__rescript__evaluate_taxonomy owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__summarize +- name: qiime2__rescript__extract_seq_segments owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__tabulate_read_counts +- name: qiime2__rescript__filter_seqs_length owner: q2d2 tool_panel_section_id: '' -- name: qiime2__deblur__denoise_16S +- name: qiime2__rescript__filter_seqs_length_by_taxon owner: q2d2 tool_panel_section_id: '' -- name: qiime2__deblur__denoise_other +- name: qiime2__rescript__filter_taxa owner: q2d2 tool_panel_section_id: '' -- name: qiime2__deblur__visualize_stats +- name: qiime2__rescript__get_bv_brc_genome_features owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_ccs +- name: qiime2__rescript__get_bv_brc_genomes owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_paired +- name: qiime2__rescript__get_bv_brc_metadata owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_pyro +- name: qiime2__rescript__get_eukaryome_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_single +- name: qiime2__rescript__get_gtdb_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__plot_base_transitions +- name: qiime2__rescript__get_midori2_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__cutadapt__demux_paired +- name: qiime2__rescript__get_ncbi_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__cutadapt__demux_single +- name: qiime2__rescript__get_ncbi_data_protein owner: q2d2 tool_panel_section_id: '' -- name: qiime2__cutadapt__trim_paired +- name: qiime2__rescript__get_ncbi_genomes owner: q2d2 tool_panel_section_id: '' -- name: qiime2__cutadapt__trim_single +- name: qiime2__rescript__get_pr2_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__add_pseudocount +- name: qiime2__rescript__get_silva_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancom +- name: qiime2__rescript__get_unite_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancombc +- name: qiime2__rescript__merge_taxa owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancombc2 +- name: qiime2__rescript__orient_reads owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancombc2_visualizer +- name: qiime2__rescript__orient_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__da_barplot +- name: qiime2__rescript__parse_silva_taxonomy owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__tabulate +- name: qiime2__rescript__reverse_transcribe owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__barplot +- name: qiime2__rescript__subsample_fasta owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__barplot2 +- name: qiime2__rescript__trim_alignment owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__collapse +- name: qiime2__quality_filter__q_score owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__filter_seqs +- name: qiime2__vizard__boxplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__filter_table +- name: qiime2__vizard__heatmap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__alpha +- name: qiime2__vizard__lineplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__alpha_average +- name: qiime2__vizard__scatterplot_2d owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__alpha_collection +- name: qiime2__alignment__mafft owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__beta +- name: qiime2__alignment__mafft_add owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__beta_average +- name: qiime2__alignment__mask owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__beta_collection +- name: qiime2__phylogeny__align_to_tree_mafft_fasttree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__core_metrics +- name: qiime2__phylogeny__align_to_tree_mafft_iqtree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__kmer_diversity +- name: qiime2__phylogeny__align_to_tree_mafft_raxml owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__resample +- name: qiime2__phylogeny__fasttree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__cluster_features_closed_reference +- name: qiime2__phylogeny__filter_table owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__cluster_features_de_novo +- name: qiime2__phylogeny__filter_tree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__cluster_features_open_reference +- name: qiime2__phylogeny__iqtree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__dereplicate_sequences +- name: qiime2__phylogeny__iqtree_ultrafast_bootstrap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__fastq_stats +- name: qiime2__phylogeny__midpoint_root owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__merge_pairs +- name: qiime2__phylogeny__raxml owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__uchime_denovo +- name: qiime2__phylogeny__raxml_rapid_bootstrap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__uchime_ref +- name: qiime2__phylogeny__robinson_foulds owner: q2d2 tool_panel_section_id: '' -- name: qiime2__emperor__biplot +- name: qiime2__fragment_insertion__classify_otus_experimental owner: q2d2 tool_panel_section_id: '' -- name: qiime2__emperor__plot +- name: qiime2__fragment_insertion__filter_features owner: q2d2 tool_panel_section_id: '' -- name: qiime2__emperor__procrustes_plot +- name: qiime2__fragment_insertion__sepp owner: q2d2 tool_panel_section_id: '' - name: qiime2__feature_classifier__blast @@ -3431,6 +3458,39 @@ tools: - name: qiime2__feature_classifier__vsearch_global owner: q2d2 tool_panel_section_id: '' +- name: qiime2__longitudinal__anova + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__feature_volatility + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__first_differences + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__first_distances + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__linear_mixed_effects + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__maturity_index + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__nmit + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__pairwise_differences + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__pairwise_distances + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__plot_feature_volatility + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__volatility + owner: q2d2 + tool_panel_section_id: '' - name: qiime2__feature_table___summarize owner: q2d2 tool_panel_section_id: '' @@ -3500,76 +3560,73 @@ tools: - name: qiime2__feature_table__transpose owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue___get_sequences - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__fondue__combine_seqs +- name: qiime2__quality_control__bowtie2_build owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__get_all +- name: qiime2__quality_control__decontam_identify owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__get_ids_from_query +- name: qiime2__quality_control__decontam_identify_batches owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__get_metadata +- name: qiime2__quality_control__decontam_score_viz owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__get_sequences +- name: qiime2__quality_control__evaluate_composition owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__merge_metadata +- name: qiime2__quality_control__evaluate_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__scrape_collection +- name: qiime2__quality_control__evaluate_taxonomy owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fragment_insertion__classify_otus_experimental +- name: qiime2__quality_control__exclude_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fragment_insertion__filter_features +- name: qiime2__quality_control__filter_reads owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fragment_insertion__sepp +- name: qiime2__metadata__distance_matrix owner: q2d2 tool_panel_section_id: '' -- name: qiime2__kmerizer__core_metrics +- name: qiime2__metadata__merge owner: q2d2 tool_panel_section_id: '' -- name: qiime2__kmerizer__seqs_to_kmers +- name: qiime2__metadata__shuffle_groups owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__anova +- name: qiime2__metadata__tabulate owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__feature_volatility +- name: qiime2__kmerizer__core_metrics owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__first_differences +- name: qiime2__kmerizer__seqs_to_kmers owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__first_distances +- name: qiime2__fondue___get_sequences owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__linear_mixed_effects +- name: qiime2__fondue__combine_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__maturity_index +- name: qiime2__fondue__get_all owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__nmit +- name: qiime2__fondue__get_ids_from_query owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__pairwise_differences +- name: qiime2__fondue__get_metadata owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__pairwise_distances +- name: qiime2__fondue__get_sequences owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__plot_feature_volatility +- name: qiime2__fondue__merge_metadata owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__volatility +- name: qiime2__fondue__scrape_collection owner: q2d2 tool_panel_section_id: '' - name: qiime2_dbotu_q2 @@ -3698,6 +3755,27 @@ tools: - name: rseqc_tin owner: nilesh tool_panel_section_id: '' +- name: samestr_compare + owner: iuc + tool_panel_section_id: '' +- name: samestr_convert + owner: iuc + tool_panel_section_id: '' +- name: samestr_extract + owner: iuc + tool_panel_section_id: '' +- name: samestr_filter + owner: iuc + tool_panel_section_id: '' +- name: samestr_merge + owner: iuc + tool_panel_section_id: '' +- name: samestr_stats + owner: iuc + tool_panel_section_id: '' +- name: samestr_summarize + owner: iuc + tool_panel_section_id: '' - name: scoary owner: iuc tool_panel_section_id: '' @@ -3822,10 +3900,10 @@ tools: owner: artbio tool_panel_section_id: '' - name: srst2 - owner: iuc + owner: nml tool_panel_section_id: '' - name: srst2 - owner: nml + owner: iuc tool_panel_section_id: '' - name: staramr_search owner: iuc @@ -3938,6 +4016,12 @@ tools: - name: varvamp owner: iuc tool_panel_section_id: '' +- name: vcontact2 + owner: iuc + tool_panel_section_id: '' +- name: vcontact2_gene2genome + owner: iuc + tool_panel_section_id: '' - name: vegan_diversity owner: iuc tool_panel_section_id: '' diff --git a/communities/microgalaxy/lab/tools/all/ImmPort_Galaxy.yaml b/communities/microgalaxy/lab/tools/all/ImmPort_Galaxy.yaml index a8c67bb3f..47a750f2c 100644 --- a/communities/microgalaxy/lab/tools/all/ImmPort_Galaxy.yaml +++ b/communities/microgalaxy/lab/tools/all/ImmPort_Galaxy.yaml @@ -1229,6 +1229,9 @@ tools: - name: kmindex_query owner: iuc tool_panel_section_id: '' +- name: kneaddata + owner: iuc + tool_panel_section_id: '' - name: kofamscan owner: iuc tool_panel_section_id: '' @@ -1286,6 +1289,9 @@ tools: - name: legsta owner: iuc tool_panel_section_id: '' +- name: liftoff + owner: iuc + tool_panel_section_id: '' - name: lighter owner: bgruening tool_panel_section_id: '' @@ -1505,6 +1511,27 @@ tools: - name: mg_toolkit_original_metadata owner: iuc tool_panel_section_id: '' +- name: mgnify_genome_search + owner: iuc + tool_panel_section_id: '' +- name: mgnify_pipelines_toolkit_classify_var_regions + owner: iuc + tool_panel_section_id: '' +- name: mgnify_pipelines_toolkit_make_asv_count_table + owner: iuc + tool_panel_section_id: '' +- name: mgnify_pipelines_toolkit_mapseq_to_asv_table + owner: iuc + tool_panel_section_id: '' +- name: mgnify_pipelines_toolkit_permute_primers + owner: iuc + tool_panel_section_id: '' +- name: mgnify_pipelines_toolkit_primer_val_classification + owner: iuc + tool_panel_section_id: '' +- name: mgnify_pipelines_toolkit_rev_comp_se_primers + owner: iuc + tool_panel_section_id: '' - name: mgnify_seqprep owner: bgruening tool_panel_section_id: '' @@ -1526,6 +1553,12 @@ tools: - name: miniprot_index owner: iuc tool_panel_section_id: '' +- name: mist_call + owner: iuc + tool_panel_section_id: '' +- name: mist_dists + owner: iuc + tool_panel_section_id: '' - name: mitos owner: iuc tool_panel_section_id: '' @@ -1976,6 +2009,9 @@ tools: - name: msstats owner: galaxyp tool_panel_section_id: '' +- name: mtnucratio + owner: iuc + tool_panel_section_id: '' - name: multigsea owner: iuc tool_panel_section_id: '' @@ -2093,6 +2129,9 @@ tools: - name: obi_clean owner: iuc tool_panel_section_id: '' +- name: obi_complement + owner: iuc + tool_panel_section_id: '' - name: obi_convert owner: iuc tool_panel_section_id: '' @@ -2105,6 +2144,18 @@ tools: - name: obi_pairing owner: iuc tool_panel_section_id: '' +- name: obi_pcr + owner: iuc + tool_panel_section_id: '' +- name: obi_refidx + owner: iuc + tool_panel_section_id: '' +- name: obi_tag + owner: iuc + tool_panel_section_id: '' +- name: obi_taxonomy + owner: iuc + tool_panel_section_id: '' - name: obi_uniq owner: iuc tool_panel_section_id: '' @@ -2726,6 +2777,9 @@ tools: - name: ppanggolin_rarefaction owner: iuc tool_panel_section_id: '' +- name: prinseq + owner: iuc + tool_panel_section_id: '' - name: prodigal owner: iuc tool_panel_section_id: '' @@ -2747,6 +2801,9 @@ tools: - name: proteinortho_summary owner: iuc tool_panel_section_id: '' +- name: psauron + owner: iuc + tool_panel_section_id: '' - name: pycoqc owner: iuc tool_panel_section_id: '' @@ -2855,262 +2912,241 @@ tools: - name: qiime_make_otu_table owner: iuc tool_panel_section_id: '' -- name: qiime2_core__tools__export - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2_core__tools__import - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2_core__tools__import_fastq - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__quality_filter__q_score - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__cull_seqs - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__degap_seqs - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__dereplicate - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__edit_taxonomy +- name: qiime2__dada2__denoise_ccs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_classifications +- name: qiime2__dada2__denoise_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_cross_validate +- name: qiime2__dada2__denoise_pyro owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_fit_classifier +- name: qiime2__dada2__denoise_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_seqs +- name: qiime2__dada2__plot_base_transitions owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_taxonomy +- name: qiime2__cutadapt__demux_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__extract_seq_segments +- name: qiime2__cutadapt__demux_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__filter_seqs_length +- name: qiime2__cutadapt__trim_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__filter_seqs_length_by_taxon +- name: qiime2__cutadapt__trim_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__filter_taxa +- name: qiime2__composition__add_pseudocount owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_bv_brc_genome_features +- name: qiime2__composition__ancom owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_bv_brc_genomes +- name: qiime2__composition__ancombc owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_bv_brc_metadata +- name: qiime2__composition__ancombc2 owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_eukaryome_data +- name: qiime2__composition__ancombc2_visualizer owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_gtdb_data +- name: qiime2__composition__da_barplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_midori2_data +- name: qiime2__composition__tabulate owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_ncbi_data +- name: qiime2__boots__alpha owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_ncbi_data_protein +- name: qiime2__boots__alpha_average owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_ncbi_genomes +- name: qiime2__boots__alpha_collection owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_pr2_data +- name: qiime2__boots__beta owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_silva_data +- name: qiime2__boots__beta_average owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_unite_data +- name: qiime2__boots__beta_collection owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__merge_taxa +- name: qiime2__boots__core_metrics owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__orient_reads +- name: qiime2__boots__kmer_diversity owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__orient_seqs +- name: qiime2__boots__resample owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__parse_silva_taxonomy +- name: qiime2__vsearch__cluster_features_closed_reference owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__reverse_transcribe +- name: qiime2__vsearch__cluster_features_de_novo owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__subsample_fasta +- name: qiime2__vsearch__cluster_features_open_reference owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__trim_alignment +- name: qiime2__vsearch__dereplicate_sequences owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__classify_samples +- name: qiime2__vsearch__fastq_stats owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__classify_samples_from_dist +- name: qiime2__vsearch__merge_pairs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__classify_samples_ncv +- name: qiime2__vsearch__uchime_denovo owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__confusion_matrix +- name: qiime2__vsearch__uchime_ref owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__fit_classifier +- name: qiime2__demux__emp_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__fit_regressor +- name: qiime2__demux__emp_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__heatmap +- name: qiime2__demux__filter_samples owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__metatable +- name: qiime2__demux__partition_samples_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__predict_classification +- name: qiime2__demux__partition_samples_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__predict_regression +- name: qiime2__demux__subsample_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__regress_samples +- name: qiime2__demux__subsample_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__regress_samples_ncv +- name: qiime2__demux__summarize owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__scatterplot +- name: qiime2__demux__tabulate_read_counts owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__split_table +- name: qiime2__deblur__denoise_16S owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__summarize +- name: qiime2__deblur__denoise_other owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__align_to_tree_mafft_fasttree +- name: qiime2__deblur__visualize_stats owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__align_to_tree_mafft_iqtree +- name: qiime2__diversity__adonis owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__align_to_tree_mafft_raxml +- name: qiime2__diversity__alpha owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__fasttree +- name: qiime2__diversity__alpha_correlation owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__filter_table +- name: qiime2__diversity__alpha_group_significance owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__filter_tree +- name: qiime2__diversity__alpha_phylogenetic owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__iqtree +- name: qiime2__diversity__alpha_rarefaction owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__iqtree_ultrafast_bootstrap +- name: qiime2__diversity__beta owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__midpoint_root +- name: qiime2__diversity__beta_correlation owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__raxml +- name: qiime2__diversity__beta_group_significance owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__raxml_rapid_bootstrap +- name: qiime2__diversity__beta_phylogenetic owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__robinson_foulds +- name: qiime2__diversity__beta_rarefaction owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__distance_matrix +- name: qiime2__diversity__bioenv owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__merge +- name: qiime2__diversity__core_metrics owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__shuffle_groups +- name: qiime2__diversity__core_metrics_phylogenetic owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__tabulate +- name: qiime2__diversity__filter_alpha_diversity owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__alpha_group_significance +- name: qiime2__diversity__filter_distance_matrix owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__collate_stats +- name: qiime2__diversity__mantel owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__facet_across +- name: qiime2__diversity__partial_procrustes owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__facet_within +- name: qiime2__diversity__pcoa owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__mann_whitney_u +- name: qiime2__diversity__pcoa_biplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__mann_whitney_u_facet +- name: qiime2__diversity__procrustes_analysis owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__plot_rainclouds +- name: qiime2__diversity__tsne owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__prep_alpha_distribution +- name: qiime2__diversity__umap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__wilcoxon_srt +- name: qiime2__emperor__biplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__wilcoxon_srt_facet +- name: qiime2__emperor__plot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__bowtie2_build +- name: qiime2__emperor__procrustes_plot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__decontam_identify +- name: qiime2_core__tools__export owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__decontam_identify_batches +- name: qiime2_core__tools__import owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__decontam_score_viz +- name: qiime2_core__tools__import_fastq owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__evaluate_composition +- name: qiime2__taxa__barplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__evaluate_seqs +- name: qiime2__taxa__barplot2 owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__evaluate_taxonomy +- name: qiime2__taxa__collapse owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__exclude_seqs +- name: qiime2__taxa__filter_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__filter_reads +- name: qiime2__taxa__filter_table owner: q2d2 tool_panel_section_id: '' - name: qiime2__diversity_lib__alpha_passthrough @@ -3149,253 +3185,244 @@ tools: - name: qiime2__diversity_lib__weighted_unifrac owner: q2d2 tool_panel_section_id: '' -- name: qiime2__alignment__mafft - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__alignment__mafft_add - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__alignment__mask - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__vizard__boxplot +- name: qiime2__stats__alpha_group_significance owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vizard__heatmap +- name: qiime2__stats__collate_stats owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vizard__lineplot +- name: qiime2__stats__facet_across owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vizard__scatterplot_2d +- name: qiime2__stats__facet_within owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__adonis +- name: qiime2__stats__mann_whitney_u owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha +- name: qiime2__stats__mann_whitney_u_facet owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_correlation +- name: qiime2__stats__plot_rainclouds owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_group_significance +- name: qiime2__stats__prep_alpha_distribution owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_phylogenetic +- name: qiime2__stats__wilcoxon_srt owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_rarefaction +- name: qiime2__stats__wilcoxon_srt_facet owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta +- name: qiime2__sample_classifier__classify_samples owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_correlation +- name: qiime2__sample_classifier__classify_samples_from_dist owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_group_significance +- name: qiime2__sample_classifier__classify_samples_ncv owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_phylogenetic +- name: qiime2__sample_classifier__confusion_matrix owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_rarefaction +- name: qiime2__sample_classifier__fit_classifier owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__bioenv +- name: qiime2__sample_classifier__fit_regressor owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__core_metrics +- name: qiime2__sample_classifier__heatmap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__core_metrics_phylogenetic +- name: qiime2__sample_classifier__metatable owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__filter_alpha_diversity +- name: qiime2__sample_classifier__predict_classification owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__filter_distance_matrix +- name: qiime2__sample_classifier__predict_regression owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__mantel +- name: qiime2__sample_classifier__regress_samples owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__partial_procrustes +- name: qiime2__sample_classifier__regress_samples_ncv owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__pcoa +- name: qiime2__sample_classifier__scatterplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__pcoa_biplot +- name: qiime2__sample_classifier__split_table owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__procrustes_analysis +- name: qiime2__sample_classifier__summarize owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__tsne +- name: qiime2__rescript__cull_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__umap +- name: qiime2__rescript__degap_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__emp_paired +- name: qiime2__rescript__dereplicate owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__emp_single +- name: qiime2__rescript__edit_taxonomy owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__filter_samples +- name: qiime2__rescript__evaluate_classifications owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__partition_samples_paired +- name: qiime2__rescript__evaluate_cross_validate owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__partition_samples_single +- name: qiime2__rescript__evaluate_fit_classifier owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__subsample_paired +- name: qiime2__rescript__evaluate_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__subsample_single +- name: qiime2__rescript__evaluate_taxonomy owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__summarize +- name: qiime2__rescript__extract_seq_segments owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__tabulate_read_counts +- name: qiime2__rescript__filter_seqs_length owner: q2d2 tool_panel_section_id: '' -- name: qiime2__deblur__denoise_16S +- name: qiime2__rescript__filter_seqs_length_by_taxon owner: q2d2 tool_panel_section_id: '' -- name: qiime2__deblur__denoise_other +- name: qiime2__rescript__filter_taxa owner: q2d2 tool_panel_section_id: '' -- name: qiime2__deblur__visualize_stats +- name: qiime2__rescript__get_bv_brc_genome_features owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_ccs +- name: qiime2__rescript__get_bv_brc_genomes owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_paired +- name: qiime2__rescript__get_bv_brc_metadata owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_pyro +- name: qiime2__rescript__get_eukaryome_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_single +- name: qiime2__rescript__get_gtdb_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__plot_base_transitions +- name: qiime2__rescript__get_midori2_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__cutadapt__demux_paired +- name: qiime2__rescript__get_ncbi_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__cutadapt__demux_single +- name: qiime2__rescript__get_ncbi_data_protein owner: q2d2 tool_panel_section_id: '' -- name: qiime2__cutadapt__trim_paired +- name: qiime2__rescript__get_ncbi_genomes owner: q2d2 tool_panel_section_id: '' -- name: qiime2__cutadapt__trim_single +- name: qiime2__rescript__get_pr2_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__add_pseudocount +- name: qiime2__rescript__get_silva_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancom +- name: qiime2__rescript__get_unite_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancombc +- name: qiime2__rescript__merge_taxa owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancombc2 +- name: qiime2__rescript__orient_reads owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancombc2_visualizer +- name: qiime2__rescript__orient_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__da_barplot +- name: qiime2__rescript__parse_silva_taxonomy owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__tabulate +- name: qiime2__rescript__reverse_transcribe owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__barplot +- name: qiime2__rescript__subsample_fasta owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__barplot2 +- name: qiime2__rescript__trim_alignment owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__collapse +- name: qiime2__quality_filter__q_score owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__filter_seqs +- name: qiime2__vizard__boxplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__filter_table +- name: qiime2__vizard__heatmap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__alpha +- name: qiime2__vizard__lineplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__alpha_average +- name: qiime2__vizard__scatterplot_2d owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__alpha_collection +- name: qiime2__alignment__mafft owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__beta +- name: qiime2__alignment__mafft_add owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__beta_average +- name: qiime2__alignment__mask owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__beta_collection +- name: qiime2__phylogeny__align_to_tree_mafft_fasttree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__core_metrics +- name: qiime2__phylogeny__align_to_tree_mafft_iqtree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__kmer_diversity +- name: qiime2__phylogeny__align_to_tree_mafft_raxml owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__resample +- name: qiime2__phylogeny__fasttree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__cluster_features_closed_reference +- name: qiime2__phylogeny__filter_table owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__cluster_features_de_novo +- name: qiime2__phylogeny__filter_tree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__cluster_features_open_reference +- name: qiime2__phylogeny__iqtree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__dereplicate_sequences +- name: qiime2__phylogeny__iqtree_ultrafast_bootstrap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__fastq_stats +- name: qiime2__phylogeny__midpoint_root owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__merge_pairs +- name: qiime2__phylogeny__raxml owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__uchime_denovo +- name: qiime2__phylogeny__raxml_rapid_bootstrap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__uchime_ref +- name: qiime2__phylogeny__robinson_foulds owner: q2d2 tool_panel_section_id: '' -- name: qiime2__emperor__biplot +- name: qiime2__fragment_insertion__classify_otus_experimental owner: q2d2 tool_panel_section_id: '' -- name: qiime2__emperor__plot +- name: qiime2__fragment_insertion__filter_features owner: q2d2 tool_panel_section_id: '' -- name: qiime2__emperor__procrustes_plot +- name: qiime2__fragment_insertion__sepp owner: q2d2 tool_panel_section_id: '' - name: qiime2__feature_classifier__blast @@ -3431,6 +3458,39 @@ tools: - name: qiime2__feature_classifier__vsearch_global owner: q2d2 tool_panel_section_id: '' +- name: qiime2__longitudinal__anova + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__feature_volatility + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__first_differences + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__first_distances + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__linear_mixed_effects + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__maturity_index + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__nmit + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__pairwise_differences + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__pairwise_distances + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__plot_feature_volatility + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__volatility + owner: q2d2 + tool_panel_section_id: '' - name: qiime2__feature_table___summarize owner: q2d2 tool_panel_section_id: '' @@ -3500,76 +3560,73 @@ tools: - name: qiime2__feature_table__transpose owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue___get_sequences - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__fondue__combine_seqs +- name: qiime2__quality_control__bowtie2_build owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__get_all +- name: qiime2__quality_control__decontam_identify owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__get_ids_from_query +- name: qiime2__quality_control__decontam_identify_batches owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__get_metadata +- name: qiime2__quality_control__decontam_score_viz owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__get_sequences +- name: qiime2__quality_control__evaluate_composition owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__merge_metadata +- name: qiime2__quality_control__evaluate_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__scrape_collection +- name: qiime2__quality_control__evaluate_taxonomy owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fragment_insertion__classify_otus_experimental +- name: qiime2__quality_control__exclude_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fragment_insertion__filter_features +- name: qiime2__quality_control__filter_reads owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fragment_insertion__sepp +- name: qiime2__metadata__distance_matrix owner: q2d2 tool_panel_section_id: '' -- name: qiime2__kmerizer__core_metrics +- name: qiime2__metadata__merge owner: q2d2 tool_panel_section_id: '' -- name: qiime2__kmerizer__seqs_to_kmers +- name: qiime2__metadata__shuffle_groups owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__anova +- name: qiime2__metadata__tabulate owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__feature_volatility +- name: qiime2__kmerizer__core_metrics owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__first_differences +- name: qiime2__kmerizer__seqs_to_kmers owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__first_distances +- name: qiime2__fondue___get_sequences owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__linear_mixed_effects +- name: qiime2__fondue__combine_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__maturity_index +- name: qiime2__fondue__get_all owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__nmit +- name: qiime2__fondue__get_ids_from_query owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__pairwise_differences +- name: qiime2__fondue__get_metadata owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__pairwise_distances +- name: qiime2__fondue__get_sequences owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__plot_feature_volatility +- name: qiime2__fondue__merge_metadata owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__volatility +- name: qiime2__fondue__scrape_collection owner: q2d2 tool_panel_section_id: '' - name: qiime2_dbotu_q2 @@ -3698,6 +3755,27 @@ tools: - name: rseqc_tin owner: nilesh tool_panel_section_id: '' +- name: samestr_compare + owner: iuc + tool_panel_section_id: '' +- name: samestr_convert + owner: iuc + tool_panel_section_id: '' +- name: samestr_extract + owner: iuc + tool_panel_section_id: '' +- name: samestr_filter + owner: iuc + tool_panel_section_id: '' +- name: samestr_merge + owner: iuc + tool_panel_section_id: '' +- name: samestr_stats + owner: iuc + tool_panel_section_id: '' +- name: samestr_summarize + owner: iuc + tool_panel_section_id: '' - name: scoary owner: iuc tool_panel_section_id: '' @@ -3822,10 +3900,10 @@ tools: owner: artbio tool_panel_section_id: '' - name: srst2 - owner: iuc + owner: nml tool_panel_section_id: '' - name: srst2 - owner: nml + owner: iuc tool_panel_section_id: '' - name: staramr_search owner: iuc @@ -3938,6 +4016,12 @@ tools: - name: varvamp owner: iuc tool_panel_section_id: '' +- name: vcontact2 + owner: iuc + tool_panel_section_id: '' +- name: vcontact2_gene2genome + owner: iuc + tool_panel_section_id: '' - name: vegan_diversity owner: iuc tool_panel_section_id: '' diff --git a/communities/microgalaxy/lab/tools/all/InteractoMIX.yaml b/communities/microgalaxy/lab/tools/all/InteractoMIX.yaml index a8c67bb3f..47a750f2c 100644 --- a/communities/microgalaxy/lab/tools/all/InteractoMIX.yaml +++ b/communities/microgalaxy/lab/tools/all/InteractoMIX.yaml @@ -1229,6 +1229,9 @@ tools: - name: kmindex_query owner: iuc tool_panel_section_id: '' +- name: kneaddata + owner: iuc + tool_panel_section_id: '' - name: kofamscan owner: iuc tool_panel_section_id: '' @@ -1286,6 +1289,9 @@ tools: - name: legsta owner: iuc tool_panel_section_id: '' +- name: liftoff + owner: iuc + tool_panel_section_id: '' - name: lighter owner: bgruening tool_panel_section_id: '' @@ -1505,6 +1511,27 @@ tools: - name: mg_toolkit_original_metadata owner: iuc tool_panel_section_id: '' +- name: mgnify_genome_search + owner: iuc + tool_panel_section_id: '' +- name: mgnify_pipelines_toolkit_classify_var_regions + owner: iuc + tool_panel_section_id: '' +- name: mgnify_pipelines_toolkit_make_asv_count_table + owner: iuc + tool_panel_section_id: '' +- name: mgnify_pipelines_toolkit_mapseq_to_asv_table + owner: iuc + tool_panel_section_id: '' +- name: mgnify_pipelines_toolkit_permute_primers + owner: iuc + tool_panel_section_id: '' +- name: mgnify_pipelines_toolkit_primer_val_classification + owner: iuc + tool_panel_section_id: '' +- name: mgnify_pipelines_toolkit_rev_comp_se_primers + owner: iuc + tool_panel_section_id: '' - name: mgnify_seqprep owner: bgruening tool_panel_section_id: '' @@ -1526,6 +1553,12 @@ tools: - name: miniprot_index owner: iuc tool_panel_section_id: '' +- name: mist_call + owner: iuc + tool_panel_section_id: '' +- name: mist_dists + owner: iuc + tool_panel_section_id: '' - name: mitos owner: iuc tool_panel_section_id: '' @@ -1976,6 +2009,9 @@ tools: - name: msstats owner: galaxyp tool_panel_section_id: '' +- name: mtnucratio + owner: iuc + tool_panel_section_id: '' - name: multigsea owner: iuc tool_panel_section_id: '' @@ -2093,6 +2129,9 @@ tools: - name: obi_clean owner: iuc tool_panel_section_id: '' +- name: obi_complement + owner: iuc + tool_panel_section_id: '' - name: obi_convert owner: iuc tool_panel_section_id: '' @@ -2105,6 +2144,18 @@ tools: - name: obi_pairing owner: iuc tool_panel_section_id: '' +- name: obi_pcr + owner: iuc + tool_panel_section_id: '' +- name: obi_refidx + owner: iuc + tool_panel_section_id: '' +- name: obi_tag + owner: iuc + tool_panel_section_id: '' +- name: obi_taxonomy + owner: iuc + tool_panel_section_id: '' - name: obi_uniq owner: iuc tool_panel_section_id: '' @@ -2726,6 +2777,9 @@ tools: - name: ppanggolin_rarefaction owner: iuc tool_panel_section_id: '' +- name: prinseq + owner: iuc + tool_panel_section_id: '' - name: prodigal owner: iuc tool_panel_section_id: '' @@ -2747,6 +2801,9 @@ tools: - name: proteinortho_summary owner: iuc tool_panel_section_id: '' +- name: psauron + owner: iuc + tool_panel_section_id: '' - name: pycoqc owner: iuc tool_panel_section_id: '' @@ -2855,262 +2912,241 @@ tools: - name: qiime_make_otu_table owner: iuc tool_panel_section_id: '' -- name: qiime2_core__tools__export - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2_core__tools__import - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2_core__tools__import_fastq - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__quality_filter__q_score - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__cull_seqs - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__degap_seqs - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__dereplicate - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__edit_taxonomy +- name: qiime2__dada2__denoise_ccs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_classifications +- name: qiime2__dada2__denoise_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_cross_validate +- name: qiime2__dada2__denoise_pyro owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_fit_classifier +- name: qiime2__dada2__denoise_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_seqs +- name: qiime2__dada2__plot_base_transitions owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_taxonomy +- name: qiime2__cutadapt__demux_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__extract_seq_segments +- name: qiime2__cutadapt__demux_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__filter_seqs_length +- name: qiime2__cutadapt__trim_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__filter_seqs_length_by_taxon +- name: qiime2__cutadapt__trim_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__filter_taxa +- name: qiime2__composition__add_pseudocount owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_bv_brc_genome_features +- name: qiime2__composition__ancom owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_bv_brc_genomes +- name: qiime2__composition__ancombc owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_bv_brc_metadata +- name: qiime2__composition__ancombc2 owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_eukaryome_data +- name: qiime2__composition__ancombc2_visualizer owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_gtdb_data +- name: qiime2__composition__da_barplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_midori2_data +- name: qiime2__composition__tabulate owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_ncbi_data +- name: qiime2__boots__alpha owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_ncbi_data_protein +- name: qiime2__boots__alpha_average owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_ncbi_genomes +- name: qiime2__boots__alpha_collection owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_pr2_data +- name: qiime2__boots__beta owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_silva_data +- name: qiime2__boots__beta_average owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_unite_data +- name: qiime2__boots__beta_collection owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__merge_taxa +- name: qiime2__boots__core_metrics owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__orient_reads +- name: qiime2__boots__kmer_diversity owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__orient_seqs +- name: qiime2__boots__resample owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__parse_silva_taxonomy +- name: qiime2__vsearch__cluster_features_closed_reference owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__reverse_transcribe +- name: qiime2__vsearch__cluster_features_de_novo owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__subsample_fasta +- name: qiime2__vsearch__cluster_features_open_reference owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__trim_alignment +- name: qiime2__vsearch__dereplicate_sequences owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__classify_samples +- name: qiime2__vsearch__fastq_stats owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__classify_samples_from_dist +- name: qiime2__vsearch__merge_pairs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__classify_samples_ncv +- name: qiime2__vsearch__uchime_denovo owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__confusion_matrix +- name: qiime2__vsearch__uchime_ref owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__fit_classifier +- name: qiime2__demux__emp_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__fit_regressor +- name: qiime2__demux__emp_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__heatmap +- name: qiime2__demux__filter_samples owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__metatable +- name: qiime2__demux__partition_samples_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__predict_classification +- name: qiime2__demux__partition_samples_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__predict_regression +- name: qiime2__demux__subsample_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__regress_samples +- name: qiime2__demux__subsample_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__regress_samples_ncv +- name: qiime2__demux__summarize owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__scatterplot +- name: qiime2__demux__tabulate_read_counts owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__split_table +- name: qiime2__deblur__denoise_16S owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__summarize +- name: qiime2__deblur__denoise_other owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__align_to_tree_mafft_fasttree +- name: qiime2__deblur__visualize_stats owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__align_to_tree_mafft_iqtree +- name: qiime2__diversity__adonis owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__align_to_tree_mafft_raxml +- name: qiime2__diversity__alpha owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__fasttree +- name: qiime2__diversity__alpha_correlation owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__filter_table +- name: qiime2__diversity__alpha_group_significance owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__filter_tree +- name: qiime2__diversity__alpha_phylogenetic owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__iqtree +- name: qiime2__diversity__alpha_rarefaction owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__iqtree_ultrafast_bootstrap +- name: qiime2__diversity__beta owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__midpoint_root +- name: qiime2__diversity__beta_correlation owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__raxml +- name: qiime2__diversity__beta_group_significance owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__raxml_rapid_bootstrap +- name: qiime2__diversity__beta_phylogenetic owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__robinson_foulds +- name: qiime2__diversity__beta_rarefaction owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__distance_matrix +- name: qiime2__diversity__bioenv owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__merge +- name: qiime2__diversity__core_metrics owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__shuffle_groups +- name: qiime2__diversity__core_metrics_phylogenetic owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__tabulate +- name: qiime2__diversity__filter_alpha_diversity owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__alpha_group_significance +- name: qiime2__diversity__filter_distance_matrix owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__collate_stats +- name: qiime2__diversity__mantel owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__facet_across +- name: qiime2__diversity__partial_procrustes owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__facet_within +- name: qiime2__diversity__pcoa owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__mann_whitney_u +- name: qiime2__diversity__pcoa_biplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__mann_whitney_u_facet +- name: qiime2__diversity__procrustes_analysis owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__plot_rainclouds +- name: qiime2__diversity__tsne owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__prep_alpha_distribution +- name: qiime2__diversity__umap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__wilcoxon_srt +- name: qiime2__emperor__biplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__wilcoxon_srt_facet +- name: qiime2__emperor__plot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__bowtie2_build +- name: qiime2__emperor__procrustes_plot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__decontam_identify +- name: qiime2_core__tools__export owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__decontam_identify_batches +- name: qiime2_core__tools__import owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__decontam_score_viz +- name: qiime2_core__tools__import_fastq owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__evaluate_composition +- name: qiime2__taxa__barplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__evaluate_seqs +- name: qiime2__taxa__barplot2 owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__evaluate_taxonomy +- name: qiime2__taxa__collapse owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__exclude_seqs +- name: qiime2__taxa__filter_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__filter_reads +- name: qiime2__taxa__filter_table owner: q2d2 tool_panel_section_id: '' - name: qiime2__diversity_lib__alpha_passthrough @@ -3149,253 +3185,244 @@ tools: - name: qiime2__diversity_lib__weighted_unifrac owner: q2d2 tool_panel_section_id: '' -- name: qiime2__alignment__mafft - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__alignment__mafft_add - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__alignment__mask - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__vizard__boxplot +- name: qiime2__stats__alpha_group_significance owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vizard__heatmap +- name: qiime2__stats__collate_stats owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vizard__lineplot +- name: qiime2__stats__facet_across owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vizard__scatterplot_2d +- name: qiime2__stats__facet_within owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__adonis +- name: qiime2__stats__mann_whitney_u owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha +- name: qiime2__stats__mann_whitney_u_facet owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_correlation +- name: qiime2__stats__plot_rainclouds owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_group_significance +- name: qiime2__stats__prep_alpha_distribution owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_phylogenetic +- name: qiime2__stats__wilcoxon_srt owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_rarefaction +- name: qiime2__stats__wilcoxon_srt_facet owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta +- name: qiime2__sample_classifier__classify_samples owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_correlation +- name: qiime2__sample_classifier__classify_samples_from_dist owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_group_significance +- name: qiime2__sample_classifier__classify_samples_ncv owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_phylogenetic +- name: qiime2__sample_classifier__confusion_matrix owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_rarefaction +- name: qiime2__sample_classifier__fit_classifier owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__bioenv +- name: qiime2__sample_classifier__fit_regressor owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__core_metrics +- name: qiime2__sample_classifier__heatmap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__core_metrics_phylogenetic +- name: qiime2__sample_classifier__metatable owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__filter_alpha_diversity +- name: qiime2__sample_classifier__predict_classification owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__filter_distance_matrix +- name: qiime2__sample_classifier__predict_regression owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__mantel +- name: qiime2__sample_classifier__regress_samples owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__partial_procrustes +- name: qiime2__sample_classifier__regress_samples_ncv owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__pcoa +- name: qiime2__sample_classifier__scatterplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__pcoa_biplot +- name: qiime2__sample_classifier__split_table owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__procrustes_analysis +- name: qiime2__sample_classifier__summarize owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__tsne +- name: qiime2__rescript__cull_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__umap +- name: qiime2__rescript__degap_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__emp_paired +- name: qiime2__rescript__dereplicate owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__emp_single +- name: qiime2__rescript__edit_taxonomy owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__filter_samples +- name: qiime2__rescript__evaluate_classifications owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__partition_samples_paired +- name: qiime2__rescript__evaluate_cross_validate owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__partition_samples_single +- name: qiime2__rescript__evaluate_fit_classifier owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__subsample_paired +- name: qiime2__rescript__evaluate_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__subsample_single +- name: qiime2__rescript__evaluate_taxonomy owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__summarize +- name: qiime2__rescript__extract_seq_segments owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__tabulate_read_counts +- name: qiime2__rescript__filter_seqs_length owner: q2d2 tool_panel_section_id: '' -- name: qiime2__deblur__denoise_16S +- name: qiime2__rescript__filter_seqs_length_by_taxon owner: q2d2 tool_panel_section_id: '' -- name: qiime2__deblur__denoise_other +- name: qiime2__rescript__filter_taxa owner: q2d2 tool_panel_section_id: '' -- name: qiime2__deblur__visualize_stats +- name: qiime2__rescript__get_bv_brc_genome_features owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_ccs +- name: qiime2__rescript__get_bv_brc_genomes owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_paired +- name: qiime2__rescript__get_bv_brc_metadata owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_pyro +- name: qiime2__rescript__get_eukaryome_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_single +- name: qiime2__rescript__get_gtdb_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__plot_base_transitions +- name: qiime2__rescript__get_midori2_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__cutadapt__demux_paired +- name: qiime2__rescript__get_ncbi_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__cutadapt__demux_single +- name: qiime2__rescript__get_ncbi_data_protein owner: q2d2 tool_panel_section_id: '' -- name: qiime2__cutadapt__trim_paired +- name: qiime2__rescript__get_ncbi_genomes owner: q2d2 tool_panel_section_id: '' -- name: qiime2__cutadapt__trim_single +- name: qiime2__rescript__get_pr2_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__add_pseudocount +- name: qiime2__rescript__get_silva_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancom +- name: qiime2__rescript__get_unite_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancombc +- name: qiime2__rescript__merge_taxa owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancombc2 +- name: qiime2__rescript__orient_reads owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancombc2_visualizer +- name: qiime2__rescript__orient_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__da_barplot +- name: qiime2__rescript__parse_silva_taxonomy owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__tabulate +- name: qiime2__rescript__reverse_transcribe owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__barplot +- name: qiime2__rescript__subsample_fasta owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__barplot2 +- name: qiime2__rescript__trim_alignment owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__collapse +- name: qiime2__quality_filter__q_score owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__filter_seqs +- name: qiime2__vizard__boxplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__filter_table +- name: qiime2__vizard__heatmap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__alpha +- name: qiime2__vizard__lineplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__alpha_average +- name: qiime2__vizard__scatterplot_2d owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__alpha_collection +- name: qiime2__alignment__mafft owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__beta +- name: qiime2__alignment__mafft_add owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__beta_average +- name: qiime2__alignment__mask owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__beta_collection +- name: qiime2__phylogeny__align_to_tree_mafft_fasttree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__core_metrics +- name: qiime2__phylogeny__align_to_tree_mafft_iqtree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__kmer_diversity +- name: qiime2__phylogeny__align_to_tree_mafft_raxml owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__resample +- name: qiime2__phylogeny__fasttree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__cluster_features_closed_reference +- name: qiime2__phylogeny__filter_table owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__cluster_features_de_novo +- name: qiime2__phylogeny__filter_tree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__cluster_features_open_reference +- name: qiime2__phylogeny__iqtree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__dereplicate_sequences +- name: qiime2__phylogeny__iqtree_ultrafast_bootstrap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__fastq_stats +- name: qiime2__phylogeny__midpoint_root owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__merge_pairs +- name: qiime2__phylogeny__raxml owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__uchime_denovo +- name: qiime2__phylogeny__raxml_rapid_bootstrap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__uchime_ref +- name: qiime2__phylogeny__robinson_foulds owner: q2d2 tool_panel_section_id: '' -- name: qiime2__emperor__biplot +- name: qiime2__fragment_insertion__classify_otus_experimental owner: q2d2 tool_panel_section_id: '' -- name: qiime2__emperor__plot +- name: qiime2__fragment_insertion__filter_features owner: q2d2 tool_panel_section_id: '' -- name: qiime2__emperor__procrustes_plot +- name: qiime2__fragment_insertion__sepp owner: q2d2 tool_panel_section_id: '' - name: qiime2__feature_classifier__blast @@ -3431,6 +3458,39 @@ tools: - name: qiime2__feature_classifier__vsearch_global owner: q2d2 tool_panel_section_id: '' +- name: qiime2__longitudinal__anova + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__feature_volatility + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__first_differences + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__first_distances + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__linear_mixed_effects + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__maturity_index + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__nmit + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__pairwise_differences + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__pairwise_distances + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__plot_feature_volatility + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__volatility + owner: q2d2 + tool_panel_section_id: '' - name: qiime2__feature_table___summarize owner: q2d2 tool_panel_section_id: '' @@ -3500,76 +3560,73 @@ tools: - name: qiime2__feature_table__transpose owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue___get_sequences - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__fondue__combine_seqs +- name: qiime2__quality_control__bowtie2_build owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__get_all +- name: qiime2__quality_control__decontam_identify owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__get_ids_from_query +- name: qiime2__quality_control__decontam_identify_batches owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__get_metadata +- name: qiime2__quality_control__decontam_score_viz owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__get_sequences +- name: qiime2__quality_control__evaluate_composition owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__merge_metadata +- name: qiime2__quality_control__evaluate_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__scrape_collection +- name: qiime2__quality_control__evaluate_taxonomy owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fragment_insertion__classify_otus_experimental +- name: qiime2__quality_control__exclude_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fragment_insertion__filter_features +- name: qiime2__quality_control__filter_reads owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fragment_insertion__sepp +- name: qiime2__metadata__distance_matrix owner: q2d2 tool_panel_section_id: '' -- name: qiime2__kmerizer__core_metrics +- name: qiime2__metadata__merge owner: q2d2 tool_panel_section_id: '' -- name: qiime2__kmerizer__seqs_to_kmers +- name: qiime2__metadata__shuffle_groups owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__anova +- name: qiime2__metadata__tabulate owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__feature_volatility +- name: qiime2__kmerizer__core_metrics owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__first_differences +- name: qiime2__kmerizer__seqs_to_kmers owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__first_distances +- name: qiime2__fondue___get_sequences owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__linear_mixed_effects +- name: qiime2__fondue__combine_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__maturity_index +- name: qiime2__fondue__get_all owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__nmit +- name: qiime2__fondue__get_ids_from_query owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__pairwise_differences +- name: qiime2__fondue__get_metadata owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__pairwise_distances +- name: qiime2__fondue__get_sequences owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__plot_feature_volatility +- name: qiime2__fondue__merge_metadata owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__volatility +- name: qiime2__fondue__scrape_collection owner: q2d2 tool_panel_section_id: '' - name: qiime2_dbotu_q2 @@ -3698,6 +3755,27 @@ tools: - name: rseqc_tin owner: nilesh tool_panel_section_id: '' +- name: samestr_compare + owner: iuc + tool_panel_section_id: '' +- name: samestr_convert + owner: iuc + tool_panel_section_id: '' +- name: samestr_extract + owner: iuc + tool_panel_section_id: '' +- name: samestr_filter + owner: iuc + tool_panel_section_id: '' +- name: samestr_merge + owner: iuc + tool_panel_section_id: '' +- name: samestr_stats + owner: iuc + tool_panel_section_id: '' +- name: samestr_summarize + owner: iuc + tool_panel_section_id: '' - name: scoary owner: iuc tool_panel_section_id: '' @@ -3822,10 +3900,10 @@ tools: owner: artbio tool_panel_section_id: '' - name: srst2 - owner: iuc + owner: nml tool_panel_section_id: '' - name: srst2 - owner: nml + owner: iuc tool_panel_section_id: '' - name: staramr_search owner: iuc @@ -3938,6 +4016,12 @@ tools: - name: varvamp owner: iuc tool_panel_section_id: '' +- name: vcontact2 + owner: iuc + tool_panel_section_id: '' +- name: vcontact2_gene2genome + owner: iuc + tool_panel_section_id: '' - name: vegan_diversity owner: iuc tool_panel_section_id: '' diff --git a/communities/microgalaxy/lab/tools/all/Lebanese_University_Galaxy.yaml b/communities/microgalaxy/lab/tools/all/Lebanese_University_Galaxy.yaml index d00d0595d..064410172 100644 --- a/communities/microgalaxy/lab/tools/all/Lebanese_University_Galaxy.yaml +++ b/communities/microgalaxy/lab/tools/all/Lebanese_University_Galaxy.yaml @@ -1226,6 +1226,9 @@ tools: - name: kmindex_query owner: iuc tool_panel_section_id: '' +- name: kneaddata + owner: iuc + tool_panel_section_id: '' - name: kofamscan owner: iuc tool_panel_section_id: '' @@ -1283,6 +1286,9 @@ tools: - name: legsta owner: iuc tool_panel_section_id: '' +- name: liftoff + owner: iuc + tool_panel_section_id: '' - name: lighter owner: bgruening tool_panel_section_id: '' @@ -1502,6 +1508,27 @@ tools: - name: mg_toolkit_original_metadata owner: iuc tool_panel_section_id: '' +- name: mgnify_genome_search + owner: iuc + tool_panel_section_id: '' +- name: mgnify_pipelines_toolkit_classify_var_regions + owner: iuc + tool_panel_section_id: '' +- name: mgnify_pipelines_toolkit_make_asv_count_table + owner: iuc + tool_panel_section_id: '' +- name: mgnify_pipelines_toolkit_mapseq_to_asv_table + owner: iuc + tool_panel_section_id: '' +- name: mgnify_pipelines_toolkit_permute_primers + owner: iuc + tool_panel_section_id: '' +- name: mgnify_pipelines_toolkit_primer_val_classification + owner: iuc + tool_panel_section_id: '' +- name: mgnify_pipelines_toolkit_rev_comp_se_primers + owner: iuc + tool_panel_section_id: '' - name: mgnify_seqprep owner: bgruening tool_panel_section_id: '' @@ -1523,6 +1550,12 @@ tools: - name: miniprot_index owner: iuc tool_panel_section_id: '' +- name: mist_call + owner: iuc + tool_panel_section_id: '' +- name: mist_dists + owner: iuc + tool_panel_section_id: '' - name: mitos owner: iuc tool_panel_section_id: '' @@ -1973,6 +2006,9 @@ tools: - name: msstats owner: galaxyp tool_panel_section_id: '' +- name: mtnucratio + owner: iuc + tool_panel_section_id: '' - name: multigsea owner: iuc tool_panel_section_id: '' @@ -2090,6 +2126,9 @@ tools: - name: obi_clean owner: iuc tool_panel_section_id: '' +- name: obi_complement + owner: iuc + tool_panel_section_id: '' - name: obi_convert owner: iuc tool_panel_section_id: '' @@ -2102,6 +2141,18 @@ tools: - name: obi_pairing owner: iuc tool_panel_section_id: '' +- name: obi_pcr + owner: iuc + tool_panel_section_id: '' +- name: obi_refidx + owner: iuc + tool_panel_section_id: '' +- name: obi_tag + owner: iuc + tool_panel_section_id: '' +- name: obi_taxonomy + owner: iuc + tool_panel_section_id: '' - name: obi_uniq owner: iuc tool_panel_section_id: '' @@ -2723,6 +2774,9 @@ tools: - name: ppanggolin_rarefaction owner: iuc tool_panel_section_id: '' +- name: prinseq + owner: iuc + tool_panel_section_id: '' - name: prodigal owner: iuc tool_panel_section_id: '' @@ -2744,6 +2798,9 @@ tools: - name: proteinortho_summary owner: iuc tool_panel_section_id: '' +- name: psauron + owner: iuc + tool_panel_section_id: '' - name: pycoqc owner: iuc tool_panel_section_id: '' @@ -2852,262 +2909,241 @@ tools: - name: qiime_make_otu_table owner: iuc tool_panel_section_id: '' -- name: qiime2_core__tools__export - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2_core__tools__import - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2_core__tools__import_fastq - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__quality_filter__q_score - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__cull_seqs - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__degap_seqs - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__dereplicate - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__edit_taxonomy +- name: qiime2__dada2__denoise_ccs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_classifications +- name: qiime2__dada2__denoise_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_cross_validate +- name: qiime2__dada2__denoise_pyro owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_fit_classifier +- name: qiime2__dada2__denoise_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_seqs +- name: qiime2__dada2__plot_base_transitions owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_taxonomy +- name: qiime2__cutadapt__demux_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__extract_seq_segments +- name: qiime2__cutadapt__demux_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__filter_seqs_length +- name: qiime2__cutadapt__trim_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__filter_seqs_length_by_taxon +- name: qiime2__cutadapt__trim_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__filter_taxa +- name: qiime2__composition__add_pseudocount owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_bv_brc_genome_features +- name: qiime2__composition__ancom owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_bv_brc_genomes +- name: qiime2__composition__ancombc owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_bv_brc_metadata +- name: qiime2__composition__ancombc2 owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_eukaryome_data +- name: qiime2__composition__ancombc2_visualizer owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_gtdb_data +- name: qiime2__composition__da_barplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_midori2_data +- name: qiime2__composition__tabulate owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_ncbi_data +- name: qiime2__boots__alpha owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_ncbi_data_protein +- name: qiime2__boots__alpha_average owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_ncbi_genomes +- name: qiime2__boots__alpha_collection owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_pr2_data +- name: qiime2__boots__beta owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_silva_data +- name: qiime2__boots__beta_average owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_unite_data +- name: qiime2__boots__beta_collection owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__merge_taxa +- name: qiime2__boots__core_metrics owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__orient_reads +- name: qiime2__boots__kmer_diversity owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__orient_seqs +- name: qiime2__boots__resample owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__parse_silva_taxonomy +- name: qiime2__vsearch__cluster_features_closed_reference owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__reverse_transcribe +- name: qiime2__vsearch__cluster_features_de_novo owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__subsample_fasta +- name: qiime2__vsearch__cluster_features_open_reference owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__trim_alignment +- name: qiime2__vsearch__dereplicate_sequences owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__classify_samples +- name: qiime2__vsearch__fastq_stats owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__classify_samples_from_dist +- name: qiime2__vsearch__merge_pairs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__classify_samples_ncv +- name: qiime2__vsearch__uchime_denovo owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__confusion_matrix +- name: qiime2__vsearch__uchime_ref owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__fit_classifier +- name: qiime2__demux__emp_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__fit_regressor +- name: qiime2__demux__emp_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__heatmap +- name: qiime2__demux__filter_samples owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__metatable +- name: qiime2__demux__partition_samples_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__predict_classification +- name: qiime2__demux__partition_samples_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__predict_regression +- name: qiime2__demux__subsample_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__regress_samples +- name: qiime2__demux__subsample_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__regress_samples_ncv +- name: qiime2__demux__summarize owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__scatterplot +- name: qiime2__demux__tabulate_read_counts owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__split_table +- name: qiime2__deblur__denoise_16S owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__summarize +- name: qiime2__deblur__denoise_other owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__align_to_tree_mafft_fasttree +- name: qiime2__deblur__visualize_stats owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__align_to_tree_mafft_iqtree +- name: qiime2__diversity__adonis owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__align_to_tree_mafft_raxml +- name: qiime2__diversity__alpha owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__fasttree +- name: qiime2__diversity__alpha_correlation owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__filter_table +- name: qiime2__diversity__alpha_group_significance owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__filter_tree +- name: qiime2__diversity__alpha_phylogenetic owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__iqtree +- name: qiime2__diversity__alpha_rarefaction owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__iqtree_ultrafast_bootstrap +- name: qiime2__diversity__beta owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__midpoint_root +- name: qiime2__diversity__beta_correlation owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__raxml +- name: qiime2__diversity__beta_group_significance owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__raxml_rapid_bootstrap +- name: qiime2__diversity__beta_phylogenetic owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__robinson_foulds +- name: qiime2__diversity__beta_rarefaction owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__distance_matrix +- name: qiime2__diversity__bioenv owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__merge +- name: qiime2__diversity__core_metrics owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__shuffle_groups +- name: qiime2__diversity__core_metrics_phylogenetic owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__tabulate +- name: qiime2__diversity__filter_alpha_diversity owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__alpha_group_significance +- name: qiime2__diversity__filter_distance_matrix owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__collate_stats +- name: qiime2__diversity__mantel owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__facet_across +- name: qiime2__diversity__partial_procrustes owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__facet_within +- name: qiime2__diversity__pcoa owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__mann_whitney_u +- name: qiime2__diversity__pcoa_biplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__mann_whitney_u_facet +- name: qiime2__diversity__procrustes_analysis owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__plot_rainclouds +- name: qiime2__diversity__tsne owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__prep_alpha_distribution +- name: qiime2__diversity__umap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__wilcoxon_srt +- name: qiime2__emperor__biplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__wilcoxon_srt_facet +- name: qiime2__emperor__plot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__bowtie2_build +- name: qiime2__emperor__procrustes_plot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__decontam_identify +- name: qiime2_core__tools__export owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__decontam_identify_batches +- name: qiime2_core__tools__import owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__decontam_score_viz +- name: qiime2_core__tools__import_fastq owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__evaluate_composition +- name: qiime2__taxa__barplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__evaluate_seqs +- name: qiime2__taxa__barplot2 owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__evaluate_taxonomy +- name: qiime2__taxa__collapse owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__exclude_seqs +- name: qiime2__taxa__filter_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__filter_reads +- name: qiime2__taxa__filter_table owner: q2d2 tool_panel_section_id: '' - name: qiime2__diversity_lib__alpha_passthrough @@ -3146,253 +3182,244 @@ tools: - name: qiime2__diversity_lib__weighted_unifrac owner: q2d2 tool_panel_section_id: '' -- name: qiime2__alignment__mafft - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__alignment__mafft_add - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__alignment__mask - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__vizard__boxplot +- name: qiime2__stats__alpha_group_significance owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vizard__heatmap +- name: qiime2__stats__collate_stats owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vizard__lineplot +- name: qiime2__stats__facet_across owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vizard__scatterplot_2d +- name: qiime2__stats__facet_within owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__adonis +- name: qiime2__stats__mann_whitney_u owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha +- name: qiime2__stats__mann_whitney_u_facet owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_correlation +- name: qiime2__stats__plot_rainclouds owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_group_significance +- name: qiime2__stats__prep_alpha_distribution owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_phylogenetic +- name: qiime2__stats__wilcoxon_srt owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_rarefaction +- name: qiime2__stats__wilcoxon_srt_facet owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta +- name: qiime2__sample_classifier__classify_samples owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_correlation +- name: qiime2__sample_classifier__classify_samples_from_dist owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_group_significance +- name: qiime2__sample_classifier__classify_samples_ncv owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_phylogenetic +- name: qiime2__sample_classifier__confusion_matrix owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_rarefaction +- name: qiime2__sample_classifier__fit_classifier owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__bioenv +- name: qiime2__sample_classifier__fit_regressor owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__core_metrics +- name: qiime2__sample_classifier__heatmap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__core_metrics_phylogenetic +- name: qiime2__sample_classifier__metatable owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__filter_alpha_diversity +- name: qiime2__sample_classifier__predict_classification owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__filter_distance_matrix +- name: qiime2__sample_classifier__predict_regression owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__mantel +- name: qiime2__sample_classifier__regress_samples owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__partial_procrustes +- name: qiime2__sample_classifier__regress_samples_ncv owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__pcoa +- name: qiime2__sample_classifier__scatterplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__pcoa_biplot +- name: qiime2__sample_classifier__split_table owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__procrustes_analysis +- name: qiime2__sample_classifier__summarize owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__tsne +- name: qiime2__rescript__cull_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__umap +- name: qiime2__rescript__degap_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__emp_paired +- name: qiime2__rescript__dereplicate owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__emp_single +- name: qiime2__rescript__edit_taxonomy owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__filter_samples +- name: qiime2__rescript__evaluate_classifications owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__partition_samples_paired +- name: qiime2__rescript__evaluate_cross_validate owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__partition_samples_single +- name: qiime2__rescript__evaluate_fit_classifier owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__subsample_paired +- name: qiime2__rescript__evaluate_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__subsample_single +- name: qiime2__rescript__evaluate_taxonomy owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__summarize +- name: qiime2__rescript__extract_seq_segments owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__tabulate_read_counts +- name: qiime2__rescript__filter_seqs_length owner: q2d2 tool_panel_section_id: '' -- name: qiime2__deblur__denoise_16S +- name: qiime2__rescript__filter_seqs_length_by_taxon owner: q2d2 tool_panel_section_id: '' -- name: qiime2__deblur__denoise_other +- name: qiime2__rescript__filter_taxa owner: q2d2 tool_panel_section_id: '' -- name: qiime2__deblur__visualize_stats +- name: qiime2__rescript__get_bv_brc_genome_features owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_ccs +- name: qiime2__rescript__get_bv_brc_genomes owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_paired +- name: qiime2__rescript__get_bv_brc_metadata owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_pyro +- name: qiime2__rescript__get_eukaryome_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_single +- name: qiime2__rescript__get_gtdb_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__plot_base_transitions +- name: qiime2__rescript__get_midori2_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__cutadapt__demux_paired +- name: qiime2__rescript__get_ncbi_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__cutadapt__demux_single +- name: qiime2__rescript__get_ncbi_data_protein owner: q2d2 tool_panel_section_id: '' -- name: qiime2__cutadapt__trim_paired +- name: qiime2__rescript__get_ncbi_genomes owner: q2d2 tool_panel_section_id: '' -- name: qiime2__cutadapt__trim_single +- name: qiime2__rescript__get_pr2_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__add_pseudocount +- name: qiime2__rescript__get_silva_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancom +- name: qiime2__rescript__get_unite_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancombc +- name: qiime2__rescript__merge_taxa owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancombc2 +- name: qiime2__rescript__orient_reads owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancombc2_visualizer +- name: qiime2__rescript__orient_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__da_barplot +- name: qiime2__rescript__parse_silva_taxonomy owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__tabulate +- name: qiime2__rescript__reverse_transcribe owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__barplot +- name: qiime2__rescript__subsample_fasta owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__barplot2 +- name: qiime2__rescript__trim_alignment owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__collapse +- name: qiime2__quality_filter__q_score owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__filter_seqs +- name: qiime2__vizard__boxplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__filter_table +- name: qiime2__vizard__heatmap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__alpha +- name: qiime2__vizard__lineplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__alpha_average +- name: qiime2__vizard__scatterplot_2d owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__alpha_collection +- name: qiime2__alignment__mafft owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__beta +- name: qiime2__alignment__mafft_add owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__beta_average +- name: qiime2__alignment__mask owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__beta_collection +- name: qiime2__phylogeny__align_to_tree_mafft_fasttree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__core_metrics +- name: qiime2__phylogeny__align_to_tree_mafft_iqtree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__kmer_diversity +- name: qiime2__phylogeny__align_to_tree_mafft_raxml owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__resample +- name: qiime2__phylogeny__fasttree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__cluster_features_closed_reference +- name: qiime2__phylogeny__filter_table owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__cluster_features_de_novo +- name: qiime2__phylogeny__filter_tree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__cluster_features_open_reference +- name: qiime2__phylogeny__iqtree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__dereplicate_sequences +- name: qiime2__phylogeny__iqtree_ultrafast_bootstrap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__fastq_stats +- name: qiime2__phylogeny__midpoint_root owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__merge_pairs +- name: qiime2__phylogeny__raxml owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__uchime_denovo +- name: qiime2__phylogeny__raxml_rapid_bootstrap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__uchime_ref +- name: qiime2__phylogeny__robinson_foulds owner: q2d2 tool_panel_section_id: '' -- name: qiime2__emperor__biplot +- name: qiime2__fragment_insertion__classify_otus_experimental owner: q2d2 tool_panel_section_id: '' -- name: qiime2__emperor__plot +- name: qiime2__fragment_insertion__filter_features owner: q2d2 tool_panel_section_id: '' -- name: qiime2__emperor__procrustes_plot +- name: qiime2__fragment_insertion__sepp owner: q2d2 tool_panel_section_id: '' - name: qiime2__feature_classifier__blast @@ -3428,6 +3455,39 @@ tools: - name: qiime2__feature_classifier__vsearch_global owner: q2d2 tool_panel_section_id: '' +- name: qiime2__longitudinal__anova + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__feature_volatility + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__first_differences + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__first_distances + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__linear_mixed_effects + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__maturity_index + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__nmit + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__pairwise_differences + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__pairwise_distances + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__plot_feature_volatility + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__volatility + owner: q2d2 + tool_panel_section_id: '' - name: qiime2__feature_table___summarize owner: q2d2 tool_panel_section_id: '' @@ -3497,76 +3557,73 @@ tools: - name: qiime2__feature_table__transpose owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue___get_sequences - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__fondue__combine_seqs +- name: qiime2__quality_control__bowtie2_build owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__get_all +- name: qiime2__quality_control__decontam_identify owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__get_ids_from_query +- name: qiime2__quality_control__decontam_identify_batches owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__get_metadata +- name: qiime2__quality_control__decontam_score_viz owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__get_sequences +- name: qiime2__quality_control__evaluate_composition owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__merge_metadata +- name: qiime2__quality_control__evaluate_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__scrape_collection +- name: qiime2__quality_control__evaluate_taxonomy owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fragment_insertion__classify_otus_experimental +- name: qiime2__quality_control__exclude_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fragment_insertion__filter_features +- name: qiime2__quality_control__filter_reads owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fragment_insertion__sepp +- name: qiime2__metadata__distance_matrix owner: q2d2 tool_panel_section_id: '' -- name: qiime2__kmerizer__core_metrics +- name: qiime2__metadata__merge owner: q2d2 tool_panel_section_id: '' -- name: qiime2__kmerizer__seqs_to_kmers +- name: qiime2__metadata__shuffle_groups owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__anova +- name: qiime2__metadata__tabulate owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__feature_volatility +- name: qiime2__kmerizer__core_metrics owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__first_differences +- name: qiime2__kmerizer__seqs_to_kmers owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__first_distances +- name: qiime2__fondue___get_sequences owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__linear_mixed_effects +- name: qiime2__fondue__combine_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__maturity_index +- name: qiime2__fondue__get_all owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__nmit +- name: qiime2__fondue__get_ids_from_query owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__pairwise_differences +- name: qiime2__fondue__get_metadata owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__pairwise_distances +- name: qiime2__fondue__get_sequences owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__plot_feature_volatility +- name: qiime2__fondue__merge_metadata owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__volatility +- name: qiime2__fondue__scrape_collection owner: q2d2 tool_panel_section_id: '' - name: qiime2_dbotu_q2 @@ -3695,6 +3752,27 @@ tools: - name: rseqc_tin owner: nilesh tool_panel_section_id: '' +- name: samestr_compare + owner: iuc + tool_panel_section_id: '' +- name: samestr_convert + owner: iuc + tool_panel_section_id: '' +- name: samestr_extract + owner: iuc + tool_panel_section_id: '' +- name: samestr_filter + owner: iuc + tool_panel_section_id: '' +- name: samestr_merge + owner: iuc + tool_panel_section_id: '' +- name: samestr_stats + owner: iuc + tool_panel_section_id: '' +- name: samestr_summarize + owner: iuc + tool_panel_section_id: '' - name: scoary owner: iuc tool_panel_section_id: '' @@ -3819,10 +3897,10 @@ tools: owner: artbio tool_panel_section_id: '' - name: srst2 - owner: iuc + owner: nml tool_panel_section_id: '' - name: srst2 - owner: nml + owner: iuc tool_panel_section_id: '' - name: staramr_search owner: iuc @@ -3935,6 +4013,12 @@ tools: - name: varvamp owner: iuc tool_panel_section_id: '' +- name: vcontact2 + owner: iuc + tool_panel_section_id: '' +- name: vcontact2_gene2genome + owner: iuc + tool_panel_section_id: '' - name: vegan_diversity owner: iuc tool_panel_section_id: '' diff --git a/communities/microgalaxy/lab/tools/all/Local_Galaxy.yaml b/communities/microgalaxy/lab/tools/all/Local_Galaxy.yaml index a8c67bb3f..47a750f2c 100644 --- a/communities/microgalaxy/lab/tools/all/Local_Galaxy.yaml +++ b/communities/microgalaxy/lab/tools/all/Local_Galaxy.yaml @@ -1229,6 +1229,9 @@ tools: - name: kmindex_query owner: iuc tool_panel_section_id: '' +- name: kneaddata + owner: iuc + tool_panel_section_id: '' - name: kofamscan owner: iuc tool_panel_section_id: '' @@ -1286,6 +1289,9 @@ tools: - name: legsta owner: iuc tool_panel_section_id: '' +- name: liftoff + owner: iuc + tool_panel_section_id: '' - name: lighter owner: bgruening tool_panel_section_id: '' @@ -1505,6 +1511,27 @@ tools: - name: mg_toolkit_original_metadata owner: iuc tool_panel_section_id: '' +- name: mgnify_genome_search + owner: iuc + tool_panel_section_id: '' +- name: mgnify_pipelines_toolkit_classify_var_regions + owner: iuc + tool_panel_section_id: '' +- name: mgnify_pipelines_toolkit_make_asv_count_table + owner: iuc + tool_panel_section_id: '' +- name: mgnify_pipelines_toolkit_mapseq_to_asv_table + owner: iuc + tool_panel_section_id: '' +- name: mgnify_pipelines_toolkit_permute_primers + owner: iuc + tool_panel_section_id: '' +- name: mgnify_pipelines_toolkit_primer_val_classification + owner: iuc + tool_panel_section_id: '' +- name: mgnify_pipelines_toolkit_rev_comp_se_primers + owner: iuc + tool_panel_section_id: '' - name: mgnify_seqprep owner: bgruening tool_panel_section_id: '' @@ -1526,6 +1553,12 @@ tools: - name: miniprot_index owner: iuc tool_panel_section_id: '' +- name: mist_call + owner: iuc + tool_panel_section_id: '' +- name: mist_dists + owner: iuc + tool_panel_section_id: '' - name: mitos owner: iuc tool_panel_section_id: '' @@ -1976,6 +2009,9 @@ tools: - name: msstats owner: galaxyp tool_panel_section_id: '' +- name: mtnucratio + owner: iuc + tool_panel_section_id: '' - name: multigsea owner: iuc tool_panel_section_id: '' @@ -2093,6 +2129,9 @@ tools: - name: obi_clean owner: iuc tool_panel_section_id: '' +- name: obi_complement + owner: iuc + tool_panel_section_id: '' - name: obi_convert owner: iuc tool_panel_section_id: '' @@ -2105,6 +2144,18 @@ tools: - name: obi_pairing owner: iuc tool_panel_section_id: '' +- name: obi_pcr + owner: iuc + tool_panel_section_id: '' +- name: obi_refidx + owner: iuc + tool_panel_section_id: '' +- name: obi_tag + owner: iuc + tool_panel_section_id: '' +- name: obi_taxonomy + owner: iuc + tool_panel_section_id: '' - name: obi_uniq owner: iuc tool_panel_section_id: '' @@ -2726,6 +2777,9 @@ tools: - name: ppanggolin_rarefaction owner: iuc tool_panel_section_id: '' +- name: prinseq + owner: iuc + tool_panel_section_id: '' - name: prodigal owner: iuc tool_panel_section_id: '' @@ -2747,6 +2801,9 @@ tools: - name: proteinortho_summary owner: iuc tool_panel_section_id: '' +- name: psauron + owner: iuc + tool_panel_section_id: '' - name: pycoqc owner: iuc tool_panel_section_id: '' @@ -2855,262 +2912,241 @@ tools: - name: qiime_make_otu_table owner: iuc tool_panel_section_id: '' -- name: qiime2_core__tools__export - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2_core__tools__import - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2_core__tools__import_fastq - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__quality_filter__q_score - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__cull_seqs - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__degap_seqs - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__dereplicate - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__edit_taxonomy +- name: qiime2__dada2__denoise_ccs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_classifications +- name: qiime2__dada2__denoise_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_cross_validate +- name: qiime2__dada2__denoise_pyro owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_fit_classifier +- name: qiime2__dada2__denoise_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_seqs +- name: qiime2__dada2__plot_base_transitions owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_taxonomy +- name: qiime2__cutadapt__demux_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__extract_seq_segments +- name: qiime2__cutadapt__demux_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__filter_seqs_length +- name: qiime2__cutadapt__trim_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__filter_seqs_length_by_taxon +- name: qiime2__cutadapt__trim_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__filter_taxa +- name: qiime2__composition__add_pseudocount owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_bv_brc_genome_features +- name: qiime2__composition__ancom owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_bv_brc_genomes +- name: qiime2__composition__ancombc owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_bv_brc_metadata +- name: qiime2__composition__ancombc2 owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_eukaryome_data +- name: qiime2__composition__ancombc2_visualizer owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_gtdb_data +- name: qiime2__composition__da_barplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_midori2_data +- name: qiime2__composition__tabulate owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_ncbi_data +- name: qiime2__boots__alpha owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_ncbi_data_protein +- name: qiime2__boots__alpha_average owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_ncbi_genomes +- name: qiime2__boots__alpha_collection owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_pr2_data +- name: qiime2__boots__beta owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_silva_data +- name: qiime2__boots__beta_average owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_unite_data +- name: qiime2__boots__beta_collection owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__merge_taxa +- name: qiime2__boots__core_metrics owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__orient_reads +- name: qiime2__boots__kmer_diversity owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__orient_seqs +- name: qiime2__boots__resample owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__parse_silva_taxonomy +- name: qiime2__vsearch__cluster_features_closed_reference owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__reverse_transcribe +- name: qiime2__vsearch__cluster_features_de_novo owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__subsample_fasta +- name: qiime2__vsearch__cluster_features_open_reference owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__trim_alignment +- name: qiime2__vsearch__dereplicate_sequences owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__classify_samples +- name: qiime2__vsearch__fastq_stats owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__classify_samples_from_dist +- name: qiime2__vsearch__merge_pairs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__classify_samples_ncv +- name: qiime2__vsearch__uchime_denovo owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__confusion_matrix +- name: qiime2__vsearch__uchime_ref owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__fit_classifier +- name: qiime2__demux__emp_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__fit_regressor +- name: qiime2__demux__emp_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__heatmap +- name: qiime2__demux__filter_samples owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__metatable +- name: qiime2__demux__partition_samples_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__predict_classification +- name: qiime2__demux__partition_samples_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__predict_regression +- name: qiime2__demux__subsample_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__regress_samples +- name: qiime2__demux__subsample_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__regress_samples_ncv +- name: qiime2__demux__summarize owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__scatterplot +- name: qiime2__demux__tabulate_read_counts owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__split_table +- name: qiime2__deblur__denoise_16S owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__summarize +- name: qiime2__deblur__denoise_other owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__align_to_tree_mafft_fasttree +- name: qiime2__deblur__visualize_stats owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__align_to_tree_mafft_iqtree +- name: qiime2__diversity__adonis owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__align_to_tree_mafft_raxml +- name: qiime2__diversity__alpha owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__fasttree +- name: qiime2__diversity__alpha_correlation owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__filter_table +- name: qiime2__diversity__alpha_group_significance owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__filter_tree +- name: qiime2__diversity__alpha_phylogenetic owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__iqtree +- name: qiime2__diversity__alpha_rarefaction owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__iqtree_ultrafast_bootstrap +- name: qiime2__diversity__beta owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__midpoint_root +- name: qiime2__diversity__beta_correlation owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__raxml +- name: qiime2__diversity__beta_group_significance owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__raxml_rapid_bootstrap +- name: qiime2__diversity__beta_phylogenetic owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__robinson_foulds +- name: qiime2__diversity__beta_rarefaction owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__distance_matrix +- name: qiime2__diversity__bioenv owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__merge +- name: qiime2__diversity__core_metrics owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__shuffle_groups +- name: qiime2__diversity__core_metrics_phylogenetic owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__tabulate +- name: qiime2__diversity__filter_alpha_diversity owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__alpha_group_significance +- name: qiime2__diversity__filter_distance_matrix owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__collate_stats +- name: qiime2__diversity__mantel owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__facet_across +- name: qiime2__diversity__partial_procrustes owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__facet_within +- name: qiime2__diversity__pcoa owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__mann_whitney_u +- name: qiime2__diversity__pcoa_biplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__mann_whitney_u_facet +- name: qiime2__diversity__procrustes_analysis owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__plot_rainclouds +- name: qiime2__diversity__tsne owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__prep_alpha_distribution +- name: qiime2__diversity__umap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__wilcoxon_srt +- name: qiime2__emperor__biplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__wilcoxon_srt_facet +- name: qiime2__emperor__plot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__bowtie2_build +- name: qiime2__emperor__procrustes_plot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__decontam_identify +- name: qiime2_core__tools__export owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__decontam_identify_batches +- name: qiime2_core__tools__import owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__decontam_score_viz +- name: qiime2_core__tools__import_fastq owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__evaluate_composition +- name: qiime2__taxa__barplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__evaluate_seqs +- name: qiime2__taxa__barplot2 owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__evaluate_taxonomy +- name: qiime2__taxa__collapse owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__exclude_seqs +- name: qiime2__taxa__filter_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__filter_reads +- name: qiime2__taxa__filter_table owner: q2d2 tool_panel_section_id: '' - name: qiime2__diversity_lib__alpha_passthrough @@ -3149,253 +3185,244 @@ tools: - name: qiime2__diversity_lib__weighted_unifrac owner: q2d2 tool_panel_section_id: '' -- name: qiime2__alignment__mafft - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__alignment__mafft_add - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__alignment__mask - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__vizard__boxplot +- name: qiime2__stats__alpha_group_significance owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vizard__heatmap +- name: qiime2__stats__collate_stats owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vizard__lineplot +- name: qiime2__stats__facet_across owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vizard__scatterplot_2d +- name: qiime2__stats__facet_within owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__adonis +- name: qiime2__stats__mann_whitney_u owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha +- name: qiime2__stats__mann_whitney_u_facet owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_correlation +- name: qiime2__stats__plot_rainclouds owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_group_significance +- name: qiime2__stats__prep_alpha_distribution owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_phylogenetic +- name: qiime2__stats__wilcoxon_srt owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_rarefaction +- name: qiime2__stats__wilcoxon_srt_facet owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta +- name: qiime2__sample_classifier__classify_samples owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_correlation +- name: qiime2__sample_classifier__classify_samples_from_dist owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_group_significance +- name: qiime2__sample_classifier__classify_samples_ncv owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_phylogenetic +- name: qiime2__sample_classifier__confusion_matrix owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_rarefaction +- name: qiime2__sample_classifier__fit_classifier owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__bioenv +- name: qiime2__sample_classifier__fit_regressor owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__core_metrics +- name: qiime2__sample_classifier__heatmap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__core_metrics_phylogenetic +- name: qiime2__sample_classifier__metatable owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__filter_alpha_diversity +- name: qiime2__sample_classifier__predict_classification owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__filter_distance_matrix +- name: qiime2__sample_classifier__predict_regression owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__mantel +- name: qiime2__sample_classifier__regress_samples owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__partial_procrustes +- name: qiime2__sample_classifier__regress_samples_ncv owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__pcoa +- name: qiime2__sample_classifier__scatterplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__pcoa_biplot +- name: qiime2__sample_classifier__split_table owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__procrustes_analysis +- name: qiime2__sample_classifier__summarize owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__tsne +- name: qiime2__rescript__cull_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__umap +- name: qiime2__rescript__degap_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__emp_paired +- name: qiime2__rescript__dereplicate owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__emp_single +- name: qiime2__rescript__edit_taxonomy owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__filter_samples +- name: qiime2__rescript__evaluate_classifications owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__partition_samples_paired +- name: qiime2__rescript__evaluate_cross_validate owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__partition_samples_single +- name: qiime2__rescript__evaluate_fit_classifier owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__subsample_paired +- name: qiime2__rescript__evaluate_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__subsample_single +- name: qiime2__rescript__evaluate_taxonomy owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__summarize +- name: qiime2__rescript__extract_seq_segments owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__tabulate_read_counts +- name: qiime2__rescript__filter_seqs_length owner: q2d2 tool_panel_section_id: '' -- name: qiime2__deblur__denoise_16S +- name: qiime2__rescript__filter_seqs_length_by_taxon owner: q2d2 tool_panel_section_id: '' -- name: qiime2__deblur__denoise_other +- name: qiime2__rescript__filter_taxa owner: q2d2 tool_panel_section_id: '' -- name: qiime2__deblur__visualize_stats +- name: qiime2__rescript__get_bv_brc_genome_features owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_ccs +- name: qiime2__rescript__get_bv_brc_genomes owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_paired +- name: qiime2__rescript__get_bv_brc_metadata owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_pyro +- name: qiime2__rescript__get_eukaryome_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_single +- name: qiime2__rescript__get_gtdb_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__plot_base_transitions +- name: qiime2__rescript__get_midori2_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__cutadapt__demux_paired +- name: qiime2__rescript__get_ncbi_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__cutadapt__demux_single +- name: qiime2__rescript__get_ncbi_data_protein owner: q2d2 tool_panel_section_id: '' -- name: qiime2__cutadapt__trim_paired +- name: qiime2__rescript__get_ncbi_genomes owner: q2d2 tool_panel_section_id: '' -- name: qiime2__cutadapt__trim_single +- name: qiime2__rescript__get_pr2_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__add_pseudocount +- name: qiime2__rescript__get_silva_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancom +- name: qiime2__rescript__get_unite_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancombc +- name: qiime2__rescript__merge_taxa owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancombc2 +- name: qiime2__rescript__orient_reads owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancombc2_visualizer +- name: qiime2__rescript__orient_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__da_barplot +- name: qiime2__rescript__parse_silva_taxonomy owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__tabulate +- name: qiime2__rescript__reverse_transcribe owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__barplot +- name: qiime2__rescript__subsample_fasta owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__barplot2 +- name: qiime2__rescript__trim_alignment owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__collapse +- name: qiime2__quality_filter__q_score owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__filter_seqs +- name: qiime2__vizard__boxplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__filter_table +- name: qiime2__vizard__heatmap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__alpha +- name: qiime2__vizard__lineplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__alpha_average +- name: qiime2__vizard__scatterplot_2d owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__alpha_collection +- name: qiime2__alignment__mafft owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__beta +- name: qiime2__alignment__mafft_add owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__beta_average +- name: qiime2__alignment__mask owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__beta_collection +- name: qiime2__phylogeny__align_to_tree_mafft_fasttree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__core_metrics +- name: qiime2__phylogeny__align_to_tree_mafft_iqtree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__kmer_diversity +- name: qiime2__phylogeny__align_to_tree_mafft_raxml owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__resample +- name: qiime2__phylogeny__fasttree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__cluster_features_closed_reference +- name: qiime2__phylogeny__filter_table owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__cluster_features_de_novo +- name: qiime2__phylogeny__filter_tree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__cluster_features_open_reference +- name: qiime2__phylogeny__iqtree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__dereplicate_sequences +- name: qiime2__phylogeny__iqtree_ultrafast_bootstrap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__fastq_stats +- name: qiime2__phylogeny__midpoint_root owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__merge_pairs +- name: qiime2__phylogeny__raxml owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__uchime_denovo +- name: qiime2__phylogeny__raxml_rapid_bootstrap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__uchime_ref +- name: qiime2__phylogeny__robinson_foulds owner: q2d2 tool_panel_section_id: '' -- name: qiime2__emperor__biplot +- name: qiime2__fragment_insertion__classify_otus_experimental owner: q2d2 tool_panel_section_id: '' -- name: qiime2__emperor__plot +- name: qiime2__fragment_insertion__filter_features owner: q2d2 tool_panel_section_id: '' -- name: qiime2__emperor__procrustes_plot +- name: qiime2__fragment_insertion__sepp owner: q2d2 tool_panel_section_id: '' - name: qiime2__feature_classifier__blast @@ -3431,6 +3458,39 @@ tools: - name: qiime2__feature_classifier__vsearch_global owner: q2d2 tool_panel_section_id: '' +- name: qiime2__longitudinal__anova + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__feature_volatility + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__first_differences + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__first_distances + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__linear_mixed_effects + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__maturity_index + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__nmit + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__pairwise_differences + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__pairwise_distances + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__plot_feature_volatility + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__volatility + owner: q2d2 + tool_panel_section_id: '' - name: qiime2__feature_table___summarize owner: q2d2 tool_panel_section_id: '' @@ -3500,76 +3560,73 @@ tools: - name: qiime2__feature_table__transpose owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue___get_sequences - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__fondue__combine_seqs +- name: qiime2__quality_control__bowtie2_build owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__get_all +- name: qiime2__quality_control__decontam_identify owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__get_ids_from_query +- name: qiime2__quality_control__decontam_identify_batches owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__get_metadata +- name: qiime2__quality_control__decontam_score_viz owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__get_sequences +- name: qiime2__quality_control__evaluate_composition owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__merge_metadata +- name: qiime2__quality_control__evaluate_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__scrape_collection +- name: qiime2__quality_control__evaluate_taxonomy owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fragment_insertion__classify_otus_experimental +- name: qiime2__quality_control__exclude_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fragment_insertion__filter_features +- name: qiime2__quality_control__filter_reads owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fragment_insertion__sepp +- name: qiime2__metadata__distance_matrix owner: q2d2 tool_panel_section_id: '' -- name: qiime2__kmerizer__core_metrics +- name: qiime2__metadata__merge owner: q2d2 tool_panel_section_id: '' -- name: qiime2__kmerizer__seqs_to_kmers +- name: qiime2__metadata__shuffle_groups owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__anova +- name: qiime2__metadata__tabulate owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__feature_volatility +- name: qiime2__kmerizer__core_metrics owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__first_differences +- name: qiime2__kmerizer__seqs_to_kmers owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__first_distances +- name: qiime2__fondue___get_sequences owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__linear_mixed_effects +- name: qiime2__fondue__combine_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__maturity_index +- name: qiime2__fondue__get_all owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__nmit +- name: qiime2__fondue__get_ids_from_query owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__pairwise_differences +- name: qiime2__fondue__get_metadata owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__pairwise_distances +- name: qiime2__fondue__get_sequences owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__plot_feature_volatility +- name: qiime2__fondue__merge_metadata owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__volatility +- name: qiime2__fondue__scrape_collection owner: q2d2 tool_panel_section_id: '' - name: qiime2_dbotu_q2 @@ -3698,6 +3755,27 @@ tools: - name: rseqc_tin owner: nilesh tool_panel_section_id: '' +- name: samestr_compare + owner: iuc + tool_panel_section_id: '' +- name: samestr_convert + owner: iuc + tool_panel_section_id: '' +- name: samestr_extract + owner: iuc + tool_panel_section_id: '' +- name: samestr_filter + owner: iuc + tool_panel_section_id: '' +- name: samestr_merge + owner: iuc + tool_panel_section_id: '' +- name: samestr_stats + owner: iuc + tool_panel_section_id: '' +- name: samestr_summarize + owner: iuc + tool_panel_section_id: '' - name: scoary owner: iuc tool_panel_section_id: '' @@ -3822,10 +3900,10 @@ tools: owner: artbio tool_panel_section_id: '' - name: srst2 - owner: iuc + owner: nml tool_panel_section_id: '' - name: srst2 - owner: nml + owner: iuc tool_panel_section_id: '' - name: staramr_search owner: iuc @@ -3938,6 +4016,12 @@ tools: - name: varvamp owner: iuc tool_panel_section_id: '' +- name: vcontact2 + owner: iuc + tool_panel_section_id: '' +- name: vcontact2_gene2genome + owner: iuc + tool_panel_section_id: '' - name: vegan_diversity owner: iuc tool_panel_section_id: '' diff --git a/communities/microgalaxy/lab/tools/all/MISSISSIPPI.yaml b/communities/microgalaxy/lab/tools/all/MISSISSIPPI.yaml index b10ec7af1..7cb2628ba 100644 --- a/communities/microgalaxy/lab/tools/all/MISSISSIPPI.yaml +++ b/communities/microgalaxy/lab/tools/all/MISSISSIPPI.yaml @@ -869,6 +869,9 @@ tools: - name: kmindex_query owner: iuc tool_panel_section_id: '' +- name: kneaddata + owner: iuc + tool_panel_section_id: '' - name: kofamscan owner: iuc tool_panel_section_id: '' @@ -926,6 +929,9 @@ tools: - name: legsta owner: iuc tool_panel_section_id: '' +- name: liftoff + owner: iuc + tool_panel_section_id: '' - name: lighter owner: bgruening tool_panel_section_id: '' @@ -1133,6 +1139,27 @@ tools: - name: mg_toolkit_original_metadata owner: iuc tool_panel_section_id: '' +- name: mgnify_genome_search + owner: iuc + tool_panel_section_id: '' +- name: mgnify_pipelines_toolkit_classify_var_regions + owner: iuc + tool_panel_section_id: '' +- name: mgnify_pipelines_toolkit_make_asv_count_table + owner: iuc + tool_panel_section_id: '' +- name: mgnify_pipelines_toolkit_mapseq_to_asv_table + owner: iuc + tool_panel_section_id: '' +- name: mgnify_pipelines_toolkit_permute_primers + owner: iuc + tool_panel_section_id: '' +- name: mgnify_pipelines_toolkit_primer_val_classification + owner: iuc + tool_panel_section_id: '' +- name: mgnify_pipelines_toolkit_rev_comp_se_primers + owner: iuc + tool_panel_section_id: '' - name: mgnify_seqprep owner: bgruening tool_panel_section_id: '' @@ -1154,6 +1181,12 @@ tools: - name: miniprot_index owner: iuc tool_panel_section_id: '' +- name: mist_call + owner: iuc + tool_panel_section_id: '' +- name: mist_dists + owner: iuc + tool_panel_section_id: '' - name: mitos owner: iuc tool_panel_section_id: '' @@ -1604,6 +1637,9 @@ tools: - name: msstats owner: galaxyp tool_panel_section_id: '' +- name: mtnucratio + owner: iuc + tool_panel_section_id: '' - name: multigsea owner: iuc tool_panel_section_id: '' @@ -1715,6 +1751,9 @@ tools: - name: obi_clean owner: iuc tool_panel_section_id: '' +- name: obi_complement + owner: iuc + tool_panel_section_id: '' - name: obi_convert owner: iuc tool_panel_section_id: '' @@ -1727,6 +1766,18 @@ tools: - name: obi_pairing owner: iuc tool_panel_section_id: '' +- name: obi_pcr + owner: iuc + tool_panel_section_id: '' +- name: obi_refidx + owner: iuc + tool_panel_section_id: '' +- name: obi_tag + owner: iuc + tool_panel_section_id: '' +- name: obi_taxonomy + owner: iuc + tool_panel_section_id: '' - name: obi_uniq owner: iuc tool_panel_section_id: '' @@ -2348,6 +2399,9 @@ tools: - name: ppanggolin_rarefaction owner: iuc tool_panel_section_id: '' +- name: prinseq + owner: iuc + tool_panel_section_id: '' - name: prodigal owner: iuc tool_panel_section_id: '' @@ -2366,6 +2420,9 @@ tools: - name: proteinortho_summary owner: iuc tool_panel_section_id: '' +- name: psauron + owner: iuc + tool_panel_section_id: '' - name: pycoqc owner: iuc tool_panel_section_id: '' @@ -2474,262 +2531,241 @@ tools: - name: qiime_make_otu_table owner: iuc tool_panel_section_id: '' -- name: qiime2_core__tools__export - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2_core__tools__import - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2_core__tools__import_fastq - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__quality_filter__q_score - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__cull_seqs - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__degap_seqs - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__dereplicate - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__edit_taxonomy +- name: qiime2__dada2__denoise_ccs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_classifications +- name: qiime2__dada2__denoise_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_cross_validate +- name: qiime2__dada2__denoise_pyro owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_fit_classifier +- name: qiime2__dada2__denoise_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_seqs +- name: qiime2__dada2__plot_base_transitions owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_taxonomy +- name: qiime2__cutadapt__demux_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__extract_seq_segments +- name: qiime2__cutadapt__demux_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__filter_seqs_length +- name: qiime2__cutadapt__trim_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__filter_seqs_length_by_taxon +- name: qiime2__cutadapt__trim_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__filter_taxa +- name: qiime2__composition__add_pseudocount owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_bv_brc_genome_features +- name: qiime2__composition__ancom owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_bv_brc_genomes +- name: qiime2__composition__ancombc owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_bv_brc_metadata +- name: qiime2__composition__ancombc2 owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_eukaryome_data +- name: qiime2__composition__ancombc2_visualizer owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_gtdb_data +- name: qiime2__composition__da_barplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_midori2_data +- name: qiime2__composition__tabulate owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_ncbi_data +- name: qiime2__boots__alpha owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_ncbi_data_protein +- name: qiime2__boots__alpha_average owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_ncbi_genomes +- name: qiime2__boots__alpha_collection owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_pr2_data +- name: qiime2__boots__beta owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_silva_data +- name: qiime2__boots__beta_average owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_unite_data +- name: qiime2__boots__beta_collection owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__merge_taxa +- name: qiime2__boots__core_metrics owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__orient_reads +- name: qiime2__boots__kmer_diversity owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__orient_seqs +- name: qiime2__boots__resample owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__parse_silva_taxonomy +- name: qiime2__vsearch__cluster_features_closed_reference owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__reverse_transcribe +- name: qiime2__vsearch__cluster_features_de_novo owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__subsample_fasta +- name: qiime2__vsearch__cluster_features_open_reference owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__trim_alignment +- name: qiime2__vsearch__dereplicate_sequences owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__classify_samples +- name: qiime2__vsearch__fastq_stats owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__classify_samples_from_dist +- name: qiime2__vsearch__merge_pairs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__classify_samples_ncv +- name: qiime2__vsearch__uchime_denovo owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__confusion_matrix +- name: qiime2__vsearch__uchime_ref owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__fit_classifier +- name: qiime2__demux__emp_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__fit_regressor +- name: qiime2__demux__emp_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__heatmap +- name: qiime2__demux__filter_samples owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__metatable +- name: qiime2__demux__partition_samples_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__predict_classification +- name: qiime2__demux__partition_samples_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__predict_regression +- name: qiime2__demux__subsample_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__regress_samples +- name: qiime2__demux__subsample_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__regress_samples_ncv +- name: qiime2__demux__summarize owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__scatterplot +- name: qiime2__demux__tabulate_read_counts owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__split_table +- name: qiime2__deblur__denoise_16S owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__summarize +- name: qiime2__deblur__denoise_other owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__align_to_tree_mafft_fasttree +- name: qiime2__deblur__visualize_stats owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__align_to_tree_mafft_iqtree +- name: qiime2__diversity__adonis owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__align_to_tree_mafft_raxml +- name: qiime2__diversity__alpha owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__fasttree +- name: qiime2__diversity__alpha_correlation owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__filter_table +- name: qiime2__diversity__alpha_group_significance owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__filter_tree +- name: qiime2__diversity__alpha_phylogenetic owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__iqtree +- name: qiime2__diversity__alpha_rarefaction owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__iqtree_ultrafast_bootstrap +- name: qiime2__diversity__beta owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__midpoint_root +- name: qiime2__diversity__beta_correlation owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__raxml +- name: qiime2__diversity__beta_group_significance owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__raxml_rapid_bootstrap +- name: qiime2__diversity__beta_phylogenetic owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__robinson_foulds +- name: qiime2__diversity__beta_rarefaction owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__distance_matrix +- name: qiime2__diversity__bioenv owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__merge +- name: qiime2__diversity__core_metrics owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__shuffle_groups +- name: qiime2__diversity__core_metrics_phylogenetic owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__tabulate +- name: qiime2__diversity__filter_alpha_diversity owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__alpha_group_significance +- name: qiime2__diversity__filter_distance_matrix owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__collate_stats +- name: qiime2__diversity__mantel owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__facet_across +- name: qiime2__diversity__partial_procrustes owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__facet_within +- name: qiime2__diversity__pcoa owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__mann_whitney_u +- name: qiime2__diversity__pcoa_biplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__mann_whitney_u_facet +- name: qiime2__diversity__procrustes_analysis owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__plot_rainclouds +- name: qiime2__diversity__tsne owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__prep_alpha_distribution +- name: qiime2__diversity__umap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__wilcoxon_srt +- name: qiime2__emperor__biplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__wilcoxon_srt_facet +- name: qiime2__emperor__plot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__bowtie2_build +- name: qiime2__emperor__procrustes_plot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__decontam_identify +- name: qiime2_core__tools__export owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__decontam_identify_batches +- name: qiime2_core__tools__import owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__decontam_score_viz +- name: qiime2_core__tools__import_fastq owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__evaluate_composition +- name: qiime2__taxa__barplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__evaluate_seqs +- name: qiime2__taxa__barplot2 owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__evaluate_taxonomy +- name: qiime2__taxa__collapse owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__exclude_seqs +- name: qiime2__taxa__filter_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__filter_reads +- name: qiime2__taxa__filter_table owner: q2d2 tool_panel_section_id: '' - name: qiime2__diversity_lib__alpha_passthrough @@ -2768,253 +2804,244 @@ tools: - name: qiime2__diversity_lib__weighted_unifrac owner: q2d2 tool_panel_section_id: '' -- name: qiime2__alignment__mafft - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__alignment__mafft_add - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__alignment__mask - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__vizard__boxplot +- name: qiime2__stats__alpha_group_significance owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vizard__heatmap +- name: qiime2__stats__collate_stats owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vizard__lineplot +- name: qiime2__stats__facet_across owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vizard__scatterplot_2d +- name: qiime2__stats__facet_within owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__adonis +- name: qiime2__stats__mann_whitney_u owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha +- name: qiime2__stats__mann_whitney_u_facet owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_correlation +- name: qiime2__stats__plot_rainclouds owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_group_significance +- name: qiime2__stats__prep_alpha_distribution owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_phylogenetic +- name: qiime2__stats__wilcoxon_srt owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_rarefaction +- name: qiime2__stats__wilcoxon_srt_facet owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta +- name: qiime2__sample_classifier__classify_samples owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_correlation +- name: qiime2__sample_classifier__classify_samples_from_dist owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_group_significance +- name: qiime2__sample_classifier__classify_samples_ncv owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_phylogenetic +- name: qiime2__sample_classifier__confusion_matrix owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_rarefaction +- name: qiime2__sample_classifier__fit_classifier owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__bioenv +- name: qiime2__sample_classifier__fit_regressor owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__core_metrics +- name: qiime2__sample_classifier__heatmap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__core_metrics_phylogenetic +- name: qiime2__sample_classifier__metatable owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__filter_alpha_diversity +- name: qiime2__sample_classifier__predict_classification owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__filter_distance_matrix +- name: qiime2__sample_classifier__predict_regression owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__mantel +- name: qiime2__sample_classifier__regress_samples owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__partial_procrustes +- name: qiime2__sample_classifier__regress_samples_ncv owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__pcoa +- name: qiime2__sample_classifier__scatterplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__pcoa_biplot +- name: qiime2__sample_classifier__split_table owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__procrustes_analysis +- name: qiime2__sample_classifier__summarize owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__tsne +- name: qiime2__rescript__cull_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__umap +- name: qiime2__rescript__degap_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__emp_paired +- name: qiime2__rescript__dereplicate owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__emp_single +- name: qiime2__rescript__edit_taxonomy owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__filter_samples +- name: qiime2__rescript__evaluate_classifications owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__partition_samples_paired +- name: qiime2__rescript__evaluate_cross_validate owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__partition_samples_single +- name: qiime2__rescript__evaluate_fit_classifier owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__subsample_paired +- name: qiime2__rescript__evaluate_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__subsample_single +- name: qiime2__rescript__evaluate_taxonomy owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__summarize +- name: qiime2__rescript__extract_seq_segments owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__tabulate_read_counts +- name: qiime2__rescript__filter_seqs_length owner: q2d2 tool_panel_section_id: '' -- name: qiime2__deblur__denoise_16S +- name: qiime2__rescript__filter_seqs_length_by_taxon owner: q2d2 tool_panel_section_id: '' -- name: qiime2__deblur__denoise_other +- name: qiime2__rescript__filter_taxa owner: q2d2 tool_panel_section_id: '' -- name: qiime2__deblur__visualize_stats +- name: qiime2__rescript__get_bv_brc_genome_features owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_ccs +- name: qiime2__rescript__get_bv_brc_genomes owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_paired +- name: qiime2__rescript__get_bv_brc_metadata owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_pyro +- name: qiime2__rescript__get_eukaryome_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_single +- name: qiime2__rescript__get_gtdb_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__plot_base_transitions +- name: qiime2__rescript__get_midori2_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__cutadapt__demux_paired +- name: qiime2__rescript__get_ncbi_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__cutadapt__demux_single +- name: qiime2__rescript__get_ncbi_data_protein owner: q2d2 tool_panel_section_id: '' -- name: qiime2__cutadapt__trim_paired +- name: qiime2__rescript__get_ncbi_genomes owner: q2d2 tool_panel_section_id: '' -- name: qiime2__cutadapt__trim_single +- name: qiime2__rescript__get_pr2_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__add_pseudocount +- name: qiime2__rescript__get_silva_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancom +- name: qiime2__rescript__get_unite_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancombc +- name: qiime2__rescript__merge_taxa owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancombc2 +- name: qiime2__rescript__orient_reads owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancombc2_visualizer +- name: qiime2__rescript__orient_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__da_barplot +- name: qiime2__rescript__parse_silva_taxonomy owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__tabulate +- name: qiime2__rescript__reverse_transcribe owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__barplot +- name: qiime2__rescript__subsample_fasta owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__barplot2 +- name: qiime2__rescript__trim_alignment owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__collapse +- name: qiime2__quality_filter__q_score owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__filter_seqs +- name: qiime2__vizard__boxplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__filter_table +- name: qiime2__vizard__heatmap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__alpha +- name: qiime2__vizard__lineplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__alpha_average +- name: qiime2__vizard__scatterplot_2d owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__alpha_collection +- name: qiime2__alignment__mafft owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__beta +- name: qiime2__alignment__mafft_add owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__beta_average +- name: qiime2__alignment__mask owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__beta_collection +- name: qiime2__phylogeny__align_to_tree_mafft_fasttree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__core_metrics +- name: qiime2__phylogeny__align_to_tree_mafft_iqtree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__kmer_diversity +- name: qiime2__phylogeny__align_to_tree_mafft_raxml owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__resample +- name: qiime2__phylogeny__fasttree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__cluster_features_closed_reference +- name: qiime2__phylogeny__filter_table owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__cluster_features_de_novo +- name: qiime2__phylogeny__filter_tree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__cluster_features_open_reference +- name: qiime2__phylogeny__iqtree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__dereplicate_sequences +- name: qiime2__phylogeny__iqtree_ultrafast_bootstrap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__fastq_stats +- name: qiime2__phylogeny__midpoint_root owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__merge_pairs +- name: qiime2__phylogeny__raxml owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__uchime_denovo +- name: qiime2__phylogeny__raxml_rapid_bootstrap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__uchime_ref +- name: qiime2__phylogeny__robinson_foulds owner: q2d2 tool_panel_section_id: '' -- name: qiime2__emperor__biplot +- name: qiime2__fragment_insertion__classify_otus_experimental owner: q2d2 tool_panel_section_id: '' -- name: qiime2__emperor__plot +- name: qiime2__fragment_insertion__filter_features owner: q2d2 tool_panel_section_id: '' -- name: qiime2__emperor__procrustes_plot +- name: qiime2__fragment_insertion__sepp owner: q2d2 tool_panel_section_id: '' - name: qiime2__feature_classifier__blast @@ -3050,6 +3077,39 @@ tools: - name: qiime2__feature_classifier__vsearch_global owner: q2d2 tool_panel_section_id: '' +- name: qiime2__longitudinal__anova + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__feature_volatility + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__first_differences + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__first_distances + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__linear_mixed_effects + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__maturity_index + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__nmit + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__pairwise_differences + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__pairwise_distances + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__plot_feature_volatility + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__volatility + owner: q2d2 + tool_panel_section_id: '' - name: qiime2__feature_table___summarize owner: q2d2 tool_panel_section_id: '' @@ -3119,76 +3179,73 @@ tools: - name: qiime2__feature_table__transpose owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue___get_sequences - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__fondue__combine_seqs +- name: qiime2__quality_control__bowtie2_build owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__get_all +- name: qiime2__quality_control__decontam_identify owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__get_ids_from_query +- name: qiime2__quality_control__decontam_identify_batches owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__get_metadata +- name: qiime2__quality_control__decontam_score_viz owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__get_sequences +- name: qiime2__quality_control__evaluate_composition owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__merge_metadata +- name: qiime2__quality_control__evaluate_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__scrape_collection +- name: qiime2__quality_control__evaluate_taxonomy owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fragment_insertion__classify_otus_experimental +- name: qiime2__quality_control__exclude_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fragment_insertion__filter_features +- name: qiime2__quality_control__filter_reads owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fragment_insertion__sepp +- name: qiime2__metadata__distance_matrix owner: q2d2 tool_panel_section_id: '' -- name: qiime2__kmerizer__core_metrics +- name: qiime2__metadata__merge owner: q2d2 tool_panel_section_id: '' -- name: qiime2__kmerizer__seqs_to_kmers +- name: qiime2__metadata__shuffle_groups owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__anova +- name: qiime2__metadata__tabulate owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__feature_volatility +- name: qiime2__kmerizer__core_metrics owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__first_differences +- name: qiime2__kmerizer__seqs_to_kmers owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__first_distances +- name: qiime2__fondue___get_sequences owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__linear_mixed_effects +- name: qiime2__fondue__combine_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__maturity_index +- name: qiime2__fondue__get_all owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__nmit +- name: qiime2__fondue__get_ids_from_query owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__pairwise_differences +- name: qiime2__fondue__get_metadata owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__pairwise_distances +- name: qiime2__fondue__get_sequences owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__plot_feature_volatility +- name: qiime2__fondue__merge_metadata owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__volatility +- name: qiime2__fondue__scrape_collection owner: q2d2 tool_panel_section_id: '' - name: qiime2_dbotu_q2 @@ -3248,6 +3305,27 @@ tools: - name: roary owner: iuc tool_panel_section_id: '' +- name: samestr_compare + owner: iuc + tool_panel_section_id: '' +- name: samestr_convert + owner: iuc + tool_panel_section_id: '' +- name: samestr_extract + owner: iuc + tool_panel_section_id: '' +- name: samestr_filter + owner: iuc + tool_panel_section_id: '' +- name: samestr_merge + owner: iuc + tool_panel_section_id: '' +- name: samestr_stats + owner: iuc + tool_panel_section_id: '' +- name: samestr_summarize + owner: iuc + tool_panel_section_id: '' - name: scoary owner: iuc tool_panel_section_id: '' @@ -3369,10 +3447,10 @@ tools: owner: iuc tool_panel_section_id: '' - name: srst2 - owner: iuc + owner: nml tool_panel_section_id: '' - name: srst2 - owner: nml + owner: iuc tool_panel_section_id: '' - name: staramr_search owner: iuc @@ -3482,6 +3560,12 @@ tools: - name: varvamp owner: iuc tool_panel_section_id: '' +- name: vcontact2 + owner: iuc + tool_panel_section_id: '' +- name: vcontact2_gene2genome + owner: iuc + tool_panel_section_id: '' - name: vegan_diversity owner: iuc tool_panel_section_id: '' diff --git a/communities/microgalaxy/lab/tools/all/Mandoiu_Lab.yaml b/communities/microgalaxy/lab/tools/all/Mandoiu_Lab.yaml index a8c67bb3f..47a750f2c 100644 --- a/communities/microgalaxy/lab/tools/all/Mandoiu_Lab.yaml +++ b/communities/microgalaxy/lab/tools/all/Mandoiu_Lab.yaml @@ -1229,6 +1229,9 @@ tools: - name: kmindex_query owner: iuc tool_panel_section_id: '' +- name: kneaddata + owner: iuc + tool_panel_section_id: '' - name: kofamscan owner: iuc tool_panel_section_id: '' @@ -1286,6 +1289,9 @@ tools: - name: legsta owner: iuc tool_panel_section_id: '' +- name: liftoff + owner: iuc + tool_panel_section_id: '' - name: lighter owner: bgruening tool_panel_section_id: '' @@ -1505,6 +1511,27 @@ tools: - name: mg_toolkit_original_metadata owner: iuc tool_panel_section_id: '' +- name: mgnify_genome_search + owner: iuc + tool_panel_section_id: '' +- name: mgnify_pipelines_toolkit_classify_var_regions + owner: iuc + tool_panel_section_id: '' +- name: mgnify_pipelines_toolkit_make_asv_count_table + owner: iuc + tool_panel_section_id: '' +- name: mgnify_pipelines_toolkit_mapseq_to_asv_table + owner: iuc + tool_panel_section_id: '' +- name: mgnify_pipelines_toolkit_permute_primers + owner: iuc + tool_panel_section_id: '' +- name: mgnify_pipelines_toolkit_primer_val_classification + owner: iuc + tool_panel_section_id: '' +- name: mgnify_pipelines_toolkit_rev_comp_se_primers + owner: iuc + tool_panel_section_id: '' - name: mgnify_seqprep owner: bgruening tool_panel_section_id: '' @@ -1526,6 +1553,12 @@ tools: - name: miniprot_index owner: iuc tool_panel_section_id: '' +- name: mist_call + owner: iuc + tool_panel_section_id: '' +- name: mist_dists + owner: iuc + tool_panel_section_id: '' - name: mitos owner: iuc tool_panel_section_id: '' @@ -1976,6 +2009,9 @@ tools: - name: msstats owner: galaxyp tool_panel_section_id: '' +- name: mtnucratio + owner: iuc + tool_panel_section_id: '' - name: multigsea owner: iuc tool_panel_section_id: '' @@ -2093,6 +2129,9 @@ tools: - name: obi_clean owner: iuc tool_panel_section_id: '' +- name: obi_complement + owner: iuc + tool_panel_section_id: '' - name: obi_convert owner: iuc tool_panel_section_id: '' @@ -2105,6 +2144,18 @@ tools: - name: obi_pairing owner: iuc tool_panel_section_id: '' +- name: obi_pcr + owner: iuc + tool_panel_section_id: '' +- name: obi_refidx + owner: iuc + tool_panel_section_id: '' +- name: obi_tag + owner: iuc + tool_panel_section_id: '' +- name: obi_taxonomy + owner: iuc + tool_panel_section_id: '' - name: obi_uniq owner: iuc tool_panel_section_id: '' @@ -2726,6 +2777,9 @@ tools: - name: ppanggolin_rarefaction owner: iuc tool_panel_section_id: '' +- name: prinseq + owner: iuc + tool_panel_section_id: '' - name: prodigal owner: iuc tool_panel_section_id: '' @@ -2747,6 +2801,9 @@ tools: - name: proteinortho_summary owner: iuc tool_panel_section_id: '' +- name: psauron + owner: iuc + tool_panel_section_id: '' - name: pycoqc owner: iuc tool_panel_section_id: '' @@ -2855,262 +2912,241 @@ tools: - name: qiime_make_otu_table owner: iuc tool_panel_section_id: '' -- name: qiime2_core__tools__export - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2_core__tools__import - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2_core__tools__import_fastq - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__quality_filter__q_score - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__cull_seqs - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__degap_seqs - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__dereplicate - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__edit_taxonomy +- name: qiime2__dada2__denoise_ccs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_classifications +- name: qiime2__dada2__denoise_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_cross_validate +- name: qiime2__dada2__denoise_pyro owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_fit_classifier +- name: qiime2__dada2__denoise_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_seqs +- name: qiime2__dada2__plot_base_transitions owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_taxonomy +- name: qiime2__cutadapt__demux_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__extract_seq_segments +- name: qiime2__cutadapt__demux_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__filter_seqs_length +- name: qiime2__cutadapt__trim_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__filter_seqs_length_by_taxon +- name: qiime2__cutadapt__trim_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__filter_taxa +- name: qiime2__composition__add_pseudocount owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_bv_brc_genome_features +- name: qiime2__composition__ancom owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_bv_brc_genomes +- name: qiime2__composition__ancombc owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_bv_brc_metadata +- name: qiime2__composition__ancombc2 owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_eukaryome_data +- name: qiime2__composition__ancombc2_visualizer owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_gtdb_data +- name: qiime2__composition__da_barplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_midori2_data +- name: qiime2__composition__tabulate owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_ncbi_data +- name: qiime2__boots__alpha owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_ncbi_data_protein +- name: qiime2__boots__alpha_average owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_ncbi_genomes +- name: qiime2__boots__alpha_collection owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_pr2_data +- name: qiime2__boots__beta owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_silva_data +- name: qiime2__boots__beta_average owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_unite_data +- name: qiime2__boots__beta_collection owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__merge_taxa +- name: qiime2__boots__core_metrics owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__orient_reads +- name: qiime2__boots__kmer_diversity owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__orient_seqs +- name: qiime2__boots__resample owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__parse_silva_taxonomy +- name: qiime2__vsearch__cluster_features_closed_reference owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__reverse_transcribe +- name: qiime2__vsearch__cluster_features_de_novo owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__subsample_fasta +- name: qiime2__vsearch__cluster_features_open_reference owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__trim_alignment +- name: qiime2__vsearch__dereplicate_sequences owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__classify_samples +- name: qiime2__vsearch__fastq_stats owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__classify_samples_from_dist +- name: qiime2__vsearch__merge_pairs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__classify_samples_ncv +- name: qiime2__vsearch__uchime_denovo owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__confusion_matrix +- name: qiime2__vsearch__uchime_ref owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__fit_classifier +- name: qiime2__demux__emp_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__fit_regressor +- name: qiime2__demux__emp_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__heatmap +- name: qiime2__demux__filter_samples owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__metatable +- name: qiime2__demux__partition_samples_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__predict_classification +- name: qiime2__demux__partition_samples_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__predict_regression +- name: qiime2__demux__subsample_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__regress_samples +- name: qiime2__demux__subsample_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__regress_samples_ncv +- name: qiime2__demux__summarize owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__scatterplot +- name: qiime2__demux__tabulate_read_counts owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__split_table +- name: qiime2__deblur__denoise_16S owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__summarize +- name: qiime2__deblur__denoise_other owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__align_to_tree_mafft_fasttree +- name: qiime2__deblur__visualize_stats owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__align_to_tree_mafft_iqtree +- name: qiime2__diversity__adonis owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__align_to_tree_mafft_raxml +- name: qiime2__diversity__alpha owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__fasttree +- name: qiime2__diversity__alpha_correlation owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__filter_table +- name: qiime2__diversity__alpha_group_significance owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__filter_tree +- name: qiime2__diversity__alpha_phylogenetic owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__iqtree +- name: qiime2__diversity__alpha_rarefaction owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__iqtree_ultrafast_bootstrap +- name: qiime2__diversity__beta owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__midpoint_root +- name: qiime2__diversity__beta_correlation owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__raxml +- name: qiime2__diversity__beta_group_significance owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__raxml_rapid_bootstrap +- name: qiime2__diversity__beta_phylogenetic owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__robinson_foulds +- name: qiime2__diversity__beta_rarefaction owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__distance_matrix +- name: qiime2__diversity__bioenv owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__merge +- name: qiime2__diversity__core_metrics owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__shuffle_groups +- name: qiime2__diversity__core_metrics_phylogenetic owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__tabulate +- name: qiime2__diversity__filter_alpha_diversity owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__alpha_group_significance +- name: qiime2__diversity__filter_distance_matrix owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__collate_stats +- name: qiime2__diversity__mantel owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__facet_across +- name: qiime2__diversity__partial_procrustes owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__facet_within +- name: qiime2__diversity__pcoa owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__mann_whitney_u +- name: qiime2__diversity__pcoa_biplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__mann_whitney_u_facet +- name: qiime2__diversity__procrustes_analysis owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__plot_rainclouds +- name: qiime2__diversity__tsne owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__prep_alpha_distribution +- name: qiime2__diversity__umap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__wilcoxon_srt +- name: qiime2__emperor__biplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__wilcoxon_srt_facet +- name: qiime2__emperor__plot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__bowtie2_build +- name: qiime2__emperor__procrustes_plot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__decontam_identify +- name: qiime2_core__tools__export owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__decontam_identify_batches +- name: qiime2_core__tools__import owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__decontam_score_viz +- name: qiime2_core__tools__import_fastq owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__evaluate_composition +- name: qiime2__taxa__barplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__evaluate_seqs +- name: qiime2__taxa__barplot2 owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__evaluate_taxonomy +- name: qiime2__taxa__collapse owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__exclude_seqs +- name: qiime2__taxa__filter_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__filter_reads +- name: qiime2__taxa__filter_table owner: q2d2 tool_panel_section_id: '' - name: qiime2__diversity_lib__alpha_passthrough @@ -3149,253 +3185,244 @@ tools: - name: qiime2__diversity_lib__weighted_unifrac owner: q2d2 tool_panel_section_id: '' -- name: qiime2__alignment__mafft - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__alignment__mafft_add - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__alignment__mask - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__vizard__boxplot +- name: qiime2__stats__alpha_group_significance owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vizard__heatmap +- name: qiime2__stats__collate_stats owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vizard__lineplot +- name: qiime2__stats__facet_across owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vizard__scatterplot_2d +- name: qiime2__stats__facet_within owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__adonis +- name: qiime2__stats__mann_whitney_u owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha +- name: qiime2__stats__mann_whitney_u_facet owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_correlation +- name: qiime2__stats__plot_rainclouds owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_group_significance +- name: qiime2__stats__prep_alpha_distribution owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_phylogenetic +- name: qiime2__stats__wilcoxon_srt owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_rarefaction +- name: qiime2__stats__wilcoxon_srt_facet owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta +- name: qiime2__sample_classifier__classify_samples owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_correlation +- name: qiime2__sample_classifier__classify_samples_from_dist owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_group_significance +- name: qiime2__sample_classifier__classify_samples_ncv owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_phylogenetic +- name: qiime2__sample_classifier__confusion_matrix owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_rarefaction +- name: qiime2__sample_classifier__fit_classifier owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__bioenv +- name: qiime2__sample_classifier__fit_regressor owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__core_metrics +- name: qiime2__sample_classifier__heatmap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__core_metrics_phylogenetic +- name: qiime2__sample_classifier__metatable owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__filter_alpha_diversity +- name: qiime2__sample_classifier__predict_classification owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__filter_distance_matrix +- name: qiime2__sample_classifier__predict_regression owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__mantel +- name: qiime2__sample_classifier__regress_samples owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__partial_procrustes +- name: qiime2__sample_classifier__regress_samples_ncv owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__pcoa +- name: qiime2__sample_classifier__scatterplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__pcoa_biplot +- name: qiime2__sample_classifier__split_table owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__procrustes_analysis +- name: qiime2__sample_classifier__summarize owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__tsne +- name: qiime2__rescript__cull_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__umap +- name: qiime2__rescript__degap_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__emp_paired +- name: qiime2__rescript__dereplicate owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__emp_single +- name: qiime2__rescript__edit_taxonomy owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__filter_samples +- name: qiime2__rescript__evaluate_classifications owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__partition_samples_paired +- name: qiime2__rescript__evaluate_cross_validate owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__partition_samples_single +- name: qiime2__rescript__evaluate_fit_classifier owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__subsample_paired +- name: qiime2__rescript__evaluate_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__subsample_single +- name: qiime2__rescript__evaluate_taxonomy owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__summarize +- name: qiime2__rescript__extract_seq_segments owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__tabulate_read_counts +- name: qiime2__rescript__filter_seqs_length owner: q2d2 tool_panel_section_id: '' -- name: qiime2__deblur__denoise_16S +- name: qiime2__rescript__filter_seqs_length_by_taxon owner: q2d2 tool_panel_section_id: '' -- name: qiime2__deblur__denoise_other +- name: qiime2__rescript__filter_taxa owner: q2d2 tool_panel_section_id: '' -- name: qiime2__deblur__visualize_stats +- name: qiime2__rescript__get_bv_brc_genome_features owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_ccs +- name: qiime2__rescript__get_bv_brc_genomes owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_paired +- name: qiime2__rescript__get_bv_brc_metadata owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_pyro +- name: qiime2__rescript__get_eukaryome_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_single +- name: qiime2__rescript__get_gtdb_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__plot_base_transitions +- name: qiime2__rescript__get_midori2_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__cutadapt__demux_paired +- name: qiime2__rescript__get_ncbi_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__cutadapt__demux_single +- name: qiime2__rescript__get_ncbi_data_protein owner: q2d2 tool_panel_section_id: '' -- name: qiime2__cutadapt__trim_paired +- name: qiime2__rescript__get_ncbi_genomes owner: q2d2 tool_panel_section_id: '' -- name: qiime2__cutadapt__trim_single +- name: qiime2__rescript__get_pr2_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__add_pseudocount +- name: qiime2__rescript__get_silva_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancom +- name: qiime2__rescript__get_unite_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancombc +- name: qiime2__rescript__merge_taxa owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancombc2 +- name: qiime2__rescript__orient_reads owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancombc2_visualizer +- name: qiime2__rescript__orient_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__da_barplot +- name: qiime2__rescript__parse_silva_taxonomy owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__tabulate +- name: qiime2__rescript__reverse_transcribe owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__barplot +- name: qiime2__rescript__subsample_fasta owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__barplot2 +- name: qiime2__rescript__trim_alignment owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__collapse +- name: qiime2__quality_filter__q_score owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__filter_seqs +- name: qiime2__vizard__boxplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__filter_table +- name: qiime2__vizard__heatmap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__alpha +- name: qiime2__vizard__lineplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__alpha_average +- name: qiime2__vizard__scatterplot_2d owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__alpha_collection +- name: qiime2__alignment__mafft owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__beta +- name: qiime2__alignment__mafft_add owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__beta_average +- name: qiime2__alignment__mask owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__beta_collection +- name: qiime2__phylogeny__align_to_tree_mafft_fasttree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__core_metrics +- name: qiime2__phylogeny__align_to_tree_mafft_iqtree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__kmer_diversity +- name: qiime2__phylogeny__align_to_tree_mafft_raxml owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__resample +- name: qiime2__phylogeny__fasttree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__cluster_features_closed_reference +- name: qiime2__phylogeny__filter_table owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__cluster_features_de_novo +- name: qiime2__phylogeny__filter_tree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__cluster_features_open_reference +- name: qiime2__phylogeny__iqtree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__dereplicate_sequences +- name: qiime2__phylogeny__iqtree_ultrafast_bootstrap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__fastq_stats +- name: qiime2__phylogeny__midpoint_root owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__merge_pairs +- name: qiime2__phylogeny__raxml owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__uchime_denovo +- name: qiime2__phylogeny__raxml_rapid_bootstrap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__uchime_ref +- name: qiime2__phylogeny__robinson_foulds owner: q2d2 tool_panel_section_id: '' -- name: qiime2__emperor__biplot +- name: qiime2__fragment_insertion__classify_otus_experimental owner: q2d2 tool_panel_section_id: '' -- name: qiime2__emperor__plot +- name: qiime2__fragment_insertion__filter_features owner: q2d2 tool_panel_section_id: '' -- name: qiime2__emperor__procrustes_plot +- name: qiime2__fragment_insertion__sepp owner: q2d2 tool_panel_section_id: '' - name: qiime2__feature_classifier__blast @@ -3431,6 +3458,39 @@ tools: - name: qiime2__feature_classifier__vsearch_global owner: q2d2 tool_panel_section_id: '' +- name: qiime2__longitudinal__anova + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__feature_volatility + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__first_differences + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__first_distances + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__linear_mixed_effects + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__maturity_index + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__nmit + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__pairwise_differences + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__pairwise_distances + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__plot_feature_volatility + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__volatility + owner: q2d2 + tool_panel_section_id: '' - name: qiime2__feature_table___summarize owner: q2d2 tool_panel_section_id: '' @@ -3500,76 +3560,73 @@ tools: - name: qiime2__feature_table__transpose owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue___get_sequences - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__fondue__combine_seqs +- name: qiime2__quality_control__bowtie2_build owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__get_all +- name: qiime2__quality_control__decontam_identify owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__get_ids_from_query +- name: qiime2__quality_control__decontam_identify_batches owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__get_metadata +- name: qiime2__quality_control__decontam_score_viz owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__get_sequences +- name: qiime2__quality_control__evaluate_composition owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__merge_metadata +- name: qiime2__quality_control__evaluate_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__scrape_collection +- name: qiime2__quality_control__evaluate_taxonomy owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fragment_insertion__classify_otus_experimental +- name: qiime2__quality_control__exclude_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fragment_insertion__filter_features +- name: qiime2__quality_control__filter_reads owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fragment_insertion__sepp +- name: qiime2__metadata__distance_matrix owner: q2d2 tool_panel_section_id: '' -- name: qiime2__kmerizer__core_metrics +- name: qiime2__metadata__merge owner: q2d2 tool_panel_section_id: '' -- name: qiime2__kmerizer__seqs_to_kmers +- name: qiime2__metadata__shuffle_groups owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__anova +- name: qiime2__metadata__tabulate owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__feature_volatility +- name: qiime2__kmerizer__core_metrics owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__first_differences +- name: qiime2__kmerizer__seqs_to_kmers owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__first_distances +- name: qiime2__fondue___get_sequences owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__linear_mixed_effects +- name: qiime2__fondue__combine_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__maturity_index +- name: qiime2__fondue__get_all owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__nmit +- name: qiime2__fondue__get_ids_from_query owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__pairwise_differences +- name: qiime2__fondue__get_metadata owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__pairwise_distances +- name: qiime2__fondue__get_sequences owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__plot_feature_volatility +- name: qiime2__fondue__merge_metadata owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__volatility +- name: qiime2__fondue__scrape_collection owner: q2d2 tool_panel_section_id: '' - name: qiime2_dbotu_q2 @@ -3698,6 +3755,27 @@ tools: - name: rseqc_tin owner: nilesh tool_panel_section_id: '' +- name: samestr_compare + owner: iuc + tool_panel_section_id: '' +- name: samestr_convert + owner: iuc + tool_panel_section_id: '' +- name: samestr_extract + owner: iuc + tool_panel_section_id: '' +- name: samestr_filter + owner: iuc + tool_panel_section_id: '' +- name: samestr_merge + owner: iuc + tool_panel_section_id: '' +- name: samestr_stats + owner: iuc + tool_panel_section_id: '' +- name: samestr_summarize + owner: iuc + tool_panel_section_id: '' - name: scoary owner: iuc tool_panel_section_id: '' @@ -3822,10 +3900,10 @@ tools: owner: artbio tool_panel_section_id: '' - name: srst2 - owner: iuc + owner: nml tool_panel_section_id: '' - name: srst2 - owner: nml + owner: iuc tool_panel_section_id: '' - name: staramr_search owner: iuc @@ -3938,6 +4016,12 @@ tools: - name: varvamp owner: iuc tool_panel_section_id: '' +- name: vcontact2 + owner: iuc + tool_panel_section_id: '' +- name: vcontact2_gene2genome + owner: iuc + tool_panel_section_id: '' - name: vegan_diversity owner: iuc tool_panel_section_id: '' diff --git a/communities/microgalaxy/lab/tools/all/Oqtans.yaml b/communities/microgalaxy/lab/tools/all/Oqtans.yaml index a8c67bb3f..47a750f2c 100644 --- a/communities/microgalaxy/lab/tools/all/Oqtans.yaml +++ b/communities/microgalaxy/lab/tools/all/Oqtans.yaml @@ -1229,6 +1229,9 @@ tools: - name: kmindex_query owner: iuc tool_panel_section_id: '' +- name: kneaddata + owner: iuc + tool_panel_section_id: '' - name: kofamscan owner: iuc tool_panel_section_id: '' @@ -1286,6 +1289,9 @@ tools: - name: legsta owner: iuc tool_panel_section_id: '' +- name: liftoff + owner: iuc + tool_panel_section_id: '' - name: lighter owner: bgruening tool_panel_section_id: '' @@ -1505,6 +1511,27 @@ tools: - name: mg_toolkit_original_metadata owner: iuc tool_panel_section_id: '' +- name: mgnify_genome_search + owner: iuc + tool_panel_section_id: '' +- name: mgnify_pipelines_toolkit_classify_var_regions + owner: iuc + tool_panel_section_id: '' +- name: mgnify_pipelines_toolkit_make_asv_count_table + owner: iuc + tool_panel_section_id: '' +- name: mgnify_pipelines_toolkit_mapseq_to_asv_table + owner: iuc + tool_panel_section_id: '' +- name: mgnify_pipelines_toolkit_permute_primers + owner: iuc + tool_panel_section_id: '' +- name: mgnify_pipelines_toolkit_primer_val_classification + owner: iuc + tool_panel_section_id: '' +- name: mgnify_pipelines_toolkit_rev_comp_se_primers + owner: iuc + tool_panel_section_id: '' - name: mgnify_seqprep owner: bgruening tool_panel_section_id: '' @@ -1526,6 +1553,12 @@ tools: - name: miniprot_index owner: iuc tool_panel_section_id: '' +- name: mist_call + owner: iuc + tool_panel_section_id: '' +- name: mist_dists + owner: iuc + tool_panel_section_id: '' - name: mitos owner: iuc tool_panel_section_id: '' @@ -1976,6 +2009,9 @@ tools: - name: msstats owner: galaxyp tool_panel_section_id: '' +- name: mtnucratio + owner: iuc + tool_panel_section_id: '' - name: multigsea owner: iuc tool_panel_section_id: '' @@ -2093,6 +2129,9 @@ tools: - name: obi_clean owner: iuc tool_panel_section_id: '' +- name: obi_complement + owner: iuc + tool_panel_section_id: '' - name: obi_convert owner: iuc tool_panel_section_id: '' @@ -2105,6 +2144,18 @@ tools: - name: obi_pairing owner: iuc tool_panel_section_id: '' +- name: obi_pcr + owner: iuc + tool_panel_section_id: '' +- name: obi_refidx + owner: iuc + tool_panel_section_id: '' +- name: obi_tag + owner: iuc + tool_panel_section_id: '' +- name: obi_taxonomy + owner: iuc + tool_panel_section_id: '' - name: obi_uniq owner: iuc tool_panel_section_id: '' @@ -2726,6 +2777,9 @@ tools: - name: ppanggolin_rarefaction owner: iuc tool_panel_section_id: '' +- name: prinseq + owner: iuc + tool_panel_section_id: '' - name: prodigal owner: iuc tool_panel_section_id: '' @@ -2747,6 +2801,9 @@ tools: - name: proteinortho_summary owner: iuc tool_panel_section_id: '' +- name: psauron + owner: iuc + tool_panel_section_id: '' - name: pycoqc owner: iuc tool_panel_section_id: '' @@ -2855,262 +2912,241 @@ tools: - name: qiime_make_otu_table owner: iuc tool_panel_section_id: '' -- name: qiime2_core__tools__export - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2_core__tools__import - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2_core__tools__import_fastq - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__quality_filter__q_score - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__cull_seqs - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__degap_seqs - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__dereplicate - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__edit_taxonomy +- name: qiime2__dada2__denoise_ccs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_classifications +- name: qiime2__dada2__denoise_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_cross_validate +- name: qiime2__dada2__denoise_pyro owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_fit_classifier +- name: qiime2__dada2__denoise_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_seqs +- name: qiime2__dada2__plot_base_transitions owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_taxonomy +- name: qiime2__cutadapt__demux_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__extract_seq_segments +- name: qiime2__cutadapt__demux_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__filter_seqs_length +- name: qiime2__cutadapt__trim_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__filter_seqs_length_by_taxon +- name: qiime2__cutadapt__trim_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__filter_taxa +- name: qiime2__composition__add_pseudocount owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_bv_brc_genome_features +- name: qiime2__composition__ancom owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_bv_brc_genomes +- name: qiime2__composition__ancombc owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_bv_brc_metadata +- name: qiime2__composition__ancombc2 owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_eukaryome_data +- name: qiime2__composition__ancombc2_visualizer owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_gtdb_data +- name: qiime2__composition__da_barplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_midori2_data +- name: qiime2__composition__tabulate owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_ncbi_data +- name: qiime2__boots__alpha owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_ncbi_data_protein +- name: qiime2__boots__alpha_average owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_ncbi_genomes +- name: qiime2__boots__alpha_collection owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_pr2_data +- name: qiime2__boots__beta owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_silva_data +- name: qiime2__boots__beta_average owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_unite_data +- name: qiime2__boots__beta_collection owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__merge_taxa +- name: qiime2__boots__core_metrics owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__orient_reads +- name: qiime2__boots__kmer_diversity owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__orient_seqs +- name: qiime2__boots__resample owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__parse_silva_taxonomy +- name: qiime2__vsearch__cluster_features_closed_reference owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__reverse_transcribe +- name: qiime2__vsearch__cluster_features_de_novo owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__subsample_fasta +- name: qiime2__vsearch__cluster_features_open_reference owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__trim_alignment +- name: qiime2__vsearch__dereplicate_sequences owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__classify_samples +- name: qiime2__vsearch__fastq_stats owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__classify_samples_from_dist +- name: qiime2__vsearch__merge_pairs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__classify_samples_ncv +- name: qiime2__vsearch__uchime_denovo owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__confusion_matrix +- name: qiime2__vsearch__uchime_ref owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__fit_classifier +- name: qiime2__demux__emp_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__fit_regressor +- name: qiime2__demux__emp_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__heatmap +- name: qiime2__demux__filter_samples owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__metatable +- name: qiime2__demux__partition_samples_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__predict_classification +- name: qiime2__demux__partition_samples_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__predict_regression +- name: qiime2__demux__subsample_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__regress_samples +- name: qiime2__demux__subsample_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__regress_samples_ncv +- name: qiime2__demux__summarize owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__scatterplot +- name: qiime2__demux__tabulate_read_counts owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__split_table +- name: qiime2__deblur__denoise_16S owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__summarize +- name: qiime2__deblur__denoise_other owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__align_to_tree_mafft_fasttree +- name: qiime2__deblur__visualize_stats owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__align_to_tree_mafft_iqtree +- name: qiime2__diversity__adonis owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__align_to_tree_mafft_raxml +- name: qiime2__diversity__alpha owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__fasttree +- name: qiime2__diversity__alpha_correlation owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__filter_table +- name: qiime2__diversity__alpha_group_significance owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__filter_tree +- name: qiime2__diversity__alpha_phylogenetic owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__iqtree +- name: qiime2__diversity__alpha_rarefaction owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__iqtree_ultrafast_bootstrap +- name: qiime2__diversity__beta owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__midpoint_root +- name: qiime2__diversity__beta_correlation owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__raxml +- name: qiime2__diversity__beta_group_significance owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__raxml_rapid_bootstrap +- name: qiime2__diversity__beta_phylogenetic owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__robinson_foulds +- name: qiime2__diversity__beta_rarefaction owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__distance_matrix +- name: qiime2__diversity__bioenv owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__merge +- name: qiime2__diversity__core_metrics owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__shuffle_groups +- name: qiime2__diversity__core_metrics_phylogenetic owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__tabulate +- name: qiime2__diversity__filter_alpha_diversity owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__alpha_group_significance +- name: qiime2__diversity__filter_distance_matrix owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__collate_stats +- name: qiime2__diversity__mantel owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__facet_across +- name: qiime2__diversity__partial_procrustes owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__facet_within +- name: qiime2__diversity__pcoa owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__mann_whitney_u +- name: qiime2__diversity__pcoa_biplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__mann_whitney_u_facet +- name: qiime2__diversity__procrustes_analysis owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__plot_rainclouds +- name: qiime2__diversity__tsne owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__prep_alpha_distribution +- name: qiime2__diversity__umap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__wilcoxon_srt +- name: qiime2__emperor__biplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__wilcoxon_srt_facet +- name: qiime2__emperor__plot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__bowtie2_build +- name: qiime2__emperor__procrustes_plot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__decontam_identify +- name: qiime2_core__tools__export owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__decontam_identify_batches +- name: qiime2_core__tools__import owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__decontam_score_viz +- name: qiime2_core__tools__import_fastq owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__evaluate_composition +- name: qiime2__taxa__barplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__evaluate_seqs +- name: qiime2__taxa__barplot2 owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__evaluate_taxonomy +- name: qiime2__taxa__collapse owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__exclude_seqs +- name: qiime2__taxa__filter_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__filter_reads +- name: qiime2__taxa__filter_table owner: q2d2 tool_panel_section_id: '' - name: qiime2__diversity_lib__alpha_passthrough @@ -3149,253 +3185,244 @@ tools: - name: qiime2__diversity_lib__weighted_unifrac owner: q2d2 tool_panel_section_id: '' -- name: qiime2__alignment__mafft - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__alignment__mafft_add - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__alignment__mask - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__vizard__boxplot +- name: qiime2__stats__alpha_group_significance owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vizard__heatmap +- name: qiime2__stats__collate_stats owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vizard__lineplot +- name: qiime2__stats__facet_across owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vizard__scatterplot_2d +- name: qiime2__stats__facet_within owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__adonis +- name: qiime2__stats__mann_whitney_u owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha +- name: qiime2__stats__mann_whitney_u_facet owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_correlation +- name: qiime2__stats__plot_rainclouds owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_group_significance +- name: qiime2__stats__prep_alpha_distribution owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_phylogenetic +- name: qiime2__stats__wilcoxon_srt owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_rarefaction +- name: qiime2__stats__wilcoxon_srt_facet owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta +- name: qiime2__sample_classifier__classify_samples owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_correlation +- name: qiime2__sample_classifier__classify_samples_from_dist owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_group_significance +- name: qiime2__sample_classifier__classify_samples_ncv owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_phylogenetic +- name: qiime2__sample_classifier__confusion_matrix owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_rarefaction +- name: qiime2__sample_classifier__fit_classifier owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__bioenv +- name: qiime2__sample_classifier__fit_regressor owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__core_metrics +- name: qiime2__sample_classifier__heatmap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__core_metrics_phylogenetic +- name: qiime2__sample_classifier__metatable owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__filter_alpha_diversity +- name: qiime2__sample_classifier__predict_classification owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__filter_distance_matrix +- name: qiime2__sample_classifier__predict_regression owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__mantel +- name: qiime2__sample_classifier__regress_samples owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__partial_procrustes +- name: qiime2__sample_classifier__regress_samples_ncv owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__pcoa +- name: qiime2__sample_classifier__scatterplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__pcoa_biplot +- name: qiime2__sample_classifier__split_table owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__procrustes_analysis +- name: qiime2__sample_classifier__summarize owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__tsne +- name: qiime2__rescript__cull_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__umap +- name: qiime2__rescript__degap_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__emp_paired +- name: qiime2__rescript__dereplicate owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__emp_single +- name: qiime2__rescript__edit_taxonomy owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__filter_samples +- name: qiime2__rescript__evaluate_classifications owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__partition_samples_paired +- name: qiime2__rescript__evaluate_cross_validate owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__partition_samples_single +- name: qiime2__rescript__evaluate_fit_classifier owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__subsample_paired +- name: qiime2__rescript__evaluate_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__subsample_single +- name: qiime2__rescript__evaluate_taxonomy owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__summarize +- name: qiime2__rescript__extract_seq_segments owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__tabulate_read_counts +- name: qiime2__rescript__filter_seqs_length owner: q2d2 tool_panel_section_id: '' -- name: qiime2__deblur__denoise_16S +- name: qiime2__rescript__filter_seqs_length_by_taxon owner: q2d2 tool_panel_section_id: '' -- name: qiime2__deblur__denoise_other +- name: qiime2__rescript__filter_taxa owner: q2d2 tool_panel_section_id: '' -- name: qiime2__deblur__visualize_stats +- name: qiime2__rescript__get_bv_brc_genome_features owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_ccs +- name: qiime2__rescript__get_bv_brc_genomes owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_paired +- name: qiime2__rescript__get_bv_brc_metadata owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_pyro +- name: qiime2__rescript__get_eukaryome_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_single +- name: qiime2__rescript__get_gtdb_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__plot_base_transitions +- name: qiime2__rescript__get_midori2_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__cutadapt__demux_paired +- name: qiime2__rescript__get_ncbi_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__cutadapt__demux_single +- name: qiime2__rescript__get_ncbi_data_protein owner: q2d2 tool_panel_section_id: '' -- name: qiime2__cutadapt__trim_paired +- name: qiime2__rescript__get_ncbi_genomes owner: q2d2 tool_panel_section_id: '' -- name: qiime2__cutadapt__trim_single +- name: qiime2__rescript__get_pr2_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__add_pseudocount +- name: qiime2__rescript__get_silva_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancom +- name: qiime2__rescript__get_unite_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancombc +- name: qiime2__rescript__merge_taxa owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancombc2 +- name: qiime2__rescript__orient_reads owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancombc2_visualizer +- name: qiime2__rescript__orient_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__da_barplot +- name: qiime2__rescript__parse_silva_taxonomy owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__tabulate +- name: qiime2__rescript__reverse_transcribe owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__barplot +- name: qiime2__rescript__subsample_fasta owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__barplot2 +- name: qiime2__rescript__trim_alignment owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__collapse +- name: qiime2__quality_filter__q_score owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__filter_seqs +- name: qiime2__vizard__boxplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__filter_table +- name: qiime2__vizard__heatmap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__alpha +- name: qiime2__vizard__lineplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__alpha_average +- name: qiime2__vizard__scatterplot_2d owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__alpha_collection +- name: qiime2__alignment__mafft owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__beta +- name: qiime2__alignment__mafft_add owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__beta_average +- name: qiime2__alignment__mask owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__beta_collection +- name: qiime2__phylogeny__align_to_tree_mafft_fasttree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__core_metrics +- name: qiime2__phylogeny__align_to_tree_mafft_iqtree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__kmer_diversity +- name: qiime2__phylogeny__align_to_tree_mafft_raxml owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__resample +- name: qiime2__phylogeny__fasttree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__cluster_features_closed_reference +- name: qiime2__phylogeny__filter_table owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__cluster_features_de_novo +- name: qiime2__phylogeny__filter_tree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__cluster_features_open_reference +- name: qiime2__phylogeny__iqtree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__dereplicate_sequences +- name: qiime2__phylogeny__iqtree_ultrafast_bootstrap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__fastq_stats +- name: qiime2__phylogeny__midpoint_root owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__merge_pairs +- name: qiime2__phylogeny__raxml owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__uchime_denovo +- name: qiime2__phylogeny__raxml_rapid_bootstrap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__uchime_ref +- name: qiime2__phylogeny__robinson_foulds owner: q2d2 tool_panel_section_id: '' -- name: qiime2__emperor__biplot +- name: qiime2__fragment_insertion__classify_otus_experimental owner: q2d2 tool_panel_section_id: '' -- name: qiime2__emperor__plot +- name: qiime2__fragment_insertion__filter_features owner: q2d2 tool_panel_section_id: '' -- name: qiime2__emperor__procrustes_plot +- name: qiime2__fragment_insertion__sepp owner: q2d2 tool_panel_section_id: '' - name: qiime2__feature_classifier__blast @@ -3431,6 +3458,39 @@ tools: - name: qiime2__feature_classifier__vsearch_global owner: q2d2 tool_panel_section_id: '' +- name: qiime2__longitudinal__anova + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__feature_volatility + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__first_differences + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__first_distances + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__linear_mixed_effects + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__maturity_index + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__nmit + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__pairwise_differences + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__pairwise_distances + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__plot_feature_volatility + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__volatility + owner: q2d2 + tool_panel_section_id: '' - name: qiime2__feature_table___summarize owner: q2d2 tool_panel_section_id: '' @@ -3500,76 +3560,73 @@ tools: - name: qiime2__feature_table__transpose owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue___get_sequences - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__fondue__combine_seqs +- name: qiime2__quality_control__bowtie2_build owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__get_all +- name: qiime2__quality_control__decontam_identify owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__get_ids_from_query +- name: qiime2__quality_control__decontam_identify_batches owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__get_metadata +- name: qiime2__quality_control__decontam_score_viz owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__get_sequences +- name: qiime2__quality_control__evaluate_composition owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__merge_metadata +- name: qiime2__quality_control__evaluate_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__scrape_collection +- name: qiime2__quality_control__evaluate_taxonomy owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fragment_insertion__classify_otus_experimental +- name: qiime2__quality_control__exclude_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fragment_insertion__filter_features +- name: qiime2__quality_control__filter_reads owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fragment_insertion__sepp +- name: qiime2__metadata__distance_matrix owner: q2d2 tool_panel_section_id: '' -- name: qiime2__kmerizer__core_metrics +- name: qiime2__metadata__merge owner: q2d2 tool_panel_section_id: '' -- name: qiime2__kmerizer__seqs_to_kmers +- name: qiime2__metadata__shuffle_groups owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__anova +- name: qiime2__metadata__tabulate owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__feature_volatility +- name: qiime2__kmerizer__core_metrics owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__first_differences +- name: qiime2__kmerizer__seqs_to_kmers owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__first_distances +- name: qiime2__fondue___get_sequences owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__linear_mixed_effects +- name: qiime2__fondue__combine_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__maturity_index +- name: qiime2__fondue__get_all owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__nmit +- name: qiime2__fondue__get_ids_from_query owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__pairwise_differences +- name: qiime2__fondue__get_metadata owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__pairwise_distances +- name: qiime2__fondue__get_sequences owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__plot_feature_volatility +- name: qiime2__fondue__merge_metadata owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__volatility +- name: qiime2__fondue__scrape_collection owner: q2d2 tool_panel_section_id: '' - name: qiime2_dbotu_q2 @@ -3698,6 +3755,27 @@ tools: - name: rseqc_tin owner: nilesh tool_panel_section_id: '' +- name: samestr_compare + owner: iuc + tool_panel_section_id: '' +- name: samestr_convert + owner: iuc + tool_panel_section_id: '' +- name: samestr_extract + owner: iuc + tool_panel_section_id: '' +- name: samestr_filter + owner: iuc + tool_panel_section_id: '' +- name: samestr_merge + owner: iuc + tool_panel_section_id: '' +- name: samestr_stats + owner: iuc + tool_panel_section_id: '' +- name: samestr_summarize + owner: iuc + tool_panel_section_id: '' - name: scoary owner: iuc tool_panel_section_id: '' @@ -3822,10 +3900,10 @@ tools: owner: artbio tool_panel_section_id: '' - name: srst2 - owner: iuc + owner: nml tool_panel_section_id: '' - name: srst2 - owner: nml + owner: iuc tool_panel_section_id: '' - name: staramr_search owner: iuc @@ -3938,6 +4016,12 @@ tools: - name: varvamp owner: iuc tool_panel_section_id: '' +- name: vcontact2 + owner: iuc + tool_panel_section_id: '' +- name: vcontact2_gene2genome + owner: iuc + tool_panel_section_id: '' - name: vegan_diversity owner: iuc tool_panel_section_id: '' diff --git a/communities/microgalaxy/lab/tools/all/Palfinder.yaml b/communities/microgalaxy/lab/tools/all/Palfinder.yaml index a8c67bb3f..47a750f2c 100644 --- a/communities/microgalaxy/lab/tools/all/Palfinder.yaml +++ b/communities/microgalaxy/lab/tools/all/Palfinder.yaml @@ -1229,6 +1229,9 @@ tools: - name: kmindex_query owner: iuc tool_panel_section_id: '' +- name: kneaddata + owner: iuc + tool_panel_section_id: '' - name: kofamscan owner: iuc tool_panel_section_id: '' @@ -1286,6 +1289,9 @@ tools: - name: legsta owner: iuc tool_panel_section_id: '' +- name: liftoff + owner: iuc + tool_panel_section_id: '' - name: lighter owner: bgruening tool_panel_section_id: '' @@ -1505,6 +1511,27 @@ tools: - name: mg_toolkit_original_metadata owner: iuc tool_panel_section_id: '' +- name: mgnify_genome_search + owner: iuc + tool_panel_section_id: '' +- name: mgnify_pipelines_toolkit_classify_var_regions + owner: iuc + tool_panel_section_id: '' +- name: mgnify_pipelines_toolkit_make_asv_count_table + owner: iuc + tool_panel_section_id: '' +- name: mgnify_pipelines_toolkit_mapseq_to_asv_table + owner: iuc + tool_panel_section_id: '' +- name: mgnify_pipelines_toolkit_permute_primers + owner: iuc + tool_panel_section_id: '' +- name: mgnify_pipelines_toolkit_primer_val_classification + owner: iuc + tool_panel_section_id: '' +- name: mgnify_pipelines_toolkit_rev_comp_se_primers + owner: iuc + tool_panel_section_id: '' - name: mgnify_seqprep owner: bgruening tool_panel_section_id: '' @@ -1526,6 +1553,12 @@ tools: - name: miniprot_index owner: iuc tool_panel_section_id: '' +- name: mist_call + owner: iuc + tool_panel_section_id: '' +- name: mist_dists + owner: iuc + tool_panel_section_id: '' - name: mitos owner: iuc tool_panel_section_id: '' @@ -1976,6 +2009,9 @@ tools: - name: msstats owner: galaxyp tool_panel_section_id: '' +- name: mtnucratio + owner: iuc + tool_panel_section_id: '' - name: multigsea owner: iuc tool_panel_section_id: '' @@ -2093,6 +2129,9 @@ tools: - name: obi_clean owner: iuc tool_panel_section_id: '' +- name: obi_complement + owner: iuc + tool_panel_section_id: '' - name: obi_convert owner: iuc tool_panel_section_id: '' @@ -2105,6 +2144,18 @@ tools: - name: obi_pairing owner: iuc tool_panel_section_id: '' +- name: obi_pcr + owner: iuc + tool_panel_section_id: '' +- name: obi_refidx + owner: iuc + tool_panel_section_id: '' +- name: obi_tag + owner: iuc + tool_panel_section_id: '' +- name: obi_taxonomy + owner: iuc + tool_panel_section_id: '' - name: obi_uniq owner: iuc tool_panel_section_id: '' @@ -2726,6 +2777,9 @@ tools: - name: ppanggolin_rarefaction owner: iuc tool_panel_section_id: '' +- name: prinseq + owner: iuc + tool_panel_section_id: '' - name: prodigal owner: iuc tool_panel_section_id: '' @@ -2747,6 +2801,9 @@ tools: - name: proteinortho_summary owner: iuc tool_panel_section_id: '' +- name: psauron + owner: iuc + tool_panel_section_id: '' - name: pycoqc owner: iuc tool_panel_section_id: '' @@ -2855,262 +2912,241 @@ tools: - name: qiime_make_otu_table owner: iuc tool_panel_section_id: '' -- name: qiime2_core__tools__export - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2_core__tools__import - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2_core__tools__import_fastq - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__quality_filter__q_score - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__cull_seqs - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__degap_seqs - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__dereplicate - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__edit_taxonomy +- name: qiime2__dada2__denoise_ccs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_classifications +- name: qiime2__dada2__denoise_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_cross_validate +- name: qiime2__dada2__denoise_pyro owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_fit_classifier +- name: qiime2__dada2__denoise_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_seqs +- name: qiime2__dada2__plot_base_transitions owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_taxonomy +- name: qiime2__cutadapt__demux_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__extract_seq_segments +- name: qiime2__cutadapt__demux_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__filter_seqs_length +- name: qiime2__cutadapt__trim_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__filter_seqs_length_by_taxon +- name: qiime2__cutadapt__trim_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__filter_taxa +- name: qiime2__composition__add_pseudocount owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_bv_brc_genome_features +- name: qiime2__composition__ancom owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_bv_brc_genomes +- name: qiime2__composition__ancombc owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_bv_brc_metadata +- name: qiime2__composition__ancombc2 owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_eukaryome_data +- name: qiime2__composition__ancombc2_visualizer owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_gtdb_data +- name: qiime2__composition__da_barplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_midori2_data +- name: qiime2__composition__tabulate owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_ncbi_data +- name: qiime2__boots__alpha owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_ncbi_data_protein +- name: qiime2__boots__alpha_average owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_ncbi_genomes +- name: qiime2__boots__alpha_collection owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_pr2_data +- name: qiime2__boots__beta owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_silva_data +- name: qiime2__boots__beta_average owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_unite_data +- name: qiime2__boots__beta_collection owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__merge_taxa +- name: qiime2__boots__core_metrics owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__orient_reads +- name: qiime2__boots__kmer_diversity owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__orient_seqs +- name: qiime2__boots__resample owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__parse_silva_taxonomy +- name: qiime2__vsearch__cluster_features_closed_reference owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__reverse_transcribe +- name: qiime2__vsearch__cluster_features_de_novo owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__subsample_fasta +- name: qiime2__vsearch__cluster_features_open_reference owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__trim_alignment +- name: qiime2__vsearch__dereplicate_sequences owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__classify_samples +- name: qiime2__vsearch__fastq_stats owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__classify_samples_from_dist +- name: qiime2__vsearch__merge_pairs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__classify_samples_ncv +- name: qiime2__vsearch__uchime_denovo owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__confusion_matrix +- name: qiime2__vsearch__uchime_ref owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__fit_classifier +- name: qiime2__demux__emp_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__fit_regressor +- name: qiime2__demux__emp_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__heatmap +- name: qiime2__demux__filter_samples owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__metatable +- name: qiime2__demux__partition_samples_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__predict_classification +- name: qiime2__demux__partition_samples_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__predict_regression +- name: qiime2__demux__subsample_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__regress_samples +- name: qiime2__demux__subsample_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__regress_samples_ncv +- name: qiime2__demux__summarize owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__scatterplot +- name: qiime2__demux__tabulate_read_counts owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__split_table +- name: qiime2__deblur__denoise_16S owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__summarize +- name: qiime2__deblur__denoise_other owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__align_to_tree_mafft_fasttree +- name: qiime2__deblur__visualize_stats owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__align_to_tree_mafft_iqtree +- name: qiime2__diversity__adonis owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__align_to_tree_mafft_raxml +- name: qiime2__diversity__alpha owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__fasttree +- name: qiime2__diversity__alpha_correlation owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__filter_table +- name: qiime2__diversity__alpha_group_significance owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__filter_tree +- name: qiime2__diversity__alpha_phylogenetic owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__iqtree +- name: qiime2__diversity__alpha_rarefaction owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__iqtree_ultrafast_bootstrap +- name: qiime2__diversity__beta owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__midpoint_root +- name: qiime2__diversity__beta_correlation owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__raxml +- name: qiime2__diversity__beta_group_significance owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__raxml_rapid_bootstrap +- name: qiime2__diversity__beta_phylogenetic owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__robinson_foulds +- name: qiime2__diversity__beta_rarefaction owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__distance_matrix +- name: qiime2__diversity__bioenv owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__merge +- name: qiime2__diversity__core_metrics owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__shuffle_groups +- name: qiime2__diversity__core_metrics_phylogenetic owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__tabulate +- name: qiime2__diversity__filter_alpha_diversity owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__alpha_group_significance +- name: qiime2__diversity__filter_distance_matrix owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__collate_stats +- name: qiime2__diversity__mantel owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__facet_across +- name: qiime2__diversity__partial_procrustes owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__facet_within +- name: qiime2__diversity__pcoa owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__mann_whitney_u +- name: qiime2__diversity__pcoa_biplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__mann_whitney_u_facet +- name: qiime2__diversity__procrustes_analysis owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__plot_rainclouds +- name: qiime2__diversity__tsne owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__prep_alpha_distribution +- name: qiime2__diversity__umap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__wilcoxon_srt +- name: qiime2__emperor__biplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__wilcoxon_srt_facet +- name: qiime2__emperor__plot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__bowtie2_build +- name: qiime2__emperor__procrustes_plot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__decontam_identify +- name: qiime2_core__tools__export owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__decontam_identify_batches +- name: qiime2_core__tools__import owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__decontam_score_viz +- name: qiime2_core__tools__import_fastq owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__evaluate_composition +- name: qiime2__taxa__barplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__evaluate_seqs +- name: qiime2__taxa__barplot2 owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__evaluate_taxonomy +- name: qiime2__taxa__collapse owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__exclude_seqs +- name: qiime2__taxa__filter_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__filter_reads +- name: qiime2__taxa__filter_table owner: q2d2 tool_panel_section_id: '' - name: qiime2__diversity_lib__alpha_passthrough @@ -3149,253 +3185,244 @@ tools: - name: qiime2__diversity_lib__weighted_unifrac owner: q2d2 tool_panel_section_id: '' -- name: qiime2__alignment__mafft - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__alignment__mafft_add - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__alignment__mask - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__vizard__boxplot +- name: qiime2__stats__alpha_group_significance owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vizard__heatmap +- name: qiime2__stats__collate_stats owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vizard__lineplot +- name: qiime2__stats__facet_across owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vizard__scatterplot_2d +- name: qiime2__stats__facet_within owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__adonis +- name: qiime2__stats__mann_whitney_u owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha +- name: qiime2__stats__mann_whitney_u_facet owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_correlation +- name: qiime2__stats__plot_rainclouds owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_group_significance +- name: qiime2__stats__prep_alpha_distribution owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_phylogenetic +- name: qiime2__stats__wilcoxon_srt owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_rarefaction +- name: qiime2__stats__wilcoxon_srt_facet owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta +- name: qiime2__sample_classifier__classify_samples owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_correlation +- name: qiime2__sample_classifier__classify_samples_from_dist owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_group_significance +- name: qiime2__sample_classifier__classify_samples_ncv owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_phylogenetic +- name: qiime2__sample_classifier__confusion_matrix owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_rarefaction +- name: qiime2__sample_classifier__fit_classifier owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__bioenv +- name: qiime2__sample_classifier__fit_regressor owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__core_metrics +- name: qiime2__sample_classifier__heatmap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__core_metrics_phylogenetic +- name: qiime2__sample_classifier__metatable owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__filter_alpha_diversity +- name: qiime2__sample_classifier__predict_classification owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__filter_distance_matrix +- name: qiime2__sample_classifier__predict_regression owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__mantel +- name: qiime2__sample_classifier__regress_samples owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__partial_procrustes +- name: qiime2__sample_classifier__regress_samples_ncv owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__pcoa +- name: qiime2__sample_classifier__scatterplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__pcoa_biplot +- name: qiime2__sample_classifier__split_table owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__procrustes_analysis +- name: qiime2__sample_classifier__summarize owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__tsne +- name: qiime2__rescript__cull_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__umap +- name: qiime2__rescript__degap_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__emp_paired +- name: qiime2__rescript__dereplicate owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__emp_single +- name: qiime2__rescript__edit_taxonomy owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__filter_samples +- name: qiime2__rescript__evaluate_classifications owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__partition_samples_paired +- name: qiime2__rescript__evaluate_cross_validate owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__partition_samples_single +- name: qiime2__rescript__evaluate_fit_classifier owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__subsample_paired +- name: qiime2__rescript__evaluate_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__subsample_single +- name: qiime2__rescript__evaluate_taxonomy owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__summarize +- name: qiime2__rescript__extract_seq_segments owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__tabulate_read_counts +- name: qiime2__rescript__filter_seqs_length owner: q2d2 tool_panel_section_id: '' -- name: qiime2__deblur__denoise_16S +- name: qiime2__rescript__filter_seqs_length_by_taxon owner: q2d2 tool_panel_section_id: '' -- name: qiime2__deblur__denoise_other +- name: qiime2__rescript__filter_taxa owner: q2d2 tool_panel_section_id: '' -- name: qiime2__deblur__visualize_stats +- name: qiime2__rescript__get_bv_brc_genome_features owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_ccs +- name: qiime2__rescript__get_bv_brc_genomes owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_paired +- name: qiime2__rescript__get_bv_brc_metadata owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_pyro +- name: qiime2__rescript__get_eukaryome_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_single +- name: qiime2__rescript__get_gtdb_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__plot_base_transitions +- name: qiime2__rescript__get_midori2_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__cutadapt__demux_paired +- name: qiime2__rescript__get_ncbi_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__cutadapt__demux_single +- name: qiime2__rescript__get_ncbi_data_protein owner: q2d2 tool_panel_section_id: '' -- name: qiime2__cutadapt__trim_paired +- name: qiime2__rescript__get_ncbi_genomes owner: q2d2 tool_panel_section_id: '' -- name: qiime2__cutadapt__trim_single +- name: qiime2__rescript__get_pr2_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__add_pseudocount +- name: qiime2__rescript__get_silva_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancom +- name: qiime2__rescript__get_unite_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancombc +- name: qiime2__rescript__merge_taxa owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancombc2 +- name: qiime2__rescript__orient_reads owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancombc2_visualizer +- name: qiime2__rescript__orient_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__da_barplot +- name: qiime2__rescript__parse_silva_taxonomy owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__tabulate +- name: qiime2__rescript__reverse_transcribe owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__barplot +- name: qiime2__rescript__subsample_fasta owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__barplot2 +- name: qiime2__rescript__trim_alignment owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__collapse +- name: qiime2__quality_filter__q_score owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__filter_seqs +- name: qiime2__vizard__boxplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__filter_table +- name: qiime2__vizard__heatmap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__alpha +- name: qiime2__vizard__lineplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__alpha_average +- name: qiime2__vizard__scatterplot_2d owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__alpha_collection +- name: qiime2__alignment__mafft owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__beta +- name: qiime2__alignment__mafft_add owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__beta_average +- name: qiime2__alignment__mask owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__beta_collection +- name: qiime2__phylogeny__align_to_tree_mafft_fasttree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__core_metrics +- name: qiime2__phylogeny__align_to_tree_mafft_iqtree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__kmer_diversity +- name: qiime2__phylogeny__align_to_tree_mafft_raxml owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__resample +- name: qiime2__phylogeny__fasttree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__cluster_features_closed_reference +- name: qiime2__phylogeny__filter_table owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__cluster_features_de_novo +- name: qiime2__phylogeny__filter_tree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__cluster_features_open_reference +- name: qiime2__phylogeny__iqtree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__dereplicate_sequences +- name: qiime2__phylogeny__iqtree_ultrafast_bootstrap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__fastq_stats +- name: qiime2__phylogeny__midpoint_root owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__merge_pairs +- name: qiime2__phylogeny__raxml owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__uchime_denovo +- name: qiime2__phylogeny__raxml_rapid_bootstrap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__uchime_ref +- name: qiime2__phylogeny__robinson_foulds owner: q2d2 tool_panel_section_id: '' -- name: qiime2__emperor__biplot +- name: qiime2__fragment_insertion__classify_otus_experimental owner: q2d2 tool_panel_section_id: '' -- name: qiime2__emperor__plot +- name: qiime2__fragment_insertion__filter_features owner: q2d2 tool_panel_section_id: '' -- name: qiime2__emperor__procrustes_plot +- name: qiime2__fragment_insertion__sepp owner: q2d2 tool_panel_section_id: '' - name: qiime2__feature_classifier__blast @@ -3431,6 +3458,39 @@ tools: - name: qiime2__feature_classifier__vsearch_global owner: q2d2 tool_panel_section_id: '' +- name: qiime2__longitudinal__anova + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__feature_volatility + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__first_differences + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__first_distances + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__linear_mixed_effects + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__maturity_index + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__nmit + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__pairwise_differences + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__pairwise_distances + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__plot_feature_volatility + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__volatility + owner: q2d2 + tool_panel_section_id: '' - name: qiime2__feature_table___summarize owner: q2d2 tool_panel_section_id: '' @@ -3500,76 +3560,73 @@ tools: - name: qiime2__feature_table__transpose owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue___get_sequences - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__fondue__combine_seqs +- name: qiime2__quality_control__bowtie2_build owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__get_all +- name: qiime2__quality_control__decontam_identify owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__get_ids_from_query +- name: qiime2__quality_control__decontam_identify_batches owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__get_metadata +- name: qiime2__quality_control__decontam_score_viz owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__get_sequences +- name: qiime2__quality_control__evaluate_composition owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__merge_metadata +- name: qiime2__quality_control__evaluate_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__scrape_collection +- name: qiime2__quality_control__evaluate_taxonomy owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fragment_insertion__classify_otus_experimental +- name: qiime2__quality_control__exclude_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fragment_insertion__filter_features +- name: qiime2__quality_control__filter_reads owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fragment_insertion__sepp +- name: qiime2__metadata__distance_matrix owner: q2d2 tool_panel_section_id: '' -- name: qiime2__kmerizer__core_metrics +- name: qiime2__metadata__merge owner: q2d2 tool_panel_section_id: '' -- name: qiime2__kmerizer__seqs_to_kmers +- name: qiime2__metadata__shuffle_groups owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__anova +- name: qiime2__metadata__tabulate owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__feature_volatility +- name: qiime2__kmerizer__core_metrics owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__first_differences +- name: qiime2__kmerizer__seqs_to_kmers owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__first_distances +- name: qiime2__fondue___get_sequences owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__linear_mixed_effects +- name: qiime2__fondue__combine_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__maturity_index +- name: qiime2__fondue__get_all owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__nmit +- name: qiime2__fondue__get_ids_from_query owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__pairwise_differences +- name: qiime2__fondue__get_metadata owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__pairwise_distances +- name: qiime2__fondue__get_sequences owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__plot_feature_volatility +- name: qiime2__fondue__merge_metadata owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__volatility +- name: qiime2__fondue__scrape_collection owner: q2d2 tool_panel_section_id: '' - name: qiime2_dbotu_q2 @@ -3698,6 +3755,27 @@ tools: - name: rseqc_tin owner: nilesh tool_panel_section_id: '' +- name: samestr_compare + owner: iuc + tool_panel_section_id: '' +- name: samestr_convert + owner: iuc + tool_panel_section_id: '' +- name: samestr_extract + owner: iuc + tool_panel_section_id: '' +- name: samestr_filter + owner: iuc + tool_panel_section_id: '' +- name: samestr_merge + owner: iuc + tool_panel_section_id: '' +- name: samestr_stats + owner: iuc + tool_panel_section_id: '' +- name: samestr_summarize + owner: iuc + tool_panel_section_id: '' - name: scoary owner: iuc tool_panel_section_id: '' @@ -3822,10 +3900,10 @@ tools: owner: artbio tool_panel_section_id: '' - name: srst2 - owner: iuc + owner: nml tool_panel_section_id: '' - name: srst2 - owner: nml + owner: iuc tool_panel_section_id: '' - name: staramr_search owner: iuc @@ -3938,6 +4016,12 @@ tools: - name: varvamp owner: iuc tool_panel_section_id: '' +- name: vcontact2 + owner: iuc + tool_panel_section_id: '' +- name: vcontact2_gene2genome + owner: iuc + tool_panel_section_id: '' - name: vegan_diversity owner: iuc tool_panel_section_id: '' diff --git a/communities/microgalaxy/lab/tools/all/PhagePromotor.yaml b/communities/microgalaxy/lab/tools/all/PhagePromotor.yaml index 3e502a6b6..47a750f2c 100644 --- a/communities/microgalaxy/lab/tools/all/PhagePromotor.yaml +++ b/communities/microgalaxy/lab/tools/all/PhagePromotor.yaml @@ -311,6 +311,9 @@ tools: - name: CryptoGenotyper owner: nml tool_panel_section_id: '' +- name: cutadapt + owner: lparsons + tool_panel_section_id: '' - name: dada2_assignTaxonomyAddspecies owner: iuc tool_panel_section_id: '' @@ -359,6 +362,9 @@ tools: - name: deeparg_short_reads owner: iuc tool_panel_section_id: '' +- name: deseq2 + owner: iuc + tool_panel_section_id: '' - name: dfast owner: ufz tool_panel_section_id: '' @@ -836,6 +842,9 @@ tools: - name: fasttree owner: iuc tool_panel_section_id: '' +- name: featurecounts + owner: iuc + tool_panel_section_id: '' - name: filter_spades_repeat owner: nml tool_panel_section_id: '' @@ -1220,6 +1229,9 @@ tools: - name: kmindex_query owner: iuc tool_panel_section_id: '' +- name: kneaddata + owner: iuc + tool_panel_section_id: '' - name: kofamscan owner: iuc tool_panel_section_id: '' @@ -1277,6 +1289,9 @@ tools: - name: legsta owner: iuc tool_panel_section_id: '' +- name: liftoff + owner: iuc + tool_panel_section_id: '' - name: lighter owner: bgruening tool_panel_section_id: '' @@ -1496,6 +1511,27 @@ tools: - name: mg_toolkit_original_metadata owner: iuc tool_panel_section_id: '' +- name: mgnify_genome_search + owner: iuc + tool_panel_section_id: '' +- name: mgnify_pipelines_toolkit_classify_var_regions + owner: iuc + tool_panel_section_id: '' +- name: mgnify_pipelines_toolkit_make_asv_count_table + owner: iuc + tool_panel_section_id: '' +- name: mgnify_pipelines_toolkit_mapseq_to_asv_table + owner: iuc + tool_panel_section_id: '' +- name: mgnify_pipelines_toolkit_permute_primers + owner: iuc + tool_panel_section_id: '' +- name: mgnify_pipelines_toolkit_primer_val_classification + owner: iuc + tool_panel_section_id: '' +- name: mgnify_pipelines_toolkit_rev_comp_se_primers + owner: iuc + tool_panel_section_id: '' - name: mgnify_seqprep owner: bgruening tool_panel_section_id: '' @@ -1517,6 +1553,12 @@ tools: - name: miniprot_index owner: iuc tool_panel_section_id: '' +- name: mist_call + owner: iuc + tool_panel_section_id: '' +- name: mist_dists + owner: iuc + tool_panel_section_id: '' - name: mitos owner: iuc tool_panel_section_id: '' @@ -1967,9 +2009,15 @@ tools: - name: msstats owner: galaxyp tool_panel_section_id: '' +- name: mtnucratio + owner: iuc + tool_panel_section_id: '' - name: multigsea owner: iuc tool_panel_section_id: '' +- name: multiqc + owner: iuc + tool_panel_section_id: '' - name: mykrobe_predict owner: iuc tool_panel_section_id: '' @@ -2081,6 +2129,9 @@ tools: - name: obi_clean owner: iuc tool_panel_section_id: '' +- name: obi_complement + owner: iuc + tool_panel_section_id: '' - name: obi_convert owner: iuc tool_panel_section_id: '' @@ -2093,6 +2144,18 @@ tools: - name: obi_pairing owner: iuc tool_panel_section_id: '' +- name: obi_pcr + owner: iuc + tool_panel_section_id: '' +- name: obi_refidx + owner: iuc + tool_panel_section_id: '' +- name: obi_tag + owner: iuc + tool_panel_section_id: '' +- name: obi_taxonomy + owner: iuc + tool_panel_section_id: '' - name: obi_uniq owner: iuc tool_panel_section_id: '' @@ -2714,6 +2777,9 @@ tools: - name: ppanggolin_rarefaction owner: iuc tool_panel_section_id: '' +- name: prinseq + owner: iuc + tool_panel_section_id: '' - name: prodigal owner: iuc tool_panel_section_id: '' @@ -2735,6 +2801,9 @@ tools: - name: proteinortho_summary owner: iuc tool_panel_section_id: '' +- name: psauron + owner: iuc + tool_panel_section_id: '' - name: pycoqc owner: iuc tool_panel_section_id: '' @@ -2843,262 +2912,241 @@ tools: - name: qiime_make_otu_table owner: iuc tool_panel_section_id: '' -- name: qiime2_core__tools__export - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2_core__tools__import - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2_core__tools__import_fastq - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__quality_filter__q_score - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__cull_seqs - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__degap_seqs - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__dereplicate - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__edit_taxonomy +- name: qiime2__dada2__denoise_ccs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_classifications +- name: qiime2__dada2__denoise_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_cross_validate +- name: qiime2__dada2__denoise_pyro owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_fit_classifier +- name: qiime2__dada2__denoise_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_seqs +- name: qiime2__dada2__plot_base_transitions owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_taxonomy +- name: qiime2__cutadapt__demux_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__extract_seq_segments +- name: qiime2__cutadapt__demux_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__filter_seqs_length +- name: qiime2__cutadapt__trim_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__filter_seqs_length_by_taxon +- name: qiime2__cutadapt__trim_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__filter_taxa +- name: qiime2__composition__add_pseudocount owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_bv_brc_genome_features +- name: qiime2__composition__ancom owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_bv_brc_genomes +- name: qiime2__composition__ancombc owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_bv_brc_metadata +- name: qiime2__composition__ancombc2 owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_eukaryome_data +- name: qiime2__composition__ancombc2_visualizer owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_gtdb_data +- name: qiime2__composition__da_barplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_midori2_data +- name: qiime2__composition__tabulate owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_ncbi_data +- name: qiime2__boots__alpha owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_ncbi_data_protein +- name: qiime2__boots__alpha_average owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_ncbi_genomes +- name: qiime2__boots__alpha_collection owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_pr2_data +- name: qiime2__boots__beta owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_silva_data +- name: qiime2__boots__beta_average owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_unite_data +- name: qiime2__boots__beta_collection owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__merge_taxa +- name: qiime2__boots__core_metrics owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__orient_reads +- name: qiime2__boots__kmer_diversity owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__orient_seqs +- name: qiime2__boots__resample owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__parse_silva_taxonomy +- name: qiime2__vsearch__cluster_features_closed_reference owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__reverse_transcribe +- name: qiime2__vsearch__cluster_features_de_novo owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__subsample_fasta +- name: qiime2__vsearch__cluster_features_open_reference owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__trim_alignment +- name: qiime2__vsearch__dereplicate_sequences owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__classify_samples +- name: qiime2__vsearch__fastq_stats owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__classify_samples_from_dist +- name: qiime2__vsearch__merge_pairs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__classify_samples_ncv +- name: qiime2__vsearch__uchime_denovo owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__confusion_matrix +- name: qiime2__vsearch__uchime_ref owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__fit_classifier +- name: qiime2__demux__emp_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__fit_regressor +- name: qiime2__demux__emp_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__heatmap +- name: qiime2__demux__filter_samples owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__metatable +- name: qiime2__demux__partition_samples_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__predict_classification +- name: qiime2__demux__partition_samples_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__predict_regression +- name: qiime2__demux__subsample_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__regress_samples +- name: qiime2__demux__subsample_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__regress_samples_ncv +- name: qiime2__demux__summarize owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__scatterplot +- name: qiime2__demux__tabulate_read_counts owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__split_table +- name: qiime2__deblur__denoise_16S owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__summarize +- name: qiime2__deblur__denoise_other owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__align_to_tree_mafft_fasttree +- name: qiime2__deblur__visualize_stats owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__align_to_tree_mafft_iqtree +- name: qiime2__diversity__adonis owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__align_to_tree_mafft_raxml +- name: qiime2__diversity__alpha owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__fasttree +- name: qiime2__diversity__alpha_correlation owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__filter_table +- name: qiime2__diversity__alpha_group_significance owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__filter_tree +- name: qiime2__diversity__alpha_phylogenetic owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__iqtree +- name: qiime2__diversity__alpha_rarefaction owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__iqtree_ultrafast_bootstrap +- name: qiime2__diversity__beta owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__midpoint_root +- name: qiime2__diversity__beta_correlation owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__raxml +- name: qiime2__diversity__beta_group_significance owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__raxml_rapid_bootstrap +- name: qiime2__diversity__beta_phylogenetic owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__robinson_foulds +- name: qiime2__diversity__beta_rarefaction owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__distance_matrix +- name: qiime2__diversity__bioenv owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__merge +- name: qiime2__diversity__core_metrics owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__shuffle_groups +- name: qiime2__diversity__core_metrics_phylogenetic owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__tabulate +- name: qiime2__diversity__filter_alpha_diversity owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__alpha_group_significance +- name: qiime2__diversity__filter_distance_matrix owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__collate_stats +- name: qiime2__diversity__mantel owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__facet_across +- name: qiime2__diversity__partial_procrustes owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__facet_within +- name: qiime2__diversity__pcoa owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__mann_whitney_u +- name: qiime2__diversity__pcoa_biplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__mann_whitney_u_facet +- name: qiime2__diversity__procrustes_analysis owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__plot_rainclouds +- name: qiime2__diversity__tsne owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__prep_alpha_distribution +- name: qiime2__diversity__umap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__wilcoxon_srt +- name: qiime2__emperor__biplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__wilcoxon_srt_facet +- name: qiime2__emperor__plot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__bowtie2_build +- name: qiime2__emperor__procrustes_plot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__decontam_identify +- name: qiime2_core__tools__export owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__decontam_identify_batches +- name: qiime2_core__tools__import owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__decontam_score_viz +- name: qiime2_core__tools__import_fastq owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__evaluate_composition +- name: qiime2__taxa__barplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__evaluate_seqs +- name: qiime2__taxa__barplot2 owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__evaluate_taxonomy +- name: qiime2__taxa__collapse owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__exclude_seqs +- name: qiime2__taxa__filter_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__filter_reads +- name: qiime2__taxa__filter_table owner: q2d2 tool_panel_section_id: '' - name: qiime2__diversity_lib__alpha_passthrough @@ -3137,253 +3185,244 @@ tools: - name: qiime2__diversity_lib__weighted_unifrac owner: q2d2 tool_panel_section_id: '' -- name: qiime2__alignment__mafft - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__alignment__mafft_add - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__alignment__mask - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__vizard__boxplot +- name: qiime2__stats__alpha_group_significance owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vizard__heatmap +- name: qiime2__stats__collate_stats owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vizard__lineplot +- name: qiime2__stats__facet_across owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vizard__scatterplot_2d +- name: qiime2__stats__facet_within owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__adonis +- name: qiime2__stats__mann_whitney_u owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha +- name: qiime2__stats__mann_whitney_u_facet owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_correlation +- name: qiime2__stats__plot_rainclouds owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_group_significance +- name: qiime2__stats__prep_alpha_distribution owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_phylogenetic +- name: qiime2__stats__wilcoxon_srt owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_rarefaction +- name: qiime2__stats__wilcoxon_srt_facet owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta +- name: qiime2__sample_classifier__classify_samples owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_correlation +- name: qiime2__sample_classifier__classify_samples_from_dist owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_group_significance +- name: qiime2__sample_classifier__classify_samples_ncv owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_phylogenetic +- name: qiime2__sample_classifier__confusion_matrix owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_rarefaction +- name: qiime2__sample_classifier__fit_classifier owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__bioenv +- name: qiime2__sample_classifier__fit_regressor owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__core_metrics +- name: qiime2__sample_classifier__heatmap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__core_metrics_phylogenetic +- name: qiime2__sample_classifier__metatable owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__filter_alpha_diversity +- name: qiime2__sample_classifier__predict_classification owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__filter_distance_matrix +- name: qiime2__sample_classifier__predict_regression owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__mantel +- name: qiime2__sample_classifier__regress_samples owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__partial_procrustes +- name: qiime2__sample_classifier__regress_samples_ncv owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__pcoa +- name: qiime2__sample_classifier__scatterplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__pcoa_biplot +- name: qiime2__sample_classifier__split_table owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__procrustes_analysis +- name: qiime2__sample_classifier__summarize owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__tsne +- name: qiime2__rescript__cull_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__umap +- name: qiime2__rescript__degap_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__emp_paired +- name: qiime2__rescript__dereplicate owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__emp_single +- name: qiime2__rescript__edit_taxonomy owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__filter_samples +- name: qiime2__rescript__evaluate_classifications owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__partition_samples_paired +- name: qiime2__rescript__evaluate_cross_validate owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__partition_samples_single +- name: qiime2__rescript__evaluate_fit_classifier owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__subsample_paired +- name: qiime2__rescript__evaluate_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__subsample_single +- name: qiime2__rescript__evaluate_taxonomy owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__summarize +- name: qiime2__rescript__extract_seq_segments owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__tabulate_read_counts +- name: qiime2__rescript__filter_seqs_length owner: q2d2 tool_panel_section_id: '' -- name: qiime2__deblur__denoise_16S +- name: qiime2__rescript__filter_seqs_length_by_taxon owner: q2d2 tool_panel_section_id: '' -- name: qiime2__deblur__denoise_other +- name: qiime2__rescript__filter_taxa owner: q2d2 tool_panel_section_id: '' -- name: qiime2__deblur__visualize_stats +- name: qiime2__rescript__get_bv_brc_genome_features owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_ccs +- name: qiime2__rescript__get_bv_brc_genomes owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_paired +- name: qiime2__rescript__get_bv_brc_metadata owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_pyro +- name: qiime2__rescript__get_eukaryome_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_single +- name: qiime2__rescript__get_gtdb_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__plot_base_transitions +- name: qiime2__rescript__get_midori2_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__cutadapt__demux_paired +- name: qiime2__rescript__get_ncbi_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__cutadapt__demux_single +- name: qiime2__rescript__get_ncbi_data_protein owner: q2d2 tool_panel_section_id: '' -- name: qiime2__cutadapt__trim_paired +- name: qiime2__rescript__get_ncbi_genomes owner: q2d2 tool_panel_section_id: '' -- name: qiime2__cutadapt__trim_single +- name: qiime2__rescript__get_pr2_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__add_pseudocount +- name: qiime2__rescript__get_silva_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancom +- name: qiime2__rescript__get_unite_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancombc +- name: qiime2__rescript__merge_taxa owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancombc2 +- name: qiime2__rescript__orient_reads owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancombc2_visualizer +- name: qiime2__rescript__orient_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__da_barplot +- name: qiime2__rescript__parse_silva_taxonomy owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__tabulate +- name: qiime2__rescript__reverse_transcribe owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__barplot +- name: qiime2__rescript__subsample_fasta owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__barplot2 +- name: qiime2__rescript__trim_alignment owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__collapse +- name: qiime2__quality_filter__q_score owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__filter_seqs +- name: qiime2__vizard__boxplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__filter_table +- name: qiime2__vizard__heatmap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__alpha +- name: qiime2__vizard__lineplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__alpha_average +- name: qiime2__vizard__scatterplot_2d owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__alpha_collection +- name: qiime2__alignment__mafft owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__beta +- name: qiime2__alignment__mafft_add owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__beta_average +- name: qiime2__alignment__mask owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__beta_collection +- name: qiime2__phylogeny__align_to_tree_mafft_fasttree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__core_metrics +- name: qiime2__phylogeny__align_to_tree_mafft_iqtree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__kmer_diversity +- name: qiime2__phylogeny__align_to_tree_mafft_raxml owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__resample +- name: qiime2__phylogeny__fasttree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__cluster_features_closed_reference +- name: qiime2__phylogeny__filter_table owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__cluster_features_de_novo +- name: qiime2__phylogeny__filter_tree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__cluster_features_open_reference +- name: qiime2__phylogeny__iqtree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__dereplicate_sequences +- name: qiime2__phylogeny__iqtree_ultrafast_bootstrap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__fastq_stats +- name: qiime2__phylogeny__midpoint_root owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__merge_pairs +- name: qiime2__phylogeny__raxml owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__uchime_denovo +- name: qiime2__phylogeny__raxml_rapid_bootstrap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__uchime_ref +- name: qiime2__phylogeny__robinson_foulds owner: q2d2 tool_panel_section_id: '' -- name: qiime2__emperor__biplot +- name: qiime2__fragment_insertion__classify_otus_experimental owner: q2d2 tool_panel_section_id: '' -- name: qiime2__emperor__plot +- name: qiime2__fragment_insertion__filter_features owner: q2d2 tool_panel_section_id: '' -- name: qiime2__emperor__procrustes_plot +- name: qiime2__fragment_insertion__sepp owner: q2d2 tool_panel_section_id: '' - name: qiime2__feature_classifier__blast @@ -3419,6 +3458,39 @@ tools: - name: qiime2__feature_classifier__vsearch_global owner: q2d2 tool_panel_section_id: '' +- name: qiime2__longitudinal__anova + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__feature_volatility + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__first_differences + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__first_distances + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__linear_mixed_effects + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__maturity_index + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__nmit + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__pairwise_differences + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__pairwise_distances + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__plot_feature_volatility + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__volatility + owner: q2d2 + tool_panel_section_id: '' - name: qiime2__feature_table___summarize owner: q2d2 tool_panel_section_id: '' @@ -3488,76 +3560,73 @@ tools: - name: qiime2__feature_table__transpose owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue___get_sequences - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__fondue__combine_seqs +- name: qiime2__quality_control__bowtie2_build owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__get_all +- name: qiime2__quality_control__decontam_identify owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__get_ids_from_query +- name: qiime2__quality_control__decontam_identify_batches owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__get_metadata +- name: qiime2__quality_control__decontam_score_viz owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__get_sequences +- name: qiime2__quality_control__evaluate_composition owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__merge_metadata +- name: qiime2__quality_control__evaluate_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__scrape_collection +- name: qiime2__quality_control__evaluate_taxonomy owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fragment_insertion__classify_otus_experimental +- name: qiime2__quality_control__exclude_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fragment_insertion__filter_features +- name: qiime2__quality_control__filter_reads owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fragment_insertion__sepp +- name: qiime2__metadata__distance_matrix owner: q2d2 tool_panel_section_id: '' -- name: qiime2__kmerizer__core_metrics +- name: qiime2__metadata__merge owner: q2d2 tool_panel_section_id: '' -- name: qiime2__kmerizer__seqs_to_kmers +- name: qiime2__metadata__shuffle_groups owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__anova +- name: qiime2__metadata__tabulate owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__feature_volatility +- name: qiime2__kmerizer__core_metrics owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__first_differences +- name: qiime2__kmerizer__seqs_to_kmers owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__first_distances +- name: qiime2__fondue___get_sequences owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__linear_mixed_effects +- name: qiime2__fondue__combine_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__maturity_index +- name: qiime2__fondue__get_all owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__nmit +- name: qiime2__fondue__get_ids_from_query owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__pairwise_differences +- name: qiime2__fondue__get_metadata owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__pairwise_distances +- name: qiime2__fondue__get_sequences owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__plot_feature_volatility +- name: qiime2__fondue__merge_metadata owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__volatility +- name: qiime2__fondue__scrape_collection owner: q2d2 tool_panel_section_id: '' - name: qiime2_dbotu_q2 @@ -3686,6 +3755,27 @@ tools: - name: rseqc_tin owner: nilesh tool_panel_section_id: '' +- name: samestr_compare + owner: iuc + tool_panel_section_id: '' +- name: samestr_convert + owner: iuc + tool_panel_section_id: '' +- name: samestr_extract + owner: iuc + tool_panel_section_id: '' +- name: samestr_filter + owner: iuc + tool_panel_section_id: '' +- name: samestr_merge + owner: iuc + tool_panel_section_id: '' +- name: samestr_stats + owner: iuc + tool_panel_section_id: '' +- name: samestr_summarize + owner: iuc + tool_panel_section_id: '' - name: scoary owner: iuc tool_panel_section_id: '' @@ -3810,10 +3900,10 @@ tools: owner: artbio tool_panel_section_id: '' - name: srst2 - owner: iuc + owner: nml tool_panel_section_id: '' - name: srst2 - owner: nml + owner: iuc tool_panel_section_id: '' - name: staramr_search owner: iuc @@ -3926,6 +4016,12 @@ tools: - name: varvamp owner: iuc tool_panel_section_id: '' +- name: vcontact2 + owner: iuc + tool_panel_section_id: '' +- name: vcontact2_gene2genome + owner: iuc + tool_panel_section_id: '' - name: vegan_diversity owner: iuc tool_panel_section_id: '' diff --git a/communities/microgalaxy/lab/tools/all/UseGalaxy_be.yaml b/communities/microgalaxy/lab/tools/all/UseGalaxy_be.yaml index 5876a16ce..c045475b6 100644 --- a/communities/microgalaxy/lab/tools/all/UseGalaxy_be.yaml +++ b/communities/microgalaxy/lab/tools/all/UseGalaxy_be.yaml @@ -266,6 +266,9 @@ tools: - name: dfast owner: ufz tool_panel_section_id: '' +- name: disco + owner: iuc + tool_panel_section_id: '' - name: dr_curve owner: ufz tool_panel_section_id: '' @@ -593,6 +596,9 @@ tools: - name: kmindex_query owner: iuc tool_panel_section_id: '' +- name: kneaddata + owner: iuc + tool_panel_section_id: '' - name: krakentools_alpha_diversity owner: iuc tool_panel_section_id: '' @@ -617,6 +623,9 @@ tools: - name: legsta owner: iuc tool_panel_section_id: '' +- name: liftoff + owner: iuc + tool_panel_section_id: '' - name: lighter owner: bgruening tool_panel_section_id: '' @@ -749,6 +758,27 @@ tools: - name: mg_toolkit_original_metadata owner: iuc tool_panel_section_id: '' +- name: mgnify_genome_search + owner: iuc + tool_panel_section_id: '' +- name: mgnify_pipelines_toolkit_classify_var_regions + owner: iuc + tool_panel_section_id: '' +- name: mgnify_pipelines_toolkit_make_asv_count_table + owner: iuc + tool_panel_section_id: '' +- name: mgnify_pipelines_toolkit_mapseq_to_asv_table + owner: iuc + tool_panel_section_id: '' +- name: mgnify_pipelines_toolkit_permute_primers + owner: iuc + tool_panel_section_id: '' +- name: mgnify_pipelines_toolkit_primer_val_classification + owner: iuc + tool_panel_section_id: '' +- name: mgnify_pipelines_toolkit_rev_comp_se_primers + owner: iuc + tool_panel_section_id: '' - name: micro_decon owner: iuc tool_panel_section_id: '' @@ -761,6 +791,18 @@ tools: - name: miniprot_index owner: iuc tool_panel_section_id: '' +- name: mist_call + owner: iuc + tool_panel_section_id: '' +- name: mist_dists + owner: iuc + tool_panel_section_id: '' +- name: mitos + owner: iuc + tool_panel_section_id: '' +- name: mitos2 + owner: iuc + tool_panel_section_id: '' - name: mmseqs2_easy_cluster owner: iuc tool_panel_section_id: '' @@ -1190,6 +1232,9 @@ tools: - name: mrbayes owner: nml tool_panel_section_id: '' +- name: mtnucratio + owner: iuc + tool_panel_section_id: '' - name: mykrobe_predict owner: iuc tool_panel_section_id: '' @@ -1274,6 +1319,9 @@ tools: - name: obi_clean owner: iuc tool_panel_section_id: '' +- name: obi_complement + owner: iuc + tool_panel_section_id: '' - name: obi_convert owner: iuc tool_panel_section_id: '' @@ -1286,6 +1334,18 @@ tools: - name: obi_pairing owner: iuc tool_panel_section_id: '' +- name: obi_pcr + owner: iuc + tool_panel_section_id: '' +- name: obi_refidx + owner: iuc + tool_panel_section_id: '' +- name: obi_tag + owner: iuc + tool_panel_section_id: '' +- name: obi_taxonomy + owner: iuc + tool_panel_section_id: '' - name: obi_uniq owner: iuc tool_panel_section_id: '' @@ -1874,6 +1934,9 @@ tools: - name: proteinortho_summary owner: iuc tool_panel_section_id: '' +- name: psauron + owner: iuc + tool_panel_section_id: '' - name: pycoqc owner: iuc tool_panel_section_id: '' @@ -1979,262 +2042,241 @@ tools: - name: qiime_make_otu_table owner: iuc tool_panel_section_id: '' -- name: qiime2_core__tools__export - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2_core__tools__import - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2_core__tools__import_fastq - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__quality_filter__q_score - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__cull_seqs - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__degap_seqs - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__dereplicate - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__edit_taxonomy +- name: qiime2__dada2__denoise_ccs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_classifications +- name: qiime2__dada2__denoise_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_cross_validate +- name: qiime2__dada2__denoise_pyro owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_fit_classifier +- name: qiime2__dada2__denoise_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_seqs +- name: qiime2__dada2__plot_base_transitions owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_taxonomy +- name: qiime2__cutadapt__demux_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__extract_seq_segments +- name: qiime2__cutadapt__demux_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__filter_seqs_length +- name: qiime2__cutadapt__trim_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__filter_seqs_length_by_taxon +- name: qiime2__cutadapt__trim_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__filter_taxa +- name: qiime2__composition__add_pseudocount owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_bv_brc_genome_features +- name: qiime2__composition__ancom owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_bv_brc_genomes +- name: qiime2__composition__ancombc owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_bv_brc_metadata +- name: qiime2__composition__ancombc2 owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_eukaryome_data +- name: qiime2__composition__ancombc2_visualizer owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_gtdb_data +- name: qiime2__composition__da_barplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_midori2_data +- name: qiime2__composition__tabulate owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_ncbi_data +- name: qiime2__boots__alpha owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_ncbi_data_protein +- name: qiime2__boots__alpha_average owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_ncbi_genomes +- name: qiime2__boots__alpha_collection owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_pr2_data +- name: qiime2__boots__beta owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_silva_data +- name: qiime2__boots__beta_average owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_unite_data +- name: qiime2__boots__beta_collection owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__merge_taxa +- name: qiime2__boots__core_metrics owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__orient_reads +- name: qiime2__boots__kmer_diversity owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__orient_seqs +- name: qiime2__boots__resample owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__parse_silva_taxonomy +- name: qiime2__vsearch__cluster_features_closed_reference owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__reverse_transcribe +- name: qiime2__vsearch__cluster_features_de_novo owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__subsample_fasta +- name: qiime2__vsearch__cluster_features_open_reference owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__trim_alignment +- name: qiime2__vsearch__dereplicate_sequences owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__classify_samples +- name: qiime2__vsearch__fastq_stats owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__classify_samples_from_dist +- name: qiime2__vsearch__merge_pairs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__classify_samples_ncv +- name: qiime2__vsearch__uchime_denovo owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__confusion_matrix +- name: qiime2__vsearch__uchime_ref owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__fit_classifier +- name: qiime2__demux__emp_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__fit_regressor +- name: qiime2__demux__emp_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__heatmap +- name: qiime2__demux__filter_samples owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__metatable +- name: qiime2__demux__partition_samples_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__predict_classification +- name: qiime2__demux__partition_samples_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__predict_regression +- name: qiime2__demux__subsample_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__regress_samples +- name: qiime2__demux__subsample_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__regress_samples_ncv +- name: qiime2__demux__summarize owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__scatterplot +- name: qiime2__demux__tabulate_read_counts owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__split_table +- name: qiime2__deblur__denoise_16S owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__summarize +- name: qiime2__deblur__denoise_other owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__align_to_tree_mafft_fasttree +- name: qiime2__deblur__visualize_stats owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__align_to_tree_mafft_iqtree +- name: qiime2__diversity__adonis owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__align_to_tree_mafft_raxml +- name: qiime2__diversity__alpha owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__fasttree +- name: qiime2__diversity__alpha_correlation owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__filter_table +- name: qiime2__diversity__alpha_group_significance owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__filter_tree +- name: qiime2__diversity__alpha_phylogenetic owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__iqtree +- name: qiime2__diversity__alpha_rarefaction owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__iqtree_ultrafast_bootstrap +- name: qiime2__diversity__beta owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__midpoint_root +- name: qiime2__diversity__beta_correlation owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__raxml +- name: qiime2__diversity__beta_group_significance owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__raxml_rapid_bootstrap +- name: qiime2__diversity__beta_phylogenetic owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__robinson_foulds +- name: qiime2__diversity__beta_rarefaction owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__distance_matrix +- name: qiime2__diversity__bioenv owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__merge +- name: qiime2__diversity__core_metrics owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__shuffle_groups +- name: qiime2__diversity__core_metrics_phylogenetic owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__tabulate +- name: qiime2__diversity__filter_alpha_diversity owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__alpha_group_significance +- name: qiime2__diversity__filter_distance_matrix owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__collate_stats +- name: qiime2__diversity__mantel owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__facet_across +- name: qiime2__diversity__partial_procrustes owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__facet_within +- name: qiime2__diversity__pcoa owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__mann_whitney_u +- name: qiime2__diversity__pcoa_biplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__mann_whitney_u_facet +- name: qiime2__diversity__procrustes_analysis owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__plot_rainclouds +- name: qiime2__diversity__tsne owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__prep_alpha_distribution +- name: qiime2__diversity__umap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__wilcoxon_srt +- name: qiime2__emperor__biplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__wilcoxon_srt_facet +- name: qiime2__emperor__plot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__bowtie2_build +- name: qiime2__emperor__procrustes_plot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__decontam_identify +- name: qiime2_core__tools__export owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__decontam_identify_batches +- name: qiime2_core__tools__import owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__decontam_score_viz +- name: qiime2_core__tools__import_fastq owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__evaluate_composition +- name: qiime2__taxa__barplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__evaluate_seqs +- name: qiime2__taxa__barplot2 owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__evaluate_taxonomy +- name: qiime2__taxa__collapse owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__exclude_seqs +- name: qiime2__taxa__filter_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__filter_reads +- name: qiime2__taxa__filter_table owner: q2d2 tool_panel_section_id: '' - name: qiime2__diversity_lib__alpha_passthrough @@ -2273,253 +2315,244 @@ tools: - name: qiime2__diversity_lib__weighted_unifrac owner: q2d2 tool_panel_section_id: '' -- name: qiime2__alignment__mafft - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__alignment__mafft_add - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__alignment__mask - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__vizard__boxplot +- name: qiime2__stats__alpha_group_significance owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vizard__heatmap +- name: qiime2__stats__collate_stats owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vizard__lineplot +- name: qiime2__stats__facet_across owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vizard__scatterplot_2d +- name: qiime2__stats__facet_within owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__adonis +- name: qiime2__stats__mann_whitney_u owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha +- name: qiime2__stats__mann_whitney_u_facet owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_correlation +- name: qiime2__stats__plot_rainclouds owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_group_significance +- name: qiime2__stats__prep_alpha_distribution owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_phylogenetic +- name: qiime2__stats__wilcoxon_srt owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_rarefaction +- name: qiime2__stats__wilcoxon_srt_facet owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta +- name: qiime2__sample_classifier__classify_samples owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_correlation +- name: qiime2__sample_classifier__classify_samples_from_dist owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_group_significance +- name: qiime2__sample_classifier__classify_samples_ncv owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_phylogenetic +- name: qiime2__sample_classifier__confusion_matrix owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_rarefaction +- name: qiime2__sample_classifier__fit_classifier owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__bioenv +- name: qiime2__sample_classifier__fit_regressor owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__core_metrics +- name: qiime2__sample_classifier__heatmap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__core_metrics_phylogenetic +- name: qiime2__sample_classifier__metatable owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__filter_alpha_diversity +- name: qiime2__sample_classifier__predict_classification owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__filter_distance_matrix +- name: qiime2__sample_classifier__predict_regression owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__mantel +- name: qiime2__sample_classifier__regress_samples owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__partial_procrustes +- name: qiime2__sample_classifier__regress_samples_ncv owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__pcoa +- name: qiime2__sample_classifier__scatterplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__pcoa_biplot +- name: qiime2__sample_classifier__split_table owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__procrustes_analysis +- name: qiime2__sample_classifier__summarize owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__tsne +- name: qiime2__rescript__cull_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__umap +- name: qiime2__rescript__degap_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__emp_paired +- name: qiime2__rescript__dereplicate owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__emp_single +- name: qiime2__rescript__edit_taxonomy owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__filter_samples +- name: qiime2__rescript__evaluate_classifications owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__partition_samples_paired +- name: qiime2__rescript__evaluate_cross_validate owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__partition_samples_single +- name: qiime2__rescript__evaluate_fit_classifier owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__subsample_paired +- name: qiime2__rescript__evaluate_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__subsample_single +- name: qiime2__rescript__evaluate_taxonomy owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__summarize +- name: qiime2__rescript__extract_seq_segments owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__tabulate_read_counts +- name: qiime2__rescript__filter_seqs_length owner: q2d2 tool_panel_section_id: '' -- name: qiime2__deblur__denoise_16S +- name: qiime2__rescript__filter_seqs_length_by_taxon owner: q2d2 tool_panel_section_id: '' -- name: qiime2__deblur__denoise_other +- name: qiime2__rescript__filter_taxa owner: q2d2 tool_panel_section_id: '' -- name: qiime2__deblur__visualize_stats +- name: qiime2__rescript__get_bv_brc_genome_features owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_ccs +- name: qiime2__rescript__get_bv_brc_genomes owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_paired +- name: qiime2__rescript__get_bv_brc_metadata owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_pyro +- name: qiime2__rescript__get_eukaryome_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_single +- name: qiime2__rescript__get_gtdb_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__plot_base_transitions +- name: qiime2__rescript__get_midori2_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__cutadapt__demux_paired +- name: qiime2__rescript__get_ncbi_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__cutadapt__demux_single +- name: qiime2__rescript__get_ncbi_data_protein owner: q2d2 tool_panel_section_id: '' -- name: qiime2__cutadapt__trim_paired +- name: qiime2__rescript__get_ncbi_genomes owner: q2d2 tool_panel_section_id: '' -- name: qiime2__cutadapt__trim_single +- name: qiime2__rescript__get_pr2_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__add_pseudocount +- name: qiime2__rescript__get_silva_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancom +- name: qiime2__rescript__get_unite_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancombc +- name: qiime2__rescript__merge_taxa owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancombc2 +- name: qiime2__rescript__orient_reads owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancombc2_visualizer +- name: qiime2__rescript__orient_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__da_barplot +- name: qiime2__rescript__parse_silva_taxonomy owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__tabulate +- name: qiime2__rescript__reverse_transcribe owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__barplot +- name: qiime2__rescript__subsample_fasta owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__barplot2 +- name: qiime2__rescript__trim_alignment owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__collapse +- name: qiime2__quality_filter__q_score owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__filter_seqs +- name: qiime2__vizard__boxplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__filter_table +- name: qiime2__vizard__heatmap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__alpha +- name: qiime2__vizard__lineplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__alpha_average +- name: qiime2__vizard__scatterplot_2d owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__alpha_collection +- name: qiime2__alignment__mafft owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__beta +- name: qiime2__alignment__mafft_add owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__beta_average +- name: qiime2__alignment__mask owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__beta_collection +- name: qiime2__phylogeny__align_to_tree_mafft_fasttree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__core_metrics +- name: qiime2__phylogeny__align_to_tree_mafft_iqtree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__kmer_diversity +- name: qiime2__phylogeny__align_to_tree_mafft_raxml owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__resample +- name: qiime2__phylogeny__fasttree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__cluster_features_closed_reference +- name: qiime2__phylogeny__filter_table owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__cluster_features_de_novo +- name: qiime2__phylogeny__filter_tree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__cluster_features_open_reference +- name: qiime2__phylogeny__iqtree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__dereplicate_sequences +- name: qiime2__phylogeny__iqtree_ultrafast_bootstrap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__fastq_stats +- name: qiime2__phylogeny__midpoint_root owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__merge_pairs +- name: qiime2__phylogeny__raxml owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__uchime_denovo +- name: qiime2__phylogeny__raxml_rapid_bootstrap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__uchime_ref +- name: qiime2__phylogeny__robinson_foulds owner: q2d2 tool_panel_section_id: '' -- name: qiime2__emperor__biplot +- name: qiime2__fragment_insertion__classify_otus_experimental owner: q2d2 tool_panel_section_id: '' -- name: qiime2__emperor__plot +- name: qiime2__fragment_insertion__filter_features owner: q2d2 tool_panel_section_id: '' -- name: qiime2__emperor__procrustes_plot +- name: qiime2__fragment_insertion__sepp owner: q2d2 tool_panel_section_id: '' - name: qiime2__feature_classifier__blast @@ -2555,6 +2588,39 @@ tools: - name: qiime2__feature_classifier__vsearch_global owner: q2d2 tool_panel_section_id: '' +- name: qiime2__longitudinal__anova + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__feature_volatility + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__first_differences + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__first_distances + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__linear_mixed_effects + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__maturity_index + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__nmit + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__pairwise_differences + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__pairwise_distances + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__plot_feature_volatility + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__volatility + owner: q2d2 + tool_panel_section_id: '' - name: qiime2__feature_table___summarize owner: q2d2 tool_panel_section_id: '' @@ -2624,76 +2690,73 @@ tools: - name: qiime2__feature_table__transpose owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue___get_sequences - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__fondue__combine_seqs +- name: qiime2__quality_control__bowtie2_build owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__get_all +- name: qiime2__quality_control__decontam_identify owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__get_ids_from_query +- name: qiime2__quality_control__decontam_identify_batches owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__get_metadata +- name: qiime2__quality_control__decontam_score_viz owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__get_sequences +- name: qiime2__quality_control__evaluate_composition owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__merge_metadata +- name: qiime2__quality_control__evaluate_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__scrape_collection +- name: qiime2__quality_control__evaluate_taxonomy owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fragment_insertion__classify_otus_experimental +- name: qiime2__quality_control__exclude_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fragment_insertion__filter_features +- name: qiime2__quality_control__filter_reads owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fragment_insertion__sepp +- name: qiime2__metadata__distance_matrix owner: q2d2 tool_panel_section_id: '' -- name: qiime2__kmerizer__core_metrics +- name: qiime2__metadata__merge owner: q2d2 tool_panel_section_id: '' -- name: qiime2__kmerizer__seqs_to_kmers +- name: qiime2__metadata__shuffle_groups owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__anova +- name: qiime2__metadata__tabulate owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__feature_volatility +- name: qiime2__kmerizer__core_metrics owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__first_differences +- name: qiime2__kmerizer__seqs_to_kmers owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__first_distances +- name: qiime2__fondue___get_sequences owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__linear_mixed_effects +- name: qiime2__fondue__combine_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__maturity_index +- name: qiime2__fondue__get_all owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__nmit +- name: qiime2__fondue__get_ids_from_query owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__pairwise_differences +- name: qiime2__fondue__get_metadata owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__pairwise_distances +- name: qiime2__fondue__get_sequences owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__plot_feature_volatility +- name: qiime2__fondue__merge_metadata owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__volatility +- name: qiime2__fondue__scrape_collection owner: q2d2 tool_panel_section_id: '' - name: qiime2_dbotu_q2 @@ -2726,6 +2789,27 @@ tools: - name: repeatexplorer_clustering owner: gga tool_panel_section_id: '' +- name: samestr_compare + owner: iuc + tool_panel_section_id: '' +- name: samestr_convert + owner: iuc + tool_panel_section_id: '' +- name: samestr_extract + owner: iuc + tool_panel_section_id: '' +- name: samestr_filter + owner: iuc + tool_panel_section_id: '' +- name: samestr_merge + owner: iuc + tool_panel_section_id: '' +- name: samestr_stats + owner: iuc + tool_panel_section_id: '' +- name: samestr_summarize + owner: iuc + tool_panel_section_id: '' - name: scoary owner: iuc tool_panel_section_id: '' @@ -2835,10 +2919,10 @@ tools: owner: artbio tool_panel_section_id: '' - name: srst2 - owner: iuc + owner: nml tool_panel_section_id: '' - name: srst2 - owner: nml + owner: iuc tool_panel_section_id: '' - name: stringmlst owner: nml @@ -2915,6 +2999,12 @@ tools: - name: vapor owner: iuc tool_panel_section_id: '' +- name: vcontact2 + owner: iuc + tool_panel_section_id: '' +- name: vcontact2_gene2genome + owner: iuc + tool_panel_section_id: '' - name: vibrant owner: ufz tool_panel_section_id: '' diff --git a/communities/microgalaxy/lab/tools/all/UseGalaxy_cz.yaml b/communities/microgalaxy/lab/tools/all/UseGalaxy_cz.yaml index 85faec102..3a275f458 100644 --- a/communities/microgalaxy/lab/tools/all/UseGalaxy_cz.yaml +++ b/communities/microgalaxy/lab/tools/all/UseGalaxy_cz.yaml @@ -350,12 +350,6 @@ tools: - name: irma owner: iuc tool_panel_section_id: '' -- name: jbrowse2 - owner: fubar - tool_panel_section_id: '' -- name: jbrowse2 - owner: fubar - tool_panel_section_id: '' - name: kaiju_addtaxonnames owner: iuc tool_panel_section_id: '' @@ -377,18 +371,21 @@ tools: - name: kmer2stats owner: iuc tool_panel_section_id: '' -- name: kmetashot - owner: bgruening - tool_panel_section_id: '' - name: kmindex_build owner: iuc tool_panel_section_id: '' - name: kmindex_query owner: iuc tool_panel_section_id: '' +- name: kneaddata + owner: iuc + tool_panel_section_id: '' - name: krocus owner: iuc tool_panel_section_id: '' +- name: liftoff + owner: iuc + tool_panel_section_id: '' - name: logol_wrapper owner: genouest tool_panel_section_id: '' @@ -461,9 +458,36 @@ tools: - name: mg_toolkit_original_metadata owner: iuc tool_panel_section_id: '' +- name: mgnify_genome_search + owner: iuc + tool_panel_section_id: '' +- name: mgnify_pipelines_toolkit_classify_var_regions + owner: iuc + tool_panel_section_id: '' +- name: mgnify_pipelines_toolkit_make_asv_count_table + owner: iuc + tool_panel_section_id: '' +- name: mgnify_pipelines_toolkit_mapseq_to_asv_table + owner: iuc + tool_panel_section_id: '' +- name: mgnify_pipelines_toolkit_permute_primers + owner: iuc + tool_panel_section_id: '' +- name: mgnify_pipelines_toolkit_primer_val_classification + owner: iuc + tool_panel_section_id: '' +- name: mgnify_pipelines_toolkit_rev_comp_se_primers + owner: iuc + tool_panel_section_id: '' - name: micro_decon owner: iuc tool_panel_section_id: '' +- name: mist_call + owner: iuc + tool_panel_section_id: '' +- name: mist_dists + owner: iuc + tool_panel_section_id: '' - name: mmseqs2_easy_cluster owner: iuc tool_panel_section_id: '' @@ -500,6 +524,9 @@ tools: - name: mrbayes owner: nml tool_panel_section_id: '' +- name: mtnucratio + owner: iuc + tool_panel_section_id: '' - name: mykrobe_predict owner: iuc tool_panel_section_id: '' @@ -578,6 +605,9 @@ tools: - name: obi_clean owner: iuc tool_panel_section_id: '' +- name: obi_complement + owner: iuc + tool_panel_section_id: '' - name: obi_convert owner: iuc tool_panel_section_id: '' @@ -590,6 +620,18 @@ tools: - name: obi_pairing owner: iuc tool_panel_section_id: '' +- name: obi_pcr + owner: iuc + tool_panel_section_id: '' +- name: obi_refidx + owner: iuc + tool_panel_section_id: '' +- name: obi_tag + owner: iuc + tool_panel_section_id: '' +- name: obi_taxonomy + owner: iuc + tool_panel_section_id: '' - name: obi_uniq owner: iuc tool_panel_section_id: '' @@ -1151,6 +1193,9 @@ tools: - name: proteinortho_summary owner: iuc tool_panel_section_id: '' +- name: psauron + owner: iuc + tool_panel_section_id: '' - name: qiime_align_seqs owner: iuc tool_panel_section_id: '' @@ -1247,364 +1292,325 @@ tools: - name: qiime_validate_mapping_file owner: iuc tool_panel_section_id: '' -- name: qiime2_core__tools__export - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2_core__tools__import - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2_core__tools__import_fastq - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__cull_seqs - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__degap_seqs - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__dereplicate - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__edit_taxonomy - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_classifications - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_cross_validate - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_fit_classifier - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_seqs - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_taxonomy - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__extract_seq_segments - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__filter_seqs_length +- name: qiime2__dada2__denoise_ccs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__filter_seqs_length_by_taxon +- name: qiime2__dada2__denoise_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__filter_taxa +- name: qiime2__dada2__denoise_pyro owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_bv_brc_genome_features +- name: qiime2__dada2__denoise_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_bv_brc_genomes +- name: qiime2__dada2__plot_base_transitions owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_bv_brc_metadata +- name: qiime2__composition__add_pseudocount owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_eukaryome_data +- name: qiime2__composition__ancom owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_gtdb_data +- name: qiime2__composition__ancombc owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_midori2_data +- name: qiime2__composition__ancombc2 owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_ncbi_data +- name: qiime2__composition__ancombc2_visualizer owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_ncbi_data_protein +- name: qiime2__composition__da_barplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_ncbi_genomes +- name: qiime2__composition__tabulate owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_pr2_data +- name: qiime2__boots__alpha owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_silva_data +- name: qiime2__boots__alpha_average owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_unite_data +- name: qiime2__boots__alpha_collection owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__merge_taxa +- name: qiime2__boots__beta owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__orient_reads +- name: qiime2__boots__beta_average owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__orient_seqs +- name: qiime2__boots__beta_collection owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__parse_silva_taxonomy +- name: qiime2__boots__core_metrics owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__reverse_transcribe +- name: qiime2__boots__kmer_diversity owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__subsample_fasta +- name: qiime2__boots__resample owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__trim_alignment +- name: qiime2__demux__emp_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__distance_matrix +- name: qiime2__demux__emp_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__merge +- name: qiime2__demux__filter_samples owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__shuffle_groups +- name: qiime2__demux__partition_samples_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__tabulate +- name: qiime2__demux__partition_samples_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__alpha_group_significance +- name: qiime2__demux__subsample_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__collate_stats +- name: qiime2__demux__subsample_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__facet_across +- name: qiime2__demux__summarize owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__facet_within +- name: qiime2__demux__tabulate_read_counts owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__mann_whitney_u +- name: qiime2__diversity__adonis owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__mann_whitney_u_facet +- name: qiime2__diversity__alpha owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__plot_rainclouds +- name: qiime2__diversity__alpha_correlation owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__prep_alpha_distribution +- name: qiime2__diversity__alpha_group_significance owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__wilcoxon_srt +- name: qiime2__diversity__alpha_phylogenetic owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__wilcoxon_srt_facet +- name: qiime2__diversity__alpha_rarefaction owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__bowtie2_build +- name: qiime2__diversity__beta owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__decontam_identify +- name: qiime2__diversity__beta_correlation owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__decontam_identify_batches +- name: qiime2__diversity__beta_group_significance owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__decontam_score_viz +- name: qiime2__diversity__beta_phylogenetic owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__evaluate_composition +- name: qiime2__diversity__beta_rarefaction owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__evaluate_seqs +- name: qiime2__diversity__bioenv owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__evaluate_taxonomy +- name: qiime2__diversity__core_metrics owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__exclude_seqs +- name: qiime2__diversity__core_metrics_phylogenetic owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__filter_reads +- name: qiime2__diversity__filter_alpha_diversity owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vizard__boxplot +- name: qiime2__diversity__filter_distance_matrix owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vizard__heatmap +- name: qiime2__diversity__mantel owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vizard__lineplot +- name: qiime2__diversity__partial_procrustes owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vizard__scatterplot_2d +- name: qiime2__diversity__pcoa owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__adonis +- name: qiime2__diversity__pcoa_biplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha +- name: qiime2__diversity__procrustes_analysis owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_correlation +- name: qiime2__diversity__tsne owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_group_significance +- name: qiime2__diversity__umap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_phylogenetic +- name: qiime2_core__tools__export owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_rarefaction +- name: qiime2_core__tools__import owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta +- name: qiime2_core__tools__import_fastq owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_correlation +- name: qiime2__taxa__barplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_group_significance +- name: qiime2__taxa__barplot2 owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_phylogenetic +- name: qiime2__taxa__collapse owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_rarefaction +- name: qiime2__taxa__filter_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__bioenv +- name: qiime2__taxa__filter_table owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__core_metrics +- name: qiime2__stats__alpha_group_significance owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__core_metrics_phylogenetic +- name: qiime2__stats__collate_stats owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__filter_alpha_diversity +- name: qiime2__stats__facet_across owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__filter_distance_matrix +- name: qiime2__stats__facet_within owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__mantel +- name: qiime2__stats__mann_whitney_u owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__partial_procrustes +- name: qiime2__stats__mann_whitney_u_facet owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__pcoa +- name: qiime2__stats__plot_rainclouds owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__pcoa_biplot +- name: qiime2__stats__prep_alpha_distribution owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__procrustes_analysis +- name: qiime2__stats__wilcoxon_srt owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__tsne +- name: qiime2__stats__wilcoxon_srt_facet owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__umap +- name: qiime2__rescript__cull_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__emp_paired +- name: qiime2__rescript__degap_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__emp_single +- name: qiime2__rescript__dereplicate owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__filter_samples +- name: qiime2__rescript__edit_taxonomy owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__partition_samples_paired +- name: qiime2__rescript__evaluate_classifications owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__partition_samples_single +- name: qiime2__rescript__evaluate_cross_validate owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__subsample_paired +- name: qiime2__rescript__evaluate_fit_classifier owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__subsample_single +- name: qiime2__rescript__evaluate_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__summarize +- name: qiime2__rescript__evaluate_taxonomy owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__tabulate_read_counts +- name: qiime2__rescript__extract_seq_segments owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_ccs +- name: qiime2__rescript__filter_seqs_length owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_paired +- name: qiime2__rescript__filter_seqs_length_by_taxon owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_pyro +- name: qiime2__rescript__filter_taxa owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_single +- name: qiime2__rescript__get_bv_brc_genome_features owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__plot_base_transitions +- name: qiime2__rescript__get_bv_brc_genomes owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__add_pseudocount +- name: qiime2__rescript__get_bv_brc_metadata owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancom +- name: qiime2__rescript__get_eukaryome_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancombc +- name: qiime2__rescript__get_gtdb_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancombc2 +- name: qiime2__rescript__get_midori2_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancombc2_visualizer +- name: qiime2__rescript__get_ncbi_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__da_barplot +- name: qiime2__rescript__get_ncbi_data_protein owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__tabulate +- name: qiime2__rescript__get_ncbi_genomes owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__barplot +- name: qiime2__rescript__get_pr2_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__barplot2 +- name: qiime2__rescript__get_silva_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__collapse +- name: qiime2__rescript__get_unite_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__filter_seqs +- name: qiime2__rescript__merge_taxa owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__filter_table +- name: qiime2__rescript__orient_reads owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__alpha +- name: qiime2__rescript__orient_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__alpha_average +- name: qiime2__rescript__parse_silva_taxonomy owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__alpha_collection +- name: qiime2__rescript__reverse_transcribe owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__beta +- name: qiime2__rescript__subsample_fasta owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__beta_average +- name: qiime2__rescript__trim_alignment owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__beta_collection +- name: qiime2__vizard__boxplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__core_metrics +- name: qiime2__vizard__heatmap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__kmer_diversity +- name: qiime2__vizard__lineplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__resample +- name: qiime2__vizard__scatterplot_2d owner: q2d2 tool_panel_section_id: '' - name: qiime2__feature_classifier__blast @@ -1709,6 +1715,51 @@ tools: - name: qiime2__feature_table__transpose owner: q2d2 tool_panel_section_id: '' +- name: qiime2__quality_control__bowtie2_build + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__quality_control__decontam_identify + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__quality_control__decontam_identify_batches + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__quality_control__decontam_score_viz + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__quality_control__evaluate_composition + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__quality_control__evaluate_seqs + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__quality_control__evaluate_taxonomy + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__quality_control__exclude_seqs + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__quality_control__filter_reads + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__metadata__distance_matrix + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__metadata__merge + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__metadata__shuffle_groups + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__metadata__tabulate + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__kmerizer__core_metrics + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__kmerizer__seqs_to_kmers + owner: q2d2 + tool_panel_section_id: '' - name: qiime2__fondue___get_sequences owner: q2d2 tool_panel_section_id: '' @@ -1733,12 +1784,6 @@ tools: - name: qiime2__fondue__scrape_collection owner: q2d2 tool_panel_section_id: '' -- name: qiime2__kmerizer__core_metrics - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__kmerizer__seqs_to_kmers - owner: q2d2 - tool_panel_section_id: '' - name: qiime2_dbotu_q2 owner: bgruening tool_panel_section_id: '' @@ -1766,6 +1811,27 @@ tools: - name: repeatexplorer_clustering owner: gga tool_panel_section_id: '' +- name: samestr_compare + owner: iuc + tool_panel_section_id: '' +- name: samestr_convert + owner: iuc + tool_panel_section_id: '' +- name: samestr_extract + owner: iuc + tool_panel_section_id: '' +- name: samestr_filter + owner: iuc + tool_panel_section_id: '' +- name: samestr_merge + owner: iuc + tool_panel_section_id: '' +- name: samestr_stats + owner: iuc + tool_panel_section_id: '' +- name: samestr_summarize + owner: iuc + tool_panel_section_id: '' - name: seqkit_fx2tab owner: iuc tool_panel_section_id: '' @@ -1862,6 +1928,12 @@ tools: - name: varvamp owner: iuc tool_panel_section_id: '' +- name: vcontact2 + owner: iuc + tool_panel_section_id: '' +- name: vcontact2_gene2genome + owner: iuc + tool_panel_section_id: '' - name: vibrant owner: ufz tool_panel_section_id: '' diff --git a/communities/microgalaxy/lab/tools/all/UseGalaxy_eu.yaml b/communities/microgalaxy/lab/tools/all/UseGalaxy_eu.yaml index 06df27665..f33aaca45 100644 --- a/communities/microgalaxy/lab/tools/all/UseGalaxy_eu.yaml +++ b/communities/microgalaxy/lab/tools/all/UseGalaxy_eu.yaml @@ -611,343 +611,304 @@ tools: - name: promer4_substitutions owner: nml tool_panel_section_id: '' -- name: qiime2__rescript__cull_seqs - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__degap_seqs - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__dereplicate - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__edit_taxonomy - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_classifications - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_cross_validate - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_fit_classifier - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_seqs - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_taxonomy - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__extract_seq_segments - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__filter_seqs_length - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__filter_seqs_length_by_taxon - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__filter_taxa - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__get_bv_brc_genome_features +- name: qiime2__dada2__denoise_ccs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_bv_brc_genomes +- name: qiime2__dada2__denoise_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_bv_brc_metadata +- name: qiime2__dada2__denoise_pyro owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_eukaryome_data +- name: qiime2__dada2__denoise_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_gtdb_data +- name: qiime2__dada2__plot_base_transitions owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_midori2_data +- name: qiime2__composition__add_pseudocount owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_ncbi_data +- name: qiime2__composition__ancom owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_ncbi_data_protein +- name: qiime2__composition__ancombc owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_ncbi_genomes +- name: qiime2__composition__ancombc2 owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_pr2_data +- name: qiime2__composition__ancombc2_visualizer owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_silva_data +- name: qiime2__composition__da_barplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_unite_data +- name: qiime2__composition__tabulate owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__merge_taxa +- name: qiime2__boots__alpha owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__orient_reads +- name: qiime2__boots__alpha_average owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__orient_seqs +- name: qiime2__boots__alpha_collection owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__parse_silva_taxonomy +- name: qiime2__boots__beta owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__reverse_transcribe +- name: qiime2__boots__beta_average owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__subsample_fasta +- name: qiime2__boots__beta_collection owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__trim_alignment +- name: qiime2__boots__core_metrics owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__distance_matrix +- name: qiime2__boots__kmer_diversity owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__merge +- name: qiime2__boots__resample owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__shuffle_groups +- name: qiime2__demux__emp_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__tabulate +- name: qiime2__demux__emp_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__alpha_group_significance +- name: qiime2__demux__filter_samples owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__collate_stats +- name: qiime2__demux__partition_samples_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__facet_across +- name: qiime2__demux__partition_samples_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__facet_within +- name: qiime2__demux__subsample_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__mann_whitney_u +- name: qiime2__demux__subsample_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__mann_whitney_u_facet +- name: qiime2__demux__summarize owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__plot_rainclouds +- name: qiime2__demux__tabulate_read_counts owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__prep_alpha_distribution +- name: qiime2__diversity__adonis owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__wilcoxon_srt +- name: qiime2__diversity__alpha owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__wilcoxon_srt_facet +- name: qiime2__diversity__alpha_correlation owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__bowtie2_build +- name: qiime2__diversity__alpha_group_significance owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__decontam_identify +- name: qiime2__diversity__alpha_phylogenetic owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__decontam_identify_batches +- name: qiime2__diversity__alpha_rarefaction owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__decontam_score_viz +- name: qiime2__diversity__beta owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__evaluate_composition +- name: qiime2__diversity__beta_correlation owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__evaluate_seqs +- name: qiime2__diversity__beta_group_significance owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__evaluate_taxonomy +- name: qiime2__diversity__beta_phylogenetic owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__exclude_seqs +- name: qiime2__diversity__beta_rarefaction owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__filter_reads +- name: qiime2__diversity__bioenv owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__adonis +- name: qiime2__diversity__core_metrics owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha +- name: qiime2__diversity__core_metrics_phylogenetic owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_correlation +- name: qiime2__diversity__filter_alpha_diversity owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_group_significance +- name: qiime2__diversity__filter_distance_matrix owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_phylogenetic +- name: qiime2__diversity__mantel owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_rarefaction +- name: qiime2__diversity__partial_procrustes owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta +- name: qiime2__diversity__pcoa owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_correlation +- name: qiime2__diversity__pcoa_biplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_group_significance +- name: qiime2__diversity__procrustes_analysis owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_phylogenetic +- name: qiime2__diversity__tsne owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_rarefaction +- name: qiime2__diversity__umap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__bioenv +- name: qiime2__taxa__barplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__core_metrics +- name: qiime2__taxa__barplot2 owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__core_metrics_phylogenetic +- name: qiime2__taxa__collapse owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__filter_alpha_diversity +- name: qiime2__taxa__filter_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__filter_distance_matrix +- name: qiime2__taxa__filter_table owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__mantel +- name: qiime2__stats__alpha_group_significance owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__partial_procrustes +- name: qiime2__stats__collate_stats owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__pcoa +- name: qiime2__stats__facet_across owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__pcoa_biplot +- name: qiime2__stats__facet_within owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__procrustes_analysis +- name: qiime2__stats__mann_whitney_u owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__tsne +- name: qiime2__stats__mann_whitney_u_facet owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__umap +- name: qiime2__stats__plot_rainclouds owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__emp_paired +- name: qiime2__stats__prep_alpha_distribution owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__emp_single +- name: qiime2__stats__wilcoxon_srt owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__filter_samples +- name: qiime2__stats__wilcoxon_srt_facet owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__partition_samples_paired +- name: qiime2__rescript__cull_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__partition_samples_single +- name: qiime2__rescript__degap_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__subsample_paired +- name: qiime2__rescript__dereplicate owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__subsample_single +- name: qiime2__rescript__edit_taxonomy owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__summarize +- name: qiime2__rescript__evaluate_classifications owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__tabulate_read_counts +- name: qiime2__rescript__evaluate_cross_validate owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_ccs +- name: qiime2__rescript__evaluate_fit_classifier owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_paired +- name: qiime2__rescript__evaluate_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_pyro +- name: qiime2__rescript__evaluate_taxonomy owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_single +- name: qiime2__rescript__extract_seq_segments owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__plot_base_transitions +- name: qiime2__rescript__filter_seqs_length owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__add_pseudocount +- name: qiime2__rescript__filter_seqs_length_by_taxon owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancom +- name: qiime2__rescript__filter_taxa owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancombc +- name: qiime2__rescript__get_bv_brc_genome_features owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancombc2 +- name: qiime2__rescript__get_bv_brc_genomes owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancombc2_visualizer +- name: qiime2__rescript__get_bv_brc_metadata owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__da_barplot +- name: qiime2__rescript__get_eukaryome_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__tabulate +- name: qiime2__rescript__get_gtdb_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__barplot +- name: qiime2__rescript__get_midori2_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__barplot2 +- name: qiime2__rescript__get_ncbi_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__collapse +- name: qiime2__rescript__get_ncbi_data_protein owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__filter_seqs +- name: qiime2__rescript__get_ncbi_genomes owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__filter_table +- name: qiime2__rescript__get_pr2_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__alpha +- name: qiime2__rescript__get_silva_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__alpha_average +- name: qiime2__rescript__get_unite_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__alpha_collection +- name: qiime2__rescript__merge_taxa owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__beta +- name: qiime2__rescript__orient_reads owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__beta_average +- name: qiime2__rescript__orient_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__beta_collection +- name: qiime2__rescript__parse_silva_taxonomy owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__core_metrics +- name: qiime2__rescript__reverse_transcribe owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__kmer_diversity +- name: qiime2__rescript__subsample_fasta owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__resample +- name: qiime2__rescript__trim_alignment owner: q2d2 tool_panel_section_id: '' - name: qiime2__feature_classifier__blast @@ -1052,6 +1013,51 @@ tools: - name: qiime2__feature_table__transpose owner: q2d2 tool_panel_section_id: '' +- name: qiime2__quality_control__bowtie2_build + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__quality_control__decontam_identify + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__quality_control__decontam_identify_batches + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__quality_control__decontam_score_viz + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__quality_control__evaluate_composition + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__quality_control__evaluate_seqs + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__quality_control__evaluate_taxonomy + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__quality_control__exclude_seqs + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__quality_control__filter_reads + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__metadata__distance_matrix + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__metadata__merge + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__metadata__shuffle_groups + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__metadata__tabulate + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__kmerizer__core_metrics + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__kmerizer__seqs_to_kmers + owner: q2d2 + tool_panel_section_id: '' - name: qiime2__fondue___get_sequences owner: q2d2 tool_panel_section_id: '' @@ -1076,12 +1082,6 @@ tools: - name: qiime2__fondue__scrape_collection owner: q2d2 tool_panel_section_id: '' -- name: qiime2__kmerizer__core_metrics - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__kmerizer__seqs_to_kmers - owner: q2d2 - tool_panel_section_id: '' - name: smalt owner: nml tool_panel_section_id: '' diff --git a/communities/microgalaxy/lab/tools/all/UseGalaxy_fr.yaml b/communities/microgalaxy/lab/tools/all/UseGalaxy_fr.yaml index a0eaede92..79da8dd59 100644 --- a/communities/microgalaxy/lab/tools/all/UseGalaxy_fr.yaml +++ b/communities/microgalaxy/lab/tools/all/UseGalaxy_fr.yaml @@ -425,6 +425,9 @@ tools: - name: kmindex_query owner: iuc tool_panel_section_id: '' +- name: kneaddata + owner: iuc + tool_panel_section_id: '' - name: Kraken2Tax owner: devteam tool_panel_section_id: '' @@ -437,6 +440,9 @@ tools: - name: legsta owner: iuc tool_panel_section_id: '' +- name: liftoff + owner: iuc + tool_panel_section_id: '' - name: lineagespot owner: iuc tool_panel_section_id: '' @@ -464,9 +470,6 @@ tools: - name: mapseq owner: iuc tool_panel_section_id: '' -- name: sanntis_marine - owner: ecology - tool_panel_section_id: '' - name: mash_dist owner: iuc tool_panel_section_id: '' @@ -536,6 +539,27 @@ tools: - name: mg_toolkit_original_metadata owner: iuc tool_panel_section_id: '' +- name: mgnify_genome_search + owner: iuc + tool_panel_section_id: '' +- name: mgnify_pipelines_toolkit_classify_var_regions + owner: iuc + tool_panel_section_id: '' +- name: mgnify_pipelines_toolkit_make_asv_count_table + owner: iuc + tool_panel_section_id: '' +- name: mgnify_pipelines_toolkit_mapseq_to_asv_table + owner: iuc + tool_panel_section_id: '' +- name: mgnify_pipelines_toolkit_permute_primers + owner: iuc + tool_panel_section_id: '' +- name: mgnify_pipelines_toolkit_primer_val_classification + owner: iuc + tool_panel_section_id: '' +- name: mgnify_pipelines_toolkit_rev_comp_se_primers + owner: iuc + tool_panel_section_id: '' - name: mgnify_seqprep owner: bgruening tool_panel_section_id: '' @@ -548,6 +572,12 @@ tools: - name: minipolish owner: bgruening tool_panel_section_id: '' +- name: mist_call + owner: iuc + tool_panel_section_id: '' +- name: mist_dists + owner: iuc + tool_panel_section_id: '' - name: mmseqs2_easy_cluster owner: iuc tool_panel_section_id: '' @@ -581,6 +611,9 @@ tools: - name: msstats owner: galaxyp tool_panel_section_id: '' +- name: mtnucratio + owner: iuc + tool_panel_section_id: '' - name: multigsea owner: iuc tool_panel_section_id: '' @@ -665,27 +698,6 @@ tools: - name: nugen_nudup owner: iuc tool_panel_section_id: '' -- name: obi_annotate - owner: iuc - tool_panel_section_id: '' -- name: obi_clean - owner: iuc - tool_panel_section_id: '' -- name: obi_convert - owner: iuc - tool_panel_section_id: '' -- name: obi_grep - owner: iuc - tool_panel_section_id: '' -- name: obi_multiplex - owner: iuc - tool_panel_section_id: '' -- name: obi_pairing - owner: iuc - tool_panel_section_id: '' -- name: obi_uniq - owner: iuc - tool_panel_section_id: '' - name: AccurateMassSearch owner: bgruening tool_panel_section_id: '' @@ -1238,355 +1250,316 @@ tools: - name: proteinortho_summary owner: iuc tool_panel_section_id: '' -- name: qiime2__rescript__cull_seqs - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__degap_seqs - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__dereplicate - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__edit_taxonomy - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_classifications - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_cross_validate - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_fit_classifier - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_seqs - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_taxonomy - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__extract_seq_segments - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__filter_seqs_length - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__filter_seqs_length_by_taxon - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__filter_taxa - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__get_bv_brc_genome_features +- name: qiime2__dada2__denoise_ccs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_bv_brc_genomes +- name: qiime2__dada2__denoise_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_bv_brc_metadata +- name: qiime2__dada2__denoise_pyro owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_eukaryome_data +- name: qiime2__dada2__denoise_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_gtdb_data +- name: qiime2__dada2__plot_base_transitions owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_midori2_data +- name: qiime2__composition__add_pseudocount owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_ncbi_data +- name: qiime2__composition__ancom owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_ncbi_data_protein +- name: qiime2__composition__ancombc owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_ncbi_genomes +- name: qiime2__composition__ancombc2 owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_pr2_data +- name: qiime2__composition__ancombc2_visualizer owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_silva_data +- name: qiime2__composition__da_barplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_unite_data +- name: qiime2__composition__tabulate owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__merge_taxa +- name: qiime2__boots__alpha owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__orient_reads +- name: qiime2__boots__alpha_average owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__orient_seqs +- name: qiime2__boots__alpha_collection owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__parse_silva_taxonomy +- name: qiime2__boots__beta owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__reverse_transcribe +- name: qiime2__boots__beta_average owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__subsample_fasta +- name: qiime2__boots__beta_collection owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__trim_alignment +- name: qiime2__boots__core_metrics owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__distance_matrix +- name: qiime2__boots__kmer_diversity owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__merge +- name: qiime2__boots__resample owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__shuffle_groups +- name: qiime2__demux__emp_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__tabulate +- name: qiime2__demux__emp_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__alpha_group_significance +- name: qiime2__demux__filter_samples owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__collate_stats +- name: qiime2__demux__partition_samples_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__facet_across +- name: qiime2__demux__partition_samples_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__facet_within +- name: qiime2__demux__subsample_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__mann_whitney_u +- name: qiime2__demux__subsample_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__mann_whitney_u_facet +- name: qiime2__demux__summarize owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__plot_rainclouds +- name: qiime2__demux__tabulate_read_counts owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__prep_alpha_distribution +- name: qiime2__diversity__adonis owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__wilcoxon_srt +- name: qiime2__diversity__alpha owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__wilcoxon_srt_facet +- name: qiime2__diversity__alpha_correlation owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__bowtie2_build +- name: qiime2__diversity__alpha_group_significance owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__decontam_identify +- name: qiime2__diversity__alpha_phylogenetic owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__decontam_identify_batches +- name: qiime2__diversity__alpha_rarefaction owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__decontam_score_viz +- name: qiime2__diversity__beta owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__evaluate_composition +- name: qiime2__diversity__beta_correlation owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__evaluate_seqs +- name: qiime2__diversity__beta_group_significance owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__evaluate_taxonomy +- name: qiime2__diversity__beta_phylogenetic owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__exclude_seqs +- name: qiime2__diversity__beta_rarefaction owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__filter_reads +- name: qiime2__diversity__bioenv owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vizard__boxplot +- name: qiime2__diversity__core_metrics owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vizard__heatmap +- name: qiime2__diversity__core_metrics_phylogenetic owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vizard__lineplot +- name: qiime2__diversity__filter_alpha_diversity owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vizard__scatterplot_2d +- name: qiime2__diversity__filter_distance_matrix owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__adonis +- name: qiime2__diversity__mantel owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha +- name: qiime2__diversity__partial_procrustes owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_correlation +- name: qiime2__diversity__pcoa owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_group_significance +- name: qiime2__diversity__pcoa_biplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_phylogenetic +- name: qiime2__diversity__procrustes_analysis owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_rarefaction +- name: qiime2__diversity__tsne owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta +- name: qiime2__diversity__umap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_correlation +- name: qiime2__taxa__barplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_group_significance +- name: qiime2__taxa__barplot2 owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_phylogenetic +- name: qiime2__taxa__collapse owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_rarefaction +- name: qiime2__taxa__filter_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__bioenv +- name: qiime2__taxa__filter_table owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__core_metrics +- name: qiime2__stats__alpha_group_significance owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__core_metrics_phylogenetic +- name: qiime2__stats__collate_stats owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__filter_alpha_diversity +- name: qiime2__stats__facet_across owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__filter_distance_matrix +- name: qiime2__stats__facet_within owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__mantel +- name: qiime2__stats__mann_whitney_u owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__partial_procrustes +- name: qiime2__stats__mann_whitney_u_facet owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__pcoa +- name: qiime2__stats__plot_rainclouds owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__pcoa_biplot +- name: qiime2__stats__prep_alpha_distribution owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__procrustes_analysis +- name: qiime2__stats__wilcoxon_srt owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__tsne +- name: qiime2__stats__wilcoxon_srt_facet owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__umap +- name: qiime2__rescript__cull_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__emp_paired +- name: qiime2__rescript__degap_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__emp_single +- name: qiime2__rescript__dereplicate owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__filter_samples +- name: qiime2__rescript__edit_taxonomy owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__partition_samples_paired +- name: qiime2__rescript__evaluate_classifications owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__partition_samples_single +- name: qiime2__rescript__evaluate_cross_validate owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__subsample_paired +- name: qiime2__rescript__evaluate_fit_classifier owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__subsample_single +- name: qiime2__rescript__evaluate_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__summarize +- name: qiime2__rescript__evaluate_taxonomy owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__tabulate_read_counts +- name: qiime2__rescript__extract_seq_segments owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_ccs +- name: qiime2__rescript__filter_seqs_length owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_paired +- name: qiime2__rescript__filter_seqs_length_by_taxon owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_pyro +- name: qiime2__rescript__filter_taxa owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_single +- name: qiime2__rescript__get_bv_brc_genome_features owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__plot_base_transitions +- name: qiime2__rescript__get_bv_brc_genomes owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__add_pseudocount +- name: qiime2__rescript__get_bv_brc_metadata owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancom +- name: qiime2__rescript__get_eukaryome_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancombc +- name: qiime2__rescript__get_gtdb_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancombc2 +- name: qiime2__rescript__get_midori2_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancombc2_visualizer +- name: qiime2__rescript__get_ncbi_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__da_barplot +- name: qiime2__rescript__get_ncbi_data_protein owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__tabulate +- name: qiime2__rescript__get_ncbi_genomes owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__barplot +- name: qiime2__rescript__get_pr2_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__barplot2 +- name: qiime2__rescript__get_silva_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__collapse +- name: qiime2__rescript__get_unite_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__filter_seqs +- name: qiime2__rescript__merge_taxa owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__filter_table +- name: qiime2__rescript__orient_reads owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__alpha +- name: qiime2__rescript__orient_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__alpha_average +- name: qiime2__rescript__parse_silva_taxonomy owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__alpha_collection +- name: qiime2__rescript__reverse_transcribe owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__beta +- name: qiime2__rescript__subsample_fasta owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__beta_average +- name: qiime2__rescript__trim_alignment owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__beta_collection +- name: qiime2__vizard__boxplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__core_metrics +- name: qiime2__vizard__heatmap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__kmer_diversity +- name: qiime2__vizard__lineplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__resample +- name: qiime2__vizard__scatterplot_2d owner: q2d2 tool_panel_section_id: '' - name: qiime2__feature_classifier__blast @@ -1691,6 +1664,51 @@ tools: - name: qiime2__feature_table__transpose owner: q2d2 tool_panel_section_id: '' +- name: qiime2__quality_control__bowtie2_build + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__quality_control__decontam_identify + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__quality_control__decontam_identify_batches + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__quality_control__decontam_score_viz + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__quality_control__evaluate_composition + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__quality_control__evaluate_seqs + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__quality_control__evaluate_taxonomy + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__quality_control__exclude_seqs + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__quality_control__filter_reads + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__metadata__distance_matrix + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__metadata__merge + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__metadata__shuffle_groups + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__metadata__tabulate + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__kmerizer__core_metrics + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__kmerizer__seqs_to_kmers + owner: q2d2 + tool_panel_section_id: '' - name: qiime2__fondue___get_sequences owner: q2d2 tool_panel_section_id: '' @@ -1715,12 +1733,6 @@ tools: - name: qiime2__fondue__scrape_collection owner: q2d2 tool_panel_section_id: '' -- name: qiime2__kmerizer__core_metrics - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__kmerizer__seqs_to_kmers - owner: q2d2 - tool_panel_section_id: '' - name: qiime2_dbotu_q2 owner: bgruening tool_panel_section_id: '' @@ -1751,6 +1763,27 @@ tools: - name: repeatexplorer_clustering owner: gga tool_panel_section_id: '' +- name: samestr_compare + owner: iuc + tool_panel_section_id: '' +- name: samestr_convert + owner: iuc + tool_panel_section_id: '' +- name: samestr_extract + owner: iuc + tool_panel_section_id: '' +- name: samestr_filter + owner: iuc + tool_panel_section_id: '' +- name: samestr_merge + owner: iuc + tool_panel_section_id: '' +- name: samestr_stats + owner: iuc + tool_panel_section_id: '' +- name: samestr_summarize + owner: iuc + tool_panel_section_id: '' - name: scoary owner: iuc tool_panel_section_id: '' @@ -1827,10 +1860,10 @@ tools: owner: artbio tool_panel_section_id: '' - name: srst2 - owner: iuc + owner: nml tool_panel_section_id: '' - name: srst2 - owner: nml + owner: iuc tool_panel_section_id: '' - name: stringmlst owner: nml @@ -1877,6 +1910,12 @@ tools: - name: varvamp owner: iuc tool_panel_section_id: '' +- name: vcontact2 + owner: iuc + tool_panel_section_id: '' +- name: vcontact2_gene2genome + owner: iuc + tool_panel_section_id: '' - name: vegan_diversity owner: iuc tool_panel_section_id: '' diff --git a/communities/microgalaxy/lab/tools/all/UseGalaxy_no.yaml b/communities/microgalaxy/lab/tools/all/UseGalaxy_no.yaml index 5b0828e59..17adcbe83 100644 --- a/communities/microgalaxy/lab/tools/all/UseGalaxy_no.yaml +++ b/communities/microgalaxy/lab/tools/all/UseGalaxy_no.yaml @@ -587,6 +587,9 @@ tools: - name: kmindex_query owner: iuc tool_panel_section_id: '' +- name: kneaddata + owner: iuc + tool_panel_section_id: '' - name: kofamscan owner: iuc tool_panel_section_id: '' @@ -614,6 +617,9 @@ tools: - name: legsta owner: iuc tool_panel_section_id: '' +- name: liftoff + owner: iuc + tool_panel_section_id: '' - name: lineagespot owner: iuc tool_panel_section_id: '' @@ -746,6 +752,27 @@ tools: - name: mg_toolkit_original_metadata owner: iuc tool_panel_section_id: '' +- name: mgnify_genome_search + owner: iuc + tool_panel_section_id: '' +- name: mgnify_pipelines_toolkit_classify_var_regions + owner: iuc + tool_panel_section_id: '' +- name: mgnify_pipelines_toolkit_make_asv_count_table + owner: iuc + tool_panel_section_id: '' +- name: mgnify_pipelines_toolkit_mapseq_to_asv_table + owner: iuc + tool_panel_section_id: '' +- name: mgnify_pipelines_toolkit_permute_primers + owner: iuc + tool_panel_section_id: '' +- name: mgnify_pipelines_toolkit_primer_val_classification + owner: iuc + tool_panel_section_id: '' +- name: mgnify_pipelines_toolkit_rev_comp_se_primers + owner: iuc + tool_panel_section_id: '' - name: mgnify_seqprep owner: bgruening tool_panel_section_id: '' @@ -761,6 +788,12 @@ tools: - name: miniprot_index owner: iuc tool_panel_section_id: '' +- name: mist_call + owner: iuc + tool_panel_section_id: '' +- name: mist_dists + owner: iuc + tool_panel_section_id: '' - name: mitos owner: iuc tool_panel_section_id: '' @@ -812,6 +845,9 @@ tools: - name: msstatstmt owner: galaxyp tool_panel_section_id: '' +- name: mtnucratio + owner: iuc + tool_panel_section_id: '' - name: multigsea owner: iuc tool_panel_section_id: '' @@ -902,6 +938,9 @@ tools: - name: obi_clean owner: iuc tool_panel_section_id: '' +- name: obi_complement + owner: iuc + tool_panel_section_id: '' - name: obi_convert owner: iuc tool_panel_section_id: '' @@ -914,6 +953,18 @@ tools: - name: obi_pairing owner: iuc tool_panel_section_id: '' +- name: obi_pcr + owner: iuc + tool_panel_section_id: '' +- name: obi_refidx + owner: iuc + tool_panel_section_id: '' +- name: obi_tag + owner: iuc + tool_panel_section_id: '' +- name: obi_taxonomy + owner: iuc + tool_panel_section_id: '' - name: obi_uniq owner: iuc tool_panel_section_id: '' @@ -1547,6 +1598,9 @@ tools: - name: proteinortho_summary owner: iuc tool_panel_section_id: '' +- name: psauron + owner: iuc + tool_panel_section_id: '' - name: pycoqc owner: iuc tool_panel_section_id: '' @@ -1646,262 +1700,241 @@ tools: - name: qiime_validate_mapping_file owner: iuc tool_panel_section_id: '' -- name: qiime2_core__tools__export - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2_core__tools__import - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2_core__tools__import_fastq - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__quality_filter__q_score - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__cull_seqs - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__degap_seqs - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__dereplicate - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__edit_taxonomy +- name: qiime2__dada2__denoise_ccs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_classifications +- name: qiime2__dada2__denoise_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_cross_validate +- name: qiime2__dada2__denoise_pyro owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_fit_classifier +- name: qiime2__dada2__denoise_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_seqs +- name: qiime2__dada2__plot_base_transitions owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_taxonomy +- name: qiime2__cutadapt__demux_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__extract_seq_segments +- name: qiime2__cutadapt__demux_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__filter_seqs_length +- name: qiime2__cutadapt__trim_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__filter_seqs_length_by_taxon +- name: qiime2__cutadapt__trim_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__filter_taxa +- name: qiime2__composition__add_pseudocount owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_bv_brc_genome_features +- name: qiime2__composition__ancom owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_bv_brc_genomes +- name: qiime2__composition__ancombc owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_bv_brc_metadata +- name: qiime2__composition__ancombc2 owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_eukaryome_data +- name: qiime2__composition__ancombc2_visualizer owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_gtdb_data +- name: qiime2__composition__da_barplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_midori2_data +- name: qiime2__composition__tabulate owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_ncbi_data +- name: qiime2__boots__alpha owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_ncbi_data_protein +- name: qiime2__boots__alpha_average owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_ncbi_genomes +- name: qiime2__boots__alpha_collection owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_pr2_data +- name: qiime2__boots__beta owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_silva_data +- name: qiime2__boots__beta_average owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_unite_data +- name: qiime2__boots__beta_collection owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__merge_taxa +- name: qiime2__boots__core_metrics owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__orient_reads +- name: qiime2__boots__kmer_diversity owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__orient_seqs +- name: qiime2__boots__resample owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__parse_silva_taxonomy +- name: qiime2__vsearch__cluster_features_closed_reference owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__reverse_transcribe +- name: qiime2__vsearch__cluster_features_de_novo owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__subsample_fasta +- name: qiime2__vsearch__cluster_features_open_reference owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__trim_alignment +- name: qiime2__vsearch__dereplicate_sequences owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__classify_samples +- name: qiime2__vsearch__fastq_stats owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__classify_samples_from_dist +- name: qiime2__vsearch__merge_pairs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__classify_samples_ncv +- name: qiime2__vsearch__uchime_denovo owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__confusion_matrix +- name: qiime2__vsearch__uchime_ref owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__fit_classifier +- name: qiime2__demux__emp_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__fit_regressor +- name: qiime2__demux__emp_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__heatmap +- name: qiime2__demux__filter_samples owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__metatable +- name: qiime2__demux__partition_samples_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__predict_classification +- name: qiime2__demux__partition_samples_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__predict_regression +- name: qiime2__demux__subsample_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__regress_samples +- name: qiime2__demux__subsample_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__regress_samples_ncv +- name: qiime2__demux__summarize owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__scatterplot +- name: qiime2__demux__tabulate_read_counts owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__split_table +- name: qiime2__deblur__denoise_16S owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__summarize +- name: qiime2__deblur__denoise_other owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__align_to_tree_mafft_fasttree +- name: qiime2__deblur__visualize_stats owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__align_to_tree_mafft_iqtree +- name: qiime2__diversity__adonis owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__align_to_tree_mafft_raxml +- name: qiime2__diversity__alpha owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__fasttree +- name: qiime2__diversity__alpha_correlation owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__filter_table +- name: qiime2__diversity__alpha_group_significance owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__filter_tree +- name: qiime2__diversity__alpha_phylogenetic owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__iqtree +- name: qiime2__diversity__alpha_rarefaction owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__iqtree_ultrafast_bootstrap +- name: qiime2__diversity__beta owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__midpoint_root +- name: qiime2__diversity__beta_correlation owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__raxml +- name: qiime2__diversity__beta_group_significance owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__raxml_rapid_bootstrap +- name: qiime2__diversity__beta_phylogenetic owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__robinson_foulds +- name: qiime2__diversity__beta_rarefaction owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__distance_matrix +- name: qiime2__diversity__bioenv owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__merge +- name: qiime2__diversity__core_metrics owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__shuffle_groups +- name: qiime2__diversity__core_metrics_phylogenetic owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__tabulate +- name: qiime2__diversity__filter_alpha_diversity owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__alpha_group_significance +- name: qiime2__diversity__filter_distance_matrix owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__collate_stats +- name: qiime2__diversity__mantel owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__facet_across +- name: qiime2__diversity__partial_procrustes owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__facet_within +- name: qiime2__diversity__pcoa owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__mann_whitney_u +- name: qiime2__diversity__pcoa_biplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__mann_whitney_u_facet +- name: qiime2__diversity__procrustes_analysis owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__plot_rainclouds +- name: qiime2__diversity__tsne owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__prep_alpha_distribution +- name: qiime2__diversity__umap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__wilcoxon_srt +- name: qiime2__emperor__biplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__wilcoxon_srt_facet +- name: qiime2__emperor__plot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__bowtie2_build +- name: qiime2__emperor__procrustes_plot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__decontam_identify +- name: qiime2_core__tools__export owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__decontam_identify_batches +- name: qiime2_core__tools__import owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__decontam_score_viz +- name: qiime2_core__tools__import_fastq owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__evaluate_composition +- name: qiime2__taxa__barplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__evaluate_seqs +- name: qiime2__taxa__barplot2 owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__evaluate_taxonomy +- name: qiime2__taxa__collapse owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__exclude_seqs +- name: qiime2__taxa__filter_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__filter_reads +- name: qiime2__taxa__filter_table owner: q2d2 tool_panel_section_id: '' - name: qiime2__diversity_lib__alpha_passthrough @@ -1940,253 +1973,244 @@ tools: - name: qiime2__diversity_lib__weighted_unifrac owner: q2d2 tool_panel_section_id: '' -- name: qiime2__alignment__mafft - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__alignment__mafft_add - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__alignment__mask - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__vizard__boxplot +- name: qiime2__stats__alpha_group_significance owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vizard__heatmap +- name: qiime2__stats__collate_stats owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vizard__lineplot +- name: qiime2__stats__facet_across owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vizard__scatterplot_2d +- name: qiime2__stats__facet_within owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__adonis +- name: qiime2__stats__mann_whitney_u owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha +- name: qiime2__stats__mann_whitney_u_facet owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_correlation +- name: qiime2__stats__plot_rainclouds owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_group_significance +- name: qiime2__stats__prep_alpha_distribution owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_phylogenetic +- name: qiime2__stats__wilcoxon_srt owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_rarefaction +- name: qiime2__stats__wilcoxon_srt_facet owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta +- name: qiime2__sample_classifier__classify_samples owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_correlation +- name: qiime2__sample_classifier__classify_samples_from_dist owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_group_significance +- name: qiime2__sample_classifier__classify_samples_ncv owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_phylogenetic +- name: qiime2__sample_classifier__confusion_matrix owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_rarefaction +- name: qiime2__sample_classifier__fit_classifier owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__bioenv +- name: qiime2__sample_classifier__fit_regressor owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__core_metrics +- name: qiime2__sample_classifier__heatmap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__core_metrics_phylogenetic +- name: qiime2__sample_classifier__metatable owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__filter_alpha_diversity +- name: qiime2__sample_classifier__predict_classification owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__filter_distance_matrix +- name: qiime2__sample_classifier__predict_regression owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__mantel +- name: qiime2__sample_classifier__regress_samples owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__partial_procrustes +- name: qiime2__sample_classifier__regress_samples_ncv owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__pcoa +- name: qiime2__sample_classifier__scatterplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__pcoa_biplot +- name: qiime2__sample_classifier__split_table owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__procrustes_analysis +- name: qiime2__sample_classifier__summarize owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__tsne +- name: qiime2__rescript__cull_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__umap +- name: qiime2__rescript__degap_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__emp_paired +- name: qiime2__rescript__dereplicate owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__emp_single +- name: qiime2__rescript__edit_taxonomy owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__filter_samples +- name: qiime2__rescript__evaluate_classifications owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__partition_samples_paired +- name: qiime2__rescript__evaluate_cross_validate owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__partition_samples_single +- name: qiime2__rescript__evaluate_fit_classifier owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__subsample_paired +- name: qiime2__rescript__evaluate_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__subsample_single +- name: qiime2__rescript__evaluate_taxonomy owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__summarize +- name: qiime2__rescript__extract_seq_segments owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__tabulate_read_counts +- name: qiime2__rescript__filter_seqs_length owner: q2d2 tool_panel_section_id: '' -- name: qiime2__deblur__denoise_16S +- name: qiime2__rescript__filter_seqs_length_by_taxon owner: q2d2 tool_panel_section_id: '' -- name: qiime2__deblur__denoise_other +- name: qiime2__rescript__filter_taxa owner: q2d2 tool_panel_section_id: '' -- name: qiime2__deblur__visualize_stats +- name: qiime2__rescript__get_bv_brc_genome_features owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_ccs +- name: qiime2__rescript__get_bv_brc_genomes owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_paired +- name: qiime2__rescript__get_bv_brc_metadata owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_pyro +- name: qiime2__rescript__get_eukaryome_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_single +- name: qiime2__rescript__get_gtdb_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__plot_base_transitions +- name: qiime2__rescript__get_midori2_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__cutadapt__demux_paired +- name: qiime2__rescript__get_ncbi_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__cutadapt__demux_single +- name: qiime2__rescript__get_ncbi_data_protein owner: q2d2 tool_panel_section_id: '' -- name: qiime2__cutadapt__trim_paired +- name: qiime2__rescript__get_ncbi_genomes owner: q2d2 tool_panel_section_id: '' -- name: qiime2__cutadapt__trim_single +- name: qiime2__rescript__get_pr2_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__add_pseudocount +- name: qiime2__rescript__get_silva_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancom +- name: qiime2__rescript__get_unite_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancombc +- name: qiime2__rescript__merge_taxa owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancombc2 +- name: qiime2__rescript__orient_reads owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancombc2_visualizer +- name: qiime2__rescript__orient_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__da_barplot +- name: qiime2__rescript__parse_silva_taxonomy owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__tabulate +- name: qiime2__rescript__reverse_transcribe owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__barplot +- name: qiime2__rescript__subsample_fasta owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__barplot2 +- name: qiime2__rescript__trim_alignment owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__collapse +- name: qiime2__quality_filter__q_score owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__filter_seqs +- name: qiime2__vizard__boxplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__filter_table +- name: qiime2__vizard__heatmap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__alpha +- name: qiime2__vizard__lineplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__alpha_average +- name: qiime2__vizard__scatterplot_2d owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__alpha_collection +- name: qiime2__alignment__mafft owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__beta +- name: qiime2__alignment__mafft_add owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__beta_average +- name: qiime2__alignment__mask owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__beta_collection +- name: qiime2__phylogeny__align_to_tree_mafft_fasttree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__core_metrics +- name: qiime2__phylogeny__align_to_tree_mafft_iqtree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__kmer_diversity +- name: qiime2__phylogeny__align_to_tree_mafft_raxml owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__resample +- name: qiime2__phylogeny__fasttree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__cluster_features_closed_reference +- name: qiime2__phylogeny__filter_table owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__cluster_features_de_novo +- name: qiime2__phylogeny__filter_tree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__cluster_features_open_reference +- name: qiime2__phylogeny__iqtree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__dereplicate_sequences +- name: qiime2__phylogeny__iqtree_ultrafast_bootstrap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__fastq_stats +- name: qiime2__phylogeny__midpoint_root owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__merge_pairs +- name: qiime2__phylogeny__raxml owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__uchime_denovo +- name: qiime2__phylogeny__raxml_rapid_bootstrap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__uchime_ref +- name: qiime2__phylogeny__robinson_foulds owner: q2d2 tool_panel_section_id: '' -- name: qiime2__emperor__biplot +- name: qiime2__fragment_insertion__classify_otus_experimental owner: q2d2 tool_panel_section_id: '' -- name: qiime2__emperor__plot +- name: qiime2__fragment_insertion__filter_features owner: q2d2 tool_panel_section_id: '' -- name: qiime2__emperor__procrustes_plot +- name: qiime2__fragment_insertion__sepp owner: q2d2 tool_panel_section_id: '' - name: qiime2__feature_classifier__blast @@ -2222,6 +2246,39 @@ tools: - name: qiime2__feature_classifier__vsearch_global owner: q2d2 tool_panel_section_id: '' +- name: qiime2__longitudinal__anova + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__feature_volatility + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__first_differences + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__first_distances + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__linear_mixed_effects + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__maturity_index + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__nmit + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__pairwise_differences + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__pairwise_distances + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__plot_feature_volatility + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__volatility + owner: q2d2 + tool_panel_section_id: '' - name: qiime2__feature_table___summarize owner: q2d2 tool_panel_section_id: '' @@ -2291,76 +2348,73 @@ tools: - name: qiime2__feature_table__transpose owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue___get_sequences - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__fondue__combine_seqs +- name: qiime2__quality_control__bowtie2_build owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__get_all +- name: qiime2__quality_control__decontam_identify owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__get_ids_from_query +- name: qiime2__quality_control__decontam_identify_batches owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__get_metadata +- name: qiime2__quality_control__decontam_score_viz owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__get_sequences +- name: qiime2__quality_control__evaluate_composition owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__merge_metadata +- name: qiime2__quality_control__evaluate_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__scrape_collection +- name: qiime2__quality_control__evaluate_taxonomy owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fragment_insertion__classify_otus_experimental +- name: qiime2__quality_control__exclude_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fragment_insertion__filter_features +- name: qiime2__quality_control__filter_reads owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fragment_insertion__sepp +- name: qiime2__metadata__distance_matrix owner: q2d2 tool_panel_section_id: '' -- name: qiime2__kmerizer__core_metrics +- name: qiime2__metadata__merge owner: q2d2 tool_panel_section_id: '' -- name: qiime2__kmerizer__seqs_to_kmers +- name: qiime2__metadata__shuffle_groups owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__anova +- name: qiime2__metadata__tabulate owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__feature_volatility +- name: qiime2__kmerizer__core_metrics owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__first_differences +- name: qiime2__kmerizer__seqs_to_kmers owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__first_distances +- name: qiime2__fondue___get_sequences owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__linear_mixed_effects +- name: qiime2__fondue__combine_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__maturity_index +- name: qiime2__fondue__get_all owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__nmit +- name: qiime2__fondue__get_ids_from_query owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__pairwise_differences +- name: qiime2__fondue__get_metadata owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__pairwise_distances +- name: qiime2__fondue__get_sequences owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__plot_feature_volatility +- name: qiime2__fondue__merge_metadata owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__volatility +- name: qiime2__fondue__scrape_collection owner: q2d2 tool_panel_section_id: '' - name: qiime2_dbotu_q2 @@ -2396,6 +2450,27 @@ tools: - name: repeatexplorer_clustering owner: gga tool_panel_section_id: '' +- name: samestr_compare + owner: iuc + tool_panel_section_id: '' +- name: samestr_convert + owner: iuc + tool_panel_section_id: '' +- name: samestr_extract + owner: iuc + tool_panel_section_id: '' +- name: samestr_filter + owner: iuc + tool_panel_section_id: '' +- name: samestr_merge + owner: iuc + tool_panel_section_id: '' +- name: samestr_stats + owner: iuc + tool_panel_section_id: '' +- name: samestr_summarize + owner: iuc + tool_panel_section_id: '' - name: scoary owner: iuc tool_panel_section_id: '' @@ -2502,10 +2577,10 @@ tools: owner: artbio tool_panel_section_id: '' - name: srst2 - owner: iuc + owner: nml tool_panel_section_id: '' - name: srst2 - owner: nml + owner: iuc tool_panel_section_id: '' - name: stringmlst owner: nml @@ -2579,6 +2654,12 @@ tools: - name: varvamp owner: iuc tool_panel_section_id: '' +- name: vcontact2 + owner: iuc + tool_panel_section_id: '' +- name: vcontact2_gene2genome + owner: iuc + tool_panel_section_id: '' - name: velvetg owner: devteam tool_panel_section_id: '' diff --git a/communities/microgalaxy/lab/tools/all/UseGalaxy_org_Main.yaml b/communities/microgalaxy/lab/tools/all/UseGalaxy_org_Main.yaml index 77ff3cfd8..e147c2916 100644 --- a/communities/microgalaxy/lab/tools/all/UseGalaxy_org_Main.yaml +++ b/communities/microgalaxy/lab/tools/all/UseGalaxy_org_Main.yaml @@ -494,15 +494,15 @@ tools: - name: kmer2stats owner: iuc tool_panel_section_id: '' -- name: kmetashot - owner: bgruening - tool_panel_section_id: '' - name: kmindex_build owner: iuc tool_panel_section_id: '' - name: kmindex_query owner: iuc tool_panel_section_id: '' +- name: kneaddata + owner: iuc + tool_panel_section_id: '' - name: kofamscan owner: iuc tool_panel_section_id: '' @@ -626,6 +626,27 @@ tools: - name: mg_toolkit_original_metadata owner: iuc tool_panel_section_id: '' +- name: mgnify_genome_search + owner: iuc + tool_panel_section_id: '' +- name: mgnify_pipelines_toolkit_classify_var_regions + owner: iuc + tool_panel_section_id: '' +- name: mgnify_pipelines_toolkit_make_asv_count_table + owner: iuc + tool_panel_section_id: '' +- name: mgnify_pipelines_toolkit_mapseq_to_asv_table + owner: iuc + tool_panel_section_id: '' +- name: mgnify_pipelines_toolkit_permute_primers + owner: iuc + tool_panel_section_id: '' +- name: mgnify_pipelines_toolkit_primer_val_classification + owner: iuc + tool_panel_section_id: '' +- name: mgnify_pipelines_toolkit_rev_comp_se_primers + owner: iuc + tool_panel_section_id: '' - name: micro_decon owner: iuc tool_panel_section_id: '' @@ -635,6 +656,12 @@ tools: - name: minipolish owner: bgruening tool_panel_section_id: '' +- name: mist_call + owner: iuc + tool_panel_section_id: '' +- name: mist_dists + owner: iuc + tool_panel_section_id: '' - name: mitos owner: iuc tool_panel_section_id: '' @@ -683,6 +710,9 @@ tools: - name: mrbayes owner: nml tool_panel_section_id: '' +- name: mtnucratio + owner: iuc + tool_panel_section_id: '' - name: multigsea owner: iuc tool_panel_section_id: '' @@ -773,6 +803,9 @@ tools: - name: obi_clean owner: iuc tool_panel_section_id: '' +- name: obi_complement + owner: iuc + tool_panel_section_id: '' - name: obi_convert owner: iuc tool_panel_section_id: '' @@ -785,6 +818,18 @@ tools: - name: obi_pairing owner: iuc tool_panel_section_id: '' +- name: obi_pcr + owner: iuc + tool_panel_section_id: '' +- name: obi_refidx + owner: iuc + tool_panel_section_id: '' +- name: obi_tag + owner: iuc + tool_panel_section_id: '' +- name: obi_taxonomy + owner: iuc + tool_panel_section_id: '' - name: obi_uniq owner: iuc tool_panel_section_id: '' @@ -1388,6 +1433,9 @@ tools: - name: proteinortho_summary owner: iuc tool_panel_section_id: '' +- name: psauron + owner: iuc + tool_panel_section_id: '' - name: qiime_align_seqs owner: iuc tool_panel_section_id: '' @@ -1490,364 +1538,316 @@ tools: - name: qiime_make_otu_table owner: iuc tool_panel_section_id: '' -- name: qiime2_core__tools__export - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2_core__tools__import - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2_core__tools__import_fastq - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__cull_seqs - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__degap_seqs - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__dereplicate - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__edit_taxonomy - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_classifications - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_cross_validate - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_fit_classifier - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_seqs - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_taxonomy - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__extract_seq_segments - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__filter_seqs_length - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__filter_seqs_length_by_taxon - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__filter_taxa - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__get_bv_brc_genome_features +- name: qiime2__dada2__denoise_ccs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_bv_brc_genomes +- name: qiime2__dada2__denoise_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_bv_brc_metadata +- name: qiime2__dada2__denoise_pyro owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_eukaryome_data +- name: qiime2__dada2__denoise_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_gtdb_data +- name: qiime2__dada2__plot_base_transitions owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_midori2_data +- name: qiime2__composition__add_pseudocount owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_ncbi_data +- name: qiime2__composition__ancom owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_ncbi_data_protein +- name: qiime2__composition__ancombc owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_ncbi_genomes +- name: qiime2__composition__ancombc2 owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_pr2_data +- name: qiime2__composition__ancombc2_visualizer owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_silva_data +- name: qiime2__composition__da_barplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_unite_data +- name: qiime2__composition__tabulate owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__merge_taxa +- name: qiime2__boots__alpha owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__orient_reads +- name: qiime2__boots__alpha_average owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__orient_seqs +- name: qiime2__boots__alpha_collection owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__parse_silva_taxonomy +- name: qiime2__boots__beta owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__reverse_transcribe +- name: qiime2__boots__beta_average owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__subsample_fasta +- name: qiime2__boots__beta_collection owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__trim_alignment +- name: qiime2__boots__core_metrics owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__distance_matrix +- name: qiime2__boots__kmer_diversity owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__merge +- name: qiime2__boots__resample owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__shuffle_groups +- name: qiime2__demux__emp_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__tabulate +- name: qiime2__demux__emp_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__alpha_group_significance +- name: qiime2__demux__filter_samples owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__collate_stats +- name: qiime2__demux__partition_samples_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__facet_across +- name: qiime2__demux__partition_samples_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__facet_within +- name: qiime2__demux__subsample_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__mann_whitney_u +- name: qiime2__demux__subsample_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__mann_whitney_u_facet +- name: qiime2__demux__summarize owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__plot_rainclouds +- name: qiime2__demux__tabulate_read_counts owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__prep_alpha_distribution +- name: qiime2__diversity__adonis owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__wilcoxon_srt +- name: qiime2__diversity__alpha owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__wilcoxon_srt_facet +- name: qiime2__diversity__alpha_correlation owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__bowtie2_build +- name: qiime2__diversity__alpha_group_significance owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__decontam_identify +- name: qiime2__diversity__alpha_phylogenetic owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__decontam_identify_batches +- name: qiime2__diversity__alpha_rarefaction owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__decontam_score_viz +- name: qiime2__diversity__beta owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__evaluate_composition +- name: qiime2__diversity__beta_correlation owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__evaluate_seqs +- name: qiime2__diversity__beta_group_significance owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__evaluate_taxonomy +- name: qiime2__diversity__beta_phylogenetic owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__exclude_seqs +- name: qiime2__diversity__beta_rarefaction owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__filter_reads +- name: qiime2__diversity__bioenv owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vizard__boxplot +- name: qiime2__diversity__core_metrics owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vizard__heatmap +- name: qiime2__diversity__core_metrics_phylogenetic owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vizard__lineplot +- name: qiime2__diversity__filter_alpha_diversity owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vizard__scatterplot_2d +- name: qiime2__diversity__filter_distance_matrix owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__adonis +- name: qiime2__diversity__mantel owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha +- name: qiime2__diversity__partial_procrustes owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_correlation +- name: qiime2__diversity__pcoa owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_group_significance +- name: qiime2__diversity__pcoa_biplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_phylogenetic +- name: qiime2__diversity__procrustes_analysis owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_rarefaction +- name: qiime2__diversity__tsne owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta +- name: qiime2__diversity__umap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_correlation +- name: qiime2__taxa__barplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_group_significance +- name: qiime2__taxa__barplot2 owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_phylogenetic +- name: qiime2__taxa__collapse owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_rarefaction +- name: qiime2__taxa__filter_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__bioenv +- name: qiime2__taxa__filter_table owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__core_metrics +- name: qiime2__stats__alpha_group_significance owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__core_metrics_phylogenetic +- name: qiime2__stats__collate_stats owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__filter_alpha_diversity +- name: qiime2__stats__facet_across owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__filter_distance_matrix +- name: qiime2__stats__facet_within owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__mantel +- name: qiime2__stats__mann_whitney_u owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__partial_procrustes +- name: qiime2__stats__mann_whitney_u_facet owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__pcoa +- name: qiime2__stats__plot_rainclouds owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__pcoa_biplot +- name: qiime2__stats__prep_alpha_distribution owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__procrustes_analysis +- name: qiime2__stats__wilcoxon_srt owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__tsne +- name: qiime2__stats__wilcoxon_srt_facet owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__umap +- name: qiime2__rescript__cull_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__emp_paired +- name: qiime2__rescript__degap_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__emp_single +- name: qiime2__rescript__dereplicate owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__filter_samples +- name: qiime2__rescript__edit_taxonomy owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__partition_samples_paired +- name: qiime2__rescript__evaluate_classifications owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__partition_samples_single +- name: qiime2__rescript__evaluate_cross_validate owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__subsample_paired +- name: qiime2__rescript__evaluate_fit_classifier owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__subsample_single +- name: qiime2__rescript__evaluate_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__summarize +- name: qiime2__rescript__evaluate_taxonomy owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__tabulate_read_counts +- name: qiime2__rescript__extract_seq_segments owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_ccs +- name: qiime2__rescript__filter_seqs_length owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_paired +- name: qiime2__rescript__filter_seqs_length_by_taxon owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_pyro +- name: qiime2__rescript__filter_taxa owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_single +- name: qiime2__rescript__get_bv_brc_genome_features owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__plot_base_transitions +- name: qiime2__rescript__get_bv_brc_genomes owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__add_pseudocount +- name: qiime2__rescript__get_bv_brc_metadata owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancom +- name: qiime2__rescript__get_eukaryome_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancombc +- name: qiime2__rescript__get_gtdb_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancombc2 +- name: qiime2__rescript__get_midori2_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancombc2_visualizer +- name: qiime2__rescript__get_ncbi_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__da_barplot +- name: qiime2__rescript__get_ncbi_data_protein owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__tabulate +- name: qiime2__rescript__get_ncbi_genomes owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__barplot +- name: qiime2__rescript__get_pr2_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__barplot2 +- name: qiime2__rescript__get_silva_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__collapse +- name: qiime2__rescript__get_unite_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__filter_seqs +- name: qiime2__rescript__merge_taxa owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__filter_table +- name: qiime2__rescript__orient_reads owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__alpha +- name: qiime2__rescript__orient_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__alpha_average +- name: qiime2__rescript__parse_silva_taxonomy owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__alpha_collection +- name: qiime2__rescript__reverse_transcribe owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__beta +- name: qiime2__rescript__subsample_fasta owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__beta_average +- name: qiime2__rescript__trim_alignment owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__beta_collection +- name: qiime2__vizard__boxplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__core_metrics +- name: qiime2__vizard__heatmap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__kmer_diversity +- name: qiime2__vizard__lineplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__resample +- name: qiime2__vizard__scatterplot_2d owner: q2d2 tool_panel_section_id: '' - name: qiime2__feature_classifier__blast @@ -1952,6 +1952,51 @@ tools: - name: qiime2__feature_table__transpose owner: q2d2 tool_panel_section_id: '' +- name: qiime2__quality_control__bowtie2_build + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__quality_control__decontam_identify + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__quality_control__decontam_identify_batches + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__quality_control__decontam_score_viz + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__quality_control__evaluate_composition + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__quality_control__evaluate_seqs + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__quality_control__evaluate_taxonomy + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__quality_control__exclude_seqs + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__quality_control__filter_reads + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__metadata__distance_matrix + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__metadata__merge + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__metadata__shuffle_groups + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__metadata__tabulate + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__kmerizer__core_metrics + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__kmerizer__seqs_to_kmers + owner: q2d2 + tool_panel_section_id: '' - name: qiime2__fondue___get_sequences owner: q2d2 tool_panel_section_id: '' @@ -1976,12 +2021,6 @@ tools: - name: qiime2__fondue__scrape_collection owner: q2d2 tool_panel_section_id: '' -- name: qiime2__kmerizer__core_metrics - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__kmerizer__seqs_to_kmers - owner: q2d2 - tool_panel_section_id: '' - name: qiime2_dbotu_q2 owner: bgruening tool_panel_section_id: '' @@ -2009,6 +2048,27 @@ tools: - name: repeatexplorer_clustering owner: gga tool_panel_section_id: '' +- name: samestr_compare + owner: iuc + tool_panel_section_id: '' +- name: samestr_convert + owner: iuc + tool_panel_section_id: '' +- name: samestr_extract + owner: iuc + tool_panel_section_id: '' +- name: samestr_filter + owner: iuc + tool_panel_section_id: '' +- name: samestr_merge + owner: iuc + tool_panel_section_id: '' +- name: samestr_stats + owner: iuc + tool_panel_section_id: '' +- name: samestr_summarize + owner: iuc + tool_panel_section_id: '' - name: scoary owner: iuc tool_panel_section_id: '' @@ -2091,10 +2151,10 @@ tools: owner: artbio tool_panel_section_id: '' - name: srst2 - owner: iuc + owner: nml tool_panel_section_id: '' - name: srst2 - owner: nml + owner: iuc tool_panel_section_id: '' - name: stringmlst owner: nml @@ -2168,6 +2228,12 @@ tools: - name: varvamp owner: iuc tool_panel_section_id: '' +- name: vcontact2 + owner: iuc + tool_panel_section_id: '' +- name: vcontact2_gene2genome + owner: iuc + tool_panel_section_id: '' - name: viralverify owner: iuc tool_panel_section_id: '' diff --git a/communities/microgalaxy/lab/tools/all/UseGalaxy_org_au.yaml b/communities/microgalaxy/lab/tools/all/UseGalaxy_org_au.yaml index 247c66295..2c67ecbe0 100644 --- a/communities/microgalaxy/lab/tools/all/UseGalaxy_org_au.yaml +++ b/communities/microgalaxy/lab/tools/all/UseGalaxy_org_au.yaml @@ -521,6 +521,9 @@ tools: - name: kmindex_query owner: iuc tool_panel_section_id: '' +- name: kneaddata + owner: iuc + tool_panel_section_id: '' - name: kofamscan owner: iuc tool_panel_section_id: '' @@ -635,6 +638,27 @@ tools: - name: mg_toolkit_original_metadata owner: iuc tool_panel_section_id: '' +- name: mgnify_genome_search + owner: iuc + tool_panel_section_id: '' +- name: mgnify_pipelines_toolkit_classify_var_regions + owner: iuc + tool_panel_section_id: '' +- name: mgnify_pipelines_toolkit_make_asv_count_table + owner: iuc + tool_panel_section_id: '' +- name: mgnify_pipelines_toolkit_mapseq_to_asv_table + owner: iuc + tool_panel_section_id: '' +- name: mgnify_pipelines_toolkit_permute_primers + owner: iuc + tool_panel_section_id: '' +- name: mgnify_pipelines_toolkit_primer_val_classification + owner: iuc + tool_panel_section_id: '' +- name: mgnify_pipelines_toolkit_rev_comp_se_primers + owner: iuc + tool_panel_section_id: '' - name: mgnify_seqprep owner: bgruening tool_panel_section_id: '' @@ -650,6 +674,12 @@ tools: - name: miniprot_index owner: iuc tool_panel_section_id: '' +- name: mist_call + owner: iuc + tool_panel_section_id: '' +- name: mist_dists + owner: iuc + tool_panel_section_id: '' - name: mitos owner: iuc tool_panel_section_id: '' @@ -692,6 +722,9 @@ tools: - name: mrbayes owner: nml tool_panel_section_id: '' +- name: mtnucratio + owner: iuc + tool_panel_section_id: '' - name: mykrobe_predict owner: iuc tool_panel_section_id: '' @@ -791,6 +824,9 @@ tools: - name: obi_clean owner: iuc tool_panel_section_id: '' +- name: obi_complement + owner: iuc + tool_panel_section_id: '' - name: obi_convert owner: iuc tool_panel_section_id: '' @@ -803,6 +839,18 @@ tools: - name: obi_pairing owner: iuc tool_panel_section_id: '' +- name: obi_pcr + owner: iuc + tool_panel_section_id: '' +- name: obi_refidx + owner: iuc + tool_panel_section_id: '' +- name: obi_tag + owner: iuc + tool_panel_section_id: '' +- name: obi_taxonomy + owner: iuc + tool_panel_section_id: '' - name: obi_uniq owner: iuc tool_panel_section_id: '' @@ -1331,6 +1379,9 @@ tools: - name: ppanggolin_rarefaction owner: iuc tool_panel_section_id: '' +- name: prinseq + owner: iuc + tool_panel_section_id: '' - name: promer4_substitutions owner: nml tool_panel_section_id: '' @@ -1346,6 +1397,9 @@ tools: - name: proteinortho_summary owner: iuc tool_panel_section_id: '' +- name: psauron + owner: iuc + tool_panel_section_id: '' - name: qiime_align_seqs owner: iuc tool_panel_section_id: '' @@ -1448,355 +1502,304 @@ tools: - name: qiime_make_otu_table owner: iuc tool_panel_section_id: '' -- name: qiime2__rescript__cull_seqs - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__degap_seqs - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__dereplicate - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__edit_taxonomy - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_classifications - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_cross_validate - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_fit_classifier - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_seqs - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_taxonomy - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__extract_seq_segments - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__filter_seqs_length - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__filter_seqs_length_by_taxon - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__filter_taxa - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__get_bv_brc_genome_features - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__get_bv_brc_genomes - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__get_bv_brc_metadata - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__get_eukaryome_data - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__get_gtdb_data +- name: qiime2__dada2__denoise_ccs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_midori2_data +- name: qiime2__dada2__denoise_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_ncbi_data +- name: qiime2__dada2__denoise_pyro owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_ncbi_data_protein +- name: qiime2__dada2__denoise_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_ncbi_genomes +- name: qiime2__dada2__plot_base_transitions owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_pr2_data +- name: qiime2__composition__add_pseudocount owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_silva_data +- name: qiime2__composition__ancom owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_unite_data +- name: qiime2__composition__ancombc owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__merge_taxa +- name: qiime2__composition__ancombc2 owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__orient_reads +- name: qiime2__composition__ancombc2_visualizer owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__orient_seqs +- name: qiime2__composition__da_barplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__parse_silva_taxonomy +- name: qiime2__composition__tabulate owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__reverse_transcribe +- name: qiime2__boots__alpha owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__subsample_fasta +- name: qiime2__boots__alpha_average owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__trim_alignment +- name: qiime2__boots__alpha_collection owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__distance_matrix +- name: qiime2__boots__beta owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__merge +- name: qiime2__boots__beta_average owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__shuffle_groups +- name: qiime2__boots__beta_collection owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__tabulate +- name: qiime2__boots__core_metrics owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__alpha_group_significance +- name: qiime2__boots__kmer_diversity owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__collate_stats +- name: qiime2__boots__resample owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__facet_across +- name: qiime2__demux__emp_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__facet_within +- name: qiime2__demux__emp_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__mann_whitney_u +- name: qiime2__demux__filter_samples owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__mann_whitney_u_facet +- name: qiime2__demux__partition_samples_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__plot_rainclouds +- name: qiime2__demux__partition_samples_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__prep_alpha_distribution +- name: qiime2__demux__subsample_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__wilcoxon_srt +- name: qiime2__demux__subsample_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__wilcoxon_srt_facet +- name: qiime2__demux__summarize owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__bowtie2_build +- name: qiime2__demux__tabulate_read_counts owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__decontam_identify +- name: qiime2__diversity__adonis owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__decontam_identify_batches +- name: qiime2__diversity__alpha owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__decontam_score_viz +- name: qiime2__diversity__alpha_correlation owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__evaluate_composition +- name: qiime2__diversity__alpha_group_significance owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__evaluate_seqs +- name: qiime2__diversity__alpha_phylogenetic owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__evaluate_taxonomy +- name: qiime2__diversity__alpha_rarefaction owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__exclude_seqs +- name: qiime2__diversity__beta owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__filter_reads +- name: qiime2__diversity__beta_correlation owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vizard__boxplot +- name: qiime2__diversity__beta_group_significance owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vizard__heatmap +- name: qiime2__diversity__beta_phylogenetic owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vizard__lineplot +- name: qiime2__diversity__beta_rarefaction owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vizard__scatterplot_2d +- name: qiime2__diversity__bioenv owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__adonis +- name: qiime2__diversity__core_metrics owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha +- name: qiime2__diversity__core_metrics_phylogenetic owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_correlation +- name: qiime2__diversity__filter_alpha_diversity owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_group_significance +- name: qiime2__diversity__filter_distance_matrix owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_phylogenetic +- name: qiime2__diversity__mantel owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_rarefaction +- name: qiime2__diversity__partial_procrustes owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta +- name: qiime2__diversity__pcoa owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_correlation +- name: qiime2__diversity__pcoa_biplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_group_significance +- name: qiime2__diversity__procrustes_analysis owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_phylogenetic +- name: qiime2__diversity__tsne owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_rarefaction +- name: qiime2__diversity__umap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__bioenv +- name: qiime2__taxa__barplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__core_metrics +- name: qiime2__taxa__barplot2 owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__core_metrics_phylogenetic +- name: qiime2__taxa__collapse owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__filter_alpha_diversity +- name: qiime2__taxa__filter_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__filter_distance_matrix +- name: qiime2__taxa__filter_table owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__mantel +- name: qiime2__stats__alpha_group_significance owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__partial_procrustes +- name: qiime2__stats__collate_stats owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__pcoa +- name: qiime2__stats__facet_across owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__pcoa_biplot +- name: qiime2__stats__facet_within owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__procrustes_analysis +- name: qiime2__stats__mann_whitney_u owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__tsne +- name: qiime2__stats__mann_whitney_u_facet owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__umap +- name: qiime2__stats__plot_rainclouds owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__emp_paired +- name: qiime2__stats__prep_alpha_distribution owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__emp_single +- name: qiime2__stats__wilcoxon_srt owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__filter_samples +- name: qiime2__stats__wilcoxon_srt_facet owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__partition_samples_paired +- name: qiime2__rescript__cull_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__partition_samples_single +- name: qiime2__rescript__degap_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__subsample_paired +- name: qiime2__rescript__dereplicate owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__subsample_single +- name: qiime2__rescript__edit_taxonomy owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__summarize +- name: qiime2__rescript__evaluate_classifications owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__tabulate_read_counts +- name: qiime2__rescript__evaluate_cross_validate owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_ccs +- name: qiime2__rescript__evaluate_fit_classifier owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_paired +- name: qiime2__rescript__evaluate_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_pyro +- name: qiime2__rescript__evaluate_taxonomy owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_single +- name: qiime2__rescript__extract_seq_segments owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__plot_base_transitions +- name: qiime2__rescript__filter_seqs_length owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__add_pseudocount +- name: qiime2__rescript__filter_seqs_length_by_taxon owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancom +- name: qiime2__rescript__filter_taxa owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancombc +- name: qiime2__rescript__get_bv_brc_genome_features owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancombc2 +- name: qiime2__rescript__get_bv_brc_genomes owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancombc2_visualizer +- name: qiime2__rescript__get_bv_brc_metadata owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__da_barplot +- name: qiime2__rescript__get_eukaryome_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__tabulate +- name: qiime2__rescript__get_gtdb_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__barplot +- name: qiime2__rescript__get_midori2_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__barplot2 +- name: qiime2__rescript__get_ncbi_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__collapse +- name: qiime2__rescript__get_ncbi_data_protein owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__filter_seqs +- name: qiime2__rescript__get_ncbi_genomes owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__filter_table +- name: qiime2__rescript__get_pr2_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__alpha +- name: qiime2__rescript__get_silva_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__alpha_average +- name: qiime2__rescript__get_unite_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__alpha_collection +- name: qiime2__rescript__merge_taxa owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__beta +- name: qiime2__rescript__orient_reads owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__beta_average +- name: qiime2__rescript__orient_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__beta_collection +- name: qiime2__rescript__parse_silva_taxonomy owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__core_metrics +- name: qiime2__rescript__reverse_transcribe owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__kmer_diversity +- name: qiime2__rescript__subsample_fasta owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__resample +- name: qiime2__rescript__trim_alignment owner: q2d2 tool_panel_section_id: '' - name: qiime2__feature_classifier__blast @@ -1901,6 +1904,51 @@ tools: - name: qiime2__feature_table__transpose owner: q2d2 tool_panel_section_id: '' +- name: qiime2__quality_control__bowtie2_build + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__quality_control__decontam_identify + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__quality_control__decontam_identify_batches + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__quality_control__decontam_score_viz + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__quality_control__evaluate_composition + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__quality_control__evaluate_seqs + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__quality_control__evaluate_taxonomy + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__quality_control__exclude_seqs + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__quality_control__filter_reads + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__metadata__distance_matrix + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__metadata__merge + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__metadata__shuffle_groups + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__metadata__tabulate + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__kmerizer__core_metrics + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__kmerizer__seqs_to_kmers + owner: q2d2 + tool_panel_section_id: '' - name: qiime2__fondue___get_sequences owner: q2d2 tool_panel_section_id: '' @@ -1925,12 +1973,6 @@ tools: - name: qiime2__fondue__scrape_collection owner: q2d2 tool_panel_section_id: '' -- name: qiime2__kmerizer__core_metrics - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__kmerizer__seqs_to_kmers - owner: q2d2 - tool_panel_section_id: '' - name: qiime2_dbotu_q2 owner: bgruening tool_panel_section_id: '' @@ -1964,6 +2006,27 @@ tools: - name: repeatexplorer_clustering owner: gga tool_panel_section_id: '' +- name: samestr_compare + owner: iuc + tool_panel_section_id: '' +- name: samestr_convert + owner: iuc + tool_panel_section_id: '' +- name: samestr_extract + owner: iuc + tool_panel_section_id: '' +- name: samestr_filter + owner: iuc + tool_panel_section_id: '' +- name: samestr_merge + owner: iuc + tool_panel_section_id: '' +- name: samestr_stats + owner: iuc + tool_panel_section_id: '' +- name: samestr_summarize + owner: iuc + tool_panel_section_id: '' - name: scoary owner: iuc tool_panel_section_id: '' @@ -2019,10 +2082,10 @@ tools: owner: artbio tool_panel_section_id: '' - name: srst2 - owner: iuc + owner: nml tool_panel_section_id: '' - name: srst2 - owner: nml + owner: iuc tool_panel_section_id: '' - name: stringmlst owner: nml @@ -2030,12 +2093,6 @@ tools: - name: '' owner: q2d2 tool_panel_section_id: '' -- name: sylph_profile - owner: bgruening - tool_panel_section_id: '' -- name: sylph_query - owner: bgruening - tool_panel_section_id: '' - name: syri owner: iuc tool_panel_section_id: '' @@ -2084,6 +2141,12 @@ tools: - name: varvamp owner: iuc tool_panel_section_id: '' +- name: vcontact2 + owner: iuc + tool_panel_section_id: '' +- name: vcontact2_gene2genome + owner: iuc + tool_panel_section_id: '' - name: vegan_diversity owner: iuc tool_panel_section_id: '' diff --git a/communities/microgalaxy/lab/tools/all/Viral_Variant_Visualizer_VVV.yaml b/communities/microgalaxy/lab/tools/all/Viral_Variant_Visualizer_VVV.yaml index 74873501c..bce8b9a6b 100644 --- a/communities/microgalaxy/lab/tools/all/Viral_Variant_Visualizer_VVV.yaml +++ b/communities/microgalaxy/lab/tools/all/Viral_Variant_Visualizer_VVV.yaml @@ -1226,6 +1226,9 @@ tools: - name: kmindex_query owner: iuc tool_panel_section_id: '' +- name: kneaddata + owner: iuc + tool_panel_section_id: '' - name: kofamscan owner: iuc tool_panel_section_id: '' @@ -1283,6 +1286,9 @@ tools: - name: legsta owner: iuc tool_panel_section_id: '' +- name: liftoff + owner: iuc + tool_panel_section_id: '' - name: lighter owner: bgruening tool_panel_section_id: '' @@ -1502,6 +1508,27 @@ tools: - name: mg_toolkit_original_metadata owner: iuc tool_panel_section_id: '' +- name: mgnify_genome_search + owner: iuc + tool_panel_section_id: '' +- name: mgnify_pipelines_toolkit_classify_var_regions + owner: iuc + tool_panel_section_id: '' +- name: mgnify_pipelines_toolkit_make_asv_count_table + owner: iuc + tool_panel_section_id: '' +- name: mgnify_pipelines_toolkit_mapseq_to_asv_table + owner: iuc + tool_panel_section_id: '' +- name: mgnify_pipelines_toolkit_permute_primers + owner: iuc + tool_panel_section_id: '' +- name: mgnify_pipelines_toolkit_primer_val_classification + owner: iuc + tool_panel_section_id: '' +- name: mgnify_pipelines_toolkit_rev_comp_se_primers + owner: iuc + tool_panel_section_id: '' - name: mgnify_seqprep owner: bgruening tool_panel_section_id: '' @@ -1523,6 +1550,12 @@ tools: - name: miniprot_index owner: iuc tool_panel_section_id: '' +- name: mist_call + owner: iuc + tool_panel_section_id: '' +- name: mist_dists + owner: iuc + tool_panel_section_id: '' - name: mitos owner: iuc tool_panel_section_id: '' @@ -1973,6 +2006,9 @@ tools: - name: msstats owner: galaxyp tool_panel_section_id: '' +- name: mtnucratio + owner: iuc + tool_panel_section_id: '' - name: multigsea owner: iuc tool_panel_section_id: '' @@ -2090,6 +2126,9 @@ tools: - name: obi_clean owner: iuc tool_panel_section_id: '' +- name: obi_complement + owner: iuc + tool_panel_section_id: '' - name: obi_convert owner: iuc tool_panel_section_id: '' @@ -2102,6 +2141,18 @@ tools: - name: obi_pairing owner: iuc tool_panel_section_id: '' +- name: obi_pcr + owner: iuc + tool_panel_section_id: '' +- name: obi_refidx + owner: iuc + tool_panel_section_id: '' +- name: obi_tag + owner: iuc + tool_panel_section_id: '' +- name: obi_taxonomy + owner: iuc + tool_panel_section_id: '' - name: obi_uniq owner: iuc tool_panel_section_id: '' @@ -2723,6 +2774,9 @@ tools: - name: ppanggolin_rarefaction owner: iuc tool_panel_section_id: '' +- name: prinseq + owner: iuc + tool_panel_section_id: '' - name: prodigal owner: iuc tool_panel_section_id: '' @@ -2744,6 +2798,9 @@ tools: - name: proteinortho_summary owner: iuc tool_panel_section_id: '' +- name: psauron + owner: iuc + tool_panel_section_id: '' - name: pycoqc owner: iuc tool_panel_section_id: '' @@ -2852,262 +2909,241 @@ tools: - name: qiime_make_otu_table owner: iuc tool_panel_section_id: '' -- name: qiime2_core__tools__export - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2_core__tools__import - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2_core__tools__import_fastq - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__quality_filter__q_score - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__cull_seqs - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__degap_seqs - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__dereplicate - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__edit_taxonomy +- name: qiime2__dada2__denoise_ccs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_classifications +- name: qiime2__dada2__denoise_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_cross_validate +- name: qiime2__dada2__denoise_pyro owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_fit_classifier +- name: qiime2__dada2__denoise_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_seqs +- name: qiime2__dada2__plot_base_transitions owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_taxonomy +- name: qiime2__cutadapt__demux_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__extract_seq_segments +- name: qiime2__cutadapt__demux_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__filter_seqs_length +- name: qiime2__cutadapt__trim_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__filter_seqs_length_by_taxon +- name: qiime2__cutadapt__trim_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__filter_taxa +- name: qiime2__composition__add_pseudocount owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_bv_brc_genome_features +- name: qiime2__composition__ancom owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_bv_brc_genomes +- name: qiime2__composition__ancombc owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_bv_brc_metadata +- name: qiime2__composition__ancombc2 owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_eukaryome_data +- name: qiime2__composition__ancombc2_visualizer owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_gtdb_data +- name: qiime2__composition__da_barplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_midori2_data +- name: qiime2__composition__tabulate owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_ncbi_data +- name: qiime2__boots__alpha owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_ncbi_data_protein +- name: qiime2__boots__alpha_average owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_ncbi_genomes +- name: qiime2__boots__alpha_collection owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_pr2_data +- name: qiime2__boots__beta owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_silva_data +- name: qiime2__boots__beta_average owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_unite_data +- name: qiime2__boots__beta_collection owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__merge_taxa +- name: qiime2__boots__core_metrics owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__orient_reads +- name: qiime2__boots__kmer_diversity owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__orient_seqs +- name: qiime2__boots__resample owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__parse_silva_taxonomy +- name: qiime2__vsearch__cluster_features_closed_reference owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__reverse_transcribe +- name: qiime2__vsearch__cluster_features_de_novo owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__subsample_fasta +- name: qiime2__vsearch__cluster_features_open_reference owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__trim_alignment +- name: qiime2__vsearch__dereplicate_sequences owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__classify_samples +- name: qiime2__vsearch__fastq_stats owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__classify_samples_from_dist +- name: qiime2__vsearch__merge_pairs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__classify_samples_ncv +- name: qiime2__vsearch__uchime_denovo owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__confusion_matrix +- name: qiime2__vsearch__uchime_ref owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__fit_classifier +- name: qiime2__demux__emp_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__fit_regressor +- name: qiime2__demux__emp_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__heatmap +- name: qiime2__demux__filter_samples owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__metatable +- name: qiime2__demux__partition_samples_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__predict_classification +- name: qiime2__demux__partition_samples_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__predict_regression +- name: qiime2__demux__subsample_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__regress_samples +- name: qiime2__demux__subsample_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__regress_samples_ncv +- name: qiime2__demux__summarize owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__scatterplot +- name: qiime2__demux__tabulate_read_counts owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__split_table +- name: qiime2__deblur__denoise_16S owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__summarize +- name: qiime2__deblur__denoise_other owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__align_to_tree_mafft_fasttree +- name: qiime2__deblur__visualize_stats owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__align_to_tree_mafft_iqtree +- name: qiime2__diversity__adonis owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__align_to_tree_mafft_raxml +- name: qiime2__diversity__alpha owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__fasttree +- name: qiime2__diversity__alpha_correlation owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__filter_table +- name: qiime2__diversity__alpha_group_significance owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__filter_tree +- name: qiime2__diversity__alpha_phylogenetic owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__iqtree +- name: qiime2__diversity__alpha_rarefaction owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__iqtree_ultrafast_bootstrap +- name: qiime2__diversity__beta owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__midpoint_root +- name: qiime2__diversity__beta_correlation owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__raxml +- name: qiime2__diversity__beta_group_significance owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__raxml_rapid_bootstrap +- name: qiime2__diversity__beta_phylogenetic owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__robinson_foulds +- name: qiime2__diversity__beta_rarefaction owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__distance_matrix +- name: qiime2__diversity__bioenv owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__merge +- name: qiime2__diversity__core_metrics owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__shuffle_groups +- name: qiime2__diversity__core_metrics_phylogenetic owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__tabulate +- name: qiime2__diversity__filter_alpha_diversity owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__alpha_group_significance +- name: qiime2__diversity__filter_distance_matrix owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__collate_stats +- name: qiime2__diversity__mantel owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__facet_across +- name: qiime2__diversity__partial_procrustes owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__facet_within +- name: qiime2__diversity__pcoa owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__mann_whitney_u +- name: qiime2__diversity__pcoa_biplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__mann_whitney_u_facet +- name: qiime2__diversity__procrustes_analysis owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__plot_rainclouds +- name: qiime2__diversity__tsne owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__prep_alpha_distribution +- name: qiime2__diversity__umap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__wilcoxon_srt +- name: qiime2__emperor__biplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__wilcoxon_srt_facet +- name: qiime2__emperor__plot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__bowtie2_build +- name: qiime2__emperor__procrustes_plot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__decontam_identify +- name: qiime2_core__tools__export owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__decontam_identify_batches +- name: qiime2_core__tools__import owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__decontam_score_viz +- name: qiime2_core__tools__import_fastq owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__evaluate_composition +- name: qiime2__taxa__barplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__evaluate_seqs +- name: qiime2__taxa__barplot2 owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__evaluate_taxonomy +- name: qiime2__taxa__collapse owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__exclude_seqs +- name: qiime2__taxa__filter_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__filter_reads +- name: qiime2__taxa__filter_table owner: q2d2 tool_panel_section_id: '' - name: qiime2__diversity_lib__alpha_passthrough @@ -3146,253 +3182,244 @@ tools: - name: qiime2__diversity_lib__weighted_unifrac owner: q2d2 tool_panel_section_id: '' -- name: qiime2__alignment__mafft - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__alignment__mafft_add - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__alignment__mask - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__vizard__boxplot +- name: qiime2__stats__alpha_group_significance owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vizard__heatmap +- name: qiime2__stats__collate_stats owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vizard__lineplot +- name: qiime2__stats__facet_across owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vizard__scatterplot_2d +- name: qiime2__stats__facet_within owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__adonis +- name: qiime2__stats__mann_whitney_u owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha +- name: qiime2__stats__mann_whitney_u_facet owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_correlation +- name: qiime2__stats__plot_rainclouds owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_group_significance +- name: qiime2__stats__prep_alpha_distribution owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_phylogenetic +- name: qiime2__stats__wilcoxon_srt owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_rarefaction +- name: qiime2__stats__wilcoxon_srt_facet owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta +- name: qiime2__sample_classifier__classify_samples owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_correlation +- name: qiime2__sample_classifier__classify_samples_from_dist owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_group_significance +- name: qiime2__sample_classifier__classify_samples_ncv owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_phylogenetic +- name: qiime2__sample_classifier__confusion_matrix owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_rarefaction +- name: qiime2__sample_classifier__fit_classifier owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__bioenv +- name: qiime2__sample_classifier__fit_regressor owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__core_metrics +- name: qiime2__sample_classifier__heatmap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__core_metrics_phylogenetic +- name: qiime2__sample_classifier__metatable owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__filter_alpha_diversity +- name: qiime2__sample_classifier__predict_classification owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__filter_distance_matrix +- name: qiime2__sample_classifier__predict_regression owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__mantel +- name: qiime2__sample_classifier__regress_samples owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__partial_procrustes +- name: qiime2__sample_classifier__regress_samples_ncv owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__pcoa +- name: qiime2__sample_classifier__scatterplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__pcoa_biplot +- name: qiime2__sample_classifier__split_table owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__procrustes_analysis +- name: qiime2__sample_classifier__summarize owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__tsne +- name: qiime2__rescript__cull_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__umap +- name: qiime2__rescript__degap_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__emp_paired +- name: qiime2__rescript__dereplicate owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__emp_single +- name: qiime2__rescript__edit_taxonomy owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__filter_samples +- name: qiime2__rescript__evaluate_classifications owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__partition_samples_paired +- name: qiime2__rescript__evaluate_cross_validate owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__partition_samples_single +- name: qiime2__rescript__evaluate_fit_classifier owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__subsample_paired +- name: qiime2__rescript__evaluate_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__subsample_single +- name: qiime2__rescript__evaluate_taxonomy owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__summarize +- name: qiime2__rescript__extract_seq_segments owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__tabulate_read_counts +- name: qiime2__rescript__filter_seqs_length owner: q2d2 tool_panel_section_id: '' -- name: qiime2__deblur__denoise_16S +- name: qiime2__rescript__filter_seqs_length_by_taxon owner: q2d2 tool_panel_section_id: '' -- name: qiime2__deblur__denoise_other +- name: qiime2__rescript__filter_taxa owner: q2d2 tool_panel_section_id: '' -- name: qiime2__deblur__visualize_stats +- name: qiime2__rescript__get_bv_brc_genome_features owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_ccs +- name: qiime2__rescript__get_bv_brc_genomes owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_paired +- name: qiime2__rescript__get_bv_brc_metadata owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_pyro +- name: qiime2__rescript__get_eukaryome_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_single +- name: qiime2__rescript__get_gtdb_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__plot_base_transitions +- name: qiime2__rescript__get_midori2_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__cutadapt__demux_paired +- name: qiime2__rescript__get_ncbi_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__cutadapt__demux_single +- name: qiime2__rescript__get_ncbi_data_protein owner: q2d2 tool_panel_section_id: '' -- name: qiime2__cutadapt__trim_paired +- name: qiime2__rescript__get_ncbi_genomes owner: q2d2 tool_panel_section_id: '' -- name: qiime2__cutadapt__trim_single +- name: qiime2__rescript__get_pr2_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__add_pseudocount +- name: qiime2__rescript__get_silva_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancom +- name: qiime2__rescript__get_unite_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancombc +- name: qiime2__rescript__merge_taxa owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancombc2 +- name: qiime2__rescript__orient_reads owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancombc2_visualizer +- name: qiime2__rescript__orient_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__da_barplot +- name: qiime2__rescript__parse_silva_taxonomy owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__tabulate +- name: qiime2__rescript__reverse_transcribe owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__barplot +- name: qiime2__rescript__subsample_fasta owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__barplot2 +- name: qiime2__rescript__trim_alignment owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__collapse +- name: qiime2__quality_filter__q_score owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__filter_seqs +- name: qiime2__vizard__boxplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__filter_table +- name: qiime2__vizard__heatmap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__alpha +- name: qiime2__vizard__lineplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__alpha_average +- name: qiime2__vizard__scatterplot_2d owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__alpha_collection +- name: qiime2__alignment__mafft owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__beta +- name: qiime2__alignment__mafft_add owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__beta_average +- name: qiime2__alignment__mask owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__beta_collection +- name: qiime2__phylogeny__align_to_tree_mafft_fasttree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__core_metrics +- name: qiime2__phylogeny__align_to_tree_mafft_iqtree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__kmer_diversity +- name: qiime2__phylogeny__align_to_tree_mafft_raxml owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__resample +- name: qiime2__phylogeny__fasttree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__cluster_features_closed_reference +- name: qiime2__phylogeny__filter_table owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__cluster_features_de_novo +- name: qiime2__phylogeny__filter_tree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__cluster_features_open_reference +- name: qiime2__phylogeny__iqtree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__dereplicate_sequences +- name: qiime2__phylogeny__iqtree_ultrafast_bootstrap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__fastq_stats +- name: qiime2__phylogeny__midpoint_root owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__merge_pairs +- name: qiime2__phylogeny__raxml owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__uchime_denovo +- name: qiime2__phylogeny__raxml_rapid_bootstrap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__uchime_ref +- name: qiime2__phylogeny__robinson_foulds owner: q2d2 tool_panel_section_id: '' -- name: qiime2__emperor__biplot +- name: qiime2__fragment_insertion__classify_otus_experimental owner: q2d2 tool_panel_section_id: '' -- name: qiime2__emperor__plot +- name: qiime2__fragment_insertion__filter_features owner: q2d2 tool_panel_section_id: '' -- name: qiime2__emperor__procrustes_plot +- name: qiime2__fragment_insertion__sepp owner: q2d2 tool_panel_section_id: '' - name: qiime2__feature_classifier__blast @@ -3428,6 +3455,39 @@ tools: - name: qiime2__feature_classifier__vsearch_global owner: q2d2 tool_panel_section_id: '' +- name: qiime2__longitudinal__anova + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__feature_volatility + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__first_differences + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__first_distances + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__linear_mixed_effects + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__maturity_index + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__nmit + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__pairwise_differences + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__pairwise_distances + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__plot_feature_volatility + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__volatility + owner: q2d2 + tool_panel_section_id: '' - name: qiime2__feature_table___summarize owner: q2d2 tool_panel_section_id: '' @@ -3497,76 +3557,73 @@ tools: - name: qiime2__feature_table__transpose owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue___get_sequences - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__fondue__combine_seqs +- name: qiime2__quality_control__bowtie2_build owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__get_all +- name: qiime2__quality_control__decontam_identify owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__get_ids_from_query +- name: qiime2__quality_control__decontam_identify_batches owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__get_metadata +- name: qiime2__quality_control__decontam_score_viz owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__get_sequences +- name: qiime2__quality_control__evaluate_composition owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__merge_metadata +- name: qiime2__quality_control__evaluate_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__scrape_collection +- name: qiime2__quality_control__evaluate_taxonomy owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fragment_insertion__classify_otus_experimental +- name: qiime2__quality_control__exclude_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fragment_insertion__filter_features +- name: qiime2__quality_control__filter_reads owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fragment_insertion__sepp +- name: qiime2__metadata__distance_matrix owner: q2d2 tool_panel_section_id: '' -- name: qiime2__kmerizer__core_metrics +- name: qiime2__metadata__merge owner: q2d2 tool_panel_section_id: '' -- name: qiime2__kmerizer__seqs_to_kmers +- name: qiime2__metadata__shuffle_groups owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__anova +- name: qiime2__metadata__tabulate owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__feature_volatility +- name: qiime2__kmerizer__core_metrics owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__first_differences +- name: qiime2__kmerizer__seqs_to_kmers owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__first_distances +- name: qiime2__fondue___get_sequences owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__linear_mixed_effects +- name: qiime2__fondue__combine_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__maturity_index +- name: qiime2__fondue__get_all owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__nmit +- name: qiime2__fondue__get_ids_from_query owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__pairwise_differences +- name: qiime2__fondue__get_metadata owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__pairwise_distances +- name: qiime2__fondue__get_sequences owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__plot_feature_volatility +- name: qiime2__fondue__merge_metadata owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__volatility +- name: qiime2__fondue__scrape_collection owner: q2d2 tool_panel_section_id: '' - name: qiime2_dbotu_q2 @@ -3695,6 +3752,27 @@ tools: - name: rseqc_tin owner: nilesh tool_panel_section_id: '' +- name: samestr_compare + owner: iuc + tool_panel_section_id: '' +- name: samestr_convert + owner: iuc + tool_panel_section_id: '' +- name: samestr_extract + owner: iuc + tool_panel_section_id: '' +- name: samestr_filter + owner: iuc + tool_panel_section_id: '' +- name: samestr_merge + owner: iuc + tool_panel_section_id: '' +- name: samestr_stats + owner: iuc + tool_panel_section_id: '' +- name: samestr_summarize + owner: iuc + tool_panel_section_id: '' - name: scoary owner: iuc tool_panel_section_id: '' @@ -3819,10 +3897,10 @@ tools: owner: artbio tool_panel_section_id: '' - name: srst2 - owner: iuc + owner: nml tool_panel_section_id: '' - name: srst2 - owner: nml + owner: iuc tool_panel_section_id: '' - name: staramr_search owner: iuc @@ -3935,6 +4013,12 @@ tools: - name: varvamp owner: iuc tool_panel_section_id: '' +- name: vcontact2 + owner: iuc + tool_panel_section_id: '' +- name: vcontact2_gene2genome + owner: iuc + tool_panel_section_id: '' - name: vegan_diversity owner: iuc tool_panel_section_id: '' diff --git a/communities/microgalaxy/lab/tools/top/APOSTL.yaml b/communities/microgalaxy/lab/tools/top/APOSTL.yaml index 81562e59c..b2d3895f0 100644 --- a/communities/microgalaxy/lab/tools/top/APOSTL.yaml +++ b/communities/microgalaxy/lab/tools/top/APOSTL.yaml @@ -776,6 +776,9 @@ tools: - name: obi_clean owner: iuc tool_panel_section_id: '' +- name: obi_complement + owner: iuc + tool_panel_section_id: '' - name: obi_convert owner: iuc tool_panel_section_id: '' @@ -788,6 +791,18 @@ tools: - name: obi_pairing owner: iuc tool_panel_section_id: '' +- name: obi_pcr + owner: iuc + tool_panel_section_id: '' +- name: obi_refidx + owner: iuc + tool_panel_section_id: '' +- name: obi_tag + owner: iuc + tool_panel_section_id: '' +- name: obi_taxonomy + owner: iuc + tool_panel_section_id: '' - name: obi_uniq owner: iuc tool_panel_section_id: '' @@ -1265,6 +1280,9 @@ tools: - name: picrust_predict_metagenomes owner: iuc tool_panel_section_id: '' +- name: prinseq + owner: iuc + tool_panel_section_id: '' - name: prodigal owner: iuc tool_panel_section_id: '' @@ -1277,262 +1295,241 @@ tools: - name: pygenomeTracks owner: iuc tool_panel_section_id: '' -- name: qiime2_core__tools__export - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2_core__tools__import - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2_core__tools__import_fastq - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__quality_filter__q_score - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__cull_seqs - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__degap_seqs - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__dereplicate - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__edit_taxonomy +- name: qiime2__dada2__denoise_ccs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_classifications +- name: qiime2__dada2__denoise_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_cross_validate +- name: qiime2__dada2__denoise_pyro owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_fit_classifier +- name: qiime2__dada2__denoise_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_seqs +- name: qiime2__dada2__plot_base_transitions owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_taxonomy +- name: qiime2__cutadapt__demux_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__extract_seq_segments +- name: qiime2__cutadapt__demux_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__filter_seqs_length +- name: qiime2__cutadapt__trim_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__filter_seqs_length_by_taxon +- name: qiime2__cutadapt__trim_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__filter_taxa +- name: qiime2__composition__add_pseudocount owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_bv_brc_genome_features +- name: qiime2__composition__ancom owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_bv_brc_genomes +- name: qiime2__composition__ancombc owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_bv_brc_metadata +- name: qiime2__composition__ancombc2 owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_eukaryome_data +- name: qiime2__composition__ancombc2_visualizer owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_gtdb_data +- name: qiime2__composition__da_barplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_midori2_data +- name: qiime2__composition__tabulate owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_ncbi_data +- name: qiime2__boots__alpha owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_ncbi_data_protein +- name: qiime2__boots__alpha_average owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_ncbi_genomes +- name: qiime2__boots__alpha_collection owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_pr2_data +- name: qiime2__boots__beta owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_silva_data +- name: qiime2__boots__beta_average owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_unite_data +- name: qiime2__boots__beta_collection owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__merge_taxa +- name: qiime2__boots__core_metrics owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__orient_reads +- name: qiime2__boots__kmer_diversity owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__orient_seqs +- name: qiime2__boots__resample owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__parse_silva_taxonomy +- name: qiime2__vsearch__cluster_features_closed_reference owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__reverse_transcribe +- name: qiime2__vsearch__cluster_features_de_novo owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__subsample_fasta +- name: qiime2__vsearch__cluster_features_open_reference owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__trim_alignment +- name: qiime2__vsearch__dereplicate_sequences owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__classify_samples +- name: qiime2__vsearch__fastq_stats owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__classify_samples_from_dist +- name: qiime2__vsearch__merge_pairs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__classify_samples_ncv +- name: qiime2__vsearch__uchime_denovo owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__confusion_matrix +- name: qiime2__vsearch__uchime_ref owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__fit_classifier +- name: qiime2__demux__emp_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__fit_regressor +- name: qiime2__demux__emp_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__heatmap +- name: qiime2__demux__filter_samples owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__metatable +- name: qiime2__demux__partition_samples_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__predict_classification +- name: qiime2__demux__partition_samples_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__predict_regression +- name: qiime2__demux__subsample_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__regress_samples +- name: qiime2__demux__subsample_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__regress_samples_ncv +- name: qiime2__demux__summarize owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__scatterplot +- name: qiime2__demux__tabulate_read_counts owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__split_table +- name: qiime2__deblur__denoise_16S owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__summarize +- name: qiime2__deblur__denoise_other owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__align_to_tree_mafft_fasttree +- name: qiime2__deblur__visualize_stats owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__align_to_tree_mafft_iqtree +- name: qiime2__diversity__adonis owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__align_to_tree_mafft_raxml +- name: qiime2__diversity__alpha owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__fasttree +- name: qiime2__diversity__alpha_correlation owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__filter_table +- name: qiime2__diversity__alpha_group_significance owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__filter_tree +- name: qiime2__diversity__alpha_phylogenetic owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__iqtree +- name: qiime2__diversity__alpha_rarefaction owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__iqtree_ultrafast_bootstrap +- name: qiime2__diversity__beta owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__midpoint_root +- name: qiime2__diversity__beta_correlation owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__raxml +- name: qiime2__diversity__beta_group_significance owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__raxml_rapid_bootstrap +- name: qiime2__diversity__beta_phylogenetic owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__robinson_foulds +- name: qiime2__diversity__beta_rarefaction owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__distance_matrix +- name: qiime2__diversity__bioenv owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__merge +- name: qiime2__diversity__core_metrics owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__shuffle_groups +- name: qiime2__diversity__core_metrics_phylogenetic owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__tabulate +- name: qiime2__diversity__filter_alpha_diversity owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__alpha_group_significance +- name: qiime2__diversity__filter_distance_matrix owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__collate_stats +- name: qiime2__diversity__mantel owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__facet_across +- name: qiime2__diversity__partial_procrustes owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__facet_within +- name: qiime2__diversity__pcoa owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__mann_whitney_u +- name: qiime2__diversity__pcoa_biplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__mann_whitney_u_facet +- name: qiime2__diversity__procrustes_analysis owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__plot_rainclouds +- name: qiime2__diversity__tsne owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__prep_alpha_distribution +- name: qiime2__diversity__umap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__wilcoxon_srt +- name: qiime2__emperor__biplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__wilcoxon_srt_facet +- name: qiime2__emperor__plot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__bowtie2_build +- name: qiime2__emperor__procrustes_plot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__decontam_identify +- name: qiime2_core__tools__export owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__decontam_identify_batches +- name: qiime2_core__tools__import owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__decontam_score_viz +- name: qiime2_core__tools__import_fastq owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__evaluate_composition +- name: qiime2__taxa__barplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__evaluate_seqs +- name: qiime2__taxa__barplot2 owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__evaluate_taxonomy +- name: qiime2__taxa__collapse owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__exclude_seqs +- name: qiime2__taxa__filter_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__filter_reads +- name: qiime2__taxa__filter_table owner: q2d2 tool_panel_section_id: '' - name: qiime2__diversity_lib__alpha_passthrough @@ -1571,253 +1568,244 @@ tools: - name: qiime2__diversity_lib__weighted_unifrac owner: q2d2 tool_panel_section_id: '' -- name: qiime2__alignment__mafft - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__alignment__mafft_add - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__alignment__mask - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__vizard__boxplot +- name: qiime2__stats__alpha_group_significance owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vizard__heatmap +- name: qiime2__stats__collate_stats owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vizard__lineplot +- name: qiime2__stats__facet_across owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vizard__scatterplot_2d +- name: qiime2__stats__facet_within owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__adonis +- name: qiime2__stats__mann_whitney_u owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha +- name: qiime2__stats__mann_whitney_u_facet owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_correlation +- name: qiime2__stats__plot_rainclouds owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_group_significance +- name: qiime2__stats__prep_alpha_distribution owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_phylogenetic +- name: qiime2__stats__wilcoxon_srt owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_rarefaction +- name: qiime2__stats__wilcoxon_srt_facet owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta +- name: qiime2__sample_classifier__classify_samples owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_correlation +- name: qiime2__sample_classifier__classify_samples_from_dist owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_group_significance +- name: qiime2__sample_classifier__classify_samples_ncv owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_phylogenetic +- name: qiime2__sample_classifier__confusion_matrix owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_rarefaction +- name: qiime2__sample_classifier__fit_classifier owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__bioenv +- name: qiime2__sample_classifier__fit_regressor owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__core_metrics +- name: qiime2__sample_classifier__heatmap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__core_metrics_phylogenetic +- name: qiime2__sample_classifier__metatable owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__filter_alpha_diversity +- name: qiime2__sample_classifier__predict_classification owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__filter_distance_matrix +- name: qiime2__sample_classifier__predict_regression owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__mantel +- name: qiime2__sample_classifier__regress_samples owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__partial_procrustes +- name: qiime2__sample_classifier__regress_samples_ncv owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__pcoa +- name: qiime2__sample_classifier__scatterplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__pcoa_biplot +- name: qiime2__sample_classifier__split_table owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__procrustes_analysis +- name: qiime2__sample_classifier__summarize owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__tsne +- name: qiime2__rescript__cull_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__umap +- name: qiime2__rescript__degap_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__emp_paired +- name: qiime2__rescript__dereplicate owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__emp_single +- name: qiime2__rescript__edit_taxonomy owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__filter_samples +- name: qiime2__rescript__evaluate_classifications owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__partition_samples_paired +- name: qiime2__rescript__evaluate_cross_validate owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__partition_samples_single +- name: qiime2__rescript__evaluate_fit_classifier owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__subsample_paired +- name: qiime2__rescript__evaluate_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__subsample_single +- name: qiime2__rescript__evaluate_taxonomy owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__summarize +- name: qiime2__rescript__extract_seq_segments owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__tabulate_read_counts +- name: qiime2__rescript__filter_seqs_length owner: q2d2 tool_panel_section_id: '' -- name: qiime2__deblur__denoise_16S +- name: qiime2__rescript__filter_seqs_length_by_taxon owner: q2d2 tool_panel_section_id: '' -- name: qiime2__deblur__denoise_other +- name: qiime2__rescript__filter_taxa owner: q2d2 tool_panel_section_id: '' -- name: qiime2__deblur__visualize_stats +- name: qiime2__rescript__get_bv_brc_genome_features owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_ccs +- name: qiime2__rescript__get_bv_brc_genomes owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_paired +- name: qiime2__rescript__get_bv_brc_metadata owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_pyro +- name: qiime2__rescript__get_eukaryome_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_single +- name: qiime2__rescript__get_gtdb_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__plot_base_transitions +- name: qiime2__rescript__get_midori2_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__cutadapt__demux_paired +- name: qiime2__rescript__get_ncbi_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__cutadapt__demux_single +- name: qiime2__rescript__get_ncbi_data_protein owner: q2d2 tool_panel_section_id: '' -- name: qiime2__cutadapt__trim_paired +- name: qiime2__rescript__get_ncbi_genomes owner: q2d2 tool_panel_section_id: '' -- name: qiime2__cutadapt__trim_single +- name: qiime2__rescript__get_pr2_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__add_pseudocount +- name: qiime2__rescript__get_silva_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancom +- name: qiime2__rescript__get_unite_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancombc +- name: qiime2__rescript__merge_taxa owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancombc2 +- name: qiime2__rescript__orient_reads owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancombc2_visualizer +- name: qiime2__rescript__orient_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__da_barplot +- name: qiime2__rescript__parse_silva_taxonomy owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__tabulate +- name: qiime2__rescript__reverse_transcribe owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__barplot +- name: qiime2__rescript__subsample_fasta owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__barplot2 +- name: qiime2__rescript__trim_alignment owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__collapse +- name: qiime2__quality_filter__q_score owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__filter_seqs +- name: qiime2__vizard__boxplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__filter_table +- name: qiime2__vizard__heatmap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__alpha +- name: qiime2__vizard__lineplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__alpha_average +- name: qiime2__vizard__scatterplot_2d owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__alpha_collection +- name: qiime2__alignment__mafft owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__beta +- name: qiime2__alignment__mafft_add owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__beta_average +- name: qiime2__alignment__mask owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__beta_collection +- name: qiime2__phylogeny__align_to_tree_mafft_fasttree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__core_metrics +- name: qiime2__phylogeny__align_to_tree_mafft_iqtree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__kmer_diversity +- name: qiime2__phylogeny__align_to_tree_mafft_raxml owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__resample +- name: qiime2__phylogeny__fasttree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__cluster_features_closed_reference +- name: qiime2__phylogeny__filter_table owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__cluster_features_de_novo +- name: qiime2__phylogeny__filter_tree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__cluster_features_open_reference +- name: qiime2__phylogeny__iqtree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__dereplicate_sequences +- name: qiime2__phylogeny__iqtree_ultrafast_bootstrap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__fastq_stats +- name: qiime2__phylogeny__midpoint_root owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__merge_pairs +- name: qiime2__phylogeny__raxml owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__uchime_denovo +- name: qiime2__phylogeny__raxml_rapid_bootstrap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__uchime_ref +- name: qiime2__phylogeny__robinson_foulds owner: q2d2 tool_panel_section_id: '' -- name: qiime2__emperor__biplot +- name: qiime2__fragment_insertion__classify_otus_experimental owner: q2d2 tool_panel_section_id: '' -- name: qiime2__emperor__plot +- name: qiime2__fragment_insertion__filter_features owner: q2d2 tool_panel_section_id: '' -- name: qiime2__emperor__procrustes_plot +- name: qiime2__fragment_insertion__sepp owner: q2d2 tool_panel_section_id: '' - name: qiime2__feature_classifier__blast @@ -1853,6 +1841,39 @@ tools: - name: qiime2__feature_classifier__vsearch_global owner: q2d2 tool_panel_section_id: '' +- name: qiime2__longitudinal__anova + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__feature_volatility + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__first_differences + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__first_distances + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__linear_mixed_effects + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__maturity_index + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__nmit + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__pairwise_differences + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__pairwise_distances + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__plot_feature_volatility + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__volatility + owner: q2d2 + tool_panel_section_id: '' - name: qiime2__feature_table___summarize owner: q2d2 tool_panel_section_id: '' @@ -1922,76 +1943,73 @@ tools: - name: qiime2__feature_table__transpose owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue___get_sequences - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__fondue__combine_seqs +- name: qiime2__quality_control__bowtie2_build owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__get_all +- name: qiime2__quality_control__decontam_identify owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__get_ids_from_query +- name: qiime2__quality_control__decontam_identify_batches owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__get_metadata +- name: qiime2__quality_control__decontam_score_viz owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__get_sequences +- name: qiime2__quality_control__evaluate_composition owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__merge_metadata +- name: qiime2__quality_control__evaluate_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__scrape_collection +- name: qiime2__quality_control__evaluate_taxonomy owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fragment_insertion__classify_otus_experimental +- name: qiime2__quality_control__exclude_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fragment_insertion__filter_features +- name: qiime2__quality_control__filter_reads owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fragment_insertion__sepp +- name: qiime2__metadata__distance_matrix owner: q2d2 tool_panel_section_id: '' -- name: qiime2__kmerizer__core_metrics +- name: qiime2__metadata__merge owner: q2d2 tool_panel_section_id: '' -- name: qiime2__kmerizer__seqs_to_kmers +- name: qiime2__metadata__shuffle_groups owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__anova +- name: qiime2__metadata__tabulate owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__feature_volatility +- name: qiime2__kmerizer__core_metrics owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__first_differences +- name: qiime2__kmerizer__seqs_to_kmers owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__first_distances +- name: qiime2__fondue___get_sequences owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__linear_mixed_effects +- name: qiime2__fondue__combine_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__maturity_index +- name: qiime2__fondue__get_all owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__nmit +- name: qiime2__fondue__get_ids_from_query owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__pairwise_differences +- name: qiime2__fondue__get_metadata owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__pairwise_distances +- name: qiime2__fondue__get_sequences owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__plot_feature_volatility +- name: qiime2__fondue__merge_metadata owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__volatility +- name: qiime2__fondue__scrape_collection owner: q2d2 tool_panel_section_id: '' - name: qualimap_bamqc diff --git a/communities/microgalaxy/lab/tools/top/CIRM-CFBP.yaml b/communities/microgalaxy/lab/tools/top/CIRM-CFBP.yaml index 81562e59c..b2d3895f0 100644 --- a/communities/microgalaxy/lab/tools/top/CIRM-CFBP.yaml +++ b/communities/microgalaxy/lab/tools/top/CIRM-CFBP.yaml @@ -776,6 +776,9 @@ tools: - name: obi_clean owner: iuc tool_panel_section_id: '' +- name: obi_complement + owner: iuc + tool_panel_section_id: '' - name: obi_convert owner: iuc tool_panel_section_id: '' @@ -788,6 +791,18 @@ tools: - name: obi_pairing owner: iuc tool_panel_section_id: '' +- name: obi_pcr + owner: iuc + tool_panel_section_id: '' +- name: obi_refidx + owner: iuc + tool_panel_section_id: '' +- name: obi_tag + owner: iuc + tool_panel_section_id: '' +- name: obi_taxonomy + owner: iuc + tool_panel_section_id: '' - name: obi_uniq owner: iuc tool_panel_section_id: '' @@ -1265,6 +1280,9 @@ tools: - name: picrust_predict_metagenomes owner: iuc tool_panel_section_id: '' +- name: prinseq + owner: iuc + tool_panel_section_id: '' - name: prodigal owner: iuc tool_panel_section_id: '' @@ -1277,262 +1295,241 @@ tools: - name: pygenomeTracks owner: iuc tool_panel_section_id: '' -- name: qiime2_core__tools__export - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2_core__tools__import - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2_core__tools__import_fastq - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__quality_filter__q_score - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__cull_seqs - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__degap_seqs - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__dereplicate - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__edit_taxonomy +- name: qiime2__dada2__denoise_ccs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_classifications +- name: qiime2__dada2__denoise_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_cross_validate +- name: qiime2__dada2__denoise_pyro owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_fit_classifier +- name: qiime2__dada2__denoise_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_seqs +- name: qiime2__dada2__plot_base_transitions owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_taxonomy +- name: qiime2__cutadapt__demux_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__extract_seq_segments +- name: qiime2__cutadapt__demux_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__filter_seqs_length +- name: qiime2__cutadapt__trim_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__filter_seqs_length_by_taxon +- name: qiime2__cutadapt__trim_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__filter_taxa +- name: qiime2__composition__add_pseudocount owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_bv_brc_genome_features +- name: qiime2__composition__ancom owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_bv_brc_genomes +- name: qiime2__composition__ancombc owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_bv_brc_metadata +- name: qiime2__composition__ancombc2 owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_eukaryome_data +- name: qiime2__composition__ancombc2_visualizer owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_gtdb_data +- name: qiime2__composition__da_barplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_midori2_data +- name: qiime2__composition__tabulate owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_ncbi_data +- name: qiime2__boots__alpha owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_ncbi_data_protein +- name: qiime2__boots__alpha_average owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_ncbi_genomes +- name: qiime2__boots__alpha_collection owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_pr2_data +- name: qiime2__boots__beta owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_silva_data +- name: qiime2__boots__beta_average owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_unite_data +- name: qiime2__boots__beta_collection owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__merge_taxa +- name: qiime2__boots__core_metrics owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__orient_reads +- name: qiime2__boots__kmer_diversity owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__orient_seqs +- name: qiime2__boots__resample owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__parse_silva_taxonomy +- name: qiime2__vsearch__cluster_features_closed_reference owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__reverse_transcribe +- name: qiime2__vsearch__cluster_features_de_novo owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__subsample_fasta +- name: qiime2__vsearch__cluster_features_open_reference owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__trim_alignment +- name: qiime2__vsearch__dereplicate_sequences owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__classify_samples +- name: qiime2__vsearch__fastq_stats owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__classify_samples_from_dist +- name: qiime2__vsearch__merge_pairs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__classify_samples_ncv +- name: qiime2__vsearch__uchime_denovo owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__confusion_matrix +- name: qiime2__vsearch__uchime_ref owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__fit_classifier +- name: qiime2__demux__emp_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__fit_regressor +- name: qiime2__demux__emp_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__heatmap +- name: qiime2__demux__filter_samples owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__metatable +- name: qiime2__demux__partition_samples_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__predict_classification +- name: qiime2__demux__partition_samples_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__predict_regression +- name: qiime2__demux__subsample_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__regress_samples +- name: qiime2__demux__subsample_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__regress_samples_ncv +- name: qiime2__demux__summarize owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__scatterplot +- name: qiime2__demux__tabulate_read_counts owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__split_table +- name: qiime2__deblur__denoise_16S owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__summarize +- name: qiime2__deblur__denoise_other owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__align_to_tree_mafft_fasttree +- name: qiime2__deblur__visualize_stats owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__align_to_tree_mafft_iqtree +- name: qiime2__diversity__adonis owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__align_to_tree_mafft_raxml +- name: qiime2__diversity__alpha owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__fasttree +- name: qiime2__diversity__alpha_correlation owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__filter_table +- name: qiime2__diversity__alpha_group_significance owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__filter_tree +- name: qiime2__diversity__alpha_phylogenetic owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__iqtree +- name: qiime2__diversity__alpha_rarefaction owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__iqtree_ultrafast_bootstrap +- name: qiime2__diversity__beta owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__midpoint_root +- name: qiime2__diversity__beta_correlation owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__raxml +- name: qiime2__diversity__beta_group_significance owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__raxml_rapid_bootstrap +- name: qiime2__diversity__beta_phylogenetic owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__robinson_foulds +- name: qiime2__diversity__beta_rarefaction owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__distance_matrix +- name: qiime2__diversity__bioenv owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__merge +- name: qiime2__diversity__core_metrics owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__shuffle_groups +- name: qiime2__diversity__core_metrics_phylogenetic owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__tabulate +- name: qiime2__diversity__filter_alpha_diversity owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__alpha_group_significance +- name: qiime2__diversity__filter_distance_matrix owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__collate_stats +- name: qiime2__diversity__mantel owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__facet_across +- name: qiime2__diversity__partial_procrustes owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__facet_within +- name: qiime2__diversity__pcoa owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__mann_whitney_u +- name: qiime2__diversity__pcoa_biplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__mann_whitney_u_facet +- name: qiime2__diversity__procrustes_analysis owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__plot_rainclouds +- name: qiime2__diversity__tsne owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__prep_alpha_distribution +- name: qiime2__diversity__umap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__wilcoxon_srt +- name: qiime2__emperor__biplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__wilcoxon_srt_facet +- name: qiime2__emperor__plot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__bowtie2_build +- name: qiime2__emperor__procrustes_plot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__decontam_identify +- name: qiime2_core__tools__export owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__decontam_identify_batches +- name: qiime2_core__tools__import owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__decontam_score_viz +- name: qiime2_core__tools__import_fastq owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__evaluate_composition +- name: qiime2__taxa__barplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__evaluate_seqs +- name: qiime2__taxa__barplot2 owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__evaluate_taxonomy +- name: qiime2__taxa__collapse owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__exclude_seqs +- name: qiime2__taxa__filter_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__filter_reads +- name: qiime2__taxa__filter_table owner: q2d2 tool_panel_section_id: '' - name: qiime2__diversity_lib__alpha_passthrough @@ -1571,253 +1568,244 @@ tools: - name: qiime2__diversity_lib__weighted_unifrac owner: q2d2 tool_panel_section_id: '' -- name: qiime2__alignment__mafft - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__alignment__mafft_add - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__alignment__mask - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__vizard__boxplot +- name: qiime2__stats__alpha_group_significance owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vizard__heatmap +- name: qiime2__stats__collate_stats owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vizard__lineplot +- name: qiime2__stats__facet_across owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vizard__scatterplot_2d +- name: qiime2__stats__facet_within owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__adonis +- name: qiime2__stats__mann_whitney_u owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha +- name: qiime2__stats__mann_whitney_u_facet owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_correlation +- name: qiime2__stats__plot_rainclouds owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_group_significance +- name: qiime2__stats__prep_alpha_distribution owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_phylogenetic +- name: qiime2__stats__wilcoxon_srt owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_rarefaction +- name: qiime2__stats__wilcoxon_srt_facet owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta +- name: qiime2__sample_classifier__classify_samples owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_correlation +- name: qiime2__sample_classifier__classify_samples_from_dist owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_group_significance +- name: qiime2__sample_classifier__classify_samples_ncv owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_phylogenetic +- name: qiime2__sample_classifier__confusion_matrix owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_rarefaction +- name: qiime2__sample_classifier__fit_classifier owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__bioenv +- name: qiime2__sample_classifier__fit_regressor owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__core_metrics +- name: qiime2__sample_classifier__heatmap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__core_metrics_phylogenetic +- name: qiime2__sample_classifier__metatable owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__filter_alpha_diversity +- name: qiime2__sample_classifier__predict_classification owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__filter_distance_matrix +- name: qiime2__sample_classifier__predict_regression owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__mantel +- name: qiime2__sample_classifier__regress_samples owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__partial_procrustes +- name: qiime2__sample_classifier__regress_samples_ncv owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__pcoa +- name: qiime2__sample_classifier__scatterplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__pcoa_biplot +- name: qiime2__sample_classifier__split_table owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__procrustes_analysis +- name: qiime2__sample_classifier__summarize owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__tsne +- name: qiime2__rescript__cull_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__umap +- name: qiime2__rescript__degap_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__emp_paired +- name: qiime2__rescript__dereplicate owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__emp_single +- name: qiime2__rescript__edit_taxonomy owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__filter_samples +- name: qiime2__rescript__evaluate_classifications owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__partition_samples_paired +- name: qiime2__rescript__evaluate_cross_validate owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__partition_samples_single +- name: qiime2__rescript__evaluate_fit_classifier owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__subsample_paired +- name: qiime2__rescript__evaluate_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__subsample_single +- name: qiime2__rescript__evaluate_taxonomy owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__summarize +- name: qiime2__rescript__extract_seq_segments owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__tabulate_read_counts +- name: qiime2__rescript__filter_seqs_length owner: q2d2 tool_panel_section_id: '' -- name: qiime2__deblur__denoise_16S +- name: qiime2__rescript__filter_seqs_length_by_taxon owner: q2d2 tool_panel_section_id: '' -- name: qiime2__deblur__denoise_other +- name: qiime2__rescript__filter_taxa owner: q2d2 tool_panel_section_id: '' -- name: qiime2__deblur__visualize_stats +- name: qiime2__rescript__get_bv_brc_genome_features owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_ccs +- name: qiime2__rescript__get_bv_brc_genomes owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_paired +- name: qiime2__rescript__get_bv_brc_metadata owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_pyro +- name: qiime2__rescript__get_eukaryome_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_single +- name: qiime2__rescript__get_gtdb_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__plot_base_transitions +- name: qiime2__rescript__get_midori2_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__cutadapt__demux_paired +- name: qiime2__rescript__get_ncbi_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__cutadapt__demux_single +- name: qiime2__rescript__get_ncbi_data_protein owner: q2d2 tool_panel_section_id: '' -- name: qiime2__cutadapt__trim_paired +- name: qiime2__rescript__get_ncbi_genomes owner: q2d2 tool_panel_section_id: '' -- name: qiime2__cutadapt__trim_single +- name: qiime2__rescript__get_pr2_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__add_pseudocount +- name: qiime2__rescript__get_silva_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancom +- name: qiime2__rescript__get_unite_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancombc +- name: qiime2__rescript__merge_taxa owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancombc2 +- name: qiime2__rescript__orient_reads owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancombc2_visualizer +- name: qiime2__rescript__orient_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__da_barplot +- name: qiime2__rescript__parse_silva_taxonomy owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__tabulate +- name: qiime2__rescript__reverse_transcribe owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__barplot +- name: qiime2__rescript__subsample_fasta owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__barplot2 +- name: qiime2__rescript__trim_alignment owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__collapse +- name: qiime2__quality_filter__q_score owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__filter_seqs +- name: qiime2__vizard__boxplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__filter_table +- name: qiime2__vizard__heatmap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__alpha +- name: qiime2__vizard__lineplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__alpha_average +- name: qiime2__vizard__scatterplot_2d owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__alpha_collection +- name: qiime2__alignment__mafft owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__beta +- name: qiime2__alignment__mafft_add owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__beta_average +- name: qiime2__alignment__mask owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__beta_collection +- name: qiime2__phylogeny__align_to_tree_mafft_fasttree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__core_metrics +- name: qiime2__phylogeny__align_to_tree_mafft_iqtree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__kmer_diversity +- name: qiime2__phylogeny__align_to_tree_mafft_raxml owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__resample +- name: qiime2__phylogeny__fasttree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__cluster_features_closed_reference +- name: qiime2__phylogeny__filter_table owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__cluster_features_de_novo +- name: qiime2__phylogeny__filter_tree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__cluster_features_open_reference +- name: qiime2__phylogeny__iqtree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__dereplicate_sequences +- name: qiime2__phylogeny__iqtree_ultrafast_bootstrap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__fastq_stats +- name: qiime2__phylogeny__midpoint_root owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__merge_pairs +- name: qiime2__phylogeny__raxml owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__uchime_denovo +- name: qiime2__phylogeny__raxml_rapid_bootstrap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__uchime_ref +- name: qiime2__phylogeny__robinson_foulds owner: q2d2 tool_panel_section_id: '' -- name: qiime2__emperor__biplot +- name: qiime2__fragment_insertion__classify_otus_experimental owner: q2d2 tool_panel_section_id: '' -- name: qiime2__emperor__plot +- name: qiime2__fragment_insertion__filter_features owner: q2d2 tool_panel_section_id: '' -- name: qiime2__emperor__procrustes_plot +- name: qiime2__fragment_insertion__sepp owner: q2d2 tool_panel_section_id: '' - name: qiime2__feature_classifier__blast @@ -1853,6 +1841,39 @@ tools: - name: qiime2__feature_classifier__vsearch_global owner: q2d2 tool_panel_section_id: '' +- name: qiime2__longitudinal__anova + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__feature_volatility + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__first_differences + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__first_distances + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__linear_mixed_effects + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__maturity_index + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__nmit + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__pairwise_differences + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__pairwise_distances + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__plot_feature_volatility + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__volatility + owner: q2d2 + tool_panel_section_id: '' - name: qiime2__feature_table___summarize owner: q2d2 tool_panel_section_id: '' @@ -1922,76 +1943,73 @@ tools: - name: qiime2__feature_table__transpose owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue___get_sequences - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__fondue__combine_seqs +- name: qiime2__quality_control__bowtie2_build owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__get_all +- name: qiime2__quality_control__decontam_identify owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__get_ids_from_query +- name: qiime2__quality_control__decontam_identify_batches owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__get_metadata +- name: qiime2__quality_control__decontam_score_viz owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__get_sequences +- name: qiime2__quality_control__evaluate_composition owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__merge_metadata +- name: qiime2__quality_control__evaluate_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__scrape_collection +- name: qiime2__quality_control__evaluate_taxonomy owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fragment_insertion__classify_otus_experimental +- name: qiime2__quality_control__exclude_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fragment_insertion__filter_features +- name: qiime2__quality_control__filter_reads owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fragment_insertion__sepp +- name: qiime2__metadata__distance_matrix owner: q2d2 tool_panel_section_id: '' -- name: qiime2__kmerizer__core_metrics +- name: qiime2__metadata__merge owner: q2d2 tool_panel_section_id: '' -- name: qiime2__kmerizer__seqs_to_kmers +- name: qiime2__metadata__shuffle_groups owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__anova +- name: qiime2__metadata__tabulate owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__feature_volatility +- name: qiime2__kmerizer__core_metrics owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__first_differences +- name: qiime2__kmerizer__seqs_to_kmers owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__first_distances +- name: qiime2__fondue___get_sequences owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__linear_mixed_effects +- name: qiime2__fondue__combine_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__maturity_index +- name: qiime2__fondue__get_all owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__nmit +- name: qiime2__fondue__get_ids_from_query owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__pairwise_differences +- name: qiime2__fondue__get_metadata owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__pairwise_distances +- name: qiime2__fondue__get_sequences owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__plot_feature_volatility +- name: qiime2__fondue__merge_metadata owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__volatility +- name: qiime2__fondue__scrape_collection owner: q2d2 tool_panel_section_id: '' - name: qualimap_bamqc diff --git a/communities/microgalaxy/lab/tools/top/ChemFlow.yaml b/communities/microgalaxy/lab/tools/top/ChemFlow.yaml index 81562e59c..b2d3895f0 100644 --- a/communities/microgalaxy/lab/tools/top/ChemFlow.yaml +++ b/communities/microgalaxy/lab/tools/top/ChemFlow.yaml @@ -776,6 +776,9 @@ tools: - name: obi_clean owner: iuc tool_panel_section_id: '' +- name: obi_complement + owner: iuc + tool_panel_section_id: '' - name: obi_convert owner: iuc tool_panel_section_id: '' @@ -788,6 +791,18 @@ tools: - name: obi_pairing owner: iuc tool_panel_section_id: '' +- name: obi_pcr + owner: iuc + tool_panel_section_id: '' +- name: obi_refidx + owner: iuc + tool_panel_section_id: '' +- name: obi_tag + owner: iuc + tool_panel_section_id: '' +- name: obi_taxonomy + owner: iuc + tool_panel_section_id: '' - name: obi_uniq owner: iuc tool_panel_section_id: '' @@ -1265,6 +1280,9 @@ tools: - name: picrust_predict_metagenomes owner: iuc tool_panel_section_id: '' +- name: prinseq + owner: iuc + tool_panel_section_id: '' - name: prodigal owner: iuc tool_panel_section_id: '' @@ -1277,262 +1295,241 @@ tools: - name: pygenomeTracks owner: iuc tool_panel_section_id: '' -- name: qiime2_core__tools__export - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2_core__tools__import - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2_core__tools__import_fastq - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__quality_filter__q_score - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__cull_seqs - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__degap_seqs - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__dereplicate - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__edit_taxonomy +- name: qiime2__dada2__denoise_ccs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_classifications +- name: qiime2__dada2__denoise_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_cross_validate +- name: qiime2__dada2__denoise_pyro owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_fit_classifier +- name: qiime2__dada2__denoise_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_seqs +- name: qiime2__dada2__plot_base_transitions owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_taxonomy +- name: qiime2__cutadapt__demux_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__extract_seq_segments +- name: qiime2__cutadapt__demux_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__filter_seqs_length +- name: qiime2__cutadapt__trim_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__filter_seqs_length_by_taxon +- name: qiime2__cutadapt__trim_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__filter_taxa +- name: qiime2__composition__add_pseudocount owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_bv_brc_genome_features +- name: qiime2__composition__ancom owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_bv_brc_genomes +- name: qiime2__composition__ancombc owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_bv_brc_metadata +- name: qiime2__composition__ancombc2 owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_eukaryome_data +- name: qiime2__composition__ancombc2_visualizer owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_gtdb_data +- name: qiime2__composition__da_barplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_midori2_data +- name: qiime2__composition__tabulate owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_ncbi_data +- name: qiime2__boots__alpha owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_ncbi_data_protein +- name: qiime2__boots__alpha_average owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_ncbi_genomes +- name: qiime2__boots__alpha_collection owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_pr2_data +- name: qiime2__boots__beta owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_silva_data +- name: qiime2__boots__beta_average owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_unite_data +- name: qiime2__boots__beta_collection owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__merge_taxa +- name: qiime2__boots__core_metrics owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__orient_reads +- name: qiime2__boots__kmer_diversity owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__orient_seqs +- name: qiime2__boots__resample owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__parse_silva_taxonomy +- name: qiime2__vsearch__cluster_features_closed_reference owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__reverse_transcribe +- name: qiime2__vsearch__cluster_features_de_novo owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__subsample_fasta +- name: qiime2__vsearch__cluster_features_open_reference owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__trim_alignment +- name: qiime2__vsearch__dereplicate_sequences owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__classify_samples +- name: qiime2__vsearch__fastq_stats owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__classify_samples_from_dist +- name: qiime2__vsearch__merge_pairs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__classify_samples_ncv +- name: qiime2__vsearch__uchime_denovo owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__confusion_matrix +- name: qiime2__vsearch__uchime_ref owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__fit_classifier +- name: qiime2__demux__emp_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__fit_regressor +- name: qiime2__demux__emp_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__heatmap +- name: qiime2__demux__filter_samples owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__metatable +- name: qiime2__demux__partition_samples_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__predict_classification +- name: qiime2__demux__partition_samples_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__predict_regression +- name: qiime2__demux__subsample_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__regress_samples +- name: qiime2__demux__subsample_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__regress_samples_ncv +- name: qiime2__demux__summarize owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__scatterplot +- name: qiime2__demux__tabulate_read_counts owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__split_table +- name: qiime2__deblur__denoise_16S owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__summarize +- name: qiime2__deblur__denoise_other owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__align_to_tree_mafft_fasttree +- name: qiime2__deblur__visualize_stats owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__align_to_tree_mafft_iqtree +- name: qiime2__diversity__adonis owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__align_to_tree_mafft_raxml +- name: qiime2__diversity__alpha owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__fasttree +- name: qiime2__diversity__alpha_correlation owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__filter_table +- name: qiime2__diversity__alpha_group_significance owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__filter_tree +- name: qiime2__diversity__alpha_phylogenetic owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__iqtree +- name: qiime2__diversity__alpha_rarefaction owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__iqtree_ultrafast_bootstrap +- name: qiime2__diversity__beta owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__midpoint_root +- name: qiime2__diversity__beta_correlation owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__raxml +- name: qiime2__diversity__beta_group_significance owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__raxml_rapid_bootstrap +- name: qiime2__diversity__beta_phylogenetic owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__robinson_foulds +- name: qiime2__diversity__beta_rarefaction owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__distance_matrix +- name: qiime2__diversity__bioenv owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__merge +- name: qiime2__diversity__core_metrics owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__shuffle_groups +- name: qiime2__diversity__core_metrics_phylogenetic owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__tabulate +- name: qiime2__diversity__filter_alpha_diversity owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__alpha_group_significance +- name: qiime2__diversity__filter_distance_matrix owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__collate_stats +- name: qiime2__diversity__mantel owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__facet_across +- name: qiime2__diversity__partial_procrustes owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__facet_within +- name: qiime2__diversity__pcoa owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__mann_whitney_u +- name: qiime2__diversity__pcoa_biplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__mann_whitney_u_facet +- name: qiime2__diversity__procrustes_analysis owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__plot_rainclouds +- name: qiime2__diversity__tsne owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__prep_alpha_distribution +- name: qiime2__diversity__umap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__wilcoxon_srt +- name: qiime2__emperor__biplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__wilcoxon_srt_facet +- name: qiime2__emperor__plot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__bowtie2_build +- name: qiime2__emperor__procrustes_plot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__decontam_identify +- name: qiime2_core__tools__export owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__decontam_identify_batches +- name: qiime2_core__tools__import owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__decontam_score_viz +- name: qiime2_core__tools__import_fastq owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__evaluate_composition +- name: qiime2__taxa__barplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__evaluate_seqs +- name: qiime2__taxa__barplot2 owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__evaluate_taxonomy +- name: qiime2__taxa__collapse owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__exclude_seqs +- name: qiime2__taxa__filter_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__filter_reads +- name: qiime2__taxa__filter_table owner: q2d2 tool_panel_section_id: '' - name: qiime2__diversity_lib__alpha_passthrough @@ -1571,253 +1568,244 @@ tools: - name: qiime2__diversity_lib__weighted_unifrac owner: q2d2 tool_panel_section_id: '' -- name: qiime2__alignment__mafft - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__alignment__mafft_add - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__alignment__mask - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__vizard__boxplot +- name: qiime2__stats__alpha_group_significance owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vizard__heatmap +- name: qiime2__stats__collate_stats owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vizard__lineplot +- name: qiime2__stats__facet_across owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vizard__scatterplot_2d +- name: qiime2__stats__facet_within owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__adonis +- name: qiime2__stats__mann_whitney_u owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha +- name: qiime2__stats__mann_whitney_u_facet owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_correlation +- name: qiime2__stats__plot_rainclouds owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_group_significance +- name: qiime2__stats__prep_alpha_distribution owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_phylogenetic +- name: qiime2__stats__wilcoxon_srt owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_rarefaction +- name: qiime2__stats__wilcoxon_srt_facet owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta +- name: qiime2__sample_classifier__classify_samples owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_correlation +- name: qiime2__sample_classifier__classify_samples_from_dist owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_group_significance +- name: qiime2__sample_classifier__classify_samples_ncv owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_phylogenetic +- name: qiime2__sample_classifier__confusion_matrix owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_rarefaction +- name: qiime2__sample_classifier__fit_classifier owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__bioenv +- name: qiime2__sample_classifier__fit_regressor owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__core_metrics +- name: qiime2__sample_classifier__heatmap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__core_metrics_phylogenetic +- name: qiime2__sample_classifier__metatable owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__filter_alpha_diversity +- name: qiime2__sample_classifier__predict_classification owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__filter_distance_matrix +- name: qiime2__sample_classifier__predict_regression owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__mantel +- name: qiime2__sample_classifier__regress_samples owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__partial_procrustes +- name: qiime2__sample_classifier__regress_samples_ncv owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__pcoa +- name: qiime2__sample_classifier__scatterplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__pcoa_biplot +- name: qiime2__sample_classifier__split_table owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__procrustes_analysis +- name: qiime2__sample_classifier__summarize owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__tsne +- name: qiime2__rescript__cull_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__umap +- name: qiime2__rescript__degap_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__emp_paired +- name: qiime2__rescript__dereplicate owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__emp_single +- name: qiime2__rescript__edit_taxonomy owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__filter_samples +- name: qiime2__rescript__evaluate_classifications owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__partition_samples_paired +- name: qiime2__rescript__evaluate_cross_validate owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__partition_samples_single +- name: qiime2__rescript__evaluate_fit_classifier owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__subsample_paired +- name: qiime2__rescript__evaluate_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__subsample_single +- name: qiime2__rescript__evaluate_taxonomy owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__summarize +- name: qiime2__rescript__extract_seq_segments owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__tabulate_read_counts +- name: qiime2__rescript__filter_seqs_length owner: q2d2 tool_panel_section_id: '' -- name: qiime2__deblur__denoise_16S +- name: qiime2__rescript__filter_seqs_length_by_taxon owner: q2d2 tool_panel_section_id: '' -- name: qiime2__deblur__denoise_other +- name: qiime2__rescript__filter_taxa owner: q2d2 tool_panel_section_id: '' -- name: qiime2__deblur__visualize_stats +- name: qiime2__rescript__get_bv_brc_genome_features owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_ccs +- name: qiime2__rescript__get_bv_brc_genomes owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_paired +- name: qiime2__rescript__get_bv_brc_metadata owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_pyro +- name: qiime2__rescript__get_eukaryome_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_single +- name: qiime2__rescript__get_gtdb_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__plot_base_transitions +- name: qiime2__rescript__get_midori2_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__cutadapt__demux_paired +- name: qiime2__rescript__get_ncbi_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__cutadapt__demux_single +- name: qiime2__rescript__get_ncbi_data_protein owner: q2d2 tool_panel_section_id: '' -- name: qiime2__cutadapt__trim_paired +- name: qiime2__rescript__get_ncbi_genomes owner: q2d2 tool_panel_section_id: '' -- name: qiime2__cutadapt__trim_single +- name: qiime2__rescript__get_pr2_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__add_pseudocount +- name: qiime2__rescript__get_silva_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancom +- name: qiime2__rescript__get_unite_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancombc +- name: qiime2__rescript__merge_taxa owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancombc2 +- name: qiime2__rescript__orient_reads owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancombc2_visualizer +- name: qiime2__rescript__orient_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__da_barplot +- name: qiime2__rescript__parse_silva_taxonomy owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__tabulate +- name: qiime2__rescript__reverse_transcribe owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__barplot +- name: qiime2__rescript__subsample_fasta owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__barplot2 +- name: qiime2__rescript__trim_alignment owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__collapse +- name: qiime2__quality_filter__q_score owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__filter_seqs +- name: qiime2__vizard__boxplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__filter_table +- name: qiime2__vizard__heatmap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__alpha +- name: qiime2__vizard__lineplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__alpha_average +- name: qiime2__vizard__scatterplot_2d owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__alpha_collection +- name: qiime2__alignment__mafft owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__beta +- name: qiime2__alignment__mafft_add owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__beta_average +- name: qiime2__alignment__mask owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__beta_collection +- name: qiime2__phylogeny__align_to_tree_mafft_fasttree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__core_metrics +- name: qiime2__phylogeny__align_to_tree_mafft_iqtree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__kmer_diversity +- name: qiime2__phylogeny__align_to_tree_mafft_raxml owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__resample +- name: qiime2__phylogeny__fasttree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__cluster_features_closed_reference +- name: qiime2__phylogeny__filter_table owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__cluster_features_de_novo +- name: qiime2__phylogeny__filter_tree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__cluster_features_open_reference +- name: qiime2__phylogeny__iqtree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__dereplicate_sequences +- name: qiime2__phylogeny__iqtree_ultrafast_bootstrap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__fastq_stats +- name: qiime2__phylogeny__midpoint_root owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__merge_pairs +- name: qiime2__phylogeny__raxml owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__uchime_denovo +- name: qiime2__phylogeny__raxml_rapid_bootstrap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__uchime_ref +- name: qiime2__phylogeny__robinson_foulds owner: q2d2 tool_panel_section_id: '' -- name: qiime2__emperor__biplot +- name: qiime2__fragment_insertion__classify_otus_experimental owner: q2d2 tool_panel_section_id: '' -- name: qiime2__emperor__plot +- name: qiime2__fragment_insertion__filter_features owner: q2d2 tool_panel_section_id: '' -- name: qiime2__emperor__procrustes_plot +- name: qiime2__fragment_insertion__sepp owner: q2d2 tool_panel_section_id: '' - name: qiime2__feature_classifier__blast @@ -1853,6 +1841,39 @@ tools: - name: qiime2__feature_classifier__vsearch_global owner: q2d2 tool_panel_section_id: '' +- name: qiime2__longitudinal__anova + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__feature_volatility + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__first_differences + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__first_distances + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__linear_mixed_effects + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__maturity_index + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__nmit + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__pairwise_differences + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__pairwise_distances + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__plot_feature_volatility + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__volatility + owner: q2d2 + tool_panel_section_id: '' - name: qiime2__feature_table___summarize owner: q2d2 tool_panel_section_id: '' @@ -1922,76 +1943,73 @@ tools: - name: qiime2__feature_table__transpose owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue___get_sequences - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__fondue__combine_seqs +- name: qiime2__quality_control__bowtie2_build owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__get_all +- name: qiime2__quality_control__decontam_identify owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__get_ids_from_query +- name: qiime2__quality_control__decontam_identify_batches owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__get_metadata +- name: qiime2__quality_control__decontam_score_viz owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__get_sequences +- name: qiime2__quality_control__evaluate_composition owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__merge_metadata +- name: qiime2__quality_control__evaluate_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__scrape_collection +- name: qiime2__quality_control__evaluate_taxonomy owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fragment_insertion__classify_otus_experimental +- name: qiime2__quality_control__exclude_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fragment_insertion__filter_features +- name: qiime2__quality_control__filter_reads owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fragment_insertion__sepp +- name: qiime2__metadata__distance_matrix owner: q2d2 tool_panel_section_id: '' -- name: qiime2__kmerizer__core_metrics +- name: qiime2__metadata__merge owner: q2d2 tool_panel_section_id: '' -- name: qiime2__kmerizer__seqs_to_kmers +- name: qiime2__metadata__shuffle_groups owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__anova +- name: qiime2__metadata__tabulate owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__feature_volatility +- name: qiime2__kmerizer__core_metrics owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__first_differences +- name: qiime2__kmerizer__seqs_to_kmers owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__first_distances +- name: qiime2__fondue___get_sequences owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__linear_mixed_effects +- name: qiime2__fondue__combine_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__maturity_index +- name: qiime2__fondue__get_all owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__nmit +- name: qiime2__fondue__get_ids_from_query owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__pairwise_differences +- name: qiime2__fondue__get_metadata owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__pairwise_distances +- name: qiime2__fondue__get_sequences owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__plot_feature_volatility +- name: qiime2__fondue__merge_metadata owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__volatility +- name: qiime2__fondue__scrape_collection owner: q2d2 tool_panel_section_id: '' - name: qualimap_bamqc diff --git a/communities/microgalaxy/lab/tools/top/Coloc-stats.yaml b/communities/microgalaxy/lab/tools/top/Coloc-stats.yaml index 81562e59c..b2d3895f0 100644 --- a/communities/microgalaxy/lab/tools/top/Coloc-stats.yaml +++ b/communities/microgalaxy/lab/tools/top/Coloc-stats.yaml @@ -776,6 +776,9 @@ tools: - name: obi_clean owner: iuc tool_panel_section_id: '' +- name: obi_complement + owner: iuc + tool_panel_section_id: '' - name: obi_convert owner: iuc tool_panel_section_id: '' @@ -788,6 +791,18 @@ tools: - name: obi_pairing owner: iuc tool_panel_section_id: '' +- name: obi_pcr + owner: iuc + tool_panel_section_id: '' +- name: obi_refidx + owner: iuc + tool_panel_section_id: '' +- name: obi_tag + owner: iuc + tool_panel_section_id: '' +- name: obi_taxonomy + owner: iuc + tool_panel_section_id: '' - name: obi_uniq owner: iuc tool_panel_section_id: '' @@ -1265,6 +1280,9 @@ tools: - name: picrust_predict_metagenomes owner: iuc tool_panel_section_id: '' +- name: prinseq + owner: iuc + tool_panel_section_id: '' - name: prodigal owner: iuc tool_panel_section_id: '' @@ -1277,262 +1295,241 @@ tools: - name: pygenomeTracks owner: iuc tool_panel_section_id: '' -- name: qiime2_core__tools__export - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2_core__tools__import - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2_core__tools__import_fastq - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__quality_filter__q_score - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__cull_seqs - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__degap_seqs - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__dereplicate - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__edit_taxonomy +- name: qiime2__dada2__denoise_ccs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_classifications +- name: qiime2__dada2__denoise_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_cross_validate +- name: qiime2__dada2__denoise_pyro owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_fit_classifier +- name: qiime2__dada2__denoise_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_seqs +- name: qiime2__dada2__plot_base_transitions owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_taxonomy +- name: qiime2__cutadapt__demux_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__extract_seq_segments +- name: qiime2__cutadapt__demux_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__filter_seqs_length +- name: qiime2__cutadapt__trim_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__filter_seqs_length_by_taxon +- name: qiime2__cutadapt__trim_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__filter_taxa +- name: qiime2__composition__add_pseudocount owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_bv_brc_genome_features +- name: qiime2__composition__ancom owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_bv_brc_genomes +- name: qiime2__composition__ancombc owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_bv_brc_metadata +- name: qiime2__composition__ancombc2 owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_eukaryome_data +- name: qiime2__composition__ancombc2_visualizer owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_gtdb_data +- name: qiime2__composition__da_barplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_midori2_data +- name: qiime2__composition__tabulate owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_ncbi_data +- name: qiime2__boots__alpha owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_ncbi_data_protein +- name: qiime2__boots__alpha_average owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_ncbi_genomes +- name: qiime2__boots__alpha_collection owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_pr2_data +- name: qiime2__boots__beta owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_silva_data +- name: qiime2__boots__beta_average owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_unite_data +- name: qiime2__boots__beta_collection owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__merge_taxa +- name: qiime2__boots__core_metrics owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__orient_reads +- name: qiime2__boots__kmer_diversity owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__orient_seqs +- name: qiime2__boots__resample owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__parse_silva_taxonomy +- name: qiime2__vsearch__cluster_features_closed_reference owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__reverse_transcribe +- name: qiime2__vsearch__cluster_features_de_novo owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__subsample_fasta +- name: qiime2__vsearch__cluster_features_open_reference owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__trim_alignment +- name: qiime2__vsearch__dereplicate_sequences owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__classify_samples +- name: qiime2__vsearch__fastq_stats owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__classify_samples_from_dist +- name: qiime2__vsearch__merge_pairs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__classify_samples_ncv +- name: qiime2__vsearch__uchime_denovo owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__confusion_matrix +- name: qiime2__vsearch__uchime_ref owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__fit_classifier +- name: qiime2__demux__emp_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__fit_regressor +- name: qiime2__demux__emp_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__heatmap +- name: qiime2__demux__filter_samples owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__metatable +- name: qiime2__demux__partition_samples_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__predict_classification +- name: qiime2__demux__partition_samples_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__predict_regression +- name: qiime2__demux__subsample_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__regress_samples +- name: qiime2__demux__subsample_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__regress_samples_ncv +- name: qiime2__demux__summarize owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__scatterplot +- name: qiime2__demux__tabulate_read_counts owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__split_table +- name: qiime2__deblur__denoise_16S owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__summarize +- name: qiime2__deblur__denoise_other owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__align_to_tree_mafft_fasttree +- name: qiime2__deblur__visualize_stats owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__align_to_tree_mafft_iqtree +- name: qiime2__diversity__adonis owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__align_to_tree_mafft_raxml +- name: qiime2__diversity__alpha owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__fasttree +- name: qiime2__diversity__alpha_correlation owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__filter_table +- name: qiime2__diversity__alpha_group_significance owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__filter_tree +- name: qiime2__diversity__alpha_phylogenetic owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__iqtree +- name: qiime2__diversity__alpha_rarefaction owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__iqtree_ultrafast_bootstrap +- name: qiime2__diversity__beta owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__midpoint_root +- name: qiime2__diversity__beta_correlation owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__raxml +- name: qiime2__diversity__beta_group_significance owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__raxml_rapid_bootstrap +- name: qiime2__diversity__beta_phylogenetic owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__robinson_foulds +- name: qiime2__diversity__beta_rarefaction owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__distance_matrix +- name: qiime2__diversity__bioenv owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__merge +- name: qiime2__diversity__core_metrics owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__shuffle_groups +- name: qiime2__diversity__core_metrics_phylogenetic owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__tabulate +- name: qiime2__diversity__filter_alpha_diversity owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__alpha_group_significance +- name: qiime2__diversity__filter_distance_matrix owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__collate_stats +- name: qiime2__diversity__mantel owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__facet_across +- name: qiime2__diversity__partial_procrustes owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__facet_within +- name: qiime2__diversity__pcoa owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__mann_whitney_u +- name: qiime2__diversity__pcoa_biplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__mann_whitney_u_facet +- name: qiime2__diversity__procrustes_analysis owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__plot_rainclouds +- name: qiime2__diversity__tsne owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__prep_alpha_distribution +- name: qiime2__diversity__umap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__wilcoxon_srt +- name: qiime2__emperor__biplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__wilcoxon_srt_facet +- name: qiime2__emperor__plot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__bowtie2_build +- name: qiime2__emperor__procrustes_plot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__decontam_identify +- name: qiime2_core__tools__export owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__decontam_identify_batches +- name: qiime2_core__tools__import owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__decontam_score_viz +- name: qiime2_core__tools__import_fastq owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__evaluate_composition +- name: qiime2__taxa__barplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__evaluate_seqs +- name: qiime2__taxa__barplot2 owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__evaluate_taxonomy +- name: qiime2__taxa__collapse owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__exclude_seqs +- name: qiime2__taxa__filter_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__filter_reads +- name: qiime2__taxa__filter_table owner: q2d2 tool_panel_section_id: '' - name: qiime2__diversity_lib__alpha_passthrough @@ -1571,253 +1568,244 @@ tools: - name: qiime2__diversity_lib__weighted_unifrac owner: q2d2 tool_panel_section_id: '' -- name: qiime2__alignment__mafft - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__alignment__mafft_add - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__alignment__mask - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__vizard__boxplot +- name: qiime2__stats__alpha_group_significance owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vizard__heatmap +- name: qiime2__stats__collate_stats owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vizard__lineplot +- name: qiime2__stats__facet_across owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vizard__scatterplot_2d +- name: qiime2__stats__facet_within owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__adonis +- name: qiime2__stats__mann_whitney_u owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha +- name: qiime2__stats__mann_whitney_u_facet owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_correlation +- name: qiime2__stats__plot_rainclouds owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_group_significance +- name: qiime2__stats__prep_alpha_distribution owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_phylogenetic +- name: qiime2__stats__wilcoxon_srt owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_rarefaction +- name: qiime2__stats__wilcoxon_srt_facet owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta +- name: qiime2__sample_classifier__classify_samples owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_correlation +- name: qiime2__sample_classifier__classify_samples_from_dist owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_group_significance +- name: qiime2__sample_classifier__classify_samples_ncv owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_phylogenetic +- name: qiime2__sample_classifier__confusion_matrix owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_rarefaction +- name: qiime2__sample_classifier__fit_classifier owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__bioenv +- name: qiime2__sample_classifier__fit_regressor owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__core_metrics +- name: qiime2__sample_classifier__heatmap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__core_metrics_phylogenetic +- name: qiime2__sample_classifier__metatable owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__filter_alpha_diversity +- name: qiime2__sample_classifier__predict_classification owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__filter_distance_matrix +- name: qiime2__sample_classifier__predict_regression owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__mantel +- name: qiime2__sample_classifier__regress_samples owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__partial_procrustes +- name: qiime2__sample_classifier__regress_samples_ncv owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__pcoa +- name: qiime2__sample_classifier__scatterplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__pcoa_biplot +- name: qiime2__sample_classifier__split_table owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__procrustes_analysis +- name: qiime2__sample_classifier__summarize owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__tsne +- name: qiime2__rescript__cull_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__umap +- name: qiime2__rescript__degap_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__emp_paired +- name: qiime2__rescript__dereplicate owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__emp_single +- name: qiime2__rescript__edit_taxonomy owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__filter_samples +- name: qiime2__rescript__evaluate_classifications owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__partition_samples_paired +- name: qiime2__rescript__evaluate_cross_validate owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__partition_samples_single +- name: qiime2__rescript__evaluate_fit_classifier owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__subsample_paired +- name: qiime2__rescript__evaluate_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__subsample_single +- name: qiime2__rescript__evaluate_taxonomy owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__summarize +- name: qiime2__rescript__extract_seq_segments owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__tabulate_read_counts +- name: qiime2__rescript__filter_seqs_length owner: q2d2 tool_panel_section_id: '' -- name: qiime2__deblur__denoise_16S +- name: qiime2__rescript__filter_seqs_length_by_taxon owner: q2d2 tool_panel_section_id: '' -- name: qiime2__deblur__denoise_other +- name: qiime2__rescript__filter_taxa owner: q2d2 tool_panel_section_id: '' -- name: qiime2__deblur__visualize_stats +- name: qiime2__rescript__get_bv_brc_genome_features owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_ccs +- name: qiime2__rescript__get_bv_brc_genomes owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_paired +- name: qiime2__rescript__get_bv_brc_metadata owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_pyro +- name: qiime2__rescript__get_eukaryome_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_single +- name: qiime2__rescript__get_gtdb_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__plot_base_transitions +- name: qiime2__rescript__get_midori2_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__cutadapt__demux_paired +- name: qiime2__rescript__get_ncbi_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__cutadapt__demux_single +- name: qiime2__rescript__get_ncbi_data_protein owner: q2d2 tool_panel_section_id: '' -- name: qiime2__cutadapt__trim_paired +- name: qiime2__rescript__get_ncbi_genomes owner: q2d2 tool_panel_section_id: '' -- name: qiime2__cutadapt__trim_single +- name: qiime2__rescript__get_pr2_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__add_pseudocount +- name: qiime2__rescript__get_silva_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancom +- name: qiime2__rescript__get_unite_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancombc +- name: qiime2__rescript__merge_taxa owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancombc2 +- name: qiime2__rescript__orient_reads owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancombc2_visualizer +- name: qiime2__rescript__orient_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__da_barplot +- name: qiime2__rescript__parse_silva_taxonomy owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__tabulate +- name: qiime2__rescript__reverse_transcribe owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__barplot +- name: qiime2__rescript__subsample_fasta owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__barplot2 +- name: qiime2__rescript__trim_alignment owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__collapse +- name: qiime2__quality_filter__q_score owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__filter_seqs +- name: qiime2__vizard__boxplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__filter_table +- name: qiime2__vizard__heatmap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__alpha +- name: qiime2__vizard__lineplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__alpha_average +- name: qiime2__vizard__scatterplot_2d owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__alpha_collection +- name: qiime2__alignment__mafft owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__beta +- name: qiime2__alignment__mafft_add owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__beta_average +- name: qiime2__alignment__mask owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__beta_collection +- name: qiime2__phylogeny__align_to_tree_mafft_fasttree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__core_metrics +- name: qiime2__phylogeny__align_to_tree_mafft_iqtree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__kmer_diversity +- name: qiime2__phylogeny__align_to_tree_mafft_raxml owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__resample +- name: qiime2__phylogeny__fasttree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__cluster_features_closed_reference +- name: qiime2__phylogeny__filter_table owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__cluster_features_de_novo +- name: qiime2__phylogeny__filter_tree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__cluster_features_open_reference +- name: qiime2__phylogeny__iqtree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__dereplicate_sequences +- name: qiime2__phylogeny__iqtree_ultrafast_bootstrap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__fastq_stats +- name: qiime2__phylogeny__midpoint_root owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__merge_pairs +- name: qiime2__phylogeny__raxml owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__uchime_denovo +- name: qiime2__phylogeny__raxml_rapid_bootstrap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__uchime_ref +- name: qiime2__phylogeny__robinson_foulds owner: q2d2 tool_panel_section_id: '' -- name: qiime2__emperor__biplot +- name: qiime2__fragment_insertion__classify_otus_experimental owner: q2d2 tool_panel_section_id: '' -- name: qiime2__emperor__plot +- name: qiime2__fragment_insertion__filter_features owner: q2d2 tool_panel_section_id: '' -- name: qiime2__emperor__procrustes_plot +- name: qiime2__fragment_insertion__sepp owner: q2d2 tool_panel_section_id: '' - name: qiime2__feature_classifier__blast @@ -1853,6 +1841,39 @@ tools: - name: qiime2__feature_classifier__vsearch_global owner: q2d2 tool_panel_section_id: '' +- name: qiime2__longitudinal__anova + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__feature_volatility + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__first_differences + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__first_distances + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__linear_mixed_effects + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__maturity_index + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__nmit + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__pairwise_differences + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__pairwise_distances + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__plot_feature_volatility + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__volatility + owner: q2d2 + tool_panel_section_id: '' - name: qiime2__feature_table___summarize owner: q2d2 tool_panel_section_id: '' @@ -1922,76 +1943,73 @@ tools: - name: qiime2__feature_table__transpose owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue___get_sequences - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__fondue__combine_seqs +- name: qiime2__quality_control__bowtie2_build owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__get_all +- name: qiime2__quality_control__decontam_identify owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__get_ids_from_query +- name: qiime2__quality_control__decontam_identify_batches owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__get_metadata +- name: qiime2__quality_control__decontam_score_viz owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__get_sequences +- name: qiime2__quality_control__evaluate_composition owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__merge_metadata +- name: qiime2__quality_control__evaluate_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__scrape_collection +- name: qiime2__quality_control__evaluate_taxonomy owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fragment_insertion__classify_otus_experimental +- name: qiime2__quality_control__exclude_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fragment_insertion__filter_features +- name: qiime2__quality_control__filter_reads owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fragment_insertion__sepp +- name: qiime2__metadata__distance_matrix owner: q2d2 tool_panel_section_id: '' -- name: qiime2__kmerizer__core_metrics +- name: qiime2__metadata__merge owner: q2d2 tool_panel_section_id: '' -- name: qiime2__kmerizer__seqs_to_kmers +- name: qiime2__metadata__shuffle_groups owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__anova +- name: qiime2__metadata__tabulate owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__feature_volatility +- name: qiime2__kmerizer__core_metrics owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__first_differences +- name: qiime2__kmerizer__seqs_to_kmers owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__first_distances +- name: qiime2__fondue___get_sequences owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__linear_mixed_effects +- name: qiime2__fondue__combine_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__maturity_index +- name: qiime2__fondue__get_all owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__nmit +- name: qiime2__fondue__get_ids_from_query owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__pairwise_differences +- name: qiime2__fondue__get_metadata owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__pairwise_distances +- name: qiime2__fondue__get_sequences owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__plot_feature_volatility +- name: qiime2__fondue__merge_metadata owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__volatility +- name: qiime2__fondue__scrape_collection owner: q2d2 tool_panel_section_id: '' - name: qualimap_bamqc diff --git a/communities/microgalaxy/lab/tools/top/GASLINI.yaml b/communities/microgalaxy/lab/tools/top/GASLINI.yaml index 81562e59c..b2d3895f0 100644 --- a/communities/microgalaxy/lab/tools/top/GASLINI.yaml +++ b/communities/microgalaxy/lab/tools/top/GASLINI.yaml @@ -776,6 +776,9 @@ tools: - name: obi_clean owner: iuc tool_panel_section_id: '' +- name: obi_complement + owner: iuc + tool_panel_section_id: '' - name: obi_convert owner: iuc tool_panel_section_id: '' @@ -788,6 +791,18 @@ tools: - name: obi_pairing owner: iuc tool_panel_section_id: '' +- name: obi_pcr + owner: iuc + tool_panel_section_id: '' +- name: obi_refidx + owner: iuc + tool_panel_section_id: '' +- name: obi_tag + owner: iuc + tool_panel_section_id: '' +- name: obi_taxonomy + owner: iuc + tool_panel_section_id: '' - name: obi_uniq owner: iuc tool_panel_section_id: '' @@ -1265,6 +1280,9 @@ tools: - name: picrust_predict_metagenomes owner: iuc tool_panel_section_id: '' +- name: prinseq + owner: iuc + tool_panel_section_id: '' - name: prodigal owner: iuc tool_panel_section_id: '' @@ -1277,262 +1295,241 @@ tools: - name: pygenomeTracks owner: iuc tool_panel_section_id: '' -- name: qiime2_core__tools__export - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2_core__tools__import - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2_core__tools__import_fastq - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__quality_filter__q_score - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__cull_seqs - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__degap_seqs - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__dereplicate - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__edit_taxonomy +- name: qiime2__dada2__denoise_ccs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_classifications +- name: qiime2__dada2__denoise_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_cross_validate +- name: qiime2__dada2__denoise_pyro owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_fit_classifier +- name: qiime2__dada2__denoise_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_seqs +- name: qiime2__dada2__plot_base_transitions owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_taxonomy +- name: qiime2__cutadapt__demux_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__extract_seq_segments +- name: qiime2__cutadapt__demux_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__filter_seqs_length +- name: qiime2__cutadapt__trim_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__filter_seqs_length_by_taxon +- name: qiime2__cutadapt__trim_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__filter_taxa +- name: qiime2__composition__add_pseudocount owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_bv_brc_genome_features +- name: qiime2__composition__ancom owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_bv_brc_genomes +- name: qiime2__composition__ancombc owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_bv_brc_metadata +- name: qiime2__composition__ancombc2 owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_eukaryome_data +- name: qiime2__composition__ancombc2_visualizer owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_gtdb_data +- name: qiime2__composition__da_barplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_midori2_data +- name: qiime2__composition__tabulate owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_ncbi_data +- name: qiime2__boots__alpha owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_ncbi_data_protein +- name: qiime2__boots__alpha_average owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_ncbi_genomes +- name: qiime2__boots__alpha_collection owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_pr2_data +- name: qiime2__boots__beta owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_silva_data +- name: qiime2__boots__beta_average owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_unite_data +- name: qiime2__boots__beta_collection owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__merge_taxa +- name: qiime2__boots__core_metrics owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__orient_reads +- name: qiime2__boots__kmer_diversity owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__orient_seqs +- name: qiime2__boots__resample owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__parse_silva_taxonomy +- name: qiime2__vsearch__cluster_features_closed_reference owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__reverse_transcribe +- name: qiime2__vsearch__cluster_features_de_novo owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__subsample_fasta +- name: qiime2__vsearch__cluster_features_open_reference owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__trim_alignment +- name: qiime2__vsearch__dereplicate_sequences owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__classify_samples +- name: qiime2__vsearch__fastq_stats owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__classify_samples_from_dist +- name: qiime2__vsearch__merge_pairs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__classify_samples_ncv +- name: qiime2__vsearch__uchime_denovo owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__confusion_matrix +- name: qiime2__vsearch__uchime_ref owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__fit_classifier +- name: qiime2__demux__emp_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__fit_regressor +- name: qiime2__demux__emp_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__heatmap +- name: qiime2__demux__filter_samples owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__metatable +- name: qiime2__demux__partition_samples_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__predict_classification +- name: qiime2__demux__partition_samples_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__predict_regression +- name: qiime2__demux__subsample_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__regress_samples +- name: qiime2__demux__subsample_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__regress_samples_ncv +- name: qiime2__demux__summarize owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__scatterplot +- name: qiime2__demux__tabulate_read_counts owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__split_table +- name: qiime2__deblur__denoise_16S owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__summarize +- name: qiime2__deblur__denoise_other owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__align_to_tree_mafft_fasttree +- name: qiime2__deblur__visualize_stats owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__align_to_tree_mafft_iqtree +- name: qiime2__diversity__adonis owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__align_to_tree_mafft_raxml +- name: qiime2__diversity__alpha owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__fasttree +- name: qiime2__diversity__alpha_correlation owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__filter_table +- name: qiime2__diversity__alpha_group_significance owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__filter_tree +- name: qiime2__diversity__alpha_phylogenetic owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__iqtree +- name: qiime2__diversity__alpha_rarefaction owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__iqtree_ultrafast_bootstrap +- name: qiime2__diversity__beta owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__midpoint_root +- name: qiime2__diversity__beta_correlation owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__raxml +- name: qiime2__diversity__beta_group_significance owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__raxml_rapid_bootstrap +- name: qiime2__diversity__beta_phylogenetic owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__robinson_foulds +- name: qiime2__diversity__beta_rarefaction owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__distance_matrix +- name: qiime2__diversity__bioenv owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__merge +- name: qiime2__diversity__core_metrics owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__shuffle_groups +- name: qiime2__diversity__core_metrics_phylogenetic owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__tabulate +- name: qiime2__diversity__filter_alpha_diversity owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__alpha_group_significance +- name: qiime2__diversity__filter_distance_matrix owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__collate_stats +- name: qiime2__diversity__mantel owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__facet_across +- name: qiime2__diversity__partial_procrustes owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__facet_within +- name: qiime2__diversity__pcoa owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__mann_whitney_u +- name: qiime2__diversity__pcoa_biplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__mann_whitney_u_facet +- name: qiime2__diversity__procrustes_analysis owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__plot_rainclouds +- name: qiime2__diversity__tsne owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__prep_alpha_distribution +- name: qiime2__diversity__umap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__wilcoxon_srt +- name: qiime2__emperor__biplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__wilcoxon_srt_facet +- name: qiime2__emperor__plot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__bowtie2_build +- name: qiime2__emperor__procrustes_plot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__decontam_identify +- name: qiime2_core__tools__export owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__decontam_identify_batches +- name: qiime2_core__tools__import owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__decontam_score_viz +- name: qiime2_core__tools__import_fastq owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__evaluate_composition +- name: qiime2__taxa__barplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__evaluate_seqs +- name: qiime2__taxa__barplot2 owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__evaluate_taxonomy +- name: qiime2__taxa__collapse owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__exclude_seqs +- name: qiime2__taxa__filter_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__filter_reads +- name: qiime2__taxa__filter_table owner: q2d2 tool_panel_section_id: '' - name: qiime2__diversity_lib__alpha_passthrough @@ -1571,253 +1568,244 @@ tools: - name: qiime2__diversity_lib__weighted_unifrac owner: q2d2 tool_panel_section_id: '' -- name: qiime2__alignment__mafft - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__alignment__mafft_add - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__alignment__mask - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__vizard__boxplot +- name: qiime2__stats__alpha_group_significance owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vizard__heatmap +- name: qiime2__stats__collate_stats owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vizard__lineplot +- name: qiime2__stats__facet_across owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vizard__scatterplot_2d +- name: qiime2__stats__facet_within owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__adonis +- name: qiime2__stats__mann_whitney_u owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha +- name: qiime2__stats__mann_whitney_u_facet owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_correlation +- name: qiime2__stats__plot_rainclouds owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_group_significance +- name: qiime2__stats__prep_alpha_distribution owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_phylogenetic +- name: qiime2__stats__wilcoxon_srt owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_rarefaction +- name: qiime2__stats__wilcoxon_srt_facet owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta +- name: qiime2__sample_classifier__classify_samples owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_correlation +- name: qiime2__sample_classifier__classify_samples_from_dist owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_group_significance +- name: qiime2__sample_classifier__classify_samples_ncv owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_phylogenetic +- name: qiime2__sample_classifier__confusion_matrix owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_rarefaction +- name: qiime2__sample_classifier__fit_classifier owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__bioenv +- name: qiime2__sample_classifier__fit_regressor owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__core_metrics +- name: qiime2__sample_classifier__heatmap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__core_metrics_phylogenetic +- name: qiime2__sample_classifier__metatable owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__filter_alpha_diversity +- name: qiime2__sample_classifier__predict_classification owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__filter_distance_matrix +- name: qiime2__sample_classifier__predict_regression owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__mantel +- name: qiime2__sample_classifier__regress_samples owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__partial_procrustes +- name: qiime2__sample_classifier__regress_samples_ncv owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__pcoa +- name: qiime2__sample_classifier__scatterplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__pcoa_biplot +- name: qiime2__sample_classifier__split_table owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__procrustes_analysis +- name: qiime2__sample_classifier__summarize owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__tsne +- name: qiime2__rescript__cull_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__umap +- name: qiime2__rescript__degap_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__emp_paired +- name: qiime2__rescript__dereplicate owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__emp_single +- name: qiime2__rescript__edit_taxonomy owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__filter_samples +- name: qiime2__rescript__evaluate_classifications owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__partition_samples_paired +- name: qiime2__rescript__evaluate_cross_validate owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__partition_samples_single +- name: qiime2__rescript__evaluate_fit_classifier owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__subsample_paired +- name: qiime2__rescript__evaluate_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__subsample_single +- name: qiime2__rescript__evaluate_taxonomy owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__summarize +- name: qiime2__rescript__extract_seq_segments owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__tabulate_read_counts +- name: qiime2__rescript__filter_seqs_length owner: q2d2 tool_panel_section_id: '' -- name: qiime2__deblur__denoise_16S +- name: qiime2__rescript__filter_seqs_length_by_taxon owner: q2d2 tool_panel_section_id: '' -- name: qiime2__deblur__denoise_other +- name: qiime2__rescript__filter_taxa owner: q2d2 tool_panel_section_id: '' -- name: qiime2__deblur__visualize_stats +- name: qiime2__rescript__get_bv_brc_genome_features owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_ccs +- name: qiime2__rescript__get_bv_brc_genomes owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_paired +- name: qiime2__rescript__get_bv_brc_metadata owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_pyro +- name: qiime2__rescript__get_eukaryome_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_single +- name: qiime2__rescript__get_gtdb_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__plot_base_transitions +- name: qiime2__rescript__get_midori2_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__cutadapt__demux_paired +- name: qiime2__rescript__get_ncbi_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__cutadapt__demux_single +- name: qiime2__rescript__get_ncbi_data_protein owner: q2d2 tool_panel_section_id: '' -- name: qiime2__cutadapt__trim_paired +- name: qiime2__rescript__get_ncbi_genomes owner: q2d2 tool_panel_section_id: '' -- name: qiime2__cutadapt__trim_single +- name: qiime2__rescript__get_pr2_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__add_pseudocount +- name: qiime2__rescript__get_silva_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancom +- name: qiime2__rescript__get_unite_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancombc +- name: qiime2__rescript__merge_taxa owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancombc2 +- name: qiime2__rescript__orient_reads owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancombc2_visualizer +- name: qiime2__rescript__orient_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__da_barplot +- name: qiime2__rescript__parse_silva_taxonomy owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__tabulate +- name: qiime2__rescript__reverse_transcribe owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__barplot +- name: qiime2__rescript__subsample_fasta owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__barplot2 +- name: qiime2__rescript__trim_alignment owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__collapse +- name: qiime2__quality_filter__q_score owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__filter_seqs +- name: qiime2__vizard__boxplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__filter_table +- name: qiime2__vizard__heatmap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__alpha +- name: qiime2__vizard__lineplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__alpha_average +- name: qiime2__vizard__scatterplot_2d owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__alpha_collection +- name: qiime2__alignment__mafft owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__beta +- name: qiime2__alignment__mafft_add owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__beta_average +- name: qiime2__alignment__mask owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__beta_collection +- name: qiime2__phylogeny__align_to_tree_mafft_fasttree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__core_metrics +- name: qiime2__phylogeny__align_to_tree_mafft_iqtree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__kmer_diversity +- name: qiime2__phylogeny__align_to_tree_mafft_raxml owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__resample +- name: qiime2__phylogeny__fasttree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__cluster_features_closed_reference +- name: qiime2__phylogeny__filter_table owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__cluster_features_de_novo +- name: qiime2__phylogeny__filter_tree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__cluster_features_open_reference +- name: qiime2__phylogeny__iqtree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__dereplicate_sequences +- name: qiime2__phylogeny__iqtree_ultrafast_bootstrap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__fastq_stats +- name: qiime2__phylogeny__midpoint_root owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__merge_pairs +- name: qiime2__phylogeny__raxml owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__uchime_denovo +- name: qiime2__phylogeny__raxml_rapid_bootstrap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__uchime_ref +- name: qiime2__phylogeny__robinson_foulds owner: q2d2 tool_panel_section_id: '' -- name: qiime2__emperor__biplot +- name: qiime2__fragment_insertion__classify_otus_experimental owner: q2d2 tool_panel_section_id: '' -- name: qiime2__emperor__plot +- name: qiime2__fragment_insertion__filter_features owner: q2d2 tool_panel_section_id: '' -- name: qiime2__emperor__procrustes_plot +- name: qiime2__fragment_insertion__sepp owner: q2d2 tool_panel_section_id: '' - name: qiime2__feature_classifier__blast @@ -1853,6 +1841,39 @@ tools: - name: qiime2__feature_classifier__vsearch_global owner: q2d2 tool_panel_section_id: '' +- name: qiime2__longitudinal__anova + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__feature_volatility + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__first_differences + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__first_distances + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__linear_mixed_effects + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__maturity_index + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__nmit + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__pairwise_differences + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__pairwise_distances + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__plot_feature_volatility + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__volatility + owner: q2d2 + tool_panel_section_id: '' - name: qiime2__feature_table___summarize owner: q2d2 tool_panel_section_id: '' @@ -1922,76 +1943,73 @@ tools: - name: qiime2__feature_table__transpose owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue___get_sequences - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__fondue__combine_seqs +- name: qiime2__quality_control__bowtie2_build owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__get_all +- name: qiime2__quality_control__decontam_identify owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__get_ids_from_query +- name: qiime2__quality_control__decontam_identify_batches owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__get_metadata +- name: qiime2__quality_control__decontam_score_viz owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__get_sequences +- name: qiime2__quality_control__evaluate_composition owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__merge_metadata +- name: qiime2__quality_control__evaluate_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__scrape_collection +- name: qiime2__quality_control__evaluate_taxonomy owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fragment_insertion__classify_otus_experimental +- name: qiime2__quality_control__exclude_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fragment_insertion__filter_features +- name: qiime2__quality_control__filter_reads owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fragment_insertion__sepp +- name: qiime2__metadata__distance_matrix owner: q2d2 tool_panel_section_id: '' -- name: qiime2__kmerizer__core_metrics +- name: qiime2__metadata__merge owner: q2d2 tool_panel_section_id: '' -- name: qiime2__kmerizer__seqs_to_kmers +- name: qiime2__metadata__shuffle_groups owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__anova +- name: qiime2__metadata__tabulate owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__feature_volatility +- name: qiime2__kmerizer__core_metrics owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__first_differences +- name: qiime2__kmerizer__seqs_to_kmers owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__first_distances +- name: qiime2__fondue___get_sequences owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__linear_mixed_effects +- name: qiime2__fondue__combine_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__maturity_index +- name: qiime2__fondue__get_all owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__nmit +- name: qiime2__fondue__get_ids_from_query owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__pairwise_differences +- name: qiime2__fondue__get_metadata owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__pairwise_distances +- name: qiime2__fondue__get_sequences owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__plot_feature_volatility +- name: qiime2__fondue__merge_metadata owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__volatility +- name: qiime2__fondue__scrape_collection owner: q2d2 tool_panel_section_id: '' - name: qualimap_bamqc diff --git a/communities/microgalaxy/lab/tools/top/Galaxy@AuBi.yaml b/communities/microgalaxy/lab/tools/top/Galaxy@AuBi.yaml index 8c36e903c..05ed349d6 100644 --- a/communities/microgalaxy/lab/tools/top/Galaxy@AuBi.yaml +++ b/communities/microgalaxy/lab/tools/top/Galaxy@AuBi.yaml @@ -269,6 +269,9 @@ tools: - name: obi_clean owner: iuc tool_panel_section_id: '' +- name: obi_complement + owner: iuc + tool_panel_section_id: '' - name: obi_convert owner: iuc tool_panel_section_id: '' @@ -281,6 +284,18 @@ tools: - name: obi_pairing owner: iuc tool_panel_section_id: '' +- name: obi_pcr + owner: iuc + tool_panel_section_id: '' +- name: obi_refidx + owner: iuc + tool_panel_section_id: '' +- name: obi_tag + owner: iuc + tool_panel_section_id: '' +- name: obi_taxonomy + owner: iuc + tool_panel_section_id: '' - name: obi_uniq owner: iuc tool_panel_section_id: '' @@ -740,364 +755,325 @@ tools: - name: phyloseq_tax_glom owner: iuc tool_panel_section_id: '' -- name: qiime2__rescript__cull_seqs - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__degap_seqs - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__dereplicate - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__edit_taxonomy - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_classifications - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_cross_validate - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_fit_classifier - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_seqs - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_taxonomy - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__extract_seq_segments - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__filter_seqs_length - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__filter_seqs_length_by_taxon - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__filter_taxa - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__get_bv_brc_genome_features +- name: qiime2__dada2__denoise_ccs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_bv_brc_genomes +- name: qiime2__dada2__denoise_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_bv_brc_metadata +- name: qiime2__dada2__denoise_pyro owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_eukaryome_data +- name: qiime2__dada2__denoise_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_gtdb_data +- name: qiime2__dada2__plot_base_transitions owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_midori2_data +- name: qiime2__composition__add_pseudocount owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_ncbi_data +- name: qiime2__composition__ancom owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_ncbi_data_protein +- name: qiime2__composition__ancombc owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_ncbi_genomes +- name: qiime2__composition__ancombc2 owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_pr2_data +- name: qiime2__composition__ancombc2_visualizer owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_silva_data +- name: qiime2__composition__da_barplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_unite_data +- name: qiime2__composition__tabulate owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__merge_taxa +- name: qiime2__boots__alpha owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__orient_reads +- name: qiime2__boots__alpha_average owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__orient_seqs +- name: qiime2__boots__alpha_collection owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__parse_silva_taxonomy +- name: qiime2__boots__beta owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__reverse_transcribe +- name: qiime2__boots__beta_average owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__subsample_fasta +- name: qiime2__boots__beta_collection owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__trim_alignment +- name: qiime2__boots__core_metrics owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__distance_matrix +- name: qiime2__boots__kmer_diversity owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__merge +- name: qiime2__boots__resample owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__shuffle_groups +- name: qiime2__demux__emp_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__tabulate +- name: qiime2__demux__emp_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__alpha_group_significance +- name: qiime2__demux__filter_samples owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__collate_stats +- name: qiime2__demux__partition_samples_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__facet_across +- name: qiime2__demux__partition_samples_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__facet_within +- name: qiime2__demux__subsample_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__mann_whitney_u +- name: qiime2__demux__subsample_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__mann_whitney_u_facet +- name: qiime2__demux__summarize owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__plot_rainclouds +- name: qiime2__demux__tabulate_read_counts owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__prep_alpha_distribution +- name: qiime2__deblur__denoise_16S owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__wilcoxon_srt +- name: qiime2__deblur__denoise_other owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__wilcoxon_srt_facet +- name: qiime2__deblur__visualize_stats owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__bowtie2_build +- name: qiime2__diversity__adonis owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__decontam_identify +- name: qiime2__diversity__alpha owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__decontam_identify_batches +- name: qiime2__diversity__alpha_correlation owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__decontam_score_viz +- name: qiime2__diversity__alpha_group_significance owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__evaluate_composition +- name: qiime2__diversity__alpha_phylogenetic owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__evaluate_seqs +- name: qiime2__diversity__alpha_rarefaction owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__evaluate_taxonomy +- name: qiime2__diversity__beta owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__exclude_seqs +- name: qiime2__diversity__beta_correlation owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__filter_reads +- name: qiime2__diversity__beta_group_significance owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vizard__boxplot +- name: qiime2__diversity__beta_phylogenetic owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vizard__heatmap +- name: qiime2__diversity__beta_rarefaction owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vizard__lineplot +- name: qiime2__diversity__bioenv owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vizard__scatterplot_2d +- name: qiime2__diversity__core_metrics owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__adonis +- name: qiime2__diversity__core_metrics_phylogenetic owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha +- name: qiime2__diversity__filter_alpha_diversity owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_correlation +- name: qiime2__diversity__filter_distance_matrix owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_group_significance +- name: qiime2__diversity__mantel owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_phylogenetic +- name: qiime2__diversity__partial_procrustes owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_rarefaction +- name: qiime2__diversity__pcoa owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta +- name: qiime2__diversity__pcoa_biplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_correlation +- name: qiime2__diversity__procrustes_analysis owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_group_significance +- name: qiime2__diversity__tsne owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_phylogenetic +- name: qiime2__diversity__umap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_rarefaction +- name: qiime2__taxa__barplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__bioenv +- name: qiime2__taxa__barplot2 owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__core_metrics +- name: qiime2__taxa__collapse owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__core_metrics_phylogenetic +- name: qiime2__taxa__filter_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__filter_alpha_diversity +- name: qiime2__taxa__filter_table owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__filter_distance_matrix +- name: qiime2__stats__alpha_group_significance owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__mantel +- name: qiime2__stats__collate_stats owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__partial_procrustes +- name: qiime2__stats__facet_across owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__pcoa +- name: qiime2__stats__facet_within owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__pcoa_biplot +- name: qiime2__stats__mann_whitney_u owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__procrustes_analysis +- name: qiime2__stats__mann_whitney_u_facet owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__tsne +- name: qiime2__stats__plot_rainclouds owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__umap +- name: qiime2__stats__prep_alpha_distribution owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__emp_paired +- name: qiime2__stats__wilcoxon_srt owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__emp_single +- name: qiime2__stats__wilcoxon_srt_facet owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__filter_samples +- name: qiime2__rescript__cull_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__partition_samples_paired +- name: qiime2__rescript__degap_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__partition_samples_single +- name: qiime2__rescript__dereplicate owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__subsample_paired +- name: qiime2__rescript__edit_taxonomy owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__subsample_single +- name: qiime2__rescript__evaluate_classifications owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__summarize +- name: qiime2__rescript__evaluate_cross_validate owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__tabulate_read_counts +- name: qiime2__rescript__evaluate_fit_classifier owner: q2d2 tool_panel_section_id: '' -- name: qiime2__deblur__denoise_16S +- name: qiime2__rescript__evaluate_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__deblur__denoise_other +- name: qiime2__rescript__evaluate_taxonomy owner: q2d2 tool_panel_section_id: '' -- name: qiime2__deblur__visualize_stats +- name: qiime2__rescript__extract_seq_segments owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_ccs +- name: qiime2__rescript__filter_seqs_length owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_paired +- name: qiime2__rescript__filter_seqs_length_by_taxon owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_pyro +- name: qiime2__rescript__filter_taxa owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_single +- name: qiime2__rescript__get_bv_brc_genome_features owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__plot_base_transitions +- name: qiime2__rescript__get_bv_brc_genomes owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__add_pseudocount +- name: qiime2__rescript__get_bv_brc_metadata owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancom +- name: qiime2__rescript__get_eukaryome_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancombc +- name: qiime2__rescript__get_gtdb_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancombc2 +- name: qiime2__rescript__get_midori2_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancombc2_visualizer +- name: qiime2__rescript__get_ncbi_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__da_barplot +- name: qiime2__rescript__get_ncbi_data_protein owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__tabulate +- name: qiime2__rescript__get_ncbi_genomes owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__barplot +- name: qiime2__rescript__get_pr2_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__barplot2 +- name: qiime2__rescript__get_silva_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__collapse +- name: qiime2__rescript__get_unite_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__filter_seqs +- name: qiime2__rescript__merge_taxa owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__filter_table +- name: qiime2__rescript__orient_reads owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__alpha +- name: qiime2__rescript__orient_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__alpha_average +- name: qiime2__rescript__parse_silva_taxonomy owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__alpha_collection +- name: qiime2__rescript__reverse_transcribe owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__beta +- name: qiime2__rescript__subsample_fasta owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__beta_average +- name: qiime2__rescript__trim_alignment owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__beta_collection +- name: qiime2__vizard__boxplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__core_metrics +- name: qiime2__vizard__heatmap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__kmer_diversity +- name: qiime2__vizard__lineplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__resample +- name: qiime2__vizard__scatterplot_2d owner: q2d2 tool_panel_section_id: '' - name: qiime2__feature_classifier__blast @@ -1202,6 +1178,51 @@ tools: - name: qiime2__feature_table__transpose owner: q2d2 tool_panel_section_id: '' +- name: qiime2__quality_control__bowtie2_build + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__quality_control__decontam_identify + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__quality_control__decontam_identify_batches + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__quality_control__decontam_score_viz + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__quality_control__evaluate_composition + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__quality_control__evaluate_seqs + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__quality_control__evaluate_taxonomy + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__quality_control__exclude_seqs + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__quality_control__filter_reads + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__metadata__distance_matrix + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__metadata__merge + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__metadata__shuffle_groups + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__metadata__tabulate + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__kmerizer__core_metrics + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__kmerizer__seqs_to_kmers + owner: q2d2 + tool_panel_section_id: '' - name: qiime2__fondue___get_sequences owner: q2d2 tool_panel_section_id: '' @@ -1226,12 +1247,6 @@ tools: - name: qiime2__fondue__scrape_collection owner: q2d2 tool_panel_section_id: '' -- name: qiime2__kmerizer__core_metrics - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__kmerizer__seqs_to_kmers - owner: q2d2 - tool_panel_section_id: '' - name: qualimap_bamqc owner: iuc tool_panel_section_id: '' diff --git a/communities/microgalaxy/lab/tools/top/Galaxy@Pasteur.yaml b/communities/microgalaxy/lab/tools/top/Galaxy@Pasteur.yaml index f17ccee89..862d0e61a 100644 --- a/communities/microgalaxy/lab/tools/top/Galaxy@Pasteur.yaml +++ b/communities/microgalaxy/lab/tools/top/Galaxy@Pasteur.yaml @@ -713,6 +713,9 @@ tools: - name: obi_clean owner: iuc tool_panel_section_id: '' +- name: obi_complement + owner: iuc + tool_panel_section_id: '' - name: obi_convert owner: iuc tool_panel_section_id: '' @@ -725,6 +728,18 @@ tools: - name: obi_pairing owner: iuc tool_panel_section_id: '' +- name: obi_pcr + owner: iuc + tool_panel_section_id: '' +- name: obi_refidx + owner: iuc + tool_panel_section_id: '' +- name: obi_tag + owner: iuc + tool_panel_section_id: '' +- name: obi_taxonomy + owner: iuc + tool_panel_section_id: '' - name: obi_uniq owner: iuc tool_panel_section_id: '' @@ -1202,268 +1217,250 @@ tools: - name: picrust_predict_metagenomes owner: iuc tool_panel_section_id: '' +- name: prinseq + owner: iuc + tool_panel_section_id: '' - name: prodigal owner: iuc tool_panel_section_id: '' - name: pygenomeTracks owner: iuc tool_panel_section_id: '' -- name: qiime2_core__tools__export - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2_core__tools__import - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2_core__tools__import_fastq - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__quality_filter__q_score - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__cull_seqs - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__degap_seqs - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__dereplicate - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__edit_taxonomy +- name: qiime2__dada2__denoise_ccs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_classifications +- name: qiime2__dada2__denoise_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_cross_validate +- name: qiime2__dada2__denoise_pyro owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_fit_classifier +- name: qiime2__dada2__denoise_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_seqs +- name: qiime2__dada2__plot_base_transitions owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_taxonomy +- name: qiime2__cutadapt__demux_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__extract_seq_segments +- name: qiime2__cutadapt__demux_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__filter_seqs_length +- name: qiime2__cutadapt__trim_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__filter_seqs_length_by_taxon +- name: qiime2__cutadapt__trim_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__filter_taxa +- name: qiime2__composition__add_pseudocount owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_bv_brc_genome_features +- name: qiime2__composition__ancom owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_bv_brc_genomes +- name: qiime2__composition__ancombc owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_bv_brc_metadata +- name: qiime2__composition__ancombc2 owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_eukaryome_data +- name: qiime2__composition__ancombc2_visualizer owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_gtdb_data +- name: qiime2__composition__da_barplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_midori2_data +- name: qiime2__composition__tabulate owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_ncbi_data +- name: qiime2__boots__alpha owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_ncbi_data_protein +- name: qiime2__boots__alpha_average owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_ncbi_genomes +- name: qiime2__boots__alpha_collection owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_pr2_data +- name: qiime2__boots__beta owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_silva_data +- name: qiime2__boots__beta_average owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_unite_data +- name: qiime2__boots__beta_collection owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__merge_taxa +- name: qiime2__boots__core_metrics owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__orient_reads +- name: qiime2__boots__kmer_diversity owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__orient_seqs +- name: qiime2__boots__resample owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__parse_silva_taxonomy +- name: qiime2__vsearch__cluster_features_closed_reference owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__reverse_transcribe +- name: qiime2__vsearch__cluster_features_de_novo owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__subsample_fasta +- name: qiime2__vsearch__cluster_features_open_reference owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__trim_alignment +- name: qiime2__vsearch__dereplicate_sequences owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__classify_samples +- name: qiime2__vsearch__fastq_stats owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__classify_samples_from_dist +- name: qiime2__vsearch__merge_pairs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__classify_samples_ncv +- name: qiime2__vsearch__uchime_denovo owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__confusion_matrix +- name: qiime2__vsearch__uchime_ref owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__fit_classifier +- name: qiime2__demux__emp_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__fit_regressor +- name: qiime2__demux__emp_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__heatmap +- name: qiime2__demux__filter_samples owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__metatable +- name: qiime2__demux__partition_samples_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__predict_classification +- name: qiime2__demux__partition_samples_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__predict_regression +- name: qiime2__demux__subsample_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__regress_samples +- name: qiime2__demux__subsample_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__regress_samples_ncv +- name: qiime2__demux__summarize owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__scatterplot +- name: qiime2__demux__tabulate_read_counts owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__split_table +- name: qiime2__deblur__denoise_16S owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__summarize +- name: qiime2__deblur__denoise_other owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__align_to_tree_mafft_fasttree +- name: qiime2__deblur__visualize_stats owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__align_to_tree_mafft_iqtree +- name: qiime2__diversity__adonis owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__align_to_tree_mafft_raxml +- name: qiime2__diversity__alpha owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__fasttree +- name: qiime2__diversity__alpha_correlation owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__filter_table +- name: qiime2__diversity__alpha_group_significance owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__filter_tree +- name: qiime2__diversity__alpha_phylogenetic owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__iqtree +- name: qiime2__diversity__alpha_rarefaction owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__iqtree_ultrafast_bootstrap +- name: qiime2__diversity__beta owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__midpoint_root +- name: qiime2__diversity__beta_correlation owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__raxml +- name: qiime2__diversity__beta_group_significance owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__raxml_rapid_bootstrap +- name: qiime2__diversity__beta_phylogenetic owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__robinson_foulds +- name: qiime2__diversity__beta_rarefaction owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__distance_matrix +- name: qiime2__diversity__bioenv owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__merge +- name: qiime2__diversity__core_metrics owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__shuffle_groups +- name: qiime2__diversity__core_metrics_phylogenetic owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__tabulate +- name: qiime2__diversity__filter_alpha_diversity owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__alpha_group_significance +- name: qiime2__diversity__filter_distance_matrix owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__collate_stats +- name: qiime2__diversity__mantel owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__facet_across +- name: qiime2__diversity__partial_procrustes owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__facet_within +- name: qiime2__diversity__pcoa owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__mann_whitney_u +- name: qiime2__diversity__pcoa_biplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__mann_whitney_u_facet +- name: qiime2__diversity__procrustes_analysis owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__plot_rainclouds +- name: qiime2__diversity__tsne owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__prep_alpha_distribution +- name: qiime2__diversity__umap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__wilcoxon_srt +- name: qiime2__emperor__biplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__wilcoxon_srt_facet +- name: qiime2__emperor__plot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__bowtie2_build +- name: qiime2__emperor__procrustes_plot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__decontam_identify +- name: qiime2_core__tools__export owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__decontam_identify_batches +- name: qiime2_core__tools__import owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__decontam_score_viz +- name: qiime2_core__tools__import_fastq owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__evaluate_composition +- name: qiime2__taxa__barplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__evaluate_seqs +- name: qiime2__taxa__barplot2 owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__evaluate_taxonomy +- name: qiime2__taxa__collapse owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__exclude_seqs +- name: qiime2__taxa__filter_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__filter_reads +- name: qiime2__taxa__filter_table owner: q2d2 tool_panel_section_id: '' - name: qiime2__diversity_lib__alpha_passthrough @@ -1502,253 +1499,244 @@ tools: - name: qiime2__diversity_lib__weighted_unifrac owner: q2d2 tool_panel_section_id: '' -- name: qiime2__alignment__mafft - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__alignment__mafft_add - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__alignment__mask - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__vizard__boxplot +- name: qiime2__stats__alpha_group_significance owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vizard__heatmap +- name: qiime2__stats__collate_stats owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vizard__lineplot +- name: qiime2__stats__facet_across owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vizard__scatterplot_2d +- name: qiime2__stats__facet_within owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__adonis +- name: qiime2__stats__mann_whitney_u owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha +- name: qiime2__stats__mann_whitney_u_facet owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_correlation +- name: qiime2__stats__plot_rainclouds owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_group_significance +- name: qiime2__stats__prep_alpha_distribution owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_phylogenetic +- name: qiime2__stats__wilcoxon_srt owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_rarefaction +- name: qiime2__stats__wilcoxon_srt_facet owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta +- name: qiime2__sample_classifier__classify_samples owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_correlation +- name: qiime2__sample_classifier__classify_samples_from_dist owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_group_significance +- name: qiime2__sample_classifier__classify_samples_ncv owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_phylogenetic +- name: qiime2__sample_classifier__confusion_matrix owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_rarefaction +- name: qiime2__sample_classifier__fit_classifier owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__bioenv +- name: qiime2__sample_classifier__fit_regressor owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__core_metrics +- name: qiime2__sample_classifier__heatmap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__core_metrics_phylogenetic +- name: qiime2__sample_classifier__metatable owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__filter_alpha_diversity +- name: qiime2__sample_classifier__predict_classification owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__filter_distance_matrix +- name: qiime2__sample_classifier__predict_regression owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__mantel +- name: qiime2__sample_classifier__regress_samples owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__partial_procrustes +- name: qiime2__sample_classifier__regress_samples_ncv owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__pcoa +- name: qiime2__sample_classifier__scatterplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__pcoa_biplot +- name: qiime2__sample_classifier__split_table owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__procrustes_analysis +- name: qiime2__sample_classifier__summarize owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__tsne +- name: qiime2__rescript__cull_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__umap +- name: qiime2__rescript__degap_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__emp_paired +- name: qiime2__rescript__dereplicate owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__emp_single +- name: qiime2__rescript__edit_taxonomy owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__filter_samples +- name: qiime2__rescript__evaluate_classifications owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__partition_samples_paired +- name: qiime2__rescript__evaluate_cross_validate owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__partition_samples_single +- name: qiime2__rescript__evaluate_fit_classifier owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__subsample_paired +- name: qiime2__rescript__evaluate_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__subsample_single +- name: qiime2__rescript__evaluate_taxonomy owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__summarize +- name: qiime2__rescript__extract_seq_segments owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__tabulate_read_counts +- name: qiime2__rescript__filter_seqs_length owner: q2d2 tool_panel_section_id: '' -- name: qiime2__deblur__denoise_16S +- name: qiime2__rescript__filter_seqs_length_by_taxon owner: q2d2 tool_panel_section_id: '' -- name: qiime2__deblur__denoise_other +- name: qiime2__rescript__filter_taxa owner: q2d2 tool_panel_section_id: '' -- name: qiime2__deblur__visualize_stats +- name: qiime2__rescript__get_bv_brc_genome_features owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_ccs +- name: qiime2__rescript__get_bv_brc_genomes owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_paired +- name: qiime2__rescript__get_bv_brc_metadata owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_pyro +- name: qiime2__rescript__get_eukaryome_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_single +- name: qiime2__rescript__get_gtdb_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__plot_base_transitions +- name: qiime2__rescript__get_midori2_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__cutadapt__demux_paired +- name: qiime2__rescript__get_ncbi_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__cutadapt__demux_single +- name: qiime2__rescript__get_ncbi_data_protein owner: q2d2 tool_panel_section_id: '' -- name: qiime2__cutadapt__trim_paired +- name: qiime2__rescript__get_ncbi_genomes owner: q2d2 tool_panel_section_id: '' -- name: qiime2__cutadapt__trim_single +- name: qiime2__rescript__get_pr2_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__add_pseudocount +- name: qiime2__rescript__get_silva_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancom +- name: qiime2__rescript__get_unite_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancombc +- name: qiime2__rescript__merge_taxa owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancombc2 +- name: qiime2__rescript__orient_reads owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancombc2_visualizer +- name: qiime2__rescript__orient_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__da_barplot +- name: qiime2__rescript__parse_silva_taxonomy owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__tabulate +- name: qiime2__rescript__reverse_transcribe owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__barplot +- name: qiime2__rescript__subsample_fasta owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__barplot2 +- name: qiime2__rescript__trim_alignment owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__collapse +- name: qiime2__quality_filter__q_score owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__filter_seqs +- name: qiime2__vizard__boxplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__filter_table +- name: qiime2__vizard__heatmap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__alpha +- name: qiime2__vizard__lineplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__alpha_average +- name: qiime2__vizard__scatterplot_2d owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__alpha_collection +- name: qiime2__alignment__mafft owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__beta +- name: qiime2__alignment__mafft_add owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__beta_average +- name: qiime2__alignment__mask owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__beta_collection +- name: qiime2__phylogeny__align_to_tree_mafft_fasttree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__core_metrics +- name: qiime2__phylogeny__align_to_tree_mafft_iqtree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__kmer_diversity +- name: qiime2__phylogeny__align_to_tree_mafft_raxml owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__resample +- name: qiime2__phylogeny__fasttree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__cluster_features_closed_reference +- name: qiime2__phylogeny__filter_table owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__cluster_features_de_novo +- name: qiime2__phylogeny__filter_tree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__cluster_features_open_reference +- name: qiime2__phylogeny__iqtree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__dereplicate_sequences +- name: qiime2__phylogeny__iqtree_ultrafast_bootstrap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__fastq_stats +- name: qiime2__phylogeny__midpoint_root owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__merge_pairs +- name: qiime2__phylogeny__raxml owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__uchime_denovo +- name: qiime2__phylogeny__raxml_rapid_bootstrap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__uchime_ref +- name: qiime2__phylogeny__robinson_foulds owner: q2d2 tool_panel_section_id: '' -- name: qiime2__emperor__biplot +- name: qiime2__fragment_insertion__classify_otus_experimental owner: q2d2 tool_panel_section_id: '' -- name: qiime2__emperor__plot +- name: qiime2__fragment_insertion__filter_features owner: q2d2 tool_panel_section_id: '' -- name: qiime2__emperor__procrustes_plot +- name: qiime2__fragment_insertion__sepp owner: q2d2 tool_panel_section_id: '' - name: qiime2__feature_classifier__blast @@ -1784,6 +1772,39 @@ tools: - name: qiime2__feature_classifier__vsearch_global owner: q2d2 tool_panel_section_id: '' +- name: qiime2__longitudinal__anova + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__feature_volatility + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__first_differences + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__first_distances + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__linear_mixed_effects + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__maturity_index + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__nmit + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__pairwise_differences + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__pairwise_distances + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__plot_feature_volatility + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__volatility + owner: q2d2 + tool_panel_section_id: '' - name: qiime2__feature_table___summarize owner: q2d2 tool_panel_section_id: '' @@ -1853,76 +1874,73 @@ tools: - name: qiime2__feature_table__transpose owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue___get_sequences - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__fondue__combine_seqs +- name: qiime2__quality_control__bowtie2_build owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__get_all +- name: qiime2__quality_control__decontam_identify owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__get_ids_from_query +- name: qiime2__quality_control__decontam_identify_batches owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__get_metadata +- name: qiime2__quality_control__decontam_score_viz owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__get_sequences +- name: qiime2__quality_control__evaluate_composition owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__merge_metadata +- name: qiime2__quality_control__evaluate_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__scrape_collection +- name: qiime2__quality_control__evaluate_taxonomy owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fragment_insertion__classify_otus_experimental +- name: qiime2__quality_control__exclude_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fragment_insertion__filter_features +- name: qiime2__quality_control__filter_reads owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fragment_insertion__sepp +- name: qiime2__metadata__distance_matrix owner: q2d2 tool_panel_section_id: '' -- name: qiime2__kmerizer__core_metrics +- name: qiime2__metadata__merge owner: q2d2 tool_panel_section_id: '' -- name: qiime2__kmerizer__seqs_to_kmers +- name: qiime2__metadata__shuffle_groups owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__anova +- name: qiime2__metadata__tabulate owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__feature_volatility +- name: qiime2__kmerizer__core_metrics owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__first_differences +- name: qiime2__kmerizer__seqs_to_kmers owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__first_distances +- name: qiime2__fondue___get_sequences owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__linear_mixed_effects +- name: qiime2__fondue__combine_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__maturity_index +- name: qiime2__fondue__get_all owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__nmit +- name: qiime2__fondue__get_ids_from_query owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__pairwise_differences +- name: qiime2__fondue__get_metadata owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__pairwise_distances +- name: qiime2__fondue__get_sequences owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__plot_feature_volatility +- name: qiime2__fondue__merge_metadata owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__volatility +- name: qiime2__fondue__scrape_collection owner: q2d2 tool_panel_section_id: '' - name: recentrifuge diff --git a/communities/microgalaxy/lab/tools/top/GalaxyTrakr.yaml b/communities/microgalaxy/lab/tools/top/GalaxyTrakr.yaml index 22d105a50..3a5b65077 100644 --- a/communities/microgalaxy/lab/tools/top/GalaxyTrakr.yaml +++ b/communities/microgalaxy/lab/tools/top/GalaxyTrakr.yaml @@ -665,6 +665,9 @@ tools: - name: obi_clean owner: iuc tool_panel_section_id: '' +- name: obi_complement + owner: iuc + tool_panel_section_id: '' - name: obi_convert owner: iuc tool_panel_section_id: '' @@ -677,6 +680,18 @@ tools: - name: obi_pairing owner: iuc tool_panel_section_id: '' +- name: obi_pcr + owner: iuc + tool_panel_section_id: '' +- name: obi_refidx + owner: iuc + tool_panel_section_id: '' +- name: obi_tag + owner: iuc + tool_panel_section_id: '' +- name: obi_taxonomy + owner: iuc + tool_panel_section_id: '' - name: obi_uniq owner: iuc tool_panel_section_id: '' @@ -1157,262 +1172,241 @@ tools: - name: pygenomeTracks owner: iuc tool_panel_section_id: '' -- name: qiime2_core__tools__export - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2_core__tools__import - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2_core__tools__import_fastq - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__quality_filter__q_score - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__cull_seqs - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__degap_seqs - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__dereplicate - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__edit_taxonomy +- name: qiime2__dada2__denoise_ccs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_classifications +- name: qiime2__dada2__denoise_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_cross_validate +- name: qiime2__dada2__denoise_pyro owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_fit_classifier +- name: qiime2__dada2__denoise_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_seqs +- name: qiime2__dada2__plot_base_transitions owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_taxonomy +- name: qiime2__cutadapt__demux_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__extract_seq_segments +- name: qiime2__cutadapt__demux_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__filter_seqs_length +- name: qiime2__cutadapt__trim_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__filter_seqs_length_by_taxon +- name: qiime2__cutadapt__trim_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__filter_taxa +- name: qiime2__composition__add_pseudocount owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_bv_brc_genome_features +- name: qiime2__composition__ancom owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_bv_brc_genomes +- name: qiime2__composition__ancombc owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_bv_brc_metadata +- name: qiime2__composition__ancombc2 owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_eukaryome_data +- name: qiime2__composition__ancombc2_visualizer owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_gtdb_data +- name: qiime2__composition__da_barplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_midori2_data +- name: qiime2__composition__tabulate owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_ncbi_data +- name: qiime2__boots__alpha owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_ncbi_data_protein +- name: qiime2__boots__alpha_average owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_ncbi_genomes +- name: qiime2__boots__alpha_collection owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_pr2_data +- name: qiime2__boots__beta owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_silva_data +- name: qiime2__boots__beta_average owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_unite_data +- name: qiime2__boots__beta_collection owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__merge_taxa +- name: qiime2__boots__core_metrics owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__orient_reads +- name: qiime2__boots__kmer_diversity owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__orient_seqs +- name: qiime2__boots__resample owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__parse_silva_taxonomy +- name: qiime2__vsearch__cluster_features_closed_reference owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__reverse_transcribe +- name: qiime2__vsearch__cluster_features_de_novo owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__subsample_fasta +- name: qiime2__vsearch__cluster_features_open_reference owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__trim_alignment +- name: qiime2__vsearch__dereplicate_sequences owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__classify_samples +- name: qiime2__vsearch__fastq_stats owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__classify_samples_from_dist +- name: qiime2__vsearch__merge_pairs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__classify_samples_ncv +- name: qiime2__vsearch__uchime_denovo owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__confusion_matrix +- name: qiime2__vsearch__uchime_ref owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__fit_classifier +- name: qiime2__demux__emp_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__fit_regressor +- name: qiime2__demux__emp_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__heatmap +- name: qiime2__demux__filter_samples owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__metatable +- name: qiime2__demux__partition_samples_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__predict_classification +- name: qiime2__demux__partition_samples_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__predict_regression +- name: qiime2__demux__subsample_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__regress_samples +- name: qiime2__demux__subsample_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__regress_samples_ncv +- name: qiime2__demux__summarize owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__scatterplot +- name: qiime2__demux__tabulate_read_counts owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__split_table +- name: qiime2__deblur__denoise_16S owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__summarize +- name: qiime2__deblur__denoise_other owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__align_to_tree_mafft_fasttree +- name: qiime2__deblur__visualize_stats owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__align_to_tree_mafft_iqtree +- name: qiime2__diversity__adonis owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__align_to_tree_mafft_raxml +- name: qiime2__diversity__alpha owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__fasttree +- name: qiime2__diversity__alpha_correlation owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__filter_table +- name: qiime2__diversity__alpha_group_significance owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__filter_tree +- name: qiime2__diversity__alpha_phylogenetic owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__iqtree +- name: qiime2__diversity__alpha_rarefaction owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__iqtree_ultrafast_bootstrap +- name: qiime2__diversity__beta owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__midpoint_root +- name: qiime2__diversity__beta_correlation owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__raxml +- name: qiime2__diversity__beta_group_significance owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__raxml_rapid_bootstrap +- name: qiime2__diversity__beta_phylogenetic owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__robinson_foulds +- name: qiime2__diversity__beta_rarefaction owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__distance_matrix +- name: qiime2__diversity__bioenv owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__merge +- name: qiime2__diversity__core_metrics owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__shuffle_groups +- name: qiime2__diversity__core_metrics_phylogenetic owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__tabulate +- name: qiime2__diversity__filter_alpha_diversity owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__alpha_group_significance +- name: qiime2__diversity__filter_distance_matrix owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__collate_stats +- name: qiime2__diversity__mantel owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__facet_across +- name: qiime2__diversity__partial_procrustes owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__facet_within +- name: qiime2__diversity__pcoa owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__mann_whitney_u +- name: qiime2__diversity__pcoa_biplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__mann_whitney_u_facet +- name: qiime2__diversity__procrustes_analysis owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__plot_rainclouds +- name: qiime2__diversity__tsne owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__prep_alpha_distribution +- name: qiime2__diversity__umap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__wilcoxon_srt +- name: qiime2__emperor__biplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__wilcoxon_srt_facet +- name: qiime2__emperor__plot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__bowtie2_build +- name: qiime2__emperor__procrustes_plot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__decontam_identify +- name: qiime2_core__tools__export owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__decontam_identify_batches +- name: qiime2_core__tools__import owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__decontam_score_viz +- name: qiime2_core__tools__import_fastq owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__evaluate_composition +- name: qiime2__taxa__barplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__evaluate_seqs +- name: qiime2__taxa__barplot2 owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__evaluate_taxonomy +- name: qiime2__taxa__collapse owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__exclude_seqs +- name: qiime2__taxa__filter_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__filter_reads +- name: qiime2__taxa__filter_table owner: q2d2 tool_panel_section_id: '' - name: qiime2__diversity_lib__alpha_passthrough @@ -1451,253 +1445,244 @@ tools: - name: qiime2__diversity_lib__weighted_unifrac owner: q2d2 tool_panel_section_id: '' -- name: qiime2__alignment__mafft - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__alignment__mafft_add - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__alignment__mask - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__vizard__boxplot +- name: qiime2__stats__alpha_group_significance owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vizard__heatmap +- name: qiime2__stats__collate_stats owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vizard__lineplot +- name: qiime2__stats__facet_across owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vizard__scatterplot_2d +- name: qiime2__stats__facet_within owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__adonis +- name: qiime2__stats__mann_whitney_u owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha +- name: qiime2__stats__mann_whitney_u_facet owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_correlation +- name: qiime2__stats__plot_rainclouds owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_group_significance +- name: qiime2__stats__prep_alpha_distribution owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_phylogenetic +- name: qiime2__stats__wilcoxon_srt owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_rarefaction +- name: qiime2__stats__wilcoxon_srt_facet owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta +- name: qiime2__sample_classifier__classify_samples owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_correlation +- name: qiime2__sample_classifier__classify_samples_from_dist owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_group_significance +- name: qiime2__sample_classifier__classify_samples_ncv owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_phylogenetic +- name: qiime2__sample_classifier__confusion_matrix owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_rarefaction +- name: qiime2__sample_classifier__fit_classifier owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__bioenv +- name: qiime2__sample_classifier__fit_regressor owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__core_metrics +- name: qiime2__sample_classifier__heatmap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__core_metrics_phylogenetic +- name: qiime2__sample_classifier__metatable owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__filter_alpha_diversity +- name: qiime2__sample_classifier__predict_classification owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__filter_distance_matrix +- name: qiime2__sample_classifier__predict_regression owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__mantel +- name: qiime2__sample_classifier__regress_samples owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__partial_procrustes +- name: qiime2__sample_classifier__regress_samples_ncv owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__pcoa +- name: qiime2__sample_classifier__scatterplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__pcoa_biplot +- name: qiime2__sample_classifier__split_table owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__procrustes_analysis +- name: qiime2__sample_classifier__summarize owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__tsne +- name: qiime2__rescript__cull_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__umap +- name: qiime2__rescript__degap_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__emp_paired +- name: qiime2__rescript__dereplicate owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__emp_single +- name: qiime2__rescript__edit_taxonomy owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__filter_samples +- name: qiime2__rescript__evaluate_classifications owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__partition_samples_paired +- name: qiime2__rescript__evaluate_cross_validate owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__partition_samples_single +- name: qiime2__rescript__evaluate_fit_classifier owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__subsample_paired +- name: qiime2__rescript__evaluate_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__subsample_single +- name: qiime2__rescript__evaluate_taxonomy owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__summarize +- name: qiime2__rescript__extract_seq_segments owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__tabulate_read_counts +- name: qiime2__rescript__filter_seqs_length owner: q2d2 tool_panel_section_id: '' -- name: qiime2__deblur__denoise_16S +- name: qiime2__rescript__filter_seqs_length_by_taxon owner: q2d2 tool_panel_section_id: '' -- name: qiime2__deblur__denoise_other +- name: qiime2__rescript__filter_taxa owner: q2d2 tool_panel_section_id: '' -- name: qiime2__deblur__visualize_stats +- name: qiime2__rescript__get_bv_brc_genome_features owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_ccs +- name: qiime2__rescript__get_bv_brc_genomes owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_paired +- name: qiime2__rescript__get_bv_brc_metadata owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_pyro +- name: qiime2__rescript__get_eukaryome_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_single +- name: qiime2__rescript__get_gtdb_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__plot_base_transitions +- name: qiime2__rescript__get_midori2_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__cutadapt__demux_paired +- name: qiime2__rescript__get_ncbi_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__cutadapt__demux_single +- name: qiime2__rescript__get_ncbi_data_protein owner: q2d2 tool_panel_section_id: '' -- name: qiime2__cutadapt__trim_paired +- name: qiime2__rescript__get_ncbi_genomes owner: q2d2 tool_panel_section_id: '' -- name: qiime2__cutadapt__trim_single +- name: qiime2__rescript__get_pr2_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__add_pseudocount +- name: qiime2__rescript__get_silva_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancom +- name: qiime2__rescript__get_unite_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancombc +- name: qiime2__rescript__merge_taxa owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancombc2 +- name: qiime2__rescript__orient_reads owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancombc2_visualizer +- name: qiime2__rescript__orient_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__da_barplot +- name: qiime2__rescript__parse_silva_taxonomy owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__tabulate +- name: qiime2__rescript__reverse_transcribe owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__barplot +- name: qiime2__rescript__subsample_fasta owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__barplot2 +- name: qiime2__rescript__trim_alignment owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__collapse +- name: qiime2__quality_filter__q_score owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__filter_seqs +- name: qiime2__vizard__boxplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__filter_table +- name: qiime2__vizard__heatmap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__alpha +- name: qiime2__vizard__lineplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__alpha_average +- name: qiime2__vizard__scatterplot_2d owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__alpha_collection +- name: qiime2__alignment__mafft owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__beta +- name: qiime2__alignment__mafft_add owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__beta_average +- name: qiime2__alignment__mask owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__beta_collection +- name: qiime2__phylogeny__align_to_tree_mafft_fasttree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__core_metrics +- name: qiime2__phylogeny__align_to_tree_mafft_iqtree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__kmer_diversity +- name: qiime2__phylogeny__align_to_tree_mafft_raxml owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__resample +- name: qiime2__phylogeny__fasttree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__cluster_features_closed_reference +- name: qiime2__phylogeny__filter_table owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__cluster_features_de_novo +- name: qiime2__phylogeny__filter_tree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__cluster_features_open_reference +- name: qiime2__phylogeny__iqtree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__dereplicate_sequences +- name: qiime2__phylogeny__iqtree_ultrafast_bootstrap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__fastq_stats +- name: qiime2__phylogeny__midpoint_root owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__merge_pairs +- name: qiime2__phylogeny__raxml owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__uchime_denovo +- name: qiime2__phylogeny__raxml_rapid_bootstrap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__uchime_ref +- name: qiime2__phylogeny__robinson_foulds owner: q2d2 tool_panel_section_id: '' -- name: qiime2__emperor__biplot +- name: qiime2__fragment_insertion__classify_otus_experimental owner: q2d2 tool_panel_section_id: '' -- name: qiime2__emperor__plot +- name: qiime2__fragment_insertion__filter_features owner: q2d2 tool_panel_section_id: '' -- name: qiime2__emperor__procrustes_plot +- name: qiime2__fragment_insertion__sepp owner: q2d2 tool_panel_section_id: '' - name: qiime2__feature_classifier__blast @@ -1733,6 +1718,39 @@ tools: - name: qiime2__feature_classifier__vsearch_global owner: q2d2 tool_panel_section_id: '' +- name: qiime2__longitudinal__anova + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__feature_volatility + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__first_differences + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__first_distances + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__linear_mixed_effects + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__maturity_index + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__nmit + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__pairwise_differences + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__pairwise_distances + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__plot_feature_volatility + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__volatility + owner: q2d2 + tool_panel_section_id: '' - name: qiime2__feature_table___summarize owner: q2d2 tool_panel_section_id: '' @@ -1802,76 +1820,73 @@ tools: - name: qiime2__feature_table__transpose owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue___get_sequences - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__fondue__combine_seqs +- name: qiime2__quality_control__bowtie2_build owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__get_all +- name: qiime2__quality_control__decontam_identify owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__get_ids_from_query +- name: qiime2__quality_control__decontam_identify_batches owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__get_metadata +- name: qiime2__quality_control__decontam_score_viz owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__get_sequences +- name: qiime2__quality_control__evaluate_composition owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__merge_metadata +- name: qiime2__quality_control__evaluate_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__scrape_collection +- name: qiime2__quality_control__evaluate_taxonomy owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fragment_insertion__classify_otus_experimental +- name: qiime2__quality_control__exclude_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fragment_insertion__filter_features +- name: qiime2__quality_control__filter_reads owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fragment_insertion__sepp +- name: qiime2__metadata__distance_matrix owner: q2d2 tool_panel_section_id: '' -- name: qiime2__kmerizer__core_metrics +- name: qiime2__metadata__merge owner: q2d2 tool_panel_section_id: '' -- name: qiime2__kmerizer__seqs_to_kmers +- name: qiime2__metadata__shuffle_groups owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__anova +- name: qiime2__metadata__tabulate owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__feature_volatility +- name: qiime2__kmerizer__core_metrics owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__first_differences +- name: qiime2__kmerizer__seqs_to_kmers owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__first_distances +- name: qiime2__fondue___get_sequences owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__linear_mixed_effects +- name: qiime2__fondue__combine_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__maturity_index +- name: qiime2__fondue__get_all owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__nmit +- name: qiime2__fondue__get_ids_from_query owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__pairwise_differences +- name: qiime2__fondue__get_metadata owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__pairwise_distances +- name: qiime2__fondue__get_sequences owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__plot_feature_volatility +- name: qiime2__fondue__merge_metadata owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__volatility +- name: qiime2__fondue__scrape_collection owner: q2d2 tool_panel_section_id: '' - name: seqkit_fx2tab diff --git a/communities/microgalaxy/lab/tools/top/HyPhy_HIV_NGS_Tools.yaml b/communities/microgalaxy/lab/tools/top/HyPhy_HIV_NGS_Tools.yaml index b528de7d7..b80db6f40 100644 --- a/communities/microgalaxy/lab/tools/top/HyPhy_HIV_NGS_Tools.yaml +++ b/communities/microgalaxy/lab/tools/top/HyPhy_HIV_NGS_Tools.yaml @@ -773,6 +773,9 @@ tools: - name: obi_clean owner: iuc tool_panel_section_id: '' +- name: obi_complement + owner: iuc + tool_panel_section_id: '' - name: obi_convert owner: iuc tool_panel_section_id: '' @@ -785,6 +788,18 @@ tools: - name: obi_pairing owner: iuc tool_panel_section_id: '' +- name: obi_pcr + owner: iuc + tool_panel_section_id: '' +- name: obi_refidx + owner: iuc + tool_panel_section_id: '' +- name: obi_tag + owner: iuc + tool_panel_section_id: '' +- name: obi_taxonomy + owner: iuc + tool_panel_section_id: '' - name: obi_uniq owner: iuc tool_panel_section_id: '' @@ -1262,6 +1277,9 @@ tools: - name: picrust_predict_metagenomes owner: iuc tool_panel_section_id: '' +- name: prinseq + owner: iuc + tool_panel_section_id: '' - name: prodigal owner: iuc tool_panel_section_id: '' @@ -1274,262 +1292,241 @@ tools: - name: pygenomeTracks owner: iuc tool_panel_section_id: '' -- name: qiime2_core__tools__export - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2_core__tools__import - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2_core__tools__import_fastq - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__quality_filter__q_score - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__cull_seqs - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__degap_seqs - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__dereplicate - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__edit_taxonomy +- name: qiime2__dada2__denoise_ccs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_classifications +- name: qiime2__dada2__denoise_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_cross_validate +- name: qiime2__dada2__denoise_pyro owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_fit_classifier +- name: qiime2__dada2__denoise_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_seqs +- name: qiime2__dada2__plot_base_transitions owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_taxonomy +- name: qiime2__cutadapt__demux_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__extract_seq_segments +- name: qiime2__cutadapt__demux_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__filter_seqs_length +- name: qiime2__cutadapt__trim_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__filter_seqs_length_by_taxon +- name: qiime2__cutadapt__trim_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__filter_taxa +- name: qiime2__composition__add_pseudocount owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_bv_brc_genome_features +- name: qiime2__composition__ancom owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_bv_brc_genomes +- name: qiime2__composition__ancombc owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_bv_brc_metadata +- name: qiime2__composition__ancombc2 owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_eukaryome_data +- name: qiime2__composition__ancombc2_visualizer owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_gtdb_data +- name: qiime2__composition__da_barplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_midori2_data +- name: qiime2__composition__tabulate owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_ncbi_data +- name: qiime2__boots__alpha owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_ncbi_data_protein +- name: qiime2__boots__alpha_average owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_ncbi_genomes +- name: qiime2__boots__alpha_collection owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_pr2_data +- name: qiime2__boots__beta owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_silva_data +- name: qiime2__boots__beta_average owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_unite_data +- name: qiime2__boots__beta_collection owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__merge_taxa +- name: qiime2__boots__core_metrics owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__orient_reads +- name: qiime2__boots__kmer_diversity owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__orient_seqs +- name: qiime2__boots__resample owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__parse_silva_taxonomy +- name: qiime2__vsearch__cluster_features_closed_reference owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__reverse_transcribe +- name: qiime2__vsearch__cluster_features_de_novo owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__subsample_fasta +- name: qiime2__vsearch__cluster_features_open_reference owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__trim_alignment +- name: qiime2__vsearch__dereplicate_sequences owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__classify_samples +- name: qiime2__vsearch__fastq_stats owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__classify_samples_from_dist +- name: qiime2__vsearch__merge_pairs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__classify_samples_ncv +- name: qiime2__vsearch__uchime_denovo owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__confusion_matrix +- name: qiime2__vsearch__uchime_ref owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__fit_classifier +- name: qiime2__demux__emp_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__fit_regressor +- name: qiime2__demux__emp_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__heatmap +- name: qiime2__demux__filter_samples owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__metatable +- name: qiime2__demux__partition_samples_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__predict_classification +- name: qiime2__demux__partition_samples_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__predict_regression +- name: qiime2__demux__subsample_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__regress_samples +- name: qiime2__demux__subsample_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__regress_samples_ncv +- name: qiime2__demux__summarize owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__scatterplot +- name: qiime2__demux__tabulate_read_counts owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__split_table +- name: qiime2__deblur__denoise_16S owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__summarize +- name: qiime2__deblur__denoise_other owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__align_to_tree_mafft_fasttree +- name: qiime2__deblur__visualize_stats owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__align_to_tree_mafft_iqtree +- name: qiime2__diversity__adonis owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__align_to_tree_mafft_raxml +- name: qiime2__diversity__alpha owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__fasttree +- name: qiime2__diversity__alpha_correlation owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__filter_table +- name: qiime2__diversity__alpha_group_significance owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__filter_tree +- name: qiime2__diversity__alpha_phylogenetic owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__iqtree +- name: qiime2__diversity__alpha_rarefaction owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__iqtree_ultrafast_bootstrap +- name: qiime2__diversity__beta owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__midpoint_root +- name: qiime2__diversity__beta_correlation owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__raxml +- name: qiime2__diversity__beta_group_significance owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__raxml_rapid_bootstrap +- name: qiime2__diversity__beta_phylogenetic owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__robinson_foulds +- name: qiime2__diversity__beta_rarefaction owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__distance_matrix +- name: qiime2__diversity__bioenv owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__merge +- name: qiime2__diversity__core_metrics owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__shuffle_groups +- name: qiime2__diversity__core_metrics_phylogenetic owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__tabulate +- name: qiime2__diversity__filter_alpha_diversity owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__alpha_group_significance +- name: qiime2__diversity__filter_distance_matrix owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__collate_stats +- name: qiime2__diversity__mantel owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__facet_across +- name: qiime2__diversity__partial_procrustes owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__facet_within +- name: qiime2__diversity__pcoa owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__mann_whitney_u +- name: qiime2__diversity__pcoa_biplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__mann_whitney_u_facet +- name: qiime2__diversity__procrustes_analysis owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__plot_rainclouds +- name: qiime2__diversity__tsne owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__prep_alpha_distribution +- name: qiime2__diversity__umap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__wilcoxon_srt +- name: qiime2__emperor__biplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__wilcoxon_srt_facet +- name: qiime2__emperor__plot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__bowtie2_build +- name: qiime2__emperor__procrustes_plot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__decontam_identify +- name: qiime2_core__tools__export owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__decontam_identify_batches +- name: qiime2_core__tools__import owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__decontam_score_viz +- name: qiime2_core__tools__import_fastq owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__evaluate_composition +- name: qiime2__taxa__barplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__evaluate_seqs +- name: qiime2__taxa__barplot2 owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__evaluate_taxonomy +- name: qiime2__taxa__collapse owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__exclude_seqs +- name: qiime2__taxa__filter_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__filter_reads +- name: qiime2__taxa__filter_table owner: q2d2 tool_panel_section_id: '' - name: qiime2__diversity_lib__alpha_passthrough @@ -1568,253 +1565,244 @@ tools: - name: qiime2__diversity_lib__weighted_unifrac owner: q2d2 tool_panel_section_id: '' -- name: qiime2__alignment__mafft - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__alignment__mafft_add - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__alignment__mask - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__vizard__boxplot +- name: qiime2__stats__alpha_group_significance owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vizard__heatmap +- name: qiime2__stats__collate_stats owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vizard__lineplot +- name: qiime2__stats__facet_across owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vizard__scatterplot_2d +- name: qiime2__stats__facet_within owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__adonis +- name: qiime2__stats__mann_whitney_u owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha +- name: qiime2__stats__mann_whitney_u_facet owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_correlation +- name: qiime2__stats__plot_rainclouds owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_group_significance +- name: qiime2__stats__prep_alpha_distribution owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_phylogenetic +- name: qiime2__stats__wilcoxon_srt owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_rarefaction +- name: qiime2__stats__wilcoxon_srt_facet owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta +- name: qiime2__sample_classifier__classify_samples owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_correlation +- name: qiime2__sample_classifier__classify_samples_from_dist owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_group_significance +- name: qiime2__sample_classifier__classify_samples_ncv owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_phylogenetic +- name: qiime2__sample_classifier__confusion_matrix owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_rarefaction +- name: qiime2__sample_classifier__fit_classifier owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__bioenv +- name: qiime2__sample_classifier__fit_regressor owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__core_metrics +- name: qiime2__sample_classifier__heatmap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__core_metrics_phylogenetic +- name: qiime2__sample_classifier__metatable owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__filter_alpha_diversity +- name: qiime2__sample_classifier__predict_classification owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__filter_distance_matrix +- name: qiime2__sample_classifier__predict_regression owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__mantel +- name: qiime2__sample_classifier__regress_samples owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__partial_procrustes +- name: qiime2__sample_classifier__regress_samples_ncv owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__pcoa +- name: qiime2__sample_classifier__scatterplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__pcoa_biplot +- name: qiime2__sample_classifier__split_table owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__procrustes_analysis +- name: qiime2__sample_classifier__summarize owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__tsne +- name: qiime2__rescript__cull_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__umap +- name: qiime2__rescript__degap_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__emp_paired +- name: qiime2__rescript__dereplicate owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__emp_single +- name: qiime2__rescript__edit_taxonomy owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__filter_samples +- name: qiime2__rescript__evaluate_classifications owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__partition_samples_paired +- name: qiime2__rescript__evaluate_cross_validate owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__partition_samples_single +- name: qiime2__rescript__evaluate_fit_classifier owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__subsample_paired +- name: qiime2__rescript__evaluate_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__subsample_single +- name: qiime2__rescript__evaluate_taxonomy owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__summarize +- name: qiime2__rescript__extract_seq_segments owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__tabulate_read_counts +- name: qiime2__rescript__filter_seqs_length owner: q2d2 tool_panel_section_id: '' -- name: qiime2__deblur__denoise_16S +- name: qiime2__rescript__filter_seqs_length_by_taxon owner: q2d2 tool_panel_section_id: '' -- name: qiime2__deblur__denoise_other +- name: qiime2__rescript__filter_taxa owner: q2d2 tool_panel_section_id: '' -- name: qiime2__deblur__visualize_stats +- name: qiime2__rescript__get_bv_brc_genome_features owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_ccs +- name: qiime2__rescript__get_bv_brc_genomes owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_paired +- name: qiime2__rescript__get_bv_brc_metadata owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_pyro +- name: qiime2__rescript__get_eukaryome_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_single +- name: qiime2__rescript__get_gtdb_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__plot_base_transitions +- name: qiime2__rescript__get_midori2_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__cutadapt__demux_paired +- name: qiime2__rescript__get_ncbi_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__cutadapt__demux_single +- name: qiime2__rescript__get_ncbi_data_protein owner: q2d2 tool_panel_section_id: '' -- name: qiime2__cutadapt__trim_paired +- name: qiime2__rescript__get_ncbi_genomes owner: q2d2 tool_panel_section_id: '' -- name: qiime2__cutadapt__trim_single +- name: qiime2__rescript__get_pr2_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__add_pseudocount +- name: qiime2__rescript__get_silva_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancom +- name: qiime2__rescript__get_unite_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancombc +- name: qiime2__rescript__merge_taxa owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancombc2 +- name: qiime2__rescript__orient_reads owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancombc2_visualizer +- name: qiime2__rescript__orient_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__da_barplot +- name: qiime2__rescript__parse_silva_taxonomy owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__tabulate +- name: qiime2__rescript__reverse_transcribe owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__barplot +- name: qiime2__rescript__subsample_fasta owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__barplot2 +- name: qiime2__rescript__trim_alignment owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__collapse +- name: qiime2__quality_filter__q_score owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__filter_seqs +- name: qiime2__vizard__boxplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__filter_table +- name: qiime2__vizard__heatmap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__alpha +- name: qiime2__vizard__lineplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__alpha_average +- name: qiime2__vizard__scatterplot_2d owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__alpha_collection +- name: qiime2__alignment__mafft owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__beta +- name: qiime2__alignment__mafft_add owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__beta_average +- name: qiime2__alignment__mask owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__beta_collection +- name: qiime2__phylogeny__align_to_tree_mafft_fasttree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__core_metrics +- name: qiime2__phylogeny__align_to_tree_mafft_iqtree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__kmer_diversity +- name: qiime2__phylogeny__align_to_tree_mafft_raxml owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__resample +- name: qiime2__phylogeny__fasttree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__cluster_features_closed_reference +- name: qiime2__phylogeny__filter_table owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__cluster_features_de_novo +- name: qiime2__phylogeny__filter_tree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__cluster_features_open_reference +- name: qiime2__phylogeny__iqtree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__dereplicate_sequences +- name: qiime2__phylogeny__iqtree_ultrafast_bootstrap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__fastq_stats +- name: qiime2__phylogeny__midpoint_root owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__merge_pairs +- name: qiime2__phylogeny__raxml owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__uchime_denovo +- name: qiime2__phylogeny__raxml_rapid_bootstrap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__uchime_ref +- name: qiime2__phylogeny__robinson_foulds owner: q2d2 tool_panel_section_id: '' -- name: qiime2__emperor__biplot +- name: qiime2__fragment_insertion__classify_otus_experimental owner: q2d2 tool_panel_section_id: '' -- name: qiime2__emperor__plot +- name: qiime2__fragment_insertion__filter_features owner: q2d2 tool_panel_section_id: '' -- name: qiime2__emperor__procrustes_plot +- name: qiime2__fragment_insertion__sepp owner: q2d2 tool_panel_section_id: '' - name: qiime2__feature_classifier__blast @@ -1850,6 +1838,39 @@ tools: - name: qiime2__feature_classifier__vsearch_global owner: q2d2 tool_panel_section_id: '' +- name: qiime2__longitudinal__anova + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__feature_volatility + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__first_differences + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__first_distances + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__linear_mixed_effects + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__maturity_index + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__nmit + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__pairwise_differences + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__pairwise_distances + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__plot_feature_volatility + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__volatility + owner: q2d2 + tool_panel_section_id: '' - name: qiime2__feature_table___summarize owner: q2d2 tool_panel_section_id: '' @@ -1919,76 +1940,73 @@ tools: - name: qiime2__feature_table__transpose owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue___get_sequences - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__fondue__combine_seqs +- name: qiime2__quality_control__bowtie2_build owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__get_all +- name: qiime2__quality_control__decontam_identify owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__get_ids_from_query +- name: qiime2__quality_control__decontam_identify_batches owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__get_metadata +- name: qiime2__quality_control__decontam_score_viz owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__get_sequences +- name: qiime2__quality_control__evaluate_composition owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__merge_metadata +- name: qiime2__quality_control__evaluate_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__scrape_collection +- name: qiime2__quality_control__evaluate_taxonomy owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fragment_insertion__classify_otus_experimental +- name: qiime2__quality_control__exclude_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fragment_insertion__filter_features +- name: qiime2__quality_control__filter_reads owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fragment_insertion__sepp +- name: qiime2__metadata__distance_matrix owner: q2d2 tool_panel_section_id: '' -- name: qiime2__kmerizer__core_metrics +- name: qiime2__metadata__merge owner: q2d2 tool_panel_section_id: '' -- name: qiime2__kmerizer__seqs_to_kmers +- name: qiime2__metadata__shuffle_groups owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__anova +- name: qiime2__metadata__tabulate owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__feature_volatility +- name: qiime2__kmerizer__core_metrics owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__first_differences +- name: qiime2__kmerizer__seqs_to_kmers owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__first_distances +- name: qiime2__fondue___get_sequences owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__linear_mixed_effects +- name: qiime2__fondue__combine_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__maturity_index +- name: qiime2__fondue__get_all owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__nmit +- name: qiime2__fondue__get_ids_from_query owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__pairwise_differences +- name: qiime2__fondue__get_metadata owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__pairwise_distances +- name: qiime2__fondue__get_sequences owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__plot_feature_volatility +- name: qiime2__fondue__merge_metadata owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__volatility +- name: qiime2__fondue__scrape_collection owner: q2d2 tool_panel_section_id: '' - name: qualimap_bamqc diff --git a/communities/microgalaxy/lab/tools/top/IPK_Galaxy_Blast_Suite.yaml b/communities/microgalaxy/lab/tools/top/IPK_Galaxy_Blast_Suite.yaml index 81562e59c..b2d3895f0 100644 --- a/communities/microgalaxy/lab/tools/top/IPK_Galaxy_Blast_Suite.yaml +++ b/communities/microgalaxy/lab/tools/top/IPK_Galaxy_Blast_Suite.yaml @@ -776,6 +776,9 @@ tools: - name: obi_clean owner: iuc tool_panel_section_id: '' +- name: obi_complement + owner: iuc + tool_panel_section_id: '' - name: obi_convert owner: iuc tool_panel_section_id: '' @@ -788,6 +791,18 @@ tools: - name: obi_pairing owner: iuc tool_panel_section_id: '' +- name: obi_pcr + owner: iuc + tool_panel_section_id: '' +- name: obi_refidx + owner: iuc + tool_panel_section_id: '' +- name: obi_tag + owner: iuc + tool_panel_section_id: '' +- name: obi_taxonomy + owner: iuc + tool_panel_section_id: '' - name: obi_uniq owner: iuc tool_panel_section_id: '' @@ -1265,6 +1280,9 @@ tools: - name: picrust_predict_metagenomes owner: iuc tool_panel_section_id: '' +- name: prinseq + owner: iuc + tool_panel_section_id: '' - name: prodigal owner: iuc tool_panel_section_id: '' @@ -1277,262 +1295,241 @@ tools: - name: pygenomeTracks owner: iuc tool_panel_section_id: '' -- name: qiime2_core__tools__export - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2_core__tools__import - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2_core__tools__import_fastq - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__quality_filter__q_score - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__cull_seqs - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__degap_seqs - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__dereplicate - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__edit_taxonomy +- name: qiime2__dada2__denoise_ccs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_classifications +- name: qiime2__dada2__denoise_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_cross_validate +- name: qiime2__dada2__denoise_pyro owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_fit_classifier +- name: qiime2__dada2__denoise_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_seqs +- name: qiime2__dada2__plot_base_transitions owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_taxonomy +- name: qiime2__cutadapt__demux_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__extract_seq_segments +- name: qiime2__cutadapt__demux_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__filter_seqs_length +- name: qiime2__cutadapt__trim_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__filter_seqs_length_by_taxon +- name: qiime2__cutadapt__trim_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__filter_taxa +- name: qiime2__composition__add_pseudocount owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_bv_brc_genome_features +- name: qiime2__composition__ancom owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_bv_brc_genomes +- name: qiime2__composition__ancombc owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_bv_brc_metadata +- name: qiime2__composition__ancombc2 owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_eukaryome_data +- name: qiime2__composition__ancombc2_visualizer owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_gtdb_data +- name: qiime2__composition__da_barplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_midori2_data +- name: qiime2__composition__tabulate owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_ncbi_data +- name: qiime2__boots__alpha owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_ncbi_data_protein +- name: qiime2__boots__alpha_average owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_ncbi_genomes +- name: qiime2__boots__alpha_collection owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_pr2_data +- name: qiime2__boots__beta owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_silva_data +- name: qiime2__boots__beta_average owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_unite_data +- name: qiime2__boots__beta_collection owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__merge_taxa +- name: qiime2__boots__core_metrics owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__orient_reads +- name: qiime2__boots__kmer_diversity owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__orient_seqs +- name: qiime2__boots__resample owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__parse_silva_taxonomy +- name: qiime2__vsearch__cluster_features_closed_reference owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__reverse_transcribe +- name: qiime2__vsearch__cluster_features_de_novo owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__subsample_fasta +- name: qiime2__vsearch__cluster_features_open_reference owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__trim_alignment +- name: qiime2__vsearch__dereplicate_sequences owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__classify_samples +- name: qiime2__vsearch__fastq_stats owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__classify_samples_from_dist +- name: qiime2__vsearch__merge_pairs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__classify_samples_ncv +- name: qiime2__vsearch__uchime_denovo owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__confusion_matrix +- name: qiime2__vsearch__uchime_ref owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__fit_classifier +- name: qiime2__demux__emp_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__fit_regressor +- name: qiime2__demux__emp_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__heatmap +- name: qiime2__demux__filter_samples owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__metatable +- name: qiime2__demux__partition_samples_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__predict_classification +- name: qiime2__demux__partition_samples_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__predict_regression +- name: qiime2__demux__subsample_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__regress_samples +- name: qiime2__demux__subsample_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__regress_samples_ncv +- name: qiime2__demux__summarize owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__scatterplot +- name: qiime2__demux__tabulate_read_counts owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__split_table +- name: qiime2__deblur__denoise_16S owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__summarize +- name: qiime2__deblur__denoise_other owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__align_to_tree_mafft_fasttree +- name: qiime2__deblur__visualize_stats owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__align_to_tree_mafft_iqtree +- name: qiime2__diversity__adonis owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__align_to_tree_mafft_raxml +- name: qiime2__diversity__alpha owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__fasttree +- name: qiime2__diversity__alpha_correlation owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__filter_table +- name: qiime2__diversity__alpha_group_significance owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__filter_tree +- name: qiime2__diversity__alpha_phylogenetic owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__iqtree +- name: qiime2__diversity__alpha_rarefaction owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__iqtree_ultrafast_bootstrap +- name: qiime2__diversity__beta owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__midpoint_root +- name: qiime2__diversity__beta_correlation owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__raxml +- name: qiime2__diversity__beta_group_significance owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__raxml_rapid_bootstrap +- name: qiime2__diversity__beta_phylogenetic owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__robinson_foulds +- name: qiime2__diversity__beta_rarefaction owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__distance_matrix +- name: qiime2__diversity__bioenv owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__merge +- name: qiime2__diversity__core_metrics owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__shuffle_groups +- name: qiime2__diversity__core_metrics_phylogenetic owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__tabulate +- name: qiime2__diversity__filter_alpha_diversity owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__alpha_group_significance +- name: qiime2__diversity__filter_distance_matrix owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__collate_stats +- name: qiime2__diversity__mantel owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__facet_across +- name: qiime2__diversity__partial_procrustes owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__facet_within +- name: qiime2__diversity__pcoa owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__mann_whitney_u +- name: qiime2__diversity__pcoa_biplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__mann_whitney_u_facet +- name: qiime2__diversity__procrustes_analysis owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__plot_rainclouds +- name: qiime2__diversity__tsne owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__prep_alpha_distribution +- name: qiime2__diversity__umap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__wilcoxon_srt +- name: qiime2__emperor__biplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__wilcoxon_srt_facet +- name: qiime2__emperor__plot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__bowtie2_build +- name: qiime2__emperor__procrustes_plot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__decontam_identify +- name: qiime2_core__tools__export owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__decontam_identify_batches +- name: qiime2_core__tools__import owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__decontam_score_viz +- name: qiime2_core__tools__import_fastq owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__evaluate_composition +- name: qiime2__taxa__barplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__evaluate_seqs +- name: qiime2__taxa__barplot2 owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__evaluate_taxonomy +- name: qiime2__taxa__collapse owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__exclude_seqs +- name: qiime2__taxa__filter_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__filter_reads +- name: qiime2__taxa__filter_table owner: q2d2 tool_panel_section_id: '' - name: qiime2__diversity_lib__alpha_passthrough @@ -1571,253 +1568,244 @@ tools: - name: qiime2__diversity_lib__weighted_unifrac owner: q2d2 tool_panel_section_id: '' -- name: qiime2__alignment__mafft - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__alignment__mafft_add - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__alignment__mask - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__vizard__boxplot +- name: qiime2__stats__alpha_group_significance owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vizard__heatmap +- name: qiime2__stats__collate_stats owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vizard__lineplot +- name: qiime2__stats__facet_across owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vizard__scatterplot_2d +- name: qiime2__stats__facet_within owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__adonis +- name: qiime2__stats__mann_whitney_u owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha +- name: qiime2__stats__mann_whitney_u_facet owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_correlation +- name: qiime2__stats__plot_rainclouds owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_group_significance +- name: qiime2__stats__prep_alpha_distribution owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_phylogenetic +- name: qiime2__stats__wilcoxon_srt owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_rarefaction +- name: qiime2__stats__wilcoxon_srt_facet owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta +- name: qiime2__sample_classifier__classify_samples owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_correlation +- name: qiime2__sample_classifier__classify_samples_from_dist owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_group_significance +- name: qiime2__sample_classifier__classify_samples_ncv owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_phylogenetic +- name: qiime2__sample_classifier__confusion_matrix owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_rarefaction +- name: qiime2__sample_classifier__fit_classifier owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__bioenv +- name: qiime2__sample_classifier__fit_regressor owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__core_metrics +- name: qiime2__sample_classifier__heatmap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__core_metrics_phylogenetic +- name: qiime2__sample_classifier__metatable owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__filter_alpha_diversity +- name: qiime2__sample_classifier__predict_classification owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__filter_distance_matrix +- name: qiime2__sample_classifier__predict_regression owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__mantel +- name: qiime2__sample_classifier__regress_samples owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__partial_procrustes +- name: qiime2__sample_classifier__regress_samples_ncv owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__pcoa +- name: qiime2__sample_classifier__scatterplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__pcoa_biplot +- name: qiime2__sample_classifier__split_table owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__procrustes_analysis +- name: qiime2__sample_classifier__summarize owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__tsne +- name: qiime2__rescript__cull_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__umap +- name: qiime2__rescript__degap_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__emp_paired +- name: qiime2__rescript__dereplicate owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__emp_single +- name: qiime2__rescript__edit_taxonomy owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__filter_samples +- name: qiime2__rescript__evaluate_classifications owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__partition_samples_paired +- name: qiime2__rescript__evaluate_cross_validate owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__partition_samples_single +- name: qiime2__rescript__evaluate_fit_classifier owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__subsample_paired +- name: qiime2__rescript__evaluate_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__subsample_single +- name: qiime2__rescript__evaluate_taxonomy owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__summarize +- name: qiime2__rescript__extract_seq_segments owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__tabulate_read_counts +- name: qiime2__rescript__filter_seqs_length owner: q2d2 tool_panel_section_id: '' -- name: qiime2__deblur__denoise_16S +- name: qiime2__rescript__filter_seqs_length_by_taxon owner: q2d2 tool_panel_section_id: '' -- name: qiime2__deblur__denoise_other +- name: qiime2__rescript__filter_taxa owner: q2d2 tool_panel_section_id: '' -- name: qiime2__deblur__visualize_stats +- name: qiime2__rescript__get_bv_brc_genome_features owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_ccs +- name: qiime2__rescript__get_bv_brc_genomes owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_paired +- name: qiime2__rescript__get_bv_brc_metadata owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_pyro +- name: qiime2__rescript__get_eukaryome_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_single +- name: qiime2__rescript__get_gtdb_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__plot_base_transitions +- name: qiime2__rescript__get_midori2_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__cutadapt__demux_paired +- name: qiime2__rescript__get_ncbi_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__cutadapt__demux_single +- name: qiime2__rescript__get_ncbi_data_protein owner: q2d2 tool_panel_section_id: '' -- name: qiime2__cutadapt__trim_paired +- name: qiime2__rescript__get_ncbi_genomes owner: q2d2 tool_panel_section_id: '' -- name: qiime2__cutadapt__trim_single +- name: qiime2__rescript__get_pr2_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__add_pseudocount +- name: qiime2__rescript__get_silva_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancom +- name: qiime2__rescript__get_unite_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancombc +- name: qiime2__rescript__merge_taxa owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancombc2 +- name: qiime2__rescript__orient_reads owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancombc2_visualizer +- name: qiime2__rescript__orient_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__da_barplot +- name: qiime2__rescript__parse_silva_taxonomy owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__tabulate +- name: qiime2__rescript__reverse_transcribe owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__barplot +- name: qiime2__rescript__subsample_fasta owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__barplot2 +- name: qiime2__rescript__trim_alignment owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__collapse +- name: qiime2__quality_filter__q_score owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__filter_seqs +- name: qiime2__vizard__boxplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__filter_table +- name: qiime2__vizard__heatmap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__alpha +- name: qiime2__vizard__lineplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__alpha_average +- name: qiime2__vizard__scatterplot_2d owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__alpha_collection +- name: qiime2__alignment__mafft owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__beta +- name: qiime2__alignment__mafft_add owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__beta_average +- name: qiime2__alignment__mask owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__beta_collection +- name: qiime2__phylogeny__align_to_tree_mafft_fasttree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__core_metrics +- name: qiime2__phylogeny__align_to_tree_mafft_iqtree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__kmer_diversity +- name: qiime2__phylogeny__align_to_tree_mafft_raxml owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__resample +- name: qiime2__phylogeny__fasttree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__cluster_features_closed_reference +- name: qiime2__phylogeny__filter_table owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__cluster_features_de_novo +- name: qiime2__phylogeny__filter_tree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__cluster_features_open_reference +- name: qiime2__phylogeny__iqtree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__dereplicate_sequences +- name: qiime2__phylogeny__iqtree_ultrafast_bootstrap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__fastq_stats +- name: qiime2__phylogeny__midpoint_root owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__merge_pairs +- name: qiime2__phylogeny__raxml owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__uchime_denovo +- name: qiime2__phylogeny__raxml_rapid_bootstrap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__uchime_ref +- name: qiime2__phylogeny__robinson_foulds owner: q2d2 tool_panel_section_id: '' -- name: qiime2__emperor__biplot +- name: qiime2__fragment_insertion__classify_otus_experimental owner: q2d2 tool_panel_section_id: '' -- name: qiime2__emperor__plot +- name: qiime2__fragment_insertion__filter_features owner: q2d2 tool_panel_section_id: '' -- name: qiime2__emperor__procrustes_plot +- name: qiime2__fragment_insertion__sepp owner: q2d2 tool_panel_section_id: '' - name: qiime2__feature_classifier__blast @@ -1853,6 +1841,39 @@ tools: - name: qiime2__feature_classifier__vsearch_global owner: q2d2 tool_panel_section_id: '' +- name: qiime2__longitudinal__anova + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__feature_volatility + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__first_differences + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__first_distances + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__linear_mixed_effects + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__maturity_index + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__nmit + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__pairwise_differences + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__pairwise_distances + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__plot_feature_volatility + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__volatility + owner: q2d2 + tool_panel_section_id: '' - name: qiime2__feature_table___summarize owner: q2d2 tool_panel_section_id: '' @@ -1922,76 +1943,73 @@ tools: - name: qiime2__feature_table__transpose owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue___get_sequences - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__fondue__combine_seqs +- name: qiime2__quality_control__bowtie2_build owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__get_all +- name: qiime2__quality_control__decontam_identify owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__get_ids_from_query +- name: qiime2__quality_control__decontam_identify_batches owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__get_metadata +- name: qiime2__quality_control__decontam_score_viz owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__get_sequences +- name: qiime2__quality_control__evaluate_composition owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__merge_metadata +- name: qiime2__quality_control__evaluate_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__scrape_collection +- name: qiime2__quality_control__evaluate_taxonomy owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fragment_insertion__classify_otus_experimental +- name: qiime2__quality_control__exclude_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fragment_insertion__filter_features +- name: qiime2__quality_control__filter_reads owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fragment_insertion__sepp +- name: qiime2__metadata__distance_matrix owner: q2d2 tool_panel_section_id: '' -- name: qiime2__kmerizer__core_metrics +- name: qiime2__metadata__merge owner: q2d2 tool_panel_section_id: '' -- name: qiime2__kmerizer__seqs_to_kmers +- name: qiime2__metadata__shuffle_groups owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__anova +- name: qiime2__metadata__tabulate owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__feature_volatility +- name: qiime2__kmerizer__core_metrics owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__first_differences +- name: qiime2__kmerizer__seqs_to_kmers owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__first_distances +- name: qiime2__fondue___get_sequences owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__linear_mixed_effects +- name: qiime2__fondue__combine_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__maturity_index +- name: qiime2__fondue__get_all owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__nmit +- name: qiime2__fondue__get_ids_from_query owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__pairwise_differences +- name: qiime2__fondue__get_metadata owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__pairwise_distances +- name: qiime2__fondue__get_sequences owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__plot_feature_volatility +- name: qiime2__fondue__merge_metadata owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__volatility +- name: qiime2__fondue__scrape_collection owner: q2d2 tool_panel_section_id: '' - name: qualimap_bamqc diff --git a/communities/microgalaxy/lab/tools/top/ImmPort_Galaxy.yaml b/communities/microgalaxy/lab/tools/top/ImmPort_Galaxy.yaml index 81562e59c..b2d3895f0 100644 --- a/communities/microgalaxy/lab/tools/top/ImmPort_Galaxy.yaml +++ b/communities/microgalaxy/lab/tools/top/ImmPort_Galaxy.yaml @@ -776,6 +776,9 @@ tools: - name: obi_clean owner: iuc tool_panel_section_id: '' +- name: obi_complement + owner: iuc + tool_panel_section_id: '' - name: obi_convert owner: iuc tool_panel_section_id: '' @@ -788,6 +791,18 @@ tools: - name: obi_pairing owner: iuc tool_panel_section_id: '' +- name: obi_pcr + owner: iuc + tool_panel_section_id: '' +- name: obi_refidx + owner: iuc + tool_panel_section_id: '' +- name: obi_tag + owner: iuc + tool_panel_section_id: '' +- name: obi_taxonomy + owner: iuc + tool_panel_section_id: '' - name: obi_uniq owner: iuc tool_panel_section_id: '' @@ -1265,6 +1280,9 @@ tools: - name: picrust_predict_metagenomes owner: iuc tool_panel_section_id: '' +- name: prinseq + owner: iuc + tool_panel_section_id: '' - name: prodigal owner: iuc tool_panel_section_id: '' @@ -1277,262 +1295,241 @@ tools: - name: pygenomeTracks owner: iuc tool_panel_section_id: '' -- name: qiime2_core__tools__export - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2_core__tools__import - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2_core__tools__import_fastq - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__quality_filter__q_score - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__cull_seqs - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__degap_seqs - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__dereplicate - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__edit_taxonomy +- name: qiime2__dada2__denoise_ccs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_classifications +- name: qiime2__dada2__denoise_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_cross_validate +- name: qiime2__dada2__denoise_pyro owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_fit_classifier +- name: qiime2__dada2__denoise_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_seqs +- name: qiime2__dada2__plot_base_transitions owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_taxonomy +- name: qiime2__cutadapt__demux_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__extract_seq_segments +- name: qiime2__cutadapt__demux_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__filter_seqs_length +- name: qiime2__cutadapt__trim_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__filter_seqs_length_by_taxon +- name: qiime2__cutadapt__trim_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__filter_taxa +- name: qiime2__composition__add_pseudocount owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_bv_brc_genome_features +- name: qiime2__composition__ancom owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_bv_brc_genomes +- name: qiime2__composition__ancombc owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_bv_brc_metadata +- name: qiime2__composition__ancombc2 owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_eukaryome_data +- name: qiime2__composition__ancombc2_visualizer owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_gtdb_data +- name: qiime2__composition__da_barplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_midori2_data +- name: qiime2__composition__tabulate owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_ncbi_data +- name: qiime2__boots__alpha owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_ncbi_data_protein +- name: qiime2__boots__alpha_average owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_ncbi_genomes +- name: qiime2__boots__alpha_collection owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_pr2_data +- name: qiime2__boots__beta owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_silva_data +- name: qiime2__boots__beta_average owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_unite_data +- name: qiime2__boots__beta_collection owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__merge_taxa +- name: qiime2__boots__core_metrics owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__orient_reads +- name: qiime2__boots__kmer_diversity owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__orient_seqs +- name: qiime2__boots__resample owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__parse_silva_taxonomy +- name: qiime2__vsearch__cluster_features_closed_reference owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__reverse_transcribe +- name: qiime2__vsearch__cluster_features_de_novo owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__subsample_fasta +- name: qiime2__vsearch__cluster_features_open_reference owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__trim_alignment +- name: qiime2__vsearch__dereplicate_sequences owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__classify_samples +- name: qiime2__vsearch__fastq_stats owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__classify_samples_from_dist +- name: qiime2__vsearch__merge_pairs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__classify_samples_ncv +- name: qiime2__vsearch__uchime_denovo owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__confusion_matrix +- name: qiime2__vsearch__uchime_ref owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__fit_classifier +- name: qiime2__demux__emp_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__fit_regressor +- name: qiime2__demux__emp_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__heatmap +- name: qiime2__demux__filter_samples owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__metatable +- name: qiime2__demux__partition_samples_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__predict_classification +- name: qiime2__demux__partition_samples_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__predict_regression +- name: qiime2__demux__subsample_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__regress_samples +- name: qiime2__demux__subsample_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__regress_samples_ncv +- name: qiime2__demux__summarize owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__scatterplot +- name: qiime2__demux__tabulate_read_counts owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__split_table +- name: qiime2__deblur__denoise_16S owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__summarize +- name: qiime2__deblur__denoise_other owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__align_to_tree_mafft_fasttree +- name: qiime2__deblur__visualize_stats owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__align_to_tree_mafft_iqtree +- name: qiime2__diversity__adonis owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__align_to_tree_mafft_raxml +- name: qiime2__diversity__alpha owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__fasttree +- name: qiime2__diversity__alpha_correlation owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__filter_table +- name: qiime2__diversity__alpha_group_significance owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__filter_tree +- name: qiime2__diversity__alpha_phylogenetic owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__iqtree +- name: qiime2__diversity__alpha_rarefaction owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__iqtree_ultrafast_bootstrap +- name: qiime2__diversity__beta owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__midpoint_root +- name: qiime2__diversity__beta_correlation owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__raxml +- name: qiime2__diversity__beta_group_significance owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__raxml_rapid_bootstrap +- name: qiime2__diversity__beta_phylogenetic owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__robinson_foulds +- name: qiime2__diversity__beta_rarefaction owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__distance_matrix +- name: qiime2__diversity__bioenv owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__merge +- name: qiime2__diversity__core_metrics owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__shuffle_groups +- name: qiime2__diversity__core_metrics_phylogenetic owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__tabulate +- name: qiime2__diversity__filter_alpha_diversity owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__alpha_group_significance +- name: qiime2__diversity__filter_distance_matrix owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__collate_stats +- name: qiime2__diversity__mantel owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__facet_across +- name: qiime2__diversity__partial_procrustes owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__facet_within +- name: qiime2__diversity__pcoa owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__mann_whitney_u +- name: qiime2__diversity__pcoa_biplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__mann_whitney_u_facet +- name: qiime2__diversity__procrustes_analysis owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__plot_rainclouds +- name: qiime2__diversity__tsne owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__prep_alpha_distribution +- name: qiime2__diversity__umap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__wilcoxon_srt +- name: qiime2__emperor__biplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__wilcoxon_srt_facet +- name: qiime2__emperor__plot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__bowtie2_build +- name: qiime2__emperor__procrustes_plot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__decontam_identify +- name: qiime2_core__tools__export owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__decontam_identify_batches +- name: qiime2_core__tools__import owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__decontam_score_viz +- name: qiime2_core__tools__import_fastq owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__evaluate_composition +- name: qiime2__taxa__barplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__evaluate_seqs +- name: qiime2__taxa__barplot2 owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__evaluate_taxonomy +- name: qiime2__taxa__collapse owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__exclude_seqs +- name: qiime2__taxa__filter_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__filter_reads +- name: qiime2__taxa__filter_table owner: q2d2 tool_panel_section_id: '' - name: qiime2__diversity_lib__alpha_passthrough @@ -1571,253 +1568,244 @@ tools: - name: qiime2__diversity_lib__weighted_unifrac owner: q2d2 tool_panel_section_id: '' -- name: qiime2__alignment__mafft - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__alignment__mafft_add - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__alignment__mask - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__vizard__boxplot +- name: qiime2__stats__alpha_group_significance owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vizard__heatmap +- name: qiime2__stats__collate_stats owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vizard__lineplot +- name: qiime2__stats__facet_across owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vizard__scatterplot_2d +- name: qiime2__stats__facet_within owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__adonis +- name: qiime2__stats__mann_whitney_u owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha +- name: qiime2__stats__mann_whitney_u_facet owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_correlation +- name: qiime2__stats__plot_rainclouds owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_group_significance +- name: qiime2__stats__prep_alpha_distribution owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_phylogenetic +- name: qiime2__stats__wilcoxon_srt owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_rarefaction +- name: qiime2__stats__wilcoxon_srt_facet owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta +- name: qiime2__sample_classifier__classify_samples owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_correlation +- name: qiime2__sample_classifier__classify_samples_from_dist owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_group_significance +- name: qiime2__sample_classifier__classify_samples_ncv owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_phylogenetic +- name: qiime2__sample_classifier__confusion_matrix owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_rarefaction +- name: qiime2__sample_classifier__fit_classifier owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__bioenv +- name: qiime2__sample_classifier__fit_regressor owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__core_metrics +- name: qiime2__sample_classifier__heatmap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__core_metrics_phylogenetic +- name: qiime2__sample_classifier__metatable owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__filter_alpha_diversity +- name: qiime2__sample_classifier__predict_classification owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__filter_distance_matrix +- name: qiime2__sample_classifier__predict_regression owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__mantel +- name: qiime2__sample_classifier__regress_samples owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__partial_procrustes +- name: qiime2__sample_classifier__regress_samples_ncv owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__pcoa +- name: qiime2__sample_classifier__scatterplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__pcoa_biplot +- name: qiime2__sample_classifier__split_table owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__procrustes_analysis +- name: qiime2__sample_classifier__summarize owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__tsne +- name: qiime2__rescript__cull_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__umap +- name: qiime2__rescript__degap_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__emp_paired +- name: qiime2__rescript__dereplicate owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__emp_single +- name: qiime2__rescript__edit_taxonomy owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__filter_samples +- name: qiime2__rescript__evaluate_classifications owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__partition_samples_paired +- name: qiime2__rescript__evaluate_cross_validate owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__partition_samples_single +- name: qiime2__rescript__evaluate_fit_classifier owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__subsample_paired +- name: qiime2__rescript__evaluate_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__subsample_single +- name: qiime2__rescript__evaluate_taxonomy owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__summarize +- name: qiime2__rescript__extract_seq_segments owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__tabulate_read_counts +- name: qiime2__rescript__filter_seqs_length owner: q2d2 tool_panel_section_id: '' -- name: qiime2__deblur__denoise_16S +- name: qiime2__rescript__filter_seqs_length_by_taxon owner: q2d2 tool_panel_section_id: '' -- name: qiime2__deblur__denoise_other +- name: qiime2__rescript__filter_taxa owner: q2d2 tool_panel_section_id: '' -- name: qiime2__deblur__visualize_stats +- name: qiime2__rescript__get_bv_brc_genome_features owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_ccs +- name: qiime2__rescript__get_bv_brc_genomes owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_paired +- name: qiime2__rescript__get_bv_brc_metadata owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_pyro +- name: qiime2__rescript__get_eukaryome_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_single +- name: qiime2__rescript__get_gtdb_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__plot_base_transitions +- name: qiime2__rescript__get_midori2_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__cutadapt__demux_paired +- name: qiime2__rescript__get_ncbi_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__cutadapt__demux_single +- name: qiime2__rescript__get_ncbi_data_protein owner: q2d2 tool_panel_section_id: '' -- name: qiime2__cutadapt__trim_paired +- name: qiime2__rescript__get_ncbi_genomes owner: q2d2 tool_panel_section_id: '' -- name: qiime2__cutadapt__trim_single +- name: qiime2__rescript__get_pr2_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__add_pseudocount +- name: qiime2__rescript__get_silva_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancom +- name: qiime2__rescript__get_unite_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancombc +- name: qiime2__rescript__merge_taxa owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancombc2 +- name: qiime2__rescript__orient_reads owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancombc2_visualizer +- name: qiime2__rescript__orient_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__da_barplot +- name: qiime2__rescript__parse_silva_taxonomy owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__tabulate +- name: qiime2__rescript__reverse_transcribe owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__barplot +- name: qiime2__rescript__subsample_fasta owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__barplot2 +- name: qiime2__rescript__trim_alignment owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__collapse +- name: qiime2__quality_filter__q_score owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__filter_seqs +- name: qiime2__vizard__boxplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__filter_table +- name: qiime2__vizard__heatmap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__alpha +- name: qiime2__vizard__lineplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__alpha_average +- name: qiime2__vizard__scatterplot_2d owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__alpha_collection +- name: qiime2__alignment__mafft owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__beta +- name: qiime2__alignment__mafft_add owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__beta_average +- name: qiime2__alignment__mask owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__beta_collection +- name: qiime2__phylogeny__align_to_tree_mafft_fasttree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__core_metrics +- name: qiime2__phylogeny__align_to_tree_mafft_iqtree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__kmer_diversity +- name: qiime2__phylogeny__align_to_tree_mafft_raxml owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__resample +- name: qiime2__phylogeny__fasttree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__cluster_features_closed_reference +- name: qiime2__phylogeny__filter_table owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__cluster_features_de_novo +- name: qiime2__phylogeny__filter_tree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__cluster_features_open_reference +- name: qiime2__phylogeny__iqtree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__dereplicate_sequences +- name: qiime2__phylogeny__iqtree_ultrafast_bootstrap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__fastq_stats +- name: qiime2__phylogeny__midpoint_root owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__merge_pairs +- name: qiime2__phylogeny__raxml owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__uchime_denovo +- name: qiime2__phylogeny__raxml_rapid_bootstrap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__uchime_ref +- name: qiime2__phylogeny__robinson_foulds owner: q2d2 tool_panel_section_id: '' -- name: qiime2__emperor__biplot +- name: qiime2__fragment_insertion__classify_otus_experimental owner: q2d2 tool_panel_section_id: '' -- name: qiime2__emperor__plot +- name: qiime2__fragment_insertion__filter_features owner: q2d2 tool_panel_section_id: '' -- name: qiime2__emperor__procrustes_plot +- name: qiime2__fragment_insertion__sepp owner: q2d2 tool_panel_section_id: '' - name: qiime2__feature_classifier__blast @@ -1853,6 +1841,39 @@ tools: - name: qiime2__feature_classifier__vsearch_global owner: q2d2 tool_panel_section_id: '' +- name: qiime2__longitudinal__anova + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__feature_volatility + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__first_differences + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__first_distances + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__linear_mixed_effects + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__maturity_index + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__nmit + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__pairwise_differences + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__pairwise_distances + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__plot_feature_volatility + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__volatility + owner: q2d2 + tool_panel_section_id: '' - name: qiime2__feature_table___summarize owner: q2d2 tool_panel_section_id: '' @@ -1922,76 +1943,73 @@ tools: - name: qiime2__feature_table__transpose owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue___get_sequences - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__fondue__combine_seqs +- name: qiime2__quality_control__bowtie2_build owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__get_all +- name: qiime2__quality_control__decontam_identify owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__get_ids_from_query +- name: qiime2__quality_control__decontam_identify_batches owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__get_metadata +- name: qiime2__quality_control__decontam_score_viz owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__get_sequences +- name: qiime2__quality_control__evaluate_composition owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__merge_metadata +- name: qiime2__quality_control__evaluate_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__scrape_collection +- name: qiime2__quality_control__evaluate_taxonomy owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fragment_insertion__classify_otus_experimental +- name: qiime2__quality_control__exclude_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fragment_insertion__filter_features +- name: qiime2__quality_control__filter_reads owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fragment_insertion__sepp +- name: qiime2__metadata__distance_matrix owner: q2d2 tool_panel_section_id: '' -- name: qiime2__kmerizer__core_metrics +- name: qiime2__metadata__merge owner: q2d2 tool_panel_section_id: '' -- name: qiime2__kmerizer__seqs_to_kmers +- name: qiime2__metadata__shuffle_groups owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__anova +- name: qiime2__metadata__tabulate owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__feature_volatility +- name: qiime2__kmerizer__core_metrics owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__first_differences +- name: qiime2__kmerizer__seqs_to_kmers owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__first_distances +- name: qiime2__fondue___get_sequences owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__linear_mixed_effects +- name: qiime2__fondue__combine_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__maturity_index +- name: qiime2__fondue__get_all owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__nmit +- name: qiime2__fondue__get_ids_from_query owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__pairwise_differences +- name: qiime2__fondue__get_metadata owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__pairwise_distances +- name: qiime2__fondue__get_sequences owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__plot_feature_volatility +- name: qiime2__fondue__merge_metadata owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__volatility +- name: qiime2__fondue__scrape_collection owner: q2d2 tool_panel_section_id: '' - name: qualimap_bamqc diff --git a/communities/microgalaxy/lab/tools/top/InteractoMIX.yaml b/communities/microgalaxy/lab/tools/top/InteractoMIX.yaml index 81562e59c..b2d3895f0 100644 --- a/communities/microgalaxy/lab/tools/top/InteractoMIX.yaml +++ b/communities/microgalaxy/lab/tools/top/InteractoMIX.yaml @@ -776,6 +776,9 @@ tools: - name: obi_clean owner: iuc tool_panel_section_id: '' +- name: obi_complement + owner: iuc + tool_panel_section_id: '' - name: obi_convert owner: iuc tool_panel_section_id: '' @@ -788,6 +791,18 @@ tools: - name: obi_pairing owner: iuc tool_panel_section_id: '' +- name: obi_pcr + owner: iuc + tool_panel_section_id: '' +- name: obi_refidx + owner: iuc + tool_panel_section_id: '' +- name: obi_tag + owner: iuc + tool_panel_section_id: '' +- name: obi_taxonomy + owner: iuc + tool_panel_section_id: '' - name: obi_uniq owner: iuc tool_panel_section_id: '' @@ -1265,6 +1280,9 @@ tools: - name: picrust_predict_metagenomes owner: iuc tool_panel_section_id: '' +- name: prinseq + owner: iuc + tool_panel_section_id: '' - name: prodigal owner: iuc tool_panel_section_id: '' @@ -1277,262 +1295,241 @@ tools: - name: pygenomeTracks owner: iuc tool_panel_section_id: '' -- name: qiime2_core__tools__export - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2_core__tools__import - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2_core__tools__import_fastq - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__quality_filter__q_score - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__cull_seqs - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__degap_seqs - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__dereplicate - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__edit_taxonomy +- name: qiime2__dada2__denoise_ccs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_classifications +- name: qiime2__dada2__denoise_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_cross_validate +- name: qiime2__dada2__denoise_pyro owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_fit_classifier +- name: qiime2__dada2__denoise_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_seqs +- name: qiime2__dada2__plot_base_transitions owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_taxonomy +- name: qiime2__cutadapt__demux_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__extract_seq_segments +- name: qiime2__cutadapt__demux_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__filter_seqs_length +- name: qiime2__cutadapt__trim_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__filter_seqs_length_by_taxon +- name: qiime2__cutadapt__trim_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__filter_taxa +- name: qiime2__composition__add_pseudocount owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_bv_brc_genome_features +- name: qiime2__composition__ancom owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_bv_brc_genomes +- name: qiime2__composition__ancombc owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_bv_brc_metadata +- name: qiime2__composition__ancombc2 owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_eukaryome_data +- name: qiime2__composition__ancombc2_visualizer owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_gtdb_data +- name: qiime2__composition__da_barplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_midori2_data +- name: qiime2__composition__tabulate owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_ncbi_data +- name: qiime2__boots__alpha owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_ncbi_data_protein +- name: qiime2__boots__alpha_average owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_ncbi_genomes +- name: qiime2__boots__alpha_collection owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_pr2_data +- name: qiime2__boots__beta owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_silva_data +- name: qiime2__boots__beta_average owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_unite_data +- name: qiime2__boots__beta_collection owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__merge_taxa +- name: qiime2__boots__core_metrics owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__orient_reads +- name: qiime2__boots__kmer_diversity owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__orient_seqs +- name: qiime2__boots__resample owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__parse_silva_taxonomy +- name: qiime2__vsearch__cluster_features_closed_reference owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__reverse_transcribe +- name: qiime2__vsearch__cluster_features_de_novo owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__subsample_fasta +- name: qiime2__vsearch__cluster_features_open_reference owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__trim_alignment +- name: qiime2__vsearch__dereplicate_sequences owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__classify_samples +- name: qiime2__vsearch__fastq_stats owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__classify_samples_from_dist +- name: qiime2__vsearch__merge_pairs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__classify_samples_ncv +- name: qiime2__vsearch__uchime_denovo owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__confusion_matrix +- name: qiime2__vsearch__uchime_ref owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__fit_classifier +- name: qiime2__demux__emp_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__fit_regressor +- name: qiime2__demux__emp_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__heatmap +- name: qiime2__demux__filter_samples owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__metatable +- name: qiime2__demux__partition_samples_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__predict_classification +- name: qiime2__demux__partition_samples_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__predict_regression +- name: qiime2__demux__subsample_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__regress_samples +- name: qiime2__demux__subsample_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__regress_samples_ncv +- name: qiime2__demux__summarize owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__scatterplot +- name: qiime2__demux__tabulate_read_counts owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__split_table +- name: qiime2__deblur__denoise_16S owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__summarize +- name: qiime2__deblur__denoise_other owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__align_to_tree_mafft_fasttree +- name: qiime2__deblur__visualize_stats owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__align_to_tree_mafft_iqtree +- name: qiime2__diversity__adonis owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__align_to_tree_mafft_raxml +- name: qiime2__diversity__alpha owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__fasttree +- name: qiime2__diversity__alpha_correlation owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__filter_table +- name: qiime2__diversity__alpha_group_significance owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__filter_tree +- name: qiime2__diversity__alpha_phylogenetic owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__iqtree +- name: qiime2__diversity__alpha_rarefaction owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__iqtree_ultrafast_bootstrap +- name: qiime2__diversity__beta owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__midpoint_root +- name: qiime2__diversity__beta_correlation owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__raxml +- name: qiime2__diversity__beta_group_significance owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__raxml_rapid_bootstrap +- name: qiime2__diversity__beta_phylogenetic owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__robinson_foulds +- name: qiime2__diversity__beta_rarefaction owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__distance_matrix +- name: qiime2__diversity__bioenv owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__merge +- name: qiime2__diversity__core_metrics owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__shuffle_groups +- name: qiime2__diversity__core_metrics_phylogenetic owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__tabulate +- name: qiime2__diversity__filter_alpha_diversity owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__alpha_group_significance +- name: qiime2__diversity__filter_distance_matrix owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__collate_stats +- name: qiime2__diversity__mantel owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__facet_across +- name: qiime2__diversity__partial_procrustes owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__facet_within +- name: qiime2__diversity__pcoa owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__mann_whitney_u +- name: qiime2__diversity__pcoa_biplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__mann_whitney_u_facet +- name: qiime2__diversity__procrustes_analysis owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__plot_rainclouds +- name: qiime2__diversity__tsne owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__prep_alpha_distribution +- name: qiime2__diversity__umap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__wilcoxon_srt +- name: qiime2__emperor__biplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__wilcoxon_srt_facet +- name: qiime2__emperor__plot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__bowtie2_build +- name: qiime2__emperor__procrustes_plot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__decontam_identify +- name: qiime2_core__tools__export owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__decontam_identify_batches +- name: qiime2_core__tools__import owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__decontam_score_viz +- name: qiime2_core__tools__import_fastq owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__evaluate_composition +- name: qiime2__taxa__barplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__evaluate_seqs +- name: qiime2__taxa__barplot2 owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__evaluate_taxonomy +- name: qiime2__taxa__collapse owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__exclude_seqs +- name: qiime2__taxa__filter_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__filter_reads +- name: qiime2__taxa__filter_table owner: q2d2 tool_panel_section_id: '' - name: qiime2__diversity_lib__alpha_passthrough @@ -1571,253 +1568,244 @@ tools: - name: qiime2__diversity_lib__weighted_unifrac owner: q2d2 tool_panel_section_id: '' -- name: qiime2__alignment__mafft - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__alignment__mafft_add - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__alignment__mask - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__vizard__boxplot +- name: qiime2__stats__alpha_group_significance owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vizard__heatmap +- name: qiime2__stats__collate_stats owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vizard__lineplot +- name: qiime2__stats__facet_across owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vizard__scatterplot_2d +- name: qiime2__stats__facet_within owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__adonis +- name: qiime2__stats__mann_whitney_u owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha +- name: qiime2__stats__mann_whitney_u_facet owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_correlation +- name: qiime2__stats__plot_rainclouds owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_group_significance +- name: qiime2__stats__prep_alpha_distribution owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_phylogenetic +- name: qiime2__stats__wilcoxon_srt owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_rarefaction +- name: qiime2__stats__wilcoxon_srt_facet owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta +- name: qiime2__sample_classifier__classify_samples owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_correlation +- name: qiime2__sample_classifier__classify_samples_from_dist owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_group_significance +- name: qiime2__sample_classifier__classify_samples_ncv owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_phylogenetic +- name: qiime2__sample_classifier__confusion_matrix owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_rarefaction +- name: qiime2__sample_classifier__fit_classifier owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__bioenv +- name: qiime2__sample_classifier__fit_regressor owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__core_metrics +- name: qiime2__sample_classifier__heatmap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__core_metrics_phylogenetic +- name: qiime2__sample_classifier__metatable owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__filter_alpha_diversity +- name: qiime2__sample_classifier__predict_classification owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__filter_distance_matrix +- name: qiime2__sample_classifier__predict_regression owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__mantel +- name: qiime2__sample_classifier__regress_samples owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__partial_procrustes +- name: qiime2__sample_classifier__regress_samples_ncv owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__pcoa +- name: qiime2__sample_classifier__scatterplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__pcoa_biplot +- name: qiime2__sample_classifier__split_table owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__procrustes_analysis +- name: qiime2__sample_classifier__summarize owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__tsne +- name: qiime2__rescript__cull_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__umap +- name: qiime2__rescript__degap_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__emp_paired +- name: qiime2__rescript__dereplicate owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__emp_single +- name: qiime2__rescript__edit_taxonomy owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__filter_samples +- name: qiime2__rescript__evaluate_classifications owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__partition_samples_paired +- name: qiime2__rescript__evaluate_cross_validate owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__partition_samples_single +- name: qiime2__rescript__evaluate_fit_classifier owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__subsample_paired +- name: qiime2__rescript__evaluate_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__subsample_single +- name: qiime2__rescript__evaluate_taxonomy owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__summarize +- name: qiime2__rescript__extract_seq_segments owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__tabulate_read_counts +- name: qiime2__rescript__filter_seqs_length owner: q2d2 tool_panel_section_id: '' -- name: qiime2__deblur__denoise_16S +- name: qiime2__rescript__filter_seqs_length_by_taxon owner: q2d2 tool_panel_section_id: '' -- name: qiime2__deblur__denoise_other +- name: qiime2__rescript__filter_taxa owner: q2d2 tool_panel_section_id: '' -- name: qiime2__deblur__visualize_stats +- name: qiime2__rescript__get_bv_brc_genome_features owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_ccs +- name: qiime2__rescript__get_bv_brc_genomes owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_paired +- name: qiime2__rescript__get_bv_brc_metadata owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_pyro +- name: qiime2__rescript__get_eukaryome_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_single +- name: qiime2__rescript__get_gtdb_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__plot_base_transitions +- name: qiime2__rescript__get_midori2_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__cutadapt__demux_paired +- name: qiime2__rescript__get_ncbi_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__cutadapt__demux_single +- name: qiime2__rescript__get_ncbi_data_protein owner: q2d2 tool_panel_section_id: '' -- name: qiime2__cutadapt__trim_paired +- name: qiime2__rescript__get_ncbi_genomes owner: q2d2 tool_panel_section_id: '' -- name: qiime2__cutadapt__trim_single +- name: qiime2__rescript__get_pr2_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__add_pseudocount +- name: qiime2__rescript__get_silva_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancom +- name: qiime2__rescript__get_unite_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancombc +- name: qiime2__rescript__merge_taxa owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancombc2 +- name: qiime2__rescript__orient_reads owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancombc2_visualizer +- name: qiime2__rescript__orient_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__da_barplot +- name: qiime2__rescript__parse_silva_taxonomy owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__tabulate +- name: qiime2__rescript__reverse_transcribe owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__barplot +- name: qiime2__rescript__subsample_fasta owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__barplot2 +- name: qiime2__rescript__trim_alignment owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__collapse +- name: qiime2__quality_filter__q_score owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__filter_seqs +- name: qiime2__vizard__boxplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__filter_table +- name: qiime2__vizard__heatmap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__alpha +- name: qiime2__vizard__lineplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__alpha_average +- name: qiime2__vizard__scatterplot_2d owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__alpha_collection +- name: qiime2__alignment__mafft owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__beta +- name: qiime2__alignment__mafft_add owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__beta_average +- name: qiime2__alignment__mask owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__beta_collection +- name: qiime2__phylogeny__align_to_tree_mafft_fasttree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__core_metrics +- name: qiime2__phylogeny__align_to_tree_mafft_iqtree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__kmer_diversity +- name: qiime2__phylogeny__align_to_tree_mafft_raxml owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__resample +- name: qiime2__phylogeny__fasttree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__cluster_features_closed_reference +- name: qiime2__phylogeny__filter_table owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__cluster_features_de_novo +- name: qiime2__phylogeny__filter_tree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__cluster_features_open_reference +- name: qiime2__phylogeny__iqtree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__dereplicate_sequences +- name: qiime2__phylogeny__iqtree_ultrafast_bootstrap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__fastq_stats +- name: qiime2__phylogeny__midpoint_root owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__merge_pairs +- name: qiime2__phylogeny__raxml owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__uchime_denovo +- name: qiime2__phylogeny__raxml_rapid_bootstrap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__uchime_ref +- name: qiime2__phylogeny__robinson_foulds owner: q2d2 tool_panel_section_id: '' -- name: qiime2__emperor__biplot +- name: qiime2__fragment_insertion__classify_otus_experimental owner: q2d2 tool_panel_section_id: '' -- name: qiime2__emperor__plot +- name: qiime2__fragment_insertion__filter_features owner: q2d2 tool_panel_section_id: '' -- name: qiime2__emperor__procrustes_plot +- name: qiime2__fragment_insertion__sepp owner: q2d2 tool_panel_section_id: '' - name: qiime2__feature_classifier__blast @@ -1853,6 +1841,39 @@ tools: - name: qiime2__feature_classifier__vsearch_global owner: q2d2 tool_panel_section_id: '' +- name: qiime2__longitudinal__anova + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__feature_volatility + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__first_differences + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__first_distances + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__linear_mixed_effects + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__maturity_index + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__nmit + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__pairwise_differences + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__pairwise_distances + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__plot_feature_volatility + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__volatility + owner: q2d2 + tool_panel_section_id: '' - name: qiime2__feature_table___summarize owner: q2d2 tool_panel_section_id: '' @@ -1922,76 +1943,73 @@ tools: - name: qiime2__feature_table__transpose owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue___get_sequences - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__fondue__combine_seqs +- name: qiime2__quality_control__bowtie2_build owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__get_all +- name: qiime2__quality_control__decontam_identify owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__get_ids_from_query +- name: qiime2__quality_control__decontam_identify_batches owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__get_metadata +- name: qiime2__quality_control__decontam_score_viz owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__get_sequences +- name: qiime2__quality_control__evaluate_composition owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__merge_metadata +- name: qiime2__quality_control__evaluate_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__scrape_collection +- name: qiime2__quality_control__evaluate_taxonomy owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fragment_insertion__classify_otus_experimental +- name: qiime2__quality_control__exclude_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fragment_insertion__filter_features +- name: qiime2__quality_control__filter_reads owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fragment_insertion__sepp +- name: qiime2__metadata__distance_matrix owner: q2d2 tool_panel_section_id: '' -- name: qiime2__kmerizer__core_metrics +- name: qiime2__metadata__merge owner: q2d2 tool_panel_section_id: '' -- name: qiime2__kmerizer__seqs_to_kmers +- name: qiime2__metadata__shuffle_groups owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__anova +- name: qiime2__metadata__tabulate owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__feature_volatility +- name: qiime2__kmerizer__core_metrics owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__first_differences +- name: qiime2__kmerizer__seqs_to_kmers owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__first_distances +- name: qiime2__fondue___get_sequences owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__linear_mixed_effects +- name: qiime2__fondue__combine_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__maturity_index +- name: qiime2__fondue__get_all owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__nmit +- name: qiime2__fondue__get_ids_from_query owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__pairwise_differences +- name: qiime2__fondue__get_metadata owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__pairwise_distances +- name: qiime2__fondue__get_sequences owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__plot_feature_volatility +- name: qiime2__fondue__merge_metadata owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__volatility +- name: qiime2__fondue__scrape_collection owner: q2d2 tool_panel_section_id: '' - name: qualimap_bamqc diff --git a/communities/microgalaxy/lab/tools/top/Lebanese_University_Galaxy.yaml b/communities/microgalaxy/lab/tools/top/Lebanese_University_Galaxy.yaml index 6d3a8c6a7..1d8985491 100644 --- a/communities/microgalaxy/lab/tools/top/Lebanese_University_Galaxy.yaml +++ b/communities/microgalaxy/lab/tools/top/Lebanese_University_Galaxy.yaml @@ -773,6 +773,9 @@ tools: - name: obi_clean owner: iuc tool_panel_section_id: '' +- name: obi_complement + owner: iuc + tool_panel_section_id: '' - name: obi_convert owner: iuc tool_panel_section_id: '' @@ -785,6 +788,18 @@ tools: - name: obi_pairing owner: iuc tool_panel_section_id: '' +- name: obi_pcr + owner: iuc + tool_panel_section_id: '' +- name: obi_refidx + owner: iuc + tool_panel_section_id: '' +- name: obi_tag + owner: iuc + tool_panel_section_id: '' +- name: obi_taxonomy + owner: iuc + tool_panel_section_id: '' - name: obi_uniq owner: iuc tool_panel_section_id: '' @@ -1262,6 +1277,9 @@ tools: - name: picrust_predict_metagenomes owner: iuc tool_panel_section_id: '' +- name: prinseq + owner: iuc + tool_panel_section_id: '' - name: prodigal owner: iuc tool_panel_section_id: '' @@ -1274,262 +1292,241 @@ tools: - name: pygenomeTracks owner: iuc tool_panel_section_id: '' -- name: qiime2_core__tools__export - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2_core__tools__import - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2_core__tools__import_fastq - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__quality_filter__q_score - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__cull_seqs - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__degap_seqs - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__dereplicate - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__edit_taxonomy +- name: qiime2__dada2__denoise_ccs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_classifications +- name: qiime2__dada2__denoise_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_cross_validate +- name: qiime2__dada2__denoise_pyro owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_fit_classifier +- name: qiime2__dada2__denoise_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_seqs +- name: qiime2__dada2__plot_base_transitions owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_taxonomy +- name: qiime2__cutadapt__demux_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__extract_seq_segments +- name: qiime2__cutadapt__demux_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__filter_seqs_length +- name: qiime2__cutadapt__trim_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__filter_seqs_length_by_taxon +- name: qiime2__cutadapt__trim_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__filter_taxa +- name: qiime2__composition__add_pseudocount owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_bv_brc_genome_features +- name: qiime2__composition__ancom owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_bv_brc_genomes +- name: qiime2__composition__ancombc owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_bv_brc_metadata +- name: qiime2__composition__ancombc2 owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_eukaryome_data +- name: qiime2__composition__ancombc2_visualizer owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_gtdb_data +- name: qiime2__composition__da_barplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_midori2_data +- name: qiime2__composition__tabulate owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_ncbi_data +- name: qiime2__boots__alpha owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_ncbi_data_protein +- name: qiime2__boots__alpha_average owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_ncbi_genomes +- name: qiime2__boots__alpha_collection owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_pr2_data +- name: qiime2__boots__beta owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_silva_data +- name: qiime2__boots__beta_average owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_unite_data +- name: qiime2__boots__beta_collection owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__merge_taxa +- name: qiime2__boots__core_metrics owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__orient_reads +- name: qiime2__boots__kmer_diversity owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__orient_seqs +- name: qiime2__boots__resample owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__parse_silva_taxonomy +- name: qiime2__vsearch__cluster_features_closed_reference owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__reverse_transcribe +- name: qiime2__vsearch__cluster_features_de_novo owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__subsample_fasta +- name: qiime2__vsearch__cluster_features_open_reference owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__trim_alignment +- name: qiime2__vsearch__dereplicate_sequences owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__classify_samples +- name: qiime2__vsearch__fastq_stats owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__classify_samples_from_dist +- name: qiime2__vsearch__merge_pairs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__classify_samples_ncv +- name: qiime2__vsearch__uchime_denovo owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__confusion_matrix +- name: qiime2__vsearch__uchime_ref owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__fit_classifier +- name: qiime2__demux__emp_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__fit_regressor +- name: qiime2__demux__emp_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__heatmap +- name: qiime2__demux__filter_samples owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__metatable +- name: qiime2__demux__partition_samples_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__predict_classification +- name: qiime2__demux__partition_samples_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__predict_regression +- name: qiime2__demux__subsample_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__regress_samples +- name: qiime2__demux__subsample_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__regress_samples_ncv +- name: qiime2__demux__summarize owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__scatterplot +- name: qiime2__demux__tabulate_read_counts owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__split_table +- name: qiime2__deblur__denoise_16S owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__summarize +- name: qiime2__deblur__denoise_other owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__align_to_tree_mafft_fasttree +- name: qiime2__deblur__visualize_stats owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__align_to_tree_mafft_iqtree +- name: qiime2__diversity__adonis owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__align_to_tree_mafft_raxml +- name: qiime2__diversity__alpha owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__fasttree +- name: qiime2__diversity__alpha_correlation owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__filter_table +- name: qiime2__diversity__alpha_group_significance owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__filter_tree +- name: qiime2__diversity__alpha_phylogenetic owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__iqtree +- name: qiime2__diversity__alpha_rarefaction owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__iqtree_ultrafast_bootstrap +- name: qiime2__diversity__beta owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__midpoint_root +- name: qiime2__diversity__beta_correlation owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__raxml +- name: qiime2__diversity__beta_group_significance owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__raxml_rapid_bootstrap +- name: qiime2__diversity__beta_phylogenetic owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__robinson_foulds +- name: qiime2__diversity__beta_rarefaction owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__distance_matrix +- name: qiime2__diversity__bioenv owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__merge +- name: qiime2__diversity__core_metrics owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__shuffle_groups +- name: qiime2__diversity__core_metrics_phylogenetic owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__tabulate +- name: qiime2__diversity__filter_alpha_diversity owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__alpha_group_significance +- name: qiime2__diversity__filter_distance_matrix owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__collate_stats +- name: qiime2__diversity__mantel owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__facet_across +- name: qiime2__diversity__partial_procrustes owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__facet_within +- name: qiime2__diversity__pcoa owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__mann_whitney_u +- name: qiime2__diversity__pcoa_biplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__mann_whitney_u_facet +- name: qiime2__diversity__procrustes_analysis owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__plot_rainclouds +- name: qiime2__diversity__tsne owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__prep_alpha_distribution +- name: qiime2__diversity__umap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__wilcoxon_srt +- name: qiime2__emperor__biplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__wilcoxon_srt_facet +- name: qiime2__emperor__plot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__bowtie2_build +- name: qiime2__emperor__procrustes_plot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__decontam_identify +- name: qiime2_core__tools__export owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__decontam_identify_batches +- name: qiime2_core__tools__import owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__decontam_score_viz +- name: qiime2_core__tools__import_fastq owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__evaluate_composition +- name: qiime2__taxa__barplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__evaluate_seqs +- name: qiime2__taxa__barplot2 owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__evaluate_taxonomy +- name: qiime2__taxa__collapse owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__exclude_seqs +- name: qiime2__taxa__filter_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__filter_reads +- name: qiime2__taxa__filter_table owner: q2d2 tool_panel_section_id: '' - name: qiime2__diversity_lib__alpha_passthrough @@ -1568,253 +1565,244 @@ tools: - name: qiime2__diversity_lib__weighted_unifrac owner: q2d2 tool_panel_section_id: '' -- name: qiime2__alignment__mafft - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__alignment__mafft_add - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__alignment__mask - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__vizard__boxplot +- name: qiime2__stats__alpha_group_significance owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vizard__heatmap +- name: qiime2__stats__collate_stats owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vizard__lineplot +- name: qiime2__stats__facet_across owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vizard__scatterplot_2d +- name: qiime2__stats__facet_within owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__adonis +- name: qiime2__stats__mann_whitney_u owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha +- name: qiime2__stats__mann_whitney_u_facet owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_correlation +- name: qiime2__stats__plot_rainclouds owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_group_significance +- name: qiime2__stats__prep_alpha_distribution owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_phylogenetic +- name: qiime2__stats__wilcoxon_srt owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_rarefaction +- name: qiime2__stats__wilcoxon_srt_facet owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta +- name: qiime2__sample_classifier__classify_samples owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_correlation +- name: qiime2__sample_classifier__classify_samples_from_dist owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_group_significance +- name: qiime2__sample_classifier__classify_samples_ncv owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_phylogenetic +- name: qiime2__sample_classifier__confusion_matrix owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_rarefaction +- name: qiime2__sample_classifier__fit_classifier owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__bioenv +- name: qiime2__sample_classifier__fit_regressor owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__core_metrics +- name: qiime2__sample_classifier__heatmap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__core_metrics_phylogenetic +- name: qiime2__sample_classifier__metatable owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__filter_alpha_diversity +- name: qiime2__sample_classifier__predict_classification owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__filter_distance_matrix +- name: qiime2__sample_classifier__predict_regression owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__mantel +- name: qiime2__sample_classifier__regress_samples owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__partial_procrustes +- name: qiime2__sample_classifier__regress_samples_ncv owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__pcoa +- name: qiime2__sample_classifier__scatterplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__pcoa_biplot +- name: qiime2__sample_classifier__split_table owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__procrustes_analysis +- name: qiime2__sample_classifier__summarize owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__tsne +- name: qiime2__rescript__cull_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__umap +- name: qiime2__rescript__degap_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__emp_paired +- name: qiime2__rescript__dereplicate owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__emp_single +- name: qiime2__rescript__edit_taxonomy owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__filter_samples +- name: qiime2__rescript__evaluate_classifications owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__partition_samples_paired +- name: qiime2__rescript__evaluate_cross_validate owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__partition_samples_single +- name: qiime2__rescript__evaluate_fit_classifier owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__subsample_paired +- name: qiime2__rescript__evaluate_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__subsample_single +- name: qiime2__rescript__evaluate_taxonomy owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__summarize +- name: qiime2__rescript__extract_seq_segments owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__tabulate_read_counts +- name: qiime2__rescript__filter_seqs_length owner: q2d2 tool_panel_section_id: '' -- name: qiime2__deblur__denoise_16S +- name: qiime2__rescript__filter_seqs_length_by_taxon owner: q2d2 tool_panel_section_id: '' -- name: qiime2__deblur__denoise_other +- name: qiime2__rescript__filter_taxa owner: q2d2 tool_panel_section_id: '' -- name: qiime2__deblur__visualize_stats +- name: qiime2__rescript__get_bv_brc_genome_features owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_ccs +- name: qiime2__rescript__get_bv_brc_genomes owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_paired +- name: qiime2__rescript__get_bv_brc_metadata owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_pyro +- name: qiime2__rescript__get_eukaryome_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_single +- name: qiime2__rescript__get_gtdb_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__plot_base_transitions +- name: qiime2__rescript__get_midori2_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__cutadapt__demux_paired +- name: qiime2__rescript__get_ncbi_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__cutadapt__demux_single +- name: qiime2__rescript__get_ncbi_data_protein owner: q2d2 tool_panel_section_id: '' -- name: qiime2__cutadapt__trim_paired +- name: qiime2__rescript__get_ncbi_genomes owner: q2d2 tool_panel_section_id: '' -- name: qiime2__cutadapt__trim_single +- name: qiime2__rescript__get_pr2_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__add_pseudocount +- name: qiime2__rescript__get_silva_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancom +- name: qiime2__rescript__get_unite_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancombc +- name: qiime2__rescript__merge_taxa owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancombc2 +- name: qiime2__rescript__orient_reads owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancombc2_visualizer +- name: qiime2__rescript__orient_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__da_barplot +- name: qiime2__rescript__parse_silva_taxonomy owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__tabulate +- name: qiime2__rescript__reverse_transcribe owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__barplot +- name: qiime2__rescript__subsample_fasta owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__barplot2 +- name: qiime2__rescript__trim_alignment owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__collapse +- name: qiime2__quality_filter__q_score owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__filter_seqs +- name: qiime2__vizard__boxplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__filter_table +- name: qiime2__vizard__heatmap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__alpha +- name: qiime2__vizard__lineplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__alpha_average +- name: qiime2__vizard__scatterplot_2d owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__alpha_collection +- name: qiime2__alignment__mafft owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__beta +- name: qiime2__alignment__mafft_add owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__beta_average +- name: qiime2__alignment__mask owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__beta_collection +- name: qiime2__phylogeny__align_to_tree_mafft_fasttree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__core_metrics +- name: qiime2__phylogeny__align_to_tree_mafft_iqtree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__kmer_diversity +- name: qiime2__phylogeny__align_to_tree_mafft_raxml owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__resample +- name: qiime2__phylogeny__fasttree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__cluster_features_closed_reference +- name: qiime2__phylogeny__filter_table owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__cluster_features_de_novo +- name: qiime2__phylogeny__filter_tree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__cluster_features_open_reference +- name: qiime2__phylogeny__iqtree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__dereplicate_sequences +- name: qiime2__phylogeny__iqtree_ultrafast_bootstrap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__fastq_stats +- name: qiime2__phylogeny__midpoint_root owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__merge_pairs +- name: qiime2__phylogeny__raxml owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__uchime_denovo +- name: qiime2__phylogeny__raxml_rapid_bootstrap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__uchime_ref +- name: qiime2__phylogeny__robinson_foulds owner: q2d2 tool_panel_section_id: '' -- name: qiime2__emperor__biplot +- name: qiime2__fragment_insertion__classify_otus_experimental owner: q2d2 tool_panel_section_id: '' -- name: qiime2__emperor__plot +- name: qiime2__fragment_insertion__filter_features owner: q2d2 tool_panel_section_id: '' -- name: qiime2__emperor__procrustes_plot +- name: qiime2__fragment_insertion__sepp owner: q2d2 tool_panel_section_id: '' - name: qiime2__feature_classifier__blast @@ -1850,6 +1838,39 @@ tools: - name: qiime2__feature_classifier__vsearch_global owner: q2d2 tool_panel_section_id: '' +- name: qiime2__longitudinal__anova + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__feature_volatility + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__first_differences + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__first_distances + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__linear_mixed_effects + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__maturity_index + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__nmit + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__pairwise_differences + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__pairwise_distances + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__plot_feature_volatility + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__volatility + owner: q2d2 + tool_panel_section_id: '' - name: qiime2__feature_table___summarize owner: q2d2 tool_panel_section_id: '' @@ -1919,76 +1940,73 @@ tools: - name: qiime2__feature_table__transpose owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue___get_sequences - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__fondue__combine_seqs +- name: qiime2__quality_control__bowtie2_build owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__get_all +- name: qiime2__quality_control__decontam_identify owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__get_ids_from_query +- name: qiime2__quality_control__decontam_identify_batches owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__get_metadata +- name: qiime2__quality_control__decontam_score_viz owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__get_sequences +- name: qiime2__quality_control__evaluate_composition owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__merge_metadata +- name: qiime2__quality_control__evaluate_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__scrape_collection +- name: qiime2__quality_control__evaluate_taxonomy owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fragment_insertion__classify_otus_experimental +- name: qiime2__quality_control__exclude_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fragment_insertion__filter_features +- name: qiime2__quality_control__filter_reads owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fragment_insertion__sepp +- name: qiime2__metadata__distance_matrix owner: q2d2 tool_panel_section_id: '' -- name: qiime2__kmerizer__core_metrics +- name: qiime2__metadata__merge owner: q2d2 tool_panel_section_id: '' -- name: qiime2__kmerizer__seqs_to_kmers +- name: qiime2__metadata__shuffle_groups owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__anova +- name: qiime2__metadata__tabulate owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__feature_volatility +- name: qiime2__kmerizer__core_metrics owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__first_differences +- name: qiime2__kmerizer__seqs_to_kmers owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__first_distances +- name: qiime2__fondue___get_sequences owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__linear_mixed_effects +- name: qiime2__fondue__combine_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__maturity_index +- name: qiime2__fondue__get_all owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__nmit +- name: qiime2__fondue__get_ids_from_query owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__pairwise_differences +- name: qiime2__fondue__get_metadata owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__pairwise_distances +- name: qiime2__fondue__get_sequences owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__plot_feature_volatility +- name: qiime2__fondue__merge_metadata owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__volatility +- name: qiime2__fondue__scrape_collection owner: q2d2 tool_panel_section_id: '' - name: qualimap_bamqc diff --git a/communities/microgalaxy/lab/tools/top/Local_Galaxy.yaml b/communities/microgalaxy/lab/tools/top/Local_Galaxy.yaml index 81562e59c..b2d3895f0 100644 --- a/communities/microgalaxy/lab/tools/top/Local_Galaxy.yaml +++ b/communities/microgalaxy/lab/tools/top/Local_Galaxy.yaml @@ -776,6 +776,9 @@ tools: - name: obi_clean owner: iuc tool_panel_section_id: '' +- name: obi_complement + owner: iuc + tool_panel_section_id: '' - name: obi_convert owner: iuc tool_panel_section_id: '' @@ -788,6 +791,18 @@ tools: - name: obi_pairing owner: iuc tool_panel_section_id: '' +- name: obi_pcr + owner: iuc + tool_panel_section_id: '' +- name: obi_refidx + owner: iuc + tool_panel_section_id: '' +- name: obi_tag + owner: iuc + tool_panel_section_id: '' +- name: obi_taxonomy + owner: iuc + tool_panel_section_id: '' - name: obi_uniq owner: iuc tool_panel_section_id: '' @@ -1265,6 +1280,9 @@ tools: - name: picrust_predict_metagenomes owner: iuc tool_panel_section_id: '' +- name: prinseq + owner: iuc + tool_panel_section_id: '' - name: prodigal owner: iuc tool_panel_section_id: '' @@ -1277,262 +1295,241 @@ tools: - name: pygenomeTracks owner: iuc tool_panel_section_id: '' -- name: qiime2_core__tools__export - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2_core__tools__import - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2_core__tools__import_fastq - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__quality_filter__q_score - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__cull_seqs - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__degap_seqs - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__dereplicate - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__edit_taxonomy +- name: qiime2__dada2__denoise_ccs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_classifications +- name: qiime2__dada2__denoise_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_cross_validate +- name: qiime2__dada2__denoise_pyro owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_fit_classifier +- name: qiime2__dada2__denoise_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_seqs +- name: qiime2__dada2__plot_base_transitions owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_taxonomy +- name: qiime2__cutadapt__demux_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__extract_seq_segments +- name: qiime2__cutadapt__demux_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__filter_seqs_length +- name: qiime2__cutadapt__trim_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__filter_seqs_length_by_taxon +- name: qiime2__cutadapt__trim_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__filter_taxa +- name: qiime2__composition__add_pseudocount owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_bv_brc_genome_features +- name: qiime2__composition__ancom owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_bv_brc_genomes +- name: qiime2__composition__ancombc owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_bv_brc_metadata +- name: qiime2__composition__ancombc2 owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_eukaryome_data +- name: qiime2__composition__ancombc2_visualizer owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_gtdb_data +- name: qiime2__composition__da_barplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_midori2_data +- name: qiime2__composition__tabulate owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_ncbi_data +- name: qiime2__boots__alpha owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_ncbi_data_protein +- name: qiime2__boots__alpha_average owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_ncbi_genomes +- name: qiime2__boots__alpha_collection owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_pr2_data +- name: qiime2__boots__beta owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_silva_data +- name: qiime2__boots__beta_average owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_unite_data +- name: qiime2__boots__beta_collection owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__merge_taxa +- name: qiime2__boots__core_metrics owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__orient_reads +- name: qiime2__boots__kmer_diversity owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__orient_seqs +- name: qiime2__boots__resample owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__parse_silva_taxonomy +- name: qiime2__vsearch__cluster_features_closed_reference owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__reverse_transcribe +- name: qiime2__vsearch__cluster_features_de_novo owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__subsample_fasta +- name: qiime2__vsearch__cluster_features_open_reference owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__trim_alignment +- name: qiime2__vsearch__dereplicate_sequences owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__classify_samples +- name: qiime2__vsearch__fastq_stats owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__classify_samples_from_dist +- name: qiime2__vsearch__merge_pairs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__classify_samples_ncv +- name: qiime2__vsearch__uchime_denovo owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__confusion_matrix +- name: qiime2__vsearch__uchime_ref owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__fit_classifier +- name: qiime2__demux__emp_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__fit_regressor +- name: qiime2__demux__emp_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__heatmap +- name: qiime2__demux__filter_samples owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__metatable +- name: qiime2__demux__partition_samples_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__predict_classification +- name: qiime2__demux__partition_samples_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__predict_regression +- name: qiime2__demux__subsample_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__regress_samples +- name: qiime2__demux__subsample_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__regress_samples_ncv +- name: qiime2__demux__summarize owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__scatterplot +- name: qiime2__demux__tabulate_read_counts owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__split_table +- name: qiime2__deblur__denoise_16S owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__summarize +- name: qiime2__deblur__denoise_other owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__align_to_tree_mafft_fasttree +- name: qiime2__deblur__visualize_stats owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__align_to_tree_mafft_iqtree +- name: qiime2__diversity__adonis owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__align_to_tree_mafft_raxml +- name: qiime2__diversity__alpha owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__fasttree +- name: qiime2__diversity__alpha_correlation owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__filter_table +- name: qiime2__diversity__alpha_group_significance owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__filter_tree +- name: qiime2__diversity__alpha_phylogenetic owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__iqtree +- name: qiime2__diversity__alpha_rarefaction owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__iqtree_ultrafast_bootstrap +- name: qiime2__diversity__beta owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__midpoint_root +- name: qiime2__diversity__beta_correlation owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__raxml +- name: qiime2__diversity__beta_group_significance owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__raxml_rapid_bootstrap +- name: qiime2__diversity__beta_phylogenetic owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__robinson_foulds +- name: qiime2__diversity__beta_rarefaction owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__distance_matrix +- name: qiime2__diversity__bioenv owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__merge +- name: qiime2__diversity__core_metrics owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__shuffle_groups +- name: qiime2__diversity__core_metrics_phylogenetic owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__tabulate +- name: qiime2__diversity__filter_alpha_diversity owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__alpha_group_significance +- name: qiime2__diversity__filter_distance_matrix owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__collate_stats +- name: qiime2__diversity__mantel owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__facet_across +- name: qiime2__diversity__partial_procrustes owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__facet_within +- name: qiime2__diversity__pcoa owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__mann_whitney_u +- name: qiime2__diversity__pcoa_biplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__mann_whitney_u_facet +- name: qiime2__diversity__procrustes_analysis owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__plot_rainclouds +- name: qiime2__diversity__tsne owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__prep_alpha_distribution +- name: qiime2__diversity__umap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__wilcoxon_srt +- name: qiime2__emperor__biplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__wilcoxon_srt_facet +- name: qiime2__emperor__plot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__bowtie2_build +- name: qiime2__emperor__procrustes_plot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__decontam_identify +- name: qiime2_core__tools__export owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__decontam_identify_batches +- name: qiime2_core__tools__import owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__decontam_score_viz +- name: qiime2_core__tools__import_fastq owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__evaluate_composition +- name: qiime2__taxa__barplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__evaluate_seqs +- name: qiime2__taxa__barplot2 owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__evaluate_taxonomy +- name: qiime2__taxa__collapse owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__exclude_seqs +- name: qiime2__taxa__filter_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__filter_reads +- name: qiime2__taxa__filter_table owner: q2d2 tool_panel_section_id: '' - name: qiime2__diversity_lib__alpha_passthrough @@ -1571,253 +1568,244 @@ tools: - name: qiime2__diversity_lib__weighted_unifrac owner: q2d2 tool_panel_section_id: '' -- name: qiime2__alignment__mafft - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__alignment__mafft_add - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__alignment__mask - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__vizard__boxplot +- name: qiime2__stats__alpha_group_significance owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vizard__heatmap +- name: qiime2__stats__collate_stats owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vizard__lineplot +- name: qiime2__stats__facet_across owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vizard__scatterplot_2d +- name: qiime2__stats__facet_within owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__adonis +- name: qiime2__stats__mann_whitney_u owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha +- name: qiime2__stats__mann_whitney_u_facet owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_correlation +- name: qiime2__stats__plot_rainclouds owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_group_significance +- name: qiime2__stats__prep_alpha_distribution owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_phylogenetic +- name: qiime2__stats__wilcoxon_srt owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_rarefaction +- name: qiime2__stats__wilcoxon_srt_facet owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta +- name: qiime2__sample_classifier__classify_samples owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_correlation +- name: qiime2__sample_classifier__classify_samples_from_dist owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_group_significance +- name: qiime2__sample_classifier__classify_samples_ncv owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_phylogenetic +- name: qiime2__sample_classifier__confusion_matrix owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_rarefaction +- name: qiime2__sample_classifier__fit_classifier owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__bioenv +- name: qiime2__sample_classifier__fit_regressor owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__core_metrics +- name: qiime2__sample_classifier__heatmap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__core_metrics_phylogenetic +- name: qiime2__sample_classifier__metatable owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__filter_alpha_diversity +- name: qiime2__sample_classifier__predict_classification owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__filter_distance_matrix +- name: qiime2__sample_classifier__predict_regression owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__mantel +- name: qiime2__sample_classifier__regress_samples owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__partial_procrustes +- name: qiime2__sample_classifier__regress_samples_ncv owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__pcoa +- name: qiime2__sample_classifier__scatterplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__pcoa_biplot +- name: qiime2__sample_classifier__split_table owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__procrustes_analysis +- name: qiime2__sample_classifier__summarize owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__tsne +- name: qiime2__rescript__cull_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__umap +- name: qiime2__rescript__degap_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__emp_paired +- name: qiime2__rescript__dereplicate owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__emp_single +- name: qiime2__rescript__edit_taxonomy owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__filter_samples +- name: qiime2__rescript__evaluate_classifications owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__partition_samples_paired +- name: qiime2__rescript__evaluate_cross_validate owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__partition_samples_single +- name: qiime2__rescript__evaluate_fit_classifier owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__subsample_paired +- name: qiime2__rescript__evaluate_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__subsample_single +- name: qiime2__rescript__evaluate_taxonomy owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__summarize +- name: qiime2__rescript__extract_seq_segments owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__tabulate_read_counts +- name: qiime2__rescript__filter_seqs_length owner: q2d2 tool_panel_section_id: '' -- name: qiime2__deblur__denoise_16S +- name: qiime2__rescript__filter_seqs_length_by_taxon owner: q2d2 tool_panel_section_id: '' -- name: qiime2__deblur__denoise_other +- name: qiime2__rescript__filter_taxa owner: q2d2 tool_panel_section_id: '' -- name: qiime2__deblur__visualize_stats +- name: qiime2__rescript__get_bv_brc_genome_features owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_ccs +- name: qiime2__rescript__get_bv_brc_genomes owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_paired +- name: qiime2__rescript__get_bv_brc_metadata owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_pyro +- name: qiime2__rescript__get_eukaryome_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_single +- name: qiime2__rescript__get_gtdb_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__plot_base_transitions +- name: qiime2__rescript__get_midori2_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__cutadapt__demux_paired +- name: qiime2__rescript__get_ncbi_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__cutadapt__demux_single +- name: qiime2__rescript__get_ncbi_data_protein owner: q2d2 tool_panel_section_id: '' -- name: qiime2__cutadapt__trim_paired +- name: qiime2__rescript__get_ncbi_genomes owner: q2d2 tool_panel_section_id: '' -- name: qiime2__cutadapt__trim_single +- name: qiime2__rescript__get_pr2_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__add_pseudocount +- name: qiime2__rescript__get_silva_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancom +- name: qiime2__rescript__get_unite_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancombc +- name: qiime2__rescript__merge_taxa owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancombc2 +- name: qiime2__rescript__orient_reads owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancombc2_visualizer +- name: qiime2__rescript__orient_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__da_barplot +- name: qiime2__rescript__parse_silva_taxonomy owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__tabulate +- name: qiime2__rescript__reverse_transcribe owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__barplot +- name: qiime2__rescript__subsample_fasta owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__barplot2 +- name: qiime2__rescript__trim_alignment owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__collapse +- name: qiime2__quality_filter__q_score owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__filter_seqs +- name: qiime2__vizard__boxplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__filter_table +- name: qiime2__vizard__heatmap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__alpha +- name: qiime2__vizard__lineplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__alpha_average +- name: qiime2__vizard__scatterplot_2d owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__alpha_collection +- name: qiime2__alignment__mafft owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__beta +- name: qiime2__alignment__mafft_add owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__beta_average +- name: qiime2__alignment__mask owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__beta_collection +- name: qiime2__phylogeny__align_to_tree_mafft_fasttree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__core_metrics +- name: qiime2__phylogeny__align_to_tree_mafft_iqtree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__kmer_diversity +- name: qiime2__phylogeny__align_to_tree_mafft_raxml owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__resample +- name: qiime2__phylogeny__fasttree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__cluster_features_closed_reference +- name: qiime2__phylogeny__filter_table owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__cluster_features_de_novo +- name: qiime2__phylogeny__filter_tree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__cluster_features_open_reference +- name: qiime2__phylogeny__iqtree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__dereplicate_sequences +- name: qiime2__phylogeny__iqtree_ultrafast_bootstrap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__fastq_stats +- name: qiime2__phylogeny__midpoint_root owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__merge_pairs +- name: qiime2__phylogeny__raxml owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__uchime_denovo +- name: qiime2__phylogeny__raxml_rapid_bootstrap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__uchime_ref +- name: qiime2__phylogeny__robinson_foulds owner: q2d2 tool_panel_section_id: '' -- name: qiime2__emperor__biplot +- name: qiime2__fragment_insertion__classify_otus_experimental owner: q2d2 tool_panel_section_id: '' -- name: qiime2__emperor__plot +- name: qiime2__fragment_insertion__filter_features owner: q2d2 tool_panel_section_id: '' -- name: qiime2__emperor__procrustes_plot +- name: qiime2__fragment_insertion__sepp owner: q2d2 tool_panel_section_id: '' - name: qiime2__feature_classifier__blast @@ -1853,6 +1841,39 @@ tools: - name: qiime2__feature_classifier__vsearch_global owner: q2d2 tool_panel_section_id: '' +- name: qiime2__longitudinal__anova + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__feature_volatility + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__first_differences + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__first_distances + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__linear_mixed_effects + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__maturity_index + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__nmit + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__pairwise_differences + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__pairwise_distances + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__plot_feature_volatility + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__volatility + owner: q2d2 + tool_panel_section_id: '' - name: qiime2__feature_table___summarize owner: q2d2 tool_panel_section_id: '' @@ -1922,76 +1943,73 @@ tools: - name: qiime2__feature_table__transpose owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue___get_sequences - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__fondue__combine_seqs +- name: qiime2__quality_control__bowtie2_build owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__get_all +- name: qiime2__quality_control__decontam_identify owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__get_ids_from_query +- name: qiime2__quality_control__decontam_identify_batches owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__get_metadata +- name: qiime2__quality_control__decontam_score_viz owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__get_sequences +- name: qiime2__quality_control__evaluate_composition owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__merge_metadata +- name: qiime2__quality_control__evaluate_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__scrape_collection +- name: qiime2__quality_control__evaluate_taxonomy owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fragment_insertion__classify_otus_experimental +- name: qiime2__quality_control__exclude_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fragment_insertion__filter_features +- name: qiime2__quality_control__filter_reads owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fragment_insertion__sepp +- name: qiime2__metadata__distance_matrix owner: q2d2 tool_panel_section_id: '' -- name: qiime2__kmerizer__core_metrics +- name: qiime2__metadata__merge owner: q2d2 tool_panel_section_id: '' -- name: qiime2__kmerizer__seqs_to_kmers +- name: qiime2__metadata__shuffle_groups owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__anova +- name: qiime2__metadata__tabulate owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__feature_volatility +- name: qiime2__kmerizer__core_metrics owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__first_differences +- name: qiime2__kmerizer__seqs_to_kmers owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__first_distances +- name: qiime2__fondue___get_sequences owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__linear_mixed_effects +- name: qiime2__fondue__combine_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__maturity_index +- name: qiime2__fondue__get_all owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__nmit +- name: qiime2__fondue__get_ids_from_query owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__pairwise_differences +- name: qiime2__fondue__get_metadata owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__pairwise_distances +- name: qiime2__fondue__get_sequences owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__plot_feature_volatility +- name: qiime2__fondue__merge_metadata owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__volatility +- name: qiime2__fondue__scrape_collection owner: q2d2 tool_panel_section_id: '' - name: qualimap_bamqc diff --git a/communities/microgalaxy/lab/tools/top/MISSISSIPPI.yaml b/communities/microgalaxy/lab/tools/top/MISSISSIPPI.yaml index 130e83670..16f6acf74 100644 --- a/communities/microgalaxy/lab/tools/top/MISSISSIPPI.yaml +++ b/communities/microgalaxy/lab/tools/top/MISSISSIPPI.yaml @@ -767,6 +767,9 @@ tools: - name: obi_clean owner: iuc tool_panel_section_id: '' +- name: obi_complement + owner: iuc + tool_panel_section_id: '' - name: obi_convert owner: iuc tool_panel_section_id: '' @@ -779,6 +782,18 @@ tools: - name: obi_pairing owner: iuc tool_panel_section_id: '' +- name: obi_pcr + owner: iuc + tool_panel_section_id: '' +- name: obi_refidx + owner: iuc + tool_panel_section_id: '' +- name: obi_tag + owner: iuc + tool_panel_section_id: '' +- name: obi_taxonomy + owner: iuc + tool_panel_section_id: '' - name: obi_uniq owner: iuc tool_panel_section_id: '' @@ -1256,6 +1271,9 @@ tools: - name: picrust_predict_metagenomes owner: iuc tool_panel_section_id: '' +- name: prinseq + owner: iuc + tool_panel_section_id: '' - name: prodigal owner: iuc tool_panel_section_id: '' @@ -1265,262 +1283,241 @@ tools: - name: pygenomeTracks owner: iuc tool_panel_section_id: '' -- name: qiime2_core__tools__export - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2_core__tools__import - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2_core__tools__import_fastq - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__quality_filter__q_score - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__cull_seqs - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__degap_seqs - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__dereplicate - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__edit_taxonomy +- name: qiime2__dada2__denoise_ccs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_classifications +- name: qiime2__dada2__denoise_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_cross_validate +- name: qiime2__dada2__denoise_pyro owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_fit_classifier +- name: qiime2__dada2__denoise_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_seqs +- name: qiime2__dada2__plot_base_transitions owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_taxonomy +- name: qiime2__cutadapt__demux_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__extract_seq_segments +- name: qiime2__cutadapt__demux_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__filter_seqs_length +- name: qiime2__cutadapt__trim_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__filter_seqs_length_by_taxon +- name: qiime2__cutadapt__trim_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__filter_taxa +- name: qiime2__composition__add_pseudocount owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_bv_brc_genome_features +- name: qiime2__composition__ancom owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_bv_brc_genomes +- name: qiime2__composition__ancombc owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_bv_brc_metadata +- name: qiime2__composition__ancombc2 owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_eukaryome_data +- name: qiime2__composition__ancombc2_visualizer owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_gtdb_data +- name: qiime2__composition__da_barplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_midori2_data +- name: qiime2__composition__tabulate owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_ncbi_data +- name: qiime2__boots__alpha owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_ncbi_data_protein +- name: qiime2__boots__alpha_average owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_ncbi_genomes +- name: qiime2__boots__alpha_collection owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_pr2_data +- name: qiime2__boots__beta owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_silva_data +- name: qiime2__boots__beta_average owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_unite_data +- name: qiime2__boots__beta_collection owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__merge_taxa +- name: qiime2__boots__core_metrics owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__orient_reads +- name: qiime2__boots__kmer_diversity owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__orient_seqs +- name: qiime2__boots__resample owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__parse_silva_taxonomy +- name: qiime2__vsearch__cluster_features_closed_reference owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__reverse_transcribe +- name: qiime2__vsearch__cluster_features_de_novo owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__subsample_fasta +- name: qiime2__vsearch__cluster_features_open_reference owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__trim_alignment +- name: qiime2__vsearch__dereplicate_sequences owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__classify_samples +- name: qiime2__vsearch__fastq_stats owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__classify_samples_from_dist +- name: qiime2__vsearch__merge_pairs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__classify_samples_ncv +- name: qiime2__vsearch__uchime_denovo owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__confusion_matrix +- name: qiime2__vsearch__uchime_ref owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__fit_classifier +- name: qiime2__demux__emp_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__fit_regressor +- name: qiime2__demux__emp_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__heatmap +- name: qiime2__demux__filter_samples owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__metatable +- name: qiime2__demux__partition_samples_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__predict_classification +- name: qiime2__demux__partition_samples_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__predict_regression +- name: qiime2__demux__subsample_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__regress_samples +- name: qiime2__demux__subsample_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__regress_samples_ncv +- name: qiime2__demux__summarize owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__scatterplot +- name: qiime2__demux__tabulate_read_counts owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__split_table +- name: qiime2__deblur__denoise_16S owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__summarize +- name: qiime2__deblur__denoise_other owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__align_to_tree_mafft_fasttree +- name: qiime2__deblur__visualize_stats owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__align_to_tree_mafft_iqtree +- name: qiime2__diversity__adonis owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__align_to_tree_mafft_raxml +- name: qiime2__diversity__alpha owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__fasttree +- name: qiime2__diversity__alpha_correlation owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__filter_table +- name: qiime2__diversity__alpha_group_significance owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__filter_tree +- name: qiime2__diversity__alpha_phylogenetic owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__iqtree +- name: qiime2__diversity__alpha_rarefaction owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__iqtree_ultrafast_bootstrap +- name: qiime2__diversity__beta owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__midpoint_root +- name: qiime2__diversity__beta_correlation owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__raxml +- name: qiime2__diversity__beta_group_significance owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__raxml_rapid_bootstrap +- name: qiime2__diversity__beta_phylogenetic owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__robinson_foulds +- name: qiime2__diversity__beta_rarefaction owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__distance_matrix +- name: qiime2__diversity__bioenv owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__merge +- name: qiime2__diversity__core_metrics owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__shuffle_groups +- name: qiime2__diversity__core_metrics_phylogenetic owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__tabulate +- name: qiime2__diversity__filter_alpha_diversity owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__alpha_group_significance +- name: qiime2__diversity__filter_distance_matrix owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__collate_stats +- name: qiime2__diversity__mantel owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__facet_across +- name: qiime2__diversity__partial_procrustes owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__facet_within +- name: qiime2__diversity__pcoa owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__mann_whitney_u +- name: qiime2__diversity__pcoa_biplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__mann_whitney_u_facet +- name: qiime2__diversity__procrustes_analysis owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__plot_rainclouds +- name: qiime2__diversity__tsne owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__prep_alpha_distribution +- name: qiime2__diversity__umap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__wilcoxon_srt +- name: qiime2__emperor__biplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__wilcoxon_srt_facet +- name: qiime2__emperor__plot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__bowtie2_build +- name: qiime2__emperor__procrustes_plot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__decontam_identify +- name: qiime2_core__tools__export owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__decontam_identify_batches +- name: qiime2_core__tools__import owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__decontam_score_viz +- name: qiime2_core__tools__import_fastq owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__evaluate_composition +- name: qiime2__taxa__barplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__evaluate_seqs +- name: qiime2__taxa__barplot2 owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__evaluate_taxonomy +- name: qiime2__taxa__collapse owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__exclude_seqs +- name: qiime2__taxa__filter_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__filter_reads +- name: qiime2__taxa__filter_table owner: q2d2 tool_panel_section_id: '' - name: qiime2__diversity_lib__alpha_passthrough @@ -1559,253 +1556,244 @@ tools: - name: qiime2__diversity_lib__weighted_unifrac owner: q2d2 tool_panel_section_id: '' -- name: qiime2__alignment__mafft - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__alignment__mafft_add - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__alignment__mask - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__vizard__boxplot +- name: qiime2__stats__alpha_group_significance owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vizard__heatmap +- name: qiime2__stats__collate_stats owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vizard__lineplot +- name: qiime2__stats__facet_across owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vizard__scatterplot_2d +- name: qiime2__stats__facet_within owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__adonis +- name: qiime2__stats__mann_whitney_u owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha +- name: qiime2__stats__mann_whitney_u_facet owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_correlation +- name: qiime2__stats__plot_rainclouds owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_group_significance +- name: qiime2__stats__prep_alpha_distribution owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_phylogenetic +- name: qiime2__stats__wilcoxon_srt owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_rarefaction +- name: qiime2__stats__wilcoxon_srt_facet owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta +- name: qiime2__sample_classifier__classify_samples owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_correlation +- name: qiime2__sample_classifier__classify_samples_from_dist owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_group_significance +- name: qiime2__sample_classifier__classify_samples_ncv owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_phylogenetic +- name: qiime2__sample_classifier__confusion_matrix owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_rarefaction +- name: qiime2__sample_classifier__fit_classifier owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__bioenv +- name: qiime2__sample_classifier__fit_regressor owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__core_metrics +- name: qiime2__sample_classifier__heatmap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__core_metrics_phylogenetic +- name: qiime2__sample_classifier__metatable owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__filter_alpha_diversity +- name: qiime2__sample_classifier__predict_classification owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__filter_distance_matrix +- name: qiime2__sample_classifier__predict_regression owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__mantel +- name: qiime2__sample_classifier__regress_samples owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__partial_procrustes +- name: qiime2__sample_classifier__regress_samples_ncv owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__pcoa +- name: qiime2__sample_classifier__scatterplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__pcoa_biplot +- name: qiime2__sample_classifier__split_table owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__procrustes_analysis +- name: qiime2__sample_classifier__summarize owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__tsne +- name: qiime2__rescript__cull_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__umap +- name: qiime2__rescript__degap_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__emp_paired +- name: qiime2__rescript__dereplicate owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__emp_single +- name: qiime2__rescript__edit_taxonomy owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__filter_samples +- name: qiime2__rescript__evaluate_classifications owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__partition_samples_paired +- name: qiime2__rescript__evaluate_cross_validate owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__partition_samples_single +- name: qiime2__rescript__evaluate_fit_classifier owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__subsample_paired +- name: qiime2__rescript__evaluate_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__subsample_single +- name: qiime2__rescript__evaluate_taxonomy owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__summarize +- name: qiime2__rescript__extract_seq_segments owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__tabulate_read_counts +- name: qiime2__rescript__filter_seqs_length owner: q2d2 tool_panel_section_id: '' -- name: qiime2__deblur__denoise_16S +- name: qiime2__rescript__filter_seqs_length_by_taxon owner: q2d2 tool_panel_section_id: '' -- name: qiime2__deblur__denoise_other +- name: qiime2__rescript__filter_taxa owner: q2d2 tool_panel_section_id: '' -- name: qiime2__deblur__visualize_stats +- name: qiime2__rescript__get_bv_brc_genome_features owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_ccs +- name: qiime2__rescript__get_bv_brc_genomes owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_paired +- name: qiime2__rescript__get_bv_brc_metadata owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_pyro +- name: qiime2__rescript__get_eukaryome_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_single +- name: qiime2__rescript__get_gtdb_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__plot_base_transitions +- name: qiime2__rescript__get_midori2_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__cutadapt__demux_paired +- name: qiime2__rescript__get_ncbi_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__cutadapt__demux_single +- name: qiime2__rescript__get_ncbi_data_protein owner: q2d2 tool_panel_section_id: '' -- name: qiime2__cutadapt__trim_paired +- name: qiime2__rescript__get_ncbi_genomes owner: q2d2 tool_panel_section_id: '' -- name: qiime2__cutadapt__trim_single +- name: qiime2__rescript__get_pr2_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__add_pseudocount +- name: qiime2__rescript__get_silva_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancom +- name: qiime2__rescript__get_unite_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancombc +- name: qiime2__rescript__merge_taxa owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancombc2 +- name: qiime2__rescript__orient_reads owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancombc2_visualizer +- name: qiime2__rescript__orient_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__da_barplot +- name: qiime2__rescript__parse_silva_taxonomy owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__tabulate +- name: qiime2__rescript__reverse_transcribe owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__barplot +- name: qiime2__rescript__subsample_fasta owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__barplot2 +- name: qiime2__rescript__trim_alignment owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__collapse +- name: qiime2__quality_filter__q_score owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__filter_seqs +- name: qiime2__vizard__boxplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__filter_table +- name: qiime2__vizard__heatmap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__alpha +- name: qiime2__vizard__lineplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__alpha_average +- name: qiime2__vizard__scatterplot_2d owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__alpha_collection +- name: qiime2__alignment__mafft owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__beta +- name: qiime2__alignment__mafft_add owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__beta_average +- name: qiime2__alignment__mask owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__beta_collection +- name: qiime2__phylogeny__align_to_tree_mafft_fasttree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__core_metrics +- name: qiime2__phylogeny__align_to_tree_mafft_iqtree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__kmer_diversity +- name: qiime2__phylogeny__align_to_tree_mafft_raxml owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__resample +- name: qiime2__phylogeny__fasttree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__cluster_features_closed_reference +- name: qiime2__phylogeny__filter_table owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__cluster_features_de_novo +- name: qiime2__phylogeny__filter_tree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__cluster_features_open_reference +- name: qiime2__phylogeny__iqtree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__dereplicate_sequences +- name: qiime2__phylogeny__iqtree_ultrafast_bootstrap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__fastq_stats +- name: qiime2__phylogeny__midpoint_root owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__merge_pairs +- name: qiime2__phylogeny__raxml owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__uchime_denovo +- name: qiime2__phylogeny__raxml_rapid_bootstrap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__uchime_ref +- name: qiime2__phylogeny__robinson_foulds owner: q2d2 tool_panel_section_id: '' -- name: qiime2__emperor__biplot +- name: qiime2__fragment_insertion__classify_otus_experimental owner: q2d2 tool_panel_section_id: '' -- name: qiime2__emperor__plot +- name: qiime2__fragment_insertion__filter_features owner: q2d2 tool_panel_section_id: '' -- name: qiime2__emperor__procrustes_plot +- name: qiime2__fragment_insertion__sepp owner: q2d2 tool_panel_section_id: '' - name: qiime2__feature_classifier__blast @@ -1841,6 +1829,39 @@ tools: - name: qiime2__feature_classifier__vsearch_global owner: q2d2 tool_panel_section_id: '' +- name: qiime2__longitudinal__anova + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__feature_volatility + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__first_differences + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__first_distances + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__linear_mixed_effects + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__maturity_index + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__nmit + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__pairwise_differences + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__pairwise_distances + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__plot_feature_volatility + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__volatility + owner: q2d2 + tool_panel_section_id: '' - name: qiime2__feature_table___summarize owner: q2d2 tool_panel_section_id: '' @@ -1910,76 +1931,73 @@ tools: - name: qiime2__feature_table__transpose owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue___get_sequences - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__fondue__combine_seqs +- name: qiime2__quality_control__bowtie2_build owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__get_all +- name: qiime2__quality_control__decontam_identify owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__get_ids_from_query +- name: qiime2__quality_control__decontam_identify_batches owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__get_metadata +- name: qiime2__quality_control__decontam_score_viz owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__get_sequences +- name: qiime2__quality_control__evaluate_composition owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__merge_metadata +- name: qiime2__quality_control__evaluate_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__scrape_collection +- name: qiime2__quality_control__evaluate_taxonomy owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fragment_insertion__classify_otus_experimental +- name: qiime2__quality_control__exclude_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fragment_insertion__filter_features +- name: qiime2__quality_control__filter_reads owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fragment_insertion__sepp +- name: qiime2__metadata__distance_matrix owner: q2d2 tool_panel_section_id: '' -- name: qiime2__kmerizer__core_metrics +- name: qiime2__metadata__merge owner: q2d2 tool_panel_section_id: '' -- name: qiime2__kmerizer__seqs_to_kmers +- name: qiime2__metadata__shuffle_groups owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__anova +- name: qiime2__metadata__tabulate owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__feature_volatility +- name: qiime2__kmerizer__core_metrics owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__first_differences +- name: qiime2__kmerizer__seqs_to_kmers owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__first_distances +- name: qiime2__fondue___get_sequences owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__linear_mixed_effects +- name: qiime2__fondue__combine_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__maturity_index +- name: qiime2__fondue__get_all owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__nmit +- name: qiime2__fondue__get_ids_from_query owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__pairwise_differences +- name: qiime2__fondue__get_metadata owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__pairwise_distances +- name: qiime2__fondue__get_sequences owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__plot_feature_volatility +- name: qiime2__fondue__merge_metadata owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__volatility +- name: qiime2__fondue__scrape_collection owner: q2d2 tool_panel_section_id: '' - name: qualimap_bamqc diff --git a/communities/microgalaxy/lab/tools/top/Mandoiu_Lab.yaml b/communities/microgalaxy/lab/tools/top/Mandoiu_Lab.yaml index 81562e59c..b2d3895f0 100644 --- a/communities/microgalaxy/lab/tools/top/Mandoiu_Lab.yaml +++ b/communities/microgalaxy/lab/tools/top/Mandoiu_Lab.yaml @@ -776,6 +776,9 @@ tools: - name: obi_clean owner: iuc tool_panel_section_id: '' +- name: obi_complement + owner: iuc + tool_panel_section_id: '' - name: obi_convert owner: iuc tool_panel_section_id: '' @@ -788,6 +791,18 @@ tools: - name: obi_pairing owner: iuc tool_panel_section_id: '' +- name: obi_pcr + owner: iuc + tool_panel_section_id: '' +- name: obi_refidx + owner: iuc + tool_panel_section_id: '' +- name: obi_tag + owner: iuc + tool_panel_section_id: '' +- name: obi_taxonomy + owner: iuc + tool_panel_section_id: '' - name: obi_uniq owner: iuc tool_panel_section_id: '' @@ -1265,6 +1280,9 @@ tools: - name: picrust_predict_metagenomes owner: iuc tool_panel_section_id: '' +- name: prinseq + owner: iuc + tool_panel_section_id: '' - name: prodigal owner: iuc tool_panel_section_id: '' @@ -1277,262 +1295,241 @@ tools: - name: pygenomeTracks owner: iuc tool_panel_section_id: '' -- name: qiime2_core__tools__export - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2_core__tools__import - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2_core__tools__import_fastq - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__quality_filter__q_score - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__cull_seqs - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__degap_seqs - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__dereplicate - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__edit_taxonomy +- name: qiime2__dada2__denoise_ccs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_classifications +- name: qiime2__dada2__denoise_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_cross_validate +- name: qiime2__dada2__denoise_pyro owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_fit_classifier +- name: qiime2__dada2__denoise_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_seqs +- name: qiime2__dada2__plot_base_transitions owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_taxonomy +- name: qiime2__cutadapt__demux_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__extract_seq_segments +- name: qiime2__cutadapt__demux_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__filter_seqs_length +- name: qiime2__cutadapt__trim_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__filter_seqs_length_by_taxon +- name: qiime2__cutadapt__trim_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__filter_taxa +- name: qiime2__composition__add_pseudocount owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_bv_brc_genome_features +- name: qiime2__composition__ancom owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_bv_brc_genomes +- name: qiime2__composition__ancombc owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_bv_brc_metadata +- name: qiime2__composition__ancombc2 owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_eukaryome_data +- name: qiime2__composition__ancombc2_visualizer owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_gtdb_data +- name: qiime2__composition__da_barplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_midori2_data +- name: qiime2__composition__tabulate owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_ncbi_data +- name: qiime2__boots__alpha owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_ncbi_data_protein +- name: qiime2__boots__alpha_average owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_ncbi_genomes +- name: qiime2__boots__alpha_collection owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_pr2_data +- name: qiime2__boots__beta owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_silva_data +- name: qiime2__boots__beta_average owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_unite_data +- name: qiime2__boots__beta_collection owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__merge_taxa +- name: qiime2__boots__core_metrics owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__orient_reads +- name: qiime2__boots__kmer_diversity owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__orient_seqs +- name: qiime2__boots__resample owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__parse_silva_taxonomy +- name: qiime2__vsearch__cluster_features_closed_reference owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__reverse_transcribe +- name: qiime2__vsearch__cluster_features_de_novo owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__subsample_fasta +- name: qiime2__vsearch__cluster_features_open_reference owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__trim_alignment +- name: qiime2__vsearch__dereplicate_sequences owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__classify_samples +- name: qiime2__vsearch__fastq_stats owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__classify_samples_from_dist +- name: qiime2__vsearch__merge_pairs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__classify_samples_ncv +- name: qiime2__vsearch__uchime_denovo owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__confusion_matrix +- name: qiime2__vsearch__uchime_ref owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__fit_classifier +- name: qiime2__demux__emp_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__fit_regressor +- name: qiime2__demux__emp_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__heatmap +- name: qiime2__demux__filter_samples owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__metatable +- name: qiime2__demux__partition_samples_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__predict_classification +- name: qiime2__demux__partition_samples_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__predict_regression +- name: qiime2__demux__subsample_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__regress_samples +- name: qiime2__demux__subsample_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__regress_samples_ncv +- name: qiime2__demux__summarize owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__scatterplot +- name: qiime2__demux__tabulate_read_counts owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__split_table +- name: qiime2__deblur__denoise_16S owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__summarize +- name: qiime2__deblur__denoise_other owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__align_to_tree_mafft_fasttree +- name: qiime2__deblur__visualize_stats owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__align_to_tree_mafft_iqtree +- name: qiime2__diversity__adonis owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__align_to_tree_mafft_raxml +- name: qiime2__diversity__alpha owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__fasttree +- name: qiime2__diversity__alpha_correlation owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__filter_table +- name: qiime2__diversity__alpha_group_significance owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__filter_tree +- name: qiime2__diversity__alpha_phylogenetic owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__iqtree +- name: qiime2__diversity__alpha_rarefaction owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__iqtree_ultrafast_bootstrap +- name: qiime2__diversity__beta owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__midpoint_root +- name: qiime2__diversity__beta_correlation owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__raxml +- name: qiime2__diversity__beta_group_significance owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__raxml_rapid_bootstrap +- name: qiime2__diversity__beta_phylogenetic owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__robinson_foulds +- name: qiime2__diversity__beta_rarefaction owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__distance_matrix +- name: qiime2__diversity__bioenv owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__merge +- name: qiime2__diversity__core_metrics owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__shuffle_groups +- name: qiime2__diversity__core_metrics_phylogenetic owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__tabulate +- name: qiime2__diversity__filter_alpha_diversity owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__alpha_group_significance +- name: qiime2__diversity__filter_distance_matrix owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__collate_stats +- name: qiime2__diversity__mantel owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__facet_across +- name: qiime2__diversity__partial_procrustes owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__facet_within +- name: qiime2__diversity__pcoa owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__mann_whitney_u +- name: qiime2__diversity__pcoa_biplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__mann_whitney_u_facet +- name: qiime2__diversity__procrustes_analysis owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__plot_rainclouds +- name: qiime2__diversity__tsne owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__prep_alpha_distribution +- name: qiime2__diversity__umap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__wilcoxon_srt +- name: qiime2__emperor__biplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__wilcoxon_srt_facet +- name: qiime2__emperor__plot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__bowtie2_build +- name: qiime2__emperor__procrustes_plot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__decontam_identify +- name: qiime2_core__tools__export owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__decontam_identify_batches +- name: qiime2_core__tools__import owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__decontam_score_viz +- name: qiime2_core__tools__import_fastq owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__evaluate_composition +- name: qiime2__taxa__barplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__evaluate_seqs +- name: qiime2__taxa__barplot2 owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__evaluate_taxonomy +- name: qiime2__taxa__collapse owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__exclude_seqs +- name: qiime2__taxa__filter_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__filter_reads +- name: qiime2__taxa__filter_table owner: q2d2 tool_panel_section_id: '' - name: qiime2__diversity_lib__alpha_passthrough @@ -1571,253 +1568,244 @@ tools: - name: qiime2__diversity_lib__weighted_unifrac owner: q2d2 tool_panel_section_id: '' -- name: qiime2__alignment__mafft - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__alignment__mafft_add - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__alignment__mask - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__vizard__boxplot +- name: qiime2__stats__alpha_group_significance owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vizard__heatmap +- name: qiime2__stats__collate_stats owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vizard__lineplot +- name: qiime2__stats__facet_across owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vizard__scatterplot_2d +- name: qiime2__stats__facet_within owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__adonis +- name: qiime2__stats__mann_whitney_u owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha +- name: qiime2__stats__mann_whitney_u_facet owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_correlation +- name: qiime2__stats__plot_rainclouds owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_group_significance +- name: qiime2__stats__prep_alpha_distribution owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_phylogenetic +- name: qiime2__stats__wilcoxon_srt owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_rarefaction +- name: qiime2__stats__wilcoxon_srt_facet owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta +- name: qiime2__sample_classifier__classify_samples owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_correlation +- name: qiime2__sample_classifier__classify_samples_from_dist owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_group_significance +- name: qiime2__sample_classifier__classify_samples_ncv owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_phylogenetic +- name: qiime2__sample_classifier__confusion_matrix owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_rarefaction +- name: qiime2__sample_classifier__fit_classifier owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__bioenv +- name: qiime2__sample_classifier__fit_regressor owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__core_metrics +- name: qiime2__sample_classifier__heatmap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__core_metrics_phylogenetic +- name: qiime2__sample_classifier__metatable owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__filter_alpha_diversity +- name: qiime2__sample_classifier__predict_classification owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__filter_distance_matrix +- name: qiime2__sample_classifier__predict_regression owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__mantel +- name: qiime2__sample_classifier__regress_samples owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__partial_procrustes +- name: qiime2__sample_classifier__regress_samples_ncv owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__pcoa +- name: qiime2__sample_classifier__scatterplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__pcoa_biplot +- name: qiime2__sample_classifier__split_table owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__procrustes_analysis +- name: qiime2__sample_classifier__summarize owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__tsne +- name: qiime2__rescript__cull_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__umap +- name: qiime2__rescript__degap_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__emp_paired +- name: qiime2__rescript__dereplicate owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__emp_single +- name: qiime2__rescript__edit_taxonomy owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__filter_samples +- name: qiime2__rescript__evaluate_classifications owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__partition_samples_paired +- name: qiime2__rescript__evaluate_cross_validate owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__partition_samples_single +- name: qiime2__rescript__evaluate_fit_classifier owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__subsample_paired +- name: qiime2__rescript__evaluate_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__subsample_single +- name: qiime2__rescript__evaluate_taxonomy owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__summarize +- name: qiime2__rescript__extract_seq_segments owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__tabulate_read_counts +- name: qiime2__rescript__filter_seqs_length owner: q2d2 tool_panel_section_id: '' -- name: qiime2__deblur__denoise_16S +- name: qiime2__rescript__filter_seqs_length_by_taxon owner: q2d2 tool_panel_section_id: '' -- name: qiime2__deblur__denoise_other +- name: qiime2__rescript__filter_taxa owner: q2d2 tool_panel_section_id: '' -- name: qiime2__deblur__visualize_stats +- name: qiime2__rescript__get_bv_brc_genome_features owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_ccs +- name: qiime2__rescript__get_bv_brc_genomes owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_paired +- name: qiime2__rescript__get_bv_brc_metadata owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_pyro +- name: qiime2__rescript__get_eukaryome_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_single +- name: qiime2__rescript__get_gtdb_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__plot_base_transitions +- name: qiime2__rescript__get_midori2_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__cutadapt__demux_paired +- name: qiime2__rescript__get_ncbi_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__cutadapt__demux_single +- name: qiime2__rescript__get_ncbi_data_protein owner: q2d2 tool_panel_section_id: '' -- name: qiime2__cutadapt__trim_paired +- name: qiime2__rescript__get_ncbi_genomes owner: q2d2 tool_panel_section_id: '' -- name: qiime2__cutadapt__trim_single +- name: qiime2__rescript__get_pr2_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__add_pseudocount +- name: qiime2__rescript__get_silva_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancom +- name: qiime2__rescript__get_unite_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancombc +- name: qiime2__rescript__merge_taxa owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancombc2 +- name: qiime2__rescript__orient_reads owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancombc2_visualizer +- name: qiime2__rescript__orient_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__da_barplot +- name: qiime2__rescript__parse_silva_taxonomy owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__tabulate +- name: qiime2__rescript__reverse_transcribe owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__barplot +- name: qiime2__rescript__subsample_fasta owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__barplot2 +- name: qiime2__rescript__trim_alignment owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__collapse +- name: qiime2__quality_filter__q_score owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__filter_seqs +- name: qiime2__vizard__boxplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__filter_table +- name: qiime2__vizard__heatmap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__alpha +- name: qiime2__vizard__lineplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__alpha_average +- name: qiime2__vizard__scatterplot_2d owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__alpha_collection +- name: qiime2__alignment__mafft owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__beta +- name: qiime2__alignment__mafft_add owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__beta_average +- name: qiime2__alignment__mask owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__beta_collection +- name: qiime2__phylogeny__align_to_tree_mafft_fasttree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__core_metrics +- name: qiime2__phylogeny__align_to_tree_mafft_iqtree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__kmer_diversity +- name: qiime2__phylogeny__align_to_tree_mafft_raxml owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__resample +- name: qiime2__phylogeny__fasttree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__cluster_features_closed_reference +- name: qiime2__phylogeny__filter_table owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__cluster_features_de_novo +- name: qiime2__phylogeny__filter_tree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__cluster_features_open_reference +- name: qiime2__phylogeny__iqtree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__dereplicate_sequences +- name: qiime2__phylogeny__iqtree_ultrafast_bootstrap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__fastq_stats +- name: qiime2__phylogeny__midpoint_root owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__merge_pairs +- name: qiime2__phylogeny__raxml owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__uchime_denovo +- name: qiime2__phylogeny__raxml_rapid_bootstrap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__uchime_ref +- name: qiime2__phylogeny__robinson_foulds owner: q2d2 tool_panel_section_id: '' -- name: qiime2__emperor__biplot +- name: qiime2__fragment_insertion__classify_otus_experimental owner: q2d2 tool_panel_section_id: '' -- name: qiime2__emperor__plot +- name: qiime2__fragment_insertion__filter_features owner: q2d2 tool_panel_section_id: '' -- name: qiime2__emperor__procrustes_plot +- name: qiime2__fragment_insertion__sepp owner: q2d2 tool_panel_section_id: '' - name: qiime2__feature_classifier__blast @@ -1853,6 +1841,39 @@ tools: - name: qiime2__feature_classifier__vsearch_global owner: q2d2 tool_panel_section_id: '' +- name: qiime2__longitudinal__anova + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__feature_volatility + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__first_differences + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__first_distances + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__linear_mixed_effects + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__maturity_index + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__nmit + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__pairwise_differences + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__pairwise_distances + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__plot_feature_volatility + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__volatility + owner: q2d2 + tool_panel_section_id: '' - name: qiime2__feature_table___summarize owner: q2d2 tool_panel_section_id: '' @@ -1922,76 +1943,73 @@ tools: - name: qiime2__feature_table__transpose owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue___get_sequences - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__fondue__combine_seqs +- name: qiime2__quality_control__bowtie2_build owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__get_all +- name: qiime2__quality_control__decontam_identify owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__get_ids_from_query +- name: qiime2__quality_control__decontam_identify_batches owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__get_metadata +- name: qiime2__quality_control__decontam_score_viz owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__get_sequences +- name: qiime2__quality_control__evaluate_composition owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__merge_metadata +- name: qiime2__quality_control__evaluate_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__scrape_collection +- name: qiime2__quality_control__evaluate_taxonomy owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fragment_insertion__classify_otus_experimental +- name: qiime2__quality_control__exclude_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fragment_insertion__filter_features +- name: qiime2__quality_control__filter_reads owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fragment_insertion__sepp +- name: qiime2__metadata__distance_matrix owner: q2d2 tool_panel_section_id: '' -- name: qiime2__kmerizer__core_metrics +- name: qiime2__metadata__merge owner: q2d2 tool_panel_section_id: '' -- name: qiime2__kmerizer__seqs_to_kmers +- name: qiime2__metadata__shuffle_groups owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__anova +- name: qiime2__metadata__tabulate owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__feature_volatility +- name: qiime2__kmerizer__core_metrics owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__first_differences +- name: qiime2__kmerizer__seqs_to_kmers owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__first_distances +- name: qiime2__fondue___get_sequences owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__linear_mixed_effects +- name: qiime2__fondue__combine_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__maturity_index +- name: qiime2__fondue__get_all owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__nmit +- name: qiime2__fondue__get_ids_from_query owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__pairwise_differences +- name: qiime2__fondue__get_metadata owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__pairwise_distances +- name: qiime2__fondue__get_sequences owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__plot_feature_volatility +- name: qiime2__fondue__merge_metadata owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__volatility +- name: qiime2__fondue__scrape_collection owner: q2d2 tool_panel_section_id: '' - name: qualimap_bamqc diff --git a/communities/microgalaxy/lab/tools/top/Oqtans.yaml b/communities/microgalaxy/lab/tools/top/Oqtans.yaml index 81562e59c..b2d3895f0 100644 --- a/communities/microgalaxy/lab/tools/top/Oqtans.yaml +++ b/communities/microgalaxy/lab/tools/top/Oqtans.yaml @@ -776,6 +776,9 @@ tools: - name: obi_clean owner: iuc tool_panel_section_id: '' +- name: obi_complement + owner: iuc + tool_panel_section_id: '' - name: obi_convert owner: iuc tool_panel_section_id: '' @@ -788,6 +791,18 @@ tools: - name: obi_pairing owner: iuc tool_panel_section_id: '' +- name: obi_pcr + owner: iuc + tool_panel_section_id: '' +- name: obi_refidx + owner: iuc + tool_panel_section_id: '' +- name: obi_tag + owner: iuc + tool_panel_section_id: '' +- name: obi_taxonomy + owner: iuc + tool_panel_section_id: '' - name: obi_uniq owner: iuc tool_panel_section_id: '' @@ -1265,6 +1280,9 @@ tools: - name: picrust_predict_metagenomes owner: iuc tool_panel_section_id: '' +- name: prinseq + owner: iuc + tool_panel_section_id: '' - name: prodigal owner: iuc tool_panel_section_id: '' @@ -1277,262 +1295,241 @@ tools: - name: pygenomeTracks owner: iuc tool_panel_section_id: '' -- name: qiime2_core__tools__export - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2_core__tools__import - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2_core__tools__import_fastq - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__quality_filter__q_score - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__cull_seqs - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__degap_seqs - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__dereplicate - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__edit_taxonomy +- name: qiime2__dada2__denoise_ccs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_classifications +- name: qiime2__dada2__denoise_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_cross_validate +- name: qiime2__dada2__denoise_pyro owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_fit_classifier +- name: qiime2__dada2__denoise_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_seqs +- name: qiime2__dada2__plot_base_transitions owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_taxonomy +- name: qiime2__cutadapt__demux_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__extract_seq_segments +- name: qiime2__cutadapt__demux_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__filter_seqs_length +- name: qiime2__cutadapt__trim_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__filter_seqs_length_by_taxon +- name: qiime2__cutadapt__trim_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__filter_taxa +- name: qiime2__composition__add_pseudocount owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_bv_brc_genome_features +- name: qiime2__composition__ancom owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_bv_brc_genomes +- name: qiime2__composition__ancombc owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_bv_brc_metadata +- name: qiime2__composition__ancombc2 owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_eukaryome_data +- name: qiime2__composition__ancombc2_visualizer owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_gtdb_data +- name: qiime2__composition__da_barplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_midori2_data +- name: qiime2__composition__tabulate owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_ncbi_data +- name: qiime2__boots__alpha owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_ncbi_data_protein +- name: qiime2__boots__alpha_average owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_ncbi_genomes +- name: qiime2__boots__alpha_collection owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_pr2_data +- name: qiime2__boots__beta owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_silva_data +- name: qiime2__boots__beta_average owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_unite_data +- name: qiime2__boots__beta_collection owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__merge_taxa +- name: qiime2__boots__core_metrics owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__orient_reads +- name: qiime2__boots__kmer_diversity owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__orient_seqs +- name: qiime2__boots__resample owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__parse_silva_taxonomy +- name: qiime2__vsearch__cluster_features_closed_reference owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__reverse_transcribe +- name: qiime2__vsearch__cluster_features_de_novo owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__subsample_fasta +- name: qiime2__vsearch__cluster_features_open_reference owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__trim_alignment +- name: qiime2__vsearch__dereplicate_sequences owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__classify_samples +- name: qiime2__vsearch__fastq_stats owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__classify_samples_from_dist +- name: qiime2__vsearch__merge_pairs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__classify_samples_ncv +- name: qiime2__vsearch__uchime_denovo owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__confusion_matrix +- name: qiime2__vsearch__uchime_ref owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__fit_classifier +- name: qiime2__demux__emp_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__fit_regressor +- name: qiime2__demux__emp_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__heatmap +- name: qiime2__demux__filter_samples owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__metatable +- name: qiime2__demux__partition_samples_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__predict_classification +- name: qiime2__demux__partition_samples_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__predict_regression +- name: qiime2__demux__subsample_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__regress_samples +- name: qiime2__demux__subsample_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__regress_samples_ncv +- name: qiime2__demux__summarize owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__scatterplot +- name: qiime2__demux__tabulate_read_counts owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__split_table +- name: qiime2__deblur__denoise_16S owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__summarize +- name: qiime2__deblur__denoise_other owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__align_to_tree_mafft_fasttree +- name: qiime2__deblur__visualize_stats owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__align_to_tree_mafft_iqtree +- name: qiime2__diversity__adonis owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__align_to_tree_mafft_raxml +- name: qiime2__diversity__alpha owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__fasttree +- name: qiime2__diversity__alpha_correlation owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__filter_table +- name: qiime2__diversity__alpha_group_significance owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__filter_tree +- name: qiime2__diversity__alpha_phylogenetic owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__iqtree +- name: qiime2__diversity__alpha_rarefaction owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__iqtree_ultrafast_bootstrap +- name: qiime2__diversity__beta owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__midpoint_root +- name: qiime2__diversity__beta_correlation owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__raxml +- name: qiime2__diversity__beta_group_significance owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__raxml_rapid_bootstrap +- name: qiime2__diversity__beta_phylogenetic owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__robinson_foulds +- name: qiime2__diversity__beta_rarefaction owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__distance_matrix +- name: qiime2__diversity__bioenv owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__merge +- name: qiime2__diversity__core_metrics owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__shuffle_groups +- name: qiime2__diversity__core_metrics_phylogenetic owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__tabulate +- name: qiime2__diversity__filter_alpha_diversity owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__alpha_group_significance +- name: qiime2__diversity__filter_distance_matrix owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__collate_stats +- name: qiime2__diversity__mantel owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__facet_across +- name: qiime2__diversity__partial_procrustes owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__facet_within +- name: qiime2__diversity__pcoa owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__mann_whitney_u +- name: qiime2__diversity__pcoa_biplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__mann_whitney_u_facet +- name: qiime2__diversity__procrustes_analysis owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__plot_rainclouds +- name: qiime2__diversity__tsne owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__prep_alpha_distribution +- name: qiime2__diversity__umap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__wilcoxon_srt +- name: qiime2__emperor__biplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__wilcoxon_srt_facet +- name: qiime2__emperor__plot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__bowtie2_build +- name: qiime2__emperor__procrustes_plot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__decontam_identify +- name: qiime2_core__tools__export owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__decontam_identify_batches +- name: qiime2_core__tools__import owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__decontam_score_viz +- name: qiime2_core__tools__import_fastq owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__evaluate_composition +- name: qiime2__taxa__barplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__evaluate_seqs +- name: qiime2__taxa__barplot2 owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__evaluate_taxonomy +- name: qiime2__taxa__collapse owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__exclude_seqs +- name: qiime2__taxa__filter_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__filter_reads +- name: qiime2__taxa__filter_table owner: q2d2 tool_panel_section_id: '' - name: qiime2__diversity_lib__alpha_passthrough @@ -1571,253 +1568,244 @@ tools: - name: qiime2__diversity_lib__weighted_unifrac owner: q2d2 tool_panel_section_id: '' -- name: qiime2__alignment__mafft - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__alignment__mafft_add - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__alignment__mask - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__vizard__boxplot +- name: qiime2__stats__alpha_group_significance owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vizard__heatmap +- name: qiime2__stats__collate_stats owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vizard__lineplot +- name: qiime2__stats__facet_across owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vizard__scatterplot_2d +- name: qiime2__stats__facet_within owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__adonis +- name: qiime2__stats__mann_whitney_u owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha +- name: qiime2__stats__mann_whitney_u_facet owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_correlation +- name: qiime2__stats__plot_rainclouds owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_group_significance +- name: qiime2__stats__prep_alpha_distribution owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_phylogenetic +- name: qiime2__stats__wilcoxon_srt owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_rarefaction +- name: qiime2__stats__wilcoxon_srt_facet owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta +- name: qiime2__sample_classifier__classify_samples owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_correlation +- name: qiime2__sample_classifier__classify_samples_from_dist owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_group_significance +- name: qiime2__sample_classifier__classify_samples_ncv owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_phylogenetic +- name: qiime2__sample_classifier__confusion_matrix owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_rarefaction +- name: qiime2__sample_classifier__fit_classifier owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__bioenv +- name: qiime2__sample_classifier__fit_regressor owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__core_metrics +- name: qiime2__sample_classifier__heatmap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__core_metrics_phylogenetic +- name: qiime2__sample_classifier__metatable owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__filter_alpha_diversity +- name: qiime2__sample_classifier__predict_classification owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__filter_distance_matrix +- name: qiime2__sample_classifier__predict_regression owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__mantel +- name: qiime2__sample_classifier__regress_samples owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__partial_procrustes +- name: qiime2__sample_classifier__regress_samples_ncv owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__pcoa +- name: qiime2__sample_classifier__scatterplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__pcoa_biplot +- name: qiime2__sample_classifier__split_table owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__procrustes_analysis +- name: qiime2__sample_classifier__summarize owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__tsne +- name: qiime2__rescript__cull_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__umap +- name: qiime2__rescript__degap_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__emp_paired +- name: qiime2__rescript__dereplicate owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__emp_single +- name: qiime2__rescript__edit_taxonomy owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__filter_samples +- name: qiime2__rescript__evaluate_classifications owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__partition_samples_paired +- name: qiime2__rescript__evaluate_cross_validate owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__partition_samples_single +- name: qiime2__rescript__evaluate_fit_classifier owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__subsample_paired +- name: qiime2__rescript__evaluate_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__subsample_single +- name: qiime2__rescript__evaluate_taxonomy owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__summarize +- name: qiime2__rescript__extract_seq_segments owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__tabulate_read_counts +- name: qiime2__rescript__filter_seqs_length owner: q2d2 tool_panel_section_id: '' -- name: qiime2__deblur__denoise_16S +- name: qiime2__rescript__filter_seqs_length_by_taxon owner: q2d2 tool_panel_section_id: '' -- name: qiime2__deblur__denoise_other +- name: qiime2__rescript__filter_taxa owner: q2d2 tool_panel_section_id: '' -- name: qiime2__deblur__visualize_stats +- name: qiime2__rescript__get_bv_brc_genome_features owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_ccs +- name: qiime2__rescript__get_bv_brc_genomes owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_paired +- name: qiime2__rescript__get_bv_brc_metadata owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_pyro +- name: qiime2__rescript__get_eukaryome_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_single +- name: qiime2__rescript__get_gtdb_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__plot_base_transitions +- name: qiime2__rescript__get_midori2_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__cutadapt__demux_paired +- name: qiime2__rescript__get_ncbi_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__cutadapt__demux_single +- name: qiime2__rescript__get_ncbi_data_protein owner: q2d2 tool_panel_section_id: '' -- name: qiime2__cutadapt__trim_paired +- name: qiime2__rescript__get_ncbi_genomes owner: q2d2 tool_panel_section_id: '' -- name: qiime2__cutadapt__trim_single +- name: qiime2__rescript__get_pr2_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__add_pseudocount +- name: qiime2__rescript__get_silva_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancom +- name: qiime2__rescript__get_unite_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancombc +- name: qiime2__rescript__merge_taxa owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancombc2 +- name: qiime2__rescript__orient_reads owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancombc2_visualizer +- name: qiime2__rescript__orient_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__da_barplot +- name: qiime2__rescript__parse_silva_taxonomy owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__tabulate +- name: qiime2__rescript__reverse_transcribe owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__barplot +- name: qiime2__rescript__subsample_fasta owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__barplot2 +- name: qiime2__rescript__trim_alignment owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__collapse +- name: qiime2__quality_filter__q_score owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__filter_seqs +- name: qiime2__vizard__boxplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__filter_table +- name: qiime2__vizard__heatmap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__alpha +- name: qiime2__vizard__lineplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__alpha_average +- name: qiime2__vizard__scatterplot_2d owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__alpha_collection +- name: qiime2__alignment__mafft owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__beta +- name: qiime2__alignment__mafft_add owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__beta_average +- name: qiime2__alignment__mask owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__beta_collection +- name: qiime2__phylogeny__align_to_tree_mafft_fasttree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__core_metrics +- name: qiime2__phylogeny__align_to_tree_mafft_iqtree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__kmer_diversity +- name: qiime2__phylogeny__align_to_tree_mafft_raxml owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__resample +- name: qiime2__phylogeny__fasttree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__cluster_features_closed_reference +- name: qiime2__phylogeny__filter_table owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__cluster_features_de_novo +- name: qiime2__phylogeny__filter_tree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__cluster_features_open_reference +- name: qiime2__phylogeny__iqtree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__dereplicate_sequences +- name: qiime2__phylogeny__iqtree_ultrafast_bootstrap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__fastq_stats +- name: qiime2__phylogeny__midpoint_root owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__merge_pairs +- name: qiime2__phylogeny__raxml owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__uchime_denovo +- name: qiime2__phylogeny__raxml_rapid_bootstrap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__uchime_ref +- name: qiime2__phylogeny__robinson_foulds owner: q2d2 tool_panel_section_id: '' -- name: qiime2__emperor__biplot +- name: qiime2__fragment_insertion__classify_otus_experimental owner: q2d2 tool_panel_section_id: '' -- name: qiime2__emperor__plot +- name: qiime2__fragment_insertion__filter_features owner: q2d2 tool_panel_section_id: '' -- name: qiime2__emperor__procrustes_plot +- name: qiime2__fragment_insertion__sepp owner: q2d2 tool_panel_section_id: '' - name: qiime2__feature_classifier__blast @@ -1853,6 +1841,39 @@ tools: - name: qiime2__feature_classifier__vsearch_global owner: q2d2 tool_panel_section_id: '' +- name: qiime2__longitudinal__anova + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__feature_volatility + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__first_differences + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__first_distances + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__linear_mixed_effects + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__maturity_index + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__nmit + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__pairwise_differences + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__pairwise_distances + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__plot_feature_volatility + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__volatility + owner: q2d2 + tool_panel_section_id: '' - name: qiime2__feature_table___summarize owner: q2d2 tool_panel_section_id: '' @@ -1922,76 +1943,73 @@ tools: - name: qiime2__feature_table__transpose owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue___get_sequences - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__fondue__combine_seqs +- name: qiime2__quality_control__bowtie2_build owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__get_all +- name: qiime2__quality_control__decontam_identify owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__get_ids_from_query +- name: qiime2__quality_control__decontam_identify_batches owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__get_metadata +- name: qiime2__quality_control__decontam_score_viz owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__get_sequences +- name: qiime2__quality_control__evaluate_composition owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__merge_metadata +- name: qiime2__quality_control__evaluate_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__scrape_collection +- name: qiime2__quality_control__evaluate_taxonomy owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fragment_insertion__classify_otus_experimental +- name: qiime2__quality_control__exclude_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fragment_insertion__filter_features +- name: qiime2__quality_control__filter_reads owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fragment_insertion__sepp +- name: qiime2__metadata__distance_matrix owner: q2d2 tool_panel_section_id: '' -- name: qiime2__kmerizer__core_metrics +- name: qiime2__metadata__merge owner: q2d2 tool_panel_section_id: '' -- name: qiime2__kmerizer__seqs_to_kmers +- name: qiime2__metadata__shuffle_groups owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__anova +- name: qiime2__metadata__tabulate owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__feature_volatility +- name: qiime2__kmerizer__core_metrics owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__first_differences +- name: qiime2__kmerizer__seqs_to_kmers owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__first_distances +- name: qiime2__fondue___get_sequences owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__linear_mixed_effects +- name: qiime2__fondue__combine_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__maturity_index +- name: qiime2__fondue__get_all owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__nmit +- name: qiime2__fondue__get_ids_from_query owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__pairwise_differences +- name: qiime2__fondue__get_metadata owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__pairwise_distances +- name: qiime2__fondue__get_sequences owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__plot_feature_volatility +- name: qiime2__fondue__merge_metadata owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__volatility +- name: qiime2__fondue__scrape_collection owner: q2d2 tool_panel_section_id: '' - name: qualimap_bamqc diff --git a/communities/microgalaxy/lab/tools/top/Palfinder.yaml b/communities/microgalaxy/lab/tools/top/Palfinder.yaml index 81562e59c..b2d3895f0 100644 --- a/communities/microgalaxy/lab/tools/top/Palfinder.yaml +++ b/communities/microgalaxy/lab/tools/top/Palfinder.yaml @@ -776,6 +776,9 @@ tools: - name: obi_clean owner: iuc tool_panel_section_id: '' +- name: obi_complement + owner: iuc + tool_panel_section_id: '' - name: obi_convert owner: iuc tool_panel_section_id: '' @@ -788,6 +791,18 @@ tools: - name: obi_pairing owner: iuc tool_panel_section_id: '' +- name: obi_pcr + owner: iuc + tool_panel_section_id: '' +- name: obi_refidx + owner: iuc + tool_panel_section_id: '' +- name: obi_tag + owner: iuc + tool_panel_section_id: '' +- name: obi_taxonomy + owner: iuc + tool_panel_section_id: '' - name: obi_uniq owner: iuc tool_panel_section_id: '' @@ -1265,6 +1280,9 @@ tools: - name: picrust_predict_metagenomes owner: iuc tool_panel_section_id: '' +- name: prinseq + owner: iuc + tool_panel_section_id: '' - name: prodigal owner: iuc tool_panel_section_id: '' @@ -1277,262 +1295,241 @@ tools: - name: pygenomeTracks owner: iuc tool_panel_section_id: '' -- name: qiime2_core__tools__export - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2_core__tools__import - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2_core__tools__import_fastq - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__quality_filter__q_score - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__cull_seqs - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__degap_seqs - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__dereplicate - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__edit_taxonomy +- name: qiime2__dada2__denoise_ccs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_classifications +- name: qiime2__dada2__denoise_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_cross_validate +- name: qiime2__dada2__denoise_pyro owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_fit_classifier +- name: qiime2__dada2__denoise_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_seqs +- name: qiime2__dada2__plot_base_transitions owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_taxonomy +- name: qiime2__cutadapt__demux_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__extract_seq_segments +- name: qiime2__cutadapt__demux_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__filter_seqs_length +- name: qiime2__cutadapt__trim_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__filter_seqs_length_by_taxon +- name: qiime2__cutadapt__trim_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__filter_taxa +- name: qiime2__composition__add_pseudocount owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_bv_brc_genome_features +- name: qiime2__composition__ancom owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_bv_brc_genomes +- name: qiime2__composition__ancombc owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_bv_brc_metadata +- name: qiime2__composition__ancombc2 owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_eukaryome_data +- name: qiime2__composition__ancombc2_visualizer owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_gtdb_data +- name: qiime2__composition__da_barplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_midori2_data +- name: qiime2__composition__tabulate owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_ncbi_data +- name: qiime2__boots__alpha owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_ncbi_data_protein +- name: qiime2__boots__alpha_average owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_ncbi_genomes +- name: qiime2__boots__alpha_collection owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_pr2_data +- name: qiime2__boots__beta owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_silva_data +- name: qiime2__boots__beta_average owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_unite_data +- name: qiime2__boots__beta_collection owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__merge_taxa +- name: qiime2__boots__core_metrics owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__orient_reads +- name: qiime2__boots__kmer_diversity owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__orient_seqs +- name: qiime2__boots__resample owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__parse_silva_taxonomy +- name: qiime2__vsearch__cluster_features_closed_reference owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__reverse_transcribe +- name: qiime2__vsearch__cluster_features_de_novo owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__subsample_fasta +- name: qiime2__vsearch__cluster_features_open_reference owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__trim_alignment +- name: qiime2__vsearch__dereplicate_sequences owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__classify_samples +- name: qiime2__vsearch__fastq_stats owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__classify_samples_from_dist +- name: qiime2__vsearch__merge_pairs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__classify_samples_ncv +- name: qiime2__vsearch__uchime_denovo owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__confusion_matrix +- name: qiime2__vsearch__uchime_ref owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__fit_classifier +- name: qiime2__demux__emp_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__fit_regressor +- name: qiime2__demux__emp_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__heatmap +- name: qiime2__demux__filter_samples owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__metatable +- name: qiime2__demux__partition_samples_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__predict_classification +- name: qiime2__demux__partition_samples_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__predict_regression +- name: qiime2__demux__subsample_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__regress_samples +- name: qiime2__demux__subsample_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__regress_samples_ncv +- name: qiime2__demux__summarize owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__scatterplot +- name: qiime2__demux__tabulate_read_counts owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__split_table +- name: qiime2__deblur__denoise_16S owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__summarize +- name: qiime2__deblur__denoise_other owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__align_to_tree_mafft_fasttree +- name: qiime2__deblur__visualize_stats owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__align_to_tree_mafft_iqtree +- name: qiime2__diversity__adonis owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__align_to_tree_mafft_raxml +- name: qiime2__diversity__alpha owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__fasttree +- name: qiime2__diversity__alpha_correlation owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__filter_table +- name: qiime2__diversity__alpha_group_significance owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__filter_tree +- name: qiime2__diversity__alpha_phylogenetic owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__iqtree +- name: qiime2__diversity__alpha_rarefaction owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__iqtree_ultrafast_bootstrap +- name: qiime2__diversity__beta owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__midpoint_root +- name: qiime2__diversity__beta_correlation owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__raxml +- name: qiime2__diversity__beta_group_significance owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__raxml_rapid_bootstrap +- name: qiime2__diversity__beta_phylogenetic owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__robinson_foulds +- name: qiime2__diversity__beta_rarefaction owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__distance_matrix +- name: qiime2__diversity__bioenv owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__merge +- name: qiime2__diversity__core_metrics owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__shuffle_groups +- name: qiime2__diversity__core_metrics_phylogenetic owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__tabulate +- name: qiime2__diversity__filter_alpha_diversity owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__alpha_group_significance +- name: qiime2__diversity__filter_distance_matrix owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__collate_stats +- name: qiime2__diversity__mantel owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__facet_across +- name: qiime2__diversity__partial_procrustes owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__facet_within +- name: qiime2__diversity__pcoa owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__mann_whitney_u +- name: qiime2__diversity__pcoa_biplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__mann_whitney_u_facet +- name: qiime2__diversity__procrustes_analysis owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__plot_rainclouds +- name: qiime2__diversity__tsne owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__prep_alpha_distribution +- name: qiime2__diversity__umap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__wilcoxon_srt +- name: qiime2__emperor__biplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__wilcoxon_srt_facet +- name: qiime2__emperor__plot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__bowtie2_build +- name: qiime2__emperor__procrustes_plot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__decontam_identify +- name: qiime2_core__tools__export owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__decontam_identify_batches +- name: qiime2_core__tools__import owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__decontam_score_viz +- name: qiime2_core__tools__import_fastq owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__evaluate_composition +- name: qiime2__taxa__barplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__evaluate_seqs +- name: qiime2__taxa__barplot2 owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__evaluate_taxonomy +- name: qiime2__taxa__collapse owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__exclude_seqs +- name: qiime2__taxa__filter_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__filter_reads +- name: qiime2__taxa__filter_table owner: q2d2 tool_panel_section_id: '' - name: qiime2__diversity_lib__alpha_passthrough @@ -1571,253 +1568,244 @@ tools: - name: qiime2__diversity_lib__weighted_unifrac owner: q2d2 tool_panel_section_id: '' -- name: qiime2__alignment__mafft - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__alignment__mafft_add - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__alignment__mask - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__vizard__boxplot +- name: qiime2__stats__alpha_group_significance owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vizard__heatmap +- name: qiime2__stats__collate_stats owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vizard__lineplot +- name: qiime2__stats__facet_across owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vizard__scatterplot_2d +- name: qiime2__stats__facet_within owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__adonis +- name: qiime2__stats__mann_whitney_u owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha +- name: qiime2__stats__mann_whitney_u_facet owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_correlation +- name: qiime2__stats__plot_rainclouds owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_group_significance +- name: qiime2__stats__prep_alpha_distribution owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_phylogenetic +- name: qiime2__stats__wilcoxon_srt owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_rarefaction +- name: qiime2__stats__wilcoxon_srt_facet owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta +- name: qiime2__sample_classifier__classify_samples owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_correlation +- name: qiime2__sample_classifier__classify_samples_from_dist owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_group_significance +- name: qiime2__sample_classifier__classify_samples_ncv owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_phylogenetic +- name: qiime2__sample_classifier__confusion_matrix owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_rarefaction +- name: qiime2__sample_classifier__fit_classifier owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__bioenv +- name: qiime2__sample_classifier__fit_regressor owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__core_metrics +- name: qiime2__sample_classifier__heatmap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__core_metrics_phylogenetic +- name: qiime2__sample_classifier__metatable owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__filter_alpha_diversity +- name: qiime2__sample_classifier__predict_classification owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__filter_distance_matrix +- name: qiime2__sample_classifier__predict_regression owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__mantel +- name: qiime2__sample_classifier__regress_samples owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__partial_procrustes +- name: qiime2__sample_classifier__regress_samples_ncv owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__pcoa +- name: qiime2__sample_classifier__scatterplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__pcoa_biplot +- name: qiime2__sample_classifier__split_table owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__procrustes_analysis +- name: qiime2__sample_classifier__summarize owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__tsne +- name: qiime2__rescript__cull_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__umap +- name: qiime2__rescript__degap_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__emp_paired +- name: qiime2__rescript__dereplicate owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__emp_single +- name: qiime2__rescript__edit_taxonomy owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__filter_samples +- name: qiime2__rescript__evaluate_classifications owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__partition_samples_paired +- name: qiime2__rescript__evaluate_cross_validate owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__partition_samples_single +- name: qiime2__rescript__evaluate_fit_classifier owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__subsample_paired +- name: qiime2__rescript__evaluate_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__subsample_single +- name: qiime2__rescript__evaluate_taxonomy owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__summarize +- name: qiime2__rescript__extract_seq_segments owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__tabulate_read_counts +- name: qiime2__rescript__filter_seqs_length owner: q2d2 tool_panel_section_id: '' -- name: qiime2__deblur__denoise_16S +- name: qiime2__rescript__filter_seqs_length_by_taxon owner: q2d2 tool_panel_section_id: '' -- name: qiime2__deblur__denoise_other +- name: qiime2__rescript__filter_taxa owner: q2d2 tool_panel_section_id: '' -- name: qiime2__deblur__visualize_stats +- name: qiime2__rescript__get_bv_brc_genome_features owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_ccs +- name: qiime2__rescript__get_bv_brc_genomes owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_paired +- name: qiime2__rescript__get_bv_brc_metadata owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_pyro +- name: qiime2__rescript__get_eukaryome_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_single +- name: qiime2__rescript__get_gtdb_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__plot_base_transitions +- name: qiime2__rescript__get_midori2_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__cutadapt__demux_paired +- name: qiime2__rescript__get_ncbi_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__cutadapt__demux_single +- name: qiime2__rescript__get_ncbi_data_protein owner: q2d2 tool_panel_section_id: '' -- name: qiime2__cutadapt__trim_paired +- name: qiime2__rescript__get_ncbi_genomes owner: q2d2 tool_panel_section_id: '' -- name: qiime2__cutadapt__trim_single +- name: qiime2__rescript__get_pr2_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__add_pseudocount +- name: qiime2__rescript__get_silva_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancom +- name: qiime2__rescript__get_unite_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancombc +- name: qiime2__rescript__merge_taxa owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancombc2 +- name: qiime2__rescript__orient_reads owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancombc2_visualizer +- name: qiime2__rescript__orient_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__da_barplot +- name: qiime2__rescript__parse_silva_taxonomy owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__tabulate +- name: qiime2__rescript__reverse_transcribe owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__barplot +- name: qiime2__rescript__subsample_fasta owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__barplot2 +- name: qiime2__rescript__trim_alignment owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__collapse +- name: qiime2__quality_filter__q_score owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__filter_seqs +- name: qiime2__vizard__boxplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__filter_table +- name: qiime2__vizard__heatmap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__alpha +- name: qiime2__vizard__lineplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__alpha_average +- name: qiime2__vizard__scatterplot_2d owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__alpha_collection +- name: qiime2__alignment__mafft owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__beta +- name: qiime2__alignment__mafft_add owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__beta_average +- name: qiime2__alignment__mask owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__beta_collection +- name: qiime2__phylogeny__align_to_tree_mafft_fasttree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__core_metrics +- name: qiime2__phylogeny__align_to_tree_mafft_iqtree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__kmer_diversity +- name: qiime2__phylogeny__align_to_tree_mafft_raxml owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__resample +- name: qiime2__phylogeny__fasttree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__cluster_features_closed_reference +- name: qiime2__phylogeny__filter_table owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__cluster_features_de_novo +- name: qiime2__phylogeny__filter_tree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__cluster_features_open_reference +- name: qiime2__phylogeny__iqtree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__dereplicate_sequences +- name: qiime2__phylogeny__iqtree_ultrafast_bootstrap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__fastq_stats +- name: qiime2__phylogeny__midpoint_root owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__merge_pairs +- name: qiime2__phylogeny__raxml owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__uchime_denovo +- name: qiime2__phylogeny__raxml_rapid_bootstrap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__uchime_ref +- name: qiime2__phylogeny__robinson_foulds owner: q2d2 tool_panel_section_id: '' -- name: qiime2__emperor__biplot +- name: qiime2__fragment_insertion__classify_otus_experimental owner: q2d2 tool_panel_section_id: '' -- name: qiime2__emperor__plot +- name: qiime2__fragment_insertion__filter_features owner: q2d2 tool_panel_section_id: '' -- name: qiime2__emperor__procrustes_plot +- name: qiime2__fragment_insertion__sepp owner: q2d2 tool_panel_section_id: '' - name: qiime2__feature_classifier__blast @@ -1853,6 +1841,39 @@ tools: - name: qiime2__feature_classifier__vsearch_global owner: q2d2 tool_panel_section_id: '' +- name: qiime2__longitudinal__anova + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__feature_volatility + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__first_differences + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__first_distances + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__linear_mixed_effects + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__maturity_index + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__nmit + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__pairwise_differences + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__pairwise_distances + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__plot_feature_volatility + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__volatility + owner: q2d2 + tool_panel_section_id: '' - name: qiime2__feature_table___summarize owner: q2d2 tool_panel_section_id: '' @@ -1922,76 +1943,73 @@ tools: - name: qiime2__feature_table__transpose owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue___get_sequences - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__fondue__combine_seqs +- name: qiime2__quality_control__bowtie2_build owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__get_all +- name: qiime2__quality_control__decontam_identify owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__get_ids_from_query +- name: qiime2__quality_control__decontam_identify_batches owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__get_metadata +- name: qiime2__quality_control__decontam_score_viz owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__get_sequences +- name: qiime2__quality_control__evaluate_composition owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__merge_metadata +- name: qiime2__quality_control__evaluate_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__scrape_collection +- name: qiime2__quality_control__evaluate_taxonomy owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fragment_insertion__classify_otus_experimental +- name: qiime2__quality_control__exclude_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fragment_insertion__filter_features +- name: qiime2__quality_control__filter_reads owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fragment_insertion__sepp +- name: qiime2__metadata__distance_matrix owner: q2d2 tool_panel_section_id: '' -- name: qiime2__kmerizer__core_metrics +- name: qiime2__metadata__merge owner: q2d2 tool_panel_section_id: '' -- name: qiime2__kmerizer__seqs_to_kmers +- name: qiime2__metadata__shuffle_groups owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__anova +- name: qiime2__metadata__tabulate owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__feature_volatility +- name: qiime2__kmerizer__core_metrics owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__first_differences +- name: qiime2__kmerizer__seqs_to_kmers owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__first_distances +- name: qiime2__fondue___get_sequences owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__linear_mixed_effects +- name: qiime2__fondue__combine_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__maturity_index +- name: qiime2__fondue__get_all owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__nmit +- name: qiime2__fondue__get_ids_from_query owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__pairwise_differences +- name: qiime2__fondue__get_metadata owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__pairwise_distances +- name: qiime2__fondue__get_sequences owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__plot_feature_volatility +- name: qiime2__fondue__merge_metadata owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__volatility +- name: qiime2__fondue__scrape_collection owner: q2d2 tool_panel_section_id: '' - name: qualimap_bamqc diff --git a/communities/microgalaxy/lab/tools/top/PhagePromotor.yaml b/communities/microgalaxy/lab/tools/top/PhagePromotor.yaml index 38cb7855f..b2d3895f0 100644 --- a/communities/microgalaxy/lab/tools/top/PhagePromotor.yaml +++ b/communities/microgalaxy/lab/tools/top/PhagePromotor.yaml @@ -71,6 +71,9 @@ tools: - name: CryptoGenotyper owner: nml tool_panel_section_id: '' +- name: cutadapt + owner: lparsons + tool_panel_section_id: '' - name: dada2_assignTaxonomyAddspecies owner: iuc tool_panel_section_id: '' @@ -707,6 +710,9 @@ tools: - name: mothur_venn owner: iuc tool_panel_section_id: '' +- name: multiqc + owner: iuc + tool_panel_section_id: '' - name: blastxml_to_tabular owner: devteam tool_panel_section_id: '' @@ -770,6 +776,9 @@ tools: - name: obi_clean owner: iuc tool_panel_section_id: '' +- name: obi_complement + owner: iuc + tool_panel_section_id: '' - name: obi_convert owner: iuc tool_panel_section_id: '' @@ -782,6 +791,18 @@ tools: - name: obi_pairing owner: iuc tool_panel_section_id: '' +- name: obi_pcr + owner: iuc + tool_panel_section_id: '' +- name: obi_refidx + owner: iuc + tool_panel_section_id: '' +- name: obi_tag + owner: iuc + tool_panel_section_id: '' +- name: obi_taxonomy + owner: iuc + tool_panel_section_id: '' - name: obi_uniq owner: iuc tool_panel_section_id: '' @@ -1259,6 +1280,9 @@ tools: - name: picrust_predict_metagenomes owner: iuc tool_panel_section_id: '' +- name: prinseq + owner: iuc + tool_panel_section_id: '' - name: prodigal owner: iuc tool_panel_section_id: '' @@ -1271,262 +1295,241 @@ tools: - name: pygenomeTracks owner: iuc tool_panel_section_id: '' -- name: qiime2_core__tools__export - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2_core__tools__import - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2_core__tools__import_fastq - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__quality_filter__q_score - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__cull_seqs - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__degap_seqs - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__dereplicate - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__edit_taxonomy +- name: qiime2__dada2__denoise_ccs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_classifications +- name: qiime2__dada2__denoise_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_cross_validate +- name: qiime2__dada2__denoise_pyro owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_fit_classifier +- name: qiime2__dada2__denoise_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_seqs +- name: qiime2__dada2__plot_base_transitions owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_taxonomy +- name: qiime2__cutadapt__demux_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__extract_seq_segments +- name: qiime2__cutadapt__demux_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__filter_seqs_length +- name: qiime2__cutadapt__trim_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__filter_seqs_length_by_taxon +- name: qiime2__cutadapt__trim_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__filter_taxa +- name: qiime2__composition__add_pseudocount owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_bv_brc_genome_features +- name: qiime2__composition__ancom owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_bv_brc_genomes +- name: qiime2__composition__ancombc owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_bv_brc_metadata +- name: qiime2__composition__ancombc2 owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_eukaryome_data +- name: qiime2__composition__ancombc2_visualizer owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_gtdb_data +- name: qiime2__composition__da_barplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_midori2_data +- name: qiime2__composition__tabulate owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_ncbi_data +- name: qiime2__boots__alpha owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_ncbi_data_protein +- name: qiime2__boots__alpha_average owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_ncbi_genomes +- name: qiime2__boots__alpha_collection owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_pr2_data +- name: qiime2__boots__beta owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_silva_data +- name: qiime2__boots__beta_average owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_unite_data +- name: qiime2__boots__beta_collection owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__merge_taxa +- name: qiime2__boots__core_metrics owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__orient_reads +- name: qiime2__boots__kmer_diversity owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__orient_seqs +- name: qiime2__boots__resample owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__parse_silva_taxonomy +- name: qiime2__vsearch__cluster_features_closed_reference owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__reverse_transcribe +- name: qiime2__vsearch__cluster_features_de_novo owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__subsample_fasta +- name: qiime2__vsearch__cluster_features_open_reference owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__trim_alignment +- name: qiime2__vsearch__dereplicate_sequences owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__classify_samples +- name: qiime2__vsearch__fastq_stats owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__classify_samples_from_dist +- name: qiime2__vsearch__merge_pairs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__classify_samples_ncv +- name: qiime2__vsearch__uchime_denovo owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__confusion_matrix +- name: qiime2__vsearch__uchime_ref owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__fit_classifier +- name: qiime2__demux__emp_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__fit_regressor +- name: qiime2__demux__emp_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__heatmap +- name: qiime2__demux__filter_samples owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__metatable +- name: qiime2__demux__partition_samples_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__predict_classification +- name: qiime2__demux__partition_samples_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__predict_regression +- name: qiime2__demux__subsample_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__regress_samples +- name: qiime2__demux__subsample_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__regress_samples_ncv +- name: qiime2__demux__summarize owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__scatterplot +- name: qiime2__demux__tabulate_read_counts owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__split_table +- name: qiime2__deblur__denoise_16S owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__summarize +- name: qiime2__deblur__denoise_other owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__align_to_tree_mafft_fasttree +- name: qiime2__deblur__visualize_stats owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__align_to_tree_mafft_iqtree +- name: qiime2__diversity__adonis owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__align_to_tree_mafft_raxml +- name: qiime2__diversity__alpha owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__fasttree +- name: qiime2__diversity__alpha_correlation owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__filter_table +- name: qiime2__diversity__alpha_group_significance owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__filter_tree +- name: qiime2__diversity__alpha_phylogenetic owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__iqtree +- name: qiime2__diversity__alpha_rarefaction owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__iqtree_ultrafast_bootstrap +- name: qiime2__diversity__beta owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__midpoint_root +- name: qiime2__diversity__beta_correlation owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__raxml +- name: qiime2__diversity__beta_group_significance owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__raxml_rapid_bootstrap +- name: qiime2__diversity__beta_phylogenetic owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__robinson_foulds +- name: qiime2__diversity__beta_rarefaction owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__distance_matrix +- name: qiime2__diversity__bioenv owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__merge +- name: qiime2__diversity__core_metrics owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__shuffle_groups +- name: qiime2__diversity__core_metrics_phylogenetic owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__tabulate +- name: qiime2__diversity__filter_alpha_diversity owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__alpha_group_significance +- name: qiime2__diversity__filter_distance_matrix owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__collate_stats +- name: qiime2__diversity__mantel owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__facet_across +- name: qiime2__diversity__partial_procrustes owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__facet_within +- name: qiime2__diversity__pcoa owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__mann_whitney_u +- name: qiime2__diversity__pcoa_biplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__mann_whitney_u_facet +- name: qiime2__diversity__procrustes_analysis owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__plot_rainclouds +- name: qiime2__diversity__tsne owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__prep_alpha_distribution +- name: qiime2__diversity__umap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__wilcoxon_srt +- name: qiime2__emperor__biplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__wilcoxon_srt_facet +- name: qiime2__emperor__plot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__bowtie2_build +- name: qiime2__emperor__procrustes_plot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__decontam_identify +- name: qiime2_core__tools__export owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__decontam_identify_batches +- name: qiime2_core__tools__import owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__decontam_score_viz +- name: qiime2_core__tools__import_fastq owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__evaluate_composition +- name: qiime2__taxa__barplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__evaluate_seqs +- name: qiime2__taxa__barplot2 owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__evaluate_taxonomy +- name: qiime2__taxa__collapse owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__exclude_seqs +- name: qiime2__taxa__filter_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__filter_reads +- name: qiime2__taxa__filter_table owner: q2d2 tool_panel_section_id: '' - name: qiime2__diversity_lib__alpha_passthrough @@ -1565,253 +1568,244 @@ tools: - name: qiime2__diversity_lib__weighted_unifrac owner: q2d2 tool_panel_section_id: '' -- name: qiime2__alignment__mafft - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__alignment__mafft_add - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__alignment__mask - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__vizard__boxplot +- name: qiime2__stats__alpha_group_significance owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vizard__heatmap +- name: qiime2__stats__collate_stats owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vizard__lineplot +- name: qiime2__stats__facet_across owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vizard__scatterplot_2d +- name: qiime2__stats__facet_within owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__adonis +- name: qiime2__stats__mann_whitney_u owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha +- name: qiime2__stats__mann_whitney_u_facet owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_correlation +- name: qiime2__stats__plot_rainclouds owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_group_significance +- name: qiime2__stats__prep_alpha_distribution owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_phylogenetic +- name: qiime2__stats__wilcoxon_srt owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_rarefaction +- name: qiime2__stats__wilcoxon_srt_facet owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta +- name: qiime2__sample_classifier__classify_samples owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_correlation +- name: qiime2__sample_classifier__classify_samples_from_dist owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_group_significance +- name: qiime2__sample_classifier__classify_samples_ncv owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_phylogenetic +- name: qiime2__sample_classifier__confusion_matrix owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_rarefaction +- name: qiime2__sample_classifier__fit_classifier owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__bioenv +- name: qiime2__sample_classifier__fit_regressor owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__core_metrics +- name: qiime2__sample_classifier__heatmap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__core_metrics_phylogenetic +- name: qiime2__sample_classifier__metatable owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__filter_alpha_diversity +- name: qiime2__sample_classifier__predict_classification owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__filter_distance_matrix +- name: qiime2__sample_classifier__predict_regression owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__mantel +- name: qiime2__sample_classifier__regress_samples owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__partial_procrustes +- name: qiime2__sample_classifier__regress_samples_ncv owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__pcoa +- name: qiime2__sample_classifier__scatterplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__pcoa_biplot +- name: qiime2__sample_classifier__split_table owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__procrustes_analysis +- name: qiime2__sample_classifier__summarize owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__tsne +- name: qiime2__rescript__cull_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__umap +- name: qiime2__rescript__degap_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__emp_paired +- name: qiime2__rescript__dereplicate owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__emp_single +- name: qiime2__rescript__edit_taxonomy owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__filter_samples +- name: qiime2__rescript__evaluate_classifications owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__partition_samples_paired +- name: qiime2__rescript__evaluate_cross_validate owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__partition_samples_single +- name: qiime2__rescript__evaluate_fit_classifier owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__subsample_paired +- name: qiime2__rescript__evaluate_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__subsample_single +- name: qiime2__rescript__evaluate_taxonomy owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__summarize +- name: qiime2__rescript__extract_seq_segments owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__tabulate_read_counts +- name: qiime2__rescript__filter_seqs_length owner: q2d2 tool_panel_section_id: '' -- name: qiime2__deblur__denoise_16S +- name: qiime2__rescript__filter_seqs_length_by_taxon owner: q2d2 tool_panel_section_id: '' -- name: qiime2__deblur__denoise_other +- name: qiime2__rescript__filter_taxa owner: q2d2 tool_panel_section_id: '' -- name: qiime2__deblur__visualize_stats +- name: qiime2__rescript__get_bv_brc_genome_features owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_ccs +- name: qiime2__rescript__get_bv_brc_genomes owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_paired +- name: qiime2__rescript__get_bv_brc_metadata owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_pyro +- name: qiime2__rescript__get_eukaryome_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_single +- name: qiime2__rescript__get_gtdb_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__plot_base_transitions +- name: qiime2__rescript__get_midori2_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__cutadapt__demux_paired +- name: qiime2__rescript__get_ncbi_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__cutadapt__demux_single +- name: qiime2__rescript__get_ncbi_data_protein owner: q2d2 tool_panel_section_id: '' -- name: qiime2__cutadapt__trim_paired +- name: qiime2__rescript__get_ncbi_genomes owner: q2d2 tool_panel_section_id: '' -- name: qiime2__cutadapt__trim_single +- name: qiime2__rescript__get_pr2_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__add_pseudocount +- name: qiime2__rescript__get_silva_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancom +- name: qiime2__rescript__get_unite_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancombc +- name: qiime2__rescript__merge_taxa owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancombc2 +- name: qiime2__rescript__orient_reads owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancombc2_visualizer +- name: qiime2__rescript__orient_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__da_barplot +- name: qiime2__rescript__parse_silva_taxonomy owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__tabulate +- name: qiime2__rescript__reverse_transcribe owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__barplot +- name: qiime2__rescript__subsample_fasta owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__barplot2 +- name: qiime2__rescript__trim_alignment owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__collapse +- name: qiime2__quality_filter__q_score owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__filter_seqs +- name: qiime2__vizard__boxplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__filter_table +- name: qiime2__vizard__heatmap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__alpha +- name: qiime2__vizard__lineplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__alpha_average +- name: qiime2__vizard__scatterplot_2d owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__alpha_collection +- name: qiime2__alignment__mafft owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__beta +- name: qiime2__alignment__mafft_add owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__beta_average +- name: qiime2__alignment__mask owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__beta_collection +- name: qiime2__phylogeny__align_to_tree_mafft_fasttree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__core_metrics +- name: qiime2__phylogeny__align_to_tree_mafft_iqtree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__kmer_diversity +- name: qiime2__phylogeny__align_to_tree_mafft_raxml owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__resample +- name: qiime2__phylogeny__fasttree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__cluster_features_closed_reference +- name: qiime2__phylogeny__filter_table owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__cluster_features_de_novo +- name: qiime2__phylogeny__filter_tree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__cluster_features_open_reference +- name: qiime2__phylogeny__iqtree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__dereplicate_sequences +- name: qiime2__phylogeny__iqtree_ultrafast_bootstrap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__fastq_stats +- name: qiime2__phylogeny__midpoint_root owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__merge_pairs +- name: qiime2__phylogeny__raxml owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__uchime_denovo +- name: qiime2__phylogeny__raxml_rapid_bootstrap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__uchime_ref +- name: qiime2__phylogeny__robinson_foulds owner: q2d2 tool_panel_section_id: '' -- name: qiime2__emperor__biplot +- name: qiime2__fragment_insertion__classify_otus_experimental owner: q2d2 tool_panel_section_id: '' -- name: qiime2__emperor__plot +- name: qiime2__fragment_insertion__filter_features owner: q2d2 tool_panel_section_id: '' -- name: qiime2__emperor__procrustes_plot +- name: qiime2__fragment_insertion__sepp owner: q2d2 tool_panel_section_id: '' - name: qiime2__feature_classifier__blast @@ -1847,6 +1841,39 @@ tools: - name: qiime2__feature_classifier__vsearch_global owner: q2d2 tool_panel_section_id: '' +- name: qiime2__longitudinal__anova + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__feature_volatility + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__first_differences + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__first_distances + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__linear_mixed_effects + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__maturity_index + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__nmit + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__pairwise_differences + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__pairwise_distances + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__plot_feature_volatility + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__volatility + owner: q2d2 + tool_panel_section_id: '' - name: qiime2__feature_table___summarize owner: q2d2 tool_panel_section_id: '' @@ -1916,76 +1943,73 @@ tools: - name: qiime2__feature_table__transpose owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue___get_sequences - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__fondue__combine_seqs +- name: qiime2__quality_control__bowtie2_build owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__get_all +- name: qiime2__quality_control__decontam_identify owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__get_ids_from_query +- name: qiime2__quality_control__decontam_identify_batches owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__get_metadata +- name: qiime2__quality_control__decontam_score_viz owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__get_sequences +- name: qiime2__quality_control__evaluate_composition owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__merge_metadata +- name: qiime2__quality_control__evaluate_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__scrape_collection +- name: qiime2__quality_control__evaluate_taxonomy owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fragment_insertion__classify_otus_experimental +- name: qiime2__quality_control__exclude_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fragment_insertion__filter_features +- name: qiime2__quality_control__filter_reads owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fragment_insertion__sepp +- name: qiime2__metadata__distance_matrix owner: q2d2 tool_panel_section_id: '' -- name: qiime2__kmerizer__core_metrics +- name: qiime2__metadata__merge owner: q2d2 tool_panel_section_id: '' -- name: qiime2__kmerizer__seqs_to_kmers +- name: qiime2__metadata__shuffle_groups owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__anova +- name: qiime2__metadata__tabulate owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__feature_volatility +- name: qiime2__kmerizer__core_metrics owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__first_differences +- name: qiime2__kmerizer__seqs_to_kmers owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__first_distances +- name: qiime2__fondue___get_sequences owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__linear_mixed_effects +- name: qiime2__fondue__combine_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__maturity_index +- name: qiime2__fondue__get_all owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__nmit +- name: qiime2__fondue__get_ids_from_query owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__pairwise_differences +- name: qiime2__fondue__get_metadata owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__pairwise_distances +- name: qiime2__fondue__get_sequences owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__plot_feature_volatility +- name: qiime2__fondue__merge_metadata owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__volatility +- name: qiime2__fondue__scrape_collection owner: q2d2 tool_panel_section_id: '' - name: qualimap_bamqc diff --git a/communities/microgalaxy/lab/tools/top/UseGalaxy_be.yaml b/communities/microgalaxy/lab/tools/top/UseGalaxy_be.yaml index f04fb746e..3a41c1743 100644 --- a/communities/microgalaxy/lab/tools/top/UseGalaxy_be.yaml +++ b/communities/microgalaxy/lab/tools/top/UseGalaxy_be.yaml @@ -179,6 +179,12 @@ tools: - name: metaphlan owner: iuc tool_panel_section_id: '' +- name: mitos + owner: iuc + tool_panel_section_id: '' +- name: mitos2 + owner: iuc + tool_panel_section_id: '' - name: mothur_align_check owner: iuc tool_panel_section_id: '' @@ -626,6 +632,9 @@ tools: - name: obi_clean owner: iuc tool_panel_section_id: '' +- name: obi_complement + owner: iuc + tool_panel_section_id: '' - name: obi_convert owner: iuc tool_panel_section_id: '' @@ -638,6 +647,18 @@ tools: - name: obi_pairing owner: iuc tool_panel_section_id: '' +- name: obi_pcr + owner: iuc + tool_panel_section_id: '' +- name: obi_refidx + owner: iuc + tool_panel_section_id: '' +- name: obi_tag + owner: iuc + tool_panel_section_id: '' +- name: obi_taxonomy + owner: iuc + tool_panel_section_id: '' - name: obi_uniq owner: iuc tool_panel_section_id: '' @@ -1106,262 +1127,241 @@ tools: - name: pycoqc owner: iuc tool_panel_section_id: '' -- name: qiime2_core__tools__export - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2_core__tools__import - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2_core__tools__import_fastq - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__quality_filter__q_score - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__cull_seqs - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__degap_seqs - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__dereplicate - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__edit_taxonomy +- name: qiime2__dada2__denoise_ccs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_classifications +- name: qiime2__dada2__denoise_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_cross_validate +- name: qiime2__dada2__denoise_pyro owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_fit_classifier +- name: qiime2__dada2__denoise_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_seqs +- name: qiime2__dada2__plot_base_transitions owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_taxonomy +- name: qiime2__cutadapt__demux_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__extract_seq_segments +- name: qiime2__cutadapt__demux_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__filter_seqs_length +- name: qiime2__cutadapt__trim_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__filter_seqs_length_by_taxon +- name: qiime2__cutadapt__trim_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__filter_taxa +- name: qiime2__composition__add_pseudocount owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_bv_brc_genome_features +- name: qiime2__composition__ancom owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_bv_brc_genomes +- name: qiime2__composition__ancombc owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_bv_brc_metadata +- name: qiime2__composition__ancombc2 owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_eukaryome_data +- name: qiime2__composition__ancombc2_visualizer owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_gtdb_data +- name: qiime2__composition__da_barplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_midori2_data +- name: qiime2__composition__tabulate owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_ncbi_data +- name: qiime2__boots__alpha owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_ncbi_data_protein +- name: qiime2__boots__alpha_average owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_ncbi_genomes +- name: qiime2__boots__alpha_collection owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_pr2_data +- name: qiime2__boots__beta owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_silva_data +- name: qiime2__boots__beta_average owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_unite_data +- name: qiime2__boots__beta_collection owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__merge_taxa +- name: qiime2__boots__core_metrics owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__orient_reads +- name: qiime2__boots__kmer_diversity owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__orient_seqs +- name: qiime2__boots__resample owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__parse_silva_taxonomy +- name: qiime2__vsearch__cluster_features_closed_reference owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__reverse_transcribe +- name: qiime2__vsearch__cluster_features_de_novo owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__subsample_fasta +- name: qiime2__vsearch__cluster_features_open_reference owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__trim_alignment +- name: qiime2__vsearch__dereplicate_sequences owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__classify_samples +- name: qiime2__vsearch__fastq_stats owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__classify_samples_from_dist +- name: qiime2__vsearch__merge_pairs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__classify_samples_ncv +- name: qiime2__vsearch__uchime_denovo owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__confusion_matrix +- name: qiime2__vsearch__uchime_ref owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__fit_classifier +- name: qiime2__demux__emp_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__fit_regressor +- name: qiime2__demux__emp_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__heatmap +- name: qiime2__demux__filter_samples owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__metatable +- name: qiime2__demux__partition_samples_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__predict_classification +- name: qiime2__demux__partition_samples_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__predict_regression +- name: qiime2__demux__subsample_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__regress_samples +- name: qiime2__demux__subsample_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__regress_samples_ncv +- name: qiime2__demux__summarize owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__scatterplot +- name: qiime2__demux__tabulate_read_counts owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__split_table +- name: qiime2__deblur__denoise_16S owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__summarize +- name: qiime2__deblur__denoise_other owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__align_to_tree_mafft_fasttree +- name: qiime2__deblur__visualize_stats owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__align_to_tree_mafft_iqtree +- name: qiime2__diversity__adonis owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__align_to_tree_mafft_raxml +- name: qiime2__diversity__alpha owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__fasttree +- name: qiime2__diversity__alpha_correlation owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__filter_table +- name: qiime2__diversity__alpha_group_significance owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__filter_tree +- name: qiime2__diversity__alpha_phylogenetic owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__iqtree +- name: qiime2__diversity__alpha_rarefaction owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__iqtree_ultrafast_bootstrap +- name: qiime2__diversity__beta owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__midpoint_root +- name: qiime2__diversity__beta_correlation owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__raxml +- name: qiime2__diversity__beta_group_significance owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__raxml_rapid_bootstrap +- name: qiime2__diversity__beta_phylogenetic owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__robinson_foulds +- name: qiime2__diversity__beta_rarefaction owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__distance_matrix +- name: qiime2__diversity__bioenv owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__merge +- name: qiime2__diversity__core_metrics owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__shuffle_groups +- name: qiime2__diversity__core_metrics_phylogenetic owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__tabulate +- name: qiime2__diversity__filter_alpha_diversity owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__alpha_group_significance +- name: qiime2__diversity__filter_distance_matrix owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__collate_stats +- name: qiime2__diversity__mantel owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__facet_across +- name: qiime2__diversity__partial_procrustes owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__facet_within +- name: qiime2__diversity__pcoa owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__mann_whitney_u +- name: qiime2__diversity__pcoa_biplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__mann_whitney_u_facet +- name: qiime2__diversity__procrustes_analysis owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__plot_rainclouds +- name: qiime2__diversity__tsne owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__prep_alpha_distribution +- name: qiime2__diversity__umap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__wilcoxon_srt +- name: qiime2__emperor__biplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__wilcoxon_srt_facet +- name: qiime2__emperor__plot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__bowtie2_build +- name: qiime2__emperor__procrustes_plot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__decontam_identify +- name: qiime2_core__tools__export owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__decontam_identify_batches +- name: qiime2_core__tools__import owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__decontam_score_viz +- name: qiime2_core__tools__import_fastq owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__evaluate_composition +- name: qiime2__taxa__barplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__evaluate_seqs +- name: qiime2__taxa__barplot2 owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__evaluate_taxonomy +- name: qiime2__taxa__collapse owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__exclude_seqs +- name: qiime2__taxa__filter_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__filter_reads +- name: qiime2__taxa__filter_table owner: q2d2 tool_panel_section_id: '' - name: qiime2__diversity_lib__alpha_passthrough @@ -1400,253 +1400,244 @@ tools: - name: qiime2__diversity_lib__weighted_unifrac owner: q2d2 tool_panel_section_id: '' -- name: qiime2__alignment__mafft - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__alignment__mafft_add - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__alignment__mask - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__vizard__boxplot +- name: qiime2__stats__alpha_group_significance owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vizard__heatmap +- name: qiime2__stats__collate_stats owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vizard__lineplot +- name: qiime2__stats__facet_across owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vizard__scatterplot_2d +- name: qiime2__stats__facet_within owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__adonis +- name: qiime2__stats__mann_whitney_u owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha +- name: qiime2__stats__mann_whitney_u_facet owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_correlation +- name: qiime2__stats__plot_rainclouds owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_group_significance +- name: qiime2__stats__prep_alpha_distribution owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_phylogenetic +- name: qiime2__stats__wilcoxon_srt owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_rarefaction +- name: qiime2__stats__wilcoxon_srt_facet owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta +- name: qiime2__sample_classifier__classify_samples owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_correlation +- name: qiime2__sample_classifier__classify_samples_from_dist owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_group_significance +- name: qiime2__sample_classifier__classify_samples_ncv owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_phylogenetic +- name: qiime2__sample_classifier__confusion_matrix owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_rarefaction +- name: qiime2__sample_classifier__fit_classifier owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__bioenv +- name: qiime2__sample_classifier__fit_regressor owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__core_metrics +- name: qiime2__sample_classifier__heatmap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__core_metrics_phylogenetic +- name: qiime2__sample_classifier__metatable owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__filter_alpha_diversity +- name: qiime2__sample_classifier__predict_classification owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__filter_distance_matrix +- name: qiime2__sample_classifier__predict_regression owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__mantel +- name: qiime2__sample_classifier__regress_samples owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__partial_procrustes +- name: qiime2__sample_classifier__regress_samples_ncv owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__pcoa +- name: qiime2__sample_classifier__scatterplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__pcoa_biplot +- name: qiime2__sample_classifier__split_table owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__procrustes_analysis +- name: qiime2__sample_classifier__summarize owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__tsne +- name: qiime2__rescript__cull_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__umap +- name: qiime2__rescript__degap_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__emp_paired +- name: qiime2__rescript__dereplicate owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__emp_single +- name: qiime2__rescript__edit_taxonomy owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__filter_samples +- name: qiime2__rescript__evaluate_classifications owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__partition_samples_paired +- name: qiime2__rescript__evaluate_cross_validate owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__partition_samples_single +- name: qiime2__rescript__evaluate_fit_classifier owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__subsample_paired +- name: qiime2__rescript__evaluate_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__subsample_single +- name: qiime2__rescript__evaluate_taxonomy owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__summarize +- name: qiime2__rescript__extract_seq_segments owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__tabulate_read_counts +- name: qiime2__rescript__filter_seqs_length owner: q2d2 tool_panel_section_id: '' -- name: qiime2__deblur__denoise_16S +- name: qiime2__rescript__filter_seqs_length_by_taxon owner: q2d2 tool_panel_section_id: '' -- name: qiime2__deblur__denoise_other +- name: qiime2__rescript__filter_taxa owner: q2d2 tool_panel_section_id: '' -- name: qiime2__deblur__visualize_stats +- name: qiime2__rescript__get_bv_brc_genome_features owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_ccs +- name: qiime2__rescript__get_bv_brc_genomes owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_paired +- name: qiime2__rescript__get_bv_brc_metadata owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_pyro +- name: qiime2__rescript__get_eukaryome_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_single +- name: qiime2__rescript__get_gtdb_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__plot_base_transitions +- name: qiime2__rescript__get_midori2_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__cutadapt__demux_paired +- name: qiime2__rescript__get_ncbi_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__cutadapt__demux_single +- name: qiime2__rescript__get_ncbi_data_protein owner: q2d2 tool_panel_section_id: '' -- name: qiime2__cutadapt__trim_paired +- name: qiime2__rescript__get_ncbi_genomes owner: q2d2 tool_panel_section_id: '' -- name: qiime2__cutadapt__trim_single +- name: qiime2__rescript__get_pr2_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__add_pseudocount +- name: qiime2__rescript__get_silva_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancom +- name: qiime2__rescript__get_unite_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancombc +- name: qiime2__rescript__merge_taxa owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancombc2 +- name: qiime2__rescript__orient_reads owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancombc2_visualizer +- name: qiime2__rescript__orient_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__da_barplot +- name: qiime2__rescript__parse_silva_taxonomy owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__tabulate +- name: qiime2__rescript__reverse_transcribe owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__barplot +- name: qiime2__rescript__subsample_fasta owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__barplot2 +- name: qiime2__rescript__trim_alignment owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__collapse +- name: qiime2__quality_filter__q_score owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__filter_seqs +- name: qiime2__vizard__boxplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__filter_table +- name: qiime2__vizard__heatmap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__alpha +- name: qiime2__vizard__lineplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__alpha_average +- name: qiime2__vizard__scatterplot_2d owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__alpha_collection +- name: qiime2__alignment__mafft owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__beta +- name: qiime2__alignment__mafft_add owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__beta_average +- name: qiime2__alignment__mask owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__beta_collection +- name: qiime2__phylogeny__align_to_tree_mafft_fasttree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__core_metrics +- name: qiime2__phylogeny__align_to_tree_mafft_iqtree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__kmer_diversity +- name: qiime2__phylogeny__align_to_tree_mafft_raxml owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__resample +- name: qiime2__phylogeny__fasttree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__cluster_features_closed_reference +- name: qiime2__phylogeny__filter_table owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__cluster_features_de_novo +- name: qiime2__phylogeny__filter_tree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__cluster_features_open_reference +- name: qiime2__phylogeny__iqtree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__dereplicate_sequences +- name: qiime2__phylogeny__iqtree_ultrafast_bootstrap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__fastq_stats +- name: qiime2__phylogeny__midpoint_root owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__merge_pairs +- name: qiime2__phylogeny__raxml owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__uchime_denovo +- name: qiime2__phylogeny__raxml_rapid_bootstrap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__uchime_ref +- name: qiime2__phylogeny__robinson_foulds owner: q2d2 tool_panel_section_id: '' -- name: qiime2__emperor__biplot +- name: qiime2__fragment_insertion__classify_otus_experimental owner: q2d2 tool_panel_section_id: '' -- name: qiime2__emperor__plot +- name: qiime2__fragment_insertion__filter_features owner: q2d2 tool_panel_section_id: '' -- name: qiime2__emperor__procrustes_plot +- name: qiime2__fragment_insertion__sepp owner: q2d2 tool_panel_section_id: '' - name: qiime2__feature_classifier__blast @@ -1682,6 +1673,39 @@ tools: - name: qiime2__feature_classifier__vsearch_global owner: q2d2 tool_panel_section_id: '' +- name: qiime2__longitudinal__anova + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__feature_volatility + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__first_differences + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__first_distances + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__linear_mixed_effects + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__maturity_index + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__nmit + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__pairwise_differences + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__pairwise_distances + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__plot_feature_volatility + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__volatility + owner: q2d2 + tool_panel_section_id: '' - name: qiime2__feature_table___summarize owner: q2d2 tool_panel_section_id: '' @@ -1751,76 +1775,73 @@ tools: - name: qiime2__feature_table__transpose owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue___get_sequences - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__fondue__combine_seqs +- name: qiime2__quality_control__bowtie2_build owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__get_all +- name: qiime2__quality_control__decontam_identify owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__get_ids_from_query +- name: qiime2__quality_control__decontam_identify_batches owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__get_metadata +- name: qiime2__quality_control__decontam_score_viz owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__get_sequences +- name: qiime2__quality_control__evaluate_composition owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__merge_metadata +- name: qiime2__quality_control__evaluate_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__scrape_collection +- name: qiime2__quality_control__evaluate_taxonomy owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fragment_insertion__classify_otus_experimental +- name: qiime2__quality_control__exclude_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fragment_insertion__filter_features +- name: qiime2__quality_control__filter_reads owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fragment_insertion__sepp +- name: qiime2__metadata__distance_matrix owner: q2d2 tool_panel_section_id: '' -- name: qiime2__kmerizer__core_metrics +- name: qiime2__metadata__merge owner: q2d2 tool_panel_section_id: '' -- name: qiime2__kmerizer__seqs_to_kmers +- name: qiime2__metadata__shuffle_groups owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__anova +- name: qiime2__metadata__tabulate owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__feature_volatility +- name: qiime2__kmerizer__core_metrics owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__first_differences +- name: qiime2__kmerizer__seqs_to_kmers owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__first_distances +- name: qiime2__fondue___get_sequences owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__linear_mixed_effects +- name: qiime2__fondue__combine_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__maturity_index +- name: qiime2__fondue__get_all owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__nmit +- name: qiime2__fondue__get_ids_from_query owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__pairwise_differences +- name: qiime2__fondue__get_metadata owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__pairwise_distances +- name: qiime2__fondue__get_sequences owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__plot_feature_volatility +- name: qiime2__fondue__merge_metadata owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__volatility +- name: qiime2__fondue__scrape_collection owner: q2d2 tool_panel_section_id: '' - name: seqkit_fx2tab diff --git a/communities/microgalaxy/lab/tools/top/UseGalaxy_cz.yaml b/communities/microgalaxy/lab/tools/top/UseGalaxy_cz.yaml index c90b3ba7b..c8d8a1ac2 100644 --- a/communities/microgalaxy/lab/tools/top/UseGalaxy_cz.yaml +++ b/communities/microgalaxy/lab/tools/top/UseGalaxy_cz.yaml @@ -134,6 +134,9 @@ tools: - name: obi_clean owner: iuc tool_panel_section_id: '' +- name: obi_complement + owner: iuc + tool_panel_section_id: '' - name: obi_convert owner: iuc tool_panel_section_id: '' @@ -146,6 +149,18 @@ tools: - name: obi_pairing owner: iuc tool_panel_section_id: '' +- name: obi_pcr + owner: iuc + tool_panel_section_id: '' +- name: obi_refidx + owner: iuc + tool_panel_section_id: '' +- name: obi_tag + owner: iuc + tool_panel_section_id: '' +- name: obi_taxonomy + owner: iuc + tool_panel_section_id: '' - name: obi_uniq owner: iuc tool_panel_section_id: '' @@ -608,364 +623,325 @@ tools: - name: picrust_predict_metagenomes owner: iuc tool_panel_section_id: '' -- name: qiime2_core__tools__export - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2_core__tools__import - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2_core__tools__import_fastq - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__cull_seqs - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__degap_seqs - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__dereplicate - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__edit_taxonomy - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_classifications - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_cross_validate - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_fit_classifier - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_seqs - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_taxonomy - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__extract_seq_segments - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__filter_seqs_length +- name: qiime2__dada2__denoise_ccs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__filter_seqs_length_by_taxon +- name: qiime2__dada2__denoise_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__filter_taxa +- name: qiime2__dada2__denoise_pyro owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_bv_brc_genome_features +- name: qiime2__dada2__denoise_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_bv_brc_genomes +- name: qiime2__dada2__plot_base_transitions owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_bv_brc_metadata +- name: qiime2__composition__add_pseudocount owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_eukaryome_data +- name: qiime2__composition__ancom owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_gtdb_data +- name: qiime2__composition__ancombc owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_midori2_data +- name: qiime2__composition__ancombc2 owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_ncbi_data +- name: qiime2__composition__ancombc2_visualizer owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_ncbi_data_protein +- name: qiime2__composition__da_barplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_ncbi_genomes +- name: qiime2__composition__tabulate owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_pr2_data +- name: qiime2__boots__alpha owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_silva_data +- name: qiime2__boots__alpha_average owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_unite_data +- name: qiime2__boots__alpha_collection owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__merge_taxa +- name: qiime2__boots__beta owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__orient_reads +- name: qiime2__boots__beta_average owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__orient_seqs +- name: qiime2__boots__beta_collection owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__parse_silva_taxonomy +- name: qiime2__boots__core_metrics owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__reverse_transcribe +- name: qiime2__boots__kmer_diversity owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__subsample_fasta +- name: qiime2__boots__resample owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__trim_alignment +- name: qiime2__demux__emp_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__distance_matrix +- name: qiime2__demux__emp_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__merge +- name: qiime2__demux__filter_samples owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__shuffle_groups +- name: qiime2__demux__partition_samples_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__tabulate +- name: qiime2__demux__partition_samples_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__alpha_group_significance +- name: qiime2__demux__subsample_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__collate_stats +- name: qiime2__demux__subsample_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__facet_across +- name: qiime2__demux__summarize owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__facet_within +- name: qiime2__demux__tabulate_read_counts owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__mann_whitney_u +- name: qiime2__diversity__adonis owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__mann_whitney_u_facet +- name: qiime2__diversity__alpha owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__plot_rainclouds +- name: qiime2__diversity__alpha_correlation owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__prep_alpha_distribution +- name: qiime2__diversity__alpha_group_significance owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__wilcoxon_srt +- name: qiime2__diversity__alpha_phylogenetic owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__wilcoxon_srt_facet +- name: qiime2__diversity__alpha_rarefaction owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__bowtie2_build +- name: qiime2__diversity__beta owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__decontam_identify +- name: qiime2__diversity__beta_correlation owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__decontam_identify_batches +- name: qiime2__diversity__beta_group_significance owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__decontam_score_viz +- name: qiime2__diversity__beta_phylogenetic owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__evaluate_composition +- name: qiime2__diversity__beta_rarefaction owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__evaluate_seqs +- name: qiime2__diversity__bioenv owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__evaluate_taxonomy +- name: qiime2__diversity__core_metrics owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__exclude_seqs +- name: qiime2__diversity__core_metrics_phylogenetic owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__filter_reads +- name: qiime2__diversity__filter_alpha_diversity owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vizard__boxplot +- name: qiime2__diversity__filter_distance_matrix owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vizard__heatmap +- name: qiime2__diversity__mantel owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vizard__lineplot +- name: qiime2__diversity__partial_procrustes owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vizard__scatterplot_2d +- name: qiime2__diversity__pcoa owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__adonis +- name: qiime2__diversity__pcoa_biplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha +- name: qiime2__diversity__procrustes_analysis owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_correlation +- name: qiime2__diversity__tsne owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_group_significance +- name: qiime2__diversity__umap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_phylogenetic +- name: qiime2_core__tools__export owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_rarefaction +- name: qiime2_core__tools__import owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta +- name: qiime2_core__tools__import_fastq owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_correlation +- name: qiime2__taxa__barplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_group_significance +- name: qiime2__taxa__barplot2 owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_phylogenetic +- name: qiime2__taxa__collapse owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_rarefaction +- name: qiime2__taxa__filter_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__bioenv +- name: qiime2__taxa__filter_table owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__core_metrics +- name: qiime2__stats__alpha_group_significance owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__core_metrics_phylogenetic +- name: qiime2__stats__collate_stats owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__filter_alpha_diversity +- name: qiime2__stats__facet_across owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__filter_distance_matrix +- name: qiime2__stats__facet_within owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__mantel +- name: qiime2__stats__mann_whitney_u owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__partial_procrustes +- name: qiime2__stats__mann_whitney_u_facet owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__pcoa +- name: qiime2__stats__plot_rainclouds owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__pcoa_biplot +- name: qiime2__stats__prep_alpha_distribution owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__procrustes_analysis +- name: qiime2__stats__wilcoxon_srt owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__tsne +- name: qiime2__stats__wilcoxon_srt_facet owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__umap +- name: qiime2__rescript__cull_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__emp_paired +- name: qiime2__rescript__degap_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__emp_single +- name: qiime2__rescript__dereplicate owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__filter_samples +- name: qiime2__rescript__edit_taxonomy owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__partition_samples_paired +- name: qiime2__rescript__evaluate_classifications owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__partition_samples_single +- name: qiime2__rescript__evaluate_cross_validate owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__subsample_paired +- name: qiime2__rescript__evaluate_fit_classifier owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__subsample_single +- name: qiime2__rescript__evaluate_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__summarize +- name: qiime2__rescript__evaluate_taxonomy owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__tabulate_read_counts +- name: qiime2__rescript__extract_seq_segments owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_ccs +- name: qiime2__rescript__filter_seqs_length owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_paired +- name: qiime2__rescript__filter_seqs_length_by_taxon owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_pyro +- name: qiime2__rescript__filter_taxa owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_single +- name: qiime2__rescript__get_bv_brc_genome_features owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__plot_base_transitions +- name: qiime2__rescript__get_bv_brc_genomes owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__add_pseudocount +- name: qiime2__rescript__get_bv_brc_metadata owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancom +- name: qiime2__rescript__get_eukaryome_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancombc +- name: qiime2__rescript__get_gtdb_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancombc2 +- name: qiime2__rescript__get_midori2_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancombc2_visualizer +- name: qiime2__rescript__get_ncbi_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__da_barplot +- name: qiime2__rescript__get_ncbi_data_protein owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__tabulate +- name: qiime2__rescript__get_ncbi_genomes owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__barplot +- name: qiime2__rescript__get_pr2_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__barplot2 +- name: qiime2__rescript__get_silva_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__collapse +- name: qiime2__rescript__get_unite_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__filter_seqs +- name: qiime2__rescript__merge_taxa owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__filter_table +- name: qiime2__rescript__orient_reads owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__alpha +- name: qiime2__rescript__orient_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__alpha_average +- name: qiime2__rescript__parse_silva_taxonomy owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__alpha_collection +- name: qiime2__rescript__reverse_transcribe owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__beta +- name: qiime2__rescript__subsample_fasta owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__beta_average +- name: qiime2__rescript__trim_alignment owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__beta_collection +- name: qiime2__vizard__boxplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__core_metrics +- name: qiime2__vizard__heatmap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__kmer_diversity +- name: qiime2__vizard__lineplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__resample +- name: qiime2__vizard__scatterplot_2d owner: q2d2 tool_panel_section_id: '' - name: qiime2__feature_classifier__blast @@ -1070,6 +1046,51 @@ tools: - name: qiime2__feature_table__transpose owner: q2d2 tool_panel_section_id: '' +- name: qiime2__quality_control__bowtie2_build + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__quality_control__decontam_identify + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__quality_control__decontam_identify_batches + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__quality_control__decontam_score_viz + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__quality_control__evaluate_composition + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__quality_control__evaluate_seqs + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__quality_control__evaluate_taxonomy + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__quality_control__exclude_seqs + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__quality_control__filter_reads + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__metadata__distance_matrix + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__metadata__merge + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__metadata__shuffle_groups + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__metadata__tabulate + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__kmerizer__core_metrics + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__kmerizer__seqs_to_kmers + owner: q2d2 + tool_panel_section_id: '' - name: qiime2__fondue___get_sequences owner: q2d2 tool_panel_section_id: '' @@ -1094,12 +1115,6 @@ tools: - name: qiime2__fondue__scrape_collection owner: q2d2 tool_panel_section_id: '' -- name: qiime2__kmerizer__core_metrics - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__kmerizer__seqs_to_kmers - owner: q2d2 - tool_panel_section_id: '' - name: seqkit_fx2tab owner: iuc tool_panel_section_id: '' diff --git a/communities/microgalaxy/lab/tools/top/UseGalaxy_eu.yaml b/communities/microgalaxy/lab/tools/top/UseGalaxy_eu.yaml index 51dd9f6d9..5fc6890b4 100644 --- a/communities/microgalaxy/lab/tools/top/UseGalaxy_eu.yaml +++ b/communities/microgalaxy/lab/tools/top/UseGalaxy_eu.yaml @@ -479,343 +479,304 @@ tools: - name: XTandemAdapter owner: bgruening tool_panel_section_id: '' -- name: qiime2__rescript__cull_seqs - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__degap_seqs - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__dereplicate - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__edit_taxonomy - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_classifications - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_cross_validate - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_fit_classifier - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_seqs - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_taxonomy - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__extract_seq_segments - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__filter_seqs_length - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__filter_seqs_length_by_taxon - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__filter_taxa - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__get_bv_brc_genome_features +- name: qiime2__dada2__denoise_ccs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_bv_brc_genomes +- name: qiime2__dada2__denoise_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_bv_brc_metadata +- name: qiime2__dada2__denoise_pyro owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_eukaryome_data +- name: qiime2__dada2__denoise_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_gtdb_data +- name: qiime2__dada2__plot_base_transitions owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_midori2_data +- name: qiime2__composition__add_pseudocount owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_ncbi_data +- name: qiime2__composition__ancom owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_ncbi_data_protein +- name: qiime2__composition__ancombc owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_ncbi_genomes +- name: qiime2__composition__ancombc2 owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_pr2_data +- name: qiime2__composition__ancombc2_visualizer owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_silva_data +- name: qiime2__composition__da_barplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_unite_data +- name: qiime2__composition__tabulate owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__merge_taxa +- name: qiime2__boots__alpha owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__orient_reads +- name: qiime2__boots__alpha_average owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__orient_seqs +- name: qiime2__boots__alpha_collection owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__parse_silva_taxonomy +- name: qiime2__boots__beta owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__reverse_transcribe +- name: qiime2__boots__beta_average owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__subsample_fasta +- name: qiime2__boots__beta_collection owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__trim_alignment +- name: qiime2__boots__core_metrics owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__distance_matrix +- name: qiime2__boots__kmer_diversity owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__merge +- name: qiime2__boots__resample owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__shuffle_groups +- name: qiime2__demux__emp_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__tabulate +- name: qiime2__demux__emp_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__alpha_group_significance +- name: qiime2__demux__filter_samples owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__collate_stats +- name: qiime2__demux__partition_samples_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__facet_across +- name: qiime2__demux__partition_samples_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__facet_within +- name: qiime2__demux__subsample_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__mann_whitney_u +- name: qiime2__demux__subsample_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__mann_whitney_u_facet +- name: qiime2__demux__summarize owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__plot_rainclouds +- name: qiime2__demux__tabulate_read_counts owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__prep_alpha_distribution +- name: qiime2__diversity__adonis owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__wilcoxon_srt +- name: qiime2__diversity__alpha owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__wilcoxon_srt_facet +- name: qiime2__diversity__alpha_correlation owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__bowtie2_build +- name: qiime2__diversity__alpha_group_significance owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__decontam_identify +- name: qiime2__diversity__alpha_phylogenetic owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__decontam_identify_batches +- name: qiime2__diversity__alpha_rarefaction owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__decontam_score_viz +- name: qiime2__diversity__beta owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__evaluate_composition +- name: qiime2__diversity__beta_correlation owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__evaluate_seqs +- name: qiime2__diversity__beta_group_significance owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__evaluate_taxonomy +- name: qiime2__diversity__beta_phylogenetic owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__exclude_seqs +- name: qiime2__diversity__beta_rarefaction owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__filter_reads +- name: qiime2__diversity__bioenv owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__adonis +- name: qiime2__diversity__core_metrics owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha +- name: qiime2__diversity__core_metrics_phylogenetic owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_correlation +- name: qiime2__diversity__filter_alpha_diversity owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_group_significance +- name: qiime2__diversity__filter_distance_matrix owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_phylogenetic +- name: qiime2__diversity__mantel owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_rarefaction +- name: qiime2__diversity__partial_procrustes owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta +- name: qiime2__diversity__pcoa owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_correlation +- name: qiime2__diversity__pcoa_biplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_group_significance +- name: qiime2__diversity__procrustes_analysis owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_phylogenetic +- name: qiime2__diversity__tsne owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_rarefaction +- name: qiime2__diversity__umap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__bioenv +- name: qiime2__taxa__barplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__core_metrics +- name: qiime2__taxa__barplot2 owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__core_metrics_phylogenetic +- name: qiime2__taxa__collapse owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__filter_alpha_diversity +- name: qiime2__taxa__filter_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__filter_distance_matrix +- name: qiime2__taxa__filter_table owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__mantel +- name: qiime2__stats__alpha_group_significance owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__partial_procrustes +- name: qiime2__stats__collate_stats owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__pcoa +- name: qiime2__stats__facet_across owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__pcoa_biplot +- name: qiime2__stats__facet_within owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__procrustes_analysis +- name: qiime2__stats__mann_whitney_u owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__tsne +- name: qiime2__stats__mann_whitney_u_facet owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__umap +- name: qiime2__stats__plot_rainclouds owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__emp_paired +- name: qiime2__stats__prep_alpha_distribution owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__emp_single +- name: qiime2__stats__wilcoxon_srt owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__filter_samples +- name: qiime2__stats__wilcoxon_srt_facet owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__partition_samples_paired +- name: qiime2__rescript__cull_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__partition_samples_single +- name: qiime2__rescript__degap_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__subsample_paired +- name: qiime2__rescript__dereplicate owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__subsample_single +- name: qiime2__rescript__edit_taxonomy owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__summarize +- name: qiime2__rescript__evaluate_classifications owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__tabulate_read_counts +- name: qiime2__rescript__evaluate_cross_validate owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_ccs +- name: qiime2__rescript__evaluate_fit_classifier owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_paired +- name: qiime2__rescript__evaluate_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_pyro +- name: qiime2__rescript__evaluate_taxonomy owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_single +- name: qiime2__rescript__extract_seq_segments owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__plot_base_transitions +- name: qiime2__rescript__filter_seqs_length owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__add_pseudocount +- name: qiime2__rescript__filter_seqs_length_by_taxon owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancom +- name: qiime2__rescript__filter_taxa owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancombc +- name: qiime2__rescript__get_bv_brc_genome_features owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancombc2 +- name: qiime2__rescript__get_bv_brc_genomes owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancombc2_visualizer +- name: qiime2__rescript__get_bv_brc_metadata owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__da_barplot +- name: qiime2__rescript__get_eukaryome_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__tabulate +- name: qiime2__rescript__get_gtdb_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__barplot +- name: qiime2__rescript__get_midori2_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__barplot2 +- name: qiime2__rescript__get_ncbi_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__collapse +- name: qiime2__rescript__get_ncbi_data_protein owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__filter_seqs +- name: qiime2__rescript__get_ncbi_genomes owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__filter_table +- name: qiime2__rescript__get_pr2_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__alpha +- name: qiime2__rescript__get_silva_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__alpha_average +- name: qiime2__rescript__get_unite_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__alpha_collection +- name: qiime2__rescript__merge_taxa owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__beta +- name: qiime2__rescript__orient_reads owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__beta_average +- name: qiime2__rescript__orient_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__beta_collection +- name: qiime2__rescript__parse_silva_taxonomy owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__core_metrics +- name: qiime2__rescript__reverse_transcribe owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__kmer_diversity +- name: qiime2__rescript__subsample_fasta owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__resample +- name: qiime2__rescript__trim_alignment owner: q2d2 tool_panel_section_id: '' - name: qiime2__feature_classifier__blast @@ -920,6 +881,51 @@ tools: - name: qiime2__feature_table__transpose owner: q2d2 tool_panel_section_id: '' +- name: qiime2__quality_control__bowtie2_build + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__quality_control__decontam_identify + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__quality_control__decontam_identify_batches + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__quality_control__decontam_score_viz + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__quality_control__evaluate_composition + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__quality_control__evaluate_seqs + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__quality_control__evaluate_taxonomy + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__quality_control__exclude_seqs + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__quality_control__filter_reads + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__metadata__distance_matrix + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__metadata__merge + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__metadata__shuffle_groups + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__metadata__tabulate + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__kmerizer__core_metrics + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__kmerizer__seqs_to_kmers + owner: q2d2 + tool_panel_section_id: '' - name: qiime2__fondue___get_sequences owner: q2d2 tool_panel_section_id: '' @@ -944,9 +950,3 @@ tools: - name: qiime2__fondue__scrape_collection owner: q2d2 tool_panel_section_id: '' -- name: qiime2__kmerizer__core_metrics - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__kmerizer__seqs_to_kmers - owner: q2d2 - tool_panel_section_id: '' diff --git a/communities/microgalaxy/lab/tools/top/UseGalaxy_fr.yaml b/communities/microgalaxy/lab/tools/top/UseGalaxy_fr.yaml index 7a837afd1..b2c3d07b2 100644 --- a/communities/microgalaxy/lab/tools/top/UseGalaxy_fr.yaml +++ b/communities/microgalaxy/lab/tools/top/UseGalaxy_fr.yaml @@ -74,27 +74,6 @@ tools: - name: ncbi_tblastx_wrapper owner: devteam tool_panel_section_id: '' -- name: obi_annotate - owner: iuc - tool_panel_section_id: '' -- name: obi_clean - owner: iuc - tool_panel_section_id: '' -- name: obi_convert - owner: iuc - tool_panel_section_id: '' -- name: obi_grep - owner: iuc - tool_panel_section_id: '' -- name: obi_multiplex - owner: iuc - tool_panel_section_id: '' -- name: obi_pairing - owner: iuc - tool_panel_section_id: '' -- name: obi_uniq - owner: iuc - tool_panel_section_id: '' - name: AccurateMassSearch owner: bgruening tool_panel_section_id: '' @@ -536,355 +515,316 @@ tools: - name: phyloseq_tax_glom owner: iuc tool_panel_section_id: '' -- name: qiime2__rescript__cull_seqs - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__degap_seqs - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__dereplicate - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__edit_taxonomy - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_classifications - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_cross_validate - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_fit_classifier - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_seqs - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_taxonomy - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__extract_seq_segments - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__filter_seqs_length - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__filter_seqs_length_by_taxon - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__filter_taxa - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__get_bv_brc_genome_features +- name: qiime2__dada2__denoise_ccs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_bv_brc_genomes +- name: qiime2__dada2__denoise_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_bv_brc_metadata +- name: qiime2__dada2__denoise_pyro owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_eukaryome_data +- name: qiime2__dada2__denoise_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_gtdb_data +- name: qiime2__dada2__plot_base_transitions owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_midori2_data +- name: qiime2__composition__add_pseudocount owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_ncbi_data +- name: qiime2__composition__ancom owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_ncbi_data_protein +- name: qiime2__composition__ancombc owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_ncbi_genomes +- name: qiime2__composition__ancombc2 owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_pr2_data +- name: qiime2__composition__ancombc2_visualizer owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_silva_data +- name: qiime2__composition__da_barplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_unite_data +- name: qiime2__composition__tabulate owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__merge_taxa +- name: qiime2__boots__alpha owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__orient_reads +- name: qiime2__boots__alpha_average owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__orient_seqs +- name: qiime2__boots__alpha_collection owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__parse_silva_taxonomy +- name: qiime2__boots__beta owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__reverse_transcribe +- name: qiime2__boots__beta_average owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__subsample_fasta +- name: qiime2__boots__beta_collection owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__trim_alignment +- name: qiime2__boots__core_metrics owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__distance_matrix +- name: qiime2__boots__kmer_diversity owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__merge +- name: qiime2__boots__resample owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__shuffle_groups +- name: qiime2__demux__emp_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__tabulate +- name: qiime2__demux__emp_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__alpha_group_significance +- name: qiime2__demux__filter_samples owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__collate_stats +- name: qiime2__demux__partition_samples_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__facet_across +- name: qiime2__demux__partition_samples_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__facet_within +- name: qiime2__demux__subsample_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__mann_whitney_u +- name: qiime2__demux__subsample_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__mann_whitney_u_facet +- name: qiime2__demux__summarize owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__plot_rainclouds +- name: qiime2__demux__tabulate_read_counts owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__prep_alpha_distribution +- name: qiime2__diversity__adonis owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__wilcoxon_srt +- name: qiime2__diversity__alpha owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__wilcoxon_srt_facet +- name: qiime2__diversity__alpha_correlation owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__bowtie2_build +- name: qiime2__diversity__alpha_group_significance owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__decontam_identify +- name: qiime2__diversity__alpha_phylogenetic owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__decontam_identify_batches +- name: qiime2__diversity__alpha_rarefaction owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__decontam_score_viz +- name: qiime2__diversity__beta owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__evaluate_composition +- name: qiime2__diversity__beta_correlation owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__evaluate_seqs +- name: qiime2__diversity__beta_group_significance owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__evaluate_taxonomy +- name: qiime2__diversity__beta_phylogenetic owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__exclude_seqs +- name: qiime2__diversity__beta_rarefaction owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__filter_reads +- name: qiime2__diversity__bioenv owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vizard__boxplot +- name: qiime2__diversity__core_metrics owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vizard__heatmap +- name: qiime2__diversity__core_metrics_phylogenetic owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vizard__lineplot +- name: qiime2__diversity__filter_alpha_diversity owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vizard__scatterplot_2d +- name: qiime2__diversity__filter_distance_matrix owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__adonis +- name: qiime2__diversity__mantel owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha +- name: qiime2__diversity__partial_procrustes owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_correlation +- name: qiime2__diversity__pcoa owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_group_significance +- name: qiime2__diversity__pcoa_biplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_phylogenetic +- name: qiime2__diversity__procrustes_analysis owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_rarefaction +- name: qiime2__diversity__tsne owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta +- name: qiime2__diversity__umap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_correlation +- name: qiime2__taxa__barplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_group_significance +- name: qiime2__taxa__barplot2 owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_phylogenetic +- name: qiime2__taxa__collapse owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_rarefaction +- name: qiime2__taxa__filter_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__bioenv +- name: qiime2__taxa__filter_table owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__core_metrics +- name: qiime2__stats__alpha_group_significance owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__core_metrics_phylogenetic +- name: qiime2__stats__collate_stats owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__filter_alpha_diversity +- name: qiime2__stats__facet_across owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__filter_distance_matrix +- name: qiime2__stats__facet_within owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__mantel +- name: qiime2__stats__mann_whitney_u owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__partial_procrustes +- name: qiime2__stats__mann_whitney_u_facet owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__pcoa +- name: qiime2__stats__plot_rainclouds owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__pcoa_biplot +- name: qiime2__stats__prep_alpha_distribution owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__procrustes_analysis +- name: qiime2__stats__wilcoxon_srt owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__tsne +- name: qiime2__stats__wilcoxon_srt_facet owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__umap +- name: qiime2__rescript__cull_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__emp_paired +- name: qiime2__rescript__degap_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__emp_single +- name: qiime2__rescript__dereplicate owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__filter_samples +- name: qiime2__rescript__edit_taxonomy owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__partition_samples_paired +- name: qiime2__rescript__evaluate_classifications owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__partition_samples_single +- name: qiime2__rescript__evaluate_cross_validate owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__subsample_paired +- name: qiime2__rescript__evaluate_fit_classifier owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__subsample_single +- name: qiime2__rescript__evaluate_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__summarize +- name: qiime2__rescript__evaluate_taxonomy owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__tabulate_read_counts +- name: qiime2__rescript__extract_seq_segments owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_ccs +- name: qiime2__rescript__filter_seqs_length owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_paired +- name: qiime2__rescript__filter_seqs_length_by_taxon owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_pyro +- name: qiime2__rescript__filter_taxa owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_single +- name: qiime2__rescript__get_bv_brc_genome_features owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__plot_base_transitions +- name: qiime2__rescript__get_bv_brc_genomes owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__add_pseudocount +- name: qiime2__rescript__get_bv_brc_metadata owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancom +- name: qiime2__rescript__get_eukaryome_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancombc +- name: qiime2__rescript__get_gtdb_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancombc2 +- name: qiime2__rescript__get_midori2_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancombc2_visualizer +- name: qiime2__rescript__get_ncbi_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__da_barplot +- name: qiime2__rescript__get_ncbi_data_protein owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__tabulate +- name: qiime2__rescript__get_ncbi_genomes owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__barplot +- name: qiime2__rescript__get_pr2_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__barplot2 +- name: qiime2__rescript__get_silva_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__collapse +- name: qiime2__rescript__get_unite_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__filter_seqs +- name: qiime2__rescript__merge_taxa owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__filter_table +- name: qiime2__rescript__orient_reads owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__alpha +- name: qiime2__rescript__orient_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__alpha_average +- name: qiime2__rescript__parse_silva_taxonomy owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__alpha_collection +- name: qiime2__rescript__reverse_transcribe owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__beta +- name: qiime2__rescript__subsample_fasta owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__beta_average +- name: qiime2__rescript__trim_alignment owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__beta_collection +- name: qiime2__vizard__boxplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__core_metrics +- name: qiime2__vizard__heatmap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__kmer_diversity +- name: qiime2__vizard__lineplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__resample +- name: qiime2__vizard__scatterplot_2d owner: q2d2 tool_panel_section_id: '' - name: qiime2__feature_classifier__blast @@ -989,6 +929,51 @@ tools: - name: qiime2__feature_table__transpose owner: q2d2 tool_panel_section_id: '' +- name: qiime2__quality_control__bowtie2_build + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__quality_control__decontam_identify + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__quality_control__decontam_identify_batches + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__quality_control__decontam_score_viz + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__quality_control__evaluate_composition + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__quality_control__evaluate_seqs + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__quality_control__evaluate_taxonomy + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__quality_control__exclude_seqs + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__quality_control__filter_reads + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__metadata__distance_matrix + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__metadata__merge + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__metadata__shuffle_groups + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__metadata__tabulate + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__kmerizer__core_metrics + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__kmerizer__seqs_to_kmers + owner: q2d2 + tool_panel_section_id: '' - name: qiime2__fondue___get_sequences owner: q2d2 tool_panel_section_id: '' @@ -1013,12 +998,6 @@ tools: - name: qiime2__fondue__scrape_collection owner: q2d2 tool_panel_section_id: '' -- name: qiime2__kmerizer__core_metrics - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__kmerizer__seqs_to_kmers - owner: q2d2 - tool_panel_section_id: '' - name: seqkit_fx2tab owner: iuc tool_panel_section_id: '' diff --git a/communities/microgalaxy/lab/tools/top/UseGalaxy_no.yaml b/communities/microgalaxy/lab/tools/top/UseGalaxy_no.yaml index 9d68f6a1f..16de93b79 100644 --- a/communities/microgalaxy/lab/tools/top/UseGalaxy_no.yaml +++ b/communities/microgalaxy/lab/tools/top/UseGalaxy_no.yaml @@ -230,6 +230,9 @@ tools: - name: obi_clean owner: iuc tool_panel_section_id: '' +- name: obi_complement + owner: iuc + tool_panel_section_id: '' - name: obi_convert owner: iuc tool_panel_section_id: '' @@ -242,6 +245,18 @@ tools: - name: obi_pairing owner: iuc tool_panel_section_id: '' +- name: obi_pcr + owner: iuc + tool_panel_section_id: '' +- name: obi_refidx + owner: iuc + tool_panel_section_id: '' +- name: obi_tag + owner: iuc + tool_panel_section_id: '' +- name: obi_taxonomy + owner: iuc + tool_panel_section_id: '' - name: obi_uniq owner: iuc tool_panel_section_id: '' @@ -725,262 +740,241 @@ tools: - name: pycoqc owner: iuc tool_panel_section_id: '' -- name: qiime2_core__tools__export - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2_core__tools__import - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2_core__tools__import_fastq - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__quality_filter__q_score - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__cull_seqs - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__degap_seqs - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__dereplicate - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__edit_taxonomy +- name: qiime2__dada2__denoise_ccs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_classifications +- name: qiime2__dada2__denoise_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_cross_validate +- name: qiime2__dada2__denoise_pyro owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_fit_classifier +- name: qiime2__dada2__denoise_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_seqs +- name: qiime2__dada2__plot_base_transitions owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_taxonomy +- name: qiime2__cutadapt__demux_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__extract_seq_segments +- name: qiime2__cutadapt__demux_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__filter_seqs_length +- name: qiime2__cutadapt__trim_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__filter_seqs_length_by_taxon +- name: qiime2__cutadapt__trim_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__filter_taxa +- name: qiime2__composition__add_pseudocount owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_bv_brc_genome_features +- name: qiime2__composition__ancom owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_bv_brc_genomes +- name: qiime2__composition__ancombc owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_bv_brc_metadata +- name: qiime2__composition__ancombc2 owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_eukaryome_data +- name: qiime2__composition__ancombc2_visualizer owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_gtdb_data +- name: qiime2__composition__da_barplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_midori2_data +- name: qiime2__composition__tabulate owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_ncbi_data +- name: qiime2__boots__alpha owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_ncbi_data_protein +- name: qiime2__boots__alpha_average owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_ncbi_genomes +- name: qiime2__boots__alpha_collection owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_pr2_data +- name: qiime2__boots__beta owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_silva_data +- name: qiime2__boots__beta_average owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_unite_data +- name: qiime2__boots__beta_collection owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__merge_taxa +- name: qiime2__boots__core_metrics owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__orient_reads +- name: qiime2__boots__kmer_diversity owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__orient_seqs +- name: qiime2__boots__resample owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__parse_silva_taxonomy +- name: qiime2__vsearch__cluster_features_closed_reference owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__reverse_transcribe +- name: qiime2__vsearch__cluster_features_de_novo owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__subsample_fasta +- name: qiime2__vsearch__cluster_features_open_reference owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__trim_alignment +- name: qiime2__vsearch__dereplicate_sequences owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__classify_samples +- name: qiime2__vsearch__fastq_stats owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__classify_samples_from_dist +- name: qiime2__vsearch__merge_pairs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__classify_samples_ncv +- name: qiime2__vsearch__uchime_denovo owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__confusion_matrix +- name: qiime2__vsearch__uchime_ref owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__fit_classifier +- name: qiime2__demux__emp_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__fit_regressor +- name: qiime2__demux__emp_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__heatmap +- name: qiime2__demux__filter_samples owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__metatable +- name: qiime2__demux__partition_samples_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__predict_classification +- name: qiime2__demux__partition_samples_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__predict_regression +- name: qiime2__demux__subsample_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__regress_samples +- name: qiime2__demux__subsample_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__regress_samples_ncv +- name: qiime2__demux__summarize owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__scatterplot +- name: qiime2__demux__tabulate_read_counts owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__split_table +- name: qiime2__deblur__denoise_16S owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__summarize +- name: qiime2__deblur__denoise_other owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__align_to_tree_mafft_fasttree +- name: qiime2__deblur__visualize_stats owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__align_to_tree_mafft_iqtree +- name: qiime2__diversity__adonis owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__align_to_tree_mafft_raxml +- name: qiime2__diversity__alpha owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__fasttree +- name: qiime2__diversity__alpha_correlation owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__filter_table +- name: qiime2__diversity__alpha_group_significance owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__filter_tree +- name: qiime2__diversity__alpha_phylogenetic owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__iqtree +- name: qiime2__diversity__alpha_rarefaction owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__iqtree_ultrafast_bootstrap +- name: qiime2__diversity__beta owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__midpoint_root +- name: qiime2__diversity__beta_correlation owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__raxml +- name: qiime2__diversity__beta_group_significance owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__raxml_rapid_bootstrap +- name: qiime2__diversity__beta_phylogenetic owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__robinson_foulds +- name: qiime2__diversity__beta_rarefaction owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__distance_matrix +- name: qiime2__diversity__bioenv owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__merge +- name: qiime2__diversity__core_metrics owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__shuffle_groups +- name: qiime2__diversity__core_metrics_phylogenetic owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__tabulate +- name: qiime2__diversity__filter_alpha_diversity owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__alpha_group_significance +- name: qiime2__diversity__filter_distance_matrix owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__collate_stats +- name: qiime2__diversity__mantel owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__facet_across +- name: qiime2__diversity__partial_procrustes owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__facet_within +- name: qiime2__diversity__pcoa owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__mann_whitney_u +- name: qiime2__diversity__pcoa_biplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__mann_whitney_u_facet +- name: qiime2__diversity__procrustes_analysis owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__plot_rainclouds +- name: qiime2__diversity__tsne owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__prep_alpha_distribution +- name: qiime2__diversity__umap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__wilcoxon_srt +- name: qiime2__emperor__biplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__wilcoxon_srt_facet +- name: qiime2__emperor__plot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__bowtie2_build +- name: qiime2__emperor__procrustes_plot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__decontam_identify +- name: qiime2_core__tools__export owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__decontam_identify_batches +- name: qiime2_core__tools__import owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__decontam_score_viz +- name: qiime2_core__tools__import_fastq owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__evaluate_composition +- name: qiime2__taxa__barplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__evaluate_seqs +- name: qiime2__taxa__barplot2 owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__evaluate_taxonomy +- name: qiime2__taxa__collapse owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__exclude_seqs +- name: qiime2__taxa__filter_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__filter_reads +- name: qiime2__taxa__filter_table owner: q2d2 tool_panel_section_id: '' - name: qiime2__diversity_lib__alpha_passthrough @@ -1019,253 +1013,244 @@ tools: - name: qiime2__diversity_lib__weighted_unifrac owner: q2d2 tool_panel_section_id: '' -- name: qiime2__alignment__mafft - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__alignment__mafft_add - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__alignment__mask - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__vizard__boxplot +- name: qiime2__stats__alpha_group_significance owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vizard__heatmap +- name: qiime2__stats__collate_stats owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vizard__lineplot +- name: qiime2__stats__facet_across owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vizard__scatterplot_2d +- name: qiime2__stats__facet_within owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__adonis +- name: qiime2__stats__mann_whitney_u owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha +- name: qiime2__stats__mann_whitney_u_facet owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_correlation +- name: qiime2__stats__plot_rainclouds owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_group_significance +- name: qiime2__stats__prep_alpha_distribution owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_phylogenetic +- name: qiime2__stats__wilcoxon_srt owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_rarefaction +- name: qiime2__stats__wilcoxon_srt_facet owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta +- name: qiime2__sample_classifier__classify_samples owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_correlation +- name: qiime2__sample_classifier__classify_samples_from_dist owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_group_significance +- name: qiime2__sample_classifier__classify_samples_ncv owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_phylogenetic +- name: qiime2__sample_classifier__confusion_matrix owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_rarefaction +- name: qiime2__sample_classifier__fit_classifier owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__bioenv +- name: qiime2__sample_classifier__fit_regressor owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__core_metrics +- name: qiime2__sample_classifier__heatmap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__core_metrics_phylogenetic +- name: qiime2__sample_classifier__metatable owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__filter_alpha_diversity +- name: qiime2__sample_classifier__predict_classification owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__filter_distance_matrix +- name: qiime2__sample_classifier__predict_regression owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__mantel +- name: qiime2__sample_classifier__regress_samples owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__partial_procrustes +- name: qiime2__sample_classifier__regress_samples_ncv owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__pcoa +- name: qiime2__sample_classifier__scatterplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__pcoa_biplot +- name: qiime2__sample_classifier__split_table owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__procrustes_analysis +- name: qiime2__sample_classifier__summarize owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__tsne +- name: qiime2__rescript__cull_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__umap +- name: qiime2__rescript__degap_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__emp_paired +- name: qiime2__rescript__dereplicate owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__emp_single +- name: qiime2__rescript__edit_taxonomy owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__filter_samples +- name: qiime2__rescript__evaluate_classifications owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__partition_samples_paired +- name: qiime2__rescript__evaluate_cross_validate owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__partition_samples_single +- name: qiime2__rescript__evaluate_fit_classifier owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__subsample_paired +- name: qiime2__rescript__evaluate_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__subsample_single +- name: qiime2__rescript__evaluate_taxonomy owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__summarize +- name: qiime2__rescript__extract_seq_segments owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__tabulate_read_counts +- name: qiime2__rescript__filter_seqs_length owner: q2d2 tool_panel_section_id: '' -- name: qiime2__deblur__denoise_16S +- name: qiime2__rescript__filter_seqs_length_by_taxon owner: q2d2 tool_panel_section_id: '' -- name: qiime2__deblur__denoise_other +- name: qiime2__rescript__filter_taxa owner: q2d2 tool_panel_section_id: '' -- name: qiime2__deblur__visualize_stats +- name: qiime2__rescript__get_bv_brc_genome_features owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_ccs +- name: qiime2__rescript__get_bv_brc_genomes owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_paired +- name: qiime2__rescript__get_bv_brc_metadata owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_pyro +- name: qiime2__rescript__get_eukaryome_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_single +- name: qiime2__rescript__get_gtdb_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__plot_base_transitions +- name: qiime2__rescript__get_midori2_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__cutadapt__demux_paired +- name: qiime2__rescript__get_ncbi_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__cutadapt__demux_single +- name: qiime2__rescript__get_ncbi_data_protein owner: q2d2 tool_panel_section_id: '' -- name: qiime2__cutadapt__trim_paired +- name: qiime2__rescript__get_ncbi_genomes owner: q2d2 tool_panel_section_id: '' -- name: qiime2__cutadapt__trim_single +- name: qiime2__rescript__get_pr2_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__add_pseudocount +- name: qiime2__rescript__get_silva_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancom +- name: qiime2__rescript__get_unite_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancombc +- name: qiime2__rescript__merge_taxa owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancombc2 +- name: qiime2__rescript__orient_reads owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancombc2_visualizer +- name: qiime2__rescript__orient_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__da_barplot +- name: qiime2__rescript__parse_silva_taxonomy owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__tabulate +- name: qiime2__rescript__reverse_transcribe owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__barplot +- name: qiime2__rescript__subsample_fasta owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__barplot2 +- name: qiime2__rescript__trim_alignment owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__collapse +- name: qiime2__quality_filter__q_score owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__filter_seqs +- name: qiime2__vizard__boxplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__filter_table +- name: qiime2__vizard__heatmap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__alpha +- name: qiime2__vizard__lineplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__alpha_average +- name: qiime2__vizard__scatterplot_2d owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__alpha_collection +- name: qiime2__alignment__mafft owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__beta +- name: qiime2__alignment__mafft_add owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__beta_average +- name: qiime2__alignment__mask owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__beta_collection +- name: qiime2__phylogeny__align_to_tree_mafft_fasttree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__core_metrics +- name: qiime2__phylogeny__align_to_tree_mafft_iqtree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__kmer_diversity +- name: qiime2__phylogeny__align_to_tree_mafft_raxml owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__resample +- name: qiime2__phylogeny__fasttree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__cluster_features_closed_reference +- name: qiime2__phylogeny__filter_table owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__cluster_features_de_novo +- name: qiime2__phylogeny__filter_tree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__cluster_features_open_reference +- name: qiime2__phylogeny__iqtree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__dereplicate_sequences +- name: qiime2__phylogeny__iqtree_ultrafast_bootstrap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__fastq_stats +- name: qiime2__phylogeny__midpoint_root owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__merge_pairs +- name: qiime2__phylogeny__raxml owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__uchime_denovo +- name: qiime2__phylogeny__raxml_rapid_bootstrap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__uchime_ref +- name: qiime2__phylogeny__robinson_foulds owner: q2d2 tool_panel_section_id: '' -- name: qiime2__emperor__biplot +- name: qiime2__fragment_insertion__classify_otus_experimental owner: q2d2 tool_panel_section_id: '' -- name: qiime2__emperor__plot +- name: qiime2__fragment_insertion__filter_features owner: q2d2 tool_panel_section_id: '' -- name: qiime2__emperor__procrustes_plot +- name: qiime2__fragment_insertion__sepp owner: q2d2 tool_panel_section_id: '' - name: qiime2__feature_classifier__blast @@ -1301,6 +1286,39 @@ tools: - name: qiime2__feature_classifier__vsearch_global owner: q2d2 tool_panel_section_id: '' +- name: qiime2__longitudinal__anova + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__feature_volatility + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__first_differences + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__first_distances + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__linear_mixed_effects + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__maturity_index + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__nmit + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__pairwise_differences + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__pairwise_distances + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__plot_feature_volatility + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__volatility + owner: q2d2 + tool_panel_section_id: '' - name: qiime2__feature_table___summarize owner: q2d2 tool_panel_section_id: '' @@ -1370,76 +1388,73 @@ tools: - name: qiime2__feature_table__transpose owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue___get_sequences - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__fondue__combine_seqs +- name: qiime2__quality_control__bowtie2_build owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__get_all +- name: qiime2__quality_control__decontam_identify owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__get_ids_from_query +- name: qiime2__quality_control__decontam_identify_batches owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__get_metadata +- name: qiime2__quality_control__decontam_score_viz owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__get_sequences +- name: qiime2__quality_control__evaluate_composition owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__merge_metadata +- name: qiime2__quality_control__evaluate_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__scrape_collection +- name: qiime2__quality_control__evaluate_taxonomy owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fragment_insertion__classify_otus_experimental +- name: qiime2__quality_control__exclude_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fragment_insertion__filter_features +- name: qiime2__quality_control__filter_reads owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fragment_insertion__sepp +- name: qiime2__metadata__distance_matrix owner: q2d2 tool_panel_section_id: '' -- name: qiime2__kmerizer__core_metrics +- name: qiime2__metadata__merge owner: q2d2 tool_panel_section_id: '' -- name: qiime2__kmerizer__seqs_to_kmers +- name: qiime2__metadata__shuffle_groups owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__anova +- name: qiime2__metadata__tabulate owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__feature_volatility +- name: qiime2__kmerizer__core_metrics owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__first_differences +- name: qiime2__kmerizer__seqs_to_kmers owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__first_distances +- name: qiime2__fondue___get_sequences owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__linear_mixed_effects +- name: qiime2__fondue__combine_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__maturity_index +- name: qiime2__fondue__get_all owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__nmit +- name: qiime2__fondue__get_ids_from_query owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__pairwise_differences +- name: qiime2__fondue__get_metadata owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__pairwise_distances +- name: qiime2__fondue__get_sequences owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__plot_feature_volatility +- name: qiime2__fondue__merge_metadata owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__volatility +- name: qiime2__fondue__scrape_collection owner: q2d2 tool_panel_section_id: '' - name: recentrifuge diff --git a/communities/microgalaxy/lab/tools/top/UseGalaxy_org_Main.yaml b/communities/microgalaxy/lab/tools/top/UseGalaxy_org_Main.yaml index d21dae02f..3fb3eedc7 100644 --- a/communities/microgalaxy/lab/tools/top/UseGalaxy_org_Main.yaml +++ b/communities/microgalaxy/lab/tools/top/UseGalaxy_org_Main.yaml @@ -239,6 +239,9 @@ tools: - name: obi_clean owner: iuc tool_panel_section_id: '' +- name: obi_complement + owner: iuc + tool_panel_section_id: '' - name: obi_convert owner: iuc tool_panel_section_id: '' @@ -251,6 +254,18 @@ tools: - name: obi_pairing owner: iuc tool_panel_section_id: '' +- name: obi_pcr + owner: iuc + tool_panel_section_id: '' +- name: obi_refidx + owner: iuc + tool_panel_section_id: '' +- name: obi_tag + owner: iuc + tool_panel_section_id: '' +- name: obi_taxonomy + owner: iuc + tool_panel_section_id: '' - name: obi_uniq owner: iuc tool_panel_section_id: '' @@ -716,364 +731,316 @@ tools: - name: picrust_predict_metagenomes owner: iuc tool_panel_section_id: '' -- name: qiime2_core__tools__export - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2_core__tools__import - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2_core__tools__import_fastq - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__cull_seqs - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__degap_seqs - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__dereplicate - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__edit_taxonomy - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_classifications - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_cross_validate - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_fit_classifier - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_seqs - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_taxonomy - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__extract_seq_segments - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__filter_seqs_length - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__filter_seqs_length_by_taxon - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__filter_taxa - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__get_bv_brc_genome_features +- name: qiime2__dada2__denoise_ccs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_bv_brc_genomes +- name: qiime2__dada2__denoise_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_bv_brc_metadata +- name: qiime2__dada2__denoise_pyro owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_eukaryome_data +- name: qiime2__dada2__denoise_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_gtdb_data +- name: qiime2__dada2__plot_base_transitions owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_midori2_data +- name: qiime2__composition__add_pseudocount owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_ncbi_data +- name: qiime2__composition__ancom owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_ncbi_data_protein +- name: qiime2__composition__ancombc owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_ncbi_genomes +- name: qiime2__composition__ancombc2 owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_pr2_data +- name: qiime2__composition__ancombc2_visualizer owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_silva_data +- name: qiime2__composition__da_barplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_unite_data +- name: qiime2__composition__tabulate owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__merge_taxa +- name: qiime2__boots__alpha owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__orient_reads +- name: qiime2__boots__alpha_average owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__orient_seqs +- name: qiime2__boots__alpha_collection owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__parse_silva_taxonomy +- name: qiime2__boots__beta owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__reverse_transcribe +- name: qiime2__boots__beta_average owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__subsample_fasta +- name: qiime2__boots__beta_collection owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__trim_alignment +- name: qiime2__boots__core_metrics owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__distance_matrix +- name: qiime2__boots__kmer_diversity owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__merge +- name: qiime2__boots__resample owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__shuffle_groups +- name: qiime2__demux__emp_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__tabulate +- name: qiime2__demux__emp_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__alpha_group_significance +- name: qiime2__demux__filter_samples owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__collate_stats +- name: qiime2__demux__partition_samples_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__facet_across +- name: qiime2__demux__partition_samples_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__facet_within +- name: qiime2__demux__subsample_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__mann_whitney_u +- name: qiime2__demux__subsample_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__mann_whitney_u_facet +- name: qiime2__demux__summarize owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__plot_rainclouds +- name: qiime2__demux__tabulate_read_counts owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__prep_alpha_distribution +- name: qiime2__diversity__adonis owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__wilcoxon_srt +- name: qiime2__diversity__alpha owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__wilcoxon_srt_facet +- name: qiime2__diversity__alpha_correlation owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__bowtie2_build +- name: qiime2__diversity__alpha_group_significance owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__decontam_identify +- name: qiime2__diversity__alpha_phylogenetic owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__decontam_identify_batches +- name: qiime2__diversity__alpha_rarefaction owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__decontam_score_viz +- name: qiime2__diversity__beta owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__evaluate_composition +- name: qiime2__diversity__beta_correlation owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__evaluate_seqs +- name: qiime2__diversity__beta_group_significance owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__evaluate_taxonomy +- name: qiime2__diversity__beta_phylogenetic owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__exclude_seqs +- name: qiime2__diversity__beta_rarefaction owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__filter_reads +- name: qiime2__diversity__bioenv owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vizard__boxplot +- name: qiime2__diversity__core_metrics owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vizard__heatmap +- name: qiime2__diversity__core_metrics_phylogenetic owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vizard__lineplot +- name: qiime2__diversity__filter_alpha_diversity owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vizard__scatterplot_2d +- name: qiime2__diversity__filter_distance_matrix owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__adonis +- name: qiime2__diversity__mantel owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha +- name: qiime2__diversity__partial_procrustes owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_correlation +- name: qiime2__diversity__pcoa owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_group_significance +- name: qiime2__diversity__pcoa_biplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_phylogenetic +- name: qiime2__diversity__procrustes_analysis owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_rarefaction +- name: qiime2__diversity__tsne owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta +- name: qiime2__diversity__umap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_correlation +- name: qiime2__taxa__barplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_group_significance +- name: qiime2__taxa__barplot2 owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_phylogenetic +- name: qiime2__taxa__collapse owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_rarefaction +- name: qiime2__taxa__filter_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__bioenv +- name: qiime2__taxa__filter_table owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__core_metrics +- name: qiime2__stats__alpha_group_significance owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__core_metrics_phylogenetic +- name: qiime2__stats__collate_stats owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__filter_alpha_diversity +- name: qiime2__stats__facet_across owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__filter_distance_matrix +- name: qiime2__stats__facet_within owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__mantel +- name: qiime2__stats__mann_whitney_u owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__partial_procrustes +- name: qiime2__stats__mann_whitney_u_facet owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__pcoa +- name: qiime2__stats__plot_rainclouds owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__pcoa_biplot +- name: qiime2__stats__prep_alpha_distribution owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__procrustes_analysis +- name: qiime2__stats__wilcoxon_srt owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__tsne +- name: qiime2__stats__wilcoxon_srt_facet owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__umap +- name: qiime2__rescript__cull_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__emp_paired +- name: qiime2__rescript__degap_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__emp_single +- name: qiime2__rescript__dereplicate owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__filter_samples +- name: qiime2__rescript__edit_taxonomy owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__partition_samples_paired +- name: qiime2__rescript__evaluate_classifications owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__partition_samples_single +- name: qiime2__rescript__evaluate_cross_validate owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__subsample_paired +- name: qiime2__rescript__evaluate_fit_classifier owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__subsample_single +- name: qiime2__rescript__evaluate_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__summarize +- name: qiime2__rescript__evaluate_taxonomy owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__tabulate_read_counts +- name: qiime2__rescript__extract_seq_segments owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_ccs +- name: qiime2__rescript__filter_seqs_length owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_paired +- name: qiime2__rescript__filter_seqs_length_by_taxon owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_pyro +- name: qiime2__rescript__filter_taxa owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_single +- name: qiime2__rescript__get_bv_brc_genome_features owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__plot_base_transitions +- name: qiime2__rescript__get_bv_brc_genomes owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__add_pseudocount +- name: qiime2__rescript__get_bv_brc_metadata owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancom +- name: qiime2__rescript__get_eukaryome_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancombc +- name: qiime2__rescript__get_gtdb_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancombc2 +- name: qiime2__rescript__get_midori2_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancombc2_visualizer +- name: qiime2__rescript__get_ncbi_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__da_barplot +- name: qiime2__rescript__get_ncbi_data_protein owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__tabulate +- name: qiime2__rescript__get_ncbi_genomes owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__barplot +- name: qiime2__rescript__get_pr2_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__barplot2 +- name: qiime2__rescript__get_silva_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__collapse +- name: qiime2__rescript__get_unite_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__filter_seqs +- name: qiime2__rescript__merge_taxa owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__filter_table +- name: qiime2__rescript__orient_reads owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__alpha +- name: qiime2__rescript__orient_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__alpha_average +- name: qiime2__rescript__parse_silva_taxonomy owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__alpha_collection +- name: qiime2__rescript__reverse_transcribe owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__beta +- name: qiime2__rescript__subsample_fasta owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__beta_average +- name: qiime2__rescript__trim_alignment owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__beta_collection +- name: qiime2__vizard__boxplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__core_metrics +- name: qiime2__vizard__heatmap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__kmer_diversity +- name: qiime2__vizard__lineplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__resample +- name: qiime2__vizard__scatterplot_2d owner: q2d2 tool_panel_section_id: '' - name: qiime2__feature_classifier__blast @@ -1178,6 +1145,51 @@ tools: - name: qiime2__feature_table__transpose owner: q2d2 tool_panel_section_id: '' +- name: qiime2__quality_control__bowtie2_build + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__quality_control__decontam_identify + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__quality_control__decontam_identify_batches + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__quality_control__decontam_score_viz + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__quality_control__evaluate_composition + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__quality_control__evaluate_seqs + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__quality_control__evaluate_taxonomy + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__quality_control__exclude_seqs + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__quality_control__filter_reads + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__metadata__distance_matrix + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__metadata__merge + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__metadata__shuffle_groups + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__metadata__tabulate + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__kmerizer__core_metrics + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__kmerizer__seqs_to_kmers + owner: q2d2 + tool_panel_section_id: '' - name: qiime2__fondue___get_sequences owner: q2d2 tool_panel_section_id: '' @@ -1202,12 +1214,6 @@ tools: - name: qiime2__fondue__scrape_collection owner: q2d2 tool_panel_section_id: '' -- name: qiime2__kmerizer__core_metrics - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__kmerizer__seqs_to_kmers - owner: q2d2 - tool_panel_section_id: '' - name: seqkit_fx2tab owner: iuc tool_panel_section_id: '' diff --git a/communities/microgalaxy/lab/tools/top/UseGalaxy_org_au.yaml b/communities/microgalaxy/lab/tools/top/UseGalaxy_org_au.yaml index 483cb77b3..b4245a2d9 100644 --- a/communities/microgalaxy/lab/tools/top/UseGalaxy_org_au.yaml +++ b/communities/microgalaxy/lab/tools/top/UseGalaxy_org_au.yaml @@ -212,6 +212,9 @@ tools: - name: obi_clean owner: iuc tool_panel_section_id: '' +- name: obi_complement + owner: iuc + tool_panel_section_id: '' - name: obi_convert owner: iuc tool_panel_section_id: '' @@ -224,6 +227,18 @@ tools: - name: obi_pairing owner: iuc tool_panel_section_id: '' +- name: obi_pcr + owner: iuc + tool_panel_section_id: '' +- name: obi_refidx + owner: iuc + tool_panel_section_id: '' +- name: obi_tag + owner: iuc + tool_panel_section_id: '' +- name: obi_taxonomy + owner: iuc + tool_panel_section_id: '' - name: obi_uniq owner: iuc tool_panel_section_id: '' @@ -668,355 +683,307 @@ tools: - name: phyloseq_tax_glom owner: iuc tool_panel_section_id: '' -- name: qiime2__rescript__cull_seqs - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__degap_seqs - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__dereplicate - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__edit_taxonomy - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_classifications - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_cross_validate - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_fit_classifier - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_seqs - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_taxonomy - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__extract_seq_segments - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__filter_seqs_length - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__filter_seqs_length_by_taxon - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__filter_taxa - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__get_bv_brc_genome_features - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__get_bv_brc_genomes - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__get_bv_brc_metadata - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__get_eukaryome_data - owner: q2d2 +- name: prinseq + owner: iuc tool_panel_section_id: '' -- name: qiime2__rescript__get_gtdb_data +- name: qiime2__dada2__denoise_ccs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_midori2_data +- name: qiime2__dada2__denoise_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_ncbi_data +- name: qiime2__dada2__denoise_pyro owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_ncbi_data_protein +- name: qiime2__dada2__denoise_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_ncbi_genomes +- name: qiime2__dada2__plot_base_transitions owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_pr2_data +- name: qiime2__composition__add_pseudocount owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_silva_data +- name: qiime2__composition__ancom owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_unite_data +- name: qiime2__composition__ancombc owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__merge_taxa +- name: qiime2__composition__ancombc2 owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__orient_reads +- name: qiime2__composition__ancombc2_visualizer owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__orient_seqs +- name: qiime2__composition__da_barplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__parse_silva_taxonomy +- name: qiime2__composition__tabulate owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__reverse_transcribe +- name: qiime2__boots__alpha owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__subsample_fasta +- name: qiime2__boots__alpha_average owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__trim_alignment +- name: qiime2__boots__alpha_collection owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__distance_matrix +- name: qiime2__boots__beta owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__merge +- name: qiime2__boots__beta_average owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__shuffle_groups +- name: qiime2__boots__beta_collection owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__tabulate +- name: qiime2__boots__core_metrics owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__alpha_group_significance +- name: qiime2__boots__kmer_diversity owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__collate_stats +- name: qiime2__boots__resample owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__facet_across +- name: qiime2__demux__emp_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__facet_within +- name: qiime2__demux__emp_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__mann_whitney_u +- name: qiime2__demux__filter_samples owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__mann_whitney_u_facet +- name: qiime2__demux__partition_samples_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__plot_rainclouds +- name: qiime2__demux__partition_samples_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__prep_alpha_distribution +- name: qiime2__demux__subsample_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__wilcoxon_srt +- name: qiime2__demux__subsample_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__wilcoxon_srt_facet +- name: qiime2__demux__summarize owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__bowtie2_build +- name: qiime2__demux__tabulate_read_counts owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__decontam_identify +- name: qiime2__diversity__adonis owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__decontam_identify_batches +- name: qiime2__diversity__alpha owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__decontam_score_viz +- name: qiime2__diversity__alpha_correlation owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__evaluate_composition +- name: qiime2__diversity__alpha_group_significance owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__evaluate_seqs +- name: qiime2__diversity__alpha_phylogenetic owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__evaluate_taxonomy +- name: qiime2__diversity__alpha_rarefaction owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__exclude_seqs +- name: qiime2__diversity__beta owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__filter_reads +- name: qiime2__diversity__beta_correlation owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vizard__boxplot +- name: qiime2__diversity__beta_group_significance owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vizard__heatmap +- name: qiime2__diversity__beta_phylogenetic owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vizard__lineplot +- name: qiime2__diversity__beta_rarefaction owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vizard__scatterplot_2d +- name: qiime2__diversity__bioenv owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__adonis +- name: qiime2__diversity__core_metrics owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha +- name: qiime2__diversity__core_metrics_phylogenetic owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_correlation +- name: qiime2__diversity__filter_alpha_diversity owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_group_significance +- name: qiime2__diversity__filter_distance_matrix owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_phylogenetic +- name: qiime2__diversity__mantel owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_rarefaction +- name: qiime2__diversity__partial_procrustes owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta +- name: qiime2__diversity__pcoa owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_correlation +- name: qiime2__diversity__pcoa_biplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_group_significance +- name: qiime2__diversity__procrustes_analysis owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_phylogenetic +- name: qiime2__diversity__tsne owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_rarefaction +- name: qiime2__diversity__umap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__bioenv +- name: qiime2__taxa__barplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__core_metrics +- name: qiime2__taxa__barplot2 owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__core_metrics_phylogenetic +- name: qiime2__taxa__collapse owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__filter_alpha_diversity +- name: qiime2__taxa__filter_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__filter_distance_matrix +- name: qiime2__taxa__filter_table owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__mantel +- name: qiime2__stats__alpha_group_significance owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__partial_procrustes +- name: qiime2__stats__collate_stats owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__pcoa +- name: qiime2__stats__facet_across owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__pcoa_biplot +- name: qiime2__stats__facet_within owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__procrustes_analysis +- name: qiime2__stats__mann_whitney_u owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__tsne +- name: qiime2__stats__mann_whitney_u_facet owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__umap +- name: qiime2__stats__plot_rainclouds owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__emp_paired +- name: qiime2__stats__prep_alpha_distribution owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__emp_single +- name: qiime2__stats__wilcoxon_srt owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__filter_samples +- name: qiime2__stats__wilcoxon_srt_facet owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__partition_samples_paired +- name: qiime2__rescript__cull_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__partition_samples_single +- name: qiime2__rescript__degap_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__subsample_paired +- name: qiime2__rescript__dereplicate owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__subsample_single +- name: qiime2__rescript__edit_taxonomy owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__summarize +- name: qiime2__rescript__evaluate_classifications owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__tabulate_read_counts +- name: qiime2__rescript__evaluate_cross_validate owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_ccs +- name: qiime2__rescript__evaluate_fit_classifier owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_paired +- name: qiime2__rescript__evaluate_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_pyro +- name: qiime2__rescript__evaluate_taxonomy owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_single +- name: qiime2__rescript__extract_seq_segments owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__plot_base_transitions +- name: qiime2__rescript__filter_seqs_length owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__add_pseudocount +- name: qiime2__rescript__filter_seqs_length_by_taxon owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancom +- name: qiime2__rescript__filter_taxa owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancombc +- name: qiime2__rescript__get_bv_brc_genome_features owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancombc2 +- name: qiime2__rescript__get_bv_brc_genomes owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancombc2_visualizer +- name: qiime2__rescript__get_bv_brc_metadata owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__da_barplot +- name: qiime2__rescript__get_eukaryome_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__tabulate +- name: qiime2__rescript__get_gtdb_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__barplot +- name: qiime2__rescript__get_midori2_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__barplot2 +- name: qiime2__rescript__get_ncbi_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__collapse +- name: qiime2__rescript__get_ncbi_data_protein owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__filter_seqs +- name: qiime2__rescript__get_ncbi_genomes owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__filter_table +- name: qiime2__rescript__get_pr2_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__alpha +- name: qiime2__rescript__get_silva_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__alpha_average +- name: qiime2__rescript__get_unite_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__alpha_collection +- name: qiime2__rescript__merge_taxa owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__beta +- name: qiime2__rescript__orient_reads owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__beta_average +- name: qiime2__rescript__orient_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__beta_collection +- name: qiime2__rescript__parse_silva_taxonomy owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__core_metrics +- name: qiime2__rescript__reverse_transcribe owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__kmer_diversity +- name: qiime2__rescript__subsample_fasta owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__resample +- name: qiime2__rescript__trim_alignment owner: q2d2 tool_panel_section_id: '' - name: qiime2__feature_classifier__blast @@ -1121,6 +1088,51 @@ tools: - name: qiime2__feature_table__transpose owner: q2d2 tool_panel_section_id: '' +- name: qiime2__quality_control__bowtie2_build + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__quality_control__decontam_identify + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__quality_control__decontam_identify_batches + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__quality_control__decontam_score_viz + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__quality_control__evaluate_composition + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__quality_control__evaluate_seqs + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__quality_control__evaluate_taxonomy + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__quality_control__exclude_seqs + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__quality_control__filter_reads + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__metadata__distance_matrix + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__metadata__merge + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__metadata__shuffle_groups + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__metadata__tabulate + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__kmerizer__core_metrics + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__kmerizer__seqs_to_kmers + owner: q2d2 + tool_panel_section_id: '' - name: qiime2__fondue___get_sequences owner: q2d2 tool_panel_section_id: '' @@ -1145,12 +1157,6 @@ tools: - name: qiime2__fondue__scrape_collection owner: q2d2 tool_panel_section_id: '' -- name: qiime2__kmerizer__core_metrics - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__kmerizer__seqs_to_kmers - owner: q2d2 - tool_panel_section_id: '' - name: seqkit_fx2tab owner: iuc tool_panel_section_id: '' diff --git a/communities/microgalaxy/lab/tools/top/Viral_Variant_Visualizer_VVV.yaml b/communities/microgalaxy/lab/tools/top/Viral_Variant_Visualizer_VVV.yaml index 4cce6ac18..209a18299 100644 --- a/communities/microgalaxy/lab/tools/top/Viral_Variant_Visualizer_VVV.yaml +++ b/communities/microgalaxy/lab/tools/top/Viral_Variant_Visualizer_VVV.yaml @@ -773,6 +773,9 @@ tools: - name: obi_clean owner: iuc tool_panel_section_id: '' +- name: obi_complement + owner: iuc + tool_panel_section_id: '' - name: obi_convert owner: iuc tool_panel_section_id: '' @@ -785,6 +788,18 @@ tools: - name: obi_pairing owner: iuc tool_panel_section_id: '' +- name: obi_pcr + owner: iuc + tool_panel_section_id: '' +- name: obi_refidx + owner: iuc + tool_panel_section_id: '' +- name: obi_tag + owner: iuc + tool_panel_section_id: '' +- name: obi_taxonomy + owner: iuc + tool_panel_section_id: '' - name: obi_uniq owner: iuc tool_panel_section_id: '' @@ -1262,6 +1277,9 @@ tools: - name: picrust_predict_metagenomes owner: iuc tool_panel_section_id: '' +- name: prinseq + owner: iuc + tool_panel_section_id: '' - name: prodigal owner: iuc tool_panel_section_id: '' @@ -1274,262 +1292,241 @@ tools: - name: pygenomeTracks owner: iuc tool_panel_section_id: '' -- name: qiime2_core__tools__export - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2_core__tools__import - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2_core__tools__import_fastq - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__quality_filter__q_score - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__cull_seqs - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__degap_seqs - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__dereplicate - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__rescript__edit_taxonomy +- name: qiime2__dada2__denoise_ccs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_classifications +- name: qiime2__dada2__denoise_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_cross_validate +- name: qiime2__dada2__denoise_pyro owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_fit_classifier +- name: qiime2__dada2__denoise_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_seqs +- name: qiime2__dada2__plot_base_transitions owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__evaluate_taxonomy +- name: qiime2__cutadapt__demux_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__extract_seq_segments +- name: qiime2__cutadapt__demux_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__filter_seqs_length +- name: qiime2__cutadapt__trim_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__filter_seqs_length_by_taxon +- name: qiime2__cutadapt__trim_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__filter_taxa +- name: qiime2__composition__add_pseudocount owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_bv_brc_genome_features +- name: qiime2__composition__ancom owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_bv_brc_genomes +- name: qiime2__composition__ancombc owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_bv_brc_metadata +- name: qiime2__composition__ancombc2 owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_eukaryome_data +- name: qiime2__composition__ancombc2_visualizer owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_gtdb_data +- name: qiime2__composition__da_barplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_midori2_data +- name: qiime2__composition__tabulate owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_ncbi_data +- name: qiime2__boots__alpha owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_ncbi_data_protein +- name: qiime2__boots__alpha_average owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_ncbi_genomes +- name: qiime2__boots__alpha_collection owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_pr2_data +- name: qiime2__boots__beta owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_silva_data +- name: qiime2__boots__beta_average owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__get_unite_data +- name: qiime2__boots__beta_collection owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__merge_taxa +- name: qiime2__boots__core_metrics owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__orient_reads +- name: qiime2__boots__kmer_diversity owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__orient_seqs +- name: qiime2__boots__resample owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__parse_silva_taxonomy +- name: qiime2__vsearch__cluster_features_closed_reference owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__reverse_transcribe +- name: qiime2__vsearch__cluster_features_de_novo owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__subsample_fasta +- name: qiime2__vsearch__cluster_features_open_reference owner: q2d2 tool_panel_section_id: '' -- name: qiime2__rescript__trim_alignment +- name: qiime2__vsearch__dereplicate_sequences owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__classify_samples +- name: qiime2__vsearch__fastq_stats owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__classify_samples_from_dist +- name: qiime2__vsearch__merge_pairs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__classify_samples_ncv +- name: qiime2__vsearch__uchime_denovo owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__confusion_matrix +- name: qiime2__vsearch__uchime_ref owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__fit_classifier +- name: qiime2__demux__emp_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__fit_regressor +- name: qiime2__demux__emp_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__heatmap +- name: qiime2__demux__filter_samples owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__metatable +- name: qiime2__demux__partition_samples_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__predict_classification +- name: qiime2__demux__partition_samples_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__predict_regression +- name: qiime2__demux__subsample_paired owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__regress_samples +- name: qiime2__demux__subsample_single owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__regress_samples_ncv +- name: qiime2__demux__summarize owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__scatterplot +- name: qiime2__demux__tabulate_read_counts owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__split_table +- name: qiime2__deblur__denoise_16S owner: q2d2 tool_panel_section_id: '' -- name: qiime2__sample_classifier__summarize +- name: qiime2__deblur__denoise_other owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__align_to_tree_mafft_fasttree +- name: qiime2__deblur__visualize_stats owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__align_to_tree_mafft_iqtree +- name: qiime2__diversity__adonis owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__align_to_tree_mafft_raxml +- name: qiime2__diversity__alpha owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__fasttree +- name: qiime2__diversity__alpha_correlation owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__filter_table +- name: qiime2__diversity__alpha_group_significance owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__filter_tree +- name: qiime2__diversity__alpha_phylogenetic owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__iqtree +- name: qiime2__diversity__alpha_rarefaction owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__iqtree_ultrafast_bootstrap +- name: qiime2__diversity__beta owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__midpoint_root +- name: qiime2__diversity__beta_correlation owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__raxml +- name: qiime2__diversity__beta_group_significance owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__raxml_rapid_bootstrap +- name: qiime2__diversity__beta_phylogenetic owner: q2d2 tool_panel_section_id: '' -- name: qiime2__phylogeny__robinson_foulds +- name: qiime2__diversity__beta_rarefaction owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__distance_matrix +- name: qiime2__diversity__bioenv owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__merge +- name: qiime2__diversity__core_metrics owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__shuffle_groups +- name: qiime2__diversity__core_metrics_phylogenetic owner: q2d2 tool_panel_section_id: '' -- name: qiime2__metadata__tabulate +- name: qiime2__diversity__filter_alpha_diversity owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__alpha_group_significance +- name: qiime2__diversity__filter_distance_matrix owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__collate_stats +- name: qiime2__diversity__mantel owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__facet_across +- name: qiime2__diversity__partial_procrustes owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__facet_within +- name: qiime2__diversity__pcoa owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__mann_whitney_u +- name: qiime2__diversity__pcoa_biplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__mann_whitney_u_facet +- name: qiime2__diversity__procrustes_analysis owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__plot_rainclouds +- name: qiime2__diversity__tsne owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__prep_alpha_distribution +- name: qiime2__diversity__umap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__wilcoxon_srt +- name: qiime2__emperor__biplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__stats__wilcoxon_srt_facet +- name: qiime2__emperor__plot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__bowtie2_build +- name: qiime2__emperor__procrustes_plot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__decontam_identify +- name: qiime2_core__tools__export owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__decontam_identify_batches +- name: qiime2_core__tools__import owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__decontam_score_viz +- name: qiime2_core__tools__import_fastq owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__evaluate_composition +- name: qiime2__taxa__barplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__evaluate_seqs +- name: qiime2__taxa__barplot2 owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__evaluate_taxonomy +- name: qiime2__taxa__collapse owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__exclude_seqs +- name: qiime2__taxa__filter_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__quality_control__filter_reads +- name: qiime2__taxa__filter_table owner: q2d2 tool_panel_section_id: '' - name: qiime2__diversity_lib__alpha_passthrough @@ -1568,253 +1565,244 @@ tools: - name: qiime2__diversity_lib__weighted_unifrac owner: q2d2 tool_panel_section_id: '' -- name: qiime2__alignment__mafft - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__alignment__mafft_add - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__alignment__mask - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__vizard__boxplot +- name: qiime2__stats__alpha_group_significance owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vizard__heatmap +- name: qiime2__stats__collate_stats owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vizard__lineplot +- name: qiime2__stats__facet_across owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vizard__scatterplot_2d +- name: qiime2__stats__facet_within owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__adonis +- name: qiime2__stats__mann_whitney_u owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha +- name: qiime2__stats__mann_whitney_u_facet owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_correlation +- name: qiime2__stats__plot_rainclouds owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_group_significance +- name: qiime2__stats__prep_alpha_distribution owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_phylogenetic +- name: qiime2__stats__wilcoxon_srt owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__alpha_rarefaction +- name: qiime2__stats__wilcoxon_srt_facet owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta +- name: qiime2__sample_classifier__classify_samples owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_correlation +- name: qiime2__sample_classifier__classify_samples_from_dist owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_group_significance +- name: qiime2__sample_classifier__classify_samples_ncv owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_phylogenetic +- name: qiime2__sample_classifier__confusion_matrix owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__beta_rarefaction +- name: qiime2__sample_classifier__fit_classifier owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__bioenv +- name: qiime2__sample_classifier__fit_regressor owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__core_metrics +- name: qiime2__sample_classifier__heatmap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__core_metrics_phylogenetic +- name: qiime2__sample_classifier__metatable owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__filter_alpha_diversity +- name: qiime2__sample_classifier__predict_classification owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__filter_distance_matrix +- name: qiime2__sample_classifier__predict_regression owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__mantel +- name: qiime2__sample_classifier__regress_samples owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__partial_procrustes +- name: qiime2__sample_classifier__regress_samples_ncv owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__pcoa +- name: qiime2__sample_classifier__scatterplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__pcoa_biplot +- name: qiime2__sample_classifier__split_table owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__procrustes_analysis +- name: qiime2__sample_classifier__summarize owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__tsne +- name: qiime2__rescript__cull_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__diversity__umap +- name: qiime2__rescript__degap_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__emp_paired +- name: qiime2__rescript__dereplicate owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__emp_single +- name: qiime2__rescript__edit_taxonomy owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__filter_samples +- name: qiime2__rescript__evaluate_classifications owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__partition_samples_paired +- name: qiime2__rescript__evaluate_cross_validate owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__partition_samples_single +- name: qiime2__rescript__evaluate_fit_classifier owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__subsample_paired +- name: qiime2__rescript__evaluate_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__subsample_single +- name: qiime2__rescript__evaluate_taxonomy owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__summarize +- name: qiime2__rescript__extract_seq_segments owner: q2d2 tool_panel_section_id: '' -- name: qiime2__demux__tabulate_read_counts +- name: qiime2__rescript__filter_seqs_length owner: q2d2 tool_panel_section_id: '' -- name: qiime2__deblur__denoise_16S +- name: qiime2__rescript__filter_seqs_length_by_taxon owner: q2d2 tool_panel_section_id: '' -- name: qiime2__deblur__denoise_other +- name: qiime2__rescript__filter_taxa owner: q2d2 tool_panel_section_id: '' -- name: qiime2__deblur__visualize_stats +- name: qiime2__rescript__get_bv_brc_genome_features owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_ccs +- name: qiime2__rescript__get_bv_brc_genomes owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_paired +- name: qiime2__rescript__get_bv_brc_metadata owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_pyro +- name: qiime2__rescript__get_eukaryome_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__denoise_single +- name: qiime2__rescript__get_gtdb_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__dada2__plot_base_transitions +- name: qiime2__rescript__get_midori2_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__cutadapt__demux_paired +- name: qiime2__rescript__get_ncbi_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__cutadapt__demux_single +- name: qiime2__rescript__get_ncbi_data_protein owner: q2d2 tool_panel_section_id: '' -- name: qiime2__cutadapt__trim_paired +- name: qiime2__rescript__get_ncbi_genomes owner: q2d2 tool_panel_section_id: '' -- name: qiime2__cutadapt__trim_single +- name: qiime2__rescript__get_pr2_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__add_pseudocount +- name: qiime2__rescript__get_silva_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancom +- name: qiime2__rescript__get_unite_data owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancombc +- name: qiime2__rescript__merge_taxa owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancombc2 +- name: qiime2__rescript__orient_reads owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__ancombc2_visualizer +- name: qiime2__rescript__orient_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__da_barplot +- name: qiime2__rescript__parse_silva_taxonomy owner: q2d2 tool_panel_section_id: '' -- name: qiime2__composition__tabulate +- name: qiime2__rescript__reverse_transcribe owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__barplot +- name: qiime2__rescript__subsample_fasta owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__barplot2 +- name: qiime2__rescript__trim_alignment owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__collapse +- name: qiime2__quality_filter__q_score owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__filter_seqs +- name: qiime2__vizard__boxplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__taxa__filter_table +- name: qiime2__vizard__heatmap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__alpha +- name: qiime2__vizard__lineplot owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__alpha_average +- name: qiime2__vizard__scatterplot_2d owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__alpha_collection +- name: qiime2__alignment__mafft owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__beta +- name: qiime2__alignment__mafft_add owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__beta_average +- name: qiime2__alignment__mask owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__beta_collection +- name: qiime2__phylogeny__align_to_tree_mafft_fasttree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__core_metrics +- name: qiime2__phylogeny__align_to_tree_mafft_iqtree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__kmer_diversity +- name: qiime2__phylogeny__align_to_tree_mafft_raxml owner: q2d2 tool_panel_section_id: '' -- name: qiime2__boots__resample +- name: qiime2__phylogeny__fasttree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__cluster_features_closed_reference +- name: qiime2__phylogeny__filter_table owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__cluster_features_de_novo +- name: qiime2__phylogeny__filter_tree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__cluster_features_open_reference +- name: qiime2__phylogeny__iqtree owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__dereplicate_sequences +- name: qiime2__phylogeny__iqtree_ultrafast_bootstrap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__fastq_stats +- name: qiime2__phylogeny__midpoint_root owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__merge_pairs +- name: qiime2__phylogeny__raxml owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__uchime_denovo +- name: qiime2__phylogeny__raxml_rapid_bootstrap owner: q2d2 tool_panel_section_id: '' -- name: qiime2__vsearch__uchime_ref +- name: qiime2__phylogeny__robinson_foulds owner: q2d2 tool_panel_section_id: '' -- name: qiime2__emperor__biplot +- name: qiime2__fragment_insertion__classify_otus_experimental owner: q2d2 tool_panel_section_id: '' -- name: qiime2__emperor__plot +- name: qiime2__fragment_insertion__filter_features owner: q2d2 tool_panel_section_id: '' -- name: qiime2__emperor__procrustes_plot +- name: qiime2__fragment_insertion__sepp owner: q2d2 tool_panel_section_id: '' - name: qiime2__feature_classifier__blast @@ -1850,6 +1838,39 @@ tools: - name: qiime2__feature_classifier__vsearch_global owner: q2d2 tool_panel_section_id: '' +- name: qiime2__longitudinal__anova + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__feature_volatility + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__first_differences + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__first_distances + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__linear_mixed_effects + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__maturity_index + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__nmit + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__pairwise_differences + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__pairwise_distances + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__plot_feature_volatility + owner: q2d2 + tool_panel_section_id: '' +- name: qiime2__longitudinal__volatility + owner: q2d2 + tool_panel_section_id: '' - name: qiime2__feature_table___summarize owner: q2d2 tool_panel_section_id: '' @@ -1919,76 +1940,73 @@ tools: - name: qiime2__feature_table__transpose owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue___get_sequences - owner: q2d2 - tool_panel_section_id: '' -- name: qiime2__fondue__combine_seqs +- name: qiime2__quality_control__bowtie2_build owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__get_all +- name: qiime2__quality_control__decontam_identify owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__get_ids_from_query +- name: qiime2__quality_control__decontam_identify_batches owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__get_metadata +- name: qiime2__quality_control__decontam_score_viz owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__get_sequences +- name: qiime2__quality_control__evaluate_composition owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__merge_metadata +- name: qiime2__quality_control__evaluate_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fondue__scrape_collection +- name: qiime2__quality_control__evaluate_taxonomy owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fragment_insertion__classify_otus_experimental +- name: qiime2__quality_control__exclude_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fragment_insertion__filter_features +- name: qiime2__quality_control__filter_reads owner: q2d2 tool_panel_section_id: '' -- name: qiime2__fragment_insertion__sepp +- name: qiime2__metadata__distance_matrix owner: q2d2 tool_panel_section_id: '' -- name: qiime2__kmerizer__core_metrics +- name: qiime2__metadata__merge owner: q2d2 tool_panel_section_id: '' -- name: qiime2__kmerizer__seqs_to_kmers +- name: qiime2__metadata__shuffle_groups owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__anova +- name: qiime2__metadata__tabulate owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__feature_volatility +- name: qiime2__kmerizer__core_metrics owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__first_differences +- name: qiime2__kmerizer__seqs_to_kmers owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__first_distances +- name: qiime2__fondue___get_sequences owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__linear_mixed_effects +- name: qiime2__fondue__combine_seqs owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__maturity_index +- name: qiime2__fondue__get_all owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__nmit +- name: qiime2__fondue__get_ids_from_query owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__pairwise_differences +- name: qiime2__fondue__get_metadata owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__pairwise_distances +- name: qiime2__fondue__get_sequences owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__plot_feature_volatility +- name: qiime2__fondue__merge_metadata owner: q2d2 tool_panel_section_id: '' -- name: qiime2__longitudinal__volatility +- name: qiime2__fondue__scrape_collection owner: q2d2 tool_panel_section_id: '' - name: qualimap_bamqc diff --git a/communities/microgalaxy/metadata/tool_status.tsv b/communities/microgalaxy/metadata/tool_status.tsv index 9080d6fc4..9a7200f19 100644 --- a/communities/microgalaxy/metadata/tool_status.tsv +++ b/communities/microgalaxy/metadata/tool_status.tsv @@ -59,7 +59,9 @@ baseline_toxicity_calculator mbernt Toxicity prediction using QSAR models False bax2bam iuc BAX to BAM converter False False bayescan iuc Detecting natural selection from population-based genetic data True False bbtools iuc BBTools is a suite of fast, multithreaded bioinformatics tools designed for analysis of DNA and RNA sequence data.BBTools can handle common sequencing file formats such as fastq, fasta, sam, scarf, fasta+qual, compressed or raw,with autodetection of quality encoding and interleaving. It is written in Java and works on any platform supportingJava, including Linux, MacOS, and Microsoft Windows and Linux; there are no dependencies other than Java (version7 or higher). Program descriptions and options are shown when running the shell scripts with no parameters. True False +bcftools_sort greg Contains a tool that sorts VCF/BCF files bctools iuc bctools is a set of tools for handling barcodes and UMIs in NGS data.bctools can be used to merge PCR duplicates according to unique molecular barcodes (UMIs),to extract barcodes from arbitrary positions relative to the read starts,to clean up readthroughs into UMIs with paired-end sequencing andhandles binary barcodes as used with uvCLAP and FLASH.License: Apache License 2.0 False False +bdei_infer pasteur Tools for fast and accurate maximum likelihood estimation of Birth-Death Exposed-Infectious (BDEI) epidemiological model parameters from phylogenetic trees. bed_to_protein_map galaxyp Converts a BED file to a tabular list of exon locations False False bellerophon iuc Filter mapped reads where the mapping spans a junction, retaining the 5-prime read. False False best_regression_subsets devteam Perform Best-subsets Regression False False @@ -76,6 +78,7 @@ biohansel nml Heidelberg and Enteritidis SNP Elucidation True False bioinformatics_cafe mbernt Miscellanea of scripts for bioinformatics False False biomformat iuc The biom-format package provides a command line interface and Python API for working with BIOM files. True False bionano bgruening Bionano Solve is a set of tools for analyzing Bionano data False False +biosigner workflow4metabolomics [W4M][Metabolomics][LC-MS][GC-MS][NMR] Discovery of significant signatures from omics data. biotradis iuc Bio-Tradis is a tool suite dedicated to essentiality analyses with TraDis data. True False biscot iuc Bionano scaffolding correction tool False False bismark bgruening A tool to map bisulfite converted sequence reads and determine cytosine methylation states False False @@ -93,6 +96,7 @@ blat_mapping devteam Coverage of the Reads in wiggle format False False blobtoolkit bgruening Identification and isolation non-target data in draft and publicly available genome assemblies. False False blockbuster rnateam Blockbuster detects blocks of overlapping reads using a gaussian-distribution approach. False False blockclust rnateam BlockClust detects transcripts with similar processing patterns. False False +bmge fmareuil ngphylogeny version of BMGE (Block Mapping and Gathering with Entropy): Selection of phylogenetic informative regions. bmtagger iuc remove contaminant reads True False bp_genbank2gff3 iuc Converts GenBank format files to GFF3 False False bracken iuc Bayesian Reestimation of Abundance with KrakEN True False @@ -106,15 +110,24 @@ bwameth iuc Fast and accurate alignment of BS-seq reads False False cactus galaxy-australia Cactus is a reference-free whole-genome multiple alignment program False False calculate_contrast_threshold iuc Calculates a contrast threshold from the CDT file generated by ``tag_pileup_frequency``. The calculated values are then used to set a uniform contrast for all the heatmaps generated downstream. False False calisp galaxyp Calgary approach to isotopes in proteomics False False +call_insertions greg Extracts aligned regions of 2 genomes and produces reference alignment and genome alignment BED files cami_amber iuc Evaluation package for the comparative assessment of genome reconstructions and taxonomic assignments True False canu bgruening Canu is a hierarchical assembly pipeline designed for high-noise single-molecule sequencing (such as the PacBio RS II/Sequel or Oxford Nanopore MinION). True False cap3 artbio cap3 wrapper False False cardinal galaxyp Statistical and computational tools for analyzing mass spectrometry imaging datasets False False cawlign iuc Codon-aware alignment of sequences to a reference. True False ccds_download_era5_af ecology Copernicus CDS Downloader for AquaINFRA marine model False False +ccqtl rplanel Set of scripts for mapping quantitative trait loci in experimental crosses using r-qtl2 cd_hit iuc Cluster or compare biological sequence datasets True False cd_hit_dup devteam simple tool for removing duplicates from sequencing reads True False cemitool iuc Gene co-expression network analysis tool True False +cfsan_snp_pipeline_call_consensus_snps greg Call the consensus base for a sample at the specified positions where high- confidence SNPs were previously called in any of the samples. +cfsan_snp_pipeline_call_sites greg Find the sites with high-confidence SNPs in a sample. +cfsan_snp_pipeline_filter_snp_regions greg Remove abnormally dense SNPs from the input VCF file, save the reserved SNPs into a new VCF file, and save the removed SNPs into another VCF file. +cfsan_snp_pipeline_map_reads greg Align the sequence reads for a specified sample to a specified reference genome +cfsan_snp_pipeline_merge_vcfs greg Merge the consensus vcf files from all samples into a single multi-vcf file. +cfsan_snp_pipeline_quast_select greg Selects the best assembly from a collection of assemblies and a combined QUAST report +cfsan_snp_pipeline_snp_matrix greg Create the SNP matrix containing the consensus base for each of the samples at the positions where high-confidence SNPs were found in any of the samples. champ_blocs ecology Compute indicators for turnover boulders fields False False charts iuc Enables advanced visualization options in Galaxy Charts False False checkm iuc Assess the quality of microbial genomes recovered from isolates, single cells, and metagenomes True False @@ -135,6 +148,7 @@ clair3 iuc Symphonizing pileup and full-alignment for high-performance long-read clc_assembly_cell peterjc Galaxy wrapper for the CLC Assembly Cell suite from CLCBio False False climate_stripes climate Create climate stripes from a tabular input file False False clinod peterjc NoD: a Nucleolar localization sequence detector for eukaryotic and viral proteins True False +clustalo fmareuil ngphylogeny version of Clustal Omega wrapper. clustalw devteam ClustalW multiple sequence alignment program for DNA or proteins True False cmems_download_ic_bc ecology Copernicus CMEMS Downloader for AquaINFRA marine model False False cmsearch_deoverlap rnateam removes lower scoring overlaps from cmsearch results. False False @@ -157,6 +171,7 @@ compleasm iuc Compleasm: a faster and more accurate reimplementation of BUSCO Tr compute_motif_frequencies_for_all_motifs devteam Compute Motif Frequencies For All Motifs, motif by motif. False False compute_motifs_frequency devteam Compute Motif Frequencies in indel flanking regions. False False concoct iuc CONCOCT (Clustering cONtigs with COverage and ComposiTion) does unsupervised binning of metagenomic contigs byusing nucleotide composition - kmer frequencies - and coverage data for multiple samples. CONCOCT can accurately(up to species level) bin metagenomic contigs. True False +conjscan odoppelt Wrapper for the MacSyFinder tool: ConjScan. consalign ecology Tool to compute a consensus sequence from several aligned fasta sequences False False consolidate_vcfs nml Combines freebayes and mpileup files for use by vcf2snvalignment False False constava iuc Calculate 'conformational states probabilities' and 'conformational state variability' from a protein structure ensemble False False @@ -181,6 +196,7 @@ custom_pro_db_annotation_data_manager galaxyp CustomProDB Annotation False False cutadapt lparsons Flexible tool to remove adapter sequences (and quality trim) high throughput sequencing reads (fasta/fastq). True False dada2 iuc DADA2 wrappers True False das_tool iuc DAS Tool for genome resolved metagenomics True False +dashing2 iuc k-mer based tool for sketching and comparison of genomic sequences data_exploration ecology Explore data through multiple statistical tools False False data_manager_eggnog_mapper galaxyp downloads eggnog data for eggnog-mapper False False data_manager_eggnog_mapper_abspath galaxyp download eggnog data for eggnog-mapper False False @@ -190,6 +206,7 @@ decontam iuc Removes decontamination features (ASVs/OTUs) using control samples decoyfasta galaxyp Galaxy tool wrapper for the transproteomic pipeline decoyFASTA tool. False False deeparg iuc A deep learning based approach to predict Antibiotic Resistance Genes (ARGs) from metagenomes True False deepsig iuc Predictor of signal peptides in proteins based on deep learning False False +defense_finder rplanel DefenseFinder is a program to systematically detect known anti-phage systems. delete_overlapping_indels devteam Delete Overlapping Indels from a chromosome indels file False False deseq2 iuc Differential gene expression analysis based on the negative binomial distribution True False detect_circular_sequences Detect circular sequences (e.g. circular contigs) in a FASTA file @@ -210,11 +227,15 @@ dot2ct rnateam Dot-Bracket to Connect Table (CT) False False dotknot bgruening DotKnot is a heuristic method for pseudoknot prediction in a given RNA sequence False False dotprep bgruening Apply unique anchor filtering to delta files and prepare Dot coordinates False False dram iuc DRAM for distilling microbial metabolism to automate the curation of microbiome function True False +draw_amr_matrix greg Accepts a collection of best AMR feature hits, an optional AMR deletions BED file, an optional AMR mutations TSV file and a AMR gene drug mappings file and draws an AMR matrix. +draw_circos greg Renders circos plots of the PIMA assembly versus the reference alignemnt. +draw_features greg Plots contigs and features of high-quality annotated assemblies drep iuc dRep compares and dereplicates genome sets True False drhip iuc Data Reduction for HyPhy with Inference Processing. A toolkit for analyzing and summarizing HyPhy evolutionary selection analysis results False False droplet_barcode_plot ebi-gxa Make a cell barcode plot for droplet single-cell RNA-seq QC False False dropletutils iuc DropletUtils - Utilities for handling droplet-based single-cell RNA-seq data False False earth ecology Access, process, visualise oceanographic data for the Earth System False False +eastr iuc EASTR detects and removes spuriously spliced alignments from RNA-seq data ecoregionalization ecology Tools to compute ecoregionalization with BRT model predictions and clustering. False False ectyper nml EC-Typer - in silico serotyping of Escherichia coli species True False edger iuc Perform RNA-Seq differential expression analysis using edgeR pipeline False False @@ -250,6 +271,7 @@ fasta_stats iuc Display summary statistics for a fasta file. False False fastani iuc Fast alignment-free computation of whole-genome Average Nucleotide Identity True False fastg2protlib galaxyp Generate FASTA from FASTG False False fastk iuc FastK: A K-mer counter (for HQ assembly data sets) True False +fastme fmareuil ngphylogeny version of Distance-based inference of phylogenetic trees. fastoma iuc FastOMA is a scalable tool for orthology inference among many genomes. True False fastp iuc Fast all-in-one preprocessing for FASTQ files True False fastplong iuc Fastplong is used for ultrafast preprocessing and quality control for long reads (Nanopore, PacBio, Cyclone, etc.). True False @@ -262,6 +284,7 @@ fastqc_stats nml Summary multiple FastQC into a single tabular line report False fastqe iuc FASTQE True False fastreer iuc fastreeR toolkit wrappers for phylogenetic trees and distance matrices from VCF and FASTA True False fastspar iuc Tool for rapid and scalable correlation estimation for compositional data. True False +fasttree fmareuil ngphylogeny version of Wrapper for the Fasttree: FastTree fasttree iuc FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences - GVL True False feature_alignment galaxyp TRIC integrates information from all available runs via a graph-based alignment strategy False False featurecounter devteam Feature coverage False False @@ -271,6 +294,7 @@ feht nml Automatically identify makers predictive of groups. False False fermikit iuc FermiKit is a de novo assembly based variant calling pipeline for deep Illumina resequencing data. False False fgsea iuc Perform gene set testing using fgsea False False filter_by_fasta_ids galaxyp Filter FASTA on the headers and/or the sequences False False +filter_contigs greg Filters contigs from an assembled fasta file that are longer than the specified length filter_density nml Filter out position based on distance between SNVs False False filter_spades_repeats nml Remove short and repeat contigs/scaffolds True False filter_stats nml SNVPhyl filter_stats False False @@ -283,6 +307,7 @@ fishertest artbio Fisher's exact test on two-column hit lists. False False flair iuc FLAIR (Full-Length Alternative Isoform analysis of RNA) for the correction, isoform definition, and alternative splicing analysis of noisy reads. False False flash iuc Fast Length Adjustment of SHort reads False False flashlfq galaxyp FlashLFQ mass-spectrometry proteomics label-free quantification True False +flavotyper iuc In silico serotyping of Flavobacterium psychrophilum from genome assemblies flye bgruening Assembly of long and error-prone reads. True False format_metaphlan2_output bebatut Format MetaPhlAn2 output to extract abundance at different taxonomic levels True False fraggenescan iuc Tool for finding (fragmented) genes in short read True False @@ -297,6 +322,7 @@ fur iuc Find unique genomic regions from target and neighbor genomes gafa earlhaminst Gene Align and Family Aggregator False False gamma iuc Gene Allele Mutation Microbial Assessment True False gatk4 iuc Genome Analysis Toolkit (GATK4) wrappers False False +gblocks fmareuil ngphylogeny version of Gblocks: automatic cleaning of alignments. gblocks earlhaminst Gblocks False False gdal ecology Geospatial Data Abstraction Library tools are all dedicated to manipulate raster and vector geospatial data formats. False False gecko iuc Ungapped genome comparison False False @@ -304,6 +330,7 @@ gemini bgruening Glimmer makes gene predictions. False False gemini iuc GEMINI: a flexible framework for exploring genome variation False False geneiobio iuc Gene.iobio is an interactive tool for variant and trio analysis. False False generate_pc_lda_matrix devteam Generate a Matrix for using PC and LDA False False +genetic_clustering ecology Tools for genetic population structure inference using LEA (sNMF) and DPAC (K-means). genetic_format_conversion ecology This tool enables the conversion and formatting of genotyping data between VCF, GENEPOP, SSR (tabular) and BayeScan formats. False False genomad ufz Identify virus and plasmid genomes from nucleotide sequences True False genomic_super_signature iuc Interpretation of RNAseq experiments through robust, efficient comparison to public databases False False @@ -355,6 +382,7 @@ hapog iuc Hapo-G - Haplotype-Aware Polishing of Genomes False False hardklor galaxyp Hardklör False False hcluster_sg earlhaminst Hierarchically clustering on a sparse graph False False hcluster_sg_parser earlhaminst Converts hcluster_sg 3-column output into lists of ids False False +heatmap iuc Generate an interactive heatmap from count and membership matrices. heinz iuc An algorithm for identification of the optimal scoring subnetwork. False False helixer genouest Gene calling with Deep Neural Networks False False hgv_fundo devteam FunDO human genes associated with disease terms False False @@ -409,6 +437,7 @@ jcvi_gff_stats iuc Compute statistics from a genome annotation in GFF3 format (u jellyfish iuc Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA True False kaiju iuc taxonomic classification of high-throughput sequencing reads True False kaptive nml Kaptive reports information about capsular (K) loci found in genome assemblies. False False +kat bgruening KAT (K-mer Analysis Toolkit) for quality control of NGS datasets and genome assemblies. kat_filter nml Filtering kmers or reads from a database of kmers hashes True False kc_align iuc Kc-Align custom tool False False kegg_pathways_completeness iuc Compute KEGG pathway/module completeness from KOs or per-contig annotation False False @@ -446,12 +475,15 @@ longdust iuc Detect low-complexity regions in long DNA sequences using k-mer sta longorf mbernt obtain longest ORF in six-frame translations True False lorikeet_spoligotype iuc Tools for M. tuberculosis DNA fingerprinting (spoligotyping) True False lotus2 earlhaminst LotuS2 OTU processing pipeline True False +lrn_risk greg Produces detected blacklisted genes and distribution of virulence factors and AMR genes for PIMA m6anet iuc m6anet to detect m6A RNA modifications from nanopore data True False maaslin2 iuc MaAsLin2 is comprehensive R package for efficiently determining multivariable association between microbial meta'omic features and clinical metadata. True False maaslin3 iuc MaAsLin 3 is the next generation of MaAsLin. This comprehensive R package efficiently determines multivariable associations between clinical metadata and microbial meta-omics features. True False macs2 iuc MACS - Model-based Analysis of ChIP-Seq False False +macsyfinder odoppelt Wrapper for the MacSyFinder tool maf_cpg_filter devteam Mask CpG/non-CpG sites from MAF file False False maf_tools iuc Utilities for working with MAF (Multiple Alignment Format) files from UCSC False False +mafft fmareuil ngphylogeny version of Mafft, Multiple alignment program for amino acid or nucleotide sequences. mafft rnateam Multiple alignment program for amino acid or nucleotide sequences True False make_nr peterjc Make a FASTA file non-redundant True False maker iuc MAKER is a portable and easily configurable genome annotation pipeline.Its purpose is to allow smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and to create genome databases. True False @@ -530,12 +562,13 @@ mothur iuc Mothur wrappers True False motus bgruening Tool for profiling the abundance of microbial taxa. True False mqc rnateam Ribosome profiling mapping quality control tool False False mqppep galaxyp MaxQuant Phosphoproteomic Enrichment Pipeline - Preprocessing and ANOVA False False +mrbayes fmareuil ngphylogeny version of MrBayes is a program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models. mrbayes nml A program for the Bayesian estimation of phylogeny. True False msconvert galaxyp msconvert Convert and/or filter mass spectrometry files (including vendor formats) using the official Docker container True False msgfplus galaxyp MSGF+ False False msms_extractor galaxyp Extract MS/MS scans from the mzML file(s) based on PSM report. False False -msstatstmt galaxyp MSstatsTMT protein significance analysis in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling True False msstatstmt galaxyp MSstats tool for analyzing mass spectrometry proteomic datasets True False +msstatstmt galaxyp MSstatsTMT protein significance analysis in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling True False mt2mq galaxyp Tool to prepare metatranscriptomic outputs from ASaiM for Metaquantome False False mtnucratio iuc Calculates Mitochondrial to Nuclear read ratio True False multigsea iuc GSEA-based pathway enrichment analysis for multi-omics data True False @@ -543,7 +576,9 @@ multiqc iuc MultiQC aggregates results from bioinformatics analyses across many multispecies_orthologous_microsats devteam Extract orthologous microsatellites False False mummer peterjc Draw dotplots using mummer, mucmer, or promer with mummerplot False False mummer4 iuc Mummer4 Tools False False +mummer4_dnadiff greg Mummer4 dnadiff muon iuc muon is a Python framework for multimodal omics analysis False False +muscle fmareuil ngphylogeny version of MUSCLE: MUltiple Sequence Comparison by Log-Expectation is computer software for multiple sequence alignment of protein and nucleotide sequences. mykrobe iuc Antibiotic resistance predictions True False mykrobe_parser nml RScript to parse the results of mykrobe predictor. True False mz_to_sqlite galaxyp Creates a SQLite database for proteomics data True False @@ -561,12 +596,14 @@ ncbi_fcs_adaptor richard-burhans FCS-adaptor detects adaptor and vector contamin ncbi_fcs_gx iuc FCS-GX detects contamination from foreign organisms in genome sequences using the genome cross-species aligner (GX). True False necat iuc Error correction and de-novo assembly for ONT Nanopore reads False False neighbors iuc Identify target and neighbor genomes for marker discovery False False +newick_utilities fmareuil ngphylogeny version of Newick display from Newick utilities. newick_utils iuc Perform operations on Newick trees True False nextclade iuc Identify differences between your sequences and a reference sequence used by Nextstrain True False nextdenovo bgruening String graph-based de novo assembler for long reads False False nfdi4earth_os4a_importer ecology A data source tool for downloading datasets via NFDI4Earth's OneStop4All search user interface. False False ngsderive iuc Forensic analysis tool for inferring properties from NGS data False False nlstradamus peterjc Find nuclear localization signals (NLSs) in protein sequences False False +noisy fmareuil ngphylogeny version of Noisy: identification of phylogenetically uninformative sites in a multiple sequence alignment. nonpareil iuc Estimate average coverage in metagenomic datasets True False novoplasty iuc NOVOPlasty is a de novo assembler and heteroplasmy/variance caller for short circular genomes. False False nucleosome_prediction bgruening Prediction of Nucleosomes Positions on the Genome False False @@ -587,6 +624,7 @@ openms bgruening OpenMS in version 2.1. True False optitype iuc Precision HLA typing from NGS data False False orfipy iuc Galaxy wrapper for ORFIPY True False orthofinder iuc Accurate inference of orthologous gene groups made easy True False +p_chunks greg Annotates plasmids pacu iuc PACU is a workflow for whole genome sequencing based phylogeny of Illumina and ONT R9/R10 data. True False pairtools iuc Flexible tools for Hi-C data processing False False pal2nal iuc Wraps PAL2NAL to convert protein alignments and nucleotide FASTA into codon-aware alignments. True False @@ -600,6 +638,7 @@ parse_mito_blast iuc Filtering blast out from querying assembly against mitochon pathview iuc Pathview is a tool set for pathway based data integration and visualization. False False patrist nml Extract Patristic Distance From a Tree False False peakachu rnateam PEAKachu is a peak-caller for CLIP- and RIP-Seq data False False +pecat bgruening Phased error correction and assembly tool for long reads pep_pointer galaxyp PepPointer categorizes peptides by their genomic coordinates. False False pepquery galaxyp A peptide-centric MS search engine for novel peptide identification and validation. False False pepquery2 galaxyp PepQuery2 peptide-centric MS search for peptide identification and validation False False @@ -612,11 +651,15 @@ pfamscan bgruening Search a FASTA sequence against a library of Pfam HMM. True F phabox ufz Identify and analyze phage contigs in metagenomic data True False pharokka iuc rapid standardised annotation tool for bacteriophage genomes and metagenomes True False phi_toolkit_report ufz Phage host interaction toolkit report generator True False +phylodeep pasteur PhyloDeep is a python library for parameter estimation and model selection from phylogenetic trees, based on deep learning. phyloseq iuc Handling and analysis of high-throughput microbiome census data True False +phyml fmareuil ngphylogeny version of Phyml, Phylogeny software based on the maximum-likelihood. phyml iuc PhyML is a phylogeny software based on the maximum-likelihood principle. True False +phyml_sms fmareuil ngphylogeny version of PhyML with Smart Model Selection version 1.7. picrust iuc PICRUSt wrappers True False picrust2 iuc PICRUSt2: Phylogenetic Investigation of Communities by Reconstruction of Unobserved States True False pileometh bgruening A tool for processing bisulfite sequencing alignments False False +pima_report greg Generates the PIMA analysis summary report pimento iuc A PrIMEr infereNce TOolkit to facilitate large-scale calling of metabarcoding amplicon sequence variants. True False pipmir rnateam A method to identify novel plant miRNA. False False piranha rnateam Piranha is a peak-caller for CLIP- and RIP-Seq data False False @@ -646,6 +689,7 @@ prokka crs4 Rapid annotation of prokaryotic genomes True False promer nml Aligns two sets of contigs and reports amino acid substitutions between them True False prot_scriber iuc Protein annotation of short human readable descriptions False False protease_prediction bgruening This tool can learn the cleavage specificity of a given class of proteases. False False +protein_mosaic_q galaxyp Calculate the Mosaic Q descriptor and visualise amino acid clustering in protein structures protein_properties bgruening Calculation of various properties from given protein sequences False False proteinortho iuc Proteinortho is a tool to detect orthologous proteins/genes within different species. True False proteomics_improviser bgruening Visualisation of PepXML files False False @@ -713,6 +757,7 @@ quality_filter devteam Filter nucleotides based on quality scores False False quantp galaxyp Correlation between protein and transcript abundance False False quantwiz_iq galaxyp Isobaric Quantitation using QuantWiz-IQ False False quasitools nml A collection of tools for analysing Viral Quasispecies False False +quast greg Quast (Quality ASsessment Tool) evaluates genome assemblies. quast iuc Quast (Quality ASsessment Tool) evaluates genome assemblies. True False quickmerge iuc Merge long-read and hybrid assemblies to increase contiguity True False quicktree iuc neighbour-joining phylogenetic inference True False @@ -729,7 +774,6 @@ rcas rnateam RCAS (RNA Centric Annotation System) for functional analysis of tra rcve devteam Compute RCVE False False rcx_boxplot recetox recetox-boxplot is a tool for plotting boxplots from a tabular/csv/parquet data file. False False rdeval richard-burhans rdeval is a General purpose, multithreaded read analysis and manipulation tool. False False -reactome_pathwaymatcher galaxyp Reactome Pathway Matcher False False read2tree iuc Infer a species tree from sequencing reads. True False read_it_and_keep iuc Rapid decontamination of SARS-CoV-2 sequencing reads True False reago rnateam Reago is tool to assembly 16S ribosomal RNA recovery from metagenomic data. True False @@ -747,6 +791,7 @@ retrieve_bold ecology Search a list of sequences in BOLD (Barcode of Life Data S revoluzer iuc revoluzer wrappers False False ribotaper rnateam A method for defining traslated ORFs using Ribosome Profiling data. False False ribowaltz iuc Calculation of optimal P-site offsets, diagnostic analysis and visual inspection of ribosome profiling data False False +rmlst_cli iuc Identify bacterial species using the PubMLST rMLST API. rnabob rnateam Fast pattern searching for RNA structural motifs False False rnacode rnateam Analyze the protein coding potential in MSA False False rnacommender rnateam RNAcommender is a tool for genome-wide recommendation of RNA-protein interactions. False False @@ -768,6 +813,7 @@ salmon_kallisto_mtx_to_10x ebi-gxa Transforms .mtx matrix and associated labels salsa iuc A tool to scaffold long read assemblies with Hi-C False False sam3_semantic_segmentation ecology SAM3 video semantic segmentation tool False False samestr iuc Strain-level analysis and comparison of metagenomic samples True False +sample_names greg Contains a tool that extracts a unique portion of the file name as the sample name, and writes it to the output. sample_seqs peterjc Sub-sample sequences files (e.g. to reduce coverage) False False samtools_depad peterjc Re-align a SAM/BAM file with a padded reference (using samtools depad) False False samtools_depth peterjc Coverage depth via samtools False False @@ -799,6 +845,7 @@ seqprep iuc Tool for merging paired-end Illumina reads and trimming adapters. Tr seqsero2 iuc Salmonella serotype prediction from genome sequencing data True False seqtk iuc Toolkit for processing sequences in FASTA/Q formats False False seqtk_nml nml Tool to downsample fastq reads False False +seqtypedetect fmareuil ngphylogeny tool: Sequence type detection (dna/protein). seqwish iuc Alignment to variation graph inducer False False seurat iuc Seurat - R toolkit for single cell genomics False False sexdeterrmine iuc Sex.DetERRmine calculates the relative coverage of sex chromosomes to determine biological sex. False False @@ -830,6 +877,7 @@ snippy iuc Contains the snippy tool for characterising microbial snps True False snv_matrix nml Generate matrix of SNV distances False False socru iuc Order and orientation of complete bacterial genomes False False sonneityping iuc Scripts for parsing Mykrobe predict results for Shigella sonnei. True False +sopa iuc sopa – Spatial-omics pipeline and analysis sortmerna rnateam SortMeRNA is a software designed to rapidly filter ribosomal RNA fragments from metatransriptomic data produced by next-generation sequencers. True False spades iuc SPAdes is an assembly toolkit containing various assembly pipelines. It implements the following 4 stages: assembly graph construction, k-bimer adjustment, construction of paired assembly graph and contig construction. True False spaln iuc Spaln (space-efficient spliced alignment) maps and aligns a set of cDNA or protein sequences onto a whole genomic sequence. False False @@ -844,8 +892,8 @@ squirrel iuc QC and Phylogenetic analysis of MPXV True False sr_bowtie artbio bowtie wrapper tool to align small RNA sequencing reads True False sr_bowtie_dataset_annotation artbio Maps iteratively small RNA sequencing datasets to reference sequences. False False srs_tools ecology Compute biodiversity indicators for remote sensing data from Sentinel 2 False False -srst2 iuc SRST2 Short Read Sequence Typing for Bacterial Pathogens True False srst2 nml Short Read Sequence Typing for Bacterial Pathogens True False +srst2 iuc SRST2 Short Read Sequence Typing for Bacterial Pathogens True False sshmm rnateam ssHMM is an RNA sequence-structure motif finder for RNA-binding protein data, such as CLIP-Seq data False False ssr_filtering ecology Tool to filter SSR genotype data for missing data and null alleles. False False stacks iuc Stacks is a software pipeline for building loci from short-read sequences, such as RAD-seq False False @@ -901,6 +949,7 @@ teloscope iuc Teloscope is a fast and comprehensive tool for matching, counting, terrabyte_ogc_api_processes ecology This tool is a wrapper for OGC API Processes (OTB) coming from terrabyte (https://docs.terrabyte.lrz.de/). False False tetoolkit iuc The TEToolkit suite improves the bioinformatic analysis of repetitive sequences, particularly transposable elements, in order to elucidate novel (and previously ignored) biological insights of their functions in development and diseases. False False tetyper iuc Type a specific transposable element (TE) of interest from paired-end sequencing data. False False +tffscan fmareuil Wrapper for the MacSyFinder tool: TFFscan. tgsgapcloser bgruening TGS-GapCloser uses error-prone long reads or preassembled contigs to fill N-gap in the genome assembly. False False thermo_raw_file_converter galaxyp Thermo RAW file converter False False tiara bgruening Tool for identification of eukaryotic sequences in the metagenomic datasets. True False @@ -918,6 +967,7 @@ translate_bed_sequences galaxyp Perform 3 frame translation of BED file augmente transtermhp iuc Finds rho-independent transcription terminators in bacterial genomes True False treebest_best earlhaminst TreeBeST best True False trim_galore bgruening Trim Galore adaptive quality and adapter trimmer True False +trimal fmareuil ngphylogeny version of trimAl: a tool for automated alignment trimming. trimal iuc Tool for automated alignment trimming False False trimns iuc TrimNs is used to trim and remove fake cut sites from bionano hybrid scaffold data in the VGP pipeline False False trinity iuc Trinity represents a method for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq datahttps://github.com/trinityrnaseq/trinityrnaseq False False @@ -925,6 +975,8 @@ trinotate iuc Trinotate is a comprehensive annotation suite designed for automat trna_prediction bgruening tRNA and tmRNA prediction from nucleotide sequences. False False trycycler iuc Trycycler toolkit wrappers True False tsebra iuc This tool has been developed to combine BRAKER predictions. True False +tsenat iuc TSENAT - Tsallis entropy analysis for transcript-level isoform complexity +txsscan odoppelt Wrapper for the MacSyFinder tool: TXSScan. ucsc_axtchain iuc Chain together genome alignments False False ucsc_blat yating-l Standalone blat sequence search command line tool False False ucsc_chainantirepeat iuc Remove repeated chains False False diff --git a/communities/microgalaxy/metadata/workflow_status.tsv b/communities/microgalaxy/metadata/workflow_status.tsv index da33a6888..f76598777 100644 --- a/communities/microgalaxy/metadata/workflow_status.tsv +++ b/communities/microgalaxy/metadata/workflow_status.tsv @@ -72,6 +72,8 @@ https://workflowhub.eu/workflows/103?version=1 3: Plant virus exploration Workfl https://workflowhub.eu/workflows/102?version=1 2: Plant virus confirmation WorkflowHub Integrated and Urban Plant Pathology Laboratory 2021-02-04 2026-05-13 True False https://workflowhub.eu/workflows/124?version=1 1: Plant virus detection with kraken2 (SE) WorkflowHub Integrated and Urban Plant Pathology Laboratory 2021-06-17 2026-05-13 True False https://workflowhub.eu/workflows/101?version=1 1: Plant virus detection with kraken2 (PE) WorkflowHub Integrated and Urban Plant Pathology Laboratory 2021-02-04 2026-05-13 True False +https://workflowhub.eu/workflows/2196?version=1 MPXV (Mpox) Phylogenetic Analysis with Squirrel WorkflowHub Melbourne Bioinformatics, Galaxy Australia Tristan Reynolds, Ammar Aziz 2026-06-18 2026-06-25 True False +https://workflowhub.eu/workflows/2195?version=1 Viral Amplicon Analysis Pipeline for ONT Data WorkflowHub Melbourne Bioinformatics, Galaxy Australia Tristan Reynolds, Ammar Aziz 2026-06-18 2026-06-25 True False https://workflowhub.eu/workflows/2098?version=1 Taxonomy Assignment with QIIME2 WorkflowHub Melbourne Bioinformatics, Galaxy Australia Tristan Reynolds, Amy Loughman 2026-03-02 2026-05-13 True False https://workflowhub.eu/workflows/1199?version=2 Taxonomy classification using Kraken2 and Bracken WorkflowHub QCIF Bioinformatics Valentine Murigneux, Mike Thang 2024-12-10 2024-12-10 True False https://workflowhub.eu/workflows/624?version=1 Analyses of shotgun metagenomics data with MetaPhlAn2 WorkflowHub QCIF Bioinformatics Valentine Murigneux, Mike Thang, Saskia Hiltemann, Bérénice Batut 2023-10-26 2026-05-13 True False @@ -87,8 +89,9 @@ https://workflowhub.eu/workflows/644?version=1 Workflow 2: Sciensano WorkflowHub https://workflowhub.eu/workflows/470?version=1 Workflow 4: Staramr WorkflowHub Seq4AMR 2023-05-11 2026-05-13 True False https://workflowhub.eu/workflows/634?version=1 Workflow 1: AbritAMR WorkflowHub Seq4AMR 2023-10-31 2026-05-13 True False https://workflowhub.eu/workflows/1189?version=2 AMR-Pathfinder WorkflowHub Seq4AMR, ErasmusMC Clinical Bioinformatics Helena Rasche, Dennis Dollée, Birgit Rijvers 2024-11-14 2026-05-13 True False +https://usegalaxy.eu/published/workflow?id=2a093e63ebf6876b Training: 16S rRNA Analysis with Nanopore Sequencing Reads https://usegalaxy.eu 2025-12-01 2026-06-12 True False +https://usegalaxy.eu/published/workflow?id=7be08f99f83c927e Sadowsky_MetaG-DBgen_02102026 https://usegalaxy.eu Subina Mehta 2026-02-10 2026-06-09 True False https://usegalaxy.eu/published/workflow?id=6ca1b4fe047a03d2 Copy of Metaproteomics_GTN shared by user engy.nasr https://usegalaxy.eu 2026-04-27 2026-04-27 True False -https://usegalaxy.eu/published/workflow?id=2a093e63ebf6876b Training: 16S rRNA Analysis with Nanopore Sequencing Reads https://usegalaxy.eu 2025-12-01 2026-03-16 True False https://usegalaxy.eu/published/workflow?id=8c91345ed468e22d MetaG_extended https://usegalaxy.eu 2025-10-01 2026-02-04 True False https://usegalaxy.eu/published/workflow?id=7491883694fff308 Metagenomic Taxonomy Analysis https://usegalaxy.eu Bérénice Batut, Géraldine Piot, Mina Hojat Ansari 2025-11-28 2025-12-17 True False https://usegalaxy.eu/published/workflow?id=7371b6918e895e0c Quality control of bins generated by MetaBAT2, MaxBin2, SemiBin, and CONCOCT https://usegalaxy.eu Bérénice Batut 2025-12-01 2025-12-08 True False diff --git a/communities/microgalaxy/resources/curated_tools.tsv b/communities/microgalaxy/resources/curated_tools.tsv index a80d527db..a42dbe300 100644 --- a/communities/microgalaxy/resources/curated_tools.tsv +++ b/communities/microgalaxy/resources/curated_tools.tsv @@ -1,371 +1,381 @@ -Suite ID Tool IDs Tool output formats Description Suite first commit date Homepage Suite version Suite conda package Latest suite conda package version Suite version status ToolShed categories EDAM operations EDAM reduced operations EDAM topics EDAM reduced topics Suite owner Suite source Suite parsed folder bio.tool ID bio.tool name bio.tool description biii ID Number of tools on UseGalaxy.org (Main) Number of tools on UseGalaxy.org.au Number of tools on UseGalaxy.eu Number of tools on UseGalaxy.fr Number of tools on APOSTL Number of tools on MBAC Metabiome Portal Number of tools on ChemFlow Number of tools on CIRM-CFBP Number of tools on Coloc-stats Number of tools on Galaxy@AuBi Number of tools on Galaxy@Pasteur Number of tools on GalaxyTrakr Number of tools on GASLINI Number of tools on HyPhy HIV NGS Tools Number of tools on ImmPort Galaxy Number of tools on InteractoMIX Number of tools on IPK Galaxy Blast Suite Number of tools on Lebanese University Galaxy Number of tools on Mandoiu Lab Number of tools on MISSISSIPPI Number of tools on Oqtans Number of tools on Palfinder Number of tools on PepSimili Number of tools on PhagePromotor Number of tools on UseGalaxy.be Number of tools on UseGalaxy.cz Number of tools on UseGalaxy.no Number of tools on Viral Variant Visualizer (VVV) Suite users (last 5 years) (usegalaxy.eu) Suite users (usegalaxy.eu) Suite runs (last 5 years) (usegalaxy.eu) Suite runs (usegalaxy.eu) Suite users (last 5 years) (usegalaxy.org) Suite users (usegalaxy.org) Suite runs (last 5 years) (usegalaxy.org) Suite runs (usegalaxy.org) Suite users (last 5 years) (usegalaxy.org.au) Suite 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epidemiology, Infectious disease iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/amrfinderplus https://github.com/galaxyproject/tools-iuc/tree/main/tools/amrfinderplus amrfinderplus AMRFinderPlus "AMRFinderPlus is designed to find acquired antimicrobial resistance genes and point mutations in protein and/or assembled nucleotide sequences.It can also search ""plus"", stress, heat, and biocide resistance and virulence factors for some organisms" 1 0 1 1 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 953 953 45130 45130 689 689 17362 17362 0 0 0 0 28 28 1863 1863 64355 64355 1670 1670 https://usegalaxy.eu/published/workflow?id=1ce523ef51f47134, https://usegalaxy.eu/published/workflow?id=2c992e509aa5dd9d, https://usegalaxy.eu/published/workflow?id=309fc4fc2e0da89c, https://usegalaxy.eu/published/workflow?id=32de10b9de8a999a, https://usegalaxy.eu/published/workflow?id=3439bd061fafcf12, https://usegalaxy.eu/published/workflow?id=34df701aa23a9fb3, 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https://usegalaxy.org/published/workflow?id=2b4b1fe82258f303, https://usegalaxy.org/published/workflow?id=3c177fdf38311118, https://usegalaxy.org/published/workflow?id=9c0fbd9f51a9857f, https://usegalaxy.org/published/workflow?id=aaf8e740b3f8e2c0, https://usegalaxy.org/published/workflow?id=d3dc805cd43b2737, https://usegalaxy.org/published/workflow?id=ef187f85b103d858, https://usegalaxy.org/published/workflow?id=f8fab0cd6fc30d92, https://usegalaxy.org/published/workflow?id=fde774a049875466, https://workflowhub.eu/workflows/1049?version=9, https://workflowhub.eu/workflows/2024?version=4 True False -ISEScan isescan txt, tabular, gff, fasta """ISEScan is a pipeline to identify IS (Insertion Sequence) elements in genome and metagenomebased on profile hidden Markov models constructed from manually curated IS elements.""" 2022-09-01 https://github.com/xiezhq/ISEScan 1.7.3 isescan 1.7.3 Up-to-date Sequence Analysis Structural variation detection Structural variation detection Genomics, DNA structural variation, Sequence analysis, Genetic variation Genomics, Sequence analysis, Genetic variation iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/isescan https://github.com/galaxyproject/tools-iuc/tree/main/tools/isescan ISEScan ISEScan Automated identification of insertion sequence elements in prokaryotic genomes. 1 1 1 1 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 392 392 67516 67516 237 237 1535 1535 116 116 7464 7464 37 37 1759 1759 78274 78274 782 782 https://usegalaxy.eu/published/workflow?id=1306ed083d91a852, https://usegalaxy.eu/published/workflow?id=2c1a6da84d891cf2, https://usegalaxy.eu/published/workflow?id=3081569659a45b9e, https://usegalaxy.eu/published/workflow?id=36ea584e0f60893e, https://usegalaxy.eu/published/workflow?id=3f5fe28793ed0c6c, https://usegalaxy.eu/published/workflow?id=4a218fb93d78ba67, https://usegalaxy.eu/published/workflow?id=61948fcaefa1418a, https://usegalaxy.eu/published/workflow?id=6b69ab27c565257b, 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https://usegalaxy.org/published/workflow?id=d3dc805cd43b2737, https://usegalaxy.org/published/workflow?id=e12324f5e3b930fd, https://usegalaxy.org/published/workflow?id=ef187f85b103d858, https://usegalaxy.org/published/workflow?id=f8fab0cd6fc30d92, https://usegalaxy.org/published/workflow?id=fb01e1a49793c8be, https://usegalaxy.org/published/workflow?id=fde774a049875466, https://workflowhub.eu/workflows/1049?version=9, https://workflowhub.eu/workflows/1062?version=1, https://workflowhub.eu/workflows/1189?version=2, https://workflowhub.eu/workflows/1495?version=1, https://workflowhub.eu/workflows/2024?version=4, https://workflowhub.eu/workflows/470?version=1 microbiome/pathogen-detection-from-nanopore-foodborne-data True False -abritamr abritamr tabular, txt A pipeline for running AMRfinderPlus and collating results into functional classes 2023-04-03 https://zenodo.org/record/7370628 1.2.0 abritamr 1.2.0 Up-to-date Sequence Analysis Antimicrobial resistance prediction Antimicrobial resistance prediction Microbiology, Public health and epidemiology, Infectious disease, Antimicrobial resistance Microbiology, Public health and epidemiology, Infectious disease iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/abritamr https://github.com/galaxyproject/tools-iuc/tree/main/tools/abritamr abritamr abriTAMR an AMR gene detection pipeline that runs AMRFinderPlus on a single (or list ) of given isolates and collates the results into a table, separating genes identified into functionally relevant groups. 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 319 319 2633 2633 0 0 0 0 97 97 880 880 3 3 5 5 3518 3518 419 419 https://usegalaxy.eu/published/workflow?id=eb5ab8bc82569eee, https://usegalaxy.org.au/published/workflow?id=7a0c4804e4d4c905, https://workflowhub.eu/workflows/634?version=1 True False -abyss abyss-pe fasta, tabular Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler 2015-04-14 https://github.com/bcgsc/abyss 2.3.10 abyss 2.3.10 Up-to-date Assembly Genome assembly, De-novo assembly, Scaffolding Genome assembly, De-novo assembly, Scaffolding Sequence assembly Sequence assembly iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/abyss https://github.com/galaxyproject/tools-iuc/tree/main/tools/abyss abyss ABySS De novo genome sequence assembler using short reads. 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 1 1 1 0 1258 1368 7148 7779 183 414 505 1305 398 398 2608 2608 11 11 16 16 11708 10277 2191 1850 True False -aldex2 aldex2 tabular, png, pdf Performs analysis Of differential abundance taking sample variation into account 2022-06-29 https://github.com/ggloor/ALDEx_bioc 1.26.0 bioconductor-aldex2 1.42.0 To update Metagenomics Statistical inference Statistical inference Gene expression, Statistics and probability Gene expression, Statistics and probability iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/aldex2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/aldex2 aldex2 ALDEx2 A differential abundance analysis for the comparison of two or more conditions. It uses a Dirichlet-multinomial model to infer abundance from counts, that has been optimized for three or more experimental replicates. Infers sampling variation and calculates the expected FDR given the biological and sampling variation using the Wilcox rank test and Welches t-test, or the glm and Kruskal Wallis tests. Reports both P and fdr values calculated by the Benjamini Hochberg correction. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 64 64 356 356 0 0 0 0 0 0 0 0 0 0 0 0 356 356 64 64 True False -amas amas_concat, amas_remove, amas_replicate, amas_split, amas_summary txt AMAS high-throughput alignment manipulation and summaries for phylogenomics 2025-12-02 https://github.com/marekborowiec/AMAS 1.0 amas 1.0 Up-to-date Phylogenetics, Sequence Analysis, Statistics Nucleic acid sequence analysis, Protein sequence analysis Nucleic acid sequence analysis, Protein sequence analysis Phylogenomics, Phylogenetics, Sequence analysis, Statistics and probability Phylogenomics, Phylogenetics, Statistics and probability iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/amas https://github.com/galaxyproject/tools-iuc/tree/main/tools/amas amas AMAS AMAS (Alignment Manipulation And Summary), a tool that works on amino acid and nucleotide alignments and combines capabilities of sequence manipulation with a function that calculates basic statistics. 0 0 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False -amplican amplican csv, tabular, html, txt, rdata, fasta AmpliCan is an analysis tool for genome editing. 2021-09-22 https://github.com/valenlab/amplican 1.14.0 bioconductor-amplican 1.32.1 To update Sequence Analysis Alignment, Standardisation and normalisation Alignment, Standardisation and normalisation PCR experiment, Statistics and probability PCR experiment, Statistics and probability iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/amplican https://github.com/galaxyproject/tools-iuc/tree/main/tools/amplican amplican amplican It performs alignment of the amplicon reads, normalizes gathered data, calculates multiple statistics (e.g. cut rates, frameshifts) and presents results in form of aggregated reports. Data and statistics can be broken down by experiments, barcodes, user defined groups, guides and amplicons allowing for quick identification of potential problems. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 18 18 85 85 0 0 0 0 0 0 0 0 0 0 0 0 85 85 18 18 True False -ampligone ampligone fastqsanger, bed AmpliGone is a tool which accurately finds and removes primer sequences from NGS reads in an amplicon experiment. 2025-07-29 https://rivm-bioinformatics.github.io/AmpliGone/latest/ 2.0.1 AmpliGone 2.0.2 To update Sequence Analysis, Fastq Manipulation iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/ampligone https://github.com/galaxyproject/tools-iuc/tree/main/tools/ampligone 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False -ancombc ancombc Performs analysis of compositions of microbiomes with bias correction. 2022-07-16 https://github.com/FrederickHuangLin/ANCOMBC 1.4.0 bioconductor-ancombc 2.12.0 To update Metagenomics DNA barcoding DNA barcoding Microbial ecology, Metagenomics, Taxonomy Microbial ecology, Metagenomics, Taxonomy iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/ancombc https://github.com/galaxyproject/tools-iuc/tree/main/tools/ancombc ancombc ANCOMBC Determine taxa whose absolute abundances, per unit volume, of the ecosystem (e.g. gut) are significantly different with changes in the covariate of interest (e.g. group). The current version of ancombc function implements Analysis of Compositions of Microbiomes with Bias Correction (ANCOM-BC) in cross-sectional data while allowing for covariate adjustment. 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 20 20 64 64 0 0 0 0 0 0 0 0 0 0 0 0 64 64 20 20 True False -antismash antismash html, txt Antismash allows the genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters 2015-02-28 https://antismash.secondarymetabolites.org 6.1.1 antismash 8.0.4 To update Sequence Analysis Sequence clustering, Gene prediction, Differential gene expression analysis Sequence clustering, Gene prediction, Differential gene expression analysis Molecular interactions, pathways and networks, Gene and protein families Molecular interactions, pathways and networks, Gene and protein families bgruening https://github.com/galaxyproject/tools-iuc/tree/master/tools/antismash https://github.com/bgruening/galaxytools/tree/master/tools/antismash antismash antiSMASH Rapid genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genomes. 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https://workflowhub.eu/workflows/642?version=25, https://workflowhub.eu/workflows/750?version=4, https://workflowhub.eu/workflows/788?version=1, https://workflowhub.eu/workflows/789?version=1 assembly/ERGA-post-assembly-QC, assembly/assembly-with-preprocessing, assembly/chloroplast-assembly, assembly/debruijn-graph-assembly, assembly/largegenome, assembly/metagenomics-assembly, assembly/mrsa-illumina, assembly/mrsa-nanopore, microbiome/metagenomics-assembly, microbiome/pathogen-detection-from-nanopore-foodborne-data, microbiome/plasmid-metagenomics-nanopore True False -bayescan BayeScan txt Detecting natural selection from population-based genetic data 2017-03-09 http://cmpg.unibe.ch/software/BayeScan/index.html 2.1 bayescan 2.1 Up-to-date Sequence Analysis Statistical inference Statistical inference Genetics, Evolutionary biology, Statistics and probability, DNA polymorphism Genetics, Evolutionary biology, Statistics and probability, DNA polymorphism iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/bayescan https://github.com/galaxyproject/tools-iuc/tree/main/tools/bayescan bayescan BayeScan BAYEsian genome SCAN for outliers, aims at identifying candidate loci under natural selection from genetic data, using differences in allele frequencies between populations. It is based on the multinomial-Dirichlet model. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 28 35 109 136 0 0 0 0 0 0 0 0 0 0 0 0 136 109 35 28 True False -bbtools bbtools_bbduk, bbtools_bbmap, bbtools_bbmerge, bbtools_bbnorm, bbtools_callvariants, bbtools_tadpole fastqsanger, tabular, fasta, txt, bam, fastq, vcf BBTools is a suite of fast, multithreaded bioinformatics tools designed for analysis of DNA and RNA sequence data.BBTools can handle common sequencing file formats such as fastq, fasta, sam, scarf, fasta+qual, compressed or raw,with autodetection of quality encoding and interleaving. It is written in Java and works on any platform supportingJava, including Linux, MacOS, and Microsoft Windows and Linux; there are no dependencies other than Java (version7 or higher). Program descriptions and options are shown when running the shell scripts with no parameters. 2021-10-04 https://jgi.doe.gov/data-and-tools/bbtools/ 39.08 bbmap 39.81 To update Sequence Analysis RNA-Seq analysis, Sequence trimming, Read mapping, Sequence contamination filtering, Read binning, Sequence alignment RNA-Seq analysis, Sequence trimming, Read mapping, Sequence contamination filtering, Read binning, Sequence alignment Sequencing, RNA splicing, Whole genome sequencing, Phylogenetics, Metagenomics, RNA-Seq RNA splicing, Whole genome sequencing, Phylogenetics, Metagenomics, RNA-Seq iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/bbtools https://github.com/galaxyproject/tools-iuc/tree/main/tools/bbtools bbmap BBMap BBMap is a fast splice-aware aligner for RNA and DNA. It is faster than almost all short-read aligners, yet retains unrivaled sensitivity and specificity, particularly for reads with many errors and indels. 6 3 6 6 0 0 0 0 0 1 6 6 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 0 413 413 25287 25287 562 562 10487 10487 172 172 3537 3537 5 5 134 134 39445 39445 1152 1152 https://usegalaxy.eu/published/workflow?id=d967194ca51ff11e, https://usegalaxy.org.au/published/workflow?id=25f65a29ce3c3ee0, https://workflowhub.eu/workflows/407?version=1, https://workflowhub.eu/workflows/519?version=1 True False -bigscape bigscape html, txt Construct sequence similarity networks of BGCs and groups them into GCF 2024-02-18 https://github.com/medema-group/BiG-SCAPE 1.1.9 bigscape 2.0.3 To update Metagenomics Clustering, Global alignment, Fold recognition Clustering, Global alignment, Fold recognition Phylogeny, Microbial ecology, Mapping, Metabolomics, Bioinformatics, Gene and protein families Phylogeny, Microbial ecology, Mapping, Metabolomics, Bioinformatics, Gene and protein families iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/bigscape https://github.com/galaxyproject/tools-iuc/tree/main/tools/bigscape BiG-SCAPE BiG-SCAPE A computational framework to explore large-scale biosynthetic diversity.BiG-SCAPE (Biosynthetic Gene Similarity Clustering and Prospecting Engine) is a software package, written in Python, that constructs sequence similarity networks of Biosynthetic Gene Clusters (BGCs) and groups them into Gene Cluster Families (GCFs). BiG-SCAPE does this by rapidly calculating a distance matrix between gene clusters based on a comparison of their protein domain content, order, copy number and sequence identity.It defines a distance metric between Gene Clusters using a combination of three indices (Jaccard Index of domain types, Domain Sequence Similarity the Adjacency...BiG-SCAPE and CORASON provide a set of tools to explore the diversity of biosynthetic gene clusters (BGCs) across large numbers of genomes, by constructing BGC sequence similarity networks, grouping BGCs into gene cluster families, and exploring gene cluster diversity linked to enzyme phylogenies. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 95 95 2449 2449 0 0 0 0 0 0 0 0 0 0 0 0 2449 2449 95 95 True False -binette binette tabular Binning refinement tool 2025-01-14 https://github.com/genotoul-bioinfo/Binette 1.2.1 binette 1.2.1 Up-to-date Metagenomics Read binning Read binning Metagenomics Metagenomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/binette https://github.com/galaxyproject/tools-iuc/tree/main/tools/binette binette Binette Binette is a fast and accurate binning refinement tool to constructs high quality MAGs from the output of multiple binning tools. 1 1 1 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 11 11 359 359 8 8 17 17 0 0 0 0 1 1 49 49 425 425 20 20 https://usegalaxy.eu/published/workflow?id=00f15824c7a9b196, https://usegalaxy.eu/published/workflow?id=7ecd92cb382d8168, https://usegalaxy.eu/published/workflow?id=ce5c9287a67e6085, https://usegalaxy.org/published/workflow?id=7251c6e0dad8f927, https://workflowhub.eu/workflows/1352?version=4, https://workflowhub.eu/workflows/2028?version=1, https://workflowhub.eu/workflows/2100?version=2 microbiome/metagenomics-binning True False -binning_refiner bin_refiner tabular Reconciles the outputs of different binning programs with the aim to improve the quality of genome bins,especially with respect to contamination levels. 2022-02-18 https://github.com/songweizhi/Binning_refiner 1.4.3 binning_refiner 1.4.3 Up-to-date Metagenomics Read binning, Sequence clustering Read binning, Sequence clustering Metagenomics, Sequence assembly, Microbial ecology Metagenomics, Sequence assembly, Microbial ecology iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/binning_refiner https://github.com/galaxyproject/tools-iuc/tree/main/tools/binning_refiner binning_refiner Binning_refiner Improving genome bins through the combination of different binning programs 0 0 1 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 64 64 236 236 0 0 0 0 0 0 0 0 0 0 0 0 236 236 64 64 True False -bio_hansel bio_hansel tabular Heidelberg and Enteritidis SNP Elucidation 2017-09-29 https://github.com/phac-nml/bio_hansel 2.6.1 bio_hansel 2.6.1 Up-to-date Sequence Analysis Genotyping, SNP detection, Genome assembly Genotyping, SNP detection, Genome assembly Whole genome sequencing, DNA polymorphism, Genotype and phenotype, Infectious disease, Agricultural science Whole genome sequencing, DNA polymorphism, Genotype and phenotype, Infectious disease, Agricultural science iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/hansel https://github.com/galaxyproject/tools-iuc/tree/main/tools/hansel Biohansel BioHansel BioHansel is a tool for performing high-resolution genotyping of bacterial isolates by identifying phylogenetically informative single nucleotide polymorphisms (SNPs), also known as canonical SNPs, in whole genome sequencing (WGS) data. The application uses a fast k-mer matching algorithm to map pathogen WGS data to canonical SNPs contained in hierarchically structured schemas and assigns genotypes based on the detected SNP profile. 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 36 39 312 397 57 63 538 592 0 0 0 0 0 0 0 0 989 850 102 93 True False -biohansel biohansel tabular, json Heidelberg and Enteritidis SNP Elucidation 2018-08-01 https://github.com/phac-nml/biohansel 2.4.0 bio_hansel 2.6.1 To update Sequence Analysis nml https://github.com/phac-nml/biohansel https://github.com/phac-nml/galaxy_tools/tree/master/tools/biohansel 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False -biomformat biom_add_metadata, biom_convert, biom_from_uc, biom_normalize_table, biom_subset_table, biom_summarize_table biom1, txt The biom-format package provides a command line interface and Python API for working with BIOM files. 2016-06-07 https://github.com/biocore/biom-format 2.1.17 biom-format 2.1.7 To update Metagenomics Formatting Formatting Laboratory information management, Sequence analysis Laboratory information management, Sequence analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/biom_format https://github.com/galaxyproject/tools-iuc/tree/main/tools/biom_format biomformat biomformat "This package includes basic tools for reading biom-format files, accessing and subsetting data tables from a biom object, as well as limited support for writing a biom-object back to a biom-format file. The design of this API is intended to match the python API and other tools included with the biom-format project, but with a decidedly ""R flavor"" that should be familiar to R users. This includes S4 classes and methods, as well as extensions of common core functions/methods." 2 2 6 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 342 356 16688 16852 374 593 2736 5533 166 235 2283 2833 0 0 0 0 25218 21707 1184 882 https://usegalaxy.eu/published/workflow?id=08e25b733cd796e6, https://usegalaxy.eu/published/workflow?id=437704898229dfb6, https://usegalaxy.eu/published/workflow?id=466bdd8ba7b67264, https://usegalaxy.eu/published/workflow?id=8f747dbff3216993, https://usegalaxy.eu/published/workflow?id=e14b81a8c0b1b7a4, https://usegalaxy.eu/published/workflow?id=fb806b88850f3427, https://usegalaxy.org.au/published/workflow?id=14e80b7f9f68ec2a, https://usegalaxy.org.au/published/workflow?id=20d472fc5563a640, https://usegalaxy.org.au/published/workflow?id=4f837b7f90d5ebac, https://usegalaxy.org.au/published/workflow?id=869440d35a618836, https://usegalaxy.org.au/published/workflow?id=ca6f29110df8dadc, https://usegalaxy.org/published/workflow?id=45f959d5bf505b15, https://usegalaxy.org/published/workflow?id=8151be18aab3a3c6, https://workflowhub.eu/workflows/1270?version=2, https://workflowhub.eu/workflows/1273?version=2, https://workflowhub.eu/workflows/142?version=1, https://workflowhub.eu/workflows/1842?version=1, https://workflowhub.eu/workflows/1856?version=1, https://workflowhub.eu/workflows/2098?version=1, https://workflowhub.eu/workflows/232?version=1, https://workflowhub.eu/workflows/233?version=1 microbiome/mgnify-amplicon True False -biotradis bacteria_tradis, tradis_essentiality, tradis_gene_insert_sites txt, tabular.gz, bam, csv, pdf Bio-Tradis is a tool suite dedicated to essentiality analyses with TraDis data. 2020-01-17 https://www.sanger.ac.uk/science/tools/bio-tradis 1.4.5 biotradis 1.4.5 Up-to-date Genome annotation Sequence analysis Sequence analysis Mobile genetic elements, Workflows Mobile genetic elements, Workflows iuc https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/biotradis https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/biotradis biotradis biotradis The Bio::TraDIS pipeline provides software utilities for the processing, mapping, and analysis of transposon insertion sequencing data. The pipeline was designed with the data from the TraDIS sequencing protocol in mind, but should work with a variety of transposon insertion sequencing protocols as long as they produce data in the expected format. 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 165 176 6369 6769 0 0 0 0 0 0 0 0 6769 6369 176 165 True False -blast2go blast2go tabular Maps BLAST results to GO annotation terms 2013-09-23 https://github.com/peterjc/galaxy_blast/tree/master/tools/blast2go 0.0.11 b2g4pipe To update Ontology Manipulation, Sequence Analysis Gene functional annotation Gene functional annotation Nucleic acid sites, features and motifs Nucleic acid sites, features and motifs peterjc https://github.com/peterjc/galaxy_blast/tree/master/tools/blast2go https://github.com/peterjc/galaxy_blast/tree/master/tools/blast2go Blast2GO Blast2GO Bioinformatics platform for high-quality functional annotation and analysis of genomic datasets. It allows analyzing and visualizing newly sequenced genomes by combining state-of-the-art methodologies, standard resources and algorithms. It allows to gain biological insights fast and easy even for completely novel genomes. Perform out-of-the-box the entire workflow of functional annotation of your transcriptomic datasets including its analysis and biological interpretation. 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 205 303 851 1255 0 0 0 0 0 0 0 0 0 1 0 10 1265 851 304 205 https://usegalaxy.eu/published/workflow?id=33312e5643279e8a True False -blast_rbh blast_reciprocal_best_hits tabular BLAST Reciprocal Best Hits (RBH) from two FASTA files 2014-05-15 https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh 0.3.0 biopython 1.70 To update Fasta Manipulation, Sequence Analysis Gene functional annotation, Nucleic acid sequence analysis Gene functional annotation, Nucleic acid sequence analysis Nucleic acid sites, features and motifs Nucleic acid sites, features and motifs peterjc https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh blast_rbh blast_rbh This tool is a short Python script to run reciprocal BLAST searches on a pair of sequence files, and extract the reciprocal best hits. 0 0 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 413 502 25833 37031 0 0 0 0 0 0 0 0 0 0 0 0 37031 25833 502 413 https://usegalaxy.eu/published/workflow?id=7f6950394a8c9c4a True False -blastxml_to_top_descr blastxml_to_top_descr tabular Make table of top BLAST match descriptions 2013-09-23 https://github.com/peterjc/galaxy_blast/tree/master/tools/blastxml_to_top_descr 0.1.2 python To update Convert Formats, Sequence Analysis, Text Manipulation Sequence alignment, Sequence annotation Sequence alignment, Sequence annotation Sequence analysis Sequence analysis peterjc https://github.com/peterjc/galaxy_blast/tree/master/tools/blastxml_to_top_descr https://github.com/peterjc/galaxy_blast/tree/master/tools/blastxml_to_top_descr blastxml_to_top_descr blastxml_to_top_descr This tool is a short Python script to parse a BLAST XML file, and extract the identifiers with description for the top matches (by default the top 3), and output these as a simple tabular file along with the query identifiers. 0 0 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 530 653 263613 265902 0 0 0 0 0 0 0 0 0 0 0 0 265902 263613 653 530 https://usegalaxy.eu/published/workflow?id=33312e5643279e8a, https://usegalaxy.eu/published/workflow?id=8f747dbff3216993, https://usegalaxy.eu/published/workflow?id=bebcbd6f0ffa55c5, https://usegalaxy.eu/published/workflow?id=e14b81a8c0b1b7a4 True False -bmtagger bmtagger remove contaminant reads 2025-11-12 https://ftp.ncbi.nlm.nih.gov/pub/agarwala/bmtagger/ 3.101 bmtagger 3.101 Up-to-date Metagenomics Data filtering, Read pre-processing Read pre-processing Metagenomics Metagenomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/bmtagger https://github.com/galaxyproject/tools-iuc/tree/main/tools/bmtagger bmtagger bmtagger Best Match Tagger for removing contaminant reads from metagenomics datasets 0 0 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False -bracken est_abundance tabular, txt Bayesian Reestimation of Abundance with KrakEN 2019-10-15 https://github.com/jenniferlu717/Bracken/releases 3.1 bracken 3.1 Up-to-date Sequence Analysis, Metagenomics Statistical calculation Statistical calculation Metagenomics, Microbial ecology Metagenomics, Microbial ecology iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/bracken https://github.com/galaxyproject/tools-iuc/tree/main/tools/bracken bracken Bracken Bracken is a companion program to Kraken 1, KrakenUniq, or Kraken 2 While Kraken classifies reads to multiple levels in the taxonomic tree, Bracken allows estimation of abundance at a single level using those classifications (e.g. Bracken can estimate abundance of species within a sample). 1 1 1 1 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1714 1714 108307 108307 804 804 27569 27569 265 265 8873 8873 59 59 12432 12432 157181 157181 2842 2842 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https://usegalaxy.org/published/workflow?id=b6a795834009ce06, https://usegalaxy.org/published/workflow?id=bdd7011a908bc1aa, https://usegalaxy.org/published/workflow?id=de9bf4c1024f8d53, https://usegalaxy.org/published/workflow?id=dfd73857c0eb2a21, https://usegalaxy.org/published/workflow?id=f378960ee55f567e, https://workflowhub.eu/workflows/1052?version=11, https://workflowhub.eu/workflows/1199?version=2, https://workflowhub.eu/workflows/1470?version=2, https://workflowhub.eu/workflows/1644?version=1, https://workflowhub.eu/workflows/1674?version=2, https://workflowhub.eu/workflows/1881?version=2, https://workflowhub.eu/workflows/1882?version=3, https://workflowhub.eu/workflows/2043?version=1 ecology/bacterial-isolate-species-contamination-checking, microbiome/taxonomic-profiling, sequence-analysis/quality-contamination-control True False -busco busco txt, tabular, png, gff3, fasta BUSCO assess genome and annotation completeness 2017-01-12 https://gitlab.com/ezlab/busco/-/releases 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taxonomic assignments 2024-05-20 https://github.com/CAMI-challenge/AMBER 2.0.7 cami-amber 2.0.7 Up-to-date Metagenomics Read binning Read binning Metagenomics Metagenomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/cami_amber https://github.com/galaxyproject/tools-iuc/tree/main/tools/cami_amber cami-amber AMBER AMBER is an evaluation package for the comparative assessment of genome reconstructions and taxonomic assignments from metagenome benchmark datasets. It provides performance metrics, results rankings, and comparative visualizations for assessing multiple programs or parameter effects. The provided metrics were used in the first community benchmarking challenge of the initiative for the Critical Assessment of Metagenomic Interpretation. 4 4 4 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 8 8 10522 10522 0 0 0 0 0 0 0 0 0 0 0 0 10522 10522 8 8 https://usegalaxy.eu/published/workflow?id=00f15824c7a9b196, https://usegalaxy.eu/published/workflow?id=17d2e76147fc940c, https://usegalaxy.eu/published/workflow?id=43098b8afe78b071, https://usegalaxy.eu/published/workflow?id=ce5c9287a67e6085, https://usegalaxy.eu/published/workflow?id=e4dabaf57668dbd1, https://workflowhub.eu/workflows/2100?version=2 True False -canu canu txt, fasta, fasta.gz Canu is a hierarchical assembly pipeline designed for high-noise single-molecule sequencing (such as the PacBio RS II/Sequel or Oxford Nanopore MinION). 2018-06-07 https://github.com/marbl/canu 2.3 canu 2.3 Up-to-date Assembly De-novo assembly De-novo assembly Genomics Genomics bgruening https://github.com/bgruening/galaxytools/tree/master/tools/canu https://github.com/bgruening/galaxytools/tree/master/tools/canu canu CANU De-novo assembly tool for long read chemistry like Nanopore data and PacBio data. 0 1 1 1 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 1644 1843 13768 17494 0 0 0 0 454 485 3744 4325 37 37 480 480 22299 17992 2365 2135 https://usegalaxy.eu/published/workflow?id=93d7a5704ec1d82d True False -cawlign cawlign fasta Codon-aware alignment of sequences to a reference. 2025-09-30 https://github.com/veg/cawlign 0.1.15 cawlign 0.1.16 To update Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/cawlign https://github.com/galaxyproject/tools-iuc/tree/main/tools/cawlign 1 0 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False -cd_hit cd_hit txt, fasta Cluster or compare biological sequence datasets 2018-02-26 http://weizhongli-lab.org/cd-hit/ 4.8.1 cd-hit 4.8.1 Up-to-date Sequence Analysis, Fasta Manipulation Sequence clustering Sequence clustering Sequencing Sequencing iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/cdhit https://github.com/galaxyproject/tools-iuc/tree/main/tools/cdhit cd-hit cd-hit Cluster a nucleotide dataset into representative sequences. 0 0 1 1 0 0 0 0 0 1 0 1 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 899 899 20148 20148 1 1 2 2 1 1 2 2 57 57 1174 1174 21326 21326 958 958 https://usegalaxy.eu/published/workflow?id=2ee0eb74e839b476, https://usegalaxy.eu/published/workflow?id=974cc681d07ec788, https://usegalaxy.eu/published/workflow?id=9b9e1e28f3683f92, https://usegalaxy.eu/published/workflow?id=bebcbd6f0ffa55c5 True False -cd_hit_dup cd_hit_dup fastqsanger, tabular simple tool for removing duplicates from sequencing reads 2015-04-28 0.0.1 cd-hit-auxtools 4.8.1 To update Metagenomics, Sequence Analysis devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/cd_hit_dup https://github.com/galaxyproject/tools-devteam/tree/main/tools/cd_hit_dup 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 501 770 7542 9437 0 0 0 0 0 0 0 0 9437 7542 770 501 https://usegalaxy.org/published/workflow?id=35c2626849348f2c True False -cemitool cemitool tabular, txt, html Gene co-expression network analysis tool 2022-10-10 https://www.bioconductor.org/packages/release/bioc/html/CEMiTool.html 1.34.0 bioconductor-cemitool 1.34.0 Up-to-date Transcriptomics, RNA, Statistics, Single Cell Enrichment analysis, Pathway or network analysis Enrichment analysis, Pathway or network analysis Gene expression, Transcriptomics, Microarray experiment Transcriptomics, Microarray experiment iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/cemitool https://github.com/galaxyproject/tools-iuc/tree/main/tools/cemitool cemitool CEMiTool It unifies the discovery and the analysis of coexpression gene modules in a fully automatic manner, while providing a user-friendly html report with high quality graphs. 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Phylogenetics, Taxonomy, Metagenomics, Data quality management iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/checkm https://github.com/galaxyproject/tools-iuc/tree/main/tools/checkm checkm CheckM CheckM provides a set of tools for assessing the quality of genomes recovered from isolates, single cells, or metagenomes. 10 10 10 10 0 0 0 0 0 0 0 10 0 0 0 0 0 0 0 0 0 0 0 0 1 10 0 0 717 717 12189 12189 179 179 1510 1510 96 96 2254 2254 50 50 1469 1469 17422 17422 1042 1042 https://usegalaxy.eu/published/workflow?id=0563f58718be932d, https://usegalaxy.eu/published/workflow?id=1e5f1d9a51032e44, https://usegalaxy.eu/published/workflow?id=3eaa913306c16146, https://usegalaxy.eu/published/workflow?id=5b940b283d91d99d, https://usegalaxy.eu/published/workflow?id=6158c3b5fc12044e, https://usegalaxy.eu/published/workflow?id=6416cfdbd5273063, https://usegalaxy.eu/published/workflow?id=667bac8d7453e5f1, https://usegalaxy.eu/published/workflow?id=8c91345ed468e22d, 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Metagenomics, Data quality management Phylogenomics, Phylogenetics, Taxonomy, Metagenomics, Data quality management iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/checkm2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/checkm2 checkm CheckM CheckM provides a set of tools for assessing the quality of genomes recovered from isolates, single cells, or metagenomes. 1 1 1 1 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 228 228 1602 1602 187 187 1322 1322 0 0 0 0 15 15 1268 1268 4192 4192 430 430 https://usegalaxy.eu/published/workflow?id=2a1dc58e51d5f01a, https://usegalaxy.eu/published/workflow?id=3303a04887a47675, https://usegalaxy.eu/published/workflow?id=368d1ac0150ea0b6, https://usegalaxy.eu/published/workflow?id=7371b6918e895e0c, https://usegalaxy.eu/published/workflow?id=7ecd92cb382d8168, https://usegalaxy.eu/published/workflow?id=ba1fda2318046543, https://usegalaxy.eu/published/workflow?id=c62d65832377e376, https://usegalaxy.eu/published/workflow?id=e532d98f4b368666, https://usegalaxy.fr/published/workflow?id=f0776f7a890b523a, https://usegalaxy.org.au/published/workflow?id=f05ed1e5c5dfffa9, https://usegalaxy.org/published/workflow?id=524602abe59b18f7, https://usegalaxy.org/published/workflow?id=5cd56232e873beab, https://usegalaxy.org/published/workflow?id=a8aee61c2cbaf6ea, https://usegalaxy.org/published/workflow?id=b76a9ce44ea019f1, https://workflowhub.eu/workflows/1352?version=4, https://workflowhub.eu/workflows/1882?version=3 genome-annotation/bacterial-genome-quality-control True False -checkv checkv_end_to_end tabular, fasta Assess quality of single-contig viral genomes 2024-09-13 https://bitbucket.org/berkeleylab/checkv/ 1.0.3 checkv 1.1.0 To update Metagenomics Sequence assembly, Validation, Read mapping Sequence assembly, Validation, Read mapping Metagenomics, Sequence assembly, Metagenomic sequencing, Mapping Metagenomics, Sequence assembly, Metagenomic sequencing, Mapping ufz https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/checkv/ https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/checkv checkv CheckV CheckV is a fully automated command-line pipeline for assessing the quality of single-contig viral genomes, including identification of host contamination for integrated proviruses, estimating completeness for genome fragments, and identification of closed genomes. 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 83 83 4527 4527 1 1 21 21 0 0 0 0 0 0 0 0 4548 4548 84 84 https://usegalaxy.eu/published/workflow?id=36de05d50c703164, https://usegalaxy.eu/published/workflow?id=62392daea25a3980, https://usegalaxy.eu/published/workflow?id=87231a6a7938cb95, https://usegalaxy.eu/published/workflow?id=c62d65832377e376 True False -chopper chopper Filtering and trimming of fastq files with long read sequencing such as PacBio or ONT. 2025-07-22 https://github.com/wdecoster/chopper 0.12.0 chopper 0.12.0 Up-to-date Sequence Analysis, Fastq Manipulation iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/chopper https://github.com/galaxyproject/tools-iuc/tree/main/tools/chopper 0 0 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 6 10 10 0 0 0 0 0 0 0 0 0 0 0 0 10 10 6 6 https://usegalaxy.eu/published/workflow?id=4eb9dfe91fc2dc67, https://usegalaxy.eu/published/workflow?id=93d7a5704ec1d82d, https://usegalaxy.eu/published/workflow?id=ece3ffe0800e6880 True False -cialign cialign fasta, txt, png, tsv Tool to clean, visualise and analyse a multiple sequence alignment 2025-08-04 https://github.com/KatyBrown/CIAlign 1.1.4 cialign 1.1.4 Up-to-date Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign 0 0 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 3 6 6 0 0 0 0 0 0 0 0 0 0 0 0 6 6 3 3 https://usegalaxy.eu/published/workflow?id=93d7a5704ec1d82d True False -clair3 clair3 vcf_bgzip Symphonizing pileup and full-alignment for high-performance long-read variant calling 2022-06-15 https://github.com/HKU-BAL/Clair3 1.0.10 clair3 2.0.1 To update Sequence Analysis, Variant Analysis Variant calling Variant calling Molecular genetics Molecular genetics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/clair3 https://github.com/galaxyproject/tools-iuc/tree/main/tools/clair3 clair3 Clair3 Clair3 is a germline small variant caller for long-reads. Clair3 makes the best of two major method categories: pileup calling handles most variant candidates with speed, and full-alignment tackles complicated candidates to maximize precision and recall. Clair3 runs fast and has superior performance, especially at lower coverage. Clair3 is simple and modular for easy deployment and integration. 1 1 1 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 328 328 5269 5269 52 52 1858 1858 13 13 246 246 2 2 54 54 7427 7427 395 395 https://usegalaxy.eu/published/workflow?id=09c7069ae409c362, https://usegalaxy.eu/published/workflow?id=3f0b104a74acf869, https://usegalaxy.eu/published/workflow?id=60e0b2a28a900178, https://usegalaxy.eu/published/workflow?id=64abcddeb516a712, https://usegalaxy.eu/published/workflow?id=6aa2891bd2b41f32, https://usegalaxy.eu/published/workflow?id=cb54883452a73019, https://usegalaxy.eu/published/workflow?id=cdf2f02428f5f83f, https://usegalaxy.eu/published/workflow?id=d215a2e554fd83bc, https://usegalaxy.org.au/published/workflow?id=0e11619979c2830c, https://usegalaxy.org.au/published/workflow?id=244ea5e94237ebad, https://usegalaxy.org.au/published/workflow?id=76a0a3af8de11622, https://usegalaxy.org.au/published/workflow?id=857e482acfcb2dba, https://usegalaxy.org/published/workflow?id=29ba77708cdafe0f, https://usegalaxy.org/published/workflow?id=38911ba6f66d80f6, https://usegalaxy.org/published/workflow?id=3e703abaeb870f6f, https://usegalaxy.org/published/workflow?id=6d778eeb176d563c, https://usegalaxy.org/published/workflow?id=cb810cdaa4915f4b, https://workflowhub.eu/workflows/1063?version=5, https://workflowhub.eu/workflows/1479?version=1 microbiome/pathogen-detection-from-nanopore-foodborne-data True False -clinod clinod tabular NoD: a Nucleolar localization sequence detector for eukaryotic and viral proteins 2013-05-02 http://www.compbio.dundee.ac.uk/www-nod/ 0.1.0 clinod 1.3 To update Sequence Analysis Nucleic acid sequence analysis Nucleic acid sequence analysis Sequence analysis Sequence analysis peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/clinod https://github.com/peterjc/pico_galaxy/tree/master/tools/clinod clinod clinod The command line NoD predictor (clinod) can be run from the command line to predict Nucleolar localization sequences (NoLSs) that are short targeting sequences responsible for the localization of proteins to the nucleolus.The predictor accepts a list of FASTA formatted sequences as an input and outputs the NOLS predictions as a result.Please note that currently, JPred secondary structure predictions are not supported by clinod. However, we are working on it. 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 31 31 585 585 0 0 0 0 0 0 0 0 585 585 31 31 True False -clustalw clustalw clustal, nhx ClustalW multiple sequence alignment program for DNA or proteins 2022-10-02 http://www.clustal.org/clustal2/ 2.1 clustalw 2.1 Up-to-date Phylogenetics, Sequence Analysis Multiple sequence alignment Multiple sequence alignment Phylogeny, Sequence analysis Phylogeny, Sequence analysis devteam https://github.com/galaxyproject/tools-iuc/tree/main/tools/clustalw https://github.com/galaxyproject/tools-iuc/tree/main/tools/clustalw clustal2 Clustal 2 (Clustal W, Clustal X) Multiple sequence alignment program with a command-line interface (Clustal W) and a graphical user interface (Clustal X). The display colours allow conserved features to be highlighted for easy viewing in the alignment. It is available for several platforms, including Windows, Macintosh PowerMac, Linux and Solaris.Names occassionally spelled also as Clustal W2, ClustalW2, ClustalW, ClustalX, Clustal2. 1 1 1 1 0 0 0 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 2268 2506 114395 117339 3966 8263 54653 99642 837 966 11073 13924 42 43 726 730 231635 180847 11778 7113 https://usegalaxy.eu/published/workflow?id=36de05d50c703164, https://usegalaxy.eu/published/workflow?id=376119528377a3ae, https://usegalaxy.eu/published/workflow?id=3e0246389fb70340, https://usegalaxy.eu/published/workflow?id=974cc681d07ec788, https://usegalaxy.eu/published/workflow?id=c8bc4af6dd3b5d02, https://usegalaxy.eu/published/workflow?id=f6a763951d815944, https://usegalaxy.org.au/published/workflow?id=b60922a253df6654, https://usegalaxy.org.au/published/workflow?id=eda40b58616a0fe4, https://usegalaxy.org/published/workflow?id=042758b8a8c5ac80, https://usegalaxy.org/published/workflow?id=07f7198b63108131, https://usegalaxy.org/published/workflow?id=18e7a954c0b6e4bc, https://usegalaxy.org/published/workflow?id=2d3063882d8239ff, https://usegalaxy.org/published/workflow?id=3d7baebefa7c9b81, https://usegalaxy.org/published/workflow?id=3ef08553982f6ffc, https://usegalaxy.org/published/workflow?id=603e5c61c57bcf3f, https://usegalaxy.org/published/workflow?id=6a1eb7e7bececba1, https://usegalaxy.org/published/workflow?id=75c2cf36253194c2, https://usegalaxy.org/published/workflow?id=7b68f97bf88f99b9, https://usegalaxy.org/published/workflow?id=87685c6247521b54, https://usegalaxy.org/published/workflow?id=8b7e03f09b0183d9, https://usegalaxy.org/published/workflow?id=a484a1e1a7335696, https://usegalaxy.org/published/workflow?id=b2fb90873471f4e7, https://usegalaxy.org/published/workflow?id=be9bd7286d38c210, https://workflowhub.eu/workflows/1060?version=1, https://workflowhub.eu/workflows/1487?version=2, https://workflowhub.eu/workflows/1541?version=1, https://workflowhub.eu/workflows/1656?version=1, https://workflowhub.eu/workflows/358?version=1 ecology/phylogeny-data-prep, genome-annotation/hpc-for-lsgc, microbiome/pathogen-detection-from-nanopore-foodborne-data True False -codeml codeml txt Detects positive selection 2017-07-19 http://abacus.gene.ucl.ac.uk/software/paml.html 4.9 paml 4.10.10 To update Phylogenetics Probabilistic sequence generation, Phylogenetic tree generation (maximum likelihood and Bayesian methods), Phylogenetic tree analysis Probabilistic sequence generation Phylogenetics, Sequence analysis Phylogenetics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/codeml https://github.com/galaxyproject/tools-iuc/tree/main/tools/codeml paml PAML Package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 72 84 62891 63000 0 0 0 0 0 0 0 0 0 0 0 0 63000 62891 84 72 True False -cojac cooc_mutbamscan, cooc_pubmut, cooc_tabmut yaml, json, tabular, tsv, csv, html co-occurrence of mutations on amplicons 2022-08-11 https://github.com/cbg-ethz/cojac 0.9.3 cojac 0.9.3 Up-to-date Metagenomics, Sequence Analysis Genetic variation Genetic variation iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/cojac https://github.com/galaxyproject/tools-iuc/tree/main/tools/cojac cojac COJAC CoOccurrence adJusted Analysis and Calling - The cojac package comprises a set of command-line tools to analyse co-occurrence of mutations on amplicons. It is useful, for example, for early detection of viral variants of concern (e.g. Alpha, Delta, Omicron) in environmental samples, and has been designed to scan for multiple SARS-CoV-2 variants in wastewater samples, as analyzed jointly by ETH Zurich, EPFL and Eawag. 2 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 13 13 2763 2763 7 7 20 20 0 0 0 0 0 0 0 0 2783 2783 20 20 https://usegalaxy.eu/published/workflow?id=d88145e7475e0b7b True False -combine_metaphlan2_humann2 combine_metaphlan_humann tabular Combine MetaPhlAn2 and HUMAnN2 outputs to relate genus/species abundances and gene families/pathways abundances 2023-07-20 0.3.0 python To update Metagenomics Aggregation Aggregation Metagenomics, Molecular interactions, pathways and networks Metagenomics, Molecular interactions, pathways and networks bebatut https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2 https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan_humann combine_metaphlan_and_humann Combine Metaphlan and HUMAnN This tool combine MetaPhlAn outputs and HUMANnN outputs 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 112 112 1972 1972 31 31 128 128 0 0 0 0 12 12 25 25 2125 2125 155 155 https://usegalaxy.eu/published/workflow?id=69eddfde874af35b, https://usegalaxy.eu/published/workflow?id=9472be79da012999, https://usegalaxy.fr/published/workflow?id=c4f6062e51d0f45e, https://workflowhub.eu/workflows/1466?version=2 microbiome/metatranscriptomics True False -comebin comebin Binning of metagenomic contigs using COntrastive Multi-viEw representation learning 2025-07-03 https://github.com/ziyewang/COMEBin 1.0.4 comebin 1.0.4 Up-to-date Metagenomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/comebin https://github.com/galaxyproject/tools-iuc/tree/main/tools/comebin 0 0 1 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 2 2 0 0 0 0 0 0 0 0 0 0 0 0 2 2 1 1 True False -comebin_bam comebin_bam bam Generate bam file for COMEBin 2025-11-07 https://github.com/ziyewang/COMEBin 1.0.4 comebin 1.0.4 Up-to-date Metagenomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/comebin_bam/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/comebin_bam 0 0 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False -compare_humann2_output compare_humann2_output tabular, txt Compare outputs of HUMAnN2 for several samples and extract similar and specific information 2022-10-19 0.2.0 To update Metagenomics Comparison Comparison Metagenomics, Gene and protein families Metagenomics, Gene and protein families bebatut https://github.com/bgruening/galaxytools/tree/master/tools/compare_humann2_output https://github.com/bgruening/galaxytools/tree/master/tools/compare_humann2_output compare_humann2_outputs Compare HUMAnN2 outputs This tool compare HUMANnN2 outputs with gene families or pathways and their relative abundances between several samples 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 23 32 248 332 0 0 0 0 0 0 0 0 0 0 0 0 332 248 32 23 True False -compleasm compleasm tsv, gff3, fasta, txt Compleasm: a faster and more accurate reimplementation of BUSCO 2023-12-04 https://github.com/huangnengCSU/compleasm 0.2.6 compleasm 0.2.7 To update Sequence Analysis Sequence assembly validation Sequence assembly validation Sequence assembly, Genomics, Transcriptomics, Sequence analysis Sequence assembly, Transcriptomics, Sequence analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/compleasm https://github.com/galaxyproject/tools-iuc/tree/main/tools/compleasm compleasm Compleasm Compleasm: a faster and more accurate reimplementation of BUSCO.It provides measures for quantitative assessment of genome assembly, gene set, and transcriptome completeness based on evolutionarily informed expectations of gene content from near-universal single-copy orthologs. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 99 99 675 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https://workflowhub.eu/workflows/67?version=1, https://workflowhub.eu/workflows/688?version=1 assembly/metagenomics-assembly, assembly/vgp_genome_assembly, contributing/create-new-tutorial, ecology/ENA_Biodiv_submission, epigenetics/atac-seq, genome-annotation/crispr-screen, genome-annotation/tnseq, microbiome/metagenomics-assembly, microbiome/metatranscriptomics, microbiome/metatranscriptomics-short, sequence-analysis/quality-control, transcriptomics/clipseq, transcriptomics/minerva-pathways, transcriptomics/ref-based, transcriptomics/rna-interactome, transcriptomics/rna-seq-reads-to-counts True False -dada2 dada2_assignTaxonomyAddspecies, dada2_dada, dada2_filterAndTrim, dada2_learnErrors, dada2_makeSequenceTable, dada2_mergePairs, dada2_plotComplexity, dada2_plotQualityProfile, dada2_primerCheck, dada2_removeBimeraDenovo, dada2_seqCounts tabular, dada2_dada, dada2_errorrates, pdf, dada2_sequencetable, dada2_mergepairs, dada2_uniques DADA2 wrappers 2019-07-05 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This pipeline inputs demultiplexed fastq files, and outputs the sequence variants and their sample-wise abundances after removing substitution and chimera errors. 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When a reliable subunit structure can be calculated from intramolecular restraints, DISCO guarantees that all satisfying oligomer structures will be discovered, yet can run in minutes to hours on only a single desktop-class computer. 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 127 163 280 453 406 435 1525 1690 0 0 0 0 0 0 0 0 2143 1805 598 533 True False -dose_response_analysis_tool dr_curve jpg, tabular A tool for analyzing and visualizing the relationship between various doses and their corresponding biological responses 2024-04-06 https://github.com/bernt-matthias/mb-galaxy-tools 3.0.1 r-drc 3.0_1 To update Ecology ufz https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/tox_tools/dose_responses https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/tox_tools/dose_responses 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False -dram dram_annotate, dram_distill, dram_merge_annotations, dram_neighborhoods, dram_strainer fasta, gff3, tabular, genbank, xlsx, html DRAM for distilling microbial metabolism to automate the curation of microbiome function 2022-09-01 https://github.com/WrightonLabCSU/DRAM 1.5.0 dram 1.5.0 Up-to-date Metagenomics Gene functional annotation Gene functional annotation Metagenomics, Biological databases, Molecular genetics Metagenomics, Biological databases, Molecular genetics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/dram https://github.com/galaxyproject/tools-iuc/tree/main/tools/dram dram DRAM Distilled and Refined Annotation of Metabolism: A tool for the annotation and curation of function for microbial and viral genomes 0 0 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 0 0 120 120 13633 13633 0 0 0 0 0 0 0 0 0 0 0 0 13633 13633 120 120 True False -drep drep_compare, drep_dereplicate dRep compares and dereplicates genome sets 2020-01-06 https://github.com/MrOlm/drep 3.6.2 drep 3.6.2 Up-to-date Metagenomics Genome comparison Genome comparison Metagenomics, Genomics, Sequence analysis Metagenomics, Sequence analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/drep https://github.com/galaxyproject/tools-iuc/tree/main/tools/drep drep dRep Fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication. 2 2 2 2 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 113 115 1708 1749 13 13 47 47 0 0 0 0 38 38 1273 1273 3069 3028 166 164 https://usegalaxy.eu/published/workflow?id=0563f58718be932d, https://usegalaxy.eu/published/workflow?id=1e5f1d9a51032e44, https://usegalaxy.eu/published/workflow?id=7ecd92cb382d8168, https://usegalaxy.eu/published/workflow?id=97312d273b6e8bd9, https://usegalaxy.eu/published/workflow?id=c62d65832377e376, https://workflowhub.eu/workflows/1352?version=4 genome-annotation/bacterial-genome-quality-control, microbiome/mags-building, microbiome/metagenomics-binning True False -ectyper ectyper tabular, txt EC-Typer - in silico serotyping of Escherichia coli species 2018-12-21 https://github.com/phac-nml/ecoli_serotyping 2.0.0 ectyper 2.0.0 Up-to-date Sequence Analysis Sequence assembly, Read pre-processing, Variant calling Sequence assembly, Read pre-processing, Variant calling Whole genome sequencing, Public health and epidemiology, Sequence assembly, Genotype and phenotype, Workflows Whole genome sequencing, Public health and epidemiology, Sequence assembly, Genotype and phenotype, Workflows nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/ectyper https://github.com/phac-nml/galaxy_tools/tree/master/tools/ectyper ectyper ECTyper Ectyper is a standalone serotyping module for Escherichia coli. 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Here, we present ETE v3, featuring numerous improvements in the underlying library of methods, and providing a novel set of standalone tools to perform common tasks in comparative genomics and phylogenetics. The new features include (i) building gene-based and supermatrix-based phylogenies using a single command, (ii) testing and visualizing evolutionary models, (iii) calculating distances between trees of different size or including duplications, and (iv) providing seamless integration with the NCBI taxonomy database. 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The new features include (i) building gene-based and supermatrix-based phylogenies using a single command, (ii) testing and visualizing evolutionary models, (iii) calculating distances between trees of different size or including duplications, and (iv) providing seamless integration with the NCBI taxonomy database. 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Any non-numeric columns will be filtered out. Your first column may contains row names, but it will also work if your first column already corresponds to the numeric values of a variable. 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False -fairy fairy_cov, fairy_sketch tabular, bcsp Fast approximate contig coverage for metagenomic binning 2024-12-20 https://github.com/bluenote-1577/fairy 0.5.8 fairy 0.5.8 Up-to-date Metagenomics Read binning, Sequence assembly validation Read binning, Sequence assembly validation Metagenomics Metagenomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/fairy https://github.com/galaxyproject/tools-iuc/tree/main/tools/fairy fairy fairy fast approximate contig coverage for metagenomic binningFairy computes multi-sample contig coverage for metagenome-assembled genome (MAG) binning.Fairy is used after metagenomic assembly and before binning. 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single-cell/scatac-preprocessing-tenx, transcriptomics/mirna-target-finder, transcriptomics/ref-based, variant-analysis/exome-seq, variant-analysis/somatic-variant-discovery, variant-analysis/somatic-variants True False -fargene fargene txt, tar.gz fARGene (Fragmented Antibiotic Resistance Gene iENntifiEr ) 2019-08-30 https://github.com/fannyhb/fargene 0.1 fargene 0.1 Up-to-date Sequence Analysis Antimicrobial resistance prediction Antimicrobial resistance prediction Metagenomics, Microbiology, Public health and epidemiology, Antimicrobial resistance Metagenomics, Microbiology, Public health and epidemiology iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/fargene https://github.com/galaxyproject/tools-iuc/tree/main/tools/fargene fargene fARGene fARGene (Fragmented Antibiotic Resistance Gene iENntifiEr ) is a tool that takes either fragmented metagenomic data or longer sequences as input and predicts and delivers full-length antiobiotic resistance genes as output. 1 0 1 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 150 159 895 1011 262 287 1203 1346 0 0 0 0 2 2 2 2 2359 2100 448 414 True False -fastani fastani tabular Fast alignment-free computation of whole-genome Average Nucleotide Identity 2020-02-17 https://github.com/ParBLiSS/FastANI 1.3 fastani 1.34 To update Sequence Analysis Genome alignment, Sequence similarity search Genome alignment, Sequence similarity search Microbiology, Genetic variation Microbiology, Genetic variation iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastani https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastani fastani FastANI FastANI is developed for fast alignment-free computation of whole-genome Average Nucleotide Identity (ANI). 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assembly/mrsa-nanopore, ecology/eDNA-taxonomic-analysis, galaxy-interface/workflow-automation, introduction/galaxy-intro-ngs-data-managment, introduction/vsi_qc, microbiome/beer-data-analysis, microbiome/mgnify-amplicon, microbiome/nanopore-16S-metagenomics, microbiome/pathogen-detection-from-nanopore-foodborne-data, sequence-analysis/quality-contamination-control, transcriptomics/differential-isoform-expression, variant-analysis/aiv-analysis, variant-analysis/pox-tiled-amplicon, variant-analysis/sars-cov-2, variant-analysis/tb-variant-analysis True False -fastplong fastplong html, json, fastq Fastplong is used for ultrafast preprocessing and quality control for long reads (Nanopore, PacBio, Cyclone, etc.). 2025-05-06 https://github.com/OpenGene/fastplong 0.4.1 fastplong 0.4.1 Up-to-date Sequence Analysis, Assembly iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastplong https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastplong 0 1 1 0 0 0 0 0 0 0 0 1 0 0 0 0 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https://usegalaxy.org.au/published/workflow?id=5d6773ed5b2f41cb, https://usegalaxy.org.au/published/workflow?id=8fe84de499e96485, https://usegalaxy.org.au/published/workflow?id=bd251174d94cde9d, https://usegalaxy.org.au/published/workflow?id=dd6f465ab1eb10b0, https://usegalaxy.org.au/published/workflow?id=e08b04291839e79a, https://usegalaxy.org/published/workflow?id=20da2dcce0ae2ca2, https://usegalaxy.org/published/workflow?id=56998cc00bcc8088, https://usegalaxy.org/published/workflow?id=7a33bc2d0970b502, https://usegalaxy.org/published/workflow?id=cf2dbc29ca20ebee, https://usegalaxy.org/published/workflow?id=d115312bcda04bf2, https://usegalaxy.org/published/workflow?id=fe262214fba1cb8e sequence-analysis/quality-control True False -fastreer fastreer_dist2tree, fastreer_fasta2dist, fastreer_vcf2dist, fastreer_vcf2tree newick, txt fastreeR toolkit wrappers for phylogenetic trees and distance matrices from VCF and FASTA 2025-11-01 https://github.com/gkanogiannis/fastreeR 2.2.0 fastreer 2.2.0 Up-to-date Phylogenetics, Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastreer https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastreer fastreer 0 0 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False -fastspar fastspar, fastspar_pvalues, fastspar_reduce tabular Tool for rapid and scalable correlation estimation for compositional data. 2025-06-16 https://github.com/scwatts/fastspar/ 1.0.0 fastspar 1.0.0 Up-to-date Metagenomics, Statistics Metagenomics, Microbial ecology Metagenomics, Microbial ecology iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastspar https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastspar FastSpar FastSpar FastSpar is a C++ implementation of the SparCC algorithm for fast correlation estimation from compositional count data such as microbiome OTU tables. 0 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 2 2 0 0 0 0 0 0 0 0 0 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RNA-Seq RNA-Seq iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/featurecounts https://github.com/galaxyproject/tools-iuc/tree/main/tools/featurecounts featurecounts FeatureCounts featureCounts is a very efficient read quantifier. It can be used to summarize RNA-seq reads and gDNA-seq reads to a variety of genomic features such as genes, exons, promoters, gene bodies and genomic bins. 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It is available in Galaxy Europe and as a stand-alone tool.GOEnrichment is flexible in that it allows the user to use any version of the Gene Ontology and any GO annotation file they desire. To enable the use of GO slims, it is accompanied by a sister tool GOSlimmer, which can convert annotation files from full GO to any specified GO slim.The tool features an optional graph clustering algorithm to reduce the redundancy in the set of enriched GO terms and simplify its output.It was developed by the BioData.pt / ELIXIR-PT team at the Instituto Gulbenkian de Ciência. 2 2 2 2 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 799 928 6000 7557 1081 1196 8060 9309 230 233 1602 1647 5 6 39 44 18557 15701 2363 2115 https://usegalaxy.eu/published/workflow?id=5f053303601cc630, https://usegalaxy.eu/published/workflow?id=7136ce9f18c74853, https://usegalaxy.org.au/published/workflow?id=d04b26372b28e8ed, https://workflowhub.eu/workflows/1515?version=1, https://workflowhub.eu/workflows/1667?version=1 single-cell/GO-enrichment, transcriptomics/goenrichment True False -goseq goseq tabular, pdf, rdata goseq does selection-unbiased testing for category enrichment amongst differentially expressed (DE) genes for RNA-seq data 2016-11-12 https://bioconductor.org/packages/release/bioc/html/goseq.html 1.50.0 bioconductor-goseq 1.62.0 To update Statistics, RNA, Micro-array Analysis Gene functional annotation Gene functional annotation RNA-Seq RNA-Seq iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/goseq https://github.com/galaxyproject/tools-iuc/tree/main/tools/goseq goseq GOseq Detect Gene Ontology and/or other user defined categories which are over/under represented in RNA-seq data. 1 1 1 1 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 1 1 1 0 3196 3921 23708 28273 3528 4089 26762 31254 640 680 4461 5015 103 104 751 784 65326 55682 8794 7467 https://usegalaxy.eu/published/workflow?id=032ad839dab7ae70, https://usegalaxy.eu/published/workflow?id=12bf85cdc8102bb5, https://usegalaxy.eu/published/workflow?id=20ada53472782c9b, https://usegalaxy.eu/published/workflow?id=63c91ea322cd2819, https://usegalaxy.eu/published/workflow?id=732fa536cdc70c96, https://usegalaxy.eu/published/workflow?id=9c7a218993788493, https://usegalaxy.eu/published/workflow?id=c1a6d11e1eab6a42, https://usegalaxy.eu/published/workflow?id=e7e26967cf6cb8d8, https://usegalaxy.eu/published/workflow?id=fa83e26e05418370, https://usegalaxy.org.au/published/workflow?id=4f0814ec9f9f8425, https://usegalaxy.org.au/published/workflow?id=5490661d0153962b, https://usegalaxy.org.au/published/workflow?id=71bad95f72c9f30d, https://usegalaxy.org.au/published/workflow?id=75113a1b41904d2a, https://usegalaxy.org.au/published/workflow?id=9f6e62f465589ca3, https://usegalaxy.org.au/published/workflow?id=e1fd89e7248b6661, https://usegalaxy.org/published/workflow?id=053f09b017c85ace, https://usegalaxy.org/published/workflow?id=3dd83e9ceaa9b749, https://usegalaxy.org/published/workflow?id=420a332da24fb9e9, https://usegalaxy.org/published/workflow?id=742120336d5ff997, https://workflowhub.eu/workflows/1194?version=1, https://workflowhub.eu/workflows/1684?version=1, https://workflowhub.eu/workflows/1699?version=1, https://workflowhub.eu/workflows/1708?version=1, https://workflowhub.eu/workflows/1713?version=2, https://workflowhub.eu/workflows/689?version=1 transcriptomics/minerva-pathways, transcriptomics/ref-based, transcriptomics/rna-seq-analysis-clustering-viz, transcriptomics/rna-seq-genes-to-pathways True False -graphlan graphlan, graphlan_annotate png, pdf, ps, eps, svg, phyloxml GraPhlAn is a software tool for producing high-quality circular representations of taxonomic and phylogenetic trees 2017-03-03 https://github.com/biobakery/graphlan graphlan 1.1.3 To update Metagenomics, Graphics, Phylogenetics Phylogenetic inference, Phylogenetic tree visualisation, Phylogenetic tree editing, Taxonomic classification Phylogenetic inference, Phylogenetic tree visualisation, Phylogenetic tree editing, Taxonomic classification Metagenomics, Phylogenetics, Phylogenomics, Cladistics Metagenomics, Phylogenetics, Phylogenomics, Cladistics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/graphlan https://github.com/galaxyproject/tools-iuc/tree/main/tools/graphlan graphlan GraPhlAn GraPhlAn is a software tool for producing high-quality circular representations of taxonomic and phylogenetic trees. GraPhlAn focuses on concise, integrative, informative, and publication-ready representations of phylogenetically- and taxonomically-driven investigation. 2 2 2 2 0 0 0 0 0 2 0 2 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 799 940 11872 13928 325 325 1773 1773 202 207 1432 1470 21 21 90 90 17261 15167 1493 1347 https://usegalaxy.eu/published/workflow?id=05f5f040337786bf, https://usegalaxy.eu/published/workflow?id=096b75501c8e0888, https://usegalaxy.eu/published/workflow?id=19de5cbae7f48103, https://usegalaxy.eu/published/workflow?id=2cf09adb1ed6c3ec, https://usegalaxy.eu/published/workflow?id=4d32b1b3ac0a7161, https://usegalaxy.eu/published/workflow?id=4f21205e71cabd37, https://usegalaxy.eu/published/workflow?id=5f0faac42b0a5062, https://usegalaxy.eu/published/workflow?id=69eddfde874af35b, https://usegalaxy.eu/published/workflow?id=713a5485e2007f90, https://usegalaxy.eu/published/workflow?id=79b4ae4403772098, https://usegalaxy.eu/published/workflow?id=7ab70660e6235cf0, https://usegalaxy.eu/published/workflow?id=87cc0cd143a12c41, https://usegalaxy.eu/published/workflow?id=994e5ff1df7d6c9e, https://usegalaxy.eu/published/workflow?id=9cbba5de2cbeeb0f, https://usegalaxy.eu/published/workflow?id=a8f829deb69b30ab, https://usegalaxy.eu/published/workflow?id=b5f848dc8e96663c, https://usegalaxy.eu/published/workflow?id=c01ef8354b585a1f, https://usegalaxy.eu/published/workflow?id=c3aa516e78ca4191, https://usegalaxy.eu/published/workflow?id=d05c6f0f3205fbd2, https://usegalaxy.eu/published/workflow?id=dfc2c53ac3103eff, https://usegalaxy.eu/published/workflow?id=ec50dd6d56f50db1, https://usegalaxy.eu/published/workflow?id=ed0ad728cf21702b, https://usegalaxy.eu/published/workflow?id=f9175e670d8dfaa1, https://usegalaxy.eu/published/workflow?id=fdca6c9d394986bf, https://usegalaxy.fr/published/workflow?id=09e8293456ee6d99, https://usegalaxy.fr/published/workflow?id=c4f6062e51d0f45e, https://workflowhub.eu/workflows/1451?version=2, https://workflowhub.eu/workflows/1466?version=2 microbiome/metatranscriptomics, microbiome/metatranscriptomics-short True False -groot groot tabular GROOT is a tool to type Antibiotic Resistance Genes (ARGs) in metagenomic samples 2024-05-14 https://github.com/will-rowe/groot 1.1.2 groot 1.1.2 Up-to-date Metagenomics Antimicrobial resistance prediction Antimicrobial resistance prediction Metagenomics, Microbiology, Genomics Metagenomics, Microbiology iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/groot https://github.com/galaxyproject/tools-iuc/tree/main/tools/groot groot GROOT Indexed variation graphs for efficient and accurate resistome profiling. 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 5 5 7 7 0 0 0 0 0 0 0 0 3 3 37 37 44 44 8 8 https://workflowhub.eu/workflows/2068?version=2 True False -gtdb_to_taxdump gtdb_to_taxdump tabular Convert GTDB taxonomy to NCBI taxdump format 2024-08-25 https://github.com/nick-youngblut/gtdb_to_taxdump 0.1.9 gtdb_to_taxdump 0.1.9 Up-to-date Metagenomics Data handling, Mapping, Generation Data handling, Mapping, Generation Computational biology Computational biology iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/gtdb_to_taxdump https://github.com/galaxyproject/tools-iuc/tree/main/tools/gtdb_to_taxdump gtdb_to_taxdump gtdb_to_taxdump Tool with multiple functions. Main functions are to create a DIAMOND database from the GTDB taxonomy data or create a NCBI taxdump format out of this data. This tool can also create a mapping between the taxonomy classification between GTDB and NCBI. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 27 27 1127 1127 0 0 0 0 0 0 0 0 0 0 0 0 1127 1127 27 27 https://usegalaxy.eu/published/workflow?id=cf0159c14418525e, https://usegalaxy.eu/published/workflow?id=e4dabaf57668dbd1, https://workflowhub.eu/workflows/2099?version=1 True False -gtdbtk gtdbtk_classify_wf txt GTDB-Tk is a software tool kit for assigning objective taxonomic classifications to bacterial and archaeal genomesbased on the Genome Database Taxonomy GTDB. It is designed to work with recent advances that allow hundreds orthousands of metagenome-assembled genomes (MAGs) to be obtained directly from environmental samples. It can alsobe applied to isolate and single-cell genomes. 2022-12-13 https://github.com/Ecogenomics/GTDBTk 2.7.2 gtdbtk 2.7.2 Up-to-date Metagenomics Genome alignment, Taxonomic classification, Sequence assembly, Query and retrieval Genome alignment, Taxonomic classification, Sequence assembly, Query and retrieval Metagenomics, Taxonomy, Phylogenetics, Database management, Proteins Metagenomics, Taxonomy, Phylogenetics, Database management, Proteins iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/gtdbtk https://github.com/galaxyproject/tools-iuc/tree/main/tools/gtdbtk GTDB-Tk GTDB-Tk a toolkit to classify genomes with the Genome Taxonomy Database.GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.GTDB-Tk is a software toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes based on the Genome Database Taxonomy GTDB. It is designed to work with recent advances that allow hundreds or thousands of metagenome-assembled genomes (MAGs) to be obtained directly from environmental samples. It can also be applied to isolate and single-cell genomes. The GTDB-Tk is open source and released under the GNU General Public License (Version 3). 1 1 1 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 462 462 3982 3982 305 305 1566 1566 177 177 1095 1095 15 15 1439 1439 8082 8082 959 959 https://usegalaxy.eu/published/workflow?id=0563f58718be932d, https://usegalaxy.eu/published/workflow?id=17d2e76147fc940c, https://usegalaxy.eu/published/workflow?id=1e5f1d9a51032e44, https://usegalaxy.eu/published/workflow?id=2c992e509aa5dd9d, https://usegalaxy.eu/published/workflow?id=7ecd92cb382d8168, https://usegalaxy.eu/published/workflow?id=c62d65832377e376, https://usegalaxy.eu/published/workflow?id=e4dabaf57668dbd1, https://usegalaxy.org/published/workflow?id=33d90e718ce500ef, https://usegalaxy.org/published/workflow?id=8d229c0f58a07ebe, https://usegalaxy.org/published/workflow?id=9b589bc76208fb1e, https://workflowhub.eu/workflows/1352?version=4, https://workflowhub.eu/workflows/2099?version=1 True False -gubbins gubbins txt, gff3, embl, fasta, phylip, csv, vcf Gubbins - bacterial recombination detection 2017-06-22 3.2.1 gubbins 3.4.3 To update Sequence Analysis Genotyping, Phylogenetic inference, Ancestral reconstruction Genotyping, Phylogenetic inference, Ancestral reconstruction Phylogeny, Genotype and phenotype, Whole genome sequencing Phylogeny, Genotype and phenotype, Whole genome sequencing iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/gubbins https://github.com/galaxyproject/tools-iuc/tree/main/tools/gubbins gubbins Gubbins Gubbins is a tool for rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences. 1 1 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 402 428 4731 5118 268 288 3847 4061 250 317 1977 2858 0 0 0 0 12037 10555 1033 920 True False -guppy_basecaller guppy-basecaller fastqsanger, txt A wrapper for the guppy basecaller tool from Oxford Nanopore Technologies 2020-11-18 http://artbio.fr 6.5.7+galaxy0 To update Nanopore artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/guppy https://github.com/ARTbio/tools-artbio/tree/main/tools/guppy 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 7 7 0 0 0 0 7 7 1 1 True False -halla halla tabular, pdf Hierarchical All-against-All association 2025-11-05 https://github.com/biobakery/halla 0.8.40 halla 0.8.40 Up-to-date Metagenomics Statistical calculation, Gene expression profiling, Essential dynamics Statistical calculation, Gene expression profiling, Essential dynamics Microbial ecology, Microarray experiment, Metabolomics, Phylogeny, Epigenetics Microbial ecology, Microarray experiment, Metabolomics, Phylogeny, Epigenetics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/halla https://github.com/galaxyproject/tools-iuc/tree/main/tools/halla halla HAllA High-sensitivity pattern discovery in large, paired multi-omic datasets. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False -hamronization hamronize_summarize, hamronize_tool tabular Convert AMR gene detection tool output to hAMRonization specification format. 2021-02-02 https://github.com/pha4ge/hAMRonization 1.1.4 hamronization 1.2.1 To update Sequence Analysis Data handling, Antimicrobial resistance prediction, Parsing Antimicrobial resistance prediction, Parsing Public health and epidemiology, Microbiology, Bioinformatics Public health and epidemiology, Microbiology, Bioinformatics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/hamronization https://github.com/galaxyproject/tools-iuc/tree/main/tools/hamronization hamronization hAMRonization Parse multiple Antimicrobial Resistance Analysis Reports into a common data structure 0 0 2 2 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 254 254 18459 18459 1 1 20 20 1 1 21 21 6 6 191 191 18691 18691 262 262 https://usegalaxy.eu/published/workflow?id=eb5ab8bc82569eee, https://workflowhub.eu/workflows/1189?version=2, https://workflowhub.eu/workflows/407?version=1, https://workflowhub.eu/workflows/470?version=1 True False -hifiasm_meta hifiasm_meta A hifiasm fork for metagenome assembly using Hifi reads. 2023-01-18 https://github.com/xfengnefx/hifiasm-meta 0.3.1 hifiasm_meta hamtv0.3.1 To update Metagenomics Sequence assembly Sequence assembly Sequence assembly, Metagenomics Sequence assembly, Metagenomics galaxy-australia https://github.com/galaxyproject/tools-iuc/tree/main/tools/hifiasm_meta https://github.com/galaxyproject/tools-iuc/tree/main/tools/hifiasm_meta hifiasm-meta Hifiasm-meta Hifiasm_meta - de novo metagenome assembler, based on hifiasm, a haplotype-resolved de novo assembler for PacBio Hifi reads. 0 1 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 40 40 229 229 0 0 0 0 16 16 368 368 0 0 0 0 597 597 56 56 True False -hivtrace hivtrace txt An application that identifies potential transmission clusters within a supplied FASTA file with an option to find potential links against the Los Alamos HIV Sequence Database. 2015-12-10 1.0.1 hivtrace 1.5.0 To update Sequence Analysis nml https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace https://github.com/phac-nml/galaxy_tools/tree/master/tools/hivtrace 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False -hmmer3 hmmer_alimask, hmmer_hmmalign, hmmer_hmmbuild, hmmer_hmmconvert, hmmer_hmmemit, hmmer_hmmfetch, hmmer_hmmscan, hmmer_hmmsearch, hmmer_jackhmmer, hmmer_nhmmer, hmmer_nhmmscan, hmmer_phmmer stockholm, hmm3, fasta HMMER is used for searching sequence databases for homologs of proteinsequences, and for making protein sequence alignments. It implementsmethods using probabilistic models called profile hidden Markov models(profile HMMs). 2015-02-16 http://hmmer.org/ 3.4 hmmer 3.4 Up-to-date Sequence Analysis Formatting, Multiple sequence alignment, Sequence profile generation, Format validation, Conversion, Sequence generation, Data retrieval, Statistical calculation, Database search, Formatting, Database search, Database search, Probabilistic sequence generation, Statistical calculation, Statistical calculation, Sequence database search, Formatting, Sequence database search, Database search, Sequence database search Formatting, Multiple sequence alignment, Sequence profile generation, Format validation, Conversion, Data retrieval, Statistical calculation, Formatting, Probabilistic sequence generation, Statistical calculation, Statistical calculation, Sequence database search, Formatting, Sequence database search, Sequence database search Sequence analysis, Sequence sites, features and motifs, Gene and protein families Sequence analysis, Sequence sites, features and motifs, Gene and protein families iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/hmmer3 https://github.com/galaxyproject/tools-iuc/tree/main/tools/hmmer3 hmmer3 HMMER3 This tool is used for searching sequence databases for homologs of protein sequences, and for making protein sequence alignments. It implements methods using probabilistic models called profile hidden Markov models. The new HMMER3 project, HMMER is now as fast as BLAST for protein search. 12 12 12 12 0 0 0 0 0 12 12 0 0 0 0 0 0 0 0 0 0 0 0 0 12 12 12 0 380 403 36302 43262 0 0 0 0 83 84 4731 4887 97 97 540 543 48692 41573 584 560 https://usegalaxy.eu/published/workflow?id=02631612a43a4d9b, https://usegalaxy.eu/published/workflow?id=0ab3e47ebd3b520e, https://usegalaxy.eu/published/workflow?id=24eaa682897379c8, https://usegalaxy.eu/published/workflow?id=3eaa913306c16146, https://usegalaxy.eu/published/workflow?id=58955868b504c60d, https://usegalaxy.eu/published/workflow?id=5be158931abca947, https://usegalaxy.eu/published/workflow?id=6158c3b5fc12044e, https://usegalaxy.eu/published/workflow?id=6416cfdbd5273063, https://usegalaxy.eu/published/workflow?id=667bac8d7453e5f1, https://usegalaxy.eu/published/workflow?id=8c91345ed468e22d, https://usegalaxy.eu/published/workflow?id=8deb08d4f228e198, https://usegalaxy.eu/published/workflow?id=9a60ecf98d4f8134, https://usegalaxy.eu/published/workflow?id=d57d41e306241396, https://usegalaxy.fr/published/workflow?id=5ec6d378e60f7ccc, https://usegalaxy.fr/published/workflow?id=7ebb54181b404733, https://usegalaxy.fr/published/workflow?id=b131218bec7eacb4, https://usegalaxy.fr/published/workflow?id=d425a77157cae2ee, https://workflowhub.eu/workflows/100?version=1, https://workflowhub.eu/workflows/37?version=1, https://workflowhub.eu/workflows/38?version=1, https://workflowhub.eu/workflows/39?version=1, https://workflowhub.eu/workflows/40?version=1 True False -humann humann, humann_barplot, humann_join_tables, humann_reduce_table, humann_regroup_table, humann_rename_table, humann_renorm_table, humann_split_stratified_table, humann_split_table, humann_unpack_pathways tabular, biom1, txt, sam, fasta, png, pdf, svg HUMAnN for functionally profiling metagenomes and metatranscriptomes at species-level resolution 2021-05-12 http://huttenhower.sph.harvard.edu/humann 3.9 humann 3.9 Up-to-date Metagenomics Species frequency estimation, Taxonomic classification, Phylogenetic analysis Species frequency estimation, Taxonomic classification, Phylogenetic analysis Metagenomics, Phylogenomics Metagenomics, Phylogenomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/humann https://github.com/galaxyproject/tools-iuc/tree/main/tools/humann humann humann HUMAnN is a pipeline for efficiently and accurately profiling the presence/absence and abundance of microbial pathways in a community from metagenomic or metatranscriptomic sequencing data (typically millions of short DNA/RNA reads). This process, referred to as functional profiling, aims to describe the metabolic potential of a microbial community and its members. More generally, functional profiling answers the question “What are the microbes in my community-of-interest doing (or are capable of doing)?” 6 10 10 10 0 0 0 0 0 10 0 9 0 0 0 0 0 0 0 0 0 0 0 0 6 10 10 0 795 795 52483 52483 123 123 3171 3171 122 122 4812 4812 17 17 987 987 61453 61453 1057 1057 https://usegalaxy.eu/published/workflow?id=21a17d6c473a88c0, https://usegalaxy.eu/published/workflow?id=23dd2253da51e22e, https://usegalaxy.eu/published/workflow?id=3118d383c81cf805, https://usegalaxy.eu/published/workflow?id=4d32b1b3ac0a7161, https://usegalaxy.eu/published/workflow?id=5ce8a472e6e95c60, https://usegalaxy.eu/published/workflow?id=5f0faac42b0a5062, https://usegalaxy.eu/published/workflow?id=69eddfde874af35b, https://usegalaxy.eu/published/workflow?id=713a5485e2007f90, https://usegalaxy.eu/published/workflow?id=87cc0cd143a12c41, https://usegalaxy.eu/published/workflow?id=9472be79da012999, https://usegalaxy.eu/published/workflow?id=a7a6d8ecc2795f58, https://usegalaxy.eu/published/workflow?id=a8f829deb69b30ab, https://usegalaxy.eu/published/workflow?id=b14845359b702444, https://usegalaxy.eu/published/workflow?id=cb2df493f5e334f7, https://usegalaxy.eu/published/workflow?id=d7e532d13a7f1ea6, https://usegalaxy.eu/published/workflow?id=fdca6c9d394986bf, https://usegalaxy.fr/published/workflow?id=c4f6062e51d0f45e, https://usegalaxy.fr/published/workflow?id=fd733565098d76c9, https://workflowhub.eu/workflows/1447?version=2, https://workflowhub.eu/workflows/1456?version=2, https://workflowhub.eu/workflows/1466?version=2 microbiome/metatranscriptomics, microbiome/metatranscriptomics-short True False -hyphy hyphy_absrel, hyphy_annotate, hyphy_b_still, hyphy_bgm, hyphy_busted, hyphy_cfel, hyphy_cln, hyphy_conv, hyphy_fade, hyphy_fel, hyphy_fubar, hyphy_gard, hyphy_infer_stasis_clusters, hyphy_meme, hyphy_prime, hyphy_relax, hyphy_slac, hyphy_sm19, hyphy_strike_ambigs markdown, hyphy_results.json, nhx, nex, fasta, json, txt Hypothesis Testing using Phylogenies 2018-06-08 http://www.hyphy.org 2.5.96 hyphy 2.5.99 To update Phylogenetics Statistical calculation Statistical calculation Phylogeny, Small molecules, Molecular interactions, pathways and networks Phylogeny, Small molecules, Molecular interactions, pathways and networks iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/hyphy https://github.com/galaxyproject/tools-iuc/tree/main/tools/hyphy HyPhy HyPhy Software package for the analysis of genetic sequences using techniques in phylogenetics, molecular evolution, and machine learning. 17 2 19 2 0 0 0 0 0 0 0 0 0 10 0 0 0 0 0 2 0 0 0 0 12 17 12 0 88 94 10953 11906 78 108 4725 8358 33 42 815 909 3 5 22 27 21200 16515 249 202 https://usegalaxy.eu/published/workflow?id=1d40d6deb2da04cc, https://usegalaxy.eu/published/workflow?id=e7f03b4bd9b3d6fd, https://usegalaxy.fr/published/workflow?id=297b71156b297a73, https://usegalaxy.org.au/published/workflow?id=42137e36791652bc, 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https://workflowhub.eu/workflows/788?version=1, https://workflowhub.eu/workflows/789?version=1 True False -icescreen icescreen tabular, txt, genbank.gz, gff3.gz, embl.gz, tar.gz, gz identification of ICEs and IMEs in Bacillota genomes. 2022-01-04 https://forgemia.inra.fr/ices_imes_analysis/icescreen 1.3.3 icescreen 1.3.3 Up-to-date Genome annotation Database search, Protein feature detection Database search, Protein feature detection Mobile genetic elements, Sequence sites, features and motifs, Genomics, Molecular interactions, pathways and networks, Structural variation Mobile genetic elements, Sequence sites, features and motifs, Genomics, Molecular interactions, pathways and networks, Structural variation iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/icescreen https://github.com/galaxyproject/tools-iuc/tree/main/tools/icescreen icescreen ICEscreen A tool to detect Firmicute ICEs and IMEs, isolated or enclosed in composite structures. 1 0 1 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 3 153 153 4 4 15 15 0 0 0 0 0 0 0 0 168 168 7 7 True False -idba idba_hybrid, idba_tran, idba_ud fasta Wrappers for the idba assembler variants. 2018-04-26 https://i.cs.hku.hk/~alse/hkubrg/projects/index.html idba 1.1.3 To update Assembly Sequence assembly Sequence assembly Sequence assembly Sequence assembly iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/idba_ud https://github.com/galaxyproject/tools-iuc/tree/main/tools/idba_ud idba IDBA A short read assembler based on iterative De Bruijn graph. 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Reads are directly assigned to taxa using the NCBI taxonomy and a reference database of protein sequences from Bacteria, Archaea, Fungi, microbial eukaryotes and viruses. 0 0 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 2 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 2 True False -kat_filter kat_@EXECUTABLE@ fastqsanger, tabular Filtering kmers or reads from a database of kmers hashes 2017-03-13 2.3 kat 2.4.2 To update Sequence Analysis nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/kat_filter 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False -khmer khmer_abundance_distribution_single, khmer_abundance_distribution, khmer_count_median, khmer_partition, khmer_extract_partitions, khmer_filter_abundance, khmer_filter_below_abundance_cutoff, khmer_normalize_by_median oxlicg, csv, txt In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more 2015-03-24 https://khmer.readthedocs.org/ 3.0.0a3 khmer 3.0.0a3 Up-to-date Assembly, Next Gen Mappers Standardisation and normalisation, De-novo assembly Standardisation and normalisation, De-novo assembly Sequence assembly Sequence assembly iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/khmer https://github.com/galaxyproject/tools-iuc/tree/main/tools/khmer khmer khmer khmer is a set of command-line tools for working with DNA shotgun sequencing data from genomes, transcriptomes, metagenomes, and single cells. khmer can make de novo assemblies faster, and sometimes better. khmer can also identify (and fix) problems with shotgun data. 8 8 8 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 1 0 0 0 0 8 8 8 0 98 116 1572 2262 169 185 1179 1564 25 25 2179 2179 0 0 0 0 6005 4930 326 292 True False -kleborate kleborate tabular Screen genome assemblies of Klebsiella pneumoniae and the Klebsiella pneumoniae species complex (KpSC) 2022-09-09 https://github.com/katholt/Kleborate 2.3.2 kleborate 3.2.4 To update Metagenomics Multilocus sequence typing, Genome assembly, Virulence prediction Multilocus sequence typing, Genome assembly, Virulence prediction Public health and epidemiology, Metagenomics, Population genomics, Sequence assembly, Whole genome sequencing Public health and epidemiology, Metagenomics, Population genomics, Sequence assembly, Whole genome sequencing iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/kleborate https://github.com/galaxyproject/tools-iuc/tree/main/tools/kleborate kleborate Kleborate Genomic surveillance framework and global population structure for Klebsiella pneumoniae.Kleborate is a tool to screen genome assemblies of Klebsiella pneumoniae and the Klebsiella pneumoniae species complex (KpSC) for:.A manuscript describing the Kleborate software in full is currently in preparation. In the meantime, if you use Kleborate, please cite the preprint: Lam, MMC. et al. Genomic surveillance framework and global population structure for Klebsiella pneumoniae. bioRxiv (2020). 0 0 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 123 123 1479 1479 0 0 0 0 0 0 0 0 0 0 0 0 1479 1479 123 123 True False -kmer2stats kmer2stats tabular A tool for creating data files for statistics based on kmers 2025-04-16 https://github.com/SantaMcCloud/kmer2stats 1.0.1 kmer2stats 1.0.3 To update Metagenomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/kmer2stats https://github.com/galaxyproject/tools-iuc/tree/main/tools/kmer2stats 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 8 8 310 310 0 0 0 0 0 0 0 0 0 0 0 0 310 310 8 8 https://usegalaxy.eu/published/workflow?id=342169b55bdc2993 True False -kmetashot kmetashot csv an alignment-free taxonomic classifier based on k-mer/minimizer counting 2025-12-18 https://github.com/gdefazio/kMetaShot 2.0 kmetashot 2.0 Up-to-date Metagenomics Metagenomics Metagenomics bgruening https://github.com/galaxyproject/tools-iuc/tree/main/tools/kmetashot https://github.com/bgruening/galaxytools/tree/master/tools/kmetashot kmetashot kMetaShot The application of 2nd and 3rd generation High Throughput Sequencing (HTS) technologies has deeply reshaped experimental method to investigate microbial communities and obtain a taxonomic and functional profile of the invetigated community. Shotgun Metagenomics allow to quickly obtain a representation of microorganisms genomes characterizing a particular environment. In order to obtain a fast e reliable taxonomic classification of microorganisms genomes we present kMetaShot, an alignment-free taxonomic classifier based on k-mer/minimizer counting. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False -kmindex kmindex_build, kmindex_query kmindex Index and query k-mers from sequencing samples using Bloom filters 2025-12-10 https://github.com/tlemane/kmindex 0.6.0 kmindex 0.6.0 Up-to-date Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/kmindex https://github.com/galaxyproject/tools-iuc/tree/main/tools/kmindex kmindex kmindex kmindex is a tool for indexing and querying sequencing samples. It is built on top of kmtricks. 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False -kofamscan kofamscan txt, zip Gene function annotation tool based on KEGG Orthology and hidden Markov model 2020-11-12 https://github.com/takaram/kofam_scan 1.3.0 kofamscan 1.3.0 Up-to-date Sequence Analysis Sequence analysis, Gene functional annotation Sequence analysis, Gene functional annotation Genomics, Structure analysis Genomics, Structure analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/kofamscan https://github.com/galaxyproject/tools-iuc/tree/main/tools/kofamscan kofamscan kofamscan KofamScan is a gene function annotation tool based on KEGG Orthology and hidden Markov model. You need KOfam database to use this tool. 0 0 1 1 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 94 94 2904 2904 0 0 0 0 0 0 0 0 2 2 3 3 2907 2907 96 96 https://usegalaxy.eu/published/workflow?id=3eaa913306c16146, https://usegalaxy.eu/published/workflow?id=6158c3b5fc12044e, https://usegalaxy.eu/published/workflow?id=6416cfdbd5273063, https://usegalaxy.eu/published/workflow?id=667bac8d7453e5f1, https://usegalaxy.eu/published/workflow?id=8deb08d4f228e198, https://usegalaxy.eu/published/workflow?id=9b9e1e28f3683f92, https://usegalaxy.eu/published/workflow?id=d57d41e306241396 True False -kraken kraken-filter, kraken-mpa-report, kraken-report, kraken-translate, kraken tabular Kraken is a system for assigning taxonomic labels to short DNAsequences, usually obtained through metagenomic studies. Previous attempts by otherbioinformatics software to accomplish this task have often used sequence alignmentor machine learning techniques that were quite slow, leading to the developmentof less sensitive but much faster abundance estimation programs. Kraken aims toachieve high sensitivity and high speed by utilizing exact alignments of k-mersand a novel classification algorithm. 2017-01-24 http://ccb.jhu.edu/software/kraken/ kraken 1.1.1 To update Metagenomics Taxonomic classification Taxonomic classification Taxonomy, Metagenomics Taxonomy, Metagenomics devteam https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/kraken https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/kraken kraken Kraken System for assigning taxonomic labels to short DNA sequences, usually obtained through metagenomic studies. Previous attempts by other bioinformatics software to accomplish this task have often used sequence alignment or machine learning techniques that were quite slow, leading to the development of less sensitive but much faster abundance estimation programs. It aims to achieve high sensitivity and high speed by utilizing exact alignments of k-mers and a novel classification algorithm. 5 5 5 5 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 2 0 5 5 5 0 1452 1453 75318 75385 2535 4229 59050 144905 904 1133 38078 44609 114 114 3720 3720 268619 176166 6929 5005 https://usegalaxy.org.au/published/workflow?id=b6bad1f167257248, https://usegalaxy.org/published/workflow?id=074a0b1bc8273c16, https://usegalaxy.org/published/workflow?id=2ec3e326c51d3147, https://usegalaxy.org/published/workflow?id=33d90e718ce500ef, https://usegalaxy.org/published/workflow?id=7321c6ad5425d347, https://usegalaxy.org/published/workflow?id=87b3305ea433b4e2, https://usegalaxy.org/published/workflow?id=a89e1018a00b883c, https://usegalaxy.org/published/workflow?id=e0c33057ac2670ba, https://usegalaxy.org/published/workflow?id=fb01e1a49793c8be True False -kraken2 kraken2 tabular Kraken2 for taxonomic designation. 2019-03-05 http://ccb.jhu.edu/software/kraken/ 2.17.1 kraken2 2.17.1 Up-to-date Metagenomics Taxonomic classification Taxonomic classification Taxonomy, Metagenomics, Microbial ecology, Microbiology Taxonomy, Metagenomics, Microbial ecology iuc https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/kraken2/kraken2 https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/kraken2/kraken2 kraken2 kraken2 Kraken 2 is the newest version of Kraken, a taxonomic classification system using exact k-mer matches to achieve high accuracy and fast classification speeds. 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https://github.com/galaxyproject/tools-iuc/tree/main/tools/legsta legsta legsta Performs in silico Legionella pneumophila sequence based typing 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 13 13 134 134 0 0 0 0 0 0 0 0 0 0 0 0 134 134 13 13 True False -lighter lighter Lighter is a kmer-based error correction method for whole genome sequencing data 2016-06-04 https://github.com/mourisl/Lighter 1.0 lighter 1.1.3 To update Sequence Analysis, Fasta Manipulation k-mer counting, Sequence read processing, Sequencing quality control, Sequencing error detection k-mer counting, Sequence read processing, Sequencing quality control, Sequencing error detection Sequencing, Whole genome sequencing, DNA, Genomics Whole genome sequencing, DNA, Genomics bgruening https://github.com/bgruening/galaxytools/tree/master/tools/lighter https://github.com/bgruening/galaxytools/tree/master/tools/lighter lighter Lighter Kmer-based error correction method for whole genome sequencing data. Lighter uses sampling (rather than counting) to obtain a set of kmers that are likely from the genome. 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https://github.com/galaxyproject/tools-iuc/tree/main/tools/longdust https://github.com/galaxyproject/tools-iuc/tree/main/tools/longdust 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False -longorf longORF fasta, tabular obtain longest ORF in six-frame translations 2018-06-01 0.3.0 To update Sequence Analysis mbernt https://github.com/bernt-matthias/mb-galaxy-tools/blob/master/tools/longorf/ https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/longorf 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False -lorikeet_spoligotype lorikeet_spoligotype txt Tools for M. tuberculosis DNA fingerprinting (spoligotyping) 2018-05-07 https://github.com/AbeelLab/lorikeet 20 lorikeet 20 Up-to-date Sequence Analysis Sequence analysis, Genotyping Sequence analysis, Genotyping Genotype and phenotype Genotype and phenotype iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/lorikeet https://github.com/galaxyproject/tools-iuc/tree/main/tools/lorikeet lorikeet lorikeet Tools for M. tuberculosis DNA fingerprinting (spoligotyping) 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 18 18 930 930 0 0 0 0 0 0 0 0 0 0 0 0 930 930 18 18 True False -lotus2 lotus2 zip, tabular, fasta, newick, txt LotuS2 OTU processing pipeline 2021-05-13 https://lotus2.earlham.ac.uk/ 2.32 lotus2 2.34.1 To update Metagenomics Sequence feature detection, DNA barcoding Sequence feature detection, DNA barcoding Metagenomics, Taxonomy, Microbial ecology Metagenomics, Taxonomy, Microbial ecology earlhaminst https://github.com/EarlhamInst/earlham-galaxytools/tree/main/tools/lotus2 https://github.com/EarlhamInst/earlham-galaxytools/tree/main/tools/lotus2 lotus2 lotus2 LotuS2 is a lightweight and user-friendly pipeline that is fast, precise, and streamlined, using extensive pre- and post-ASV/OTU clustering steps to further increase data quality. High data usage rates and reliability enable high-throughput microbiome analysis in minutes. 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 249 249 1979 1979 0 0 0 0 22 22 417 417 2 2 5 5 2401 2401 273 273 https://usegalaxy.eu/published/workflow?id=466bdd8ba7b67264, https://workflowhub.eu/workflows/1460?version=1 microbiome/lotus2-identifying-fungi, microbiome/mgnify-amplicon True False -m6anet m6anet tabular m6anet to detect m6A RNA modifications from nanopore data 2023-10-25 https://m6anet.readthedocs.io/en/latest 2.1.0 m6anet 2.1.0 Up-to-date Sequence Analysis Quantification, Imputation, Gene expression profiling Quantification, Imputation, Gene expression profiling RNA-Seq, Transcriptomics, RNA, Machine learning RNA-Seq, Transcriptomics, RNA, Machine learning iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/m6anet https://github.com/galaxyproject/tools-iuc/tree/main/tools/m6anet m6Anet m6Anet Detection of m6A from direct RNA sequencing using a Multiple Instance Learning framework. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 12 12 47 47 0 0 0 0 0 0 0 0 0 0 0 0 47 47 12 12 True False -maaslin2 maaslin2 zip, tabular, rdata, pdf MaAsLin2 is comprehensive R package for efficiently determining multivariable association between microbial meta'omic features and clinical metadata. 2021-11-05 http://huttenhower.sph.harvard.edu/maaslin 1.18.0 bioconductor-maaslin2 1.18.0 Up-to-date Metagenomics Filtering, Statistical calculation, Standardisation and normalisation, Visualisation Filtering, Standardisation and normalisation, Visualisation Metagenomics, Statistics and probability Metagenomics, Statistics and probability iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/maaslin2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/maaslin2 maaslin2 MaAsLin2 MaAsLin2 is comprehensive R package for efficiently determining multivariable association between phenotypes, environments, exposures, covariates and microbial meta’omic features. MaAsLin2 relies on general linear models to accommodate most modern epidemiological study designs, including cross-sectional and longitudinal, and offers a variety of data exploration, normalization, and transformation methods. 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 100 100 3676 3676 0 0 0 0 0 0 0 0 2 2 4 4 3680 3680 102 102 https://usegalaxy.eu/published/workflow?id=466bdd8ba7b67264, https://usegalaxy.eu/published/workflow?id=4ddf2ec5c460d622, https://usegalaxy.eu/published/workflow?id=e1296dbcf34499b0, https://usegalaxy.eu/published/workflow?id=e69b555faa6bb962 True False -maaslin3 maaslin3 tabular, png, pdf MaAsLin 3 is the next generation of MaAsLin. 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https://github.com/peterjc/galaxy_blast/tree/master/tools/make_nr make_nr make_nr Make a FASTA file non-redundant, with a Galaxy wrapperThis tool is copyright 2018 by Peter Cock, The James Hutton Institute, UK. All rights reserved.This tool is a short Python script intended to be run prior to calling the NCBI BLAST+ command line tool makeblastdb or in other settings where you want to collapse duplicated sequences in a FASTA file to a single representative. 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False -maker maker, maker_map_ids gff3, gff, tabular MAKER is a portable and easily configurable genome annotation pipeline.Its purpose is to allow smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and to create genome databases. 2017-10-04 http://www.yandell-lab.org/software/maker.html 2.31.11 maker 3.01.04 To update Sequence Analysis Genome annotation Genome annotation Genomics, DNA, Sequence analysis Genomics, DNA, Sequence analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/maker https://github.com/galaxyproject/tools-iuc/tree/main/tools/maker maker MAKER Portable and easily configurable genome annotation pipeline. It’s purpose is to allow smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and to create genome databases. 2 2 2 2 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 1323 1455 7332 8835 1701 1808 9536 10359 904 904 4968 4989 33 33 211 211 24394 22047 4200 3961 https://usegalaxy.eu/published/workflow?id=26ad77bc07a7e512, https://usegalaxy.eu/published/workflow?id=6ca20e710f4f3ffb, https://usegalaxy.org.au/published/workflow?id=7a87dfe5bdd30040, https://usegalaxy.org.au/published/workflow?id=7e40485d1ed45b7c, https://usegalaxy.org/published/workflow?id=65b4051e722228b8, https://usegalaxy.org/published/workflow?id=c42c66d1b627c5a5, https://usegalaxy.org/published/workflow?id=dbe08700353dfc43, https://workflowhub.eu/workflows/1323?version=1, https://workflowhub.eu/workflows/1504?version=1, https://workflowhub.eu/workflows/1549?version=1 genome-annotation/annotation-with-maker, genome-annotation/annotation-with-maker-short True False -mapseq mapseq tabular fast and accurate sequence read classification tool designed to assign taxonomy and OTU classifications to ribosomal RNA sequences. 2023-08-02 https://github.com/jfmrod/MAPseq 2.1.1b perl To update Metagenomics k-mer counting k-mer counting Functional, regulatory and non-coding RNA, Sequence analysis, Sequence sites, features and motifs Functional, regulatory and non-coding RNA, Sequence analysis, Sequence sites, features and motifs iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/mapseq https://github.com/galaxyproject/tools-iuc/tree/main/tools/mapseq mapseq MAPseq Highly efficient k-mer search with confidence estimates, for rRNA sequence analysis . 1 0 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 64 64 9612 9612 24 24 434 434 0 0 0 0 0 0 0 0 10046 10046 88 88 https://usegalaxy.eu/published/workflow?id=08e25b733cd796e6, https://usegalaxy.eu/published/workflow?id=437704898229dfb6, https://usegalaxy.eu/published/workflow?id=fb806b88850f3427, 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generation, Clustering, Principal component plotting Imputation, Visualisation, Protein quantification, Standardisation and normalisation, Heat map generation, Clustering Proteomics experiment, Proteomics, Statistics and probability Proteomics experiment, Proteomics, Statistics and probability galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant maxquant MaxQuant Quantitative proteomics software package designed for analyzing large mass-spectrometric data sets. It is specifically aimed at high-resolution MS data. 2 2 2 2 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 1628 1682 7932 8757 775 775 3791 3791 407 416 3720 3831 3 3 33 33 16412 15476 2876 2813 https://usegalaxy.eu/published/workflow?id=0135ee4b3fa0cbce, https://usegalaxy.eu/published/workflow?id=41e9882300fa2386, https://usegalaxy.eu/published/workflow?id=607ca3a9d45bd080, https://usegalaxy.eu/published/workflow?id=8af41219411062ad, https://usegalaxy.eu/published/workflow?id=912b81c444e35045, https://usegalaxy.eu/published/workflow?id=96d198ed953449fd, https://usegalaxy.eu/published/workflow?id=9e0d784860d6cc91, https://usegalaxy.eu/published/workflow?id=a49275eb8b2b2ecb, https://usegalaxy.eu/published/workflow?id=c4119ea7ffd29094, https://usegalaxy.eu/published/workflow?id=d789165f4e0c50eb, https://usegalaxy.eu/published/workflow?id=eb54512829d8509c, https://usegalaxy.org.au/published/workflow?id=1727d16fa4dec19c, https://usegalaxy.org.au/published/workflow?id=43a951ec514498f6, https://usegalaxy.org.au/published/workflow?id=781457327e644c7e, https://usegalaxy.org.au/published/workflow?id=b0a79310e0dc3fb4, https://usegalaxy.org.au/published/workflow?id=ba217a34d7e1b5ee, https://usegalaxy.org/published/workflow?id=2404d5e5b1817825, https://usegalaxy.org/published/workflow?id=e97da2da9e0290a7, https://workflowhub.eu/workflows/1177?version=1, https://workflowhub.eu/workflows/1225?version=1, https://workflowhub.eu/workflows/1396?version=1, https://workflowhub.eu/workflows/1401?version=1, https://workflowhub.eu/workflows/1420?version=1, https://workflowhub.eu/workflows/1421?version=1, https://workflowhub.eu/workflows/1435?version=1, https://workflowhub.eu/workflows/1448?version=1, https://workflowhub.eu/workflows/1468?version=1 microbiome/clinical-mp-2-discovery, microbiome/clinical-mp-4-quantitation, proteomics/DIA_lib_OSW, proteomics/clinical-mp-2-discovery, proteomics/clinical-mp-4-quantitation, proteomics/maxquant-label-free, proteomics/maxquant-msstats-dda-lfq, proteomics/maxquant-msstats-tmt True False -mcl mcl tabular The Markov Cluster Algorithm, a cluster algorithm for graphs 2022-05-12 https://micans.org/mcl/man/mcl.html 22.282 mcl 22.282 Up-to-date Sequence Analysis Clustering, Network analysis, Gene regulatory network analysis Clustering, Gene regulatory network analysis Molecular interactions, pathways and networks Molecular interactions, pathways and networks iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/mcl https://github.com/galaxyproject/tools-iuc/tree/main/tools/mcl mcl MCL MCL is a clustering algorithm widely used in bioinformatics and gaining traction in other fields. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 18 18 153 153 0 0 0 0 0 0 0 0 0 0 0 0 153 153 18 18 True False -medaka medaka_consensus, medaka_consensus_pipeline, medaka_variant h5, txt, fasta, bam, bed, vcf, tabular Sequence correction provided by ONT Research 2020-02-23 https://github.com/nanoporetech/medaka 2.1.1 medaka 2.2.2 To update Sequence Analysis Base-calling, Variant calling, Sequence assembly Base-calling, Variant calling, Sequence assembly Sequence assembly, Machine learning Sequence assembly, Machine learning iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/medaka https://github.com/galaxyproject/tools-iuc/tree/main/tools/medaka medaka Medaka medaka is a tool to create consensus sequences and variant calls from nanopore sequencing data. 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It makes use of succinct de Bruijn graph to achieve low memory usage, whereas its goal is not to make memory usage as low as possible. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 1 1 1 0 200 212 763 862 113 113 338 338 33 33 150 150 6 6 80 80 1430 1331 364 352 https://usegalaxy.eu/published/workflow?id=62c47e3c9d4f3aa3, https://workflowhub.eu/workflows/1390?version=2, https://workflowhub.eu/workflows/1634?version=1 assembly/metagenomics-assembly, microbiome/metagenomics-assembly True False -megan megan_blast2lca, megan_blast2rma, megan_daa2info, megan_daa2rma, megan_daa_meganizer, megan_read_extractor, megan_sam2rma txt, rma6, daa MEGAN Community Edition - Interactive exploration and analysis of large-scale microbiome sequencing data. MEGAN is a tool for studying the taxonomic content of a set of DNA reads, typically collected in a metagenomics project.In a preprocessing step, a sequence alignment of all reads against a suitable database of reference DNA or proteinsequences must be performed to produce an input file for the program. MEGAN is suitable for DNA reads (metagenomedata), RNA reads (metatranscriptome data), peptide sequences (metaproteomics data) and, using a suitable synonymsfile that maps SILVA ids to taxon ids, for 16S rRNA data (amplicon sequencing). 2021-11-24 https://github.com/husonlab/megan-ce 6.21.7 megan 6.25.10 To update Sequence Analysis Sequence analysis, Taxonomic classification Sequence analysis, Taxonomic classification Sequence analysis Sequence analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/megan https://github.com/galaxyproject/tools-iuc/tree/main/tools/megan megan MEGAN Metagenome Analysis Software - MEGAN (MEtaGenome ANalyzer) is a new computer program that allows laptop analysis of large metagenomic datasets. In a preprocessing step, the set of DNA reads (or contigs) is compared against databases of known sequences using BLAST or another comparison tool. MEGAN can then be used to compute and interactively explore the taxonomical content of the dataset, employing the NCBI taxonomy to summarize and order the results. 0 1 7 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 0 0 250 250 5164 5164 0 0 0 0 5 5 72 72 3 3 4 4 5240 5240 258 258 True False -meningotype meningotype tabular Assign sequence type to N. meningitidis genome assemblies 2023-06-06 https://github.com/MDU-PHL/meningotype 0.8.5 meningotype 0.8.6b To update Sequence Analysis Genotyping, Multilocus sequence typing Multilocus sequence typing Microbiology, Genotype and phenotype Microbiology, Genotype and phenotype iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/meningotype https://github.com/galaxyproject/tools-iuc/tree/main/tools/meningotype meningotype meningotype In silico typing of Neisseria meningitidis contigs. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False -merqury merqury, merquryplot txt Merqury is 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Metaeuk combines the fast andsensitive homology search capabilities of MMseqs2 with a dynamic programmingprocedure to recover optimal exons sets. It reduces redundancies in multiplediscoveries of the same gene and resolves conflicting gene predictions onthe same strand. 2020-08-04 https://github.com/soedinglab/metaeuk 7.bba0d80 metaeuk 6.a5d39d9 To update Sequence Analysis, Genome annotation Homology-based gene prediction Homology-based gene prediction Metagenomics, Gene and protein families Metagenomics, Gene and protein families iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/metaeuk https://github.com/galaxyproject/tools-iuc/tree/main/tools/metaeuk MetaEuk MetaEuk MetaEuk - sensitive, high-throughput gene discovery and annotation for large-scale eukaryotic metagenomics 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 57 58 507 509 0 0 0 0 0 0 0 0 0 0 0 0 509 507 58 57 https://usegalaxy.eu/published/workflow?id=9b9e1e28f3683f92 True False -metagene_annotator metagene_annotator txt, tabular, bed MetaGeneAnnotator gene-finding program for prokaryote and phage 2018-03-21 http://metagene.nig.ac.jp/ 1.0 metagene_annotator 1.0 Up-to-date Sequence Analysis Sequence annotation Sequence annotation Genomics, Model organisms, Data submission, annotation and curation Genomics, Model organisms, Data submission, annotation and curation galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metagene_annotator metageneannotator MetaGeneAnnotator Prokaryotic gene finding program from environmental genome shotgun sequences or metagenomic sequences. 0 0 1 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 439 457 20971 21069 0 0 0 0 0 0 0 0 0 0 0 0 21069 20971 457 439 https://usegalaxy.eu/published/workflow?id=3dcf09e75d707573, https://usegalaxy.eu/published/workflow?id=799b924edd3c401b, https://usegalaxy.eu/published/workflow?id=9b9e1e28f3683f92, https://usegalaxy.eu/published/workflow?id=a644e6b450dabca8 True False -metagenomeseq_normalization metagenomeseq_normalizaton tabular, txt metagenomeSeq Normalization 2017-03-27 https://bioconductor.org/packages/3.18/bioc/html/metagenomeSeq.html 1.16.0-0.0.1 bioconductor-metagenomeseq 1.52.0 To update Metagenomics Sequence visualisation, Statistical calculation Sequence visualisation, Statistical calculation Metagenomics, Sequencing Metagenomics, Sequencing iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/metagenomeseq https://github.com/galaxyproject/tools-iuc/tree/main/tools/metagenomeseq metagenomeseq metagenomeSeq Designed to determine features (be it Operational Taxanomic Unit (OTU), species, etc.) that are differentially abundant between two or more groups of multiple samples. It is designed to address the effects of both normalization and under-sampling of microbial communities on disease association detection and the testing of feature correlations. 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 15 23 521 763 28 56 261 530 0 0 0 0 0 0 0 0 1293 782 79 43 True False -metamdbg metamdbg_asm, metamdbg_gfa fasta.gz, tar.gz, txt, gfa1 MetaMDBG is a fast and low-memory assembler for long and accurate metagenomics reads. 2025-02-04 https://github.com/GaetanBenoitDev/metaMDBG 1.4 metamdbg 1.4 Up-to-date Assembly, Metagenomics Genome assembly Genome assembly Metagenomics Metagenomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/metamdbg https://github.com/galaxyproject/tools-iuc/tree/main/tools/metamdbg metamdbg metaMDBG MetaMDBG is a fast and low-memory assembler for long and accurate metagenomics reads (e.g. PacBio HiFi, Nanopore r10.4). It is based on the minimizer de-Brujin graph (MDBG), which have been reimplemetend specifically for metagenomics assembly. 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https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo metanovo MetaNovo An open-source pipeline for probabilistic peptide discovery in complex metaproteomic datasets. 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 40 40 5000 5000 5 5 34 34 4 4 92 92 0 0 0 0 5126 5126 49 49 https://usegalaxy.eu/published/workflow?id=2f7e13eb26c8cd18, https://usegalaxy.eu/published/workflow?id=7cfbf4b7bd3f30d3, https://usegalaxy.eu/published/workflow?id=c6aecbdbeb27585f, https://usegalaxy.eu/published/workflow?id=d7c7a4d6c8072167, https://usegalaxy.eu/published/workflow?id=f2b45a7ff4f449e6, https://usegalaxy.org.au/published/workflow?id=351f3fab960c013b, https://usegalaxy.org/published/workflow?id=2be8ecd5922d23d1, https://workflowhub.eu/workflows/1216?version=1, https://workflowhub.eu/workflows/1461?version=1, https://workflowhub.eu/workflows/1474?version=1 microbiome/clinical-mp-1-database-generation, proteomics/clinical-mp-1-database-generation True False -metaphlan customize_metaphlan_database, extract_metaphlan_database, merge_metaphlan_tables, metaphlan fasta, json, tabular, sam, biom1, fastqsanger MetaPhlAn for Metagenomic Phylogenetic Analysis 2021-03-11 https://github.com/biobakery/MetaPhlAn 4.2.4 metaphlan 4.2.4 Up-to-date Metagenomics Taxonomic classification, Taxonomic classification Taxonomic classification, Taxonomic classification Metagenomics, Phylogenomics Metagenomics, Phylogenomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/metaphlan https://github.com/galaxyproject/tools-iuc/tree/main/tools/metaphlan metaphlan MetaPhlAn Computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data. 1 2 4 4 0 1 0 0 0 4 0 3 0 0 0 0 0 0 0 0 0 0 0 0 1 4 4 0 1552 1552 30934 31014 1122 1122 20021 20021 314 314 6347 6347 28 28 211 211 57593 57513 3016 3016 https://usegalaxy.eu/published/workflow?id=05f5f040337786bf, https://usegalaxy.eu/published/workflow?id=19de5cbae7f48103, 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to finish: read quality control, assembly, visualization, taxonomic profiling, extracting draft genomes (binning), and functional annotation. 0 2 2 2 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 100 1596 1596 0 0 0 0 67 67 587 587 0 0 0 0 2183 2183 167 167 True False -mg_toolkit mg_toolkit_bulk_download, mg_toolkit_original_metadata tsv Metagenomics toolkit enables scientists to download all of the sample metadata for a given study or sequence to a single csv file. 2024-07-12 https://github.com/EBI-Metagenomics/emg-toolkit 0.10.4 mg-toolkit 0.10.4 Up-to-date Metagenomics Data retrieval Data retrieval Metagenomics Metagenomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/mg_toolkit https://github.com/galaxyproject/tools-iuc/tree/main/tools/mg_toolkit mg-toolkit mg-toolkit Metagenomics toolkit enables scientists to download all of the sample metadata for a given study or sequence to a single csv file. 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10 10 21 21 0 0 0 0 0 0 0 0 0 0 0 0 21 21 10 10 True False -mgnify_seqprep mgnify_seqprep fastq.gz A modifiied vesion of SeqPrep. Made for use with the MGnify pipelines. 2024-05-14 https://github.com/jstjohn/SeqPrep 1.2 To update Fastq Manipulation, Sequence Analysis Nucleic acid design Nucleic acid design Genomics, Sequence assembly, Sequencing, Probes and primers Genomics, Sequence assembly, Sequencing, Probes and primers bgruening https://github.com/bgruening/galaxytools/tree/master/tools/mgnify_seqprep https://github.com/bgruening/galaxytools/tree/master/tools/mgnify_seqprep seqprep SeqPrep Strips adapters and optionally merges overlapping paired-end (or paired-end contamination in mate-pair libraries) illumina style reads. 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 6 6 1348 1348 109 109 444 444 0 0 0 0 0 0 0 0 1792 1792 115 115 https://usegalaxy.eu/published/workflow?id=0609a4b1941d1a68, https://usegalaxy.eu/published/workflow?id=9fddc44294236e8f, https://usegalaxy.org/published/workflow?id=20b7ae4b517a80fd, https://usegalaxy.org/published/workflow?id=a71fcbc60caae8b6, https://workflowhub.eu/workflows/1272?version=2, https://workflowhub.eu/workflows/1854?version=1 microbiome/mgnify-amplicon True False -micro_decon micro_decon csv An R package for removing contamination from metabarcoding (e.g., microbiome) datasets post-sequencing 2025-08-05 https://github.com/donaldtmcknight/microdecon 1.0.2 To update Metagenomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/micro_decon https://github.com/galaxyproject/tools-iuc/tree/main/tools/micro_decon 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False -minia minia fasta Short-read assembler based on a de Bruijn graph 2020-04-08 https://gatb.inria.fr/software/minia/ 3.2.6 minia 3.2.6 Up-to-date Assembly Genome assembly Genome assembly Sequence assembly Sequence assembly iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/minia https://github.com/galaxyproject/tools-iuc/tree/main/tools/minia minia Minia Short-read assembler based on a de Bruijn graph, capable of assembling a human genome on a desktop computer in a day. 0 1 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 272 287 6758 7224 0 0 0 0 77 77 357 357 0 0 0 0 7581 7115 364 349 https://usegalaxy.eu/published/workflow?id=9ba580ba8b01db40 True False -miniasm miniasm tabular Miniasm - Ultrafast de novo assembly for long noisy reads (though having no consensus step) 2019-06-18 https://github.com/lh3/miniasm 0.3_r179 miniasm 0.3 To update Assembly De-novo assembly De-novo assembly Genomics, Sequence assembly Genomics, Sequence assembly iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/miniasm https://github.com/galaxyproject/tools-iuc/tree/main/tools/miniasm miniasm miniasm Miniasm is a very fast OLC-based de novo assembler for noisy long reads. It takes all-vs-all read self-mappings (typically by minimap) as input and outputs an assembly graph in the GFA format. 1 1 1 1 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 571 687 11506 14702 474 538 9124 10016 88 96 1235 1277 16 16 166 166 26161 22031 1337 1149 https://usegalaxy.eu/published/workflow?id=249c115413f17f28, https://usegalaxy.eu/published/workflow?id=32d2f5340098bcbd, https://usegalaxy.eu/published/workflow?id=39837ca09374598b, https://usegalaxy.eu/published/workflow?id=44e53ea319e07daa, https://usegalaxy.eu/published/workflow?id=b4de76c0a4d0e23a, https://usegalaxy.eu/published/workflow?id=c48807045e258dd8, https://usegalaxy.eu/published/workflow?id=dc7107896a3f2964, https://usegalaxy.org.au/published/workflow?id=d9571b3dfef34e5e, https://workflowhub.eu/workflows/1477?version=1, https://workflowhub.eu/workflows/406?version=1 microbiome/plasmid-metagenomics-nanopore True False -minipolish minipolish gfa1 Polishing miniasm assemblies 2022-10-19 https://github.com/rrwick/Minipolish 0.2.1 minipolish 0.2.1 Up-to-date Sequence Analysis Localised reassembly, Read depth analysis Localised reassembly, Read depth analysis Sequence assembly, Sequencing Sequence assembly, Sequencing bgruening https://github.com/bgruening/galaxytools/tree/master/tools/minipolish https://github.com/bgruening/galaxytools/tree/master/tools/minipolish minipolish minipolish A tool that bridges the output of miniasm (long-read assembly) and racon (assembly polishing) together to polish a draft assembly. It also provides read depth information in contigs. 0 0 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 43 43 278 278 0 0 0 0 0 0 0 0 0 0 0 0 278 278 43 43 True False -miniprot miniprot, miniprot_index gff3, binary Align a protein sequence against a genome with affine gap penalty, splicing and frameshift. 2022-09-19 https://github.com/lh3/miniprot 0.18 miniprot 0.18 Up-to-date Sequence Analysis Sequence alignment, Protein sequence analysis Sequence alignment, Protein sequence analysis Sequence sites, features and motifs, Sequence analysis Sequence sites, features and motifs, Sequence analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/miniprot https://github.com/galaxyproject/tools-iuc/tree/main/tools/miniprot miniprot miniprot Miniprot aligns a protein sequence against a genome with affine gap penalty, splicing and frameshift. 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MMseqs2 is open source software implemented in C++ for Linux, MacOS, and (as beta version, via cygwin) Windows. The software is designed to run on multiple cores and servers and exhibits very good scalability. MMseqs2 can run 10000 times faster than BLAST. At 100 times its speed it achieves almost the same sensitivity. It can perform profile searches with the same sensitivity as PSI-BLAST at over 400 times its speed.MMseqs2 includes Linclust, the first clustering algorithm whose runtime scales linearly With Linclust we clustered 1.6 billion metagenomic sequence fragments in 10 h on a single server to 50% sequence identity. 2 0 7 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 42 42 260 260 0 0 0 0 0 0 0 0 3 3 29 29 289 289 45 45 https://usegalaxy.eu/published/workflow?id=62392daea25a3980, https://workflowhub.eu/workflows/2024?version=4 True False -mmuphin mmuphin tabular, pdf MMUPHin is an R package implementing meta-analysis methods for microbial community profiles 2024-11-22 https://huttenhower.sph.harvard.edu/mmuphin 1.16.0 bioconductor-mmuphin 1.16.0 Up-to-date Metagenomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/mmuphin https://github.com/galaxyproject/tools-iuc/tree/main/tools/mmuphin mmuphin mmuphin MMUPHin is an R package for meta-analysis tasks of microbiome cohorts. It has function interfaces for: a) covariate-controlled batch- and cohort effect adjustment, b) meta-analysis differential abundance testing, c) meta-analysis unsupervised discrete structure (clustering) discovery, and d) meta-analysis unsupervised continuous structure discovery. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 3 14 14 0 0 0 0 0 0 0 0 0 0 0 0 14 14 3 3 https://usegalaxy.eu/published/workflow?id=466bdd8ba7b67264 True False -mob_suite mob_recon, mob_typer tabular, fasta MOB-suite is a set of software tools for clustering, reconstruction and typing of plasmids from draft assemblies 2018-04-30 https://github.com/phac-nml/mob-suite 3.1.9 mob_suite 3.1.9 Up-to-date Sequence Analysis Clustering, Sequence analysis Clustering, Sequence analysis Metagenomics, Sequence assembly, Genotype and phenotype, Mobile genetic elements, Genomics Metagenomics, Sequence assembly, Genotype and phenotype, Mobile genetic elements nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/mob-suite https://github.com/phac-nml/galaxy_tools/tree/master/tools/mob_suite mob_suite mob_suite MOB-suite: Software tools for clustering, reconstruction and typing of plasmids from draft assembliesThe MOB-suite depends on a series of databases which are too large to be hosted in git-hub. 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mothur_cluster_split, mothur_cluster, mothur_collect_shared, mothur_collect_single, mothur_consensus_seqs, mothur_cooccurrence, mothur_corr_axes, mothur_count_groups, mothur_count_seqs, mothur_create_database, mothur_degap_seqs, mothur_deunique_seqs, mothur_deunique_tree, mothur_dist_seqs, mothur_dist_shared, mothur_fastq_info, mothur_filter_seqs, mothur_filter_shared, mothur_get_communitytype, mothur_get_coremicrobiome, mothur_get_dists, mothur_get_group, mothur_get_groups, mothur_get_label, mothur_get_lineage, mothur_get_mimarkspackage, mothur_get_otulabels, mothur_get_otulist, mothur_get_oturep, mothur_get_otus, mothur_get_rabund, mothur_get_relabund, mothur_get_sabund, mothur_get_seqs, mothur_get_sharedseqs, mothur_heatmap_bin, mothur_heatmap_sim, mothur_homova, mothur_indicator, mothur_lefse, mothur_libshuff, mothur_list_otulabels, mothur_list_seqs, mothur_make_biom, mothur_make_contigs, mothur_make_design, mothur_make_fastq, mothur_make_group, mothur_make_lefse, mothur_make_lookup, mothur_make_shared, mothur_make_sra, mothur_mantel, mothur_merge_count, mothur_merge_files, mothur_merge_groups, mothur_merge_sfffiles, mothur_merge_taxsummary, mothur_metastats, mothur_mimarks_attributes, mothur_nmds, mothur_normalize_shared, mothur_otu_association, mothur_otu_hierarchy, mothur_pairwise_seqs, mothur_parse_list, mothur_parsimony, mothur_pca, mothur_pcoa, mothur_pcr_seqs, mothur_phylo_diversity, mothur_phylotype, mothur_pre_cluster, mothur_primer_design, mothur_rarefaction_shared, mothur_rarefaction_single, mothur_remove_dists, mothur_remove_groups, mothur_remove_lineage, mothur_remove_otulabels, mothur_remove_otus, mothur_remove_rare, mothur_remove_seqs, mothur_rename_seqs, mothur_reverse_seqs, mothur_screen_seqs, mothur_sens_spec, mothur_seq_error, mothur_sffinfo, mothur_shhh_flows, mothur_shhh_seqs, mothur_sort_seqs, mothur_split_abund, mothur_split_groups, mothur_sub_sample, mothur_summary_qual, mothur_summary_seqs, mothur_summary_shared, mothur_summary_single, mothur_summary_tax, mothur_taxonomy_to_krona, mothur_tree_shared, mothur_trim_flows, mothur_trim_seqs, mothur_unifrac_unweighted, mothur_unifrac_weighted, mothur_unique_seqs, mothur_venn mothur.align.check, mothur.align, mothur.align.report, mothur.accnos, tabular, mothur.shared, mothur.cons.taxonomy, mothur.tax.summary, txt, mothur.freq, mothur.quan, mothur.count_table, mothur.seq.taxonomy, mothur.tre, mothur.lower.dist, mothur.rabund, mothur.sabund, mothur.list, mothur.names, mothur.axes, mothur.groups, mothur.pair.dist, fasta, qual454, fastq, mothur.filter, mothur.design, mothur.otu.corr, mothur.relabund, svg, qual, mothur.sff.flow, sff, xml, mothur.summary Mothur wrappers 2016-06-24 https://www.mothur.org 1.0 mothur 1.48.5 To update Metagenomics DNA barcoding, Sequencing quality control, Sequence clustering, Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic analysis DNA barcoding, Sequencing quality control, Sequence clustering, 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Metagenomics bgruening https://github.com/bgruening/galaxytools/tree/master/tools/motus https://github.com/bgruening/galaxytools/tree/master/tools/motus mOTUs Metagenomic operational taxonomic units (mOTUs) Metagenomic operational taxonomic units (mOTUs) enable high-accuracy taxonomic profiling of known (sequenced) and unknown microorganisms at species-level resolution from shotgun metagenomic or metatranscriptomic data. 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microbiome/host-removal, microbiome/mags-building, microbiome/metatranscriptomics, microbiome/metatranscriptomics-short, microbiome/mgnify-amplicon, microbiome/nanopore-16S-metagenomics, microbiome/pathogen-detection-from-nanopore-foodborne-data, sequence-analysis/mapping, sequence-analysis/quality-control, single-cell/scrna-preprocessing, single-cell/scrna-preprocessing-tenx, transcriptomics/differential-isoform-expression, transcriptomics/full-de-novo, transcriptomics/minerva-pathways, transcriptomics/mirna-target-finder, transcriptomics/ref-based, transcriptomics/rna-seq-reads-to-counts, variant-analysis/exome-seq, variant-analysis/sars-cov-2, variant-analysis/somatic-variant-discovery, variant-analysis/somatic-variants, variant-analysis/tb-variant-analysis True False -mykrobe mykrobe_predict csv Antibiotic resistance predictions 2017-12-18 https://github.com/Mykrobe-tools/mykrobe 0.10.0 mykrobe 0.13.0 To update Sequence Analysis Antimicrobial resistance prediction, Variant calling, Genotyping, Sequence trimming Antimicrobial resistance prediction, Variant calling, Genotyping, Sequence trimming Whole genome sequencing, Genotype and phenotype, Probes and primers, Genetic variation, Metagenomics Whole genome sequencing, Genotype and phenotype, Probes and primers, Genetic variation, Metagenomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/mykrobe https://github.com/galaxyproject/tools-iuc/tree/main/tools/mykrobe Mykrobe Mykrobe Antibiotic resistance prediction for Mycobacterium tuberculosis from genome sequence data with Mykrobe.Antibiotic resistance prediction in minutes.Table of Contents generated with DocToc.AMR prediction (Mykrobe predictor).Before attempting to install with bioconda, please ensure you have your channels set up as specified in the documentation. If you don't, you may run into issues with an older version of mykrobe being installed 0 0 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False -mykrobe_parser mykrobe_parseR csv RScript to parse the results of mykrobe predictor. 2018-09-28 https://github.com/phac-nml/mykrobe-parser 0.1.4.1 r-base To update Sequence Analysis nml https://github.com/phac-nml/mykrobe-parser https://github.com/phac-nml/galaxy_tools/tree/master/tools/mykrobe_parser 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False -mz_to_sqlite mz_to_sqlite mz.sqlite Creates a SQLite database for proteomics data 2015-06-01 https://github.com/galaxyproteomics/mzToSQLite 2.1.1+galaxy0 mztosqlite 2.1.1 To update Proteomics Conversion, Peptide database search Conversion, Peptide database search Proteomics, Biological databases Proteomics, Biological databases galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mz_to_sqlite https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mz_to_sqlite mztosqlite mzToSQLite Convert proteomics data files into a SQLite databaseExtract data from proteomics mzIdentML and mass spec scan files: mzML, MGF, etc and store in a SQLite database.The intended purpose is to provide a Galaxy dataset that can support an interactive Galaxy visualization plugin. 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 136 146 868 959 17 17 83 83 18 18 336 336 0 0 0 0 1378 1287 181 171 https://usegalaxy.eu/published/workflow?id=03e52c8c71710cae, https://usegalaxy.eu/published/workflow?id=0aee7ffa5f6384bd, https://usegalaxy.eu/published/workflow?id=2a7e63d1cc583002, https://usegalaxy.eu/published/workflow?id=41d096891bada138, https://usegalaxy.eu/published/workflow?id=41e9882300fa2386, https://usegalaxy.eu/published/workflow?id=6e5f0d05c91876c2, https://usegalaxy.eu/published/workflow?id=8a85663218676b59, https://usegalaxy.eu/published/workflow?id=9a8b5e99ca9500e3, https://usegalaxy.eu/published/workflow?id=b89cf3cb6a25c999, https://usegalaxy.eu/published/workflow?id=eb54512829d8509c, https://usegalaxy.eu/published/workflow?id=edea08c943ff9c5e, https://usegalaxy.org.au/published/workflow?id=1b9bfe7ce484fdc2, https://usegalaxy.org/published/workflow?id=f4486159b08900a4, https://workflowhub.eu/workflows/1429?version=2 proteomics/proteogenomics-dbsearch True False -nanocompore nanocompore_db, nanocompore_sampcomp tabular, tar, txt Nanocompore compares 2 ONT nanopore direct RNA sequencing datasets from different experimental conditions expected to have a significant impact on RNA modifications. It is recommended to have at least 2 replicates per condition. For example one can use a control condition with a significantly reduced number of modifications such as a cell line for which a modification writing enzyme was knocked-down or knocked-out. Alternatively, on a smaller scale transcripts of interests could be synthesized in-vitro. 2020-04-27 https://nanocompore.rna.rocks/ 1.0.0rc3.post2 nanocompore 1.0.4 To update Sequence Analysis Post-translation modification site prediction, PolyA signal detection, Genotyping, k-mer counting PolyA signal detection, Genotyping, k-mer counting Functional, regulatory and non-coding RNA, RNA-Seq, Gene transcripts, Transcriptomics, Transcription factors and regulatory sites Functional, regulatory and non-coding RNA, RNA-Seq, Gene transcripts, Transcriptomics, Transcription factors and regulatory sites iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanocompore https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanocompore Nanocompore Nanocompore RNA modifications detection by comparative Nanopore direct RNA sequencing.RNA modifications detection from Nanopore dRNA-Seq data.Nanocompore identifies differences in ONT nanopore sequencing raw signal corresponding to RNA modifications by comparing 2 samples.Analyses performed for the nanocompore paper.Nanocompore compares 2 ONT nanopore direct RNA sequencing datasets from different experimental conditions expected to have a significant impact on RNA modifications. It is recommended to have at least 2 replicates per condition. For example one can use a control condition with a significantly reduced number of modifications such as a cell line for which a modification writing enzyme was knocked-down or knocked-out. 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update Sequence Analysis Sequence assembly validation, Differential protein expression profiling Sequence assembly validation, Differential protein expression profiling Proteomics, Sequence analysis, Statistics and probability Proteomics, Sequence analysis, Statistics and probability iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/omark https://github.com/galaxyproject/tools-iuc/tree/main/tools/omark omark OMArk OMArk is a software for proteome (protein-coding gene repertoire) quality assessment. 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https://github.com/urmi-21/orfipy 0.0.4 orfipy 0.0.4 Up-to-date Sequence Analysis Coding region prediction, Database search, Transcriptome assembly, De-novo assembly Coding region prediction, Database search, Transcriptome assembly, De-novo assembly Computer science, RNA-Seq, Transcriptomics, Small molecules Computer science, RNA-Seq, Transcriptomics, Small molecules iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/orfipy https://github.com/galaxyproject/tools-iuc/tree/main/tools/orfipy orfipy orfipy A fast and flexible tool for extracting ORFs.orfipy is a tool written in python/cython to extract ORFs in extremely an fast and flexible manner. Other popular ORF searching tools are OrfM and getorf. Compared to OrfM and getorf, orfipy provides the most options to fine tune ORF searches. orfipy uses multiple CPU cores and is particularly faster for data containing multiple smaller fasta sequences such as de-novo transcriptome assemblies. 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It finds orthogroups and orthologs, infers rooted gene trees for all orthogroups and identifies all of the gene duplcation events in those gene trees. It also infers a rooted species tree for the species being analysed and maps the gene duplication events from the gene trees to branches in the species tree. OrthoFinder also provides comprehensive statistics for comparative genomic analyses. 1 1 1 1 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 1 1 0 0 801 801 3870 3870 0 0 0 0 133 133 1450 1450 36 36 221 221 5541 5541 970 970 https://usegalaxy.eu/published/workflow?id=d8492b49aed84d4f, https://usegalaxy.eu/published/workflow?id=e5becc6d66b2568c True False -pacu pacu_map, pacu_snp bam, html PACU is a workflow for whole genome sequencing based phylogeny of Illumina and ONT R9/R10 data. 2024-08-13 https://github.com/BioinformaticsPlatformWIV-ISP/PACU 0.0.5 pacu_snp 1.0.0 To update Sequence Analysis, Phylogenetics Clustering Clustering Phylogenetics, Sequence analysis Phylogenetics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/pacu https://github.com/galaxyproject/tools-iuc/tree/main/tools/pacu pacu PACU PACU is a workflow for whole genome sequencing based phylogeny of Illumina and ONT R9/R10 data.PACU stands for the Prokaryotic Awesome variant Calling Utility and is named after an omnivorous fish (that eats both Illumina and ONT reads). 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 19 19 223 223 0 0 0 0 0 0 0 0 0 0 0 0 223 223 19 19 True False -pal2nal pal2nal txt, html Wraps PAL2NAL to convert protein alignments and nucleotide FASTA into codon-aware alignments. 2025-11-09 http://www.bork.embl.de/pal2nal pal2nal 14.1 To update Sequence Analysis, Phylogenetics iuc https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal https://github.com/galaxyproject/tools-iuc/tree/main/tools/pal2nal 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False -pampa pampa_communitymetrics, pampa_presabs, pampa_glmcomm, pampa_glmsp, pampa_plotglm tabular, txt Tools to compute and analyse biodiversity metrics 2020-06-06 0.0.2 To update Ecology ecology https://github.com/ColineRoyaux/PAMPA-Galaxy https://github.com/galaxyecology/tools-ecology/tree/master/tools/PAMPA 0 5 5 5 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 5 5 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Pipeline. 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 67 67 297 297 0 0 0 0 39 39 312 312 0 0 0 0 609 609 106 106 True False -panta panta json, tsv, csv, txt, fasta Efficient inference of large prokaryotic pangenomes with PanTA. 2025-09-15 https://github.com/amromics/panta 1.0.1 panta 1.0.1 Up-to-date Genome annotation, Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta 0 0 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False -peptideshaker fasta_cli, ident_params, peptide_shaker, search_gui fasta, json, zip, mzid, peptideshaker_archive, txt, tabular, searchgui_archive PeptideShaker and SearchGUI 2015-01-31 http://compomics.github.io searchgui 4.3.15 To update Proteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker 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Description Suite first commit date Homepage Suite version Suite conda package Latest suite conda package version Suite version status ToolShed categories EDAM operations EDAM reduced operations EDAM topics EDAM reduced topics Suite owner Suite source Suite parsed folder bio.tool ID bio.tool name bio.tool description biii ID Related Workflows Related Tutorials Number of tools on UseGalaxy.org (Main) Number of tools on UseGalaxy.org.au Number of tools on UseGalaxy.eu Number of tools on UseGalaxy.fr Number of tools on APOSTL Number of tools on ChemFlow Number of tools on CIRM-CFBP Number of tools on Coloc-stats Number of tools on Galaxy@AuBi Number of tools on Galaxy@Pasteur Number of tools on GalaxyTrakr Number of tools on GASLINI Number of tools on HyPhy HIV NGS Tools Number of tools on ImmPort Galaxy Number of tools on InteractoMIX Number of tools on IPK Galaxy Blast Suite Number of tools on Lebanese University Galaxy Number of tools on Mandoiu Lab Number of tools on MISSISSIPPI 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"""AMRFinderPlus is designed to find acquired antimicrobial resistance genes and point mutations in protein and/or assembled nucleotide sequences.It can also search ""plus"", stress, heat, and biocide resistance and virulence factors for some organisms." 2023-05-12 https://github.com/ncbi/amr 4.2.7 ncbi-amrfinderplus 4.2.7 Up-to-date Sequence Analysis Antimicrobial resistance prediction Antimicrobial resistance prediction Microbiology, Public health and epidemiology, Infectious disease Microbiology, Public health and epidemiology, Infectious disease iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/amrfinderplus https://github.com/galaxyproject/tools-iuc/tree/master/tools/amrfinderplus amrfinderplus AMRFinderPlus "AMRFinderPlus is designed to find acquired antimicrobial resistance genes and point mutations in protein and/or assembled nucleotide sequences.It can also search ""plus"", stress, heat, and biocide resistance and virulence factors for some organisms" 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https://github.com/galaxyproject/tools-iuc/tree/main/tools/abritamr https://github.com/galaxyproject/tools-iuc/tree/master/tools/abritamr abritamr abriTAMR an AMR gene detection pipeline that runs AMRFinderPlus on a single (or list ) of given isolates and collates the results into a table, separating genes identified into functionally relevant groups. https://usegalaxy.eu/published/workflow?id=eb5ab8bc82569eee, https://usegalaxy.org.au/published/workflow?id=7a0c4804e4d4c905, https://workflowhub.eu/workflows/634?version=1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 319 319 2633 2633 0 0 0 0 97 97 880 880 3 3 5 5 3518 3518 419 419 True False +abyss abyss-pe fasta, tabular Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler 2015-04-14 https://github.com/bcgsc/abyss @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ abyss 2.3.10 To update Assembly Genome assembly, De-novo assembly, Scaffolding Genome assembly, De-novo assembly, Scaffolding Sequence assembly Sequence assembly iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/abyss https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss abyss ABySS De novo genome sequence assembler using short reads. 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 1 1 1 0 1258 1368 7148 7779 183 414 505 1305 398 398 2608 2608 11 11 16 16 11708 10277 2191 1850 True False +aldex2 aldex2 tabular, png, pdf Performs analysis Of differential abundance taking sample variation into account 2022-06-29 https://github.com/ggloor/ALDEx_bioc 1.26.0 bioconductor-aldex2 1.42.0 To update Metagenomics Statistical inference Statistical inference Gene expression, Statistics and probability Gene expression, Statistics and probability iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/aldex2 https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 aldex2 ALDEx2 A differential abundance analysis for the comparison of two or more conditions. It uses a Dirichlet-multinomial model to infer abundance from counts, that has been optimized for three or more experimental replicates. Infers sampling variation and calculates the expected FDR given the biological and sampling variation using the Wilcox rank test and Welches t-test, or the glm and Kruskal Wallis tests. Reports both P and fdr values calculated by the Benjamini Hochberg correction. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 64 64 356 356 0 0 0 0 0 0 0 0 0 0 0 0 356 356 64 64 True False +amas amas_concat, amas_remove, amas_replicate, amas_split, amas_summary txt AMAS high-throughput alignment manipulation and summaries for phylogenomics 2025-12-02 https://github.com/marekborowiec/AMAS 1.0 amas 1.0 Up-to-date Phylogenetics, Sequence Analysis, Statistics Nucleic acid sequence analysis, Protein sequence analysis Nucleic acid sequence analysis, Protein sequence analysis Phylogenomics, Phylogenetics, Sequence analysis, Statistics and probability Phylogenomics, Phylogenetics, Statistics and probability iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/amas https://github.com/galaxyproject/tools-iuc/tree/master/tools/amas amas AMAS AMAS (Alignment Manipulation And Summary), a tool that works on amino acid and nucleotide alignments and combines capabilities of sequence manipulation with a function that calculates basic statistics. 0 0 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False +amplican amplican csv, tabular, html, txt, rdata, fasta AmpliCan is an analysis tool for genome editing. 2021-09-22 https://github.com/valenlab/amplican 1.14.0 bioconductor-amplican 1.32.1 To update Sequence Analysis Alignment, Standardisation and normalisation Alignment, Standardisation and normalisation PCR experiment, Statistics and probability PCR experiment, Statistics and probability iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/amplican https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican amplican amplican It performs alignment of the amplicon reads, normalizes gathered data, calculates multiple statistics (e.g. cut rates, frameshifts) and presents results in form of aggregated reports. 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It integrates and cross-links with a large number of in silico secondary metabolite analysis tools that have been published earlier. https://usegalaxy.eu/published/workflow?id=0461bbd1f96292e2, https://usegalaxy.eu/published/workflow?id=0ab3e47ebd3b520e, https://usegalaxy.eu/published/workflow?id=24eaa682897379c8, https://usegalaxy.eu/published/workflow?id=33312e5643279e8a, https://usegalaxy.eu/published/workflow?id=5be158931abca947, https://usegalaxy.eu/published/workflow?id=6984990d0ac2e1e6, https://usegalaxy.eu/published/workflow?id=6a5c39c1d38a10c2, https://usegalaxy.eu/published/workflow?id=6d87481be47902e1, https://usegalaxy.eu/published/workflow?id=9a60ecf98d4f8134, https://usegalaxy.eu/published/workflow?id=a448400f69594135, https://usegalaxy.eu/published/workflow?id=bf48b0eb15e8ff75, https://usegalaxy.eu/published/workflow?id=cc59ae1a9878942c, https://usegalaxy.eu/published/workflow?id=edbaf66c1e97ebdb, https://usegalaxy.eu/published/workflow?id=f141db5179ea8422, 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https://github.com/galaxyproject/tools-iuc/tree/main/tools/argnorm https://github.com/galaxyproject/tools-iuc/tree/master/tools/argnorm argnorm argNorm argNorm is a tool to normalize antibiotic resistance genes (ARGs) by mapping them to the antibiotic resistance ontology (ARO) created by the CARD database.argNorm also enhances antibiotic resistance gene annotations by providing drug categorization of the drugs that antibiotic resistance genes confer resistance to. https://workflowhub.eu/workflows/2024?version=4, https://workflowhub.eu/workflows/2068?version=2 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 48 48 211 211 0 0 0 0 0 0 0 0 3 3 91 91 302 302 51 51 True False +artic artic_guppyplex, artic_minion bam, tabular, vcf_bgzip, fasta, txt The artic pipeline is designed to help run the artic bioinformatics protocols;for example the nCoV-2019 novel coronavirus protocol.Features include: read filtering, primer trimming, amplicon coverage normalisation,variant calling and consensus 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https://workflowhub.eu/workflows/642?version=25, https://workflowhub.eu/workflows/750?version=4, https://workflowhub.eu/workflows/788?version=1, https://workflowhub.eu/workflows/789?version=1 assembly/ERGA-post-assembly-QC, assembly/assembly-with-preprocessing, assembly/chloroplast-assembly, assembly/debruijn-graph-assembly, assembly/largegenome, assembly/metagenomics-assembly, assembly/mrsa-illumina, assembly/mrsa-nanopore, microbiome/metagenomics-assembly, microbiome/pathogen-detection-from-nanopore-foodborne-data, microbiome/plasmid-metagenomics-nanopore 2 2 2 2 0 0 0 0 2 2 0 0 0 0 0 0 0 0 2 0 0 0 2 2 2 0 5065 5359 74766 78507 4846 5038 63998 65491 3140 3234 25266 26126 317 319 9763 9780 179904 173793 13950 13368 True False +bayescan BayeScan txt Detecting natural selection from population-based genetic data 2017-03-09 http://cmpg.unibe.ch/software/BayeScan/index.html 2.1 bayescan 2.1 Up-to-date Sequence Analysis Statistical inference Statistical inference Genetics, Evolutionary biology, Statistics and probability, DNA polymorphism Genetics, Evolutionary biology, Statistics and probability, DNA polymorphism iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/bayescan https://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan bayescan BayeScan BAYEsian genome SCAN for outliers, aims at identifying candidate loci under natural selection from genetic data, using differences in allele frequencies between populations. It is based on the multinomial-Dirichlet model. https://usegalaxy.eu/published/workflow?id=5dc5e056c5f4e0da, https://usegalaxy.eu/published/workflow?id=8f5c84fb0d286050 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 28 35 109 136 0 0 0 0 0 0 0 0 0 0 0 0 136 109 35 28 True False +bbtools bbtools_bbduk, bbtools_bbmap, bbtools_bbmerge, bbtools_bbnorm, bbtools_callvariants, bbtools_tadpole fastqsanger, tabular, fasta, txt, bam, fastq, vcf BBTools is a suite of fast, multithreaded bioinformatics tools designed for analysis of DNA and RNA sequence data.BBTools can handle common sequencing file formats such as fastq, fasta, sam, scarf, fasta+qual, compressed or raw,with autodetection of quality encoding and interleaving. It is written in Java and works on any platform supportingJava, including Linux, MacOS, and Microsoft Windows and Linux; there are no dependencies other than Java (version7 or higher). Program descriptions and options are shown when running the shell scripts with no parameters. 2021-10-04 https://jgi.doe.gov/data-and-tools/bbtools/ 39.08 bbmap 39.81 To update Sequence Analysis RNA-Seq analysis, Sequence trimming, Read mapping, Sequence contamination filtering, Read binning, Sequence alignment RNA-Seq analysis, Sequence trimming, Read mapping, Sequence contamination filtering, Read binning, Sequence alignment Sequencing, RNA splicing, Whole genome sequencing, Phylogenetics, Metagenomics, RNA-Seq RNA splicing, Whole genome sequencing, Phylogenetics, Metagenomics, RNA-Seq iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/bbtools https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools bbmap BBMap BBMap is a fast splice-aware aligner for RNA and DNA. It is faster than almost all short-read aligners, yet retains unrivaled sensitivity and specificity, particularly for reads with many errors and indels. https://usegalaxy.eu/published/workflow?id=d967194ca51ff11e, https://usegalaxy.org.au/published/workflow?id=25f65a29ce3c3ee0, https://workflowhub.eu/workflows/407?version=1, https://workflowhub.eu/workflows/519?version=1 6 4 6 6 0 0 0 0 1 6 6 0 0 0 0 0 0 0 0 0 0 0 0 4 0 0 413 413 25287 25287 562 562 10487 10487 172 172 3537 3537 5 5 134 134 39445 39445 1152 1152 True False +bigscape bigscape html, txt Construct sequence similarity networks of BGCs and groups them into GCF 2024-02-18 https://github.com/medema-group/BiG-SCAPE @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ bigscape 2.0.3 To update Metagenomics Clustering, Global alignment, Fold recognition Clustering, Global alignment, Fold recognition Phylogeny, Microbial ecology, Mapping, Metabolomics, Bioinformatics, Gene and protein families Phylogeny, Microbial ecology, Mapping, Metabolomics, Bioinformatics, Gene and protein families iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/bigscape https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape BiG-SCAPE BiG-SCAPE A computational framework to explore large-scale biosynthetic diversity.BiG-SCAPE (Biosynthetic Gene Similarity Clustering and Prospecting Engine) is a software package, written in Python, that constructs sequence similarity networks of Biosynthetic Gene Clusters (BGCs) and groups them into Gene Cluster Families (GCFs). BiG-SCAPE does this by rapidly calculating a distance matrix between gene clusters based on a comparison of their protein domain content, order, copy number and sequence identity.It defines a distance metric between Gene Clusters using a combination of three indices (Jaccard Index of domain types, Domain Sequence Similarity the Adjacency...BiG-SCAPE and CORASON provide a set of tools to explore the diversity of biosynthetic gene clusters (BGCs) across large numbers of genomes, by constructing BGC sequence similarity networks, grouping BGCs into gene cluster families, and exploring gene cluster diversity linked to enzyme phylogenies. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 95 95 2449 2449 0 0 0 0 0 0 0 0 0 0 0 0 2449 2449 95 95 True False +binette binette tabular Binning refinement tool 2025-01-14 https://github.com/genotoul-bioinfo/Binette @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ binette 1.2.1 To update Metagenomics Read binning Read binning Metagenomics Metagenomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/binette https://github.com/galaxyproject/tools-iuc/tree/master/tools/binette binette Binette Binette is a fast and accurate binning refinement tool to constructs high quality MAGs from the output of multiple binning tools. https://usegalaxy.eu/published/workflow?id=00f15824c7a9b196, https://usegalaxy.eu/published/workflow?id=7ecd92cb382d8168, https://usegalaxy.eu/published/workflow?id=ce5c9287a67e6085, https://usegalaxy.org/published/workflow?id=7251c6e0dad8f927, https://workflowhub.eu/workflows/1352?version=4, https://workflowhub.eu/workflows/2028?version=1, https://workflowhub.eu/workflows/2100?version=2 microbiome/metagenomics-binning 1 1 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 11 11 359 359 8 8 17 17 0 0 0 0 1 1 49 49 425 425 20 20 True False +binning_refiner bin_refiner tabular Reconciles the outputs of different binning programs with the aim to improve the quality of genome bins,especially with respect to contamination levels. 2022-02-18 https://github.com/songweizhi/Binning_refiner 1.4.3 binning_refiner 1.4.3 Up-to-date Metagenomics Read binning, Sequence clustering Read binning, Sequence clustering Metagenomics, Sequence assembly, Microbial ecology Metagenomics, Sequence assembly, Microbial ecology iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/binning_refiner https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner binning_refiner Binning_refiner Improving genome bins through the combination of different binning programs 0 0 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 64 64 236 236 0 0 0 0 0 0 0 0 0 0 0 0 236 236 64 64 True False +bio_hansel bio_hansel tabular Heidelberg and Enteritidis SNP Elucidation 2017-09-29 https://github.com/phac-nml/bio_hansel 2.6.1 bio_hansel 2.6.1 Up-to-date Sequence Analysis Genotyping, SNP detection, Genome assembly Genotyping, SNP detection, Genome assembly Whole genome sequencing, DNA polymorphism, Genotype and phenotype, Infectious disease, Agricultural science Whole genome sequencing, DNA polymorphism, Genotype and phenotype, Infectious disease, Agricultural science iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/hansel https://github.com/galaxyproject/tools-iuc/tree/master/tools/hansel Biohansel BioHansel BioHansel is a tool for performing high-resolution genotyping of bacterial isolates by identifying phylogenetically informative single nucleotide polymorphisms (SNPs), also known as canonical SNPs, in whole genome sequencing (WGS) data. The application uses a fast k-mer matching algorithm to map pathogen WGS data to canonical SNPs contained in hierarchically structured schemas and assigns genotypes based on the detected SNP profile. 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 36 39 312 397 57 63 538 592 0 0 0 0 0 0 0 0 989 850 102 93 True False +biohansel biohansel tabular, json Heidelberg and Enteritidis SNP Elucidation 2018-08-01 https://github.com/phac-nml/biohansel 2.4.0 bio_hansel 2.6.1 To update Sequence Analysis nml https://github.com/phac-nml/biohansel https://github.com/phac-nml/galaxy_tools/tree/master/tools/biohansel 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False +biomformat biom_add_metadata, biom_convert, biom_from_uc, biom_normalize_table, biom_subset_table, biom_summarize_table biom1, txt The biom-format package provides a command line interface and Python API for working with BIOM files. 2016-06-07 https://github.com/biocore/biom-format 2.1.17 biom-format 2.1.7 To update Metagenomics Formatting Formatting Laboratory information management, Sequence analysis Laboratory information management, Sequence analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/biom_format https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format biomformat biomformat "This package includes basic tools for reading biom-format files, accessing and subsetting data tables from a biom object, as well as limited support for writing a biom-object back to a biom-format file. The design of this API is intended to match the python API and other tools included with the biom-format project, but with a decidedly ""R flavor"" that should be familiar to R users. This includes S4 classes and methods, as well as extensions of common core functions/methods." https://usegalaxy.eu/published/workflow?id=08e25b733cd796e6, https://usegalaxy.eu/published/workflow?id=437704898229dfb6, https://usegalaxy.eu/published/workflow?id=466bdd8ba7b67264, https://usegalaxy.eu/published/workflow?id=8f747dbff3216993, https://usegalaxy.eu/published/workflow?id=e14b81a8c0b1b7a4, https://usegalaxy.eu/published/workflow?id=fb806b88850f3427, https://usegalaxy.org.au/published/workflow?id=14e80b7f9f68ec2a, https://usegalaxy.org.au/published/workflow?id=20d472fc5563a640, https://usegalaxy.org.au/published/workflow?id=4f837b7f90d5ebac, https://usegalaxy.org.au/published/workflow?id=869440d35a618836, https://usegalaxy.org.au/published/workflow?id=ca6f29110df8dadc, https://usegalaxy.org/published/workflow?id=45f959d5bf505b15, https://usegalaxy.org/published/workflow?id=8151be18aab3a3c6, https://workflowhub.eu/workflows/1270?version=2, https://workflowhub.eu/workflows/1273?version=2, https://workflowhub.eu/workflows/142?version=1, https://workflowhub.eu/workflows/1842?version=1, https://workflowhub.eu/workflows/1856?version=1, https://workflowhub.eu/workflows/2098?version=1, https://workflowhub.eu/workflows/232?version=1, https://workflowhub.eu/workflows/233?version=1 microbiome/mgnify-amplicon 2 2 6 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 342 356 16688 16852 374 593 2736 5533 166 235 2283 2833 0 0 0 0 25218 21707 1184 882 True False +biotradis bacteria_tradis, tradis_essentiality, tradis_gene_insert_sites txt, tabular.gz, bam, csv, pdf Bio-Tradis is a tool suite dedicated to essentiality analyses with TraDis data. 2020-01-17 https://www.sanger.ac.uk/science/tools/bio-tradis 1.4.5 biotradis 1.4.5 Up-to-date Genome annotation Sequence analysis Sequence analysis Mobile genetic elements, Workflows Mobile genetic elements, Workflows iuc https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/biotradis https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis biotradis biotradis The Bio::TraDIS pipeline provides software utilities for the processing, mapping, and analysis of transposon insertion sequencing data. The pipeline was designed with the data from the TraDIS sequencing protocol in mind, but should work with a variety of transposon insertion sequencing protocols as long as they produce data in the expected format. 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 165 176 6369 6769 0 0 0 0 0 0 0 0 6769 6369 176 165 True False +blast2go blast2go tabular Maps BLAST results to GO annotation terms 2013-09-23 https://github.com/peterjc/galaxy_blast/tree/master/tools/blast2go 0.0.11 b2g4pipe To update Ontology Manipulation, Sequence Analysis Gene functional annotation Gene functional annotation Nucleic acid sites, features and motifs Nucleic acid sites, features and motifs peterjc https://github.com/peterjc/galaxy_blast/tree/master/tools/blast2go https://github.com/peterjc/galaxy_blast/tree/master/tools/blast2go Blast2GO Blast2GO Bioinformatics platform for high-quality functional annotation and analysis of genomic datasets. It allows analyzing and visualizing newly sequenced genomes by combining state-of-the-art methodologies, standard resources and algorithms. It allows to gain biological insights fast and easy even for completely novel genomes. Perform out-of-the-box the entire workflow of functional annotation of your transcriptomic datasets including its analysis and biological interpretation. https://usegalaxy.eu/published/workflow?id=33312e5643279e8a 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 205 303 851 1255 0 0 0 0 0 0 0 0 0 1 0 10 1265 851 304 205 True False +blast_rbh blast_reciprocal_best_hits tabular BLAST Reciprocal Best Hits (RBH) from two FASTA files 2014-05-15 https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh 0.3.0 biopython 1.70 To update Fasta Manipulation, Sequence Analysis Gene functional annotation, Nucleic acid sequence analysis Gene functional annotation, Nucleic acid sequence analysis Nucleic acid sites, features and motifs Nucleic acid sites, features and motifs peterjc https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh blast_rbh blast_rbh This tool is a short Python script to run reciprocal BLAST searches on a pair of sequence files, and extract the reciprocal best hits. https://usegalaxy.eu/published/workflow?id=7f6950394a8c9c4a 0 0 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 413 502 25833 37031 0 0 0 0 0 0 0 0 0 0 0 0 37031 25833 502 413 True False +blastxml_to_top_descr blastxml_to_top_descr tabular Make table of top BLAST match descriptions 2013-09-23 https://github.com/peterjc/galaxy_blast/tree/master/tools/blastxml_to_top_descr 0.1.2 python To update Convert Formats, Sequence Analysis, Text Manipulation Sequence alignment, Sequence annotation Sequence alignment, Sequence annotation Sequence analysis Sequence analysis peterjc https://github.com/peterjc/galaxy_blast/tree/master/tools/blastxml_to_top_descr https://github.com/peterjc/galaxy_blast/tree/master/tools/blastxml_to_top_descr blastxml_to_top_descr blastxml_to_top_descr This tool is a short Python script to parse a BLAST XML file, and extract the identifiers with description for the top matches (by default the top 3), and output these as a simple tabular file along with the query identifiers. https://usegalaxy.eu/published/workflow?id=33312e5643279e8a, https://usegalaxy.eu/published/workflow?id=8f747dbff3216993, https://usegalaxy.eu/published/workflow?id=bebcbd6f0ffa55c5, https://usegalaxy.eu/published/workflow?id=e14b81a8c0b1b7a4 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 530 653 263613 265902 0 0 0 0 0 0 0 0 0 0 0 0 265902 263613 653 530 True False +bmtagger bmtagger remove contaminant reads 2025-11-12 https://ftp.ncbi.nlm.nih.gov/pub/agarwala/bmtagger/ @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ bmtagger 3.101 To update Metagenomics Data filtering, Read pre-processing Read pre-processing Metagenomics Metagenomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/bmtagger https://github.com/galaxyproject/tools-iuc/tree/master/tools/bmtagger bmtagger bmtagger Best Match Tagger for removing contaminant reads from metagenomics datasets 0 0 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False +bracken est_abundance tabular, txt Bayesian Reestimation of Abundance with KrakEN 2019-10-15 https://github.com/jenniferlu717/Bracken/releases 3.1 bracken 3.1p1 To update Sequence Analysis, Metagenomics Statistical calculation Statistical calculation Metagenomics, Microbial ecology Metagenomics, Microbial ecology iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/bracken https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken bracken Bracken Bracken is a companion program to Kraken 1, KrakenUniq, or Kraken 2 While Kraken classifies reads to multiple levels in the taxonomic tree, Bracken allows estimation of abundance at a single level using those classifications (e.g. Bracken can estimate abundance of species within a sample). https://usegalaxy.eu/published/workflow?id=0a82eb8b44d9d502, https://usegalaxy.eu/published/workflow?id=0abd32dbc5207b88, 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https://usegalaxy.org.au/published/workflow?id=2120112358db8e01, https://usegalaxy.org.au/published/workflow?id=41331c03339e2b19, https://usegalaxy.org.au/published/workflow?id=92fcdd490831c6c5, https://usegalaxy.org.au/published/workflow?id=a335b9c9103b57ad, https://usegalaxy.org/published/workflow?id=074a0b1bc8273c16, https://usegalaxy.org/published/workflow?id=1643187038d1ff86, https://usegalaxy.org/published/workflow?id=1be5c982c2d36a6c, https://usegalaxy.org/published/workflow?id=2572128d91500ba1, https://usegalaxy.org/published/workflow?id=2a782ad24271f570, https://usegalaxy.org/published/workflow?id=323c651ca583c9e5, https://usegalaxy.org/published/workflow?id=4f698eaeef30e364, https://usegalaxy.org/published/workflow?id=5308dc1278cef0b5, https://usegalaxy.org/published/workflow?id=623fc80c7f91a33a, https://usegalaxy.org/published/workflow?id=9ba6da7dae465d3e, https://usegalaxy.org/published/workflow?id=9f68718f025bed30, https://usegalaxy.org/published/workflow?id=b6a795834009ce06, https://usegalaxy.org/published/workflow?id=bdd7011a908bc1aa, https://usegalaxy.org/published/workflow?id=de9bf4c1024f8d53, https://usegalaxy.org/published/workflow?id=dfd73857c0eb2a21, https://usegalaxy.org/published/workflow?id=f378960ee55f567e, https://workflowhub.eu/workflows/1052?version=11, https://workflowhub.eu/workflows/1199?version=2, https://workflowhub.eu/workflows/1470?version=2, https://workflowhub.eu/workflows/1644?version=1, https://workflowhub.eu/workflows/1674?version=2, https://workflowhub.eu/workflows/1881?version=2, https://workflowhub.eu/workflows/1882?version=3, https://workflowhub.eu/workflows/2043?version=1 ecology/bacterial-isolate-species-contamination-checking, microbiome/taxonomic-profiling, sequence-analysis/quality-contamination-control 1 1 1 1 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1714 1714 108307 108307 804 804 27569 27569 265 265 8873 8873 59 59 12432 12432 157181 157181 2842 2842 True False +busco busco txt, tabular, png, gff3, fasta BUSCO assess genome and annotation completeness 2017-01-12 https://gitlab.com/ezlab/busco/-/releases 5.8.0 busco 6.1.0 To update Sequence Analysis, Genome annotation Sequence assembly validation Sequence assembly validation Sequence assembly, Genomics, Transcriptomics, Sequence analysis Sequence assembly, Transcriptomics, Sequence analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/busco https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco busco BUSCO Provides measures for quantitative assessment of genome assembly, gene set, and transcriptome completeness based on evolutionarily informed expectations of gene content from near-universal single-copy orthologs. https://usegalaxy.cz/published/workflow?id=932f4901960a595a, https://usegalaxy.eu/published/workflow?id=002a51bdef00e14d, https://usegalaxy.eu/published/workflow?id=007ce6405d196df3, https://usegalaxy.eu/published/workflow?id=01fe4c590e608103, 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8866 256712 250519 14600 14188 True False +cami_amber biobox_add_taxid, cami_amber, cami_amber_add, cami_amber_convert tabular, html Evaluation package for the comparative assessment of genome reconstructions and taxonomic assignments 2024-05-20 https://github.com/CAMI-challenge/AMBER 2.0.7 cami-amber 2.0.7 Up-to-date Metagenomics Read binning Read binning Metagenomics Metagenomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/cami_amber https://github.com/galaxyproject/tools-iuc/tree/master/tools/cami_amber cami-amber AMBER AMBER is an evaluation package for the comparative assessment of genome reconstructions and taxonomic assignments from metagenome benchmark datasets. It provides performance metrics, results rankings, and comparative visualizations for assessing multiple programs or parameter effects. The provided metrics were used in the first community benchmarking challenge of the initiative for the Critical Assessment of Metagenomic Interpretation. https://usegalaxy.eu/published/workflow?id=00f15824c7a9b196, https://usegalaxy.eu/published/workflow?id=17d2e76147fc940c, https://usegalaxy.eu/published/workflow?id=43098b8afe78b071, https://usegalaxy.eu/published/workflow?id=ce5c9287a67e6085, https://usegalaxy.eu/published/workflow?id=e4dabaf57668dbd1, https://workflowhub.eu/workflows/2100?version=2 4 4 4 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 8 8 10522 10522 0 0 0 0 0 0 0 0 0 0 0 0 10522 10522 8 8 True False +canu canu txt, fasta, fasta.gz Canu is a hierarchical assembly pipeline designed for high-noise single-molecule sequencing (such as the PacBio RS II/Sequel or Oxford Nanopore MinION). 2018-06-07 https://github.com/marbl/canu @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ canu 2.3 To update Assembly De-novo assembly De-novo assembly Genomics Genomics bgruening https://github.com/bgruening/galaxytools/tree/master/tools/canu https://github.com/bgruening/galaxytools/tree/master/tools/canu canu CANU De-novo assembly tool for long read chemistry like Nanopore data and PacBio data. https://usegalaxy.eu/published/workflow?id=93d7a5704ec1d82d, https://usegalaxy.org.au/published/workflow?id=344b2ad2604939bc 0 1 1 1 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 1644 1843 13768 17494 0 0 0 0 454 485 3744 4325 37 37 480 480 22299 17992 2365 2135 True False +cawlign cawlign fasta Codon-aware alignment of sequences to a reference. 2025-09-30 https://github.com/veg/cawlign 0.1.15 cawlign 0.1.16 To update Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/cawlign https://github.com/galaxyproject/tools-iuc/tree/master/tools/cawlign 1 0 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False +cd_hit cd_hit txt, fasta Cluster or compare biological sequence datasets 2018-02-26 http://weizhongli-lab.org/cd-hit/ 4.8.1 cd-hit 4.8.1 Up-to-date Sequence Analysis, Fasta Manipulation Sequence clustering Sequence clustering Sequencing Sequencing iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/cdhit https://github.com/galaxyproject/tools-iuc/tree/master/tools/cdhit cd-hit cd-hit Cluster a nucleotide dataset into representative sequences. https://usegalaxy.eu/published/workflow?id=2ee0eb74e839b476, https://usegalaxy.eu/published/workflow?id=974cc681d07ec788, https://usegalaxy.eu/published/workflow?id=9b9e1e28f3683f92, https://usegalaxy.eu/published/workflow?id=bebcbd6f0ffa55c5 0 0 1 1 0 0 0 0 1 0 1 0 0 0 0 0 1 0 0 0 0 0 1 1 1 0 899 899 20148 20148 1 1 2 2 1 1 2 2 57 57 1174 1174 21326 21326 958 958 True False +cd_hit_dup cd_hit_dup fastqsanger, tabular simple tool for removing duplicates from sequencing reads 2015-04-28 0.0.1 cd-hit-auxtools 4.8.1 To update Metagenomics, Sequence Analysis devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/cd_hit_dup https://github.com/galaxyproject/tools-devteam/tree/master/tools/cd_hit_dup https://usegalaxy.org/published/workflow?id=35c2626849348f2c 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 501 770 7542 9437 0 0 0 0 0 0 0 0 9437 7542 770 501 True False +cemitool cemitool tabular, txt, html Gene co-expression network analysis tool 2022-10-10 https://www.bioconductor.org/packages/release/bioc/html/CEMiTool.html 1.34.0 bioconductor-cemitool 1.34.0 Up-to-date Transcriptomics, RNA, Statistics, Single Cell Enrichment analysis, Pathway or network analysis Enrichment analysis, Pathway or network analysis Gene expression, Transcriptomics, Microarray experiment Transcriptomics, Microarray experiment iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/cemitool https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool cemitool CEMiTool It unifies the discovery and the analysis of coexpression gene modules in a fully automatic manner, while providing a user-friendly html report with high quality graphs. Our tool evaluates if modules contain genes that are over-represented by specific pathways or that are altered in a specific sample group. Additionally, CEMiTool is able to integrate transcriptomic data with interactome information, identifying the potential hubs on each network. 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 45 45 354 354 87 87 584 584 6 6 154 154 0 0 0 0 1092 1092 138 138 True False +checkm checkm_analyze, checkm_lineage_set, checkm_lineage_wf, checkm_plot, checkm_qa, checkm_taxon_set, checkm_taxonomy_wf, checkm_tetra, checkm_tree, checkm_tree_qa tabular, zip, fasta, phyloxml, json, newick Assess the quality of microbial genomes recovered from isolates, single cells, and metagenomes 2022-07-29 https://github.com/Ecogenomics/CheckM 1.2.5 checkm-genome 1.2.5 Up-to-date Metagenomics Sequence assembly validation, Validation, Sequence composition calculation, Sequencing quality control, Statistical calculation Sequence assembly validation, Sequence composition calculation, Statistical calculation Genomics, Phylogenomics, Phylogenetics, Taxonomy, Metagenomics, Data quality management Phylogenomics, Phylogenetics, Taxonomy, Metagenomics, Data quality management iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/checkm https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm checkm CheckM CheckM provides a set of tools for assessing the quality of genomes recovered from isolates, single cells, or metagenomes. https://usegalaxy.eu/published/workflow?id=0563f58718be932d, https://usegalaxy.eu/published/workflow?id=1e5f1d9a51032e44, https://usegalaxy.eu/published/workflow?id=3eaa913306c16146, https://usegalaxy.eu/published/workflow?id=5b940b283d91d99d, https://usegalaxy.eu/published/workflow?id=6158c3b5fc12044e, https://usegalaxy.eu/published/workflow?id=6416cfdbd5273063, https://usegalaxy.eu/published/workflow?id=667bac8d7453e5f1, https://usegalaxy.eu/published/workflow?id=8c91345ed468e22d, https://usegalaxy.eu/published/workflow?id=8deb08d4f228e198, https://usegalaxy.eu/published/workflow?id=97312d273b6e8bd9, https://usegalaxy.eu/published/workflow?id=d57d41e306241396, https://usegalaxy.org.au/published/workflow?id=2120112358db8e01, https://usegalaxy.org.au/published/workflow?id=41331c03339e2b19, https://usegalaxy.org.au/published/workflow?id=92fcdd490831c6c5, https://usegalaxy.org/published/workflow?id=7251c6e0dad8f927, https://usegalaxy.org/published/workflow?id=80565301ada0d3eb, https://workflowhub.eu/workflows/1352?version=4 microbiome/mags-building, microbiome/metagenomics-binning 10 10 10 10 0 0 0 0 0 0 10 0 0 0 0 0 0 0 0 0 0 0 1 10 0 0 717 717 12189 12189 179 179 1510 1510 96 96 2254 2254 50 50 1469 1469 17422 17422 1042 1042 True False +checkm2 checkm2 tabular Rapid assessment of genome bin quality using machine learning 2024-11-08 https://github.com/chklovski/CheckM2 @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ checkm2 1.1.0 To update Metagenomics Sequence assembly validation, Validation, Sequence composition calculation, Sequencing quality control, Statistical calculation Sequence assembly validation, Sequence composition calculation, Statistical calculation Genomics, Phylogenomics, Phylogenetics, Taxonomy, Metagenomics, Data quality management Phylogenomics, Phylogenetics, Taxonomy, Metagenomics, Data quality management iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/checkm2 https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm2 checkm CheckM CheckM provides a set of tools for assessing the quality of genomes recovered from isolates, single cells, or metagenomes. https://usegalaxy.eu/published/workflow?id=2a1dc58e51d5f01a, https://usegalaxy.eu/published/workflow?id=3303a04887a47675, https://usegalaxy.eu/published/workflow?id=368d1ac0150ea0b6, https://usegalaxy.eu/published/workflow?id=7371b6918e895e0c, https://usegalaxy.eu/published/workflow?id=7ecd92cb382d8168, https://usegalaxy.eu/published/workflow?id=ba1fda2318046543, https://usegalaxy.eu/published/workflow?id=c62d65832377e376, https://usegalaxy.eu/published/workflow?id=e532d98f4b368666, https://usegalaxy.fr/published/workflow?id=f0776f7a890b523a, https://usegalaxy.org.au/published/workflow?id=f05ed1e5c5dfffa9, https://usegalaxy.org/published/workflow?id=524602abe59b18f7, https://usegalaxy.org/published/workflow?id=5cd56232e873beab, https://usegalaxy.org/published/workflow?id=a8aee61c2cbaf6ea, https://usegalaxy.org/published/workflow?id=b76a9ce44ea019f1, https://workflowhub.eu/workflows/1352?version=4, https://workflowhub.eu/workflows/1882?version=3 genome-annotation/bacterial-genome-quality-control 1 1 1 1 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 228 228 1602 1602 187 187 1322 1322 0 0 0 0 15 15 1268 1268 4192 4192 430 430 True False +checkv checkv_end_to_end tabular, fasta Assess quality of single-contig viral genomes 2024-09-13 https://bitbucket.org/berkeleylab/checkv/ @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ checkv 1.1.1 To update Metagenomics Sequence assembly, Validation, Read mapping Sequence assembly, Validation, Read mapping Metagenomics, Sequence assembly, Metagenomic sequencing, Mapping Metagenomics, Sequence assembly, Metagenomic sequencing, Mapping ufz https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/checkv/ https://github.com/Helmholtz-UFZ/galaxy-tools/tree/master/tools/checkv checkv CheckV CheckV is a fully automated command-line pipeline for assessing the quality of single-contig viral genomes, including identification of host contamination for integrated proviruses, estimating completeness for genome fragments, and identification of closed genomes. https://usegalaxy.eu/published/workflow?id=36de05d50c703164, https://usegalaxy.eu/published/workflow?id=62392daea25a3980, https://usegalaxy.eu/published/workflow?id=87231a6a7938cb95, https://usegalaxy.eu/published/workflow?id=c62d65832377e376 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 83 83 4527 4527 1 1 21 21 0 0 0 0 0 0 0 0 4548 4548 84 84 True False +chopper chopper Filtering and trimming of fastq files with long read sequencing such as PacBio or ONT. 2025-07-22 https://github.com/wdecoster/chopper @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ chopper 0.13.0 To update Sequence Analysis, Fastq Manipulation iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/chopper https://github.com/galaxyproject/tools-iuc/tree/master/tools/chopper https://usegalaxy.eu/published/workflow?id=1ae9a523ef719a3d, https://usegalaxy.eu/published/workflow?id=4eb9dfe91fc2dc67, https://usegalaxy.eu/published/workflow?id=5cd71f9a190cae1b, https://usegalaxy.eu/published/workflow?id=93d7a5704ec1d82d, https://usegalaxy.eu/published/workflow?id=ece3ffe0800e6880 0 0 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 6 10 10 0 0 0 0 0 0 0 0 0 0 0 0 10 10 6 6 True False +cialign cialign fasta, txt, png, tsv Tool to clean, visualise and analyse a multiple sequence alignment 2025-08-04 https://github.com/KatyBrown/CIAlign 1.1.4 cialign 1.1.4 Up-to-date Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign https://github.com/galaxyproject/tools-iuc/tree/master/tools/cialign https://usegalaxy.eu/published/workflow?id=93d7a5704ec1d82d 0 0 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 3 6 6 0 0 0 0 0 0 0 0 0 0 0 0 6 6 3 3 True False +clair3 clair3 vcf_bgzip Symphonizing pileup and full-alignment for high-performance long-read variant calling 2022-06-15 https://github.com/HKU-BAL/Clair3 @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ clair3 2.0.2 To update Sequence Analysis, Variant Analysis Variant calling Variant calling Molecular genetics Molecular genetics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/clair3 https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 clair3 Clair3 Clair3 is a germline small variant caller for long-reads. Clair3 makes the best of two major method categories: pileup calling handles most variant candidates with speed, and full-alignment tackles complicated candidates to maximize precision and recall. Clair3 runs fast and has superior performance, especially at lower coverage. Clair3 is simple and modular for easy deployment and integration. https://usegalaxy.eu/published/workflow?id=09c7069ae409c362, https://usegalaxy.eu/published/workflow?id=3f0b104a74acf869, https://usegalaxy.eu/published/workflow?id=60e0b2a28a900178, https://usegalaxy.eu/published/workflow?id=64abcddeb516a712, https://usegalaxy.eu/published/workflow?id=6aa2891bd2b41f32, https://usegalaxy.eu/published/workflow?id=cb54883452a73019, https://usegalaxy.eu/published/workflow?id=cdf2f02428f5f83f, https://usegalaxy.eu/published/workflow?id=d215a2e554fd83bc, https://usegalaxy.org.au/published/workflow?id=0e11619979c2830c, https://usegalaxy.org.au/published/workflow?id=244ea5e94237ebad, https://usegalaxy.org.au/published/workflow?id=76a0a3af8de11622, https://usegalaxy.org.au/published/workflow?id=857e482acfcb2dba, https://usegalaxy.org/published/workflow?id=29ba77708cdafe0f, https://usegalaxy.org/published/workflow?id=38911ba6f66d80f6, https://usegalaxy.org/published/workflow?id=3e703abaeb870f6f, https://usegalaxy.org/published/workflow?id=6d778eeb176d563c, https://usegalaxy.org/published/workflow?id=cb810cdaa4915f4b, https://workflowhub.eu/workflows/1063?version=5, https://workflowhub.eu/workflows/1479?version=1 microbiome/pathogen-detection-from-nanopore-foodborne-data 1 1 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 328 328 5269 5269 52 52 1858 1858 13 13 246 246 2 2 54 54 7427 7427 395 395 True False +clinod clinod tabular NoD: a Nucleolar localization sequence detector for eukaryotic and viral proteins 2013-05-02 http://www.compbio.dundee.ac.uk/www-nod/ 0.1.0 clinod 1.3 To update Sequence Analysis Nucleic acid sequence analysis Nucleic acid sequence analysis Sequence analysis Sequence analysis peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/clinod https://github.com/peterjc/pico_galaxy/tree/master/tools/clinod clinod clinod The command line NoD predictor (clinod) can be run from the command line to predict Nucleolar localization sequences (NoLSs) that are short targeting sequences responsible for the localization of proteins to the nucleolus.The predictor accepts a list of FASTA formatted sequences as an input and outputs the NOLS predictions as a result.Please note that currently, JPred secondary structure predictions are not supported by clinod. However, we are working on it. 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 31 31 585 585 0 0 0 0 0 0 0 0 585 585 31 31 True False +clustalw clustalw clustal, nhx ClustalW multiple sequence alignment program for DNA or proteins 2022-10-02 http://www.clustal.org/clustal2/ 2.1 clustalw 2.1 Up-to-date Phylogenetics, Sequence Analysis Multiple sequence alignment Multiple sequence alignment Phylogeny, Sequence analysis Phylogeny, Sequence analysis devteam https://github.com/galaxyproject/tools-iuc/tree/main/tools/clustalw https://github.com/galaxyproject/tools-iuc/tree/master/tools/clustalw clustal2 Clustal 2 (Clustal W, Clustal X) Multiple sequence alignment program with a command-line interface (Clustal W) and a graphical user interface (Clustal X). The display colours allow conserved features to be highlighted for easy viewing in the alignment. It is available for several platforms, including Windows, Macintosh PowerMac, Linux and Solaris.Names occassionally spelled also as Clustal W2, ClustalW2, ClustalW, ClustalX, Clustal2. https://usegalaxy.eu/published/workflow?id=36de05d50c703164, https://usegalaxy.eu/published/workflow?id=376119528377a3ae, https://usegalaxy.eu/published/workflow?id=3e0246389fb70340, https://usegalaxy.eu/published/workflow?id=974cc681d07ec788, https://usegalaxy.eu/published/workflow?id=c8bc4af6dd3b5d02, https://usegalaxy.eu/published/workflow?id=f6a763951d815944, https://usegalaxy.org.au/published/workflow?id=b60922a253df6654, https://usegalaxy.org.au/published/workflow?id=eda40b58616a0fe4, https://usegalaxy.org/published/workflow?id=042758b8a8c5ac80, https://usegalaxy.org/published/workflow?id=07f7198b63108131, https://usegalaxy.org/published/workflow?id=18e7a954c0b6e4bc, https://usegalaxy.org/published/workflow?id=2d3063882d8239ff, https://usegalaxy.org/published/workflow?id=3d7baebefa7c9b81, https://usegalaxy.org/published/workflow?id=3ef08553982f6ffc, https://usegalaxy.org/published/workflow?id=603e5c61c57bcf3f, https://usegalaxy.org/published/workflow?id=6a1eb7e7bececba1, https://usegalaxy.org/published/workflow?id=75c2cf36253194c2, https://usegalaxy.org/published/workflow?id=7b68f97bf88f99b9, https://usegalaxy.org/published/workflow?id=87685c6247521b54, https://usegalaxy.org/published/workflow?id=8b7e03f09b0183d9, https://usegalaxy.org/published/workflow?id=a484a1e1a7335696, https://usegalaxy.org/published/workflow?id=b2fb90873471f4e7, https://usegalaxy.org/published/workflow?id=be9bd7286d38c210, https://usegalaxy.org/published/workflow?id=f7bf58d66cafcf1f, https://workflowhub.eu/workflows/1060?version=1, https://workflowhub.eu/workflows/1487?version=2, https://workflowhub.eu/workflows/1541?version=1, https://workflowhub.eu/workflows/1656?version=1, https://workflowhub.eu/workflows/358?version=1 ecology/phylogeny-data-prep, genome-annotation/hpc-for-lsgc, microbiome/pathogen-detection-from-nanopore-foodborne-data 1 1 1 1 0 0 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 2268 2506 114395 117339 3966 8263 54653 99642 837 966 11073 13924 42 43 726 730 231635 180847 11778 7113 True False +codeml codeml txt Detects positive selection 2017-07-19 http://abacus.gene.ucl.ac.uk/software/paml.html 4.9 paml 4.10.10 To update Phylogenetics Probabilistic sequence generation, Phylogenetic tree generation (maximum likelihood and Bayesian methods), Phylogenetic tree analysis Probabilistic sequence generation Phylogenetics, Sequence analysis Phylogenetics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/codeml https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml paml PAML Package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 72 84 62891 63000 0 0 0 0 0 0 0 0 0 0 0 0 63000 62891 84 72 True False +cojac cooc_mutbamscan, cooc_pubmut, cooc_tabmut yaml, json, tabular, tsv, csv, html co-occurrence of mutations on amplicons 2022-08-11 https://github.com/cbg-ethz/cojac 0.9.3 cojac 0.9.3 Up-to-date Metagenomics, Sequence Analysis Genetic variation Genetic variation iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/cojac https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac cojac COJAC CoOccurrence adJusted Analysis and Calling - The cojac package comprises a set of command-line tools to analyse co-occurrence of mutations on amplicons. It is useful, for example, for early detection of viral variants of concern (e.g. Alpha, Delta, Omicron) in environmental samples, and has been designed to scan for multiple SARS-CoV-2 variants in wastewater samples, as analyzed jointly by ETH Zurich, EPFL and Eawag. https://usegalaxy.eu/published/workflow?id=d88145e7475e0b7b 2 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 13 13 2763 2763 7 7 20 20 0 0 0 0 0 0 0 0 2783 2783 20 20 True False +combine_metaphlan2_humann2 combine_metaphlan_humann tabular Combine MetaPhlAn2 and HUMAnN2 outputs to relate genus/species abundances and gene families/pathways abundances 2023-07-20 0.3.0 python To update Metagenomics Aggregation Aggregation Metagenomics, Molecular interactions, pathways and networks Metagenomics, Molecular interactions, pathways and networks bebatut https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2 https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan_humann combine_metaphlan_and_humann Combine Metaphlan and HUMAnN This tool combine MetaPhlAn outputs and HUMANnN outputs https://usegalaxy.eu/published/workflow?id=69eddfde874af35b, https://usegalaxy.eu/published/workflow?id=9472be79da012999, https://usegalaxy.fr/published/workflow?id=c4f6062e51d0f45e, https://workflowhub.eu/workflows/1466?version=2 microbiome/metatranscriptomics 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 112 112 1972 1972 31 31 128 128 0 0 0 0 12 12 25 25 2125 2125 155 155 True False +comebin comebin Binning of metagenomic contigs using COntrastive Multi-viEw representation learning 2025-07-03 https://github.com/ziyewang/COMEBin 1.0.4 comebin 1.0.4 Up-to-date Metagenomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/comebin https://github.com/galaxyproject/tools-iuc/tree/master/tools/comebin 0 0 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 2 2 0 0 0 0 0 0 0 0 0 0 0 0 2 2 1 1 True False +comebin_bam comebin_bam bam Generate bam file for COMEBin 2025-11-07 https://github.com/ziyewang/COMEBin 1.0.4 comebin 1.0.4 Up-to-date Metagenomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/comebin_bam/ https://github.com/galaxyproject/tools-iuc/tree/master/tools/comebin_bam 0 0 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False +compare_humann2_output compare_humann2_output tabular, txt Compare outputs of HUMAnN2 for several samples and extract similar and specific information 2022-10-19 0.2.0 To update Metagenomics Comparison Comparison Metagenomics, Gene and protein families Metagenomics, Gene and protein families bebatut https://github.com/bgruening/galaxytools/tree/master/tools/compare_humann2_output https://github.com/bgruening/galaxytools/tree/master/tools/compare_humann2_output compare_humann2_outputs Compare HUMAnN2 outputs This tool compare HUMANnN2 outputs with gene families or pathways and their relative abundances between several samples 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 23 32 248 332 0 0 0 0 0 0 0 0 0 0 0 0 332 248 32 23 True False +compleasm compleasm tsv, gff3, fasta, txt Compleasm: a faster and more accurate reimplementation of BUSCO 2023-12-04 https://github.com/huangnengCSU/compleasm 0.2.6 compleasm 0.2.8 To update Sequence Analysis Sequence assembly validation Sequence assembly validation Sequence assembly, Genomics, Transcriptomics, Sequence analysis Sequence assembly, Transcriptomics, Sequence analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/compleasm https://github.com/galaxyproject/tools-iuc/tree/master/tools/compleasm compleasm Compleasm Compleasm: a faster and more accurate reimplementation of BUSCO.It provides measures for quantitative assessment of genome assembly, gene set, and transcriptome completeness based on evolutionarily informed expectations of gene content from near-universal single-copy orthologs. https://usegalaxy.eu/published/workflow?id=04844dddcc4e8aa7, 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The core algorithm of both programs involves gene calling, mapping of predicted ORFs against the nr protein database, and voting-based classification of the entire contig / MAG based on classification of the individual ORFs. https://usegalaxy.eu/published/workflow?id=02631612a43a4d9b, https://usegalaxy.eu/published/workflow?id=3eaa913306c16146, https://usegalaxy.eu/published/workflow?id=6158c3b5fc12044e, https://usegalaxy.eu/published/workflow?id=6416cfdbd5273063, https://usegalaxy.eu/published/workflow?id=667bac8d7453e5f1, https://usegalaxy.eu/published/workflow?id=7be08f99f83c927e, https://usegalaxy.eu/published/workflow?id=8c91345ed468e22d, https://usegalaxy.eu/published/workflow?id=8deb08d4f228e198, https://usegalaxy.eu/published/workflow?id=9a97c6eb4fe015e7, https://usegalaxy.eu/published/workflow?id=d57d41e306241396, https://usegalaxy.org/published/workflow?id=33d90e718ce500ef 5 2 5 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 5 0 257 267 17418 17676 216 231 1590 1750 84 85 848 875 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https://workflowhub.eu/workflows/1717?version=2, https://workflowhub.eu/workflows/338?version=1, https://workflowhub.eu/workflows/412?version=1 transcriptomics/de-novo, transcriptomics/mirna-target-finder, transcriptomics/network-analysis-with-heinz, transcriptomics/ref-based, transcriptomics/rna-seq-analysis-clustering-viz, transcriptomics/srna 1 1 1 1 0 0 0 0 1 1 1 0 0 0 0 0 0 0 1 0 0 0 1 1 1 0 13707 15994 110682 133936 27214 37996 191581 286575 2980 3614 19899 24448 820 824 4511 4530 449489 326673 58428 44721 True False +dfast dfast tabular, fasta, embl, genbank, gff3, txt Prokaryotic genome annotation 2025-04-16 https://github.com/nigyta/dfast_core/ @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ dfast 1.4.0 To update Genome annotation Genome annotation Genome annotation Nucleic acid structure analysis, Genomics, Sequence analysis Nucleic acid structure analysis, Genomics, Sequence analysis ufz https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/dfast/ https://github.com/Helmholtz-UFZ/galaxy-tools/tree/master/tools/dfast dfast DFAST Flexible prokaryotic genome annotation pipeline for faster genome publication. 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False +diamond bg_diamond, bg_diamond_makedb, bg_diamond_view txt, dmnd DIAMOND is a new alignment tool for aligning short DNA sequencing reads to a protein reference database such as NCBI-NR. 2021-03-21 https://github.com/bbuchfink/diamond 2.2.2 diamond 2.2.2 Up-to-date Sequence Analysis Sequence alignment analysis Sequence alignment analysis Sequence analysis, Proteins Sequence analysis, Proteins bgruening https://github.com/galaxyproject/tools-iuc/tree/main/tools/diamond https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond diamond Diamond Sequence aligner for protein and translated DNA searches and functions as a drop-in replacement for the NCBI BLAST software tools. It is suitable for protein-protein search as well as DNA-protein search on short reads and longer sequences including contigs and assemblies, providing a speedup of BLAST ranging up to x20,000. https://usegalaxy.eu/published/workflow?id=2ee0eb74e839b476, https://usegalaxy.eu/published/workflow?id=559f079f6510aa24, https://usegalaxy.eu/published/workflow?id=86900be4282d4b1d, https://usegalaxy.eu/published/workflow?id=9b9e1e28f3683f92, https://usegalaxy.eu/published/workflow?id=a2c46deea34d9d80, https://usegalaxy.eu/published/workflow?id=bc32937d505135ab, https://usegalaxy.eu/published/workflow?id=bebcbd6f0ffa55c5, https://usegalaxy.eu/published/workflow?id=ff4d5beb6ce1809d, https://usegalaxy.org.au/published/workflow?id=0a3fb089674de144, https://usegalaxy.org.au/published/workflow?id=a07809974079a317, https://usegalaxy.org/published/workflow?id=b0f85c802c1ea7f8, https://usegalaxy.org/published/workflow?id=e0c33057ac2670ba, https://workflowhub.eu/workflows/1103?version=3, https://workflowhub.eu/workflows/1104?version=2, https://workflowhub.eu/workflows/1518?version=1, https://workflowhub.eu/workflows/1641?version=1 assembly/ERGA-post-assembly-QC, genome-annotation/functional, genome-annotation/gene-centric, sequence-analysis/ncbi-blast-against-the-madland 3 3 3 3 0 0 0 0 3 3 0 0 0 0 0 1 0 0 0 0 0 0 3 3 3 0 1620 1706 112648 114376 665 1048 35921 43599 446 448 65850 66062 125 125 2180 2208 226245 216599 3327 2856 True False +disco disco txt, fasta DISCO is a overlap-layout-consensus (OLC) metagenome assembler 2017-10-26 http://disco.omicsbio.org/ @WRAPPER_VERSION@.1 disco 1.3 To update Metagenomics, Assembly Protein sequence analysis Protein sequence analysis Structure determination Structure determination iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/disco https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco disco DISCO DISCO is software to perform structure determination of protein homo-oligomers with cyclic symmetry.DISCO computes oligomeric protein structures using geometric constraints derived from RDCs and intermolecular distance restraints such as NOEs or disulfide bonds. When a reliable subunit structure can be calculated from intramolecular restraints, DISCO guarantees that all satisfying oligomer structures will be discovered, yet can run in minutes to hours on only a single desktop-class computer. 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 127 163 280 453 406 435 1525 1690 0 0 0 0 0 0 0 0 2143 1805 598 533 True False +dose_response_analysis_tool dr_curve jpg, tabular A tool for analyzing and visualizing the relationship between various doses and their corresponding biological responses 2024-04-06 https://github.com/bernt-matthias/mb-galaxy-tools @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ r-drc 3.0_1 To update Ecology ufz https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/tox_tools/dose_responses https://github.com/Helmholtz-UFZ/galaxy-tools/tree/master/tools/tox_tools/dose_responses 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False +dram dram_annotate, dram_distill, dram_merge_annotations, dram_neighborhoods, dram_strainer fasta, gff3, tabular, genbank, xlsx, html DRAM for distilling microbial metabolism to automate the curation of microbiome function 2022-09-01 https://github.com/WrightonLabCSU/DRAM 1.5.0 dram 1.5.0 Up-to-date Metagenomics Gene functional annotation Gene functional annotation Metagenomics, Biological databases, Molecular genetics Metagenomics, Biological databases, Molecular genetics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/dram https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram dram DRAM Distilled and Refined Annotation of Metabolism: A tool for the annotation and curation of function for microbial and viral genomes 0 0 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 0 0 120 120 13633 13633 0 0 0 0 0 0 0 0 0 0 0 0 13633 13633 120 120 True False +drep drep_compare, drep_dereplicate dRep compares and dereplicates genome sets 2020-01-06 https://github.com/MrOlm/drep 3.6.2 drep 3.7.1 To update Metagenomics Genome comparison Genome comparison Metagenomics, Genomics, Sequence analysis Metagenomics, Sequence analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/drep https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep drep dRep Fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication. https://usegalaxy.eu/published/workflow?id=0563f58718be932d, https://usegalaxy.eu/published/workflow?id=1e5f1d9a51032e44, https://usegalaxy.eu/published/workflow?id=7ecd92cb382d8168, https://usegalaxy.eu/published/workflow?id=97312d273b6e8bd9, https://usegalaxy.eu/published/workflow?id=c62d65832377e376, https://workflowhub.eu/workflows/1352?version=4 genome-annotation/bacterial-genome-quality-control, microbiome/mags-building, microbiome/metagenomics-binning 2 2 2 2 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 113 115 1708 1749 13 13 47 47 0 0 0 0 38 38 1273 1273 3069 3028 166 164 True False +ectyper ectyper tabular, txt EC-Typer - in silico serotyping of Escherichia coli species 2018-12-21 https://github.com/phac-nml/ecoli_serotyping @VERSION@ ectyper 2.0.0 To update Sequence Analysis Sequence assembly, Read pre-processing, Variant calling Sequence assembly, Read pre-processing, Variant calling Whole genome sequencing, Public health and epidemiology, Sequence assembly, Genotype and phenotype, Workflows Whole genome sequencing, Public health and epidemiology, Sequence assembly, Genotype and phenotype, Workflows nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/ectyper https://github.com/phac-nml/galaxy_tools/tree/master/tools/ectyper ectyper ECTyper Ectyper is a standalone serotyping module for Escherichia coli. It supports fasta and fastq file formats. (Galaxy Version 1.0.0) https://usegalaxy.eu/published/workflow?id=b90585626a793502 0 1 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 218 218 30463 30463 1 1 10 10 0 0 0 0 0 0 0 0 30473 30473 219 219 True False +effectivet3 effectiveT3 tabular Find bacterial type III effectors in protein sequences 2013-04-30 http://effectors.org 0.0.21 effectiveT3 1.0.1 To update Sequence Analysis Sequence classification Sequence classification Sequence analysis Sequence analysis peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/effectiveT3 https://github.com/peterjc/pico_galaxy/tree/master/tools/effectiveT3 effectivet3 EffectiveT3 Prediction of putative Type-III secreted proteins. 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False +eggnog_mapper eggnog_mapper, eggnog_mapper_annotate, eggnog_mapper_search eggnog-mapper fast functional annotation of novel sequences 2019-11-11 https://github.com/eggnogdb/eggnog-mapper 2.1.13 eggnog-mapper 2.1.13 Up-to-date Proteomics Homology-based gene prediction, Genome annotation, Fold recognition, Information extraction, Query and retrieval Homology-based gene prediction, Genome annotation, Fold recognition, Information extraction, Query and retrieval Metagenomics, Phylogeny, Transcriptomics, Workflows, Sequence analysis Metagenomics, Phylogeny, Transcriptomics, Workflows, Sequence analysis galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper eggnog-mapper-v2 eggNOG-mapper v2 EggNOG-mapper is a tool for fast functional annotation of novel sequences. 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needle Galaxy wrappers for EMBOSS6 tools 2025-01-17 http://emboss.open-bio.org/ 6.6.0 emboss 6.6.0 Up-to-date Sequence Analysis, Fasta Manipulation Sequence analysis, Local alignment, Sequence alignment analysis, Global alignment, Sequence alignment Sequence analysis, Local alignment, Sequence alignment analysis, Global alignment, Sequence alignment Molecular biology, Sequence analysis, Biology Molecular biology, Sequence analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/emboss https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss emboss EMBOSS Diverse suite of tools for sequence analysis; many programs analagous to GCG; context-sensitive help for each tool. 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 62 62 419 419 0 0 0 0 0 0 0 0 0 0 0 0 419 419 62 62 True False +emboss_5 EMBOSS: antigenic1, EMBOSS: backtranseq2, EMBOSS: banana3, EMBOSS: biosed4, EMBOSS: btwisted5, EMBOSS: cai6, EMBOSS: cai_custom6, EMBOSS: chaos7, EMBOSS: charge8, EMBOSS: 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coderet, compseq, cpgplot, cpgreport, cusp, dan, diffseq, digest, dreg, einverted, epestfind, table, equicktandem, est2genome, etandem, freak, fuzznuc, fuzzpro, fuzztran, garnier, geecee, motif, hmoment, isochore, markx0, simple, needle, newcpgreport, newcpgseek, noreturn, oddcomp, palindrome, dbmotif, pepcoil, pepinfo, pepstats, polydot, preg, prettyseq, primersearch, seqmatchall, showfeat, sixpack, supermatcher, syco, textsearch, seqtable, vectorstrip, srs, wobble, wordcount, match Galaxy wrappers for EMBOSS version 5.0.0 tools 2017-01-11 http://emboss.open-bio.org/ 5.0.0 emboss 6.6.0 To update Sequence Analysis, Fasta Manipulation Sequence analysis, Local alignment, Sequence alignment analysis, Global alignment, Sequence alignment Sequence analysis, Local alignment, Sequence alignment analysis, Global alignment, Sequence alignment Molecular biology, Sequence analysis, Biology Molecular biology, Sequence analysis devteam https://github.com/galaxyproject/tools-iuc/tree/main/tools/emboss_5 https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 emboss EMBOSS Diverse suite of tools for sequence analysis; many programs analagous to GCG; context-sensitive help for each tool. https://usegalaxy.eu/published/workflow?id=0293e155386d3f3a, https://usegalaxy.eu/published/workflow?id=04a4dcac3fd922c5, https://usegalaxy.eu/published/workflow?id=0ed8817a90caa2b1, https://usegalaxy.eu/published/workflow?id=1031e4c4f18e020e, https://usegalaxy.eu/published/workflow?id=1f88311a8e365c17, https://usegalaxy.eu/published/workflow?id=2c79eee5ca5a3b09, https://usegalaxy.eu/published/workflow?id=33312e5643279e8a, https://usegalaxy.eu/published/workflow?id=402b14906a03b2ef, https://usegalaxy.eu/published/workflow?id=6e1fe7372e93fae0, https://usegalaxy.eu/published/workflow?id=90f993a1b245eb68, https://usegalaxy.eu/published/workflow?id=9275d0c90a8713d6, https://usegalaxy.eu/published/workflow?id=93d1035a307fe63d, 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https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete ete ete The Environment for Tree Exploration (ETE) is a computational framework that simplifies the reconstruction, analysis, and visualization of phylogenetic trees and multiple sequence alignments. Here, we present ETE v3, featuring numerous improvements in the underlying library of methods, and providing a novel set of standalone tools to perform common tasks in comparative genomics and phylogenetics. The new features include (i) building gene-based and supermatrix-based phylogenies using a single command, (ii) testing and visualizing evolutionary models, (iii) calculating distances between trees of different size or including duplications, and (iv) providing seamless integration with the NCBI taxonomy database. 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Here, we present ETE v3, featuring numerous improvements in the underlying library of methods, and providing a novel set of standalone tools to perform common tasks in comparative genomics and phylogenetics. The new features include (i) building gene-based and supermatrix-based phylogenies using a single command, (ii) testing and visualizing evolutionary models, (iii) calculating distances between trees of different size or including duplications, and (iv) providing seamless integration with the NCBI taxonomy database. ETE is freely available at http://etetoolkit.org https://workflowhub.eu/workflows/1650?version=1 sequence-analysis/tapscan-streptophyte-algae 0 0 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 130 130 1626 1626 0 0 0 0 0 0 0 0 4 4 5 5 1631 1631 134 134 True False +eukcc eukcc_single tabular Galaxy wrapper for EukCC 2025-07-25 https://github.com/EBI-Metagenomics/EukCC 2.1.3 eukcc 2.1.3 Up-to-date Metagenomics Sequence assembly validation Sequence assembly validation Metagenomics Metagenomics ufz https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/eukcc https://github.com/Helmholtz-UFZ/galaxy-tools/tree/master/tools/eukcc eukcc EukCC EukCC is a completeness and contamination estimator for metagenomic assembled microbial eukaryotic genomes. 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False +eukrep eukrep fasta, txt Classification of Eukaryotic and Prokaryotic sequences from metagenomic datasets 2025-07-30 https://github.com/patrickwest/EukRep @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ eukrep 0.6.7 To update Metagenomics Nucleic acid sequence analysis Nucleic acid sequence analysis Metagenomics Metagenomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/eukrep https://github.com/galaxyproject/tools-iuc/tree/master/tools/eukrep eukrep EukRep Classification of Eukaryotic and Prokaryotic sequences from metagenomic datasets 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False +export2graphlan export2graphlan txt export2graphlan is a conversion software tool for producing both annotation and tree file for GraPhlAn 2017-03-03 https://bitbucket.org/CibioCM/export2graphlan/overview @VERSION@+@GALAXY_VERSION@ export2graphlan 0.22 To update Metagenomics Conversion Conversion Taxonomy, Metabolomics, Biomarkers Taxonomy, Metabolomics, Biomarkers iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/export2graphlan https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan export2graphlan export2graphlan export2graphlan is a conversion software tool for producing both annotation and tree file for GraPhlAn. In particular, the annotation file tries to highlight specific sub-trees deriving automatically from input file what nodes are important. https://usegalaxy.eu/published/workflow?id=05f5f040337786bf, https://usegalaxy.eu/published/workflow?id=096b75501c8e0888, https://usegalaxy.eu/published/workflow?id=19de5cbae7f48103, https://usegalaxy.eu/published/workflow?id=2cf09adb1ed6c3ec, https://usegalaxy.eu/published/workflow?id=4d32b1b3ac0a7161, https://usegalaxy.eu/published/workflow?id=4f21205e71cabd37, https://usegalaxy.eu/published/workflow?id=5f0faac42b0a5062, https://usegalaxy.eu/published/workflow?id=69eddfde874af35b, https://usegalaxy.eu/published/workflow?id=713a5485e2007f90, https://usegalaxy.eu/published/workflow?id=79b4ae4403772098, https://usegalaxy.eu/published/workflow?id=7ab70660e6235cf0, https://usegalaxy.eu/published/workflow?id=87cc0cd143a12c41, https://usegalaxy.eu/published/workflow?id=994e5ff1df7d6c9e, https://usegalaxy.eu/published/workflow?id=9cbba5de2cbeeb0f, https://usegalaxy.eu/published/workflow?id=a8f829deb69b30ab, https://usegalaxy.eu/published/workflow?id=b5f848dc8e96663c, https://usegalaxy.eu/published/workflow?id=c01ef8354b585a1f, https://usegalaxy.eu/published/workflow?id=c3aa516e78ca4191, https://usegalaxy.eu/published/workflow?id=d05c6f0f3205fbd2, https://usegalaxy.eu/published/workflow?id=dfc2c53ac3103eff, https://usegalaxy.eu/published/workflow?id=ed0ad728cf21702b, https://usegalaxy.eu/published/workflow?id=f9175e670d8dfaa1, https://usegalaxy.eu/published/workflow?id=fdca6c9d394986bf, https://usegalaxy.fr/published/workflow?id=09e8293456ee6d99, https://usegalaxy.fr/published/workflow?id=c4f6062e51d0f45e, https://workflowhub.eu/workflows/1451?version=2, https://workflowhub.eu/workflows/1466?version=2 microbiome/metatranscriptomics, microbiome/metatranscriptomics-short 1 1 1 1 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 589 710 6276 7303 193 213 712 791 122 123 616 632 16 16 43 43 8769 7647 1062 920 True False +ez_histograms ez_histograms pdf, tabular ggplot2 histograms and density plots 2024-02-07 https://github.com/tidyverse/ggplot2 @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ r-ggplot2 2.2.1 To update Visualization, Statistics Data analysis, Statistical calculation, Visualisation Statistical calculation, Visualisation Ecology Ecology artbio https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms https://github.com/ARTbio/tools-artbio/tree/master/tools/ez_histograms ez_histograms ez_histograms This tool produces histograms or density plots from any tabular datasets, using ggplot2.You may provide headerless tables as well as tables with column headers. Any non-numeric columns will be filtered out. Your first column may contains row names, but it will also work if your first column already corresponds to the numeric values of a variable. 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False +fairy fairy_cov, fairy_sketch tabular, bcsp Fast approximate contig coverage for metagenomic binning 2024-12-20 https://github.com/bluenote-1577/fairy 0.5.8 fairy 0.5.8 Up-to-date Metagenomics Read binning, Sequence assembly validation Read binning, Sequence assembly validation Metagenomics Metagenomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/fairy https://github.com/galaxyproject/tools-iuc/tree/master/tools/fairy fairy fairy fast approximate contig coverage for metagenomic binningFairy computes multi-sample contig coverage for metagenome-assembled genome (MAG) binning.Fairy is used after metagenomic assembly and before binning. It can- Calculate coverage 100x-1000x faster than read alignment (e.g. BWA)- Give comparable bins for multi-sample binning (short read or nanopore reads)- Output formats that are compatible with MetaBAT2, MaxBin2, SemiBin2, and more 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 148 148 0 0 0 0 0 0 0 0 0 0 0 0 148 148 5 5 True False +falco falco html, txt A high throughput sequence QC analysis tool 2024-04-17 https://github.com/smithlabcode/falco/ @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ falco 1.3.2 To update Sequence Analysis Sequencing quality control, Visualisation, Read mapping Sequencing quality control, Visualisation, Read mapping Workflows, Mapping, Imaging Workflows, Mapping, Imaging iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/falco https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco falco Falco A high-speed FastQC emulation for quality control of sequencing data. https://usegalaxy.eu/published/workflow?id=046e5c9726c75a3c, 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2019-08-30 https://github.com/fannyhb/fargene 0.1 fargene 0.1 Up-to-date Sequence Analysis Antimicrobial resistance prediction Antimicrobial resistance prediction Metagenomics, Microbiology, Public health and epidemiology, Antimicrobial resistance Metagenomics, Microbiology, Public health and epidemiology iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/fargene https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene fargene fARGene fARGene (Fragmented Antibiotic Resistance Gene iENntifiEr ) is a tool that takes either fragmented metagenomic data or longer sequences as input and predicts and delivers full-length antiobiotic resistance genes as output. 1 0 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 150 159 895 1011 262 287 1203 1346 0 0 0 0 2 2 2 2 2359 2100 448 414 True False +fastani fastani tabular Fast alignment-free computation of whole-genome Average Nucleotide Identity 2020-02-17 https://github.com/ParBLiSS/FastANI 1.3 fastani 1.34 To update Sequence Analysis Genome alignment, Sequence similarity search Genome alignment, Sequence similarity search Microbiology, Genetic variation Microbiology, Genetic variation iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastani https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastani fastani FastANI FastANI is developed for fast alignment-free computation of whole-genome Average Nucleotide Identity (ANI). ANI is defined as mean nucleotide identity of orthologous gene pairs shared between two microbial genomes. FastANI supports pairwise comparison of both complete and draft genome assemblies. https://usegalaxy.eu/published/workflow?id=2a1dc58e51d5f01a, https://usegalaxy.eu/published/workflow?id=bf48b0eb15e8ff75 0 1 1 1 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1182 1205 29436 29626 1 1 18 18 133 133 1799 1799 64 64 949 949 32392 32202 1403 1380 True False +fastk fastk_fastk, fastk_histex, fastk_logex fastk_ktab_tar, fastk_hist, fastk_ktab, txt, tabular FastK: A K-mer counter (for HQ assembly data sets) 2024-05-03 https://github.com/thegenemyers/FASTK 1.1.0 fastk 1.2 To update Assembly k-mer counting, Sequence analysis k-mer counting, Sequence analysis Genomics, Sequence analysis Genomics, Sequence analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastk https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk fastk FASTK FastK is a k‑mer counter that is optimized for processing high quality DNA assembly data sets such as those produced with an Illumina instrument or a PacBio run in HiFi mode. 3 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 46 46 742 742 45 45 389 389 0 0 0 0 0 0 0 0 1131 1131 91 91 True False +fastoma fastoma xml, html, ipynb, tabular, newick FastOMA is a scalable tool for orthology inference among many genomes. 2025-12-26 https://github.com/dessimozlab/FastOMA 0.5.1 To update Phylogenetics, Sequence Analysis Phylogenetic tree reconciliation, Protein sequence analysis, Genome comparison, Sequence clustering, Phylogenetic inference (from molecular sequences) Phylogenetic tree reconciliation, Protein sequence analysis, Genome comparison, Sequence clustering, Phylogenetic inference (from molecular sequences) Comparative genomics Comparative genomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastoma https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastoma fastoma FastOMA FastOMA is a scalable software package to infer orthology relationship. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False +fastp fastp html, json Fast all-in-one preprocessing for FASTQ files 2018-03-08 https://github.com/OpenGene/fastp 1.3.5 fastp 1.3.6 To update Sequence Analysis Sequencing quality control, Sequence contamination filtering Sequence contamination filtering Sequence analysis, Probes and primers Probes and primers iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastp https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp fastp fastp A tool designed to provide fast all-in-one preprocessing for FastQ files. 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27815 True False +fastplong fastplong html, json, fastq Fastplong is used for ultrafast preprocessing and quality control for long reads (Nanopore, PacBio, Cyclone, etc.). 2025-05-06 https://github.com/OpenGene/fastplong @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ fastplong 0.4.1 To update Sequence Analysis, Assembly iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastplong https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastplong https://usegalaxy.org.au/published/workflow?id=aa1d123c0a0929f3, https://workflowhub.eu/workflows/2195?version=1 0 1 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 40 40 309 309 0 0 0 0 8 8 217 217 0 0 0 0 526 526 48 48 True False +fastqe fastqe html FASTQE 2020-07-13 https://fastqe.com/ 0.3.1 fastqe 0.5.2 To update Sequence Analysis Sequencing quality control Sequencing quality control Sequence analysis, Sequencing Sequence analysis, Sequencing iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastqe https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe fastqe FASTQE Compute quality stats for FASTQ files and print those stats as emoji... for some reason. https://usegalaxy.eu/published/workflow?id=055eae88be2d4dd7, https://usegalaxy.eu/published/workflow?id=2a274e0e4ba45c77, https://usegalaxy.eu/published/workflow?id=340aa3ae5468deb0, https://usegalaxy.eu/published/workflow?id=4c736e255f4a740f, https://usegalaxy.eu/published/workflow?id=519e0ffdfd1790bc, https://usegalaxy.eu/published/workflow?id=76a63b1710da5e60, https://usegalaxy.eu/published/workflow?id=a8d814a6d86e9661, https://usegalaxy.eu/published/workflow?id=c65d98740ca64104, https://usegalaxy.eu/published/workflow?id=d38f1f6a499a27fb, https://usegalaxy.eu/published/workflow?id=d3ae8c51061330f3, https://usegalaxy.eu/published/workflow?id=d5780c37232e3181, https://usegalaxy.eu/published/workflow?id=f6b1300a9f4b9084, https://usegalaxy.org.au/published/workflow?id=115151c2c8998d44, https://usegalaxy.org.au/published/workflow?id=178db14511c8f293, https://usegalaxy.org.au/published/workflow?id=1f63ec596e578b1c, https://usegalaxy.org.au/published/workflow?id=2afeae1ec03c0b57, https://usegalaxy.org.au/published/workflow?id=43f2dabbc1932e30, https://usegalaxy.org.au/published/workflow?id=47cacc06d404a8c6, https://usegalaxy.org.au/published/workflow?id=5d6773ed5b2f41cb, https://usegalaxy.org.au/published/workflow?id=8fe84de499e96485, https://usegalaxy.org.au/published/workflow?id=bd251174d94cde9d, https://usegalaxy.org.au/published/workflow?id=dd6f465ab1eb10b0, https://usegalaxy.org.au/published/workflow?id=e08b04291839e79a, https://usegalaxy.org/published/workflow?id=20da2dcce0ae2ca2, https://usegalaxy.org/published/workflow?id=56998cc00bcc8088, https://usegalaxy.org/published/workflow?id=7a33bc2d0970b502, https://usegalaxy.org/published/workflow?id=cf2dbc29ca20ebee, https://usegalaxy.org/published/workflow?id=d115312bcda04bf2, https://usegalaxy.org/published/workflow?id=fe262214fba1cb8e sequence-analysis/quality-control 1 1 1 1 0 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 3154 3177 6904 6978 6143 6198 13534 13627 1316 1323 3505 3549 291 291 510 510 24664 24453 10989 10904 True False +fastreer fastreer_dist2tree, fastreer_fasta2dist, fastreer_vcf2dist, fastreer_vcf2tree newick, txt fastreeR toolkit wrappers for phylogenetic trees and distance matrices from VCF and FASTA 2025-11-01 https://github.com/gkanogiannis/fastreeR 2.2.0 fastreer 2.2.0 Up-to-date Phylogenetics, Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastreer https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastreer fastreer 0 0 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False +fastspar fastspar, fastspar_pvalues, fastspar_reduce tabular Tool for rapid and scalable correlation estimation for compositional data. 2025-06-16 https://github.com/scwatts/fastspar/ 1.0.0 fastspar 1.0.0 Up-to-date Metagenomics, Statistics Metagenomics, Microbial ecology Metagenomics, Microbial ecology iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastspar https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastspar FastSpar FastSpar FastSpar is a C++ implementation of the SparCC algorithm for fast correlation estimation from compositional count data such as microbiome OTU tables. 0 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 2 2 0 0 0 0 0 0 0 0 0 0 0 0 2 2 1 1 True False +fasttree fasttree nhx, txt FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences - GVL 2018-02-02 http://www.microbesonline.org/fasttree/ @VERSION@ fasttree 2.2.0 To update Phylogenetics Phylogenetic tree generation (from molecular sequences), Phylogenetic tree generation (maximum likelihood and Bayesian methods) Phylogenetics, Sequence analysis Phylogenetics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/fasttree https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree fasttree FastTree Infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences. https://usegalaxy.eu/published/workflow?id=36de05d50c703164, https://usegalaxy.eu/published/workflow?id=376119528377a3ae, https://usegalaxy.eu/published/workflow?id=46ef864fe9468894, https://usegalaxy.eu/published/workflow?id=73a9598202d0fb7d, https://usegalaxy.eu/published/workflow?id=9155ed0e7a6a7b60, https://usegalaxy.eu/published/workflow?id=974cc681d07ec788, https://usegalaxy.eu/published/workflow?id=b1a799497c366eef, https://usegalaxy.eu/published/workflow?id=c8bc4af6dd3b5d02, https://usegalaxy.eu/published/workflow?id=ce21961260fe4351, https://usegalaxy.eu/published/workflow?id=d07fe8b5a045c176, https://usegalaxy.eu/published/workflow?id=dc57118a95b10a80, 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https://workflowhub.eu/workflows/1559?version=1 evolution/abc_intro_phylo, evolution/bacterial-comparative-genomics, microbiome/pathogen-detection-from-nanopore-foodborne-data 1 1 1 1 0 0 0 0 1 1 1 0 0 0 0 0 0 0 1 0 0 0 1 1 1 0 1826 1923 84447 85175 2879 3069 29857 32881 829 967 8573 9437 82 84 411 416 127909 123288 6043 5616 True False +featurecounts featurecounts tabular, bam featureCounts counts the number of reads aligned to defined masked regions in a reference genome 2016-02-09 https://subread.sourceforge.net/ @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ subread 2.1.1 To update RNA, Transcriptomics, Sequence Analysis Read summarisation, RNA-Seq quantification Read summarisation, RNA-Seq quantification RNA-Seq RNA-Seq iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/featurecounts https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts featurecounts FeatureCounts featureCounts is a very efficient read quantifier. It can be used to summarize RNA-seq reads and gDNA-seq reads to a variety of genomic features such as genes, exons, promoters, gene bodies and genomic bins. 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Filtlong Filtlong is a tool for filtering long reads by quality. It can take a set of long reads and produce a smaller, better subset. It uses both read length (longer is better) and read identity (higher is better) when choosing which reads pass the filter. https://usegalaxy.eu/published/workflow?id=07c92110c3fffcf8, https://usegalaxy.eu/published/workflow?id=30dc526dcfa500df, https://usegalaxy.eu/published/workflow?id=346b46e6316c6950, https://usegalaxy.eu/published/workflow?id=4ddbffe4b3fef275, https://usegalaxy.eu/published/workflow?id=5500de2961f7470c, https://usegalaxy.eu/published/workflow?id=5826e573b6f93762, https://usegalaxy.eu/published/workflow?id=6f878d8b43ef1521, https://usegalaxy.eu/published/workflow?id=83a1b8949d87e3da, https://usegalaxy.eu/published/workflow?id=86cf02cc0868d238, https://usegalaxy.eu/published/workflow?id=968f0ac2617aa524, https://usegalaxy.eu/published/workflow?id=a337bfb2eb1e583f, https://usegalaxy.eu/published/workflow?id=a84bac86ec183d46, https://usegalaxy.eu/published/workflow?id=ab646c6ab6de7061, https://usegalaxy.eu/published/workflow?id=bf48b0eb15e8ff75, https://usegalaxy.eu/published/workflow?id=c3bfedf33bb00069, https://usegalaxy.eu/published/workflow?id=c9ef2d2ce92e2dfb, https://usegalaxy.eu/published/workflow?id=d0339e4a794f4922, https://usegalaxy.eu/published/workflow?id=ea485dbabc76488d, https://usegalaxy.eu/published/workflow?id=eb5ab8bc82569eee, https://usegalaxy.eu/published/workflow?id=ecf48fa50af560a0, https://usegalaxy.org.au/published/workflow?id=2e29b21cdec7d0cc, https://usegalaxy.org.au/published/workflow?id=35f39173f0ac9179, https://usegalaxy.org.au/published/workflow?id=4871f853090e8be8, https://usegalaxy.org.au/published/workflow?id=b7aa22291322e505, https://usegalaxy.org.au/published/workflow?id=c997a34b55425155, https://usegalaxy.org.au/published/workflow?id=d69a765cfc82a399, https://usegalaxy.org.au/published/workflow?id=fc664a96d8099652, https://usegalaxy.org/published/workflow?id=2a0e8cd16fb21fa1, https://usegalaxy.org/published/workflow?id=2ded909e7e3a9962, https://usegalaxy.org/published/workflow?id=48dafc35989f13b1, https://usegalaxy.org/published/workflow?id=547f86db467bf620, https://usegalaxy.org/published/workflow?id=7fc8b2398b6f093f, https://usegalaxy.org/published/workflow?id=8421cbcadcbc8b79, https://usegalaxy.org/published/workflow?id=87045af52d500e91, https://usegalaxy.org/published/workflow?id=a4543d00cdbede5f, https://usegalaxy.org/published/workflow?id=c451e4dca9981ed0, https://usegalaxy.org/published/workflow?id=cc6ee582a6e5cae2, https://usegalaxy.org/published/workflow?id=d5436cee11a34de9, https://usegalaxy.org/published/workflow?id=e1dcdc125122f561, https://workflowhub.eu/workflows/1613?version=2, https://workflowhub.eu/workflows/51?version=1 assembly/mrsa-nanopore 1 1 1 1 0 0 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 2169 2318 79820 82849 1410 1424 72145 72255 830 830 17538 17538 27 27 150 150 172792 169653 4599 4436 True False +flashlfq flashlfq txt, tabular FlashLFQ mass-spectrometry proteomics label-free quantification 2017-12-06 https://github.com/smith-chem-wisc/FlashLFQ 1.0.3.1 flashlfq 2.1.4 To update Proteomics Label-free quantification Label-free quantification Proteomics experiment, Proteomics Proteomics experiment, Proteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq flashlfq FlashLFQ FlashLFQ is an ultrafast label-free quantification algorithm for mass-spectrometry proteomics. https://usegalaxy.eu/published/workflow?id=ba3a5d59b3879764, https://usegalaxy.eu/published/workflow?id=cd675ab32d3e7833, https://usegalaxy.eu/published/workflow?id=d0e062aee910086a, https://usegalaxy.eu/published/workflow?id=fc42cc9467c6ee8d, https://workflowhub.eu/workflows/1450?version=1 proteomics/metaquantome-data-creation 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 47 59 516 760 0 0 0 0 16 16 216 226 0 0 0 0 986 732 75 63 True False +flye flye fasta, graph_dot, gfa1, tabular, txt Assembly of long and error-prone reads. 2018-09-22 https://github.com/fenderglass/Flye/ 2.9.6 flye 2.9.6 Up-to-date Assembly Genome assembly, De-novo assembly, Mapping assembly, Cross-assembly Genome assembly, De-novo assembly, Mapping assembly, Cross-assembly Sequence assembly, Metagenomics, Whole genome sequencing, Genomics Sequence assembly, Metagenomics, Whole genome sequencing bgruening https://github.com/bgruening/galaxytools/tree/master/tools/flye https://github.com/bgruening/galaxytools/tree/master/tools/flye Flye Flye Flye is a de novo assembler for single molecule sequencing reads, such as those produced by PacBio and Oxford Nanopore Technologies. It is designed for a wide range of datasets, from small bacterial projects to large mammalian-scale assemblies. The package represents a complete pipeline: it takes raw PB / ONT reads as input and outputs polished contigs. https://usegalaxy.eu/published/workflow?id=0ebfab0e957b7267, https://usegalaxy.eu/published/workflow?id=152223c8aed27357, https://usegalaxy.eu/published/workflow?id=1c4c2eaaf177ba2c, https://usegalaxy.eu/published/workflow?id=2b888e200dfd91bc, https://usegalaxy.eu/published/workflow?id=2c992e509aa5dd9d, https://usegalaxy.eu/published/workflow?id=30b514cfb9cce524, https://usegalaxy.eu/published/workflow?id=34a07bf6407510ef, https://usegalaxy.eu/published/workflow?id=368d1ac0150ea0b6, https://usegalaxy.eu/published/workflow?id=36cba3f275da3f70, https://usegalaxy.eu/published/workflow?id=4ddbffe4b3fef275, https://usegalaxy.eu/published/workflow?id=5500de2961f7470c, https://usegalaxy.eu/published/workflow?id=585c21b7b1d864fc, https://usegalaxy.eu/published/workflow?id=5cd71f9a190cae1b, https://usegalaxy.eu/published/workflow?id=6b79f4974f73593a, 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https://workflowhub.eu/workflows/1062?version=1, https://workflowhub.eu/workflows/1114?version=1, https://workflowhub.eu/workflows/1495?version=1, https://workflowhub.eu/workflows/1595?version=1, https://workflowhub.eu/workflows/1613?version=2, https://workflowhub.eu/workflows/1617?version=1, https://workflowhub.eu/workflows/1621?version=1, https://workflowhub.eu/workflows/2011?version=1, https://workflowhub.eu/workflows/225?version=1, https://workflowhub.eu/workflows/51?version=1, https://workflowhub.eu/workflows/750?version=4, https://workflowhub.eu/workflows/788?version=1 assembly/chloroplast-assembly, assembly/hifi-assembly, assembly/hybrid_denovo_assembly, assembly/largegenome, assembly/mrsa-nanopore, microbiome/pathogen-detection-from-nanopore-foodborne-data 1 1 1 1 0 0 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 4818 4961 49679 51133 4110 4110 36053 36053 2250 2274 13882 14419 185 185 1088 1088 102693 100702 11530 11363 True False +format_metaphlan2_output format_metaphlan2_output tabular Format MetaPhlAn2 output to extract abundance at different taxonomic levels 2022-10-19 0.2.0 To update Metagenomics Formatting Formatting Taxonomy, Metagenomics Taxonomy, Metagenomics bebatut https://github.com/bgruening/galaxytools/tree/master/tools/format_metaphlan2_output/ https://github.com/bgruening/galaxytools/tree/master/tools/format_metaphlan2_output format_metaphlan2_output Format metaphlan2 output This tool format output file of MetaPhlan2 containing community content (abundance) at all taxonomic levels (from kingdom to strains). https://usegalaxy.eu/published/workflow?id=096b75501c8e0888, https://usegalaxy.eu/published/workflow?id=2cf09adb1ed6c3ec, https://usegalaxy.eu/published/workflow?id=7ab70660e6235cf0, https://usegalaxy.eu/published/workflow?id=994e5ff1df7d6c9e, https://usegalaxy.eu/published/workflow?id=9cbba5de2cbeeb0f, https://usegalaxy.eu/published/workflow?id=a8f829deb69b30ab, https://usegalaxy.eu/published/workflow?id=c01ef8354b585a1f, https://usegalaxy.eu/published/workflow?id=c3aa516e78ca4191, https://usegalaxy.eu/published/workflow?id=d05c6f0f3205fbd2, https://usegalaxy.eu/published/workflow?id=dfc2c53ac3103eff, https://usegalaxy.eu/published/workflow?id=ed0ad728cf21702b, https://usegalaxy.eu/published/workflow?id=f9175e670d8dfaa1 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 555 731 6485 7678 0 0 0 0 0 0 0 0 0 0 0 0 7678 6485 731 555 True False +fraggenescan fraggenescan tabular, fasta, gff Tool for finding (fragmented) genes in short read 2017-09-04 https://sourceforge.net/projects/fraggenescan/ @WRAPPER_VERSION@.0 fraggenescan 1.32 To update Sequence Analysis Gene prediction Gene prediction Genetics, Sequence analysis Genetics, Sequence analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/fraggenescan https://github.com/galaxyproject/tools-iuc/tree/master/tools/fraggenescan fraggenescan FragGeneScan Application for finding (fragmented) genes in short reads https://usegalaxy.eu/published/workflow?id=02631612a43a4d9b, https://usegalaxy.eu/published/workflow?id=3eaa913306c16146, https://usegalaxy.eu/published/workflow?id=401746888e8b3aa8, https://usegalaxy.eu/published/workflow?id=534f5fc25bc887ca, https://usegalaxy.eu/published/workflow?id=58955868b504c60d, https://usegalaxy.eu/published/workflow?id=6158c3b5fc12044e, https://usegalaxy.eu/published/workflow?id=6416cfdbd5273063, https://usegalaxy.eu/published/workflow?id=667bac8d7453e5f1, https://usegalaxy.eu/published/workflow?id=7be08f99f83c927e, https://usegalaxy.eu/published/workflow?id=8c7958cb05fba814, https://usegalaxy.eu/published/workflow?id=8c91345ed468e22d, https://usegalaxy.eu/published/workflow?id=8deb08d4f228e198, https://usegalaxy.eu/published/workflow?id=9382f9bbbdddb5ad, https://usegalaxy.eu/published/workflow?id=9a97c6eb4fe015e7, https://usegalaxy.eu/published/workflow?id=a8417c63e9e22afb, https://usegalaxy.eu/published/workflow?id=d4a95588e6e50893, https://usegalaxy.eu/published/workflow?id=d57d41e306241396 0 1 1 1 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 160 193 1267 1643 0 0 0 0 48 48 1171 1208 2 2 12 12 2863 2450 243 210 True False +fragpipe fragpipe, fragpipe_manifest_generator txt, csv, tsv, tabular Data analysis for mass spectrometry-based proteomics. 2022-07-21 https://fragpipe.nesvilab.org/ 23.0 fragpipe 24.0 To update Proteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe https://usegalaxy.eu/published/workflow?id=4c7fabcb345f5990, https://usegalaxy.eu/published/workflow?id=8ef3379dded2490a, https://usegalaxy.eu/published/workflow?id=bee2a7669a7dea5b, https://usegalaxy.org.au/published/workflow?id=9365a7de314c9f85, https://usegalaxy.org/published/workflow?id=e3a30c0583183c1e, https://workflowhub.eu/workflows/1410?version=1, https://workflowhub.eu/workflows/1793?version=1 proteomics/neoantigen-fragpipe-discovery 2 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 41 41 435 435 23 23 70 70 0 0 0 0 0 0 0 0 505 505 64 64 True False +freqsap freqsap tabular Get frequencies of single amino-acid polymorphisms based on nucleid-acid polymorphism for different populations from UniProt and DbSNP. 2025-07-18 https://github.com/RECETOX/galaxytools 1.1.1 freqsap 1.1.1 Up-to-date Proteomics recetox https://github.com/RECETOX/galaxytools/tree/main/tools/freqsap https://github.com/RECETOX/galaxytools/tree/master/tools/freqsap 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False +freyja freyja_aggregate_plot, freyja_boot, freyja_demix, freyja_variants tabular, html, pdf, csv lineage abundances estimation 2022-07-05 https://github.com/andersen-lab/Freyja 2.0.1 freyja 2.0.3 To update Metagenomics, Sequence Analysis RNA-Seq quantification RNA-Seq quantification Metagenomics Metagenomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/freyja https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja freyja Freyja Recover relative lineage abundances from mixed SARS-CoV-2 samples from a sequencing dataset https://usegalaxy.eu/published/workflow?id=4a764275d4bf9f31, https://usegalaxy.eu/published/workflow?id=d88145e7475e0b7b 2 0 4 0 0 0 0 0 0 0 4 0 0 0 0 0 0 0 0 0 0 0 0 4 0 0 58 58 24576 24576 15 15 327 327 0 0 0 0 0 0 0 0 24903 24903 73 73 True False +frogs_core FROGS_Core_Companion, FROGS_Core_Main Suite for metabarcoding analysis 2025-07-25 http://frogs.inrae.fr/ 5.1.0 To update Metagenomics frogs https://github.com/geraldinepascal/FROGS-wrappers/ https://github.com/geraldinepascal/FROGS-wrappers/tree/master/tools/frogs_core 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False +frogs_func FROGS_Func Suite for metabarcoding analysis 2025-08-27 http://frogs.inrae.fr/ 5.1.0 To update Metagenomics frogs https://github.com/geraldinepascal/FROGS-wrappers/ https://github.com/geraldinepascal/FROGS-wrappers/tree/master/tools/frogs_func 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False +frogs_stat FROGS_Stat Suite for metabarcoding analysis 2025-07-23 http://frogs.inrae.fr/ 5.1.0 To update Metagenomics frogs https://github.com/geraldinepascal/FROGS-wrappers/ https://github.com/geraldinepascal/FROGS-wrappers/tree/master/tools/frogs_stat 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False +funannotate funannotate_annotate, funannotate_clean, funannotate_compare, funannotate_predict, funannotate_sort genbank, tabular, fasta, txt, gff3, json, html Funannotate is a genome prediction, annotation, and comparison software package. 2021-08-26 https://funannotate.readthedocs.io 1.8.17 To update Genome annotation Genome annotation Genome annotation Genomics Genomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/funannotate https://github.com/galaxyproject/tools-iuc/tree/master/tools/funannotate funannotate funannotate funannotate is a pipeline for genome annotation (built specifically for fungi, but will also work with higher eukaryotes). https://usegalaxy.cz/published/workflow?id=932f4901960a595a, https://usegalaxy.eu/published/workflow?id=07c92110c3fffcf8, https://usegalaxy.eu/published/workflow?id=e5becc6d66b2568c, https://usegalaxy.org.au/published/workflow?id=4e161a8f5098cc49, https://usegalaxy.org.au/published/workflow?id=52065a4100b11184, https://usegalaxy.org.au/published/workflow?id=a9068ea858222e2b, https://usegalaxy.org/published/workflow?id=7251c6e0dad8f927, https://usegalaxy.org/published/workflow?id=c42c66d1b627c5a5, https://workflowhub.eu/workflows/1525?version=1, https://workflowhub.eu/workflows/1656?version=1, https://workflowhub.eu/workflows/358?version=1, https://workflowhub.eu/workflows/754?version=1 ecology/phylogeny-data-prep, genome-annotation/funannotate 3 5 5 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 0 0 891 891 14118 14118 209 209 1453 1453 310 310 8597 8597 88 88 1505 1505 25673 25673 1498 1498 True False +gamma gamma_s, gamma tabular, gff, fasta Gene Allele Mutation Microbial Assessment 2025-08-06 https://github.com/rastanton/GAMMA @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ GAMMA 2.2 To update Metagenomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/gamma https://github.com/galaxyproject/tools-iuc/tree/master/tools/gamma 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False +genomad genomad_end_to_end Identify virus and plasmid genomes from nucleotide sequences 2024-06-17 https://github.com/apcamargo/genomad/ @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ genomad 1.12.0 To update Metagenomics Sequence annotation, Taxonomic classification Sequence annotation, Taxonomic classification Sequence analysis Sequence analysis ufz https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/genomad/ https://github.com/Helmholtz-UFZ/galaxy-tools/tree/master/tools/genomad genomad geNomad geNomad is a tool that identifies virus and plasmid genomes from nucleotide sequences. 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https://workflowhub.eu/workflows/641?version=33, https://workflowhub.eu/workflows/642?version=25, https://workflowhub.eu/workflows/643?version=5, https://workflowhub.eu/workflows/645?version=17, https://workflowhub.eu/workflows/701?version=1, https://workflowhub.eu/workflows/702?version=1, https://workflowhub.eu/workflows/751?version=19, https://workflowhub.eu/workflows/788?version=1, https://workflowhub.eu/workflows/789?version=1 assembly/ERGA-post-assembly-QC, assembly/assembly-decontamination, assembly/vgp_genome_assembly 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 1105 1105 19582 19582 735 735 15352 15352 183 183 4128 4128 5 5 453 453 39515 39515 2028 2028 True False +gi2taxonomy Fetch Taxonomic Ranks taxonomy Fetch taxonomic representation 2014-01-27 https://bitbucket.org/natefoo/taxonomy 1.1.1 taxonomy 0.10.5 To update Metagenomics Database search, ID mapping Database search, ID mapping Taxonomy Taxonomy devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/gi2taxonomy https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/gi2taxonomy gi2taxonomy gi2taxonomy The tool fetches taxonomic information for a list of sequence identifiers (i.e. GI numbers, as used by the National Center for Biotechnology Information (NCBI). https://usegalaxy.org/published/workflow?id=19c9c8cc3c813bda, https://usegalaxy.org/published/workflow?id=2f7638035fb889ac, https://usegalaxy.org/published/workflow?id=55aa743125c2465d, https://usegalaxy.org/published/workflow?id=59347cc210c4cdbc, https://usegalaxy.org/published/workflow?id=7294f75ad01ca7ed, https://usegalaxy.org/published/workflow?id=7b67ffcf1b7c2232, https://usegalaxy.org/published/workflow?id=85d825931edf4a64, https://usegalaxy.org/published/workflow?id=896d29573ea3e574, https://usegalaxy.org/published/workflow?id=d851f8436497dd1c 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 68 116 244 713 17 1798 113 14058 0 0 0 0 0 1 0 6 14777 357 1915 85 True False +glimmer_hmm GlimmerHMM is a new gene finder based on a Generalized Hidden Markov Model (GHMM) 2015-02-28 https://ccb.jhu.edu/software/glimmerhmm/ To update Sequence Analysis bgruening https://github.com/bgruening/galaxytools/tree/master/tools/glimmer_hmm https://github.com/bgruening/galaxytools/tree/master/tools/glimmer_hmm 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False +goenrichment goenrichment, goslimmer tabular, png Performs GO Enrichment analysis. 2018-12-28 https://github.com/DanFaria/GOEnrichment @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ goenrichment 2.0.1 To update Genome annotation Gene-set enrichment analysis Gene-set enrichment analysis Transcriptomics Transcriptomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/goenrichment https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment goenrichment GOEnrichment GOEnrichment is a tool for performing GO enrichment analysis of gene sets, such as those obtained from RNA-seq or Microarray experiments, to help characterize them at the functional level. It is available in Galaxy Europe and as a stand-alone tool.GOEnrichment is flexible in that it allows the user to use any version of the Gene Ontology and any GO annotation file they desire. To enable the use of GO slims, it is accompanied by a sister tool GOSlimmer, which can convert annotation files from full GO to any specified GO slim.The tool features an optional graph clustering algorithm to reduce the redundancy in the set of enriched GO terms and simplify its output.It was developed by the BioData.pt / ELIXIR-PT team at the Instituto Gulbenkian de Ciência. https://usegalaxy.eu/published/workflow?id=5f053303601cc630, https://usegalaxy.eu/published/workflow?id=7136ce9f18c74853, https://usegalaxy.org.au/published/workflow?id=d04b26372b28e8ed, https://workflowhub.eu/workflows/1515?version=1, https://workflowhub.eu/workflows/1667?version=1 single-cell/GO-enrichment, transcriptomics/goenrichment 2 2 2 2 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 799 928 6000 7557 1081 1196 8060 9309 230 233 1602 1647 5 6 39 44 18557 15701 2363 2115 True False +goseq goseq tabular, pdf, rdata goseq does selection-unbiased testing for category enrichment amongst differentially expressed (DE) genes for RNA-seq data 2016-11-12 https://bioconductor.org/packages/release/bioc/html/goseq.html @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ bioconductor-goseq 1.62.0 To update Statistics, RNA, Micro-array Analysis Gene functional annotation Gene functional annotation RNA-Seq RNA-Seq iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/goseq https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq goseq GOseq Detect Gene Ontology and/or other user defined categories which are over/under represented in RNA-seq data. https://usegalaxy.eu/published/workflow?id=032ad839dab7ae70, https://usegalaxy.eu/published/workflow?id=12bf85cdc8102bb5, https://usegalaxy.eu/published/workflow?id=20ada53472782c9b, https://usegalaxy.eu/published/workflow?id=63c91ea322cd2819, https://usegalaxy.eu/published/workflow?id=732fa536cdc70c96, https://usegalaxy.eu/published/workflow?id=9c7a218993788493, https://usegalaxy.eu/published/workflow?id=c1a6d11e1eab6a42, https://usegalaxy.eu/published/workflow?id=e18ef811e7ad487d, https://usegalaxy.eu/published/workflow?id=e7e26967cf6cb8d8, https://usegalaxy.eu/published/workflow?id=f9aea278cd2b5ee4, https://usegalaxy.eu/published/workflow?id=fa83e26e05418370, https://usegalaxy.org.au/published/workflow?id=4f0814ec9f9f8425, https://usegalaxy.org.au/published/workflow?id=5490661d0153962b, https://usegalaxy.org.au/published/workflow?id=71bad95f72c9f30d, https://usegalaxy.org.au/published/workflow?id=75113a1b41904d2a, https://usegalaxy.org.au/published/workflow?id=9f6e62f465589ca3, https://usegalaxy.org.au/published/workflow?id=e1fd89e7248b6661, https://usegalaxy.org/published/workflow?id=053f09b017c85ace, https://usegalaxy.org/published/workflow?id=3dd83e9ceaa9b749, https://usegalaxy.org/published/workflow?id=420a332da24fb9e9, https://usegalaxy.org/published/workflow?id=742120336d5ff997, https://workflowhub.eu/workflows/1194?version=1, https://workflowhub.eu/workflows/1684?version=1, https://workflowhub.eu/workflows/1699?version=1, https://workflowhub.eu/workflows/1708?version=1, https://workflowhub.eu/workflows/1713?version=2, https://workflowhub.eu/workflows/689?version=1 transcriptomics/minerva-pathways, transcriptomics/ref-based, transcriptomics/rna-seq-analysis-clustering-viz, transcriptomics/rna-seq-genes-to-pathways 1 1 1 1 0 0 0 0 1 0 0 0 0 0 0 0 0 0 1 0 0 0 1 1 1 0 3196 3921 23708 28273 3528 4089 26762 31254 640 680 4461 5015 103 104 751 784 65326 55682 8794 7467 True False +graphlan graphlan, graphlan_annotate png, pdf, ps, eps, svg, phyloxml GraPhlAn is a software tool for producing high-quality circular representations of taxonomic and phylogenetic trees 2017-03-03 https://github.com/biobakery/graphlan 1.1.3 graphlan 1.1.3 Up-to-date Metagenomics, Graphics, Phylogenetics Phylogenetic inference, Phylogenetic tree visualisation, Phylogenetic tree editing, Taxonomic classification Phylogenetic inference, Phylogenetic tree visualisation, Phylogenetic tree editing, Taxonomic classification Metagenomics, Phylogenetics, Phylogenomics, Cladistics Metagenomics, Phylogenetics, Phylogenomics, Cladistics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/graphlan https://github.com/galaxyproject/tools-iuc/tree/master/tools/graphlan graphlan GraPhlAn GraPhlAn is a software tool for producing high-quality circular representations of taxonomic and phylogenetic trees. GraPhlAn focuses on concise, integrative, informative, and publication-ready representations of phylogenetically- and taxonomically-driven investigation. https://usegalaxy.eu/published/workflow?id=05f5f040337786bf, https://usegalaxy.eu/published/workflow?id=096b75501c8e0888, https://usegalaxy.eu/published/workflow?id=19de5cbae7f48103, https://usegalaxy.eu/published/workflow?id=2cf09adb1ed6c3ec, https://usegalaxy.eu/published/workflow?id=4d32b1b3ac0a7161, https://usegalaxy.eu/published/workflow?id=4f21205e71cabd37, https://usegalaxy.eu/published/workflow?id=5f0faac42b0a5062, https://usegalaxy.eu/published/workflow?id=69eddfde874af35b, https://usegalaxy.eu/published/workflow?id=713a5485e2007f90, https://usegalaxy.eu/published/workflow?id=79b4ae4403772098, https://usegalaxy.eu/published/workflow?id=7ab70660e6235cf0, https://usegalaxy.eu/published/workflow?id=87cc0cd143a12c41, https://usegalaxy.eu/published/workflow?id=994e5ff1df7d6c9e, https://usegalaxy.eu/published/workflow?id=9cbba5de2cbeeb0f, https://usegalaxy.eu/published/workflow?id=a8f829deb69b30ab, https://usegalaxy.eu/published/workflow?id=b5f848dc8e96663c, https://usegalaxy.eu/published/workflow?id=c01ef8354b585a1f, https://usegalaxy.eu/published/workflow?id=c3aa516e78ca4191, https://usegalaxy.eu/published/workflow?id=d05c6f0f3205fbd2, https://usegalaxy.eu/published/workflow?id=dfc2c53ac3103eff, https://usegalaxy.eu/published/workflow?id=ec50dd6d56f50db1, https://usegalaxy.eu/published/workflow?id=ed0ad728cf21702b, https://usegalaxy.eu/published/workflow?id=f9175e670d8dfaa1, https://usegalaxy.eu/published/workflow?id=fdca6c9d394986bf, https://usegalaxy.fr/published/workflow?id=09e8293456ee6d99, https://usegalaxy.fr/published/workflow?id=c4f6062e51d0f45e, https://workflowhub.eu/workflows/1451?version=2, https://workflowhub.eu/workflows/1466?version=2 microbiome/metatranscriptomics, microbiome/metatranscriptomics-short 2 2 2 2 0 0 0 0 2 0 2 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 799 940 11872 13928 325 325 1773 1773 202 207 1432 1470 21 21 90 90 17261 15167 1493 1347 True False +groot groot tabular GROOT is a tool to type Antibiotic Resistance Genes (ARGs) in metagenomic samples 2024-05-14 https://github.com/will-rowe/groot @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ groot 1.1.2 To update Metagenomics Antimicrobial resistance prediction Antimicrobial resistance prediction Metagenomics, Microbiology, Genomics Metagenomics, Microbiology iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/groot https://github.com/galaxyproject/tools-iuc/tree/master/tools/groot groot GROOT Indexed variation graphs for efficient and accurate resistome profiling. https://workflowhub.eu/workflows/2068?version=2 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 5 5 7 7 0 0 0 0 0 0 0 0 3 3 37 37 44 44 8 8 True False +gtdb_to_taxdump gtdb_to_taxdump tabular Convert GTDB taxonomy to NCBI taxdump format 2024-08-25 https://github.com/nick-youngblut/gtdb_to_taxdump 0.1.9 gtdb_to_taxdump 0.1.9 Up-to-date Metagenomics Data handling, Mapping, Generation Data handling, Mapping, Generation Computational biology Computational biology iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/gtdb_to_taxdump https://github.com/galaxyproject/tools-iuc/tree/master/tools/gtdb_to_taxdump gtdb_to_taxdump gtdb_to_taxdump Tool with multiple functions. Main functions are to create a DIAMOND database from the GTDB taxonomy data or create a NCBI taxdump format out of this data. This tool can also create a mapping between the taxonomy classification between GTDB and NCBI. https://usegalaxy.eu/published/workflow?id=cf0159c14418525e, https://usegalaxy.eu/published/workflow?id=e4dabaf57668dbd1, https://workflowhub.eu/workflows/2099?version=2 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 27 27 1127 1127 0 0 0 0 0 0 0 0 0 0 0 0 1127 1127 27 27 True False +gtdbtk gtdbtk_classify_wf txt GTDB-Tk is a software tool kit for assigning objective taxonomic classifications to bacterial and archaeal genomesbased on the Genome Database Taxonomy GTDB. It is designed to work with recent advances that allow hundreds orthousands of metagenome-assembled genomes (MAGs) to be obtained directly from environmental samples. It can alsobe applied to isolate and single-cell genomes. 2022-12-13 https://github.com/Ecogenomics/GTDBTk 2.7.2 gtdbtk 2.7.2 Up-to-date Metagenomics Genome alignment, Taxonomic classification, Sequence assembly, Query and retrieval Genome alignment, Taxonomic classification, Sequence assembly, Query and retrieval Metagenomics, Taxonomy, Phylogenetics, Database management, Proteins Metagenomics, Taxonomy, Phylogenetics, Database management, Proteins iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/gtdbtk https://github.com/galaxyproject/tools-iuc/tree/master/tools/gtdbtk GTDB-Tk GTDB-Tk a toolkit to classify genomes with the Genome Taxonomy Database.GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.GTDB-Tk is a software toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes based on the Genome Database Taxonomy GTDB. It is designed to work with recent advances that allow hundreds or thousands of metagenome-assembled genomes (MAGs) to be obtained directly from environmental samples. It can also be applied to isolate and single-cell genomes. The GTDB-Tk is open source and released under the GNU General Public License (Version 3). https://usegalaxy.eu/published/workflow?id=0563f58718be932d, https://usegalaxy.eu/published/workflow?id=17d2e76147fc940c, https://usegalaxy.eu/published/workflow?id=1e5f1d9a51032e44, https://usegalaxy.eu/published/workflow?id=2c992e509aa5dd9d, https://usegalaxy.eu/published/workflow?id=7ecd92cb382d8168, https://usegalaxy.eu/published/workflow?id=c62d65832377e376, https://usegalaxy.eu/published/workflow?id=e4dabaf57668dbd1, https://usegalaxy.org/published/workflow?id=33d90e718ce500ef, https://usegalaxy.org/published/workflow?id=84233173d92fa506, https://usegalaxy.org/published/workflow?id=8d229c0f58a07ebe, https://usegalaxy.org/published/workflow?id=9b589bc76208fb1e, https://workflowhub.eu/workflows/1352?version=4, https://workflowhub.eu/workflows/2099?version=2 1 1 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 462 462 3982 3982 305 305 1566 1566 177 177 1095 1095 15 15 1439 1439 8082 8082 959 959 True False +gubbins gubbins txt, gff3, embl, fasta, phylip, csv, vcf Gubbins - bacterial recombination detection 2017-06-22 @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ gubbins 3.4.3 To update Sequence Analysis Genotyping, Phylogenetic inference, Ancestral reconstruction Genotyping, Phylogenetic inference, Ancestral reconstruction Phylogeny, Genotype and phenotype, Whole genome sequencing Phylogeny, Genotype and phenotype, Whole genome sequencing iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/gubbins https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins gubbins Gubbins Gubbins is a tool for rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences. 1 1 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 402 428 4731 5118 268 288 3847 4061 250 317 1977 2858 0 0 0 0 12037 10555 1033 920 True False +guppy_basecaller guppy-basecaller fastqsanger, txt A wrapper for the guppy basecaller tool from Oxford Nanopore Technologies 2020-11-18 http://artbio.fr 6.5.7 To update Nanopore artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/guppy https://github.com/ARTbio/tools-artbio/tree/master/tools/guppy 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 7 7 0 0 0 0 7 7 1 1 True False +halla halla tabular, pdf Hierarchical All-against-All association 2025-11-05 https://github.com/biobakery/halla @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ halla 0.8.40 To update Metagenomics Statistical calculation, Gene expression profiling, Essential dynamics Statistical calculation, Gene expression profiling, Essential dynamics Microbial ecology, Microarray experiment, Metabolomics, Phylogeny, Epigenetics Microbial ecology, Microarray experiment, Metabolomics, Phylogeny, Epigenetics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/halla https://github.com/galaxyproject/tools-iuc/tree/master/tools/halla halla HAllA High-sensitivity pattern discovery in large, paired multi-omic datasets. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False +hamronization hamronize_summarize, hamronize_tool tabular Convert AMR gene detection tool output to hAMRonization specification format. 2021-02-02 https://github.com/pha4ge/hAMRonization 1.1.4 hamronization 1.2.1 To update Sequence Analysis Data handling, Antimicrobial resistance prediction, Parsing Antimicrobial resistance prediction, Parsing Public health and epidemiology, Microbiology, Bioinformatics Public health and epidemiology, Microbiology, Bioinformatics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/hamronization https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization hamronization hAMRonization Parse multiple Antimicrobial Resistance Analysis Reports into a common data structure https://usegalaxy.eu/published/workflow?id=eb5ab8bc82569eee, https://workflowhub.eu/workflows/1189?version=2, https://workflowhub.eu/workflows/407?version=1, https://workflowhub.eu/workflows/470?version=1 0 0 2 2 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 254 254 18459 18459 1 1 20 20 1 1 21 21 6 6 191 191 18691 18691 262 262 True False +hifiasm_meta hifiasm_meta A hifiasm fork for metagenome assembly using Hifi reads. 2023-01-18 https://github.com/xfengnefx/hifiasm-meta 0.3.1 hifiasm_meta hamtv0.3.1 To update Metagenomics Sequence assembly Sequence assembly Sequence assembly, Metagenomics Sequence assembly, Metagenomics galaxy-australia https://github.com/galaxyproject/tools-iuc/tree/main/tools/hifiasm_meta https://github.com/galaxyproject/tools-iuc/tree/master/tools/hifiasm_meta hifiasm-meta Hifiasm-meta Hifiasm_meta - de novo metagenome assembler, based on hifiasm, a haplotype-resolved de novo assembler for PacBio Hifi reads. 0 1 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 40 40 229 229 0 0 0 0 16 16 368 368 0 0 0 0 597 597 56 56 True False +hivtrace hivtrace txt An application that identifies potential transmission clusters within a supplied FASTA file with an option to find potential links against the Los Alamos HIV Sequence Database. 2015-12-10 1.0.1 hivtrace 1.5.0 To update Sequence Analysis nml https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace https://github.com/phac-nml/galaxy_tools/tree/master/tools/hivtrace 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False +hmmer3 hmmer_alimask, hmmer_hmmalign, hmmer_hmmbuild, hmmer_hmmconvert, hmmer_hmmemit, hmmer_hmmfetch, hmmer_hmmscan, hmmer_hmmsearch, hmmer_jackhmmer, hmmer_nhmmer, hmmer_nhmmscan, hmmer_phmmer stockholm, hmm3, fasta HMMER is used for searching sequence databases for homologs of proteinsequences, and for making protein sequence alignments. It implementsmethods using probabilistic models called profile hidden Markov models(profile HMMs). 2015-02-16 http://hmmer.org/ 3.4 hmmer 3.4 Up-to-date Sequence Analysis Formatting, Multiple sequence alignment, Sequence profile generation, Format validation, Conversion, Sequence generation, Data retrieval, Statistical calculation, Database search, Formatting, Database search, Database search, Probabilistic sequence generation, Statistical calculation, Statistical calculation, Sequence database search, Formatting, Sequence database search, Database search, Sequence database search Formatting, Multiple sequence alignment, Sequence profile generation, Format validation, Conversion, Data retrieval, Statistical calculation, Formatting, Probabilistic sequence generation, Statistical calculation, Statistical calculation, Sequence database search, Formatting, Sequence database search, Sequence database search Sequence analysis, Sequence sites, features and motifs, Gene and protein families Sequence analysis, Sequence sites, features and motifs, Gene and protein families iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/hmmer3 https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 hmmer3 HMMER3 This tool is used for searching sequence databases for homologs of protein sequences, and for making protein sequence alignments. It implements methods using probabilistic models called profile hidden Markov models. The new HMMER3 project, HMMER is now as fast as BLAST for protein search. https://usegalaxy.eu/published/workflow?id=02631612a43a4d9b, https://usegalaxy.eu/published/workflow?id=0ab3e47ebd3b520e, https://usegalaxy.eu/published/workflow?id=24eaa682897379c8, https://usegalaxy.eu/published/workflow?id=3eaa913306c16146, https://usegalaxy.eu/published/workflow?id=58955868b504c60d, https://usegalaxy.eu/published/workflow?id=5be158931abca947, https://usegalaxy.eu/published/workflow?id=6158c3b5fc12044e, https://usegalaxy.eu/published/workflow?id=6416cfdbd5273063, https://usegalaxy.eu/published/workflow?id=667bac8d7453e5f1, https://usegalaxy.eu/published/workflow?id=8c91345ed468e22d, https://usegalaxy.eu/published/workflow?id=8deb08d4f228e198, https://usegalaxy.eu/published/workflow?id=9a60ecf98d4f8134, https://usegalaxy.eu/published/workflow?id=d57d41e306241396, https://usegalaxy.fr/published/workflow?id=5ec6d378e60f7ccc, https://usegalaxy.fr/published/workflow?id=7ebb54181b404733, https://usegalaxy.fr/published/workflow?id=b131218bec7eacb4, https://usegalaxy.fr/published/workflow?id=d425a77157cae2ee, https://usegalaxy.org/published/workflow?id=84b447be2f1c5870, https://workflowhub.eu/workflows/100?version=1, https://workflowhub.eu/workflows/37?version=1, https://workflowhub.eu/workflows/38?version=1, https://workflowhub.eu/workflows/39?version=1, https://workflowhub.eu/workflows/40?version=1 12 12 12 12 0 0 0 0 12 12 0 0 0 0 0 0 0 0 0 0 0 0 12 12 12 0 380 403 36302 43262 0 0 0 0 83 84 4731 4887 97 97 540 543 48692 41573 584 560 True False +humann humann, humann_barplot, humann_join_tables, humann_reduce_table, humann_regroup_table, humann_rename_table, humann_renorm_table, humann_split_stratified_table, humann_split_table, humann_unpack_pathways tabular, biom1, txt, sam, fasta, png, pdf, svg HUMAnN for functionally profiling metagenomes and metatranscriptomes at species-level resolution 2021-05-12 http://huttenhower.sph.harvard.edu/humann 3.9 humann 3.9 Up-to-date Metagenomics Species frequency estimation, Taxonomic classification, Phylogenetic analysis Species frequency estimation, Taxonomic classification, Phylogenetic analysis Metagenomics, Phylogenomics Metagenomics, Phylogenomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/humann https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann humann humann HUMAnN is a pipeline for efficiently and accurately profiling the presence/absence and abundance of microbial pathways in a community from metagenomic or metatranscriptomic sequencing data (typically millions of short DNA/RNA reads). This process, referred to as functional profiling, aims to describe the metabolic potential of a microbial community and its members. More generally, functional profiling answers the question “What are the microbes in my community-of-interest doing (or are capable of doing)?” https://usegalaxy.eu/published/workflow?id=21a17d6c473a88c0, https://usegalaxy.eu/published/workflow?id=23dd2253da51e22e, https://usegalaxy.eu/published/workflow?id=3118d383c81cf805, https://usegalaxy.eu/published/workflow?id=4d32b1b3ac0a7161, https://usegalaxy.eu/published/workflow?id=5ce8a472e6e95c60, https://usegalaxy.eu/published/workflow?id=5f0faac42b0a5062, https://usegalaxy.eu/published/workflow?id=69eddfde874af35b, https://usegalaxy.eu/published/workflow?id=713a5485e2007f90, https://usegalaxy.eu/published/workflow?id=87cc0cd143a12c41, https://usegalaxy.eu/published/workflow?id=9472be79da012999, https://usegalaxy.eu/published/workflow?id=a7a6d8ecc2795f58, https://usegalaxy.eu/published/workflow?id=a8f829deb69b30ab, https://usegalaxy.eu/published/workflow?id=b14845359b702444, https://usegalaxy.eu/published/workflow?id=cb2df493f5e334f7, https://usegalaxy.eu/published/workflow?id=d7e532d13a7f1ea6, https://usegalaxy.eu/published/workflow?id=fdca6c9d394986bf, https://usegalaxy.fr/published/workflow?id=c4f6062e51d0f45e, https://usegalaxy.fr/published/workflow?id=fd733565098d76c9, https://workflowhub.eu/workflows/1447?version=2, https://workflowhub.eu/workflows/1456?version=2, https://workflowhub.eu/workflows/1466?version=2 microbiome/metatranscriptomics, microbiome/metatranscriptomics-short 6 10 10 10 0 0 0 0 10 0 9 0 0 0 0 0 0 0 0 0 0 0 6 10 10 0 795 795 52483 52483 123 123 3171 3171 122 122 4812 4812 17 17 987 987 61453 61453 1057 1057 True False +hyphy hyphy_absrel, hyphy_annotate, hyphy_b_still, hyphy_bgm, hyphy_busted, hyphy_cfel, hyphy_cln, hyphy_conv, hyphy_fade, hyphy_fel, hyphy_fubar, hyphy_gard, hyphy_infer_stasis_clusters, hyphy_meme, hyphy_prime, hyphy_relax, hyphy_slac, hyphy_sm19, hyphy_strike_ambigs markdown, hyphy_results.json, nhx, nex, fasta, json, txt Hypothesis Testing using Phylogenies 2018-06-08 http://www.hyphy.org 2.5.96 hyphy 2.5.100 To update Phylogenetics Statistical calculation Statistical calculation Phylogeny, Small molecules, Molecular interactions, pathways and networks Phylogeny, Small molecules, Molecular interactions, pathways and networks iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/hyphy https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy HyPhy HyPhy Software package for the analysis of genetic sequences using techniques in phylogenetics, molecular evolution, and machine learning. https://usegalaxy.eu/published/workflow?id=1d40d6deb2da04cc, https://usegalaxy.eu/published/workflow?id=e7f03b4bd9b3d6fd, https://usegalaxy.fr/published/workflow?id=297b71156b297a73, https://usegalaxy.org.au/published/workflow?id=42137e36791652bc, https://usegalaxy.org/published/workflow?id=2d1ca299c1b058f6, https://usegalaxy.org/published/workflow?id=a46ad0b9240d1a13, https://usegalaxy.org/published/workflow?id=e1cc0886cd27b92e 17 2 19 2 0 0 0 0 0 0 0 0 10 0 0 0 0 0 2 0 0 0 12 17 12 0 88 94 10953 11906 78 108 4725 8358 33 42 815 909 3 5 22 27 21200 16515 249 202 True False +hypo hypo fasta, txt Super Fast & Accurate Polisher for Long Read Genome Assemblies 2021-11-15 https://github.com/kensung-lab/hypo 1.0.3 hypo 1.0.3 Up-to-date Assembly Optimisation and refinement, Genome assembly Optimisation and refinement, Genome assembly Sequence assembly, Genomics Sequence assembly, Genomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/hypo https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo HyPo HyPo HyPo, a Hybrid Polisher, utilizes short as well as long reads within a single run to polish a long reads assembly of small and large genomes. https://usegalaxy.eu/published/workflow?id=83a1b8949d87e3da, https://workflowhub.eu/workflows/788?version=1, https://workflowhub.eu/workflows/789?version=1 0 0 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 107 107 575 575 0 0 0 0 0 0 0 0 0 0 0 0 575 575 107 107 True False +icescreen icescreen tabular, txt, genbank.gz, gff3.gz, embl.gz, tar.gz, gz identification of ICEs and IMEs in Bacillota genomes. 2022-01-04 https://forgemia.inra.fr/ices_imes_analysis/icescreen 1.3.3 icescreen 1.3.3 Up-to-date Genome annotation Database search, Protein feature detection Database search, Protein feature detection Mobile genetic elements, Sequence sites, features and motifs, Genomics, Molecular interactions, pathways and networks, Structural variation Mobile genetic elements, Sequence sites, features and motifs, Genomics, Molecular interactions, pathways and networks, Structural variation iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/icescreen https://github.com/galaxyproject/tools-iuc/tree/master/tools/icescreen icescreen ICEscreen A tool to detect Firmicute ICEs and IMEs, isolated or enclosed in composite structures. 1 0 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 3 153 153 4 4 15 15 0 0 0 0 0 0 0 0 168 168 7 7 True False +idba idba_hybrid, idba_tran, idba_ud fasta Wrappers for the idba assembler variants. 2018-04-26 https://i.cs.hku.hk/~alse/hkubrg/projects/index.html 1.1.3 idba 1.1.3 Up-to-date Assembly Sequence assembly Sequence assembly Sequence assembly Sequence assembly iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/idba_ud https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud idba IDBA A short read assembler based on iterative De Bruijn graph. It is developed under 64-bit Linux, but should be suitable for all unix-like system. 3 0 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 3 3 0 106 126 944 1353 146 169 1199 1700 0 0 0 0 1 1 3 3 3056 2146 296 253 True False +instrain instrain_compare, instrain_profile tabular, pdf, zip InStrain is a tool for analysis of co-occurring genome populations from metagenomes 2021-08-11 https://instrain.readthedocs.io/ 1.5.3 instrain 1.10.0 To update Metagenomics SNP detection, Genome comparison SNP detection, Genome comparison Mapping, Metagenomics Mapping, Metagenomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/instrain https://github.com/galaxyproject/tools-iuc/tree/master/tools/instrain instrain InStrain InStrain is a tool for analysis of co-occurring genome populations from metagenomes that allows highly accurate genome comparisons, analysis of coverage, microdiversity, and linkage, and sensitive SNP detection with gene localization and synonymous non-synonymous identification 0 0 2 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 22 22 208 208 0 0 0 0 0 0 0 0 0 0 0 0 208 208 22 22 True False +integronfinder integron_finder txt, tsv """IntegronFinder identify integrons with high accuracy and sensitivity.It searches for attC sites using covariance models, for integron-integrases using HMM profiles, and for other features (promoters, attI site) using pattern matching""" 2022-09-22 https://github.com/gem-pasteur/Integron_Finder 2.0.5 integron_finder 2.0.6 To update Sequence Analysis Nucleic acid feature detection, Sequence motif recognition, Protein feature detection, Genome annotation Nucleic acid feature detection, Sequence motif recognition, Protein feature detection, Genome annotation Functional genomics, Mobile genetic elements, Molecular biology, Sequence analysis Functional genomics, Mobile genetic elements, Molecular biology, Sequence analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/integron_finder https://github.com/galaxyproject/tools-iuc/tree/master/tools/integron_finder integron_finder Integron Finder A tool to detect Integron in DNA sequences. https://usegalaxy.eu/published/workflow?id=1306ed083d91a852, https://usegalaxy.eu/published/workflow?id=2c1a6da84d891cf2, https://usegalaxy.eu/published/workflow?id=36ea584e0f60893e, https://usegalaxy.eu/published/workflow?id=3f5fe28793ed0c6c, https://usegalaxy.eu/published/workflow?id=4a218fb93d78ba67, https://usegalaxy.eu/published/workflow?id=61948fcaefa1418a, https://usegalaxy.eu/published/workflow?id=6b69ab27c565257b, https://usegalaxy.eu/published/workflow?id=8792eaecb69fbc26, https://usegalaxy.eu/published/workflow?id=a18aed4b03ffd27e, https://usegalaxy.eu/published/workflow?id=b1afc8d1e81fc904, https://usegalaxy.eu/published/workflow?id=bcd50e655809cfcb, https://usegalaxy.eu/published/workflow?id=d8db0b2e30370b84, https://usegalaxy.eu/published/workflow?id=dfb8e0f3c534000e, 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genome-annotation/bacterial-genome-annotation 1 1 1 1 0 0 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 390 390 64428 64428 252 252 7167 7167 132 132 12061 12061 34 34 2504 2504 86160 86160 808 808 True False +interproscan interproscan tabular, xml, gff3, json Interproscan queries the interpro database and provides annotations. 2021-11-15 http://www.ebi.ac.uk/Tools/pfa/iprscan5/ 5.59-91.0 interproscan 5.59_91.0 To update Sequence Analysis Sequence motif recognition, Protein feature detection Sequence motif recognition, Protein feature detection Gene and protein families, Sequence analysis Gene and protein families, Sequence analysis bgruening https://github.com/galaxyproject/tools-iuc/tree/main/tools/interproscan https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan interproscan_ebi InterProScan (EBI) Scan sequences against the InterPro protein signature databases. https://usegalaxy.cz/published/workflow?id=932f4901960a595a, https://usegalaxy.eu/published/workflow?id=02631612a43a4d9b, https://usegalaxy.eu/published/workflow?id=0293e155386d3f3a, https://usegalaxy.eu/published/workflow?id=0b9071d5dfa38559, https://usegalaxy.eu/published/workflow?id=2d2862b48918b22f, https://usegalaxy.eu/published/workflow?id=33312e5643279e8a, https://usegalaxy.eu/published/workflow?id=3eaa913306c16146, https://usegalaxy.eu/published/workflow?id=58955868b504c60d, https://usegalaxy.eu/published/workflow?id=6158c3b5fc12044e, https://usegalaxy.eu/published/workflow?id=6416cfdbd5273063, https://usegalaxy.eu/published/workflow?id=667bac8d7453e5f1, https://usegalaxy.eu/published/workflow?id=8c91345ed468e22d, https://usegalaxy.eu/published/workflow?id=8deb08d4f228e198, https://usegalaxy.eu/published/workflow?id=9a95556ec171d405, https://usegalaxy.eu/published/workflow?id=9a97c6eb4fe015e7, https://usegalaxy.eu/published/workflow?id=a448400f69594135, https://usegalaxy.eu/published/workflow?id=b9c938d1af08124b, https://usegalaxy.eu/published/workflow?id=cc59ae1a9878942c, https://usegalaxy.eu/published/workflow?id=d57d41e306241396, https://usegalaxy.eu/published/workflow?id=e5becc6d66b2568c, https://usegalaxy.org.au/published/workflow?id=35f39173f0ac9179, https://usegalaxy.org.au/published/workflow?id=7559224fc32dce3a, https://usegalaxy.org.au/published/workflow?id=876163677f1cccc4, https://usegalaxy.org.au/published/workflow?id=a9068ea858222e2b, https://usegalaxy.org/published/workflow?id=92613e1e0b13aa0a, https://usegalaxy.org/published/workflow?id=c451e4dca9981ed0, https://workflowhub.eu/workflows/1262?version=1, https://workflowhub.eu/workflows/1521?version=1, https://workflowhub.eu/workflows/1525?version=1, https://workflowhub.eu/workflows/1663?version=1, https://workflowhub.eu/workflows/2118?version=1, https://workflowhub.eu/workflows/754?version=1, https://workflowhub.eu/workflows/755?version=1 ecology/marine_omics_bgc, genome-annotation/funannotate, genome-annotation/functional 1 1 1 1 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 2350 2550 44154 69658 486 486 3914 3914 799 804 13188 13204 144 144 9435 9435 96211 70691 3984 3779 True False +iphop iphop_predict csv Integrated Phage Host Prediction 2024-10-14 https://bitbucket.org/srouxjgi/iphop/ @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ iphop 1.4.2 To update Metagenomics Sample comparison Sample comparison ufz https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/iphop/ https://github.com/Helmholtz-UFZ/galaxy-tools/tree/master/tools/iphop iphop iPHoP An automated command-line pipeline for predicting host genus of novel bacteriophages and archaeoviruses based on their genome sequences. https://usegalaxy.eu/published/workflow?id=62392daea25a3980, https://usegalaxy.eu/published/workflow?id=c62d65832377e376 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 9 9 26 26 0 0 0 0 0 0 0 0 0 0 0 0 26 26 9 9 True False +iprscan5 Interproscan queries the interpro database and provides annotations. 2015-02-28 http://www.ebi.ac.uk/Tools/pfa/iprscan5/ To update Sequence Analysis bgruening https://github.com/bgruening/galaxytools/tree/master/tools/iprscan5 https://github.com/bgruening/galaxytools/tree/master/tools/iprscan5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False +iqtree iqtree nhx, mldist, nex, iqtree, data, txt Efficient phylogenomic software by maximum likelihood 2017-09-26 http://www.iqtree.org/ 2.4.0 iqtree 3.1.2 To update Phylogenetics Phylogenetic analysis, Sequence analysis Phylogenetic analysis, Sequence analysis Phylogenetics Phylogenetics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/iqtree https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree iqtree iqtree A fast and effective stochastic algorithm to infer phylogenetic trees by maximum likelihood. 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jellyfish jellyfish, txt, fasta, tsv Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA 2021-04-07 https://github.com/gmarcais/Jellyfish @WRAPPER_VERSION@+@VERSION_SUFFIX@ kmer-jellyfish 2.3.1 To update Assembly k-mer counting k-mer counting Sequence analysis, Genomics Sequence analysis, Genomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/jellyfish https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish Jellyfish Jellyfish A command-line algorithm for counting k-mers in DNA sequence. https://usegalaxy.eu/published/workflow?id=342169b55bdc2993, https://usegalaxy.eu/published/workflow?id=bc32937d505135ab 0 1 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 369 369 4901 4901 0 0 0 0 87 87 1492 1492 35 35 1519 1519 7912 7912 491 491 True False +kaiju kaiju_addtaxonnames, kaiju_mergeoutputs, kaiju_kaiju, kaiju_kaiju2krona, kaiju_kaiju2table tabular taxonomic classification of high-throughput sequencing reads 2025-04-22 https://github.com/bioinformatics-centre/kaiju 1.10.1 kaiju 1.10.1 Up-to-date Metagenomics Taxonomic classification Taxonomic classification Metagenomics Metagenomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/kaiju https://github.com/galaxyproject/tools-iuc/tree/master/tools/kaiju kaiju Kaiju Program for the taxonomic assignment of high-throughput sequencing reads, e.g., Illumina or Roche/454, from whole-genome sequencing of metagenomic DNA. Reads are directly assigned to taxa using the NCBI taxonomy and a reference database of protein sequences from Bacteria, Archaea, Fungi, microbial eukaryotes and viruses. 0 0 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 2 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 2 True False +kat_filter kat_@EXECUTABLE@ fastqsanger, tabular Filtering kmers or reads from a database of kmers hashes 2017-03-13 2.3 kat 2.4.2 To update Sequence Analysis nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/kat_filter 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False +khmer khmer_abundance_distribution_single, khmer_abundance_distribution, khmer_count_median, khmer_partition, khmer_extract_partitions, khmer_filter_abundance, khmer_filter_below_abundance_cutoff, khmer_normalize_by_median oxlicg, csv, txt In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more 2015-03-24 https://khmer.readthedocs.org/ 3.0.0a3 khmer 3.0.0a3 Up-to-date Assembly, Next Gen Mappers Standardisation and normalisation, De-novo assembly Standardisation and normalisation, De-novo assembly Sequence assembly Sequence assembly iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/khmer https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer khmer khmer khmer is a set of command-line tools for working with DNA shotgun sequencing data from genomes, transcriptomes, metagenomes, and single cells. khmer can make de novo assemblies faster, and sometimes better. khmer can also identify (and fix) problems with shotgun data. 8 8 8 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 1 0 0 0 8 8 8 0 98 116 1572 2262 169 185 1179 1564 25 25 2179 2179 0 0 0 0 6005 4930 326 292 True False +kleborate kleborate tabular Screen genome assemblies of Klebsiella pneumoniae and the Klebsiella pneumoniae species complex (KpSC) 2022-09-09 https://github.com/katholt/Kleborate @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ kleborate 3.2.4 To update Metagenomics Multilocus sequence typing, Genome assembly, Virulence prediction Multilocus sequence typing, Genome assembly, Virulence prediction Public health and epidemiology, Metagenomics, Population genomics, Sequence assembly, Whole genome sequencing Public health and epidemiology, Metagenomics, Population genomics, Sequence assembly, Whole genome sequencing iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/kleborate https://github.com/galaxyproject/tools-iuc/tree/master/tools/kleborate kleborate Kleborate Genomic surveillance framework and global population structure for Klebsiella pneumoniae.Kleborate is a tool to screen genome assemblies of Klebsiella pneumoniae and the Klebsiella pneumoniae species complex (KpSC) for:.A manuscript describing the Kleborate software in full is currently in preparation. In the meantime, if you use Kleborate, please cite the preprint: Lam, MMC. et al. Genomic surveillance framework and global population structure for Klebsiella pneumoniae. bioRxiv (2020). 0 0 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 123 123 1479 1479 0 0 0 0 0 0 0 0 0 0 0 0 1479 1479 123 123 True False +kmer2stats kmer2stats tabular A tool for creating data files for statistics based on kmers 2025-04-16 https://github.com/SantaMcCloud/kmer2stats @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ kmer2stats 1.0.3 To update Metagenomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/kmer2stats https://github.com/galaxyproject/tools-iuc/tree/master/tools/kmer2stats https://usegalaxy.eu/published/workflow?id=342169b55bdc2993 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 8 8 310 310 0 0 0 0 0 0 0 0 0 0 0 0 310 310 8 8 True False +kmetashot kmetashot csv an alignment-free taxonomic classifier based on k-mer/minimizer counting 2025-12-18 https://github.com/gdefazio/kMetaShot @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ kmetashot 2.0 To update Metagenomics Metagenomics Metagenomics bgruening https://github.com/galaxyproject/tools-iuc/tree/main/tools/kmetashot https://github.com/bgruening/galaxytools/tree/master/tools/kmetashot kmetashot kMetaShot The application of 2nd and 3rd generation High Throughput Sequencing (HTS) technologies has deeply reshaped experimental method to investigate microbial communities and obtain a taxonomic and functional profile of the invetigated community. Shotgun Metagenomics allow to quickly obtain a representation of microorganisms genomes characterizing a particular environment. In order to obtain a fast e reliable taxonomic classification of microorganisms genomes we present kMetaShot, an alignment-free taxonomic classifier based on k-mer/minimizer counting. microbiome/mags-building 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False +kmindex kmindex_build, kmindex_query kmindex Index and query k-mers from sequencing samples using Bloom filters 2025-12-10 https://github.com/tlemane/kmindex 0.6.0 kmindex 0.6.0 Up-to-date Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/kmindex https://github.com/galaxyproject/tools-iuc/tree/master/tools/kmindex kmindex kmindex kmindex is a tool for indexing and querying sequencing samples. It is built on top of kmtricks. 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False +kneaddata kneaddata txt Quality control and contaminant removal for metagenomic data 2026-02-04 https://github.com/biobakery/kneaddata 0.12.1 kneaddata 0.12.4 To update Metagenomics, Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/kneaddata https://github.com/galaxyproject/tools-iuc/tree/master/tools/kneaddata https://usegalaxy.eu/published/workflow?id=8e13c87e751e88d8 0 0 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False +kofamscan kofamscan txt, zip Gene function annotation tool based on KEGG Orthology and hidden Markov model 2020-11-12 https://github.com/takaram/kofam_scan @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ kofamscan 1.3.0 To update Sequence Analysis Sequence analysis, Gene functional annotation Sequence analysis, Gene functional annotation Genomics, Structure analysis Genomics, Structure analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/kofamscan https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan kofamscan kofamscan KofamScan is a gene function annotation tool based on KEGG Orthology and hidden Markov model. You need KOfam database to use this tool. https://usegalaxy.eu/published/workflow?id=3eaa913306c16146, https://usegalaxy.eu/published/workflow?id=6158c3b5fc12044e, https://usegalaxy.eu/published/workflow?id=6416cfdbd5273063, https://usegalaxy.eu/published/workflow?id=667bac8d7453e5f1, https://usegalaxy.eu/published/workflow?id=8deb08d4f228e198, https://usegalaxy.eu/published/workflow?id=9b9e1e28f3683f92, https://usegalaxy.eu/published/workflow?id=d57d41e306241396 0 0 1 1 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 94 94 2904 2904 0 0 0 0 0 0 0 0 2 2 3 3 2907 2907 96 96 True False +kraken kraken-filter, kraken-mpa-report, kraken-report, kraken-translate, kraken tabular Kraken is a system for assigning taxonomic labels to short DNAsequences, usually obtained through metagenomic studies. Previous attempts by otherbioinformatics software to accomplish this task have often used sequence alignmentor machine learning techniques that were quite slow, leading to the developmentof less sensitive but much faster abundance estimation programs. Kraken aims toachieve high sensitivity and high speed by utilizing exact alignments of k-mersand a novel classification algorithm. 2017-01-24 http://ccb.jhu.edu/software/kraken/ 1.3.1 kraken 1.1.1 To update Metagenomics Taxonomic classification Taxonomic classification Taxonomy, Metagenomics Taxonomy, Metagenomics devteam https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/kraken https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/kraken kraken Kraken System for assigning taxonomic labels to short DNA sequences, usually obtained through metagenomic studies. Previous attempts by other bioinformatics software to accomplish this task have often used sequence alignment or machine learning techniques that were quite slow, leading to the development of less sensitive but much faster abundance estimation programs. It aims to achieve high sensitivity and high speed by utilizing exact alignments of k-mers and a novel classification algorithm. https://usegalaxy.org.au/published/workflow?id=b6bad1f167257248, https://usegalaxy.org/published/workflow?id=074a0b1bc8273c16, https://usegalaxy.org/published/workflow?id=2ec3e326c51d3147, https://usegalaxy.org/published/workflow?id=33d90e718ce500ef, https://usegalaxy.org/published/workflow?id=7321c6ad5425d347, https://usegalaxy.org/published/workflow?id=87b3305ea433b4e2, https://usegalaxy.org/published/workflow?id=a89e1018a00b883c, https://usegalaxy.org/published/workflow?id=e0c33057ac2670ba, https://usegalaxy.org/published/workflow?id=fb01e1a49793c8be 5 5 5 5 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 5 0 1452 1453 75318 75385 2535 4229 59050 144905 904 1133 38078 44609 114 114 3720 3720 268619 176166 6929 5005 True False +kraken2 kraken2 tabular Kraken2 for taxonomic designation. 2019-03-05 http://ccb.jhu.edu/software/kraken/ 2.17.1 kraken2 2.17.1 Up-to-date Metagenomics Taxonomic classification Taxonomic classification Taxonomy, Metagenomics, Microbial ecology, Microbiology Taxonomy, Metagenomics, Microbial ecology iuc https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/kraken2/kraken2 https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/kraken2/kraken2 kraken2 kraken2 Kraken 2 is the newest version of Kraken, a taxonomic classification system using exact k-mer matches to achieve high accuracy and fast classification speeds. This classifier matches each k-mer within a query sequence to the lowest common ancestor (LCA) of all genomes containing the given k-mer. The k-mer assignments inform the classification algorithm.Any assumption that Kraken’s raw read assignments can be directly translated into species or strain-level abundance estimates is flawed. Bracken (Bayesian Reestimation of Abundance after Classification with KrakEN), estimates species abundances in metagenomics samples by probabilistically re-distributing reads in the taxonomic tree. 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18602 18602 64 64 5824 5824 226351 226351 5016 5016 True False +krocus krocus tabular, fastq Predict MLST directly from uncorrected long reads 2019-09-03 https://github.com/quadram-institute-bioscience/krocus 1.0.1 krocus 1.0.3 To update Sequence Analysis Multilocus sequence typing, k-mer counting Multilocus sequence typing, k-mer counting Public health and epidemiology Public health and epidemiology iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/krocus https://github.com/galaxyproject/tools-iuc/tree/master/tools/krocus krocus krocus Predict MLST directly from uncorrected long reads 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False +lca_wrapper lca1 taxonomy Find lowest diagnostic rank 2014-01-27 https://bitbucket.org/natefoo/taxonomy 1.0.1 taxonomy 0.10.5 To update Metagenomics devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/lca_wrapper https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/lca_wrapper https://usegalaxy.org/published/workflow?id=19c9c8cc3c813bda, https://usegalaxy.org/published/workflow?id=2f7638035fb889ac, https://usegalaxy.org/published/workflow?id=55aa743125c2465d, https://usegalaxy.org/published/workflow?id=59347cc210c4cdbc, https://usegalaxy.org/published/workflow?id=7294f75ad01ca7ed, https://usegalaxy.org/published/workflow?id=7b67ffcf1b7c2232, https://usegalaxy.org/published/workflow?id=85d825931edf4a64, https://usegalaxy.org/published/workflow?id=896d29573ea3e574, https://usegalaxy.org/published/workflow?id=d851f8436497dd1c 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 3 20 11 137 14 1112 112 6136 0 0 0 0 0 0 0 0 6273 123 1132 17 True False +legsta legsta tabular Performs in silico Legionella pneumophila sequence based typing. 2022-02-21 https://github.com/tseemann/legsta 0.5.2 legsta 0.5.2 Up-to-date Sequence Analysis Sequence analysis Sequence analysis Public health and epidemiology Public health and epidemiology iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/legsta https://github.com/galaxyproject/tools-iuc/tree/master/tools/legsta legsta legsta Performs in silico Legionella pneumophila sequence based typing 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 13 13 134 134 0 0 0 0 0 0 0 0 0 0 0 0 134 134 13 13 True False +liftoff liftoff gff3, txt Lift gene annotations between genome assemblies using Liftoff 2026-02-02 https://github.com/agshumate/Liftoff @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ liftoff 1.6.3 To update Sequence Analysis Genome assembly, Mapping assembly, Mapping Genome assembly, Mapping assembly, Mapping Gene transcripts, Sequence assembly, Mapping, Gene expression, RNA immunoprecipitation Gene transcripts, Sequence assembly, Mapping, Gene expression, RNA immunoprecipitation iuc https://github.com/galaxyproject/tools-iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/liftoff liftoff Liftoff An accurate gene annotation mapping tool. https://usegalaxy.org/published/workflow?id=84b447be2f1c5870 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False +lighter lighter Lighter is a kmer-based error correction method for whole genome sequencing data 2016-06-04 https://github.com/mourisl/Lighter 1.0 lighter 1.1.3 To update Sequence Analysis, Fasta Manipulation k-mer counting, Sequence read processing, Sequencing quality control, Sequencing error detection k-mer counting, Sequence read processing, Sequencing quality control, Sequencing error detection Sequencing, Whole genome sequencing, DNA, Genomics Whole genome sequencing, DNA, Genomics bgruening https://github.com/bgruening/galaxytools/tree/master/tools/lighter https://github.com/bgruening/galaxytools/tree/master/tools/lighter lighter Lighter Kmer-based error correction method for whole genome sequencing data. Lighter uses sampling (rather than counting) to obtain a set of kmers that are likely from the genome. 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Genotyping Sequence analysis, Genotyping Genotype and phenotype Genotype and phenotype iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/lorikeet https://github.com/galaxyproject/tools-iuc/tree/master/tools/lorikeet lorikeet lorikeet Tools for M. tuberculosis DNA fingerprinting (spoligotyping) 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 18 18 930 930 0 0 0 0 0 0 0 0 0 0 0 0 930 930 18 18 True False +lotus2 lotus2 zip, tabular, fasta, newick, txt LotuS2 OTU processing pipeline 2021-05-13 https://lotus2.earlham.ac.uk/ @VERSION@ lotus2 2.34.1 To update Metagenomics Sequence feature detection, DNA barcoding Sequence feature detection, DNA barcoding Metagenomics, Taxonomy, Microbial ecology Metagenomics, Taxonomy, Microbial ecology earlhaminst https://github.com/EarlhamInst/earlham-galaxytools/tree/main/tools/lotus2 https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 lotus2 lotus2 LotuS2 is a lightweight and user-friendly pipeline that is fast, precise, 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High data usage rates and reliability enable high-throughput microbiome analysis in minutes. https://usegalaxy.eu/published/workflow?id=466bdd8ba7b67264, https://workflowhub.eu/workflows/1460?version=1 microbiome/lotus2-identifying-fungi, microbiome/mgnify-amplicon 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 249 249 1979 1979 0 0 0 0 22 22 417 417 2 2 5 5 2401 2401 273 273 True False +m6anet m6anet tabular m6anet to detect m6A RNA modifications from nanopore data 2023-10-25 https://m6anet.readthedocs.io/en/latest @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ m6anet 2.1.0 To update Sequence Analysis Quantification, Imputation, Gene expression profiling Quantification, Imputation, Gene expression profiling RNA-Seq, Transcriptomics, RNA, Machine learning RNA-Seq, Transcriptomics, RNA, Machine learning iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/m6anet https://github.com/galaxyproject/tools-iuc/tree/master/tools/m6anet m6Anet m6Anet Detection of m6A from direct RNA sequencing using a Multiple Instance Learning framework. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 12 12 47 47 0 0 0 0 0 0 0 0 0 0 0 0 47 47 12 12 True False +maaslin2 maaslin2 zip, tabular, rdata, pdf MaAsLin2 is comprehensive R package for efficiently determining multivariable association between microbial meta'omic features and clinical metadata. 2021-11-05 http://huttenhower.sph.harvard.edu/maaslin 1.18.0 bioconductor-maaslin2 1.18.0 Up-to-date Metagenomics Filtering, Statistical calculation, Standardisation and normalisation, Visualisation Filtering, Standardisation and normalisation, Visualisation Metagenomics, Statistics and probability Metagenomics, Statistics and probability iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/maaslin2 https://github.com/galaxyproject/tools-iuc/tree/master/tools/maaslin2 maaslin2 MaAsLin2 MaAsLin2 is comprehensive R package for efficiently determining multivariable association between phenotypes, environments, exposures, covariates and microbial meta’omic features. 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https://workflowhub.eu/workflows/1559?version=1, https://workflowhub.eu/workflows/1627?version=1, https://workflowhub.eu/workflows/1650?version=1, https://workflowhub.eu/workflows/1839?version=1 evolution/abc_intro_phylo, genome-annotation/gene-centric, sequence-analysis/tapscan-streptophyte-algae, sequence-analysis/viral_primer_design, variant-analysis/aiv-analysis, variant-analysis/pox-tiled-amplicon 2 2 2 2 0 0 0 0 2 0 2 0 0 0 0 0 0 0 2 0 0 0 2 2 2 0 2844 3060 164403 217226 4659 6641 99571 145229 1279 1462 23332 25716 158 160 5367 5382 393553 292673 11323 8940 True False +make_nr make_nr fasta Make a FASTA file non-redundant 2018-11-06 https://github.com/peterjc/galaxy_blast/tree/master/tools/make_nr 0.0.3 biopython 1.70 To update Fasta Manipulation, Sequence Analysis Sequence alignment, Genome annotation Sequence alignment, Genome annotation Molecular biology, Sequence analysis Molecular biology, Sequence analysis peterjc https://github.com/peterjc/galaxy_blast/tree/master/tools/make_nr https://github.com/peterjc/galaxy_blast/tree/master/tools/make_nr make_nr make_nr Make a FASTA file non-redundant, with a Galaxy wrapperThis tool is copyright 2018 by Peter Cock, The James Hutton Institute, UK. All rights reserved.This tool is a short Python script intended to be run prior to calling the NCBI BLAST+ command line tool makeblastdb or in other settings where you want to collapse duplicated sequences in a FASTA file to a single representative. 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False +maker maker, maker_map_ids gff3, gff, tabular MAKER is a portable and easily configurable genome annotation pipeline.Its purpose is to allow smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and to create genome databases. 2017-10-04 http://www.yandell-lab.org/software/maker.html 2.31.11 maker 3.01.04 To update Sequence Analysis Genome annotation Genome annotation Genomics, DNA, Sequence analysis Genomics, DNA, Sequence analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/maker https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker maker MAKER Portable and easily configurable genome annotation pipeline. It’s purpose is to allow smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and to create genome databases. https://usegalaxy.eu/published/workflow?id=26ad77bc07a7e512, https://usegalaxy.eu/published/workflow?id=6ca20e710f4f3ffb, https://usegalaxy.org.au/published/workflow?id=7a87dfe5bdd30040, https://usegalaxy.org.au/published/workflow?id=7e40485d1ed45b7c, https://usegalaxy.org/published/workflow?id=65b4051e722228b8, https://usegalaxy.org/published/workflow?id=c42c66d1b627c5a5, https://usegalaxy.org/published/workflow?id=dbe08700353dfc43, https://workflowhub.eu/workflows/1323?version=1, https://workflowhub.eu/workflows/1504?version=1, https://workflowhub.eu/workflows/1549?version=1 genome-annotation/annotation-with-maker, genome-annotation/annotation-with-maker-short 2 2 2 2 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 1323 1455 7332 8835 1701 1808 9536 10359 904 904 4968 4989 33 33 211 211 24394 22047 4200 3961 True False +mapseq mapseq tabular fast and accurate sequence read classification tool designed to assign taxonomy and OTU classifications to ribosomal RNA sequences. 2023-08-02 https://github.com/jfmrod/MAPseq @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ perl To update Metagenomics k-mer counting k-mer counting Functional, regulatory and non-coding RNA, Sequence analysis, Sequence sites, features and motifs Functional, regulatory and non-coding RNA, Sequence analysis, Sequence sites, features and motifs iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/mapseq https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq mapseq MAPseq Highly efficient k-mer search with confidence estimates, for rRNA sequence analysis . https://usegalaxy.eu/published/workflow?id=08e25b733cd796e6, https://usegalaxy.eu/published/workflow?id=437704898229dfb6, https://usegalaxy.eu/published/workflow?id=fb806b88850f3427, https://usegalaxy.org/published/workflow?id=45f959d5bf505b15, 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3 3 29 29 15005 14906 96 88 True False +maxbin2 maxbin2 fasta, tabular, txt, pdf clusters metagenomic contigs into bins 2019-10-24 https://downloads.jbei.org/data/microbial_communities/MaxBin/MaxBin.html @MAXBIN_VERSION@ maxbin2 2.2.7 To update Metagenomics Sequence assembly Sequence assembly Metagenomics, Sequence assembly, Microbiology Metagenomics, Sequence assembly, Microbiology mbernt https://github.com/galaxyproject/tools-iuc/tree/main/tools/maxbin2 https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2 maxbin MaxBin Software for binning assembled metagenomic sequences based on an Expectation-Maximization algorithm. https://usegalaxy.eu/published/workflow?id=00f15824c7a9b196, https://usegalaxy.eu/published/workflow?id=02631612a43a4d9b, https://usegalaxy.eu/published/workflow?id=0563f58718be932d, https://usegalaxy.eu/published/workflow?id=1e5f1d9a51032e44, https://usegalaxy.eu/published/workflow?id=6158c3b5fc12044e, 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2015-01-23 https://www.maxquant.org/ 2.0.3.0 maxquant 2.0.3.0 Up-to-date Proteomics Imputation, Visualisation, Protein quantification, Statistical calculation, Standardisation and normalisation, Heat map generation, Clustering, Principal component plotting Imputation, Visualisation, Protein quantification, Standardisation and normalisation, Heat map generation, Clustering Proteomics experiment, Proteomics, Statistics and probability Proteomics experiment, Proteomics, Statistics and probability galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant maxquant MaxQuant Quantitative proteomics software package designed for analyzing large mass-spectrometric data sets. It is specifically aimed at high-resolution MS data. https://usegalaxy.eu/published/workflow?id=0135ee4b3fa0cbce, https://usegalaxy.eu/published/workflow?id=41e9882300fa2386, https://usegalaxy.eu/published/workflow?id=607ca3a9d45bd080, https://usegalaxy.eu/published/workflow?id=8af41219411062ad, https://usegalaxy.eu/published/workflow?id=912b81c444e35045, https://usegalaxy.eu/published/workflow?id=96d198ed953449fd, https://usegalaxy.eu/published/workflow?id=9e0d784860d6cc91, https://usegalaxy.eu/published/workflow?id=a49275eb8b2b2ecb, https://usegalaxy.eu/published/workflow?id=c4119ea7ffd29094, https://usegalaxy.eu/published/workflow?id=d789165f4e0c50eb, https://usegalaxy.eu/published/workflow?id=eb54512829d8509c, https://usegalaxy.org.au/published/workflow?id=1727d16fa4dec19c, https://usegalaxy.org.au/published/workflow?id=43a951ec514498f6, https://usegalaxy.org.au/published/workflow?id=781457327e644c7e, https://usegalaxy.org.au/published/workflow?id=b0a79310e0dc3fb4, https://usegalaxy.org.au/published/workflow?id=ba217a34d7e1b5ee, https://usegalaxy.org/published/workflow?id=2404d5e5b1817825, https://usegalaxy.org/published/workflow?id=e97da2da9e0290a7, https://workflowhub.eu/workflows/1177?version=1, https://workflowhub.eu/workflows/1225?version=1, https://workflowhub.eu/workflows/1396?version=1, https://workflowhub.eu/workflows/1401?version=1, https://workflowhub.eu/workflows/1420?version=1, https://workflowhub.eu/workflows/1421?version=1, https://workflowhub.eu/workflows/1435?version=1, https://workflowhub.eu/workflows/1448?version=1, https://workflowhub.eu/workflows/1468?version=1 microbiome/clinical-mp-2-discovery, microbiome/clinical-mp-4-quantitation, proteomics/DIA_lib_OSW, proteomics/clinical-mp-2-discovery, proteomics/clinical-mp-4-quantitation, proteomics/maxquant-label-free, proteomics/maxquant-msstats-dda-lfq, proteomics/maxquant-msstats-tmt 2 2 2 2 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 1628 1682 7932 8757 775 775 3791 3791 407 416 3720 3831 3 3 33 33 16412 15476 2876 2813 True False +mcl mcl tabular The Markov Cluster Algorithm, a cluster algorithm for graphs 2022-05-12 https://micans.org/mcl/man/mcl.html @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ mcl 22.282 To update Sequence Analysis Clustering, Network analysis, Gene regulatory network analysis Clustering, Gene regulatory network analysis Molecular interactions, pathways and networks Molecular interactions, pathways and networks iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/mcl https://github.com/galaxyproject/tools-iuc/tree/master/tools/mcl mcl MCL MCL is a clustering algorithm widely used in bioinformatics and gaining traction in other fields. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 18 18 153 153 0 0 0 0 0 0 0 0 0 0 0 0 153 153 18 18 True False +medaka medaka_consensus, medaka_consensus_pipeline, medaka_variant h5, txt, fasta, bam, bed, vcf, tabular Sequence correction provided by ONT Research 2020-02-23 https://github.com/nanoporetech/medaka 2.1.1 medaka 2.2.2 To update Sequence Analysis Base-calling, Variant calling, Sequence assembly Base-calling, Variant calling, Sequence assembly Sequence assembly, Machine learning Sequence assembly, Machine learning iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/medaka https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka medaka Medaka medaka is a tool to create consensus sequences and variant calls from nanopore sequencing data. 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It makes use of succinct de Bruijn graph to achieve low memory usage, whereas its goal is not to make memory usage as low as possible. https://usegalaxy.eu/published/workflow?id=0563f58718be932d, https://usegalaxy.eu/published/workflow?id=1524b189069b42a5, https://usegalaxy.eu/published/workflow?id=1e5f1d9a51032e44, https://usegalaxy.eu/published/workflow?id=2ee0eb74e839b476, https://usegalaxy.eu/published/workflow?id=401746888e8b3aa8, https://usegalaxy.eu/published/workflow?id=534f5fc25bc887ca, https://usegalaxy.eu/published/workflow?id=62c47e3c9d4f3aa3, https://usegalaxy.eu/published/workflow?id=7d84b0419296857d, https://usegalaxy.eu/published/workflow?id=7ecd92cb382d8168, https://usegalaxy.eu/published/workflow?id=97312d273b6e8bd9, https://usegalaxy.eu/published/workflow?id=98bfad0c684011e9, https://usegalaxy.eu/published/workflow?id=9b9e1e28f3683f92, https://usegalaxy.eu/published/workflow?id=a8417c63e9e22afb, https://usegalaxy.eu/published/workflow?id=b37800d990cceb83, https://usegalaxy.eu/published/workflow?id=bebcbd6f0ffa55c5, https://usegalaxy.eu/published/workflow?id=ce5c16ac23c4fbb1, https://usegalaxy.eu/published/workflow?id=d4a95588e6e50893, https://usegalaxy.eu/published/workflow?id=f141db5179ea8422, https://usegalaxy.org/published/workflow?id=7251c6e0dad8f927, https://workflowhub.eu/workflows/1352?version=4, https://workflowhub.eu/workflows/1390?version=2, https://workflowhub.eu/workflows/1480?version=1, https://workflowhub.eu/workflows/1631?version=1, https://workflowhub.eu/workflows/1634?version=1, https://workflowhub.eu/workflows/2024?version=4, https://workflowhub.eu/workflows/2036?version=1, https://workflowhub.eu/workflows/2038?version=1 assembly/metagenomics-assembly, microbiome/metagenomics-assembly 1 1 1 1 0 0 0 0 1 1 1 0 0 0 0 0 0 0 1 0 0 0 1 1 1 0 2052 2197 22340 24371 2823 2929 23973 24874 615 632 9338 9643 54 54 1387 1387 60275 57038 5812 5544 True False +megahit_contig2fastg megahit_contig2fastg fastg A subprogram within the Megahit toolkit for converting contigs to assembly graphs (fastg) 2018-11-08 https://github.com/voutcn/megahit/blob/master/tools/toolkit.cpp @VERSION@+@GALAXY_VERSION@ megahit 1.2.9 To update Sequence Analysis, Assembly, Metagenomics Genome assembly Genome assembly Metagenomics, Sequencing, Ecology, Sequence assembly Metagenomics, Sequencing, Sequence assembly iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/megahit_contig2fastg https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit_contig2fastg megahit MEGAHIT Single node assembler for large and complex metagenomics NGS reads, such as soil. It makes use of succinct de Bruijn graph to achieve low memory usage, whereas its goal is not to make memory usage as low as possible. https://usegalaxy.eu/published/workflow?id=62c47e3c9d4f3aa3, https://workflowhub.eu/workflows/1390?version=2, https://workflowhub.eu/workflows/1634?version=1 assembly/metagenomics-assembly, microbiome/metagenomics-assembly 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 1 1 1 0 200 212 763 862 113 113 338 338 33 33 150 150 6 6 80 80 1430 1331 364 352 True False +megan megan_blast2lca, megan_blast2rma, megan_daa2info, megan_daa2rma, megan_daa_meganizer, megan_read_extractor, megan_sam2rma txt, rma6, daa MEGAN Community Edition - Interactive exploration and analysis of large-scale microbiome sequencing data. MEGAN is a tool for studying the taxonomic content of a set of DNA reads, typically collected in a metagenomics project.In a preprocessing step, a sequence alignment of all reads against a suitable database of reference DNA or proteinsequences must be performed to produce an input file for the program. MEGAN is suitable for DNA reads (metagenomedata), RNA reads (metatranscriptome data), peptide sequences (metaproteomics data) and, using a suitable synonymsfile that maps SILVA ids to taxon ids, for 16S rRNA data (amplicon sequencing). 2021-11-24 https://github.com/husonlab/megan-ce 6.21.7 megan 6.25.10 To update Sequence Analysis Sequence analysis, Taxonomic classification Sequence analysis, Taxonomic classification Sequence analysis Sequence analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/megan https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan megan MEGAN Metagenome Analysis Software - MEGAN (MEtaGenome ANalyzer) is a new computer program that allows laptop analysis of large metagenomic datasets. In a preprocessing step, the set of DNA reads (or contigs) is compared against databases of known sequences using BLAST or another comparison tool. MEGAN can then be used to compute and interactively explore the taxonomical content of the dataset, employing the NCBI taxonomy to summarize and order the results. 0 1 7 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 0 0 250 250 5164 5164 0 0 0 0 5 5 72 72 3 3 4 4 5240 5240 258 258 True False +meningotype meningotype tabular Assign sequence type to N. meningitidis genome assemblies 2023-06-06 https://github.com/MDU-PHL/meningotype @TOOL_VERSION@ meningotype 0.8.6b To update Sequence Analysis Genotyping, Multilocus sequence typing Multilocus sequence typing Microbiology, Genotype and phenotype Microbiology, Genotype and phenotype iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/meningotype https://github.com/galaxyproject/tools-iuc/tree/master/tools/meningotype meningotype meningotype In silico typing of Neisseria meningitidis contigs. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False +merqury merqury, merquryplot txt Merqury 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genome sequencing, Genomics, Sequence analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/meryl https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl meryl Meryl Meryl is a tool for counting and working with sets of k-mers that was originally developed for use in the Celera Assembler and has since been migrated and maintained as part of Canu. https://usegalaxy.eu/published/workflow?id=0ccb3838765a8b84, https://usegalaxy.eu/published/workflow?id=10bde4e7f8dbd0c4, https://usegalaxy.eu/published/workflow?id=41c48e4632684f76, https://usegalaxy.eu/published/workflow?id=59f35cb60b3d989d, https://usegalaxy.org.au/published/workflow?id=0296e7daa3a2b072, https://usegalaxy.org.au/published/workflow?id=0512ed898dee714e, https://usegalaxy.org.au/published/workflow?id=0a4324fc4a74dde8, https://usegalaxy.org.au/published/workflow?id=1e6d9e24f4caf776, https://usegalaxy.org.au/published/workflow?id=2a610a038c326937, 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https://workflowhub.eu/workflows/632?version=15 7 7 7 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 55 55 1850 1850 77 77 1478 1478 0 0 0 0 0 0 0 0 3328 3328 132 132 True False +metabat2 metabat2_jgi_summarize_bam_contig_depths, metabat2 tabular, fasta, txt MetaBAT2 (Metagenome Binning based on Abundance and Tetranucleotide frequency) is an automated metagenome binningsoftware that integrates empirical probabilistic distances of genome abundance and tetranucleotide frequency. 2022-01-28 https://bitbucket.org/berkeleylab/metabat/src/master/ 2.18.23 metabat2 2.18_23_gc869c52 To update Metagenomics Read binning, Sequence assembly, Genome annotation Read binning, Sequence assembly, Genome annotation Metagenomics, Sequence assembly, Metagenomic sequencing Metagenomics, Sequence assembly, Metagenomic sequencing iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/metabat2 https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2 MetaBAT_2 MetaBAT 2 "an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies | MetaBAT2 clusters metagenomic contigs into different ""bins"", each of which should correspond to a putative genome | MetaBAT2 uses nucleotide composition information and source strain abundance (measured by depth-of-coverage by aligning the reads to the contigs) to perform binning" https://usegalaxy.eu/published/workflow?id=00f15824c7a9b196, https://usegalaxy.eu/published/workflow?id=0563f58718be932d, https://usegalaxy.eu/published/workflow?id=1e5f1d9a51032e44, https://usegalaxy.eu/published/workflow?id=43098b8afe78b071, https://usegalaxy.eu/published/workflow?id=7ecd92cb382d8168, https://usegalaxy.eu/published/workflow?id=97312d273b6e8bd9, https://usegalaxy.eu/published/workflow?id=ce5c9287a67e6085, https://usegalaxy.org/published/workflow?id=9b589bc76208fb1e, https://workflowhub.eu/workflows/1352?version=4, https://workflowhub.eu/workflows/2028?version=1, https://workflowhub.eu/workflows/2100?version=2 microbiome/metagenomics-binning 2 2 2 2 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 2 2 0 0 670 670 14194 14194 375 375 2591 2591 167 167 1738 1738 18 18 1359 1359 19882 19882 1230 1230 True False +metabuli metabuli_classify tabular, html, txt Classifying metagenomes by jointly analysing both DNA and amino acid (AA) sequences 2024-06-04 https://github.com/steineggerlab/Metabuli 1.0.5 metabuli 1.2.0 To update Sequence Analysis, Metagenomics Taxonomic classification Taxonomic classification Taxonomy Taxonomy iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/metabuli https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabuli metabuli metabuli Metabuli: specific and sensitive metagenomic classification via joint analysis of DNA and amino acid 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False +metaeuk metaeuk_easy_predict fasta, gff MetaEuk is a modular toolkit designed for large-scale gene discovery andannotation in eukaryotic metagenomic contigs. Metaeuk combines the fast andsensitive homology search capabilities of MMseqs2 with a dynamic programmingprocedure to recover optimal exons sets. It reduces redundancies in multiplediscoveries of the same gene and resolves conflicting gene predictions onthe same strand. 2020-08-04 https://github.com/soedinglab/metaeuk @TOOL_VERSION@ metaeuk 6.a5d39d9 To update Sequence Analysis, Genome annotation Homology-based gene prediction Homology-based gene prediction Metagenomics, Gene and protein families Metagenomics, Gene and protein families iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/metaeuk https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk MetaEuk MetaEuk MetaEuk - sensitive, high-throughput gene discovery and annotation for large-scale eukaryotic metagenomics https://usegalaxy.eu/published/workflow?id=9b9e1e28f3683f92 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 57 58 507 509 0 0 0 0 0 0 0 0 0 0 0 0 509 507 58 57 True False +metagene_annotator metagene_annotator txt, tabular, bed MetaGeneAnnotator gene-finding program for prokaryote and phage 2018-03-21 http://metagene.nig.ac.jp/ @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ metagene_annotator 1.0 To update Sequence Analysis Sequence annotation Sequence annotation Genomics, Model organisms, Data submission, annotation and curation Genomics, Model organisms, Data submission, annotation and curation galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metagene_annotator metageneannotator MetaGeneAnnotator Prokaryotic gene finding program from environmental genome shotgun sequences or metagenomic sequences. https://usegalaxy.eu/published/workflow?id=3dcf09e75d707573, https://usegalaxy.eu/published/workflow?id=799b924edd3c401b, https://usegalaxy.eu/published/workflow?id=9b9e1e28f3683f92, https://usegalaxy.eu/published/workflow?id=a644e6b450dabca8 0 0 1 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 439 457 20971 21069 0 0 0 0 0 0 0 0 0 0 0 0 21069 20971 457 439 True False +metagenomeseq_normalization metagenomeseq_normalizaton tabular, txt metagenomeSeq Normalization 2017-03-27 https://bioconductor.org/packages/3.18/bioc/html/metagenomeSeq.html 1.16.0-0.0.1 bioconductor-metagenomeseq 1.52.0 To update Metagenomics Sequence visualisation, Statistical calculation Sequence visualisation, Statistical calculation Metagenomics, Sequencing Metagenomics, Sequencing iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/metagenomeseq https://github.com/galaxyproject/tools-iuc/tree/master/tools/metagenomeseq metagenomeseq metagenomeSeq Designed to determine features (be it Operational Taxanomic Unit (OTU), species, etc.) that are differentially abundant between two or more groups of multiple samples. It is designed to address the effects of both normalization and under-sampling of microbial communities on disease association detection and the testing of feature correlations. 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 15 23 521 763 28 56 261 530 0 0 0 0 0 0 0 0 1293 782 79 43 True False +metamdbg metamdbg_asm, metamdbg_gfa fasta.gz, tar.gz, txt, gfa1 MetaMDBG is a fast and low-memory assembler for long and accurate metagenomics reads. 2025-02-04 https://github.com/GaetanBenoitDev/metaMDBG 1.4 metamdbg 1.4 Up-to-date Assembly, Metagenomics Genome assembly Genome assembly Metagenomics Metagenomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/metamdbg https://github.com/galaxyproject/tools-iuc/tree/master/tools/metamdbg metamdbg metaMDBG MetaMDBG is a fast and low-memory assembler for long and accurate metagenomics reads (e.g. PacBio HiFi, Nanopore r10.4). It is based on the minimizer de-Brujin graph (MDBG), which have been reimplemetend specifically for metagenomics assembly. MetaMDBG combines an efficient multi-k approach in minimizer-space for dealing with uneven species coverages, and a novel abundance-based filtering method for simplifying strain complexity. 2 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False +metanovo metanovo fasta, csv Produce targeted databases for mass spectrometry analysis. 2022-03-29 https://github.com/uct-cbio/proteomics-pipelines @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ metanovo 1.9.4 To update Proteomics Target-Decoy, de Novo sequencing, Tag-based peptide identification, Protein identification, Expression analysis Target-Decoy, de Novo sequencing, Tag-based peptide identification, Protein identification, Expression analysis Proteomics, Microbial ecology, Metagenomics, Proteomics experiment, Small molecules Proteomics, Microbial ecology, Metagenomics, Proteomics experiment, Small molecules galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo metanovo MetaNovo An open-source pipeline for probabilistic peptide discovery in complex metaproteomic datasets. https://usegalaxy.eu/published/workflow?id=2f7e13eb26c8cd18, https://usegalaxy.eu/published/workflow?id=7cfbf4b7bd3f30d3, https://usegalaxy.eu/published/workflow?id=c6aecbdbeb27585f, https://usegalaxy.eu/published/workflow?id=d7c7a4d6c8072167, https://usegalaxy.eu/published/workflow?id=f2b45a7ff4f449e6, https://usegalaxy.org.au/published/workflow?id=351f3fab960c013b, https://usegalaxy.org/published/workflow?id=2be8ecd5922d23d1, https://workflowhub.eu/workflows/1216?version=1, https://workflowhub.eu/workflows/1461?version=1, https://workflowhub.eu/workflows/1474?version=1 microbiome/clinical-mp-1-database-generation, proteomics/clinical-mp-1-database-generation 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 40 40 5000 5000 5 5 34 34 4 4 92 92 0 0 0 0 5126 5126 49 49 True False +metaphlan customize_metaphlan_database, extract_metaphlan_database, merge_metaphlan_tables, metaphlan fasta, json, tabular, sam, biom1, fastqsanger MetaPhlAn for Metagenomic Phylogenetic Analysis 2021-03-11 https://github.com/biobakery/MetaPhlAn 4.2.4 metaphlan 4.2.4 Up-to-date Metagenomics Taxonomic classification, Taxonomic classification Taxonomic classification, Taxonomic classification Metagenomics, Phylogenomics Metagenomics, Phylogenomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/metaphlan https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan metaphlan MetaPhlAn Computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data. https://usegalaxy.eu/published/workflow?id=052f35a526798020, https://usegalaxy.eu/published/workflow?id=05f5f040337786bf, https://usegalaxy.eu/published/workflow?id=19de5cbae7f48103, https://usegalaxy.eu/published/workflow?id=21a17d6c473a88c0, https://usegalaxy.eu/published/workflow?id=39d36a7ce0ef268d, https://usegalaxy.eu/published/workflow?id=4d32b1b3ac0a7161, https://usegalaxy.eu/published/workflow?id=4f0daf8e9dd54127, https://usegalaxy.eu/published/workflow?id=4f21205e71cabd37, https://usegalaxy.eu/published/workflow?id=5f0faac42b0a5062, https://usegalaxy.eu/published/workflow?id=69eddfde874af35b, https://usegalaxy.eu/published/workflow?id=713a5485e2007f90, https://usegalaxy.eu/published/workflow?id=7491883694fff308, https://usegalaxy.eu/published/workflow?id=79b4ae4403772098, https://usegalaxy.eu/published/workflow?id=87cc0cd143a12c41, https://usegalaxy.eu/published/workflow?id=9472be79da012999, https://usegalaxy.eu/published/workflow?id=a8f829deb69b30ab, https://usegalaxy.eu/published/workflow?id=b14845359b702444, https://usegalaxy.eu/published/workflow?id=cb2df493f5e334f7, https://usegalaxy.eu/published/workflow?id=fdca6c9d394986bf, https://usegalaxy.fr/published/workflow?id=09e8293456ee6d99, https://usegalaxy.fr/published/workflow?id=c4f6062e51d0f45e, https://usegalaxy.org.au/published/workflow?id=6b7e565258a9da2a, https://workflowhub.eu/workflows/1451?version=2, https://workflowhub.eu/workflows/1466?version=2, https://workflowhub.eu/workflows/1470?version=2, https://workflowhub.eu/workflows/624?version=1 microbiome/metatranscriptomics, microbiome/metatranscriptomics-short, microbiome/taxonomic-profiling 1 2 4 4 0 0 0 0 4 0 3 0 0 0 0 0 0 0 0 0 0 0 1 4 4 0 1552 1552 30934 31014 1122 1122 20021 20021 314 314 6347 6347 28 28 211 211 57593 57513 3016 3016 True False +metaquantome metaquantome_db, metaquantome_expand, metaquantome_filter, metaquantome_sample, metaquantome_stat, metaquantome_viz tar, tabular, html quantitative analysis of microbiome taxonomy and function 2018-11-27 https://github.com/galaxyproteomics/metaquantome/ 2.0.4 metaquantome 2.0.4 Up-to-date Proteomics Principal component visualisation, Visualisation, Functional clustering, Query and retrieval, Differential protein expression analysis, Heat map generation, Quantification, Indexing, Filtering, Statistical inference Principal component visualisation, Functional clustering, Query and retrieval, Heat map generation, Quantification, Indexing, Filtering, Statistical inference Proteomics, Metatranscriptomics, Microbial ecology, Proteomics experiment, Metagenomics Proteomics, Metatranscriptomics, Microbial ecology, Proteomics experiment, Metagenomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome metaQuantome metaQuantome metaQuantome software suite analyzes the state of a microbiome by leveraging complex taxonomic and functional hierarchies to summarize peptide-level quantitative information. metaQuantome offers differential abundance analysis, principal components analysis, and clustered heat map visualizations, as well as exploratory analysis for a single sample or experimental condition. https://usegalaxy.eu/published/workflow?id=4c364c6be27981ba, https://usegalaxy.eu/published/workflow?id=695f7defb516d80d, https://usegalaxy.eu/published/workflow?id=ce7f7c6eef526d67, https://usegalaxy.eu/published/workflow?id=dc438d4ae1866df8, https://usegalaxy.eu/published/workflow?id=e5a89ef7b5f1c1d9, https://usegalaxy.org.au/published/workflow?id=cada735fa0716570, https://usegalaxy.org.au/published/workflow?id=f8183bba3a1d150d, https://workflowhub.eu/workflows/1453?version=1, https://workflowhub.eu/workflows/1459?version=1 proteomics/metaquantome-function, proteomics/metaquantome-taxonomy 0 6 6 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 6 6 0 80 89 2277 3166 0 0 0 0 27 27 2323 2323 0 0 0 0 5489 4600 116 107 True False +metasbt metasbt_index, metasbt_profile tabular, tar Microbial genomes characterization with Sequence Bloom Trees 2025-08-22 https://github.com/cumbof/MetaSBT 0.1.5 sed To update Metagenomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/metasbt https://github.com/galaxyproject/tools-iuc/tree/master/tools/metasbt 2 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False +metawrapmg_binning metawrapmg_binning, metawrapmg_bin_refinement A flexible pipeline for genome-resolved metagenomic data analysis 2024-04-12 https://github.com/bxlab/metaWRAP 1.3.0 metawrap-mg 1.3.0 Up-to-date Metagenomics Read binning, Sequence assembly, Genome annotation, Sequence trimming, Demultiplexing Read binning, Sequence assembly, Genome annotation, Sequence trimming, Demultiplexing Whole genome sequencing, Metagenomic sequencing, Metagenomics Whole genome sequencing, Metagenomic sequencing, Metagenomics galaxy-australia https://github.com/galaxyproject/tools-iuc/tree/main/tools/metawrapmg https://github.com/galaxyproject/tools-iuc/tree/master/tools/metawrapmg metawrap MetaWRAP MetaWRAP aims to be an easy-to-use metagenomic wrapper suite that accomplishes the core tasks of metagenomic analysis from start to finish: read quality control, assembly, visualization, taxonomic profiling, extracting draft genomes (binning), and functional annotation. 0 2 2 2 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 100 1596 1596 0 0 0 0 67 67 587 587 0 0 0 0 2183 2183 167 167 True False +mg_toolkit mg_toolkit_bulk_download, mg_toolkit_original_metadata tsv Metagenomics toolkit enables scientists to download all of the sample metadata for a given study or sequence to a single csv file. 2024-07-12 https://github.com/EBI-Metagenomics/emg-toolkit 0.10.4 mg-toolkit 0.10.4 Up-to-date Metagenomics Data retrieval Data retrieval Metagenomics Metagenomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/mg_toolkit https://github.com/galaxyproject/tools-iuc/tree/master/tools/mg_toolkit mg-toolkit mg-toolkit Metagenomics toolkit enables scientists to download all of the sample metadata for a given study or sequence to a single csv file. 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10 10 21 21 0 0 0 0 0 0 0 0 0 0 0 0 21 21 10 10 True False +mgnify_genome_search mgnify_genome_search tabular Queue genomes against registered genome from MGnify Database 2026-01-26 https://github.com/SantaMcCloud/MGnify-genome-search @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ mgnify-genome-search 1.0.0 To update Metagenomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/mgnify_genome_search https://github.com/galaxyproject/tools-iuc/tree/master/tools/mgnify_genome_search 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False +mgnify_pipelines_toolkit mgnify_pipelines_toolkit_classify_var_regions, mgnify_pipelines_toolkit_make_asv_count_table, mgnify_pipelines_toolkit_mapseq_to_asv_table, mgnify_pipelines_toolkit_permute_primers, mgnify_pipelines_toolkit_primer_val_classification, mgnify_pipelines_toolkit_rev_comp_se_primers json, tabular, txt, tsv, fasta Utilities for use in the MGnify pipelines 2026-04-22 https://github.com/EBI-Metagenomics/mgnify-pipelines-toolkit 1.5.1 mgnify-pipelines-toolkit 1.5.2 To update Metagenomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/mgnify_pipelines_toolkit https://github.com/galaxyproject/tools-iuc/tree/master/tools/mgnify_pipelines_toolkit 0 0 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False +mgnify_seqprep mgnify_seqprep fastq.gz A modifiied vesion of SeqPrep. Made for use with the MGnify pipelines. 2024-05-14 https://github.com/jstjohn/SeqPrep 1.2 To update Fastq Manipulation, Sequence Analysis Nucleic acid design Nucleic acid design Genomics, Sequence assembly, Sequencing, Probes and primers Genomics, Sequence assembly, Sequencing, Probes and primers bgruening https://github.com/bgruening/galaxytools/tree/master/tools/mgnify_seqprep https://github.com/bgruening/galaxytools/tree/master/tools/mgnify_seqprep seqprep SeqPrep Strips adapters and optionally merges overlapping paired-end (or paired-end contamination in mate-pair libraries) illumina style reads. https://usegalaxy.eu/published/workflow?id=0609a4b1941d1a68, https://usegalaxy.eu/published/workflow?id=9fddc44294236e8f, https://usegalaxy.org/published/workflow?id=20b7ae4b517a80fd, https://usegalaxy.org/published/workflow?id=a71fcbc60caae8b6, https://workflowhub.eu/workflows/1272?version=2, https://workflowhub.eu/workflows/1854?version=1 microbiome/mgnify-amplicon 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 6 6 1348 1348 109 109 444 444 0 0 0 0 0 0 0 0 1792 1792 115 115 True False +micro_decon micro_decon csv An R package for removing contamination from metabarcoding (e.g., microbiome) datasets post-sequencing 2025-08-05 https://github.com/donaldtmcknight/microdecon 1.0.2 To update Metagenomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/micro_decon https://github.com/galaxyproject/tools-iuc/tree/master/tools/micro_decon 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False +minia minia fasta Short-read assembler based on a de Bruijn graph 2020-04-08 https://gatb.inria.fr/software/minia/ @TOOL_VERSION@ minia 3.2.6 To update Assembly Genome assembly Genome assembly Sequence assembly Sequence assembly iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/minia https://github.com/galaxyproject/tools-iuc/tree/master/tools/minia minia Minia Short-read assembler based on a de Bruijn graph, capable of assembling a human genome on a desktop computer in a day. https://usegalaxy.eu/published/workflow?id=9ba580ba8b01db40 0 1 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 272 287 6758 7224 0 0 0 0 77 77 357 357 0 0 0 0 7581 7115 364 349 True False +miniasm miniasm tabular Miniasm - Ultrafast de novo assembly for long noisy reads (though having no consensus step) 2019-06-18 https://github.com/lh3/miniasm @TOOL_VERSION@ miniasm 0.3 To update Assembly De-novo assembly De-novo assembly Genomics, Sequence assembly Genomics, Sequence assembly iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/miniasm https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniasm miniasm miniasm Miniasm is a very fast OLC-based de novo assembler for noisy long reads. It takes all-vs-all read self-mappings (typically by minimap) as input and outputs an assembly graph in the GFA format. https://usegalaxy.eu/published/workflow?id=249c115413f17f28, https://usegalaxy.eu/published/workflow?id=32d2f5340098bcbd, https://usegalaxy.eu/published/workflow?id=39837ca09374598b, https://usegalaxy.eu/published/workflow?id=44e53ea319e07daa, https://usegalaxy.eu/published/workflow?id=b4de76c0a4d0e23a, https://usegalaxy.eu/published/workflow?id=c48807045e258dd8, https://usegalaxy.eu/published/workflow?id=dc7107896a3f2964, https://usegalaxy.org.au/published/workflow?id=d9571b3dfef34e5e, https://workflowhub.eu/workflows/1477?version=1, https://workflowhub.eu/workflows/406?version=1 microbiome/plasmid-metagenomics-nanopore 1 1 1 1 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 571 687 11506 14702 474 538 9124 10016 88 96 1235 1277 16 16 166 166 26161 22031 1337 1149 True False +minipolish minipolish gfa1 Polishing miniasm assemblies 2022-10-19 https://github.com/rrwick/Minipolish 0.2.1 minipolish 0.2.1 Up-to-date Sequence Analysis Localised reassembly, Read depth analysis Localised reassembly, Read depth analysis Sequence assembly, Sequencing Sequence assembly, Sequencing bgruening https://github.com/bgruening/galaxytools/tree/master/tools/minipolish https://github.com/bgruening/galaxytools/tree/master/tools/minipolish minipolish minipolish A tool that bridges the output of miniasm (long-read assembly) and racon (assembly polishing) together to polish a draft assembly. It also provides read depth information in contigs. 0 0 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 43 43 278 278 0 0 0 0 0 0 0 0 0 0 0 0 278 278 43 43 True False +miniprot miniprot, miniprot_index gff3, binary Align a protein sequence against a genome with affine gap penalty, splicing and frameshift. 2022-09-19 https://github.com/lh3/miniprot 0.18 miniprot 0.18 Up-to-date Sequence Analysis Sequence alignment, Protein sequence analysis Sequence alignment, Protein sequence analysis Sequence sites, features and motifs, Sequence analysis Sequence sites, features and motifs, Sequence analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/miniprot https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot miniprot miniprot Miniprot aligns a protein sequence against a genome with affine gap penalty, splicing and frameshift. It is primarily intended for annotating protein-coding genes in a new species using known genes from other species. https://usegalaxy.eu/published/workflow?id=0c92c3c322c3effe 2 0 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 100 100 5038 5038 42 42 364 364 0 0 0 0 25 25 283 283 5685 5685 167 167 True False +mist_typing mist_call, mist_dists tabular, json Wrappers for Minimap2-inferred Sequence Typing (MiST). 2026-01-08 https://github.com/BioinformaticsPlatformWIV-ISP/MiST 1.2.0 mist_typing 1.2.0 Up-to-date Sequence Analysis, Phylogenetics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/mist_typing https://github.com/galaxyproject/tools-iuc/tree/master/tools/mist_typing 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False +mitos mitos, mitos2 bed, tabular, gff, txt, fasta, pdf, zip de-novo annotation of metazoan mitochondrial genomes 2020-02-18 http://mitos.bioinf.uni-leipzig.de/ @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ mitos 2.1.10 To update Sequence Analysis Genome annotation Genome annotation Zoology, Whole genome sequencing Zoology, Whole genome sequencing iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/mitos https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos mitos MITOS De novo metazoan mitochondrial genome annotation. https://usegalaxy.eu/published/workflow?id=0de5fcc38ef1501d, https://usegalaxy.eu/published/workflow?id=2d0400b5d05c6c10, https://usegalaxy.org/published/workflow?id=110ad20060b03e02 1 1 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 1326 1336 267673 268177 772 772 84561 84561 151 151 15492 15492 6 6 109 109 368339 367835 2265 2255 True False +mlst mlst, mlst_list tabular, fasta, txt Scan contig files against PubMLST typing schemes 2016-12-13 https://github.com/tseemann/mlst 2.22.0 mlst 2.35.0 To update Sequence Analysis Multilocus sequence typing Multilocus sequence typing Immunoproteins and antigens Immunoproteins and antigens iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/mlst https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst mlst MLST Multi Locus Sequence Typing from an assembled genome or from a set of reads. https://usegalaxy.eu/published/workflow?id=2b888e200dfd91bc, https://usegalaxy.eu/published/workflow?id=309fc4fc2e0da89c, https://usegalaxy.eu/published/workflow?id=368d1ac0150ea0b6, https://usegalaxy.eu/published/workflow?id=37da7b42cb063a3a, https://usegalaxy.eu/published/workflow?id=42c0da2e86318b37, https://usegalaxy.eu/published/workflow?id=49c46d7653d6c349, https://usegalaxy.eu/published/workflow?id=5826e573b6f93762, https://usegalaxy.eu/published/workflow?id=5b940b283d91d99d, https://usegalaxy.eu/published/workflow?id=81eeeaa94eb36f36, https://usegalaxy.eu/published/workflow?id=9219557de92e0203, https://usegalaxy.eu/published/workflow?id=a337bfb2eb1e583f, https://usegalaxy.eu/published/workflow?id=a601e36ce9928094, 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https://usegalaxy.org/published/workflow?id=8111bb9bb26bb665, https://usegalaxy.org/published/workflow?id=c65bec6c332bf740, https://usegalaxy.org/published/workflow?id=fb01e1a49793c8be microbiome/pathogen-detection-from-nanopore-foodborne-data 2 2 2 2 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 1786 1918 24365 26341 1356 1420 12903 13604 1137 1439 12595 15564 22 22 99 99 55608 49962 4799 4301 True False +mmseqs2 mmseqs2_easy_cluster, mmseqs2_easy_linclust_clustering, mmseqs2_easy_linsearch, mmseqs2_easy_rbh, mmseqs2_easy_search, mmseqs2_easy_taxonomy, mmseqs2_taxonomy_assignment tabular, txt, html MMseqs2 is an ultra fast and sensitive sequence search and clustering suite 2025-03-27 https://github.com/soedinglab/MMseqs2 17-b804f mmseqs2 17.b804f To update Sequence Analysis, Metagenomics Sequence similarity search, Sequence alignment, Sequence clustering, Taxonomic classification Sequence similarity search, Sequence alignment, Sequence clustering, Taxonomic classification Metagenomics, Sequence analysis, Proteins, Nucleic acids, Gene and protein families, Taxonomy Metagenomics, Sequence analysis, Nucleic acids, Gene and protein families, Taxonomy iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/mmseqs2 https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmseqs2 MMseqs2 MMseqs2 MMseqs2 (Many-against-Many sequence searching) is a software suite to search and cluster huge protein and nucleotide sequence sets. MMseqs2 is open source software implemented in C++ for Linux, MacOS, and (as beta version, via cygwin) Windows. The software is designed to run on multiple cores and servers and exhibits very good scalability. MMseqs2 can run 10000 times faster than BLAST. At 100 times its speed it achieves almost the same sensitivity. It can perform profile searches with the same sensitivity as PSI-BLAST at over 400 times its speed.MMseqs2 includes Linclust, the first clustering algorithm whose runtime scales linearly With Linclust we clustered 1.6 billion metagenomic sequence fragments in 10 h on a single server to 50% sequence identity. https://usegalaxy.eu/published/workflow?id=62392daea25a3980, https://workflowhub.eu/workflows/2024?version=4 2 0 7 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 42 42 260 260 0 0 0 0 0 0 0 0 3 3 29 29 289 289 45 45 True False +mmuphin mmuphin tabular, pdf MMUPHin is an R package implementing meta-analysis methods for microbial community profiles 2024-11-22 https://huttenhower.sph.harvard.edu/mmuphin 1.16.0 bioconductor-mmuphin 1.16.0 Up-to-date Metagenomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/mmuphin https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmuphin mmuphin mmuphin MMUPHin is an R package for meta-analysis tasks of microbiome cohorts. It has function interfaces for: a) covariate-controlled batch- and cohort effect adjustment, b) meta-analysis differential abundance testing, c) meta-analysis unsupervised discrete structure (clustering) discovery, and d) meta-analysis unsupervised continuous structure discovery. https://usegalaxy.eu/published/workflow?id=466bdd8ba7b67264 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 3 14 14 0 0 0 0 0 0 0 0 0 0 0 0 14 14 3 3 True False +mob_suite mob_recon, mob_typer tabular, fasta MOB-suite is a set of software tools for clustering, reconstruction and typing of plasmids from draft assemblies 2018-04-30 https://github.com/phac-nml/mob-suite 3.1.9 mob_suite 3.1.9 Up-to-date Sequence Analysis Clustering, Sequence analysis Clustering, Sequence analysis Metagenomics, Sequence assembly, Genotype and phenotype, Mobile genetic elements, Genomics Metagenomics, Sequence assembly, Genotype and phenotype, Mobile genetic elements nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/mob-suite https://github.com/phac-nml/galaxy_tools/tree/master/tools/mob_suite mob_suite mob_suite MOB-suite: Software tools for clustering, reconstruction and typing of plasmids from draft assembliesThe MOB-suite depends on a series of databases which are too large to be hosted in git-hub. They can be downloaded or updated by running mob_init or if running any of the tools for the first time, the databases will download and initialize automatically if you do not specify an alternate database location. https://usegalaxy.eu/published/workflow?id=2c992e509aa5dd9d, https://usegalaxy.eu/published/workflow?id=d0339e4a794f4922, https://workflowhub.eu/workflows/407?version=1 0 2 2 2 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 620 620 162457 162457 1 1 42 42 199 199 66525 66525 12 12 58 58 229082 229082 832 832 True False +mothur mothur_align_check, mothur_align_seqs, mothur_amova, mothur_anosim, mothur_bin_seqs, mothur_biom_info, mothur_chimera_bellerophon, mothur_chimera_ccode, mothur_chimera_check, mothur_chimera_perseus, mothur_chimera_pintail, mothur_chimera_slayer, mothur_chimera_uchime, mothur_chimera_vsearch, mothur_chop_seqs, mothur_classify_otu, mothur_classify_seqs, mothur_classify_tree, mothur_clearcut, mothur_cluster_classic, mothur_cluster_fragments, mothur_cluster_split, mothur_cluster, mothur_collect_shared, mothur_collect_single, mothur_consensus_seqs, mothur_cooccurrence, mothur_corr_axes, mothur_count_groups, mothur_count_seqs, mothur_create_database, mothur_degap_seqs, mothur_deunique_seqs, mothur_deunique_tree, mothur_dist_seqs, mothur_dist_shared, mothur_fastq_info, mothur_filter_seqs, mothur_filter_shared, mothur_get_communitytype, mothur_get_coremicrobiome, mothur_get_dists, mothur_get_group, mothur_get_groups, mothur_get_label, mothur_get_lineage, mothur_get_mimarkspackage, mothur_get_otulabels, mothur_get_otulist, mothur_get_oturep, mothur_get_otus, mothur_get_rabund, mothur_get_relabund, mothur_get_sabund, mothur_get_seqs, mothur_get_sharedseqs, mothur_heatmap_bin, mothur_heatmap_sim, mothur_homova, mothur_indicator, mothur_lefse, mothur_libshuff, mothur_list_otulabels, mothur_list_seqs, mothur_make_biom, mothur_make_contigs, mothur_make_design, mothur_make_fastq, mothur_make_group, mothur_make_lefse, mothur_make_lookup, mothur_make_shared, mothur_make_sra, mothur_mantel, mothur_merge_count, mothur_merge_files, mothur_merge_groups, mothur_merge_sfffiles, mothur_merge_taxsummary, mothur_metastats, mothur_mimarks_attributes, mothur_nmds, mothur_normalize_shared, mothur_otu_association, mothur_otu_hierarchy, mothur_pairwise_seqs, mothur_parse_list, mothur_parsimony, mothur_pca, mothur_pcoa, mothur_pcr_seqs, mothur_phylo_diversity, mothur_phylotype, mothur_pre_cluster, mothur_primer_design, mothur_rarefaction_shared, mothur_rarefaction_single, mothur_remove_dists, mothur_remove_groups, mothur_remove_lineage, mothur_remove_otulabels, mothur_remove_otus, mothur_remove_rare, mothur_remove_seqs, mothur_rename_seqs, mothur_reverse_seqs, mothur_screen_seqs, mothur_sens_spec, mothur_seq_error, mothur_sffinfo, mothur_shhh_flows, mothur_shhh_seqs, mothur_sort_seqs, mothur_split_abund, mothur_split_groups, mothur_sub_sample, mothur_summary_qual, mothur_summary_seqs, mothur_summary_shared, mothur_summary_single, mothur_summary_tax, mothur_taxonomy_to_krona, mothur_tree_shared, mothur_trim_flows, mothur_trim_seqs, mothur_unifrac_unweighted, mothur_unifrac_weighted, mothur_unique_seqs, mothur_venn mothur.align.check, mothur.align, mothur.align.report, mothur.accnos, tabular, mothur.shared, mothur.cons.taxonomy, mothur.tax.summary, txt, mothur.freq, mothur.quan, mothur.count_table, mothur.seq.taxonomy, mothur.tre, mothur.lower.dist, mothur.rabund, mothur.sabund, mothur.list, mothur.names, mothur.axes, mothur.groups, mothur.pair.dist, fasta, qual454, fastq, mothur.filter, mothur.design, mothur.otu.corr, mothur.relabund, svg, qual, mothur.sff.flow, sff, xml, mothur.summary Mothur wrappers 2016-06-24 https://www.mothur.org 1.39.5.0 mothur 1.48.5 To update Metagenomics DNA barcoding, Sequencing quality control, Sequence clustering, Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic analysis DNA barcoding, Sequencing quality control, Sequence 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bgruening https://github.com/bgruening/galaxytools/tree/master/tools/motus https://github.com/bgruening/galaxytools/tree/master/tools/motus mOTUs Metagenomic operational taxonomic units (mOTUs) Metagenomic operational taxonomic units (mOTUs) enable high-accuracy taxonomic profiling of known (sequenced) and unknown microorganisms at species-level resolution from shotgun metagenomic or metatranscriptomic data. The method clusters single-copy phylogenetic marker gene sequences from metagenomes and reference genomes into mOTUs to quantify their abundances in meta-omics data with very high precision and recall. 0 0 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 40 40 377 377 0 0 0 0 0 0 0 0 0 0 0 0 377 377 40 40 True False +mrbayes mrbayes txt A program for the Bayesian estimation of phylogeny. 2015-12-04 1.0.2 mrbayes 3.2.7 To update Sequence Analysis nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/mrbayes https://usegalaxy.eu/published/workflow?id=93d7a5704ec1d82d 0 0 1 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 4 18 18 0 0 0 0 0 0 0 0 0 0 0 0 18 18 4 4 True False +msconvert msconvert msconvert Convert and/or filter mass spectrometry files (including vendor formats) using the official Docker container 2015-01-23 http://proteowizard.sourceforge.net/tools.shtml 3.0.26121 To update Proteomics Filtering, Formatting Filtering, Formatting Proteomics, Proteomics experiment Proteomics, Proteomics experiment galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert msconvert msConvert msConvert is a command-line utility for converting between various mass spectrometry data formats, including from raw data from several commercial companies (with vendor libraries, Windows-only). 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https://workflowhub.eu/workflows/1471?version=1, https://workflowhub.eu/workflows/1582?version=1, https://workflowhub.eu/workflows/1791?version=1 metabolomics/gc_ms_with_xcms, microbiome/clinical-mp-2-discovery, proteomics/DIA_Analysis_OSW, proteomics/clinical-mp-2-discovery, proteomics/encyclopedia, proteomics/metaquantome-data-creation, proteomics/neoantigen-peptide-verification, proteomics/protein-id-oms 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 550 604 58574 66339 133 133 2254 2254 76 76 4844 4844 108 113 7765 7906 81343 73437 926 867 True False +msstatstmt msstatstmt txt, tabular, pdf MSstatsTMT protein significance analysis in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling 2021-01-20 http://msstats.org/msstatstmt/ @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ bioconductor-msstatstmt 2.18.0 To update Proteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt https://usegalaxy.eu/published/workflow?id=755ede37d94dc456, https://usegalaxy.eu/published/workflow?id=8f3cafa3bc59ff82, https://usegalaxy.eu/published/workflow?id=d148459a4d4b91f1, https://usegalaxy.org.au/published/workflow?id=050a66ff6d4c2b53, https://usegalaxy.org/published/workflow?id=3f797bfb67130883, https://workflowhub.eu/workflows/1219?version=1, https://workflowhub.eu/workflows/1401?version=1, https://workflowhub.eu/workflows/1433?version=1, https://workflowhub.eu/workflows/1482?version=1 microbiome/clinical-mp-5-data-interpretation, proteomics/clinical-mp-5-data-interpretation, proteomics/maxquant-msstats-tmt 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 113 113 844 844 10 10 47 47 18 18 693 693 0 0 0 0 1584 1584 141 141 True False +msstatstmt msstats txt, tabular, pdf MSstats tool for analyzing mass spectrometry proteomic datasets 2020-07-25 https://github.com/MeenaChoi/MSstats @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ bioconductor-msstats 4.18.1 To update Proteomics Spectrum calculation, Tag-based peptide identification, Differential protein expression profiling Spectrum calculation, Tag-based peptide identification, Differential protein expression profiling Proteomics, Proteomics experiment, Protein expression Proteomics, Proteomics experiment, Protein expression galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats msstatstmt MSstatsTMT Tools for detecting differentially abundant peptides and proteins in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling https://usegalaxy.org.au/published/workflow?id=1727d16fa4dec19c, https://workflowhub.eu/workflows/1426?version=1, https://workflowhub.eu/workflows/1458?version=1, https://workflowhub.eu/workflows/1462?version=1 proteomics/DIA_Analysis_MSstats, proteomics/maxquant-label-free, proteomics/maxquant-msstats-dda-lfq 1 1 1 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 800 803 2969 3004 283 283 1456 1456 99 99 1605 1605 0 0 0 0 6065 6030 1185 1182 True False +mtnucratio mtnucratio txt, json Calculates Mitochondrial to Nuclear read ratio 2026-03-18 https://github.com/TCLamnidis/mtnucratio @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ mtnucratio 0.7.1 To update Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/mtnucratio https://github.com/galaxyproject/tools-iuc/tree/master/tools/mtnucratio 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False +multigsea multigsea tabular GSEA-based pathway enrichment analysis for multi-omics data 2023-06-07 https://bioconductor.org/packages/devel/bioc/html/multiGSEA.html 1.12.0 bioconductor-multigsea 1.20.0 To update Transcriptomics, Proteomics, Statistics, Single Cell Gene-set enrichment analysis, Aggregation, Pathway analysis Gene-set enrichment analysis, Aggregation, Pathway analysis Metabolomics, Molecular interactions, pathways and networks, Proteomics, Transcriptomics, Small molecules Metabolomics, Molecular interactions, pathways and networks, Proteomics, Transcriptomics, Small molecules iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/multigsea https://github.com/galaxyproject/tools-iuc/tree/master/tools/multigsea multiGSEA multiGSEA A GSEA-based pathway enrichment analysis for multi-omics data.multiGSEA: a GSEA-based pathway enrichment analysis for multi-omics data, BMC Bioinformatics 21, 561 (2020).Combining GSEA-based pathway enrichment with multi omics data integration. https://workflowhub.eu/workflows/1388?version=1 proteomics/multiGSEA-tutorial 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 65 65 212 212 0 0 0 0 5 5 46 46 0 0 0 0 258 258 70 70 True False +multiqc multiqc html, tabular MultiQC aggregates results from bioinformatics analyses across many samples into a single report 2017-09-21 http://multiqc.info/ 1.35 multiqc 1.35 Up-to-date Fastq Manipulation, Statistics, Visualization Validation, Sequencing quality control Sequencing quality control Sequencing, Bioinformatics, Sequence analysis, Genomics Sequencing, Bioinformatics, Sequence analysis, Genomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/multiqc https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc multiqc MultiQC MultiQC aggregates results from multiple bioinformatics analyses across many samples into a single report. It searches a given directory for analysis logs and compiles a HTML report. 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https://workflowhub.eu/workflows/612?version=26, https://workflowhub.eu/workflows/625?version=31, https://workflowhub.eu/workflows/628?version=1, https://workflowhub.eu/workflows/641?version=33, https://workflowhub.eu/workflows/642?version=25, https://workflowhub.eu/workflows/676?version=1, https://workflowhub.eu/workflows/688?version=1, https://workflowhub.eu/workflows/876?version=1 assembly/assembly-with-preprocessing, assembly/general-introduction, assembly/hybrid_denovo_assembly, assembly/largegenome, assembly/unicycler-assembly, contributing/create-new-tutorial-content, ecology/ENA_Biodiv_submission, ecology/ref-based-rad-seq, epigenetics/cut_and_run, galaxy-interface/workflow-automation, galaxy-interface/workflow-fairification, genome-annotation/crispr-screen, introduction/galaxy-intro-ngs-data-managment, introduction/vsi_qc, microbiome/host-removal, microbiome/mags-building, microbiome/metatranscriptomics, microbiome/metatranscriptomics-short, microbiome/mgnify-amplicon, microbiome/nanopore-16S-metagenomics, microbiome/pathogen-detection-from-nanopore-foodborne-data, sequence-analysis/mapping, sequence-analysis/quality-control, single-cell/scrna-preprocessing, single-cell/scrna-preprocessing-tenx, transcriptomics/differential-isoform-expression, transcriptomics/full-de-novo, transcriptomics/minerva-pathways, transcriptomics/mirna-target-finder, transcriptomics/ref-based, transcriptomics/rna-seq-reads-to-counts, variant-analysis/exome-seq, variant-analysis/sars-cov-2, variant-analysis/somatic-variant-discovery, variant-analysis/somatic-variants, variant-analysis/tb-variant-analysis 1 1 1 1 0 0 0 0 1 1 1 0 0 0 0 0 0 0 1 0 0 0 1 1 1 0 24162 26916 223019 248625 32289 38522 203104 241071 7040 7764 49577 54957 2276 2280 43768 43966 588619 519468 75482 65767 True False +mykrobe mykrobe_predict csv Antibiotic resistance predictions 2017-12-18 https://github.com/Mykrobe-tools/mykrobe 0.10.0 mykrobe 0.13.0 To update Sequence Analysis Antimicrobial resistance prediction, Variant calling, Genotyping, Sequence trimming Antimicrobial resistance prediction, Variant calling, Genotyping, Sequence trimming Whole genome sequencing, Genotype and phenotype, Probes and primers, Genetic variation, Metagenomics Whole genome sequencing, Genotype and phenotype, Probes and primers, Genetic variation, Metagenomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/mykrobe https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe Mykrobe Mykrobe Antibiotic resistance prediction for Mycobacterium tuberculosis from genome sequence data with Mykrobe.Antibiotic resistance prediction in minutes.Table of Contents generated with DocToc.AMR prediction (Mykrobe predictor).Before attempting to install with bioconda, please ensure you have your channels set up as specified in the documentation. If you don't, you may run into issues with an older version of mykrobe being installed 0 0 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False +mykrobe_parser mykrobe_parseR csv RScript to parse the results of mykrobe predictor. 2018-09-28 https://github.com/phac-nml/mykrobe-parser @VERSION@ r-base To update Sequence Analysis nml https://github.com/phac-nml/mykrobe-parser https://github.com/phac-nml/galaxy_tools/tree/master/tools/mykrobe_parser 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False +mz_to_sqlite mz_to_sqlite mz.sqlite Creates a SQLite database for proteomics data 2015-06-01 https://github.com/galaxyproteomics/mzToSQLite 2.1.1 mztosqlite 2.1.1 Up-to-date Proteomics Conversion, Peptide database search Conversion, Peptide database search Proteomics, Biological databases Proteomics, Biological databases galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mz_to_sqlite https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mz_to_sqlite mztosqlite mzToSQLite Convert proteomics data files into a SQLite databaseExtract data from proteomics mzIdentML and mass spec scan files: mzML, MGF, etc and store in a SQLite database.The intended purpose is to provide a Galaxy dataset that can support an interactive Galaxy visualization plugin. https://usegalaxy.eu/published/workflow?id=03e52c8c71710cae, https://usegalaxy.eu/published/workflow?id=0aee7ffa5f6384bd, https://usegalaxy.eu/published/workflow?id=2a7e63d1cc583002, https://usegalaxy.eu/published/workflow?id=41d096891bada138, https://usegalaxy.eu/published/workflow?id=41e9882300fa2386, https://usegalaxy.eu/published/workflow?id=6e5f0d05c91876c2, https://usegalaxy.eu/published/workflow?id=8a85663218676b59, https://usegalaxy.eu/published/workflow?id=9a8b5e99ca9500e3, https://usegalaxy.eu/published/workflow?id=b89cf3cb6a25c999, https://usegalaxy.eu/published/workflow?id=eb54512829d8509c, https://usegalaxy.eu/published/workflow?id=edea08c943ff9c5e, https://usegalaxy.org.au/published/workflow?id=1b9bfe7ce484fdc2, https://usegalaxy.org/published/workflow?id=f4486159b08900a4, https://workflowhub.eu/workflows/1429?version=2 proteomics/proteogenomics-dbsearch 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 136 146 868 959 17 17 83 83 18 18 336 336 0 0 0 0 1378 1287 181 171 True False +nanocompore nanocompore_db, nanocompore_sampcomp tabular, tar, txt Nanocompore compares 2 ONT nanopore direct RNA sequencing datasets from different experimental conditions expected to have a significant impact on RNA modifications. It is recommended to have at least 2 replicates per condition. For example one can use a control condition with a significantly reduced number of modifications such as a cell line for which a modification writing enzyme was knocked-down or knocked-out. Alternatively, on a smaller scale transcripts of interests could be synthesized in-vitro. 2020-04-28 https://nanocompore.rna.rocks/ 1.0.0rc3.post2 nanocompore 1.0.4 To update Sequence Analysis Post-translation modification site prediction, PolyA signal detection, Genotyping, k-mer counting PolyA signal detection, Genotyping, k-mer counting Functional, regulatory and non-coding RNA, RNA-Seq, Gene transcripts, Transcriptomics, Transcription factors and regulatory sites Functional, regulatory and non-coding RNA, RNA-Seq, Gene transcripts, Transcriptomics, Transcription factors and regulatory sites iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanocompore https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore Nanocompore Nanocompore RNA modifications detection by comparative Nanopore direct RNA sequencing.RNA modifications detection from Nanopore dRNA-Seq data.Nanocompore identifies differences in ONT nanopore sequencing raw signal corresponding to RNA modifications by comparing 2 samples.Analyses performed for the nanocompore paper.Nanocompore compares 2 ONT nanopore direct RNA sequencing datasets from different experimental conditions expected to have a significant impact on RNA modifications. It is recommended to have at least 2 replicates per condition. For example one can use a control condition with a significantly reduced number of modifications such as a cell line for which a modification writing enzyme was knocked-down or knocked-out. Alternatively, on a smaller scale transcripts of interests could be synthesized in-vitro https://usegalaxy.eu/published/workflow?id=778923dd04996e07, https://usegalaxy.eu/published/workflow?id=77db45ad90b4033d 0 1 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 5 7 27 839 0 0 0 0 5 5 365 371 0 0 0 0 1210 392 12 10 True False +nanoplot nanoplot html, tabular Plotting tool for long read sequencing data and alignments 2018-09-24 https://github.com/wdecoster/NanoPlot @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ nanoplot 1.47.1 To update Visualization Scatter plot plotting, Box-Whisker plot plotting Scatter plot plotting, Box-Whisker plot plotting Genomics Genomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanoplot https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot nanoplot NanoPlot NanoPlot is a tool with various visualizations of sequencing data in bam, cram, fastq, fasta or platform-specific TSV summaries, mainly intended for long-read sequencing from 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https://workflowhub.eu/workflows/1585?version=1, https://workflowhub.eu/workflows/1612?version=1, https://workflowhub.eu/workflows/1613?version=2, https://workflowhub.eu/workflows/1616?version=1, https://workflowhub.eu/workflows/1617?version=1, https://workflowhub.eu/workflows/222?version=1, https://workflowhub.eu/workflows/406?version=1, https://workflowhub.eu/workflows/521?version=1, https://workflowhub.eu/workflows/697?version=1 assembly/assembly-with-preprocessing, assembly/chloroplast-assembly, assembly/largegenome, assembly/mrsa-nanopore, microbiome/pathogen-detection-from-nanopore-foodborne-data, microbiome/plasmid-metagenomics-nanopore, sequence-analysis/quality-control 1 1 1 1 0 0 0 0 1 1 1 0 0 0 0 0 0 0 1 0 0 0 1 1 1 0 7663 7942 168514 173861 4903 5029 72856 74900 2940 2983 25741 26566 295 297 3814 3828 279155 270925 16251 15801 True False +nanopolishcomp nanopolishcomp_eventaligncollapse, nanopolishcomp_freqmethcalculate tabular, txt, bed NanopolishComp contains 2 modules. 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Freq_meth_calculate methylation frequency at genomic CpG sites from the output of nanopolish call-methylation. 2020-04-27 https://a-slide.github.io/NanopolishComp 0.6.11 nanopolishcomp 0.6.12 To update Sequence Analysis Methylation analysis, Collapsing methods Methylation analysis, Collapsing methods Sequence analysis, Sequencing, Genetic variation Sequence analysis, Sequencing, Genetic variation iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanopolishcomp https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanopolishcomp nanopolishcomp NanopolishComp NanopolishComp is a Python3 package for downstream analyses of Nanopolish output files.It is a companion package for Nanopolish. https://usegalaxy.eu/published/workflow?id=77db45ad90b4033d 0 0 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 36 38 709 1129 0 0 0 0 0 0 0 0 1 1 1 1 1130 710 39 37 True False +ncbi_blast_plus blastxml_to_tabular, get_species_taxids, ncbi_blastdbcmd_info, ncbi_blastdbcmd_wrapper, 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obi_pairing, obi_pcr, obi_refidx, obi_tag, obi_taxonomy, obi_uniq csv, fasta OBITools is a set of programs developed to simplify the manipulation of sequence files 2017-03-22 https://github.com/metabarcoding/obitools4 4.4.45 obitools4 4.4.45 Up-to-date Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/obitools https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools https://usegalaxy.eu/published/workflow?id=513389e1a8c6bba9, https://usegalaxy.eu/published/workflow?id=afad9a17a80bb26d, https://usegalaxy.eu/published/workflow?id=edf7e2128f5aef8d, https://usegalaxy.org.au/published/workflow?id=470eb26144325590, https://workflowhub.eu/workflows/1702?version=1, https://workflowhub.eu/workflows/655?version=1 ecology/Obitools-metabarcoding 0 5 12 12 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 5 5 0 329 331 30430 30600 0 0 0 0 49 49 2343 2343 11 11 202 202 33145 32975 391 389 True False +omark omark txt, omq, pdf, png, sum, ump Proteome quality assessment software 2023-11-15 https://github.com/DessimozLab/OMArk 0.3.1 To update Sequence Analysis Sequence assembly validation, Differential protein expression profiling Sequence assembly validation, Differential protein expression profiling Proteomics, Sequence analysis, Statistics and probability Proteomics, Sequence analysis, Statistics and probability iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/omark https://github.com/galaxyproject/tools-iuc/tree/master/tools/omark omark OMArk OMArk is a software for proteome (protein-coding gene repertoire) quality assessment. It provides measures of proteome completeness, characterizes the consistency of all protein coding genes with regard to their homologs, and identifies the presence of contamination from other species. OMArk relies on the OMA orthology database, from which it exploits orthology relationships, and on the OMAmer software for fast placement of all proteins into gene families. https://usegalaxy.eu/published/workflow?id=31bc2a44fb89aa89, https://usegalaxy.eu/published/workflow?id=327beb1edda305ff, https://usegalaxy.eu/published/workflow?id=3d604dad4f1f5b3d, https://usegalaxy.eu/published/workflow?id=4077e77b6af919c4, https://usegalaxy.eu/published/workflow?id=6550f72070b24082, https://usegalaxy.eu/published/workflow?id=8976041ef89e4548, https://usegalaxy.org.au/published/workflow?id=dd9272826e6dd98d, https://usegalaxy.org.au/published/workflow?id=e263fcb6c98e231b, https://usegalaxy.org.au/published/workflow?id=ec7efff3d3249177, https://usegalaxy.org/published/workflow?id=4605309321799e9b, https://usegalaxy.org/published/workflow?id=80a7124c40438cc9, https://usegalaxy.org/published/workflow?id=f4111a169255535c, https://workflowhub.eu/workflows/1096?version=2, 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OpenSwathDIAPreScoring, OpenSwathDecoyGenerator, OpenSwathFeatureXMLToTSV, OpenSwathFileSplitter, OpenSwathMzMLFileCacher, OpenSwathRTNormalizer, OpenSwathRewriteToFeatureXML, OpenSwathWorkflow, PTModel, PTPredict, PeakPickerHiRes, PeakPickerIterative, PeakPickerWavelet, PepNovoAdapter, PeptideIndexer, PhosphoScoring, PrecursorIonSelector, PrecursorMassCorrector, ProteinInference, ProteinQuantifier, ProteinResolver, QCCalculator, QCEmbedder, QCExporter, QCExtractor, QCImporter, QCMerger, QCShrinker, RNPxl, RNPxlXICFilter, RTEvaluation, RTModel, RTPredict, SemanticValidator, SequenceCoverageCalculator, SimpleSearchEngine, SpecLibCreator, SpectraFilterBernNorm, SpectraFilterMarkerMower, SpectraFilterNLargest, SpectraFilterNormalizer, SpectraFilterParentPeakMower, SpectraFilterScaler, SpectraFilterSqrtMower, SpectraFilterThresholdMower, SpectraFilterWindowMower, SpectraMerger, SvmTheoreticalSpectrumGeneratorTrainer, TICCalculator, TMTAnalyzer, TOFCalibration, TextExporter, TopPerc, 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https://usegalaxy.org/published/workflow?id=9865fee6c68fc201, https://usegalaxy.org/published/workflow?id=f9048d9678e21f36, https://workflowhub.eu/workflows/1394?version=1, https://workflowhub.eu/workflows/1399?version=1, https://workflowhub.eu/workflows/1421?version=1, https://workflowhub.eu/workflows/1424?version=1, https://workflowhub.eu/workflows/1434?version=1, https://workflowhub.eu/workflows/1438?version=1, https://workflowhub.eu/workflows/1446?version=1, https://workflowhub.eu/workflows/1449?version=1, https://workflowhub.eu/workflows/1452?version=1, https://workflowhub.eu/workflows/1463?version=1, https://workflowhub.eu/workflows/613?version=3 proteomics/DIA_Analysis_OSW, proteomics/DIA_lib_OSW, proteomics/database-handling, proteomics/ntails, proteomics/protein-id-oms, proteomics/protein-id-sg-ps, proteomics/protein-quant-sil 7 34 135 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 27 135 134 0 583 698 30109 114383 10 10 417 417 33 34 1321 1325 0 0 0 0 116125 31847 742 626 True False +orfipy orfipy bed6, bed12, fasta Galaxy wrapper for ORFIPY 2022-04-07 https://github.com/urmi-21/orfipy 0.0.4 orfipy 0.0.4 Up-to-date Sequence Analysis Coding region prediction, Database search, Transcriptome assembly, De-novo assembly Coding region prediction, Database search, Transcriptome assembly, De-novo assembly Computer science, RNA-Seq, Transcriptomics, Small molecules Computer science, RNA-Seq, Transcriptomics, Small molecules iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/orfipy https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy orfipy orfipy A fast and flexible tool for extracting ORFs.orfipy is a tool written in python/cython to extract ORFs in extremely an fast and flexible manner. Other popular ORF searching tools are OrfM and getorf. Compared to OrfM and getorf, orfipy provides the most options to fine tune ORF searches. orfipy uses multiple CPU cores and is particularly faster for data containing multiple smaller fasta sequences such as de-novo transcriptome assemblies. 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It finds orthogroups and orthologs, infers rooted gene trees for all orthogroups and identifies all of the gene duplcation events in those gene trees. It also infers a rooted species tree for the species being analysed and maps the gene duplication events from the gene trees to branches in the species tree. OrthoFinder also provides comprehensive statistics for comparative genomic analyses. https://usegalaxy.eu/published/workflow?id=d8492b49aed84d4f, https://usegalaxy.eu/published/workflow?id=e0c709127e9a42ae, https://usegalaxy.eu/published/workflow?id=e5becc6d66b2568c, https://usegalaxy.org/published/workflow?id=84b447be2f1c5870 1 1 1 1 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 1 1 0 0 801 801 3870 3870 0 0 0 0 133 133 1450 1450 36 36 221 221 5541 5541 970 970 True False +pacu pacu_map, pacu_snp bam, html PACU is a workflow for whole genome sequencing based phylogeny of Illumina and ONT R9/R10 data. 2024-08-13 https://github.com/BioinformaticsPlatformWIV-ISP/PACU 0.0.5 pacu_snp 1.0.0 To update Sequence Analysis, Phylogenetics Clustering Clustering Phylogenetics, Sequence analysis Phylogenetics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/pacu https://github.com/galaxyproject/tools-iuc/tree/master/tools/pacu pacu PACU PACU is a workflow for whole genome sequencing based phylogeny of Illumina and ONT R9/R10 data.PACU stands for the Prokaryotic Awesome variant Calling Utility and is named after an omnivorous fish (that eats both Illumina and ONT reads). 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 19 19 223 223 0 0 0 0 0 0 0 0 0 0 0 0 223 223 19 19 True False +pal2nal pal2nal txt, html Wraps PAL2NAL to convert protein alignments and nucleotide FASTA into codon-aware alignments. 2025-11-09 http://www.bork.embl.de/pal2nal @TOOL_VERSION@+galaxy@WRAPPER_VERSION@ pal2nal 14.1 To update Sequence Analysis, Phylogenetics iuc https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal https://github.com/galaxyproject/tools-iuc/tree/master/tools/pal2nal 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False +pampa pampa_communitymetrics, pampa_presabs, pampa_glmcomm, pampa_glmsp, pampa_plotglm tabular, txt Tools to compute and analyse biodiversity metrics 2020-06-06 0.0.2 To update Ecology ecology 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https://github.com/galaxyproject/tools-iuc/tree/main/tools/panaroo https://github.com/galaxyproject/tools-iuc/tree/master/tools/panaroo panaroo Panaroo Producing Polished Prokaryotic Pangenomes with the Panaroo Pipeline. 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 67 67 297 297 0 0 0 0 39 39 312 312 0 0 0 0 609 609 106 106 True False +panta panta json, tsv, csv, txt, fasta Efficient inference of large prokaryotic pangenomes with PanTA. 2025-09-15 https://github.com/amromics/panta 1.0.1 panta 1.0.1 Up-to-date Genome annotation, Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta https://github.com/galaxyproject/tools-iuc/tree/master/tools/panta 0 0 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False +peptideshaker fasta_cli, ident_params, peptide_shaker, search_gui fasta, json, zip, mzid, peptideshaker_archive, txt, tabular, searchgui_archive PeptideShaker and SearchGUI 2015-01-31 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+pfamscan pfamscan tabular Search a FASTA sequence against a library of Pfam HMM. 2023-02-02 http://ftp.ebi.ac.uk/pub/databases/Pfam/Tools/ @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ pfam_scan 1.6 To update Sequence Analysis Protein sequence analysis Protein sequence analysis Sequence analysis Sequence analysis bgruening https://github.com/bgruening/galaxytools/tree/master/tools/pfamscan https://github.com/bgruening/galaxytools/tree/master/tools/pfamscan pfamscan PfamScan This tool is used to search a FASTA sequence against a library of Pfam HMM. https://usegalaxy.eu/published/workflow?id=11eba1b28ec87963, https://usegalaxy.eu/published/workflow?id=1f9a9a7998ef5ab3, https://usegalaxy.eu/published/workflow?id=47a0407867a90f95, https://usegalaxy.eu/published/workflow?id=87231a6a7938cb95, https://usegalaxy.eu/published/workflow?id=9b025479fade745d, https://usegalaxy.eu/published/workflow?id=b7a3cbcd32734e8b, https://usegalaxy.org.au/published/workflow?id=6e1e24f9e0326930, https://workflowhub.eu/workflows/1688?version=1 transcriptomics/differential-isoform-expression 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 146 146 7522 7522 143 143 881 881 33 33 545 545 1 1 1 1 8949 8949 323 323 True False +phabox phabox_cherry, phabox_contamination, phabox_end_to_end, phabox_phagcn, phabox_phamer, phabox_phatyp, phabox_phavip, phabox_tree, phabox_votu tabular Identify and analyze phage contigs in metagenomic data 2024-11-12 https://github.com/KennthShang/PhaBOX 2.1.11 phabox 2.1.13 To update Metagenomics Sequence assembly, Taxonomic classification, Visualisation Sequence assembly, Taxonomic classification, Visualisation Metagenomics, Microbial ecology, Sequence assembly, Taxonomy Metagenomics, Microbial ecology, Sequence assembly, Taxonomy ufz https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox https://github.com/Helmholtz-UFZ/galaxy-tools/tree/master/tools/phabox phabox PhaBOX Web server for identifying and characterizing phage contigs in metagenomic data. 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False pharokka pharokka genbank, gff, zip rapid standardised annotation tool for bacteriophage genomes and metagenomes 2023-02-14 https://github.com/gbouras13/pharokka 1.3.2 " pharokka - " To update Genome annotation Genome annotation, Antimicrobial resistance prediction, tRNA gene prediction, Formatting, Sequence assembly Genome annotation, Antimicrobial resistance prediction, tRNA gene prediction, Formatting, Sequence assembly Metagenomics, Sequence sites, features and motifs, Workflows, Functional, regulatory and non-coding RNA Metagenomics, Sequence sites, features and motifs, Workflows, Functional, regulatory and non-coding RNA iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/pharokka https://github.com/galaxyproject/tools-iuc/tree/main/tools/pharokka pharokka Pharokka Pharokka is a rapid standardised annotation tool for bacteriophage genomes and metagenomes. 0 1 1 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 0 0 1 0 0 766 766 16933 16933 1 1 21 21 117 117 1202 1202 0 0 0 0 18156 18156 884 884 https://usegalaxy.eu/published/workflow?id=46ef864fe9468894, https://usegalaxy.eu/published/workflow?id=62392daea25a3980 True False -phi_toolkit_report phi_toolkit_report html, tsv Phage host interaction toolkit report generator 2025-06-04 https://git.ufz.de/borimcor/phage-host-analysis 0.3.0 bioconductor-biostrings 2.78.0 To update Metagenomics ufz https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phi-toolkit https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/phi-toolkit 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 https://usegalaxy.eu/published/workflow?id=c62d65832377e376 True False -phyloseq phyloseq_add_rank_names, phyloseq_from_biom, phyloseq_from_dada2, phyloseq_plot_bar, phyloseq_plot_ordination, phyloseq_plot_richness, phyloseq_tax_glom phyloseq, pdf, tabular Handling and analysis of high-throughput microbiome census data 2022-03-03 https://www.bioconductor.org/packages/release/bioc/html/phyloseq.html 1.54.0 bioconductor-phyloseq 1.54.0 Up-to-date Metagenomics Deposition, Analysis, Visualisation Deposition, Analysis, Visualisation Microbiology, Sequence analysis, Metagenomics Microbiology, Sequence analysis, Metagenomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/phyloseq https://github.com/galaxyproject/tools-iuc/tree/main/tools/phyloseq phyloseq phyloseq Provides a set of classes and tools to facilitate the import, storage, analysis, and graphical display of microbiome census data. 4 1 7 6 0 0 0 0 0 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 3 3 0 251 251 3161 3161 156 156 1022 1022 35 35 190 190 14 14 163 163 4536 4536 456 456 https://usegalaxy.eu/published/workflow?id=466bdd8ba7b67264, https://usegalaxy.eu/published/workflow?id=e3918808605cf8cd, https://usegalaxy.org/published/workflow?id=4faff660f6defa10, https://workflowhub.eu/workflows/1395?version=2 microbiome/dada-16S True False -phyml phyml nhx, txt PhyML is a phylogeny software based on the maximum-likelihood principle. 2019-05-27 http://www.atgc-montpellier.fr/phyml/ 3.3.20220408 phyml 3.3.20220408 Up-to-date Phylogenetics Phylogenetic tree generation (maximum likelihood and Bayesian methods) Phylogenetics, Bioinformatics, Phylogenetics Phylogenetics, Bioinformatics, Phylogenetics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/phyml https://github.com/galaxyproject/tools-iuc/tree/main/tools/phyml phyml PhyML Phylogenetic estimation software using Maximum Likelihood 0 1 1 1 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 286 335 2452 2654 0 0 0 0 215 240 1475 1564 79 79 334 334 4552 4261 654 580 https://usegalaxy.fr/published/workflow?id=63b49f322ec366b5, https://usegalaxy.fr/published/workflow?id=894143d81af8dff0 True False -picrust picrust_categorize, picrust_compare_biom, picrust_format_tree_and_trait_table, picrust_metagenome_contributions, picrust_normalize_by_copy_number, picrust_predict_metagenomes tabular, nhx PICRUSt wrappers 2016-11-08 https://picrust.github.io/picrust/ 1.1.1 picrust 1.1.4 To update Metagenomics Phylogenetic reconstruction, Expression analysis, Genome annotation, DNA barcoding Phylogenetic reconstruction, Expression analysis, Genome annotation, DNA barcoding Metagenomics, Microbial ecology, Functional, regulatory and non-coding RNA, Metagenomic sequencing Metagenomics, Microbial ecology, Functional, regulatory and non-coding RNA, Metagenomic sequencing iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/picrust https://github.com/galaxyproject/tools-iuc/tree/main/tools/picrust picrust PICRUSt PICRUSt (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) is a bioinformatics software package designed to predict metagenome functional content from marker gene (e.g., 16S rRNA) surveys and full genomes. 0 6 6 6 0 0 0 0 0 6 0 0 0 0 0 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of Unobserved States) is a software for predicting functional abundances based only on marker gene sequences. 0 7 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 0 0 327 327 6432 6432 1 1 1 1 64 64 2888 2888 0 0 0 0 9321 9321 392 392 https://usegalaxy.eu/published/workflow?id=be9ff4159593cc34 True False -pimento pimento_are_there_primers, pimento_auto, pimento_choose_primer_cutoff, pimento_find_cutoffs, pimento_gen_bcv, pimento_std txt, fasta, tsv A PrIMEr infereNce TOolkit to facilitate large-scale calling of metabarcoding amplicon sequence variants. 2025-08-04 https://github.com/EBI-Metagenomics/PIMENTO 1.0.3 mi-pimento 1.0.3 Up-to-date Metagenomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/pimento https://github.com/galaxyproject/tools-iuc/tree/main/tools/pimento 0 0 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 2 2 0 0 0 0 0 0 0 0 0 0 0 0 2 2 1 1 True False -pirate pirate txt, tsv, fasta, newick, gfa1, gff, pdf Pangenome Iterative Refinement and Threshold Evaluation. 2026-01-31 https://github.com/SionBayliss/PIRATE 1.0.5 pirate 1.0.5 Up-to-date Sequence Analysis, Genome annotation iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/pirate https://github.com/galaxyproject/tools-iuc/tree/main/tools/pirate 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False -plasclass plasclass tabular PlasClass is a tool to classify sequences of plasmid or chromosomal origin 2025-07-31 https://github.com/Shamir-Lab/PlasClass 0.1.1 plasclass 0.1.1 Up-to-date Sequence Analysis Sequence classification, Sequence assembly, k-mer counting Sequence classification, Sequence assembly, k-mer counting Metagenomics, Sequence assembly, DNA, Metagenomic sequencing Metagenomics, Sequence assembly, DNA, Metagenomic sequencing iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/plasclass https://github.com/galaxyproject/tools-iuc/tree/main/tools/plasclass PlasClass PlasClass PlasClass is a tool for easy classification of sequences as either plasmid or chromosomal. 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0 68330 66494 1888 1720 https://usegalaxy.eu/published/workflow?id=152223c8aed27357, https://usegalaxy.eu/published/workflow?id=249c115413f17f28, https://usegalaxy.eu/published/workflow?id=3081569659a45b9e, https://usegalaxy.eu/published/workflow?id=32d2f5340098bcbd, https://usegalaxy.eu/published/workflow?id=39837ca09374598b, https://usegalaxy.eu/published/workflow?id=44e53ea319e07daa, https://usegalaxy.eu/published/workflow?id=9219557de92e0203, https://usegalaxy.eu/published/workflow?id=b4de76c0a4d0e23a, https://usegalaxy.eu/published/workflow?id=c48807045e258dd8, https://usegalaxy.eu/published/workflow?id=dc7107896a3f2964, https://usegalaxy.org.au/published/workflow?id=d9571b3dfef34e5e, https://usegalaxy.org/published/workflow?id=33d90e718ce500ef, https://workflowhub.eu/workflows/1477?version=1, https://workflowhub.eu/workflows/406?version=1 microbiome/plasmid-metagenomics-nanopore True False -plasmidfinder plasmidfinder json, fasta, tabular, txt Identify plasmids in total or partial sequenced isolates of bacteria. 2022-09-19 https://bitbucket.org/genomicepidemiology/plasmidfinder/src/master/ 2.1.6 plasmidfinder 2.1.6 Up-to-date Sequence Analysis Genome assembly, Scaffolding, Multilocus sequence typing Genome assembly, Scaffolding, Multilocus sequence typing Whole genome sequencing, Sequence assembly, Mapping, Probes and primers Whole genome sequencing, Sequence assembly, Mapping, Probes and primers iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/plasmidfinder https://github.com/galaxyproject/tools-iuc/tree/main/tools/plasmidfinder PlasmidFinder PlasmidFinder PlasmidFinder is a tool for the identification and typing of Plasmid Replicons in Whole-Genome Sequencing (WGS). 1 1 1 1 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 1015 1015 35994 35994 623 623 11939 11939 211 211 3278 3278 48 48 10730 10730 61941 61941 1897 1897 https://usegalaxy.eu/published/workflow?id=1306ed083d91a852, https://usegalaxy.eu/published/workflow?id=2a1dc58e51d5f01a, 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https://usegalaxy.org.au/published/workflow?id=05f3abecd4ddd4a1, https://usegalaxy.org.au/published/workflow?id=09ec031656620fb5, https://usegalaxy.org/published/workflow?id=04c5ea133de3204c, https://usegalaxy.org/published/workflow?id=3940186d02245b1d, https://usegalaxy.org/published/workflow?id=49da012e2839c046, https://usegalaxy.org/published/workflow?id=4f8bdd61c524b901, https://usegalaxy.org/published/workflow?id=649cdc14757e5755, https://usegalaxy.org/published/workflow?id=67ca17ab34b10772, https://usegalaxy.org/published/workflow?id=8cb8a588a0495cfa, https://usegalaxy.org/published/workflow?id=993534c11310a207, https://usegalaxy.org/published/workflow?id=d2a5f6a5181aada5, https://workflowhub.eu/workflows/1050?version=13, https://workflowhub.eu/workflows/1513?version=1 genome-annotation/bacterial-genome-annotation True False -plasmidspades plasmidspades fasta, tabular, txt Genome assembler for assemblying plasmid 2016-06-06 1.1 spades 4.2.0 To update Assembly nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/plasmidspades 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False -polypolish polypolish fasta, tabular, txt """Polypolish is a tool for polishing genome assemblies with short reads.Polypolish uses SAM files where each read has been aligned to all possible locations (not just a single best location).This allows it to repair errors in repeat regions that other alignment-based polishers cannot fix.""" 2022-09-22 https://github.com/rrwick/Polypolish 0.6.1 polypolish 0.6.1 Up-to-date Sequence Analysis Genome assembly, Read mapping, Mapping assembly, Sequencing error detection Genome assembly, Read mapping, Mapping assembly, Sequencing error detection Sequence assembly, Sequence composition, complexity and repeats, Mapping Sequence assembly, Sequence composition, complexity and repeats, Mapping iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/polypolish https://github.com/galaxyproject/tools-iuc/tree/main/tools/polypolish Polypolish Polypolish Polypolish is a tool for polishing genome assemblies with short reads. Unlike other tools in this category, Polypolish uses SAM files where each read has been aligned to all possible locations (not just a single best location). This allows it to repair errors in repeat regions that other alignment-based polishers cannot fix. 0 1 1 1 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 147 147 1066 1066 0 0 0 0 26 26 615 615 10 10 79 79 1760 1760 183 183 https://usegalaxy.eu/published/workflow?id=2c992e509aa5dd9d, https://workflowhub.eu/workflows/1613?version=2 assembly/mrsa-nanopore True False -ppanggolin ppanggolin_all, ppanggolin_msa, ppanggolin_projection, ppanggolin_rarefaction tsv, fasta, json, xml, html, csv, txt, h5, tar.gz, tabular Microbial Partitioned PanGenome 2025-01-22 https://github.com/labgem/PPanGGOLiN 2.3.0 ppanggolin 2.3.0 Up-to-date Genome annotation Rarefaction, Essential dynamics, Sequence assembly, Genome annotation Rarefaction, Essential dynamics, Sequence assembly, Genome annotation Metagenomics, Gene and protein families, Model organisms, Public health and epidemiology, Mapping Metagenomics, Gene and protein families, Model organisms, Public health and epidemiology, Mapping iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/ppanggolin https://github.com/galaxyproject/tools-iuc/tree/main/tools/ppanggolin ppanggolin PPanGGOLiN PPanGGOLiN is a software suite used to create and manipulate prokaryotic pangenomes from a set of either genomic DNA sequences or provided genome annotations. It is designed to scale up to tens of thousands of genomes. It has the specificity to partition the pangenome using a statistical approach rather than using fixed thresholds which gives it the ability to work with low-quality data such as Metagenomic Assembled Genomes (MAGs) or Single-cell Amplified Genomes (SAGs) thus taking advantage of large scale environmental studies and letting users study the pangenome of uncultivable species 0 0 4 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 55 55 249 249 0 0 0 0 0 0 0 0 16 16 67 67 316 316 71 71 genome-annotation/bacterial-pangenomics True False -prodigal prodigal genbank, fasta, tabular A protein-coding gene prediction software tool for bacterial and archaeal genomes 2024-03-14 https://github.com/hyattpd/Prodigal 2.6.3 prodigal 2.6.3 Up-to-date Genome annotation Genome annotation Genome annotation Genomics, Sequence analysis Genomics, Sequence analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/prodigal https://github.com/galaxyproject/tools-iuc/tree/main/tools/prodigal prodigal Prodigal Fast, reliable protein-coding gene prediction for prokaryotic genomes. 1 1 1 1 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 611 611 6456 6456 0 0 0 0 70 70 1515 1515 19 19 1487 1487 9458 9458 700 700 https://usegalaxy.eu/published/workflow?id=2ee0eb74e839b476, https://usegalaxy.eu/published/workflow?id=62392daea25a3980, https://usegalaxy.eu/published/workflow?id=6dbbf39e07a5212e, https://usegalaxy.eu/published/workflow?id=b9c938d1af08124b, https://usegalaxy.org/published/workflow?id=d3c400275889ce4b, https://workflowhub.eu/workflows/1663?version=1, https://workflowhub.eu/workflows/2024?version=4 ecology/marine_omics_bgc True False -prokka prokka gff3, genbank, fasta, asn1, txt, tabular Rapid annotation of prokaryotic genomes 2016-10-07 http://github.com/tseemann/prokka 1.14.6 prokka 1.15.6 To update Sequence Analysis Gene prediction, Coding region prediction, Genome annotation Coding region prediction, Genome annotation Genomics, Model organisms, Virology Genomics, 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developed and supported bioinformatics. 15 15 15 15 0 0 0 0 0 15 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 15 0 0 5 5 30 30 17 17 47 47 5 5 6 6 1 1 4 4 87 87 28 28 True False -qiime2 qiime2__phylogeny__align_to_tree_mafft_fasttree, qiime2__phylogeny__align_to_tree_mafft_iqtree, qiime2__phylogeny__align_to_tree_mafft_raxml, qiime2__phylogeny__fasttree, qiime2__phylogeny__filter_table, qiime2__phylogeny__filter_tree, qiime2__phylogeny__iqtree, qiime2__phylogeny__iqtree_ultrafast_bootstrap, qiime2__phylogeny__midpoint_root, qiime2__phylogeny__raxml, qiime2__phylogeny__raxml_rapid_bootstrap, qiime2__phylogeny__robinson_foulds qza 2022-08-26 https://github.com/qiime2/q2-phylogeny 2026.1.0+q2galaxy.2026.1.0 To update Metagenomics, Sequence Analysis, Statistics Demultiplexing, Visualisation, Taxonomic classification Demultiplexing, Visualisation, Taxonomic classification Microbial ecology, Metatranscriptomics, Metagenomics Microbial ecology, Metatranscriptomics, Metagenomics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__phylogeny https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__phylogeny qiime2 QIIME 2 QIIME 2 is an AI-ready microbiome multi-omics data science platform that is trusted, free, open source, extensible, and community developed and supported bioinformatics. 12 12 12 12 0 0 0 0 0 12 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 12 0 0 167 167 880 880 93 93 338 338 66 66 373 373 13 13 91 91 1682 1682 339 339 https://usegalaxy.eu/published/workflow?id=7c07e87c77dcee05 True False -qiime2 qiime2__metadata__distance_matrix, qiime2__metadata__merge, qiime2__metadata__shuffle_groups, qiime2__metadata__tabulate qza, qzv 2022-08-26 https://github.com/qiime2/q2-metadata 2026.1.0+q2galaxy.2026.1.0 To update Metagenomics, Sequence Analysis, Statistics Demultiplexing, Visualisation, Taxonomic classification Demultiplexing, Visualisation, Taxonomic classification Microbial ecology, Metatranscriptomics, Metagenomics Microbial ecology, Metatranscriptomics, Metagenomics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__metadata https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__metadata qiime2 QIIME 2 QIIME 2 is an AI-ready microbiome multi-omics data science platform that is trusted, free, open source, extensible, and community developed and supported bioinformatics. 3 3 3 3 0 0 0 0 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 331 331 2227 2227 292 292 1317 1317 94 94 744 744 39 39 269 269 4557 4557 756 756 https://usegalaxy.eu/published/workflow?id=3d0039098a87642c, https://usegalaxy.eu/published/workflow?id=5223c9554718114d, https://usegalaxy.eu/published/workflow?id=851b97ea3d1de9f7, https://usegalaxy.eu/published/workflow?id=b3d48f81329926fc, https://usegalaxy.eu/published/workflow?id=da17a4d690eb0ff3, https://usegalaxy.eu/published/workflow?id=e1f08a63fbc8e173, https://usegalaxy.eu/published/workflow?id=e2af8c661e98f4f4, 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Taxonomic classification Microbial ecology, Metatranscriptomics, Metagenomics Microbial ecology, Metatranscriptomics, Metagenomics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__stats https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__stats qiime2 QIIME 2 QIIME 2 is an AI-ready microbiome multi-omics data science platform that is trusted, free, open source, extensible, and community developed and supported bioinformatics. 0 0 9 0 0 0 0 0 0 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False -qiime2 qiime2__quality_control__bowtie2_build, qiime2__quality_control__decontam_identify, qiime2__quality_control__decontam_identify_batches, qiime2__quality_control__decontam_score_viz, qiime2__quality_control__evaluate_composition, qiime2__quality_control__evaluate_seqs, qiime2__quality_control__evaluate_taxonomy, qiime2__quality_control__exclude_seqs, qiime2__quality_control__filter_reads qza, qzv 2022-08-26 https://github.com/qiime2/q2-quality-control 2026.1.0+q2galaxy.2026.1.0 To update Metagenomics, Sequence Analysis, Statistics Demultiplexing, Visualisation, Taxonomic classification Demultiplexing, Visualisation, Taxonomic classification Microbial ecology, Metatranscriptomics, Metagenomics Microbial ecology, Metatranscriptomics, Metagenomics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control qiime2 QIIME 2 QIIME 2 is an AI-ready microbiome multi-omics data science platform that is trusted, free, open source, extensible, and community developed and supported bioinformatics. 6 6 6 6 0 0 0 0 0 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 0 0 4 4 6 6 11 11 105 105 4 4 11 11 0 0 0 0 122 122 19 19 True False -qiime2 qiime2__diversity_lib__alpha_passthrough, qiime2__diversity_lib__beta_passthrough, qiime2__diversity_lib__beta_phylogenetic_meta_passthrough, qiime2__diversity_lib__beta_phylogenetic_passthrough, qiime2__diversity_lib__bray_curtis, qiime2__diversity_lib__faith_pd, qiime2__diversity_lib__jaccard, qiime2__diversity_lib__observed_features, qiime2__diversity_lib__pielou_evenness, qiime2__diversity_lib__shannon_entropy, qiime2__diversity_lib__unweighted_unifrac, qiime2__diversity_lib__weighted_unifrac qza 2022-08-26 https://github.com/qiime2/q2-diversity-lib 2026.1.0+q2galaxy.2026.1.0 To update Metagenomics, Sequence Analysis, Statistics Demultiplexing, Visualisation, Taxonomic classification Demultiplexing, Visualisation, Taxonomic classification Microbial ecology, Metatranscriptomics, Metagenomics Microbial ecology, Metatranscriptomics, Metagenomics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib qiime2 QIIME 2 QIIME 2 is an AI-ready microbiome multi-omics data science platform that is trusted, free, open 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and community developed and supported bioinformatics. 3 3 3 3 0 0 0 0 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 67 67 390 390 35 35 78 78 16 16 114 114 14 14 69 69 651 651 132 132 True False -qiime2 qiime2__vizard__boxplot, qiime2__vizard__heatmap, qiime2__vizard__lineplot, qiime2__vizard__scatterplot_2d qzv 2024-10-30 https://github.com/qiime2/q2-vizard 2026.1.0+q2galaxy.2026.1.0 To update Metagenomics, Sequence Analysis, Statistics Demultiplexing, Visualisation, Taxonomic classification Demultiplexing, Visualisation, Taxonomic classification Microbial ecology, Metatranscriptomics, Metagenomics Microbial ecology, Metatranscriptomics, Metagenomics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vizard https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vizard qiime2 QIIME 2 QIIME 2 is an AI-ready microbiome multi-omics data science platform that is trusted, free, open source, extensible, and community developed and supported bioinformatics. 0 0 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To update Metagenomics, Sequence Analysis, Statistics Demultiplexing, Visualisation, Taxonomic classification Demultiplexing, Visualisation, Taxonomic classification Microbial ecology, Metatranscriptomics, Metagenomics Microbial ecology, Metatranscriptomics, Metagenomics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity qiime2 QIIME 2 QIIME 2 is an AI-ready microbiome multi-omics data science platform that is trusted, free, open source, extensible, and community developed and supported bioinformatics. 21 22 22 21 0 0 0 0 0 22 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 21 0 0 135 135 3770 3770 88 88 2286 2286 60 60 1211 1211 26 26 360 360 7627 7627 309 309 https://usegalaxy.eu/published/workflow?id=457a3de5c1512707, https://usegalaxy.eu/published/workflow?id=6e5fad1de09af683, https://usegalaxy.eu/published/workflow?id=a91c46b9e0c1d635, 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https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__demux qiime2 QIIME 2 QIIME 2 is an AI-ready microbiome multi-omics data science platform that is trusted, free, open source, extensible, and community developed and supported bioinformatics. 6 6 6 6 0 0 0 0 0 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 0 0 289 289 1358 1358 251 251 1071 1071 91 91 1146 1146 28 28 127 127 3702 3702 659 659 https://usegalaxy.eu/published/workflow?id=3d0039098a87642c, https://usegalaxy.eu/published/workflow?id=5528702f49c33d83, https://usegalaxy.eu/published/workflow?id=5d401d357500617f, https://usegalaxy.eu/published/workflow?id=86b31ac8a7720e41, https://usegalaxy.eu/published/workflow?id=b1f68ff8158d0b85, https://usegalaxy.eu/published/workflow?id=b2975bb705d3e851, https://usegalaxy.eu/published/workflow?id=be9ff4159593cc34, https://usegalaxy.eu/published/workflow?id=c0b5b499b149005f, https://usegalaxy.eu/published/workflow?id=c58941443cec9380, 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-qiime2 qiime2__deblur__denoise_16S, qiime2__deblur__denoise_other, qiime2__deblur__visualize_stats qza, qzv 2022-08-26 https://github.com/biocore/deblur 2026.1.0+q2galaxy.2026.1.0 To update Metagenomics, Sequence Analysis, Statistics Demultiplexing, Visualisation, Taxonomic classification Demultiplexing, Visualisation, Taxonomic classification Microbial ecology, Metatranscriptomics, Metagenomics Microbial ecology, Metatranscriptomics, Metagenomics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__deblur https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__deblur qiime2 QIIME 2 QIIME 2 is an AI-ready microbiome multi-omics data science platform that is trusted, free, open source, extensible, and community developed and supported bioinformatics. 3 3 3 3 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 40 40 225 225 24 24 78 78 9 9 177 177 1 1 8 8 488 488 74 74 True False -qiime2 qiime2__dada2__denoise_ccs, qiime2__dada2__denoise_paired, 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2026.1.0+q2galaxy.2026.1.0 To update Metagenomics, Sequence Analysis, Statistics Demultiplexing, Visualisation, Taxonomic classification Demultiplexing, Visualisation, Taxonomic classification Microbial ecology, Metatranscriptomics, Metagenomics Microbial ecology, Metatranscriptomics, Metagenomics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt qiime2 QIIME 2 QIIME 2 is an AI-ready microbiome multi-omics data science platform that is trusted, free, open source, extensible, and community developed and supported bioinformatics. 4 4 4 4 0 0 0 0 0 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 0 73 73 364 364 69 69 273 273 7 7 213 213 3 3 31 31 881 881 152 152 True False -qiime2 qiime2__composition__add_pseudocount, qiime2__composition__ancom, qiime2__composition__ancombc, qiime2__composition__ancombc2, qiime2__composition__ancombc2_visualizer, qiime2__composition__da_barplot, qiime2__composition__tabulate qza, qzv 2022-08-26 https://github.com/qiime2/q2-composition 2026.1.0+0.g4b3aa86.dirty-q2galaxy.2026.1.0 To update Metagenomics, Sequence Analysis, Statistics Demultiplexing, Visualisation, Taxonomic classification Demultiplexing, Visualisation, Taxonomic classification Microbial ecology, Metatranscriptomics, Metagenomics Microbial ecology, Metatranscriptomics, Metagenomics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition qiime2 QIIME 2 QIIME 2 is an AI-ready microbiome multi-omics data science platform that is trusted, free, open source, extensible, and community developed and supported bioinformatics. 4 4 4 2 0 0 0 0 0 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 0 26 26 388 388 31 31 256 256 8 8 325 325 9 9 89 89 1058 1058 74 74 True False -qiime2 qiime2__taxa__barplot, qiime2__taxa__barplot2, qiime2__taxa__collapse, qiime2__taxa__filter_seqs, qiime2__taxa__filter_table qzv, qza 2022-08-26 https://github.com/qiime2/q2-taxa 2026.1.0+q2galaxy.2026.1.0 To update Metagenomics, Sequence Analysis, Statistics Demultiplexing, Visualisation, Taxonomic classification Demultiplexing, Visualisation, Taxonomic classification Microbial ecology, Metatranscriptomics, Metagenomics Microbial ecology, Metatranscriptomics, Metagenomics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa qiime2 QIIME 2 QIIME 2 is an AI-ready microbiome multi-omics data science platform that is trusted, free, open source, extensible, and community developed and supported bioinformatics. 4 4 4 4 0 0 0 0 0 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 0 266 266 2747 2747 159 159 1008 1008 78 78 690 690 22 22 236 236 4681 4681 525 525 https://usegalaxy.eu/published/workflow?id=be9ff4159593cc34, https://usegalaxy.eu/published/workflow?id=e2af8c661e98f4f4, 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microbiome/metagenomics-assembly True False -quickmerge quickmerge fasta, tabular Merge long-read and hybrid assemblies to increase contiguity 2022-07-08 https://github.com/mahulchak/quickmerge 0.3 quickmerge 0.3 Up-to-date Assembly Genome assembly, Scaffolding, De-novo assembly, Genotyping Genome assembly, Scaffolding, De-novo assembly, Genotyping Structural variation, Sequence assembly, DNA polymorphism, Whole genome sequencing, Genotype and phenotype Structural variation, Sequence assembly, DNA polymorphism, Whole genome sequencing, Genotype and phenotype iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/quickmerge https://github.com/galaxyproject/tools-iuc/tree/main/tools/quickmerge quickmerge quickmerge Quickmerge is a program that uses complementary information from genomes assembled with long reads in order to improve contiguity, and works with assemblies derived from both Pacific Biosciences or Oxford Nanopore. Quickmerge will even work with hybrid assemblies made by combining long reads and Illumina short reads. 0 0 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False -quicktree quicktree newick neighbour-joining phylogenetic inference 2024-11-21 https://github.com/khowe/quicktree 2.5 quicktree 2.5 Up-to-date Phylogenetics Phylogenetic inference (from molecular sequences) Phylogenetic inference (from molecular sequences) Phylogenetics Phylogenetics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/quicktree https://github.com/galaxyproject/tools-iuc/tree/main/tools/quicktree quicktree QuickTree QuickTree is an efficient implementation of the Neighbor-Joining algorithm (PMID: 3447015), capable of reconstructing phylogenies from huge alignments in time less than the age of the universe. 0 0 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 69 69 466 466 0 0 0 0 0 0 0 0 0 0 0 0 466 466 69 69 https://workflowhub.eu/workflows/1650?version=1 sequence-analysis/tapscan-streptophyte-algae True False -racon racon fasta Consensus module for raw de novo DNA assembly of long uncorrected reads. 2018-06-11 https://github.com/isovic/racon 1.5.0 racon 1.5.0 Up-to-date Sequence Analysis Genome assembly, Mapping assembly Genome assembly, Mapping assembly Whole genome sequencing, Sequence assembly Whole genome sequencing, Sequence assembly bgruening https://github.com/bgruening/galaxytools/tree/master/tools/racon https://github.com/bgruening/galaxytools/tree/master/tools/racon Racon Racon Consensus module for raw de novo DNA assembly of long uncorrected readsRacon is intended as a standalone consensus module to correct raw contigs generated by rapid assembly methods which do not include a consensus step. The goal of Racon is to generate genomic consensus which is of similar or better quality compared to the output generated by assembly methods which employ both error correction and consensus steps, while providing a speedup of several times compared to those methods. 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It leverages the OMA database and a set of input reads, bypassing many of the standard steps typically required in phylogenomic analysis. In particular, it avoids for read filtering, assembly, gene prediction, gene annotation, all-vs-all comparison, orthology prediction, alignment, and concatenation. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False -read_it_and_keep read_it_and_keep Rapid decontamination of SARS-CoV-2 sequencing reads 2022-01-28 https://github.com/GenomePathogenAnalysisService/read-it-and-keep 0.2.2 read-it-and-keep 0.3.0 To update Sequence Analysis Filtering, Genome alignment Filtering, Genome alignment Pathology, Genomics Pathology, Genomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/read_it_and_keep https://github.com/galaxyproject/tools-iuc/tree/main/tools/read_it_and_keep read_it_and_keep read_it_and_keep Read-it-and-keep is a bioinformatics tool designed to filter and extract sequencing reads according to user-defined criteria, such as the presence of specific motifs or coverage of regions of interest. This type of filtering can be particularly useful for targeted analyses, where only relevant sequences are retained for further study, optimising computing and storage resources. 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 81 81 3781 3781 8 8 9 9 0 0 0 0 0 0 0 0 3790 3790 89 89 https://usegalaxy.eu/published/workflow?id=3fb550d7c2bc390a, https://usegalaxy.eu/published/workflow?id=4a764275d4bf9f31, https://usegalaxy.eu/published/workflow?id=629e57958afed44c, https://usegalaxy.eu/published/workflow?id=7c986f4d14c6a539, https://usegalaxy.eu/published/workflow?id=d88145e7475e0b7b, https://usegalaxy.eu/published/workflow?id=d967194ca51ff11e, https://workflowhub.eu/workflows/519?version=1, https://workflowhub.eu/workflows/521?version=1 True False -reago reago fasta Reago is tool to assembly 16S ribosomal RNA recovery from metagenomic data. 2015-12-09 https://github.com/chengyuan/reago-1.1 1.1 reago 1.1 Up-to-date Metagenomics, RNA Sequence assembly Sequence assembly Sequence assembly, RNA, Metagenomics, Microbiology Sequence assembly, RNA, Metagenomics, Microbiology rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago reago REAGO This is an assembly tool for 16S ribosomal RNA recovery from metagenomic data. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 7 18 18 0 0 0 0 0 0 0 0 0 0 0 0 18 18 7 7 True False -recentrifuge recentrifuge html, txt, tabular, xlsx """With Recentrifuge, researchers can analyze results from taxonomic classifiers using interactive charts with emphasis on the confidence level of the classifications.In addition to contamination-subtracted samples.Recentrifuge provides shared and exclusive taxa per sample,thus enabling robust contamination removal and comparative analysis in environmental and clinical metagenomics.""" 2022-05-04 https://github.com/khyox/recentrifuge 1.16.1 recentrifuge 2.1.1 To update Metagenomics 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https://usegalaxy.org/published/workflow?id=de9bf4c1024f8d53, https://usegalaxy.org/published/workflow?id=dfd73857c0eb2a21, https://usegalaxy.org/published/workflow?id=f378960ee55f567e, https://workflowhub.eu/workflows/1052?version=11, https://workflowhub.eu/workflows/1644?version=1, https://workflowhub.eu/workflows/1674?version=2, https://workflowhub.eu/workflows/1881?version=2, https://workflowhub.eu/workflows/1882?version=3, https://workflowhub.eu/workflows/2043?version=1 ecology/bacterial-isolate-species-contamination-checking, sequence-analysis/quality-contamination-control True False -remove_terminal_stop_codons remove_terminal_stop_codons fasta Remove terminal stop codons from coding sequences 2025-12-04 https://github.com/veg/CAPHEINE 1.0.0 biopython 1.70 To update Phylogenetics, Sequence Analysis, Fasta Manipulation iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/remove_terminal_stop_codons https://github.com/galaxyproject/tools-iuc/tree/main/tools/remove_terminal_stop_codons 1 0 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False -repeatexplorer2 repeatexplorer_clustering html Tool for annotation of repeats from unassembled shotgun reads. 2023-11-01 https://github.com/repeatexplorer/repex_tarean 2.3.8 To update Genome annotation gga https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 83 83 369 369 0 0 0 0 0 0 0 0 0 0 0 0 369 369 83 83 True False -roary roary tabular, fasta, csv, nhx, dot, embl, txt Roary the pangenome pipeline 2017-06-21 https://sanger-pathogens.github.io/Roary/ 3.13.0 roary 3.13.0 Up-to-date Sequence Analysis Genome assembly Genome assembly DNA, Genomics, Mapping DNA, Genomics, Mapping iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/roary https://github.com/galaxyproject/tools-iuc/tree/main/tools/roary roary Roary A high speed stand alone pan genome pipeline, which takes annotated assemblies in GFF3 format (produced by Prokka (Seemann, 2014)) and calculates the pan genome. 1 1 1 1 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 2251 2377 21218 23887 2319 2454 17744 18851 653 749 5251 7169 47 47 187 187 50094 44400 5627 5270 https://usegalaxy.eu/published/workflow?id=46ef864fe9468894, https://usegalaxy.eu/published/workflow?id=628062a8cf93261f, https://usegalaxy.eu/published/workflow?id=94c3d329c31c712f, https://usegalaxy.eu/published/workflow?id=b1a799497c366eef, https://usegalaxy.eu/published/workflow?id=e16e524c557d7928, https://usegalaxy.org.au/published/workflow?id=05f3abecd4ddd4a1, https://usegalaxy.org.au/published/workflow?id=3fd2195b6928d5e0, https://usegalaxy.org/published/workflow?id=23a87246c646eb8a, https://usegalaxy.org/published/workflow?id=78d8b738f5715a8a, https://usegalaxy.org/published/workflow?id=80565301ada0d3eb True False -rseqc rseqc_FPKM_count, rseqc_RNA_fragment_size, rseqc_RPKM_saturation, rseqc_bam2wig, rseqc_bam_stat, rseqc_clipping_profile, rseqc_deletion_profile, rseqc_geneBody_coverage, rseqc_geneBody_coverage2, rseqc_infer_experiment, rseqc_inner_distance, rseqc_insertion_profile, rseqc_junction_annotation, rseqc_junction_saturation, rseqc_mismatch_profile, rseqc_read_GC, rseqc_read_NVC, rseqc_read_distribution, rseqc_read_duplication, rseqc_read_hexamer, rseqc_read_quality, rseqc_tin tabular, wig, txt, pdf an RNA-seq quality control package 2017-02-27 https://code.google.com/p/rseqc/ 5.0.3 rseqc 5.0.4 To update Convert Formats, Sequence Analysis, RNA, Transcriptomics, Visualization Data handling Data handling Sequencing Sequencing nilesh https://github.com/galaxyproject/tools-iuc/tree/main/tools/rseqc https://github.com/galaxyproject/tools-iuc/tree/main/tools/rseqc rseqc RSeQC Provides a number of useful modules that can comprehensively evaluate high throughput sequence data especially RNA-seq data. 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https://workflowhub.eu/workflows/1695?version=1, https://workflowhub.eu/workflows/688?version=1 transcriptomics/differential-isoform-expression, transcriptomics/minerva-pathways, transcriptomics/ref-based, transcriptomics/rna-seq-reads-to-counts True False -scoary scoary tabular, newick Scoary calculates the assocations between all genes in the accessory genome and the traits. 2021-03-18 https://github.com/AdmiralenOla/Scoary 1.6.16 scoary 1.6.16 Up-to-date Metagenomics Analysis Analysis Genotype and phenotype, Model organisms, GWAS study, Functional genomics Genotype and phenotype, Model organisms, GWAS study, Functional genomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/scoary https://github.com/galaxyproject/tools-iuc/tree/main/tools/scoary scoary Scoary Pan-genome wide association studies and is designed to take the gene_presence_absence.csv file from Roary as well as a traits file created by the user and calculate the assocations between all genes in the accessory genome (all genes that are present in i genomes where 1 < i < N) and the traits. It reports a list of genes sorted by strength of association per trait. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 113 113 1366 1366 0 0 0 0 0 0 0 0 0 0 0 0 1366 1366 113 113 True False -semibin semibin_bin, semibin_concatenate_fasta, semibin_generate_cannot_links, semibin_generate_sequence_features, semibin, semibin_train fasta, csv SemiBin: Semi-supervised Metagenomic Binning Using Siamese Neural Networks 2022-10-14 https://semibin.readthedocs.io/en/latest/ 2.1.0 semibin 2.2.1 To update Metagenomics Sequence assembly, Read binning Sequence assembly, Read binning Metagenomics, Machine learning, Microbial ecology, Sequence assembly Metagenomics, Machine learning, Microbial ecology, Sequence assembly iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin semibin SemiBin Command tool for metagenomic binning with semi-supervised deep learning using information from reference genomes. 1 6 6 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 6 0 0 53 53 2779 2779 9 9 18 18 0 0 0 0 2 2 75 75 2872 2872 64 64 https://usegalaxy.eu/published/workflow?id=00f15824c7a9b196, https://usegalaxy.eu/published/workflow?id=0563f58718be932d, https://usegalaxy.eu/published/workflow?id=1e5f1d9a51032e44, https://usegalaxy.eu/published/workflow?id=43098b8afe78b071, https://usegalaxy.eu/published/workflow?id=7ecd92cb382d8168, https://usegalaxy.eu/published/workflow?id=97312d273b6e8bd9, https://usegalaxy.eu/published/workflow?id=ce5c9287a67e6085, https://workflowhub.eu/workflows/1352?version=4, https://workflowhub.eu/workflows/2028?version=1, https://workflowhub.eu/workflows/2100?version=2 microbiome/metagenomics-binning True False -seqkit seqkit_fx2tab, seqkit_grep, seqkit_head, seqkit_locate, seqkit_sort, seqkit_split2, seqkit_stats, seqkit_translate tabular, txt A cross-platform and ultrafast toolkit for FASTA/Q file manipulation 2022-06-01 https://bioinf.shenwei.me/seqkit/ 2.13.0 seqkit 2.13.0 Up-to-date Sequence Analysis DNA transcription, Sequence trimming, DNA translation, Sequence conversion DNA transcription, Sequence trimming, DNA translation Database management, Sequence analysis Database management, Sequence analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqkit https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqkit seqkit seqkit FASTA and FASTQ are basic and ubiquitous formats for storing nucleotide and protein sequences. Common manipulations of FASTA/Q file include converting, searching, filtering, deduplication, splitting, shuffling, and sampling. Existing tools only implement some of these manipulations, and not particularly efficiently, and some are only available for certain operating systems. Furthermore, the complicated installation process of required packages and running environments can render these programs less user friendly. SeqKit demonstrates competitive performance in execution time and memory usage compared to similar tools. The efficiency and usability of SeqKit enable researchers to rapidly accomplish common FASTA/Q file manipulations. 3 6 8 5 0 0 0 0 0 0 0 4 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 0 396 396 13926 13926 0 0 0 0 120 120 2190 2190 69 69 648 648 16764 16764 585 585 https://usegalaxy.org.au/published/workflow?id=7559224fc32dce3a, https://usegalaxy.org.au/published/workflow?id=7a0c4804e4d4c905, https://usegalaxy.org.au/published/workflow?id=ed3e48a73b5aaa56, https://workflowhub.eu/workflows/2024?version=4, https://workflowhub.eu/workflows/2036?version=1, https://workflowhub.eu/workflows/2038?version=1, https://workflowhub.eu/workflows/601?version=2, https://workflowhub.eu/workflows/602?version=2, https://workflowhub.eu/workflows/697?version=1 True False -seqprep seqprep fastq.gz Tool for merging paired-end Illumina reads and trimming adapters. 2024-01-15 https://github.com/jstjohn/SeqPrep 1.3.2 seqprep 1.3.2 Up-to-date Fastq Manipulation, Sequence Analysis Nucleic acid design Nucleic acid design Genomics, Sequence assembly, Sequencing, Probes and primers Genomics, Sequence assembly, Sequencing, Probes and primers iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqprep https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqprep seqprep SeqPrep Strips adapters and optionally merges overlapping paired-end (or paired-end contamination in mate-pair libraries) illumina style reads. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 227 227 3602 3602 0 0 0 0 0 0 0 0 0 0 0 0 3602 3602 227 227 microbiome/mgnify-amplicon True False -seqsero2 seqsero2 tabular, txt Salmonella serotype prediction from genome sequencing data 2023-11-07 https://github.com/denglab/SeqSero2 1.3.2 seqsero2 1.3.2 Up-to-date Sequence Analysis Genome indexing, Antimicrobial resistance prediction, Genome alignment Genome indexing, Antimicrobial resistance prediction, Genome alignment Whole genome sequencing, Sequence assembly, Genomics Whole genome sequencing, Sequence assembly, Genomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqsero2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqsero2 seqsero2 SeqSero2 "rapid and improved Salmonella serotype determination using whole genome sequencing data | SeqSero-Salmonella Serotyping by Whole Genome Sequencing | Salmonella Serotyping by Whole Genome Sequencing | Online version: http://www.denglab.info/SeqSero2 | Salmonella serotype prediction from genome sequencing data | Citation: SeqSero, Zhang et al. 2015; SeqSero2, Zhang et al. 2019 | Salmonella serotype derterminants databases | Upon executing the command, a directory named 'SeqSero_result_Time_your_run' will be created. Your result will be stored in 'SeqSero_result.txt' in that directory. And the assembled alleles can also be found in the directory if using ""-m a"" (allele mode)" 0 0 1 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 116 116 14011 14011 0 0 0 0 0 0 0 0 2 2 2 2 14013 14013 118 118 https://usegalaxy.eu/published/workflow?id=fde21b5f5c169114, https://workflowhub.eu/workflows/407?version=1 True False -shovill shovill txt, fasta, unsorted.bam, gfa1 Faster de novo assembly pipeline based around Spades 2017-10-24 https://github.com/tseemann/shovill 1.4.2 shovill 1.4.2 Up-to-date Assembly Genome assembly Genome assembly Genomics, Microbiology, Sequence assembly Genomics, Microbiology, Sequence assembly iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/shovill https://github.com/galaxyproject/tools-iuc/tree/main/tools/shovill shovill shovill Shovill is a pipeline for assembly of bacterial isolate genomes from Illumina paired-end reads. Shovill uses SPAdes at its core, but alters the steps before and after the primary assembly step to get similar results in less time. Shovill also supports other assemblers like SKESA, Velvet and Megahit, so you can take advantage of the pre- and post-processing the Shovill provides with those too. 1 1 1 1 0 0 0 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 3269 3491 70801 76107 4933 5212 51724 55190 1425 1669 30312 35794 83 83 9136 9136 176227 161973 10455 9710 https://usegalaxy.eu/published/workflow?id=0404013d5c27210d, https://usegalaxy.eu/published/workflow?id=1ea8bfbe6cb04531, https://usegalaxy.eu/published/workflow?id=309fc4fc2e0da89c, https://usegalaxy.eu/published/workflow?id=3303a04887a47675, https://usegalaxy.eu/published/workflow?id=3d937648809ca4e7, https://usegalaxy.eu/published/workflow?id=4216424f032c055f, https://usegalaxy.eu/published/workflow?id=42c0da2e86318b37, https://usegalaxy.eu/published/workflow?id=4f245ac304ab76d9, https://usegalaxy.eu/published/workflow?id=5b893b69a1b6748f, https://usegalaxy.eu/published/workflow?id=5b940b283d91d99d, https://usegalaxy.eu/published/workflow?id=628062a8cf93261f, 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https://workflowhub.eu/workflows/407?version=1, https://workflowhub.eu/workflows/470?version=1 assembly/mrsa-illumina True False -sistr_cmd sistr_cmd csv, json, tabular, fasta SISTR in silico serotyping tool 2017-02-20 https://github.com/phac-nml/sistr_cmd 1.1.3 sistr_cmd 1.1.3 Up-to-date Sequence Analysis Genome assembly, Visualisation, Multilocus sequence typing Genome assembly, Visualisation, Multilocus sequence typing Whole genome sequencing, Immunoproteins and antigens, Sequence assembly, Zoology, Public health and epidemiology Whole genome sequencing, Immunoproteins and antigens, Sequence assembly, Zoology, Public health and epidemiology nml https://github.com/phac-nml/sistr_cmd https://github.com/phac-nml/galaxy_tools/tree/master/tools/sistr_cmd SISTR SISTR The Salmonella In Silico Typing Resource (SISTR) is an open-source and freely available web application for rapid in silico typing and serovar prediction from Salmonella genome assemblies using cgMLST and O and H antigen gene searching. 0 1 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 395 397 5345 5466 0 0 0 0 91 95 907 1010 0 0 0 0 6476 6252 492 486 https://usegalaxy.eu/published/workflow?id=628062a8cf93261f, https://usegalaxy.eu/published/workflow?id=94c3d329c31c712f, https://usegalaxy.eu/published/workflow?id=cbe3769f1abb9fa5, https://usegalaxy.eu/published/workflow?id=fde21b5f5c169114, https://usegalaxy.org.au/published/workflow?id=2120112358db8e01, https://usegalaxy.org.au/published/workflow?id=92fcdd490831c6c5, https://workflowhub.eu/workflows/407?version=1 True False -smallgenomeutilities smgu_frameshift_deletions_checks tabular Set of utilities for manipulating small viral genome data. 2023-05-30 https://github.com/cbg-ethz/smallgenomeutilities 0.5.2 smallgenomeutilities 0.5.2 Up-to-date Sequence Analysis Read pre-processing, Sequence alignment, Genetic variation analysis Read pre-processing, Sequence alignment, Genetic variation analysis Genomics, Population genetics, Workflows, Virology, Sequencing Genomics, Population genetics, Workflows, Virology, Sequencing iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/smallgenomeutilities https://github.com/galaxyproject/tools-iuc/tree/main/tools/smallgenomeutilities v-pipe V-pipe Bioinformatics pipeline for the analysis of next-generation sequencing data derived from intra-host viral populations. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 15 15 168 168 0 0 0 0 0 0 0 0 0 0 0 0 168 168 15 15 True False -smalt smalt cigar SMALT aligns DNA sequencing reads with a reference genome. 2017-09-19 http://www.sanger.ac.uk/science/tools/smalt-0 0.7.6 smalt 0.7.6 Up-to-date Sequence Analysis nml https://sourceforge.net/projects/smalt/ https://github.com/phac-nml/galaxy_tools/tree/master/tools/smalt 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False -snap snap, snap_training gff, fasta, snaphmm SNAP is a general purpose gene finding program suitable for both eukaryotic and prokaryotic genomes. 2017-10-12 https://github.com/KorfLab/SNAP 2013_11_29 snap 2013_11_29 Up-to-date Sequence Analysis Gene prediction Gene prediction DNA, DNA polymorphism, Genetics DNA polymorphism, Genetics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/snap https://github.com/galaxyproject/tools-iuc/tree/main/tools/snap snap SNAP The Semi-HMM-based Nucleic Acid Parser is a gene prediction tool. 1 1 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 348 410 1443 1821 258 292 813 939 100 101 578 594 0 0 0 0 3354 2834 803 706 https://usegalaxy.eu/published/workflow?id=26ad77bc07a7e512, https://usegalaxy.eu/published/workflow?id=6ca20e710f4f3ffb, https://usegalaxy.org.au/published/workflow?id=7a87dfe5bdd30040, https://usegalaxy.org.au/published/workflow?id=7e40485d1ed45b7c, https://usegalaxy.org/published/workflow?id=c42c66d1b627c5a5, https://workflowhub.eu/workflows/1504?version=1 genome-annotation/annotation-with-maker True False -snippy snippy_core, snippy, snippy_clean_full_aln fasta, tabular, txt, vcf, gff3, bam, zip Contains the snippy tool for characterising microbial snps 2017-07-13 https://github.com/tseemann/snippy snippy 4.6.0 To update Sequence Analysis Phylogenetic tree visualisation, Phylogenetic tree generation, Variant calling Phylogenetic tree visualisation, Variant calling Genomics, Model organisms, DNA polymorphism, Phylogenetics Genomics, Model organisms, DNA polymorphism, Phylogenetics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/snippy https://github.com/galaxyproject/tools-iuc/tree/main/tools/snippy snippy snippy Rapid haploid variant calling and core SNP phylogeny generation. 3 3 3 3 0 0 0 0 0 0 0 3 0 0 0 0 0 0 0 0 0 0 0 0 3 3 3 0 3483 3838 188403 199916 4057 4306 138187 142349 2223 2852 67168 78979 60 60 8769 8769 430013 402527 11056 9823 https://usegalaxy.eu/published/workflow?id=2b25eaebd3987612, https://usegalaxy.eu/published/workflow?id=2c79eee5ca5a3b09, 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https://usegalaxy.org/published/workflow?id=e7ce46762faccaac, https://usegalaxy.org/published/workflow?id=ee4679b3e9e830b7, https://workflowhub.eu/workflows/1035?version=1, https://workflowhub.eu/workflows/1573?version=1, https://workflowhub.eu/workflows/1639?version=1, https://workflowhub.eu/workflows/1647?version=2, https://workflowhub.eu/workflows/2049?version=1 evolution/mtb_transmission, variant-analysis/microbial-variants, variant-analysis/tb-variant-analysis True False -sonneityping sonneityping tabular Scripts for parsing Mykrobe predict results for Shigella sonnei. 2021-09-16 https://github.com/katholt/sonneityping 20210201 sonneityping 20210201 Up-to-date Sequence Analysis Antimicrobial resistance prediction, Variant calling, Genotyping Antimicrobial resistance prediction, Variant calling, Genotyping Whole genome sequencing, Genotype and phenotype, Genetic variation, Metagenomics Whole genome sequencing, Genotype and phenotype, Genetic variation, Metagenomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/sonneityping https://github.com/galaxyproject/tools-iuc/tree/main/tools/sonneityping sonneityping sonneityping Scripts for parsing Mykrobe predict results for Shigella sonnei. 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 2 2 2 2 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 2 True False -sortmerna bg_sortmerna bam, tabular, txt SortMeRNA is a software designed to rapidly filter ribosomal RNA fragments from metatransriptomic data produced by next-generation sequencers. 2015-02-28 http://bioinfo.lifl.fr/RNA/sortmerna/ 5.0.0 sortmerna 4.3.7 To update RNA Sequence similarity search, Sequence comparison, Sequence alignment analysis Sequence similarity search, Sequence alignment analysis Metatranscriptomics, Metagenomics Metatranscriptomics, Metagenomics rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna sortmerna SortMeRNA Sequence analysis tool for filtering, mapping and OTU-picking NGS reads. 1 1 1 1 0 0 0 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1135 1352 23920 26406 581 581 6479 6479 219 225 3668 3882 116 116 648 651 37418 34715 2274 2051 https://usegalaxy.eu/published/workflow?id=096b75501c8e0888, https://usegalaxy.eu/published/workflow?id=2cf09adb1ed6c3ec, https://usegalaxy.eu/published/workflow?id=385cc7df70d7916b, https://usegalaxy.eu/published/workflow?id=401746888e8b3aa8, https://usegalaxy.eu/published/workflow?id=4d32b1b3ac0a7161, https://usegalaxy.eu/published/workflow?id=5f0faac42b0a5062, https://usegalaxy.eu/published/workflow?id=69eddfde874af35b, https://usegalaxy.eu/published/workflow?id=72e3e5fdc766e24a, https://usegalaxy.eu/published/workflow?id=7ab70660e6235cf0, https://usegalaxy.eu/published/workflow?id=87cc0cd143a12c41, https://usegalaxy.eu/published/workflow?id=9382f9bbbdddb5ad, https://usegalaxy.eu/published/workflow?id=9472be79da012999, 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https://workflowhub.eu/workflows/1466?version=2 microbiome/metatranscriptomics, microbiome/metatranscriptomics-short True False -spades spades_biosyntheticspades, spades_coronaspades, spades_metaplasmidspades, metaspades, spades_metaviralspades, spades_plasmidspades, rnaspades, spades_rnaviralspades, spades fasta, txt SPAdes is an assembly toolkit containing various assembly pipelines. It implements the following 4 stages: assembly graph construction, k-bimer adjustment, construction of paired assembly graph and contig construction. 2016-12-21 https://github.com/ablab/spades 4.2.0 spades 4.2.0 Up-to-date Assembly, RNA, Metagenomics Genome assembly Genome assembly Sequence assembly Sequence assembly iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/spades https://github.com/galaxyproject/tools-iuc/tree/main/tools/spades spades SPAdes St. Petersburg genome assembler – is intended for both standard isolates and single-cell MDA bacteria assemblies. SPAdes 3.9 works with Illumina or IonTorrent reads and is capable of providing hybrid assemblies using PacBio, Oxford Nanopore and Sanger reads. Additional contigs can be provided and can be used as long reads. 9 9 9 9 0 1 0 0 0 2 3 3 0 0 0 0 0 0 0 3 0 0 0 0 3 9 3 0 8250 8882 104429 116176 14023 14731 147425 154112 5211 6722 62902 76811 373 380 2677 2762 349861 317433 30715 27857 https://usegalaxy.eu/published/workflow?id=007ce6405d196df3, https://usegalaxy.eu/published/workflow?id=02631612a43a4d9b, https://usegalaxy.eu/published/workflow?id=1860e02bcb894a64, https://usegalaxy.eu/published/workflow?id=37da7b42cb063a3a, https://usegalaxy.eu/published/workflow?id=49c46d7653d6c349, https://usegalaxy.eu/published/workflow?id=579ff83177c5ee09, https://usegalaxy.eu/published/workflow?id=62c47e3c9d4f3aa3, https://usegalaxy.eu/published/workflow?id=7b755497d168cb13, https://usegalaxy.eu/published/workflow?id=7ecd92cb382d8168, https://usegalaxy.eu/published/workflow?id=87231a6a7938cb95, https://usegalaxy.eu/published/workflow?id=8c7958cb05fba814, https://usegalaxy.eu/published/workflow?id=9382f9bbbdddb5ad, 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https://workflowhub.eu/workflows/1634?version=1, https://workflowhub.eu/workflows/2046?version=1, https://workflowhub.eu/workflows/2047?version=1, https://workflowhub.eu/workflows/2048?version=1, https://workflowhub.eu/workflows/434?version=1, https://workflowhub.eu/workflows/52?version=1, https://workflowhub.eu/workflows/68?version=1 assembly/debruijn-graph-assembly, assembly/metagenomics-assembly, microbiome/metagenomics-assembly True False -spotyping spotyping txt, excel.xls, pdf SpoTyping allows fast and accurate in silico Mycobacterium spoligotyping from sequence reads 2018-05-07 https://github.com/xiaeryu/SpoTyping-v2.0 2.1 spotyping 2.1 Up-to-date Sequence Analysis Variant pattern analysis Variant pattern analysis Microbiology, Sequencing, Sequence composition, complexity and repeats, Genetic variation Microbiology, Sequencing, Sequence composition, complexity and repeats, Genetic variation iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/spotyping https://github.com/galaxyproject/tools-iuc/tree/main/tools/spotyping spotyping SpoTyping Fast and accurate in silico Mycobacterium spoligotyping from sequence reads. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 34 34 2042 2042 0 0 0 0 0 0 0 0 0 0 0 0 2042 2042 34 34 True False -squirrel squirrel_phylo, squirrel_qc nexus, fasta, svg, png, csv QC and Phylogenetic analysis of MPXV 2025-01-16 https://github.com/aineniamh/squirrel 1.0.13 squirrel 1.3.2 To update Phylogenetics Phylogenetic analysis, Sequencing quality control Phylogenetic analysis, Sequencing quality control Virology Virology iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/squirrel https://github.com/galaxyproject/tools-iuc/tree/main/tools/squirrel squirrel squirrel Some QUIck Reconstruction to Resolve Evolutionary LinksSquirrel provides a rapid way of producing reliable alignments for MPXV and also enable maximum-likelihood phylogenetics pipeline tree estimation. 0 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 7 7 0 0 0 0 41 41 193 193 0 0 0 0 200 200 43 43 https://usegalaxy.org.au/published/workflow?id=b9fd488b0938d323 True False -sr_bowtie bowtieForSmallRNA tabular bowtie wrapper tool to align small RNA sequencing reads 2017-09-02 http://artbio.fr 2.3.1 bowtie 1.3.1 To update RNA, Next Gen Mappers Microbiology, Biology Microbiology artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie https://github.com/ARTbio/tools-artbio/tree/main/tools/sr_bowtie sr_bowtie sr_bowtie "Bowtie_ is a short read aligner designed to be ultrafast and memory-efficient. It is developed by Ben Langmead and Cole Trapnell. Please cite: Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biology 10:R25... _Bowtie: http://bowtie-bio.sourceforge.net/index.shtmlA generic ""Map with Bowtie for Illumina"" Galaxy tool is available in the main Galaxy distribution.However, this Bowtie wrapper tool only takes FASTQ files as inputs.The sRbowtie wrapper works with short (-v bowtie mode) reads inputs, in fasta or fastq format, and proposes a simplified set of configurations suited to small RNA analysis." 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 2 2 98 98 0 0 0 0 0 0 0 0 98 98 2 2 True False -srst2 srst2 tabular, fasta SRST2 Short Read Sequence Typing for Bacterial Pathogens 2022-08-22 http://katholt.github.io/srst2/ 0.2.0 samtools 1.23.1 To update Metagenomics Multilocus sequence typing Multilocus sequence typing Whole genome sequencing, Public health and epidemiology, Comparative genomics Whole genome sequencing, Public health and epidemiology, Comparative genomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/srst2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/srst2 srst2 srst2 Short Read Sequence Typing for Bacterial Pathogens 0 0 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 68 68 407 407 1 1 71 71 0 0 0 0 0 0 0 0 478 478 69 69 https://workflowhub.eu/workflows/407?version=1 True False -srst2 srst2 bam, tabular, fasta Short Read Sequence Typing for Bacterial Pathogens 2015-12-02 0.3.7 srst2 0.2.0 To update Sequence Analysis nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/srst2 0 0 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 68 68 407 407 1 1 71 71 0 0 0 0 0 0 0 0 478 478 69 69 https://workflowhub.eu/workflows/407?version=1 True False -staramr staramr_search tabular, txt, xlsx Scan genome contigs against the ResFinder, PlasmidFinder, and PointFinder antimicrobial resistance databases. 2024-09-19 https://github.com/phac-nml/staramr 0.12.2 staramr 0.12.2 Up-to-date Sequence Analysis Antimicrobial resistance prediction Antimicrobial resistance prediction Microbiology, Public health and epidemiology, Infectious disease Microbiology, Public health and epidemiology, Infectious disease iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/staramr https://github.com/galaxyproject/tools-iuc/tree/main/tools/staramr staramr staramr staramr (*AMR) scans bacterial genome contigs against the ResFinder, PointFinder, and PlasmidFinder databases (used by the ResFinder webservice and other webservices offered by the Center for Genomic Epidemiology) and compiles a summary report of detected antimicrobial resistance genes. The star|* in staramr indicates that it can handle all of the ResFinder, PointFinder, and PlasmidFinder databases. 1 1 1 1 0 0 0 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 2921 3072 31443 33124 2130 2130 14763 14763 1173 1182 8989 9237 97 97 9838 9838 66962 65033 6481 6321 https://usegalaxy.eu/published/workflow?id=007ce6405d196df3, https://usegalaxy.eu/published/workflow?id=152223c8aed27357, https://usegalaxy.eu/published/workflow?id=1ce523ef51f47134, https://usegalaxy.eu/published/workflow?id=249c115413f17f28, https://usegalaxy.eu/published/workflow?id=2e0075791f7fa384, https://usegalaxy.eu/published/workflow?id=32d2f5340098bcbd, https://usegalaxy.eu/published/workflow?id=32de10b9de8a999a, https://usegalaxy.eu/published/workflow?id=34df701aa23a9fb3, https://usegalaxy.eu/published/workflow?id=374797e58377c40f, https://usegalaxy.eu/published/workflow?id=39837ca09374598b, https://usegalaxy.eu/published/workflow?id=41d207d06a32ba05, https://usegalaxy.eu/published/workflow?id=44e53ea319e07daa, https://usegalaxy.eu/published/workflow?id=46b6812817c57a01, https://usegalaxy.eu/published/workflow?id=4ddbffe4b3fef275, https://usegalaxy.eu/published/workflow?id=628062a8cf93261f, https://usegalaxy.eu/published/workflow?id=6d87481be47902e1, https://usegalaxy.eu/published/workflow?id=7aa32aba3fde0708, https://usegalaxy.eu/published/workflow?id=9219557de92e0203, https://usegalaxy.eu/published/workflow?id=94c3d329c31c712f, https://usegalaxy.eu/published/workflow?id=a06b1ed5cd25922f, https://usegalaxy.eu/published/workflow?id=abe85758e77c78e6, https://usegalaxy.eu/published/workflow?id=b203dec6ee6da2fd, https://usegalaxy.eu/published/workflow?id=b2b46e71046b1999, https://usegalaxy.eu/published/workflow?id=b4de76c0a4d0e23a, https://usegalaxy.eu/published/workflow?id=b60a3e0427f2f519, https://usegalaxy.eu/published/workflow?id=c48807045e258dd8, https://usegalaxy.eu/published/workflow?id=d0339e4a794f4922, https://usegalaxy.eu/published/workflow?id=dc7107896a3f2964, https://usegalaxy.eu/published/workflow?id=e37cc0b64774561b, https://usegalaxy.eu/published/workflow?id=ea485dbabc76488d, https://usegalaxy.eu/published/workflow?id=eb5ab8bc82569eee, https://usegalaxy.eu/published/workflow?id=ecf48fa50af560a0, https://usegalaxy.eu/published/workflow?id=f30f8e7dcd50cd0d, https://usegalaxy.eu/published/workflow?id=ffd365c037373673, https://usegalaxy.org.au/published/workflow?id=05f3abecd4ddd4a1, https://usegalaxy.org.au/published/workflow?id=2120112358db8e01, https://usegalaxy.org.au/published/workflow?id=2e29b21cdec7d0cc, https://usegalaxy.org.au/published/workflow?id=35f39173f0ac9179, https://usegalaxy.org.au/published/workflow?id=92fcdd490831c6c5, https://usegalaxy.org.au/published/workflow?id=c9b7de574fb2f2d5, https://usegalaxy.org.au/published/workflow?id=d9571b3dfef34e5e, https://usegalaxy.org/published/workflow?id=2078a54de1f2628d, https://usegalaxy.org/published/workflow?id=2b4b1fe82258f303, https://usegalaxy.org/published/workflow?id=3c177fdf38311118, https://usegalaxy.org/published/workflow?id=547f86db467bf620, https://usegalaxy.org/published/workflow?id=aaf8e740b3f8e2c0, https://usegalaxy.org/published/workflow?id=d3dc805cd43b2737, https://usegalaxy.org/published/workflow?id=d4f0a7ccb09f1e55, https://usegalaxy.org/published/workflow?id=ef187f85b103d858, https://usegalaxy.org/published/workflow?id=f8fab0cd6fc30d92, https://usegalaxy.org/published/workflow?id=fde774a049875466, https://workflowhub.eu/workflows/1049?version=9, https://workflowhub.eu/workflows/1189?version=2, https://workflowhub.eu/workflows/1477?version=1, https://workflowhub.eu/workflows/1488?version=2, https://workflowhub.eu/workflows/2024?version=4, https://workflowhub.eu/workflows/406?version=1, https://workflowhub.eu/workflows/470?version=1 genome-annotation/amr-gene-detection, microbiome/plasmid-metagenomics-nanopore True False -stringmlst stringmlst tabular, txt, fastqsanger Rapid and accurate identification of the sequence type (ST) 2016-10-19 1.1.0 stringMLST 0.6.3 To update Sequence Analysis nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/stringmlst 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False -structure structure txt for using multi-locus genotype data to investigate population structure. 2017-09-22 https://web.stanford.edu/group/pritchardlab/structure.html 2.3.4 structure 2.3.4 Up-to-date Phylogenetics, Variant Analysis Genetic variation analysis Genetic variation analysis Population genetics Population genetics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/structure https://github.com/galaxyproject/tools-iuc/tree/main/tools/structure structure Structure The program structureis a free software package for using multi-locus genotype data to investigate population structure. Its uses include inferring the presence of distinct populations, assigning individuals to populations, studying hybrid zones, identifying migrants and admixed individuals, and estimating population allele frequencies in situations where many individuals are migrants or admixed. 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 138 155 3903 4354 0 0 0 0 0 0 0 0 3 3 330 330 4684 4233 158 141 True False -suite_qiime2_core 2022-08-29 To update Statistics, Sequence Analysis, Metagenomics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tool_collections/suite_qiime2_core 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False -sylph sylph_profile, sylph_query tabular sylph - fast and precise species-level metagenomic profiling with ANIs 2024-10-08 https://github.com/bluenote-1577/sylph 0.8.1 sylph 0.9.0 To update Metagenomics Taxonomic classification Taxonomic classification Metagenomics Metagenomics bgruening https://github.com/bgruening/galaxytools/main/tools/sylph https://github.com/bgruening/galaxytools/tree/master/tools/sylph sylph sylph fast and precise species-level metagenomic profiling with ANIs 2 0 2 2 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 9 9 257 257 1 1 1 1 0 0 0 0 1 1 12 12 270 270 11 11 https://usegalaxy.eu/published/workflow?id=7491883694fff308, https://usegalaxy.eu/published/workflow?id=cb2df493f5e334f7, https://workflowhub.eu/workflows/2068?version=2 True False -syri syri tabular, vcf Synteny and Rearrangement Identifier 2025-04-16 https://github.com/schneebergerlab/syri 1.7.1 syri 1.7.1 Up-to-date Sequence Analysis Haplotype mapping, Variant calling, Genotyping, Sequence assembly, Read mapping Haplotype mapping, Variant calling, Genotyping, Sequence assembly, Read mapping DNA polymorphism, Sequence assembly, DNA structural variation, Mapping, Sequencing DNA polymorphism, Sequence assembly, Mapping, Sequencing iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/syri https://github.com/galaxyproject/tools-iuc/tree/main/tools/syri SyRI SyRI SyRI is tool for finding genomic rearrangements and local sequence differences from whole-genome assemblies.Genomic differences range from single nucleotide differences to complex structural variations. Current methods typically annotate sequence differences ranging from SNPs to large indels accurately but do not unravel the full complexity of structural rearrangements, including inversions, translocations, and duplications, where highly similar sequence changes in location, orientation, or copy number. Here, we present SyRI, a pairwise whole-genome comparison tool for chromosome-level assemblies. SyRI starts by finding rearranged regions and then searches for differences in the sequences, which are distinguished for residing in syntenic or rearranged regions. This distinction is important as rearranged regions are inherited differently compared to syntenic regions. 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 22 22 84 84 0 0 0 0 0 0 0 0 5 5 76 76 160 160 27 27 https://usegalaxy.fr/published/workflow?id=356dced9687596b7, https://usegalaxy.fr/published/workflow?id=ce4acd38084ee9ef True False -t2ps Draw_phylogram pdf Draw phylogeny 2014-01-27 https://bitbucket.org/natefoo/taxonomy 1.0.0 taxonomy 0.10.5 To update Metagenomics Phylogenetic tree visualisation Phylogenetic tree visualisation Phylogenomics Phylogenomics devteam https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/t2ps https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/t2ps t2ps Draw phylogeny """Given taxonomy representation (produced by *Fetch taxonomic representation* tool) this utility produces a graphical representations of phylogenetic tree in PDF format."" - Galaxy tool wrapper" 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 64 93 405 479 13 1240 102 7952 0 0 0 0 0 0 0 0 8431 507 1333 77 https://usegalaxy.org/published/workflow?id=19c9c8cc3c813bda, https://usegalaxy.org/published/workflow?id=2f7638035fb889ac, https://usegalaxy.org/published/workflow?id=55aa743125c2465d, https://usegalaxy.org/published/workflow?id=59347cc210c4cdbc, https://usegalaxy.org/published/workflow?id=7294f75ad01ca7ed, https://usegalaxy.org/published/workflow?id=7b67ffcf1b7c2232, https://usegalaxy.org/published/workflow?id=85d825931edf4a64, https://usegalaxy.org/published/workflow?id=896d29573ea3e574, https://usegalaxy.org/published/workflow?id=d851f8436497dd1c True False -t2t_report t2t_report tabular Summarize taxonomy 2014-01-27 https://bitbucket.org/natefoo/taxonomy 1.0.0 taxonomy 0.10.5 To update Metagenomics devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/t2t_report https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/t2t_report 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 55 82 745 1071 16 1143 118 7194 0 0 0 0 0 0 0 0 8265 863 1225 71 https://usegalaxy.org/published/workflow?id=19c9c8cc3c813bda, https://usegalaxy.org/published/workflow?id=2f7638035fb889ac, https://usegalaxy.org/published/workflow?id=55aa743125c2465d, https://usegalaxy.org/published/workflow?id=59347cc210c4cdbc, https://usegalaxy.org/published/workflow?id=7b67ffcf1b7c2232, https://usegalaxy.org/published/workflow?id=85d825931edf4a64, https://usegalaxy.org/published/workflow?id=896d29573ea3e574, https://usegalaxy.org/published/workflow?id=d851f8436497dd1c True False -t_coffee t_coffee clustal, nhx, fasta, msf, phylip, pir, txt, html T-Coffee 2016-12-13 https://tcoffee.org/ 13.45.0.4846264 t-coffee 13.46.0.919e8c6b To update Sequence Analysis earlhaminst https://github.com/EarlhamInst/earlham-galaxytools/tree/main/tools/t_coffee https://github.com/EarlhamInst/earlham-galaxytools/tree/main/tools/t_coffee 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 274 311 3958 9664 1 1 1 1 0 0 0 0 0 0 0 0 9665 3959 312 275 True False -taxonkit name2taxid, profile2cami tabular, tsv TaxonKit - A Practical and Efficient NCBI Taxonomy Toolkit 2024-07-26 https://bioinf.shenwei.me/taxonkit/ 0.20.0 taxonkit 0.20.0 Up-to-date Metagenomics Formatting, Data retrieval Formatting, Data retrieval Taxonomy, Biotechnology, Ecology Taxonomy, Biotechnology, Ecology iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/taxonkit https://github.com/galaxyproject/tools-iuc/tree/main/tools/taxonkit taxonkit TaxonKit TaxonKit is a practical and efficient NCBI taxonomy toolkit. 1 1 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 12 12 1094 1094 0 0 0 0 0 0 0 0 0 0 0 0 1094 1094 12 12 https://usegalaxy.eu/published/workflow?id=cf0159c14418525e, https://usegalaxy.eu/published/workflow?id=e4dabaf57668dbd1, 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We call those tools taxonomic profilers. They each come with their own particular tabular output format. Across the profilers, relative abundances can be reported in read counts, fractions, or percentages, as well as any number of additional columns with extra information. We therefore decided to take the lessons learnt to heart and provide our own solution to deal with this pasticcio. With taxpasta you can ingest all of those formats and, at a minimum, output taxonomy identifiers and their integer counts. 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Each terminator found by the program is assigned a confidence value that estimates its probability of being a true terminator 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 59 62 467 502 49 55 170 216 0 0 0 0 0 0 0 0 718 637 117 108 True False -treebest_best treebest_best nhx TreeBeST best 2015-08-06 https://treesoft.sourceforge.net/treebest.shtml 1.9.2.post0 treebest 1.9.2.post1 To update Phylogenetics Phylogenetic tree visualisation, Phylogenetic analysis, Phylogenetic inference (from molecular sequences) Phylogenetic tree visualisation, Phylogenetic inference (from molecular sequences) Phylogenetics Phylogenetics earlhaminst https://github.com/EarlhamInst/earlham-galaxytools/tree/main/tools/TreeBest https://github.com/EarlhamInst/earlham-galaxytools/tree/main/tools/TreeBest treebest TreeBeST TreeBeST, which stands for (gene) Tree Building guided by Species Tree, is a versatile program that builds, manipulates and displays phylogenetic trees. 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trycycler 0.5.6 To update Assembly Genome assembly, Sequence trimming, Scaffold gap completion, Sequence assembly validation Genome assembly, Sequence trimming, Scaffold gap completion, Sequence assembly validation Sequence assembly, DNA, Human biology, Whole genome sequencing, Genomics Sequence assembly, DNA, Human biology, Whole genome sequencing, Genomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/trycycler https://github.com/galaxyproject/tools-iuc/tree/main/tools/trycycler trycycler Trycycler Trycycler: consensus long-read assemblies for bacterial genomes 0 5 5 5 0 0 0 0 0 5 0 5 0 0 0 0 0 0 0 0 0 0 0 0 0 5 0 0 122 122 15743 15743 0 0 0 0 57 57 6233 6233 3 3 27 27 22003 22003 182 182 True False -tsebra tsebra gtf, txt This tool has been developed to combine BRAKER predictions. 2023-10-19 https://github.com/Gaius-Augustus/TSEBRA 1.1.2.5 tsebra 1.1.2.5 Up-to-date Genome annotation Homology-based gene prediction, Alternative splicing prediction Homology-based gene prediction, Alternative splicing prediction Gene expression, RNA-Seq, Gene transcripts, Model organisms Gene expression, RNA-Seq, Gene transcripts, Model organisms iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/tsebra https://github.com/galaxyproject/tools-iuc/tree/main/tools/tsebra tsebra TSEBRA TSEBRA is a combiner tool that selects transcripts from gene predictions based on the support by extrisic evidence in form of introns and start/stop codons. 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https://usegalaxy.org.au/published/workflow?id=050a66ff6d4c2b53, https://usegalaxy.org.au/published/workflow?id=f9f685d6150e48c5, https://usegalaxy.org/published/workflow?id=3f797bfb67130883, https://workflowhub.eu/workflows/1219?version=1, https://workflowhub.eu/workflows/1433?version=1, https://workflowhub.eu/workflows/1443?version=2, https://workflowhub.eu/workflows/1450?version=1, https://workflowhub.eu/workflows/1482?version=1 microbiome/clinical-mp-5-data-interpretation, proteomics/clinical-mp-5-data-interpretation, proteomics/metaproteomics, proteomics/metaquantome-data-creation True False -uniprotxml_downloader uniprotxml_downloader uniprotxml Download UniProt proteome in XML or fasta format 2016-03-08 https://www.uniprot.org/help/programmatic_access 2.5.0 requests To update Proteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader 1 1 1 0 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proteomics/clinical-mp-1-database-generation, proteomics/clinical-mp-3-verification True False -usher usher_matutils, usher_ripples, usher txt, tabular, vcf, protobuf3, json, newick UShER toolkit wrappers 2021-05-11 https://github.com/yatisht/usher 0.6.6 usher 0.6.6 Up-to-date Phylogenetics Classification, Phylogenetic tree visualisation, Phylogenetic inference (from molecular sequences) Classification, Phylogenetic tree visualisation, Phylogenetic inference (from molecular sequences) Phylogeny, Evolutionary biology, Cladistics, Genotype and phenotype, Phylogenomics Cladistics, Genotype and phenotype, Phylogenomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher usher usher The UShER toolkit includes a set of tools for for rapid, accurate placement of samples to existing phylogenies. While not restricted to SARS-CoV-2 phylogenetic analyses, it has enabled real-time phylogenetic analyses and genomic contact tracing in that its placement is orders of magnitude faster and more memory-efficient than previous methods. 0 0 3 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 5 5 1060 1060 0 0 0 0 0 0 0 0 0 0 0 0 1060 1060 5 5 True False -valet valet pdf A pipeline for detecting mis-assemblies in metagenomic assemblies. 2017-11-16 https://github.com/marbl/VALET valet 1.0 To update Metagenomics Sequence assembly, Sequence assembly visualisation Sequence assembly, Sequence assembly visualisation Metagenomics, Sequence assembly Metagenomics, Sequence assembly iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/valet https://github.com/galaxyproject/tools-iuc/tree/main/tools/valet valet VALET VALET is a pipeline for detecting mis-assemblies in metagenomic assemblies. 1 0 1 1 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 74 101 449 711 67 76 160 249 0 0 0 0 0 0 0 0 960 609 177 141 https://usegalaxy.eu/published/workflow?id=1524b189069b42a5, https://usegalaxy.eu/published/workflow?id=579ff83177c5ee09 True False -vapor vapor tabular, fasta Classify Influenza samples from raw short read sequence data 2022-08-24 https://github.com/wm75/vaporup 1.0.3 vapor 1.0.3 Up-to-date Sequence Analysis Data retrieval, De-novo assembly, Read mapping Data retrieval, De-novo assembly, Read mapping Whole genome sequencing, Mapping, Sequence assembly Whole genome sequencing, Mapping, Sequence assembly iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/vapor https://github.com/galaxyproject/tools-iuc/tree/main/tools/vapor vapor VAPOR VAPOR is a tool for classification of Influenza samples from raw short read sequence data for downstream bioinformatics analysis. VAPOR is provided with a fasta file of full-length sequences (> 20,000) for a given segment, a set of reads, and attempts to retrieve a reference that is closest to the sample strain. 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 188 188 197466 197466 127 127 1849 1849 0 0 0 0 0 0 0 0 199315 199315 315 315 https://usegalaxy.eu/published/workflow?id=4db391b405f2ed38, https://usegalaxy.eu/published/workflow?id=629e57958afed44c, https://usegalaxy.eu/published/workflow?id=7c986f4d14c6a539, https://usegalaxy.eu/published/workflow?id=a15dabcadb63b46d, https://usegalaxy.eu/published/workflow?id=c789ab71876c6ead, https://usegalaxy.eu/published/workflow?id=cd25f70f71683ab6, https://usegalaxy.eu/published/workflow?id=e353c6a106fa9e4c, https://usegalaxy.org/published/workflow?id=1518c8c50747a1c1, https://usegalaxy.org/published/workflow?id=97263f3308077ff0, https://usegalaxy.org/published/workflow?id=f7d9656f4cb77079, https://workflowhub.eu/workflows/1260?version=3 variant-analysis/aiv-analysis True False -varvamp varvamp txt, fasta, bed, tabular, pdf Variable VirusAMPlicons (varVAMP) is a tool to design primers for highly diverse viruses 2024-01-27 https://github.com/jonas-fuchs/varVAMP/ 1.3 varvamp 1.3.2 To update Sequence Analysis PCR primer design PCR primer design Virology, Probes and primers Virology, Probes and primers iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/varvamp https://github.com/galaxyproject/tools-iuc/tree/main/tools/varvamp varvamp varVAMP variable VirusAMPlicons (varVAMP) is a tool to design primers for highly diverse viruses. The input is an alignment of your viral (full-genome) sequences. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 55 55 912 912 0 0 0 0 0 0 0 0 0 0 0 0 912 912 55 55 https://workflowhub.eu/workflows/1627?version=1 sequence-analysis/viral_primer_design True False -vegan vegan_diversity, vegan_fisher_alpha, vegan_rarefaction tabular, png, txt an R package fo community ecologist 2015-08-27 https://cran.r-project.org/package=vegan 2.4-3 r-vegan 2.3_4 To update Metagenomics Standardisation and normalisation, Analysis Standardisation and normalisation, Analysis Ecology, Phylogenetics, Environmental science Ecology, Phylogenetics, Environmental science iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/vegan https://github.com/galaxyproject/tools-iuc/tree/main/tools/vegan vegan vegan Ordination methods, diversity analysis and other functions for community and vegetation ecologists 3 0 3 0 0 0 0 0 0 0 0 3 0 0 0 0 0 0 0 0 0 0 0 0 3 3 3 0 101 116 2314 2547 167 318 3493 5788 0 0 0 0 0 0 0 0 8335 5807 434 268 True False -velvet velvetg, velveth txt, afg, fasta, tabular, velvet de novo genomic assembler specially designed for short read sequencing technologies 2020-06-09 https://www.ebi.ac.uk/~zerbino/velvet/ velvet 1.2.10 To update Assembly Formatting, De-novo assembly Formatting, De-novo assembly Sequence assembly Sequence assembly devteam https://github.com/galaxyproject/tools-iuc/tree/main/tools/velvet https://github.com/galaxyproject/tools-iuc/tree/main/tools/velvet velvet Velvet A de novo genomic assembler specially designed for short read sequencing technologies, such as Solexa or 454 or SOLiD. 2 2 2 2 0 0 0 0 0 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 0 0 2567 2888 27621 32158 4951 5263 52855 57273 2097 2221 30746 33121 109 109 1097 1097 123649 112319 10481 9724 https://usegalaxy.eu/published/workflow?id=01dc0619e050dc91, https://usegalaxy.eu/published/workflow?id=56edd22d14392691, https://usegalaxy.eu/published/workflow?id=6d87481be47902e1, 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https://workflowhub.eu/workflows/2048?version=1 assembly/debruijn-graph-assembly, assembly/general-introduction True False -vibrant vibrant txt, fasta, genbank, tabular Virus Identification By iteRative ANnoTation 2024-09-11 https://github.com/AnantharamanLab/VIBRANT 1.2.1 vibrant 1.2.1 Up-to-date Metagenomics Sequence trimming, Scaffolding, Genome annotation Sequence trimming, Scaffolding, Genome annotation Metagenomics, Microbial ecology, Sequence assembly, Molecular interactions, pathways and networks, Endocrinology and metabolism Metagenomics, Microbial ecology, Sequence assembly, Molecular interactions, pathways and networks, Endocrinology and metabolism ufz https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/vibrant VIBRANT VIBRANT Automated recovery, annotation and curation of microbial viruses, and evaluation of virome function from genomic sequences.Virus Identification By iteRative ANnoTation.Discovery Environment Applications List.Created by upendra_35, last modified on Nov 04, 2019.If you find VIBRANT useful please consider citing our preprint on bioRxiv:.Kieft, K., Zhou, Z., and Anantharaman, K. (2019). VIBRANT: Automated recovery, annotation and curation of microbial viruses, and evaluation of virome function from genomic sequences. BioRxiv 855387.VIBRANT is a tool for automated recovery and annotation of bacterial and archaeal viruses, determination of genome completeness, and characterization of virome function from metagenomic assemblies.The QuickStart tutorial provides an introduction to basic DE functionality and navigation.Please work through the tutorial and use the intercom button on the bottom right of this page if you have any questions 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 65 65 1586 1586 0 0 0 0 0 0 0 0 0 0 0 0 1586 1586 65 65 https://usegalaxy.eu/published/workflow?id=87231a6a7938cb95, https://usegalaxy.eu/published/workflow?id=c62d65832377e376 True False -viralverify viralverify fasta, csv, txt, genbank Contigs prediction as viral, chromosomal, plasmidic or uncertain. 2025-07-04 https://github.com/ablab/viralVerify 1.1 viralverify 1.1 Up-to-date Sequence Analysis, Metagenomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/viralverify https://github.com/galaxyproject/tools-iuc/tree/main/tools/viralverify 0 0 1 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False -virannot virannot_blast2tsv, virannot_otu, virAnnot_rps2tsv tabular, xlsx, zip virAnnot wrappers 2025-08-04 https://github.com/marieBvr/virAnnot 1.2.0 biopython 1.70 To update Metagenomics Sequence annotation, Sequence clustering, Sequence cluster visualisation Sequence annotation, Sequence clustering, Sequence cluster visualisation Metagenomics, Virology, Microbial ecology Metagenomics, Virology, Microbial ecology iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/virannot https://github.com/galaxyproject/tools-iuc/tree/main/tools/virannot virannot virAnnot "VirAnnot was build to ease the assembly, blast search, taxonomic annotation and OTUs assignation of viral metagenomic HTS data. It is used in Virologie team of UMR1332 BFP laboratory at INRAE. VirAnnot also takes part of the Euphresco project ""Plant Health Bioinformatics Network"". See more.It is designed to identify viruses in plant metagenomic data but it can be used to assemble and annotate any sequences with the NCBI taxonomy." 0 0 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 16 16 336 336 0 0 0 0 0 0 0 0 2 2 14 14 350 350 18 18 https://usegalaxy.eu/published/workflow?id=17f73aba442315e6, https://usegalaxy.eu/published/workflow?id=86465932556bc96c True False -virsorter virsorter fasta, tabular, txt VirSorter2 applies a multi-classifier, expert-guided approach to detect diverse DNA and RNA virus genomes. 2024-06-20 https://github.com/jiarong/VirSorter2/ 2.2.4 virsorter 2.2.4 Up-to-date Metagenomics Taxonomic classification Taxonomic classification Metagenomics Metagenomics ufz https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/virsorter https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/virsorter virsorter virsorter Identify DNA and RNA virus sequences. 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 144 144 2379 2379 0 0 0 0 0 0 0 0 0 0 0 0 2379 2379 144 144 https://usegalaxy.eu/published/workflow?id=62392daea25a3980, https://usegalaxy.eu/published/workflow?id=87231a6a7938cb95 True False -vrhyme vrhyme tabular, txt, fasta Tool for dereplication and binning virus genomes from metagenomes. 2025-05-14 https://github.com/AnantharamanLab/vRhyme 1.1.0 vrhyme 1.1.0 Up-to-date Metagenomics Scaffolding, Read binning, Read mapping, Sequence trimming Scaffolding, Read binning, Read mapping, Sequence trimming Metagenomics, Microbial ecology, Model organisms, Machine learning, Sequence assembly Metagenomics, Microbial ecology, Model organisms, Machine learning, Sequence assembly bgruening https://github.com/bgruening/galaxytools/tree/master/tools/vrhyme https://github.com/bgruening/galaxytools/tree/master/tools/vrhyme vRhyme vRhyme vRhyme enables binning of viral genomes from metagenomes. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 6 47 47 0 0 0 0 0 0 0 0 0 0 0 0 47 47 6 6 https://usegalaxy.eu/published/workflow?id=62392daea25a3980 True False -vsearch vsearch_alignment, vsearch_chimera_detection, vsearch_clustering, vsearch_dereplication, vsearch_masking, vsearch_search, vsearch_shuffling, vsearch_sorting fasta, tabular VSEARCH including searching, clustering, chimera detection, dereplication, sorting, masking and shuffling of sequences. 2014-11-30 https://github.com/torognes/vsearch 2.8.3 vsearch 2.31.0 To update Sequence Analysis DNA mapping, Chimera detection DNA mapping, Chimera detection Metagenomics, Sequence analysis Metagenomics, Sequence analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/vsearch https://github.com/galaxyproject/tools-iuc/tree/main/tools/vsearch vsearch VSEARCH High-throughput search and clustering sequence analysis tool. It supports de novo and reference based chimera detection, clustering, full-length and prefix dereplication, reverse complementation, masking, all-vs-all pairwise global alignment, exact and global alignment searching, shuffling, subsampling and sorting. It also supports FASTQ file analysis, filtering and conversion. 8 8 8 8 0 0 0 0 0 8 8 8 0 0 0 0 0 0 0 8 0 0 0 0 8 8 8 0 226 259 13600 15795 323 642 14828 59476 82 97 6641 7811 11 12 285 286 83368 35354 1010 642 https://usegalaxy.eu/published/workflow?id=401746888e8b3aa8, https://usegalaxy.eu/published/workflow?id=4eb9dfe91fc2dc67, https://usegalaxy.eu/published/workflow?id=8a7caaa658744441, https://usegalaxy.eu/published/workflow?id=9382f9bbbdddb5ad, https://usegalaxy.eu/published/workflow?id=9cbba5de2cbeeb0f, https://usegalaxy.eu/published/workflow?id=a8417c63e9e22afb, https://usegalaxy.eu/published/workflow?id=c3aa516e78ca4191, https://usegalaxy.org.au/published/workflow?id=14e80b7f9f68ec2a, https://usegalaxy.org.au/published/workflow?id=869440d35a618836, https://workflowhub.eu/workflows/232?version=1, https://workflowhub.eu/workflows/233?version=1 True False + " To update Genome annotation Genome annotation, Antimicrobial resistance prediction, tRNA gene prediction, Formatting, Sequence assembly Genome annotation, Antimicrobial resistance prediction, tRNA gene prediction, Formatting, Sequence assembly Metagenomics, Sequence sites, features and motifs, Workflows, Functional, regulatory and non-coding RNA Metagenomics, Sequence sites, features and motifs, Workflows, Functional, regulatory and non-coding RNA iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/pharokka https://github.com/galaxyproject/tools-iuc/tree/master/tools/pharokka pharokka Pharokka Pharokka is a rapid standardised annotation tool for bacteriophage genomes and metagenomes. https://usegalaxy.eu/published/workflow?id=46ef864fe9468894, https://usegalaxy.eu/published/workflow?id=62392daea25a3980 0 1 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 766 766 16933 16933 1 1 21 21 117 117 1202 1202 0 0 0 0 18156 18156 884 884 True False +phi_toolkit_report phi_toolkit_report html, tsv Phage host interaction toolkit report generator 2025-06-04 https://git.ufz.de/borimcor/phage-host-analysis @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ bioconductor-biostrings 2.78.0 To update Metagenomics ufz https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phi-toolkit https://github.com/Helmholtz-UFZ/galaxy-tools/tree/master/tools/phi-toolkit https://usegalaxy.eu/published/workflow?id=c62d65832377e376 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False +phyloseq phyloseq_add_rank_names, phyloseq_from_biom, phyloseq_from_dada2, phyloseq_plot_bar, phyloseq_plot_ordination, phyloseq_plot_richness, phyloseq_tax_glom phyloseq, pdf, tabular Handling and analysis of high-throughput microbiome census data 2022-03-03 https://www.bioconductor.org/packages/release/bioc/html/phyloseq.html 1.54.0 bioconductor-phyloseq 1.54.0 Up-to-date Metagenomics Deposition, Analysis, Visualisation Deposition, Analysis, Visualisation Microbiology, Sequence analysis, Metagenomics Microbiology, Sequence analysis, Metagenomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/phyloseq https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq phyloseq phyloseq Provides a set of classes and tools to facilitate the import, storage, analysis, and graphical display of microbiome census data. https://usegalaxy.eu/published/workflow?id=466bdd8ba7b67264, https://usegalaxy.eu/published/workflow?id=e3918808605cf8cd, https://usegalaxy.org/published/workflow?id=4faff660f6defa10, https://workflowhub.eu/workflows/1395?version=2 microbiome/dada-16S 4 1 7 6 0 0 0 0 4 0 0 0 0 0 0 0 0 0 0 0 0 0 1 3 3 0 251 251 3161 3161 156 156 1022 1022 35 35 190 190 14 14 163 163 4536 4536 456 456 True False +phyml phyml nhx, txt PhyML is a phylogeny software based on the maximum-likelihood principle. 2019-05-27 http://www.atgc-montpellier.fr/phyml/ @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ phyml 3.3.20220408 To update Phylogenetics Phylogenetic tree generation (maximum likelihood and Bayesian methods) Phylogenetics, Bioinformatics, Phylogenetics Phylogenetics, Bioinformatics, Phylogenetics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/phyml https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml phyml PhyML Phylogenetic estimation software using Maximum Likelihood https://usegalaxy.fr/published/workflow?id=63b49f322ec366b5, https://usegalaxy.fr/published/workflow?id=894143d81af8dff0 0 1 1 1 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 286 335 2452 2654 0 0 0 0 215 240 1475 1564 79 79 334 334 4552 4261 654 580 True False +picrust picrust_categorize, picrust_compare_biom, picrust_format_tree_and_trait_table, picrust_metagenome_contributions, picrust_normalize_by_copy_number, picrust_predict_metagenomes tabular, nhx PICRUSt wrappers 2016-11-08 https://picrust.github.io/picrust/ 1.1.1 picrust 1.1.4 To update Metagenomics Phylogenetic reconstruction, Expression analysis, Genome annotation, DNA barcoding Phylogenetic reconstruction, Expression analysis, Genome annotation, DNA barcoding Metagenomics, Microbial ecology, Functional, regulatory and non-coding RNA, Metagenomic sequencing Metagenomics, Microbial ecology, Functional, regulatory and non-coding RNA, Metagenomic sequencing iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/picrust https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust picrust PICRUSt PICRUSt (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) is a bioinformatics software package designed to predict metagenome functional content from marker gene (e.g., 16S rRNA) surveys and full genomes. 0 6 6 6 0 0 0 0 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 0 44 63 562 1142 0 0 0 0 38 41 2348 2626 20 20 442 442 4210 3352 124 102 True False +picrust2 picrust2_add_descriptions, picrust2_hsp, picrust2_metagenome_pipeline, picrust2_pathway_pipeline, picrust2_pipeline, picrust2_place_seqs, picrust2_shuffle_predictions tabular PICRUSt2: Phylogenetic Investigation of Communities by Reconstruction of Unobserved States 2021-07-09 https://github.com/picrust/picrust2/wiki 2.5.3 picrust2 2.6.3 To update Metagenomics Phylogenetic reconstruction, Expression analysis, Rarefaction, Pathway analysis Phylogenetic reconstruction, Expression analysis, Rarefaction, Pathway analysis Metagenomics, Microbiology, Phylogenetics, Metagenomic sequencing Metagenomics, Microbiology, Phylogenetics, Metagenomic sequencing iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/picrust2 https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust2 picrust2 PICRUSt2 PICRUSt2 (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) is a software for predicting functional abundances based only on marker gene sequences. https://usegalaxy.eu/published/workflow?id=be9ff4159593cc34 0 7 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 0 0 327 327 6432 6432 1 1 1 1 64 64 2888 2888 0 0 0 0 9321 9321 392 392 True False +pimento pimento_are_there_primers, pimento_auto, pimento_choose_primer_cutoff, pimento_find_cutoffs, pimento_gen_bcv, pimento_std txt, fasta, tsv A PrIMEr infereNce TOolkit to facilitate large-scale calling of metabarcoding amplicon sequence variants. 2025-08-04 https://github.com/EBI-Metagenomics/PIMENTO 1.0.3 mi-pimento 1.0.3 Up-to-date Metagenomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/pimento https://github.com/galaxyproject/tools-iuc/tree/master/tools/pimento 0 0 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 2 2 0 0 0 0 0 0 0 0 0 0 0 0 2 2 1 1 True False +pirate pirate txt, tsv, fasta, newick, gfa1, gff, pdf Pangenome Iterative Refinement and Threshold Evaluation. 2026-01-31 https://github.com/SionBayliss/PIRATE 1.0.5 pirate 1.0.5 Up-to-date Sequence Analysis, Genome annotation iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/pirate https://github.com/galaxyproject/tools-iuc/tree/master/tools/pirate 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False +plasclass plasclass tabular PlasClass is a tool to classify sequences of plasmid or chromosomal origin 2025-07-31 https://github.com/Shamir-Lab/PlasClass @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ plasclass 0.1.1 To update Sequence Analysis Sequence classification, Sequence assembly, k-mer counting Sequence classification, Sequence assembly, k-mer counting Metagenomics, Sequence assembly, DNA, Metagenomic sequencing Metagenomics, Sequence assembly, DNA, Metagenomic sequencing iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/plasclass https://github.com/galaxyproject/tools-iuc/tree/master/tools/plasclass PlasClass PlasClass PlasClass is a tool for easy classification of sequences as either plasmid or chromosomal. For example, it can be used to classify the contigs in a (metagenomic) assembly. https://usegalaxy.eu/published/workflow?id=d0339e4a794f4922 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False +plasflow PlasFlow tabular, fasta PlasFlow - Prediction of plasmid sequences in metagenomic contigs. 2018-09-05 https://github.com/smaegol/PlasFlow @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ plasflow 1.1.0 To update Sequence Analysis Sequence analysis Sequence analysis Metagenomics, Sequence assembly, Mobile genetic elements, Machine learning Metagenomics, Sequence assembly, Mobile genetic elements, Machine learning iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/plasflow https://github.com/galaxyproject/tools-iuc/tree/master/tools/plasflow plasflow PlasFlow PlasFlow is a set of scripts used for prediction of plasmid sequences in metagenomic contigs. https://usegalaxy.eu/published/workflow?id=152223c8aed27357, https://usegalaxy.eu/published/workflow?id=249c115413f17f28, https://usegalaxy.eu/published/workflow?id=3081569659a45b9e, https://usegalaxy.eu/published/workflow?id=32d2f5340098bcbd, https://usegalaxy.eu/published/workflow?id=39837ca09374598b, https://usegalaxy.eu/published/workflow?id=44e53ea319e07daa, https://usegalaxy.eu/published/workflow?id=9219557de92e0203, https://usegalaxy.eu/published/workflow?id=b4de76c0a4d0e23a, https://usegalaxy.eu/published/workflow?id=c48807045e258dd8, https://usegalaxy.eu/published/workflow?id=dc7107896a3f2964, https://usegalaxy.org.au/published/workflow?id=d9571b3dfef34e5e, https://usegalaxy.org/published/workflow?id=33d90e718ce500ef, https://workflowhub.eu/workflows/1477?version=1, https://workflowhub.eu/workflows/406?version=1 microbiome/plasmid-metagenomics-nanopore 1 1 1 1 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 876 1004 55069 56639 757 797 7929 8195 87 87 3496 3496 0 0 0 0 68330 66494 1888 1720 True False +plasmidfinder plasmidfinder json, fasta, tabular, txt Identify plasmids in total or partial sequenced isolates of bacteria. 2022-09-19 https://bitbucket.org/genomicepidemiology/plasmidfinder/src/master/ 2.1.6 plasmidfinder 2.1.6 Up-to-date Sequence Analysis Genome assembly, Scaffolding, Multilocus sequence typing Genome assembly, Scaffolding, Multilocus sequence typing Whole genome sequencing, Sequence assembly, Mapping, Probes and primers Whole genome sequencing, Sequence assembly, Mapping, Probes and primers iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/plasmidfinder https://github.com/galaxyproject/tools-iuc/tree/master/tools/plasmidfinder PlasmidFinder PlasmidFinder PlasmidFinder is a tool for the identification and typing of Plasmid Replicons in Whole-Genome Sequencing (WGS). https://usegalaxy.eu/published/workflow?id=1306ed083d91a852, https://usegalaxy.eu/published/workflow?id=2a1dc58e51d5f01a, https://usegalaxy.eu/published/workflow?id=2c1a6da84d891cf2, https://usegalaxy.eu/published/workflow?id=36ea584e0f60893e, https://usegalaxy.eu/published/workflow?id=3f5fe28793ed0c6c, https://usegalaxy.eu/published/workflow?id=4a218fb93d78ba67, https://usegalaxy.eu/published/workflow?id=61948fcaefa1418a, https://usegalaxy.eu/published/workflow?id=6b69ab27c565257b, https://usegalaxy.eu/published/workflow?id=8792eaecb69fbc26, https://usegalaxy.eu/published/workflow?id=a18aed4b03ffd27e, https://usegalaxy.eu/published/workflow?id=b1afc8d1e81fc904, https://usegalaxy.eu/published/workflow?id=bcd50e655809cfcb, https://usegalaxy.eu/published/workflow?id=d0339e4a794f4922, https://usegalaxy.eu/published/workflow?id=d8db0b2e30370b84, https://usegalaxy.eu/published/workflow?id=dfb8e0f3c534000e, https://usegalaxy.eu/published/workflow?id=fd63b9884fda75b6, https://usegalaxy.eu/published/workflow?id=ffd365c037373673, https://usegalaxy.fr/published/workflow?id=7964ddc68853458f, https://usegalaxy.org.au/published/workflow?id=05f3abecd4ddd4a1, https://usegalaxy.org.au/published/workflow?id=09ec031656620fb5, https://usegalaxy.org/published/workflow?id=04c5ea133de3204c, https://usegalaxy.org/published/workflow?id=3940186d02245b1d, https://usegalaxy.org/published/workflow?id=49da012e2839c046, https://usegalaxy.org/published/workflow?id=4f8bdd61c524b901, https://usegalaxy.org/published/workflow?id=649cdc14757e5755, https://usegalaxy.org/published/workflow?id=67ca17ab34b10772, https://usegalaxy.org/published/workflow?id=8cb8a588a0495cfa, https://usegalaxy.org/published/workflow?id=993534c11310a207, https://usegalaxy.org/published/workflow?id=d2a5f6a5181aada5, https://workflowhub.eu/workflows/1050?version=13, https://workflowhub.eu/workflows/1513?version=1 genome-annotation/bacterial-genome-annotation 1 1 1 1 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 1015 1015 35994 35994 623 623 11939 11939 211 211 3278 3278 48 48 10730 10730 61941 61941 1897 1897 True False +plasmidspades plasmidspades fasta, tabular, txt Genome assembler for assemblying plasmid 2016-06-06 1.1 spades 4.3.0 To update Assembly nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/plasmidspades 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False +polypolish polypolish fasta, tabular, txt """Polypolish is a tool for polishing genome assemblies with short reads.Polypolish uses SAM files where each read has been aligned to all possible locations (not just a single best location).This allows it to repair errors in repeat regions that other alignment-based polishers cannot fix.""" 2022-09-22 https://github.com/rrwick/Polypolish 0.6.1 polypolish 0.6.1 Up-to-date Sequence Analysis Genome assembly, Read mapping, Mapping assembly, Sequencing error detection Genome assembly, Read mapping, Mapping assembly, Sequencing error detection Sequence assembly, Sequence composition, complexity and repeats, Mapping Sequence assembly, Sequence composition, complexity and repeats, Mapping iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/polypolish https://github.com/galaxyproject/tools-iuc/tree/master/tools/polypolish Polypolish Polypolish Polypolish is a tool for polishing genome assemblies with short reads. Unlike other tools in this category, Polypolish uses SAM files where each read has been aligned to all possible locations (not just a single best location). This allows it to repair errors in repeat regions that other alignment-based polishers cannot fix. https://usegalaxy.eu/published/workflow?id=2c992e509aa5dd9d, https://workflowhub.eu/workflows/1613?version=2 assembly/mrsa-nanopore 0 1 1 1 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 147 147 1066 1066 0 0 0 0 26 26 615 615 10 10 79 79 1760 1760 183 183 True False +ppanggolin ppanggolin_all, ppanggolin_msa, ppanggolin_projection, ppanggolin_rarefaction tsv, fasta, json, xml, html, csv, txt, h5, tar.gz, tabular Microbial Partitioned PanGenome 2025-01-22 https://github.com/labgem/PPanGGOLiN 2.3.0 ppanggolin 2.3.0 Up-to-date Genome annotation Rarefaction, Essential dynamics, Sequence assembly, Genome annotation Rarefaction, Essential dynamics, Sequence assembly, Genome annotation Metagenomics, Gene and protein families, Model organisms, Public health and epidemiology, Mapping Metagenomics, Gene and protein families, Model organisms, Public health and epidemiology, Mapping iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/ppanggolin https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin ppanggolin PPanGGOLiN PPanGGOLiN is a software suite used to create and manipulate prokaryotic pangenomes from a set of either genomic DNA sequences or provided genome annotations. It is designed to scale up to tens of thousands of genomes. It has the specificity to partition the pangenome using a statistical approach rather than using fixed thresholds which gives it the ability to work with low-quality data such as Metagenomic Assembled Genomes (MAGs) or Single-cell Amplified Genomes (SAGs) thus taking advantage of large scale environmental studies and letting users study the pangenome of uncultivable species genome-annotation/bacterial-pangenomics 0 0 4 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 55 55 249 249 0 0 0 0 0 0 0 0 16 16 67 67 316 316 71 71 True False +prinseq prinseq PRINSEQ is a tool for easy and rapid quality control and data processing of metagenomic and metatranscriptomic datasets 2016-05-30 http://prinseq.sourceforge.net/manual.html @TOOL_VERSION prinseq 0.20.4 To update Fastq Manipulation, Metagenomics Read pre-processing, Sequence trimming, Sequence contamination filtering Read pre-processing, Sequence trimming, Sequence contamination filtering Transcriptomics, Metagenomics, Genomics Transcriptomics, Metagenomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/prinseq https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq prinseq PRINSEQ PRINSEQ is a sequence processing tool that can be used to filter, reformat and trim genomic and metagenomic sequence data. It generates summary statistics of the input in graphical and tabular formats that can be used for quality control steps. PRINSEQ is available as both standalone and web-based versions. https://usegalaxy.eu/published/workflow?id=0609a4b1941d1a68, https://usegalaxy.eu/published/workflow?id=76e9cd837ea5e7da, https://usegalaxy.eu/published/workflow?id=8f415b0c409f56f7, https://usegalaxy.eu/published/workflow?id=9fddc44294236e8f, https://usegalaxy.eu/published/workflow?id=d6ff6be33b8bfe85, https://usegalaxy.eu/published/workflow?id=da19c0eaa757fa39, https://usegalaxy.org/published/workflow?id=20b7ae4b517a80fd, https://usegalaxy.org/published/workflow?id=46f184a0e95f3c1c, https://usegalaxy.org/published/workflow?id=5f878c4cc3bff68c, https://usegalaxy.org/published/workflow?id=a71fcbc60caae8b6, https://usegalaxy.org/published/workflow?id=afb67b4b9952f57d, https://workflowhub.eu/workflows/1271?version=3, https://workflowhub.eu/workflows/1272?version=2, https://workflowhub.eu/workflows/1850?version=1, https://workflowhub.eu/workflows/1854?version=1 microbiome/mgnify-amplicon 1 0 1 1 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 345 412 15643 16651 1317 1501 10523 12474 0 0 0 0 11 11 17 17 29142 26183 1924 1673 True False +prodigal prodigal genbank, fasta, tabular A protein-coding gene prediction software tool for bacterial and archaeal genomes 2024-03-14 https://github.com/hyattpd/Prodigal @VERSION@ prodigal 2.6.3 To update Genome annotation Genome annotation Genome annotation Genomics, Sequence analysis Genomics, Sequence analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/prodigal https://github.com/galaxyproject/tools-iuc/tree/master/tools/prodigal prodigal Prodigal Fast, reliable protein-coding gene prediction for prokaryotic genomes. https://usegalaxy.eu/published/workflow?id=2ee0eb74e839b476, https://usegalaxy.eu/published/workflow?id=62392daea25a3980, https://usegalaxy.eu/published/workflow?id=6dbbf39e07a5212e, https://usegalaxy.eu/published/workflow?id=b9c938d1af08124b, https://usegalaxy.org/published/workflow?id=d3c400275889ce4b, https://workflowhub.eu/workflows/1663?version=1, https://workflowhub.eu/workflows/2024?version=4 ecology/marine_omics_bgc 1 1 1 1 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 611 611 6456 6456 0 0 0 0 70 70 1515 1515 19 19 1487 1487 9458 9458 700 700 True False +prokka prokka gff3, genbank, fasta, asn1, txt, tabular Rapid annotation of prokaryotic genomes 2016-10-07 http://github.com/tseemann/prokka @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ prokka 1.15.6 To update Sequence Analysis Gene prediction, Coding region prediction, Genome annotation Coding region prediction, Genome annotation Genomics, Model organisms, Virology Genomics, Model organisms, Virology crs4 https://github.com/galaxyproject/tools-iuc/tree/main/tools/prokka https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka prokka Prokka Software tool to annotate bacterial, archaeal and viral genomes quickly and produce standards-compliant output files. https://usegalaxy.eu/published/workflow?id=007ce6405d196df3, 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https://github.com/qiime2/galaxy-tools/tree/master/tools/suite_qiime2__demux qiime2 QIIME 2 QIIME 2 is an AI-ready microbiome multi-omics data science platform that is trusted, free, open source, extensible, and community developed and supported bioinformatics. https://usegalaxy.eu/published/workflow?id=3d0039098a87642c, https://usegalaxy.eu/published/workflow?id=5528702f49c33d83, https://usegalaxy.eu/published/workflow?id=5d401d357500617f, https://usegalaxy.eu/published/workflow?id=86b31ac8a7720e41, https://usegalaxy.eu/published/workflow?id=b1f68ff8158d0b85, https://usegalaxy.eu/published/workflow?id=b2975bb705d3e851, https://usegalaxy.eu/published/workflow?id=be9ff4159593cc34, https://usegalaxy.eu/published/workflow?id=c0b5b499b149005f, https://usegalaxy.eu/published/workflow?id=c58941443cec9380, https://usegalaxy.eu/published/workflow?id=ca5da5179cefec8b, https://usegalaxy.eu/published/workflow?id=fb96000c99db2fa8, https://usegalaxy.org.au/published/workflow?id=19b0f96df6d09b4e, 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qiime2_core__tools__import_fastq qza 2022-08-25 https://qiime2.org 2026.1.0+dist.h02a552c2 To update Metagenomics, Sequence Analysis, Statistics Demultiplexing, Visualisation, Taxonomic classification Demultiplexing, Visualisation, Taxonomic classification Microbial ecology, Metatranscriptomics, Metagenomics Microbial ecology, Metatranscriptomics, Metagenomics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2_core__tools https://github.com/qiime2/galaxy-tools/tree/master/tools/suite_qiime2_core__tools qiime2 QIIME 2 QIIME 2 is an AI-ready microbiome multi-omics data science platform that is trusted, free, open source, extensible, and community developed and supported bioinformatics. https://usegalaxy.eu/published/workflow?id=3d0039098a87642c, https://usegalaxy.eu/published/workflow?id=457a3de5c1512707, https://usegalaxy.eu/published/workflow?id=5528702f49c33d83, https://usegalaxy.eu/published/workflow?id=5d401d357500617f, 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https://github.com/qiime2/galaxy-tools/tree/master/tools/suite_qiime2__diversity_lib qiime2 QIIME 2 QIIME 2 is an AI-ready microbiome multi-omics data science platform that is trusted, free, open source, extensible, and community developed and supported bioinformatics. https://usegalaxy.org/published/workflow?id=7251c6e0dad8f927 12 12 12 12 0 0 0 0 12 0 0 0 0 0 0 0 0 0 0 0 0 0 0 12 0 0 4 4 33 33 8 8 47 47 6 6 2850 2850 2 2 3 3 2933 2933 20 20 True False +qiime2 qiime2__stats__alpha_group_significance, qiime2__stats__collate_stats, qiime2__stats__facet_across, qiime2__stats__facet_within, qiime2__stats__mann_whitney_u, qiime2__stats__mann_whitney_u_facet, qiime2__stats__plot_rainclouds, qiime2__stats__prep_alpha_distribution, qiime2__stats__wilcoxon_srt, qiime2__stats__wilcoxon_srt_facet qza, qzv 2024-10-30 https://github.com/qiime2/q2-stats 2026.1.0+q2galaxy.2026.1.0 To update Metagenomics, Sequence Analysis, Statistics Demultiplexing, Visualisation, Taxonomic classification Demultiplexing, Visualisation, Taxonomic classification Microbial ecology, Metatranscriptomics, Metagenomics Microbial ecology, Metatranscriptomics, Metagenomics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__stats https://github.com/qiime2/galaxy-tools/tree/master/tools/suite_qiime2__stats qiime2 QIIME 2 QIIME 2 is an AI-ready microbiome multi-omics data science platform that is trusted, free, open source, extensible, and community developed and supported bioinformatics. 0 9 9 0 0 0 0 0 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False +qiime2 qiime2__sample_classifier__classify_samples, qiime2__sample_classifier__classify_samples_from_dist, qiime2__sample_classifier__classify_samples_ncv, qiime2__sample_classifier__confusion_matrix, qiime2__sample_classifier__fit_classifier, qiime2__sample_classifier__fit_regressor, qiime2__sample_classifier__heatmap, qiime2__sample_classifier__metatable, 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developed and supported bioinformatics. 15 15 15 15 0 0 0 0 15 0 0 0 0 0 0 0 0 0 0 0 0 0 0 15 0 0 5 5 30 30 17 17 47 47 5 5 6 6 1 1 4 4 87 87 28 28 True False +qiime2 qiime2__rescript__cull_seqs, qiime2__rescript__degap_seqs, qiime2__rescript__dereplicate, qiime2__rescript__edit_taxonomy, qiime2__rescript__evaluate_classifications, qiime2__rescript__evaluate_cross_validate, qiime2__rescript__evaluate_fit_classifier, qiime2__rescript__evaluate_seqs, qiime2__rescript__evaluate_taxonomy, qiime2__rescript__extract_seq_segments, qiime2__rescript__filter_seqs_length, qiime2__rescript__filter_seqs_length_by_taxon, qiime2__rescript__filter_taxa, qiime2__rescript__get_bv_brc_genome_features, qiime2__rescript__get_bv_brc_genomes, qiime2__rescript__get_bv_brc_metadata, qiime2__rescript__get_eukaryome_data, qiime2__rescript__get_gtdb_data, qiime2__rescript__get_midori2_data, qiime2__rescript__get_ncbi_data, qiime2__rescript__get_ncbi_data_protein, qiime2__rescript__get_ncbi_genomes, qiime2__rescript__get_pr2_data, qiime2__rescript__get_silva_data, qiime2__rescript__get_unite_data, qiime2__rescript__merge_taxa, qiime2__rescript__orient_reads, qiime2__rescript__orient_seqs, qiime2__rescript__parse_silva_taxonomy, qiime2__rescript__reverse_transcribe, qiime2__rescript__subsample_fasta, qiime2__rescript__trim_alignment qza, qzv 2024-04-25 https://github.com/nbokulich/RESCRIPt 2026.1.0+q2galaxy.2026.1.0 To update Metagenomics, Sequence Analysis, Statistics Demultiplexing, Visualisation, Taxonomic classification Demultiplexing, Visualisation, Taxonomic classification Microbial ecology, Metatranscriptomics, Metagenomics Microbial ecology, Metatranscriptomics, Metagenomics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript https://github.com/qiime2/galaxy-tools/tree/master/tools/suite_qiime2__rescript qiime2 QIIME 2 QIIME 2 is an AI-ready microbiome multi-omics data science platform that is trusted, free, open source, extensible, and 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qiime2__alignment__mafft_add, qiime2__alignment__mask qza 2022-08-25 https://github.com/qiime2/q2-alignment 2026.1.0+q2galaxy.2026.1.0 To update Metagenomics, Sequence Analysis, Statistics Demultiplexing, Visualisation, Taxonomic classification Demultiplexing, Visualisation, Taxonomic classification Microbial ecology, Metatranscriptomics, Metagenomics Microbial ecology, Metatranscriptomics, Metagenomics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment https://github.com/qiime2/galaxy-tools/tree/master/tools/suite_qiime2__alignment qiime2 QIIME 2 QIIME 2 is an AI-ready microbiome multi-omics data science platform that is trusted, free, open source, extensible, and community developed and supported bioinformatics. 3 3 3 3 0 0 0 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 67 67 390 390 35 35 78 78 16 16 114 114 14 14 69 69 651 651 132 132 True False +qiime2 qiime2__phylogeny__align_to_tree_mafft_fasttree, qiime2__phylogeny__align_to_tree_mafft_iqtree, 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Sequence assembly, DNA polymorphism, Whole genome sequencing, Genotype and phenotype iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/quickmerge https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge quickmerge quickmerge Quickmerge is a program that uses complementary information from genomes assembled with long reads in order to improve contiguity, and works with assemblies derived from both Pacific Biosciences or Oxford Nanopore. Quickmerge will even work with hybrid assemblies made by combining long reads and Illumina short reads. 0 0 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False +quicktree quicktree newick neighbour-joining phylogenetic inference 2024-11-21 https://github.com/khowe/quicktree @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ quicktree 2.5 To update Phylogenetics Phylogenetic inference (from molecular sequences) Phylogenetic inference (from molecular sequences) Phylogenetics Phylogenetics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/quicktree https://github.com/galaxyproject/tools-iuc/tree/master/tools/quicktree quicktree QuickTree QuickTree is an efficient implementation of the Neighbor-Joining algorithm (PMID: 3447015), capable of reconstructing phylogenies from huge alignments in time less than the age of the universe. https://workflowhub.eu/workflows/1650?version=1 sequence-analysis/tapscan-streptophyte-algae 0 0 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 69 69 466 466 0 0 0 0 0 0 0 0 0 0 0 0 466 466 69 69 True False +racon racon fasta Consensus module for raw de novo DNA assembly of long uncorrected reads. 2018-06-11 https://github.com/isovic/racon 1.5.0 racon 1.5.0 Up-to-date Sequence Analysis Genome assembly, Mapping assembly Genome assembly, Mapping assembly Whole genome sequencing, Sequence assembly Whole genome sequencing, Sequence assembly bgruening https://github.com/bgruening/galaxytools/tree/master/tools/racon https://github.com/bgruening/galaxytools/tree/master/tools/racon Racon Racon Consensus module for raw de novo DNA assembly of long uncorrected readsRacon is intended as a standalone consensus module to correct raw contigs generated by rapid assembly methods which do not include a consensus step. The goal of Racon is to generate genomic consensus which is of similar or better quality compared to the output generated by assembly methods which employ both error correction and consensus steps, while providing a speedup of several times compared to those methods. It supports data produced by both Pacific Biosciences and Oxford Nanopore Technologies. https://usegalaxy.eu/published/workflow?id=1ae9a523ef719a3d, https://usegalaxy.eu/published/workflow?id=249c115413f17f28, https://usegalaxy.eu/published/workflow?id=32d2f5340098bcbd, https://usegalaxy.eu/published/workflow?id=39837ca09374598b, https://usegalaxy.eu/published/workflow?id=44e53ea319e07daa, https://usegalaxy.eu/published/workflow?id=4eb9dfe91fc2dc67, https://usegalaxy.eu/published/workflow?id=5500de2961f7470c, https://usegalaxy.eu/published/workflow?id=5826e573b6f93762, https://usegalaxy.eu/published/workflow?id=8b2f53745e720d0f, https://usegalaxy.eu/published/workflow?id=a337bfb2eb1e583f, https://usegalaxy.eu/published/workflow?id=a4f50449afde4a05, https://usegalaxy.eu/published/workflow?id=a84bac86ec183d46, https://usegalaxy.eu/published/workflow?id=b4de76c0a4d0e23a, https://usegalaxy.eu/published/workflow?id=c48807045e258dd8, https://usegalaxy.eu/published/workflow?id=dc7107896a3f2964, https://usegalaxy.org.au/published/workflow?id=0c421197e022f323, https://usegalaxy.org.au/published/workflow?id=1ff6aabb7e3954ac, https://usegalaxy.org.au/published/workflow?id=45e9910f46a210d8, https://usegalaxy.org.au/published/workflow?id=d9571b3dfef34e5e, https://usegalaxy.org/published/workflow?id=bcdc5ce2ea8700fc, https://workflowhub.eu/workflows/1477?version=1, https://workflowhub.eu/workflows/1599?version=1, https://workflowhub.eu/workflows/1604?version=1, https://workflowhub.eu/workflows/227?version=1, https://workflowhub.eu/workflows/228?version=1, https://workflowhub.eu/workflows/406?version=1, https://workflowhub.eu/workflows/51?version=1, https://workflowhub.eu/workflows/563?version=1 assembly/largegenome, microbiome/plasmid-metagenomics-nanopore 1 1 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1046 1151 32503 37525 683 683 23074 23074 263 268 9144 9214 31 31 320 320 70133 65041 2133 2023 True False +rasusa rasusa bam Randomly subsample sequencing reads to a specified coverage 2024-02-16 https://github.com/mbhall88/rasusa @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ rasusa 4.1.0 To update Sequence Analysis Sequence assembly validation, Sequencing quality control Sequence assembly validation Genomics, Sequence analysis, Sequence assembly, Sequencing, RNA-Seq Genomics, Sequence analysis, Sequence assembly, RNA-Seq iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/rasusa https://github.com/galaxyproject/tools-iuc/tree/master/tools/rasusa rasusa rasusa Rasusa: Randomly subsample sequencing reads to aspecified coverageProduces an unbiased subsample of your reads 0 0 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 24 24 104 104 0 0 0 0 0 0 0 0 0 0 0 0 104 104 24 24 True False +raxml raxml txt, nhx RAxML - A Maximum Likelihood based phylogenetic inference 2015-11-05 http://www.exelixis-lab.org/web/software/raxml/ @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ raxml 8.2.13 To update Phylogenetics Sequence analysis, Phylogenetic tree analysis Sequence analysis Phylogenetics, Sequence analysis Phylogenetics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml raxml RAxML A tool for Phylogenetic Analysis and Post-Analysis of Large Phylogenies. https://usegalaxy.eu/published/workflow?id=470656ef317c9dd5, https://usegalaxy.eu/published/workflow?id=875b3ca170ac12a1, https://usegalaxy.org/published/workflow?id=7251c6e0dad8f927, https://usegalaxy.org/published/workflow?id=d4f0a7ccb09f1e55, https://workflowhub.eu/workflows/1577?version=1 evolution/mtb_phylogeny 1 1 1 1 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1422 1464 15492 16986 1144 1144 19599 19633 731 1034 5870 7945 21 21 305 305 44869 41266 3663 3318 True False +raxmlng raxmlng txt, nhx, json RAxML-NG - A Maximum Likelihood based phylogenetic tree inference 2025-12-20 http://www.exelixis-lab.org/web/software/raxml-ng/ 2.0.2 raxml-ng 2.0.2 Up-to-date Phylogenetics Phylogenetic tree generation (maximum likelihood and Bayesian methods), Phylogenetic tree bootstrapping Phylogenetic tree bootstrapping Phylogenetics, Agricultural science, Phylogenomics Phylogenetics, Agricultural science, Phylogenomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxmlng https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxmlng RAxML-NG RAxML-NG Phylogenetic tree inference tool which uses maximum-likelihood (ML) optimality criterion. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False +read2tree read2tree newick Infer a species tree from sequencing reads. 2025-11-23 https://github.com/DessimozLab/read2tree @TOOL_VERSION@ read2tree 2.0.1 To update Phylogenetics Phylogenomics Phylogenomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/read2tree https://github.com/galaxyproject/tools-iuc/tree/master/tools/read2tree read2tree read2tree read2tree is a software tool for generating alignment matrices and performing tree inference directly from sequencing reads. It leverages the OMA database and a set of input reads, bypassing many of the standard steps typically required in phylogenomic analysis. In particular, it avoids for read filtering, assembly, gene prediction, gene annotation, all-vs-all comparison, orthology prediction, alignment, and concatenation. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False +read_it_and_keep read_it_and_keep Rapid decontamination of SARS-CoV-2 sequencing reads 2022-01-28 https://github.com/GenomePathogenAnalysisService/read-it-and-keep @TOOL_VERSION@ read-it-and-keep 0.3.0 To update Sequence Analysis Filtering, Genome alignment Filtering, Genome alignment Pathology, Genomics Pathology, Genomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/read_it_and_keep https://github.com/galaxyproject/tools-iuc/tree/master/tools/read_it_and_keep read_it_and_keep read_it_and_keep Read-it-and-keep is a bioinformatics tool designed to filter and extract sequencing reads according to user-defined criteria, such as the presence of specific motifs or coverage of regions of interest. This type of filtering can be particularly useful for targeted analyses, where only relevant sequences are retained for further study, optimising computing and storage resources. https://usegalaxy.eu/published/workflow?id=3fb550d7c2bc390a, https://usegalaxy.eu/published/workflow?id=4a764275d4bf9f31, https://usegalaxy.eu/published/workflow?id=629e57958afed44c, https://usegalaxy.eu/published/workflow?id=7c986f4d14c6a539, https://usegalaxy.eu/published/workflow?id=d88145e7475e0b7b, https://usegalaxy.eu/published/workflow?id=d967194ca51ff11e, https://workflowhub.eu/workflows/519?version=1, https://workflowhub.eu/workflows/521?version=1 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 81 81 3781 3781 8 8 9 9 0 0 0 0 0 0 0 0 3790 3790 89 89 True False +reago reago fasta Reago is tool to assembly 16S ribosomal RNA recovery from metagenomic data. 2015-12-09 https://github.com/chengyuan/reago-1.1 @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ reago 1.1 To update Metagenomics, RNA Sequence assembly Sequence assembly Sequence assembly, RNA, Metagenomics, Microbiology Sequence assembly, RNA, Metagenomics, Microbiology rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago reago REAGO This is an assembly tool for 16S ribosomal RNA recovery from metagenomic data. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 7 18 18 0 0 0 0 0 0 0 0 0 0 0 0 18 18 7 7 True False +recentrifuge recentrifuge html, txt, tabular, xlsx """With Recentrifuge, researchers can analyze results from taxonomic classifiers using interactive charts with emphasis on the confidence level of the classifications.In addition to contamination-subtracted samples.Recentrifuge provides shared and exclusive taxa per sample,thus enabling robust contamination removal and comparative analysis in environmental and clinical metagenomics.""" 2022-05-04 https://github.com/khyox/recentrifuge 1.16.1 recentrifuge 2.1.1 To update Metagenomics Taxonomic classification, Expression analysis, Cross-assembly Taxonomic classification, Expression analysis, Cross-assembly Metagenomics, Microbial ecology, Metagenomic sequencing Metagenomics, Microbial ecology, Metagenomic sequencing iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/recentrifuge https://github.com/galaxyproject/tools-iuc/tree/master/tools/recentrifuge Recentrifuge Recentrifuge Robust comparative analysis and contamination removal for metagenomics. https://usegalaxy.eu/published/workflow?id=0a82eb8b44d9d502, https://usegalaxy.eu/published/workflow?id=0abd32dbc5207b88, https://usegalaxy.eu/published/workflow?id=0c47571d20535426, https://usegalaxy.eu/published/workflow?id=2fa2f67603772413, https://usegalaxy.eu/published/workflow?id=47e14222073e7192, https://usegalaxy.eu/published/workflow?id=884a4415b669690c, https://usegalaxy.eu/published/workflow?id=aafcfcb585c5ca75, https://usegalaxy.eu/published/workflow?id=bb63b5bb983fd49c, 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https://usegalaxy.org/published/workflow?id=f378960ee55f567e, https://workflowhub.eu/workflows/1052?version=11, https://workflowhub.eu/workflows/1644?version=1, https://workflowhub.eu/workflows/1674?version=2, https://workflowhub.eu/workflows/1881?version=2, https://workflowhub.eu/workflows/1882?version=3, https://workflowhub.eu/workflows/2043?version=1 ecology/bacterial-isolate-species-contamination-checking, sequence-analysis/quality-contamination-control 1 1 1 1 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 306 306 2546 2546 160 160 593 593 37 37 105 105 27 27 2397 2397 5641 5641 530 530 True False +remove_terminal_stop_codons remove_terminal_stop_codons fasta Remove terminal stop codons from coding sequences 2025-12-04 https://github.com/veg/CAPHEINE @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ biopython 1.70 To update Phylogenetics, Sequence Analysis, Fasta Manipulation iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/remove_terminal_stop_codons https://github.com/galaxyproject/tools-iuc/tree/master/tools/remove_terminal_stop_codons 1 0 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False +repeatexplorer2 repeatexplorer_clustering html Tool for annotation of repeats from unassembled shotgun reads. 2023-11-01 https://github.com/repeatexplorer/repex_tarean 2.3.8 To update Genome annotation gga https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 83 83 369 369 0 0 0 0 0 0 0 0 0 0 0 0 369 369 83 83 True False +roary roary tabular, fasta, csv, nhx, dot, embl, txt Roary the pangenome pipeline 2017-06-21 https://sanger-pathogens.github.io/Roary/ @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ roary 3.13.0 To update Sequence Analysis Genome assembly Genome assembly DNA, Genomics, Mapping DNA, Genomics, Mapping iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/roary https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary roary Roary A high speed stand alone pan genome pipeline, which takes annotated assemblies in GFF3 format (produced by Prokka (Seemann, 2014)) and calculates the pan genome. https://usegalaxy.eu/published/workflow?id=46ef864fe9468894, https://usegalaxy.eu/published/workflow?id=628062a8cf93261f, https://usegalaxy.eu/published/workflow?id=94c3d329c31c712f, https://usegalaxy.eu/published/workflow?id=b1a799497c366eef, https://usegalaxy.eu/published/workflow?id=e16e524c557d7928, https://usegalaxy.org.au/published/workflow?id=05f3abecd4ddd4a1, https://usegalaxy.org.au/published/workflow?id=3fd2195b6928d5e0, https://usegalaxy.org/published/workflow?id=23a87246c646eb8a, https://usegalaxy.org/published/workflow?id=78d8b738f5715a8a, https://usegalaxy.org/published/workflow?id=80565301ada0d3eb 1 1 1 1 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 2251 2377 21218 23887 2319 2454 17744 18851 653 749 5251 7169 47 47 187 187 50094 44400 5627 5270 True False +rseqc rseqc_FPKM_count, rseqc_RNA_fragment_size, rseqc_RPKM_saturation, rseqc_bam2wig, rseqc_bam_stat, rseqc_clipping_profile, rseqc_deletion_profile, rseqc_geneBody_coverage, rseqc_geneBody_coverage2, rseqc_infer_experiment, rseqc_inner_distance, rseqc_insertion_profile, rseqc_junction_annotation, rseqc_junction_saturation, rseqc_mismatch_profile, rseqc_read_GC, rseqc_read_NVC, rseqc_read_distribution, rseqc_read_duplication, rseqc_read_hexamer, rseqc_read_quality, rseqc_tin tabular, wig, txt, pdf an RNA-seq quality control package 2017-02-27 https://code.google.com/p/rseqc/ 5.0.3 rseqc 5.0.4 To update Convert Formats, Sequence Analysis, RNA, Transcriptomics, Visualization Data handling Data handling Sequencing Sequencing nilesh https://github.com/galaxyproject/tools-iuc/tree/main/tools/rseqc https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc rseqc RSeQC Provides a number of useful modules that can comprehensively evaluate high throughput sequence data especially RNA-seq data. Some basic modules quickly inspect sequence quality, nucleotide composition bias, PCR bias and GC bias, while RNA-seq specific modules evaluate sequencing saturation, mapped reads distribution, coverage uniformity, strand specificity, transcript level RNA integrity etc. https://usegalaxy.eu/published/workflow?id=165a9bfc79856c2f, https://usegalaxy.eu/published/workflow?id=1ee43d90b69829e9, https://usegalaxy.eu/published/workflow?id=1f9a9a7998ef5ab3, https://usegalaxy.eu/published/workflow?id=20ada53472782c9b, https://usegalaxy.eu/published/workflow?id=47a0407867a90f95, https://usegalaxy.eu/published/workflow?id=5e4135eeb4972709, https://usegalaxy.eu/published/workflow?id=8ef65d7fefeac22d, https://usegalaxy.eu/published/workflow?id=93d1035a307fe63d, https://usegalaxy.eu/published/workflow?id=985044b4b2c51425, https://usegalaxy.eu/published/workflow?id=9b025479fade745d, https://usegalaxy.eu/published/workflow?id=9c7a218993788493, 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https://usegalaxy.org/published/workflow?id=a743746151101352, https://usegalaxy.org/published/workflow?id=b1a98a2d5ebda1c5, https://usegalaxy.org/published/workflow?id=cbcf04cac4c6d0b8, https://usegalaxy.org/published/workflow?id=cdd68689c095252c, https://usegalaxy.org/published/workflow?id=cf988e9e8003e3ef, https://usegalaxy.org/published/workflow?id=d9d3ccdcd7d91bb6, https://usegalaxy.org/published/workflow?id=e035be74e3c85bf5, https://usegalaxy.org/published/workflow?id=e151b279b0b45a57, https://usegalaxy.org/published/workflow?id=eb4b32fcf4a9f64a, https://usegalaxy.org/published/workflow?id=fb789920b057fe8d, https://workflowhub.eu/workflows/1103?version=3, https://workflowhub.eu/workflows/1675?version=1, https://workflowhub.eu/workflows/1688?version=1, https://workflowhub.eu/workflows/1692?version=1, https://workflowhub.eu/workflows/1695?version=1, https://workflowhub.eu/workflows/688?version=1 transcriptomics/differential-isoform-expression, transcriptomics/minerva-pathways, transcriptomics/ref-based, transcriptomics/rna-seq-reads-to-counts 22 22 22 22 0 0 0 0 22 0 0 0 0 0 0 0 0 0 22 0 0 0 22 22 22 0 4113 5223 155237 181534 4079 5016 146353 197501 629 697 28108 32069 809 810 78294 78366 489470 407992 11746 9630 True False +samestr samestr_compare, samestr_convert, samestr_extract, samestr_filter, samestr_merge, samestr_stats, samestr_summarize tabular, fasta, fasta.gz, npz Strain-level analysis and comparison of metagenomic samples 2026-04-15 https://github.com/danielpodlesny/samestr 1.2025.111 samestr 1.2025.111 Up-to-date Metagenomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/samestr https://github.com/galaxyproject/tools-iuc/tree/master/tools/samestr https://usegalaxy.eu/published/workflow?id=052f35a526798020 0 0 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False +scoary scoary tabular, newick Scoary calculates the assocations between all genes in the accessory genome and the traits. 2021-03-18 https://github.com/AdmiralenOla/Scoary @TOOL_VERSION@ scoary 1.6.16 To update Metagenomics Analysis Analysis Genotype and phenotype, Model organisms, GWAS study, Functional genomics Genotype and phenotype, Model organisms, GWAS study, Functional genomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/scoary https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary scoary Scoary Pan-genome wide association studies and is designed to take the gene_presence_absence.csv file from Roary as well as a traits file created by the user and calculate the assocations between all genes in the accessory genome (all genes that are present in i genomes where 1 < i < N) and the traits. It reports a list of genes sorted by strength of association per trait. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 113 113 1366 1366 0 0 0 0 0 0 0 0 0 0 0 0 1366 1366 113 113 True False +semibin semibin_bin, semibin_concatenate_fasta, semibin_generate_cannot_links, semibin_generate_sequence_features, semibin, semibin_train fasta, csv SemiBin: Semi-supervised Metagenomic Binning Using Siamese Neural Networks 2022-10-14 https://semibin.readthedocs.io/en/latest/ 2.1.0 semibin 2.3.0 To update Metagenomics Sequence assembly, Read binning Sequence assembly, Read binning Metagenomics, Machine learning, Microbial ecology, Sequence assembly Metagenomics, Machine learning, Microbial ecology, Sequence assembly iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin semibin SemiBin Command tool for metagenomic binning with semi-supervised deep learning using information from reference genomes. https://usegalaxy.eu/published/workflow?id=00f15824c7a9b196, https://usegalaxy.eu/published/workflow?id=0563f58718be932d, https://usegalaxy.eu/published/workflow?id=1e5f1d9a51032e44, https://usegalaxy.eu/published/workflow?id=43098b8afe78b071, https://usegalaxy.eu/published/workflow?id=7ecd92cb382d8168, https://usegalaxy.eu/published/workflow?id=97312d273b6e8bd9, https://usegalaxy.eu/published/workflow?id=ce5c9287a67e6085, https://workflowhub.eu/workflows/1352?version=4, https://workflowhub.eu/workflows/2028?version=1, https://workflowhub.eu/workflows/2100?version=2 microbiome/metagenomics-binning 1 6 6 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 6 0 0 53 53 2779 2779 9 9 18 18 0 0 0 0 2 2 75 75 2872 2872 64 64 True False +seqkit seqkit_fx2tab, seqkit_grep, seqkit_head, seqkit_locate, seqkit_sort, seqkit_split2, seqkit_stats, seqkit_translate tabular, txt A cross-platform and ultrafast toolkit for FASTA/Q file manipulation 2022-06-01 https://bioinf.shenwei.me/seqkit/ 2.13.0 seqkit 2.13.0 Up-to-date Sequence Analysis DNA transcription, Sequence trimming, DNA translation, Sequence conversion DNA transcription, Sequence trimming, DNA translation Database management, Sequence analysis Database management, Sequence analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqkit https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit seqkit seqkit FASTA and FASTQ are basic and ubiquitous formats for storing nucleotide and protein sequences. Common manipulations of FASTA/Q file include converting, searching, filtering, deduplication, splitting, shuffling, and sampling. Existing tools only implement some of these manipulations, and not particularly efficiently, and some are only available for certain operating systems. Furthermore, the complicated installation process of required packages and running environments can render these programs less user friendly. SeqKit demonstrates competitive performance in execution time and memory usage compared to similar tools. The efficiency and usability of SeqKit enable researchers to rapidly accomplish common FASTA/Q file manipulations. https://usegalaxy.eu/published/workflow?id=8ee6213aec38e4cc, https://usegalaxy.eu/published/workflow?id=e0c709127e9a42ae, https://usegalaxy.org.au/published/workflow?id=7559224fc32dce3a, https://usegalaxy.org.au/published/workflow?id=7a0c4804e4d4c905, https://usegalaxy.org.au/published/workflow?id=ed3e48a73b5aaa56, https://workflowhub.eu/workflows/2024?version=4, https://workflowhub.eu/workflows/2036?version=1, https://workflowhub.eu/workflows/2038?version=1, https://workflowhub.eu/workflows/601?version=2, https://workflowhub.eu/workflows/602?version=2, https://workflowhub.eu/workflows/697?version=1 3 6 8 5 0 0 0 0 0 0 4 0 0 0 0 0 0 0 0 0 0 0 0 4 0 0 396 396 13926 13926 0 0 0 0 120 120 2190 2190 69 69 648 648 16764 16764 585 585 True False +seqprep seqprep fastq.gz Tool for merging paired-end Illumina reads and trimming adapters. 2024-01-15 https://github.com/jstjohn/SeqPrep 1.3.2 seqprep 1.3.2 Up-to-date Fastq Manipulation, Sequence Analysis Nucleic acid design Nucleic acid design Genomics, Sequence assembly, Sequencing, Probes and primers Genomics, Sequence assembly, Sequencing, Probes and primers iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqprep https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep seqprep SeqPrep Strips adapters and optionally merges overlapping paired-end (or paired-end contamination in mate-pair libraries) illumina style reads. microbiome/mgnify-amplicon 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 227 227 3602 3602 0 0 0 0 0 0 0 0 0 0 0 0 3602 3602 227 227 True False +seqsero2 seqsero2 tabular, txt Salmonella serotype prediction from genome sequencing data 2023-11-07 https://github.com/denglab/SeqSero2 1.3.2 seqsero2 1.3.2 Up-to-date Sequence Analysis Genome indexing, Antimicrobial resistance prediction, Genome alignment Genome indexing, Antimicrobial resistance prediction, Genome alignment Whole genome sequencing, Sequence assembly, Genomics Whole genome sequencing, Sequence assembly, Genomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqsero2 https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 seqsero2 SeqSero2 "rapid and improved Salmonella serotype determination using whole genome sequencing data | SeqSero-Salmonella Serotyping by Whole Genome Sequencing | Salmonella Serotyping by Whole Genome Sequencing | Online version: http://www.denglab.info/SeqSero2 | Salmonella serotype prediction from genome sequencing data | Citation: SeqSero, Zhang et al. 2015; SeqSero2, Zhang et al. 2019 | Salmonella serotype derterminants databases | Upon executing the command, a directory named 'SeqSero_result_Time_your_run' will be created. Your result will be stored in 'SeqSero_result.txt' in that directory. And the assembled alleles can also be found in the directory if using ""-m a"" (allele mode)" https://usegalaxy.eu/published/workflow?id=fde21b5f5c169114, https://workflowhub.eu/workflows/407?version=1 0 0 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 116 116 14011 14011 0 0 0 0 0 0 0 0 2 2 2 2 14013 14013 118 118 True False +shovill shovill txt, fasta, unsorted.bam, gfa1 Faster de novo assembly pipeline based around Spades 2017-10-24 https://github.com/tseemann/shovill @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ shovill 1.4.2 To update Assembly Genome assembly Genome assembly Genomics, Microbiology, Sequence assembly Genomics, Microbiology, Sequence assembly iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/shovill https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill shovill shovill Shovill is a pipeline for assembly of bacterial isolate genomes from Illumina paired-end reads. Shovill uses SPAdes at its core, but alters the steps before and after the primary assembly step to get similar results in less time. Shovill also supports other assemblers like SKESA, Velvet and Megahit, so you can take advantage of the pre- and post-processing the Shovill provides with those too. https://usegalaxy.eu/published/workflow?id=0404013d5c27210d, https://usegalaxy.eu/published/workflow?id=1ea8bfbe6cb04531, https://usegalaxy.eu/published/workflow?id=309fc4fc2e0da89c, https://usegalaxy.eu/published/workflow?id=3303a04887a47675, https://usegalaxy.eu/published/workflow?id=3d937648809ca4e7, https://usegalaxy.eu/published/workflow?id=4216424f032c055f, https://usegalaxy.eu/published/workflow?id=42c0da2e86318b37, https://usegalaxy.eu/published/workflow?id=4f245ac304ab76d9, https://usegalaxy.eu/published/workflow?id=5b893b69a1b6748f, https://usegalaxy.eu/published/workflow?id=5b940b283d91d99d, https://usegalaxy.eu/published/workflow?id=628062a8cf93261f, https://usegalaxy.eu/published/workflow?id=723e718f37e9ab91, https://usegalaxy.eu/published/workflow?id=7aa32aba3fde0708, 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https://usegalaxy.org.au/published/workflow?id=7a0c4804e4d4c905, https://usegalaxy.org.au/published/workflow?id=92fcdd490831c6c5, https://usegalaxy.org.au/published/workflow?id=d78f885b4b86635f, https://usegalaxy.org.au/published/workflow?id=f2541030f6d70b59, https://usegalaxy.org.au/published/workflow?id=fa76b66785ce38b8, https://usegalaxy.org/published/workflow?id=0e30324072570abb, https://usegalaxy.org/published/workflow?id=109092d8dbda4398, https://usegalaxy.org/published/workflow?id=1c7af480caf150bd, https://usegalaxy.org/published/workflow?id=3cf46c167ccb374f, https://usegalaxy.org/published/workflow?id=4161cfd67ed94b5d, https://usegalaxy.org/published/workflow?id=4d1279007d0137fa, https://usegalaxy.org/published/workflow?id=524602abe59b18f7, https://usegalaxy.org/published/workflow?id=5cd56232e873beab, https://usegalaxy.org/published/workflow?id=84233173d92fa506, https://usegalaxy.org/published/workflow?id=8ebc2b1ae24ed884, https://usegalaxy.org/published/workflow?id=9ac1e4efe310b3b3, https://usegalaxy.org/published/workflow?id=9e5c5ddb60a24889, https://usegalaxy.org/published/workflow?id=b76a9ce44ea019f1, https://usegalaxy.org/published/workflow?id=c454c930ccfb0d3f, https://usegalaxy.org/published/workflow?id=d4c790a45978bb9e, https://usegalaxy.org/published/workflow?id=d4f0a7ccb09f1e55, https://usegalaxy.org/published/workflow?id=db08887d7d6dc147, https://usegalaxy.org/published/workflow?id=e2ab3d3219a648a7, https://usegalaxy.org/published/workflow?id=e75bd7d392e65209, https://usegalaxy.org/published/workflow?id=f4d623a19b32370e, https://workflowhub.eu/workflows/100?version=1, https://workflowhub.eu/workflows/102?version=1, https://workflowhub.eu/workflows/103?version=1, https://workflowhub.eu/workflows/1043?version=12, https://workflowhub.eu/workflows/1189?version=2, https://workflowhub.eu/workflows/1602?version=2, https://workflowhub.eu/workflows/1767?version=1, https://workflowhub.eu/workflows/407?version=1, https://workflowhub.eu/workflows/470?version=1 assembly/mrsa-illumina 1 1 1 1 0 0 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 3269 3491 70801 76107 4933 5212 51724 55190 1425 1669 30312 35794 83 83 9136 9136 176227 161973 10455 9710 True False +sistr_cmd sistr_cmd csv, json, tabular, fasta SISTR in silico serotyping tool 2017-02-20 https://github.com/phac-nml/sistr_cmd @VERSION@ sistr_cmd 1.1.3 To update Sequence Analysis Genome assembly, Visualisation, Multilocus sequence typing Genome assembly, Visualisation, Multilocus sequence typing Whole genome sequencing, Immunoproteins and antigens, Sequence assembly, Zoology, Public health and epidemiology Whole genome sequencing, Immunoproteins and antigens, Sequence assembly, Zoology, Public health and epidemiology nml https://github.com/phac-nml/sistr_cmd https://github.com/phac-nml/galaxy_tools/tree/master/tools/sistr_cmd SISTR SISTR The Salmonella In Silico Typing Resource (SISTR) is an open-source and freely available web application for rapid in silico typing and serovar prediction from Salmonella genome assemblies using cgMLST and O and H antigen gene searching. https://usegalaxy.eu/published/workflow?id=628062a8cf93261f, https://usegalaxy.eu/published/workflow?id=94c3d329c31c712f, https://usegalaxy.eu/published/workflow?id=cbe3769f1abb9fa5, https://usegalaxy.eu/published/workflow?id=fde21b5f5c169114, https://usegalaxy.org.au/published/workflow?id=2120112358db8e01, https://usegalaxy.org.au/published/workflow?id=41331c03339e2b19, https://usegalaxy.org.au/published/workflow?id=92fcdd490831c6c5, https://workflowhub.eu/workflows/407?version=1 0 1 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 395 397 5345 5466 0 0 0 0 91 95 907 1010 0 0 0 0 6476 6252 492 486 True False +smallgenomeutilities smgu_frameshift_deletions_checks tabular Set of utilities for manipulating small viral genome data. 2023-05-30 https://github.com/cbg-ethz/smallgenomeutilities 0.5.2 smallgenomeutilities 0.5.2 Up-to-date Sequence Analysis Read pre-processing, Sequence alignment, Genetic variation analysis Read pre-processing, Sequence alignment, Genetic variation analysis Genomics, Population genetics, Workflows, Virology, Sequencing Genomics, Population genetics, Workflows, Virology, Sequencing iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/smallgenomeutilities https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities v-pipe V-pipe Bioinformatics pipeline for the analysis of next-generation sequencing data derived from intra-host viral populations. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 15 15 168 168 0 0 0 0 0 0 0 0 0 0 0 0 168 168 15 15 True False +smalt smalt cigar SMALT aligns DNA sequencing reads with a reference genome. 2017-09-19 http://www.sanger.ac.uk/science/tools/smalt-0 @VERSION@ smalt 0.7.6 To update Sequence Analysis nml https://sourceforge.net/projects/smalt/ https://github.com/phac-nml/galaxy_tools/tree/master/tools/smalt 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False +snap snap, snap_training gff, fasta, snaphmm SNAP is a general purpose gene finding program suitable for both eukaryotic and prokaryotic genomes. 2017-10-12 https://github.com/KorfLab/SNAP 2013_11_29 snap 2013_11_29 Up-to-date Sequence Analysis Gene prediction Gene prediction DNA, DNA polymorphism, Genetics DNA polymorphism, Genetics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/snap https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap snap SNAP The Semi-HMM-based Nucleic Acid Parser is a gene prediction tool. https://usegalaxy.eu/published/workflow?id=26ad77bc07a7e512, https://usegalaxy.eu/published/workflow?id=6ca20e710f4f3ffb, https://usegalaxy.org.au/published/workflow?id=7a87dfe5bdd30040, https://usegalaxy.org.au/published/workflow?id=7e40485d1ed45b7c, https://usegalaxy.org/published/workflow?id=c42c66d1b627c5a5, https://workflowhub.eu/workflows/1504?version=1 genome-annotation/annotation-with-maker 1 1 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 348 410 1443 1821 258 292 813 939 100 101 578 594 0 0 0 0 3354 2834 803 706 True False +snippy snippy_core, snippy, snippy_clean_full_aln fasta, tabular, txt, vcf, gff3, bam, zip Contains the snippy tool for characterising microbial snps 2017-07-13 https://github.com/tseemann/snippy 4.6.0 snippy 4.6.0 Up-to-date Sequence Analysis Phylogenetic tree visualisation, Phylogenetic tree generation, Variant calling Phylogenetic tree visualisation, Variant calling Genomics, Model organisms, DNA polymorphism, Phylogenetics Genomics, Model organisms, DNA polymorphism, Phylogenetics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/snippy https://github.com/galaxyproject/tools-iuc/tree/master/tools/snippy snippy snippy Rapid haploid variant calling and core SNP phylogeny generation. https://usegalaxy.eu/published/workflow?id=2b25eaebd3987612, https://usegalaxy.eu/published/workflow?id=2c79eee5ca5a3b09, https://usegalaxy.eu/published/workflow?id=309fc4fc2e0da89c, https://usegalaxy.eu/published/workflow?id=3a8fde248a4d0383, https://usegalaxy.eu/published/workflow?id=3ff4dbcc7a602e6b, https://usegalaxy.eu/published/workflow?id=461d71caea871db8, https://usegalaxy.eu/published/workflow?id=464b642261ed7452, https://usegalaxy.eu/published/workflow?id=4f9f7065975b3f97, https://usegalaxy.eu/published/workflow?id=515ef1601bc24a6c, https://usegalaxy.eu/published/workflow?id=628062a8cf93261f, https://usegalaxy.eu/published/workflow?id=65249196143d7930, https://usegalaxy.eu/published/workflow?id=6d87481be47902e1, https://usegalaxy.eu/published/workflow?id=920aab45ff028ed4, https://usegalaxy.eu/published/workflow?id=94c3d329c31c712f, https://usegalaxy.eu/published/workflow?id=968f0ac2617aa524, https://usegalaxy.eu/published/workflow?id=a183da6b56cd1d60, https://usegalaxy.eu/published/workflow?id=b556b0a67ad979da, https://usegalaxy.eu/published/workflow?id=b681f7b677b23168, https://usegalaxy.eu/published/workflow?id=c38e3ac59d8b86d6, https://usegalaxy.eu/published/workflow?id=c9ef2d2ce92e2dfb, https://usegalaxy.eu/published/workflow?id=d92f9c33dded693f, https://usegalaxy.eu/published/workflow?id=fde21b5f5c169114, https://usegalaxy.org.au/published/workflow?id=1719e0eb54b41f68, https://usegalaxy.org.au/published/workflow?id=5693811cd933d2a2, https://usegalaxy.org.au/published/workflow?id=a61d4bda54de7cd1, https://usegalaxy.org.au/published/workflow?id=fa76b66785ce38b8, https://usegalaxy.org/published/workflow?id=00596e862edb23f2, https://usegalaxy.org/published/workflow?id=23a87246c646eb8a, https://usegalaxy.org/published/workflow?id=562bcaa9b4d2e8a4, https://usegalaxy.org/published/workflow?id=5674956f5c18b85b, https://usegalaxy.org/published/workflow?id=69d8863d40524120, https://usegalaxy.org/published/workflow?id=7dd6e4150bb81ad1, https://usegalaxy.org/published/workflow?id=80ac6adead9f97d8, https://usegalaxy.org/published/workflow?id=d4f0a7ccb09f1e55, https://usegalaxy.org/published/workflow?id=e7ce46762faccaac, https://usegalaxy.org/published/workflow?id=ee4679b3e9e830b7, https://workflowhub.eu/workflows/1035?version=1, https://workflowhub.eu/workflows/1573?version=1, https://workflowhub.eu/workflows/1639?version=1, https://workflowhub.eu/workflows/1647?version=2, https://workflowhub.eu/workflows/2049?version=1 evolution/mtb_transmission, variant-analysis/microbial-variants, variant-analysis/tb-variant-analysis 3 3 3 3 0 0 0 0 0 0 3 0 0 0 0 0 0 0 0 0 0 0 3 3 3 0 3483 3838 188403 199916 4057 4306 138187 142349 2223 2852 67168 78979 60 60 8769 8769 430013 402527 11056 9823 True False +sonneityping sonneityping tabular Scripts for parsing Mykrobe predict results for Shigella sonnei. 2021-09-16 https://github.com/katholt/sonneityping 20210201 sonneityping 20210201 Up-to-date Sequence Analysis Antimicrobial resistance prediction, Variant calling, Genotyping Antimicrobial resistance prediction, Variant calling, Genotyping Whole genome sequencing, Genotype and phenotype, Genetic variation, Metagenomics Whole genome sequencing, Genotype and phenotype, Genetic variation, Metagenomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/sonneityping https://github.com/galaxyproject/tools-iuc/tree/master/tools/sonneityping sonneityping sonneityping Scripts for parsing Mykrobe predict results for Shigella sonnei. 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 2 2 2 2 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 2 True False +sortmerna bg_sortmerna bam, tabular, txt SortMeRNA is a software designed to rapidly filter ribosomal RNA fragments from metatransriptomic data produced by next-generation sequencers. 2015-02-28 http://bioinfo.lifl.fr/RNA/sortmerna/ 5.0.0 sortmerna 4.3.7 To update RNA Sequence similarity search, Sequence comparison, Sequence alignment analysis Sequence similarity search, Sequence alignment analysis Metatranscriptomics, Metagenomics Metatranscriptomics, Metagenomics rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna sortmerna SortMeRNA Sequence analysis tool for filtering, mapping and OTU-picking NGS reads. https://usegalaxy.eu/published/workflow?id=096b75501c8e0888, https://usegalaxy.eu/published/workflow?id=2cf09adb1ed6c3ec, https://usegalaxy.eu/published/workflow?id=385cc7df70d7916b, https://usegalaxy.eu/published/workflow?id=401746888e8b3aa8, https://usegalaxy.eu/published/workflow?id=4d32b1b3ac0a7161, https://usegalaxy.eu/published/workflow?id=5f0faac42b0a5062, https://usegalaxy.eu/published/workflow?id=69eddfde874af35b, https://usegalaxy.eu/published/workflow?id=72e3e5fdc766e24a, https://usegalaxy.eu/published/workflow?id=7ab70660e6235cf0, https://usegalaxy.eu/published/workflow?id=87cc0cd143a12c41, 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https://usegalaxy.org.au/published/workflow?id=408a31694e9c85e6, https://workflowhub.eu/workflows/1444?version=2, https://workflowhub.eu/workflows/1466?version=2 microbiome/metatranscriptomics, microbiome/metatranscriptomics-short 1 1 1 1 0 0 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1135 1352 23920 26406 581 581 6479 6479 219 225 3668 3882 116 116 648 651 37418 34715 2274 2051 True False +spades spades_biosyntheticspades, spades_coronaspades, spades_metaplasmidspades, metaspades, spades_metaviralspades, spades_plasmidspades, rnaspades, spades_rnaviralspades, spades fasta, txt SPAdes is an assembly toolkit containing various assembly pipelines. It implements the following 4 stages: assembly graph construction, k-bimer adjustment, construction of paired assembly graph and contig construction. 2016-12-21 https://github.com/ablab/spades 4.3.0 spades 4.3.0 Up-to-date Assembly, RNA, Metagenomics Genome assembly Genome assembly Sequence assembly Sequence assembly iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/spades https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades spades SPAdes St. Petersburg genome assembler – is intended for both standard isolates and single-cell MDA bacteria assemblies. SPAdes 3.9 works with Illumina or IonTorrent reads and is capable of providing hybrid assemblies using PacBio, Oxford Nanopore and Sanger reads. Additional contigs can be provided and can be used as long reads. https://usegalaxy.eu/published/workflow?id=007ce6405d196df3, https://usegalaxy.eu/published/workflow?id=02631612a43a4d9b, https://usegalaxy.eu/published/workflow?id=1860e02bcb894a64, https://usegalaxy.eu/published/workflow?id=37da7b42cb063a3a, https://usegalaxy.eu/published/workflow?id=49c46d7653d6c349, https://usegalaxy.eu/published/workflow?id=579ff83177c5ee09, https://usegalaxy.eu/published/workflow?id=62c47e3c9d4f3aa3, https://usegalaxy.eu/published/workflow?id=7b755497d168cb13, https://usegalaxy.eu/published/workflow?id=7ecd92cb382d8168, https://usegalaxy.eu/published/workflow?id=87231a6a7938cb95, https://usegalaxy.eu/published/workflow?id=8c7958cb05fba814, https://usegalaxy.eu/published/workflow?id=9382f9bbbdddb5ad, https://usegalaxy.eu/published/workflow?id=93d1035a307fe63d, https://usegalaxy.eu/published/workflow?id=98bfad0c684011e9, https://usegalaxy.eu/published/workflow?id=9a97c6eb4fe015e7, 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https://usegalaxy.org/published/workflow?id=7251c6e0dad8f927, https://usegalaxy.org/published/workflow?id=84233173d92fa506, https://usegalaxy.org/published/workflow?id=87b3305ea433b4e2, https://usegalaxy.org/published/workflow?id=8a350e0d96e937a5, https://usegalaxy.org/published/workflow?id=8d229c0f58a07ebe, https://usegalaxy.org/published/workflow?id=8eb22336826a0f75, https://usegalaxy.org/published/workflow?id=9203f914b3e498a1, https://usegalaxy.org/published/workflow?id=9ba6da7dae465d3e, https://usegalaxy.org/published/workflow?id=9c0fbd9f51a9857f, https://usegalaxy.org/published/workflow?id=ae81cc0e8263d03e, https://usegalaxy.org/published/workflow?id=d3357032209bbd02, https://usegalaxy.org/published/workflow?id=e0c33057ac2670ba, https://usegalaxy.org/published/workflow?id=fb01e1a49793c8be, https://workflowhub.eu/workflows/1390?version=2, https://workflowhub.eu/workflows/1626?version=1, https://workflowhub.eu/workflows/1634?version=1, https://workflowhub.eu/workflows/2046?version=1, https://workflowhub.eu/workflows/2047?version=1, https://workflowhub.eu/workflows/2048?version=1, https://workflowhub.eu/workflows/434?version=1, https://workflowhub.eu/workflows/52?version=1, https://workflowhub.eu/workflows/68?version=1 assembly/debruijn-graph-assembly, assembly/metagenomics-assembly, microbiome/metagenomics-assembly 9 9 9 9 0 0 0 0 2 3 3 0 0 0 0 0 0 0 3 0 0 0 3 9 3 0 8250 8882 104429 116176 14023 14731 147425 154112 5211 6722 62902 76811 373 380 2677 2762 349861 317433 30715 27857 True False +spotyping spotyping txt, excel.xls, pdf SpoTyping allows fast and accurate in silico Mycobacterium spoligotyping from sequence reads 2018-05-08 https://github.com/xiaeryu/SpoTyping-v2.0 2.1 spotyping 2.1 Up-to-date Sequence Analysis Variant pattern analysis Variant pattern analysis Microbiology, Sequencing, Sequence composition, complexity and repeats, Genetic variation Microbiology, Sequencing, Sequence composition, complexity and repeats, Genetic variation iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/spotyping https://github.com/galaxyproject/tools-iuc/tree/master/tools/spotyping spotyping SpoTyping Fast and accurate in silico Mycobacterium spoligotyping from sequence reads. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 34 34 2042 2042 0 0 0 0 0 0 0 0 0 0 0 0 2042 2042 34 34 True False +squirrel squirrel_phylo, squirrel_qc nexus, fasta, svg, png, csv QC and Phylogenetic analysis of MPXV 2025-01-16 https://github.com/aineniamh/squirrel 1.0.13 squirrel 1.3.2 To update Phylogenetics Phylogenetic analysis, Sequencing quality control Phylogenetic analysis, Sequencing quality control Virology Virology iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/squirrel https://github.com/galaxyproject/tools-iuc/tree/master/tools/squirrel squirrel squirrel Some QUIck Reconstruction to Resolve Evolutionary LinksSquirrel provides a rapid way of producing reliable alignments for MPXV and also enable maximum-likelihood phylogenetics pipeline tree estimation. https://usegalaxy.org.au/published/workflow?id=b9fd488b0938d323, https://workflowhub.eu/workflows/2196?version=1 0 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 7 7 0 0 0 0 41 41 193 193 0 0 0 0 200 200 43 43 True False +sr_bowtie bowtieForSmallRNA tabular bowtie wrapper tool to align small RNA sequencing reads 2017-09-02 http://artbio.fr 2.3.1 bowtie 1.3.1 To update RNA, Next Gen Mappers Microbiology, Biology Microbiology artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie sr_bowtie sr_bowtie "Bowtie_ is a short read aligner designed to be ultrafast and memory-efficient. It is developed by Ben Langmead and Cole Trapnell. Please cite: Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biology 10:R25... _Bowtie: http://bowtie-bio.sourceforge.net/index.shtmlA generic ""Map with Bowtie for Illumina"" Galaxy tool is available in the main Galaxy distribution.However, this Bowtie wrapper tool only takes FASTQ files as inputs.The sRbowtie wrapper works with short (-v bowtie mode) reads inputs, in fasta or fastq format, and proposes a simplified set of configurations suited to small RNA analysis." 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 2 2 98 98 0 0 0 0 0 0 0 0 98 98 2 2 True False +srst2 srst2 bam, tabular, fasta Short Read Sequence Typing for Bacterial Pathogens 2015-12-02 0.3.7 srst2 0.2.0 To update Sequence Analysis nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/srst2 https://workflowhub.eu/workflows/407?version=1 0 0 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 68 68 407 407 1 1 71 71 0 0 0 0 0 0 0 0 478 478 69 69 True False +srst2 srst2 tabular, fasta SRST2 Short Read Sequence Typing for Bacterial Pathogens 2022-08-22 http://katholt.github.io/srst2/ 0.2.0 samtools 1.23.1 To update Metagenomics Multilocus sequence typing Multilocus sequence typing Whole genome sequencing, Public health and epidemiology, Comparative genomics Whole genome sequencing, Public health and epidemiology, Comparative genomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/srst2 https://github.com/galaxyproject/tools-iuc/tree/master/tools/srst2 srst2 srst2 Short Read Sequence Typing for Bacterial Pathogens https://workflowhub.eu/workflows/407?version=1 0 0 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 68 68 407 407 1 1 71 71 0 0 0 0 0 0 0 0 478 478 69 69 True False +staramr staramr_search tabular, txt, xlsx Scan genome contigs against the ResFinder, PlasmidFinder, and PointFinder antimicrobial resistance databases. 2024-09-19 https://github.com/phac-nml/staramr @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ staramr 0.12.3 To update Sequence Analysis Antimicrobial resistance prediction Antimicrobial resistance prediction Microbiology, Public health and epidemiology, Infectious disease Microbiology, Public health and epidemiology, Infectious disease iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/staramr https://github.com/galaxyproject/tools-iuc/tree/master/tools/staramr staramr staramr staramr (*AMR) scans bacterial genome contigs against the ResFinder, PointFinder, and PlasmidFinder databases (used by the ResFinder webservice and other webservices offered by the Center for Genomic Epidemiology) and compiles a summary report of detected antimicrobial resistance genes. The star|* in staramr indicates that it can handle all of the ResFinder, PointFinder, and PlasmidFinder databases. https://usegalaxy.eu/published/workflow?id=007ce6405d196df3, https://usegalaxy.eu/published/workflow?id=152223c8aed27357, https://usegalaxy.eu/published/workflow?id=1ce523ef51f47134, https://usegalaxy.eu/published/workflow?id=249c115413f17f28, https://usegalaxy.eu/published/workflow?id=2e0075791f7fa384, https://usegalaxy.eu/published/workflow?id=32d2f5340098bcbd, https://usegalaxy.eu/published/workflow?id=32de10b9de8a999a, https://usegalaxy.eu/published/workflow?id=34df701aa23a9fb3, https://usegalaxy.eu/published/workflow?id=374797e58377c40f, https://usegalaxy.eu/published/workflow?id=39837ca09374598b, https://usegalaxy.eu/published/workflow?id=41d207d06a32ba05, https://usegalaxy.eu/published/workflow?id=44e53ea319e07daa, https://usegalaxy.eu/published/workflow?id=46b6812817c57a01, https://usegalaxy.eu/published/workflow?id=4ddbffe4b3fef275, https://usegalaxy.eu/published/workflow?id=628062a8cf93261f, https://usegalaxy.eu/published/workflow?id=6d87481be47902e1, https://usegalaxy.eu/published/workflow?id=7aa32aba3fde0708, https://usegalaxy.eu/published/workflow?id=9219557de92e0203, https://usegalaxy.eu/published/workflow?id=94c3d329c31c712f, https://usegalaxy.eu/published/workflow?id=a06b1ed5cd25922f, https://usegalaxy.eu/published/workflow?id=abe85758e77c78e6, https://usegalaxy.eu/published/workflow?id=b203dec6ee6da2fd, https://usegalaxy.eu/published/workflow?id=b2b46e71046b1999, https://usegalaxy.eu/published/workflow?id=b46d67d91391053d, https://usegalaxy.eu/published/workflow?id=b4de76c0a4d0e23a, https://usegalaxy.eu/published/workflow?id=b60a3e0427f2f519, https://usegalaxy.eu/published/workflow?id=c48807045e258dd8, https://usegalaxy.eu/published/workflow?id=d0339e4a794f4922, https://usegalaxy.eu/published/workflow?id=dc7107896a3f2964, https://usegalaxy.eu/published/workflow?id=e37cc0b64774561b, https://usegalaxy.eu/published/workflow?id=ea485dbabc76488d, https://usegalaxy.eu/published/workflow?id=eb5ab8bc82569eee, https://usegalaxy.eu/published/workflow?id=ecf48fa50af560a0, https://usegalaxy.eu/published/workflow?id=f30f8e7dcd50cd0d, https://usegalaxy.eu/published/workflow?id=ffd365c037373673, https://usegalaxy.org.au/published/workflow?id=05f3abecd4ddd4a1, https://usegalaxy.org.au/published/workflow?id=2120112358db8e01, https://usegalaxy.org.au/published/workflow?id=2e29b21cdec7d0cc, https://usegalaxy.org.au/published/workflow?id=35f39173f0ac9179, https://usegalaxy.org.au/published/workflow?id=41331c03339e2b19, https://usegalaxy.org.au/published/workflow?id=92fcdd490831c6c5, https://usegalaxy.org.au/published/workflow?id=c9b7de574fb2f2d5, https://usegalaxy.org.au/published/workflow?id=d9571b3dfef34e5e, https://usegalaxy.org/published/workflow?id=2078a54de1f2628d, https://usegalaxy.org/published/workflow?id=2b4b1fe82258f303, https://usegalaxy.org/published/workflow?id=3c177fdf38311118, https://usegalaxy.org/published/workflow?id=547f86db467bf620, https://usegalaxy.org/published/workflow?id=aaf8e740b3f8e2c0, https://usegalaxy.org/published/workflow?id=d3dc805cd43b2737, https://usegalaxy.org/published/workflow?id=d4f0a7ccb09f1e55, https://usegalaxy.org/published/workflow?id=ef187f85b103d858, https://usegalaxy.org/published/workflow?id=f8fab0cd6fc30d92, https://usegalaxy.org/published/workflow?id=fde774a049875466, https://workflowhub.eu/workflows/1049?version=9, https://workflowhub.eu/workflows/1189?version=2, https://workflowhub.eu/workflows/1477?version=1, https://workflowhub.eu/workflows/1488?version=2, https://workflowhub.eu/workflows/2024?version=4, https://workflowhub.eu/workflows/406?version=1, https://workflowhub.eu/workflows/470?version=1 genome-annotation/amr-gene-detection, microbiome/plasmid-metagenomics-nanopore 1 1 1 1 0 0 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 2921 3072 31443 33124 2130 2130 14763 14763 1173 1182 8989 9237 97 97 9838 9838 66962 65033 6481 6321 True False +stringmlst stringmlst tabular, txt, fastqsanger Rapid and accurate identification of the sequence type (ST) 2016-10-19 1.1.0 stringMLST 0.6.3 To update Sequence Analysis nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/stringmlst 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False +structure structure txt for using multi-locus genotype data to investigate population structure. 2017-09-22 https://web.stanford.edu/group/pritchardlab/structure.html @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ structure 2.3.4 To update Phylogenetics, Variant Analysis Genetic variation analysis Genetic variation analysis Population genetics Population genetics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/structure https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure structure Structure The program structureis a free software package for using multi-locus genotype data to investigate population structure. Its uses include inferring the presence of distinct populations, assigning individuals to populations, studying hybrid zones, identifying migrants and admixed individuals, and estimating population allele frequencies in situations where many individuals are migrants or admixed. 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 138 155 3903 4354 0 0 0 0 0 0 0 0 3 3 330 330 4684 4233 158 141 True False +suite_qiime2_core 2022-08-29 To update Statistics, Sequence Analysis, Metagenomics q2d2 https://github.com/qiime2/galaxy-tools/tree/master/tool_collections/suite_qiime2_core 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False +sylph sylph_profile, sylph_query tabular sylph - fast and precise species-level metagenomic profiling with ANIs 2024-10-08 https://github.com/bluenote-1577/sylph 0.8.1 sylph 0.9.0 To update Metagenomics Taxonomic classification Taxonomic classification Metagenomics Metagenomics bgruening https://github.com/bgruening/galaxytools/main/tools/sylph https://github.com/bgruening/galaxytools/tree/master/tools/sylph sylph sylph fast and precise species-level metagenomic profiling with ANIs https://usegalaxy.eu/published/workflow?id=7491883694fff308, https://usegalaxy.eu/published/workflow?id=cb2df493f5e334f7, https://workflowhub.eu/workflows/2068?version=2 2 2 2 2 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 9 9 257 257 1 1 1 1 0 0 0 0 1 1 12 12 270 270 11 11 True False +syri syri tabular, vcf Synteny and Rearrangement Identifier 2025-04-16 https://github.com/schneebergerlab/syri 1.7.1 syri 1.7.1 Up-to-date Sequence Analysis Haplotype mapping, Variant calling, Genotyping, Sequence assembly, Read mapping Haplotype mapping, Variant calling, Genotyping, Sequence assembly, Read mapping DNA polymorphism, Sequence assembly, DNA structural variation, Mapping, Sequencing DNA polymorphism, Sequence assembly, Mapping, Sequencing iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/syri https://github.com/galaxyproject/tools-iuc/tree/master/tools/syri SyRI SyRI SyRI is tool for finding genomic rearrangements and local sequence differences from whole-genome assemblies.Genomic differences range from single nucleotide differences to complex structural variations. Current methods typically annotate sequence differences ranging from SNPs to large indels accurately but do not unravel the full complexity of structural rearrangements, including inversions, translocations, and duplications, where highly similar sequence changes in location, orientation, or copy number. Here, we present SyRI, a pairwise whole-genome comparison tool for chromosome-level assemblies. SyRI starts by finding rearranged regions and then searches for differences in the sequences, which are distinguished for residing in syntenic or rearranged regions. This distinction is important as rearranged regions are inherited differently compared to syntenic regions. https://usegalaxy.fr/published/workflow?id=356dced9687596b7, https://usegalaxy.fr/published/workflow?id=ce4acd38084ee9ef 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 22 22 84 84 0 0 0 0 0 0 0 0 5 5 76 76 160 160 27 27 True False +t2ps Draw_phylogram pdf Draw phylogeny 2014-01-27 https://bitbucket.org/natefoo/taxonomy 1.0.0 taxonomy 0.10.5 To update Metagenomics Phylogenetic tree visualisation Phylogenetic tree visualisation Phylogenomics Phylogenomics devteam https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/t2ps https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/t2ps t2ps Draw phylogeny """Given taxonomy representation (produced by *Fetch taxonomic representation* tool) this utility produces a graphical representations of phylogenetic tree in PDF format."" - Galaxy tool wrapper" https://usegalaxy.org/published/workflow?id=19c9c8cc3c813bda, https://usegalaxy.org/published/workflow?id=2f7638035fb889ac, https://usegalaxy.org/published/workflow?id=55aa743125c2465d, https://usegalaxy.org/published/workflow?id=59347cc210c4cdbc, https://usegalaxy.org/published/workflow?id=7294f75ad01ca7ed, https://usegalaxy.org/published/workflow?id=7b67ffcf1b7c2232, https://usegalaxy.org/published/workflow?id=85d825931edf4a64, https://usegalaxy.org/published/workflow?id=896d29573ea3e574, https://usegalaxy.org/published/workflow?id=d851f8436497dd1c 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 64 93 405 479 13 1240 102 7952 0 0 0 0 0 0 0 0 8431 507 1333 77 True False +t2t_report t2t_report tabular Summarize taxonomy 2014-01-27 https://bitbucket.org/natefoo/taxonomy 1.0.0 taxonomy 0.10.5 To update Metagenomics devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/t2t_report https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/t2t_report https://usegalaxy.org/published/workflow?id=19c9c8cc3c813bda, https://usegalaxy.org/published/workflow?id=2f7638035fb889ac, https://usegalaxy.org/published/workflow?id=55aa743125c2465d, https://usegalaxy.org/published/workflow?id=59347cc210c4cdbc, https://usegalaxy.org/published/workflow?id=7b67ffcf1b7c2232, https://usegalaxy.org/published/workflow?id=85d825931edf4a64, https://usegalaxy.org/published/workflow?id=896d29573ea3e574, https://usegalaxy.org/published/workflow?id=d851f8436497dd1c 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 55 82 745 1071 16 1143 118 7194 0 0 0 0 0 0 0 0 8265 863 1225 71 True False +t_coffee t_coffee clustal, nhx, fasta, msf, phylip, pir, txt, html T-Coffee 2016-12-13 https://tcoffee.org/ @TOOL_VERSION@ t-coffee 13.46.0.919e8c6b To update Sequence Analysis earlhaminst https://github.com/EarlhamInst/earlham-galaxytools/tree/main/tools/t_coffee https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 274 311 3958 9664 1 1 1 1 0 0 0 0 0 0 0 0 9665 3959 312 275 True False +taxonkit name2taxid, profile2cami tabular, tsv TaxonKit - A Practical and Efficient NCBI Taxonomy Toolkit 2024-07-26 https://bioinf.shenwei.me/taxonkit/ 0.20.0 taxonkit 0.20.0 Up-to-date Metagenomics Formatting, Data retrieval Formatting, Data retrieval Taxonomy, Biotechnology, Ecology Taxonomy, Biotechnology, Ecology iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/taxonkit https://github.com/galaxyproject/tools-iuc/tree/master/tools/taxonkit taxonkit TaxonKit TaxonKit is a practical and efficient NCBI taxonomy toolkit. https://usegalaxy.eu/published/workflow?id=cf0159c14418525e, https://usegalaxy.eu/published/workflow?id=e4dabaf57668dbd1, https://workflowhub.eu/workflows/2099?version=2 1 1 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 12 12 1094 1094 0 0 0 0 0 0 0 0 0 0 0 0 1094 1094 12 12 True False +taxonomy_krona_chart taxonomy_krona_chart html Krona pie chart from taxonomic profile 2015-08-06 http://sourceforge.net/projects/krona/ 2.7.1 krona 2.8.1 To update Assembly Visualisation Visualisation Metagenomics Metagenomics crs4 https://github.com/galaxyproject/tools-iuc/tree/main/tools/taxonomy_krona_chart https://github.com/galaxyproject/tools-iuc/tree/master/tools/taxonomy_krona_chart krona Krona Krona creates interactive HTML5 charts of hierarchical data (such as taxonomic abundance in a metagenome). https://usegalaxy.eu/published/workflow?id=007ce6405d196df3, https://usegalaxy.eu/published/workflow?id=0590554db9794d13, https://usegalaxy.eu/published/workflow?id=05f5f040337786bf, https://usegalaxy.eu/published/workflow?id=08e25b733cd796e6, https://usegalaxy.eu/published/workflow?id=08eb5e55109c4d9c, https://usegalaxy.eu/published/workflow?id=096b75501c8e0888, https://usegalaxy.eu/published/workflow?id=0bafeb17c21ebc9c, 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biom1 standardise taxonomic profiles 2023-08-30 https://taxpasta.readthedocs.io/en/latest/ @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ taxpasta 0.7.0 To update Sequence Analysis Standardisation and normalisation, Aggregation, Formatting, Conversion Standardisation and normalisation, Aggregation, Formatting, Conversion Taxonomy, Metagenomics Taxonomy, Metagenomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/taxpasta https://github.com/galaxyproject/tools-iuc/tree/master/tools/taxpasta taxpasta taxpasta TAXonomic Profile Aggregation and STAndardisationThe main purpose of taxpasta is to standardise taxonomic profiles created by a range of bioinformatics tools. We call those tools taxonomic profilers. They each come with their own particular tabular output format. Across the profilers, relative abundances can be reported in read counts, fractions, or percentages, as well as any number of additional columns with extra information. We therefore decided to take the lessons learnt to heart and provide our own solution to deal with this pasticcio. With taxpasta you can ingest all of those formats and, at a minimum, output taxonomy identifiers and their integer counts. Taxpasta can not only standardise profiles but also merge them across samples for the same profiler into a single table. https://usegalaxy.eu/published/workflow?id=7491883694fff308, https://usegalaxy.eu/published/workflow?id=b14845359b702444, https://usegalaxy.eu/published/workflow?id=cb2df493f5e334f7 0 0 1 1 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 51 51 323 323 0 0 0 0 0 0 0 0 1 1 18 18 341 341 52 52 True False +tb-profiler tb_profiler_collate, tb_profiler_profile tabular, csv, txt, json, vcf, bam, pdf Processes M. tuberculosis sequence data to infer strain type and identify known drug resistance markers. 2019-04-02 https://github.com/jodyphelan/TBProfiler 6.6.5 tb-profiler 6.7.0 To update Sequence Analysis Antimicrobial resistance prediction Antimicrobial resistance prediction iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/tb-profiler https://github.com/galaxyproject/tools-iuc/tree/master/tools/tb-profiler tb-profiler tb-profiler A tool for drug resistance prediction from _M. tuberculosis_ genomic data (sequencing reads, alignments or variants). https://usegalaxy.eu/published/workflow?id=2b25eaebd3987612, https://usegalaxy.eu/published/workflow?id=2c79eee5ca5a3b09, https://usegalaxy.eu/published/workflow?id=3ff4dbcc7a602e6b, https://usegalaxy.eu/published/workflow?id=461d71caea871db8, https://usegalaxy.eu/published/workflow?id=89ed570bc0703472, https://usegalaxy.eu/published/workflow?id=c38e3ac59d8b86d6, https://usegalaxy.eu/published/workflow?id=d0d6dae0d1eecc21, https://usegalaxy.org.au/published/workflow?id=5693811cd933d2a2, https://usegalaxy.org.au/published/workflow?id=a61d4bda54de7cd1, https://usegalaxy.org/published/workflow?id=e7ce46762faccaac, https://workflowhub.eu/workflows/1035?version=1, https://workflowhub.eu/workflows/1564?version=1, https://workflowhub.eu/workflows/1647?version=2, https://workflowhub.eu/workflows/2049?version=1 evolution/mtb_transmission, variant-analysis/tb-variant-analysis 1 2 2 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 491 535 15947 16201 490 506 11483 11641 199 201 10939 10981 0 0 0 0 38823 38369 1242 1180 True False +tiara tiara tabular, txt Tool for identification of eukaryotic sequences in the metagenomic datasets. 2024-05-23 https://github.com/ibe-uw/tiara 1.0.3 tiara To update Metagenomics, Sequence Analysis Genome comparison, Data retrieval, Variant calling, Genome visualisation, Structural variation detection Genome comparison, Data retrieval, Variant calling, Genome visualisation, Structural variation detection Sequencing, Genomics, DNA polymorphism, DNA structural variation Sequencing, Genomics, DNA polymorphism bgruening https://github.com/bgruening/galaxytools/tree/master/tools/tiara https://github.com/bgruening/galaxytools/tree/master/tools/tiara Tiara TIARA Total Integrated Archive of Short-Read and Array (TIARA) database, contains personal genomic information obtained from next generation sequencing (NGS) techniques and ultra-high-resolution comparative genomic hybridization (CGH) arrays. 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292 292 True False +transtermhp transtermhp gff3 Finds rho-independent transcription terminators in bacterial genomes 2015-10-08 https://transterm.cbcb.umd.edu 2.09.1 transtermhp 2.09 To update Sequence Analysis Transcriptional regulatory element prediction Transcriptional regulatory element prediction Transcription factors and regulatory sites Transcription factors and regulatory sites iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/transtermhp https://github.com/galaxyproject/tools-iuc/tree/master/tools/transtermhp transtermhp TransTermHP TransTermHP finds rho-independent transcription terminators in bacterial genomes. Each terminator found by the program is assigned a confidence value that estimates its probability of being a true terminator 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 59 62 467 502 49 55 170 216 0 0 0 0 0 0 0 0 718 637 117 108 True False +treebest_best treebest_best nhx TreeBeST best 2015-08-06 https://treesoft.sourceforge.net/treebest.shtml 1.9.2.post0 treebest 1.9.2.post1 To update Phylogenetics Phylogenetic tree visualisation, Phylogenetic analysis, Phylogenetic inference (from molecular sequences) Phylogenetic tree visualisation, Phylogenetic inference (from molecular sequences) Phylogenetics Phylogenetics earlhaminst https://github.com/EarlhamInst/earlham-galaxytools/tree/main/tools/TreeBest https://github.com/TGAC/earlham-galaxytools/tree/master/tools/TreeBest treebest TreeBeST TreeBeST, which stands for (gene) Tree Building guided by Species Tree, is a versatile program that builds, manipulates and displays phylogenetic trees. 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It has been largely used in the TreeFam database, Ensembl Compara and OPTIC database of Chris Ponting group. 0 0 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 45 58 966 1033 0 0 0 0 0 0 0 0 1 1 1 1 1034 967 59 46 True False +trim_galore trim_galore txt Trim Galore adaptive quality and adapter trimmer 2015-02-28 http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/ 0.6.10 trim-galore 2.3.0 To update Sequence Analysis, Fastq Manipulation Sequence trimming, Primer removal, Read pre-processing Sequence trimming, Primer removal, Read pre-processing Sequence analysis Sequence analysis bgruening https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore trim_galore Trim Galore A wrapper tool around Cutadapt and FastQC to consistently apply quality and adapter trimming to FastQ files, with some extra functionality for MspI-digested RRBS-type (Reduced Representation Bisufite-Seq) libraries. 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metaproteomics information 2015-04-03 https://github.com/galaxyproteomics/tools-galaxyp 6.2.4 python To update Proteomics Prediction and recognition, Visualisation Prediction and recognition, Visualisation Proteomics, Proteogenomics, Biodiversity, Workflows Proteomics, Proteogenomics, Biodiversity, Workflows galaxyp https://unipept.ugent.be/apidocs https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/unipept unipept Unipept Metaproteomics data analysis with a focus on interactive data visualizations. https://usegalaxy.eu/published/workflow?id=00e246ea459b0991, https://usegalaxy.eu/published/workflow?id=02700454f57eb556, https://usegalaxy.eu/published/workflow?id=0e0be913c3e27022, https://usegalaxy.eu/published/workflow?id=1706bfa819bbfa89, https://usegalaxy.eu/published/workflow?id=17a1433d0b681d4a, https://usegalaxy.eu/published/workflow?id=229a955d29bd4064, https://usegalaxy.eu/published/workflow?id=28af61ead68e0976, 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microbiome/clinical-mp-3-verification, proteomics/clinical-mp-1-database-generation, proteomics/clinical-mp-3-verification 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 239 313 1805 2133 73 73 143 143 41 41 1139 1139 0 0 0 0 3415 3087 427 353 True False +usher usher_matutils, usher_ripples, usher txt, tabular, vcf, protobuf3, json, newick UShER toolkit wrappers 2021-05-11 https://github.com/yatisht/usher 0.6.6 usher 0.6.6 Up-to-date Phylogenetics Classification, Phylogenetic tree visualisation, Phylogenetic inference (from molecular sequences) Classification, Phylogenetic tree visualisation, Phylogenetic inference (from molecular sequences) Phylogeny, Evolutionary biology, Cladistics, Genotype and phenotype, Phylogenomics Cladistics, Genotype and phenotype, Phylogenomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher usher usher The UShER toolkit includes a set of tools for for rapid, accurate placement of samples to existing phylogenies. While not restricted to SARS-CoV-2 phylogenetic analyses, it has enabled real-time phylogenetic analyses and genomic contact tracing in that its placement is orders of magnitude faster and more memory-efficient than previous methods. 0 0 3 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 5 5 1060 1060 0 0 0 0 0 0 0 0 0 0 0 0 1060 1060 5 5 True False +valet valet pdf A pipeline for detecting mis-assemblies in metagenomic assemblies. 2017-11-16 https://github.com/marbl/VALET @WRAPPER_VERSION@.0 valet 1.0 To update Metagenomics Sequence assembly, Sequence assembly visualisation Sequence assembly, Sequence assembly visualisation Metagenomics, Sequence assembly Metagenomics, Sequence assembly iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/valet https://github.com/galaxyproject/tools-iuc/tree/master/tools/valet valet VALET VALET is a pipeline for detecting mis-assemblies in metagenomic assemblies. https://usegalaxy.eu/published/workflow?id=1524b189069b42a5, https://usegalaxy.eu/published/workflow?id=579ff83177c5ee09 1 0 1 1 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 74 101 449 711 67 76 160 249 0 0 0 0 0 0 0 0 960 609 177 141 True False +vapor vapor tabular, fasta Classify Influenza samples from raw short read sequence data 2022-08-24 https://github.com/wm75/vaporup @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ vapor 1.0.3 To update Sequence Analysis Data retrieval, De-novo assembly, Read mapping Data retrieval, De-novo assembly, Read mapping Whole genome sequencing, Mapping, Sequence assembly Whole genome sequencing, Mapping, Sequence assembly iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/vapor https://github.com/galaxyproject/tools-iuc/tree/master/tools/vapor vapor VAPOR VAPOR is a tool for classification of Influenza samples from raw short read sequence data for downstream bioinformatics analysis. VAPOR is provided with a fasta file of full-length sequences (> 20,000) for a given segment, a set of reads, and attempts to retrieve a reference that is closest to the sample strain. https://usegalaxy.eu/published/workflow?id=4db391b405f2ed38, https://usegalaxy.eu/published/workflow?id=629e57958afed44c, https://usegalaxy.eu/published/workflow?id=7c986f4d14c6a539, https://usegalaxy.eu/published/workflow?id=a15dabcadb63b46d, https://usegalaxy.eu/published/workflow?id=c789ab71876c6ead, https://usegalaxy.eu/published/workflow?id=cd25f70f71683ab6, https://usegalaxy.eu/published/workflow?id=e353c6a106fa9e4c, https://usegalaxy.org/published/workflow?id=1518c8c50747a1c1, https://usegalaxy.org/published/workflow?id=97263f3308077ff0, https://usegalaxy.org/published/workflow?id=f7d9656f4cb77079, https://workflowhub.eu/workflows/1260?version=3 variant-analysis/aiv-analysis 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 188 188 197466 197466 127 127 1849 1849 0 0 0 0 0 0 0 0 199315 199315 315 315 True False +varvamp varvamp txt, fasta, bed, tabular, pdf Variable VirusAMPlicons (varVAMP) is a tool to design primers for highly diverse viruses 2024-01-27 https://github.com/jonas-fuchs/varVAMP/ 1.3 varvamp 1.3.2 To update Sequence Analysis PCR primer design PCR primer design Virology, Probes and primers Virology, Probes and primers iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/varvamp https://github.com/galaxyproject/tools-iuc/tree/master/tools/varvamp varvamp varVAMP variable VirusAMPlicons (varVAMP) is a tool to design primers for highly diverse viruses. The input is an alignment of your viral (full-genome) sequences. https://workflowhub.eu/workflows/1627?version=1 sequence-analysis/viral_primer_design 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 55 55 912 912 0 0 0 0 0 0 0 0 0 0 0 0 912 912 55 55 True False +vcontact2 vcontact2, vcontact2_gene2genome csv, tabular Tool to provide taxonomic context of metagenomic sequencing data 2025-11-10 https://bitbucket.org/MAVERICLab/vcontact2/src/master/ 0.11.3 python To update Metagenomics Deposition, Taxonomic classification, Genome annotation Deposition, Taxonomic classification, Genome annotation Taxonomy, Metagenomics, Microbial ecology Taxonomy, Metagenomics, Microbial ecology iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/vcontact2 https://github.com/galaxyproject/tools-iuc/tree/master/tools/vcontact2 vConTACT vConTACT Network-based application utilizing whole genome gene-sharing profiles for virus taxonomy that integrates distance-based hierarchical clustering and confidence scores for all taxonomic predictions. https://usegalaxy.eu/published/workflow?id=62392daea25a3980 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False +vegan vegan_diversity, vegan_fisher_alpha, vegan_rarefaction tabular, png, txt an R package fo community ecologist 2015-08-27 https://cran.r-project.org/package=vegan 2.4-3 r-vegan 2.3_4 To update Metagenomics Standardisation and normalisation, Analysis Standardisation and normalisation, Analysis Ecology, Phylogenetics, Environmental science Ecology, Phylogenetics, Environmental science iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/vegan https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan vegan vegan Ordination methods, diversity analysis and other functions for community and vegetation ecologists 3 0 3 0 0 0 0 0 0 0 3 0 0 0 0 0 0 0 0 0 0 0 3 3 3 0 101 116 2314 2547 167 318 3493 5788 0 0 0 0 0 0 0 0 8335 5807 434 268 True False +velvet velvetg, velveth txt, afg, fasta, tabular, velvet de novo genomic assembler specially designed for short read sequencing technologies 2020-06-09 https://www.ebi.ac.uk/~zerbino/velvet/ 1.2.10.3 velvet 1.2.10 To update Assembly Formatting, De-novo assembly Formatting, De-novo assembly Sequence assembly Sequence assembly devteam https://github.com/galaxyproject/tools-iuc/tree/main/tools/velvet https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvet velvet Velvet A de novo genomic assembler specially designed for short read sequencing technologies, such as Solexa or 454 or SOLiD. https://usegalaxy.eu/published/workflow?id=01dc0619e050dc91, https://usegalaxy.eu/published/workflow?id=56edd22d14392691, https://usegalaxy.eu/published/workflow?id=6d87481be47902e1, https://usegalaxy.eu/published/workflow?id=842e0ea7b1eb56af, https://usegalaxy.eu/published/workflow?id=b7c2440621968526, https://usegalaxy.eu/published/workflow?id=ef83f7fd2176a244, 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https://usegalaxy.org/published/workflow?id=1c7af480caf150bd, https://usegalaxy.org/published/workflow?id=2b1cdf79e8df5a78, https://usegalaxy.org/published/workflow?id=3cf46c167ccb374f, https://usegalaxy.org/published/workflow?id=4e1ae78405034ad3, https://usegalaxy.org/published/workflow?id=51c485af11d90700, https://usegalaxy.org/published/workflow?id=7a33bc2d0970b502, https://usegalaxy.org/published/workflow?id=ae6e37c90b8f2a86, https://usegalaxy.org/published/workflow?id=c30f6ca171896908, https://usegalaxy.org/published/workflow?id=c43c3836f51479c0, https://usegalaxy.org/published/workflow?id=e2ab3d3219a648a7, https://usegalaxy.org/published/workflow?id=e745c45651d829b8, https://usegalaxy.org/published/workflow?id=f6bd33dedc7c6c12, https://usegalaxy.org/published/workflow?id=f926e70bee242785, https://workflowhub.eu/workflows/1622?version=1, https://workflowhub.eu/workflows/2048?version=1 assembly/debruijn-graph-assembly, assembly/general-introduction 2 2 2 2 0 0 0 0 2 2 0 0 0 0 0 0 0 0 0 0 0 0 2 2 0 0 2567 2888 27621 32158 4951 5263 52855 57273 2097 2221 30746 33121 109 109 1097 1097 123649 112319 10481 9724 True False +vibrant vibrant txt, fasta, genbank, tabular Virus Identification By iteRative ANnoTation 2024-09-11 https://github.com/AnantharamanLab/VIBRANT @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ vibrant 1.2.1 To update Metagenomics Sequence trimming, Scaffolding, Genome annotation Sequence trimming, Scaffolding, Genome annotation Metagenomics, Microbial ecology, Sequence assembly, Molecular interactions, pathways and networks, Endocrinology and metabolism Metagenomics, Microbial ecology, Sequence assembly, Molecular interactions, pathways and networks, Endocrinology and metabolism ufz https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant https://github.com/Helmholtz-UFZ/galaxy-tools/tree/master/tools/vibrant VIBRANT VIBRANT Automated recovery, annotation and curation of microbial viruses, and evaluation of virome function from genomic sequences.Virus Identification By iteRative ANnoTation.Discovery Environment Applications List.Created by upendra_35, last modified on Nov 04, 2019.If you find VIBRANT useful please consider citing our preprint on bioRxiv:.Kieft, K., Zhou, Z., and Anantharaman, K. (2019). VIBRANT: Automated recovery, annotation and curation of microbial viruses, and evaluation of virome function from genomic sequences. BioRxiv 855387.VIBRANT is a tool for automated recovery and annotation of bacterial and archaeal viruses, determination of genome completeness, and characterization of virome function from metagenomic assemblies.The QuickStart tutorial provides an introduction to basic DE functionality and navigation.Please work through the tutorial and use the intercom button on the bottom right of this page if you have any questions https://usegalaxy.eu/published/workflow?id=87231a6a7938cb95, https://usegalaxy.eu/published/workflow?id=c62d65832377e376 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 65 65 1586 1586 0 0 0 0 0 0 0 0 0 0 0 0 1586 1586 65 65 True False +viralverify viralverify fasta, csv, txt, genbank Contigs prediction as viral, chromosomal, plasmidic or uncertain. 2025-07-04 https://github.com/ablab/viralVerify @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ viralverify 1.1 To update Sequence Analysis, Metagenomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/viralverify https://github.com/galaxyproject/tools-iuc/tree/master/tools/viralverify 0 0 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False +virannot virannot_blast2tsv, virannot_otu, virAnnot_rps2tsv tabular, xlsx, zip virAnnot wrappers 2025-08-04 https://github.com/marieBvr/virAnnot 1.2.0 biopython 1.70 To update Metagenomics Sequence annotation, Sequence clustering, Sequence cluster visualisation Sequence annotation, Sequence clustering, Sequence cluster visualisation Metagenomics, Virology, Microbial ecology Metagenomics, Virology, Microbial ecology iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/virannot https://github.com/galaxyproject/tools-iuc/tree/master/tools/virannot virannot virAnnot "VirAnnot was build to ease the assembly, blast search, taxonomic annotation and OTUs assignation of viral metagenomic HTS data. It is used in Virologie team of UMR1332 BFP laboratory at INRAE. VirAnnot also takes part of the Euphresco project ""Plant Health Bioinformatics Network"". See more.It is designed to identify viruses in plant metagenomic data but it can be used to assemble and annotate any sequences with the NCBI taxonomy." https://usegalaxy.eu/published/workflow?id=17f73aba442315e6, https://usegalaxy.eu/published/workflow?id=86465932556bc96c 0 0 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 16 16 336 336 0 0 0 0 0 0 0 0 2 2 14 14 350 350 18 18 True False +virsorter virsorter fasta, tabular, txt VirSorter2 applies a multi-classifier, expert-guided approach to detect diverse DNA and RNA virus genomes. 2024-06-20 https://github.com/jiarong/VirSorter2/ @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ virsorter 2.2.4 To update Metagenomics Taxonomic classification Taxonomic classification Metagenomics Metagenomics ufz https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/virsorter https://github.com/Helmholtz-UFZ/galaxy-tools/tree/master/tools/virsorter virsorter virsorter Identify DNA and RNA virus sequences. https://usegalaxy.eu/published/workflow?id=62392daea25a3980, https://usegalaxy.eu/published/workflow?id=87231a6a7938cb95 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 144 144 2379 2379 0 0 0 0 0 0 0 0 0 0 0 0 2379 2379 144 144 True False +vrhyme vrhyme tabular, txt, fasta Tool for dereplication and binning virus genomes from metagenomes. 2025-05-14 https://github.com/AnantharamanLab/vRhyme 1.1.0 vrhyme 1.1.0 Up-to-date Metagenomics Scaffolding, Read binning, Read mapping, Sequence trimming Scaffolding, Read binning, Read mapping, Sequence trimming Metagenomics, Microbial ecology, Model organisms, Machine learning, Sequence assembly Metagenomics, Microbial ecology, Model organisms, Machine learning, Sequence assembly bgruening https://github.com/bgruening/galaxytools/tree/master/tools/vrhyme https://github.com/bgruening/galaxytools/tree/master/tools/vrhyme vRhyme vRhyme vRhyme enables binning of viral genomes from metagenomes. https://usegalaxy.eu/published/workflow?id=62392daea25a3980 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 6 47 47 0 0 0 0 0 0 0 0 0 0 0 0 47 47 6 6 True False +vsearch vsearch_alignment, vsearch_chimera_detection, vsearch_clustering, vsearch_dereplication, vsearch_masking, vsearch_search, vsearch_shuffling, vsearch_sorting fasta, tabular VSEARCH including searching, clustering, chimera detection, dereplication, sorting, masking and shuffling of sequences. 2014-11-30 https://github.com/torognes/vsearch 2.8.3 vsearch 2.31.0 To update Sequence Analysis DNA mapping, Chimera detection DNA mapping, Chimera detection Metagenomics, Sequence analysis Metagenomics, Sequence analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/vsearch https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch vsearch VSEARCH High-throughput search and clustering sequence analysis tool. It supports de novo and reference based chimera detection, clustering, full-length and prefix dereplication, reverse complementation, masking, all-vs-all pairwise global alignment, exact and global alignment searching, shuffling, subsampling and sorting. It also supports FASTQ file analysis, filtering and conversion. https://usegalaxy.eu/published/workflow?id=1ae9a523ef719a3d, https://usegalaxy.eu/published/workflow?id=401746888e8b3aa8, https://usegalaxy.eu/published/workflow?id=4eb9dfe91fc2dc67, https://usegalaxy.eu/published/workflow?id=8a7caaa658744441, https://usegalaxy.eu/published/workflow?id=9382f9bbbdddb5ad, https://usegalaxy.eu/published/workflow?id=9cbba5de2cbeeb0f, https://usegalaxy.eu/published/workflow?id=a8417c63e9e22afb, https://usegalaxy.eu/published/workflow?id=c3aa516e78ca4191, https://usegalaxy.org.au/published/workflow?id=14e80b7f9f68ec2a, https://usegalaxy.org.au/published/workflow?id=869440d35a618836, https://workflowhub.eu/workflows/232?version=1, https://workflowhub.eu/workflows/233?version=1 8 8 8 8 0 0 0 0 8 8 8 0 0 0 0 0 0 0 8 0 0 0 8 8 8 0 226 259 13600 15795 323 642 14828 59476 82 97 6641 7811 11 12 285 286 83368 35354 1010 642 True False diff --git a/communities/microgalaxy/resources/curated_tools.yml b/communities/microgalaxy/resources/curated_tools.yml index a23850947..161ee863d 100644 --- a/communities/microgalaxy/resources/curated_tools.yml +++ b/communities/microgalaxy/resources/curated_tools.yml @@ -20,12 +20,10 @@ Number of tools on ImmPort Galaxy: 0 Number of tools on InteractoMIX: 0 Number of tools on Lebanese University Galaxy: 0 - Number of tools on MBAC Metabiome Portal: 0 Number of tools on MISSISSIPPI: 0 Number of tools on Mandoiu Lab: 0 Number of tools on Oqtans: 0 Number of tools on Palfinder: 0 - Number of tools on PepSimili: 0 Number of tools on PhagePromotor: 0 Number of tools on UseGalaxy.be: 0 Number of tools on UseGalaxy.cz: 0 @@ -106,12 +104,10 @@ Number of tools on ImmPort Galaxy: 0 Number of tools on InteractoMIX: 0 Number of tools on Lebanese University Galaxy: 0 - Number of tools on MBAC Metabiome Portal: 0 Number of tools on MISSISSIPPI: 0 Number of tools on Mandoiu Lab: 0 Number of tools on Oqtans: 0 Number of tools on Palfinder: 0 - Number of tools on PepSimili: 0 Number of tools on PhagePromotor: 0 Number of tools on UseGalaxy.be: 0 Number of tools on UseGalaxy.cz: 1 @@ -127,7 +123,7 @@ Suite conda package: treebest Suite first commit date: '2015-08-06' Suite owner: earlhaminst - Suite parsed folder: https://github.com/EarlhamInst/earlham-galaxytools/tree/main/tools/TreeBest + Suite parsed folder: https://github.com/TGAC/earlham-galaxytools/tree/master/tools/TreeBest Suite runs (last 5 years) (usegalaxy.eu): 966 Suite runs (last 5 years) (usegalaxy.fr): 1 Suite runs (last 5 years) (usegalaxy.org): 0 @@ -198,12 +194,10 @@ Number of tools on ImmPort Galaxy: 0 Number of tools on InteractoMIX: 0 Number of tools on Lebanese University Galaxy: 0 - 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Number of tools on PepSimili: 0 Number of tools on PhagePromotor: 0 Number of tools on UseGalaxy.be: 0 Number of tools on UseGalaxy.cz: 4 @@ -2406,15 +2351,15 @@ Number of tools on UseGalaxy.fr: 2 Number of tools on UseGalaxy.no: 0 Number of tools on UseGalaxy.org (Main): 4 - Number of tools on UseGalaxy.org.au: 4 + Number of tools on UseGalaxy.org.au: 6 Number of tools on Viral Variant Visualizer (VVV): 0 Related Tutorials: [] Related Workflows: [] Suite ID: qiime2 Suite conda package: null - Suite first commit date: '2022-08-26' + Suite first commit date: '2022-08-25' Suite owner: q2d2 - Suite parsed folder: https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition + Suite parsed folder: https://github.com/qiime2/galaxy-tools/tree/master/tools/suite_qiime2__composition Suite runs (last 5 years) (usegalaxy.eu): 388 Suite runs (last 5 years) (usegalaxy.fr): 89 Suite runs (last 5 years) (usegalaxy.org): 256 @@ -2458,7 +2403,7 @@ UseGalaxy.cz: 4 UseGalaxy.eu: 4 UseGalaxy.fr: 2 - UseGalaxy.or: 4 + UseGalaxy.or: 6 biii ID: null bio.tool ID: qiime2 bio.tool description: QIIME 2 is an AI-ready microbiome multi-omics data science @@ -2498,12 +2443,10 @@ Number of tools on ImmPort Galaxy: 0 Number of tools on InteractoMIX: 0 Number of tools on Lebanese University Galaxy: 0 - Number of tools on MBAC Metabiome Portal: 0 Number of tools on MISSISSIPPI: 0 Number of tools on Mandoiu Lab: 0 Number of tools on Oqtans: 0 Number of tools on Palfinder: 0 - Number of tools on PepSimili: 0 Number of tools on PhagePromotor: 0 Number of tools on UseGalaxy.be: 0 Number of tools on UseGalaxy.cz: 4 @@ -2517,9 +2460,9 @@ Related Workflows: [] Suite ID: qiime2 Suite conda package: null - Suite first commit date: '2022-08-26' + Suite first commit date: '2022-08-25' Suite owner: q2d2 - Suite parsed folder: https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt + Suite parsed folder: https://github.com/qiime2/galaxy-tools/tree/master/tools/suite_qiime2__cutadapt Suite runs (last 5 years) (usegalaxy.eu): 364 Suite runs (last 5 years) (usegalaxy.fr): 31 Suite runs (last 5 years) (usegalaxy.org): 273 @@ -2599,12 +2542,10 @@ Number of tools on ImmPort Galaxy: 0 Number of tools on InteractoMIX: 0 Number of tools on Lebanese University Galaxy: 0 - Number of tools on MBAC Metabiome Portal: 0 Number of tools on MISSISSIPPI: 0 Number of tools on Mandoiu Lab: 0 Number of tools on Oqtans: 0 Number of tools on Palfinder: 0 - Number of tools on PepSimili: 0 Number of tools on PhagePromotor: 0 Number of tools on UseGalaxy.be: 0 Number of tools on UseGalaxy.cz: 4 @@ -2632,9 +2573,9 @@ - https://workflowhub.eu/workflows/892?version=3 Suite ID: qiime2 Suite conda package: null - Suite first commit date: '2022-08-26' + Suite first commit date: '2022-08-25' Suite owner: q2d2 - Suite parsed folder: https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 + Suite parsed folder: https://github.com/qiime2/galaxy-tools/tree/master/tools/suite_qiime2__dada2 Suite runs (last 5 years) (usegalaxy.eu): 2670 Suite runs (last 5 years) (usegalaxy.fr): 182 Suite runs (last 5 years) (usegalaxy.org): 1230 @@ -2716,12 +2657,10 @@ Number of tools on ImmPort Galaxy: 0 Number of tools on InteractoMIX: 0 Number of tools on Lebanese University Galaxy: 0 - Number of tools on MBAC Metabiome Portal: 0 Number of tools on MISSISSIPPI: 0 Number of tools on Mandoiu Lab: 0 Number of tools on Oqtans: 0 Number of tools on Palfinder: 0 - Number of tools on PepSimili: 0 Number of tools on PhagePromotor: 0 Number of tools on UseGalaxy.be: 0 Number of tools on UseGalaxy.cz: 3 @@ -2735,9 +2674,9 @@ Related Workflows: [] Suite ID: qiime2 Suite conda package: null - Suite first commit date: '2022-08-26' + Suite first commit date: '2022-08-25' Suite owner: q2d2 - Suite parsed folder: https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__deblur + Suite parsed folder: https://github.com/qiime2/galaxy-tools/tree/master/tools/suite_qiime2__deblur Suite runs (last 5 years) (usegalaxy.eu): 225 Suite runs (last 5 years) (usegalaxy.fr): 8 Suite runs (last 5 years) (usegalaxy.org): 78 @@ -2817,12 +2756,10 @@ Number of tools on ImmPort Galaxy: 0 Number of tools on InteractoMIX: 0 Number of tools on Lebanese University Galaxy: 0 - Number of tools on MBAC Metabiome Portal: 0 Number of tools on MISSISSIPPI: 0 Number of tools on Mandoiu Lab: 0 Number of tools on Oqtans: 0 Number of tools on Palfinder: 0 - Number of tools on PepSimili: 0 Number of tools on PhagePromotor: 0 Number of tools on UseGalaxy.be: 0 Number of tools on UseGalaxy.cz: 6 @@ -2861,9 +2798,9 @@ - https://workflowhub.eu/workflows/893?version=3 Suite ID: qiime2 Suite conda package: null - Suite first commit date: '2022-08-26' + Suite first commit date: '2022-08-25' Suite owner: q2d2 - Suite parsed folder: https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__demux + Suite parsed folder: https://github.com/qiime2/galaxy-tools/tree/master/tools/suite_qiime2__demux Suite runs (last 5 years) (usegalaxy.eu): 1358 Suite runs (last 5 years) (usegalaxy.fr): 127 Suite runs (last 5 years) (usegalaxy.org): 1071 @@ -2949,12 +2886,10 @@ Number of tools on ImmPort Galaxy: 0 Number of tools on InteractoMIX: 0 Number of tools on Lebanese University Galaxy: 0 - Number of tools on MBAC Metabiome Portal: 0 Number of tools on MISSISSIPPI: 0 Number of tools on Mandoiu Lab: 0 Number of tools on Oqtans: 0 Number of tools on Palfinder: 0 - Number of tools on PepSimili: 0 Number of tools on PhagePromotor: 0 Number of tools on UseGalaxy.be: 0 Number of tools on UseGalaxy.cz: 21 @@ -2975,9 +2910,9 @@ - https://usegalaxy.org/published/workflow?id=ef28b1c267b5a318 Suite ID: qiime2 Suite conda package: null - Suite first commit date: '2022-08-26' + Suite first commit date: '2022-08-25' Suite owner: q2d2 - Suite parsed folder: https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity + Suite parsed folder: https://github.com/qiime2/galaxy-tools/tree/master/tools/suite_qiime2__diversity Suite runs (last 5 years) (usegalaxy.eu): 3770 Suite runs (last 5 years) (usegalaxy.fr): 360 Suite runs (last 5 years) (usegalaxy.org): 2286 @@ -3077,12 +3012,10 @@ Number of tools on ImmPort Galaxy: 0 Number of tools on InteractoMIX: 0 Number of tools on Lebanese University Galaxy: 0 - Number of tools on MBAC Metabiome Portal: 0 Number of tools on MISSISSIPPI: 0 Number of tools on Mandoiu Lab: 0 Number of tools on Oqtans: 0 Number of tools on Palfinder: 0 - Number of tools on PepSimili: 0 Number of tools on PhagePromotor: 0 Number of tools on UseGalaxy.be: 0 Number of tools on UseGalaxy.cz: 12 @@ -3097,9 +3030,9 @@ - https://usegalaxy.org/published/workflow?id=7251c6e0dad8f927 Suite ID: qiime2 Suite conda package: null - Suite first commit date: '2022-08-26' + Suite first commit date: '2022-08-25' Suite owner: q2d2 - Suite parsed folder: https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib + Suite parsed folder: https://github.com/qiime2/galaxy-tools/tree/master/tools/suite_qiime2__diversity_lib Suite runs (last 5 years) (usegalaxy.eu): 33 Suite runs (last 5 years) (usegalaxy.fr): 3 Suite runs (last 5 years) (usegalaxy.org): 47 @@ -3187,12 +3120,10 @@ Number of tools on ImmPort Galaxy: 0 Number of tools on InteractoMIX: 0 Number of tools on Lebanese University Galaxy: 0 - Number of tools on MBAC Metabiome Portal: 0 Number of tools on MISSISSIPPI: 0 Number of tools on Mandoiu Lab: 0 Number of tools on Oqtans: 0 Number of tools on Palfinder: 0 - Number of tools on PepSimili: 0 Number of tools on PhagePromotor: 0 Number of tools on UseGalaxy.be: 0 Number of tools on UseGalaxy.cz: 3 @@ -3206,9 +3137,9 @@ Related Workflows: [] Suite ID: qiime2 Suite conda package: null - Suite first commit date: '2022-08-26' + Suite first commit date: '2022-08-25' Suite owner: q2d2 - Suite parsed folder: https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__emperor + Suite parsed folder: https://github.com/qiime2/galaxy-tools/tree/master/tools/suite_qiime2__emperor Suite runs (last 5 years) (usegalaxy.eu): 142 Suite runs (last 5 years) (usegalaxy.fr): 27 Suite runs (last 5 years) (usegalaxy.org): 198 @@ -3287,12 +3218,10 @@ Number of tools on ImmPort Galaxy: 0 Number of tools on InteractoMIX: 0 Number of tools on Lebanese University Galaxy: 0 - Number of tools on MBAC Metabiome Portal: 0 Number of tools on MISSISSIPPI: 0 Number of tools on Mandoiu Lab: 0 Number of tools on Oqtans: 0 Number of tools on Palfinder: 0 - Number of tools on PepSimili: 0 Number of tools on PhagePromotor: 0 Number of tools on UseGalaxy.be: 0 Number of tools on UseGalaxy.cz: 10 @@ -3310,9 +3239,9 @@ - https://workflowhub.eu/workflows/2098?version=1 Suite ID: qiime2 Suite conda package: null - Suite first commit date: '2022-08-26' + Suite first commit date: '2022-08-25' Suite owner: q2d2 - Suite parsed folder: https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_classifier + Suite parsed folder: https://github.com/qiime2/galaxy-tools/tree/master/tools/suite_qiime2__feature_classifier Suite runs (last 5 years) (usegalaxy.eu): 3046 Suite runs (last 5 years) (usegalaxy.fr): 178 Suite runs (last 5 years) (usegalaxy.org): 1256 @@ -3399,12 +3328,10 @@ Number of tools on ImmPort Galaxy: 0 Number of tools on InteractoMIX: 0 Number of tools on Lebanese University Galaxy: 0 - Number of tools on MBAC Metabiome Portal: 0 Number of tools on MISSISSIPPI: 0 Number of tools on Mandoiu Lab: 0 Number of tools on Oqtans: 0 Number of tools on Palfinder: 0 - Number of tools on PepSimili: 0 Number of tools on PhagePromotor: 0 Number of tools on UseGalaxy.be: 0 Number of tools on UseGalaxy.cz: 17 @@ -3433,9 +3360,9 @@ - https://workflowhub.eu/workflows/892?version=3 Suite ID: qiime2 Suite conda package: null - Suite first commit date: '2022-08-26' + Suite first commit date: '2022-08-25' Suite owner: q2d2 - Suite parsed folder: https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table + Suite parsed folder: https://github.com/qiime2/galaxy-tools/tree/master/tools/suite_qiime2__feature_table Suite runs (last 5 years) (usegalaxy.eu): 5335 Suite runs (last 5 years) (usegalaxy.fr): 591 Suite runs (last 5 years) (usegalaxy.org): 1938 @@ -3535,12 +3462,10 @@ Number of tools on ImmPort Galaxy: 0 Number of tools on InteractoMIX: 0 Number of tools on Lebanese University Galaxy: 0 - Number of tools on MBAC Metabiome Portal: 0 Number of tools on MISSISSIPPI: 0 Number of tools on Mandoiu Lab: 0 Number of tools on Oqtans: 0 Number of tools on Palfinder: 0 - Number of tools on PepSimili: 0 Number of tools on PhagePromotor: 0 Number of tools on UseGalaxy.be: 0 Number of tools on UseGalaxy.cz: 0 @@ -3556,7 +3481,7 @@ Suite conda package: null Suite first commit date: '2025-11-01' Suite owner: q2d2 - Suite parsed folder: https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__fondue + Suite parsed folder: https://github.com/qiime2/galaxy-tools/tree/master/tools/suite_qiime2__fondue Suite runs (last 5 years) (usegalaxy.eu): 0 Suite runs (last 5 years) (usegalaxy.fr): 0 Suite runs (last 5 years) (usegalaxy.org): 0 @@ -3636,12 +3561,10 @@ Number of tools on ImmPort Galaxy: 0 Number of tools on InteractoMIX: 0 Number of tools on Lebanese University Galaxy: 0 - Number of tools on MBAC Metabiome Portal: 0 Number of tools on MISSISSIPPI: 0 Number of tools on Mandoiu Lab: 0 Number of tools on Oqtans: 0 Number of tools on Palfinder: 0 - Number of tools on PepSimili: 0 Number of tools on PhagePromotor: 0 Number of tools on UseGalaxy.be: 0 Number of tools on UseGalaxy.cz: 3 @@ -3656,9 +3579,9 @@ - https://usegalaxy.eu/published/workflow?id=6ad6d87618c4e405 Suite ID: qiime2 Suite conda package: null - Suite first commit date: '2022-08-26' + Suite first commit date: '2022-08-25' Suite owner: q2d2 - Suite parsed folder: https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__fragment_insertion + Suite parsed folder: https://github.com/qiime2/galaxy-tools/tree/master/tools/suite_qiime2__fragment_insertion Suite runs (last 5 years) (usegalaxy.eu): 81 Suite runs (last 5 years) (usegalaxy.fr): 2 Suite runs (last 5 years) (usegalaxy.org): 59 @@ -3737,12 +3660,10 @@ Number of tools on ImmPort Galaxy: 0 Number of tools on InteractoMIX: 0 Number of tools on Lebanese University Galaxy: 0 - Number of tools on MBAC Metabiome Portal: 0 Number of tools on MISSISSIPPI: 0 Number of tools on Mandoiu Lab: 0 Number of tools on Oqtans: 0 Number of tools on Palfinder: 0 - Number of tools on PepSimili: 0 Number of tools on PhagePromotor: 0 Number of tools on UseGalaxy.be: 0 Number of tools on UseGalaxy.cz: 0 @@ -3758,7 +3679,7 @@ Suite conda package: null Suite first commit date: '2025-11-01' Suite owner: q2d2 - Suite parsed folder: https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__kmerizer + Suite parsed folder: https://github.com/qiime2/galaxy-tools/tree/master/tools/suite_qiime2__kmerizer Suite runs (last 5 years) (usegalaxy.eu): 0 Suite runs (last 5 years) (usegalaxy.fr): 0 Suite runs (last 5 years) (usegalaxy.org): 0 @@ -3833,12 +3754,10 @@ Number of tools on ImmPort Galaxy: 0 Number of tools on InteractoMIX: 0 Number of tools on Lebanese University Galaxy: 0 - Number of tools on MBAC Metabiome Portal: 0 Number of tools on MISSISSIPPI: 0 Number of tools on Mandoiu Lab: 0 Number of tools on Oqtans: 0 Number of tools on Palfinder: 0 - Number of tools on PepSimili: 0 Number of tools on PhagePromotor: 0 Number of tools on UseGalaxy.be: 0 Number of tools on UseGalaxy.cz: 11 @@ -3852,9 +3771,9 @@ Related Workflows: [] Suite ID: qiime2 Suite conda package: null - Suite first commit date: '2022-08-26' + Suite first commit date: '2022-08-25' Suite owner: q2d2 - Suite parsed folder: https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal + Suite parsed folder: https://github.com/qiime2/galaxy-tools/tree/master/tools/suite_qiime2__longitudinal Suite runs (last 5 years) (usegalaxy.eu): 63 Suite runs (last 5 years) (usegalaxy.fr): 8 Suite runs (last 5 years) (usegalaxy.org): 60 @@ -3942,12 +3861,10 @@ Number of tools on ImmPort Galaxy: 0 Number of tools on InteractoMIX: 0 Number of tools on Lebanese University Galaxy: 0 - Number of tools on MBAC Metabiome Portal: 0 Number of tools on MISSISSIPPI: 0 Number of tools on Mandoiu Lab: 0 Number of tools on Oqtans: 0 Number of tools on Palfinder: 0 - Number of tools on PepSimili: 0 Number of tools on PhagePromotor: 0 Number of tools on UseGalaxy.be: 0 Number of tools on UseGalaxy.cz: 3 @@ -3975,9 +3892,9 @@ - https://workflowhub.eu/workflows/892?version=3 Suite ID: qiime2 Suite conda package: null - Suite first commit date: '2022-08-26' + Suite first commit date: '2022-08-25' Suite owner: q2d2 - Suite parsed folder: https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__metadata + Suite parsed folder: https://github.com/qiime2/galaxy-tools/tree/master/tools/suite_qiime2__metadata Suite runs (last 5 years) (usegalaxy.eu): 2227 Suite runs (last 5 years) (usegalaxy.fr): 269 Suite runs (last 5 years) (usegalaxy.org): 1317 @@ -4058,12 +3975,10 @@ Number of tools on ImmPort Galaxy: 0 Number of tools on InteractoMIX: 0 Number of tools on Lebanese University Galaxy: 0 - Number of tools on MBAC Metabiome Portal: 0 Number of tools on MISSISSIPPI: 0 Number of tools on Mandoiu Lab: 0 Number of tools on Oqtans: 0 Number of tools on Palfinder: 0 - Number of tools on PepSimili: 0 Number of tools on PhagePromotor: 0 Number of tools on UseGalaxy.be: 0 Number of tools on UseGalaxy.cz: 12 @@ -4078,9 +3993,9 @@ - https://usegalaxy.eu/published/workflow?id=7c07e87c77dcee05 Suite ID: qiime2 Suite conda package: null - Suite first commit date: '2022-08-26' + Suite first commit date: '2022-08-25' Suite owner: q2d2 - Suite parsed folder: https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__phylogeny + Suite parsed folder: https://github.com/qiime2/galaxy-tools/tree/master/tools/suite_qiime2__phylogeny Suite runs (last 5 years) (usegalaxy.eu): 880 Suite runs (last 5 years) (usegalaxy.fr): 91 Suite runs (last 5 years) (usegalaxy.org): 338 @@ -4168,12 +4083,10 @@ Number of tools on ImmPort Galaxy: 0 Number of tools on InteractoMIX: 0 Number of tools on Lebanese University Galaxy: 0 - Number of tools on MBAC Metabiome Portal: 0 Number of tools on MISSISSIPPI: 0 Number of tools on Mandoiu Lab: 0 Number of tools on Oqtans: 0 Number of tools on Palfinder: 0 - Number of tools on PepSimili: 0 Number of tools on PhagePromotor: 0 Number of tools on UseGalaxy.be: 0 Number of tools on UseGalaxy.cz: 6 @@ -4187,9 +4100,9 @@ Related Workflows: [] Suite ID: qiime2 Suite conda package: null - Suite first commit date: '2022-08-26' + Suite first commit date: '2022-08-25' Suite owner: q2d2 - Suite parsed folder: https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control + Suite parsed folder: https://github.com/qiime2/galaxy-tools/tree/master/tools/suite_qiime2__quality_control Suite runs (last 5 years) (usegalaxy.eu): 6 Suite runs (last 5 years) (usegalaxy.fr): 0 Suite runs (last 5 years) (usegalaxy.org): 105 @@ -4275,12 +4188,10 @@ Number of tools on ImmPort Galaxy: 0 Number of tools on InteractoMIX: 0 Number of tools on Lebanese University Galaxy: 0 - Number of tools on MBAC Metabiome Portal: 0 Number of tools on MISSISSIPPI: 0 Number of tools on Mandoiu Lab: 0 Number of tools on Oqtans: 0 Number of tools on Palfinder: 0 - Number of tools on PepSimili: 0 Number of tools on PhagePromotor: 0 Number of tools on UseGalaxy.be: 0 Number of tools on UseGalaxy.cz: 1 @@ -4294,9 +4205,9 @@ Related Workflows: [] Suite ID: qiime2 Suite conda package: null - Suite first commit date: '2022-08-26' + Suite first commit date: '2022-08-25' Suite owner: q2d2 - Suite parsed folder: https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_filter + Suite parsed folder: https://github.com/qiime2/galaxy-tools/tree/master/tools/suite_qiime2__quality_filter Suite runs (last 5 years) (usegalaxy.eu): 55 Suite runs (last 5 years) (usegalaxy.fr): 21 Suite runs (last 5 years) (usegalaxy.org): 39 @@ -4373,12 +4284,10 @@ Number of tools on ImmPort Galaxy: 0 Number of tools on InteractoMIX: 0 Number of tools on Lebanese University Galaxy: 0 - Number of tools on MBAC Metabiome Portal: 0 Number of tools on MISSISSIPPI: 0 Number of tools on Mandoiu Lab: 0 Number of tools on Oqtans: 0 Number of tools on Palfinder: 0 - Number of tools on PepSimili: 0 Number of tools on PhagePromotor: 0 Number of tools on UseGalaxy.be: 0 Number of tools on UseGalaxy.cz: 0 @@ -4386,7 +4295,7 @@ Number of tools on UseGalaxy.fr: 0 Number of tools on UseGalaxy.no: 0 Number of tools on UseGalaxy.org (Main): 0 - Number of tools on UseGalaxy.org.au: 0 + Number of tools on UseGalaxy.org.au: 3 Number of tools on Viral Variant Visualizer (VVV): 0 Related Tutorials: [] Related Workflows: [] @@ -4394,7 +4303,7 @@ Suite conda package: null Suite first commit date: '2024-04-25' Suite owner: q2d2 - Suite parsed folder: https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript + Suite parsed folder: https://github.com/qiime2/galaxy-tools/tree/master/tools/suite_qiime2__rescript Suite runs (last 5 years) (usegalaxy.eu): 18 Suite runs (last 5 years) (usegalaxy.fr): 0 Suite runs (last 5 years) (usegalaxy.org): 0 @@ -4461,6 +4370,7 @@ - Statistics availability: UseGalaxy.eu: 3 + UseGalaxy.or: 3 biii ID: null bio.tool ID: qiime2 bio.tool description: QIIME 2 is an AI-ready microbiome multi-omics data science @@ -4500,12 +4410,10 @@ Number of tools on ImmPort Galaxy: 0 Number of tools on InteractoMIX: 0 Number of tools on Lebanese University Galaxy: 0 - Number of tools on MBAC Metabiome Portal: 0 Number of tools on MISSISSIPPI: 0 Number of tools on Mandoiu Lab: 0 Number of tools on Oqtans: 0 Number of tools on Palfinder: 0 - Number of tools on PepSimili: 0 Number of tools on PhagePromotor: 0 Number of tools on UseGalaxy.be: 0 Number of tools on UseGalaxy.cz: 15 @@ -4519,9 +4427,9 @@ Related Workflows: [] Suite ID: qiime2 Suite conda package: null - Suite first commit date: '2022-08-26' + Suite first commit date: '2022-08-25' Suite owner: q2d2 - Suite parsed folder: https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier + Suite parsed folder: https://github.com/qiime2/galaxy-tools/tree/master/tools/suite_qiime2__sample_classifier Suite runs (last 5 years) (usegalaxy.eu): 30 Suite runs (last 5 years) (usegalaxy.fr): 4 Suite runs (last 5 years) (usegalaxy.org): 47 @@ -4613,12 +4521,10 @@ Number of tools on ImmPort Galaxy: 0 Number of tools on InteractoMIX: 0 Number of tools on Lebanese University Galaxy: 0 - Number of tools on MBAC Metabiome Portal: 0 Number of tools on MISSISSIPPI: 0 Number of tools on Mandoiu Lab: 0 Number of tools on Oqtans: 0 Number of tools on Palfinder: 0 - Number of tools on PepSimili: 0 Number of tools on PhagePromotor: 0 Number of tools on UseGalaxy.be: 0 Number of tools on UseGalaxy.cz: 0 @@ -4626,7 +4532,7 @@ Number of tools on UseGalaxy.fr: 0 Number of tools on UseGalaxy.no: 0 Number of tools on UseGalaxy.org (Main): 0 - Number of tools on UseGalaxy.org.au: 0 + Number of tools on UseGalaxy.org.au: 9 Number of tools on Viral Variant Visualizer (VVV): 0 Related Tutorials: [] Related Workflows: [] @@ -4634,7 +4540,7 @@ Suite conda package: null Suite first commit date: '2024-10-30' Suite owner: q2d2 - Suite parsed folder: https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__stats + Suite parsed folder: https://github.com/qiime2/galaxy-tools/tree/master/tools/suite_qiime2__stats Suite runs (last 5 years) (usegalaxy.eu): 0 Suite runs (last 5 years) (usegalaxy.fr): 0 Suite runs (last 5 years) (usegalaxy.org): 0 @@ -4679,6 +4585,7 @@ - Statistics availability: UseGalaxy.eu: 9 + UseGalaxy.or: 9 biii ID: null bio.tool ID: qiime2 bio.tool description: QIIME 2 is an AI-ready microbiome multi-omics data science @@ -4718,12 +4625,10 @@ Number of tools on ImmPort Galaxy: 0 Number of tools on InteractoMIX: 0 Number of tools on Lebanese University Galaxy: 0 - Number of tools on MBAC Metabiome Portal: 0 Number of tools on MISSISSIPPI: 0 Number of tools on Mandoiu Lab: 0 Number of tools on Oqtans: 0 Number of tools on Palfinder: 0 - Number of tools on PepSimili: 0 Number of tools on PhagePromotor: 0 Number of tools on UseGalaxy.be: 0 Number of tools on UseGalaxy.cz: 4 @@ -4740,9 +4645,9 @@ - https://workflowhub.eu/workflows/2098?version=1 Suite ID: qiime2 Suite conda package: null - Suite first commit date: '2022-08-26' + Suite first commit date: '2022-08-25' Suite owner: q2d2 - Suite parsed folder: https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa + Suite parsed folder: https://github.com/qiime2/galaxy-tools/tree/master/tools/suite_qiime2__taxa Suite runs (last 5 years) (usegalaxy.eu): 2747 Suite runs (last 5 years) (usegalaxy.fr): 236 Suite runs (last 5 years) (usegalaxy.org): 1008 @@ -4824,12 +4729,10 @@ Number of tools on ImmPort Galaxy: 0 Number of tools on InteractoMIX: 0 Number of tools on Lebanese University Galaxy: 0 - Number of tools on MBAC Metabiome Portal: 0 Number of tools on MISSISSIPPI: 0 Number of tools on Mandoiu Lab: 0 Number of tools on Oqtans: 0 Number of tools on Palfinder: 0 - Number of tools on PepSimili: 0 Number of tools on PhagePromotor: 0 Number of tools on UseGalaxy.be: 0 Number of tools on UseGalaxy.cz: 0 @@ -4837,7 +4740,7 @@ Number of tools on UseGalaxy.fr: 0 Number of tools on UseGalaxy.no: 0 Number of tools on UseGalaxy.org (Main): 0 - Number of tools on UseGalaxy.org.au: 0 + Number of tools on UseGalaxy.org.au: 4 Number of tools on Viral Variant Visualizer (VVV): 0 Related Tutorials: [] Related Workflows: [] @@ -4845,7 +4748,7 @@ Suite conda package: null Suite first commit date: '2024-10-30' Suite owner: q2d2 - Suite parsed folder: https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vizard + Suite parsed folder: https://github.com/qiime2/galaxy-tools/tree/master/tools/suite_qiime2__vizard Suite runs (last 5 years) (usegalaxy.eu): 20 Suite runs (last 5 years) (usegalaxy.fr): 0 Suite runs (last 5 years) (usegalaxy.org): 0 @@ -4883,6 +4786,7 @@ - Statistics availability: UseGalaxy.eu: 4 + UseGalaxy.or: 4 biii ID: null bio.tool ID: qiime2 bio.tool description: QIIME 2 is an AI-ready microbiome multi-omics data science @@ -4922,12 +4826,10 @@ Number of tools on ImmPort Galaxy: 0 Number of tools on InteractoMIX: 0 Number of tools on Lebanese University Galaxy: 0 - Number of tools on MBAC Metabiome Portal: 0 Number of tools on MISSISSIPPI: 0 Number of tools on Mandoiu Lab: 0 Number of tools on Oqtans: 0 Number of tools on Palfinder: 0 - Number of tools on PepSimili: 0 Number of tools on PhagePromotor: 0 Number of tools on UseGalaxy.be: 0 Number of tools on UseGalaxy.cz: 8 @@ -4941,9 +4843,9 @@ Related Workflows: [] Suite ID: qiime2 Suite conda package: null - Suite first commit date: '2022-08-26' + Suite first commit date: '2022-08-25' Suite owner: q2d2 - Suite parsed folder: https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch + Suite parsed folder: https://github.com/qiime2/galaxy-tools/tree/master/tools/suite_qiime2__vsearch Suite runs (last 5 years) (usegalaxy.eu): 409 Suite runs (last 5 years) (usegalaxy.fr): 77 Suite runs (last 5 years) (usegalaxy.org): 280 @@ -5028,19 +4930,17 @@ Number of tools on ImmPort Galaxy: 0 Number of tools on InteractoMIX: 0 Number of tools on Lebanese University Galaxy: 0 - 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Number of tools on MBAC Metabiome Portal: 0 Number of tools on MISSISSIPPI: 0 Number of tools on Mandoiu Lab: 0 Number of tools on Oqtans: 0 Number of tools on Palfinder: 0 - Number of tools on PepSimili: 0 Number of tools on PhagePromotor: 0 Number of tools on UseGalaxy.be: 0 Number of tools on UseGalaxy.cz: 0 @@ -5169,7 +5067,7 @@ Suite conda package: null Suite first commit date: '2022-08-29' Suite owner: q2d2 - Suite parsed folder: https://github.com/qiime2/galaxy-tools/tree/main/tool_collections/suite_qiime2_core + Suite parsed folder: https://github.com/qiime2/galaxy-tools/tree/master/tool_collections/suite_qiime2_core Suite runs (last 5 years) (usegalaxy.eu): 0 Suite runs (last 5 years) (usegalaxy.fr): 0 Suite runs (last 5 years) (usegalaxy.org): 0 @@ -5226,12 +5124,10 @@ Number of tools on ImmPort Galaxy: 0 Number of tools on InteractoMIX: 0 Number of tools on Lebanese University Galaxy: 0 - Number of tools on MBAC Metabiome Portal: 0 Number of tools on MISSISSIPPI: 0 Number of tools on Mandoiu Lab: 0 Number of tools on Oqtans: 0 Number of tools on Palfinder: 0 - Number of tools on PepSimili: 0 Number of tools on PhagePromotor: 0 Number of tools on UseGalaxy.be: 0 Number of tools on UseGalaxy.cz: 0 @@ -5248,7 +5144,7 @@ Suite conda package: cd-hit-auxtools Suite first commit date: '2015-04-28' Suite owner: devteam - Suite parsed folder: https://github.com/galaxyproject/tools-devteam/tree/main/tools/cd_hit_dup + Suite parsed folder: https://github.com/galaxyproject/tools-devteam/tree/master/tools/cd_hit_dup Suite runs (last 5 years) (usegalaxy.eu): 0 Suite runs (last 5 years) (usegalaxy.fr): 0 Suite runs (last 5 years) (usegalaxy.org): 7542 @@ -5314,12 +5210,10 @@ Number of tools on ImmPort Galaxy: 0 Number of tools on InteractoMIX: 0 Number of tools on Lebanese University Galaxy: 0 - Number of tools on MBAC Metabiome Portal: 0 Number of tools on MISSISSIPPI: 0 Number of tools on Mandoiu Lab: 0 Number of tools on Oqtans: 0 Number of tools on Palfinder: 0 - Number of tools on PepSimili: 0 Number of tools on PhagePromotor: 0 Number of tools on UseGalaxy.be: 1 Number of tools on UseGalaxy.cz: 1 @@ -5344,7 +5238,7 @@ Suite conda package: taxonomy Suite first commit date: '2014-01-27' Suite owner: devteam - Suite parsed folder: https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/gi2taxonomy + Suite parsed folder: https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/gi2taxonomy Suite runs (last 5 years) (usegalaxy.eu): 244 Suite runs (last 5 years) (usegalaxy.fr): 0 Suite runs (last 5 years) (usegalaxy.org): 113 @@ -5406,12 +5300,10 @@ Number of tools on ImmPort Galaxy: 0 Number of tools on InteractoMIX: 0 Number of tools on Lebanese University Galaxy: 0 - Number of tools on MBAC Metabiome Portal: 0 Number of tools on MISSISSIPPI: 0 Number of tools on Mandoiu Lab: 0 Number of tools on Oqtans: 0 Number of tools on Palfinder: 0 - Number of tools on PepSimili: 0 Number of tools on PhagePromotor: 0 Number of tools on UseGalaxy.be: 1 Number of tools on UseGalaxy.cz: 1 @@ -5445,7 +5337,7 @@ Suite conda package: gawk Suite first commit date: '2015-08-05' Suite owner: devteam - Suite parsed folder: https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/kraken2tax + Suite parsed folder: https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/kraken2tax Suite runs (last 5 years) (usegalaxy.eu): 33158 Suite runs (last 5 years) (usegalaxy.fr): 0 Suite runs (last 5 years) (usegalaxy.org): 18299 @@ -5467,7 +5359,7 @@ Suite users (usegalaxy.org): 2555 Suite users (usegalaxy.org.au): 576 Suite users on main servers: 4507 - 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Number of tools on MBAC Metabiome Portal: 0 Number of tools on MISSISSIPPI: 0 Number of tools on Mandoiu Lab: 0 Number of tools on Oqtans: 0 Number of tools on Palfinder: 0 - Number of tools on PepSimili: 0 Number of tools on PhagePromotor: 0 Number of tools on UseGalaxy.be: 1 Number of tools on UseGalaxy.cz: 1 @@ -5632,7 +5520,7 @@ Suite conda package: taxonomy Suite first commit date: '2014-01-27' Suite owner: devteam - Suite parsed folder: https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/t2ps + Suite parsed folder: https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/t2ps Suite runs (last 5 years) (usegalaxy.eu): 405 Suite runs (last 5 years) (usegalaxy.fr): 0 Suite runs (last 5 years) (usegalaxy.org): 102 @@ -5695,12 +5583,10 @@ Number of tools on ImmPort Galaxy: 0 Number of tools on InteractoMIX: 0 Number of tools on Lebanese University Galaxy: 0 - Number of tools on MBAC Metabiome Portal: 0 Number of tools on MISSISSIPPI: 0 Number of tools on Mandoiu Lab: 0 Number of tools on Oqtans: 0 Number of tools on Palfinder: 0 - Number of tools on PepSimili: 0 Number of tools on PhagePromotor: 0 Number of tools on UseGalaxy.be: 1 Number of tools on UseGalaxy.cz: 1 @@ -5724,7 +5610,7 @@ Suite conda package: taxonomy Suite first commit date: '2014-01-27' Suite owner: devteam - Suite parsed folder: https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/t2t_report + Suite parsed folder: https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/t2t_report Suite runs (last 5 years) (usegalaxy.eu): 745 Suite runs (last 5 years) (usegalaxy.fr): 0 Suite runs (last 5 years) (usegalaxy.org): 118 @@ -5796,12 +5682,10 @@ Number of tools on ImmPort Galaxy: 0 Number of tools on InteractoMIX: 0 Number of tools on Lebanese University Galaxy: 0 - Number of tools on MBAC Metabiome Portal: 0 Number of tools on MISSISSIPPI: 0 Number of tools on Mandoiu Lab: 0 Number of tools on Oqtans: 0 Number of tools on Palfinder: 0 - Number of tools on PepSimili: 0 Number of tools on PhagePromotor: 0 Number of tools on UseGalaxy.be: 1 Number of tools on UseGalaxy.cz: 1 @@ -5829,6 +5713,7 @@ - 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https://usegalaxy.org.au/published/workflow?id=344b2ad2604939bc Suite ID: canu Suite conda package: canu Suite first commit date: '2018-06-07' @@ -5955,8 +5839,8 @@ Suite users (usegalaxy.org): 0 Suite users (usegalaxy.org.au): 485 Suite users on main servers: 2365 - Suite version: '2.3' - Suite version status: Up-to-date + Suite version: '@TOOL_VERSION@+galaxy@VERSION_SUFFIX@' + Suite version status: To update To keep: true Tool IDs: - canu @@ -6005,12 +5889,10 @@ Number of tools on ImmPort Galaxy: 0 Number of tools on InteractoMIX: 0 Number of tools on Lebanese University Galaxy: 0 - Number of tools on MBAC Metabiome Portal: 0 Number of tools on MISSISSIPPI: 0 Number of tools on Mandoiu Lab: 0 Number of tools on Oqtans: 0 Number of tools on Palfinder: 0 - Number of tools on PepSimili: 0 Number of tools on PhagePromotor: 0 Number of tools on UseGalaxy.be: 1 Number of tools on UseGalaxy.cz: 1 @@ -6100,12 +5982,10 @@ Number of tools on ImmPort Galaxy: 0 Number of tools on InteractoMIX: 0 Number of tools on Lebanese University Galaxy: 0 - Number of tools on MBAC Metabiome Portal: 0 Number of tools on MISSISSIPPI: 0 Number of tools on Mandoiu Lab: 0 Number of tools on Oqtans: 0 Number of tools on Palfinder: 0 - Number of tools on PepSimili: 0 Number of tools on PhagePromotor: 0 Number of tools on UseGalaxy.be: 0 Number of tools on UseGalaxy.cz: 1 @@ -6197,12 +6077,10 @@ Number of tools on ImmPort Galaxy: 0 Number of tools on InteractoMIX: 0 Number of tools on Lebanese University Galaxy: 0 - Number of tools on MBAC Metabiome Portal: 0 Number of tools on MISSISSIPPI: 0 Number of tools on Mandoiu Lab: 0 Number of tools on Oqtans: 0 Number of tools on Palfinder: 0 - Number of tools on PepSimili: 0 Number of tools on PhagePromotor: 0 Number of tools on UseGalaxy.be: 1 Number of tools on UseGalaxy.cz: 1 @@ -6232,6 +6110,7 @@ - https://usegalaxy.eu/published/workflow?id=4ddbffe4b3fef275 - https://usegalaxy.eu/published/workflow?id=5500de2961f7470c - https://usegalaxy.eu/published/workflow?id=585c21b7b1d864fc + - https://usegalaxy.eu/published/workflow?id=5cd71f9a190cae1b - 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Number of tools on PepSimili: 0 Number of tools on PhagePromotor: 0 Number of tools on UseGalaxy.be: 1 Number of tools on UseGalaxy.cz: 1 @@ -6486,12 +6366,10 @@ Number of tools on ImmPort Galaxy: 0 Number of tools on InteractoMIX: 0 Number of tools on Lebanese University Galaxy: 0 - Number of tools on MBAC Metabiome Portal: 0 Number of tools on MISSISSIPPI: 0 Number of tools on Mandoiu Lab: 0 Number of tools on Oqtans: 0 Number of tools on Palfinder: 0 - Number of tools on PepSimili: 0 Number of tools on PhagePromotor: 0 Number of tools on UseGalaxy.be: 1 Number of tools on UseGalaxy.cz: 1 @@ -6780,6 +6658,8 @@ - https://usegalaxy.org.au/published/workflow?id=53cbacc71790c41b - https://usegalaxy.org.au/published/workflow?id=543fb2d9431a7e13 - https://usegalaxy.org.au/published/workflow?id=5550585ffc3d8d0e + - https://usegalaxy.org.au/published/workflow?id=586a218c9b29d99a + - https://usegalaxy.org.au/published/workflow?id=58f97e4a249796cb - https://usegalaxy.org.au/published/workflow?id=5b0c0e34394afed1 - 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Number of tools on MBAC Metabiome Portal: 0 Number of tools on MISSISSIPPI: 0 Number of tools on Mandoiu Lab: 0 Number of tools on Oqtans: 0 Number of tools on Palfinder: 0 - Number of tools on PepSimili: 0 Number of tools on PhagePromotor: 0 Number of tools on UseGalaxy.be: 0 Number of tools on UseGalaxy.cz: 0 @@ -7328,12 +7207,10 @@ Number of tools on ImmPort Galaxy: 0 Number of tools on InteractoMIX: 0 Number of tools on Lebanese University Galaxy: 0 - Number of tools on MBAC Metabiome Portal: 0 Number of tools on MISSISSIPPI: 0 Number of tools on Mandoiu Lab: 0 Number of tools on Oqtans: 0 Number of tools on Palfinder: 0 - Number of tools on PepSimili: 0 Number of tools on PhagePromotor: 0 Number of tools on UseGalaxy.be: 0 Number of tools on UseGalaxy.cz: 1 @@ -7346,6 +7223,8 @@ Related Tutorials: [] Related Workflows: - https://usegalaxy.eu/published/workflow?id=4eb9dfe91fc2dc67 + - https://usegalaxy.eu/published/workflow?id=6e3f8dd5fdfbcfbe + - https://usegalaxy.eu/published/workflow?id=9cce01219994b52e Suite ID: itsx Suite conda package: itsx Suite first commit date: '2022-05-02' @@ -7419,7 +7298,7 @@ - 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https://usegalaxy.eu/published/workflow?id=07c92110c3fffcf8 - https://usegalaxy.eu/published/workflow?id=1ce406de61de8492 @@ -7482,6 +7360,7 @@ - https://workflowhub.eu/workflows/1715?version=3 - https://workflowhub.eu/workflows/2036?version=1 - https://workflowhub.eu/workflows/2038?version=1 + - https://workflowhub.eu/workflows/2180?version=1 Suite ID: jbrowse2 Suite conda package: jbrowse2 Suite first commit date: '2024-06-04' @@ -7519,6 +7398,7 @@ - Sequence Analysis availability: UseGalaxy.be: 1 + UseGalaxy.cz: 1 UseGalaxy.eu: 1 UseGalaxy.fr: 1 UseGalaxy.or: 1 @@ -7550,22 +7430,21 @@ Number of tools on ImmPort Galaxy: 0 Number of tools on InteractoMIX: 0 Number of tools on Lebanese University Galaxy: 0 - Number of tools on MBAC Metabiome Portal: 0 Number of tools on MISSISSIPPI: 0 Number of tools on Mandoiu Lab: 0 Number of tools on Oqtans: 0 Number of tools on Palfinder: 0 - Number of tools on PepSimili: 0 Number of tools on PhagePromotor: 0 Number of tools on UseGalaxy.be: 0 - Number of tools on UseGalaxy.cz: 0 + Number of tools on UseGalaxy.cz: 1 Number of tools on UseGalaxy.eu: 1 Number of tools on UseGalaxy.fr: 0 Number of tools on UseGalaxy.no: 0 - 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Number of tools on MBAC Metabiome Portal: 0 Number of tools on MISSISSIPPI: 0 Number of tools on Mandoiu Lab: 0 Number of tools on Oqtans: 0 Number of tools on Palfinder: 0 - Number of tools on PepSimili: 0 Number of tools on PhagePromotor: 0 Number of tools on UseGalaxy.be: 0 Number of tools on UseGalaxy.cz: 1 @@ -10710,7 +10546,7 @@ Suite conda package: argnorm Suite first commit date: '2024-08-28' Suite owner: iuc - Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/argnorm + Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/master/tools/argnorm Suite runs (last 5 years) (usegalaxy.eu): 211 Suite runs (last 5 years) (usegalaxy.fr): 91 Suite runs (last 5 years) (usegalaxy.org): 0 @@ -10732,7 +10568,7 @@ Suite users (usegalaxy.org): 0 Suite users (usegalaxy.org.au): 0 Suite users on main servers: 51 - Suite version: 1.0.0 + Suite version: '@VERSION@+galaxy@VERSION_SUFFIX@' Suite version status: To update To keep: true Tool IDs: @@ -10768,7 +10604,7 @@ EDAM topics: - Genomics Homepage: https://github.com/artic-network/fieldbioinformatics - Latest suite conda package version: 1.10.1 + Latest suite conda package version: 1.11.0 Number of tools on APOSTL: 0 Number of tools on CIRM-CFBP: 0 Number of tools on ChemFlow: 0 @@ -10782,12 +10618,10 @@ Number of tools on ImmPort Galaxy: 0 Number of tools on InteractoMIX: 0 Number of tools on Lebanese University Galaxy: 0 - Number of tools on MBAC Metabiome Portal: 0 Number of tools on MISSISSIPPI: 0 Number of tools on Mandoiu Lab: 0 Number of tools on Oqtans: 0 Number of tools on Palfinder: 0 - Number of tools on PepSimili: 0 Number of tools on PhagePromotor: 0 Number of tools on UseGalaxy.be: 1 Number of tools on UseGalaxy.cz: 2 @@ -10800,12 +10634,13 @@ Related Tutorials: [] Related Workflows: - https://usegalaxy.org.au/published/workflow?id=aa1d123c0a0929f3 + - https://workflowhub.eu/workflows/2195?version=1 - https://workflowhub.eu/workflows/521?version=1 Suite ID: artic Suite conda package: artic Suite first commit date: '2020-04-17' Suite owner: iuc - Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/artic + Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic Suite runs (last 5 years) (usegalaxy.eu): 13444 Suite runs (last 5 years) (usegalaxy.fr): 0 Suite runs (last 5 years) (usegalaxy.org): 0 @@ -10874,12 +10709,10 @@ Number of tools on ImmPort Galaxy: 0 Number of tools on InteractoMIX: 0 Number of tools on Lebanese University Galaxy: 0 - Number of tools on MBAC Metabiome Portal: 0 Number of tools on MISSISSIPPI: 0 Number of tools on Mandoiu Lab: 0 Number of tools on Oqtans: 0 Number of tools on Palfinder: 0 - Number of tools on PepSimili: 0 Number of tools on PhagePromotor: 0 Number of tools on UseGalaxy.be: 0 Number of tools on UseGalaxy.cz: 0 @@ -10895,7 +10728,7 @@ Suite conda package: rjchallis-assembly-stats Suite first commit date: '2023-06-21' Suite owner: iuc - Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/assembly-stats + Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/master/tools/assembly-stats Suite runs (last 5 years) (usegalaxy.eu): 0 Suite runs (last 5 years) (usegalaxy.fr): 32 Suite runs (last 5 years) (usegalaxy.org): 0 @@ -10954,12 +10787,10 @@ Number of tools on ImmPort Galaxy: 0 Number of tools on InteractoMIX: 0 Number of tools on Lebanese University Galaxy: 0 - Number of tools on MBAC Metabiome Portal: 0 Number of tools on MISSISSIPPI: 0 Number of tools on Mandoiu Lab: 0 Number of tools on Oqtans: 0 Number of tools on Palfinder: 0 - Number of tools on PepSimili: 0 Number of tools on PhagePromotor: 0 Number of tools on UseGalaxy.be: 0 Number of tools on UseGalaxy.cz: 0 @@ -10975,7 +10806,7 @@ Suite conda package: autobigs-cli Suite first commit date: '2025-02-24' Suite owner: iuc - Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/autobigs + Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/master/tools/autobigs Suite runs (last 5 years) (usegalaxy.eu): 53 Suite runs (last 5 years) (usegalaxy.fr): 0 Suite runs (last 5 years) (usegalaxy.org): 0 @@ -10997,7 +10828,7 @@ Suite users (usegalaxy.org): 0 Suite users (usegalaxy.org.au): 0 Suite users on main servers: 31 - Suite version: 0.6.2 + Suite version: '@TOOL_VERSION@+galaxy@VERSION_SUFFIX@' Suite version status: To update To keep: true Tool IDs: @@ -11047,12 +10878,10 @@ Number of tools on ImmPort Galaxy: 0 Number of tools on InteractoMIX: 0 Number of tools on Lebanese University Galaxy: 0 - Number of tools on MBAC Metabiome Portal: 0 Number of tools on MISSISSIPPI: 0 Number of tools on Mandoiu Lab: 0 Number of tools on Oqtans: 0 Number of tools on Palfinder: 0 - Number of tools on PepSimili: 0 Number of tools on PhagePromotor: 0 Number of tools on UseGalaxy.be: 1 Number of tools on UseGalaxy.cz: 1 @@ -11083,6 +10912,7 @@ - https://usegalaxy.eu/published/workflow?id=968f0ac2617aa524 - https://usegalaxy.eu/published/workflow?id=a18aed4b03ffd27e - https://usegalaxy.eu/published/workflow?id=b1afc8d1e81fc904 + - https://usegalaxy.eu/published/workflow?id=b46d67d91391053d - https://usegalaxy.eu/published/workflow?id=bcd50e655809cfcb - https://usegalaxy.eu/published/workflow?id=cc59ae1a9878942c - https://usegalaxy.eu/published/workflow?id=d0339e4a794f4922 @@ -11106,6 +10936,7 @@ - https://usegalaxy.org/published/workflow?id=69d8863d40524120 - https://usegalaxy.org/published/workflow?id=7dd6e4150bb81ad1 - https://usegalaxy.org/published/workflow?id=80ac6adead9f97d8 + - https://usegalaxy.org/published/workflow?id=84233173d92fa506 - https://usegalaxy.org/published/workflow?id=8cb8a588a0495cfa - https://usegalaxy.org/published/workflow?id=993534c11310a207 - https://usegalaxy.org/published/workflow?id=9c0fbd9f51a9857f @@ -11118,7 +10949,7 @@ Suite conda package: bakta Suite first commit date: '2022-09-01' Suite owner: iuc - Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/bakta + Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/master/tools/bakta Suite runs (last 5 years) (usegalaxy.eu): 67465 Suite runs (last 5 years) (usegalaxy.fr): 3664 Suite runs (last 5 years) (usegalaxy.org): 14351 @@ -11180,7 +11011,7 @@ - Genomics - Sequence assembly Homepage: https://github.com/rrwick/Bandage - Latest suite conda package version: 2026.4.1 + Latest suite conda package version: 2026.6.1 Number of tools on APOSTL: 0 Number of tools on CIRM-CFBP: 0 Number of tools on ChemFlow: 0 @@ -11194,12 +11025,10 @@ Number of tools on ImmPort Galaxy: 0 Number of tools on InteractoMIX: 0 Number of tools on Lebanese University Galaxy: 0 - Number of tools on MBAC Metabiome Portal: 0 Number of tools on MISSISSIPPI: 2 Number of tools on Mandoiu Lab: 0 Number of tools on Oqtans: 0 Number of tools on Palfinder: 0 - Number of tools on PepSimili: 0 Number of tools on PhagePromotor: 0 Number of tools on UseGalaxy.be: 2 Number of tools on UseGalaxy.cz: 2 @@ -11280,6 +11109,7 @@ - https://usegalaxy.eu/published/workflow?id=585c21b7b1d864fc - https://usegalaxy.eu/published/workflow?id=5ad406442ec21345 - https://usegalaxy.eu/published/workflow?id=5b893b69a1b6748f + - https://usegalaxy.eu/published/workflow?id=5cd71f9a190cae1b - https://usegalaxy.eu/published/workflow?id=5e1906290f5b4d8a - https://usegalaxy.eu/published/workflow?id=62c47e3c9d4f3aa3 - https://usegalaxy.eu/published/workflow?id=6573f3b1606b7f09 @@ -11522,6 +11352,7 @@ - https://usegalaxy.org/published/workflow?id=81f1f0fd6d9235fd - https://usegalaxy.org/published/workflow?id=84161f4f8bf77474 - https://usegalaxy.org/published/workflow?id=864da6858d34df08 + - https://usegalaxy.org/published/workflow?id=87045af52d500e91 - https://usegalaxy.org/published/workflow?id=8a350e0d96e937a5 - https://usegalaxy.org/published/workflow?id=8cfbaa14cff5a633 - https://usegalaxy.org/published/workflow?id=8ebc2b1ae24ed884 @@ -11537,6 +11368,7 @@ - https://usegalaxy.org/published/workflow?id=9ddfdc9d6cacea88 - https://usegalaxy.org/published/workflow?id=9e5c5ddb60a24889 - https://usegalaxy.org/published/workflow?id=a0366d691ecadfd5 + - https://usegalaxy.org/published/workflow?id=a4543d00cdbede5f - https://usegalaxy.org/published/workflow?id=a8e0f77cd6ef49f9 - https://usegalaxy.org/published/workflow?id=ab0be4897d5355ac - https://usegalaxy.org/published/workflow?id=acada5044d64a30a @@ -11608,7 +11440,7 @@ Suite conda package: bandage_ng Suite first commit date: '2018-09-06' Suite owner: iuc - Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/bandage + Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage Suite runs (last 5 years) (usegalaxy.eu): 74766 Suite runs (last 5 years) (usegalaxy.fr): 9763 Suite runs (last 5 years) (usegalaxy.org): 63998 @@ -11685,12 +11517,10 @@ Number of tools on ImmPort Galaxy: 0 Number of tools on InteractoMIX: 0 Number of tools on Lebanese University Galaxy: 0 - Number of tools on MBAC Metabiome Portal: 0 Number of tools on MISSISSIPPI: 0 Number of tools on Mandoiu Lab: 0 Number of tools on Oqtans: 0 Number of tools on Palfinder: 0 - Number of tools on PepSimili: 0 Number of tools on PhagePromotor: 0 Number of tools on UseGalaxy.be: 1 Number of tools on UseGalaxy.cz: 1 @@ -11701,12 +11531,14 @@ Number of tools on UseGalaxy.org.au: 0 Number of tools on Viral Variant Visualizer (VVV): 0 Related Tutorials: [] - Related Workflows: [] + Related Workflows: + - https://usegalaxy.eu/published/workflow?id=5dc5e056c5f4e0da + - https://usegalaxy.eu/published/workflow?id=8f5c84fb0d286050 Suite ID: bayescan Suite conda package: bayescan Suite first commit date: '2017-03-09' Suite owner: iuc - Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/bayescan + Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan Suite runs (last 5 years) (usegalaxy.eu): 109 Suite runs (last 5 years) (usegalaxy.fr): 0 Suite runs (last 5 years) (usegalaxy.org): 0 @@ -11798,12 +11630,10 @@ Number of tools on ImmPort Galaxy: 0 Number of tools on InteractoMIX: 0 Number of tools on Lebanese University Galaxy: 0 - Number of tools on MBAC Metabiome Portal: 0 Number of tools on MISSISSIPPI: 0 Number of tools on Mandoiu Lab: 0 Number of tools on Oqtans: 0 Number of tools on Palfinder: 0 - Number of tools on PepSimili: 0 Number of tools on PhagePromotor: 0 Number of tools on UseGalaxy.be: 0 Number of tools on UseGalaxy.cz: 4 @@ -11811,7 +11641,7 @@ Number of tools on UseGalaxy.fr: 6 Number of tools on UseGalaxy.no: 0 Number of tools on UseGalaxy.org (Main): 6 - Number of tools on UseGalaxy.org.au: 3 + Number of tools on UseGalaxy.org.au: 4 Number of tools on Viral Variant Visualizer (VVV): 0 Related Tutorials: [] Related Workflows: @@ -11823,7 +11653,7 @@ Suite conda package: bbmap Suite first commit date: '2021-10-04' Suite owner: iuc - Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/bbtools + Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools Suite runs (last 5 years) (usegalaxy.eu): 25287 Suite runs (last 5 years) (usegalaxy.fr): 134 Suite runs (last 5 years) (usegalaxy.org): 10487 @@ -11869,7 +11699,7 @@ UseGalaxy.cz: 4 UseGalaxy.eu: 6 UseGalaxy.fr: 6 - UseGalaxy.or: 3 + UseGalaxy.or: 4 biii ID: null bio.tool ID: bbmap bio.tool description: BBMap is a fast splice-aware aligner for RNA and DNA. It @@ -11916,12 +11746,10 @@ Number of tools on ImmPort Galaxy: 0 Number of tools on InteractoMIX: 0 Number of tools on Lebanese University Galaxy: 0 - Number of tools on MBAC Metabiome Portal: 0 Number of tools on MISSISSIPPI: 0 Number of tools on Mandoiu Lab: 0 Number of tools on Oqtans: 0 Number of tools on Palfinder: 0 - Number of tools on PepSimili: 0 Number of tools on PhagePromotor: 0 Number of tools on UseGalaxy.be: 0 Number of tools on UseGalaxy.cz: 0 @@ -11937,7 +11765,7 @@ Suite conda package: bigscape Suite first commit date: '2024-02-18' Suite owner: iuc - Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/bigscape + Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape Suite runs (last 5 years) (usegalaxy.eu): 2449 Suite runs (last 5 years) (usegalaxy.fr): 0 Suite runs (last 5 years) (usegalaxy.org): 0 @@ -11959,7 +11787,7 @@ Suite users (usegalaxy.org): 0 Suite users (usegalaxy.org.au): 0 Suite users on main servers: 95 - Suite version: 1.1.9 + Suite version: '@TOOL_VERSION@+galaxy@VERSION_SUFFIX@' Suite version status: To update To keep: true Tool IDs: @@ -12011,12 +11839,10 @@ Number of tools on ImmPort Galaxy: 0 Number of tools on InteractoMIX: 0 Number of tools on Lebanese University Galaxy: 0 - Number of tools on MBAC Metabiome Portal: 0 Number of tools on MISSISSIPPI: 0 Number of tools on Mandoiu Lab: 0 Number of tools on Oqtans: 0 Number of tools on Palfinder: 0 - Number of tools on PepSimili: 0 Number of tools on PhagePromotor: 0 Number of tools on UseGalaxy.be: 1 Number of tools on UseGalaxy.cz: 1 @@ -12040,7 +11866,7 @@ Suite conda package: binette Suite first commit date: '2025-01-14' Suite owner: iuc - Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/binette + Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/master/tools/binette Suite runs (last 5 years) (usegalaxy.eu): 359 Suite runs (last 5 years) (usegalaxy.fr): 49 Suite runs (last 5 years) (usegalaxy.org): 17 @@ -12062,8 +11888,8 @@ Suite users (usegalaxy.org): 8 Suite users (usegalaxy.org.au): 0 Suite users on main servers: 20 - Suite version: 1.2.1 - Suite version status: Up-to-date + Suite version: '@TOOL_VERSION@+galaxy@VERSION_SUFFIX@' + Suite version status: To update To keep: true Tool IDs: - binette @@ -12114,12 +11940,10 @@ Number of tools on ImmPort Galaxy: 0 Number of tools on InteractoMIX: 0 Number of tools on Lebanese University Galaxy: 0 - Number of tools on MBAC Metabiome Portal: 0 Number of tools on MISSISSIPPI: 0 Number of tools on Mandoiu Lab: 0 Number of tools on Oqtans: 0 Number of tools on Palfinder: 0 - Number of tools on PepSimili: 0 Number of tools on PhagePromotor: 0 Number of tools on UseGalaxy.be: 0 Number of tools on UseGalaxy.cz: 1 @@ -12135,7 +11959,7 @@ Suite conda package: binning_refiner Suite first commit date: '2022-02-18' Suite owner: iuc - Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/binning_refiner + Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner Suite runs (last 5 years) (usegalaxy.eu): 236 Suite runs (last 5 years) (usegalaxy.fr): 0 Suite runs (last 5 years) (usegalaxy.org): 0 @@ -12203,12 +12027,10 @@ Number of tools on ImmPort Galaxy: 0 Number of tools on InteractoMIX: 0 Number of tools on Lebanese University Galaxy: 0 - Number of tools on MBAC Metabiome Portal: 0 Number of tools on MISSISSIPPI: 0 Number of tools on Mandoiu Lab: 0 Number of tools on Oqtans: 0 Number of tools on Palfinder: 0 - Number of tools on PepSimili: 0 Number of tools on PhagePromotor: 0 Number of tools on UseGalaxy.be: 1 Number of tools on UseGalaxy.cz: 1 @@ -12246,7 +12068,7 @@ Suite conda package: biom-format Suite first commit date: '2016-06-07' Suite owner: iuc - Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/biom_format + Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format Suite runs (last 5 years) (usegalaxy.eu): 16688 Suite runs (last 5 years) (usegalaxy.fr): 0 Suite runs (last 5 years) (usegalaxy.org): 2736 @@ -12324,12 +12146,10 @@ Number of tools on ImmPort Galaxy: 0 Number of tools on InteractoMIX: 0 Number of tools on Lebanese University Galaxy: 0 - Number of tools on MBAC Metabiome Portal: 0 Number of tools on MISSISSIPPI: 0 Number of tools on Mandoiu Lab: 0 Number of tools on Oqtans: 0 Number of tools on Palfinder: 0 - Number of tools on PepSimili: 0 Number of tools on PhagePromotor: 0 Number of tools on UseGalaxy.be: 0 Number of tools on UseGalaxy.cz: 0 @@ -12345,7 +12165,7 @@ Suite conda package: bmtagger Suite first commit date: '2025-11-12' Suite owner: iuc - Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/bmtagger + Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/master/tools/bmtagger Suite runs (last 5 years) (usegalaxy.eu): 0 Suite runs (last 5 years) (usegalaxy.fr): 0 Suite runs (last 5 years) (usegalaxy.org): 0 @@ -12367,8 +12187,8 @@ Suite users (usegalaxy.org): 0 Suite users (usegalaxy.org.au): 0 Suite users on main servers: 0 - Suite version: '3.101' - Suite version status: Up-to-date + Suite version: '@TOOL_VERSION@+galaxy@VERSION_SUFFIX@' + Suite version status: To update To keep: true Tool IDs: - bmtagger @@ -12395,7 +12215,7 @@ - Metagenomics - Microbial ecology Homepage: https://github.com/jenniferlu717/Bracken/releases - Latest suite conda package version: '3.1' + Latest suite conda package version: 3.1p1 Number of tools on APOSTL: 0 Number of tools on CIRM-CFBP: 0 Number of tools on ChemFlow: 0 @@ -12409,12 +12229,10 @@ Number of tools on ImmPort Galaxy: 0 Number of tools on InteractoMIX: 0 Number of tools on Lebanese University Galaxy: 0 - Number of tools on MBAC Metabiome Portal: 0 Number of tools on MISSISSIPPI: 0 Number of tools on Mandoiu Lab: 0 Number of tools on Oqtans: 0 Number of tools on Palfinder: 0 - Number of tools on PepSimili: 0 Number of tools on PhagePromotor: 0 Number of tools on UseGalaxy.be: 1 Number of tools on UseGalaxy.cz: 1 @@ -12448,6 +12266,7 @@ - https://usegalaxy.eu/published/workflow?id=ebb131f2a6172081 - https://usegalaxy.fr/published/workflow?id=3d3b40398d1cd1ae - https://usegalaxy.org.au/published/workflow?id=2120112358db8e01 + - https://usegalaxy.org.au/published/workflow?id=41331c03339e2b19 - https://usegalaxy.org.au/published/workflow?id=92fcdd490831c6c5 - https://usegalaxy.org.au/published/workflow?id=a335b9c9103b57ad - https://usegalaxy.org/published/workflow?id=074a0b1bc8273c16 @@ -12478,7 +12297,7 @@ Suite conda package: bracken Suite first commit date: '2019-10-15' Suite owner: iuc - Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/bracken + Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken Suite runs (last 5 years) (usegalaxy.eu): 108307 Suite runs (last 5 years) (usegalaxy.fr): 12432 Suite runs (last 5 years) (usegalaxy.org): 27569 @@ -12501,7 +12320,7 @@ Suite users (usegalaxy.org.au): 265 Suite users on main servers: 2842 Suite version: '3.1' - Suite version status: Up-to-date + Suite version status: To update To keep: true Tool IDs: - est_abundance @@ -12541,7 +12360,7 @@ - Transcriptomics - Sequence analysis Homepage: https://gitlab.com/ezlab/busco/-/releases - Latest suite conda package version: 6.0.0 + Latest suite conda package version: 6.1.0 Number of tools on APOSTL: 0 Number of tools on CIRM-CFBP: 0 Number of tools on ChemFlow: 0 @@ -12555,12 +12374,10 @@ Number of tools on ImmPort Galaxy: 0 Number of tools on InteractoMIX: 0 Number of tools on Lebanese University Galaxy: 0 - Number of tools on MBAC Metabiome Portal: 0 Number of tools on MISSISSIPPI: 0 Number of tools on Mandoiu Lab: 0 Number of tools on Oqtans: 0 Number of tools on Palfinder: 0 - Number of tools on PepSimili: 0 Number of tools on PhagePromotor: 0 Number of tools on UseGalaxy.be: 1 Number of tools on UseGalaxy.cz: 1 @@ -12755,6 +12572,7 @@ - https://usegalaxy.eu/published/workflow?id=e935d2c8ffb52588 - https://usegalaxy.eu/published/workflow?id=ec79f14ab91cd933 - https://usegalaxy.eu/published/workflow?id=f08b29e4cef76cd5 + - https://usegalaxy.eu/published/workflow?id=f15643eaf62f76a8 - https://usegalaxy.eu/published/workflow?id=f1ca4289ee4f67bb - https://usegalaxy.eu/published/workflow?id=f1e2577699125607 - https://usegalaxy.eu/published/workflow?id=f38745208494d4ab @@ -13010,6 +12828,7 @@ - https://usegalaxy.org/published/workflow?id=80a7124c40438cc9 - https://usegalaxy.org/published/workflow?id=81f1f0fd6d9235fd - https://usegalaxy.org/published/workflow?id=84161f4f8bf77474 + - https://usegalaxy.org/published/workflow?id=84233173d92fa506 - https://usegalaxy.org/published/workflow?id=864da6858d34df08 - https://usegalaxy.org/published/workflow?id=86c67855acbf6124 - https://usegalaxy.org/published/workflow?id=88327cb2e0fe3c25 @@ -13122,7 +12941,7 @@ Suite conda package: busco Suite first commit date: '2017-01-12' Suite owner: iuc - Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/busco + Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco Suite runs (last 5 years) (usegalaxy.eu): 134029 Suite runs (last 5 years) (usegalaxy.fr): 8860 Suite runs (last 5 years) (usegalaxy.org): 58403 @@ -13197,12 +13016,10 @@ Number of tools on ImmPort Galaxy: 0 Number of tools on InteractoMIX: 0 Number of tools on Lebanese University Galaxy: 0 - Number of tools on MBAC Metabiome Portal: 0 Number of tools on MISSISSIPPI: 0 Number of tools on Mandoiu Lab: 0 Number of tools on Oqtans: 0 Number of tools on Palfinder: 0 - Number of tools on PepSimili: 0 Number of tools on PhagePromotor: 0 Number of tools on UseGalaxy.be: 0 Number of tools on UseGalaxy.cz: 3 @@ -13224,7 +13041,7 @@ Suite conda package: cami-amber Suite first commit date: '2024-05-20' Suite owner: iuc - Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/cami_amber + Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/master/tools/cami_amber Suite runs (last 5 years) (usegalaxy.eu): 10522 Suite runs (last 5 years) (usegalaxy.fr): 0 Suite runs (last 5 years) (usegalaxy.org): 0 @@ -13308,12 +13125,10 @@ Number of tools on ImmPort Galaxy: 0 Number of tools on InteractoMIX: 0 Number of tools on Lebanese University Galaxy: 0 - Number of tools on MBAC Metabiome Portal: 0 Number of tools on MISSISSIPPI: 0 Number of tools on Mandoiu Lab: 0 Number of tools on Oqtans: 0 Number of tools on Palfinder: 0 - Number of tools on PepSimili: 0 Number of tools on PhagePromotor: 0 Number of tools on UseGalaxy.be: 5 Number of tools on UseGalaxy.cz: 5 @@ -13330,6 +13145,7 @@ - https://usegalaxy.eu/published/workflow?id=6158c3b5fc12044e - https://usegalaxy.eu/published/workflow?id=6416cfdbd5273063 - https://usegalaxy.eu/published/workflow?id=667bac8d7453e5f1 + - https://usegalaxy.eu/published/workflow?id=7be08f99f83c927e - https://usegalaxy.eu/published/workflow?id=8c91345ed468e22d - https://usegalaxy.eu/published/workflow?id=8deb08d4f228e198 - https://usegalaxy.eu/published/workflow?id=9a97c6eb4fe015e7 @@ -13339,7 +13155,7 @@ Suite conda package: cat Suite first commit date: '2019-11-27' Suite owner: iuc - Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/cat + Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/master/tools/cat Suite runs (last 5 years) (usegalaxy.eu): 17418 Suite runs (last 5 years) (usegalaxy.fr): 0 Suite runs (last 5 years) (usegalaxy.org): 1590 @@ -13413,12 +13229,10 @@ Number of tools on ImmPort Galaxy: 0 Number of tools on InteractoMIX: 0 Number of tools on Lebanese University Galaxy: 0 - Number of tools on MBAC Metabiome Portal: 0 Number of tools on MISSISSIPPI: 0 Number of tools on Mandoiu Lab: 0 Number of tools on Oqtans: 0 Number of tools on Palfinder: 0 - Number of tools on PepSimili: 0 Number of tools on PhagePromotor: 0 Number of tools on UseGalaxy.be: 0 Number of tools on UseGalaxy.cz: 1 @@ -13434,7 +13248,7 @@ Suite conda package: cawlign Suite first commit date: '2025-09-30' Suite owner: iuc - Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/cawlign + Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/master/tools/cawlign Suite runs (last 5 years) (usegalaxy.eu): 0 Suite runs (last 5 years) (usegalaxy.fr): 0 Suite runs (last 5 years) (usegalaxy.org): 0 @@ -13498,12 +13312,10 @@ Number of tools on ImmPort Galaxy: 0 Number of tools on InteractoMIX: 0 Number of tools on Lebanese University Galaxy: 1 - Number of tools on MBAC Metabiome Portal: 0 Number of tools on MISSISSIPPI: 0 Number of tools on Mandoiu Lab: 0 Number of tools on Oqtans: 0 Number of tools on Palfinder: 0 - 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Number of tools on PepSimili: 0 Number of tools on PhagePromotor: 0 Number of tools on UseGalaxy.be: 0 Number of tools on UseGalaxy.cz: 1 @@ -13880,7 +13687,7 @@ Suite conda package: checkm2 Suite first commit date: '2024-11-08' Suite owner: iuc - Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/checkm2 + Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm2 Suite runs (last 5 years) (usegalaxy.eu): 1602 Suite runs (last 5 years) (usegalaxy.fr): 1268 Suite runs (last 5 years) (usegalaxy.org): 1322 @@ -13902,8 +13709,8 @@ Suite users (usegalaxy.org): 187 Suite users (usegalaxy.org.au): 0 Suite users on main servers: 430 - Suite version: 1.1.0 - Suite version status: Up-to-date + Suite version: '@TOOL_VERSION@+galaxy@VERSION_SUFFIX@' + Suite version status: To update To keep: true Tool IDs: - checkm2 @@ -13929,7 +13736,7 @@ EDAM reduced topics: [] EDAM topics: [] Homepage: https://github.com/wdecoster/chopper - Latest suite conda package version: 0.12.0 + Latest suite conda package version: 0.13.0 Number of tools on APOSTL: 0 Number of tools on CIRM-CFBP: 0 Number of tools on ChemFlow: 0 @@ -13943,12 +13750,10 @@ Number of tools on ImmPort Galaxy: 0 Number of tools on InteractoMIX: 0 Number of tools on Lebanese University Galaxy: 0 - Number of tools on MBAC Metabiome Portal: 0 Number of tools on MISSISSIPPI: 0 Number of tools on Mandoiu Lab: 0 Number of tools on Oqtans: 0 Number of tools on Palfinder: 0 - Number of tools on PepSimili: 0 Number of tools on PhagePromotor: 0 Number of tools on UseGalaxy.be: 0 Number of tools on UseGalaxy.cz: 0 @@ -13960,14 +13765,16 @@ Number of tools on Viral Variant Visualizer (VVV): 0 Related Tutorials: [] Related Workflows: + - https://usegalaxy.eu/published/workflow?id=1ae9a523ef719a3d - https://usegalaxy.eu/published/workflow?id=4eb9dfe91fc2dc67 + - https://usegalaxy.eu/published/workflow?id=5cd71f9a190cae1b - https://usegalaxy.eu/published/workflow?id=93d7a5704ec1d82d - https://usegalaxy.eu/published/workflow?id=ece3ffe0800e6880 Suite ID: chopper Suite conda package: chopper Suite first commit date: '2025-07-22' Suite owner: iuc - Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/chopper + Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/master/tools/chopper Suite runs (last 5 years) (usegalaxy.eu): 10 Suite runs (last 5 years) (usegalaxy.fr): 0 Suite runs (last 5 years) (usegalaxy.org): 0 @@ -13989,8 +13796,8 @@ Suite users (usegalaxy.org): 0 Suite users (usegalaxy.org.au): 0 Suite users on main servers: 6 - Suite version: 0.12.0 - Suite version status: Up-to-date + Suite version: '@TOOL_VERSION@+galaxy@VERSION_SUFFIX@' + Suite version status: To update To keep: true Tool IDs: - chopper @@ -14025,12 +13832,10 @@ Number of tools on ImmPort Galaxy: 0 Number of tools on InteractoMIX: 0 Number of tools on Lebanese University Galaxy: 0 - Number of tools on MBAC Metabiome Portal: 0 Number of tools on MISSISSIPPI: 0 Number of tools on Mandoiu Lab: 0 Number of tools on Oqtans: 0 Number of tools on Palfinder: 0 - Number of tools on PepSimili: 0 Number of tools on PhagePromotor: 0 Number of tools on UseGalaxy.be: 0 Number of tools on UseGalaxy.cz: 0 @@ -14047,7 +13852,7 @@ Suite conda package: cialign Suite first commit date: '2025-08-04' Suite owner: iuc - Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign + Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/master/tools/cialign Suite runs (last 5 years) (usegalaxy.eu): 6 Suite runs (last 5 years) (usegalaxy.fr): 0 Suite runs (last 5 years) (usegalaxy.org): 0 @@ -14099,7 +13904,7 @@ EDAM topics: - Molecular genetics Homepage: https://github.com/HKU-BAL/Clair3 - Latest suite conda package version: 2.0.1 + Latest suite conda package version: 2.0.2 Number of tools on APOSTL: 0 Number of tools on CIRM-CFBP: 0 Number of tools on ChemFlow: 0 @@ -14113,12 +13918,10 @@ Number of tools on ImmPort Galaxy: 0 Number of tools on InteractoMIX: 0 Number of tools on Lebanese University Galaxy: 0 - Number of tools on MBAC Metabiome Portal: 0 Number of tools on MISSISSIPPI: 0 Number of tools on Mandoiu Lab: 0 Number of tools on Oqtans: 0 Number of tools on Palfinder: 0 - Number of tools on PepSimili: 0 Number of tools on PhagePromotor: 0 Number of tools on UseGalaxy.be: 1 Number of tools on UseGalaxy.cz: 1 @@ -14154,7 +13957,7 @@ Suite conda package: clair3 Suite first commit date: '2022-06-15' Suite owner: iuc - Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/clair3 + Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 Suite runs (last 5 years) (usegalaxy.eu): 5269 Suite runs (last 5 years) (usegalaxy.fr): 54 Suite runs (last 5 years) (usegalaxy.org): 1858 @@ -14176,7 +13979,7 @@ Suite users (usegalaxy.org): 52 Suite users (usegalaxy.org.au): 13 Suite users on main servers: 395 - Suite version: 1.0.10 + Suite version: '@TOOL_VERSION@+galaxy@VERSION_SUFFIX@' Suite version status: To update To keep: true Tool IDs: @@ -14228,12 +14031,10 @@ Number of tools on ImmPort Galaxy: 0 Number of tools on InteractoMIX: 0 Number of tools on Lebanese University Galaxy: 0 - Number of tools on MBAC Metabiome Portal: 0 Number of tools on MISSISSIPPI: 0 Number of tools on Mandoiu Lab: 0 Number of tools on Oqtans: 0 Number of tools on Palfinder: 0 - Number of tools on PepSimili: 0 Number of tools on PhagePromotor: 0 Number of tools on UseGalaxy.be: 1 Number of tools on UseGalaxy.cz: 1 @@ -14271,6 +14072,7 @@ - https://usegalaxy.org/published/workflow?id=a484a1e1a7335696 - https://usegalaxy.org/published/workflow?id=b2fb90873471f4e7 - https://usegalaxy.org/published/workflow?id=be9bd7286d38c210 + - https://usegalaxy.org/published/workflow?id=f7bf58d66cafcf1f - https://workflowhub.eu/workflows/1060?version=1 - https://workflowhub.eu/workflows/1487?version=2 - https://workflowhub.eu/workflows/1541?version=1 @@ -14280,7 +14082,7 @@ Suite conda package: clustalw Suite first commit date: '2022-10-02' Suite owner: devteam - 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Suite version: 1.3.3 - Suite version status: Up-to-date + Suite version: 1.3.5 + Suite version status: To update To keep: true Tool IDs: - fastp @@ -19697,12 +19473,10 @@ Number of tools on ImmPort Galaxy: 0 Number of tools on InteractoMIX: 0 Number of tools on Lebanese University Galaxy: 0 - Number of tools on MBAC Metabiome Portal: 0 Number of tools on MISSISSIPPI: 0 Number of tools on Mandoiu Lab: 0 Number of tools on Oqtans: 0 Number of tools on Palfinder: 0 - Number of tools on PepSimili: 0 Number of tools on PhagePromotor: 0 Number of tools on UseGalaxy.be: 0 Number of tools on UseGalaxy.cz: 0 @@ -19715,11 +19489,12 @@ Related Tutorials: [] Related Workflows: - https://usegalaxy.org.au/published/workflow?id=aa1d123c0a0929f3 + - https://workflowhub.eu/workflows/2195?version=1 Suite ID: fastplong Suite conda package: fastplong Suite first commit date: '2025-05-06' Suite owner: iuc - Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastplong + Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastplong Suite runs (last 5 years) (usegalaxy.eu): 309 Suite runs (last 5 years) (usegalaxy.fr): 0 Suite runs (last 5 years) (usegalaxy.org): 0 @@ -19741,8 +19516,8 @@ Suite users (usegalaxy.org): 0 Suite users (usegalaxy.org.au): 8 Suite users on main servers: 48 - Suite version: 0.4.1 - Suite version status: Up-to-date + Suite version: '@TOOL_VERSION@+galaxy@VERSION_SUFFIX@' + Suite version status: To update To keep: true Tool IDs: - fastplong @@ -19787,12 +19562,10 @@ Number of tools on ImmPort Galaxy: 0 Number of tools on InteractoMIX: 0 Number of tools on Lebanese University Galaxy: 0 - Number of tools on MBAC Metabiome Portal: 0 Number of tools on MISSISSIPPI: 0 Number of tools on Mandoiu Lab: 0 Number of tools on Oqtans: 0 Number of tools on Palfinder: 0 - Number of tools on PepSimili: 0 Number of tools on PhagePromotor: 0 Number of tools on UseGalaxy.be: 1 Number of tools on UseGalaxy.cz: 1 @@ -19838,7 +19611,7 @@ Suite conda package: fastqe Suite first commit date: '2020-07-13' Suite owner: iuc - Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastqe + Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe Suite runs (last 5 years) (usegalaxy.eu): 6904 Suite runs (last 5 years) (usegalaxy.fr): 510 Suite runs (last 5 years) (usegalaxy.org): 13534 @@ -19860,7 +19633,7 @@ Suite users (usegalaxy.org): 6198 Suite users (usegalaxy.org.au): 1323 Suite users on main servers: 10989 - 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Suite version: null + Suite version: '@WRAPPER_VERSION@.0' Suite version status: To update To keep: true Tool IDs: @@ -21046,12 +20817,10 @@ Number of tools on ImmPort Galaxy: 0 Number of tools on InteractoMIX: 0 Number of tools on Lebanese University Galaxy: 0 - Number of tools on MBAC Metabiome Portal: 0 Number of tools on MISSISSIPPI: 0 Number of tools on Mandoiu Lab: 0 Number of tools on Oqtans: 0 Number of tools on Palfinder: 0 - Number of tools on PepSimili: 0 Number of tools on PhagePromotor: 0 Number of tools on UseGalaxy.be: 0 Number of tools on UseGalaxy.cz: 4 @@ -21069,7 +20838,7 @@ Suite conda package: freyja Suite first commit date: '2022-07-05' Suite owner: iuc - Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/freyja + Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja Suite runs (last 5 years) (usegalaxy.eu): 24576 Suite runs (last 5 years) (usegalaxy.fr): 0 Suite runs (last 5 years) (usegalaxy.org): 327 @@ -21142,12 +20911,10 @@ Number of tools on ImmPort Galaxy: 0 Number of tools on InteractoMIX: 0 Number of tools on Lebanese University Galaxy: 0 - 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Number of tools on MBAC Metabiome Portal: 0 Number of tools on MISSISSIPPI: 0 Number of tools on Mandoiu Lab: 0 Number of tools on Oqtans: 0 Number of tools on Palfinder: 0 - Number of tools on PepSimili: 0 Number of tools on PhagePromotor: 0 Number of tools on UseGalaxy.be: 0 Number of tools on UseGalaxy.cz: 1 @@ -21938,15 +21693,16 @@ - https://usegalaxy.eu/published/workflow?id=c62d65832377e376 - https://usegalaxy.eu/published/workflow?id=e4dabaf57668dbd1 - https://usegalaxy.org/published/workflow?id=33d90e718ce500ef + - https://usegalaxy.org/published/workflow?id=84233173d92fa506 - https://usegalaxy.org/published/workflow?id=8d229c0f58a07ebe - https://usegalaxy.org/published/workflow?id=9b589bc76208fb1e - https://workflowhub.eu/workflows/1352?version=4 - - https://workflowhub.eu/workflows/2099?version=1 + - https://workflowhub.eu/workflows/2099?version=2 Suite ID: gtdbtk Suite conda package: gtdbtk Suite first commit date: '2022-12-13' Suite owner: iuc - Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/gtdbtk + Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/master/tools/gtdbtk Suite runs (last 5 years) (usegalaxy.eu): 3982 Suite runs (last 5 years) (usegalaxy.fr): 1439 Suite runs (last 5 years) (usegalaxy.org): 1566 @@ -22027,12 +21783,10 @@ Number of tools on ImmPort Galaxy: 0 Number of tools on InteractoMIX: 0 Number of tools on Lebanese University Galaxy: 0 - Number of tools on MBAC Metabiome Portal: 0 Number of tools on MISSISSIPPI: 0 Number of tools on Mandoiu Lab: 0 Number of tools on Oqtans: 0 Number of tools on Palfinder: 0 - Number of tools on PepSimili: 0 Number of tools on PhagePromotor: 0 Number of tools on UseGalaxy.be: 1 Number of tools on UseGalaxy.cz: 1 @@ -22048,7 +21802,7 @@ Suite conda package: gubbins Suite first commit date: '2017-06-22' Suite owner: iuc - Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/gubbins + Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins Suite runs (last 5 years) (usegalaxy.eu): 4731 Suite runs (last 5 years) (usegalaxy.fr): 0 Suite runs (last 5 years) (usegalaxy.org): 3847 @@ -22070,7 +21824,7 @@ Suite users (usegalaxy.org): 288 Suite users (usegalaxy.org.au): 317 Suite users on main servers: 1033 - Suite version: 3.2.1 + Suite version: '@TOOL_VERSION@+galaxy@VERSION_SUFFIX@' Suite version status: To update To keep: true Tool IDs: @@ -22133,12 +21887,10 @@ Number of tools on ImmPort Galaxy: 0 Number of tools on InteractoMIX: 0 Number of tools on Lebanese University Galaxy: 0 - Number of tools on MBAC Metabiome Portal: 0 Number of tools on MISSISSIPPI: 0 Number of tools on Mandoiu Lab: 0 Number of tools on Oqtans: 0 Number of tools on Palfinder: 0 - Number of tools on PepSimili: 0 Number of tools on PhagePromotor: 0 Number of tools on UseGalaxy.be: 0 Number of tools on UseGalaxy.cz: 0 @@ -22154,7 +21906,7 @@ Suite conda package: halla Suite first commit date: '2025-11-05' Suite owner: iuc - Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/halla + Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/master/tools/halla Suite runs (last 5 years) (usegalaxy.eu): 0 Suite runs (last 5 years) (usegalaxy.fr): 0 Suite runs (last 5 years) (usegalaxy.org): 0 @@ -22176,8 +21928,8 @@ Suite users (usegalaxy.org): 0 Suite users (usegalaxy.org.au): 0 Suite users on main servers: 0 - Suite version: 0.8.40 - Suite version status: Up-to-date + Suite version: '@TOOL_VERSION@+galaxy@VERSION_SUFFIX@' + Suite version status: To update To keep: true Tool IDs: - halla @@ -22226,12 +21978,10 @@ Number of tools on ImmPort Galaxy: 0 Number of tools on InteractoMIX: 0 Number of tools on Lebanese University Galaxy: 0 - Number of tools on MBAC Metabiome Portal: 0 Number of tools on MISSISSIPPI: 0 Number of tools on Mandoiu Lab: 0 Number of tools on Oqtans: 0 Number of tools on Palfinder: 0 - Number of tools on PepSimili: 0 Number of tools on PhagePromotor: 0 Number of tools on UseGalaxy.be: 0 Number of tools on UseGalaxy.cz: 2 @@ -22251,7 +22001,7 @@ Suite conda package: hamronization Suite first commit date: '2021-02-02' Suite owner: iuc - Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/hamronization + Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization Suite runs (last 5 years) (usegalaxy.eu): 18459 Suite runs (last 5 years) (usegalaxy.fr): 191 Suite runs (last 5 years) (usegalaxy.org): 20 @@ -22329,12 +22079,10 @@ Number of tools on ImmPort Galaxy: 0 Number of tools on InteractoMIX: 0 Number of tools on Lebanese University Galaxy: 0 - Number of tools on MBAC Metabiome Portal: 0 Number of tools on MISSISSIPPI: 0 Number of tools on Mandoiu Lab: 0 Number of tools on Oqtans: 0 Number of tools on Palfinder: 0 - Number of tools on PepSimili: 0 Number of tools on PhagePromotor: 0 Number of tools on UseGalaxy.be: 1 Number of tools on UseGalaxy.cz: 1 @@ -22350,7 +22098,7 @@ Suite conda package: bio_hansel Suite first commit date: '2017-09-29' Suite owner: iuc - Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/hansel + Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/master/tools/hansel Suite runs (last 5 years) (usegalaxy.eu): 312 Suite runs (last 5 years) (usegalaxy.fr): 0 Suite runs (last 5 years) (usegalaxy.org): 538 @@ -22423,12 +22171,10 @@ Number of tools on ImmPort Galaxy: 0 Number of tools on InteractoMIX: 0 Number of tools on Lebanese University Galaxy: 0 - Number of tools on MBAC Metabiome Portal: 0 Number of tools on MISSISSIPPI: 0 Number of tools on Mandoiu Lab: 0 Number of tools on Oqtans: 0 Number of tools on Palfinder: 0 - Number of tools on PepSimili: 0 Number of tools on PhagePromotor: 0 Number of tools on UseGalaxy.be: 0 Number of tools on UseGalaxy.cz: 1 @@ -22444,7 +22190,7 @@ Suite conda package: hifiasm_meta Suite first commit date: '2023-01-18' Suite owner: galaxy-australia - Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/hifiasm_meta + Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/master/tools/hifiasm_meta Suite runs (last 5 years) (usegalaxy.eu): 229 Suite runs (last 5 years) (usegalaxy.fr): 0 Suite runs (last 5 years) (usegalaxy.org): 0 @@ -22547,12 +22293,10 @@ Number of tools on ImmPort Galaxy: 0 Number of tools on InteractoMIX: 0 Number of tools on Lebanese University Galaxy: 0 - Number of tools on MBAC Metabiome Portal: 0 Number of tools on MISSISSIPPI: 0 Number of tools on Mandoiu Lab: 0 Number of tools on Oqtans: 0 Number of tools on Palfinder: 0 - Number of tools on PepSimili: 0 Number of tools on PhagePromotor: 0 Number of tools on UseGalaxy.be: 12 Number of tools on UseGalaxy.cz: 12 @@ -22581,6 +22325,7 @@ - https://usegalaxy.fr/published/workflow?id=7ebb54181b404733 - https://usegalaxy.fr/published/workflow?id=b131218bec7eacb4 - https://usegalaxy.fr/published/workflow?id=d425a77157cae2ee + - https://usegalaxy.org/published/workflow?id=84b447be2f1c5870 - https://workflowhub.eu/workflows/100?version=1 - https://workflowhub.eu/workflows/37?version=1 - https://workflowhub.eu/workflows/38?version=1 @@ -22590,7 +22335,7 @@ Suite conda package: hmmer Suite first commit date: '2015-02-16' Suite owner: iuc - Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/hmmer3 + Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 Suite runs (last 5 years) (usegalaxy.eu): 36302 Suite runs (last 5 years) (usegalaxy.fr): 540 Suite runs (last 5 years) (usegalaxy.org): 0 @@ -22680,12 +22425,10 @@ Number of tools on ImmPort Galaxy: 0 Number of tools on InteractoMIX: 0 Number of tools on Lebanese University Galaxy: 0 - Number of tools on MBAC Metabiome Portal: 0 Number of tools on MISSISSIPPI: 0 Number of tools on Mandoiu Lab: 0 Number of tools on Oqtans: 0 Number of tools on Palfinder: 0 - Number of tools on PepSimili: 0 Number of tools on PhagePromotor: 0 Number of tools on UseGalaxy.be: 6 Number of tools on UseGalaxy.cz: 10 @@ -22724,7 +22467,7 @@ Suite conda package: humann Suite first commit date: '2021-05-12' Suite owner: iuc - Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/humann + Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann Suite runs (last 5 years) (usegalaxy.eu): 52483 Suite runs (last 5 years) (usegalaxy.fr): 987 Suite runs (last 5 years) (usegalaxy.org): 3171 @@ -22803,7 +22546,7 @@ - Small molecules - Molecular interactions, pathways and networks Homepage: http://www.hyphy.org - Latest suite conda package version: 2.5.99 + Latest suite conda package version: 2.5.100 Number of tools on APOSTL: 0 Number of tools on CIRM-CFBP: 0 Number of tools on ChemFlow: 0 @@ -22817,12 +22560,10 @@ Number of tools on ImmPort Galaxy: 0 Number of tools on InteractoMIX: 0 Number of tools on Lebanese University Galaxy: 0 - Number of tools on MBAC Metabiome Portal: 0 Number of tools on MISSISSIPPI: 2 Number of tools on Mandoiu Lab: 0 Number of tools on Oqtans: 0 Number of tools on Palfinder: 0 - Number of tools on PepSimili: 0 Number of tools on PhagePromotor: 0 Number of tools on UseGalaxy.be: 12 Number of tools on UseGalaxy.cz: 17 @@ -22845,7 +22586,7 @@ Suite conda package: hyphy Suite first commit date: '2018-06-08' Suite owner: iuc - Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/hyphy + Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy Suite runs (last 5 years) (usegalaxy.eu): 10953 Suite runs (last 5 years) (usegalaxy.fr): 22 Suite runs (last 5 years) (usegalaxy.org): 4725 @@ -22941,12 +22682,10 @@ Number of tools on ImmPort Galaxy: 0 Number of tools on InteractoMIX: 0 Number of tools on Lebanese University Galaxy: 0 - Number of tools on MBAC Metabiome Portal: 0 Number of tools on MISSISSIPPI: 0 Number of tools on Mandoiu Lab: 0 Number of tools on Oqtans: 0 Number of tools on Palfinder: 0 - Number of tools on PepSimili: 0 Number of tools on PhagePromotor: 0 Number of tools on UseGalaxy.be: 0 Number of tools on UseGalaxy.cz: 1 @@ -22965,7 +22704,7 @@ Suite conda package: hypo Suite first commit date: '2021-11-15' Suite owner: iuc - Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/hypo + Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo Suite runs (last 5 years) (usegalaxy.eu): 575 Suite runs (last 5 years) (usegalaxy.fr): 0 Suite runs (last 5 years) (usegalaxy.org): 0 @@ -23040,12 +22779,10 @@ Number of tools on ImmPort Galaxy: 0 Number of tools on InteractoMIX: 0 Number of tools on Lebanese University Galaxy: 0 - Number of tools on MBAC Metabiome Portal: 0 Number of tools on MISSISSIPPI: 0 Number of tools on Mandoiu Lab: 0 Number of tools on Oqtans: 0 Number of tools on Palfinder: 0 - Number of tools on PepSimili: 0 Number of tools on PhagePromotor: 0 Number of tools on UseGalaxy.be: 0 Number of tools on UseGalaxy.cz: 0 @@ -23061,7 +22798,7 @@ Suite conda package: icescreen Suite first commit date: '2022-01-04' Suite owner: iuc - Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/icescreen + Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/master/tools/icescreen Suite runs (last 5 years) (usegalaxy.eu): 153 Suite runs (last 5 years) (usegalaxy.fr): 0 Suite runs (last 5 years) (usegalaxy.org): 15 @@ -23132,12 +22869,10 @@ Number of tools on ImmPort Galaxy: 0 Number of tools on InteractoMIX: 0 Number of tools on Lebanese University Galaxy: 0 - Number of tools on MBAC Metabiome Portal: 0 Number of tools on MISSISSIPPI: 0 Number of tools on Mandoiu Lab: 0 Number of tools on Oqtans: 0 Number of tools on Palfinder: 0 - Number of tools on PepSimili: 0 Number of tools on PhagePromotor: 0 Number of tools on UseGalaxy.be: 3 Number of tools on UseGalaxy.cz: 3 @@ -23153,7 +22888,7 @@ Suite conda package: idba Suite first commit date: '2018-04-26' Suite owner: iuc - Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/idba_ud + Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud Suite runs (last 5 years) (usegalaxy.eu): 944 Suite runs (last 5 years) (usegalaxy.fr): 3 Suite runs (last 5 years) (usegalaxy.org): 1199 @@ -23175,8 +22910,8 @@ Suite users (usegalaxy.org): 169 Suite users (usegalaxy.org.au): 0 Suite users on main servers: 296 - Suite version: null - Suite version status: To update + Suite version: 1.1.3 + Suite version status: Up-to-date To keep: true Tool IDs: - idba_hybrid @@ -23228,12 +22963,10 @@ Number of tools on ImmPort Galaxy: 0 Number of tools on InteractoMIX: 0 Number of tools on Lebanese University Galaxy: 0 - Number of tools on MBAC Metabiome Portal: 0 Number of tools on MISSISSIPPI: 0 Number of tools on Mandoiu Lab: 0 Number of tools on Oqtans: 0 Number of tools on Palfinder: 0 - Number of tools on PepSimili: 0 Number of tools on PhagePromotor: 0 Number of tools on UseGalaxy.be: 0 Number of tools on UseGalaxy.cz: 2 @@ -23249,7 +22982,7 @@ Suite conda package: instrain Suite first commit date: '2021-08-11' Suite owner: iuc - Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/instrain + Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/master/tools/instrain Suite runs (last 5 years) (usegalaxy.eu): 208 Suite runs (last 5 years) (usegalaxy.fr): 0 Suite runs (last 5 years) (usegalaxy.org): 0 @@ -23332,12 +23065,10 @@ Number of tools on ImmPort Galaxy: 0 Number of tools on InteractoMIX: 0 Number of tools on Lebanese University Galaxy: 0 - Number of tools on MBAC Metabiome Portal: 0 Number of tools on MISSISSIPPI: 0 Number of tools on Mandoiu Lab: 0 Number of tools on Oqtans: 0 Number of tools on Palfinder: 0 - Number of tools on PepSimili: 0 Number of tools on PhagePromotor: 0 Number of tools on UseGalaxy.be: 1 Number of tools on UseGalaxy.cz: 1 @@ -23383,7 +23114,7 @@ Suite conda package: integron_finder Suite first commit date: '2022-09-22' Suite owner: iuc - Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/integron_finder + Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/master/tools/integron_finder Suite runs (last 5 years) (usegalaxy.eu): 64428 Suite runs (last 5 years) (usegalaxy.fr): 2504 Suite runs (last 5 years) (usegalaxy.org): 7167 @@ -23448,18 +23179,16 @@ Number of tools on GASLINI: 0 Number of tools on Galaxy@AuBi: 1 Number of tools on Galaxy@Pasteur: 0 - Number of tools on GalaxyTrakr: 0 + Number of tools on GalaxyTrakr: 1 Number of tools on HyPhy HIV NGS Tools: 0 Number of tools on IPK Galaxy Blast Suite: 0 Number of tools on ImmPort Galaxy: 0 Number of tools on InteractoMIX: 0 Number of tools on Lebanese University Galaxy: 0 - Number of tools on MBAC Metabiome Portal: 0 Number of tools on MISSISSIPPI: 0 Number of tools on Mandoiu Lab: 0 Number of tools on Oqtans: 0 Number of tools on Palfinder: 0 - Number of tools on PepSimili: 0 Number of tools on PhagePromotor: 0 Number of tools on UseGalaxy.be: 1 Number of tools on UseGalaxy.cz: 1 @@ -23476,6 +23205,7 @@ Related Workflows: - https://usegalaxy.cz/published/workflow?id=932f4901960a595a - https://usegalaxy.eu/published/workflow?id=02631612a43a4d9b + - https://usegalaxy.eu/published/workflow?id=0293e155386d3f3a - https://usegalaxy.eu/published/workflow?id=0b9071d5dfa38559 - https://usegalaxy.eu/published/workflow?id=2d2862b48918b22f - https://usegalaxy.eu/published/workflow?id=33312e5643279e8a @@ -23493,8 +23223,6 @@ - https://usegalaxy.eu/published/workflow?id=cc59ae1a9878942c - https://usegalaxy.eu/published/workflow?id=d57d41e306241396 - https://usegalaxy.eu/published/workflow?id=e5becc6d66b2568c - - https://usegalaxy.fr/published/workflow?id=20e1c40739fad57b - - https://usegalaxy.fr/published/workflow?id=3b65122efecd004f - https://usegalaxy.org.au/published/workflow?id=35f39173f0ac9179 - https://usegalaxy.org.au/published/workflow?id=7559224fc32dce3a - https://usegalaxy.org.au/published/workflow?id=876163677f1cccc4 @@ -23512,7 +23240,7 @@ Suite conda package: interproscan Suite first commit date: '2021-11-15' Suite owner: bgruening - Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/interproscan + Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan Suite runs (last 5 years) (usegalaxy.eu): 44154 Suite runs (last 5 years) (usegalaxy.fr): 9435 Suite runs (last 5 years) (usegalaxy.org): 3914 @@ -23584,12 +23312,10 @@ Number of tools on ImmPort Galaxy: 0 Number of tools on InteractoMIX: 0 Number of tools on Lebanese University Galaxy: 0 - Number of tools on MBAC Metabiome Portal: 0 Number of tools on MISSISSIPPI: 0 Number of tools on Mandoiu Lab: 0 Number of tools on Oqtans: 0 Number of tools on Palfinder: 0 - Number of tools on PepSimili: 0 Number of tools on PhagePromotor: 0 Number of tools on UseGalaxy.be: 1 Number of tools on UseGalaxy.cz: 1 @@ -23606,6 +23332,7 @@ Related Workflows: - https://usegalaxy.eu/published/workflow?id=293b914eda3fbb1f - https://usegalaxy.eu/published/workflow?id=4db391b405f2ed38 + - https://usegalaxy.eu/published/workflow?id=54d04d62d8723672 - https://usegalaxy.eu/published/workflow?id=628062a8cf93261f - https://usegalaxy.eu/published/workflow?id=7878f33525c4bb6c - https://usegalaxy.eu/published/workflow?id=93d7a5704ec1d82d @@ -23645,7 +23372,7 @@ Suite conda package: iqtree Suite first commit date: '2017-09-26' Suite owner: iuc - Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/iqtree + Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree Suite runs (last 5 years) (usegalaxy.eu): 44137 Suite runs (last 5 years) (usegalaxy.fr): 229 Suite runs (last 5 years) (usegalaxy.org): 34112 @@ -23704,7 +23431,7 @@ EDAM reduced topics: [] EDAM topics: [] Homepage: https://wonder.cdc.gov/amd/flu/irma/irma.html - Latest suite conda package version: 1.3.3 + Latest suite conda package version: 1.3.4 Number of tools on APOSTL: 0 Number of tools on CIRM-CFBP: 0 Number of tools on ChemFlow: 0 @@ -23718,12 +23445,10 @@ Number of tools on ImmPort Galaxy: 0 Number of tools on InteractoMIX: 0 Number of tools on Lebanese University Galaxy: 0 - Number of tools on MBAC Metabiome Portal: 0 Number of tools on MISSISSIPPI: 0 Number of tools on Mandoiu Lab: 0 Number of tools on Oqtans: 0 Number of tools on Palfinder: 0 - Number of tools on PepSimili: 0 Number of tools on PhagePromotor: 0 Number of tools on UseGalaxy.be: 0 Number of tools on UseGalaxy.cz: 0 @@ -23739,7 +23464,7 @@ Suite conda package: irma Suite first commit date: '2024-11-09' Suite owner: iuc - Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/irma + Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/master/tools/irma Suite runs (last 5 years) (usegalaxy.eu): 16450 Suite runs (last 5 years) (usegalaxy.fr): 0 Suite runs (last 5 years) (usegalaxy.org): 0 @@ -23761,7 +23486,7 @@ Suite users (usegalaxy.org): 0 Suite users (usegalaxy.org.au): 0 Suite users on main servers: 12 - Suite version: 1.2.0 + Suite version: '@TOOL_VERSION@+galaxy@VERSION_SUFFIX@' Suite version status: To update To keep: true Tool IDs: @@ -23809,12 +23534,10 @@ Number of tools on ImmPort Galaxy: 0 Number of tools on InteractoMIX: 0 Number of tools on Lebanese University Galaxy: 0 - Number of tools on MBAC Metabiome Portal: 0 Number of tools on MISSISSIPPI: 0 Number of tools on Mandoiu Lab: 0 Number of tools on Oqtans: 0 Number of tools on Palfinder: 0 - Number of tools on PepSimili: 0 Number of tools on PhagePromotor: 0 Number of tools on UseGalaxy.be: 1 Number of tools on UseGalaxy.cz: 1 @@ -23859,7 +23582,7 @@ Suite conda package: isescan Suite first commit date: '2022-09-01' Suite owner: iuc - Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/isescan + Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/master/tools/isescan Suite runs (last 5 years) (usegalaxy.eu): 67516 Suite runs (last 5 years) (usegalaxy.fr): 1759 Suite runs (last 5 years) (usegalaxy.org): 1535 @@ -23930,12 +23653,10 @@ Number of tools on ImmPort Galaxy: 0 Number of tools on InteractoMIX: 0 Number of tools on Lebanese University Galaxy: 0 - Number of tools on MBAC Metabiome Portal: 0 Number of tools on MISSISSIPPI: 4 Number of tools on Mandoiu Lab: 0 Number of tools on Oqtans: 0 Number of tools on Palfinder: 0 - Number of tools on PepSimili: 0 Number of tools on PhagePromotor: 0 Number of tools on UseGalaxy.be: 5 Number of tools on UseGalaxy.cz: 5 @@ -24087,7 +23808,7 @@ Suite conda package: ivar Suite first commit date: '2020-03-21' Suite owner: iuc - Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/ivar + Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar Suite runs (last 5 years) (usegalaxy.eu): 1414011 Suite runs (last 5 years) (usegalaxy.fr): 7502 Suite runs (last 5 years) (usegalaxy.org): 147224 @@ -24162,12 +23883,10 @@ Number of tools on ImmPort Galaxy: 0 Number of tools on InteractoMIX: 0 Number of tools on Lebanese University Galaxy: 0 - Number of tools on MBAC Metabiome Portal: 0 Number of tools on MISSISSIPPI: 2 Number of tools on Mandoiu Lab: 0 Number of tools on Oqtans: 0 Number of tools on Palfinder: 0 - Number of tools on PepSimili: 0 Number of tools on PhagePromotor: 0 Number of tools on UseGalaxy.be: 2 Number of tools on UseGalaxy.cz: 2 @@ -24323,7 +24042,7 @@ Suite conda package: jbrowse Suite first commit date: '2015-05-01' Suite owner: iuc - Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/jbrowse + Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse Suite runs (last 5 years) (usegalaxy.eu): 26043 Suite runs (last 5 years) (usegalaxy.fr): 1697 Suite runs (last 5 years) (usegalaxy.org): 22125 @@ -24391,7 +24110,7 @@ - Gene structure - Sequence assembly Homepage: https://jbrowse.org - Latest suite conda package version: 4.2.1 + Latest suite conda package version: 4.3.0 Number of tools on APOSTL: 0 Number of tools on CIRM-CFBP: 0 Number of tools on ChemFlow: 0 @@ -24405,15 +24124,13 @@ Number of tools on ImmPort Galaxy: 0 Number of tools on InteractoMIX: 0 Number of tools on Lebanese University Galaxy: 0 - Number of tools on MBAC Metabiome Portal: 0 Number of tools on MISSISSIPPI: 0 Number of tools on Mandoiu Lab: 0 Number of tools on Oqtans: 0 Number of tools on Palfinder: 0 - Number of tools on PepSimili: 0 Number of tools on PhagePromotor: 0 Number of tools on UseGalaxy.be: 1 - Number of tools on UseGalaxy.cz: 0 + Number of tools on UseGalaxy.cz: 1 Number of tools on UseGalaxy.eu: 1 Number of tools on UseGalaxy.fr: 1 Number of tools on UseGalaxy.no: 0 @@ -24423,6 +24140,7 @@ Related Tutorials: - epigenetics/formation_of_super-structures_on_xi - transcriptomics/ref-based + - visualisation/jbrowse2 Related Workflows: - https://usegalaxy.eu/published/workflow?id=07c92110c3fffcf8 - https://usegalaxy.eu/published/workflow?id=1ce406de61de8492 @@ -24454,11 +24172,12 @@ - https://workflowhub.eu/workflows/1715?version=3 - https://workflowhub.eu/workflows/2036?version=1 - https://workflowhub.eu/workflows/2038?version=1 + - https://workflowhub.eu/workflows/2180?version=1 Suite ID: jbrowse2 Suite conda package: jbrowse2 Suite first commit date: '2021-09-30' Suite owner: fubar - Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/jbrowse2 + Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 Suite runs (last 5 years) (usegalaxy.eu): 3765 Suite runs (last 5 years) (usegalaxy.fr): 0 Suite runs (last 5 years) (usegalaxy.org): 1248 @@ -24491,6 +24210,7 @@ - Sequence Analysis availability: UseGalaxy.be: 1 + UseGalaxy.cz: 1 UseGalaxy.eu: 1 UseGalaxy.fr: 1 UseGalaxy.or: 1 @@ -24527,12 +24247,10 @@ Number of tools on ImmPort Galaxy: 0 Number of tools on InteractoMIX: 0 Number of tools on Lebanese University Galaxy: 0 - Number of tools on MBAC Metabiome Portal: 0 Number of tools on MISSISSIPPI: 0 Number of tools on Mandoiu Lab: 0 Number of tools on Oqtans: 0 Number of tools on Palfinder: 0 - Number of tools on PepSimili: 0 Number of tools on PhagePromotor: 0 Number of tools on UseGalaxy.be: 0 Number of tools on UseGalaxy.cz: 1 @@ -24550,7 +24268,7 @@ Suite conda package: kmer-jellyfish Suite first commit date: '2021-04-07' Suite owner: iuc - Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/jellyfish + Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish Suite runs (last 5 years) (usegalaxy.eu): 4901 Suite runs (last 5 years) (usegalaxy.fr): 1519 Suite runs (last 5 years) (usegalaxy.org): 0 @@ -24572,7 +24290,7 @@ Suite users (usegalaxy.org): 0 Suite users (usegalaxy.org.au): 87 Suite users on main servers: 491 - Suite version: null + Suite version: '@WRAPPER_VERSION@+@VERSION_SUFFIX@' Suite version status: To update To keep: true Tool IDs: @@ -24619,12 +24337,10 @@ Number of tools on ImmPort Galaxy: 0 Number of tools on InteractoMIX: 0 Number of tools on Lebanese University Galaxy: 0 - Number of tools on MBAC Metabiome Portal: 0 Number of tools on MISSISSIPPI: 0 Number of tools on Mandoiu Lab: 0 Number of tools on Oqtans: 0 Number of tools on Palfinder: 0 - Number of tools on PepSimili: 0 Number of tools on PhagePromotor: 0 Number of tools on UseGalaxy.be: 0 Number of tools on UseGalaxy.cz: 0 @@ -24640,7 +24356,7 @@ Suite conda package: kaiju Suite first commit date: '2025-04-22' Suite owner: iuc - Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/kaiju + Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/master/tools/kaiju Suite runs (last 5 years) (usegalaxy.eu): 2 Suite runs (last 5 years) (usegalaxy.fr): 0 Suite runs (last 5 years) (usegalaxy.org): 0 @@ -24713,12 +24429,10 @@ Number of tools on ImmPort Galaxy: 0 Number of tools on InteractoMIX: 0 Number of tools on Lebanese University Galaxy: 0 - Number of tools on MBAC Metabiome Portal: 0 Number of tools on MISSISSIPPI: 1 Number of tools on Mandoiu Lab: 0 Number of tools on Oqtans: 0 Number of tools on Palfinder: 0 - Number of tools on PepSimili: 0 Number of tools on PhagePromotor: 0 Number of tools on UseGalaxy.be: 8 Number of tools on UseGalaxy.cz: 8 @@ -24734,7 +24448,7 @@ Suite conda package: khmer Suite first commit date: '2015-03-24' Suite owner: iuc - Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/khmer + Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer Suite runs (last 5 years) (usegalaxy.eu): 1572 Suite runs (last 5 years) (usegalaxy.fr): 0 Suite runs (last 5 years) (usegalaxy.org): 1179 @@ -24826,12 +24540,10 @@ Number of tools on ImmPort Galaxy: 0 Number of tools on InteractoMIX: 0 Number of tools on Lebanese University Galaxy: 0 - Number of tools on MBAC Metabiome Portal: 0 Number of tools on MISSISSIPPI: 0 Number of tools on Mandoiu Lab: 0 Number of tools on Oqtans: 0 Number of tools on Palfinder: 0 - Number of tools on PepSimili: 0 Number of tools on PhagePromotor: 0 Number of tools on UseGalaxy.be: 0 Number of tools on UseGalaxy.cz: 1 @@ -24847,7 +24559,7 @@ Suite conda package: kleborate Suite first commit date: '2022-09-09' Suite owner: iuc - Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/kleborate + Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/master/tools/kleborate Suite runs (last 5 years) (usegalaxy.eu): 1479 Suite runs (last 5 years) (usegalaxy.fr): 0 Suite runs (last 5 years) (usegalaxy.org): 0 @@ -24869,7 +24581,7 @@ Suite users (usegalaxy.org): 0 Suite users (usegalaxy.org.au): 0 Suite users on main servers: 123 - Suite version: 2.3.2 + Suite version: '@TOOL_VERSION@+galaxy@VERSION_SUFFIX@' Suite version status: To update To keep: true Tool IDs: @@ -24912,12 +24624,10 @@ Number of tools on ImmPort Galaxy: 0 Number of tools on InteractoMIX: 0 Number of tools on Lebanese University Galaxy: 0 - Number of tools on MBAC Metabiome Portal: 0 Number of tools on MISSISSIPPI: 0 Number of tools on Mandoiu Lab: 0 Number of tools on Oqtans: 0 Number of tools on Palfinder: 0 - Number of tools on PepSimili: 0 Number of tools on PhagePromotor: 0 Number of tools on UseGalaxy.be: 0 Number of tools on UseGalaxy.cz: 0 @@ -24934,7 +24644,7 @@ Suite conda package: kmer2stats Suite first commit date: '2025-04-16' Suite owner: iuc - Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/kmer2stats + Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/master/tools/kmer2stats Suite runs (last 5 years) (usegalaxy.eu): 310 Suite runs (last 5 years) (usegalaxy.fr): 0 Suite runs (last 5 years) (usegalaxy.org): 0 @@ -24956,7 +24666,7 @@ Suite users (usegalaxy.org): 0 Suite users (usegalaxy.org.au): 0 Suite users on main servers: 8 - Suite version: 1.0.1 + Suite version: '@TOOL_VERSION@+galaxy@VERSION_SUFFIX@' Suite version status: To update To keep: true Tool IDs: @@ -24993,12 +24703,10 @@ Number of tools on ImmPort Galaxy: 0 Number of tools on InteractoMIX: 0 Number of tools on Lebanese University Galaxy: 0 - Number of tools on MBAC Metabiome Portal: 0 Number of tools on MISSISSIPPI: 0 Number of tools on Mandoiu Lab: 0 Number of tools on Oqtans: 0 Number of tools on Palfinder: 0 - Number of tools on PepSimili: 0 Number of tools on PhagePromotor: 0 Number of tools on UseGalaxy.be: 0 Number of tools on UseGalaxy.cz: 0 @@ -25014,7 +24722,7 @@ Suite conda package: kmindex Suite first commit date: '2025-12-10' Suite owner: iuc - Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/kmindex + Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/master/tools/kmindex Suite runs (last 5 years) (usegalaxy.eu): 0 Suite runs (last 5 years) (usegalaxy.fr): 0 Suite runs (last 5 years) (usegalaxy.org): 0 @@ -25053,6 +24761,85 @@ bio.tool description: kmindex is a tool for indexing and querying sequencing samples. It is built on top of kmtricks. bio.tool name: kmindex +- Deprecated: false + Description: Quality control and contaminant removal for metagenomic data + EDAM operations: [] + EDAM reduced operations: [] + EDAM reduced topics: [] + EDAM topics: [] + Homepage: https://github.com/biobakery/kneaddata + Latest suite conda package version: 0.12.4 + Number of tools on APOSTL: 0 + Number of tools on CIRM-CFBP: 0 + Number of tools on ChemFlow: 0 + Number of tools on Coloc-stats: 0 + Number of tools on GASLINI: 0 + Number of tools on Galaxy@AuBi: 0 + Number of tools on Galaxy@Pasteur: 0 + Number of tools on GalaxyTrakr: 1 + Number of tools on HyPhy HIV NGS Tools: 0 + Number of tools on IPK Galaxy Blast Suite: 0 + Number of tools on ImmPort Galaxy: 0 + Number of tools on InteractoMIX: 0 + Number of tools on Lebanese University Galaxy: 0 + Number of tools on MISSISSIPPI: 0 + Number of tools on Mandoiu Lab: 0 + Number of tools on Oqtans: 0 + Number of tools on Palfinder: 0 + Number of tools on PhagePromotor: 0 + Number of tools on UseGalaxy.be: 0 + Number of tools on UseGalaxy.cz: 0 + Number of tools on UseGalaxy.eu: 1 + Number of tools on UseGalaxy.fr: 0 + Number of tools on UseGalaxy.no: 0 + Number of tools on UseGalaxy.org (Main): 0 + Number of tools on UseGalaxy.org.au: 0 + Number of tools on Viral Variant Visualizer (VVV): 0 + Related Tutorials: [] + Related Workflows: + - https://usegalaxy.eu/published/workflow?id=8e13c87e751e88d8 + Suite ID: kneaddata + Suite conda package: kneaddata + Suite first commit date: '2026-02-04' + Suite owner: iuc + Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/master/tools/kneaddata + Suite runs (last 5 years) (usegalaxy.eu): 0 + Suite runs (last 5 years) (usegalaxy.fr): 0 + Suite runs (last 5 years) (usegalaxy.org): 0 + Suite runs (last 5 years) (usegalaxy.org.au): 0 + Suite runs (last 5 years) on main servers: 0 + Suite runs (usegalaxy.eu): 0 + Suite runs (usegalaxy.fr): 0 + Suite runs (usegalaxy.org): 0 + Suite runs (usegalaxy.org.au): 0 + Suite runs on main servers: 0 + Suite source: https://github.com/galaxyproject/tools-iuc/tree/main/tools/kneaddata + Suite users (last 5 years) (usegalaxy.eu): 0 + Suite users (last 5 years) (usegalaxy.fr): 0 + Suite users (last 5 years) (usegalaxy.org): 0 + Suite users (last 5 years) (usegalaxy.org.au): 0 + Suite users (last 5 years) on main servers: 0 + Suite users (usegalaxy.eu): 0 + Suite users (usegalaxy.fr): 0 + Suite users (usegalaxy.org): 0 + Suite users (usegalaxy.org.au): 0 + Suite users on main servers: 0 + Suite version: 0.12.1 + Suite version status: To update + To keep: true + Tool IDs: + - kneaddata + Tool output formats: + - txt + ToolShed categories: + - Metagenomics + - Sequence Analysis + availability: + UseGalaxy.eu: 1 + biii ID: null + bio.tool ID: null + bio.tool description: null + bio.tool name: null - Deprecated: false Description: Gene function annotation tool based on KEGG Orthology and hidden Markov model @@ -25083,12 +24870,10 @@ Number of tools on ImmPort Galaxy: 0 Number of tools on InteractoMIX: 0 Number of tools on Lebanese University Galaxy: 0 - Number of tools on MBAC Metabiome Portal: 0 Number of tools on MISSISSIPPI: 0 Number of tools on Mandoiu Lab: 0 Number of tools on Oqtans: 0 Number of tools on Palfinder: 0 - Number of tools on PepSimili: 0 Number of tools on PhagePromotor: 0 Number of tools on UseGalaxy.be: 1 Number of tools on UseGalaxy.cz: 1 @@ -25111,7 +24896,7 @@ Suite conda package: kofamscan Suite first commit date: '2020-11-12' Suite owner: iuc - Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/kofamscan + Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan Suite runs (last 5 years) (usegalaxy.eu): 2904 Suite runs (last 5 years) (usegalaxy.fr): 3 Suite runs (last 5 years) (usegalaxy.org): 0 @@ -25133,8 +24918,8 @@ Suite users (usegalaxy.org): 0 Suite users (usegalaxy.org.au): 0 Suite users on main servers: 96 - Suite version: 1.3.0 - Suite version status: Up-to-date + Suite version: '@TOOL_VERSION@+galaxy@VERSION_SUFFIX@' + Suite version status: To update To keep: true Tool IDs: - kofamscan @@ -25183,12 +24968,10 @@ Number of tools on ImmPort Galaxy: 0 Number of tools on InteractoMIX: 0 Number of tools on Lebanese University Galaxy: 0 - Number of tools on MBAC Metabiome Portal: 0 Number of tools on MISSISSIPPI: 0 Number of tools on Mandoiu Lab: 0 Number of tools on Oqtans: 0 Number of tools on Palfinder: 0 - Number of tools on PepSimili: 0 Number of tools on PhagePromotor: 0 Number of tools on UseGalaxy.be: 1 Number of tools on UseGalaxy.cz: 1 @@ -25211,7 +24994,7 @@ Suite conda package: kraken-biom Suite first commit date: '2022-09-03' Suite owner: iuc - Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/kraken_biom + Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/master/tools/kraken_biom Suite runs (last 5 years) (usegalaxy.eu): 4747 Suite runs (last 5 years) (usegalaxy.fr): 17 Suite runs (last 5 years) (usegalaxy.org): 150 @@ -25283,12 +25066,10 @@ Number of tools on ImmPort Galaxy: 0 Number of tools on InteractoMIX: 0 Number of tools on Lebanese University Galaxy: 0 - Number of tools on MBAC Metabiome Portal: 0 Number of tools on MISSISSIPPI: 0 Number of tools on Mandoiu Lab: 0 Number of tools on Oqtans: 0 Number of tools on Palfinder: 0 - Number of tools on PepSimili: 0 Number of tools on PhagePromotor: 0 Number of tools on UseGalaxy.be: 1 Number of tools on UseGalaxy.cz: 1 @@ -25306,7 +25087,7 @@ Suite conda package: biopython Suite first commit date: '2016-06-01' Suite owner: iuc - Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/kraken_taxonomy_report + Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/master/tools/kraken_taxonomy_report Suite runs (last 5 years) (usegalaxy.eu): 5719 Suite runs (last 5 years) (usegalaxy.fr): 25 Suite runs (last 5 years) (usegalaxy.org): 5613 @@ -25328,7 +25109,7 @@ Suite users (usegalaxy.org): 1717 Suite users (usegalaxy.org.au): 148 Suite users on main servers: 3030 - Suite version: 0.0.3 + Suite version: '@TOOL_VERSION@+galaxy@VERSION_SUFFIX@' Suite version status: To update To keep: true Tool IDs: @@ -25378,12 +25159,10 @@ Number of tools on ImmPort Galaxy: 0 Number of tools on InteractoMIX: 0 Number of tools on Lebanese University Galaxy: 0 - Number of tools on MBAC Metabiome Portal: 0 Number of tools on MISSISSIPPI: 0 Number of tools on Mandoiu Lab: 0 Number of tools on Oqtans: 0 Number of tools on Palfinder: 0 - Number of tools on PepSimili: 0 Number of tools on PhagePromotor: 0 Number of tools on UseGalaxy.be: 4 Number of tools on UseGalaxy.cz: 6 @@ -25460,7 +25239,7 @@ Suite conda package: krakentools Suite first commit date: '2023-01-13' Suite owner: iuc - Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/krakentools + Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools Suite runs (last 5 years) (usegalaxy.eu): 161915 Suite runs (last 5 years) (usegalaxy.fr): 5824 Suite runs (last 5 years) (usegalaxy.org): 40010 @@ -25537,12 +25316,10 @@ Number of tools on ImmPort Galaxy: 0 Number of tools on InteractoMIX: 0 Number of tools on Lebanese University Galaxy: 0 - Number of tools on MBAC Metabiome Portal: 0 Number of tools on MISSISSIPPI: 0 Number of tools on Mandoiu Lab: 0 Number of tools on Oqtans: 0 Number of tools on Palfinder: 0 - Number of tools on PepSimili: 0 Number of tools on PhagePromotor: 0 Number of tools on UseGalaxy.be: 0 Number of tools on UseGalaxy.cz: 0 @@ -25558,7 +25335,7 @@ Suite conda package: krocus Suite first commit date: '2019-09-03' Suite owner: iuc - Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/krocus + Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/master/tools/krocus Suite runs (last 5 years) (usegalaxy.eu): 0 Suite runs (last 5 years) (usegalaxy.fr): 0 Suite runs (last 5 years) (usegalaxy.org): 0 @@ -25621,12 +25398,10 @@ Number of tools on ImmPort Galaxy: 0 Number of tools on InteractoMIX: 0 Number of tools on Lebanese University Galaxy: 0 - Number of tools on MBAC Metabiome Portal: 0 Number of tools on MISSISSIPPI: 0 Number of tools on Mandoiu Lab: 0 Number of tools on Oqtans: 0 Number of tools on Palfinder: 0 - Number of tools on PepSimili: 0 Number of tools on PhagePromotor: 0 Number of tools on UseGalaxy.be: 0 Number of tools on UseGalaxy.cz: 1 @@ -25642,7 +25417,7 @@ Suite conda package: legsta Suite first commit date: '2022-02-21' Suite owner: iuc - Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/legsta + Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/master/tools/legsta Suite runs (last 5 years) (usegalaxy.eu): 134 Suite runs (last 5 years) (usegalaxy.fr): 0 Suite runs (last 5 years) (usegalaxy.org): 0 @@ -25680,6 +25455,102 @@ bio.tool ID: legsta bio.tool description: Performs in silico Legionella pneumophila sequence based typing bio.tool name: legsta +- Deprecated: false + Description: Lift gene annotations between genome assemblies using Liftoff + EDAM operations: + - Genome assembly + - Mapping assembly + - Mapping + EDAM reduced operations: + - Genome assembly + - Mapping assembly + - Mapping + EDAM reduced topics: + - Gene transcripts + - Sequence assembly + - Mapping + - Gene expression + - RNA immunoprecipitation + EDAM topics: + - Gene transcripts + - Sequence assembly + - Mapping + - Gene expression + - RNA immunoprecipitation + Homepage: https://github.com/agshumate/Liftoff + Latest suite conda package version: 1.6.3 + Number of tools on APOSTL: 0 + Number of tools on CIRM-CFBP: 0 + Number of tools on ChemFlow: 0 + Number of tools on Coloc-stats: 0 + Number of tools on GASLINI: 0 + Number of tools on Galaxy@AuBi: 0 + Number of tools on Galaxy@Pasteur: 0 + Number of tools on GalaxyTrakr: 0 + Number of tools on HyPhy HIV NGS Tools: 0 + Number of tools on IPK Galaxy Blast Suite: 0 + Number of tools on ImmPort Galaxy: 0 + Number of tools on InteractoMIX: 0 + Number of tools on Lebanese University Galaxy: 0 + Number of tools on MISSISSIPPI: 0 + Number of tools on Mandoiu Lab: 0 + Number of tools on Oqtans: 0 + Number of tools on Palfinder: 0 + Number of tools on PhagePromotor: 0 + Number of tools on UseGalaxy.be: 0 + Number of tools on UseGalaxy.cz: 0 + Number of tools on UseGalaxy.eu: 1 + Number of tools on UseGalaxy.fr: 0 + Number of tools on UseGalaxy.no: 0 + Number of tools on UseGalaxy.org (Main): 1 + Number of tools on UseGalaxy.org.au: 1 + Number of tools on Viral Variant Visualizer (VVV): 0 + Related Tutorials: [] + Related Workflows: + - https://usegalaxy.org/published/workflow?id=84b447be2f1c5870 + Suite ID: liftoff + Suite conda package: liftoff + Suite first commit date: '2026-02-02' + Suite owner: iuc + Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/master/tools/liftoff + Suite runs (last 5 years) (usegalaxy.eu): 0 + Suite runs (last 5 years) (usegalaxy.fr): 0 + Suite runs (last 5 years) (usegalaxy.org): 0 + Suite runs (last 5 years) (usegalaxy.org.au): 0 + Suite runs (last 5 years) on main servers: 0 + Suite runs (usegalaxy.eu): 0 + Suite runs (usegalaxy.fr): 0 + Suite runs (usegalaxy.org): 0 + Suite runs (usegalaxy.org.au): 0 + Suite runs on main servers: 0 + Suite source: https://github.com/galaxyproject/tools-iuc + Suite users (last 5 years) (usegalaxy.eu): 0 + Suite users (last 5 years) (usegalaxy.fr): 0 + Suite users (last 5 years) (usegalaxy.org): 0 + Suite users (last 5 years) (usegalaxy.org.au): 0 + Suite users (last 5 years) on main servers: 0 + Suite users (usegalaxy.eu): 0 + Suite users (usegalaxy.fr): 0 + Suite users (usegalaxy.org): 0 + Suite users (usegalaxy.org.au): 0 + Suite users on main servers: 0 + Suite version: '@TOOL_VERSION@+galaxy@VERSION_SUFFIX@' + Suite version status: To update + To keep: true + Tool IDs: + - liftoff + Tool output formats: + - gff3 + - txt + ToolShed categories: + - Sequence Analysis + availability: + UseGalaxy.eu: 1 + UseGalaxy.or: 1 + biii ID: null + bio.tool ID: liftoff + bio.tool description: An accurate gene annotation mapping tool. + bio.tool name: Liftoff - Deprecated: false Description: Perform RNA-Seq differential expression analysis using limma voom pipeline EDAM operations: @@ -25707,12 +25578,10 @@ Number of tools on ImmPort Galaxy: 0 Number of tools on InteractoMIX: 0 Number of tools on Lebanese University Galaxy: 0 - Number of tools on MBAC Metabiome Portal: 0 Number of tools on MISSISSIPPI: 0 Number of tools on Mandoiu Lab: 0 Number of tools on Oqtans: 0 Number of tools on Palfinder: 0 - Number of tools on PepSimili: 0 Number of tools on PhagePromotor: 0 Number of tools on UseGalaxy.be: 1 Number of tools on UseGalaxy.cz: 1 @@ -25735,7 +25604,6 @@ - https://usegalaxy.eu/published/workflow?id=21dd4bd16579fc12 - https://usegalaxy.eu/published/workflow?id=227d97974573aaf2 - 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https://usegalaxy.eu/published/workflow?id=8ab363878cd34ef0 - https://usegalaxy.eu/published/workflow?id=8bc1c3b9e665ea37 - https://usegalaxy.eu/published/workflow?id=8cd275b30524b383 @@ -25787,6 +25657,7 @@ - https://usegalaxy.org/published/workflow?id=aac2ae0419f7d515 - https://usegalaxy.org/published/workflow?id=b094b6e1e7d48416 - https://usegalaxy.org/published/workflow?id=b3823d276917baf0 + - https://usegalaxy.org/published/workflow?id=b750b0fdf74855dc - https://usegalaxy.org/published/workflow?id=cd56ed91856fcc6f - https://usegalaxy.org/published/workflow?id=d5514e327878b531 - https://usegalaxy.org/published/workflow?id=ddb737f2ad0589e8 @@ -25799,7 +25670,7 @@ Suite conda package: bioconductor-limma Suite first commit date: '2017-05-24' Suite owner: iuc - Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/limma_voom + Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom Suite runs (last 5 years) (usegalaxy.eu): 27013 Suite runs (last 5 years) (usegalaxy.fr): 329 Suite runs (last 5 years) (usegalaxy.org): 50381 @@ -25821,7 +25692,7 @@ Suite users (usegalaxy.org): 6265 Suite users (usegalaxy.org.au): 1003 Suite users on main servers: 10460 - Suite version: 3.58.1 + Suite version: '@TOOL_VERSION@+galaxy@VERSION_SUFFIX@' Suite version status: To update To keep: true Tool IDs: @@ -25880,12 +25751,10 @@ Number of tools on ImmPort Galaxy: 0 Number of tools on InteractoMIX: 0 Number of tools on Lebanese University Galaxy: 0 - Number of tools on MBAC Metabiome Portal: 0 Number of tools on MISSISSIPPI: 0 Number of tools on Mandoiu Lab: 0 Number of tools on Oqtans: 0 Number of tools on Palfinder: 0 - Number of tools on PepSimili: 0 Number of tools on PhagePromotor: 0 Number of tools on UseGalaxy.be: 0 Number of tools on UseGalaxy.cz: 1 @@ -25901,7 +25770,7 @@ Suite conda package: r-base Suite first commit date: '2023-07-04' Suite owner: iuc - Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/lineagespot + Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot Suite runs (last 5 years) (usegalaxy.eu): 39 Suite runs (last 5 years) (usegalaxy.fr): 0 Suite runs (last 5 years) (usegalaxy.org): 0 @@ -25923,7 +25792,7 @@ Suite users (usegalaxy.org): 0 Suite users (usegalaxy.org.au): 0 Suite users on main servers: 4 - Suite version: 1.6.0 + Suite version: '@TOOL_VERSION@+galaxy@VERSION_SUFFIX@' Suite version status: To update To keep: true Tool IDs: @@ -25963,12 +25832,10 @@ Number of tools on ImmPort Galaxy: 0 Number of tools on InteractoMIX: 0 Number of tools on Lebanese University Galaxy: 0 - Number of tools on MBAC Metabiome Portal: 0 Number of tools on MISSISSIPPI: 0 Number of tools on Mandoiu Lab: 0 Number of tools on Oqtans: 0 Number of tools on Palfinder: 0 - Number of tools on PepSimili: 0 Number of tools on PhagePromotor: 0 Number of tools on UseGalaxy.be: 0 Number of tools on UseGalaxy.cz: 0 @@ -25984,7 +25851,7 @@ Suite conda package: longdust Suite first commit date: '2025-10-01' Suite owner: iuc - Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/longdust + Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/master/tools/longdust Suite runs (last 5 years) (usegalaxy.eu): 0 Suite runs (last 5 years) (usegalaxy.fr): 0 Suite runs (last 5 years) (usegalaxy.org): 0 @@ -26049,12 +25916,10 @@ Number of tools on ImmPort Galaxy: 0 Number of tools on InteractoMIX: 0 Number of tools on Lebanese University Galaxy: 0 - Number of tools on MBAC Metabiome Portal: 0 Number of tools on MISSISSIPPI: 0 Number of tools on Mandoiu Lab: 0 Number of tools on Oqtans: 0 Number of tools on Palfinder: 0 - Number of tools on PepSimili: 0 Number of tools on PhagePromotor: 0 Number of tools on UseGalaxy.be: 0 Number of tools on UseGalaxy.cz: 1 @@ -26070,7 +25935,7 @@ Suite conda package: lorikeet Suite first commit date: '2018-05-07' Suite owner: iuc - Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/lorikeet + Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/master/tools/lorikeet Suite runs (last 5 years) (usegalaxy.eu): 930 Suite runs (last 5 years) (usegalaxy.fr): 0 Suite runs (last 5 years) (usegalaxy.org): 0 @@ -26092,8 +25957,8 @@ Suite users (usegalaxy.org): 0 Suite users (usegalaxy.org.au): 0 Suite users on main servers: 18 - Suite version: '20' - Suite version status: Up-to-date + Suite version: '@TOOL_VERSION@' + Suite version status: To update To keep: true Tool IDs: - 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Suite version: 2.1.0 - Suite version status: Up-to-date + Suite version: '@TOOL_VERSION@+galaxy@VERSION_SUFFIX@' + Suite version status: To update To keep: true Tool IDs: - m6anet @@ -26236,12 +26099,10 @@ Number of tools on ImmPort Galaxy: 0 Number of tools on InteractoMIX: 0 Number of tools on Lebanese University Galaxy: 0 - Number of tools on MBAC Metabiome Portal: 0 Number of tools on MISSISSIPPI: 0 Number of tools on Mandoiu Lab: 0 Number of tools on Oqtans: 0 Number of tools on Palfinder: 0 - Number of tools on PepSimili: 0 Number of tools on PhagePromotor: 0 Number of tools on UseGalaxy.be: 0 Number of tools on UseGalaxy.cz: 1 @@ -26261,7 +26122,7 @@ Suite conda package: bioconductor-maaslin2 Suite first commit date: '2021-11-05' Suite owner: iuc - Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/maaslin2 + Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/master/tools/maaslin2 Suite runs (last 5 years) (usegalaxy.eu): 3676 Suite runs (last 5 years) (usegalaxy.fr): 4 Suite runs (last 5 years) (usegalaxy.org): 0 @@ -26331,12 +26192,10 @@ Number of tools on ImmPort Galaxy: 0 Number of tools on InteractoMIX: 0 Number of tools on Lebanese University Galaxy: 0 - 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Number of tools on MBAC Metabiome Portal: 0 Number of tools on MISSISSIPPI: 1 Number of tools on Mandoiu Lab: 0 Number of tools on Oqtans: 0 Number of tools on Palfinder: 0 - Number of tools on PepSimili: 1 Number of tools on PhagePromotor: 0 Number of tools on UseGalaxy.be: 1 Number of tools on UseGalaxy.cz: 1 @@ -27148,7 +26997,7 @@ Suite conda package: megahit Suite first commit date: '2017-09-22' Suite owner: iuc - Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/megahit + Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit Suite runs (last 5 years) (usegalaxy.eu): 22340 Suite runs (last 5 years) (usegalaxy.fr): 1387 Suite runs (last 5 years) (usegalaxy.org): 23973 @@ -27170,8 +27019,8 @@ Suite users (usegalaxy.org): 2929 Suite users (usegalaxy.org.au): 632 Suite users on main servers: 5812 - Suite version: 1.2.9 - Suite version status: Up-to-date + Suite version: '@TOOL_VERSION@' + Suite version status: To update To keep: true Tool IDs: - megahit @@ -27226,12 +27075,10 @@ Number of tools on ImmPort Galaxy: 0 Number of tools on InteractoMIX: 0 Number of tools on Lebanese University Galaxy: 0 - Number of tools on MBAC Metabiome Portal: 0 Number of tools on MISSISSIPPI: 1 Number of tools on Mandoiu Lab: 0 Number of tools on Oqtans: 0 Number of tools on Palfinder: 0 - Number of tools on PepSimili: 0 Number of tools on PhagePromotor: 0 Number of tools on UseGalaxy.be: 1 Number of tools on UseGalaxy.cz: 1 @@ -27250,9 +27097,9 @@ - https://workflowhub.eu/workflows/1634?version=1 Suite ID: megahit_contig2fastg Suite conda package: megahit - Suite first commit date: '2018-11-09' + Suite first commit date: '2018-11-08' Suite owner: iuc - Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/megahit_contig2fastg + Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit_contig2fastg Suite runs (last 5 years) (usegalaxy.eu): 763 Suite runs (last 5 years) (usegalaxy.fr): 80 Suite runs (last 5 years) (usegalaxy.org): 338 @@ -27274,7 +27121,7 @@ Suite users (usegalaxy.org): 113 Suite users (usegalaxy.org.au): 33 Suite users on main servers: 364 - Suite version: 1.1.3 + Suite version: '@VERSION@+@GALAXY_VERSION@' Suite version status: To update To keep: true Tool IDs: @@ -27332,12 +27179,10 @@ Number of tools on ImmPort Galaxy: 0 Number of tools on InteractoMIX: 0 Number of tools on Lebanese University Galaxy: 0 - Number of tools on MBAC Metabiome Portal: 0 Number of tools on MISSISSIPPI: 0 Number of tools on Mandoiu Lab: 0 Number of tools on Oqtans: 0 Number of tools on Palfinder: 0 - Number of tools on PepSimili: 0 Number of tools on PhagePromotor: 0 Number of tools on UseGalaxy.be: 0 Number of tools on UseGalaxy.cz: 7 @@ -27353,7 +27198,7 @@ Suite conda package: megan Suite first commit date: '2021-11-24' Suite owner: iuc - Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/megan + Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan Suite runs (last 5 years) (usegalaxy.eu): 5164 Suite runs (last 5 years) (usegalaxy.fr): 4 Suite runs (last 5 years) (usegalaxy.org): 0 @@ -27434,12 +27279,10 @@ Number of tools on ImmPort Galaxy: 0 Number of tools on InteractoMIX: 0 Number of tools on Lebanese University Galaxy: 0 - 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Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/meryl + Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl Suite runs (last 5 years) (usegalaxy.eu): 1850 Suite runs (last 5 years) (usegalaxy.fr): 0 Suite runs (last 5 years) (usegalaxy.org): 1478 @@ -28120,6 +27960,7 @@ availability: UseGalaxy.cz: 3 UseGalaxy.eu: 7 + UseGalaxy.fr: 2 UseGalaxy.or: 7 biii ID: null bio.tool ID: meryl @@ -28162,12 +28003,10 @@ Number of tools on ImmPort Galaxy: 0 Number of tools on InteractoMIX: 0 Number of tools on Lebanese University Galaxy: 0 - Number of tools on MBAC Metabiome Portal: 0 Number of tools on MISSISSIPPI: 0 Number of tools on Mandoiu Lab: 0 Number of tools on Oqtans: 0 Number of tools on Palfinder: 0 - Number of tools on PepSimili: 1 Number of tools on PhagePromotor: 0 Number of tools on UseGalaxy.be: 2 Number of tools on UseGalaxy.cz: 2 @@ -28195,7 +28034,7 @@ Suite conda package: metabat2 Suite first commit date: '2022-01-28' Suite owner: iuc - Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/metabat2 + Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2 Suite runs (last 5 years) (usegalaxy.eu): 14194 Suite runs (last 5 years) (usegalaxy.fr): 1359 Suite runs (last 5 years) (usegalaxy.org): 2591 @@ -28269,12 +28108,10 @@ Number of tools on ImmPort Galaxy: 0 Number of tools on InteractoMIX: 0 Number of tools on Lebanese University Galaxy: 0 - Number of tools on MBAC Metabiome Portal: 0 Number of tools on MISSISSIPPI: 0 Number of tools on Mandoiu Lab: 0 Number of tools on Oqtans: 0 Number of tools on Palfinder: 0 - Number of tools on PepSimili: 0 Number of tools on PhagePromotor: 0 Number of tools on UseGalaxy.be: 0 Number of tools on UseGalaxy.cz: 0 @@ -28290,7 +28127,7 @@ Suite conda package: metabuli Suite first commit date: '2024-06-04' Suite owner: iuc - Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/metabuli + Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabuli Suite runs (last 5 years) (usegalaxy.eu): 0 Suite runs (last 5 years) (usegalaxy.fr): 0 Suite runs (last 5 years) (usegalaxy.org): 0 @@ -28362,12 +28199,10 @@ Number of tools on ImmPort Galaxy: 0 Number of tools on InteractoMIX: 0 Number of tools on Lebanese University Galaxy: 0 - Number of tools on MBAC Metabiome Portal: 0 Number of tools on MISSISSIPPI: 0 Number of tools on Mandoiu Lab: 0 Number of tools on Oqtans: 0 Number of tools on Palfinder: 0 - Number of tools on PepSimili: 0 Number of tools on PhagePromotor: 0 Number of tools on UseGalaxy.be: 1 Number of tools on UseGalaxy.cz: 1 @@ -28384,7 +28219,7 @@ Suite conda package: metaeuk Suite first commit date: '2020-08-04' Suite owner: iuc - Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/metaeuk + Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk Suite runs (last 5 years) (usegalaxy.eu): 507 Suite runs (last 5 years) (usegalaxy.fr): 0 Suite runs (last 5 years) (usegalaxy.org): 0 @@ -28406,7 +28241,7 @@ Suite users (usegalaxy.org): 0 Suite users (usegalaxy.org.au): 0 Suite users on main servers: 58 - Suite version: 7.bba0d80 + Suite version: '@TOOL_VERSION@' Suite version status: To update To keep: true Tool IDs: @@ -28456,12 +28291,10 @@ Number of tools on ImmPort Galaxy: 0 Number of tools on InteractoMIX: 0 Number of tools on Lebanese University Galaxy: 0 - Number of tools on MBAC Metabiome Portal: 0 Number of tools on MISSISSIPPI: 0 Number of tools on Mandoiu Lab: 0 Number of tools on Oqtans: 0 Number of tools on Palfinder: 0 - Number of tools on PepSimili: 0 Number of tools on PhagePromotor: 0 Number of tools on UseGalaxy.be: 1 Number of tools on UseGalaxy.cz: 1 @@ -28477,7 +28310,7 @@ Suite conda package: bioconductor-metagenomeseq Suite first commit date: '2017-03-27' Suite owner: iuc - Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/metagenomeseq + Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/master/tools/metagenomeseq Suite runs (last 5 years) (usegalaxy.eu): 521 Suite runs (last 5 years) (usegalaxy.fr): 0 Suite runs (last 5 years) (usegalaxy.org): 261 @@ -28550,12 +28383,10 @@ Number of tools on ImmPort Galaxy: 0 Number of tools on InteractoMIX: 0 Number of tools on Lebanese University Galaxy: 0 - Number of tools on MBAC Metabiome Portal: 0 Number of tools on MISSISSIPPI: 0 Number of tools on Mandoiu Lab: 0 Number of tools on Oqtans: 0 Number of tools on Palfinder: 0 - Number of tools on PepSimili: 0 Number of tools on PhagePromotor: 0 Number of tools on UseGalaxy.be: 0 Number of tools on UseGalaxy.cz: 0 @@ -28571,7 +28402,7 @@ Suite conda package: metamdbg Suite first commit date: '2025-02-04' Suite owner: iuc - Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/metamdbg + Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/master/tools/metamdbg Suite runs (last 5 years) (usegalaxy.eu): 0 Suite runs (last 5 years) (usegalaxy.fr): 0 Suite runs (last 5 years) (usegalaxy.org): 0 @@ -28648,12 +28479,10 @@ Number of tools on ImmPort Galaxy: 0 Number of tools on InteractoMIX: 0 Number of tools on Lebanese University Galaxy: 0 - Number of tools on MBAC Metabiome Portal: 1 Number of tools on MISSISSIPPI: 0 Number of tools on Mandoiu Lab: 0 Number of tools on Oqtans: 0 Number of tools on Palfinder: 0 - Number of tools on PepSimili: 0 Number of tools on PhagePromotor: 0 Number of tools on UseGalaxy.be: 1 Number of tools on UseGalaxy.cz: 4 @@ -28668,6 +28497,7 @@ - microbiome/metatranscriptomics-short - microbiome/taxonomic-profiling Related Workflows: + - https://usegalaxy.eu/published/workflow?id=052f35a526798020 - https://usegalaxy.eu/published/workflow?id=05f5f040337786bf - https://usegalaxy.eu/published/workflow?id=19de5cbae7f48103 - https://usegalaxy.eu/published/workflow?id=21a17d6c473a88c0 @@ -28697,7 +28527,7 @@ Suite conda package: metaphlan Suite first commit date: '2021-03-11' Suite owner: iuc - Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/metaphlan + Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan Suite runs (last 5 years) (usegalaxy.eu): 30934 Suite runs (last 5 years) (usegalaxy.fr): 211 Suite runs (last 5 years) (usegalaxy.org): 20021 @@ -28769,12 +28599,10 @@ Number of tools on ImmPort Galaxy: 0 Number of tools on InteractoMIX: 0 Number of tools on Lebanese University Galaxy: 0 - Number of tools on MBAC Metabiome Portal: 0 Number of tools on MISSISSIPPI: 0 Number of tools on Mandoiu Lab: 0 Number of tools on Oqtans: 0 Number of tools on Palfinder: 0 - Number of tools on PepSimili: 0 Number of tools on PhagePromotor: 0 Number of tools on UseGalaxy.be: 0 Number of tools on UseGalaxy.cz: 0 @@ -28790,7 +28618,7 @@ Suite conda package: sed Suite first commit date: '2025-08-22' Suite owner: iuc - Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/metasbt + Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/master/tools/metasbt Suite runs (last 5 years) (usegalaxy.eu): 0 Suite runs (last 5 years) (usegalaxy.fr): 0 Suite runs (last 5 years) (usegalaxy.org): 0 @@ -28867,12 +28695,10 @@ Number of tools on ImmPort Galaxy: 0 Number of tools on InteractoMIX: 0 Number of tools on Lebanese University Galaxy: 0 - Number of tools on MBAC Metabiome Portal: 0 Number of tools on MISSISSIPPI: 0 Number of tools on Mandoiu Lab: 0 Number of tools on Oqtans: 0 Number of tools on Palfinder: 0 - Number of tools on PepSimili: 0 Number of tools on PhagePromotor: 0 Number of tools on UseGalaxy.be: 0 Number of tools on UseGalaxy.cz: 0 @@ -28886,9 +28712,9 @@ Related Workflows: [] Suite ID: metawrapmg_binning Suite conda package: metawrap-mg - Suite first commit date: '2024-04-11' + Suite first commit date: '2024-04-12' Suite owner: galaxy-australia - Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/metawrapmg + Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/master/tools/metawrapmg Suite runs (last 5 years) (usegalaxy.eu): 1596 Suite runs (last 5 years) (usegalaxy.fr): 0 Suite runs (last 5 years) (usegalaxy.org): 0 @@ -28956,12 +28782,10 @@ Number of tools on ImmPort Galaxy: 0 Number of tools on InteractoMIX: 0 Number of tools on Lebanese University Galaxy: 0 - Number of tools on MBAC Metabiome Portal: 0 Number of tools on MISSISSIPPI: 0 Number of tools on Mandoiu Lab: 0 Number of tools on Oqtans: 0 Number of tools on Palfinder: 0 - Number of tools on PepSimili: 0 Number of tools on PhagePromotor: 0 Number of tools on UseGalaxy.be: 0 Number of tools on UseGalaxy.cz: 0 @@ -28977,7 +28801,7 @@ Suite conda package: mg-toolkit Suite first commit date: '2024-07-12' Suite owner: iuc - Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/mg_toolkit + Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/master/tools/mg_toolkit Suite runs (last 5 years) (usegalaxy.eu): 21 Suite runs (last 5 years) (usegalaxy.fr): 0 Suite runs (last 5 years) (usegalaxy.org): 0 @@ -29016,6 +28840,169 @@ bio.tool description: Metagenomics toolkit enables scientists to download all of the sample metadata for a given study or sequence to a single csv file. bio.tool name: mg-toolkit +- Deprecated: false + Description: Queue genomes against registered genome from MGnify Database + EDAM operations: [] + EDAM reduced operations: [] + EDAM reduced topics: [] + EDAM topics: [] + Homepage: https://github.com/SantaMcCloud/MGnify-genome-search + Latest suite conda package version: 1.0.0 + Number of tools on APOSTL: 0 + Number of tools on CIRM-CFBP: 0 + Number of tools on ChemFlow: 0 + Number of tools on Coloc-stats: 0 + Number of tools on GASLINI: 0 + Number of tools on Galaxy@AuBi: 0 + Number of tools on Galaxy@Pasteur: 0 + Number of tools on GalaxyTrakr: 0 + Number of tools on HyPhy HIV NGS Tools: 0 + Number of tools on IPK Galaxy Blast Suite: 0 + Number of tools on ImmPort Galaxy: 0 + Number of tools on InteractoMIX: 0 + Number of tools on Lebanese University Galaxy: 0 + Number of tools on MISSISSIPPI: 0 + Number of tools on Mandoiu Lab: 0 + Number of tools on Oqtans: 0 + Number of tools on Palfinder: 0 + Number of tools on PhagePromotor: 0 + Number of tools on UseGalaxy.be: 0 + Number of tools on UseGalaxy.cz: 0 + Number of tools on UseGalaxy.eu: 1 + Number of tools on UseGalaxy.fr: 0 + Number of tools on UseGalaxy.no: 0 + Number of tools on UseGalaxy.org (Main): 0 + Number of tools on UseGalaxy.org.au: 0 + Number of tools on Viral Variant Visualizer (VVV): 0 + Related Tutorials: [] + Related Workflows: [] + Suite ID: mgnify_genome_search + Suite conda package: mgnify-genome-search + Suite first commit date: '2026-01-26' + Suite owner: iuc + Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/master/tools/mgnify_genome_search + Suite runs (last 5 years) (usegalaxy.eu): 0 + Suite runs (last 5 years) (usegalaxy.fr): 0 + Suite runs (last 5 years) (usegalaxy.org): 0 + Suite runs (last 5 years) (usegalaxy.org.au): 0 + Suite runs (last 5 years) on main servers: 0 + Suite runs (usegalaxy.eu): 0 + Suite runs (usegalaxy.fr): 0 + Suite runs (usegalaxy.org): 0 + Suite runs (usegalaxy.org.au): 0 + Suite runs on main servers: 0 + Suite source: https://github.com/galaxyproject/tools-iuc/tree/main/tools/mgnify_genome_search + Suite users (last 5 years) (usegalaxy.eu): 0 + Suite users (last 5 years) (usegalaxy.fr): 0 + Suite users (last 5 years) (usegalaxy.org): 0 + Suite users (last 5 years) (usegalaxy.org.au): 0 + Suite users (last 5 years) on main servers: 0 + Suite users (usegalaxy.eu): 0 + Suite users (usegalaxy.fr): 0 + Suite users (usegalaxy.org): 0 + Suite users (usegalaxy.org.au): 0 + Suite users on main servers: 0 + Suite version: '@TOOL_VERSION@+galaxy@VERSION_SUFFIX@' + Suite version status: To update + To keep: true + Tool IDs: + - mgnify_genome_search + Tool output formats: + - tabular + ToolShed categories: + - Metagenomics + availability: + UseGalaxy.eu: 1 + biii ID: null + bio.tool ID: null + bio.tool description: null + bio.tool name: null +- Deprecated: false + Description: Utilities for use in the MGnify pipelines + EDAM operations: [] + EDAM reduced operations: [] + EDAM reduced topics: [] + EDAM topics: [] + Homepage: https://github.com/EBI-Metagenomics/mgnify-pipelines-toolkit + Latest suite conda package version: 1.5.2 + Number of tools on APOSTL: 0 + Number of tools on CIRM-CFBP: 0 + Number of tools on ChemFlow: 0 + Number of tools on Coloc-stats: 0 + Number of tools on GASLINI: 0 + Number of tools on Galaxy@AuBi: 0 + Number of tools on Galaxy@Pasteur: 0 + Number of tools on GalaxyTrakr: 0 + Number of tools on HyPhy HIV NGS Tools: 0 + Number of tools on IPK Galaxy Blast Suite: 0 + Number of tools on ImmPort Galaxy: 0 + Number of tools on InteractoMIX: 0 + Number of tools on Lebanese University Galaxy: 0 + Number of tools on MISSISSIPPI: 0 + Number of tools on Mandoiu Lab: 0 + Number of tools on Oqtans: 0 + Number of tools on Palfinder: 0 + Number of tools on PhagePromotor: 0 + Number of tools on UseGalaxy.be: 0 + Number of tools on UseGalaxy.cz: 0 + Number of tools on UseGalaxy.eu: 6 + Number of tools on UseGalaxy.fr: 0 + Number of tools on UseGalaxy.no: 0 + Number of tools on UseGalaxy.org (Main): 0 + Number of tools on UseGalaxy.org.au: 0 + Number of tools on Viral Variant Visualizer (VVV): 0 + Related Tutorials: [] + Related Workflows: [] + Suite ID: mgnify_pipelines_toolkit + Suite conda package: mgnify-pipelines-toolkit + Suite first commit date: '2026-04-22' + Suite owner: iuc + Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/master/tools/mgnify_pipelines_toolkit + Suite runs (last 5 years) (usegalaxy.eu): 0 + Suite runs (last 5 years) (usegalaxy.fr): 0 + Suite runs (last 5 years) (usegalaxy.org): 0 + Suite runs (last 5 years) (usegalaxy.org.au): 0 + Suite runs (last 5 years) on main servers: 0 + Suite runs (usegalaxy.eu): 0 + Suite runs (usegalaxy.fr): 0 + Suite runs (usegalaxy.org): 0 + Suite runs (usegalaxy.org.au): 0 + Suite runs on main servers: 0 + Suite source: https://github.com/galaxyproject/tools-iuc/tree/main/tools/mgnify_pipelines_toolkit + Suite users (last 5 years) (usegalaxy.eu): 0 + Suite users (last 5 years) (usegalaxy.fr): 0 + Suite users (last 5 years) (usegalaxy.org): 0 + Suite users (last 5 years) (usegalaxy.org.au): 0 + Suite users (last 5 years) on main servers: 0 + Suite users (usegalaxy.eu): 0 + Suite users (usegalaxy.fr): 0 + Suite users (usegalaxy.org): 0 + Suite users (usegalaxy.org.au): 0 + Suite users on main servers: 0 + Suite version: 1.5.1 + Suite version status: To update + To keep: true + Tool IDs: + - mgnify_pipelines_toolkit_classify_var_regions + - mgnify_pipelines_toolkit_make_asv_count_table + - mgnify_pipelines_toolkit_mapseq_to_asv_table + - mgnify_pipelines_toolkit_permute_primers + - mgnify_pipelines_toolkit_primer_val_classification + - mgnify_pipelines_toolkit_rev_comp_se_primers + Tool output formats: + - json + - tabular + - txt + - tsv + - fasta + ToolShed categories: + - Metagenomics + availability: + UseGalaxy.eu: 6 + biii ID: null + bio.tool ID: null + bio.tool description: null + bio.tool name: null - Deprecated: false Description: An R package for removing contamination from metabarcoding (e.g., microbiome) datasets post-sequencing @@ -29038,12 +29025,10 @@ Number of tools on ImmPort Galaxy: 0 Number of tools on InteractoMIX: 0 Number of tools on Lebanese University Galaxy: 0 - Number of tools on MBAC Metabiome Portal: 0 Number of tools on MISSISSIPPI: 0 Number of tools on Mandoiu Lab: 0 Number of tools on Oqtans: 0 Number of tools on Palfinder: 0 - Number of tools on PepSimili: 0 Number of tools on PhagePromotor: 0 Number of tools on UseGalaxy.be: 0 Number of tools on UseGalaxy.cz: 0 @@ -29059,7 +29044,7 @@ Suite conda package: null Suite first commit date: '2025-08-05' Suite owner: iuc - Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/micro_decon + Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/master/tools/micro_decon Suite runs (last 5 years) (usegalaxy.eu): 0 Suite runs (last 5 years) (usegalaxy.fr): 0 Suite runs (last 5 years) (usegalaxy.org): 0 @@ -29121,12 +29106,10 @@ Number of tools on ImmPort Galaxy: 0 Number of tools on InteractoMIX: 0 Number of tools on Lebanese University Galaxy: 0 - Number of tools on MBAC Metabiome Portal: 0 Number of tools on MISSISSIPPI: 0 Number of tools on Mandoiu Lab: 0 Number of tools on Oqtans: 0 Number of tools on Palfinder: 0 - Number of tools on PepSimili: 0 Number of tools on PhagePromotor: 0 Number of tools on UseGalaxy.be: 1 Number of tools on UseGalaxy.cz: 1 @@ -29143,7 +29126,7 @@ Suite conda package: minia Suite first commit date: '2020-04-08' Suite owner: iuc - Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/minia + Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/master/tools/minia Suite runs (last 5 years) (usegalaxy.eu): 6758 Suite runs (last 5 years) (usegalaxy.fr): 0 Suite runs (last 5 years) (usegalaxy.org): 0 @@ -29165,8 +29148,8 @@ Suite users (usegalaxy.org): 0 Suite users (usegalaxy.org.au): 77 Suite users on main servers: 364 - Suite version: 3.2.6 - Suite version status: Up-to-date + Suite version: '@TOOL_VERSION@' + Suite version status: To update To keep: true Tool IDs: - minia @@ -29213,12 +29196,10 @@ Number of tools on ImmPort Galaxy: 0 Number of tools on InteractoMIX: 0 Number of tools on Lebanese University Galaxy: 0 - Number of tools on MBAC Metabiome Portal: 0 Number of tools on MISSISSIPPI: 0 Number of tools on Mandoiu Lab: 0 Number of tools on Oqtans: 0 Number of tools on Palfinder: 0 - Number of tools on PepSimili: 0 Number of tools on PhagePromotor: 0 Number of tools on UseGalaxy.be: 1 Number of tools on UseGalaxy.cz: 1 @@ -29245,7 +29226,7 @@ Suite conda package: miniasm Suite first commit date: '2019-06-18' Suite owner: iuc - Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/miniasm + Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniasm Suite runs (last 5 years) (usegalaxy.eu): 11506 Suite runs (last 5 years) (usegalaxy.fr): 166 Suite runs (last 5 years) (usegalaxy.org): 9124 @@ -29267,7 +29248,7 @@ Suite users (usegalaxy.org): 538 Suite users (usegalaxy.org.au): 96 Suite users on main servers: 1337 - Suite version: 0.3_r179 + Suite version: '@TOOL_VERSION@' Suite version status: To update To keep: true Tool IDs: @@ -29319,12 +29300,10 @@ Number of tools on ImmPort Galaxy: 0 Number of tools on InteractoMIX: 0 Number of tools on Lebanese University Galaxy: 0 - Number of tools on MBAC Metabiome Portal: 0 Number of tools on MISSISSIPPI: 0 Number of tools on Mandoiu Lab: 0 Number of tools on Oqtans: 0 Number of tools on Palfinder: 0 - Number of tools on PepSimili: 0 Number of tools on PhagePromotor: 0 Number of tools on UseGalaxy.be: 0 Number of tools on UseGalaxy.cz: 2 @@ -29341,7 +29320,7 @@ Suite conda package: miniprot Suite first commit date: '2022-09-19' Suite owner: iuc - Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/miniprot + Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot Suite runs (last 5 years) (usegalaxy.eu): 5038 Suite runs (last 5 years) (usegalaxy.fr): 283 Suite runs (last 5 years) (usegalaxy.org): 364 @@ -29385,6 +29364,86 @@ gap penalty, splicing and frameshift. It is primarily intended for annotating protein-coding genes in a new species using known genes from other species. bio.tool name: miniprot +- Deprecated: false + Description: Wrappers for Minimap2-inferred Sequence Typing (MiST). + EDAM operations: [] + EDAM reduced operations: [] + EDAM reduced topics: [] + EDAM topics: [] + Homepage: https://github.com/BioinformaticsPlatformWIV-ISP/MiST + Latest suite conda package version: 1.2.0 + Number of tools on APOSTL: 0 + Number of tools on CIRM-CFBP: 0 + Number of tools on ChemFlow: 0 + Number of tools on Coloc-stats: 0 + Number of tools on GASLINI: 0 + Number of tools on Galaxy@AuBi: 0 + Number of tools on Galaxy@Pasteur: 0 + Number of tools on GalaxyTrakr: 0 + Number of tools on HyPhy HIV NGS Tools: 0 + Number of tools on IPK Galaxy Blast Suite: 0 + Number of tools on ImmPort Galaxy: 0 + Number of tools on InteractoMIX: 0 + Number of tools on Lebanese University Galaxy: 0 + Number of tools on MISSISSIPPI: 0 + Number of tools on Mandoiu Lab: 0 + Number of tools on Oqtans: 0 + Number of tools on Palfinder: 0 + Number of tools on PhagePromotor: 0 + Number of tools on UseGalaxy.be: 0 + Number of tools on UseGalaxy.cz: 0 + Number of tools on UseGalaxy.eu: 2 + Number of tools on UseGalaxy.fr: 0 + Number of tools on UseGalaxy.no: 0 + Number of tools on UseGalaxy.org (Main): 0 + Number of tools on UseGalaxy.org.au: 0 + Number of tools on Viral Variant Visualizer (VVV): 0 + Related Tutorials: [] + Related Workflows: [] + Suite ID: mist_typing + Suite conda package: mist_typing + Suite first commit date: '2026-01-08' + Suite owner: iuc + Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/master/tools/mist_typing + Suite runs (last 5 years) (usegalaxy.eu): 0 + Suite runs (last 5 years) (usegalaxy.fr): 0 + Suite runs (last 5 years) (usegalaxy.org): 0 + Suite runs (last 5 years) (usegalaxy.org.au): 0 + Suite runs (last 5 years) on main servers: 0 + Suite runs (usegalaxy.eu): 0 + Suite runs (usegalaxy.fr): 0 + Suite runs (usegalaxy.org): 0 + Suite runs (usegalaxy.org.au): 0 + Suite runs on main servers: 0 + Suite source: https://github.com/galaxyproject/tools-iuc/tree/main/tools/mist_typing + Suite users (last 5 years) (usegalaxy.eu): 0 + Suite users (last 5 years) (usegalaxy.fr): 0 + Suite users (last 5 years) (usegalaxy.org): 0 + Suite users (last 5 years) (usegalaxy.org.au): 0 + Suite users (last 5 years) on main servers: 0 + Suite users (usegalaxy.eu): 0 + Suite users (usegalaxy.fr): 0 + Suite users (usegalaxy.org): 0 + Suite users (usegalaxy.org.au): 0 + Suite users on main servers: 0 + Suite version: 1.2.0 + Suite version status: Up-to-date + To keep: true + Tool IDs: + - mist_call + - mist_dists + Tool output formats: + - tabular + - json + ToolShed categories: + - Sequence Analysis + - Phylogenetics + availability: + UseGalaxy.eu: 2 + biii ID: null + bio.tool ID: null + bio.tool description: null + bio.tool name: null - Deprecated: false Description: de-novo annotation of metazoan mitochondrial genomes EDAM operations: @@ -29412,14 +29471,12 @@ Number of tools on ImmPort Galaxy: 0 Number of tools on InteractoMIX: 0 Number of tools on Lebanese University Galaxy: 0 - Number of tools on MBAC Metabiome Portal: 0 Number of tools on MISSISSIPPI: 0 Number of tools on Mandoiu Lab: 0 Number of tools on Oqtans: 0 Number of tools on Palfinder: 0 - Number of tools on PepSimili: 0 Number of tools on PhagePromotor: 0 - Number of tools on UseGalaxy.be: 2 + Number of tools on UseGalaxy.be: 1 Number of tools on UseGalaxy.cz: 2 Number of tools on UseGalaxy.eu: 2 Number of tools on UseGalaxy.fr: 2 @@ -29436,7 +29493,7 @@ Suite conda package: mitos Suite first commit date: '2020-02-18' Suite owner: iuc - Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/mitos + Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos Suite runs (last 5 years) (usegalaxy.eu): 267673 Suite runs (last 5 years) (usegalaxy.fr): 109 Suite runs (last 5 years) (usegalaxy.org): 84561 @@ -29458,7 +29515,7 @@ Suite users (usegalaxy.org): 772 Suite users (usegalaxy.org.au): 151 Suite users on main servers: 2265 - Suite version: 1.1.7 + Suite version: '@TOOL_VERSION@+galaxy@VERSION_SUFFIX@' Suite version status: To update To keep: true Tool IDs: @@ -29475,7 +29532,7 @@ ToolShed categories: - Sequence Analysis availability: - UseGalaxy.be: 2 + UseGalaxy.be: 1 UseGalaxy.cz: 2 UseGalaxy.eu: 2 UseGalaxy.fr: 2 @@ -29496,7 +29553,7 @@ EDAM topics: - Immunoproteins and antigens Homepage: https://github.com/tseemann/mlst - Latest suite conda package version: 2.33.1 + Latest suite conda package version: 2.35.0 Number of tools on APOSTL: 0 Number of tools on CIRM-CFBP: 0 Number of tools on ChemFlow: 0 @@ -29510,12 +29567,10 @@ Number of tools on ImmPort Galaxy: 0 Number of tools on InteractoMIX: 0 Number of tools on Lebanese University Galaxy: 0 - Number of tools on MBAC Metabiome Portal: 0 Number of tools on MISSISSIPPI: 0 Number of tools on Mandoiu Lab: 0 Number of tools on Oqtans: 0 Number of tools on Palfinder: 0 - Number of tools on PepSimili: 0 Number of tools on PhagePromotor: 0 Number of tools on UseGalaxy.be: 2 Number of tools on UseGalaxy.cz: 2 @@ -29546,6 +29601,7 @@ - https://usegalaxy.eu/published/workflow?id=fde21b5f5c169114 - https://usegalaxy.eu/published/workflow?id=ffd365c037373673 - https://usegalaxy.org.au/published/workflow?id=2120112358db8e01 + - https://usegalaxy.org.au/published/workflow?id=41331c03339e2b19 - https://usegalaxy.org.au/published/workflow?id=59618ed15510f531 - https://usegalaxy.org.au/published/workflow?id=7a0c4804e4d4c905 - https://usegalaxy.org.au/published/workflow?id=914330feb75ea9ab @@ -29559,9 +29615,9 @@ - https://usegalaxy.org/published/workflow?id=fb01e1a49793c8be Suite ID: mlst Suite conda package: mlst - Suite first commit date: '2016-12-12' + Suite first commit date: '2016-12-13' Suite owner: iuc - 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Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/mykrobe + Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe Suite runs (last 5 years) (usegalaxy.eu): 0 Suite runs (last 5 years) (usegalaxy.fr): 0 Suite runs (last 5 years) (usegalaxy.org): 0 @@ -32385,12 +32524,10 @@ Number of tools on ImmPort Galaxy: 0 Number of tools on InteractoMIX: 0 Number of tools on Lebanese University Galaxy: 0 - Number of tools on MBAC Metabiome Portal: 0 Number of tools on MISSISSIPPI: 0 Number of tools on Mandoiu Lab: 0 Number of tools on Oqtans: 0 Number of tools on Palfinder: 0 - Number of tools on PepSimili: 0 Number of tools on PhagePromotor: 0 Number of tools on UseGalaxy.be: 2 Number of tools on UseGalaxy.cz: 2 @@ -32406,9 +32543,9 @@ - https://usegalaxy.eu/published/workflow?id=77db45ad90b4033d Suite ID: nanocompore Suite conda package: nanocompore - Suite first commit date: '2020-04-27' + Suite first commit date: '2020-04-28' Suite owner: iuc - Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanocompore + Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore Suite runs (last 5 years) (usegalaxy.eu): 27 Suite runs (last 5 years) (usegalaxy.fr): 0 Suite runs (last 5 years) (usegalaxy.org): 0 @@ -32475,7 +32612,7 @@ EDAM topics: - Genomics Homepage: https://github.com/wdecoster/NanoPlot - Latest suite conda package version: 1.46.2 + Latest suite conda package version: 1.47.1 Number of tools on APOSTL: 0 Number of tools on CIRM-CFBP: 0 Number of tools on ChemFlow: 0 @@ -32489,12 +32626,10 @@ Number of tools on ImmPort Galaxy: 0 Number of tools on InteractoMIX: 0 Number of tools on Lebanese University Galaxy: 0 - Number of tools on MBAC Metabiome Portal: 0 Number of tools on MISSISSIPPI: 1 Number of tools on Mandoiu Lab: 0 Number of tools on Oqtans: 0 Number of tools on Palfinder: 0 - Number of tools on PepSimili: 0 Number of tools on PhagePromotor: 0 Number of tools on UseGalaxy.be: 1 Number of tools on UseGalaxy.cz: 1 @@ -32518,6 +32653,7 @@ - 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https://usegalaxy.org/published/workflow?id=80ac6adead9f97d8 + - https://usegalaxy.org/published/workflow?id=8421cbcadcbc8b79 + - https://usegalaxy.org/published/workflow?id=87045af52d500e91 + - https://usegalaxy.org/published/workflow?id=a4543d00cdbede5f - https://usegalaxy.org/published/workflow?id=a8b9252fad5fe06a - https://usegalaxy.org/published/workflow?id=b7817a12dbee583c - https://usegalaxy.org/published/workflow?id=bff206b4625375bc @@ -32630,7 +32770,7 @@ Suite conda package: nanoplot Suite first commit date: '2018-09-24' Suite owner: iuc - Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanoplot + Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot Suite runs (last 5 years) (usegalaxy.eu): 168514 Suite runs (last 5 years) (usegalaxy.fr): 3814 Suite runs (last 5 years) (usegalaxy.org): 72856 @@ -32652,8 +32792,8 @@ Suite users (usegalaxy.org): 5029 Suite users (usegalaxy.org.au): 2983 Suite users on main servers: 16251 - Suite version: 1.46.2 - Suite version status: Up-to-date + Suite version: '@TOOL_VERSION@+galaxy@VERSION_SUFFIX@' + Suite version status: To update To keep: true Tool IDs: - nanoplot @@ -32708,12 +32848,10 @@ Number of tools on ImmPort Galaxy: 0 Number of tools on InteractoMIX: 0 Number of tools on Lebanese University Galaxy: 0 - Number of tools on MBAC Metabiome Portal: 0 Number of tools on MISSISSIPPI: 0 Number of tools on Mandoiu Lab: 0 Number of tools on Oqtans: 0 Number of tools on Palfinder: 0 - Number of tools on PepSimili: 0 Number of tools on PhagePromotor: 0 Number of tools on UseGalaxy.be: 2 Number of tools on UseGalaxy.cz: 2 @@ -32730,7 +32868,7 @@ Suite conda package: nanopolishcomp Suite first commit date: '2020-04-27' Suite owner: iuc - Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanopolishcomp + Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanopolishcomp Suite runs (last 5 years) (usegalaxy.eu): 709 Suite runs (last 5 years) (usegalaxy.fr): 1 Suite runs (last 5 years) (usegalaxy.org): 0 @@ -32807,12 +32945,10 @@ Number of tools on ImmPort Galaxy: 0 Number of tools on InteractoMIX: 0 Number of tools on Lebanese University Galaxy: 0 - Number of tools on MBAC Metabiome Portal: 0 Number of tools on MISSISSIPPI: 0 Number of tools on Mandoiu Lab: 0 Number of tools on Oqtans: 0 Number of tools on Palfinder: 0 - Number of tools on PepSimili: 0 Number of tools on PhagePromotor: 0 Number of tools on UseGalaxy.be: 1 Number of tools on UseGalaxy.cz: 1 @@ -32829,6 +32965,10 @@ - https://usegalaxy.eu/published/workflow?id=c36560c74416fbbf - https://usegalaxy.eu/published/workflow?id=ce5378e3c2507524 - https://usegalaxy.eu/published/workflow?id=e035ac55551b2744 + - https://usegalaxy.org.au/published/workflow?id=586a218c9b29d99a + - https://usegalaxy.org.au/published/workflow?id=58f97e4a249796cb + - https://usegalaxy.org.au/published/workflow?id=a5b356c8baef01cf + - https://usegalaxy.org.au/published/workflow?id=dce03a1f302668c5 - https://usegalaxy.org/published/workflow?id=529b410bd03b66aa - https://usegalaxy.org/published/workflow?id=5d1cc6450f699345 - https://usegalaxy.org/published/workflow?id=927b8f90ad9603a7 @@ -32839,7 +32979,7 @@ Suite conda package: ncbi-fcs-gx Suite first commit date: '2023-09-21' Suite owner: iuc - Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_fcs_gx + Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_fcs_gx Suite runs (last 5 years) (usegalaxy.eu): 2259 Suite runs (last 5 years) (usegalaxy.fr): 9 Suite runs (last 5 years) (usegalaxy.org): 26859 @@ -32915,12 +33055,10 @@ Number of tools on ImmPort Galaxy: 0 Number of tools on InteractoMIX: 0 Number of tools on Lebanese University Galaxy: 0 - Number of tools on MBAC Metabiome Portal: 0 Number of tools on MISSISSIPPI: 0 Number of tools on Mandoiu Lab: 0 Number of tools on Oqtans: 0 Number of tools on Palfinder: 0 - Number of tools on PepSimili: 0 Number of tools on PhagePromotor: 0 Number of tools on UseGalaxy.be: 1 Number of tools on UseGalaxy.cz: 1 @@ -32984,7 +33122,7 @@ Suite conda package: newick_utils Suite first commit date: '2018-10-01' Suite owner: iuc - Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/newick_utils + Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/master/tools/newick_utils Suite runs (last 5 years) (usegalaxy.eu): 51682 Suite runs (last 5 years) (usegalaxy.fr): 310 Suite runs (last 5 years) (usegalaxy.org): 18983 @@ -33006,8 +33144,8 @@ Suite users (usegalaxy.org): 2332 Suite users (usegalaxy.org.au): 1145 Suite users on main servers: 5419 - Suite version: 1.6+galaxy1 - Suite version status: To update + Suite version: '1.6' + Suite version status: Up-to-date To keep: true Tool IDs: - newick_display @@ -33061,12 +33199,10 @@ Number of tools on ImmPort Galaxy: 0 Number of tools on InteractoMIX: 0 Number of tools on Lebanese University Galaxy: 0 - Number of tools on MBAC Metabiome Portal: 0 Number of tools on MISSISSIPPI: 1 Number of tools on Mandoiu Lab: 0 Number of tools on Oqtans: 0 Number of tools on Palfinder: 0 - Number of tools on PepSimili: 0 Number of tools on PhagePromotor: 0 Number of tools on UseGalaxy.be: 0 Number of tools on UseGalaxy.cz: 2 @@ -33106,7 +33242,7 @@ Suite conda package: nextalign Suite first commit date: '2021-03-29' Suite owner: iuc - Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/nextclade + Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade Suite runs (last 5 years) (usegalaxy.eu): 4718 Suite runs (last 5 years) (usegalaxy.fr): 723 Suite runs (last 5 years) (usegalaxy.org): 11632 @@ -33174,12 +33310,10 @@ Number of tools on ImmPort Galaxy: 0 Number of tools on InteractoMIX: 0 Number of tools on Lebanese University Galaxy: 0 - Number of tools on MBAC Metabiome Portal: 0 Number of tools on MISSISSIPPI: 0 Number of tools on Mandoiu Lab: 0 Number of tools on Oqtans: 0 Number of tools on Palfinder: 0 - Number of tools on PepSimili: 0 Number of tools on PhagePromotor: 0 Number of tools on UseGalaxy.be: 1 Number of tools on UseGalaxy.cz: 1 @@ -33195,7 +33329,7 @@ Suite conda package: nonpareil Suite first commit date: '2017-11-03' Suite owner: iuc - Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/nonpareil + Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil Suite runs (last 5 years) (usegalaxy.eu): 105 Suite runs (last 5 years) (usegalaxy.fr): 0 Suite runs (last 5 years) (usegalaxy.org): 122 @@ -33269,12 +33403,10 @@ Number of tools on ImmPort Galaxy: 0 Number of tools on InteractoMIX: 0 Number of tools on Lebanese University Galaxy: 0 - Number of tools on MBAC Metabiome Portal: 0 Number of tools on MISSISSIPPI: 0 Number of tools on Mandoiu Lab: 0 Number of tools on Oqtans: 0 Number of tools on Palfinder: 0 - Number of tools on PepSimili: 0 Number of tools on PhagePromotor: 0 Number of tools on UseGalaxy.be: 0 Number of tools on UseGalaxy.cz: 0 @@ -33290,7 +33422,7 @@ Suite conda package: nudup Suite first commit date: '2016-11-18' Suite owner: iuc - Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/nugen_nudup + Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/master/tools/nugen_nudup Suite runs (last 5 years) (usegalaxy.eu): 0 Suite runs (last 5 years) (usegalaxy.fr): 0 Suite runs (last 5 years) (usegalaxy.org): 0 @@ -33340,7 +33472,7 @@ EDAM reduced topics: [] EDAM topics: [] Homepage: https://github.com/metabarcoding/obitools4 - Latest suite conda package version: 4.4.42 + Latest suite conda package version: 4.4.45 Number of tools on APOSTL: 0 Number of tools on CIRM-CFBP: 0 Number of tools on ChemFlow: 0 @@ -33354,17 +33486,15 @@ Number of tools on ImmPort Galaxy: 0 Number of tools on InteractoMIX: 0 Number of tools on Lebanese University Galaxy: 0 - Number of tools on MBAC Metabiome Portal: 0 Number of tools on MISSISSIPPI: 0 Number of tools on Mandoiu Lab: 0 Number of tools on Oqtans: 0 Number of tools on Palfinder: 0 - Number of tools on PepSimili: 0 Number of tools on PhagePromotor: 0 Number of tools on UseGalaxy.be: 4 Number of tools on UseGalaxy.cz: 5 - Number of tools on UseGalaxy.eu: 7 - Number of tools on UseGalaxy.fr: 5 + Number of tools on UseGalaxy.eu: 12 + Number of tools on UseGalaxy.fr: 12 Number of tools on UseGalaxy.no: 5 Number of tools on UseGalaxy.org (Main): 0 Number of tools on UseGalaxy.org.au: 5 @@ -33382,7 +33512,7 @@ Suite conda package: obitools4 Suite first commit date: '2017-03-22' Suite owner: iuc - Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/obitools + Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools Suite runs (last 5 years) (usegalaxy.eu): 30430 Suite runs (last 5 years) (usegalaxy.fr): 202 Suite runs (last 5 years) (usegalaxy.org): 0 @@ -33404,26 +33534,32 @@ Suite users (usegalaxy.org): 0 Suite users (usegalaxy.org.au): 49 Suite users on main servers: 391 - Suite version: 4.4.42 + Suite version: 4.4.45 Suite version status: Up-to-date To keep: true Tool IDs: - obi_annotate - obi_clean + - obi_complement - obi_convert - obi_grep - obi_multiplex - obi_pairing + - obi_pcr + - obi_refidx + - obi_tag + - obi_taxonomy - obi_uniq Tool output formats: + - csv - fasta ToolShed categories: - Sequence Analysis availability: UseGalaxy.be: 4 UseGalaxy.cz: 5 - UseGalaxy.eu: 7 - UseGalaxy.fr: 5 + UseGalaxy.eu: 12 + UseGalaxy.fr: 12 UseGalaxy.no: 5 UseGalaxy.or: 5 biii ID: null @@ -33461,12 +33597,10 @@ Number of tools on ImmPort Galaxy: 0 Number of tools on InteractoMIX: 0 Number of tools on Lebanese University Galaxy: 0 - Number of tools on MBAC Metabiome Portal: 0 Number of tools on MISSISSIPPI: 0 Number of tools on Mandoiu Lab: 0 Number of tools on Oqtans: 0 Number of tools on Palfinder: 0 - Number of tools on PepSimili: 0 Number of tools on PhagePromotor: 0 Number of tools on UseGalaxy.be: 1 Number of tools on UseGalaxy.cz: 1 @@ -33502,7 +33636,7 @@ Suite conda package: null Suite first commit date: '2023-11-15' Suite owner: iuc - Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/omark + Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/master/tools/omark Suite runs (last 5 years) (usegalaxy.eu): 707 Suite runs (last 5 years) (usegalaxy.fr): 347 Suite runs (last 5 years) (usegalaxy.org): 44 @@ -33590,12 +33724,10 @@ Number of tools on ImmPort Galaxy: 0 Number of tools on InteractoMIX: 0 Number of tools on Lebanese University Galaxy: 0 - Number of tools on MBAC Metabiome Portal: 0 Number of tools on MISSISSIPPI: 0 Number of tools on Mandoiu Lab: 0 Number of tools on Oqtans: 0 Number of tools on Palfinder: 0 - Number of tools on PepSimili: 0 Number of tools on PhagePromotor: 0 Number of tools on UseGalaxy.be: 0 Number of tools on UseGalaxy.cz: 1 @@ -33613,7 +33745,7 @@ Suite conda package: orfipy Suite first commit date: '2022-04-07' Suite owner: iuc - Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/orfipy + Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy Suite runs (last 5 years) (usegalaxy.eu): 1509 Suite runs (last 5 years) (usegalaxy.fr): 0 Suite runs (last 5 years) (usegalaxy.org): 2776 @@ -33681,7 +33813,7 @@ - Comparative genomics - Sequence analysis Homepage: https://github.com/davidemms/OrthoFinder - Latest suite conda package version: 3.1.4 + Latest suite conda package version: 3.1.5 Number of tools on APOSTL: 0 Number of tools on CIRM-CFBP: 0 Number of tools on ChemFlow: 0 @@ -33695,12 +33827,10 @@ Number of tools on ImmPort Galaxy: 0 Number of tools on InteractoMIX: 0 Number of tools on Lebanese University Galaxy: 0 - Number of tools on MBAC Metabiome Portal: 0 Number of tools on MISSISSIPPI: 0 Number of tools on Mandoiu Lab: 0 Number of tools on Oqtans: 0 Number of tools on Palfinder: 0 - Number of tools on PepSimili: 0 Number of tools on PhagePromotor: 0 Number of tools on UseGalaxy.be: 1 Number of tools on UseGalaxy.cz: 1 @@ -33713,12 +33843,14 @@ Related Tutorials: [] Related Workflows: - https://usegalaxy.eu/published/workflow?id=d8492b49aed84d4f + - https://usegalaxy.eu/published/workflow?id=e0c709127e9a42ae - https://usegalaxy.eu/published/workflow?id=e5becc6d66b2568c + - https://usegalaxy.org/published/workflow?id=84b447be2f1c5870 Suite ID: orthofinder Suite conda package: orthofinder Suite first commit date: '2017-05-22' Suite owner: iuc - Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/orthofinder + Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder Suite runs (last 5 years) (usegalaxy.eu): 3870 Suite runs (last 5 years) (usegalaxy.fr): 221 Suite runs (last 5 years) (usegalaxy.org): 0 @@ -33795,12 +33927,10 @@ Number of tools on ImmPort Galaxy: 0 Number of tools on InteractoMIX: 0 Number of tools on Lebanese University Galaxy: 0 - Number of tools on MBAC Metabiome Portal: 0 Number of tools on MISSISSIPPI: 0 Number of tools on Mandoiu Lab: 0 Number of tools on Oqtans: 0 Number of tools on Palfinder: 0 - Number of tools on PepSimili: 0 Number of tools on PhagePromotor: 0 Number of tools on UseGalaxy.be: 0 Number of tools on UseGalaxy.cz: 0 @@ -33816,7 +33946,7 @@ Suite conda package: pacu_snp Suite first commit date: '2024-08-13' Suite owner: iuc - Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/pacu + Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/master/tools/pacu Suite runs (last 5 years) (usegalaxy.eu): 223 Suite runs (last 5 years) (usegalaxy.fr): 0 Suite runs (last 5 years) (usegalaxy.org): 0 @@ -33881,12 +34011,10 @@ Number of tools on ImmPort Galaxy: 0 Number of tools on InteractoMIX: 0 Number of tools on Lebanese University Galaxy: 0 - Number of tools on MBAC Metabiome Portal: 0 Number of tools on MISSISSIPPI: 0 Number of tools on Mandoiu Lab: 0 Number of tools on Oqtans: 0 Number of tools on Palfinder: 0 - Number of tools on PepSimili: 0 Number of tools on PhagePromotor: 0 Number of tools on UseGalaxy.be: 0 Number of tools on UseGalaxy.cz: 0 @@ -33902,7 +34030,7 @@ Suite conda package: pal2nal Suite first commit date: '2025-11-09' Suite owner: iuc - Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/pal2nal + Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/master/tools/pal2nal Suite runs (last 5 years) (usegalaxy.eu): 0 Suite runs (last 5 years) (usegalaxy.fr): 0 Suite runs (last 5 years) (usegalaxy.org): 0 @@ -33924,7 +34052,7 @@ Suite users (usegalaxy.org): 0 Suite users (usegalaxy.org.au): 0 Suite users on main servers: 0 - Suite version: null + Suite version: '@TOOL_VERSION@+galaxy@WRAPPER_VERSION@' Suite version status: To update To keep: true Tool IDs: @@ -33964,7 +34092,7 @@ - Plant biology - Sequencing Homepage: https://github.com/gtonkinhill/panaroo/releases - Latest suite conda package version: 1.6.0 + Latest suite conda package version: 1.7.0 Number of tools on APOSTL: 0 Number of tools on CIRM-CFBP: 0 Number of tools on ChemFlow: 0 @@ -33978,12 +34106,10 @@ Number of tools on ImmPort Galaxy: 0 Number of tools on InteractoMIX: 0 Number of tools on Lebanese University Galaxy: 0 - Number of tools on MBAC Metabiome Portal: 0 Number of tools on MISSISSIPPI: 0 Number of tools on Mandoiu Lab: 0 Number of tools on Oqtans: 0 Number of tools on Palfinder: 0 - Number of tools on PepSimili: 0 Number of tools on PhagePromotor: 0 Number of tools on UseGalaxy.be: 0 Number of tools on UseGalaxy.cz: 0 @@ -33999,7 +34125,7 @@ Suite conda package: panaroo Suite first commit date: '2025-02-28' Suite owner: galaxy-australia - Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/panaroo + Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/master/tools/panaroo Suite runs (last 5 years) (usegalaxy.eu): 297 Suite runs (last 5 years) (usegalaxy.fr): 0 Suite runs (last 5 years) (usegalaxy.org): 0 @@ -34021,7 +34147,7 @@ Suite users (usegalaxy.org): 0 Suite users (usegalaxy.org.au): 39 Suite users on main servers: 106 - Suite version: 1.6.0 + Suite version: 1.7.0 Suite version status: Up-to-date To keep: true Tool IDs: @@ -34059,12 +34185,10 @@ Number of tools on ImmPort Galaxy: 0 Number of tools on InteractoMIX: 0 Number of tools on Lebanese University Galaxy: 0 - Number of tools on MBAC Metabiome Portal: 0 Number of tools on MISSISSIPPI: 0 Number of tools on Mandoiu Lab: 0 Number of tools on Oqtans: 0 Number of tools on Palfinder: 0 - Number of tools on PepSimili: 0 Number of tools on PhagePromotor: 0 Number of tools on UseGalaxy.be: 0 Number of tools on UseGalaxy.cz: 0 @@ -34080,7 +34204,7 @@ Suite conda package: panta Suite first commit date: '2025-09-15' Suite owner: iuc - Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta + Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/master/tools/panta Suite runs (last 5 years) (usegalaxy.eu): 0 Suite runs (last 5 years) (usegalaxy.fr): 0 Suite runs (last 5 years) (usegalaxy.org): 0 @@ -34161,12 +34285,10 @@ Number of tools on ImmPort Galaxy: 0 Number of tools on InteractoMIX: 0 Number of tools on Lebanese University Galaxy: 0 - Number of tools on MBAC Metabiome Portal: 0 Number of tools on MISSISSIPPI: 0 Number of tools on Mandoiu Lab: 0 Number of tools on Oqtans: 0 Number of tools on Palfinder: 0 - Number of tools on PepSimili: 1 Number of tools on PhagePromotor: 0 Number of tools on UseGalaxy.be: 0 Number of tools on UseGalaxy.cz: 1 @@ -34184,7 +34306,7 @@ Suite conda package: "\n pharokka\n " Suite first commit date: '2023-02-14' Suite owner: iuc - Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/pharokka + Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/master/tools/pharokka Suite runs (last 5 years) (usegalaxy.eu): 16933 Suite runs (last 5 years) (usegalaxy.fr): 0 Suite runs (last 5 years) (usegalaxy.org): 21 @@ -34260,12 +34382,10 @@ Number of tools on ImmPort Galaxy: 0 Number of tools on InteractoMIX: 0 Number of tools on Lebanese University Galaxy: 0 - Number of tools on MBAC Metabiome Portal: 0 Number of tools on MISSISSIPPI: 0 Number of tools on Mandoiu Lab: 0 Number of tools on Oqtans: 0 Number of tools on Palfinder: 0 - Number of tools on PepSimili: 0 Number of tools on PhagePromotor: 0 Number of tools on UseGalaxy.be: 1 Number of tools on UseGalaxy.cz: 3 @@ -34286,7 +34406,7 @@ Suite conda package: bioconductor-phyloseq Suite first commit date: '2022-03-03' Suite owner: iuc - Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/phyloseq + Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq Suite runs (last 5 years) (usegalaxy.eu): 3161 Suite runs (last 5 years) (usegalaxy.fr): 163 Suite runs (last 5 years) (usegalaxy.org): 1022 @@ -34365,12 +34485,10 @@ Number of tools on ImmPort Galaxy: 0 Number of tools on InteractoMIX: 0 Number of tools on Lebanese University Galaxy: 0 - Number of tools on MBAC Metabiome Portal: 0 Number of tools on MISSISSIPPI: 0 Number of tools on Mandoiu Lab: 0 Number of tools on Oqtans: 0 Number of tools on Palfinder: 0 - Number of tools on PepSimili: 0 Number of tools on PhagePromotor: 0 Number of tools on UseGalaxy.be: 1 Number of tools on UseGalaxy.cz: 1 @@ -34388,7 +34506,7 @@ Suite conda package: phyml Suite first commit date: '2019-05-27' Suite owner: iuc - Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/phyml + Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml Suite runs (last 5 years) (usegalaxy.eu): 2452 Suite runs (last 5 years) (usegalaxy.fr): 334 Suite runs (last 5 years) (usegalaxy.org): 0 @@ -34410,8 +34528,8 @@ Suite users (usegalaxy.org): 0 Suite users (usegalaxy.org.au): 240 Suite users on main servers: 654 - Suite version: 3.3.20220408 - Suite version status: Up-to-date + Suite version: '@TOOL_VERSION@+galaxy@VERSION_SUFFIX@' + Suite version status: To update To keep: true Tool IDs: - phyml @@ -34468,12 +34586,10 @@ Number of tools on ImmPort Galaxy: 0 Number of tools on InteractoMIX: 0 Number of tools on Lebanese University Galaxy: 0 - Number of tools on MBAC Metabiome Portal: 0 Number of tools on MISSISSIPPI: 0 Number of tools on Mandoiu Lab: 0 Number of tools on Oqtans: 0 Number of tools on Palfinder: 0 - Number of tools on PepSimili: 0 Number of tools on PhagePromotor: 0 Number of tools on UseGalaxy.be: 0 Number of tools on UseGalaxy.cz: 5 @@ -34489,7 +34605,7 @@ Suite conda package: picrust Suite first commit date: '2016-11-08' Suite owner: iuc - Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/picrust + Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust Suite runs (last 5 years) (usegalaxy.eu): 562 Suite runs (last 5 years) (usegalaxy.fr): 442 Suite runs (last 5 years) (usegalaxy.org): 0 @@ -34577,12 +34693,10 @@ Number of tools on ImmPort Galaxy: 0 Number of tools on InteractoMIX: 0 Number of tools on Lebanese University Galaxy: 0 - Number of tools on MBAC Metabiome Portal: 0 Number of tools on MISSISSIPPI: 0 Number of tools on Mandoiu Lab: 0 Number of tools on Oqtans: 0 Number of tools on Palfinder: 0 - Number of tools on PepSimili: 0 Number of tools on PhagePromotor: 0 Number of tools on UseGalaxy.be: 0 Number of tools on UseGalaxy.cz: 7 @@ -34599,7 +34713,7 @@ Suite conda package: picrust2 Suite first commit date: '2021-07-09' Suite owner: iuc - Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/picrust2 + Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust2 Suite runs (last 5 years) (usegalaxy.eu): 6432 Suite runs (last 5 years) (usegalaxy.fr): 0 Suite runs (last 5 years) (usegalaxy.org): 1 @@ -34668,12 +34782,10 @@ Number of tools on ImmPort Galaxy: 0 Number of tools on InteractoMIX: 0 Number of tools on Lebanese University Galaxy: 0 - Number of tools on MBAC Metabiome Portal: 0 Number of tools on MISSISSIPPI: 0 Number of tools on Mandoiu Lab: 0 Number of tools on Oqtans: 0 Number of tools on Palfinder: 0 - Number of tools on PepSimili: 0 Number of tools on PhagePromotor: 0 Number of tools on UseGalaxy.be: 0 Number of tools on UseGalaxy.cz: 0 @@ -34689,7 +34801,7 @@ Suite conda package: mi-pimento Suite first commit date: '2025-08-04' Suite owner: iuc - Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/pimento + Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/master/tools/pimento Suite runs (last 5 years) (usegalaxy.eu): 2 Suite runs (last 5 years) (usegalaxy.fr): 0 Suite runs (last 5 years) (usegalaxy.org): 0 @@ -34754,12 +34866,10 @@ Number of tools on ImmPort Galaxy: 0 Number of tools on InteractoMIX: 0 Number of tools on Lebanese University Galaxy: 0 - Number of tools on MBAC Metabiome Portal: 0 Number of tools on MISSISSIPPI: 0 Number of tools on Mandoiu Lab: 0 Number of tools on Oqtans: 0 Number of tools on Palfinder: 0 - Number of tools on PepSimili: 0 Number of tools on PhagePromotor: 0 Number of tools on UseGalaxy.be: 0 Number of tools on UseGalaxy.cz: 0 @@ -34775,7 +34885,7 @@ Suite conda package: pirate Suite first commit date: '2026-01-31' Suite owner: iuc - Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/pirate + Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/master/tools/pirate Suite runs (last 5 years) (usegalaxy.eu): 0 Suite runs (last 5 years) (usegalaxy.fr): 0 Suite runs (last 5 years) (usegalaxy.org): 0 @@ -34855,12 +34965,10 @@ Number of tools on ImmPort Galaxy: 0 Number of tools on InteractoMIX: 0 Number of tools on Lebanese University Galaxy: 0 - Number of tools on MBAC Metabiome Portal: 0 Number of tools on MISSISSIPPI: 0 Number of tools on Mandoiu Lab: 0 Number of tools on Oqtans: 0 Number of tools on Palfinder: 0 - Number of tools on PepSimili: 0 Number of tools on PhagePromotor: 0 Number of tools on UseGalaxy.be: 0 Number of tools on UseGalaxy.cz: 0 @@ -34877,7 +34985,7 @@ Suite conda package: plasclass Suite first commit date: '2025-07-31' Suite owner: iuc - Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/plasclass + Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/master/tools/plasclass Suite runs (last 5 years) (usegalaxy.eu): 0 Suite runs (last 5 years) (usegalaxy.fr): 0 Suite runs (last 5 years) (usegalaxy.org): 0 @@ -34899,8 +35007,8 @@ Suite users (usegalaxy.org): 0 Suite users (usegalaxy.org.au): 0 Suite users on main servers: 0 - Suite version: 0.1.1 - Suite version status: Up-to-date + Suite version: '@TOOL_VERSION@+galaxy@VERSION_SUFFIX@' + Suite version status: To update To keep: true Tool IDs: - plasclass @@ -34947,12 +35055,10 @@ Number of tools on ImmPort Galaxy: 0 Number of tools on InteractoMIX: 0 Number of tools on Lebanese University Galaxy: 0 - Number of tools on MBAC Metabiome Portal: 0 Number of tools on MISSISSIPPI: 0 Number of tools on Mandoiu Lab: 0 Number of tools on Oqtans: 0 Number of tools on Palfinder: 0 - Number of tools on PepSimili: 0 Number of tools on PhagePromotor: 0 Number of tools on UseGalaxy.be: 1 Number of tools on UseGalaxy.cz: 1 @@ -34983,7 +35089,7 @@ Suite conda package: plasflow Suite first commit date: '2018-09-05' Suite owner: iuc - Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/plasflow + Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/master/tools/plasflow Suite runs (last 5 years) (usegalaxy.eu): 55069 Suite runs (last 5 years) (usegalaxy.fr): 0 Suite runs (last 5 years) (usegalaxy.org): 7929 @@ -35005,8 +35111,8 @@ Suite users (usegalaxy.org): 797 Suite users (usegalaxy.org.au): 87 Suite users on main servers: 1888 - Suite version: 1.1.0 - Suite version status: Up-to-date + Suite version: '@TOOL_VERSION@+galaxy@VERSION_SUFFIX@' + Suite version status: To update To keep: true Tool IDs: - PlasFlow @@ -35062,12 +35168,10 @@ Number of tools on ImmPort Galaxy: 0 Number of tools on InteractoMIX: 0 Number of tools on Lebanese University Galaxy: 0 - Number of tools on MBAC Metabiome Portal: 0 Number of tools on MISSISSIPPI: 0 Number of tools on Mandoiu Lab: 0 Number of tools on Oqtans: 0 Number of tools on Palfinder: 0 - Number of tools on PepSimili: 0 Number of tools on PhagePromotor: 0 Number of tools on UseGalaxy.be: 1 Number of tools on UseGalaxy.cz: 1 @@ -35115,7 +35219,7 @@ Suite conda package: plasmidfinder Suite first commit date: '2022-09-19' Suite owner: iuc - Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/plasmidfinder + Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/master/tools/plasmidfinder Suite runs (last 5 years) (usegalaxy.eu): 35994 Suite runs (last 5 years) (usegalaxy.fr): 10730 Suite runs (last 5 years) (usegalaxy.org): 11939 @@ -35198,12 +35302,10 @@ Number of tools on ImmPort Galaxy: 0 Number of tools on InteractoMIX: 0 Number of tools on Lebanese University Galaxy: 0 - Number of tools on MBAC Metabiome Portal: 0 Number of tools on MISSISSIPPI: 0 Number of tools on Mandoiu Lab: 0 Number of tools on Oqtans: 0 Number of tools on Palfinder: 0 - Number of tools on PepSimili: 0 Number of tools on PhagePromotor: 0 Number of tools on UseGalaxy.be: 1 Number of tools on UseGalaxy.cz: 1 @@ -35222,7 +35324,7 @@ Suite conda package: polypolish Suite first commit date: '2022-09-22' Suite owner: iuc - Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/polypolish + Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/master/tools/polypolish Suite runs (last 5 years) (usegalaxy.eu): 1066 Suite runs (last 5 years) (usegalaxy.fr): 79 Suite runs (last 5 years) (usegalaxy.org): 0 @@ -35308,12 +35410,10 @@ Number of tools on ImmPort Galaxy: 0 Number of tools on InteractoMIX: 0 Number of tools on Lebanese University Galaxy: 0 - Number of tools on MBAC Metabiome Portal: 0 Number of tools on MISSISSIPPI: 0 Number of tools on Mandoiu Lab: 0 Number of tools on Oqtans: 0 Number of tools on Palfinder: 0 - Number of tools on PepSimili: 0 Number of tools on PhagePromotor: 0 Number of tools on UseGalaxy.be: 0 Number of tools on UseGalaxy.cz: 0 @@ -35330,7 +35430,7 @@ Suite conda package: ppanggolin Suite first commit date: '2025-01-22' Suite owner: iuc - Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/ppanggolin + Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin Suite runs (last 5 years) (usegalaxy.eu): 249 Suite runs (last 5 years) (usegalaxy.fr): 67 Suite runs (last 5 years) (usegalaxy.org): 0 @@ -35387,6 +35487,120 @@ (SAGs) thus taking advantage of large scale environmental studies and letting users study the pangenome of uncultivable species bio.tool name: PPanGGOLiN +- Deprecated: false + Description: PRINSEQ is a tool for easy and rapid quality control and data processing + of metagenomic and metatranscriptomic datasets + EDAM operations: + - Read pre-processing + - Sequence trimming + - Sequence contamination filtering + EDAM reduced operations: + - Read pre-processing + - Sequence trimming + - Sequence contamination filtering + EDAM reduced topics: + - Transcriptomics + - Metagenomics + EDAM topics: + - Transcriptomics + - Metagenomics + - Genomics + Homepage: http://prinseq.sourceforge.net/manual.html + Latest suite conda package version: 0.20.4 + Number of tools on APOSTL: 0 + Number of tools on CIRM-CFBP: 0 + Number of tools on ChemFlow: 0 + Number of tools on Coloc-stats: 0 + Number of tools on GASLINI: 0 + Number of tools on Galaxy@AuBi: 1 + Number of tools on Galaxy@Pasteur: 0 + Number of tools on GalaxyTrakr: 1 + Number of tools on HyPhy HIV NGS Tools: 0 + Number of tools on IPK Galaxy Blast Suite: 0 + Number of tools on ImmPort Galaxy: 0 + Number of tools on InteractoMIX: 0 + Number of tools on Lebanese University Galaxy: 0 + Number of tools on MISSISSIPPI: 0 + Number of tools on Mandoiu Lab: 0 + Number of tools on Oqtans: 0 + Number of tools on Palfinder: 0 + Number of tools on PhagePromotor: 0 + Number of tools on UseGalaxy.be: 1 + Number of tools on UseGalaxy.cz: 1 + Number of tools on UseGalaxy.eu: 1 + Number of tools on UseGalaxy.fr: 1 + Number of tools on UseGalaxy.no: 1 + Number of tools on UseGalaxy.org (Main): 1 + Number of tools on UseGalaxy.org.au: 0 + Number of tools on Viral Variant Visualizer (VVV): 0 + Related Tutorials: + - microbiome/mgnify-amplicon + Related Workflows: + - https://usegalaxy.eu/published/workflow?id=0609a4b1941d1a68 + - https://usegalaxy.eu/published/workflow?id=76e9cd837ea5e7da + - https://usegalaxy.eu/published/workflow?id=8f415b0c409f56f7 + - https://usegalaxy.eu/published/workflow?id=9fddc44294236e8f + - https://usegalaxy.eu/published/workflow?id=d6ff6be33b8bfe85 + - https://usegalaxy.eu/published/workflow?id=da19c0eaa757fa39 + - https://usegalaxy.org/published/workflow?id=20b7ae4b517a80fd + - https://usegalaxy.org/published/workflow?id=46f184a0e95f3c1c + - https://usegalaxy.org/published/workflow?id=5f878c4cc3bff68c + - https://usegalaxy.org/published/workflow?id=a71fcbc60caae8b6 + - https://usegalaxy.org/published/workflow?id=afb67b4b9952f57d + - https://workflowhub.eu/workflows/1271?version=3 + - https://workflowhub.eu/workflows/1272?version=2 + - https://workflowhub.eu/workflows/1850?version=1 + - https://workflowhub.eu/workflows/1854?version=1 + Suite ID: prinseq + Suite conda package: prinseq + Suite first commit date: '2016-05-30' + Suite owner: iuc + Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq + Suite runs (last 5 years) (usegalaxy.eu): 15643 + Suite runs (last 5 years) (usegalaxy.fr): 17 + Suite runs (last 5 years) (usegalaxy.org): 10523 + Suite runs (last 5 years) (usegalaxy.org.au): 0 + Suite runs (last 5 years) on main servers: 26183 + Suite runs (usegalaxy.eu): 16651 + Suite runs (usegalaxy.fr): 17 + Suite runs (usegalaxy.org): 12474 + Suite runs (usegalaxy.org.au): 0 + Suite runs on main servers: 29142 + Suite source: https://github.com/galaxyproject/tools-iuc/tree/main/tools/prinseq + Suite users (last 5 years) (usegalaxy.eu): 345 + Suite users (last 5 years) (usegalaxy.fr): 11 + Suite users (last 5 years) (usegalaxy.org): 1317 + Suite users (last 5 years) (usegalaxy.org.au): 0 + Suite users (last 5 years) on main servers: 1673 + Suite users (usegalaxy.eu): 412 + Suite users (usegalaxy.fr): 11 + Suite users (usegalaxy.org): 1501 + Suite users (usegalaxy.org.au): 0 + Suite users on main servers: 1924 + Suite version: '@TOOL_VERSION' + Suite version status: To update + To keep: true + Tool IDs: + - prinseq + Tool output formats: [] + ToolShed categories: + - Fastq Manipulation + - Metagenomics + availability: + UseGalaxy.be: 1 + UseGalaxy.cz: 1 + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + UseGalaxy.no: 1 + UseGalaxy.or: 1 + biii ID: null + bio.tool ID: prinseq + bio.tool description: PRINSEQ is a sequence processing tool that can be used to + filter, reformat and trim genomic and metagenomic sequence data. It generates + summary statistics of the input in graphical and tabular formats that can be used + for quality control steps. PRINSEQ is available as both standalone and web-based + versions. + bio.tool name: PRINSEQ - Deprecated: false Description: A protein-coding gene prediction software tool for bacterial and archaeal genomes @@ -35415,12 +35629,10 @@ Number of tools on ImmPort Galaxy: 0 Number of tools on InteractoMIX: 0 Number of tools on Lebanese University Galaxy: 0 - Number of tools on MBAC Metabiome Portal: 0 Number of tools on MISSISSIPPI: 0 Number of tools on Mandoiu Lab: 0 Number of tools on Oqtans: 0 Number of tools on Palfinder: 0 - Number of tools on PepSimili: 0 Number of tools on PhagePromotor: 0 Number of tools on UseGalaxy.be: 1 Number of tools on UseGalaxy.cz: 1 @@ -35444,7 +35656,7 @@ Suite conda package: prodigal Suite first commit date: '2024-03-14' Suite owner: iuc - Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/prodigal + Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/master/tools/prodigal Suite runs (last 5 years) (usegalaxy.eu): 6456 Suite runs (last 5 years) (usegalaxy.fr): 1487 Suite runs (last 5 years) (usegalaxy.org): 0 @@ -35466,8 +35678,8 @@ Suite users (usegalaxy.org): 0 Suite users (usegalaxy.org.au): 70 Suite users on main servers: 700 - Suite version: 2.6.3 - Suite version status: Up-to-date + Suite version: '@VERSION@' + Suite version status: To update To keep: true Tool IDs: - prodigal @@ -35520,12 +35732,10 @@ Number of tools on ImmPort Galaxy: 0 Number of tools on InteractoMIX: 0 Number of tools on Lebanese University Galaxy: 0 - Number of tools on MBAC Metabiome Portal: 0 Number of tools on MISSISSIPPI: 1 Number of tools on Mandoiu Lab: 0 Number of tools on Oqtans: 0 Number of tools on Palfinder: 0 - Number of tools on PepSimili: 1 Number of tools on PhagePromotor: 0 Number of tools on UseGalaxy.be: 1 Number of tools on UseGalaxy.cz: 1 @@ -35574,12 +35784,14 @@ - https://usegalaxy.eu/published/workflow?id=ce8bf03d3df24806 - https://usegalaxy.eu/published/workflow?id=cf8591391a17a914 - https://usegalaxy.eu/published/workflow?id=d92f9c33dded693f + - https://usegalaxy.eu/published/workflow?id=e0c709127e9a42ae - https://usegalaxy.eu/published/workflow?id=e16e524c557d7928 - https://usegalaxy.eu/published/workflow?id=e1894c36f1ab4ab4 - 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Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/prokka + Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka Suite runs (last 5 years) (usegalaxy.eu): 819587 Suite runs (last 5 years) (usegalaxy.fr): 7463 Suite runs (last 5 years) (usegalaxy.org): 462648 @@ -35651,7 +35864,7 @@ Suite users (usegalaxy.org): 16587 Suite users (usegalaxy.org.au): 6142 Suite users on main servers: 34251 - Suite version: 1.14.6 + Suite version: '@TOOL_VERSION@+galaxy@VERSION_SUFFIX@' Suite version status: To update To keep: true Tool IDs: @@ -35705,12 +35918,10 @@ Number of tools on ImmPort Galaxy: 0 Number of tools on InteractoMIX: 0 Number of tools on Lebanese University Galaxy: 0 - Number of tools on MBAC Metabiome Portal: 0 Number of tools on MISSISSIPPI: 0 Number of tools on Mandoiu Lab: 0 Number of tools on Oqtans: 0 Number of tools on Palfinder: 0 - Number of tools on PepSimili: 0 Number of tools on PhagePromotor: 0 Number of tools on UseGalaxy.be: 3 Number of tools on UseGalaxy.cz: 3 @@ -35729,7 +35940,7 @@ Suite conda package: proteinortho Suite first commit date: '2020-02-05' Suite owner: iuc - Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/proteinortho + Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/master/tools/proteinortho Suite runs (last 5 years) (usegalaxy.eu): 5028 Suite runs (last 5 years) (usegalaxy.fr): 23 Suite runs (last 5 years) (usegalaxy.org): 0 @@ -35774,6 +35985,85 @@ bio.tool description: Proteinortho is a tool to detect orthologous genes within different species bio.tool name: Proteinortho +- Deprecated: false + Description: PSAURON is a machine learning model for rapid assessment of protein + coding gene annotation + EDAM operations: [] + EDAM reduced operations: [] + EDAM reduced topics: [] + EDAM topics: [] + Homepage: https://github.com/salzberg-lab/PSAURON/ + Latest suite conda package version: 1.1.3 + Number of tools on APOSTL: 0 + Number of tools on CIRM-CFBP: 0 + Number of tools on ChemFlow: 0 + Number of tools on Coloc-stats: 0 + Number of tools on GASLINI: 0 + Number of tools on Galaxy@AuBi: 0 + Number of tools on Galaxy@Pasteur: 0 + Number of tools on GalaxyTrakr: 0 + Number of tools on HyPhy HIV NGS Tools: 0 + Number of tools on IPK Galaxy Blast Suite: 0 + Number of tools on ImmPort Galaxy: 0 + Number of tools on InteractoMIX: 0 + Number of tools on Lebanese University Galaxy: 0 + Number of tools on MISSISSIPPI: 0 + Number of tools on Mandoiu Lab: 0 + Number of tools on Oqtans: 0 + Number of tools on Palfinder: 0 + Number of tools on PhagePromotor: 0 + Number of tools on UseGalaxy.be: 0 + Number of tools on UseGalaxy.cz: 0 + Number of tools on UseGalaxy.eu: 1 + Number of tools on UseGalaxy.fr: 1 + Number of tools on UseGalaxy.no: 0 + Number of tools on UseGalaxy.org (Main): 0 + Number of tools on UseGalaxy.org.au: 0 + Number of tools on Viral Variant Visualizer (VVV): 0 + Related Tutorials: [] + Related Workflows: [] + Suite ID: psauron + Suite conda package: psauron + Suite first commit date: '2026-02-20' + Suite owner: iuc + Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/master/tools/psauron + Suite runs (last 5 years) (usegalaxy.eu): 0 + Suite runs (last 5 years) (usegalaxy.fr): 0 + Suite runs (last 5 years) (usegalaxy.org): 0 + Suite runs (last 5 years) (usegalaxy.org.au): 0 + Suite runs (last 5 years) on main servers: 0 + Suite runs (usegalaxy.eu): 0 + Suite runs (usegalaxy.fr): 0 + Suite runs (usegalaxy.org): 0 + Suite runs (usegalaxy.org.au): 0 + Suite runs on main servers: 0 + Suite source: https://github.com/galaxyproject/tools-iuc/tree/main/tools/psauron + Suite users (last 5 years) (usegalaxy.eu): 0 + Suite users (last 5 years) (usegalaxy.fr): 0 + Suite users (last 5 years) (usegalaxy.org): 0 + Suite users (last 5 years) (usegalaxy.org.au): 0 + Suite users (last 5 years) on main servers: 0 + Suite users (usegalaxy.eu): 0 + Suite users (usegalaxy.fr): 0 + Suite users (usegalaxy.org): 0 + Suite users (usegalaxy.org.au): 0 + Suite users on main servers: 0 + Suite version: 1.1.3 + Suite version status: Up-to-date + To keep: true + Tool IDs: + - psauron + Tool output formats: + - csv + ToolShed categories: + - Genome annotation + availability: + UseGalaxy.eu: 1 + UseGalaxy.fr: 1 + biii ID: null + bio.tool ID: null + bio.tool description: null + bio.tool name: null - Deprecated: false Description: QC metrics for ONT Basecalling EDAM operations: @@ -35805,12 +36095,10 @@ Number of tools on ImmPort Galaxy: 0 Number of tools on InteractoMIX: 0 Number of tools on Lebanese University Galaxy: 0 - Number of tools on MBAC Metabiome Portal: 0 Number of tools on MISSISSIPPI: 0 Number of tools on Mandoiu Lab: 0 Number of tools on Oqtans: 0 Number of tools on Palfinder: 0 - Number of tools on PepSimili: 0 Number of tools on PhagePromotor: 0 Number of tools on UseGalaxy.be: 0 Number of tools on UseGalaxy.cz: 1 @@ -35841,7 +36129,7 @@ Suite conda package: pycoqc Suite first commit date: '2021-03-02' Suite owner: iuc - Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/pycoqc + Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc Suite runs (last 5 years) (usegalaxy.eu): 23549 Suite runs (last 5 years) (usegalaxy.fr): 322 Suite runs (last 5 years) (usegalaxy.org): 4440 @@ -35915,12 +36203,10 @@ Number of tools on ImmPort Galaxy: 0 Number of tools on InteractoMIX: 0 Number of tools on Lebanese University Galaxy: 0 - 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Number of tools on MBAC Metabiome Portal: 0 Number of tools on MISSISSIPPI: 0 Number of tools on Mandoiu Lab: 0 Number of tools on Oqtans: 0 Number of tools on Palfinder: 0 - Number of tools on PepSimili: 0 Number of tools on PhagePromotor: 0 Number of tools on UseGalaxy.be: 0 Number of tools on UseGalaxy.cz: 0 @@ -36963,7 +37253,7 @@ Suite conda package: quickmerge Suite first commit date: '2022-07-08' Suite owner: iuc - Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/quickmerge + Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge Suite runs (last 5 years) (usegalaxy.eu): 0 Suite runs (last 5 years) (usegalaxy.fr): 0 Suite runs (last 5 years) (usegalaxy.org): 0 @@ -36985,8 +37275,8 @@ Suite users (usegalaxy.org): 0 Suite users (usegalaxy.org.au): 0 Suite users on main servers: 0 - Suite version: '0.3' - Suite version status: Up-to-date + Suite version: '@TOOL_VERSION@+galaxy@VERSION_SUFFIX@' + Suite version status: To update To keep: true Tool IDs: - quickmerge @@ -37031,12 +37321,10 @@ Number of tools on ImmPort Galaxy: 0 Number of tools on InteractoMIX: 0 Number of tools on Lebanese University Galaxy: 0 - Number of tools on MBAC Metabiome Portal: 0 Number of tools on MISSISSIPPI: 0 Number of tools on Mandoiu Lab: 0 Number of tools on Oqtans: 0 Number of tools on Palfinder: 0 - Number of tools on PepSimili: 0 Number of tools on PhagePromotor: 0 Number of tools on UseGalaxy.be: 1 Number of tools on UseGalaxy.cz: 0 @@ -37054,7 +37342,7 @@ Suite conda package: quicktree Suite first commit date: '2024-11-21' Suite owner: iuc - Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/quicktree + Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/master/tools/quicktree Suite runs (last 5 years) (usegalaxy.eu): 466 Suite runs (last 5 years) (usegalaxy.fr): 0 Suite runs (last 5 years) (usegalaxy.org): 0 @@ -37076,8 +37364,8 @@ Suite users (usegalaxy.org): 0 Suite users (usegalaxy.org.au): 0 Suite users on main servers: 69 - Suite version: '2.5' - Suite version status: Up-to-date + Suite version: '@TOOL_VERSION@+galaxy@VERSION_SUFFIX@' + Suite version status: To update To keep: true Tool IDs: - quicktree @@ -37127,12 +37415,10 @@ Number of tools on ImmPort Galaxy: 0 Number of tools on InteractoMIX: 0 Number of tools on Lebanese University Galaxy: 0 - Number of tools on MBAC Metabiome Portal: 0 Number of tools on MISSISSIPPI: 0 Number of tools on Mandoiu Lab: 0 Number of tools on Oqtans: 0 Number of tools on Palfinder: 0 - Number of tools on PepSimili: 0 Number of tools on PhagePromotor: 0 Number of tools on UseGalaxy.be: 0 Number of tools on UseGalaxy.cz: 0 @@ -37148,7 +37434,7 @@ Suite conda package: rasusa Suite first commit date: '2024-02-16' Suite owner: iuc - Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/rasusa + Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/master/tools/rasusa Suite runs (last 5 years) (usegalaxy.eu): 104 Suite runs (last 5 years) (usegalaxy.fr): 0 Suite runs (last 5 years) (usegalaxy.org): 0 @@ -37170,8 +37456,8 @@ Suite users (usegalaxy.org): 0 Suite users (usegalaxy.org.au): 0 Suite users on main servers: 24 - Suite version: 4.1.0 - Suite version status: Up-to-date + Suite version: '@TOOL_VERSION@+galaxy@VERSION_SUFFIX@' + Suite version status: To update To keep: true Tool IDs: - rasusa @@ -37214,12 +37500,10 @@ Number of tools on ImmPort Galaxy: 0 Number of tools on InteractoMIX: 0 Number of tools on Lebanese University Galaxy: 0 - Number of tools on MBAC Metabiome Portal: 0 Number of tools on MISSISSIPPI: 0 Number of tools on Mandoiu Lab: 0 Number of tools on Oqtans: 0 Number of tools on Palfinder: 0 - Number of tools on PepSimili: 0 Number of tools on PhagePromotor: 0 Number of tools on UseGalaxy.be: 1 Number of tools on UseGalaxy.cz: 1 @@ -37241,7 +37525,7 @@ Suite conda package: raxml Suite first commit date: '2015-11-05' Suite owner: iuc - Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml + Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml Suite runs (last 5 years) (usegalaxy.eu): 15492 Suite runs (last 5 years) (usegalaxy.fr): 305 Suite runs (last 5 years) (usegalaxy.org): 19599 @@ -37263,7 +37547,7 @@ Suite users (usegalaxy.org): 1144 Suite users (usegalaxy.org.au): 1034 Suite users on main servers: 3663 - Suite version: 8.2.12 + Suite version: '@TOOL_VERSION@+galaxy@VERSION_SUFFIX@' Suite version status: To update To keep: true Tool IDs: @@ -37301,7 +37585,7 @@ - Agricultural science - Phylogenomics Homepage: http://www.exelixis-lab.org/web/software/raxml-ng/ - Latest suite conda package version: 2.0.1 + Latest suite conda package version: 2.0.2 Number of tools on APOSTL: 0 Number of tools on CIRM-CFBP: 0 Number of tools on ChemFlow: 0 @@ -37315,12 +37599,10 @@ Number of tools on ImmPort Galaxy: 0 Number of tools on InteractoMIX: 0 Number of tools on Lebanese University Galaxy: 0 - Number of tools on MBAC Metabiome Portal: 0 Number of tools on MISSISSIPPI: 0 Number of tools on Mandoiu Lab: 0 Number of tools on Oqtans: 0 Number of tools on Palfinder: 0 - Number of tools on PepSimili: 0 Number of tools on PhagePromotor: 0 Number of tools on UseGalaxy.be: 0 Number of tools on UseGalaxy.cz: 0 @@ -37336,7 +37618,7 @@ Suite conda package: raxml-ng Suite first commit date: '2025-12-20' Suite owner: iuc - Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxmlng + Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxmlng Suite runs (last 5 years) (usegalaxy.eu): 0 Suite runs (last 5 years) (usegalaxy.fr): 0 Suite runs (last 5 years) (usegalaxy.org): 0 @@ -37358,7 +37640,7 @@ Suite users (usegalaxy.org): 0 Suite users (usegalaxy.org.au): 0 Suite users on main servers: 0 - Suite version: 2.0.1 + Suite version: 2.0.2 Suite version status: Up-to-date To keep: true Tool IDs: @@ -37399,12 +37681,10 @@ Number of tools on ImmPort Galaxy: 0 Number of tools on InteractoMIX: 0 Number of tools on Lebanese University Galaxy: 0 - Number of tools on MBAC Metabiome Portal: 0 Number of tools on MISSISSIPPI: 0 Number of tools on Mandoiu Lab: 0 Number of tools on Oqtans: 0 Number of tools on Palfinder: 0 - Number of tools on PepSimili: 0 Number of tools on PhagePromotor: 0 Number of tools on UseGalaxy.be: 0 Number of tools on UseGalaxy.cz: 0 @@ -37420,7 +37700,7 @@ Suite conda package: read2tree Suite first commit date: '2025-11-23' Suite owner: iuc - Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/read2tree + Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/master/tools/read2tree Suite runs (last 5 years) (usegalaxy.eu): 0 Suite runs (last 5 years) (usegalaxy.fr): 0 Suite runs (last 5 years) (usegalaxy.org): 0 @@ -37442,8 +37722,8 @@ Suite users (usegalaxy.org): 0 Suite users (usegalaxy.org.au): 0 Suite users on main servers: 0 - Suite version: 2.0.1 - Suite version status: Up-to-date + Suite version: '@TOOL_VERSION@' + Suite version status: To update To keep: true Tool IDs: - read2tree @@ -37491,12 +37771,10 @@ Number of tools on ImmPort Galaxy: 0 Number of tools on InteractoMIX: 0 Number of tools on Lebanese University Galaxy: 0 - Number of tools on MBAC Metabiome Portal: 0 Number of tools on MISSISSIPPI: 0 Number of tools on Mandoiu Lab: 0 Number of tools on Oqtans: 0 Number of tools on Palfinder: 0 - Number of tools on PepSimili: 0 Number of tools on PhagePromotor: 0 Number of tools on UseGalaxy.be: 0 Number of tools on UseGalaxy.cz: 1 @@ -37520,7 +37798,7 @@ Suite conda package: read-it-and-keep Suite first commit date: '2022-01-28' Suite owner: iuc - Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/read_it_and_keep + Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/master/tools/read_it_and_keep Suite runs (last 5 years) (usegalaxy.eu): 3781 Suite runs (last 5 years) (usegalaxy.fr): 0 Suite runs (last 5 years) (usegalaxy.org): 9 @@ -37542,7 +37820,7 @@ Suite users (usegalaxy.org): 8 Suite users (usegalaxy.org.au): 0 Suite users on main servers: 89 - Suite version: 0.2.2 + Suite version: '@TOOL_VERSION@' Suite version status: To update To keep: true Tool IDs: @@ -37599,12 +37877,10 @@ Number of tools on ImmPort Galaxy: 0 Number of tools on InteractoMIX: 0 Number of tools on Lebanese University Galaxy: 0 - Number of tools on MBAC Metabiome Portal: 0 Number of tools on MISSISSIPPI: 0 Number of tools on Mandoiu Lab: 0 Number of tools on Oqtans: 0 Number of tools on Palfinder: 0 - Number of tools on PepSimili: 0 Number of tools on PhagePromotor: 0 Number of tools on UseGalaxy.be: 1 Number of tools on UseGalaxy.cz: 1 @@ -37653,7 +37929,7 @@ Suite conda package: recentrifuge Suite first commit date: '2022-05-04' Suite owner: iuc - 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Suite version: 1.0.0 + Suite version: '@TOOL_VERSION@+galaxy@VERSION_SUFFIX@' Suite version status: To update To keep: true Tool IDs: @@ -37810,12 +38084,10 @@ Number of tools on ImmPort Galaxy: 0 Number of tools on InteractoMIX: 0 Number of tools on Lebanese University Galaxy: 0 - Number of tools on MBAC Metabiome Portal: 0 Number of tools on MISSISSIPPI: 0 Number of tools on Mandoiu Lab: 0 Number of tools on Oqtans: 0 Number of tools on Palfinder: 0 - Number of tools on PepSimili: 0 Number of tools on PhagePromotor: 0 Number of tools on UseGalaxy.be: 1 Number of tools on UseGalaxy.cz: 1 @@ -37841,7 +38113,7 @@ Suite conda package: roary Suite first commit date: '2017-06-21' Suite owner: iuc - Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/roary + Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary Suite runs (last 5 years) (usegalaxy.eu): 21218 Suite runs (last 5 years) (usegalaxy.fr): 187 Suite runs (last 5 years) (usegalaxy.org): 17744 @@ -37863,8 +38135,8 @@ Suite users (usegalaxy.org): 2454 Suite users (usegalaxy.org.au): 749 Suite users on main servers: 5627 - Suite version: 3.13.0 - Suite version status: Up-to-date + Suite version: '@TOOL_VERSION@+galaxy@VERSION_SUFFIX@' + Suite version status: To update To keep: true Tool IDs: - roary @@ -37916,12 +38188,10 @@ Number of tools on ImmPort Galaxy: 0 Number of tools on InteractoMIX: 0 Number of tools on Lebanese University Galaxy: 0 - Number of tools on MBAC Metabiome Portal: 0 Number of tools on MISSISSIPPI: 22 Number of tools on Mandoiu Lab: 0 Number of tools on Oqtans: 0 Number of tools on Palfinder: 0 - Number of tools on PepSimili: 0 Number of tools on PhagePromotor: 0 Number of tools on UseGalaxy.be: 22 Number of tools on UseGalaxy.cz: 22 @@ -37953,6 +38223,8 @@ - https://usegalaxy.eu/published/workflow?id=b7a3cbcd32734e8b - https://usegalaxy.eu/published/workflow?id=cc37667c2d1f9056 - https://usegalaxy.eu/published/workflow?id=ccef778cfd9024d1 + - https://usegalaxy.eu/published/workflow?id=e18ef811e7ad487d + - https://usegalaxy.eu/published/workflow?id=f2042ad9c10cea31 - https://usegalaxy.eu/published/workflow?id=f33b5135ee99e0dc - https://usegalaxy.fr/published/workflow?id=334189184455d9a2 - https://usegalaxy.fr/published/workflow?id=5d83e0886f2a7465 @@ -37970,7 +38242,6 @@ - https://usegalaxy.org.au/published/workflow?id=ce7f6a1c824920e2 - https://usegalaxy.org.au/published/workflow?id=e1fd89e7248b6661 - https://usegalaxy.org/published/workflow?id=044c5ce43f2e1829 - - https://usegalaxy.org/published/workflow?id=582f3de3971fc38c - https://usegalaxy.org/published/workflow?id=5944c5effd56b0d6 - https://usegalaxy.org/published/workflow?id=682b1c7e2ad9d443 - https://usegalaxy.org/published/workflow?id=7022c4d9af725e5c @@ -37986,11 +38257,9 @@ - https://usegalaxy.org/published/workflow?id=d9d3ccdcd7d91bb6 - https://usegalaxy.org/published/workflow?id=e035be74e3c85bf5 - https://usegalaxy.org/published/workflow?id=e151b279b0b45a57 - - https://usegalaxy.org/published/workflow?id=e33f6a058c5f57e5 - https://usegalaxy.org/published/workflow?id=eb4b32fcf4a9f64a - https://usegalaxy.org/published/workflow?id=fb789920b057fe8d - 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https://usegalaxy.eu/published/workflow?id=052f35a526798020 + Suite ID: samestr + Suite conda package: samestr + Suite first commit date: '2026-04-15' + Suite owner: iuc + Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/master/tools/samestr + Suite runs (last 5 years) (usegalaxy.eu): 0 + Suite runs (last 5 years) (usegalaxy.fr): 0 + Suite runs (last 5 years) (usegalaxy.org): 0 + Suite runs (last 5 years) (usegalaxy.org.au): 0 + Suite runs (last 5 years) on main servers: 0 + Suite runs (usegalaxy.eu): 0 + Suite runs (usegalaxy.fr): 0 + Suite runs (usegalaxy.org): 0 + Suite runs (usegalaxy.org.au): 0 + Suite runs on main servers: 0 + Suite source: https://github.com/galaxyproject/tools-iuc/tree/main/tools/samestr + Suite users (last 5 years) (usegalaxy.eu): 0 + Suite users (last 5 years) (usegalaxy.fr): 0 + Suite users (last 5 years) (usegalaxy.org): 0 + Suite users (last 5 years) (usegalaxy.org.au): 0 + Suite users (last 5 years) on main servers: 0 + Suite users (usegalaxy.eu): 0 + Suite users (usegalaxy.fr): 0 + Suite users (usegalaxy.org): 0 + Suite users (usegalaxy.org.au): 0 + Suite users on main servers: 0 + Suite version: 1.2025.111 + Suite version status: Up-to-date + To keep: true + Tool IDs: + - samestr_compare + - samestr_convert + - samestr_extract + - samestr_filter + - samestr_merge + - samestr_stats + - samestr_summarize + Tool output formats: + - tabular + - fasta + - fasta.gz + - npz + ToolShed categories: + - Metagenomics + availability: + UseGalaxy.eu: 7 + biii ID: null + bio.tool ID: null + bio.tool description: null + bio.tool name: null - Deprecated: false Description: Scoary calculates the assocations between all genes in the accessory genome and the traits. @@ -38107,12 +38463,10 @@ Number of tools on ImmPort Galaxy: 0 Number of tools on InteractoMIX: 0 Number of tools on Lebanese University Galaxy: 0 - Number of tools on MBAC Metabiome Portal: 0 Number of tools on MISSISSIPPI: 0 Number of tools on Mandoiu Lab: 0 Number of tools on Oqtans: 0 Number of tools on Palfinder: 0 - Number of tools on PepSimili: 0 Number of tools on PhagePromotor: 0 Number of tools on UseGalaxy.be: 0 Number of tools on UseGalaxy.cz: 1 @@ -38128,7 +38482,7 @@ Suite conda package: scoary Suite first commit date: '2021-03-18' Suite owner: iuc - Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/scoary + Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary Suite runs (last 5 years) (usegalaxy.eu): 1366 Suite runs (last 5 years) (usegalaxy.fr): 0 Suite runs (last 5 years) (usegalaxy.org): 0 @@ -38150,8 +38504,8 @@ Suite users (usegalaxy.org): 0 Suite users (usegalaxy.org.au): 0 Suite users on main servers: 113 - Suite version: 1.6.16 - Suite version status: Up-to-date + Suite version: '@TOOL_VERSION@' + Suite version status: To update To keep: true Tool IDs: - scoary @@ -38191,7 +38545,7 @@ - Microbial ecology - Sequence assembly Homepage: https://semibin.readthedocs.io/en/latest/ - Latest suite conda package version: 2.2.1 + Latest suite conda package version: 2.3.0 Number of tools on APOSTL: 0 Number of tools on CIRM-CFBP: 0 Number of tools on ChemFlow: 0 @@ -38205,12 +38559,10 @@ Number of tools on ImmPort Galaxy: 0 Number of tools on InteractoMIX: 0 Number of tools on Lebanese University Galaxy: 0 - Number of tools on MBAC Metabiome Portal: 0 Number of tools on MISSISSIPPI: 0 Number of tools on Mandoiu Lab: 0 Number of tools on Oqtans: 0 Number of tools on Palfinder: 0 - Number of tools on PepSimili: 0 Number of tools on PhagePromotor: 0 Number of tools on UseGalaxy.be: 1 Number of tools on UseGalaxy.cz: 6 @@ -38237,7 +38589,7 @@ Suite conda package: semibin Suite first commit date: '2022-10-14' Suite owner: iuc - Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin + Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin Suite runs (last 5 years) (usegalaxy.eu): 2779 Suite runs (last 5 years) (usegalaxy.fr): 75 Suite runs (last 5 years) (usegalaxy.org): 18 @@ -38317,12 +38669,10 @@ Number of tools on ImmPort Galaxy: 0 Number of tools on InteractoMIX: 0 Number of tools on Lebanese University Galaxy: 0 - Number of tools on MBAC Metabiome Portal: 0 Number of tools on MISSISSIPPI: 0 Number of tools on Mandoiu Lab: 0 Number of tools on Oqtans: 0 Number of tools on Palfinder: 0 - Number of tools on PepSimili: 0 Number of tools on PhagePromotor: 0 Number of tools on UseGalaxy.be: 0 Number of tools on UseGalaxy.cz: 4 @@ -38334,6 +38684,8 @@ Number of tools on Viral Variant Visualizer (VVV): 0 Related Tutorials: [] Related Workflows: + - https://usegalaxy.eu/published/workflow?id=8ee6213aec38e4cc + - https://usegalaxy.eu/published/workflow?id=e0c709127e9a42ae - https://usegalaxy.org.au/published/workflow?id=7559224fc32dce3a - https://usegalaxy.org.au/published/workflow?id=7a0c4804e4d4c905 - https://usegalaxy.org.au/published/workflow?id=ed3e48a73b5aaa56 @@ -38347,7 +38699,7 @@ Suite conda package: seqkit Suite first commit date: '2022-06-01' Suite owner: iuc - Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqkit + Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit Suite runs (last 5 years) (usegalaxy.eu): 13926 Suite runs (last 5 years) (usegalaxy.fr): 648 Suite runs (last 5 years) (usegalaxy.org): 0 @@ -38435,12 +38787,10 @@ Number of tools on ImmPort Galaxy: 0 Number of tools on InteractoMIX: 0 Number of tools on Lebanese University Galaxy: 0 - Number of tools on MBAC Metabiome Portal: 0 Number of tools on MISSISSIPPI: 0 Number of tools on Mandoiu Lab: 0 Number of tools on Oqtans: 0 Number of tools on Palfinder: 0 - Number of tools on PepSimili: 0 Number of tools on PhagePromotor: 0 Number of tools on UseGalaxy.be: 0 Number of tools on UseGalaxy.cz: 0 @@ -38457,7 +38807,7 @@ Suite conda package: seqprep Suite first commit date: '2024-01-15' Suite owner: iuc - Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqprep + Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep Suite runs (last 5 years) (usegalaxy.eu): 3602 Suite runs (last 5 years) (usegalaxy.fr): 0 Suite runs (last 5 years) (usegalaxy.org): 0 @@ -38529,12 +38879,10 @@ Number of tools on ImmPort Galaxy: 0 Number of tools on InteractoMIX: 0 Number of tools on Lebanese University Galaxy: 0 - Number of tools on MBAC Metabiome Portal: 0 Number of tools on MISSISSIPPI: 0 Number of tools on Mandoiu Lab: 0 Number of tools on Oqtans: 0 Number of tools on Palfinder: 0 - Number of tools on PepSimili: 0 Number of tools on PhagePromotor: 0 Number of tools on UseGalaxy.be: 0 Number of tools on UseGalaxy.cz: 0 @@ -38552,7 +38900,7 @@ Suite conda package: seqsero2 Suite first commit date: '2023-11-07' Suite owner: iuc - Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqsero2 + Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 Suite runs (last 5 years) (usegalaxy.eu): 14011 Suite runs (last 5 years) (usegalaxy.fr): 2 Suite runs (last 5 years) (usegalaxy.org): 0 @@ -38628,12 +38976,10 @@ Number of tools on ImmPort Galaxy: 0 Number of tools on InteractoMIX: 0 Number of tools on Lebanese University Galaxy: 0 - Number of tools on MBAC Metabiome Portal: 0 Number of tools on MISSISSIPPI: 0 Number of tools on Mandoiu Lab: 0 Number of tools on Oqtans: 0 Number of tools on Palfinder: 0 - Number of tools on PepSimili: 0 Number of tools on PhagePromotor: 0 Number of tools on UseGalaxy.be: 1 Number of tools on UseGalaxy.cz: 1 @@ -38673,6 +39019,7 @@ - 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Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/shovill + Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill Suite runs (last 5 years) (usegalaxy.eu): 70801 Suite runs (last 5 years) (usegalaxy.fr): 9136 Suite runs (last 5 years) (usegalaxy.org): 51724 @@ -38733,8 +39081,8 @@ Suite users (usegalaxy.org): 5212 Suite users (usegalaxy.org.au): 1669 Suite users on main servers: 10455 - Suite version: 1.4.2 - Suite version status: Up-to-date + Suite version: '@TOOL_VERSION@+galaxy@VERSION_SUFFIX@' + Suite version status: To update To keep: true Tool IDs: - shovill @@ -38798,12 +39146,10 @@ Number of tools on ImmPort Galaxy: 0 Number of tools on InteractoMIX: 0 Number of tools on Lebanese University Galaxy: 0 - Number of tools on MBAC Metabiome Portal: 0 Number of tools on MISSISSIPPI: 0 Number of tools on Mandoiu Lab: 0 Number of tools on Oqtans: 0 Number of tools on Palfinder: 0 - Number of tools on PepSimili: 0 Number of tools on PhagePromotor: 0 Number of tools on UseGalaxy.be: 0 Number of tools on UseGalaxy.cz: 1 @@ -38819,7 +39165,7 @@ Suite conda package: smallgenomeutilities Suite first commit date: '2023-05-30' Suite owner: iuc - Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/smallgenomeutilities + Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities Suite runs (last 5 years) (usegalaxy.eu): 168 Suite runs (last 5 years) (usegalaxy.fr): 0 Suite runs (last 5 years) (usegalaxy.org): 0 @@ -38887,12 +39233,10 @@ Number of tools on ImmPort Galaxy: 0 Number of tools on InteractoMIX: 0 Number of tools on Lebanese University Galaxy: 0 - Number of tools on MBAC Metabiome Portal: 0 Number of tools on MISSISSIPPI: 0 Number of tools on Mandoiu Lab: 0 Number of tools on Oqtans: 0 Number of tools on Palfinder: 0 - Number of tools on PepSimili: 0 Number of tools on PhagePromotor: 0 Number of tools on UseGalaxy.be: 1 Number of tools on UseGalaxy.cz: 1 @@ -38915,7 +39259,7 @@ Suite conda package: snap Suite first commit date: '2017-10-12' Suite owner: iuc - Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/snap + Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap Suite runs (last 5 years) (usegalaxy.eu): 1443 Suite runs (last 5 years) (usegalaxy.fr): 0 Suite runs (last 5 years) (usegalaxy.org): 813 @@ -38994,12 +39338,10 @@ Number of tools on ImmPort Galaxy: 0 Number of tools on InteractoMIX: 0 Number of tools on Lebanese University Galaxy: 0 - Number of tools on MBAC Metabiome Portal: 0 Number of tools on MISSISSIPPI: 0 Number of tools on Mandoiu Lab: 0 Number of tools on Oqtans: 0 Number of tools on Palfinder: 0 - Number of tools on PepSimili: 0 Number of tools on PhagePromotor: 0 Number of tools on UseGalaxy.be: 3 Number of tools on UseGalaxy.cz: 3 @@ -39059,7 +39401,7 @@ Suite conda package: snippy Suite first commit date: '2017-07-13' Suite owner: iuc - Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/snippy + Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/master/tools/snippy Suite runs (last 5 years) (usegalaxy.eu): 188403 Suite runs (last 5 years) (usegalaxy.fr): 8769 Suite runs (last 5 years) (usegalaxy.org): 138187 @@ -39081,8 +39423,8 @@ Suite users (usegalaxy.org): 4306 Suite users (usegalaxy.org.au): 2852 Suite users on main servers: 11056 - Suite version: null - Suite version status: To update + Suite version: 4.6.0 + Suite version status: Up-to-date To keep: true Tool IDs: - snippy_core @@ -39144,12 +39486,10 @@ Number of tools on ImmPort Galaxy: 0 Number of tools on InteractoMIX: 0 Number of tools on Lebanese University Galaxy: 0 - Number of tools on MBAC Metabiome Portal: 0 Number of tools on MISSISSIPPI: 0 Number of tools on Mandoiu Lab: 0 Number of tools on Oqtans: 0 Number of tools on Palfinder: 0 - Number of tools on PepSimili: 0 Number of tools on PhagePromotor: 0 Number of tools on UseGalaxy.be: 0 Number of tools on UseGalaxy.cz: 1 @@ -39165,7 +39505,7 @@ Suite conda package: sonneityping Suite first commit date: '2021-09-16' Suite owner: iuc - Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/sonneityping + Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/master/tools/sonneityping Suite runs (last 5 years) (usegalaxy.eu): 2 Suite runs (last 5 years) (usegalaxy.fr): 0 Suite runs (last 5 years) (usegalaxy.org): 0 @@ -39217,7 +39557,7 @@ EDAM topics: - Sequence assembly Homepage: https://github.com/ablab/spades - Latest suite conda package version: 4.2.0 + Latest suite conda package version: 4.3.0 Number of tools on APOSTL: 0 Number of tools on CIRM-CFBP: 0 Number of tools on ChemFlow: 0 @@ -39231,12 +39571,10 @@ Number of tools on ImmPort Galaxy: 0 Number of tools on InteractoMIX: 0 Number of tools on Lebanese University Galaxy: 0 - Number of tools on MBAC Metabiome Portal: 1 Number of tools on MISSISSIPPI: 3 Number of tools on Mandoiu Lab: 0 Number of tools on Oqtans: 0 Number of tools on Palfinder: 0 - Number of tools on PepSimili: 0 Number of tools on PhagePromotor: 0 Number of tools on UseGalaxy.be: 3 Number of tools on UseGalaxy.cz: 9 @@ -39298,10 +39636,12 @@ - https://usegalaxy.org/published/workflow?id=65bd891fe65ff78c - https://usegalaxy.org/published/workflow?id=71f8a4090877f171 - https://usegalaxy.org/published/workflow?id=7251c6e0dad8f927 + - https://usegalaxy.org/published/workflow?id=84233173d92fa506 - https://usegalaxy.org/published/workflow?id=87b3305ea433b4e2 - https://usegalaxy.org/published/workflow?id=8a350e0d96e937a5 - https://usegalaxy.org/published/workflow?id=8d229c0f58a07ebe - https://usegalaxy.org/published/workflow?id=8eb22336826a0f75 + - https://usegalaxy.org/published/workflow?id=9203f914b3e498a1 - https://usegalaxy.org/published/workflow?id=9ba6da7dae465d3e - https://usegalaxy.org/published/workflow?id=9c0fbd9f51a9857f - https://usegalaxy.org/published/workflow?id=ae81cc0e8263d03e @@ -39321,7 +39661,7 @@ Suite conda package: spades Suite first commit date: '2016-12-21' Suite owner: iuc - Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/spades + Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades Suite runs (last 5 years) (usegalaxy.eu): 104429 Suite runs (last 5 years) (usegalaxy.fr): 2677 Suite runs (last 5 years) (usegalaxy.org): 147425 @@ -39343,7 +39683,7 @@ Suite users (usegalaxy.org): 14731 Suite users (usegalaxy.org.au): 6722 Suite users on main servers: 30715 - Suite version: 4.2.0 + Suite version: 4.3.0 Suite version status: Up-to-date To keep: true Tool IDs: @@ -39410,12 +39750,10 @@ Number of tools on ImmPort Galaxy: 0 Number of tools on InteractoMIX: 0 Number of tools on Lebanese University Galaxy: 0 - Number of tools on MBAC Metabiome Portal: 0 Number of tools on MISSISSIPPI: 0 Number of tools on Mandoiu Lab: 0 Number of tools on Oqtans: 0 Number of tools on Palfinder: 0 - Number of tools on PepSimili: 0 Number of tools on PhagePromotor: 0 Number of tools on UseGalaxy.be: 0 Number of tools on UseGalaxy.cz: 1 @@ -39429,9 +39767,9 @@ Related Workflows: [] Suite ID: spotyping Suite conda package: spotyping - Suite first commit date: '2018-05-07' + Suite first commit date: '2018-05-08' Suite owner: iuc - Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/spotyping + Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/master/tools/spotyping Suite runs (last 5 years) (usegalaxy.eu): 2042 Suite runs (last 5 years) (usegalaxy.fr): 0 Suite runs (last 5 years) (usegalaxy.org): 0 @@ -39499,12 +39837,10 @@ Number of tools on ImmPort Galaxy: 0 Number of tools on InteractoMIX: 0 Number of tools on Lebanese University Galaxy: 0 - Number of tools on MBAC Metabiome Portal: 0 Number of tools on MISSISSIPPI: 0 Number of tools on Mandoiu Lab: 0 Number of tools on Oqtans: 0 Number of tools on Palfinder: 0 - Number of tools on PepSimili: 0 Number of tools on PhagePromotor: 0 Number of tools on UseGalaxy.be: 0 Number of tools on UseGalaxy.cz: 0 @@ -39517,11 +39853,12 @@ Related Tutorials: [] Related Workflows: - https://usegalaxy.org.au/published/workflow?id=b9fd488b0938d323 + - https://workflowhub.eu/workflows/2196?version=1 Suite ID: squirrel Suite conda package: squirrel Suite first commit date: '2025-01-16' Suite owner: iuc - Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/squirrel + Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/master/tools/squirrel Suite runs (last 5 years) (usegalaxy.eu): 7 Suite runs (last 5 years) (usegalaxy.fr): 0 Suite runs (last 5 years) (usegalaxy.org): 0 @@ -39595,12 +39932,10 @@ Number of tools on ImmPort Galaxy: 0 Number of tools on InteractoMIX: 0 Number of tools on Lebanese University Galaxy: 0 - Number of tools on MBAC Metabiome Portal: 0 Number of tools on MISSISSIPPI: 0 Number of tools on Mandoiu Lab: 0 Number of tools on Oqtans: 0 Number of tools on Palfinder: 0 - Number of tools on PepSimili: 0 Number of tools on PhagePromotor: 0 Number of tools on UseGalaxy.be: 0 Number of tools on UseGalaxy.cz: 1 @@ -39617,7 +39952,7 @@ Suite conda package: samtools Suite first commit date: '2022-08-22' Suite owner: iuc - Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/srst2 + Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/master/tools/srst2 Suite runs (last 5 years) (usegalaxy.eu): 407 Suite runs (last 5 years) (usegalaxy.fr): 0 Suite runs (last 5 years) (usegalaxy.org): 71 @@ -39672,7 +40007,7 @@ - Public health and epidemiology - Infectious disease Homepage: https://github.com/phac-nml/staramr - Latest suite conda package version: 0.12.2 + Latest suite conda package version: 0.12.3 Number of tools on APOSTL: 0 Number of tools on CIRM-CFBP: 0 Number of tools on ChemFlow: 0 @@ -39686,12 +40021,10 @@ Number of tools on ImmPort Galaxy: 0 Number of tools on InteractoMIX: 0 Number of tools on Lebanese University Galaxy: 0 - Number of tools on MBAC Metabiome Portal: 0 Number of tools on MISSISSIPPI: 0 Number of tools on Mandoiu Lab: 0 Number of tools on Oqtans: 0 Number of tools on Palfinder: 0 - Number of tools on PepSimili: 0 Number of tools on PhagePromotor: 0 Number of tools on UseGalaxy.be: 1 Number of tools on UseGalaxy.cz: 1 @@ -39728,6 +40061,7 @@ - https://usegalaxy.eu/published/workflow?id=abe85758e77c78e6 - https://usegalaxy.eu/published/workflow?id=b203dec6ee6da2fd - https://usegalaxy.eu/published/workflow?id=b2b46e71046b1999 + - https://usegalaxy.eu/published/workflow?id=b46d67d91391053d - https://usegalaxy.eu/published/workflow?id=b4de76c0a4d0e23a - https://usegalaxy.eu/published/workflow?id=b60a3e0427f2f519 - https://usegalaxy.eu/published/workflow?id=c48807045e258dd8 @@ -39743,6 +40077,7 @@ - https://usegalaxy.org.au/published/workflow?id=2120112358db8e01 - https://usegalaxy.org.au/published/workflow?id=2e29b21cdec7d0cc - https://usegalaxy.org.au/published/workflow?id=35f39173f0ac9179 + - https://usegalaxy.org.au/published/workflow?id=41331c03339e2b19 - https://usegalaxy.org.au/published/workflow?id=92fcdd490831c6c5 - https://usegalaxy.org.au/published/workflow?id=c9b7de574fb2f2d5 - https://usegalaxy.org.au/published/workflow?id=d9571b3dfef34e5e @@ -39767,7 +40102,7 @@ Suite conda package: staramr Suite first commit date: '2024-09-19' Suite owner: iuc - Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/staramr + Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/master/tools/staramr Suite runs (last 5 years) (usegalaxy.eu): 31443 Suite runs (last 5 years) (usegalaxy.fr): 9838 Suite runs (last 5 years) (usegalaxy.org): 14763 @@ -39789,8 +40124,8 @@ Suite users (usegalaxy.org): 2130 Suite users (usegalaxy.org.au): 1182 Suite users on main servers: 6481 - Suite version: 0.12.2 - Suite version status: Up-to-date + Suite version: '@TOOL_VERSION@+galaxy@VERSION_SUFFIX@' + Suite version status: To update To keep: true Tool IDs: - staramr_search @@ -39841,12 +40176,10 @@ Number of tools on ImmPort Galaxy: 0 Number of tools on InteractoMIX: 0 Number of tools on Lebanese University Galaxy: 0 - Number of tools on MBAC Metabiome Portal: 0 Number of tools on MISSISSIPPI: 0 Number of tools on Mandoiu Lab: 0 Number of tools on Oqtans: 0 Number of tools on Palfinder: 0 - Number of tools on PepSimili: 0 Number of tools on PhagePromotor: 0 Number of tools on UseGalaxy.be: 1 Number of tools on UseGalaxy.cz: 1 @@ -39862,7 +40195,7 @@ Suite conda package: structure Suite first commit date: '2017-09-22' Suite owner: iuc - Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/structure + Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure Suite runs (last 5 years) (usegalaxy.eu): 3903 Suite runs (last 5 years) (usegalaxy.fr): 330 Suite runs (last 5 years) (usegalaxy.org): 0 @@ -39884,8 +40217,8 @@ Suite users (usegalaxy.org): 0 Suite users (usegalaxy.org.au): 0 Suite users on main servers: 158 - Suite version: 2.3.4 - Suite version status: Up-to-date + Suite version: '@TOOL_VERSION@+galaxy@VERSION_SUFFIX@' + Suite version status: To update To keep: true Tool IDs: - structure @@ -39950,12 +40283,10 @@ Number of tools on ImmPort Galaxy: 0 Number of tools on InteractoMIX: 0 Number of tools on Lebanese University Galaxy: 0 - Number of tools on MBAC Metabiome Portal: 0 Number of tools on MISSISSIPPI: 0 Number of tools on Mandoiu Lab: 0 Number of tools on Oqtans: 0 Number of tools on Palfinder: 0 - Number of tools on PepSimili: 0 Number of tools on PhagePromotor: 0 Number of tools on UseGalaxy.be: 0 Number of tools on UseGalaxy.cz: 0 @@ -39973,7 +40304,7 @@ Suite conda package: syri Suite first commit date: '2025-04-16' Suite owner: iuc - Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/syri + Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/master/tools/syri Suite runs (last 5 years) (usegalaxy.eu): 84 Suite runs (last 5 years) (usegalaxy.fr): 76 Suite runs (last 5 years) (usegalaxy.org): 0 @@ -40053,12 +40384,10 @@ Number of tools on ImmPort Galaxy: 0 Number of tools on InteractoMIX: 0 Number of tools on Lebanese University Galaxy: 0 - Number of tools on MBAC Metabiome Portal: 0 Number of tools on MISSISSIPPI: 0 Number of tools on Mandoiu Lab: 0 Number of tools on Oqtans: 0 Number of tools on Palfinder: 0 - Number of tools on PepSimili: 0 Number of tools on PhagePromotor: 0 Number of tools on UseGalaxy.be: 0 Number of tools on UseGalaxy.cz: 1 @@ -40072,12 +40401,12 @@ Related Workflows: - https://usegalaxy.eu/published/workflow?id=cf0159c14418525e - https://usegalaxy.eu/published/workflow?id=e4dabaf57668dbd1 - - https://workflowhub.eu/workflows/2099?version=1 + - https://workflowhub.eu/workflows/2099?version=2 Suite ID: taxonkit Suite conda package: taxonkit Suite first commit date: '2024-07-26' Suite owner: iuc - Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/taxonkit + Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/master/tools/taxonkit Suite runs (last 5 years) (usegalaxy.eu): 1094 Suite runs (last 5 years) (usegalaxy.fr): 0 Suite runs (last 5 years) (usegalaxy.org): 0 @@ -40144,12 +40473,10 @@ Number of tools on ImmPort Galaxy: 0 Number of tools on InteractoMIX: 0 Number of tools on Lebanese University Galaxy: 0 - Number of tools on MBAC Metabiome Portal: 0 Number of tools on MISSISSIPPI: 0 Number of tools on Mandoiu Lab: 0 Number of tools on Oqtans: 0 Number of tools on Palfinder: 0 - Number of tools on PepSimili: 1 Number of tools on PhagePromotor: 0 Number of tools on UseGalaxy.be: 1 Number of tools on UseGalaxy.cz: 1 @@ -40304,7 +40631,7 @@ Suite conda package: krona Suite first commit date: '2015-08-06' Suite owner: crs4 - Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/taxonomy_krona_chart + Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/master/tools/taxonomy_krona_chart Suite runs (last 5 years) (usegalaxy.eu): 48617 Suite runs (last 5 years) (usegalaxy.fr): 565 Suite runs (last 5 years) (usegalaxy.org): 33268 @@ -40326,7 +40653,7 @@ Suite users (usegalaxy.org): 7659 Suite users (usegalaxy.org.au): 2042 Suite users on main servers: 17738 - Suite version: 2.7.1+galaxy0 + Suite version: 2.7.1 Suite version status: To update To keep: true Tool IDs: @@ -40380,12 +40707,10 @@ Number of tools on ImmPort Galaxy: 0 Number of tools on InteractoMIX: 0 Number of tools on Lebanese University Galaxy: 0 - Number of tools on MBAC Metabiome Portal: 0 Number of tools on MISSISSIPPI: 0 Number of tools on Mandoiu Lab: 0 Number of tools on Oqtans: 0 Number of tools on Palfinder: 0 - Number of tools on PepSimili: 0 Number of tools on PhagePromotor: 0 Number of tools on UseGalaxy.be: 0 Number of tools on UseGalaxy.cz: 0 @@ -40404,7 +40729,7 @@ Suite conda package: taxpasta Suite first commit date: '2023-08-30' Suite owner: iuc - Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/taxpasta + Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/master/tools/taxpasta Suite runs (last 5 years) (usegalaxy.eu): 323 Suite runs (last 5 years) (usegalaxy.fr): 18 Suite runs (last 5 years) (usegalaxy.org): 0 @@ -40426,8 +40751,8 @@ Suite users (usegalaxy.org): 0 Suite users (usegalaxy.org.au): 0 Suite users on main servers: 52 - Suite version: 0.7.0 - Suite version status: Up-to-date + Suite version: '@TOOL_VERSION@+galaxy@VERSION_SUFFIX@' + Suite version status: To update To keep: true Tool IDs: - taxpasta @@ -40477,12 +40802,10 @@ Number of tools on ImmPort Galaxy: 0 Number of tools on InteractoMIX: 0 Number of tools on Lebanese University Galaxy: 0 - Number of tools on MBAC Metabiome Portal: 0 Number of tools on MISSISSIPPI: 0 Number of tools on Mandoiu Lab: 0 Number of tools on Oqtans: 0 Number of tools on Palfinder: 0 - Number of tools on PepSimili: 0 Number of tools on PhagePromotor: 0 Number of tools on UseGalaxy.be: 1 Number of tools on UseGalaxy.cz: 1 @@ -40514,7 +40837,7 @@ Suite conda package: tb-profiler Suite first commit date: '2019-04-02' Suite owner: iuc - Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/tb-profiler + Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/master/tools/tb-profiler Suite runs (last 5 years) (usegalaxy.eu): 15947 Suite runs (last 5 years) (usegalaxy.fr): 0 Suite runs (last 5 years) (usegalaxy.org): 11483 @@ -40579,7 +40902,7 @@ - Bioinformatics - Sequence analysis Homepage: https://gitlab.com/ifb-elixirfr/abromics/tooldistillator - Latest suite conda package version: 1.0.5 + Latest suite conda package version: 1.0.6 Number of tools on APOSTL: 0 Number of tools on CIRM-CFBP: 0 Number of tools on ChemFlow: 0 @@ -40593,12 +40916,10 @@ Number of tools on ImmPort Galaxy: 0 Number of tools on InteractoMIX: 0 Number of tools on Lebanese University Galaxy: 0 - Number of tools on MBAC Metabiome Portal: 0 Number of tools on MISSISSIPPI: 0 Number of tools on Mandoiu Lab: 0 Number of tools on Oqtans: 0 Number of tools on Palfinder: 0 - Number of tools on PepSimili: 0 Number of tools on PhagePromotor: 0 Number of tools on UseGalaxy.be: 0 Number of tools on UseGalaxy.cz: 2 @@ -40709,7 +41030,7 @@ Suite conda package: tooldistillator Suite first commit date: '2024-04-30' Suite owner: iuc - Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/tooldistillator + Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator Suite runs (last 5 years) (usegalaxy.eu): 5042 Suite runs (last 5 years) (usegalaxy.fr): 19253 Suite runs (last 5 years) (usegalaxy.org): 1550 @@ -40731,7 +41052,7 @@ Suite users (usegalaxy.org): 162 Suite users (usegalaxy.org.au): 0 Suite users on main servers: 292 - Suite version: 1.0.5 + Suite version: 1.0.6 Suite version status: Up-to-date To keep: true Tool IDs: @@ -40779,12 +41100,10 @@ Number of tools on ImmPort Galaxy: 0 Number of tools on InteractoMIX: 0 Number of tools on Lebanese University Galaxy: 0 - Number of tools on MBAC Metabiome Portal: 0 Number of tools on MISSISSIPPI: 0 Number of tools on Mandoiu Lab: 0 Number of tools on Oqtans: 0 Number of tools on Palfinder: 0 - Number of tools on PepSimili: 0 Number of tools on PhagePromotor: 0 Number of tools on UseGalaxy.be: 1 Number of tools on UseGalaxy.cz: 1 @@ -40800,7 +41119,7 @@ Suite conda package: transtermhp Suite first commit date: '2015-10-08' Suite owner: iuc - Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/transtermhp + Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/master/tools/transtermhp Suite runs (last 5 years) (usegalaxy.eu): 467 Suite runs (last 5 years) (usegalaxy.fr): 0 Suite runs (last 5 years) (usegalaxy.org): 170 @@ -40822,7 +41141,7 @@ Suite users (usegalaxy.org): 55 Suite users (usegalaxy.org.au): 0 Suite users on main servers: 117 - Suite version: null + Suite version: 2.09.1 Suite version status: To update To keep: true Tool IDs: @@ -40882,12 +41201,10 @@ Number of tools on ImmPort Galaxy: 0 Number of tools on InteractoMIX: 0 Number of tools on Lebanese University Galaxy: 0 - Number of tools on MBAC Metabiome Portal: 0 Number of tools on MISSISSIPPI: 0 Number of tools on Mandoiu Lab: 0 Number of tools on Oqtans: 0 Number of tools on Palfinder: 0 - Number of tools on PepSimili: 0 Number of tools on PhagePromotor: 0 Number of tools on UseGalaxy.be: 0 Number of tools on UseGalaxy.cz: 5 @@ -40903,7 +41220,7 @@ Suite conda package: trycycler Suite first commit date: '2021-02-11' Suite owner: iuc - Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/trycycler + Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler Suite runs (last 5 years) (usegalaxy.eu): 15743 Suite runs (last 5 years) (usegalaxy.fr): 27 Suite runs (last 5 years) (usegalaxy.org): 0 @@ -40982,12 +41299,10 @@ Number of tools on ImmPort Galaxy: 0 Number of tools on InteractoMIX: 0 Number of tools on Lebanese University Galaxy: 0 - Number of tools on MBAC Metabiome Portal: 0 Number of tools on MISSISSIPPI: 0 Number of tools on Mandoiu Lab: 0 Number of tools on Oqtans: 0 Number of tools on Palfinder: 0 - Number of tools on PepSimili: 0 Number of tools on PhagePromotor: 0 Number of tools on UseGalaxy.be: 0 Number of tools on UseGalaxy.cz: 0 @@ -41003,7 +41318,7 @@ Suite conda package: tsebra Suite first commit date: '2023-10-19' Suite owner: iuc - Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/tsebra + Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsebra Suite runs (last 5 years) (usegalaxy.eu): 51 Suite runs (last 5 years) (usegalaxy.fr): 0 Suite runs (last 5 years) (usegalaxy.org): 0 @@ -41078,12 +41393,10 @@ Number of tools on ImmPort Galaxy: 0 Number of tools on InteractoMIX: 0 Number of tools on Lebanese University Galaxy: 0 - Number of tools on MBAC Metabiome Portal: 0 Number of tools on MISSISSIPPI: 1 Number of tools on Mandoiu Lab: 0 Number of tools on Oqtans: 0 Number of tools on Palfinder: 0 - Number of tools on PepSimili: 0 Number of tools on PhagePromotor: 0 Number of tools on UseGalaxy.be: 1 Number of tools on UseGalaxy.cz: 1 @@ -41163,7 +41476,7 @@ Suite conda package: unicycler Suite first commit date: '2017-05-08' Suite owner: iuc - Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/unicycler + Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler Suite runs (last 5 years) (usegalaxy.eu): 83521 Suite runs (last 5 years) (usegalaxy.fr): 2160 Suite runs (last 5 years) (usegalaxy.org): 65067 @@ -41185,8 +41498,8 @@ Suite users (usegalaxy.org): 8769 Suite users (usegalaxy.org.au): 2613 Suite users on main servers: 16860 - Suite version: 0.5.1 - Suite version status: Up-to-date + Suite version: '@TOOL_VERSION@+galaxy@VERSION_SUFFIX@' + Suite version status: To update To keep: true Tool IDs: - unicycler @@ -41243,12 +41556,10 @@ Number of tools on ImmPort Galaxy: 0 Number of tools on InteractoMIX: 0 Number of tools on Lebanese University Galaxy: 0 - Number of tools on MBAC Metabiome Portal: 0 Number of tools on MISSISSIPPI: 0 Number of tools on Mandoiu Lab: 0 Number of tools on Oqtans: 0 Number of tools on Palfinder: 0 - Number of tools on PepSimili: 0 Number of tools on PhagePromotor: 0 Number of tools on UseGalaxy.be: 0 Number of tools on UseGalaxy.cz: 2 @@ -41264,7 +41575,7 @@ Suite conda package: usher Suite first commit date: '2021-05-11' Suite owner: iuc - Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher + Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher Suite runs (last 5 years) (usegalaxy.eu): 1060 Suite runs (last 5 years) (usegalaxy.fr): 0 Suite runs (last 5 years) (usegalaxy.org): 0 @@ -41342,12 +41653,10 @@ Number of tools on ImmPort Galaxy: 0 Number of tools on InteractoMIX: 0 Number of tools on Lebanese University Galaxy: 0 - Number of tools on MBAC Metabiome Portal: 0 Number of tools on MISSISSIPPI: 0 Number of tools on Mandoiu Lab: 0 Number of tools on Oqtans: 0 Number of tools on Palfinder: 0 - Number of tools on PepSimili: 0 Number of tools on PhagePromotor: 0 Number of tools on UseGalaxy.be: 1 Number of tools on UseGalaxy.cz: 1 @@ -41365,7 +41674,7 @@ Suite conda package: valet Suite first commit date: '2017-11-16' Suite owner: iuc - Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/valet + Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/master/tools/valet Suite runs (last 5 years) (usegalaxy.eu): 449 Suite runs (last 5 years) (usegalaxy.fr): 0 Suite runs (last 5 years) (usegalaxy.org): 160 @@ -41387,7 +41696,7 @@ Suite users (usegalaxy.org): 76 Suite users (usegalaxy.org.au): 0 Suite users on main servers: 177 - Suite version: null + Suite version: '@WRAPPER_VERSION@.0' Suite version status: To update To keep: true Tool IDs: @@ -41441,12 +41750,10 @@ Number of tools on ImmPort Galaxy: 0 Number of tools on InteractoMIX: 0 Number of tools on Lebanese University Galaxy: 0 - Number of tools on MBAC Metabiome Portal: 0 Number of tools on MISSISSIPPI: 0 Number of tools on Mandoiu Lab: 0 Number of tools on Oqtans: 0 Number of tools on Palfinder: 0 - Number of tools on PepSimili: 0 Number of tools on PhagePromotor: 0 Number of tools on UseGalaxy.be: 0 Number of tools on UseGalaxy.cz: 1 @@ -41474,7 +41781,7 @@ Suite conda package: vapor Suite first commit date: '2022-08-24' Suite owner: iuc - Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/vapor + Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/master/tools/vapor Suite runs (last 5 years) (usegalaxy.eu): 197466 Suite runs (last 5 years) (usegalaxy.fr): 0 Suite runs (last 5 years) (usegalaxy.org): 1849 @@ -41496,8 +41803,8 @@ Suite users (usegalaxy.org): 127 Suite users (usegalaxy.org.au): 0 Suite users on main servers: 315 - Suite version: 1.0.3 - Suite version status: Up-to-date + Suite version: '@TOOL_VERSION@+galaxy@VERSION_SUFFIX@' + Suite version status: To update To keep: true Tool IDs: - vapor @@ -41546,12 +41853,10 @@ Number of tools on ImmPort Galaxy: 0 Number of tools on InteractoMIX: 0 Number of tools on Lebanese University Galaxy: 0 - Number of tools on MBAC Metabiome Portal: 0 Number of tools on MISSISSIPPI: 0 Number of tools on Mandoiu Lab: 0 Number of tools on Oqtans: 0 Number of tools on Palfinder: 0 - Number of tools on PepSimili: 0 Number of tools on PhagePromotor: 0 Number of tools on UseGalaxy.be: 1 Number of tools on UseGalaxy.cz: 0 @@ -41569,7 +41874,7 @@ Suite conda package: varvamp Suite first commit date: '2024-01-27' Suite owner: iuc - Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/varvamp + Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/master/tools/varvamp Suite runs (last 5 years) (usegalaxy.eu): 912 Suite runs (last 5 years) (usegalaxy.fr): 0 Suite runs (last 5 years) (usegalaxy.org): 0 @@ -41613,6 +41918,100 @@ for highly diverse viruses. The input is an alignment of your viral (full-genome) sequences. bio.tool name: varVAMP +- Deprecated: false + Description: Tool to provide taxonomic context of metagenomic sequencing data + EDAM operations: + - Deposition + - Taxonomic classification + - Genome annotation + EDAM reduced operations: + - Deposition + - Taxonomic classification + - Genome annotation + EDAM reduced topics: + - Taxonomy + - Metagenomics + - Microbial ecology + EDAM topics: + - Taxonomy + - Metagenomics + - Microbial ecology + Homepage: https://bitbucket.org/MAVERICLab/vcontact2/src/master/ + Latest suite conda package version: null + Number of tools on APOSTL: 0 + Number of tools on CIRM-CFBP: 0 + Number of tools on ChemFlow: 0 + Number of tools on Coloc-stats: 0 + Number of tools on GASLINI: 0 + Number of tools on Galaxy@AuBi: 0 + Number of tools on Galaxy@Pasteur: 0 + Number of tools on GalaxyTrakr: 0 + Number of tools on HyPhy HIV NGS Tools: 0 + Number of tools on IPK Galaxy Blast Suite: 0 + Number of 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years) (usegalaxy.fr): 0 + Suite runs (last 5 years) (usegalaxy.org): 0 + Suite runs (last 5 years) (usegalaxy.org.au): 0 + Suite runs (last 5 years) on main servers: 0 + Suite runs (usegalaxy.eu): 0 + Suite runs (usegalaxy.fr): 0 + Suite runs (usegalaxy.org): 0 + Suite runs (usegalaxy.org.au): 0 + Suite runs on main servers: 0 + Suite source: https://github.com/galaxyproject/tools-iuc/tree/main/tools/vcontact2 + Suite users (last 5 years) (usegalaxy.eu): 0 + Suite users (last 5 years) (usegalaxy.fr): 0 + Suite users (last 5 years) (usegalaxy.org): 0 + Suite users (last 5 years) (usegalaxy.org.au): 0 + Suite users (last 5 years) on main servers: 0 + Suite users (usegalaxy.eu): 0 + Suite users (usegalaxy.fr): 0 + Suite users (usegalaxy.org): 0 + Suite users (usegalaxy.org.au): 0 + Suite users on main servers: 0 + Suite version: 0.11.3 + Suite version status: To update + To keep: true + Tool IDs: + - vcontact2 + - vcontact2_gene2genome + Tool output formats: + - csv + - tabular + ToolShed categories: + - Metagenomics + availability: + UseGalaxy.eu: 2 + biii ID: null + bio.tool ID: vConTACT + bio.tool description: Network-based application utilizing whole genome gene-sharing + profiles for virus taxonomy that integrates distance-based hierarchical clustering + and confidence scores for all taxonomic predictions. + bio.tool name: vConTACT - Deprecated: false Description: an R package fo community ecologist EDAM operations: @@ -41644,12 +42043,10 @@ Number of tools on ImmPort Galaxy: 0 Number of tools on InteractoMIX: 0 Number of tools on Lebanese University Galaxy: 0 - Number of tools on MBAC Metabiome Portal: 0 Number of tools on MISSISSIPPI: 0 Number of tools on Mandoiu Lab: 0 Number of tools on Oqtans: 0 Number of tools on Palfinder: 0 - Number of tools on PepSimili: 0 Number of tools on PhagePromotor: 0 Number of tools on UseGalaxy.be: 3 Number of tools on UseGalaxy.cz: 3 @@ -41665,7 +42062,7 @@ Suite conda package: r-vegan Suite first commit date: '2015-08-27' Suite owner: iuc - Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/vegan + Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan Suite runs (last 5 years) (usegalaxy.eu): 2314 Suite runs (last 5 years) (usegalaxy.fr): 0 Suite runs (last 5 years) (usegalaxy.org): 3493 @@ -41739,12 +42136,10 @@ Number of tools on ImmPort Galaxy: 0 Number of tools on InteractoMIX: 0 Number of tools on Lebanese University Galaxy: 0 - Number of tools on MBAC Metabiome Portal: 0 Number of tools on MISSISSIPPI: 0 Number of tools on Mandoiu Lab: 0 Number of tools on Oqtans: 0 Number of tools on Palfinder: 0 - Number of tools on PepSimili: 0 Number of tools on PhagePromotor: 0 Number of tools on UseGalaxy.be: 2 Number of tools on UseGalaxy.cz: 2 @@ -41771,6 +42166,7 @@ - https://usegalaxy.org.au/published/workflow?id=874492eb776ba813 - https://usegalaxy.org.au/published/workflow?id=8b6739a000780d99 - 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@@ -41865,12 +42261,10 @@ Number of tools on ImmPort Galaxy: 0 Number of tools on InteractoMIX: 0 Number of tools on Lebanese University Galaxy: 0 - Number of tools on MBAC Metabiome Portal: 0 Number of tools on MISSISSIPPI: 0 Number of tools on Mandoiu Lab: 0 Number of tools on Oqtans: 0 Number of tools on Palfinder: 0 - Number of tools on PepSimili: 0 Number of tools on PhagePromotor: 0 Number of tools on UseGalaxy.be: 0 Number of tools on UseGalaxy.cz: 0 @@ -41886,7 +42280,7 @@ Suite conda package: viralverify Suite first commit date: '2025-07-04' Suite owner: iuc - Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/viralverify + Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/master/tools/viralverify Suite runs (last 5 years) (usegalaxy.eu): 0 Suite runs (last 5 years) (usegalaxy.fr): 0 Suite runs (last 5 years) (usegalaxy.org): 0 @@ -41908,8 +42302,8 @@ Suite users (usegalaxy.org): 0 Suite users (usegalaxy.org.au): 0 Suite users on main servers: 0 - Suite version: '1.1' - Suite version status: Up-to-date + Suite version: '@TOOL_VERSION@+galaxy@VERSION_SUFFIX@' + Suite version status: To update To keep: true Tool IDs: - viralverify @@ -41961,12 +42355,10 @@ Number of tools on ImmPort Galaxy: 0 Number of tools on InteractoMIX: 0 Number of tools on Lebanese University Galaxy: 0 - Number of tools on MBAC Metabiome Portal: 0 Number of tools on MISSISSIPPI: 0 Number of tools on Mandoiu Lab: 0 Number of tools on Oqtans: 0 Number of tools on Palfinder: 0 - Number of tools on PepSimili: 0 Number of tools on PhagePromotor: 0 Number of tools on UseGalaxy.be: 0 Number of tools on UseGalaxy.cz: 0 @@ -41984,7 +42376,7 @@ Suite conda package: biopython Suite first commit date: '2025-08-04' Suite owner: iuc - Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/main/tools/virannot + Suite parsed folder: https://github.com/galaxyproject/tools-iuc/tree/master/tools/virannot Suite runs (last 5 years) (usegalaxy.eu): 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tools on Mandoiu Lab: 0 Number of tools on Oqtans: 0 Number of tools on Palfinder: 0 - Number of tools on PepSimili: 0 Number of tools on PhagePromotor: 0 Number of tools on UseGalaxy.be: 0 Number of tools on UseGalaxy.cz: 0 @@ -43131,12 +43510,10 @@ Number of tools on ImmPort Galaxy: 0 Number of tools on InteractoMIX: 0 Number of tools on Lebanese University Galaxy: 0 - Number of tools on MBAC Metabiome Portal: 0 Number of tools on MISSISSIPPI: 0 Number of tools on Mandoiu Lab: 0 Number of tools on Oqtans: 0 Number of tools on Palfinder: 0 - Number of tools on PepSimili: 0 Number of tools on PhagePromotor: 0 Number of tools on UseGalaxy.be: 2 Number of tools on UseGalaxy.cz: 2 @@ -43185,7 +43562,7 @@ - https://workflowhub.eu/workflows/1468?version=1 Suite ID: maxquant Suite conda package: maxquant - Suite first commit date: '2015-01-24' + Suite first commit date: '2015-01-23' Suite owner: galaxyp Suite parsed folder: 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Number of tools on Lebanese University Galaxy: 0 - Number of tools on MBAC Metabiome Portal: 0 Number of tools on MISSISSIPPI: 0 Number of tools on Mandoiu Lab: 0 Number of tools on Oqtans: 0 Number of tools on Palfinder: 0 - Number of tools on PepSimili: 0 Number of tools on PhagePromotor: 0 Number of tools on UseGalaxy.be: 1 Number of tools on UseGalaxy.cz: 1 @@ -43423,8 +43796,8 @@ Suite users (usegalaxy.org): 5 Suite users (usegalaxy.org.au): 4 Suite users on main servers: 49 - Suite version: 1.9.4 - Suite version status: Up-to-date + Suite version: '@TOOL_VERSION@+galaxy@VERSION_SUFFIX@' + Suite version status: To update To keep: true Tool IDs: - metanovo @@ -43492,12 +43865,10 @@ Number of tools on ImmPort Galaxy: 0 Number of tools on InteractoMIX: 0 Number of tools on Lebanese University Galaxy: 0 - Number of tools on MBAC Metabiome Portal: 0 Number of tools on MISSISSIPPI: 0 Number of tools on Mandoiu Lab: 0 Number of tools on Oqtans: 0 Number of tools on Palfinder: 0 - Number 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(last 5 years) (usegalaxy.org): 0 @@ -46302,8 +46630,8 @@ Suite users (usegalaxy.org): 0 Suite users (usegalaxy.org.au): 0 Suite users on main servers: 9 - Suite version: 1.4.2 - Suite version status: Up-to-date + Suite version: '@TOOL_VERSION@+galaxy@VERSION_SUFFIX@' + Suite version status: To update To keep: true Tool IDs: - iphop_predict @@ -46340,12 +46668,10 @@ Number of tools on ImmPort Galaxy: 0 Number of tools on InteractoMIX: 0 Number of tools on Lebanese University Galaxy: 0 - Number of tools on MBAC Metabiome Portal: 0 Number of tools on MISSISSIPPI: 0 Number of tools on Mandoiu Lab: 0 Number of tools on Oqtans: 0 Number of tools on Palfinder: 0 - Number of tools on PepSimili: 0 Number of tools on PhagePromotor: 0 Number of tools on UseGalaxy.be: 0 Number of tools on UseGalaxy.cz: 0 @@ -46361,7 +46687,7 @@ Suite conda package: null Suite first commit date: '2018-06-01' Suite owner: mbernt - Suite parsed folder: https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/longorf + Suite parsed folder: https://github.com/Helmholtz-UFZ/galaxy-tools/tree/master/tools/longorf Suite runs (last 5 years) (usegalaxy.eu): 0 Suite runs (last 5 years) (usegalaxy.fr): 0 Suite runs (last 5 years) (usegalaxy.org): 0 @@ -46433,12 +46759,10 @@ Number of tools on ImmPort Galaxy: 0 Number of tools on InteractoMIX: 0 Number of tools on Lebanese University Galaxy: 0 - Number of tools on MBAC Metabiome Portal: 0 Number of tools on MISSISSIPPI: 0 Number of tools on Mandoiu Lab: 0 Number of tools on Oqtans: 0 Number of tools on Palfinder: 0 - Number of tools on PepSimili: 0 Number of tools on PhagePromotor: 0 Number of tools on UseGalaxy.be: 0 Number of tools on UseGalaxy.cz: 0 @@ -46454,7 +46778,7 @@ Suite conda package: phabox Suite first commit date: '2024-11-12' Suite owner: ufz - Suite parsed folder: https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/phabox + Suite parsed folder: https://github.com/Helmholtz-UFZ/galaxy-tools/tree/master/tools/phabox Suite runs (last 5 years) (usegalaxy.eu): 0 Suite runs (last 5 years) (usegalaxy.fr): 0 Suite runs (last 5 years) (usegalaxy.org): 0 @@ -46520,12 +46844,10 @@ Number of tools on ImmPort Galaxy: 0 Number of tools on InteractoMIX: 0 Number of tools on Lebanese University Galaxy: 0 - Number of tools on MBAC Metabiome Portal: 0 Number of tools on MISSISSIPPI: 0 Number of tools on Mandoiu Lab: 0 Number of tools on Oqtans: 0 Number of tools on Palfinder: 0 - Number of tools on PepSimili: 0 Number of tools on PhagePromotor: 0 Number of tools on UseGalaxy.be: 0 Number of tools on UseGalaxy.cz: 0 @@ -46542,7 +46864,7 @@ Suite conda package: bioconductor-biostrings Suite first commit date: '2025-06-04' Suite owner: ufz - Suite parsed folder: https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/phi-toolkit + Suite parsed folder: https://github.com/Helmholtz-UFZ/galaxy-tools/tree/master/tools/phi-toolkit Suite runs (last 5 years) (usegalaxy.eu): 0 Suite runs (last 5 years) (usegalaxy.fr): 0 Suite runs (last 5 years) (usegalaxy.org): 0 @@ -46564,7 +46886,7 @@ Suite users (usegalaxy.org): 0 Suite users (usegalaxy.org.au): 0 Suite users on main servers: 0 - Suite version: 0.3.0 + Suite version: '@TOOL_VERSION@+galaxy@VERSION_SUFFIX@' Suite version status: To update To keep: true Tool IDs: @@ -46603,12 +46925,10 @@ Number of tools on ImmPort Galaxy: 0 Number of tools on InteractoMIX: 0 Number of tools on Lebanese University Galaxy: 0 - Number of tools on MBAC Metabiome Portal: 0 Number of tools on MISSISSIPPI: 0 Number of tools on Mandoiu Lab: 0 Number of tools on Oqtans: 0 Number of tools on Palfinder: 0 - Number of tools on PepSimili: 0 Number of tools on PhagePromotor: 0 Number of tools on UseGalaxy.be: 0 Number of tools on UseGalaxy.cz: 0 @@ -46624,7 +46944,7 @@ Suite conda package: r-drc Suite first commit date: '2024-04-06' Suite owner: ufz - Suite parsed folder: https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/tox_tools/dose_responses + Suite parsed folder: https://github.com/Helmholtz-UFZ/galaxy-tools/tree/master/tools/tox_tools/dose_responses Suite runs (last 5 years) (usegalaxy.eu): 0 Suite runs (last 5 years) (usegalaxy.fr): 0 Suite runs (last 5 years) (usegalaxy.org): 0 @@ -46646,7 +46966,7 @@ Suite users (usegalaxy.org): 0 Suite users (usegalaxy.org.au): 0 Suite users on main servers: 0 - Suite version: 3.0.1 + Suite version: '@TOOL_VERSION@+galaxy@VERSION_SUFFIX@' Suite version status: To update To keep: true Tool IDs: @@ -46698,12 +47018,10 @@ Number of tools on ImmPort Galaxy: 0 Number of tools on InteractoMIX: 0 Number of tools on Lebanese University Galaxy: 0 - Number of tools on MBAC Metabiome Portal: 0 Number of tools on MISSISSIPPI: 0 Number of tools on Mandoiu Lab: 0 Number of tools on Oqtans: 0 Number of tools on Palfinder: 0 - Number of tools on PepSimili: 0 Number of tools on PhagePromotor: 0 Number of tools on UseGalaxy.be: 0 Number of tools on UseGalaxy.cz: 0 @@ -46721,7 +47039,7 @@ Suite conda package: vibrant Suite first commit date: '2024-09-11' Suite owner: ufz - Suite parsed folder: https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/vibrant + Suite parsed folder: https://github.com/Helmholtz-UFZ/galaxy-tools/tree/master/tools/vibrant Suite runs (last 5 years) (usegalaxy.eu): 1586 Suite runs (last 5 years) (usegalaxy.fr): 0 Suite runs (last 5 years) (usegalaxy.org): 0 @@ -46743,8 +47061,8 @@ Suite users (usegalaxy.org): 0 Suite users (usegalaxy.org.au): 0 Suite users on main servers: 65 - Suite version: 1.2.1 - Suite version status: Up-to-date + Suite version: '@TOOL_VERSION@+galaxy@VERSION_SUFFIX@' + Suite version status: To update To keep: true Tool IDs: - vibrant @@ -46799,12 +47117,10 @@ Number of tools on ImmPort Galaxy: 0 Number of tools on InteractoMIX: 0 Number of tools on Lebanese University Galaxy: 0 - Number of tools on MBAC Metabiome Portal: 0 Number of tools on MISSISSIPPI: 0 Number of tools on Mandoiu Lab: 0 Number of tools on Oqtans: 0 Number of tools on Palfinder: 0 - Number of tools on PepSimili: 0 Number of tools on PhagePromotor: 0 Number of tools on UseGalaxy.be: 0 Number of tools on UseGalaxy.cz: 0 @@ -46822,7 +47138,7 @@ Suite conda package: virsorter Suite first commit date: '2024-06-20' Suite owner: ufz - Suite parsed folder: https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/virsorter + Suite parsed folder: https://github.com/Helmholtz-UFZ/galaxy-tools/tree/master/tools/virsorter Suite runs (last 5 years) (usegalaxy.eu): 2379 Suite runs (last 5 years) (usegalaxy.fr): 0 Suite runs (last 5 years) (usegalaxy.org): 0 @@ -46844,8 +47160,8 @@ Suite users (usegalaxy.org): 0 Suite users (usegalaxy.org.au): 0 Suite users on main servers: 144 - Suite version: 2.2.4 - Suite version status: Up-to-date + Suite version: '@TOOL_VERSION@+galaxy@VERSION_SUFFIX@' + Suite version status: To update To keep: true Tool IDs: - virsorter diff --git a/communities/microgalaxy/resources/curated_tools_w_biotools.tsv b/communities/microgalaxy/resources/curated_tools_w_biotools.tsv index f20d2daae..dedf21280 100644 --- a/communities/microgalaxy/resources/curated_tools_w_biotools.tsv +++ b/communities/microgalaxy/resources/curated_tools_w_biotools.tsv @@ -132,6 +132,7 @@ kraken_taxonomy_report Kraken-Taxonomy-Report Visualisation, Classification Meta krakentools KrakenTools Visualisation, Aggregation Taxonomy, Metagenomics krocus krocus Multilocus sequence typing, k-mer counting Public health and epidemiology legsta legsta Sequence analysis Public health and epidemiology +liftoff Liftoff Genome assembly, Mapping assembly, Mapping Gene transcripts, Sequence assembly, Mapping, Gene expression, RNA immunoprecipitation lighter Lighter k-mer counting, Sequence read processing, Sequencing quality control, Sequencing error detection Sequencing, Whole genome sequencing, DNA, Genomics limma_voom limma RNA-Seq analysis Molecular biology, Genetics lineagespot lineagespot Variant calling Metagenomics, Gene transcripts, Evolutionary biology, Sequencing, Genetic variation @@ -208,13 +209,14 @@ plasflow PlasFlow Sequence analysis Metagenomics, Sequence assembly, Mobile gene plasmidfinder PlasmidFinder Genome assembly, Scaffolding, Multilocus sequence typing Whole genome sequencing, Sequence assembly, Mapping, Probes and primers polypolish Polypolish Genome assembly, Read mapping, Mapping assembly, Sequencing error detection Sequence assembly, Sequence composition, complexity and repeats, Mapping ppanggolin PPanGGOLiN Rarefaction, Essential dynamics, Sequence assembly, Genome annotation Metagenomics, Gene and protein families, Model organisms, Public health and epidemiology, Mapping +prinseq PRINSEQ Read pre-processing, Sequence trimming, Sequence contamination filtering Transcriptomics, Metagenomics, Genomics prodigal Prodigal Genome annotation Genomics, Sequence analysis prokka Prokka Gene prediction, Coding region prediction, Genome annotation Genomics, Model organisms, Virology proteinortho Proteinortho Sequence clustering, Sequence analysis Comparative genomics pycoqc pycoQC Sequencing quality control, Statistical calculation Sequence analysis, Data quality management, Sequencing pygenometracks pyGenomeTracks Visualisation, Formatting Model organisms, Imaging, Workflows -qiime qiime_core Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control Microbial ecology, Phylogeny, Metagenomics, Metatranscriptomics qiime qiime_add_on Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control Microbial ecology, Phylogeny, Metagenomics, Metatranscriptomics +qiime qiime_core Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control Microbial ecology, Phylogeny, Metagenomics, Metatranscriptomics qiime2 QIIME 2 Demultiplexing, Visualisation, Taxonomic classification Microbial ecology, Metatranscriptomics, Metagenomics qiime2 QIIME 2 Demultiplexing, Visualisation, Taxonomic classification Microbial ecology, Metatranscriptomics, Metagenomics qiime2 QIIME 2 Demultiplexing, Visualisation, Taxonomic classification Microbial ecology, Metatranscriptomics, Metagenomics @@ -296,6 +298,7 @@ usher usher Classification, Phylogenetic tree visualisation, Phylogenetic infere valet VALET Sequence assembly, Sequence assembly visualisation Metagenomics, Sequence assembly vapor VAPOR Data retrieval, De-novo assembly, Read mapping Whole genome sequencing, Mapping, Sequence assembly varvamp varVAMP PCR primer design Virology, Probes and primers +vcontact2 vConTACT Deposition, Taxonomic classification, Genome annotation Taxonomy, Metagenomics, Microbial ecology vegan vegan Standardisation and normalisation, Analysis Ecology, Phylogenetics, Environmental science velvet Velvet Formatting, De-novo assembly Sequence assembly vibrant VIBRANT Sequence trimming, Scaffolding, Genome annotation Metagenomics, Microbial ecology, Sequence assembly, Molecular interactions, pathways and networks, Endocrinology and metabolism diff --git a/communities/microgalaxy/resources/curated_tools_wo_biotools.tsv b/communities/microgalaxy/resources/curated_tools_wo_biotools.tsv index 0f43d7a57..6410465b0 100644 --- a/communities/microgalaxy/resources/curated_tools_wo_biotools.tsv +++ b/communities/microgalaxy/resources/curated_tools_wo_biotools.tsv @@ -27,6 +27,7 @@ hivtrace https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace iprscan5 http://www.ebi.ac.uk/Tools/pfa/iprscan5/ https://github.com/bgruening/galaxytools/tree/master/tools/iprscan5 kat_filter kmer2stats https://github.com/SantaMcCloud/kmer2stats https://github.com/galaxyproject/tools-iuc/tree/main/tools/kmer2stats +kneaddata https://github.com/biobakery/kneaddata https://github.com/galaxyproject/tools-iuc/tree/main/tools/kneaddata kraken2tax https://bitbucket.org/natefoo/taxonomy https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/taxonomy/kraken2tax/ lca_wrapper https://bitbucket.org/natefoo/taxonomy https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/lca_wrapper logol http://logol.genouest.org/web/app.php/logol https://github.com/genouest/galaxy-tools/tree/master/tools/logol @@ -35,9 +36,13 @@ longorf https://github.com/bernt-matthias/mb-galaxy-tools/blob/master/tools/lon maaslin3 https://github.com/biobakery/maaslin3 https://github.com/galaxyproject/tools-iuc/tree/main/tools/maaslin3 marine_omics https://github.com/Finn-Lab/SanntiS https://github.com/galaxyecology/tools-ecology/tree/master/tools/marine_omics metasbt https://github.com/cumbof/MetaSBT https://github.com/galaxyproject/tools-iuc/tree/main/tools/metasbt +mgnify_genome_search https://github.com/SantaMcCloud/MGnify-genome-search https://github.com/galaxyproject/tools-iuc/tree/main/tools/mgnify_genome_search +mgnify_pipelines_toolkit https://github.com/EBI-Metagenomics/mgnify-pipelines-toolkit https://github.com/galaxyproject/tools-iuc/tree/main/tools/mgnify_pipelines_toolkit micro_decon https://github.com/donaldtmcknight/microdecon https://github.com/galaxyproject/tools-iuc/tree/main/tools/micro_decon +mist_typing https://github.com/BioinformaticsPlatformWIV-ISP/MiST https://github.com/galaxyproject/tools-iuc/tree/main/tools/mist_typing mrbayes msstatstmt http://msstats.org/msstatstmt/ https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt +mtnucratio https://github.com/TCLamnidis/mtnucratio https://github.com/galaxyproject/tools-iuc/tree/main/tools/mtnucratio mykrobe_parser https://github.com/phac-nml/mykrobe-parser https://github.com/phac-nml/mykrobe-parser ncbi_blast_plus https://blast.ncbi.nlm.nih.gov/ https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus ncbi_egapx https://github.com/ncbi/egapx https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_egapx @@ -52,9 +57,11 @@ pimento https://github.com/EBI-Metagenomics/PIMENTO https://github.com/galaxypro pirate https://github.com/SionBayliss/PIRATE https://github.com/galaxyproject/tools-iuc/tree/main/tools/pirate plasmidspades promer https://github.com/phac-nml/promer https://github.com/phac-nml/promer +psauron https://github.com/salzberg-lab/PSAURON/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/psauron qualifilter https://github.com/galaxyproject/tools-iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualifilter remove_terminal_stop_codons https://github.com/veg/CAPHEINE https://github.com/galaxyproject/tools-iuc/tree/main/tools/remove_terminal_stop_codons repeatexplorer2 https://github.com/repeatexplorer/repex_tarean https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 +samestr https://github.com/danielpodlesny/samestr https://github.com/galaxyproject/tools-iuc/tree/main/tools/samestr smalt http://www.sanger.ac.uk/science/tools/smalt-0 https://sourceforge.net/projects/smalt/ srst2 stringmlst diff --git a/communities/microgalaxy/resources/curated_workflows.json b/communities/microgalaxy/resources/curated_workflows.json index 60e251232..aec524da1 100644 --- a/communities/microgalaxy/resources/curated_workflows.json +++ b/communities/microgalaxy/resources/curated_workflows.json @@ -1,4 +1,104 @@ [ + { + "create_time": "2026-06-18", + "creators": [ + "Tristan Reynolds", + "Ammar Aziz" + ], + "deprecated": false, + "doi": "10.48546/workflowhub.workflow.2196.1", + "edam_operation": [ + "Sequencing quality control", + "Phylogenetic analysis" + ], + "edam_topic": [ + "Bioinformatics", + "Biomedical science", + "Genomics", + "Virology" + ], + "id": "2196", + "keep": true, + "latest_version": 1, + "license": "MIT", + "link": "https://workflowhub.eu/workflows/2196?version=1", + "name": "MPXV (Mpox) Phylogenetic Analysis with Squirrel", + "number_of_steps": 3, + "projects": [ + "Melbourne Bioinformatics", + "Galaxy Australia" + ], + "source": "WorkflowHub", + "tags": [ + "amplicon", + "mpox", + "ont", + "virus", + "mpxv", + "phylogeny" + ], + "tools": [ + "squirrel_phylo", + "regex1", + "squirrel_qc" + ], + "update_time": "2026-06-25", + "versions": 1 + }, + { + "create_time": "2026-06-18", + "creators": [ + "Tristan Reynolds", + "Ammar Aziz" + ], + "deprecated": false, + "doi": "10.48546/workflowhub.workflow.2195.1", + "edam_operation": [ + "Sequencing quality control", + "Sequence alignment", + "Validation", + "Mapping" + ], + "edam_topic": [ + "Bioinformatics", + "Biomedical science", + "Genomics", + "Virology" + ], + "id": "2195", + "keep": true, + "latest_version": 1, + "license": "MIT", + "link": "https://workflowhub.eu/workflows/2195?version=1", + "name": "Viral Amplicon Analysis Pipeline for ONT Data", + "number_of_steps": 12, + "projects": [ + "Melbourne Bioinformatics", + "Galaxy Australia" + ], + "source": "WorkflowHub", + "tags": [ + "amplicon", + "mpox", + "ont", + "virus", + "mpxv", + "phylogeny" + ], + "tools": [ + "artic_minion", + "multiqc", + "mosdepth", + "XY_Plot_1", + "regex1", + "__BUILD_LIST__", + "tp_cat", + "fastplong", + "bedtools_makewindowsbed" + ], + "update_time": "2026-06-25", + "versions": 1 + }, { "create_time": "2026-03-02", "creators": [ @@ -8,10 +108,10 @@ "deprecated": false, "doi": "10.48546/workflowhub.workflow.2098.1", "edam_operation": [ - "Visualisation", + "Taxonomic classification", "Formatting", "Demultiplexing", - "Taxonomic classification" + "Visualisation" ], "edam_topic": [ "Taxonomy" @@ -34,20 +134,20 @@ "taxonomic-classification" ], "tools": [ - "qiime2__feature_classifier__classify_sklearn", - "qiime2__feature_table__summarize", - "qiime2_core__tools__import", - "qiime2__taxa__barplot", - "qiime2__feature_classifier__fit_classifier_naive_bayes", "qiime2__feature_table__tabulate_seqs", - "qiime2__feature_classifier__extract_reads", + "biom_convert", "csv_to_tabular", "tp_easyjoin_tool", - "Remove beginning1", - "biom_convert", + "qiime2_core__tools__import", + "qiime2__feature_classifier__classify_sklearn", + "qiime2__feature_table__summarize", + "tabular_to_csv", + "qiime2__taxa__barplot", "qiime_extract_viz", + "qiime2__feature_classifier__fit_classifier_naive_bayes", "qiime2_core__tools__export", - "tabular_to_csv" + "qiime2__feature_classifier__extract_reads", + "Remove beginning1" ], "update_time": "2026-05-13", "versions": 1 @@ -62,11 +162,11 @@ "doi": null, "edam_operation": [ "Data parsing", - "Gene functional annotation", - "Validation", "Taxonomic classification", + "Gene functional annotation", "Sequencing quality control", - "Antimicrobial resistance prediction" + "Antimicrobial resistance prediction", + "Validation" ], "edam_topic": [], "id": "2068", @@ -82,23 +182,23 @@ "source": "WorkflowHub", "tags": [], "tools": [ - "table_pandas_rename_column", - "multiqc", + "tooldistillator_summarize", + "__RELABEL_FROM_FILE__", "groot", "collection_element_identifiers", - "tooldistillator_summarize", - "tooldistillator", - "Remove a collection level so that outputs can be taken into account by tooldistillator\n__FLATTEN__", - "__FILTER_FAILED_DATASETS__", - "tp_text_file_with_recurring_lines", - "__UNZIP_COLLECTION__", "sylph_profile", + "deeparg_short_reads", + "fastq_paired_end_interlacer", "argnorm", - "__RELABEL_FROM_FILE__", + "table_pandas_rename_column", + "multiqc", "Removal of the first line because it is not necessary for tooldistillator\nRemove beginning1", + "tp_text_file_with_recurring_lines", + "tooldistillator", + "__UNZIP_COLLECTION__", "Removal of the first argNorm line that causes a multiQC error\nRemove beginning1", - "fastq_paired_end_interlacer", - "deeparg_short_reads" + "__FILTER_FAILED_DATASETS__", + "Remove a collection level so that outputs can be taken into account by tooldistillator\n__FLATTEN__" ], "update_time": "2026-05-14", "versions": 2 @@ -113,8 +213,8 @@ "deprecated": false, "doi": null, "edam_operation": [ - "Multilocus sequence typing", - "Data parsing" + "Data parsing", + "Multilocus sequence typing" ], "edam_topic": [], "id": "2055", @@ -130,9 +230,9 @@ "source": "WorkflowHub", "tags": [], "tools": [ - "coreprofiler_allele_calling", + "tooldistillator", "tooldistillator_summarize", - "tooldistillator" + "coreprofiler_allele_calling" ], "update_time": "2026-05-14", "versions": 2 @@ -143,19 +243,19 @@ "deprecated": false, "doi": null, "edam_operation": [ - "Phylogenetic tree visualisation", - "Sequence alignment", - "Validation", + "Taxonomic classification", "Antimicrobial resistance prediction", - "Phylogenetic tree generation", "Variant calling", - "Sequence analysis", - "Local alignment", + "Sequence alignment", + "Phylogenetic tree visualisation", + "Sequencing quality control", "Sequence contamination filtering", - "Global alignment", "Sequence alignment analysis", - "Taxonomic classification", - "Sequencing quality control" + "Phylogenetic tree generation", + "Validation", + "Global alignment", + "Sequence analysis", + "Local alignment" ], "edam_topic": [], "id": "1647", @@ -176,20 +276,20 @@ "tuberculosis" ], "tools": [ - "bcftools_consensus", + "fastp", "tp_awk_tool", - "tb_profiler_profile", + "qualimap_bamqc", + "EMBOSS: seqret84", "kraken2", - "__FLATTEN__", - "multiqc", "mosdepth", + "__FLATTEN__", + "tp_sed_tool", "snippy", - "qualimap_bamqc", + "multiqc", + "bcftools_consensus", "tb_variant_filter", - "tbvcfreport", - "fastp", - "tp_sed_tool", - "EMBOSS: seqret84" + "tb_profiler_profile", + "tbvcfreport" ], "update_time": "2026-01-12", "versions": 2 @@ -200,14 +300,14 @@ "deprecated": false, "doi": null, "edam_operation": [ - "Visualisation", "Statistical calculation", - "Read mapping", - "Cross-assembly", - "Sequence contamination filtering", - "Expression analysis", "Taxonomic classification", - "Sequencing quality control" + "Expression analysis", + "Sequencing quality control", + "Sequence contamination filtering", + "Read mapping", + "Visualisation", + "Cross-assembly" ], "edam_topic": [], "id": "2043", @@ -227,11 +327,11 @@ "sequence-analysis" ], "tools": [ - "falco", - "kraken2", - "est_abundance", "fastp", - "recentrifuge" + "recentrifuge", + "est_abundance", + "kraken2", + "falco" ], "update_time": "2025-12-22", "versions": 1 @@ -242,11 +342,11 @@ "deprecated": false, "doi": null, "edam_operation": [ - "Visualisation", "Statistical calculation", "Taxonomic classification", + "Aggregation", "Genome annotation", - "Aggregation" + "Visualisation" ], "edam_topic": [], "id": "1470", @@ -266,15 +366,15 @@ "microbiome" ], "tools": [ - "interactive_tool_phinch", "metaphlan", - "kraken2", "taxonomy_krona_chart", "krakentools_kreport2krona", - "__UNZIP_COLLECTION__", "est_abundance", - "interactive_tool_pavian", - "kraken_biom" + "kraken_biom", + "kraken2", + "interactive_tool_phinch", + "__UNZIP_COLLECTION__", + "interactive_tool_pavian" ], "update_time": "2025-12-22", "versions": 2 @@ -285,10 +385,10 @@ "deprecated": false, "doi": null, "edam_operation": [ - "Cross-assembly", "Statistical calculation", "Taxonomic classification", - "Expression analysis" + "Expression analysis", + "Cross-assembly" ], "edam_topic": [], "id": "1674", @@ -308,9 +408,9 @@ "galaxy" ], "tools": [ - "kraken2", "est_abundance", - "recentrifuge" + "recentrifuge", + "kraken2" ], "update_time": "2025-12-22", "versions": 2 @@ -323,8 +423,8 @@ "edam_operation": [ "Sequence assembly", "Read mapping", - "Genome annotation", "Sequence clustering", + "Genome annotation", "Read binning" ], "edam_topic": [], @@ -348,19 +448,19 @@ ], "tools": [ "bowtie2", - "metabat2", - "__BUILD_LIST__", "concoct_coverage_table", - "metabat2_jgi_summarize_bam_contig_depths", + "concoct_merge_cut_up_clustering", "concoct_extract_fasta_bins", - "semibin", - "concoct", + "concoct_cut_up_fasta", "samtools_sort", - "maxbin2", - "binette", "Fasta_to_Contig2Bin", - "concoct_merge_cut_up_clustering", - "concoct_cut_up_fasta" + "concoct", + "__BUILD_LIST__", + "binette", + "semibin", + "maxbin2", + "metabat2", + "metabat2_jgi_summarize_bam_contig_depths" ], "update_time": "2025-12-08", "versions": 1 @@ -375,16 +475,16 @@ "deprecated": false, "doi": null, "edam_operation": [ - "Visualisation", - "Sequence composition calculation", - "Sequence assembly validation", "Statistical calculation", - "Validation", - "Cross-assembly", - "Data parsing", - "Expression analysis", "Taxonomic classification", - "Sequencing quality control" + "Expression analysis", + "Sequence assembly validation", + "Data parsing", + "Sequencing quality control", + "Validation", + "Sequence composition calculation", + "Visualisation", + "Cross-assembly" ], "edam_topic": [], "id": "1882", @@ -400,15 +500,15 @@ "source": "WorkflowHub", "tags": [], "tools": [ - "pick_value", - "kraken2", "tooldistillator_summarize", - "tooldistillator", + "recentrifuge", + "checkm2", "est_abundance", - "quast", + "kraken2", + "pick_value", "collapse_dataset", - "checkm2", - "recentrifuge" + "tooldistillator", + "quast" ], "update_time": "2026-05-13", "versions": 3 @@ -421,19 +521,19 @@ "deprecated": false, "doi": null, "edam_operation": [ - "Methylation analysis", + "Read mapping", + "Generation", + "Variant classification", + "Variant calling", + "Tree-based sequence alignment", "Sequence alignment", "Genome indexing", - "SNP detection", + "Sequencing quality control", + "Sequence contamination filtering", "Validation", - "Read mapping", - "Variant calling", + "Methylation analysis", "Primer removal", - "Sequence contamination filtering", - "Generation", - "Tree-based sequence alignment", - "Variant classification", - "Sequencing quality control" + "SNP detection" ], "edam_topic": [], "id": "155", @@ -451,21 +551,21 @@ "virology" ], "tools": [ - "ivar_consensus", + "fastp", + "ivar_variants", + "nextclade", + "ivar_trim", "samtools_view", + "ivar_consensus", + "qualimap_bamqc", "multiqc", "__FLATTEN__", - "nextclade", - "samtools_stats", - "pangolin", - "bwa_mem", - "qualimap_bamqc", - "ivar_trim", - "fastp", + "tp_sed_tool", "snpeff_sars_cov_2", + "samtools_stats", "tp_cat", - "tp_sed_tool", - "ivar_variants" + "pangolin", + "bwa_mem" ], "update_time": "2026-05-13", "versions": 7 @@ -479,14 +579,14 @@ "doi": null, "edam_operation": [ "Formatting", + "Generation", "Sequence alignment", "Genome indexing", - "SNP detection", + "Sequencing quality control", + "Sequence contamination filtering", "Validation", "Read mapping", - "Sequence contamination filtering", - "Generation", - "Sequencing quality control" + "SNP detection" ], "edam_topic": [], "id": "113", @@ -507,17 +607,17 @@ "emergen_validated" ], "tools": [ + "lofreq_filter", + "fastp", + "picard_MarkDuplicates", + "lofreq_viterbi", "samtools_view", + "lofreq_call", "multiqc", + "snpeff_sars_cov_2", "samtools_stats", - "bwa_mem", - "lofreq_viterbi", "lofreq_indelqual", - "fastp", - "picard_MarkDuplicates", - "lofreq_call", - "lofreq_filter", - "snpeff_sars_cov_2" + "bwa_mem" ], "update_time": "2026-05-14", "versions": 4 @@ -531,14 +631,14 @@ "deprecated": false, "doi": null, "edam_operation": [ - "Sequence alignment", - "Genome indexing", + "Sequencing quality control", + "Sequence contamination filtering", + "Generation", "Validation", "Read mapping", + "Sequence alignment", "Primer removal", - "Sequence contamination filtering", - "Generation", - "Sequencing quality control" + "Genome indexing" ], "edam_topic": [], "id": "1876", @@ -556,28 +656,28 @@ "virology" ], "tools": [ + "ivar_variants", + "__FLATTEN__", + "snpSift_extractFields", + "map_param_value", + "collapse_dataset", + "tp_cat", + "fastp", "samtools_view", - "__FILTER_FAILED_DATASETS__", - "qualimap_bamqc", - "tp_sed_tool", "snpEff", - "__FLATTEN__", + "tp_find_and_replace", + "calculate_numeric_param", "samtools_stats", - "bwa_mem", "lofreq_viterbi", - "calculate_numeric_param", - "collapse_dataset", - "ivar_variants", + "snpEff_build_gb", "ivar_consensus", - "tp_find_and_replace", - "map_param_value", - "ivar_trim", - "fastp", - "tp_cat", - "snpSift_extractFields", "pick_value", + "ivar_trim", + "qualimap_bamqc", "multiqc", - "snpEff_build_gb" + "tp_sed_tool", + "__FILTER_FAILED_DATASETS__", + "bwa_mem" ], "update_time": "2026-05-13", "versions": 2 @@ -593,22 +693,22 @@ "deprecated": false, "doi": null, "edam_operation": [ + "Data retrieval", + "Generation", "Multiple sequence alignment", - "Sequence alignment", - "Genome indexing", + "Data handling", + "De-novo assembly", "Sequence file editing", - "Phylogenetic analysis", - "Read mapping", - "Sequence analysis", - "Primer removal", + "Sequence alignment", "Base position variability plotting", + "Genome indexing", + "Sequencing quality control", "Sequence contamination filtering", - "Data retrieval", "Sequence alignment analysis", - "Data handling", - "Generation", - "Sequencing quality control", - "De-novo assembly" + "Sequence analysis", + "Read mapping", + "Primer removal", + "Phylogenetic analysis" ], "edam_topic": [], "id": "1260", @@ -626,41 +726,41 @@ "virology" ], "tools": [ - "wc_gnu", - "samtools_view", - "__FILTER_FAILED_DATASETS__", - "tp_text_file_with_recurring_lines", - "qualimap_bamqc", - "bwa mem will fail if no reference for any segment got suggested by vapor, i.e. the reference genome is empty. In that case, we need to skip further analysis of the sample.\n__FILTER_FAILED_DATASETS__", - "__HARMONIZELISTS__", - "Show beginning1", - "Filter1", - "__FLATTEN__", "collection_element_identifiers", - "bwa_mem", - "__RELABEL_FROM_FILE__", - "__APPLY_RULES__", - "__MERGE_COLLECTION__", - "collapse_dataset", "Paste1", - "bamtools_split_ref", + "__FLATTEN__", "snipit", - "Grep1", - "ivar_consensus", + "bwa mem will fail if no reference for any segment got suggested by vapor, i.e. the reference genome is empty. In that case, we need to skip further analysis of the sample.\n__FILTER_FAILED_DATASETS__", + "collapse_dataset", + "bamtools_split_ref", + "tp_cat", + "Show beginning1", "param_value_from_file", - "tp_find_and_replace", - "__UNZIP_COLLECTION__", - "tp_easyjoin_tool", "fastp", - "tp_cat", - "Cut1", + "samtools_view", + "tp_find_and_replace", "rbc_mafft", + "tp_text_file_with_recurring_lines", + "__APPLY_RULES__", "__FILTER_FROM_FILE__", - "vapor", + "ivar_consensus", + "__HARMONIZELISTS__", + "__DUPLICATE_FILE_TO_COLLECTION__", "This seemingly no-op transformation will remove samples with no remaining segment results (cases where vapor failed for every segment).\n__APPLY_RULES__", - "seqtk_subseq", + "Grep1", "iqtree", - "__DUPLICATE_FILE_TO_COLLECTION__" + "vapor", + "__RELABEL_FROM_FILE__", + "wc_gnu", + "seqtk_subseq", + "tp_easyjoin_tool", + "qualimap_bamqc", + "__MERGE_COLLECTION__", + "__UNZIP_COLLECTION__", + "__FILTER_FAILED_DATASETS__", + "Filter1", + "Cut1", + "bwa_mem" ], "update_time": "2026-05-13", "versions": 3 @@ -674,18 +774,18 @@ "deprecated": false, "doi": null, "edam_operation": [ + "Generation", "Sequence alignment", "Genome indexing", + "Sequencing quality control", + "Sequence contamination filtering", + "Sequence alignment analysis", "Validation", - "Read mapping", + "Global alignment", "Sequence analysis", + "Read mapping", "Primer removal", - "Local alignment", - "Sequence contamination filtering", - "Global alignment", - "Sequence alignment analysis", - "Generation", - "Sequencing quality control" + "Local alignment" ], "edam_topic": [], "id": "439", @@ -704,31 +804,31 @@ "pox" ], "tools": [ - "compose_text_param", + "collection_element_identifiers", + "__FLATTEN__", + "EMBOSS: maskseq51", + "tp_cat", + "datamash_ops", + "param_value_from_file", + "fastp", "samtools_view", - "__FILTER_FAILED_DATASETS__", - "qualimap_bamqc", - "tp_sed_tool", - "fasta_compute_length", "samtools_merge", - "__FLATTEN__", - "collection_element_identifiers", "samtools_stats", - "bwa_mem", "__APPLY_RULES__", "__ZIP_COLLECTION__", - "Grep1", "ivar_consensus", - "param_value_from_file", - "split_file_to_collection", - "ivar_trim", - "fastp", - "tp_cat", - "Cut1", "__SORTLIST__", - "EMBOSS: maskseq51", + "Grep1", + "fasta_compute_length", + "ivar_trim", + "qualimap_bamqc", "multiqc", - "datamash_ops" + "split_file_to_collection", + "compose_text_param", + "tp_sed_tool", + "__FILTER_FAILED_DATASETS__", + "Cut1", + "bwa_mem" ], "update_time": "2026-05-13", "versions": 4 @@ -740,8 +840,8 @@ "doi": null, "edam_operation": [ "k-mer counting", - "Visualisation", "Formatting", + "Visualisation", "Mapping" ], "edam_topic": [], @@ -766,10 +866,10 @@ ], "tools": [ "", - "tp_awk_tool", - "__FILTER_FROM_FILE__", "bedtools_maskfastabed", "mapseq", + "tp_awk_tool", + "__FILTER_FROM_FILE__", "collection_element_identifiers", "taxonomy_krona_chart", "biom_convert", @@ -784,8 +884,8 @@ "deprecated": false, "doi": null, "edam_operation": [ - "Visualisation", - "Analysis" + "Analysis", + "Visualisation" ], "edam_topic": [], "id": "1855", @@ -805,10 +905,10 @@ "microbiome" ], "tools": [ - "collection_column_join", - "ampvis2_load", "tp_awk_tool", + "collection_column_join", "collapse_dataset", + "ampvis2_load", "query_tabular" ], "update_time": "2025-08-11", @@ -820,14 +920,14 @@ "deprecated": false, "doi": null, "edam_operation": [ - "Sequence trimming", - "Sequence composition calculation", - "Nucleic acid design", "Statistical calculation", + "Sequencing quality control", + "Sequence contamination filtering", + "Sequence trimming", "Validation", + "Nucleic acid design", "Read pre-processing", - "Sequence contamination filtering", - "Sequencing quality control" + "Sequence composition calculation" ], "edam_topic": [], "id": "1854", @@ -850,17 +950,17 @@ "name:microgalaxy" ], "tools": [ + "fastp", "cshl_fasta_formatter", "tp_find_and_replace", - "fastq_to_fasta_python", "multiqc", + "trimmomatic", "fastqc", "__UNZIP_COLLECTION__", - "prinseq", "mgnify_seqprep", - "fastp", - "trimmomatic", - "fastq_filter" + "fastq_filter", + "prinseq", + "fastq_to_fasta_python" ], "update_time": "2025-08-11", "versions": 1 @@ -893,11 +993,11 @@ ], "tools": [ "", - "fastq_dl", - "CONVERTER_uncompressed_to_gz", "tp_awk_tool", + "CONVERTER_uncompressed_to_gz", "CONVERTER_gz_to_uncompressed", - "__MERGE_COLLECTION__" + "__MERGE_COLLECTION__", + "fastq_dl" ], "update_time": "2025-08-11", "versions": 1 @@ -929,9 +1029,9 @@ "name:microgalaxy" ], "tools": [ - "Grouping1", - "collection_column_join", "tp_awk_tool", + "collection_column_join", + "Grouping1", "filter_tabular", "query_tabular" ], @@ -944,13 +1044,13 @@ "deprecated": false, "doi": null, "edam_operation": [ - "Sequence trimming", - "Read pre-processing", - "Sequence composition calculation", - "Sequence contamination filtering", + "Sequencing quality control", "Statistical calculation", + "Sequence contamination filtering", + "Sequence trimming", "Validation", - "Sequencing quality control" + "Read pre-processing", + "Sequence composition calculation" ], "edam_topic": [], "id": "1850", @@ -975,12 +1075,12 @@ "tools": [ "cshl_fasta_formatter", "tp_find_and_replace", - "fastq_to_fasta_python", "multiqc", + "trimmomatic", "fastqc", + "fastq_filter", "prinseq", - "trimmomatic", - "fastq_filter" + "fastq_to_fasta_python" ], "update_time": "2025-08-11", "versions": 1 @@ -991,13 +1091,13 @@ "deprecated": false, "doi": null, "edam_operation": [ - "Visualisation", - "Alignment", - "Formatting", - "Mapping", "k-mer counting", + "Formatting", "Comparison", - "Nucleic acid feature detection" + "Mapping", + "Alignment", + "Nucleic acid feature detection", + "Visualisation" ], "edam_topic": [], "id": "1842", @@ -1021,19 +1121,19 @@ ], "tools": [ "", - "bedtools_getfastabed", - "tp_awk_tool", "cshl_fasta_formatter", - "__FILTER_FROM_FILE__", - "infernal_cmsearch", + "tp_awk_tool", "mapseq", "collection_element_identifiers", + "__FILTER_FROM_FILE__", "taxonomy_krona_chart", - "cmsearch_deoverlap", "biom_convert", + "cmsearch_deoverlap", + "infernal_cmsearch", + "bedtools_getfastabed", "gops_concat_1", - "__FILTER_EMPTY_DATASETS__", - "query_tabular" + "query_tabular", + "__FILTER_EMPTY_DATASETS__" ], "update_time": "2025-08-11", "versions": 1 @@ -1044,8 +1144,8 @@ "deprecated": false, "doi": null, "edam_operation": [ - "Species frequency estimation", "Taxonomic classification", + "Species frequency estimation", "Phylogenetic analysis" ], "edam_topic": [], @@ -1067,15 +1167,15 @@ "metagenomics" ], "tools": [ - "Grep1", "humann_rename_table", + "humann_regroup_table", "tp_find_and_replace", "combine_metaphlan2_humann2", - "Cut1", - "humann_renorm_table", - "humann_regroup_table", "humann_unpack_pathways", - "humann_split_stratified_table" + "humann_split_stratified_table", + "humann_renorm_table", + "Grep1", + "Cut1" ], "update_time": "2025-07-14", "versions": 2 @@ -1086,11 +1186,11 @@ "deprecated": false, "doi": null, "edam_operation": [ - "Visualisation", "DNA barcoding", - "Deposition", "Analysis", - "Variant calling" + "Variant calling", + "Deposition", + "Visualisation" ], "edam_topic": [], "id": "1395", @@ -1110,24 +1210,24 @@ "microbiome" ], "tools": [ - "dada2_filterAndTrim", + "dada2_dada", + "Add_a_column1", + "dada2_makeSequenceTable", + "dada2_plotQualityProfile", + "collection_element_identifiers", + "__SORTLIST__", "dada2_learnErrors", + "tp_replace_in_line", + "dada2_seqCounts", "dada2_assignTaxonomyAddspecies", + "cat1", + "dada2_filterAndTrim", + "__UNZIP_COLLECTION__", "tp_replace_in_column", - "collection_element_identifiers", "phyloseq_from_dada2", - "dada2_makeSequenceTable", - "dada2_seqCounts", - "tp_replace_in_line", - "__UNZIP_COLLECTION__", - "dada2_dada", - "dada2_mergePairs", - "dada2_removeBimeraDenovo", - "cat1", - "Add_a_column1", "tp_head_tool", - "dada2_plotQualityProfile", - "__SORTLIST__" + "dada2_removeBimeraDenovo", + "dada2_mergePairs" ], "update_time": "2025-07-07", "versions": 2 @@ -1138,25 +1238,25 @@ "deprecated": false, "doi": null, "edam_operation": [ - "Sequence comparison", - "Phylogenetic tree visualisation", - "Visualisation", - "Sequence composition calculation", "Statistical calculation", "Phylogenetic inference", - "Validation", - "Primer removal", - "Sequence alignment analysis", + "Conversion", "Sequencing quality control", + "Sequence alignment analysis", + "Sequence comparison", + "Sequence composition calculation", "Phylogenetic analysis", - "Sequence trimming", - "Phylogenetic tree editing", - "Read pre-processing", - "Species frequency estimation", "Taxonomic classification", + "Aggregation", + "Species frequency estimation", + "Phylogenetic tree visualisation", "Sequence similarity search", - "Conversion", - "Aggregation" + "Phylogenetic tree editing", + "Sequence trimming", + "Validation", + "Read pre-processing", + "Primer removal", + "Visualisation" ], "edam_topic": [], "id": "1466", @@ -1176,28 +1276,28 @@ "microbiome" ], "tools": [ - "Grouping1", - "metaphlan", - "fastqc", - "tp_sort_header_tool", - "humann", - "humann_unpack_pathways", - "graphlan", - "Grep1", - "humann_rename_table", - "tp_find_and_replace", - "combine_metaphlan_humann", - "Cut1", + "graphlan_annotate", "bg_sortmerna", - "fastq_paired_end_interlacer", - "humann_split_stratified_table", - "multiqc", "cutadapt", "taxonomy_krona_chart", - "graphlan_annotate", - "humann_renorm_table", + "tp_find_and_replace", + "export2graphlan", + "humann_split_stratified_table", + "metaphlan", "humann_regroup_table", - "export2graphlan" + "fastq_paired_end_interlacer", + "Grouping1", + "humann_renorm_table", + "Grep1", + "graphlan", + "humann", + "tp_sort_header_tool", + "humann_rename_table", + "multiqc", + "fastqc", + "humann_unpack_pathways", + "combine_metaphlan_humann", + "Cut1" ], "update_time": "2025-06-23", "versions": 2 @@ -1208,12 +1308,12 @@ "deprecated": false, "doi": null, "edam_operation": [ - "Phylogenetic tree visualisation", - "Visualisation", + "Taxonomic classification", "Phylogenetic inference", + "Conversion", + "Phylogenetic tree visualisation", "Phylogenetic tree editing", - "Taxonomic classification", - "Conversion" + "Visualisation" ], "edam_topic": [], "id": "1451", @@ -1233,12 +1333,12 @@ "microbiome" ], "tools": [ - "graphlan", "metaphlan", - "taxonomy_krona_chart", "graphlan_annotate", + "taxonomy_krona_chart", + "export2graphlan", "Cut1", - "export2graphlan" + "graphlan" ], "update_time": "2025-06-23", "versions": 2 @@ -1249,16 +1349,16 @@ "deprecated": false, "doi": null, "edam_operation": [ - "Sequence trimming", - "Sequence composition calculation", "Statistical calculation", - "Validation", - "Primer removal", - "Read pre-processing", "Sequence similarity search", + "Primer removal", + "Sequencing quality control", + "Sequence trimming", "Sequence alignment analysis", "Sequence comparison", - "Sequencing quality control" + "Validation", + "Read pre-processing", + "Sequence composition calculation" ], "edam_topic": [], "id": "1444", @@ -1278,11 +1378,11 @@ "microbiome" ], "tools": [ + "fastq_paired_end_interlacer", "multiqc", "fastqc", - "cutadapt", "bg_sortmerna", - "fastq_paired_end_interlacer" + "cutadapt" ], "update_time": "2025-06-23", "versions": 2 @@ -1293,8 +1393,8 @@ "deprecated": false, "doi": null, "edam_operation": [ - "Species frequency estimation", "Taxonomic classification", + "Species frequency estimation", "Phylogenetic analysis" ], "edam_topic": [], @@ -1315,15 +1415,15 @@ "microbiome" ], "tools": [ - "Grep1", "humann_rename_table", - "humann", - "tp_find_and_replace", - "humann_renorm_table", - "tp_sort_header_tool", "humann_regroup_table", + "tp_find_and_replace", "humann_unpack_pathways", - "humann_split_stratified_table" + "humann_split_stratified_table", + "humann_renorm_table", + "Grep1", + "humann", + "tp_sort_header_tool" ], "update_time": "2025-06-23", "versions": 2 @@ -1335,11 +1435,11 @@ "doi": null, "edam_operation": [ "Visualisation", - "Local alignment", - "Sequence assembly validation", "Read mapping", - "Genome assembly", - "Sequence assembly visualisation" + "Sequence assembly validation", + "Sequence assembly visualisation", + "Local alignment", + "Genome assembly" ], "edam_topic": [], "id": "1390", @@ -1359,15 +1459,15 @@ "microbiome" ], "tools": [ - "collection_column_join", "bowtie2", "megahit_contig2fastg", - "bandage_info", - "bandage_image", + "collection_column_join", "metaspades", - "quast", + "bandage_image", + "bandage_info", + "megahit", "coverm_contig", - "megahit" + "quast" ], "update_time": "2025-06-16", "versions": 2 @@ -1378,8 +1478,8 @@ "deprecated": false, "doi": null, "edam_operation": [ - "Sequence contamination filtering", - "Sequencing quality control" + "Sequencing quality control", + "Sequence contamination filtering" ], "edam_topic": [], "id": "1723", @@ -1399,10 +1499,10 @@ "galaxy" ], "tools": [ - "ncbi_blastn_wrapper", - "Count1", + "fastp", "cshl_fastq_to_fasta", - "fastp" + "ncbi_blastn_wrapper", + "Count1" ], "update_time": "2025-06-02", "versions": 1 @@ -1413,14 +1513,14 @@ "deprecated": false, "doi": null, "edam_operation": [ - "Visualisation", "Statistical calculation", - "Read mapping", - "Cross-assembly", - "Sequence contamination filtering", - "Expression analysis", "Taxonomic classification", - "Sequencing quality control" + "Expression analysis", + "Sequencing quality control", + "Sequence contamination filtering", + "Read mapping", + "Visualisation", + "Cross-assembly" ], "edam_topic": [], "id": "1644", @@ -1440,11 +1540,11 @@ "sequence-analysis" ], "tools": [ - "falco", - "kraken2", - "est_abundance", "fastp", - "recentrifuge" + "recentrifuge", + "est_abundance", + "kraken2", + "falco" ], "update_time": "2025-06-02", "versions": 1 @@ -1455,11 +1555,11 @@ "deprecated": false, "doi": null, "edam_operation": [ - "Local alignment", - "Sequence alignment", - "Global alignment", "Sequence alignment analysis", - "Sequence analysis" + "Global alignment", + "Sequence analysis", + "Sequence alignment", + "Local alignment" ], "edam_topic": [], "id": "1632", @@ -1479,14 +1579,14 @@ "variant-analysis" ], "tools": [ - "Grep1", - "param_value_from_file", + "Add_a_column1", "compose_text_param", "EMBOSS: maskseq51", + "Grep1", "datamash_ops", - "Cut1", "fasta_compute_length", - "Add_a_column1" + "Cut1", + "param_value_from_file" ], "update_time": "2025-06-02", "versions": 1 @@ -1497,16 +1597,16 @@ "deprecated": false, "doi": null, "edam_operation": [ + "Pairwise sequence alignment", "Aggregation", - "Mapping assembly", "Antimicrobial resistance prediction", - "Sequence analysis", "Box-Whisker plot plotting", - "Pairwise sequence alignment", - "Genome assembly", - "Sequence assembly visualisation", + "De-novo assembly", "Scatter plot plotting", - "De-novo assembly" + "Sequence assembly visualisation", + "Sequence analysis", + "Mapping assembly", + "Genome assembly" ], "edam_topic": [], "id": "1477", @@ -1527,14 +1627,14 @@ ], "tools": [ "unicycler", - "racon", - "staramr_search", - "miniasm", - "nanoplot", "bandage_image", + "miniasm", + "staramr_search", "PlasFlow", - "gfa_to_fa", - "minimap2" + "nanoplot", + "minimap2", + "racon", + "gfa_to_fa" ], "update_time": "2025-06-02", "versions": 1 @@ -1545,13 +1645,13 @@ "deprecated": false, "doi": null, "edam_operation": [ - "Visualisation", - "Sequence clustering", - "DNA barcoding", "Taxonomic classification", + "DNA barcoding", "Sequence read processing", "Sequencing quality control", - "Phylogenetic analysis" + "Sequence clustering", + "Phylogenetic analysis", + "Visualisation" ], "edam_topic": [], "id": "1476", @@ -1571,21 +1671,21 @@ "microbiome" ], "tools": [ - "mothur_pre_cluster", - "mothur_make_group", + "mothur_unique_seqs", + "mothur_cluster_split", "mothur_summary_seqs", "mothur_count_seqs", - "mothur_unique_seqs", + "mothur_make_shared", + "mothur_make_biom", "mothur_merge_files", - "mothur_align_seqs", - "mothur_filter_seqs", - "mothur_cluster_split", "mothur_screen_seqs", + "mothur_filter_seqs", + "mothur_make_group", "mothur_classify_seqs", - "mothur_make_shared", - "krona-text", "mothur_classify_otu", - "mothur_make_biom" + "mothur_align_seqs", + "mothur_pre_cluster", + "krona-text" ], "update_time": "2025-06-02", "versions": 1 @@ -1596,13 +1696,13 @@ "deprecated": false, "doi": null, "edam_operation": [ - "Visualisation", - "Sequence composition calculation", + "Sequencing quality control", "Sequence contamination filtering", + "Taxonomic classification", "Statistical calculation", "Validation", - "Taxonomic classification", - "Sequencing quality control" + "Sequence composition calculation", + "Visualisation" ], "edam_topic": [], "id": "1473", @@ -1622,15 +1722,15 @@ "microbiome" ], "tools": [ + "fastp", + "datamash_reverse", + "taxonomy_krona_chart", "multiqc", "kraken2", + "tp_replace_in_line", "fastqc", - "taxonomy_krona_chart", "porechop", - "tp_replace_in_line", - "fastp", - "Remove beginning1", - "datamash_reverse" + "Remove beginning1" ], "update_time": "2025-06-02", "versions": 1 @@ -1661,12 +1761,12 @@ "microbiome" ], "tools": [ - "humann2", - "taxonomy_krona_chart", "metaphlan2krona", + "metaphlan2", "humann2_renorm_table", - "humann2_regroup_table", - "metaphlan2" + "taxonomy_krona_chart", + "humann2", + "humann2_regroup_table" ], "update_time": "2025-06-02", "versions": 1 @@ -1677,8 +1777,8 @@ "deprecated": false, "doi": null, "edam_operation": [ - "Visualisation", - "Pairwise sequence alignment" + "Pairwise sequence alignment", + "Visualisation" ], "edam_topic": [], "id": "1469", @@ -1700,24 +1800,24 @@ "name:microgalaxy" ], "tools": [ - "Grouping1", + "Add_a_column1", "CONVERTER_fasta_to_tabular", "tp_sorted_uniq", - "sort1", - "Filter1", - "MQoutputfilter", - "tp_replace_in_column", "histogram_rpy", - "tp_tail_tool", "join1", + "Grouping1", + "cat1", + "tp_tail_tool", "count_gff_features", + "ggplot2_histogram", + "minimap2", + "add_column_headers", + "tp_replace_in_column", + "Filter1", "tab2fasta", "Cut1", - "cat1", - "add_column_headers", - "Add_a_column1", - "ggplot2_histogram", - "minimap2" + "MQoutputfilter", + "sort1" ], "update_time": "2025-06-02", "versions": 1 @@ -1728,16 +1828,16 @@ "deprecated": false, "doi": null, "edam_operation": [ - "Visualisation", - "Phylogenetic tree reconstruction", - "Sequence clustering", - "Phylogenetic tree generation", - "DNA barcoding", - "Phylogenetic tree analysis", "Taxonomic classification", + "DNA barcoding", "Sequence read processing", "Sequencing quality control", - "Phylogenetic analysis" + "Phylogenetic tree generation", + "Phylogenetic tree reconstruction", + "Sequence clustering", + "Phylogenetic tree analysis", + "Phylogenetic analysis", + "Visualisation" ], "edam_topic": [], "id": "1465", @@ -1757,39 +1857,39 @@ "microbiome" ], "tools": [ - "mothur_pre_cluster", - "mothur_make_contigs", "mothur_count_seqs", - "mothur_cluster", - "mothur_unique_seqs", - "mothur_venn", - "mothur_classify_seqs", - "mothur_make_shared", - "mothur_make_biom", - "mothur_summary_seqs", - "mothur_cluster_split", "mothur_chimera_vsearch", + "mothur_get_groups", "mothur_screen_seqs", - "mothur_remove_lineage", - "mothur_summary_single", + "mothur_rarefaction_single", + "mothur_align_seqs", + "newick_display", + "mothur_make_shared", + "taxonomy_krona_chart", + "mothur_cluster", "mothur_remove_seqs", - "XY_Plot_1", + "mothur_summary_single", + "mothur_sub_sample", "mothur_remove_groups", - "mothur_taxonomy_to_krona", + "mothur_classify_seqs", + "mothur_seq_error", "mothur_count_groups", - "mothur_align_seqs", - "mothur_filter_seqs", - "mothur_dist_shared", + "mothur_cluster_split", "mothur_tree_shared", - "mothur_dist_seqs", + "mothur_summary_seqs", + "mothur_make_contigs", + "mothur_dist_shared", + "mothur_dist_seqs", + "XY_Plot_1", + "mothur_filter_seqs", + "mothur_remove_lineage", "mothur_classify_otu", + "mothur_pre_cluster", + "mothur_unique_seqs", + "mothur_venn", "mothur_heatmap_sim", - "mothur_rarefaction_single", - "mothur_sub_sample", - "newick_display", - "taxonomy_krona_chart", - "mothur_seq_error", - "mothur_get_groups" + "mothur_make_biom", + "mothur_taxonomy_to_krona" ], "update_time": "2025-06-02", "versions": 1 @@ -1800,8 +1900,8 @@ "deprecated": false, "doi": null, "edam_operation": [ - "Sequence feature detection", - "DNA barcoding" + "DNA barcoding", + "Sequence feature detection" ], "edam_topic": [], "id": "1460", @@ -1835,13 +1935,13 @@ "deprecated": false, "doi": null, "edam_operation": [ - "Visualisation", - "Sequence composition calculation", + "Sequencing quality control", "Sequence contamination filtering", - "Statistical calculation", "Taxonomic classification", + "Statistical calculation", "Aggregation", - "Sequencing quality control" + "Sequence composition calculation", + "Visualisation" ], "edam_topic": [], "id": "1439", @@ -1861,13 +1961,13 @@ "microbiome" ], "tools": [ - "kraken2", - "Filter1", - "fastqc", + "fastp", "taxonomy_krona_chart", "krakentools_kreport2krona", - "porechop", - "fastp" + "kraken2", + "fastqc", + "Filter1", + "porechop" ], "update_time": "2025-06-02", "versions": 1 @@ -1878,8 +1978,8 @@ "deprecated": false, "doi": null, "edam_operation": [ - "Visualisation", - "Aggregation" + "Aggregation", + "Visualisation" ], "edam_topic": [], "id": "1431", @@ -1911,13 +2011,13 @@ "deprecated": false, "doi": null, "edam_operation": [ - "Visualisation", - "Sequence clustering", - "DNA barcoding", "Taxonomic classification", + "DNA barcoding", "Sequence read processing", "Sequencing quality control", - "Phylogenetic analysis" + "Sequence clustering", + "Phylogenetic analysis", + "Visualisation" ], "edam_topic": [], "id": "1428", @@ -1937,9 +2037,9 @@ "microbiome" ], "tools": [ + "mothur_remove_lineage", "mothur_summary_seqs", - "mothur_classify_seqs", - "mothur_remove_lineage" + "mothur_classify_seqs" ], "update_time": "2025-06-02", "versions": 1 @@ -1950,13 +2050,13 @@ "deprecated": false, "doi": null, "edam_operation": [ - "Visualisation", - "Sequence clustering", - "DNA barcoding", "Taxonomic classification", + "DNA barcoding", "Sequence read processing", "Sequencing quality control", - "Phylogenetic analysis" + "Sequence clustering", + "Phylogenetic analysis", + "Visualisation" ], "edam_topic": [], "id": "1422", @@ -1976,10 +2076,10 @@ "microbiome" ], "tools": [ + "mothur_unique_seqs", "mothur_summary_seqs", "mothur_count_seqs", - "mothur_screen_seqs", - "mothur_unique_seqs" + "mothur_screen_seqs" ], "update_time": "2025-06-02", "versions": 1 @@ -1990,16 +2090,16 @@ "deprecated": false, "doi": null, "edam_operation": [ - "Visualisation", - "Phylogenetic tree reconstruction", - "Sequence clustering", - "Phylogenetic tree generation", - "DNA barcoding", - "Phylogenetic tree analysis", "Taxonomic classification", + "DNA barcoding", "Sequence read processing", "Sequencing quality control", - "Phylogenetic analysis" + "Phylogenetic tree generation", + "Phylogenetic tree reconstruction", + "Sequence clustering", + "Phylogenetic tree analysis", + "Phylogenetic analysis", + "Visualisation" ], "edam_topic": [], "id": "1418", @@ -2019,12 +2119,12 @@ "microbiome" ], "tools": [ + "mothur_tree_shared", + "mothur_venn", "mothur_heatmap_sim", - "newick_display", "mothur_dist_shared", - "mothur_venn", "collapse_dataset", - "mothur_tree_shared" + "newick_display" ], "update_time": "2025-06-02", "versions": 1 @@ -2035,13 +2135,13 @@ "deprecated": false, "doi": null, "edam_operation": [ - "Visualisation", - "Sequence clustering", - "DNA barcoding", "Taxonomic classification", + "DNA barcoding", "Sequence read processing", "Sequencing quality control", - "Phylogenetic analysis" + "Sequence clustering", + "Phylogenetic analysis", + "Visualisation" ], "edam_topic": [], "id": "1412", @@ -2074,13 +2174,13 @@ "deprecated": false, "doi": null, "edam_operation": [ - "Visualisation", - "Sequence clustering", - "DNA barcoding", "Taxonomic classification", + "DNA barcoding", "Sequence read processing", "Sequencing quality control", - "Phylogenetic analysis" + "Sequence clustering", + "Phylogenetic analysis", + "Visualisation" ], "edam_topic": [], "id": "1408", @@ -2100,10 +2200,10 @@ "microbiome" ], "tools": [ - "mothur_rarefaction_single", + "mothur_cluster", "mothur_dist_seqs", "mothur_make_shared", - "mothur_cluster" + "mothur_rarefaction_single" ], "update_time": "2025-06-02", "versions": 1 @@ -2114,13 +2214,13 @@ "deprecated": false, "doi": null, "edam_operation": [ - "Visualisation", - "Sequence clustering", - "DNA barcoding", "Taxonomic classification", + "DNA barcoding", "Sequence read processing", "Sequencing quality control", - "Phylogenetic analysis" + "Sequence clustering", + "Phylogenetic analysis", + "Visualisation" ], "edam_topic": [], "id": "1404", @@ -2140,12 +2240,12 @@ "microbiome" ], "tools": [ - "mothur_remove_groups", - "mothur_sub_sample", - "mothur_count_groups", "mothur_cluster_split", "mothur_make_shared", - "mothur_classify_otu" + "mothur_sub_sample", + "mothur_remove_groups", + "mothur_classify_otu", + "mothur_count_groups" ], "update_time": "2025-06-02", "versions": 1 @@ -2156,13 +2256,13 @@ "deprecated": false, "doi": null, "edam_operation": [ - "Visualisation", - "Sequence clustering", - "DNA barcoding", "Taxonomic classification", + "DNA barcoding", "Sequence read processing", "Sequencing quality control", - "Phylogenetic analysis" + "Sequence clustering", + "Phylogenetic analysis", + "Visualisation" ], "edam_topic": [], "id": "1400", @@ -2182,13 +2282,13 @@ "microbiome" ], "tools": [ - "mothur_pre_cluster", - "mothur_summary_seqs", "mothur_unique_seqs", - "mothur_filter_seqs", + "mothur_summary_seqs", "mothur_chimera_vsearch", + "mothur_remove_seqs", "mothur_screen_seqs", - "mothur_remove_seqs" + "mothur_filter_seqs", + "mothur_pre_cluster" ], "update_time": "2025-06-02", "versions": 1 @@ -2220,24 +2320,24 @@ "source": "WorkflowHub", "tags": [], "tools": [ + "tp_cut_tool", + "clair3", + "table_compute", + "samtools_depth", "bcftools_consensus", + "CONVERTER_gz_to_uncompressed", "Paste1", - "samtools_coverage", - "regexColumn1", "bcftools_norm", - "CONVERTER_gz_to_uncompressed", - "snpSift_filter", - "tp_cut_tool", "Cut1", "snpSift_extractFields", - "clair3", + "samtools_coverage", + "snpSift_filter", "collapse_dataset", - "Remove beginning1", - "table_compute", - "tp_head_tool", + "minimap2", "Count1", - "samtools_depth", - "minimap2" + "tp_head_tool", + "Remove beginning1", + "regexColumn1" ], "update_time": "2026-05-14", "versions": 5 @@ -2266,11 +2366,11 @@ "tags": [], "tools": [ "", - "fastq_dl", - "CONVERTER_uncompressed_to_gz", "tp_awk_tool", + "CONVERTER_uncompressed_to_gz", "CONVERTER_gz_to_uncompressed", - "__MERGE_COLLECTION__" + "__MERGE_COLLECTION__", + "fastq_dl" ], "update_time": "2026-05-14", "versions": 2 @@ -2285,8 +2385,8 @@ "doi": null, "edam_operation": [ "k-mer counting", - "Visualisation", "Formatting", + "Visualisation", "Mapping" ], "edam_topic": [], @@ -2304,10 +2404,10 @@ "tags": [], "tools": [ "", - "tp_awk_tool", - "__FILTER_FROM_FILE__", "bedtools_maskfastabed", "mapseq", + "tp_awk_tool", + "__FILTER_FROM_FILE__", "collection_element_identifiers", "taxonomy_krona_chart", "biom_convert", @@ -2325,14 +2425,14 @@ "deprecated": false, "doi": null, "edam_operation": [ - "Sequence trimming", - "Sequence composition calculation", - "Nucleic acid design", "Statistical calculation", + "Sequencing quality control", + "Sequence contamination filtering", + "Sequence trimming", "Validation", + "Nucleic acid design", "Read pre-processing", - "Sequence contamination filtering", - "Sequencing quality control" + "Sequence composition calculation" ], "edam_topic": [], "id": "1272", @@ -2348,17 +2448,17 @@ "source": "WorkflowHub", "tags": [], "tools": [ + "fastp", "cshl_fasta_formatter", "tp_find_and_replace", - "fastq_to_fasta_python", "multiqc", + "trimmomatic", "fastqc", "__UNZIP_COLLECTION__", - "prinseq", "mgnify_seqprep", - "fastp", - "trimmomatic", - "fastq_filter" + "fastq_filter", + "prinseq", + "fastq_to_fasta_python" ], "update_time": "2026-05-14", "versions": 2 @@ -2372,13 +2472,13 @@ "deprecated": false, "doi": null, "edam_operation": [ - "Sequence trimming", - "Read pre-processing", - "Sequence composition calculation", - "Sequence contamination filtering", + "Sequencing quality control", "Statistical calculation", + "Sequence contamination filtering", + "Sequence trimming", "Validation", - "Sequencing quality control" + "Read pre-processing", + "Sequence composition calculation" ], "edam_topic": [], "id": "1271", @@ -2396,12 +2496,12 @@ "tools": [ "cshl_fasta_formatter", "tp_find_and_replace", - "fastq_to_fasta_python", "multiqc", + "trimmomatic", "fastqc", + "fastq_filter", "prinseq", - "trimmomatic", - "fastq_filter" + "fastq_to_fasta_python" ], "update_time": "2026-05-14", "versions": 3 @@ -2415,13 +2515,13 @@ "deprecated": false, "doi": null, "edam_operation": [ - "Visualisation", - "Alignment", - "Formatting", - "Mapping", "k-mer counting", + "Formatting", "Comparison", - "Nucleic acid feature detection" + "Mapping", + "Alignment", + "Nucleic acid feature detection", + "Visualisation" ], "edam_topic": [], "id": "1270", @@ -2438,19 +2538,19 @@ "tags": [], "tools": [ "", - "bedtools_getfastabed", - "tp_awk_tool", "cshl_fasta_formatter", - "__FILTER_FROM_FILE__", - "infernal_cmsearch", + "tp_awk_tool", "mapseq", "collection_element_identifiers", + "__FILTER_FROM_FILE__", "taxonomy_krona_chart", - "cmsearch_deoverlap", "biom_convert", + "cmsearch_deoverlap", + "infernal_cmsearch", + "bedtools_getfastabed", "gops_concat_1", - "__FILTER_EMPTY_DATASETS__", - "query_tabular" + "query_tabular", + "__FILTER_EMPTY_DATASETS__" ], "update_time": "2026-05-14", "versions": 2 @@ -2477,9 +2577,9 @@ "source": "WorkflowHub", "tags": [], "tools": [ - "Grouping1", - "collection_column_join", "tp_awk_tool", + "collection_column_join", + "Grouping1", "filter_tabular", "query_tabular" ], @@ -2494,16 +2594,16 @@ "deprecated": false, "doi": null, "edam_operation": [ - "Visualisation", - "Filtering", - "Formatting", "Statistical calculation", "Imputation", - "Standardisation and normalisation", + "Formatting", "Heat map generation", + "Filtering", + "Standardisation and normalisation", "Protein quantification", + "Clustering", "Principal component plotting", - "Clustering" + "Visualisation" ], "edam_topic": [], "id": "1225", @@ -2519,23 +2619,23 @@ "source": "WorkflowHub", "tags": [], "tools": [ + "query_tabular", + "peptide_shaker", + "Remove beginning1", + "tp_cat", + "search_gui", "Grouping1", - "Grep1", - "fasta2tab", - "fasta_merge_files_and_filter_unique_sequences", - "Filter1", + "fasta_cli", "ident_params", - "Remove beginning1", + "maxquant", "msconvert", - "Cut1", - "query_tabular", "dbbuilder", - "fasta_cli", + "Grep1", "filter_tabular", - "tp_cat", - "search_gui", - "peptide_shaker", - "maxquant" + "Filter1", + "fasta_merge_files_and_filter_unique_sequences", + "Cut1", + "fasta2tab" ], "update_time": "2026-05-13", "versions": 1 @@ -2549,10 +2649,10 @@ "deprecated": false, "doi": "10.48546/workflowhub.workflow.1199.2", "edam_operation": [ - "Visualisation", "Statistical calculation", "Taxonomic classification", - "Aggregation" + "Aggregation", + "Visualisation" ], "edam_topic": [ "Metagenomics", @@ -2576,24 +2676,24 @@ "shotgun" ], "tools": [ + "__RELABEL_FROM_FILE__", "collection_column_join", - "krakentools_beta_diversity", + "cat_multiple", "Prepare alpha diversity summary file\nPaste1", - "Prepare alpha diversity summary file (paste Simpson and Fisher results)\nPaste1", - "kraken2", - "Prepare alpha diversity summary file (paste sample identifiers and Simpson results)\nPaste1", - "taxonomy_krona_chart", "collection_element_identifiers", + "krakentools_combine_kreports", "krakentools_kreport2krona", - "Fisher results contains a header line we want to exclude \"Fisher's alpha...loading\"\nShow tail1", + "krakentools_beta_diversity", "est_abundance", - "__RELABEL_FROM_FILE__", + "taxonomy_krona_chart", + "kraken2", + "Prepare alpha diversity summary file (paste sample identifiers and Simpson results)\nPaste1", + "Prepare alpha diversity summary file (paste Simpson and Fisher results)\nPaste1", "add_line_to_file", - "regex1", "krakentools_alpha_diversity", - "cat_multiple", + "regex1", "Extract column name and fraction_total_reads from Bracken report\nCut1", - "krakentools_combine_kreports" + "Fisher results contains a header line we want to exclude \"Fisher's alpha...loading\"\nShow tail1" ], "update_time": "2024-12-10", "versions": 2 @@ -2606,8 +2706,8 @@ "deprecated": false, "doi": null, "edam_operation": [ - "Visualisation", - "Prediction and recognition" + "Prediction and recognition", + "Visualisation" ], "edam_topic": [], "id": "1219", @@ -2623,8 +2723,8 @@ "source": "WorkflowHub", "tags": [], "tools": [ - "Grep1", "msstatstmt", + "Grep1", "unipept" ], "update_time": "2026-05-13", @@ -2652,17 +2752,17 @@ "source": "WorkflowHub", "tags": [], "tools": [ - "Grouping1", - "fasta_merge_files_and_filter_unique_sequences", "Filter1", "uniprotxml_downloader", + "Grouping1", "Cut1", - "pepquery2", - "tp_cat", + "collapse_dataset", "dbbuilder", + "query_tabular", + "tp_cat", + "fasta_merge_files_and_filter_unique_sequences", "Remove beginning1", - "collapse_dataset", - "query_tabular" + "pepquery2" ], "update_time": "2026-05-13", "versions": 1 @@ -2675,11 +2775,11 @@ "deprecated": false, "doi": null, "edam_operation": [ + "de Novo sequencing", + "Target-Decoy", "Expression analysis", - "Protein identification", "Tag-based peptide identification", - "de Novo sequencing", - "Target-Decoy" + "Protein identification" ], "edam_topic": [], "id": "1216", @@ -2711,10 +2811,10 @@ "deprecated": false, "doi": null, "edam_operation": [ - "Parsing", + "Antimicrobial resistance prediction", "Data handling", - "Genome assembly", - "Antimicrobial resistance prediction" + "Parsing", + "Genome assembly" ], "edam_topic": [], "id": "1189", @@ -2736,24 +2836,24 @@ ], "tools": [ "", - "hamronize_summarize", - "tp_text_file_with_recurring_lines", - "cat1", - "hamronize_tool", - "abricate", - "addValue", - "__APPLY_RULES__", - "__MERGE_COLLECTION__", - "collapse_dataset", + "cat_multi_datasets", "shovill", - "Grep1", - "cast", - "tp_find_and_replace", - "Cut1", "tp_split_on_column", - "datamash_ops", "staramr_search", - "cat_multi_datasets" + "collapse_dataset", + "datamash_ops", + "abricate", + "hamronize_tool", + "tp_find_and_replace", + "cat1", + "tp_text_file_with_recurring_lines", + "cast", + "__APPLY_RULES__", + "addValue", + "Grep1", + "hamronize_summarize", + "__MERGE_COLLECTION__", + "Cut1" ], "update_time": "2026-05-13", "versions": 2 @@ -2766,14 +2866,14 @@ "deprecated": false, "doi": null, "edam_operation": [ - "Visualisation", "Statistical calculation", "Imputation", - "Standardisation and normalisation", "Heat map generation", + "Standardisation and normalisation", "Protein quantification", + "Clustering", "Principal component plotting", - "Clustering" + "Visualisation" ], "edam_topic": [], "id": "1177", @@ -2789,13 +2889,13 @@ "source": "WorkflowHub", "tags": [], "tools": [ - "maxquant", - "Quantified-Proteins\nGrouping1", + "extracting microbial Proteins\nGrep1", "extract proteins\nCut1", - "extract peptides\nCut1", "Quantified-Peptides\nGrouping1", - "extracting microbial Proteins\nGrep1", - "extracting microbial Peptides\nGrep1" + "extracting microbial Peptides\nGrep1", + "Quantified-Proteins\nGrouping1", + "maxquant", + "extract peptides\nCut1" ], "update_time": "2026-05-14", "versions": 1 @@ -2811,8 +2911,8 @@ "doi": null, "edam_operation": [ "Data parsing", - "Genome assembly", - "Sequence assembly visualisation" + "Sequence assembly visualisation", + "Genome assembly" ], "edam_topic": [], "id": "1043", @@ -2836,11 +2936,11 @@ "quality" ], "tools": [ - "bandage_info", - "bandage_image", - "tooldistillator", "tooldistillator_summarize", - "shovill" + "shovill", + "bandage_image", + "bandage_info", + "tooldistillator" ], "update_time": "2026-05-13", "versions": 12 @@ -2855,13 +2955,13 @@ "deprecated": false, "doi": null, "edam_operation": [ - "Cross-assembly", - "Data parsing", + "Sequencing quality control", "Sequence contamination filtering", + "Data parsing", + "Taxonomic classification", "Expression analysis", "Statistical calculation", - "Taxonomic classification", - "Sequencing quality control" + "Cross-assembly" ], "edam_topic": [], "id": "1052", @@ -2886,14 +2986,14 @@ "trimming" ], "tools": [ - "kraken2", - "tooldistillator_summarize", - "tooldistillator", - "__UNZIP_COLLECTION__", - "est_abundance", "fastp", + "tooldistillator_summarize", "recentrifuge", - "__ZIP_COLLECTION__" + "__ZIP_COLLECTION__", + "est_abundance", + "kraken2", + "__UNZIP_COLLECTION__", + "tooldistillator" ], "update_time": "2026-05-14", "versions": 11 @@ -2904,22 +3004,22 @@ "deprecated": false, "doi": null, "edam_operation": [ - "Visualisation", - "Multilocus sequence typing", - "Sequence alignment", - "Genome indexing", - "Read mapping", + "Genome alignment", + "Read binning", "Sequence contamination filtering", "Clustering", - "Genome alignment", - "Parsing", + "Antimicrobial resistance prediction", "Data handling", - "Genome assembly", + "Sequence alignment", + "Parsing", + "Genome indexing", "RNA-Seq analysis", "Sequence trimming", - "Antimicrobial resistance prediction", - "Read binning", - "Sequence analysis" + "Sequence analysis", + "Read mapping", + "Multilocus sequence typing", + "Visualisation", + "Genome assembly" ], "edam_topic": [], "id": "407", @@ -2938,17 +3038,17 @@ "antimicrobial resistance" ], "tools": [ - "kma_map", - "hamronize_summarize", "seqsero2", - "bbtools_bbduk", - "__UNZIP_COLLECTION__", - "srst2", "shovill", - "mob_recon", + "bbtools_tadpole", "hamronize_tool", + "bbtools_bbduk", "sistr_cmd", - "bbtools_tadpole" + "mob_recon", + "kma_map", + "__UNZIP_COLLECTION__", + "hamronize_summarize", + "srst2" ], "update_time": "2026-05-13", "versions": 1 @@ -2984,10 +3084,10 @@ "deprecated": false, "doi": null, "edam_operation": [ - "Parsing", + "Antimicrobial resistance prediction", "Data handling", - "Genome assembly", - "Antimicrobial resistance prediction" + "Parsing", + "Genome assembly" ], "edam_topic": [], "id": "470", @@ -3009,13 +3109,13 @@ "antimicrobial resistance" ], "tools": [ - "hamronize_summarize", - "tp_find_and_replace", "abricate", + "shovill", + "hamronize_tool", + "tp_find_and_replace", "staramr_search", "collapse_dataset", - "shovill", - "hamronize_tool" + "hamronize_summarize" ], "update_time": "2026-05-13", "versions": 1 @@ -3069,9 +3169,9 @@ "source": "WorkflowHub", "tags": [], "tools": [ - "Phylogenetic tree for diversity analysis", + "Rarefaction", "Taxonomic analysis", - "Rarefaction" + "Phylogenetic tree for diversity analysis" ], "update_time": "2026-05-14", "versions": 2 @@ -3086,15 +3186,15 @@ "deprecated": false, "doi": "10.48546/workflowhub.workflow.1062.1", "edam_operation": [ - "Antimicrobial resistance prediction", "Base-calling", + "Antimicrobial resistance prediction", + "De-novo assembly", "Variant calling", + "Sequence assembly visualisation", + "Sequence assembly", "Cross-assembly", "Mapping assembly", - "Sequence assembly", - "Genome assembly", - "Sequence assembly visualisation", - "De-novo assembly" + "Genome assembly" ], "edam_topic": [], "id": "1062", @@ -3110,18 +3210,18 @@ "source": "WorkflowHub", "tags": [], "tools": [ - "medaka_consensus_pipeline", - "param_value_from_file", - "compose_text_param", - "__BUILD_LIST__", - "tp_find_and_replace", "abricate", "collection_element_identifiers", "bandage_image", - "split_file_to_collection", "flye", - "fasta2tab", - "tab2fasta" + "tp_find_and_replace", + "split_file_to_collection", + "compose_text_param", + "__BUILD_LIST__", + "tab2fasta", + "medaka_consensus_pipeline", + "param_value_from_file", + "fasta2tab" ], "update_time": "2026-05-13", "versions": 1 @@ -3136,14 +3236,12 @@ "deprecated": false, "doi": "10.48546/workflowhub.workflow.1060.1", "edam_operation": [ - "Phylogenetic tree generation (from molecular sequences)", + "Phylogenetic tree generation", "Visualisation", - "Phylogenetic tree generation (maximum likelihood and Bayesian methods)", "Multiple sequence alignment", - "Mapping", "Phylogenetic tree reconstruction", "Phylogenetic tree analysis", - "Phylogenetic tree generation" + "Mapping" ], "edam_topic": [], "id": "1060", @@ -3159,28 +3257,28 @@ "source": "WorkflowHub", "tags": [], "tools": [ - "Grouping1", + "tp_split_on_column", + "ggplot2_heatmap", + "bedtools_getfastabed", + "collapse_dataset", + "regex1", + "tp_replace_in_column", + "fasta_merge_files_and_filter_unique_sequences", + "newick_display", "regexColumn1", - "clustalw", - "__FILTER_FAILED_DATASETS__", + "tp_multijoin_tool", + "Count1", + "__FILTER_EMPTY_DATASETS__", "fasta2tab", "tp_sorted_uniq", - "fasta_merge_files_and_filter_unique_sequences", - "collapse_dataset", - "__FILTER_EMPTY_DATASETS__", - "bedtools_getfastabed", - "tp_multijoin_tool", - "ggplot2_heatmap", - "Cut1", - "Remove beginning1", + "Grouping1", "fasttree", - "tp_split_on_column", + "tab2fasta", + "Remove beginning1", "collection_column_join", - "tp_replace_in_column", - "newick_display", - "regex1", - "Count1", - "tab2fasta" + "clustalw", + "__FILTER_FAILED_DATASETS__", + "Cut1" ], "update_time": "2026-05-13", "versions": 1 @@ -3195,9 +3293,9 @@ "deprecated": false, "doi": "10.48546/workflowhub.workflow.1059.1", "edam_operation": [ - "Visualisation", "Taxonomic classification", - "Aggregation" + "Aggregation", + "Visualisation" ], "edam_topic": [], "id": "1059", @@ -3213,9 +3311,9 @@ "source": "WorkflowHub", "tags": [], "tools": [ + "krakentools_kreport2krona", "kraken2", - "taxonomy_krona_chart", - "krakentools_kreport2krona" + "taxonomy_krona_chart" ], "update_time": "2026-05-13", "versions": 1 @@ -3231,14 +3329,14 @@ "doi": null, "edam_operation": [ "Scaffolding", - "Multilocus sequence typing", - "Structural variation detection", - "Sequence motif recognition", "Genome annotation", + "Nucleic acid feature detection", "Data parsing", - "Genome assembly", "Protein feature detection", - "Nucleic acid feature detection" + "Structural variation detection", + "Sequence motif recognition", + "Multilocus sequence typing", + "Genome assembly" ], "edam_topic": [], "id": "1050", @@ -3261,12 +3359,12 @@ "genome-annotation" ], "tools": [ + "tooldistillator_summarize", + "integron_finder", + "plasmidfinder", "isescan", "bakta", - "integron_finder", - "tooldistillator_summarize", - "tooldistillator", - "plasmidfinder" + "tooldistillator" ], "update_time": "2026-05-13", "versions": 13 @@ -3308,10 +3406,10 @@ "fasta" ], "tools": [ + "tooldistillator_summarize", "abricate", "amrfinderplus", "staramr_search", - "tooldistillator_summarize", "tooldistillator" ], "update_time": "2026-05-13", @@ -3325,19 +3423,19 @@ "deprecated": false, "doi": null, "edam_operation": [ - "Phylogenetic tree visualisation", - "Sequence alignment", - "Validation", + "Taxonomic classification", "Antimicrobial resistance prediction", - "Phylogenetic tree generation", "Variant calling", - "Sequence analysis", - "Local alignment", + "Sequence alignment", + "Phylogenetic tree visualisation", + "Sequencing quality control", "Sequence contamination filtering", - "Global alignment", "Sequence alignment analysis", - "Taxonomic classification", - "Sequencing quality control" + "Phylogenetic tree generation", + "Validation", + "Global alignment", + "Sequence analysis", + "Local alignment" ], "edam_topic": [ "Genetic variation", @@ -3362,20 +3460,20 @@ "tuberculosis" ], "tools": [ - "bcftools_consensus", + "fastp", "tp_awk_tool", - "tb_profiler_profile", + "qualimap_bamqc", + "EMBOSS: seqret84", "kraken2", - "__FLATTEN__", - "multiqc", "mosdepth", + "__FLATTEN__", + "tp_sed_tool", "snippy", - "qualimap_bamqc", + "multiqc", + "bcftools_consensus", "tb_variant_filter", - "tbvcfreport", - "fastp", - "tp_sed_tool", - "EMBOSS: seqret84" + "tb_profiler_profile", + "tbvcfreport" ], "update_time": "2026-05-13", "versions": 1 @@ -3407,17 +3505,17 @@ "name:amplicon" ], "tools": [ - "dada2_filterAndTrim", + "dada2_dada", + "dada2_makeSequenceTable", + "__APPLY_RULES__", + "dada2_plotQualityProfile", "dada2_learnErrors", "dada2_assignTaxonomyAddspecies", - "dada2_makeSequenceTable", "dada2_seqCounts", + "dada2_filterAndTrim", "__UNZIP_COLLECTION__", "dada2_removeBimeraDenovo", - "__APPLY_RULES__", - "dada2_mergePairs", - "dada2_plotQualityProfile", - "dada2_dada" + "dada2_mergePairs" ], "update_time": "2026-05-14", "versions": 3 @@ -3448,11 +3546,11 @@ "genome-annotation" ], "tools": [ - "jbrowse", - "iframe", "create_or_update", - "list_organism", - "create_account" + "iframe", + "jbrowse", + "create_account", + "list_organism" ], "update_time": "2025-11-04", "versions": 1 @@ -3468,8 +3566,8 @@ "deprecated": false, "doi": "10.48546/workflowhub.workflow.624.1", "edam_operation": [ - "Visualisation", - "Taxonomic classification" + "Taxonomic classification", + "Visualisation" ], "edam_topic": [ "Metagenomic sequencing", @@ -3493,14 +3591,14 @@ ], "tools": [ "", - "humann2", - "taxonomy_krona_chart", "metaphlan2krona", + "metaphlan2", + "taxonomy_krona_chart", "humann2_renorm_table", - "humann2_regroup_table", - "Cut1", "merge_metaphlan_tables", - "metaphlan2" + "humann2", + "humann2_regroup_table", + "Cut1" ], "update_time": "2026-05-13", "versions": 1 @@ -3516,18 +3614,18 @@ "deprecated": false, "doi": null, "edam_operation": [ - "Visualisation", - "Phylogenetic tree reconstruction", - "Sequence clustering", - "Phylogenetic tree generation", - "DNA barcoding", - "Phylogenetic tree analysis", "Taxonomic classification", + "DNA barcoding", "Sequence read processing", "Sequencing quality control", - "Phylogenetic analysis" - ], - "edam_topic": [], + "Phylogenetic tree generation", + "Phylogenetic tree reconstruction", + "Sequence clustering", + "Phylogenetic tree analysis", + "Phylogenetic analysis", + "Visualisation" + ], + "edam_topic": [], "id": "653", "keep": true, "latest_version": 1, @@ -3543,10 +3641,10 @@ "metagenomics" ], "tools": [ - "mothur_dist_shared", "mothur_tree_shared", "mothur_heatmap_sim", - "newick_display" + "newick_display", + "mothur_dist_shared" ], "update_time": "2026-05-13", "versions": 1 @@ -3562,13 +3660,13 @@ "deprecated": false, "doi": null, "edam_operation": [ - "Visualisation", - "Sequence clustering", - "DNA barcoding", "Taxonomic classification", + "DNA barcoding", "Sequence read processing", "Sequencing quality control", - "Phylogenetic analysis" + "Sequence clustering", + "Phylogenetic analysis", + "Visualisation" ], "edam_topic": [], "id": "652", @@ -3604,13 +3702,13 @@ "deprecated": false, "doi": null, "edam_operation": [ - "Visualisation", - "Sequence clustering", - "DNA barcoding", "Taxonomic classification", + "DNA barcoding", "Sequence read processing", "Sequencing quality control", - "Phylogenetic analysis" + "Sequence clustering", + "Phylogenetic analysis", + "Visualisation" ], "edam_topic": [], "id": "651", @@ -3628,11 +3726,11 @@ "metagenomics" ], "tools": [ - "mothur_sub_sample", - "mothur_count_groups", "mothur_cluster_split", "mothur_make_shared", - "mothur_classify_otu" + "mothur_sub_sample", + "mothur_classify_otu", + "mothur_count_groups" ], "update_time": "2026-05-13", "versions": 1 @@ -3648,13 +3746,13 @@ "deprecated": false, "doi": null, "edam_operation": [ - "Visualisation", - "Sequence clustering", - "DNA barcoding", "Taxonomic classification", + "DNA barcoding", "Sequence read processing", "Sequencing quality control", - "Phylogenetic analysis" + "Sequence clustering", + "Phylogenetic analysis", + "Visualisation" ], "edam_topic": [], "id": "650", @@ -3672,8 +3770,8 @@ "metagenomics" ], "tools": [ - "mothur_classify_seqs", - "mothur_remove_lineage" + "mothur_remove_lineage", + "mothur_classify_seqs" ], "update_time": "2026-05-13", "versions": 1 @@ -3689,13 +3787,13 @@ "deprecated": false, "doi": null, "edam_operation": [ - "Visualisation", - "Sequence clustering", - "DNA barcoding", "Taxonomic classification", + "DNA barcoding", "Sequence read processing", "Sequencing quality control", - "Phylogenetic analysis" + "Sequence clustering", + "Phylogenetic analysis", + "Visualisation" ], "edam_topic": [], "id": "648", @@ -3713,10 +3811,10 @@ "metagenomics" ], "tools": [ + "mothur_unique_seqs", "mothur_summary_seqs", "mothur_count_seqs", - "mothur_screen_seqs", - "mothur_unique_seqs" + "mothur_screen_seqs" ], "update_time": "2026-05-13", "versions": 1 @@ -3732,13 +3830,13 @@ "deprecated": false, "doi": null, "edam_operation": [ - "Visualisation", - "Sequence clustering", - "DNA barcoding", "Taxonomic classification", + "DNA barcoding", "Sequence read processing", "Sequencing quality control", - "Phylogenetic analysis" + "Sequence clustering", + "Phylogenetic analysis", + "Visualisation" ], "edam_topic": [], "id": "649", @@ -3756,13 +3854,13 @@ "metagenomics" ], "tools": [ - "mothur_pre_cluster", - "mothur_summary_seqs", "mothur_unique_seqs", - "mothur_filter_seqs", + "mothur_summary_seqs", "mothur_chimera_vsearch", + "mothur_remove_seqs", "mothur_screen_seqs", - "mothur_remove_seqs" + "mothur_filter_seqs", + "mothur_pre_cluster" ], "update_time": "2026-05-13", "versions": 1 @@ -3773,9 +3871,9 @@ "deprecated": false, "doi": null, "edam_operation": [ - "Genome assembly", + "Sequencing quality control", "Sequence contamination filtering", - "Sequencing quality control" + "Genome assembly" ], "edam_topic": [], "id": "103", @@ -3807,13 +3905,13 @@ "deprecated": false, "doi": null, "edam_operation": [ - "Read pre-processing", - "Sequence contamination filtering", + "Sequencing quality control", "Formatting", + "Sequence contamination filtering", "Pairwise sequence alignment", - "Genome assembly", - "Sequencing quality control", - "Variant calling" + "Variant calling", + "Read pre-processing", + "Genome assembly" ], "edam_topic": [], "id": "102", @@ -3835,13 +3933,13 @@ "reads_selection" ], "tools": [ - "fasta_merge_files_and_filter_unique_sequences", "ncbi_blastn_wrapper", - "samtools_stats", - "picard_SamToFastq", "shovill", + "picard_SamToFastq", "ngsutils_bam_filter", - "minimap2" + "minimap2", + "samtools_stats", + "fasta_merge_files_and_filter_unique_sequences" ], "update_time": "2026-05-13", "versions": 1 @@ -3855,16 +3953,16 @@ "deprecated": false, "doi": null, "edam_operation": [ + "Pairwise sequence alignment", "Aggregation", - "Mapping assembly", "Antimicrobial resistance prediction", - "Sequence analysis", "Box-Whisker plot plotting", - "Pairwise sequence alignment", - "Genome assembly", - "Sequence assembly visualisation", + "De-novo assembly", "Scatter plot plotting", - "De-novo assembly" + "Sequence assembly visualisation", + "Sequence analysis", + "Mapping assembly", + "Genome assembly" ], "edam_topic": [ "Microbiology" @@ -3885,14 +3983,14 @@ ], "tools": [ "unicycler", - "racon", - "staramr_search", - "miniasm", - "nanoplot", "bandage_image", + "miniasm", + "staramr_search", "PlasFlow", - "gfa_to_fa", - "minimap2" + "nanoplot", + "minimap2", + "racon", + "gfa_to_fa" ], "update_time": "2026-05-13", "versions": 1 @@ -3903,8 +4001,8 @@ "deprecated": false, "doi": null, "edam_operation": [ - "Visualisation", - "Taxonomic classification" + "Taxonomic classification", + "Visualisation" ], "edam_topic": [], "id": "124", @@ -3923,8 +4021,8 @@ "kraken" ], "tools": [ - "kraken2", "Kraken2Tax", + "kraken2", "taxonomy_krona_chart" ], "update_time": "2026-05-13", @@ -3936,8 +4034,8 @@ "deprecated": false, "doi": null, "edam_operation": [ - "Visualisation", - "Taxonomic classification" + "Taxonomic classification", + "Visualisation" ], "edam_topic": [], "id": "101", @@ -3956,8 +4054,8 @@ "kraken" ], "tools": [ - "kraken2", "Kraken2Tax", + "kraken2", "taxonomy_krona_chart" ], "update_time": "2026-05-13", @@ -3971,11 +4069,11 @@ "deprecated": false, "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Sequence assembly validation", "Statistical calculation", + "Sequencing quality control", "Validation", - "Sequencing quality control" + "Sequence composition calculation", + "Sequence assembly validation" ], "edam_topic": [], "id": "f0776f7a890b523a", @@ -3992,91 +4090,149 @@ "name:microgalaxy" ], "tools": [ + "__RELABEL_FROM_FILE__", + "checkm2", + "collection_element_identifiers", "multiqc", "__FLATTEN__", - "collection_element_identifiers", - "__RELABEL_FROM_FILE__", "__MERGE_COLLECTION__", - "regex1", - "checkm2" + "regex1" ], "update_time": "2025-12-08", "versions": 1 }, { - "create_time": "2026-04-27", + "create_time": "2025-12-01", "creators": [], "deprecated": false, "doi": "", "edam_operation": [ - "Visualisation", - "Prediction and recognition" + "Sequencing quality control", + "Sequence contamination filtering", + "Taxonomic classification", + "Statistical calculation", + "Validation", + "Sequence composition calculation", + "Visualisation" ], "edam_topic": [], - "id": "6ca1b4fe047a03d2", + "id": "2a093e63ebf6876b", "keep": true, - "latest_version": 1, + "latest_version": 3, "license": null, - "link": "https://usegalaxy.eu/published/workflow?id=6ca1b4fe047a03d2", - "name": "Copy of Metaproteomics_GTN shared by user engy.nasr", + "link": "https://usegalaxy.eu/published/workflow?id=2a093e63ebf6876b", + "name": "Training: 16S rRNA Analysis with Nanopore Sequencing Reads", "number_of_steps": null, "projects": [], "source": "https://usegalaxy.eu", "tags": [ - "proteomics", + "metagenomics", "name:microgalaxy" ], "tools": [ - "search_gui", - "peptide_shaker", - "sqlite_to_tabular", + "fastp", + "datamash_reverse", + "taxonomy_krona_chart", + "multiqc", + "kraken2", + "tp_replace_in_line", + "fastqc", + "porechop", + "Remove beginning1" + ], + "update_time": "2026-06-12", + "versions": 3 + }, + { + "create_time": "2026-02-10", + "creators": [ + "Subina Mehta" + ], + "deprecated": false, + "doi": "", + "edam_operation": [ + "Statistical calculation", + "Taxonomic classification", + "Genome annotation", + "Sequencing quality control", + "Sequence trimming", + "Sequence assembly", + "Fold recognition", + "Information extraction", + "Homology-based gene prediction", + "Gene prediction", + "Read pre-processing", + "Coding region prediction", + "Primer removal", + "Query and retrieval", + "Sequence composition calculation" + ], + "edam_topic": [], + "id": "7be08f99f83c927e", + "keep": true, + "latest_version": 1, + "license": "CC-BY-4.0", + "link": "https://usegalaxy.eu/published/workflow?id=7be08f99f83c927e", + "name": "Sadowsky_MetaG-DBgen_02102026", + "number_of_steps": null, + "projects": [], + "source": "https://usegalaxy.eu", + "tags": [ + "name:microgalaxy" + ], + "tools": [ + "validate_fasta_database", + "Remove beginning1", + "regexColumn1", + "cat_bins", + "trim_galore", + "fastqc", + "eggnog_mapper", + "collapse_dataset", + "regex1", "query_tabular", - "unipept" + "tp_cat", + "tab2fasta", + "fasta_merge_files_and_filter_unique_sequences", + "maxbin2", + "fasta2tab", + "fraggenescan" ], - "update_time": "2026-04-27", + "update_time": "2026-06-09", "versions": 1 }, { - "create_time": "2025-12-01", + "create_time": "2026-04-27", "creators": [], "deprecated": false, "doi": "", "edam_operation": [ - "Visualisation", - "Sequence composition calculation", - "Sequence contamination filtering", - "Statistical calculation", - "Validation", - "Taxonomic classification", - "Sequencing quality control" + "Prediction and recognition", + "Visualisation" ], "edam_topic": [], - "id": "2a093e63ebf6876b", + "id": "6ca1b4fe047a03d2", "keep": true, - "latest_version": 2, + "latest_version": 1, "license": null, - "link": "https://usegalaxy.eu/published/workflow?id=2a093e63ebf6876b", - "name": "Training: 16S rRNA Analysis with Nanopore Sequencing Reads", + "link": "https://usegalaxy.eu/published/workflow?id=6ca1b4fe047a03d2", + "name": "Copy of Metaproteomics_GTN shared by user engy.nasr", "number_of_steps": null, "projects": [], "source": "https://usegalaxy.eu", "tags": [ - "metagenomics", + "proteomics", "name:microgalaxy" ], "tools": [ - "multiqc", - "kraken2", - "fastqc", - "taxonomy_krona_chart", - "porechop", - "tp_replace_in_line", - "fastp", - "Remove beginning1", - "datamash_reverse" + "peptide_shaker", + "unipept", + "search_gui", + "sqlite_to_tabular", + "query_tabular" ], - "update_time": "2026-03-16", - "versions": 2 + "update_time": "2026-04-27", + "versions": 1 }, { "create_time": "2025-10-01", @@ -4084,32 +4240,32 @@ "deprecated": false, "doi": "", "edam_operation": [ - "Visualisation", - "Sequence composition calculation", - "Formatting", "Statistical calculation", - "Validation", - "Sequence database search", + "Formatting", + "Visualisation", "Format validation", - "Primer removal", - "Coding region prediction", - "Local alignment", - "Sequence assembly", - "Database search", - "Sequence profile generation", + "Conversion", + "Probabilistic sequence generation", "Sequencing quality control", + "Sequence assembly", "Protein feature detection", - "Sequence trimming", - "Multiple sequence alignment", - "Sequence assembly validation", + "Gene prediction", "Sequence motif recognition", + "Coding region prediction", + "Sequence composition calculation", "Sequence generation", - "Read pre-processing", + "Database search", + "Sequence database search", "Data retrieval", - "Gene prediction", "Taxonomic classification", - "Conversion", - "Probabilistic sequence generation" + "Multiple sequence alignment", + "Sequence assembly validation", + "Sequence trimming", + "Sequence profile generation", + "Validation", + "Read pre-processing", + "Primer removal", + "Local alignment" ], "edam_topic": [], "id": "8c91345ed468e22d", @@ -4125,22 +4281,22 @@ "name:microgalaxy" ], "tools": [ + "coverm_genome", "fasplit", "tp_awk_tool", "tp_grep_tool", + "sort1", + "cat_bins", + "trim_galore", "fastqc", "checkm_lineage_wf", - "hmmer_hmmscan", - "coverm_genome", - "quast", "coverm_contig", - "fraggenescan", - "maxbin2", - "cat_bins", - "tp_cat", - "trim_galore", + "hmmer_hmmscan", "interproscan", - "sort1" + "tp_cat", + "maxbin2", + "quast", + "fraggenescan" ], "update_time": "2026-02-04", "versions": 0 @@ -4155,13 +4311,13 @@ "deprecated": false, "doi": "", "edam_operation": [ - "Visualisation", - "Formatting", "Statistical calculation", "Taxonomic classification", - "Conversion", + "Standardisation and normalisation", + "Formatting", "Aggregation", - "Standardisation and normalisation" + "Conversion", + "Visualisation" ], "edam_topic": [], "id": "7491883694fff308", @@ -4181,18 +4337,18 @@ ], "tools": [ "metaphlan", - "kraken2", + "metaphlan2krona", "collection_element_identifiers", + "sylph_profile", "taxonomy_krona_chart", - "metaphlan2krona", "krakentools_kreport2krona", - "taxpasta", "est_abundance", - "sylph_profile", + "kraken2", + "cat1", "add_line_to_file", + "taxpasta", "datamash_transpose", - "Remove beginning1", - "cat1" + "Remove beginning1" ], "update_time": "2025-12-17", "versions": 3 @@ -4205,11 +4361,11 @@ "deprecated": false, "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Sequence assembly validation", "Statistical calculation", + "Sequencing quality control", "Validation", - "Sequencing quality control" + "Sequence composition calculation", + "Sequence assembly validation" ], "edam_topic": [], "id": "7371b6918e895e0c", @@ -4226,13 +4382,13 @@ "name:microgalaxy" ], "tools": [ + "__RELABEL_FROM_FILE__", + "checkm2", + "collection_element_identifiers", "multiqc", "__FLATTEN__", - "collection_element_identifiers", - "__RELABEL_FROM_FILE__", "__MERGE_COLLECTION__", - "regex1", - "checkm2" + "regex1" ], "update_time": "2025-12-08", "versions": 16 @@ -4246,19 +4402,19 @@ "deprecated": false, "doi": "", "edam_operation": [ - "Visualisation", - "Sequence feature detection", - "Sequence composition calculation", - "Filtering", - "Formatting", "Statistical calculation", - "Deposition", - "Validation", - "Analysis", - "Standardisation and normalisation", - "Classification", + "Formatting", "DNA barcoding", - "Sequencing quality control" + "Filtering", + "Sequence feature detection", + "Sequencing quality control", + "Standardisation and normalisation", + "Analysis", + "Validation", + "Deposition", + "Sequence composition calculation", + "Visualisation", + "Classification" ], "edam_topic": [], "id": "466bdd8ba7b67264", @@ -4277,34 +4433,34 @@ "name:pallori" ], "tools": [ - "compose_text_param", + "__FLATTEN__", "ampvis2_heatmap", - "fastqc", - "bg_column_arrange_by_header", - "ampvis2_subset_samples", "datamash_transpose", - "unzip", - "biom_convert", - "maaslin2", - "volcanoplot", - "__FLATTEN__", - "calculate_numeric_param", - "mmuphin", - "phyloseq_tax_glom", + "regex1", "ampvis2_load", + "mmuphin", + "maaslin2", + "ampvis2_ordinate", + "unzip", "param_value_from_file", + "phyloseq_from_biom", "tp_awk_tool", + "phyloseq_add_rank_names", + "calculate_numeric_param", + "ampvis2_export_otu", + "bg_column_arrange_by_header", + "volcanoplot", "tp_cut_tool", - "tp_easyjoin_tool", + "biom_convert", "Remove beginning1", + "tp_easyjoin_tool", "multiqc", - "ampvis2_ordinate", - "phyloseq_from_biom", - "phyloseq_add_rank_names", - "ampvis2_export_otu", - "regex1", "lotus2", - "decontam" + "compose_text_param", + "fastqc", + "ampvis2_subset_samples", + "decontam", + "phyloseq_tax_glom" ], "update_time": "2025-11-18", "versions": 193 @@ -4318,15 +4474,15 @@ "deprecated": false, "doi": "", "edam_operation": [ - "Visualisation", - "Formatting", "Statistical calculation", - "Standardisation and normalisation", - "Species frequency estimation", "Taxonomic classification", - "Conversion", + "Formatting", "Aggregation", - "Phylogenetic analysis" + "Species frequency estimation", + "Conversion", + "Standardisation and normalisation", + "Phylogenetic analysis", + "Visualisation" ], "edam_topic": [], "id": "cb2df493f5e334f7", @@ -4345,35 +4501,35 @@ "name:microgalaxy" ], "tools": [ - "metaphlan", - "tp_text_file_with_recurring_lines", - "est_abundance", - "datamash_transpose", - "cat1", - "tp_sed_tool", - "sort1", - "humann", - "kraken2", "collection_element_identifiers", "krakentools_kreport2krona", - "csv_to_tabular", - "collapse_dataset", - "humann_unpack_pathways", - "humann_rename_table", - "tp_awk_tool", "tp_replace_in_line", - "__UNZIP_COLLECTION__", - "add_line_to_file", - "tp_easyjoin_tool", - "Remove beginning1", + "collapse_dataset", + "datamash_transpose", "krakentools_alpha_diversity", - "fastq_paired_end_interlacer", - "collection_column_join", + "tp_awk_tool", + "csv_to_tabular", "taxonomy_krona_chart", + "est_abundance", + "kraken2", + "cat1", + "tp_text_file_with_recurring_lines", "taxpasta", + "metaphlan", + "humann_regroup_table", "sylph_profile", + "fastq_paired_end_interlacer", "humann_renorm_table", - "humann_regroup_table" + "Remove beginning1", + "humann", + "sort1", + "humann_rename_table", + "collection_column_join", + "tp_easyjoin_tool", + "tp_sed_tool", + "humann_unpack_pathways", + "add_line_to_file", + "__UNZIP_COLLECTION__" ], "update_time": "2025-11-13", "versions": 18 @@ -4387,13 +4543,13 @@ "deprecated": false, "doi": "", "edam_operation": [ - "Read summarisation", - "Sequence composition calculation", - "RNA-Seq quantification", + "Sequencing quality control", "Statistical calculation", - "Sequence alignment", "Validation", - "Sequencing quality control" + "Read summarisation", + "Sequence alignment", + "Sequence composition calculation", + "RNA-Seq quantification" ], "edam_topic": [], "id": "ca9d3233b0912765", @@ -4414,14 +4570,14 @@ "name:transcriptomics" ], "tools": [ + "umi_tools_dedup", "collection_column_join", + "umi_tools_extract", "multiqc", "fastqc", - "__FILTER_FAILED_DATASETS__", "featurecounts", - "umi_tools_dedup", - "rna_star", - "umi_tools_extract" + "__FILTER_FAILED_DATASETS__", + "rna_star" ], "update_time": "2025-06-26", "versions": 48 @@ -4436,34 +4592,34 @@ "deprecated": false, "doi": "", "edam_operation": [ - "Visualisation", - "Sequence composition calculation", - "Formatting", "Statistical calculation", + "Formatting", "Gene functional annotation", - "Validation", - "Sequence database search", + "Visualisation", "Format validation", - "Primer removal", - "Coding region prediction", - "Local alignment", - "Sequence assembly", - "Database search", - "Sequence profile generation", + "Conversion", + "Probabilistic sequence generation", "Sequencing quality control", + "Sequence assembly", "Protein feature detection", - "Sequence trimming", - "Multiple sequence alignment", - "Sequence assembly validation", + "Gene prediction", "Sequence motif recognition", + "Coding region prediction", + "Sequence composition calculation", "Sequence generation", - "Sequence analysis", - "Read pre-processing", + "Database search", + "Sequence database search", "Data retrieval", - "Gene prediction", "Taxonomic classification", - "Conversion", - "Probabilistic sequence generation" + "Multiple sequence alignment", + "Sequence assembly validation", + "Sequence trimming", + "Sequence profile generation", + "Validation", + "Sequence analysis", + "Read pre-processing", + "Primer removal", + "Local alignment" ], "edam_topic": [], "id": "667bac8d7453e5f1", @@ -4481,23 +4637,23 @@ "name:mags" ], "tools": [ - "fasplit", - "tp_awk_tool", - "tp_grep_tool", - "fastqc", - "checkm_lineage_wf", - "hmmer_hmmscan", "coverm_genome", - "quast", - "coverm_contig", - "fraggenescan", - "maxbin2", - "tp_cat", + "fasplit", + "tp_awk_tool", + "tp_grep_tool", + "sort1", "cat_bins", - "kofamscan", "trim_galore", + "fastqc", + "checkm_lineage_wf", "interproscan", - "sort1" + "coverm_contig", + "hmmer_hmmscan", + "kofamscan", + "tp_cat", + "maxbin2", + "quast", + "fraggenescan" ], "update_time": "2024-12-21", "versions": 14 @@ -4523,23 +4679,23 @@ "deprecated": false, "doi": "", "edam_operation": [ - "Sequence comparison", - "Phylogenetic tree visualisation", - "Visualisation", - "Sequence composition calculation", - "Formatting", "Statistical calculation", "Phylogenetic inference", - "Validation", - "Primer removal", - "Sequence alignment analysis", + "Taxonomic classification", + "Formatting", + "Conversion", + "Phylogenetic tree visualisation", + "Sequence similarity search", + "Sequence composition calculation", + "Phylogenetic tree editing", "Sequencing quality control", "Sequence trimming", - "Phylogenetic tree editing", + "Sequence alignment analysis", + "Sequence comparison", + "Validation", "Read pre-processing", - "Taxonomic classification", - "Sequence similarity search", - "Conversion" + "Primer removal", + "Visualisation" ], "edam_topic": [], "id": "096b75501c8e0888", @@ -4559,27 +4715,27 @@ "name:microgalaxy" ], "tools": [ - "Grouping1", - "group_humann2_uniref_abundances_to_go", - "fastqc", + "graphlan_annotate", "humann2_renorm_table", - "humann2_unpack_pathways", - "tp_sort_header_tool", + "combine_metaphlan2_humann2", + "bg_sortmerna", + "cutadapt", "humann2_genefamilies_genus_level", + "taxonomy_krona_chart", + "export2graphlan", + "metaphlan2", + "fastq_paired_end_interlacer", + "group_humann2_uniref_abundances_to_go", + "Grouping1", + "Grep1", "humann2", + "graphlan", + "tp_sort_header_tool", "metaphlan2krona", - "Grep1", + "humann2_unpack_pathways", "format_metaphlan2_output", - "graphlan", - "bg_sortmerna", - "fastq_paired_end_interlacer", "multiqc", - "combine_metaphlan2_humann2", - "cutadapt", - "taxonomy_krona_chart", - "graphlan_annotate", - "export2graphlan", - "metaphlan2" + "fastqc" ], "update_time": "2024-12-20", "versions": 3 @@ -4603,16 +4759,16 @@ "deprecated": false, "doi": "", "edam_operation": [ - "Sequence trimming", - "Sequence composition calculation", "Statistical calculation", - "Gene expression profiling", - "Primer removal", - "Read pre-processing", "Sequence similarity search", + "Sequencing quality control", + "Gene expression profiling", + "Sequence trimming", "Sequence alignment analysis", "Sequence comparison", - "Sequencing quality control" + "Read pre-processing", + "Primer removal", + "Sequence composition calculation" ], "edam_topic": [], "id": "fd90652d475ed739", @@ -4630,12 +4786,12 @@ "microbiome" ], "tools": [ - "collection_column_join", "kallisto_quant", - "fastqc", - "__UNZIP_COLLECTION__", + "collection_column_join", "trim_galore", - "bg_sortmerna" + "fastqc", + "bg_sortmerna", + "__UNZIP_COLLECTION__" ], "update_time": "2024-12-20", "versions": 6 @@ -4649,8 +4805,8 @@ "doi": "", "edam_operation": [ "Sequence alignment analysis", - "Multiple sequence alignment", - "Phylogenetic tree generation" + "Phylogenetic tree generation", + "Multiple sequence alignment" ], "edam_topic": [], "id": "a2c46deea34d9d80", @@ -4667,20 +4823,20 @@ "name:microgalaxy" ], "tools": [ + "Add_a_column1", + "tab2fasta", "tp_split_on_column", - "regexColumn1", + "gops_intersect_1", "rbc_mafft", - "bg_diamond_view", - "Filter1", - "bg_diamond", "join1", - "tab2fasta", - "collapse_dataset", - "Cut1", + "bg_diamond", "cat1", + "collapse_dataset", "rapidnj", - "Add_a_column1", - "gops_intersect_1" + "Filter1", + "bg_diamond_view", + "Cut1", + "regexColumn1" ], "update_time": "2024-12-05", "versions": 2 @@ -4697,8 +4853,8 @@ "deprecated": false, "doi": "", "edam_operation": [ - "Visualisation", - "Prediction and recognition" + "Prediction and recognition", + "Visualisation" ], "edam_topic": [], "id": "cefc49c13ff73231", @@ -4717,11 +4873,11 @@ "name:microgalaxy" ], "tools": [ - "search_gui", "peptide_shaker", + "unipept", + "search_gui", "sqlite_to_tabular", - "query_tabular", - "unipept" + "query_tabular" ], "update_time": "2024-11-21", "versions": 40 @@ -4755,10 +4911,10 @@ "limma-rle" ], "tools": [ + "__EXTRACT_DATASET__", + "map_param_value", "Grep1", "__BUILD_LIST__", - "map_param_value", - "__EXTRACT_DATASET__", "__FILTER_EMPTY_DATASETS__" ], "update_time": "2024-11-21", @@ -4776,11 +4932,11 @@ "deprecated": false, "doi": "", "edam_operation": [ - "Visualisation", - "Label-free quantification", + "Formatting", "Prediction and recognition", "Filtering", - "Formatting" + "Visualisation", + "Label-free quantification" ], "edam_topic": [], "id": "cd675ab32d3e7833", @@ -4797,18 +4953,18 @@ "name:microgalaxy" ], "tools": [ - "tp_replace_in_column", + "peptide_shaker", + "search_gui", + "unipept", "flashlfq", - "Filter1", - "msconvert", "tp_replace_in_line", "Cut1", "regex1", - "Remove beginning1", - "search_gui", - "peptide_shaker", + "msconvert", + "tp_replace_in_column", "query_tabular", - "unipept" + "Filter1", + "Remove beginning1" ], "update_time": "2024-11-21", "versions": 1 @@ -4826,16 +4982,16 @@ "deprecated": false, "doi": "", "edam_operation": [ - "Visualisation", - "Statistical inference", "Quantification", - "Heat map generation", - "Query and retrieval", - "Indexing", "Differential protein expression analysis", + "Query and retrieval", "Principal component visualisation", + "Indexing", + "Heat map generation", "Filtering", - "Functional clustering" + "Functional clustering", + "Statistical inference", + "Visualisation" ], "edam_topic": [], "id": "e5a89ef7b5f1c1d9", @@ -4852,12 +5008,12 @@ "name:microgalaxy" ], "tools": [ - "metaquantome_db", - "metaquantome_sample", "metaquantome_stat", - "metaquantome_filter", + "metaquantome_expand", "metaquantome_viz", - "metaquantome_expand" + "metaquantome_db", + "metaquantome_filter", + "metaquantome_sample" ], "update_time": "2024-11-21", "versions": 3 @@ -4873,10 +5029,10 @@ "deprecated": false, "doi": "", "edam_operation": [ - "Cross-assembly", "Taxonomic classification", + "Expression analysis", "Read mapping", - "Expression analysis" + "Cross-assembly" ], "edam_topic": [], "id": "c09159d7aad0f264", @@ -4895,10 +5051,10 @@ ], "tools": [ "bowtie2", - "kraken2", + "recentrifuge", "fastq_to_tabular", + "kraken2", "filter_tabular", - "recentrifuge", "seq_filter_by_id" ], "update_time": "2024-11-21", @@ -4915,11 +5071,11 @@ "deprecated": false, "doi": "", "edam_operation": [ - "Read summarisation", - "RNA-Seq quantification", + "Sequencing quality control", "Validation", + "Read summarisation", "Read mapping", - "Sequencing quality control" + "RNA-Seq quantification" ], "edam_topic": [], "id": "63478edcea3f449a", @@ -4937,8 +5093,8 @@ "name:microgalaxy" ], "tools": [ - "featurecounts", "bowtie2", + "featurecounts", "multiqc" ], "update_time": "2024-11-21", @@ -4955,10 +5111,10 @@ "deprecated": false, "doi": "", "edam_operation": [ - "Sequence composition calculation", + "Sequencing quality control", "Statistical calculation", "Validation", - "Sequencing quality control" + "Sequence composition calculation" ], "edam_topic": [], "id": "1ef76b7b86e15792", @@ -4976,9 +5132,9 @@ "name:microgalaxy" ], "tools": [ - "trimmomatic", "fastqc", - "multiqc" + "multiqc", + "trimmomatic" ], "update_time": "2024-11-21", "versions": 6 @@ -5034,26 +5190,26 @@ "name:microgalaxy" ], "tools": [ - "mergeCols1", - "bedtools_complementbed", - "tp_sort_header_tool", - "tp_sed_tool", - "cat1", "bedtools_sortbed", - "fasta_compute_length", - "Filter1", - "addValue", - "join1", "collapse_dataset", "bedtools_intersectbed", - "random_lines1", - "Grep1", "tp_cat", - "Cut1", - "fasta_filter_by_length", - "tp_grep_tool", "datamash_ops", - "lastz_wrapper_2" + "bedtools_complementbed", + "cat1", + "join1", + "mergeCols1", + "lastz_wrapper_2", + "tp_grep_tool", + "addValue", + "fasta_filter_by_length", + "Grep1", + "fasta_compute_length", + "tp_sort_header_tool", + "random_lines1", + "tp_sed_tool", + "Filter1", + "Cut1" ], "update_time": "2023-12-14", "versions": 0 @@ -5067,8 +5223,8 @@ "doi": "", "edam_operation": [ "Sequence alignment analysis", - "Multiple sequence alignment", - "Phylogenetic tree generation" + "Phylogenetic tree generation", + "Multiple sequence alignment" ], "edam_topic": [], "id": "86900be4282d4b1d", @@ -5086,20 +5242,20 @@ "name:microgalaxy" ], "tools": [ + "Add_a_column1", + "tab2fasta", "tp_split_on_column", - "regexColumn1", + "gops_intersect_1", "rbc_mafft", - "bg_diamond_view", - "Filter1", - "bg_diamond", "join1", - "tab2fasta", - "collapse_dataset", - "Cut1", + "bg_diamond", "cat1", + "collapse_dataset", "rapidnj", - "Add_a_column1", - "gops_intersect_1" + "Filter1", + "bg_diamond_view", + "Cut1", + "regexColumn1" ], "update_time": "2023-12-14", "versions": 0 @@ -5127,11 +5283,11 @@ "name:microgalaxy" ], "tools": [ - "jbrowse", - "iframe", "create_or_update", - "list_organism", - "create_account" + "iframe", + "jbrowse", + "create_account", + "list_organism" ], "update_time": "2023-12-14", "versions": 0 @@ -5142,24 +5298,24 @@ "deprecated": false, "doi": "", "edam_operation": [ - "Genome assembly", + "Base-calling", + "Pairwise sequence alignment", "Sequence visualisation", - "Gene prediction", - "Genome annotation", - "Sequence analysis", + "De-novo assembly", "Variant calling", - "Base-calling", - "Antimicrobial resistance prediction", + "Scatter plot plotting", + "Genome annotation", + "Sequence assembly", + "Gene prediction", + "Genome visualisation", + "Mapping assembly", "Coding region prediction", "Cross-assembly", - "Mapping assembly", - "Sequence assembly", + "Antimicrobial resistance prediction", "Box-Whisker plot plotting", - "Genome visualisation", - "Pairwise sequence alignment", "Sequence assembly visualisation", - "Scatter plot plotting", - "De-novo assembly" + "Sequence analysis", + "Genome assembly" ], "edam_topic": [], "id": "152223c8aed27357", @@ -5176,42 +5332,42 @@ "name:microgalaxy" ], "tools": [ - "jbrowse", - "bg_column_arrange_by_header", - "gff2bed1", - "tp_text_file_with_recurring_lines", - "circos_gc_skew", - "trimmomatic", - "fasta2tab", - "fasta_compute_length", - "Add_a_column1", - "circos_interval_to_tile", - "tp_sort_header_tool", - "minimap2", - "Filter1", + "circos_wiggle_to_scatter", + "tp_split_on_column", "bandage_image", - "nanoplot", - "join1", + "flye", + "deeptools_bam_coverage", + "staramr_search", "PlasFlow", - "circos", + "regex1", + "jbrowse", + "tp_cat", "tp_head_tool", - "deeptools_bam_coverage", - "Grep1", + "ncbi_blastn_wrapper", + "medaka_consensus_pipeline", + "gff2bed1", + "circos", + "tbl2gff3", + "join1", + "trimmomatic", + "tp_text_file_with_recurring_lines", + "prokka", + "nanoplot", + "bg_column_arrange_by_header", + "fasta2tab", + "Add_a_column1", "tp_cut_tool", + "minimap2", + "Grep1", + "tab2fasta", + "fasta_compute_length", + "tp_sort_header_tool", + "circos_interval_to_tile", "tp_easyjoin_tool", - "tp_cat", "regex_replace", - "Cut1", - "tp_split_on_column", - "medaka_consensus_pipeline", - "circos_wiggle_to_scatter", - "ncbi_blastn_wrapper", - "staramr_search", - "prokka", - "regex1", - "flye", - "tbl2gff3", - "tab2fasta" + "circos_gc_skew", + "Filter1", + "Cut1" ], "update_time": "2023-12-14", "versions": 0 @@ -5237,11 +5393,11 @@ "name:microgalaxy" ], "tools": [ + "snp_dists", "bcftools_consensus", - "snp_sites", "tb_variant_filter", - "tp_cat", - "snp_dists" + "snp_sites", + "tp_cat" ], "update_time": "2023-12-14", "versions": 0 @@ -5253,8 +5409,8 @@ "doi": "", "edam_operation": [ "Phylogenetic tree visualisation", - "Variant calling", - "Phylogenetic tree generation" + "Phylogenetic tree generation", + "Variant calling" ], "edam_topic": [], "id": "3a8fde248a4d0383", @@ -5271,10 +5427,10 @@ "name:microgalaxy" ], "tools": [ - "trimmomatic", - "tb_variant_filter", + "snippy", "__MERGE_COLLECTION__", - "snippy" + "tb_variant_filter", + "trimmomatic" ], "update_time": "2023-12-14", "versions": 0 @@ -5302,14 +5458,14 @@ "name:microgalaxy" ], "tools": [ + "addName", "samtools_view", - "tb_profiler_profile", "tp_grep_tool", + "tp_sed_tool", "tp_replace_in_line", "__MERGE_COLLECTION__", "tp_cat", - "addName", - "tp_sed_tool" + "tb_profiler_profile" ], "update_time": "2023-12-14", "versions": 0 @@ -5340,12 +5496,12 @@ ], "tools": [ "bowtie2", - "bcftools_norm", "tp_awk_tool", - "snpSift_filter", + "bcftools_view", + "bcftools_norm", "vcf2tsv", - "freebayes", - "bcftools_view" + "snpSift_filter", + "freebayes" ], "update_time": "2023-12-13", "versions": 2 @@ -5376,14 +5532,14 @@ ], "tools": [ "bowtie2", - "samtools_coverage", + "collection_element_identifiers", + "samtools_depth", "bcftools_norm", "vcf2tsv", - "collection_element_identifiers", - "freebayes", - "tp_cat", "collapse_dataset", - "samtools_depth" + "samtools_coverage", + "tp_cat", + "freebayes" ], "update_time": "2023-12-13", "versions": 13 @@ -5396,11 +5552,11 @@ "deprecated": false, "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Sequence assembly validation", "Statistical calculation", + "Sequencing quality control", "Validation", - "Sequencing quality control" + "Sequence composition calculation", + "Sequence assembly validation" ], "edam_topic": [], "id": "a8aee61c2cbaf6ea", @@ -5417,13 +5573,13 @@ "name:microgalaxy" ], "tools": [ + "__RELABEL_FROM_FILE__", + "checkm2", + "collection_element_identifiers", "multiqc", "__FLATTEN__", - "collection_element_identifiers", - "__RELABEL_FROM_FILE__", "__MERGE_COLLECTION__", - "regex1", - "checkm2" + "regex1" ], "update_time": "2025-12-08", "versions": 1 @@ -5455,11 +5611,11 @@ "name:microgalaxy" ], "tools": [ - "fastq_dl", - "CONVERTER_uncompressed_to_gz", "tp_awk_tool", + "CONVERTER_uncompressed_to_gz", "CONVERTER_gz_to_uncompressed", - "__MERGE_COLLECTION__" + "__MERGE_COLLECTION__", + "fastq_dl" ], "update_time": "2025-04-25", "versions": 1 @@ -5475,8 +5631,8 @@ "doi": "", "edam_operation": [ "k-mer counting", - "Visualisation", "Formatting", + "Visualisation", "Mapping" ], "edam_topic": [], @@ -5496,10 +5652,10 @@ "name:microgalaxy" ], "tools": [ - "tp_awk_tool", - "__FILTER_FROM_FILE__", "bedtools_maskfastabed", "mapseq", + "tp_awk_tool", + "__FILTER_FROM_FILE__", "collection_element_identifiers", "taxonomy_krona_chart", "biom_convert", @@ -5518,14 +5674,14 @@ "deprecated": false, "doi": "", "edam_operation": [ - "Sequence trimming", - "Sequence composition calculation", - "Nucleic acid design", "Statistical calculation", + "Sequencing quality control", + "Sequence contamination filtering", + "Sequence trimming", "Validation", + "Nucleic acid design", "Read pre-processing", - "Sequence contamination filtering", - "Sequencing quality control" + "Sequence composition calculation" ], "edam_topic": [], "id": "a71fcbc60caae8b6", @@ -5544,17 +5700,17 @@ "name:microgalaxy" ], "tools": [ + "fastp", "cshl_fasta_formatter", "tp_find_and_replace", - "fastq_to_fasta_python", "multiqc", + "trimmomatic", "fastqc", "__UNZIP_COLLECTION__", - "prinseq", "mgnify_seqprep", - "fastp", - "trimmomatic", - "fastq_filter" + "fastq_filter", + "prinseq", + "fastq_to_fasta_python" ], "update_time": "2025-04-25", "versions": 1 @@ -5569,13 +5725,13 @@ "deprecated": false, "doi": "", "edam_operation": [ - "Sequence trimming", - "Read pre-processing", - "Sequence composition calculation", - "Sequence contamination filtering", + "Sequencing quality control", "Statistical calculation", + "Sequence contamination filtering", + "Sequence trimming", "Validation", - "Sequencing quality control" + "Read pre-processing", + "Sequence composition calculation" ], "edam_topic": [], "id": "5f878c4cc3bff68c", @@ -5596,12 +5752,12 @@ "tools": [ "cshl_fasta_formatter", "tp_find_and_replace", - "fastq_to_fasta_python", "multiqc", + "trimmomatic", "fastqc", + "fastq_filter", "prinseq", - "trimmomatic", - "fastq_filter" + "fastq_to_fasta_python" ], "update_time": "2025-04-25", "versions": 1 @@ -5636,24 +5792,24 @@ "name:iwc" ], "tools": [ + "tp_cut_tool", + "clair3", + "table_compute", + "samtools_depth", "bcftools_consensus", + "CONVERTER_gz_to_uncompressed", "Paste1", - "samtools_coverage", - "regexColumn1", "bcftools_norm", - "CONVERTER_gz_to_uncompressed", - "snpSift_filter", - "tp_cut_tool", "Cut1", "snpSift_extractFields", - "clair3", + "samtools_coverage", + "snpSift_filter", "collapse_dataset", - "Remove beginning1", - "table_compute", - "tp_head_tool", + "minimap2", "Count1", - "samtools_depth", - "minimap2" + "tp_head_tool", + "Remove beginning1", + "regexColumn1" ], "update_time": "2025-04-25", "versions": 1 @@ -5668,13 +5824,13 @@ "deprecated": false, "doi": "", "edam_operation": [ - "Sequence trimming", - "Read pre-processing", - "Sequence composition calculation", - "Sequence contamination filtering", + "Sequencing quality control", "Statistical calculation", + "Sequence contamination filtering", + "Sequence trimming", "Validation", - "Sequencing quality control" + "Read pre-processing", + "Sequence composition calculation" ], "edam_topic": [], "id": "afb67b4b9952f57d", @@ -5695,12 +5851,12 @@ "tools": [ "cshl_fasta_formatter", "tp_find_and_replace", - "fastq_to_fasta_python", "multiqc", + "trimmomatic", "fastqc", + "fastq_filter", "prinseq", - "trimmomatic", - "fastq_filter" + "fastq_to_fasta_python" ], "update_time": "2025-04-25", "versions": 1 @@ -5735,24 +5891,24 @@ "name:iwc" ], "tools": [ + "tp_cut_tool", + "clair3", + "table_compute", + "samtools_depth", "bcftools_consensus", + "CONVERTER_gz_to_uncompressed", "Paste1", - "samtools_coverage", - "regexColumn1", "bcftools_norm", - "CONVERTER_gz_to_uncompressed", - "snpSift_filter", - "tp_cut_tool", "Cut1", "snpSift_extractFields", - "clair3", + "samtools_coverage", + "snpSift_filter", "collapse_dataset", - "Remove beginning1", - "table_compute", - "tp_head_tool", + "minimap2", "Count1", - "samtools_depth", - "minimap2" + "tp_head_tool", + "Remove beginning1", + "regexColumn1" ], "update_time": "2025-04-25", "versions": 1 @@ -5784,11 +5940,11 @@ "name:microgalaxy" ], "tools": [ - "fastq_dl", - "CONVERTER_uncompressed_to_gz", "tp_awk_tool", + "CONVERTER_uncompressed_to_gz", "CONVERTER_gz_to_uncompressed", - "__MERGE_COLLECTION__" + "__MERGE_COLLECTION__", + "fastq_dl" ], "update_time": "2025-04-25", "versions": 1 @@ -5804,8 +5960,8 @@ "doi": "", "edam_operation": [ "k-mer counting", - "Visualisation", "Formatting", + "Visualisation", "Mapping" ], "edam_topic": [], @@ -5825,10 +5981,10 @@ "name:microgalaxy" ], "tools": [ - "tp_awk_tool", - "__FILTER_FROM_FILE__", "bedtools_maskfastabed", "mapseq", + "tp_awk_tool", + "__FILTER_FROM_FILE__", "collection_element_identifiers", "taxonomy_krona_chart", "biom_convert", @@ -5847,14 +6003,14 @@ "deprecated": false, "doi": "", "edam_operation": [ - "Sequence trimming", - "Sequence composition calculation", - "Nucleic acid design", "Statistical calculation", + "Sequencing quality control", + "Sequence contamination filtering", + "Sequence trimming", "Validation", + "Nucleic acid design", "Read pre-processing", - "Sequence contamination filtering", - "Sequencing quality control" + "Sequence composition calculation" ], "edam_topic": [], "id": "20b7ae4b517a80fd", @@ -5873,17 +6029,17 @@ "name:microgalaxy" ], "tools": [ + "fastp", "cshl_fasta_formatter", "tp_find_and_replace", - "fastq_to_fasta_python", "multiqc", + "trimmomatic", "fastqc", "__UNZIP_COLLECTION__", - "prinseq", "mgnify_seqprep", - "fastp", - "trimmomatic", - "fastq_filter" + "fastq_filter", + "prinseq", + "fastq_to_fasta_python" ], "update_time": "2025-04-25", "versions": 1 @@ -5898,13 +6054,13 @@ "deprecated": false, "doi": "", "edam_operation": [ - "Sequence trimming", - "Read pre-processing", - "Sequence composition calculation", - "Sequence contamination filtering", + "Sequencing quality control", "Statistical calculation", + "Sequence contamination filtering", + "Sequence trimming", "Validation", - "Sequencing quality control" + "Read pre-processing", + "Sequence composition calculation" ], "edam_topic": [], "id": "46f184a0e95f3c1c", @@ -5925,12 +6081,12 @@ "tools": [ "cshl_fasta_formatter", "tp_find_and_replace", - "fastq_to_fasta_python", "multiqc", + "trimmomatic", "fastqc", + "fastq_filter", "prinseq", - "trimmomatic", - "fastq_filter" + "fastq_to_fasta_python" ], "update_time": "2025-04-25", "versions": 1 @@ -5945,19 +6101,19 @@ "deprecated": false, "doi": "", "edam_operation": [ - "Visualisation", - "Sequence composition calculation", "Statistical calculation", - "Validation", - "Sequence contamination filtering", - "Box-Whisker plot plotting", - "Sequence alignment analysis", "Taxonomic classification", - "Data handling", "Pairwise sequence alignment", + "Box-Whisker plot plotting", "Aggregation", + "Data handling", "Scatter plot plotting", - "Sequencing quality control" + "Sequencing quality control", + "Sequence contamination filtering", + "Sequence alignment analysis", + "Validation", + "Sequence composition calculation", + "Visualisation" ], "edam_topic": [], "id": "a8b9252fad5fe06a", @@ -5977,23 +6133,23 @@ "name:iwc" ], "tools": [ + "Add_a_column1", + "fastp", "collection_column_join", - "Grep1", - "samtools_fastx", - "regexColumn1", "multiqc", "kraken2", + "samtools_fastx", "fastqc", - "bamtools_split_mapped", + "collapse_dataset", "nanoplot", - "porechop", + "minimap2", + "Grep1", "__FILTER_FAILED_DATASETS__", - "krakentools_extract_kraken_reads", - "fastp", - "collapse_dataset", + "bamtools_split_mapped", + "porechop", "Cut1", - "Add_a_column1", - "minimap2" + "regexColumn1", + "krakentools_extract_kraken_reads" ], "update_time": "2025-04-25", "versions": 1 @@ -6006,11 +6162,11 @@ "deprecated": false, "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Sequence assembly validation", "Statistical calculation", + "Sequencing quality control", "Validation", - "Sequencing quality control" + "Sequence composition calculation", + "Sequence assembly validation" ], "edam_topic": [], "id": "f05ed1e5c5dfffa9", @@ -6027,13 +6183,13 @@ "name:microgalaxy" ], "tools": [ + "__RELABEL_FROM_FILE__", + "checkm2", + "collection_element_identifiers", "multiqc", "__FLATTEN__", - "collection_element_identifiers", - "__RELABEL_FROM_FILE__", "__MERGE_COLLECTION__", - "regex1", - "checkm2" + "regex1" ], "update_time": "2025-12-08", "versions": 1 @@ -6068,24 +6224,24 @@ "name:iwc" ], "tools": [ + "tp_cut_tool", + "clair3", + "table_compute", + "samtools_depth", "bcftools_consensus", + "CONVERTER_gz_to_uncompressed", "Paste1", - "samtools_coverage", - "regexColumn1", "bcftools_norm", - "CONVERTER_gz_to_uncompressed", - "snpSift_filter", - "tp_cut_tool", "Cut1", "snpSift_extractFields", - "clair3", + "samtools_coverage", + "snpSift_filter", "collapse_dataset", - "Remove beginning1", - "table_compute", - "tp_head_tool", + "minimap2", "Count1", - "samtools_depth", - "minimap2" + "tp_head_tool", + "Remove beginning1", + "regexColumn1" ], "update_time": "2025-04-25", "versions": 1 @@ -6120,24 +6276,24 @@ "name:iwc" ], "tools": [ + "tp_cut_tool", + "clair3", + "table_compute", + "samtools_depth", "bcftools_consensus", + "CONVERTER_gz_to_uncompressed", "Paste1", - "samtools_coverage", - "regexColumn1", "bcftools_norm", - "CONVERTER_gz_to_uncompressed", - "snpSift_filter", - "tp_cut_tool", "Cut1", "snpSift_extractFields", - "clair3", + "samtools_coverage", + "snpSift_filter", "collapse_dataset", - "Remove beginning1", - "table_compute", - "tp_head_tool", + "minimap2", "Count1", - "samtools_depth", - "minimap2" + "tp_head_tool", + "Remove beginning1", + "regexColumn1" ], "update_time": "2025-04-25", "versions": 1 diff --git a/communities/microgalaxy/resources/curated_workflows.tsv b/communities/microgalaxy/resources/curated_workflows.tsv index 6e3b5d442..8453fd035 100644 --- a/communities/microgalaxy/resources/curated_workflows.tsv +++ b/communities/microgalaxy/resources/curated_workflows.tsv @@ -1,151 +1,154 @@ Name Source ID Link Creators Tags Creation time Update time Latest version Versions Number of steps Tools EDAM operations EDAM topics License DOI Projects To keep Deprecated -metagenomic-raw-reads-amr-analysis/main WorkflowHub 2068 https://workflowhub.eu/workflows/2068?version=2 ABRomics None, Hugo Lefeuvre 2026-02-26 2026-05-14 2 2 20.0 "table_pandas_rename_column, multiqc, groot, collection_element_identifiers, tooldistillator_summarize, tooldistillator, Remove a collection level so that outputs can be taken into account by tooldistillator -__FLATTEN__, __FILTER_FAILED_DATASETS__, tp_text_file_with_recurring_lines, __UNZIP_COLLECTION__, sylph_profile, argnorm, __RELABEL_FROM_FILE__, Removal of the first line because it is not necessary for tooldistillator -Remove beginning1, Removal of the first argNorm line that causes a multiQC error -Remove beginning1, fastq_paired_end_interlacer, deeparg_short_reads" Data parsing, Gene functional annotation, Validation, Taxonomic classification, Sequencing quality control, Antimicrobial resistance prediction GPL-3.0-or-later Intergalactic Workflow Commission (IWC) True False -cgmlst-bacterial-genome/main WorkflowHub 2055 https://workflowhub.eu/workflows/2055?version=2 ABRomics None, Clea Siguret, Hugo Lefeuvre 2026-03-13 2026-05-14 2 2 3.0 coreprofiler_allele_calling, tooldistillator_summarize, tooldistillator Multilocus sequence typing, Data parsing GPL-3.0-or-later Intergalactic Workflow Commission (IWC) True False -bacterial-quality-and-contamination-control-post-assembly/main WorkflowHub 1882 https://workflowhub.eu/workflows/1882?version=3 ABRomics None, Pierre Marin, Clea Siguret 2025-12-04 2026-05-13 3 3 14.0 pick_value, kraken2, tooldistillator_summarize, tooldistillator, est_abundance, quast, collapse_dataset, checkm2, recentrifuge Visualisation, Sequence composition calculation, Sequence assembly validation, Statistical calculation, Validation, Cross-assembly, Data parsing, Expression analysis, Taxonomic classification, Sequencing quality control GPL-3.0-or-later Intergalactic Workflow Commission (IWC) True False -sars-cov-2-pe-illumina-artic-ivar-analysis/SARS-COV-2-ILLUMINA-AMPLICON-IVAR-PANGOLIN-NEXTCLADE WorkflowHub 155 https://workflowhub.eu/workflows/155?version=7 Peter van Heusden virology 2026-03-10 2026-05-13 7 7 16.0 ivar_consensus, samtools_view, multiqc, __FLATTEN__, nextclade, samtools_stats, pangolin, bwa_mem, qualimap_bamqc, ivar_trim, fastp, snpeff_sars_cov_2, tp_cat, tp_sed_tool, ivar_variants Methylation analysis, Sequence alignment, Genome indexing, SNP detection, Validation, Read mapping, Variant calling, Primer removal, Sequence contamination filtering, Generation, Tree-based sequence alignment, Variant classification, Sequencing quality control MIT Intergalactic Workflow Commission (IWC) True False -sars-cov-2-pe-illumina-wgs-variant-calling/COVID-19-PE-WGS-ILLUMINA WorkflowHub 113 https://workflowhub.eu/workflows/113?version=4 Wolfgang Maier virology, covid-19, covid19.galaxyproject.org, emergen_validated 2021-12-21 2026-05-14 4 4 11.0 samtools_view, multiqc, samtools_stats, bwa_mem, lofreq_viterbi, lofreq_indelqual, fastp, picard_MarkDuplicates, lofreq_call, lofreq_filter, snpeff_sars_cov_2 Formatting, Sequence alignment, Genome indexing, SNP detection, Validation, Read mapping, Sequence contamination filtering, Generation, Sequencing quality control MIT Intergalactic Workflow Commission (IWC) True False -generic-non-segmented-viral-variant-calling/main WorkflowHub 1876 https://workflowhub.eu/workflows/1876?version=2 Peter van Heusden, Wolfgang Maier virology 2025-12-05 2026-05-13 2 2 23.0 samtools_view, __FILTER_FAILED_DATASETS__, qualimap_bamqc, tp_sed_tool, snpEff, __FLATTEN__, samtools_stats, bwa_mem, lofreq_viterbi, calculate_numeric_param, collapse_dataset, ivar_variants, ivar_consensus, tp_find_and_replace, map_param_value, ivar_trim, fastp, tp_cat, snpSift_extractFields, pick_value, multiqc, snpEff_build_gb Sequence alignment, Genome indexing, Validation, Read mapping, Primer removal, Sequence contamination filtering, Generation, Sequencing quality control AGPL-3.0-or-later Intergalactic Workflow Commission (IWC) True False -influenza-isolates-consensus-and-subtyping/main WorkflowHub 1260 https://workflowhub.eu/workflows/1260?version=3 Viktoria Isabel Schwarz, Wolfgang Maier, Aaron Kolbecher, Saim Momin virology 2026-02-12 2026-05-13 3 3 68.0 "wc_gnu, samtools_view, __FILTER_FAILED_DATASETS__, tp_text_file_with_recurring_lines, qualimap_bamqc, bwa mem will fail if no reference for any segment got suggested by vapor, i.e. the reference genome is empty. In that case, we need to skip further analysis of the sample. -__FILTER_FAILED_DATASETS__, __HARMONIZELISTS__, Show beginning1, Filter1, __FLATTEN__, collection_element_identifiers, bwa_mem, __RELABEL_FROM_FILE__, __APPLY_RULES__, __MERGE_COLLECTION__, collapse_dataset, Paste1, bamtools_split_ref, snipit, Grep1, ivar_consensus, param_value_from_file, tp_find_and_replace, __UNZIP_COLLECTION__, tp_easyjoin_tool, fastp, tp_cat, Cut1, rbc_mafft, __FILTER_FROM_FILE__, vapor, This seemingly no-op transformation will remove samples with no remaining segment results (cases where vapor failed for every segment). -__APPLY_RULES__, seqtk_subseq, iqtree, __DUPLICATE_FILE_TO_COLLECTION__" Multiple sequence alignment, Sequence alignment, Genome indexing, Sequence file editing, Phylogenetic analysis, Read mapping, Sequence analysis, Primer removal, Base position variability plotting, Sequence contamination filtering, Data retrieval, Sequence alignment analysis, Data handling, Generation, Sequencing quality control, De-novo assembly AGPL-3.0-or-later Intergalactic Workflow Commission (IWC) True False -pox-virus-amplicon/main WorkflowHub 439 https://workflowhub.eu/workflows/439?version=4 Viktoria Isabel Schwarz, Wolfgang Maier virology, pox 2025-10-11 2026-05-13 4 4 40.0 compose_text_param, samtools_view, __FILTER_FAILED_DATASETS__, qualimap_bamqc, tp_sed_tool, fasta_compute_length, samtools_merge, __FLATTEN__, collection_element_identifiers, samtools_stats, bwa_mem, __APPLY_RULES__, __ZIP_COLLECTION__, Grep1, ivar_consensus, param_value_from_file, split_file_to_collection, ivar_trim, fastp, tp_cat, Cut1, __SORTLIST__, EMBOSS: maskseq51, multiqc, datamash_ops Sequence alignment, Genome indexing, Validation, Read mapping, Sequence analysis, Primer removal, Local alignment, Sequence contamination filtering, Global alignment, Sequence alignment analysis, Generation, Sequencing quality control MIT Intergalactic Workflow Commission (IWC) True False -allele-based-pathogen-identification/main WorkflowHub 1063 https://workflowhub.eu/workflows/1063?version=5 Engy Nasr, Bérénice Batut, Paul Zierep 2025-03-26 2026-05-14 5 5 23.0 bcftools_consensus, Paste1, samtools_coverage, regexColumn1, bcftools_norm, CONVERTER_gz_to_uncompressed, snpSift_filter, tp_cut_tool, Cut1, snpSift_extractFields, clair3, collapse_dataset, Remove beginning1, table_compute, tp_head_tool, Count1, samtools_depth, minimap2 Pairwise sequence alignment, Variant calling MIT Intergalactic Workflow Commission (IWC) True False -mgnify-amplicon-pipeline-v5-complete/main WorkflowHub 1274 https://workflowhub.eu/workflows/1274?version=2 Rand Zoabi, Paul Zierep 2025-03-26 2026-05-14 2 2 20.0 , fastq_dl, CONVERTER_uncompressed_to_gz, tp_awk_tool, CONVERTER_gz_to_uncompressed, __MERGE_COLLECTION__ Apache-2.0 Intergalactic Workflow Commission (IWC) True False -mgnify-amplicon-pipeline-v5-its/main WorkflowHub 1273 https://workflowhub.eu/workflows/1273?version=2 Rand Zoabi, Paul Zierep 2025-03-26 2026-05-14 2 2 30.0 , tp_awk_tool, __FILTER_FROM_FILE__, bedtools_maskfastabed, mapseq, collection_element_identifiers, taxonomy_krona_chart, biom_convert, __FILTER_EMPTY_DATASETS__ k-mer counting, Visualisation, Formatting, Mapping Apache-2.0 Intergalactic Workflow Commission (IWC) True False -mgnify-amplicon-pipeline-v5-quality-control-paired-end/main WorkflowHub 1272 https://workflowhub.eu/workflows/1272?version=2 Rand Zoabi, Paul Zierep 2025-03-26 2026-05-14 2 2 17.0 cshl_fasta_formatter, tp_find_and_replace, fastq_to_fasta_python, multiqc, fastqc, __UNZIP_COLLECTION__, prinseq, mgnify_seqprep, fastp, trimmomatic, fastq_filter Sequence trimming, Sequence composition calculation, Nucleic acid design, Statistical calculation, Validation, Read pre-processing, Sequence contamination filtering, Sequencing quality control Apache-2.0 Intergalactic Workflow Commission (IWC) True False -mgnify-amplicon-pipeline-v5-quality-control-single-end/main WorkflowHub 1271 https://workflowhub.eu/workflows/1271?version=3 Rand Zoabi, Paul Zierep 2025-03-26 2026-05-14 3 3 14.0 cshl_fasta_formatter, tp_find_and_replace, fastq_to_fasta_python, multiqc, fastqc, prinseq, trimmomatic, fastq_filter Sequence trimming, Read pre-processing, Sequence composition calculation, Sequence contamination filtering, Statistical calculation, Validation, Sequencing quality control Apache-2.0 Intergalactic Workflow Commission (IWC) True False -mgnify-amplicon-pipeline-v5-rrna-prediction/main WorkflowHub 1270 https://workflowhub.eu/workflows/1270?version=2 Rand Zoabi, Paul Zierep 2025-03-26 2026-05-14 2 2 47.0 , bedtools_getfastabed, tp_awk_tool, cshl_fasta_formatter, __FILTER_FROM_FILE__, infernal_cmsearch, mapseq, collection_element_identifiers, taxonomy_krona_chart, cmsearch_deoverlap, biom_convert, gops_concat_1, __FILTER_EMPTY_DATASETS__, query_tabular Visualisation, Alignment, Formatting, Mapping, k-mer counting, Comparison, Nucleic acid feature detection Apache-2.0 Intergalactic Workflow Commission (IWC) True False -mgnify-amplicon-taxonomic-summary-tables/main WorkflowHub 1269 https://workflowhub.eu/workflows/1269?version=2 Rand Zoabi 2025-03-26 2026-05-14 2 2 10.0 Grouping1, collection_column_join, tp_awk_tool, filter_tabular, query_tabular MIT Intergalactic Workflow Commission (IWC) True False -clinicalmp-discovery/main WorkflowHub 1225 https://workflowhub.eu/workflows/1225?version=1 Subina Mehta 2024-12-10 2026-05-13 1 1 24.0 Grouping1, Grep1, fasta2tab, fasta_merge_files_and_filter_unique_sequences, Filter1, ident_params, Remove beginning1, msconvert, Cut1, query_tabular, dbbuilder, fasta_cli, filter_tabular, tp_cat, search_gui, peptide_shaker, maxquant Visualisation, Filtering, Formatting, Statistical calculation, Imputation, Standardisation and normalisation, Heat map generation, Protein quantification, Principal component plotting, Clustering CC-BY-4.0 Intergalactic Workflow Commission (IWC) True False -clinicalmp-data-interpretation/main WorkflowHub 1219 https://workflowhub.eu/workflows/1219?version=1 GalaxyP 2024-11-26 2026-05-13 1 1 6.0 Grep1, msstatstmt, unipept Visualisation, Prediction and recognition CC-BY-4.0 Intergalactic Workflow Commission (IWC) True False -clinicalmp-verification/main WorkflowHub 1218 https://workflowhub.eu/workflows/1218?version=1 Pratik Jagtap 2024-11-26 2026-05-13 1 1 19.0 Grouping1, fasta_merge_files_and_filter_unique_sequences, Filter1, uniprotxml_downloader, Cut1, pepquery2, tp_cat, dbbuilder, Remove beginning1, collapse_dataset, query_tabular CC-BY-4.0 Intergalactic Workflow Commission (IWC) True False -clinicalmp-database-generation/main WorkflowHub 1216 https://workflowhub.eu/workflows/1216?version=1 Subina Mehta 2024-11-23 2026-05-13 1 1 3.0 metanovo, fasta_merge_files_and_filter_unique_sequences Expression analysis, Protein identification, Tag-based peptide identification, de Novo sequencing, Target-Decoy CC-BY-4.0 Intergalactic Workflow Commission (IWC) True False -clinicalmp-quantitation/main WorkflowHub 1177 https://workflowhub.eu/workflows/1177?version=1 GalaxyP 2024-10-07 2026-05-14 1 1 7.0 "maxquant, Quantified-Proteins -Grouping1, extract proteins -Cut1, extract peptides +metagenomic-raw-reads-amr-analysis/main WorkflowHub 2068 https://workflowhub.eu/workflows/2068?version=2 ABRomics None, Hugo Lefeuvre 2026-02-26 2026-05-14 2 2 20.0 "tooldistillator_summarize, __RELABEL_FROM_FILE__, groot, collection_element_identifiers, sylph_profile, deeparg_short_reads, fastq_paired_end_interlacer, argnorm, table_pandas_rename_column, multiqc, Removal of the first line because it is not necessary for tooldistillator +Remove beginning1, tp_text_file_with_recurring_lines, tooldistillator, __UNZIP_COLLECTION__, Removal of the first argNorm line that causes a multiQC error +Remove beginning1, __FILTER_FAILED_DATASETS__, Remove a collection level so that outputs can be taken into account by tooldistillator +__FLATTEN__" Data parsing, Taxonomic classification, Gene functional annotation, Sequencing quality control, Antimicrobial resistance prediction, Validation GPL-3.0-or-later Intergalactic Workflow Commission (IWC) True False +cgmlst-bacterial-genome/main WorkflowHub 2055 https://workflowhub.eu/workflows/2055?version=2 ABRomics None, Clea Siguret, Hugo Lefeuvre 2026-03-13 2026-05-14 2 2 3.0 tooldistillator, tooldistillator_summarize, coreprofiler_allele_calling Data parsing, Multilocus sequence typing GPL-3.0-or-later Intergalactic Workflow Commission (IWC) True False +bacterial-quality-and-contamination-control-post-assembly/main WorkflowHub 1882 https://workflowhub.eu/workflows/1882?version=3 ABRomics None, Pierre Marin, Clea Siguret 2025-12-04 2026-05-13 3 3 14.0 tooldistillator_summarize, recentrifuge, checkm2, est_abundance, kraken2, pick_value, collapse_dataset, tooldistillator, quast Statistical calculation, Taxonomic classification, Expression analysis, Sequence assembly validation, Data parsing, Sequencing quality control, Validation, Sequence composition calculation, Visualisation, Cross-assembly GPL-3.0-or-later Intergalactic Workflow Commission (IWC) True False +sars-cov-2-pe-illumina-artic-ivar-analysis/SARS-COV-2-ILLUMINA-AMPLICON-IVAR-PANGOLIN-NEXTCLADE WorkflowHub 155 https://workflowhub.eu/workflows/155?version=7 Peter van Heusden virology 2026-03-10 2026-05-13 7 7 16.0 fastp, ivar_variants, nextclade, ivar_trim, samtools_view, ivar_consensus, qualimap_bamqc, multiqc, __FLATTEN__, tp_sed_tool, snpeff_sars_cov_2, samtools_stats, tp_cat, pangolin, bwa_mem Read mapping, Generation, Variant classification, Variant calling, Tree-based sequence alignment, Sequence alignment, Genome indexing, Sequencing quality control, Sequence contamination filtering, Validation, Methylation analysis, Primer removal, SNP detection MIT Intergalactic Workflow Commission (IWC) True False +sars-cov-2-pe-illumina-wgs-variant-calling/COVID-19-PE-WGS-ILLUMINA WorkflowHub 113 https://workflowhub.eu/workflows/113?version=4 Wolfgang Maier virology, covid-19, covid19.galaxyproject.org, emergen_validated 2021-12-21 2026-05-14 4 4 11.0 lofreq_filter, fastp, picard_MarkDuplicates, lofreq_viterbi, samtools_view, lofreq_call, multiqc, snpeff_sars_cov_2, samtools_stats, lofreq_indelqual, bwa_mem Formatting, Generation, Sequence alignment, Genome indexing, Sequencing quality control, Sequence contamination filtering, Validation, Read mapping, SNP detection MIT Intergalactic Workflow Commission (IWC) True False +generic-non-segmented-viral-variant-calling/main WorkflowHub 1876 https://workflowhub.eu/workflows/1876?version=2 Peter van Heusden, Wolfgang Maier virology 2025-12-05 2026-05-13 2 2 23.0 ivar_variants, __FLATTEN__, snpSift_extractFields, map_param_value, collapse_dataset, tp_cat, fastp, samtools_view, snpEff, tp_find_and_replace, calculate_numeric_param, samtools_stats, lofreq_viterbi, snpEff_build_gb, ivar_consensus, pick_value, ivar_trim, qualimap_bamqc, multiqc, tp_sed_tool, __FILTER_FAILED_DATASETS__, bwa_mem Sequencing quality control, Sequence contamination filtering, Generation, Validation, Read mapping, Sequence alignment, Primer removal, Genome indexing AGPL-3.0-or-later Intergalactic Workflow Commission (IWC) True False +influenza-isolates-consensus-and-subtyping/main WorkflowHub 1260 https://workflowhub.eu/workflows/1260?version=3 Viktoria Isabel Schwarz, Wolfgang Maier, Aaron Kolbecher, Saim Momin virology 2026-02-12 2026-05-13 3 3 68.0 "collection_element_identifiers, Paste1, __FLATTEN__, snipit, bwa mem will fail if no reference for any segment got suggested by vapor, i.e. the reference genome is empty. In that case, we need to skip further analysis of the sample. +__FILTER_FAILED_DATASETS__, collapse_dataset, bamtools_split_ref, tp_cat, Show beginning1, param_value_from_file, fastp, samtools_view, tp_find_and_replace, rbc_mafft, tp_text_file_with_recurring_lines, __APPLY_RULES__, __FILTER_FROM_FILE__, ivar_consensus, __HARMONIZELISTS__, __DUPLICATE_FILE_TO_COLLECTION__, This seemingly no-op transformation will remove samples with no remaining segment results (cases where vapor failed for every segment). +__APPLY_RULES__, Grep1, iqtree, vapor, __RELABEL_FROM_FILE__, wc_gnu, seqtk_subseq, tp_easyjoin_tool, qualimap_bamqc, __MERGE_COLLECTION__, __UNZIP_COLLECTION__, __FILTER_FAILED_DATASETS__, Filter1, Cut1, bwa_mem" Data retrieval, Generation, Multiple sequence alignment, Data handling, De-novo assembly, Sequence file editing, Sequence alignment, Base position variability plotting, Genome indexing, Sequencing quality control, Sequence contamination filtering, Sequence alignment analysis, Sequence analysis, Read mapping, Primer removal, Phylogenetic analysis AGPL-3.0-or-later Intergalactic Workflow Commission (IWC) True False +pox-virus-amplicon/main WorkflowHub 439 https://workflowhub.eu/workflows/439?version=4 Viktoria Isabel Schwarz, Wolfgang Maier virology, pox 2025-10-11 2026-05-13 4 4 40.0 collection_element_identifiers, __FLATTEN__, EMBOSS: maskseq51, tp_cat, datamash_ops, param_value_from_file, fastp, samtools_view, samtools_merge, samtools_stats, __APPLY_RULES__, __ZIP_COLLECTION__, ivar_consensus, __SORTLIST__, Grep1, fasta_compute_length, ivar_trim, qualimap_bamqc, multiqc, split_file_to_collection, compose_text_param, tp_sed_tool, __FILTER_FAILED_DATASETS__, Cut1, bwa_mem Generation, Sequence alignment, Genome indexing, Sequencing quality control, Sequence contamination filtering, Sequence alignment analysis, Validation, Global alignment, Sequence analysis, Read mapping, Primer removal, Local alignment MIT Intergalactic Workflow Commission (IWC) True False +allele-based-pathogen-identification/main WorkflowHub 1063 https://workflowhub.eu/workflows/1063?version=5 Engy Nasr, Bérénice Batut, Paul Zierep 2025-03-26 2026-05-14 5 5 23.0 tp_cut_tool, clair3, table_compute, samtools_depth, bcftools_consensus, CONVERTER_gz_to_uncompressed, Paste1, bcftools_norm, Cut1, snpSift_extractFields, samtools_coverage, snpSift_filter, collapse_dataset, minimap2, Count1, tp_head_tool, Remove beginning1, regexColumn1 Pairwise sequence alignment, Variant calling MIT Intergalactic Workflow Commission (IWC) True False +mgnify-amplicon-pipeline-v5-complete/main WorkflowHub 1274 https://workflowhub.eu/workflows/1274?version=2 Rand Zoabi, Paul Zierep 2025-03-26 2026-05-14 2 2 20.0 , tp_awk_tool, CONVERTER_uncompressed_to_gz, CONVERTER_gz_to_uncompressed, __MERGE_COLLECTION__, fastq_dl Apache-2.0 Intergalactic Workflow Commission (IWC) True False +mgnify-amplicon-pipeline-v5-its/main WorkflowHub 1273 https://workflowhub.eu/workflows/1273?version=2 Rand Zoabi, Paul Zierep 2025-03-26 2026-05-14 2 2 30.0 , bedtools_maskfastabed, mapseq, tp_awk_tool, __FILTER_FROM_FILE__, collection_element_identifiers, taxonomy_krona_chart, biom_convert, __FILTER_EMPTY_DATASETS__ k-mer counting, Formatting, Visualisation, Mapping Apache-2.0 Intergalactic Workflow Commission (IWC) True False +mgnify-amplicon-pipeline-v5-quality-control-paired-end/main WorkflowHub 1272 https://workflowhub.eu/workflows/1272?version=2 Rand Zoabi, Paul Zierep 2025-03-26 2026-05-14 2 2 17.0 fastp, cshl_fasta_formatter, tp_find_and_replace, multiqc, trimmomatic, fastqc, __UNZIP_COLLECTION__, mgnify_seqprep, fastq_filter, prinseq, fastq_to_fasta_python Statistical calculation, Sequencing quality control, Sequence contamination filtering, Sequence trimming, Validation, Nucleic acid design, Read pre-processing, Sequence composition calculation Apache-2.0 Intergalactic Workflow Commission (IWC) True False +mgnify-amplicon-pipeline-v5-quality-control-single-end/main WorkflowHub 1271 https://workflowhub.eu/workflows/1271?version=3 Rand Zoabi, Paul Zierep 2025-03-26 2026-05-14 3 3 14.0 cshl_fasta_formatter, tp_find_and_replace, multiqc, trimmomatic, fastqc, fastq_filter, prinseq, fastq_to_fasta_python Sequencing quality control, Statistical calculation, Sequence contamination filtering, Sequence trimming, Validation, Read pre-processing, Sequence composition calculation Apache-2.0 Intergalactic Workflow Commission (IWC) True False +mgnify-amplicon-pipeline-v5-rrna-prediction/main WorkflowHub 1270 https://workflowhub.eu/workflows/1270?version=2 Rand Zoabi, Paul Zierep 2025-03-26 2026-05-14 2 2 47.0 , cshl_fasta_formatter, tp_awk_tool, mapseq, collection_element_identifiers, __FILTER_FROM_FILE__, taxonomy_krona_chart, biom_convert, cmsearch_deoverlap, infernal_cmsearch, bedtools_getfastabed, gops_concat_1, query_tabular, __FILTER_EMPTY_DATASETS__ k-mer counting, Formatting, Comparison, Mapping, Alignment, Nucleic acid feature detection, Visualisation Apache-2.0 Intergalactic Workflow Commission (IWC) True False +mgnify-amplicon-taxonomic-summary-tables/main WorkflowHub 1269 https://workflowhub.eu/workflows/1269?version=2 Rand Zoabi 2025-03-26 2026-05-14 2 2 10.0 tp_awk_tool, collection_column_join, Grouping1, filter_tabular, query_tabular MIT Intergalactic Workflow Commission (IWC) True False +clinicalmp-discovery/main WorkflowHub 1225 https://workflowhub.eu/workflows/1225?version=1 Subina Mehta 2024-12-10 2026-05-13 1 1 24.0 query_tabular, peptide_shaker, Remove beginning1, tp_cat, search_gui, Grouping1, fasta_cli, ident_params, maxquant, msconvert, dbbuilder, Grep1, filter_tabular, Filter1, fasta_merge_files_and_filter_unique_sequences, Cut1, fasta2tab Statistical calculation, Imputation, Formatting, Heat map generation, Filtering, Standardisation and normalisation, Protein quantification, Clustering, Principal component plotting, Visualisation CC-BY-4.0 Intergalactic Workflow Commission (IWC) True False +clinicalmp-data-interpretation/main WorkflowHub 1219 https://workflowhub.eu/workflows/1219?version=1 GalaxyP 2024-11-26 2026-05-13 1 1 6.0 msstatstmt, Grep1, unipept Prediction and recognition, Visualisation CC-BY-4.0 Intergalactic Workflow Commission (IWC) True False +clinicalmp-verification/main WorkflowHub 1218 https://workflowhub.eu/workflows/1218?version=1 Pratik Jagtap 2024-11-26 2026-05-13 1 1 19.0 Filter1, uniprotxml_downloader, Grouping1, Cut1, collapse_dataset, dbbuilder, query_tabular, tp_cat, fasta_merge_files_and_filter_unique_sequences, Remove beginning1, pepquery2 CC-BY-4.0 Intergalactic Workflow Commission (IWC) True False +clinicalmp-database-generation/main WorkflowHub 1216 https://workflowhub.eu/workflows/1216?version=1 Subina Mehta 2024-11-23 2026-05-13 1 1 3.0 metanovo, fasta_merge_files_and_filter_unique_sequences de Novo sequencing, Target-Decoy, Expression analysis, Tag-based peptide identification, Protein identification CC-BY-4.0 Intergalactic Workflow Commission (IWC) True False +clinicalmp-quantitation/main WorkflowHub 1177 https://workflowhub.eu/workflows/1177?version=1 GalaxyP 2024-10-07 2026-05-14 1 1 7.0 "extracting microbial Proteins +Grep1, extract proteins Cut1, Quantified-Peptides -Grouping1, extracting microbial Proteins -Grep1, extracting microbial Peptides -Grep1" Visualisation, Statistical calculation, Imputation, Standardisation and normalisation, Heat map generation, Protein quantification, Principal component plotting, Clustering CC-BY-4.0 Intergalactic Workflow Commission (IWC) True False -bacterial-genome-assembly/main WorkflowHub 1043 https://workflowhub.eu/workflows/1043?version=12 Abromics None, Pierre Marin, Clea Siguret abromics, assembly, fastq, genomics, bacterial-genomics, paired-end, quality 2025-12-04 2026-05-13 12 12 5.0 bandage_info, bandage_image, tooldistillator, tooldistillator_summarize, shovill Data parsing, Genome assembly, Sequence assembly visualisation GPL-3.0-or-later Intergalactic Workflow Commission (IWC) True False -quality-and-contamination-control/main WorkflowHub 1052 https://workflowhub.eu/workflows/1052?version=11 ABRomics None, Pierre Marin, Clea Siguret abromics, fastq, genomics, bacterial-genomics, paired-end, quality, taxonomy-assignment, trimming 2025-06-19 2026-05-14 11 11 8.0 kraken2, tooldistillator_summarize, tooldistillator, __UNZIP_COLLECTION__, est_abundance, fastp, recentrifuge, __ZIP_COLLECTION__ Cross-assembly, Data parsing, Sequence contamination filtering, Expression analysis, Statistical calculation, Taxonomic classification, Sequencing quality control GPL-3.0-or-later Intergalactic Workflow Commission (IWC) True False -qiime2-III-VI-downsteam/QIIME2-III-V-Phylogeny-Rarefaction-Taxonomic-Analysis WorkflowHub 1090 https://workflowhub.eu/workflows/1090?version=2 Debjyoti Ghosh 2024-11-26 2026-05-14 2 2 3.0 Phylogenetic tree for diversity analysis, Taxonomic analysis, Rarefaction MIT Intergalactic Workflow Commission (IWC) True False -gene-based-pathogen-identification/main WorkflowHub 1062 https://workflowhub.eu/workflows/1062?version=1 Engy Nasr, Bérénice Batut, Paul Zierep 2024-06-26 2026-05-13 1 1 15.0 medaka_consensus_pipeline, param_value_from_file, compose_text_param, __BUILD_LIST__, tp_find_and_replace, abricate, collection_element_identifiers, bandage_image, split_file_to_collection, flye, fasta2tab, tab2fasta Antimicrobial resistance prediction, Base-calling, Variant calling, Cross-assembly, Mapping assembly, Sequence assembly, Genome assembly, Sequence assembly visualisation, De-novo assembly MIT 10.48546/workflowhub.workflow.1062.1 Intergalactic Workflow Commission (IWC) True False -pathogen-detection-pathogfair-samples-aggregation-and-visualisation/main WorkflowHub 1060 https://workflowhub.eu/workflows/1060?version=1 Engy Nasr, Bérénice Batut, Paul Zierep 2024-06-26 2026-05-13 1 1 60.0 Grouping1, regexColumn1, clustalw, __FILTER_FAILED_DATASETS__, fasta2tab, tp_sorted_uniq, fasta_merge_files_and_filter_unique_sequences, collapse_dataset, __FILTER_EMPTY_DATASETS__, bedtools_getfastabed, tp_multijoin_tool, ggplot2_heatmap, Cut1, Remove beginning1, fasttree, tp_split_on_column, collection_column_join, tp_replace_in_column, newick_display, regex1, Count1, tab2fasta Phylogenetic tree generation (from molecular sequences), Visualisation, Phylogenetic tree generation (maximum likelihood and Bayesian methods), Multiple sequence alignment, Mapping, Phylogenetic tree reconstruction, Phylogenetic tree analysis, Phylogenetic tree generation MIT 10.48546/workflowhub.workflow.1060.1 Intergalactic Workflow Commission (IWC) True False -taxonomy-profiling-and-visualization-with-krona/main WorkflowHub 1059 https://workflowhub.eu/workflows/1059?version=1 Engy Nasr, Bérénice Batut, Paul Zierep 2024-06-26 2026-05-13 1 1 3.0 kraken2, taxonomy_krona_chart, krakentools_kreport2krona Visualisation, Taxonomic classification, Aggregation MIT 10.48546/workflowhub.workflow.1059.1 Intergalactic Workflow Commission (IWC) True False -bacterial_genome_annotation/main WorkflowHub 1050 https://workflowhub.eu/workflows/1050?version=13 ABRomics None, Pierre Marin, Clea Siguret abromics, annotation, genomics, bacterial-genomics, fasta, genome-annotation 2025-12-06 2026-05-13 13 13 6.0 isescan, bakta, integron_finder, tooldistillator_summarize, tooldistillator, plasmidfinder Scaffolding, Multilocus sequence typing, Structural variation detection, Sequence motif recognition, Genome annotation, Data parsing, Genome assembly, Protein feature detection, Nucleic acid feature detection GPL-3.0-or-later Intergalactic Workflow Commission (IWC) True False -amr_gene_detection/main WorkflowHub 1049 https://workflowhub.eu/workflows/1049?version=9 ABRomics None, Pierre Marin, Clea Siguret abromics, amr, amr-detection, genomics, antibiotic-resistance, antimicrobial resistance, antimicrobial-resistance-genes, bacterial-genomics, fasta 2025-12-04 2026-05-13 9 9 5.0 abricate, amrfinderplus, staramr_search, tooldistillator_summarize, tooldistillator Data parsing, Antimicrobial resistance prediction GPL-3.0-or-later Intergalactic Workflow Commission (IWC) True False -dada2/main WorkflowHub 790 https://workflowhub.eu/workflows/790?version=3 Matthias Bernt name:amplicon 2025-03-26 2026-05-14 3 3 14.0 dada2_filterAndTrim, dada2_learnErrors, dada2_assignTaxonomyAddspecies, dada2_makeSequenceTable, dada2_seqCounts, __UNZIP_COLLECTION__, dada2_removeBimeraDenovo, __APPLY_RULES__, dada2_mergePairs, dada2_plotQualityProfile, dada2_dada DNA barcoding, Variant calling MIT Intergalactic Workflow Commission (IWC) True False -Refining Genome Annotations with Apollo (prokaryotes) WorkflowHub 749 https://workflowhub.eu/workflows/749?version=1 Anthony Bretaudeau genome-annotation 2024-02-14 2025-11-04 1 1 5.0 jbrowse, iframe, create_or_update, list_organism, create_account Genome visualisation CC-BY-4.0 10.48546/workflowhub.workflow.749.1 EuroScienceGateway True False -TB Variant Analysis v1.0 WorkflowHub 1647 https://workflowhub.eu/workflows/1647?version=2 gtn, galaxy, pathogen, tuberculosis 2026-01-12 2026-01-12 2 2 15.0 bcftools_consensus, tp_awk_tool, tb_profiler_profile, kraken2, __FLATTEN__, multiqc, mosdepth, snippy, qualimap_bamqc, tb_variant_filter, tbvcfreport, fastp, tp_sed_tool, EMBOSS: seqret84 Phylogenetic tree visualisation, Sequence alignment, Validation, Antimicrobial resistance prediction, Phylogenetic tree generation, Variant calling, Sequence analysis, Local alignment, Sequence contamination filtering, Global alignment, Sequence alignment analysis, Taxonomic classification, Sequencing quality control AGPL-3.0-or-later Galaxy Training Network True False -Quality and contamination control in bacterial isolate using Illumina MiSeq Data WorkflowHub 2043 https://workflowhub.eu/workflows/2043?version=1 gtn, galaxy, sequence-analysis 2025-12-22 2025-12-22 1 1 5.0 falco, kraken2, est_abundance, fastp, recentrifuge Visualisation, Statistical calculation, Read mapping, Cross-assembly, Sequence contamination filtering, Expression analysis, Taxonomic classification, Sequencing quality control GPL-3.0-or-later Galaxy Training Network True False -Taxonomic Profiling and Visualization of Metagenomic Data WorkflowHub 1470 https://workflowhub.eu/workflows/1470?version=2 gtn, galaxy, microbiome 2025-12-22 2025-12-22 2 2 10.0 interactive_tool_phinch, metaphlan, kraken2, taxonomy_krona_chart, krakentools_kreport2krona, __UNZIP_COLLECTION__, est_abundance, interactive_tool_pavian, kraken_biom Visualisation, Statistical calculation, Taxonomic classification, Genome annotation, Aggregation MIT Galaxy Training Network True False -Checking expected species and contamination in bacterial isolate WorkflowHub 1674 https://workflowhub.eu/workflows/1674?version=2 ecology, gtn, galaxy 2025-12-22 2025-12-22 2 2 3.0 kraken2, est_abundance, recentrifuge Cross-assembly, Statistical calculation, Taxonomic classification, Expression analysis GPL-3.0-or-later Galaxy Training Network True False -Metagenomic Binning WorkflowHub 2028 https://workflowhub.eu/workflows/2028?version=1 gtn, galaxy, microgalaxy, binning, microbiome 2025-12-08 2025-12-08 1 1 17.0 bowtie2, metabat2, __BUILD_LIST__, concoct_coverage_table, metabat2_jgi_summarize_bam_contig_depths, concoct_extract_fasta_bins, semibin, concoct, samtools_sort, maxbin2, binette, Fasta_to_Contig2Bin, concoct_merge_cut_up_clustering, concoct_cut_up_fasta Sequence assembly, Read mapping, Genome annotation, Sequence clustering, Read binning MIT Galaxy Training Network True False -MGnify's amplicon pipeline v5.0 - ITS WorkflowHub 1856 https://workflowhub.eu/workflows/1856?version=1 amplicon, gtn, galaxy, metagenomics, mgnify_amplicon, name:microgalaxy 2025-08-11 2025-08-11 1 1 30.0 , tp_awk_tool, __FILTER_FROM_FILE__, bedtools_maskfastabed, mapseq, collection_element_identifiers, taxonomy_krona_chart, biom_convert, __FILTER_EMPTY_DATASETS__ k-mer counting, Visualisation, Formatting, Mapping Apache-2.0 Galaxy Training Network True False -MAPseq to ampvis2 WorkflowHub 1855 https://workflowhub.eu/workflows/1855?version=1 gtn, galaxy, microbiome 2025-08-11 2025-08-11 1 1 9.0 collection_column_join, ampvis2_load, tp_awk_tool, collapse_dataset, query_tabular Visualisation, Analysis MIT Galaxy Training Network True False -MGnify's amplicon pipeline v5.0 - Quality control PE WorkflowHub 1854 https://workflowhub.eu/workflows/1854?version=1 amplicon, gtn, galaxy, metagenomics, mgnify_amplicon, name:microgalaxy 2025-08-11 2025-08-11 1 1 17.0 cshl_fasta_formatter, tp_find_and_replace, fastq_to_fasta_python, multiqc, fastqc, __UNZIP_COLLECTION__, prinseq, mgnify_seqprep, fastp, trimmomatic, fastq_filter Sequence trimming, Sequence composition calculation, Nucleic acid design, Statistical calculation, Validation, Read pre-processing, Sequence contamination filtering, Sequencing quality control Apache-2.0 Galaxy Training Network True False -MGnify's amplicon pipeline v5.0 WorkflowHub 1853 https://workflowhub.eu/workflows/1853?version=1 amplicon, gtn, galaxy, metagenomics, mgnify_amplicon, name:microgalaxy 2025-08-11 2025-08-11 1 1 20.0 , fastq_dl, CONVERTER_uncompressed_to_gz, tp_awk_tool, CONVERTER_gz_to_uncompressed, __MERGE_COLLECTION__ Apache-2.0 Galaxy Training Network True False -MGnify amplicon summary tables WorkflowHub 1851 https://workflowhub.eu/workflows/1851?version=1 amplicon, gtn, galaxy, metagenomics, mgnify_amplicon, name:microgalaxy 2025-08-11 2025-08-11 1 1 10.0 Grouping1, collection_column_join, tp_awk_tool, filter_tabular, query_tabular MIT Galaxy Training Network True False -MGnify's amplicon pipeline v5.0 - Quality control SE WorkflowHub 1850 https://workflowhub.eu/workflows/1850?version=1 amplicon, gtn, galaxy, metagenomics, mgnify_amplicon, name:microgalaxy 2025-08-11 2025-08-11 1 1 14.0 cshl_fasta_formatter, tp_find_and_replace, fastq_to_fasta_python, multiqc, fastqc, prinseq, trimmomatic, fastq_filter Sequence trimming, Read pre-processing, Sequence composition calculation, Sequence contamination filtering, Statistical calculation, Validation, Sequencing quality control Apache-2.0 Galaxy Training Network True False -MGnify's amplicon pipeline v5.0 - rRNA prediction WorkflowHub 1842 https://workflowhub.eu/workflows/1842?version=1 amplicon, gtn, galaxy, metagenomics, mgnify_amplicon, name:microgalaxy 2025-08-04 2025-08-11 1 1 47.0 , bedtools_getfastabed, tp_awk_tool, cshl_fasta_formatter, __FILTER_FROM_FILE__, infernal_cmsearch, mapseq, collection_element_identifiers, taxonomy_krona_chart, cmsearch_deoverlap, biom_convert, gops_concat_1, __FILTER_EMPTY_DATASETS__, query_tabular Visualisation, Alignment, Formatting, Mapping, k-mer counting, Comparison, Nucleic acid feature detection Apache-2.0 Galaxy Training Network True False -Workflow 3: Functional Information (quick) WorkflowHub 1447 https://workflowhub.eu/workflows/1447?version=2 asaim, gtn, galaxy, metagenomics 2025-07-14 2025-07-14 2 2 12.0 Grep1, humann_rename_table, tp_find_and_replace, combine_metaphlan2_humann2, Cut1, humann_renorm_table, humann_regroup_table, humann_unpack_pathways, humann_split_stratified_table Species frequency estimation, Taxonomic classification, Phylogenetic analysis MIT Galaxy Training Network True False -Building an amplicon sequence variant (ASV) table from 16S data using DADA2 WorkflowHub 1395 https://workflowhub.eu/workflows/1395?version=2 gtn, galaxy, microbiome 2025-07-07 2025-07-07 2 2 21.0 dada2_filterAndTrim, dada2_learnErrors, dada2_assignTaxonomyAddspecies, tp_replace_in_column, collection_element_identifiers, phyloseq_from_dada2, dada2_makeSequenceTable, dada2_seqCounts, tp_replace_in_line, __UNZIP_COLLECTION__, dada2_dada, dada2_mergePairs, dada2_removeBimeraDenovo, cat1, Add_a_column1, tp_head_tool, dada2_plotQualityProfile, __SORTLIST__ Visualisation, DNA barcoding, Deposition, Analysis, Variant calling MIT Galaxy Training Network True False -Metatranscriptomics analysis using microbiome RNA-seq data WorkflowHub 1466 https://workflowhub.eu/workflows/1466?version=2 gtn, galaxy, microbiome 2025-06-23 2025-06-23 2 2 33.0 Grouping1, metaphlan, fastqc, tp_sort_header_tool, humann, humann_unpack_pathways, graphlan, Grep1, humann_rename_table, tp_find_and_replace, combine_metaphlan_humann, Cut1, bg_sortmerna, fastq_paired_end_interlacer, humann_split_stratified_table, multiqc, cutadapt, taxonomy_krona_chart, graphlan_annotate, humann_renorm_table, humann_regroup_table, export2graphlan Sequence comparison, Phylogenetic tree visualisation, Visualisation, Sequence composition calculation, Statistical calculation, Phylogenetic inference, Validation, Primer removal, Sequence alignment analysis, Sequencing quality control, Phylogenetic analysis, Sequence trimming, Phylogenetic tree editing, Read pre-processing, Species frequency estimation, Taxonomic classification, Sequence similarity search, Conversion, Aggregation MIT Galaxy Training Network True False -Metatranscriptomics analysis using microbiome RNA-seq data - Workflow 2: Community profile WorkflowHub 1451 https://workflowhub.eu/workflows/1451?version=2 gtn, galaxy, microbiome 2025-06-23 2025-06-23 2 2 6.0 graphlan, metaphlan, taxonomy_krona_chart, graphlan_annotate, Cut1, export2graphlan Phylogenetic tree visualisation, Visualisation, Phylogenetic inference, Phylogenetic tree editing, Taxonomic classification, Conversion MIT Galaxy Training Network True False -Metatranscriptomics analysis using microbiome RNA-seq data - Workflow 1: Preprocessing WorkflowHub 1444 https://workflowhub.eu/workflows/1444?version=2 gtn, galaxy, microbiome 2025-06-23 2025-06-23 2 2 6.0 multiqc, fastqc, cutadapt, bg_sortmerna, fastq_paired_end_interlacer Sequence trimming, Sequence composition calculation, Statistical calculation, Validation, Primer removal, Read pre-processing, Sequence similarity search, Sequence alignment analysis, Sequence comparison, Sequencing quality control MIT Galaxy Training Network True False -Metatranscriptomics analysis using microbiome RNA-seq data - Workflow 3: Functional Information WorkflowHub 1456 https://workflowhub.eu/workflows/1456?version=2 gtn, galaxy, microbiome 2025-06-23 2025-06-23 2 2 18.0 Grep1, humann_rename_table, humann, tp_find_and_replace, humann_renorm_table, tp_sort_header_tool, humann_regroup_table, humann_unpack_pathways, humann_split_stratified_table Species frequency estimation, Taxonomic classification, Phylogenetic analysis MIT Galaxy Training Network True False -Assembly of metagenomic sequencing data WorkflowHub 1390 https://workflowhub.eu/workflows/1390?version=2 gtn, galaxy, microbiome 2025-06-16 2025-06-16 2 2 9.0 collection_column_join, bowtie2, megahit_contig2fastg, bandage_info, bandage_image, metaspades, quast, coverm_contig, megahit Visualisation, Local alignment, Sequence assembly validation, Read mapping, Genome assembly, Sequence assembly visualisation MIT Galaxy Training Network True False -Taxonomic Analysis of eDNA WorkflowHub 1723 https://workflowhub.eu/workflows/1723?version=1 ecology, gtn, galaxy 2025-06-02 2025-06-02 1 1 8.0 ncbi_blastn_wrapper, Count1, cshl_fastq_to_fasta, fastp Sequence contamination filtering, Sequencing quality control CC-BY-4.0 Galaxy Training Network True False -Quality and contamination control in bacterial isolate using Illumina MiSeq Data WorkflowHub 1644 https://workflowhub.eu/workflows/1644?version=1 gtn, galaxy, sequence-analysis 2025-06-02 2025-06-02 1 1 6.0 falco, kraken2, est_abundance, fastp, recentrifuge Visualisation, Statistical calculation, Read mapping, Cross-assembly, Sequence contamination filtering, Expression analysis, Taxonomic classification, Sequencing quality control GPL-3.0-or-later Galaxy Training Network True False -pox-virus-tiled-amplicon-ref-masking WorkflowHub 1632 https://workflowhub.eu/workflows/1632?version=1 gtn, galaxy, variant-analysis 2025-06-02 2025-06-02 1 1 14.0 Grep1, param_value_from_file, compose_text_param, EMBOSS: maskseq51, datamash_ops, Cut1, fasta_compute_length, Add_a_column1 Local alignment, Sequence alignment, Global alignment, Sequence alignment analysis, Sequence analysis MIT Galaxy Training Network True False -Copy Of GTN Training - Antibiotic Resistance Detection WorkflowHub 1477 https://workflowhub.eu/workflows/1477?version=1 gtn, galaxy, microbiome 2025-06-02 2025-06-02 1 1 12.0 unicycler, racon, staramr_search, miniasm, nanoplot, bandage_image, PlasFlow, gfa_to_fa, minimap2 Aggregation, Mapping assembly, Antimicrobial resistance prediction, Sequence analysis, Box-Whisker plot plotting, Pairwise sequence alignment, Genome assembly, Sequence assembly visualisation, Scatter plot plotting, De-novo assembly CC-BY-4.0 Galaxy Training Network True False -Amplicon Tutorial WorkflowHub 1476 https://workflowhub.eu/workflows/1476?version=1 gtn, galaxy, microbiome 2025-06-02 2025-06-02 1 1 17.0 mothur_pre_cluster, mothur_make_group, mothur_summary_seqs, mothur_count_seqs, mothur_unique_seqs, mothur_merge_files, mothur_align_seqs, mothur_filter_seqs, mothur_cluster_split, mothur_screen_seqs, mothur_classify_seqs, mothur_make_shared, krona-text, mothur_classify_otu, mothur_make_biom Visualisation, Sequence clustering, DNA barcoding, Taxonomic classification, Sequence read processing, Sequencing quality control, Phylogenetic analysis CC-BY-4.0 Galaxy Training Network True False -Training: 16S rRNA Analysis with Nanopore Sequencing Reads WorkflowHub 1473 https://workflowhub.eu/workflows/1473?version=1 gtn, galaxy, microbiome 2025-06-02 2025-06-02 1 1 11.0 multiqc, kraken2, fastqc, taxonomy_krona_chart, porechop, tp_replace_in_line, fastp, Remove beginning1, datamash_reverse Visualisation, Sequence composition calculation, Sequence contamination filtering, Statistical calculation, Validation, Taxonomic classification, Sequencing quality control CC-BY-4.0 Galaxy Training Network True False -"WGS Part In ""Analyses Of Metagenomics Data - The Global Picture""" WorkflowHub 1472 https://workflowhub.eu/workflows/1472?version=1 gtn, galaxy, microbiome 2025-06-02 2025-06-02 1 1 7.0 humann2, taxonomy_krona_chart, metaphlan2krona, humann2_renorm_table, humann2_regroup_table, metaphlan2 Visualisation CC-BY-4.0 Galaxy Training Network True False -Query a metaplasmidome database to identify and annotate plasmids in metagenomes WorkflowHub 1469 https://workflowhub.eu/workflows/1469?version=1 gtn, galaxy, metagenomics, metaplasmidome, name:microgalaxy 2025-06-02 2025-06-02 1 1 47.0 Grouping1, CONVERTER_fasta_to_tabular, tp_sorted_uniq, sort1, Filter1, MQoutputfilter, tp_replace_in_column, histogram_rpy, tp_tail_tool, join1, count_gff_features, tab2fasta, Cut1, cat1, add_column_headers, Add_a_column1, ggplot2_histogram, minimap2 Visualisation, Pairwise sequence alignment MIT Galaxy Training Network True False -Training: 16S rRNA Sequencing With Mothur: Main Tutorial WorkflowHub 1465 https://workflowhub.eu/workflows/1465?version=1 gtn, galaxy, microbiome 2025-06-02 2025-06-02 1 1 38.0 mothur_pre_cluster, mothur_make_contigs, mothur_count_seqs, mothur_cluster, mothur_unique_seqs, mothur_venn, mothur_classify_seqs, mothur_make_shared, mothur_make_biom, mothur_summary_seqs, mothur_cluster_split, mothur_chimera_vsearch, mothur_screen_seqs, mothur_remove_lineage, mothur_summary_single, mothur_remove_seqs, XY_Plot_1, mothur_remove_groups, mothur_taxonomy_to_krona, mothur_count_groups, mothur_align_seqs, mothur_filter_seqs, mothur_dist_shared, mothur_tree_shared, mothur_dist_seqs, mothur_classify_otu, mothur_heatmap_sim, mothur_rarefaction_single, mothur_sub_sample, newick_display, taxonomy_krona_chart, mothur_seq_error, mothur_get_groups Visualisation, Phylogenetic tree reconstruction, Sequence clustering, Phylogenetic tree generation, DNA barcoding, Phylogenetic tree analysis, Taxonomic classification, Sequence read processing, Sequencing quality control, Phylogenetic analysis CC-BY-4.0 Galaxy Training Network True False -Workflow for Identifying MF from ITS2 sequencing using LotuS2 - tutorial example run' WorkflowHub 1460 https://workflowhub.eu/workflows/1460?version=1 ecology, fungi, gtn, galaxy, lotus2, metagenomics 2025-06-02 2025-06-02 1 1 1.0 lotus2 Sequence feature detection, DNA barcoding MIT Galaxy Training Network True False -Identification of the micro-organisms in a beer using Nanopore sequencing WorkflowHub 1439 https://workflowhub.eu/workflows/1439?version=1 gtn, galaxy, microbiome 2025-06-02 2025-06-02 1 1 8.0 kraken2, Filter1, fastqc, taxonomy_krona_chart, krakentools_kreport2krona, porechop, fastp Visualisation, Sequence composition calculation, Sequence contamination filtering, Statistical calculation, Taxonomic classification, Aggregation, Sequencing quality control MIT Galaxy Training Network True False -Calculating diversity from microbiome taxonomic data WorkflowHub 1431 https://workflowhub.eu/workflows/1431?version=1 gtn, galaxy, name:gtn 2025-06-02 2025-06-02 1 1 6.0 krakentools_alpha_diversity, krakentools_beta_diversity Visualisation, Aggregation MIT Galaxy Training Network True False -Workflow 3: Classification [Galaxy Training: 16S Microbial Analysis With Mothur] WorkflowHub 1428 https://workflowhub.eu/workflows/1428?version=1 gtn, galaxy, microbiome 2025-06-02 2025-06-02 1 1 3.0 mothur_summary_seqs, mothur_classify_seqs, mothur_remove_lineage Visualisation, Sequence clustering, DNA barcoding, Taxonomic classification, Sequence read processing, Sequencing quality control, Phylogenetic analysis MIT Galaxy Training Network True False -Workflow 1: Quality Control [Galaxy Training: 16S Microbial Analysis With Mothur] WorkflowHub 1422 https://workflowhub.eu/workflows/1422?version=1 gtn, galaxy, microbiome 2025-06-02 2025-06-02 1 1 5.0 mothur_summary_seqs, mothur_count_seqs, mothur_screen_seqs, mothur_unique_seqs Visualisation, Sequence clustering, DNA barcoding, Taxonomic classification, Sequence read processing, Sequencing quality control, Phylogenetic analysis MIT Galaxy Training Network True False -Workflow7: Beta Diversity [Galaxy Training: 16S Microbial Analysis With Mothur] WorkflowHub 1418 https://workflowhub.eu/workflows/1418?version=1 gtn, galaxy, microbiome 2025-06-02 2025-06-02 1 1 6.0 mothur_heatmap_sim, newick_display, mothur_dist_shared, mothur_venn, collapse_dataset, mothur_tree_shared Visualisation, Phylogenetic tree reconstruction, Sequence clustering, Phylogenetic tree generation, DNA barcoding, Phylogenetic tree analysis, Taxonomic classification, Sequence read processing, Sequencing quality control, Phylogenetic analysis MIT Galaxy Training Network True False -Workflow 6: Alpha Diversity [Galaxy Training: 16S Microbial Analysis With Mothur] WorkflowHub 1412 https://workflowhub.eu/workflows/1412?version=1 gtn, galaxy, microbiome 2025-06-02 2025-06-02 1 1 3.0 XY_Plot_1, mothur_rarefaction_single, mothur_summary_single Visualisation, Sequence clustering, DNA barcoding, Taxonomic classification, Sequence read processing, Sequencing quality control, Phylogenetic analysis MIT Galaxy Training Network True False -Workflow 4: Mock OTU Clustering [Galaxy Training: 16S Microbial Analysis With Mothur] WorkflowHub 1408 https://workflowhub.eu/workflows/1408?version=1 gtn, galaxy, microbiome 2025-06-02 2025-06-02 1 1 4.0 mothur_rarefaction_single, mothur_dist_seqs, mothur_make_shared, mothur_cluster Visualisation, Sequence clustering, DNA barcoding, Taxonomic classification, Sequence read processing, Sequencing quality control, Phylogenetic analysis MIT Galaxy Training Network True False -Workflow 5: OTU Clustering [Galaxy Training: 16S Microbial Analysis With Mothur] WorkflowHub 1404 https://workflowhub.eu/workflows/1404?version=1 gtn, galaxy, microbiome 2025-06-02 2025-06-02 1 1 6.0 mothur_remove_groups, mothur_sub_sample, mothur_count_groups, mothur_cluster_split, mothur_make_shared, mothur_classify_otu Visualisation, Sequence clustering, DNA barcoding, Taxonomic classification, Sequence read processing, Sequencing quality control, Phylogenetic analysis MIT Galaxy Training Network True False -Workflow 2: Data Cleaning And Chimera Removal [Galaxy Training: 16S Microbial Analysis With Mothur] WorkflowHub 1400 https://workflowhub.eu/workflows/1400?version=1 gtn, galaxy, microbiome 2025-06-02 2025-06-02 1 1 9.0 mothur_pre_cluster, mothur_summary_seqs, mothur_unique_seqs, mothur_filter_seqs, mothur_chimera_vsearch, mothur_screen_seqs, mothur_remove_seqs Visualisation, Sequence clustering, DNA barcoding, Taxonomic classification, Sequence read processing, Sequencing quality control, Phylogenetic analysis MIT Galaxy Training Network True False -GTN Training - Antibiotic Resistance Detection WorkflowHub 406 https://workflowhub.eu/workflows/406?version=1 Saskia Hiltemann, Willem de Koning metagenomics 2022-11-24 2026-05-13 1 1 12.0 unicycler, racon, staramr_search, miniasm, nanoplot, bandage_image, PlasFlow, gfa_to_fa, minimap2 Aggregation, Mapping assembly, Antimicrobial resistance prediction, Sequence analysis, Box-Whisker plot plotting, Pairwise sequence alignment, Genome assembly, Sequence assembly visualisation, Scatter plot plotting, De-novo assembly Microbiology CC-BY-4.0 Galaxy Training Network True False -3: Plant virus exploration WorkflowHub 103 https://workflowhub.eu/workflows/103?version=1 de_novo, virology, exploration 2021-02-04 2026-05-13 1 1 2.0 fastp, shovill Genome assembly, Sequence contamination filtering, Sequencing quality control Apache-2.0 Integrated and Urban Plant Pathology Laboratory True False -2: Plant virus confirmation WorkflowHub 102 https://workflowhub.eu/workflows/102?version=1 assembly, virology, blast, mapping, reads_selection 2021-02-04 2026-05-13 1 1 7.0 fasta_merge_files_and_filter_unique_sequences, ncbi_blastn_wrapper, samtools_stats, picard_SamToFastq, shovill, ngsutils_bam_filter, minimap2 Read pre-processing, Sequence contamination filtering, Formatting, Pairwise sequence alignment, Genome assembly, Sequencing quality control, Variant calling Apache-2.0 Integrated and Urban Plant Pathology Laboratory True False -1: Plant virus detection with kraken2 (SE) WorkflowHub 124 https://workflowhub.eu/workflows/124?version=1 virology, kraken 2021-06-17 2026-05-13 1 1 3.0 kraken2, Kraken2Tax, taxonomy_krona_chart Visualisation, Taxonomic classification Apache-2.0 Integrated and Urban Plant Pathology Laboratory True False -1: Plant virus detection with kraken2 (PE) WorkflowHub 101 https://workflowhub.eu/workflows/101?version=1 virology, kraken 2021-02-04 2026-05-13 1 1 3.0 kraken2, Kraken2Tax, taxonomy_krona_chart Visualisation, Taxonomic classification Apache-2.0 Integrated and Urban Plant Pathology Laboratory True False -Taxonomy Assignment with QIIME2 WorkflowHub 2098 https://workflowhub.eu/workflows/2098?version=1 Tristan Reynolds, Amy Loughman amplicon, microbiome, taxonomic-classification 2026-03-02 2026-05-13 1 1 19.0 qiime2__feature_classifier__classify_sklearn, qiime2__feature_table__summarize, qiime2_core__tools__import, qiime2__taxa__barplot, qiime2__feature_classifier__fit_classifier_naive_bayes, qiime2__feature_table__tabulate_seqs, qiime2__feature_classifier__extract_reads, csv_to_tabular, tp_easyjoin_tool, Remove beginning1, biom_convert, qiime_extract_viz, qiime2_core__tools__export, tabular_to_csv Visualisation, Formatting, Demultiplexing, Taxonomic classification Taxonomy CC-BY-4.0 10.48546/workflowhub.workflow.2098.1 Melbourne Bioinformatics, Galaxy Australia True False -Taxonomy classification using Kraken2 and Bracken WorkflowHub 1199 https://workflowhub.eu/workflows/1199?version=2 Valentine Murigneux, Mike Thang gucfg2galaxy, metagenomics, name:collection, shotgun 2024-12-10 2024-12-10 2 2 29.0 "collection_column_join, krakentools_beta_diversity, Prepare alpha diversity summary file +Grouping1, extracting microbial Peptides +Grep1, Quantified-Proteins +Grouping1, maxquant, extract peptides +Cut1" Statistical calculation, Imputation, Heat map generation, Standardisation and normalisation, Protein quantification, Clustering, Principal component plotting, Visualisation CC-BY-4.0 Intergalactic Workflow Commission (IWC) True False +bacterial-genome-assembly/main WorkflowHub 1043 https://workflowhub.eu/workflows/1043?version=12 Abromics None, Pierre Marin, Clea Siguret abromics, assembly, fastq, genomics, bacterial-genomics, paired-end, quality 2025-12-04 2026-05-13 12 12 5.0 tooldistillator_summarize, shovill, bandage_image, bandage_info, tooldistillator Data parsing, Sequence assembly visualisation, Genome assembly GPL-3.0-or-later Intergalactic Workflow Commission (IWC) True False +quality-and-contamination-control/main WorkflowHub 1052 https://workflowhub.eu/workflows/1052?version=11 ABRomics None, Pierre Marin, Clea Siguret abromics, fastq, genomics, bacterial-genomics, paired-end, quality, taxonomy-assignment, trimming 2025-06-19 2026-05-14 11 11 8.0 fastp, tooldistillator_summarize, recentrifuge, __ZIP_COLLECTION__, est_abundance, kraken2, __UNZIP_COLLECTION__, tooldistillator Sequencing quality control, Sequence contamination filtering, Data parsing, Taxonomic classification, Expression analysis, Statistical calculation, Cross-assembly GPL-3.0-or-later Intergalactic Workflow Commission (IWC) True False +qiime2-III-VI-downsteam/QIIME2-III-V-Phylogeny-Rarefaction-Taxonomic-Analysis WorkflowHub 1090 https://workflowhub.eu/workflows/1090?version=2 Debjyoti Ghosh 2024-11-26 2026-05-14 2 2 3.0 Rarefaction, Taxonomic analysis, Phylogenetic tree for diversity analysis MIT Intergalactic Workflow Commission (IWC) True False +gene-based-pathogen-identification/main WorkflowHub 1062 https://workflowhub.eu/workflows/1062?version=1 Engy Nasr, Bérénice Batut, Paul Zierep 2024-06-26 2026-05-13 1 1 15.0 abricate, collection_element_identifiers, bandage_image, flye, tp_find_and_replace, split_file_to_collection, compose_text_param, __BUILD_LIST__, tab2fasta, medaka_consensus_pipeline, param_value_from_file, fasta2tab Base-calling, Antimicrobial resistance prediction, De-novo assembly, Variant calling, Sequence assembly visualisation, Sequence assembly, Cross-assembly, Mapping assembly, Genome assembly MIT 10.48546/workflowhub.workflow.1062.1 Intergalactic Workflow Commission (IWC) True False +pathogen-detection-pathogfair-samples-aggregation-and-visualisation/main WorkflowHub 1060 https://workflowhub.eu/workflows/1060?version=1 Engy Nasr, Bérénice Batut, Paul Zierep 2024-06-26 2026-05-13 1 1 60.0 tp_split_on_column, ggplot2_heatmap, bedtools_getfastabed, collapse_dataset, regex1, tp_replace_in_column, fasta_merge_files_and_filter_unique_sequences, newick_display, regexColumn1, tp_multijoin_tool, Count1, __FILTER_EMPTY_DATASETS__, fasta2tab, tp_sorted_uniq, Grouping1, fasttree, tab2fasta, Remove beginning1, collection_column_join, clustalw, __FILTER_FAILED_DATASETS__, Cut1 Phylogenetic tree generation, Visualisation, Multiple sequence alignment, Phylogenetic tree reconstruction, Phylogenetic tree analysis, Mapping MIT 10.48546/workflowhub.workflow.1060.1 Intergalactic Workflow Commission (IWC) True False +taxonomy-profiling-and-visualization-with-krona/main WorkflowHub 1059 https://workflowhub.eu/workflows/1059?version=1 Engy Nasr, Bérénice Batut, Paul Zierep 2024-06-26 2026-05-13 1 1 3.0 krakentools_kreport2krona, kraken2, taxonomy_krona_chart Taxonomic classification, Aggregation, Visualisation MIT 10.48546/workflowhub.workflow.1059.1 Intergalactic Workflow Commission (IWC) True False +bacterial_genome_annotation/main WorkflowHub 1050 https://workflowhub.eu/workflows/1050?version=13 ABRomics None, Pierre Marin, Clea Siguret abromics, annotation, genomics, bacterial-genomics, fasta, genome-annotation 2025-12-06 2026-05-13 13 13 6.0 tooldistillator_summarize, integron_finder, plasmidfinder, isescan, bakta, tooldistillator Scaffolding, Genome annotation, Nucleic acid feature detection, Data parsing, Protein feature detection, Structural variation detection, Sequence motif recognition, Multilocus sequence typing, Genome assembly GPL-3.0-or-later Intergalactic Workflow Commission (IWC) True False +amr_gene_detection/main WorkflowHub 1049 https://workflowhub.eu/workflows/1049?version=9 ABRomics None, Pierre Marin, Clea Siguret abromics, amr, amr-detection, genomics, antibiotic-resistance, antimicrobial resistance, antimicrobial-resistance-genes, bacterial-genomics, fasta 2025-12-04 2026-05-13 9 9 5.0 tooldistillator_summarize, abricate, amrfinderplus, staramr_search, tooldistillator Data parsing, Antimicrobial resistance prediction GPL-3.0-or-later Intergalactic Workflow Commission (IWC) True False +dada2/main WorkflowHub 790 https://workflowhub.eu/workflows/790?version=3 Matthias Bernt name:amplicon 2025-03-26 2026-05-14 3 3 14.0 dada2_dada, dada2_makeSequenceTable, __APPLY_RULES__, dada2_plotQualityProfile, dada2_learnErrors, dada2_assignTaxonomyAddspecies, dada2_seqCounts, dada2_filterAndTrim, __UNZIP_COLLECTION__, dada2_removeBimeraDenovo, dada2_mergePairs DNA barcoding, Variant calling MIT Intergalactic Workflow Commission (IWC) True False +Refining Genome Annotations with Apollo (prokaryotes) WorkflowHub 749 https://workflowhub.eu/workflows/749?version=1 Anthony Bretaudeau genome-annotation 2024-02-14 2025-11-04 1 1 5.0 create_or_update, iframe, jbrowse, create_account, list_organism Genome visualisation CC-BY-4.0 10.48546/workflowhub.workflow.749.1 EuroScienceGateway True False +TB Variant Analysis v1.0 WorkflowHub 1647 https://workflowhub.eu/workflows/1647?version=2 gtn, galaxy, pathogen, tuberculosis 2026-01-12 2026-01-12 2 2 15.0 fastp, tp_awk_tool, qualimap_bamqc, EMBOSS: seqret84, kraken2, mosdepth, __FLATTEN__, tp_sed_tool, snippy, multiqc, bcftools_consensus, tb_variant_filter, tb_profiler_profile, tbvcfreport Taxonomic classification, Antimicrobial resistance prediction, Variant calling, Sequence alignment, Phylogenetic tree visualisation, Sequencing quality control, Sequence contamination filtering, Sequence alignment analysis, Phylogenetic tree generation, Validation, Global alignment, Sequence analysis, Local alignment AGPL-3.0-or-later Galaxy Training Network True False +Quality and contamination control in bacterial isolate using Illumina MiSeq Data WorkflowHub 2043 https://workflowhub.eu/workflows/2043?version=1 gtn, galaxy, sequence-analysis 2025-12-22 2025-12-22 1 1 5.0 fastp, recentrifuge, est_abundance, kraken2, falco Statistical calculation, Taxonomic classification, Expression analysis, Sequencing quality control, Sequence contamination filtering, Read mapping, Visualisation, Cross-assembly GPL-3.0-or-later Galaxy Training Network True False +Taxonomic Profiling and Visualization of Metagenomic Data WorkflowHub 1470 https://workflowhub.eu/workflows/1470?version=2 gtn, galaxy, microbiome 2025-12-22 2025-12-22 2 2 10.0 metaphlan, taxonomy_krona_chart, krakentools_kreport2krona, est_abundance, kraken_biom, kraken2, interactive_tool_phinch, __UNZIP_COLLECTION__, interactive_tool_pavian Statistical calculation, Taxonomic classification, Aggregation, Genome annotation, Visualisation MIT Galaxy Training Network True False +Checking expected species and contamination in bacterial isolate WorkflowHub 1674 https://workflowhub.eu/workflows/1674?version=2 ecology, gtn, galaxy 2025-12-22 2025-12-22 2 2 3.0 est_abundance, recentrifuge, kraken2 Statistical calculation, Taxonomic classification, Expression analysis, Cross-assembly GPL-3.0-or-later Galaxy Training Network True False +Metagenomic Binning WorkflowHub 2028 https://workflowhub.eu/workflows/2028?version=1 gtn, galaxy, microgalaxy, binning, microbiome 2025-12-08 2025-12-08 1 1 17.0 bowtie2, concoct_coverage_table, concoct_merge_cut_up_clustering, concoct_extract_fasta_bins, concoct_cut_up_fasta, samtools_sort, Fasta_to_Contig2Bin, concoct, __BUILD_LIST__, binette, semibin, maxbin2, metabat2, metabat2_jgi_summarize_bam_contig_depths Sequence assembly, Read mapping, Sequence clustering, Genome annotation, Read binning MIT Galaxy Training Network True False +MGnify's amplicon pipeline v5.0 - ITS WorkflowHub 1856 https://workflowhub.eu/workflows/1856?version=1 amplicon, gtn, galaxy, metagenomics, mgnify_amplicon, name:microgalaxy 2025-08-11 2025-08-11 1 1 30.0 , bedtools_maskfastabed, mapseq, tp_awk_tool, __FILTER_FROM_FILE__, collection_element_identifiers, taxonomy_krona_chart, biom_convert, __FILTER_EMPTY_DATASETS__ k-mer counting, Formatting, Visualisation, Mapping Apache-2.0 Galaxy Training Network True False +MAPseq to ampvis2 WorkflowHub 1855 https://workflowhub.eu/workflows/1855?version=1 gtn, galaxy, microbiome 2025-08-11 2025-08-11 1 1 9.0 tp_awk_tool, collection_column_join, collapse_dataset, ampvis2_load, query_tabular Analysis, Visualisation MIT Galaxy Training Network True False +MGnify's amplicon pipeline v5.0 - Quality control PE WorkflowHub 1854 https://workflowhub.eu/workflows/1854?version=1 amplicon, gtn, galaxy, metagenomics, mgnify_amplicon, name:microgalaxy 2025-08-11 2025-08-11 1 1 17.0 fastp, cshl_fasta_formatter, tp_find_and_replace, multiqc, trimmomatic, fastqc, __UNZIP_COLLECTION__, mgnify_seqprep, fastq_filter, prinseq, fastq_to_fasta_python Statistical calculation, Sequencing quality control, Sequence contamination filtering, Sequence trimming, Validation, Nucleic acid design, Read pre-processing, Sequence composition calculation Apache-2.0 Galaxy Training Network True False +MGnify's amplicon pipeline v5.0 WorkflowHub 1853 https://workflowhub.eu/workflows/1853?version=1 amplicon, gtn, galaxy, metagenomics, mgnify_amplicon, name:microgalaxy 2025-08-11 2025-08-11 1 1 20.0 , tp_awk_tool, CONVERTER_uncompressed_to_gz, CONVERTER_gz_to_uncompressed, __MERGE_COLLECTION__, fastq_dl Apache-2.0 Galaxy Training Network True False +MGnify amplicon summary tables WorkflowHub 1851 https://workflowhub.eu/workflows/1851?version=1 amplicon, gtn, galaxy, metagenomics, mgnify_amplicon, name:microgalaxy 2025-08-11 2025-08-11 1 1 10.0 tp_awk_tool, collection_column_join, Grouping1, filter_tabular, query_tabular MIT Galaxy Training Network True False +MGnify's amplicon pipeline v5.0 - Quality control SE WorkflowHub 1850 https://workflowhub.eu/workflows/1850?version=1 amplicon, gtn, galaxy, metagenomics, mgnify_amplicon, name:microgalaxy 2025-08-11 2025-08-11 1 1 14.0 cshl_fasta_formatter, tp_find_and_replace, multiqc, trimmomatic, fastqc, fastq_filter, prinseq, fastq_to_fasta_python Sequencing quality control, Statistical calculation, Sequence contamination filtering, Sequence trimming, Validation, Read pre-processing, Sequence composition calculation Apache-2.0 Galaxy Training Network True False +MGnify's amplicon pipeline v5.0 - rRNA prediction WorkflowHub 1842 https://workflowhub.eu/workflows/1842?version=1 amplicon, gtn, galaxy, metagenomics, mgnify_amplicon, name:microgalaxy 2025-08-04 2025-08-11 1 1 47.0 , cshl_fasta_formatter, tp_awk_tool, mapseq, collection_element_identifiers, __FILTER_FROM_FILE__, taxonomy_krona_chart, biom_convert, cmsearch_deoverlap, infernal_cmsearch, bedtools_getfastabed, gops_concat_1, query_tabular, __FILTER_EMPTY_DATASETS__ k-mer counting, Formatting, Comparison, Mapping, Alignment, Nucleic acid feature detection, Visualisation Apache-2.0 Galaxy Training Network True False +Workflow 3: Functional Information (quick) WorkflowHub 1447 https://workflowhub.eu/workflows/1447?version=2 asaim, gtn, galaxy, metagenomics 2025-07-14 2025-07-14 2 2 12.0 humann_rename_table, humann_regroup_table, tp_find_and_replace, combine_metaphlan2_humann2, humann_unpack_pathways, humann_split_stratified_table, humann_renorm_table, Grep1, Cut1 Taxonomic classification, Species frequency estimation, Phylogenetic analysis MIT Galaxy Training Network True False +Building an amplicon sequence variant (ASV) table from 16S data using DADA2 WorkflowHub 1395 https://workflowhub.eu/workflows/1395?version=2 gtn, galaxy, microbiome 2025-07-07 2025-07-07 2 2 21.0 dada2_dada, Add_a_column1, dada2_makeSequenceTable, dada2_plotQualityProfile, collection_element_identifiers, __SORTLIST__, dada2_learnErrors, tp_replace_in_line, dada2_seqCounts, dada2_assignTaxonomyAddspecies, cat1, dada2_filterAndTrim, __UNZIP_COLLECTION__, tp_replace_in_column, phyloseq_from_dada2, tp_head_tool, dada2_removeBimeraDenovo, dada2_mergePairs DNA barcoding, Analysis, Variant calling, Deposition, Visualisation MIT Galaxy Training Network True False +Metatranscriptomics analysis using microbiome RNA-seq data WorkflowHub 1466 https://workflowhub.eu/workflows/1466?version=2 gtn, galaxy, microbiome 2025-06-23 2025-06-23 2 2 33.0 graphlan_annotate, bg_sortmerna, cutadapt, taxonomy_krona_chart, tp_find_and_replace, export2graphlan, humann_split_stratified_table, metaphlan, humann_regroup_table, fastq_paired_end_interlacer, Grouping1, humann_renorm_table, Grep1, graphlan, humann, tp_sort_header_tool, humann_rename_table, multiqc, fastqc, humann_unpack_pathways, combine_metaphlan_humann, Cut1 Statistical calculation, Phylogenetic inference, Conversion, Sequencing quality control, Sequence alignment analysis, Sequence comparison, Sequence composition calculation, Phylogenetic analysis, Taxonomic classification, Aggregation, Species frequency estimation, Phylogenetic tree visualisation, Sequence similarity search, Phylogenetic tree editing, Sequence trimming, Validation, Read pre-processing, Primer removal, Visualisation MIT Galaxy Training Network True False +Metatranscriptomics analysis using microbiome RNA-seq data - Workflow 2: Community profile WorkflowHub 1451 https://workflowhub.eu/workflows/1451?version=2 gtn, galaxy, microbiome 2025-06-23 2025-06-23 2 2 6.0 metaphlan, graphlan_annotate, taxonomy_krona_chart, export2graphlan, Cut1, graphlan Taxonomic classification, Phylogenetic inference, Conversion, Phylogenetic tree visualisation, Phylogenetic tree editing, Visualisation MIT Galaxy Training Network True False +Metatranscriptomics analysis using microbiome RNA-seq data - Workflow 1: Preprocessing WorkflowHub 1444 https://workflowhub.eu/workflows/1444?version=2 gtn, galaxy, microbiome 2025-06-23 2025-06-23 2 2 6.0 fastq_paired_end_interlacer, multiqc, fastqc, bg_sortmerna, cutadapt Statistical calculation, Sequence similarity search, Primer removal, Sequencing quality control, Sequence trimming, Sequence alignment analysis, Sequence comparison, Validation, Read pre-processing, Sequence composition calculation MIT Galaxy Training Network True False +Metatranscriptomics analysis using microbiome RNA-seq data - Workflow 3: Functional Information WorkflowHub 1456 https://workflowhub.eu/workflows/1456?version=2 gtn, galaxy, microbiome 2025-06-23 2025-06-23 2 2 18.0 humann_rename_table, humann_regroup_table, tp_find_and_replace, humann_unpack_pathways, humann_split_stratified_table, humann_renorm_table, Grep1, humann, tp_sort_header_tool Taxonomic classification, Species frequency estimation, Phylogenetic analysis MIT Galaxy Training Network True False +Assembly of metagenomic sequencing data WorkflowHub 1390 https://workflowhub.eu/workflows/1390?version=2 gtn, galaxy, microbiome 2025-06-16 2025-06-16 2 2 9.0 bowtie2, megahit_contig2fastg, collection_column_join, metaspades, bandage_image, bandage_info, megahit, coverm_contig, quast Visualisation, Read mapping, Sequence assembly validation, Sequence assembly visualisation, Local alignment, Genome assembly MIT Galaxy Training Network True False +Taxonomic Analysis of eDNA WorkflowHub 1723 https://workflowhub.eu/workflows/1723?version=1 ecology, gtn, galaxy 2025-06-02 2025-06-02 1 1 8.0 fastp, cshl_fastq_to_fasta, ncbi_blastn_wrapper, Count1 Sequencing quality control, Sequence contamination filtering CC-BY-4.0 Galaxy Training Network True False +Quality and contamination control in bacterial isolate using Illumina MiSeq Data WorkflowHub 1644 https://workflowhub.eu/workflows/1644?version=1 gtn, galaxy, sequence-analysis 2025-06-02 2025-06-02 1 1 6.0 fastp, recentrifuge, est_abundance, kraken2, falco Statistical calculation, Taxonomic classification, Expression analysis, Sequencing quality control, Sequence contamination filtering, Read mapping, Visualisation, Cross-assembly GPL-3.0-or-later Galaxy Training Network True False +pox-virus-tiled-amplicon-ref-masking WorkflowHub 1632 https://workflowhub.eu/workflows/1632?version=1 gtn, galaxy, variant-analysis 2025-06-02 2025-06-02 1 1 14.0 Add_a_column1, compose_text_param, EMBOSS: maskseq51, Grep1, datamash_ops, fasta_compute_length, Cut1, param_value_from_file Sequence alignment analysis, Global alignment, Sequence analysis, Sequence alignment, Local alignment MIT Galaxy Training Network True False +Copy Of GTN Training - Antibiotic Resistance Detection WorkflowHub 1477 https://workflowhub.eu/workflows/1477?version=1 gtn, galaxy, microbiome 2025-06-02 2025-06-02 1 1 12.0 unicycler, bandage_image, miniasm, staramr_search, PlasFlow, nanoplot, minimap2, racon, gfa_to_fa Pairwise sequence alignment, Aggregation, Antimicrobial resistance prediction, Box-Whisker plot plotting, De-novo assembly, Scatter plot plotting, Sequence assembly visualisation, Sequence analysis, Mapping assembly, Genome assembly CC-BY-4.0 Galaxy Training Network True False +Amplicon Tutorial WorkflowHub 1476 https://workflowhub.eu/workflows/1476?version=1 gtn, galaxy, microbiome 2025-06-02 2025-06-02 1 1 17.0 mothur_unique_seqs, mothur_cluster_split, mothur_summary_seqs, mothur_count_seqs, mothur_make_shared, mothur_make_biom, mothur_merge_files, mothur_screen_seqs, mothur_filter_seqs, mothur_make_group, mothur_classify_seqs, mothur_classify_otu, mothur_align_seqs, mothur_pre_cluster, krona-text Taxonomic classification, DNA barcoding, Sequence read processing, Sequencing quality control, Sequence clustering, Phylogenetic analysis, Visualisation CC-BY-4.0 Galaxy Training Network True False +Training: 16S rRNA Analysis with Nanopore Sequencing Reads WorkflowHub 1473 https://workflowhub.eu/workflows/1473?version=1 gtn, galaxy, microbiome 2025-06-02 2025-06-02 1 1 11.0 fastp, datamash_reverse, taxonomy_krona_chart, multiqc, kraken2, tp_replace_in_line, fastqc, porechop, Remove beginning1 Sequencing quality control, Sequence contamination filtering, Taxonomic classification, Statistical calculation, Validation, Sequence composition calculation, Visualisation CC-BY-4.0 Galaxy Training Network True False +"WGS Part In ""Analyses Of Metagenomics Data - The Global Picture""" WorkflowHub 1472 https://workflowhub.eu/workflows/1472?version=1 gtn, galaxy, microbiome 2025-06-02 2025-06-02 1 1 7.0 metaphlan2krona, metaphlan2, humann2_renorm_table, taxonomy_krona_chart, humann2, humann2_regroup_table Visualisation CC-BY-4.0 Galaxy Training Network True False +Query a metaplasmidome database to identify and annotate plasmids in metagenomes WorkflowHub 1469 https://workflowhub.eu/workflows/1469?version=1 gtn, galaxy, metagenomics, metaplasmidome, name:microgalaxy 2025-06-02 2025-06-02 1 1 47.0 Add_a_column1, CONVERTER_fasta_to_tabular, tp_sorted_uniq, histogram_rpy, join1, Grouping1, cat1, tp_tail_tool, count_gff_features, ggplot2_histogram, minimap2, add_column_headers, tp_replace_in_column, Filter1, tab2fasta, Cut1, MQoutputfilter, sort1 Pairwise sequence alignment, Visualisation MIT Galaxy Training Network True False +Training: 16S rRNA Sequencing With Mothur: Main Tutorial WorkflowHub 1465 https://workflowhub.eu/workflows/1465?version=1 gtn, galaxy, microbiome 2025-06-02 2025-06-02 1 1 38.0 mothur_count_seqs, mothur_chimera_vsearch, mothur_get_groups, mothur_screen_seqs, mothur_rarefaction_single, mothur_align_seqs, newick_display, mothur_make_shared, taxonomy_krona_chart, mothur_cluster, mothur_remove_seqs, mothur_summary_single, mothur_sub_sample, mothur_remove_groups, mothur_classify_seqs, mothur_seq_error, mothur_count_groups, mothur_cluster_split, mothur_tree_shared, mothur_summary_seqs, mothur_make_contigs, mothur_dist_shared, mothur_dist_seqs, XY_Plot_1, mothur_filter_seqs, mothur_remove_lineage, mothur_classify_otu, mothur_pre_cluster, mothur_unique_seqs, mothur_venn, mothur_heatmap_sim, mothur_make_biom, mothur_taxonomy_to_krona Taxonomic classification, DNA barcoding, Sequence read processing, Sequencing quality control, Phylogenetic tree generation, Phylogenetic tree reconstruction, Sequence clustering, Phylogenetic tree analysis, Phylogenetic analysis, Visualisation CC-BY-4.0 Galaxy Training Network True False +Workflow for Identifying MF from ITS2 sequencing using LotuS2 - tutorial example run' WorkflowHub 1460 https://workflowhub.eu/workflows/1460?version=1 ecology, fungi, gtn, galaxy, lotus2, metagenomics 2025-06-02 2025-06-02 1 1 1.0 lotus2 DNA barcoding, Sequence feature detection MIT Galaxy Training Network True False +Identification of the micro-organisms in a beer using Nanopore sequencing WorkflowHub 1439 https://workflowhub.eu/workflows/1439?version=1 gtn, galaxy, microbiome 2025-06-02 2025-06-02 1 1 8.0 fastp, taxonomy_krona_chart, krakentools_kreport2krona, kraken2, fastqc, Filter1, porechop Sequencing quality control, Sequence contamination filtering, Taxonomic classification, Statistical calculation, Aggregation, Sequence composition calculation, Visualisation MIT Galaxy Training Network True False +Calculating diversity from microbiome taxonomic data WorkflowHub 1431 https://workflowhub.eu/workflows/1431?version=1 gtn, galaxy, name:gtn 2025-06-02 2025-06-02 1 1 6.0 krakentools_alpha_diversity, krakentools_beta_diversity Aggregation, Visualisation MIT Galaxy Training Network True False +Workflow 3: Classification [Galaxy Training: 16S Microbial Analysis With Mothur] WorkflowHub 1428 https://workflowhub.eu/workflows/1428?version=1 gtn, galaxy, microbiome 2025-06-02 2025-06-02 1 1 3.0 mothur_remove_lineage, mothur_summary_seqs, mothur_classify_seqs Taxonomic classification, DNA barcoding, Sequence read processing, Sequencing quality control, Sequence clustering, Phylogenetic analysis, Visualisation MIT Galaxy Training Network True False +Workflow 1: Quality Control [Galaxy Training: 16S Microbial Analysis With Mothur] WorkflowHub 1422 https://workflowhub.eu/workflows/1422?version=1 gtn, galaxy, microbiome 2025-06-02 2025-06-02 1 1 5.0 mothur_unique_seqs, mothur_summary_seqs, mothur_count_seqs, mothur_screen_seqs Taxonomic classification, DNA barcoding, Sequence read processing, Sequencing quality control, Sequence clustering, Phylogenetic analysis, Visualisation MIT Galaxy Training Network True False +Workflow7: Beta Diversity [Galaxy Training: 16S Microbial Analysis With Mothur] WorkflowHub 1418 https://workflowhub.eu/workflows/1418?version=1 gtn, galaxy, microbiome 2025-06-02 2025-06-02 1 1 6.0 mothur_tree_shared, mothur_venn, mothur_heatmap_sim, mothur_dist_shared, collapse_dataset, newick_display Taxonomic classification, DNA barcoding, Sequence read processing, Sequencing quality control, Phylogenetic tree generation, Phylogenetic tree reconstruction, Sequence clustering, Phylogenetic tree analysis, Phylogenetic analysis, Visualisation MIT Galaxy Training Network True False +Workflow 6: Alpha Diversity [Galaxy Training: 16S Microbial Analysis With Mothur] WorkflowHub 1412 https://workflowhub.eu/workflows/1412?version=1 gtn, galaxy, microbiome 2025-06-02 2025-06-02 1 1 3.0 XY_Plot_1, mothur_rarefaction_single, mothur_summary_single Taxonomic classification, DNA barcoding, Sequence read processing, Sequencing quality control, Sequence clustering, Phylogenetic analysis, Visualisation MIT Galaxy Training Network True False +Workflow 4: Mock OTU Clustering [Galaxy Training: 16S Microbial Analysis With Mothur] WorkflowHub 1408 https://workflowhub.eu/workflows/1408?version=1 gtn, galaxy, microbiome 2025-06-02 2025-06-02 1 1 4.0 mothur_cluster, mothur_dist_seqs, mothur_make_shared, mothur_rarefaction_single Taxonomic classification, DNA barcoding, Sequence read processing, Sequencing quality control, Sequence clustering, Phylogenetic analysis, Visualisation MIT Galaxy Training Network True False +Workflow 5: OTU Clustering [Galaxy Training: 16S Microbial Analysis With Mothur] WorkflowHub 1404 https://workflowhub.eu/workflows/1404?version=1 gtn, galaxy, microbiome 2025-06-02 2025-06-02 1 1 6.0 mothur_cluster_split, mothur_make_shared, mothur_sub_sample, mothur_remove_groups, mothur_classify_otu, mothur_count_groups Taxonomic classification, DNA barcoding, Sequence read processing, Sequencing quality control, Sequence clustering, Phylogenetic analysis, Visualisation MIT Galaxy Training Network True False +Workflow 2: Data Cleaning And Chimera Removal [Galaxy Training: 16S Microbial Analysis With Mothur] WorkflowHub 1400 https://workflowhub.eu/workflows/1400?version=1 gtn, galaxy, microbiome 2025-06-02 2025-06-02 1 1 9.0 mothur_unique_seqs, mothur_summary_seqs, mothur_chimera_vsearch, mothur_remove_seqs, mothur_screen_seqs, mothur_filter_seqs, mothur_pre_cluster Taxonomic classification, DNA barcoding, Sequence read processing, Sequencing quality control, Sequence clustering, Phylogenetic analysis, Visualisation MIT Galaxy Training Network True False +GTN Training - Antibiotic Resistance Detection WorkflowHub 406 https://workflowhub.eu/workflows/406?version=1 Saskia Hiltemann, Willem de Koning metagenomics 2022-11-24 2026-05-13 1 1 12.0 unicycler, bandage_image, miniasm, staramr_search, PlasFlow, nanoplot, minimap2, racon, gfa_to_fa Pairwise sequence alignment, Aggregation, Antimicrobial resistance prediction, Box-Whisker plot plotting, De-novo assembly, Scatter plot plotting, Sequence assembly visualisation, Sequence analysis, Mapping assembly, Genome assembly Microbiology CC-BY-4.0 Galaxy Training Network True False +3: Plant virus exploration WorkflowHub 103 https://workflowhub.eu/workflows/103?version=1 de_novo, virology, exploration 2021-02-04 2026-05-13 1 1 2.0 fastp, shovill Sequencing quality control, Sequence contamination filtering, Genome assembly Apache-2.0 Integrated and Urban Plant Pathology Laboratory True False +2: Plant virus confirmation WorkflowHub 102 https://workflowhub.eu/workflows/102?version=1 assembly, virology, blast, mapping, reads_selection 2021-02-04 2026-05-13 1 1 7.0 ncbi_blastn_wrapper, shovill, picard_SamToFastq, ngsutils_bam_filter, minimap2, samtools_stats, fasta_merge_files_and_filter_unique_sequences Sequencing quality control, Formatting, Sequence contamination filtering, Pairwise sequence alignment, Variant calling, Read pre-processing, Genome assembly Apache-2.0 Integrated and Urban Plant Pathology Laboratory True False +1: Plant virus detection with kraken2 (SE) WorkflowHub 124 https://workflowhub.eu/workflows/124?version=1 virology, kraken 2021-06-17 2026-05-13 1 1 3.0 Kraken2Tax, kraken2, taxonomy_krona_chart Taxonomic classification, Visualisation Apache-2.0 Integrated and Urban Plant Pathology Laboratory True False +1: Plant virus detection with kraken2 (PE) WorkflowHub 101 https://workflowhub.eu/workflows/101?version=1 virology, kraken 2021-02-04 2026-05-13 1 1 3.0 Kraken2Tax, kraken2, taxonomy_krona_chart Taxonomic classification, Visualisation Apache-2.0 Integrated and Urban Plant Pathology Laboratory True False +MPXV (Mpox) Phylogenetic Analysis with Squirrel WorkflowHub 2196 https://workflowhub.eu/workflows/2196?version=1 Tristan Reynolds, Ammar Aziz amplicon, mpox, ont, virus, mpxv, phylogeny 2026-06-18 2026-06-25 1 1 3.0 squirrel_phylo, regex1, squirrel_qc Sequencing quality control, Phylogenetic analysis Bioinformatics, Biomedical science, Genomics, Virology MIT 10.48546/workflowhub.workflow.2196.1 Melbourne Bioinformatics, Galaxy Australia True False +Viral Amplicon Analysis Pipeline for ONT Data WorkflowHub 2195 https://workflowhub.eu/workflows/2195?version=1 Tristan Reynolds, Ammar Aziz amplicon, mpox, ont, virus, mpxv, phylogeny 2026-06-18 2026-06-25 1 1 12.0 artic_minion, multiqc, mosdepth, XY_Plot_1, regex1, __BUILD_LIST__, tp_cat, fastplong, bedtools_makewindowsbed Sequencing quality control, Sequence alignment, Validation, Mapping Bioinformatics, Biomedical science, Genomics, Virology MIT 10.48546/workflowhub.workflow.2195.1 Melbourne Bioinformatics, Galaxy Australia True False +Taxonomy Assignment with QIIME2 WorkflowHub 2098 https://workflowhub.eu/workflows/2098?version=1 Tristan Reynolds, Amy Loughman amplicon, microbiome, taxonomic-classification 2026-03-02 2026-05-13 1 1 19.0 qiime2__feature_table__tabulate_seqs, biom_convert, csv_to_tabular, tp_easyjoin_tool, qiime2_core__tools__import, qiime2__feature_classifier__classify_sklearn, qiime2__feature_table__summarize, tabular_to_csv, qiime2__taxa__barplot, qiime_extract_viz, qiime2__feature_classifier__fit_classifier_naive_bayes, qiime2_core__tools__export, qiime2__feature_classifier__extract_reads, Remove beginning1 Taxonomic classification, Formatting, Demultiplexing, Visualisation Taxonomy CC-BY-4.0 10.48546/workflowhub.workflow.2098.1 Melbourne Bioinformatics, Galaxy Australia True False +Taxonomy classification using Kraken2 and Bracken WorkflowHub 1199 https://workflowhub.eu/workflows/1199?version=2 Valentine Murigneux, Mike Thang gucfg2galaxy, metagenomics, name:collection, shotgun 2024-12-10 2024-12-10 2 2 29.0 "__RELABEL_FROM_FILE__, collection_column_join, cat_multiple, Prepare alpha diversity summary file +Paste1, collection_element_identifiers, krakentools_combine_kreports, krakentools_kreport2krona, krakentools_beta_diversity, est_abundance, taxonomy_krona_chart, kraken2, Prepare alpha diversity summary file (paste sample identifiers and Simpson results) Paste1, Prepare alpha diversity summary file (paste Simpson and Fisher results) -Paste1, kraken2, Prepare alpha diversity summary file (paste sample identifiers and Simpson results) -Paste1, taxonomy_krona_chart, collection_element_identifiers, krakentools_kreport2krona, Fisher results contains a header line we want to exclude ""Fisher's alpha...loading"" -Show tail1, est_abundance, __RELABEL_FROM_FILE__, add_line_to_file, regex1, krakentools_alpha_diversity, cat_multiple, Extract column name and fraction_total_reads from Bracken report -Cut1, krakentools_combine_kreports" Visualisation, Statistical calculation, Taxonomic classification, Aggregation Metagenomics, Taxonomy CC-BY-4.0 10.48546/workflowhub.workflow.1199.2 QCIF Bioinformatics True False -Analyses of shotgun metagenomics data with MetaPhlAn2 WorkflowHub 624 https://workflowhub.eu/workflows/624?version=1 Valentine Murigneux, Mike Thang, Saskia Hiltemann, Bérénice Batut gucfg2galaxy, metagenomics, shotgun 2023-10-26 2026-05-13 1 1 17.0 , humann2, taxonomy_krona_chart, metaphlan2krona, humann2_renorm_table, humann2_regroup_table, Cut1, merge_metaphlan_tables, metaphlan2 Visualisation, Taxonomic classification Metagenomic sequencing, Metagenomics CC-BY-4.0 10.48546/workflowhub.workflow.624.1 QCIF Bioinformatics True False -Workflow 7 : Beta Diversity [16S Microbial Analysis With Mothur] WorkflowHub 653 https://workflowhub.eu/workflows/653?version=1 Saskia Hiltemann, Bérénice Batut, Dave Clements, Ahmed Mehdi metagenomics 2023-11-09 2026-05-13 1 1 4.0 mothur_dist_shared, mothur_tree_shared, mothur_heatmap_sim, newick_display Visualisation, Phylogenetic tree reconstruction, Sequence clustering, Phylogenetic tree generation, DNA barcoding, Phylogenetic tree analysis, Taxonomic classification, Sequence read processing, Sequencing quality control, Phylogenetic analysis CC-BY-4.0 QCIF Bioinformatics True False -Workflow 6: Alpha Diversity [16S Microbial Analysis With Mothur] WorkflowHub 652 https://workflowhub.eu/workflows/652?version=1 Saskia Hiltemann, Bérénice Batut, Dave Clements, Ahmed Mehdi metagenomics 2023-11-09 2026-05-13 1 1 3.0 XY_Plot_1, mothur_rarefaction_single, mothur_summary_single Visualisation, Sequence clustering, DNA barcoding, Taxonomic classification, Sequence read processing, Sequencing quality control, Phylogenetic analysis CC-BY-4.0 QCIF Bioinformatics True False -Workflow 5: OTU Clustering [16S Microbial Analysis With Mothur] WorkflowHub 651 https://workflowhub.eu/workflows/651?version=1 Saskia Hiltemann, Bérénice Batut, Dave Clements, Ahmed Mehdi metagenomics 2023-11-09 2026-05-13 1 1 5.0 mothur_sub_sample, mothur_count_groups, mothur_cluster_split, mothur_make_shared, mothur_classify_otu Visualisation, Sequence clustering, DNA barcoding, Taxonomic classification, Sequence read processing, Sequencing quality control, Phylogenetic analysis CC-BY-4.0 QCIF Bioinformatics True False -Workflow 3: Classification [Galaxy Training: 16S Microbial Analysis With Mothur] WorkflowHub 650 https://workflowhub.eu/workflows/650?version=1 Saskia Hiltemann, Bérénice Batut, Dave Clements, Ahmed Mehdi metagenomics 2023-11-09 2026-05-13 1 1 2.0 mothur_classify_seqs, mothur_remove_lineage Visualisation, Sequence clustering, DNA barcoding, Taxonomic classification, Sequence read processing, Sequencing quality control, Phylogenetic analysis CC-BY-4.0 QCIF Bioinformatics True False -Workflow 1: Further Quality Control [16S Microbial Analysis With Mothur] WorkflowHub 648 https://workflowhub.eu/workflows/648?version=1 Saskia Hiltemann, Bérénice Batut, Dave Clements, Ahmed Mehdi metagenomics 2023-11-09 2026-05-13 1 1 5.0 mothur_summary_seqs, mothur_count_seqs, mothur_screen_seqs, mothur_unique_seqs Visualisation, Sequence clustering, DNA barcoding, Taxonomic classification, Sequence read processing, Sequencing quality control, Phylogenetic analysis CC-BY-4.0 QCIF Bioinformatics True False -Workflow 2: Data Cleaning And Chimera Removal [16S Microbial Analysis With Mothur] WorkflowHub 649 https://workflowhub.eu/workflows/649?version=1 Saskia Hiltemann, Bérénice Batut, Dave Clements, Ahmed Mehdi metagenomics 2023-11-09 2026-05-13 1 1 9.0 mothur_pre_cluster, mothur_summary_seqs, mothur_unique_seqs, mothur_filter_seqs, mothur_chimera_vsearch, mothur_screen_seqs, mothur_remove_seqs Visualisation, Sequence clustering, DNA barcoding, Taxonomic classification, Sequence read processing, Sequencing quality control, Phylogenetic analysis CC-BY-4.0 QCIF Bioinformatics True False -TB Variant Analysis v1.0 WorkflowHub 1035 https://workflowhub.eu/workflows/1035?version=1 Peter van Heusden pathogen, tuberculosis 2024-06-07 2026-05-13 1 1 15.0 bcftools_consensus, tp_awk_tool, tb_profiler_profile, kraken2, __FLATTEN__, multiqc, mosdepth, snippy, qualimap_bamqc, tb_variant_filter, tbvcfreport, fastp, tp_sed_tool, EMBOSS: seqret84 Phylogenetic tree visualisation, Sequence alignment, Validation, Antimicrobial resistance prediction, Phylogenetic tree generation, Variant calling, Sequence analysis, Local alignment, Sequence contamination filtering, Global alignment, Sequence alignment analysis, Taxonomic classification, Sequencing quality control Genetic variation, Infectious disease, Microbiology, Public health and epidemiology, Sequence assembly AGPL-3.0-or-later SANBI Pathogen Bioinformatics True False -Workflow 3: AMR - SeqSero2/SISTR WorkflowHub 407 https://workflowhub.eu/workflows/407?version=1 bioinformatics, antimicrobial resistance 2022-11-24 2026-05-13 1 1 14.0 kma_map, hamronize_summarize, seqsero2, bbtools_bbduk, __UNZIP_COLLECTION__, srst2, shovill, mob_recon, hamronize_tool, sistr_cmd, bbtools_tadpole Visualisation, Multilocus sequence typing, Sequence alignment, Genome indexing, Read mapping, Sequence contamination filtering, Clustering, Genome alignment, Parsing, Data handling, Genome assembly, RNA-Seq analysis, Sequence trimming, Antimicrobial resistance prediction, Read binning, Sequence analysis GPL-3.0 Seq4AMR True False +Paste1, add_line_to_file, krakentools_alpha_diversity, regex1, Extract column name and fraction_total_reads from Bracken report +Cut1, Fisher results contains a header line we want to exclude ""Fisher's alpha...loading"" +Show tail1" Statistical calculation, Taxonomic classification, Aggregation, Visualisation Metagenomics, Taxonomy CC-BY-4.0 10.48546/workflowhub.workflow.1199.2 QCIF Bioinformatics True False +Analyses of shotgun metagenomics data with MetaPhlAn2 WorkflowHub 624 https://workflowhub.eu/workflows/624?version=1 Valentine Murigneux, Mike Thang, Saskia Hiltemann, Bérénice Batut gucfg2galaxy, metagenomics, shotgun 2023-10-26 2026-05-13 1 1 17.0 , metaphlan2krona, metaphlan2, taxonomy_krona_chart, humann2_renorm_table, merge_metaphlan_tables, humann2, humann2_regroup_table, Cut1 Taxonomic classification, Visualisation Metagenomic sequencing, Metagenomics CC-BY-4.0 10.48546/workflowhub.workflow.624.1 QCIF Bioinformatics True False +Workflow 7 : Beta Diversity [16S Microbial Analysis With Mothur] WorkflowHub 653 https://workflowhub.eu/workflows/653?version=1 Saskia Hiltemann, Bérénice Batut, Dave Clements, Ahmed Mehdi metagenomics 2023-11-09 2026-05-13 1 1 4.0 mothur_tree_shared, mothur_heatmap_sim, newick_display, mothur_dist_shared Taxonomic classification, DNA barcoding, Sequence read processing, Sequencing quality control, Phylogenetic tree generation, Phylogenetic tree reconstruction, Sequence clustering, Phylogenetic tree analysis, Phylogenetic analysis, Visualisation CC-BY-4.0 QCIF Bioinformatics True False +Workflow 6: Alpha Diversity [16S Microbial Analysis With Mothur] WorkflowHub 652 https://workflowhub.eu/workflows/652?version=1 Saskia Hiltemann, Bérénice Batut, Dave Clements, Ahmed Mehdi metagenomics 2023-11-09 2026-05-13 1 1 3.0 XY_Plot_1, mothur_rarefaction_single, mothur_summary_single Taxonomic classification, DNA barcoding, Sequence read processing, Sequencing quality control, Sequence clustering, Phylogenetic analysis, Visualisation CC-BY-4.0 QCIF Bioinformatics True False +Workflow 5: OTU Clustering [16S Microbial Analysis With Mothur] WorkflowHub 651 https://workflowhub.eu/workflows/651?version=1 Saskia Hiltemann, Bérénice Batut, Dave Clements, Ahmed Mehdi metagenomics 2023-11-09 2026-05-13 1 1 5.0 mothur_cluster_split, mothur_make_shared, mothur_sub_sample, mothur_classify_otu, mothur_count_groups Taxonomic classification, DNA barcoding, Sequence read processing, Sequencing quality control, Sequence clustering, Phylogenetic analysis, Visualisation CC-BY-4.0 QCIF Bioinformatics True False +Workflow 3: Classification [Galaxy Training: 16S Microbial Analysis With Mothur] WorkflowHub 650 https://workflowhub.eu/workflows/650?version=1 Saskia Hiltemann, Bérénice Batut, Dave Clements, Ahmed Mehdi metagenomics 2023-11-09 2026-05-13 1 1 2.0 mothur_remove_lineage, mothur_classify_seqs Taxonomic classification, DNA barcoding, Sequence read processing, Sequencing quality control, Sequence clustering, Phylogenetic analysis, Visualisation CC-BY-4.0 QCIF Bioinformatics True False +Workflow 1: Further Quality Control [16S Microbial Analysis With Mothur] WorkflowHub 648 https://workflowhub.eu/workflows/648?version=1 Saskia Hiltemann, Bérénice Batut, Dave Clements, Ahmed Mehdi metagenomics 2023-11-09 2026-05-13 1 1 5.0 mothur_unique_seqs, mothur_summary_seqs, mothur_count_seqs, mothur_screen_seqs Taxonomic classification, DNA barcoding, Sequence read processing, Sequencing quality control, Sequence clustering, Phylogenetic analysis, Visualisation CC-BY-4.0 QCIF Bioinformatics True False +Workflow 2: Data Cleaning And Chimera Removal [16S Microbial Analysis With Mothur] WorkflowHub 649 https://workflowhub.eu/workflows/649?version=1 Saskia Hiltemann, Bérénice Batut, Dave Clements, Ahmed Mehdi metagenomics 2023-11-09 2026-05-13 1 1 9.0 mothur_unique_seqs, mothur_summary_seqs, mothur_chimera_vsearch, mothur_remove_seqs, mothur_screen_seqs, mothur_filter_seqs, mothur_pre_cluster Taxonomic classification, DNA barcoding, Sequence read processing, Sequencing quality control, Sequence clustering, Phylogenetic analysis, Visualisation CC-BY-4.0 QCIF Bioinformatics True False +TB Variant Analysis v1.0 WorkflowHub 1035 https://workflowhub.eu/workflows/1035?version=1 Peter van Heusden pathogen, tuberculosis 2024-06-07 2026-05-13 1 1 15.0 fastp, tp_awk_tool, qualimap_bamqc, EMBOSS: seqret84, kraken2, mosdepth, __FLATTEN__, tp_sed_tool, snippy, multiqc, bcftools_consensus, tb_variant_filter, tb_profiler_profile, tbvcfreport Taxonomic classification, Antimicrobial resistance prediction, Variant calling, Sequence alignment, Phylogenetic tree visualisation, Sequencing quality control, Sequence contamination filtering, Sequence alignment analysis, Phylogenetic tree generation, Validation, Global alignment, Sequence analysis, Local alignment Genetic variation, Infectious disease, Microbiology, Public health and epidemiology, Sequence assembly AGPL-3.0-or-later SANBI Pathogen Bioinformatics True False +Workflow 3: AMR - SeqSero2/SISTR WorkflowHub 407 https://workflowhub.eu/workflows/407?version=1 bioinformatics, antimicrobial resistance 2022-11-24 2026-05-13 1 1 14.0 seqsero2, shovill, bbtools_tadpole, hamronize_tool, bbtools_bbduk, sistr_cmd, mob_recon, kma_map, __UNZIP_COLLECTION__, hamronize_summarize, srst2 Genome alignment, Read binning, Sequence contamination filtering, Clustering, Antimicrobial resistance prediction, Data handling, Sequence alignment, Parsing, Genome indexing, RNA-Seq analysis, Sequence trimming, Sequence analysis, Read mapping, Multilocus sequence typing, Visualisation, Genome assembly GPL-3.0 Seq4AMR True False Workflow 2: Sciensano WorkflowHub 644 https://workflowhub.eu/workflows/644?version=1 2023-11-07 2026-05-13 1 1 1.0 pipeline_stec_1.0 CC-BY-4.0 Seq4AMR True False -Workflow 4: Staramr WorkflowHub 470 https://workflowhub.eu/workflows/470?version=1 10.3390/microorganisms10020292, amr, amr-detection, bioinformatics, antimicrobial resistance 2023-05-11 2026-05-13 1 1 10.0 hamronize_summarize, tp_find_and_replace, abricate, staramr_search, collapse_dataset, shovill, hamronize_tool Parsing, Data handling, Genome assembly, Antimicrobial resistance prediction GPL-3.0 Seq4AMR True False +Workflow 4: Staramr WorkflowHub 470 https://workflowhub.eu/workflows/470?version=1 10.3390/microorganisms10020292, amr, amr-detection, bioinformatics, antimicrobial resistance 2023-05-11 2026-05-13 1 1 10.0 abricate, shovill, hamronize_tool, tp_find_and_replace, staramr_search, collapse_dataset, hamronize_summarize Antimicrobial resistance prediction, Data handling, Parsing, Genome assembly GPL-3.0 Seq4AMR True False Workflow 1: AbritAMR WorkflowHub 634 https://workflowhub.eu/workflows/634?version=1 2023-10-31 2026-05-13 1 1 1.0 abritamr Antimicrobial resistance prediction CC-BY-4.0 Seq4AMR True False -AMR-Pathfinder WorkflowHub 1189 https://workflowhub.eu/workflows/1189?version=2 Helena Rasche, Dennis Dollée, Birgit Rijvers amr, amr-detection, benchamrking 2024-11-14 2026-05-13 2 2 36.0 , hamronize_summarize, tp_text_file_with_recurring_lines, cat1, hamronize_tool, abricate, addValue, __APPLY_RULES__, __MERGE_COLLECTION__, collapse_dataset, shovill, Grep1, cast, tp_find_and_replace, Cut1, tp_split_on_column, datamash_ops, staramr_search, cat_multi_datasets Parsing, Data handling, Genome assembly, Antimicrobial resistance prediction MIT Seq4AMR, ErasmusMC Clinical Bioinformatics True False -Copy of Metaproteomics_GTN shared by user engy.nasr https://usegalaxy.eu 6ca1b4fe047a03d2 https://usegalaxy.eu/published/workflow?id=6ca1b4fe047a03d2 proteomics, name:microgalaxy 2026-04-27 2026-04-27 1 1 search_gui, peptide_shaker, sqlite_to_tabular, query_tabular, unipept Visualisation, Prediction and recognition True False -Training: 16S rRNA Analysis with Nanopore Sequencing Reads https://usegalaxy.eu 2a093e63ebf6876b https://usegalaxy.eu/published/workflow?id=2a093e63ebf6876b metagenomics, name:microgalaxy 2025-12-01 2026-03-16 2 2 multiqc, kraken2, fastqc, taxonomy_krona_chart, porechop, tp_replace_in_line, fastp, Remove beginning1, datamash_reverse Visualisation, Sequence composition calculation, Sequence contamination filtering, Statistical calculation, Validation, Taxonomic classification, Sequencing quality control True False -MetaG_extended https://usegalaxy.eu 8c91345ed468e22d https://usegalaxy.eu/published/workflow?id=8c91345ed468e22d name:microgalaxy 2025-10-01 2026-02-04 0 0 fasplit, tp_awk_tool, tp_grep_tool, fastqc, checkm_lineage_wf, hmmer_hmmscan, coverm_genome, quast, coverm_contig, fraggenescan, maxbin2, cat_bins, tp_cat, trim_galore, interproscan, sort1 Visualisation, Sequence composition calculation, Formatting, Statistical calculation, Validation, Sequence database search, Format validation, Primer removal, Coding region prediction, Local alignment, Sequence assembly, Database search, Sequence profile generation, Sequencing quality control, Protein feature detection, Sequence trimming, Multiple sequence alignment, Sequence assembly validation, Sequence motif recognition, Sequence generation, Read pre-processing, Data retrieval, Gene prediction, Taxonomic classification, Conversion, Probabilistic sequence generation True False -Metagenomic Taxonomy Analysis https://usegalaxy.eu 7491883694fff308 https://usegalaxy.eu/published/workflow?id=7491883694fff308 Bérénice Batut, Géraldine Piot, Mina Hojat Ansari name:metagenomics, microbiome, diversity, name:microgalaxy 2025-11-28 2025-12-17 3 3 metaphlan, kraken2, collection_element_identifiers, taxonomy_krona_chart, metaphlan2krona, krakentools_kreport2krona, taxpasta, est_abundance, sylph_profile, add_line_to_file, datamash_transpose, Remove beginning1, cat1 Visualisation, Formatting, Statistical calculation, Taxonomic classification, Conversion, Aggregation, Standardisation and normalisation MIT True False -Quality control of bins generated by MetaBAT2, MaxBin2, SemiBin, and CONCOCT https://usegalaxy.eu 7371b6918e895e0c https://usegalaxy.eu/published/workflow?id=7371b6918e895e0c Bérénice Batut microbiome, name:microgalaxy 2025-12-01 2025-12-08 16 16 multiqc, __FLATTEN__, collection_element_identifiers, __RELABEL_FROM_FILE__, __MERGE_COLLECTION__, regex1, checkm2 Sequence composition calculation, Sequence assembly validation, Statistical calculation, Validation, Sequencing quality control MIT True False -pAllori Amplicon 16S Pre-Processing and Taxonomy Classification https://usegalaxy.eu 466bdd8ba7b67264 https://usegalaxy.eu/published/workflow?id=466bdd8ba7b67264 Engy Nasr, Paul Zierep name:microgalaxy, name:16s, name:metagenomics, name:pallori 2023-06-30 2025-11-18 193 193 compose_text_param, ampvis2_heatmap, fastqc, bg_column_arrange_by_header, ampvis2_subset_samples, datamash_transpose, unzip, biom_convert, maaslin2, volcanoplot, __FLATTEN__, calculate_numeric_param, mmuphin, phyloseq_tax_glom, ampvis2_load, param_value_from_file, tp_awk_tool, tp_cut_tool, tp_easyjoin_tool, Remove beginning1, multiqc, ampvis2_ordinate, phyloseq_from_biom, phyloseq_add_rank_names, ampvis2_export_otu, regex1, lotus2, decontam Visualisation, Sequence feature detection, Sequence composition calculation, Filtering, Formatting, Statistical calculation, Deposition, Validation, Analysis, Standardisation and normalisation, Classification, DNA barcoding, Sequencing quality control MIT True False -Metagenomic Taxonomy and Functional Analysis https://usegalaxy.eu cb2df493f5e334f7 https://usegalaxy.eu/published/workflow?id=cb2df493f5e334f7 Bérénice Batut, Géraldine Piot name:metagenomics, microbiome, diversity, name:microgalaxy 2024-12-20 2025-11-13 18 18 metaphlan, tp_text_file_with_recurring_lines, est_abundance, datamash_transpose, cat1, tp_sed_tool, sort1, humann, kraken2, collection_element_identifiers, krakentools_kreport2krona, csv_to_tabular, collapse_dataset, humann_unpack_pathways, humann_rename_table, tp_awk_tool, tp_replace_in_line, __UNZIP_COLLECTION__, add_line_to_file, tp_easyjoin_tool, Remove beginning1, krakentools_alpha_diversity, fastq_paired_end_interlacer, collection_column_join, taxonomy_krona_chart, taxpasta, sylph_profile, humann_renorm_table, humann_regroup_table Visualisation, Formatting, Statistical calculation, Standardisation and normalisation, Species frequency estimation, Taxonomic classification, Conversion, Aggregation, Phylogenetic analysis MIT True False -pAllori Blood RNA https://usegalaxy.eu ca9d3233b0912765 https://usegalaxy.eu/published/workflow?id=ca9d3233b0912765 Engy Nasr, Paul Zierep name:microgalaxy, name:pallori, name:bloodrna, name:umi, name:barcode, name:transcriptomics 2023-07-02 2025-06-26 48 48 collection_column_join, multiqc, fastqc, __FILTER_FAILED_DATASETS__, featurecounts, umi_tools_dedup, rna_star, umi_tools_extract Read summarisation, Sequence composition calculation, RNA-Seq quantification, Statistical calculation, Sequence alignment, Validation, Sequencing quality control MIT True False -MetaG: Preparation, Building and Annotation of Metagenomics Assembled Genomes https://usegalaxy.eu 667bac8d7453e5f1 https://usegalaxy.eu/published/workflow?id=667bac8d7453e5f1 Valerie C. Schiml, Magnus Ø. Arntzen, Bérénice Batut name:microgalaxy, name:microbiome, name:mags 2024-09-30 2024-12-21 14 14 fasplit, tp_awk_tool, tp_grep_tool, fastqc, checkm_lineage_wf, hmmer_hmmscan, coverm_genome, quast, coverm_contig, fraggenescan, maxbin2, tp_cat, cat_bins, kofamscan, trim_galore, interproscan, sort1 Visualisation, Sequence composition calculation, Formatting, Statistical calculation, Gene functional annotation, Validation, Sequence database search, Format validation, Primer removal, Coding region prediction, Local alignment, Sequence assembly, Database search, Sequence profile generation, Sequencing quality control, Protein feature detection, Sequence trimming, Multiple sequence alignment, Sequence assembly validation, Sequence motif recognition, Sequence generation, Sequence analysis, Read pre-processing, Data retrieval, Gene prediction, Taxonomic classification, Conversion, Probabilistic sequence generation MIT True False -ASaiM-MT: Metatranscriptomics Analysis of Microbes https://usegalaxy.eu 096b75501c8e0888 https://usegalaxy.eu/published/workflow?id=096b75501c8e0888 Subina Mehta, Marie Crane, Emma Leith, Bérénice Batut, Saskia Hiltemann, Magnus Ø Arntzen, Benoit J. Kunath, Phillip B. Pope, Francesco Delogu, Ray Sajulga, Praveen Kumar, James E. Johnson, Timothy J. Griffin, Pratik D. Jagtap asaim, metatranscriptomics, rna-seq, microbiome, name:microgalaxy 2024-12-20 2024-12-20 3 3 Grouping1, group_humann2_uniref_abundances_to_go, fastqc, humann2_renorm_table, humann2_unpack_pathways, tp_sort_header_tool, humann2_genefamilies_genus_level, humann2, metaphlan2krona, Grep1, format_metaphlan2_output, graphlan, bg_sortmerna, fastq_paired_end_interlacer, multiqc, combine_metaphlan2_humann2, cutadapt, taxonomy_krona_chart, graphlan_annotate, export2graphlan, metaphlan2 Sequence comparison, Phylogenetic tree visualisation, Visualisation, Sequence composition calculation, Formatting, Statistical calculation, Phylogenetic inference, Validation, Primer removal, Sequence alignment analysis, Sequencing quality control, Sequence trimming, Phylogenetic tree editing, Read pre-processing, Taxonomic classification, Sequence similarity search, Conversion MIT True False -MetaT: Metatranscriptomics data analysis https://usegalaxy.eu fd90652d475ed739 https://usegalaxy.eu/published/workflow?id=fd90652d475ed739 Valerie C. Schiml, Magnus Ø. Arntzen, Francesco Delogu, Praveen Kumar, Benoit Kunath, Bérénice Batut, Subina Mehta, James E. Johnson, Björn Grüning, Phillip B. Pope, Pratik D. Jagtap, Timothy J. Griffin name:microgalaxy, metatranscriptomics, microbiome 2024-11-21 2024-12-20 6 6 collection_column_join, kallisto_quant, fastqc, __UNZIP_COLLECTION__, trim_galore, bg_sortmerna Sequence trimming, Sequence composition calculation, Statistical calculation, Gene expression profiling, Primer removal, Read pre-processing, Sequence similarity search, Sequence alignment analysis, Sequence comparison, Sequencing quality control MIT True False -Halophiles workup of Comparative gene analysis https://usegalaxy.eu a2c46deea34d9d80 https://usegalaxy.eu/published/workflow?id=a2c46deea34d9d80 Anton Nekrutenko genome-annotation, name:microgalaxy 2024-12-03 2024-12-05 2 2 tp_split_on_column, regexColumn1, rbc_mafft, bg_diamond_view, Filter1, bg_diamond, join1, tab2fasta, collapse_dataset, Cut1, cat1, rapidnj, Add_a_column1, gops_intersect_1 Sequence alignment analysis, Multiple sequence alignment, Phylogenetic tree generation True False -Metaproteomics workflow https://usegalaxy.eu cefc49c13ff73231 https://usegalaxy.eu/published/workflow?id=cefc49c13ff73231 Timothy Griffin, Pratik Jagtap, James Johnson, Clemens Blank, Subina Mehta name:metaproteomics, name:galaxyp, name:massspectrometry, name:microgalaxy 2024-11-21 2024-11-21 40 40 search_gui, peptide_shaker, sqlite_to_tabular, query_tabular, unipept Visualisation, Prediction and recognition MIT True False -Feature-Count Table Normalization https://usegalaxy.eu 6239178d7cc4ac68 https://usegalaxy.eu/published/workflow?id=6239178d7cc4ac68 Johannes Effenberger name:microgalaxy, normalization, softmax, relative-abundance, sigmoid, css, limma-tmm, limma-rle 2024-11-21 2024-11-21 5 5 Grep1, __BUILD_LIST__, map_param_value, __EXTRACT_DATASET__, __FILTER_EMPTY_DATASETS__ MIT True False -metaQuantome_datacreation_workflow https://usegalaxy.eu cd675ab32d3e7833 https://usegalaxy.eu/published/workflow?id=cd675ab32d3e7833 Subina Metha, Timothy J. Griffin, Pratik Jagtap, Emma Leith, Marie Crane proteomics, name:microgalaxy 2024-11-21 2024-11-21 1 1 tp_replace_in_column, flashlfq, Filter1, msconvert, tp_replace_in_line, Cut1, regex1, Remove beginning1, search_gui, peptide_shaker, query_tabular, unipept Visualisation, Label-free quantification, Prediction and recognition, Filtering, Formatting MIT True False -metaquantome-function-worklow https://usegalaxy.eu e5a89ef7b5f1c1d9 https://usegalaxy.eu/published/workflow?id=e5a89ef7b5f1c1d9 Subina Mehta, Timothy J. Griffin, Pratik Jagtap, Emma Leith, Marie Crane, Praveen Kumar proteomics, name:microgalaxy 2024-11-21 2024-11-21 3 3 metaquantome_db, metaquantome_sample, metaquantome_stat, metaquantome_filter, metaquantome_viz, metaquantome_expand Visualisation, Statistical inference, Quantification, Heat map generation, Query and retrieval, Indexing, Differential protein expression analysis, Principal component visualisation, Filtering, Functional clustering MIT True False -Cloud Aerosol MT-MG Contamination Filtering https://usegalaxy.eu c09159d7aad0f264 https://usegalaxy.eu/published/workflow?id=c09159d7aad0f264 Engy Nasr , Bérénice Batut, Raphaëlle Péguilhan, Pierre Amato metagenomics, metatranscriptomics, name:microgalaxy 2024-11-21 2024-11-21 2 2 bowtie2, kraken2, fastq_to_tabular, filter_tabular, recentrifuge, seq_filter_by_id Cross-assembly, Taxonomic classification, Read mapping, Expression analysis MIT True False - Cloud-Aerosole MT-MG Functional Profiling https://usegalaxy.eu 63478edcea3f449a https://usegalaxy.eu/published/workflow?id=63478edcea3f449a Engy Nasr, Bérénice Batut, Raphaëlle Péguilhan, Pierre Amato metagenomics, metatranscriptomics, name:microgalaxy 2024-11-21 2024-11-21 4 4 featurecounts, bowtie2, multiqc Read summarisation, RNA-Seq quantification, Validation, Read mapping, Sequencing quality control MIT True False -Cloud-Aerosole MT-MG Pre-Processing https://usegalaxy.eu 1ef76b7b86e15792 https://usegalaxy.eu/published/workflow?id=1ef76b7b86e15792 Engy Nasr, Bérénice Batut, Raphaëlle Péguilhan, Pierre Amato metagenomics, metatranscriptomics, name:microgalaxy 2024-11-21 2024-11-21 6 6 trimmomatic, fastqc, multiqc Sequence composition calculation, Statistical calculation, Validation, Sequencing quality control MIT True False +AMR-Pathfinder WorkflowHub 1189 https://workflowhub.eu/workflows/1189?version=2 Helena Rasche, Dennis Dollée, Birgit Rijvers amr, amr-detection, benchamrking 2024-11-14 2026-05-13 2 2 36.0 , cat_multi_datasets, shovill, tp_split_on_column, staramr_search, collapse_dataset, datamash_ops, abricate, hamronize_tool, tp_find_and_replace, cat1, tp_text_file_with_recurring_lines, cast, __APPLY_RULES__, addValue, Grep1, hamronize_summarize, __MERGE_COLLECTION__, Cut1 Antimicrobial resistance prediction, Data handling, Parsing, Genome assembly MIT Seq4AMR, ErasmusMC Clinical Bioinformatics True False +Training: 16S rRNA Analysis with Nanopore Sequencing Reads https://usegalaxy.eu 2a093e63ebf6876b https://usegalaxy.eu/published/workflow?id=2a093e63ebf6876b metagenomics, name:microgalaxy 2025-12-01 2026-06-12 3 3 fastp, datamash_reverse, taxonomy_krona_chart, multiqc, kraken2, tp_replace_in_line, fastqc, porechop, Remove beginning1 Sequencing quality control, Sequence contamination filtering, Taxonomic classification, Statistical calculation, Validation, Sequence composition calculation, Visualisation True False +Sadowsky_MetaG-DBgen_02102026 https://usegalaxy.eu 7be08f99f83c927e https://usegalaxy.eu/published/workflow?id=7be08f99f83c927e Subina Mehta name:microgalaxy 2026-02-10 2026-06-09 1 1 validate_fasta_database, Remove beginning1, regexColumn1, cat_bins, trim_galore, fastqc, eggnog_mapper, collapse_dataset, regex1, query_tabular, tp_cat, tab2fasta, fasta_merge_files_and_filter_unique_sequences, maxbin2, fasta2tab, fraggenescan Statistical calculation, Taxonomic classification, Genome annotation, Sequencing quality control, Sequence trimming, Sequence assembly, Fold recognition, Information extraction, Homology-based gene prediction, Gene prediction, Read pre-processing, Coding region prediction, Primer removal, Query and retrieval, Sequence composition calculation CC-BY-4.0 True False +Copy of Metaproteomics_GTN shared by user engy.nasr https://usegalaxy.eu 6ca1b4fe047a03d2 https://usegalaxy.eu/published/workflow?id=6ca1b4fe047a03d2 proteomics, name:microgalaxy 2026-04-27 2026-04-27 1 1 peptide_shaker, unipept, search_gui, sqlite_to_tabular, query_tabular Prediction and recognition, Visualisation True False +MetaG_extended https://usegalaxy.eu 8c91345ed468e22d https://usegalaxy.eu/published/workflow?id=8c91345ed468e22d name:microgalaxy 2025-10-01 2026-02-04 0 0 coverm_genome, fasplit, tp_awk_tool, tp_grep_tool, sort1, cat_bins, trim_galore, fastqc, checkm_lineage_wf, coverm_contig, hmmer_hmmscan, interproscan, tp_cat, maxbin2, quast, fraggenescan Statistical calculation, Formatting, Visualisation, Format validation, Conversion, Probabilistic sequence generation, Sequencing quality control, Sequence assembly, Protein feature detection, Gene prediction, Sequence motif recognition, Coding region prediction, Sequence composition calculation, Sequence generation, Database search, Sequence database search, Data retrieval, Taxonomic classification, Multiple sequence alignment, Sequence assembly validation, Sequence trimming, Sequence profile generation, Validation, Read pre-processing, Primer removal, Local alignment True False +Metagenomic Taxonomy Analysis https://usegalaxy.eu 7491883694fff308 https://usegalaxy.eu/published/workflow?id=7491883694fff308 Bérénice Batut, Géraldine Piot, Mina Hojat Ansari name:metagenomics, microbiome, diversity, name:microgalaxy 2025-11-28 2025-12-17 3 3 metaphlan, metaphlan2krona, collection_element_identifiers, sylph_profile, taxonomy_krona_chart, krakentools_kreport2krona, est_abundance, kraken2, cat1, add_line_to_file, taxpasta, datamash_transpose, Remove beginning1 Statistical calculation, Taxonomic classification, Standardisation and normalisation, Formatting, Aggregation, Conversion, Visualisation MIT True False +Quality control of bins generated by MetaBAT2, MaxBin2, SemiBin, and CONCOCT https://usegalaxy.eu 7371b6918e895e0c https://usegalaxy.eu/published/workflow?id=7371b6918e895e0c Bérénice Batut microbiome, name:microgalaxy 2025-12-01 2025-12-08 16 16 __RELABEL_FROM_FILE__, checkm2, collection_element_identifiers, multiqc, __FLATTEN__, __MERGE_COLLECTION__, regex1 Statistical calculation, Sequencing quality control, Validation, Sequence composition calculation, Sequence assembly validation MIT True False +pAllori Amplicon 16S Pre-Processing and Taxonomy Classification https://usegalaxy.eu 466bdd8ba7b67264 https://usegalaxy.eu/published/workflow?id=466bdd8ba7b67264 Engy Nasr, Paul Zierep name:microgalaxy, name:16s, name:metagenomics, name:pallori 2023-06-30 2025-11-18 193 193 __FLATTEN__, ampvis2_heatmap, datamash_transpose, regex1, ampvis2_load, mmuphin, maaslin2, ampvis2_ordinate, unzip, param_value_from_file, phyloseq_from_biom, tp_awk_tool, phyloseq_add_rank_names, calculate_numeric_param, ampvis2_export_otu, bg_column_arrange_by_header, volcanoplot, tp_cut_tool, biom_convert, Remove beginning1, tp_easyjoin_tool, multiqc, lotus2, compose_text_param, fastqc, ampvis2_subset_samples, decontam, phyloseq_tax_glom Statistical calculation, Formatting, DNA barcoding, Filtering, Sequence feature detection, Sequencing quality control, Standardisation and normalisation, Analysis, Validation, Deposition, Sequence composition calculation, Visualisation, Classification MIT True False +Metagenomic Taxonomy and Functional Analysis https://usegalaxy.eu cb2df493f5e334f7 https://usegalaxy.eu/published/workflow?id=cb2df493f5e334f7 Bérénice Batut, Géraldine Piot name:metagenomics, microbiome, diversity, name:microgalaxy 2024-12-20 2025-11-13 18 18 collection_element_identifiers, krakentools_kreport2krona, tp_replace_in_line, collapse_dataset, datamash_transpose, krakentools_alpha_diversity, tp_awk_tool, csv_to_tabular, taxonomy_krona_chart, est_abundance, kraken2, cat1, tp_text_file_with_recurring_lines, taxpasta, metaphlan, humann_regroup_table, sylph_profile, fastq_paired_end_interlacer, humann_renorm_table, Remove beginning1, humann, sort1, humann_rename_table, collection_column_join, tp_easyjoin_tool, tp_sed_tool, humann_unpack_pathways, add_line_to_file, __UNZIP_COLLECTION__ Statistical calculation, Taxonomic classification, Formatting, Aggregation, Species frequency estimation, Conversion, Standardisation and normalisation, Phylogenetic analysis, Visualisation MIT True False +pAllori Blood RNA https://usegalaxy.eu ca9d3233b0912765 https://usegalaxy.eu/published/workflow?id=ca9d3233b0912765 Engy Nasr, Paul Zierep name:microgalaxy, name:pallori, name:bloodrna, name:umi, name:barcode, name:transcriptomics 2023-07-02 2025-06-26 48 48 umi_tools_dedup, collection_column_join, umi_tools_extract, multiqc, fastqc, featurecounts, __FILTER_FAILED_DATASETS__, rna_star Sequencing quality control, Statistical calculation, Validation, Read summarisation, Sequence alignment, Sequence composition calculation, RNA-Seq quantification MIT True False +MetaG: Preparation, Building and Annotation of Metagenomics Assembled Genomes https://usegalaxy.eu 667bac8d7453e5f1 https://usegalaxy.eu/published/workflow?id=667bac8d7453e5f1 Valerie C. Schiml, Magnus Ø. Arntzen, Bérénice Batut name:microgalaxy, name:microbiome, name:mags 2024-09-30 2024-12-21 14 14 coverm_genome, fasplit, tp_awk_tool, tp_grep_tool, sort1, cat_bins, trim_galore, fastqc, checkm_lineage_wf, interproscan, coverm_contig, hmmer_hmmscan, kofamscan, tp_cat, maxbin2, quast, fraggenescan Statistical calculation, Formatting, Gene functional annotation, Visualisation, Format validation, Conversion, Probabilistic sequence generation, Sequencing quality control, Sequence assembly, Protein feature detection, Gene prediction, Sequence motif recognition, Coding region prediction, Sequence composition calculation, Sequence generation, Database search, Sequence database search, Data retrieval, Taxonomic classification, Multiple sequence alignment, Sequence assembly validation, Sequence trimming, Sequence profile generation, Validation, Sequence analysis, Read pre-processing, Primer removal, Local alignment MIT True False +ASaiM-MT: Metatranscriptomics Analysis of Microbes https://usegalaxy.eu 096b75501c8e0888 https://usegalaxy.eu/published/workflow?id=096b75501c8e0888 Subina Mehta, Marie Crane, Emma Leith, Bérénice Batut, Saskia Hiltemann, Magnus Ø Arntzen, Benoit J. Kunath, Phillip B. Pope, Francesco Delogu, Ray Sajulga, Praveen Kumar, James E. Johnson, Timothy J. Griffin, Pratik D. Jagtap asaim, metatranscriptomics, rna-seq, microbiome, name:microgalaxy 2024-12-20 2024-12-20 3 3 graphlan_annotate, humann2_renorm_table, combine_metaphlan2_humann2, bg_sortmerna, cutadapt, humann2_genefamilies_genus_level, taxonomy_krona_chart, export2graphlan, metaphlan2, fastq_paired_end_interlacer, group_humann2_uniref_abundances_to_go, Grouping1, Grep1, humann2, graphlan, tp_sort_header_tool, metaphlan2krona, humann2_unpack_pathways, format_metaphlan2_output, multiqc, fastqc Statistical calculation, Phylogenetic inference, Taxonomic classification, Formatting, Conversion, Phylogenetic tree visualisation, Sequence similarity search, Sequence composition calculation, Phylogenetic tree editing, Sequencing quality control, Sequence trimming, Sequence alignment analysis, Sequence comparison, Validation, Read pre-processing, Primer removal, Visualisation MIT True False +MetaT: Metatranscriptomics data analysis https://usegalaxy.eu fd90652d475ed739 https://usegalaxy.eu/published/workflow?id=fd90652d475ed739 Valerie C. Schiml, Magnus Ø. Arntzen, Francesco Delogu, Praveen Kumar, Benoit Kunath, Bérénice Batut, Subina Mehta, James E. Johnson, Björn Grüning, Phillip B. Pope, Pratik D. Jagtap, Timothy J. Griffin name:microgalaxy, metatranscriptomics, microbiome 2024-11-21 2024-12-20 6 6 kallisto_quant, collection_column_join, trim_galore, fastqc, bg_sortmerna, __UNZIP_COLLECTION__ Statistical calculation, Sequence similarity search, Sequencing quality control, Gene expression profiling, Sequence trimming, Sequence alignment analysis, Sequence comparison, Read pre-processing, Primer removal, Sequence composition calculation MIT True False +Halophiles workup of Comparative gene analysis https://usegalaxy.eu a2c46deea34d9d80 https://usegalaxy.eu/published/workflow?id=a2c46deea34d9d80 Anton Nekrutenko genome-annotation, name:microgalaxy 2024-12-03 2024-12-05 2 2 Add_a_column1, tab2fasta, tp_split_on_column, gops_intersect_1, rbc_mafft, join1, bg_diamond, cat1, collapse_dataset, rapidnj, Filter1, bg_diamond_view, Cut1, regexColumn1 Sequence alignment analysis, Phylogenetic tree generation, Multiple sequence alignment True False +Metaproteomics workflow https://usegalaxy.eu cefc49c13ff73231 https://usegalaxy.eu/published/workflow?id=cefc49c13ff73231 Timothy Griffin, Pratik Jagtap, James Johnson, Clemens Blank, Subina Mehta name:metaproteomics, name:galaxyp, name:massspectrometry, name:microgalaxy 2024-11-21 2024-11-21 40 40 peptide_shaker, unipept, search_gui, sqlite_to_tabular, query_tabular Prediction and recognition, Visualisation MIT True False +Feature-Count Table Normalization https://usegalaxy.eu 6239178d7cc4ac68 https://usegalaxy.eu/published/workflow?id=6239178d7cc4ac68 Johannes Effenberger name:microgalaxy, normalization, softmax, relative-abundance, sigmoid, css, limma-tmm, limma-rle 2024-11-21 2024-11-21 5 5 __EXTRACT_DATASET__, map_param_value, Grep1, __BUILD_LIST__, __FILTER_EMPTY_DATASETS__ MIT True False +metaQuantome_datacreation_workflow https://usegalaxy.eu cd675ab32d3e7833 https://usegalaxy.eu/published/workflow?id=cd675ab32d3e7833 Subina Metha, Timothy J. Griffin, Pratik Jagtap, Emma Leith, Marie Crane proteomics, name:microgalaxy 2024-11-21 2024-11-21 1 1 peptide_shaker, search_gui, unipept, flashlfq, tp_replace_in_line, Cut1, regex1, msconvert, tp_replace_in_column, query_tabular, Filter1, Remove beginning1 Formatting, Prediction and recognition, Filtering, Visualisation, Label-free quantification MIT True False +metaquantome-function-worklow https://usegalaxy.eu e5a89ef7b5f1c1d9 https://usegalaxy.eu/published/workflow?id=e5a89ef7b5f1c1d9 Subina Mehta, Timothy J. Griffin, Pratik Jagtap, Emma Leith, Marie Crane, Praveen Kumar proteomics, name:microgalaxy 2024-11-21 2024-11-21 3 3 metaquantome_stat, metaquantome_expand, metaquantome_viz, metaquantome_db, metaquantome_filter, metaquantome_sample Quantification, Differential protein expression analysis, Query and retrieval, Principal component visualisation, Indexing, Heat map generation, Filtering, Functional clustering, Statistical inference, Visualisation MIT True False +Cloud Aerosol MT-MG Contamination Filtering https://usegalaxy.eu c09159d7aad0f264 https://usegalaxy.eu/published/workflow?id=c09159d7aad0f264 Engy Nasr , Bérénice Batut, Raphaëlle Péguilhan, Pierre Amato metagenomics, metatranscriptomics, name:microgalaxy 2024-11-21 2024-11-21 2 2 bowtie2, recentrifuge, fastq_to_tabular, kraken2, filter_tabular, seq_filter_by_id Taxonomic classification, Expression analysis, Read mapping, Cross-assembly MIT True False + Cloud-Aerosole MT-MG Functional Profiling https://usegalaxy.eu 63478edcea3f449a https://usegalaxy.eu/published/workflow?id=63478edcea3f449a Engy Nasr, Bérénice Batut, Raphaëlle Péguilhan, Pierre Amato metagenomics, metatranscriptomics, name:microgalaxy 2024-11-21 2024-11-21 4 4 bowtie2, featurecounts, multiqc Sequencing quality control, Validation, Read summarisation, Read mapping, RNA-Seq quantification MIT True False +Cloud-Aerosole MT-MG Pre-Processing https://usegalaxy.eu 1ef76b7b86e15792 https://usegalaxy.eu/published/workflow?id=1ef76b7b86e15792 Engy Nasr, Bérénice Batut, Raphaëlle Péguilhan, Pierre Amato metagenomics, metatranscriptomics, name:microgalaxy 2024-11-21 2024-11-21 6 6 fastqc, multiqc, trimmomatic Sequencing quality control, Statistical calculation, Validation, Sequence composition calculation MIT True False Mgnify ML https://usegalaxy.eu 011f701c5a55bfdf https://usegalaxy.eu/published/workflow?id=011f701c5a55bfdf name:microgalaxy 2023-10-10 2024-03-15 128 128 interactive_tool_jupyter_notebook, __BUILD_LIST__ True False -Ecoli Comparison https://usegalaxy.eu 0e492839192d26e0 https://usegalaxy.eu/published/workflow?id=0e492839192d26e0 assembly, name:microgalaxy 2023-12-14 2023-12-14 0 0 mergeCols1, bedtools_complementbed, tp_sort_header_tool, tp_sed_tool, cat1, bedtools_sortbed, fasta_compute_length, Filter1, addValue, join1, collapse_dataset, bedtools_intersectbed, random_lines1, Grep1, tp_cat, Cut1, fasta_filter_by_length, tp_grep_tool, datamash_ops, lastz_wrapper_2 Read mapping, Sequence alignment, Mapping True False -Comparative gene analysis https://usegalaxy.eu 86900be4282d4b1d https://usegalaxy.eu/published/workflow?id=86900be4282d4b1d Anton Nekrutenko vgp, genome-annotation, name:microgalaxy 2023-12-14 2023-12-14 0 0 tp_split_on_column, regexColumn1, rbc_mafft, bg_diamond_view, Filter1, bg_diamond, join1, tab2fasta, collapse_dataset, Cut1, cat1, rapidnj, Add_a_column1, gops_intersect_1 Sequence alignment analysis, Multiple sequence alignment, Phylogenetic tree generation True False -Apollo Load Test https://usegalaxy.eu 3c233cc56d4df8b0 https://usegalaxy.eu/published/workflow?id=3c233cc56d4df8b0 genome-annotation, name:microgalaxy 2023-12-14 2023-12-14 0 0 jbrowse, iframe, create_or_update, list_organism, create_account Genome visualisation True False -Flye-AMR workflow EMC/WMDI - v3.5 (imported from URL) https://usegalaxy.eu 152223c8aed27357 https://usegalaxy.eu/published/workflow?id=152223c8aed27357 wmdi, name:microgalaxy 2023-12-14 2023-12-14 0 0 jbrowse, bg_column_arrange_by_header, gff2bed1, tp_text_file_with_recurring_lines, circos_gc_skew, trimmomatic, fasta2tab, fasta_compute_length, Add_a_column1, circos_interval_to_tile, tp_sort_header_tool, minimap2, Filter1, bandage_image, nanoplot, join1, PlasFlow, circos, tp_head_tool, deeptools_bam_coverage, Grep1, tp_cut_tool, tp_easyjoin_tool, tp_cat, regex_replace, Cut1, tp_split_on_column, medaka_consensus_pipeline, circos_wiggle_to_scatter, ncbi_blastn_wrapper, staramr_search, prokka, regex1, flye, tbl2gff3, tab2fasta Genome assembly, Sequence visualisation, Gene prediction, Genome annotation, Sequence analysis, Variant calling, Base-calling, Antimicrobial resistance prediction, Coding region prediction, Cross-assembly, Mapping assembly, Sequence assembly, Box-Whisker plot plotting, Genome visualisation, Pairwise sequence alignment, Sequence assembly visualisation, Scatter plot plotting, De-novo assembly True False -From VCFs to SNP distance matrix https://usegalaxy.eu 6d333ed886aab471 https://usegalaxy.eu/published/workflow?id=6d333ed886aab471 evolution, name:microgalaxy 2023-12-14 2023-12-14 0 0 bcftools_consensus, snp_sites, tb_variant_filter, tp_cat, snp_dists True False -From Fastqs to VCFs and BAMs https://usegalaxy.eu 3a8fde248a4d0383 https://usegalaxy.eu/published/workflow?id=3a8fde248a4d0383 evolution, name:microgalaxy 2023-12-14 2023-12-14 0 0 trimmomatic, tb_variant_filter, __MERGE_COLLECTION__, snippy Phylogenetic tree visualisation, Variant calling, Phylogenetic tree generation True False -From BAMs to drug resistance prediction with TB-profiler https://usegalaxy.eu d0d6dae0d1eecc21 https://usegalaxy.eu/published/workflow?id=d0d6dae0d1eecc21 evolution, name:microgalaxy 2023-12-14 2023-12-14 0 0 samtools_view, tb_profiler_profile, tp_grep_tool, tp_replace_in_line, __MERGE_COLLECTION__, tp_cat, addName, tp_sed_tool Antimicrobial resistance prediction True False -Compute Allel Frequency Table from paired reads https://usegalaxy.eu 21a39ac4c1becb31 https://usegalaxy.eu/published/workflow?id=21a39ac4c1becb31 name:microgalaxy, hpylori 2023-12-13 2023-12-13 2 2 bowtie2, bcftools_norm, tp_awk_tool, snpSift_filter, vcf2tsv, freebayes, bcftools_view Read mapping, Statistical calculation, Variant calling True False -Reference genome choice (indels, coverage, depth) for short reads https://usegalaxy.eu 61fe08fb3d5e83f8 https://usegalaxy.eu/published/workflow?id=61fe08fb3d5e83f8 name:microgalaxy, hpylori 2023-10-27 2023-12-13 13 13 bowtie2, samtools_coverage, bcftools_norm, vcf2tsv, collection_element_identifiers, freebayes, tp_cat, collapse_dataset, samtools_depth Read mapping, Statistical calculation, Variant calling True False -Quality control of bins generated by MetaBAT2, MaxBin2, SemiBin, and CONCOCT https://usegalaxy.fr f0776f7a890b523a https://usegalaxy.fr/published/workflow?id=f0776f7a890b523a Bérénice Batut microbiome, name:microgalaxy 2025-12-08 2025-12-08 1 1 multiqc, __FLATTEN__, collection_element_identifiers, __RELABEL_FROM_FILE__, __MERGE_COLLECTION__, regex1, checkm2 Sequence composition calculation, Sequence assembly validation, Statistical calculation, Validation, Sequencing quality control MIT True False -Quality control of bins generated by MetaBAT2, MaxBin2, SemiBin, and CONCOCT https://usegalaxy.org a8aee61c2cbaf6ea https://usegalaxy.org/published/workflow?id=a8aee61c2cbaf6ea Bérénice Batut microbiome, name:microgalaxy 2025-12-08 2025-12-08 1 1 multiqc, __FLATTEN__, collection_element_identifiers, __RELABEL_FROM_FILE__, __MERGE_COLLECTION__, regex1, checkm2 Sequence composition calculation, Sequence assembly validation, Statistical calculation, Validation, Sequencing quality control MIT True False -MGnify's amplicon pipeline v5.0 (release v0.1) https://usegalaxy.org 8e863bbef37cc36b https://usegalaxy.org/published/workflow?id=8e863bbef37cc36b EMBL's European Bioinformatics Institute, Rand Zoabi, Paul Zierep mgnify_amplicon, metagenomics, amplicon, name:microgalaxy 2025-02-06 2025-04-25 1 1 fastq_dl, CONVERTER_uncompressed_to_gz, tp_awk_tool, CONVERTER_gz_to_uncompressed, __MERGE_COLLECTION__ Apache-2.0 True False -MGnify's amplicon pipeline v5.0 - ITS (release v0.1) https://usegalaxy.org 45f959d5bf505b15 https://usegalaxy.org/published/workflow?id=45f959d5bf505b15 EMBL's European Bioinformatics Institute, Rand Zoabi, Paul Zierep mgnify_amplicon, amplicon, metagenomics, name:microgalaxy 2025-02-06 2025-04-25 1 1 tp_awk_tool, __FILTER_FROM_FILE__, bedtools_maskfastabed, mapseq, collection_element_identifiers, taxonomy_krona_chart, biom_convert, __FILTER_EMPTY_DATASETS__ k-mer counting, Visualisation, Formatting, Mapping Apache-2.0 True False -MGnify's amplicon pipeline v5.0 - Quality control PE (release v0.1) https://usegalaxy.org a71fcbc60caae8b6 https://usegalaxy.org/published/workflow?id=a71fcbc60caae8b6 EMBL's European Bioinformatics Institute, Rand Zoabi, Paul Zierep mgnify_amplicon, amplicon, metagenomics, name:microgalaxy 2025-02-06 2025-04-25 1 1 cshl_fasta_formatter, tp_find_and_replace, fastq_to_fasta_python, multiqc, fastqc, __UNZIP_COLLECTION__, prinseq, mgnify_seqprep, fastp, trimmomatic, fastq_filter Sequence trimming, Sequence composition calculation, Nucleic acid design, Statistical calculation, Validation, Read pre-processing, Sequence contamination filtering, Sequencing quality control Apache-2.0 True False -MGnify's amplicon pipeline v5.0 - Quality control SE (release v0.1) https://usegalaxy.org 5f878c4cc3bff68c https://usegalaxy.org/published/workflow?id=5f878c4cc3bff68c MGnify - EMBL, Rand Zoabi, Paul Zierep mgnify_amplicon, amplicon, metagenomics, name:microgalaxy 2025-02-06 2025-04-25 1 1 cshl_fasta_formatter, tp_find_and_replace, fastq_to_fasta_python, multiqc, fastqc, prinseq, trimmomatic, fastq_filter Sequence trimming, Read pre-processing, Sequence composition calculation, Sequence contamination filtering, Statistical calculation, Validation, Sequencing quality control Apache-2.0 True False -Allele-based Pathogen Identification (release v0.1.3) https://usegalaxy.org 3e703abaeb870f6f https://usegalaxy.org/published/workflow?id=3e703abaeb870f6f Engy Nasr, Bérénice Batut, Paul Zierep name:collection, name:microgalaxy, name:pathogfair, name:iwc 2025-03-06 2025-04-25 1 1 bcftools_consensus, Paste1, samtools_coverage, regexColumn1, bcftools_norm, CONVERTER_gz_to_uncompressed, snpSift_filter, tp_cut_tool, Cut1, snpSift_extractFields, clair3, collapse_dataset, Remove beginning1, table_compute, tp_head_tool, Count1, samtools_depth, minimap2 Pairwise sequence alignment, Variant calling MIT True False -MGnify's amplicon pipeline v5.0 - Quality control SE (release v0.2) https://usegalaxy.org afb67b4b9952f57d https://usegalaxy.org/published/workflow?id=afb67b4b9952f57d MGnify - EMBL, Rand Zoabi, Paul Zierep mgnify_amplicon, amplicon, metagenomics, name:microgalaxy 2025-03-06 2025-04-25 1 1 cshl_fasta_formatter, tp_find_and_replace, fastq_to_fasta_python, multiqc, fastqc, prinseq, trimmomatic, fastq_filter Sequence trimming, Read pre-processing, Sequence composition calculation, Sequence contamination filtering, Statistical calculation, Validation, Sequencing quality control Apache-2.0 True False -Allele-based Pathogen Identification (release v0.1.4) https://usegalaxy.org cb810cdaa4915f4b https://usegalaxy.org/published/workflow?id=cb810cdaa4915f4b Engy Nasr, Bérénice Batut, Paul Zierep name:collection, name:microgalaxy, name:pathogfair, name:iwc 2025-03-13 2025-04-25 1 1 bcftools_consensus, Paste1, samtools_coverage, regexColumn1, bcftools_norm, CONVERTER_gz_to_uncompressed, snpSift_filter, tp_cut_tool, Cut1, snpSift_extractFields, clair3, collapse_dataset, Remove beginning1, table_compute, tp_head_tool, Count1, samtools_depth, minimap2 Pairwise sequence alignment, Variant calling MIT True False -MGnify's amplicon pipeline v5.0 (release v0.2) https://usegalaxy.org 77de7101effbff3d https://usegalaxy.org/published/workflow?id=77de7101effbff3d EMBL's European Bioinformatics Institute, Rand Zoabi, Paul Zierep mgnify_amplicon, metagenomics, amplicon, name:microgalaxy 2025-03-13 2025-04-25 1 1 fastq_dl, CONVERTER_uncompressed_to_gz, tp_awk_tool, CONVERTER_gz_to_uncompressed, __MERGE_COLLECTION__ Apache-2.0 True False -MGnify's amplicon pipeline v5.0 - ITS (release v0.2) https://usegalaxy.org 8151be18aab3a3c6 https://usegalaxy.org/published/workflow?id=8151be18aab3a3c6 EMBL's European Bioinformatics Institute, Rand Zoabi, Paul Zierep mgnify_amplicon, amplicon, metagenomics, name:microgalaxy 2025-03-13 2025-04-25 1 1 tp_awk_tool, __FILTER_FROM_FILE__, bedtools_maskfastabed, mapseq, collection_element_identifiers, taxonomy_krona_chart, biom_convert, __FILTER_EMPTY_DATASETS__ k-mer counting, Visualisation, Formatting, Mapping Apache-2.0 True False -MGnify's amplicon pipeline v5.0 - Quality control PE (release v0.2) https://usegalaxy.org 20b7ae4b517a80fd https://usegalaxy.org/published/workflow?id=20b7ae4b517a80fd EMBL's European Bioinformatics Institute, Rand Zoabi, Paul Zierep mgnify_amplicon, amplicon, metagenomics, name:microgalaxy 2025-03-13 2025-04-25 1 1 cshl_fasta_formatter, tp_find_and_replace, fastq_to_fasta_python, multiqc, fastqc, __UNZIP_COLLECTION__, prinseq, mgnify_seqprep, fastp, trimmomatic, fastq_filter Sequence trimming, Sequence composition calculation, Nucleic acid design, Statistical calculation, Validation, Read pre-processing, Sequence contamination filtering, Sequencing quality control Apache-2.0 True False -MGnify's amplicon pipeline v5.0 - Quality control SE (release v0.3) https://usegalaxy.org 46f184a0e95f3c1c https://usegalaxy.org/published/workflow?id=46f184a0e95f3c1c MGnify - EMBL, Rand Zoabi, Paul Zierep mgnify_amplicon, amplicon, metagenomics, name:microgalaxy 2025-03-13 2025-04-25 1 1 cshl_fasta_formatter, tp_find_and_replace, fastq_to_fasta_python, multiqc, fastqc, prinseq, trimmomatic, fastq_filter Sequence trimming, Read pre-processing, Sequence composition calculation, Sequence contamination filtering, Statistical calculation, Validation, Sequencing quality control Apache-2.0 True False -Nanopore Preprocessing (release v0.1) https://usegalaxy.org a8b9252fad5fe06a https://usegalaxy.org/published/workflow?id=a8b9252fad5fe06a Bérénice Batut, Engy Nasr, Paul Zierep name:collection, name:microgalaxy, name:pathogfair, name:nanopore, name:iwc 2025-03-20 2025-04-25 1 1 collection_column_join, Grep1, samtools_fastx, regexColumn1, multiqc, kraken2, fastqc, bamtools_split_mapped, nanoplot, porechop, __FILTER_FAILED_DATASETS__, krakentools_extract_kraken_reads, fastp, collapse_dataset, Cut1, Add_a_column1, minimap2 Visualisation, Sequence composition calculation, Statistical calculation, Validation, Sequence contamination filtering, Box-Whisker plot plotting, Sequence alignment analysis, Taxonomic classification, Data handling, Pairwise sequence alignment, Aggregation, Scatter plot plotting, Sequencing quality control MIT True False -Quality control of bins generated by MetaBAT2, MaxBin2, SemiBin, and CONCOCT https://usegalaxy.org.au f05ed1e5c5dfffa9 https://usegalaxy.org.au/published/workflow?id=f05ed1e5c5dfffa9 Bérénice Batut microbiome, name:microgalaxy 2025-12-08 2025-12-08 1 1 multiqc, __FLATTEN__, collection_element_identifiers, __RELABEL_FROM_FILE__, __MERGE_COLLECTION__, regex1, checkm2 Sequence composition calculation, Sequence assembly validation, Statistical calculation, Validation, Sequencing quality control MIT True False -Allele-based Pathogen Identification (release v0.1.3) https://usegalaxy.org.au 0e11619979c2830c https://usegalaxy.org.au/published/workflow?id=0e11619979c2830c Engy Nasr, Bérénice Batut, Paul Zierep name:collection, name:microgalaxy, name:pathogfair, name:iwc 2025-03-06 2025-04-25 1 1 bcftools_consensus, Paste1, samtools_coverage, regexColumn1, bcftools_norm, CONVERTER_gz_to_uncompressed, snpSift_filter, tp_cut_tool, Cut1, snpSift_extractFields, clair3, collapse_dataset, Remove beginning1, table_compute, tp_head_tool, Count1, samtools_depth, minimap2 Pairwise sequence alignment, Variant calling MIT True False -Allele-based Pathogen Identification (release v0.1.4) https://usegalaxy.org.au 76a0a3af8de11622 https://usegalaxy.org.au/published/workflow?id=76a0a3af8de11622 Engy Nasr, Bérénice Batut, Paul Zierep name:collection, name:microgalaxy, name:pathogfair, name:iwc 2025-03-13 2025-04-25 1 1 bcftools_consensus, Paste1, samtools_coverage, regexColumn1, bcftools_norm, CONVERTER_gz_to_uncompressed, snpSift_filter, tp_cut_tool, Cut1, snpSift_extractFields, clair3, collapse_dataset, Remove beginning1, table_compute, tp_head_tool, Count1, samtools_depth, minimap2 Pairwise sequence alignment, Variant calling MIT True False +Ecoli Comparison https://usegalaxy.eu 0e492839192d26e0 https://usegalaxy.eu/published/workflow?id=0e492839192d26e0 assembly, name:microgalaxy 2023-12-14 2023-12-14 0 0 bedtools_sortbed, collapse_dataset, bedtools_intersectbed, tp_cat, datamash_ops, bedtools_complementbed, cat1, join1, mergeCols1, lastz_wrapper_2, tp_grep_tool, addValue, fasta_filter_by_length, Grep1, fasta_compute_length, tp_sort_header_tool, random_lines1, tp_sed_tool, Filter1, Cut1 Read mapping, Sequence alignment, Mapping True False +Comparative gene analysis https://usegalaxy.eu 86900be4282d4b1d https://usegalaxy.eu/published/workflow?id=86900be4282d4b1d Anton Nekrutenko vgp, genome-annotation, name:microgalaxy 2023-12-14 2023-12-14 0 0 Add_a_column1, tab2fasta, tp_split_on_column, gops_intersect_1, rbc_mafft, join1, bg_diamond, cat1, collapse_dataset, rapidnj, Filter1, bg_diamond_view, Cut1, regexColumn1 Sequence alignment analysis, Phylogenetic tree generation, Multiple sequence alignment True False +Apollo Load Test https://usegalaxy.eu 3c233cc56d4df8b0 https://usegalaxy.eu/published/workflow?id=3c233cc56d4df8b0 genome-annotation, name:microgalaxy 2023-12-14 2023-12-14 0 0 create_or_update, iframe, jbrowse, create_account, list_organism Genome visualisation True False +Flye-AMR workflow EMC/WMDI - v3.5 (imported from URL) https://usegalaxy.eu 152223c8aed27357 https://usegalaxy.eu/published/workflow?id=152223c8aed27357 wmdi, name:microgalaxy 2023-12-14 2023-12-14 0 0 circos_wiggle_to_scatter, tp_split_on_column, bandage_image, flye, deeptools_bam_coverage, staramr_search, PlasFlow, regex1, jbrowse, tp_cat, tp_head_tool, ncbi_blastn_wrapper, medaka_consensus_pipeline, gff2bed1, circos, tbl2gff3, join1, trimmomatic, tp_text_file_with_recurring_lines, prokka, nanoplot, bg_column_arrange_by_header, fasta2tab, Add_a_column1, tp_cut_tool, minimap2, Grep1, tab2fasta, fasta_compute_length, tp_sort_header_tool, circos_interval_to_tile, tp_easyjoin_tool, regex_replace, circos_gc_skew, Filter1, Cut1 Base-calling, Pairwise sequence alignment, Sequence visualisation, De-novo assembly, Variant calling, Scatter plot plotting, Genome annotation, Sequence assembly, Gene prediction, Genome visualisation, Mapping assembly, Coding region prediction, Cross-assembly, Antimicrobial resistance prediction, Box-Whisker plot plotting, Sequence assembly visualisation, Sequence analysis, Genome assembly True False +From VCFs to SNP distance matrix https://usegalaxy.eu 6d333ed886aab471 https://usegalaxy.eu/published/workflow?id=6d333ed886aab471 evolution, name:microgalaxy 2023-12-14 2023-12-14 0 0 snp_dists, bcftools_consensus, tb_variant_filter, snp_sites, tp_cat True False +From Fastqs to VCFs and BAMs https://usegalaxy.eu 3a8fde248a4d0383 https://usegalaxy.eu/published/workflow?id=3a8fde248a4d0383 evolution, name:microgalaxy 2023-12-14 2023-12-14 0 0 snippy, __MERGE_COLLECTION__, tb_variant_filter, trimmomatic Phylogenetic tree visualisation, Phylogenetic tree generation, Variant calling True False +From BAMs to drug resistance prediction with TB-profiler https://usegalaxy.eu d0d6dae0d1eecc21 https://usegalaxy.eu/published/workflow?id=d0d6dae0d1eecc21 evolution, name:microgalaxy 2023-12-14 2023-12-14 0 0 addName, samtools_view, tp_grep_tool, tp_sed_tool, tp_replace_in_line, __MERGE_COLLECTION__, tp_cat, tb_profiler_profile Antimicrobial resistance prediction True False +Compute Allel Frequency Table from paired reads https://usegalaxy.eu 21a39ac4c1becb31 https://usegalaxy.eu/published/workflow?id=21a39ac4c1becb31 name:microgalaxy, hpylori 2023-12-13 2023-12-13 2 2 bowtie2, tp_awk_tool, bcftools_view, bcftools_norm, vcf2tsv, snpSift_filter, freebayes Read mapping, Statistical calculation, Variant calling True False +Reference genome choice (indels, coverage, depth) for short reads https://usegalaxy.eu 61fe08fb3d5e83f8 https://usegalaxy.eu/published/workflow?id=61fe08fb3d5e83f8 name:microgalaxy, hpylori 2023-10-27 2023-12-13 13 13 bowtie2, collection_element_identifiers, samtools_depth, bcftools_norm, vcf2tsv, collapse_dataset, samtools_coverage, tp_cat, freebayes Read mapping, Statistical calculation, Variant calling True False +Quality control of bins generated by MetaBAT2, MaxBin2, SemiBin, and CONCOCT https://usegalaxy.fr f0776f7a890b523a https://usegalaxy.fr/published/workflow?id=f0776f7a890b523a Bérénice Batut microbiome, name:microgalaxy 2025-12-08 2025-12-08 1 1 __RELABEL_FROM_FILE__, checkm2, collection_element_identifiers, multiqc, __FLATTEN__, __MERGE_COLLECTION__, regex1 Statistical calculation, Sequencing quality control, Validation, Sequence composition calculation, Sequence assembly validation MIT True False +Quality control of bins generated by MetaBAT2, MaxBin2, SemiBin, and CONCOCT https://usegalaxy.org a8aee61c2cbaf6ea https://usegalaxy.org/published/workflow?id=a8aee61c2cbaf6ea Bérénice Batut microbiome, name:microgalaxy 2025-12-08 2025-12-08 1 1 __RELABEL_FROM_FILE__, checkm2, collection_element_identifiers, multiqc, __FLATTEN__, __MERGE_COLLECTION__, regex1 Statistical calculation, Sequencing quality control, Validation, Sequence composition calculation, Sequence assembly validation MIT True False +MGnify's amplicon pipeline v5.0 (release v0.1) https://usegalaxy.org 8e863bbef37cc36b https://usegalaxy.org/published/workflow?id=8e863bbef37cc36b EMBL's European Bioinformatics Institute, Rand Zoabi, Paul Zierep mgnify_amplicon, metagenomics, amplicon, name:microgalaxy 2025-02-06 2025-04-25 1 1 tp_awk_tool, CONVERTER_uncompressed_to_gz, CONVERTER_gz_to_uncompressed, __MERGE_COLLECTION__, fastq_dl Apache-2.0 True False +MGnify's amplicon pipeline v5.0 - ITS (release v0.1) https://usegalaxy.org 45f959d5bf505b15 https://usegalaxy.org/published/workflow?id=45f959d5bf505b15 EMBL's European Bioinformatics Institute, Rand Zoabi, Paul Zierep mgnify_amplicon, amplicon, metagenomics, name:microgalaxy 2025-02-06 2025-04-25 1 1 bedtools_maskfastabed, mapseq, tp_awk_tool, __FILTER_FROM_FILE__, collection_element_identifiers, taxonomy_krona_chart, biom_convert, __FILTER_EMPTY_DATASETS__ k-mer counting, Formatting, Visualisation, Mapping Apache-2.0 True False +MGnify's amplicon pipeline v5.0 - Quality control PE (release v0.1) https://usegalaxy.org a71fcbc60caae8b6 https://usegalaxy.org/published/workflow?id=a71fcbc60caae8b6 EMBL's European Bioinformatics Institute, Rand Zoabi, Paul Zierep mgnify_amplicon, amplicon, metagenomics, name:microgalaxy 2025-02-06 2025-04-25 1 1 fastp, cshl_fasta_formatter, tp_find_and_replace, multiqc, trimmomatic, fastqc, __UNZIP_COLLECTION__, mgnify_seqprep, fastq_filter, prinseq, fastq_to_fasta_python Statistical calculation, Sequencing quality control, Sequence contamination filtering, Sequence trimming, Validation, Nucleic acid design, Read pre-processing, Sequence composition calculation Apache-2.0 True False +MGnify's amplicon pipeline v5.0 - Quality control SE (release v0.1) https://usegalaxy.org 5f878c4cc3bff68c https://usegalaxy.org/published/workflow?id=5f878c4cc3bff68c MGnify - EMBL, Rand Zoabi, Paul Zierep mgnify_amplicon, amplicon, metagenomics, name:microgalaxy 2025-02-06 2025-04-25 1 1 cshl_fasta_formatter, tp_find_and_replace, multiqc, trimmomatic, fastqc, fastq_filter, prinseq, fastq_to_fasta_python Sequencing quality control, Statistical calculation, Sequence contamination filtering, Sequence trimming, Validation, Read pre-processing, Sequence composition calculation Apache-2.0 True False +Allele-based Pathogen Identification (release v0.1.3) https://usegalaxy.org 3e703abaeb870f6f https://usegalaxy.org/published/workflow?id=3e703abaeb870f6f Engy Nasr, Bérénice Batut, Paul Zierep name:collection, name:microgalaxy, name:pathogfair, name:iwc 2025-03-06 2025-04-25 1 1 tp_cut_tool, clair3, table_compute, samtools_depth, bcftools_consensus, CONVERTER_gz_to_uncompressed, Paste1, bcftools_norm, Cut1, snpSift_extractFields, samtools_coverage, snpSift_filter, collapse_dataset, minimap2, Count1, tp_head_tool, Remove beginning1, regexColumn1 Pairwise sequence alignment, Variant calling MIT True False +MGnify's amplicon pipeline v5.0 - Quality control SE (release v0.2) https://usegalaxy.org afb67b4b9952f57d https://usegalaxy.org/published/workflow?id=afb67b4b9952f57d MGnify - EMBL, Rand Zoabi, Paul Zierep mgnify_amplicon, amplicon, metagenomics, name:microgalaxy 2025-03-06 2025-04-25 1 1 cshl_fasta_formatter, tp_find_and_replace, multiqc, trimmomatic, fastqc, fastq_filter, prinseq, fastq_to_fasta_python Sequencing quality control, Statistical calculation, Sequence contamination filtering, Sequence trimming, Validation, Read pre-processing, Sequence composition calculation Apache-2.0 True False +Allele-based Pathogen Identification (release v0.1.4) https://usegalaxy.org cb810cdaa4915f4b https://usegalaxy.org/published/workflow?id=cb810cdaa4915f4b Engy Nasr, Bérénice Batut, Paul Zierep name:collection, name:microgalaxy, name:pathogfair, name:iwc 2025-03-13 2025-04-25 1 1 tp_cut_tool, clair3, table_compute, samtools_depth, bcftools_consensus, CONVERTER_gz_to_uncompressed, Paste1, bcftools_norm, Cut1, snpSift_extractFields, samtools_coverage, snpSift_filter, collapse_dataset, minimap2, Count1, tp_head_tool, Remove beginning1, regexColumn1 Pairwise sequence alignment, Variant calling MIT True False +MGnify's amplicon pipeline v5.0 (release v0.2) https://usegalaxy.org 77de7101effbff3d https://usegalaxy.org/published/workflow?id=77de7101effbff3d EMBL's European Bioinformatics Institute, Rand Zoabi, Paul Zierep mgnify_amplicon, metagenomics, amplicon, name:microgalaxy 2025-03-13 2025-04-25 1 1 tp_awk_tool, CONVERTER_uncompressed_to_gz, CONVERTER_gz_to_uncompressed, __MERGE_COLLECTION__, fastq_dl Apache-2.0 True False +MGnify's amplicon pipeline v5.0 - ITS (release v0.2) https://usegalaxy.org 8151be18aab3a3c6 https://usegalaxy.org/published/workflow?id=8151be18aab3a3c6 EMBL's European Bioinformatics Institute, Rand Zoabi, Paul Zierep mgnify_amplicon, amplicon, metagenomics, name:microgalaxy 2025-03-13 2025-04-25 1 1 bedtools_maskfastabed, mapseq, tp_awk_tool, __FILTER_FROM_FILE__, collection_element_identifiers, taxonomy_krona_chart, biom_convert, __FILTER_EMPTY_DATASETS__ k-mer counting, Formatting, Visualisation, Mapping Apache-2.0 True False +MGnify's amplicon pipeline v5.0 - Quality control PE (release v0.2) https://usegalaxy.org 20b7ae4b517a80fd https://usegalaxy.org/published/workflow?id=20b7ae4b517a80fd EMBL's European Bioinformatics Institute, Rand Zoabi, Paul Zierep mgnify_amplicon, amplicon, metagenomics, name:microgalaxy 2025-03-13 2025-04-25 1 1 fastp, cshl_fasta_formatter, tp_find_and_replace, multiqc, trimmomatic, fastqc, __UNZIP_COLLECTION__, mgnify_seqprep, fastq_filter, prinseq, fastq_to_fasta_python Statistical calculation, Sequencing quality control, Sequence contamination filtering, Sequence trimming, Validation, Nucleic acid design, Read pre-processing, Sequence composition calculation Apache-2.0 True False +MGnify's amplicon pipeline v5.0 - Quality control SE (release v0.3) https://usegalaxy.org 46f184a0e95f3c1c https://usegalaxy.org/published/workflow?id=46f184a0e95f3c1c MGnify - EMBL, Rand Zoabi, Paul Zierep mgnify_amplicon, amplicon, metagenomics, name:microgalaxy 2025-03-13 2025-04-25 1 1 cshl_fasta_formatter, tp_find_and_replace, multiqc, trimmomatic, fastqc, fastq_filter, prinseq, fastq_to_fasta_python Sequencing quality control, Statistical calculation, Sequence contamination filtering, Sequence trimming, Validation, Read pre-processing, Sequence composition calculation Apache-2.0 True False +Nanopore Preprocessing (release v0.1) https://usegalaxy.org a8b9252fad5fe06a https://usegalaxy.org/published/workflow?id=a8b9252fad5fe06a Bérénice Batut, Engy Nasr, Paul Zierep name:collection, name:microgalaxy, name:pathogfair, name:nanopore, name:iwc 2025-03-20 2025-04-25 1 1 Add_a_column1, fastp, collection_column_join, multiqc, kraken2, samtools_fastx, fastqc, collapse_dataset, nanoplot, minimap2, Grep1, __FILTER_FAILED_DATASETS__, bamtools_split_mapped, porechop, Cut1, regexColumn1, krakentools_extract_kraken_reads Statistical calculation, Taxonomic classification, Pairwise sequence alignment, Box-Whisker plot plotting, Aggregation, Data handling, Scatter plot plotting, Sequencing quality control, Sequence contamination filtering, Sequence alignment analysis, Validation, Sequence composition calculation, Visualisation MIT True False +Quality control of bins generated by MetaBAT2, MaxBin2, SemiBin, and CONCOCT https://usegalaxy.org.au f05ed1e5c5dfffa9 https://usegalaxy.org.au/published/workflow?id=f05ed1e5c5dfffa9 Bérénice Batut microbiome, name:microgalaxy 2025-12-08 2025-12-08 1 1 __RELABEL_FROM_FILE__, checkm2, collection_element_identifiers, multiqc, __FLATTEN__, __MERGE_COLLECTION__, regex1 Statistical calculation, Sequencing quality control, Validation, Sequence composition calculation, Sequence assembly validation MIT True False +Allele-based Pathogen Identification (release v0.1.3) https://usegalaxy.org.au 0e11619979c2830c https://usegalaxy.org.au/published/workflow?id=0e11619979c2830c Engy Nasr, Bérénice Batut, Paul Zierep name:collection, name:microgalaxy, name:pathogfair, name:iwc 2025-03-06 2025-04-25 1 1 tp_cut_tool, clair3, table_compute, samtools_depth, bcftools_consensus, CONVERTER_gz_to_uncompressed, Paste1, bcftools_norm, Cut1, snpSift_extractFields, samtools_coverage, snpSift_filter, collapse_dataset, minimap2, Count1, tp_head_tool, Remove beginning1, regexColumn1 Pairwise sequence alignment, Variant calling MIT True False +Allele-based Pathogen Identification (release v0.1.4) https://usegalaxy.org.au 76a0a3af8de11622 https://usegalaxy.org.au/published/workflow?id=76a0a3af8de11622 Engy Nasr, Bérénice Batut, Paul Zierep name:collection, name:microgalaxy, name:pathogfair, name:iwc 2025-03-13 2025-04-25 1 1 tp_cut_tool, clair3, table_compute, samtools_depth, bcftools_consensus, CONVERTER_gz_to_uncompressed, Paste1, bcftools_norm, Cut1, snpSift_extractFields, samtools_coverage, snpSift_filter, collapse_dataset, minimap2, Count1, tp_head_tool, Remove beginning1, regexColumn1 Pairwise sequence alignment, Variant calling MIT True False diff --git a/communities/microgalaxy/resources/curated_workflows.yml b/communities/microgalaxy/resources/curated_workflows.yml index 09ec93841..4598908c7 100644 --- a/communities/microgalaxy/resources/curated_workflows.yml +++ b/communities/microgalaxy/resources/curated_workflows.yml @@ -1,3 +1,87 @@ +- create_time: '2026-06-18' + creators: + - Tristan Reynolds + - Ammar Aziz + deprecated: false + doi: 10.48546/workflowhub.workflow.2196.1 + edam_operation: + - Sequencing quality control + - Phylogenetic analysis + edam_topic: + - Bioinformatics + - Biomedical science + - Genomics + - Virology + id: '2196' + keep: true + latest_version: 1 + license: MIT + link: https://workflowhub.eu/workflows/2196?version=1 + name: MPXV (Mpox) Phylogenetic Analysis with Squirrel + number_of_steps: 3 + projects: + - Melbourne Bioinformatics + - Galaxy Australia + source: WorkflowHub + tags: + - amplicon + - mpox + - ont + - virus + - mpxv + - phylogeny + tools: + - squirrel_phylo + - regex1 + - squirrel_qc + update_time: '2026-06-25' + versions: 1 +- create_time: '2026-06-18' + creators: + - Tristan Reynolds + - Ammar Aziz + deprecated: false + doi: 10.48546/workflowhub.workflow.2195.1 + edam_operation: + - Sequencing quality control + - Sequence alignment + - Validation + - Mapping + edam_topic: + - Bioinformatics + - Biomedical science + - Genomics + - Virology + id: '2195' + keep: true + latest_version: 1 + license: MIT + link: https://workflowhub.eu/workflows/2195?version=1 + name: Viral Amplicon Analysis Pipeline for ONT Data + number_of_steps: 12 + projects: + - Melbourne Bioinformatics + - Galaxy Australia + source: WorkflowHub + tags: + - amplicon + - mpox + - ont + - virus + - mpxv + - phylogeny + tools: + - artic_minion + - multiqc + - mosdepth + - XY_Plot_1 + - regex1 + - __BUILD_LIST__ + - tp_cat + - fastplong + - bedtools_makewindowsbed + update_time: '2026-06-25' + versions: 1 - create_time: '2026-03-02' creators: - Tristan Reynolds @@ -5,10 +89,10 @@ deprecated: false doi: 10.48546/workflowhub.workflow.2098.1 edam_operation: - - Visualisation + - Taxonomic classification - Formatting - Demultiplexing - - Taxonomic classification + - Visualisation edam_topic: - Taxonomy id: '2098' @@ -27,20 +111,20 @@ - microbiome - taxonomic-classification tools: + - qiime2__feature_table__tabulate_seqs + - biom_convert + - csv_to_tabular + - tp_easyjoin_tool + - qiime2_core__tools__import - qiime2__feature_classifier__classify_sklearn - qiime2__feature_table__summarize - - qiime2_core__tools__import + - tabular_to_csv - qiime2__taxa__barplot + - qiime_extract_viz - qiime2__feature_classifier__fit_classifier_naive_bayes - - qiime2__feature_table__tabulate_seqs + - qiime2_core__tools__export - qiime2__feature_classifier__extract_reads - - csv_to_tabular - - tp_easyjoin_tool - Remove beginning1 - - biom_convert - - qiime_extract_viz - - qiime2_core__tools__export - - tabular_to_csv update_time: '2026-05-13' versions: 1 - create_time: '2026-02-26' @@ -51,11 +135,11 @@ doi: null edam_operation: - Data parsing - - Gene functional annotation - - Validation - Taxonomic classification + - Gene functional annotation - Sequencing quality control - Antimicrobial resistance prediction + - Validation edam_topic: [] id: '2068' keep: true @@ -69,29 +153,29 @@ source: WorkflowHub tags: [] tools: - - table_pandas_rename_column - - multiqc + - tooldistillator_summarize + - __RELABEL_FROM_FILE__ - groot - collection_element_identifiers - - tooldistillator_summarize - - tooldistillator - - 'Remove a collection level so that outputs can be taken into account by tooldistillator - - __FLATTEN__' - - __FILTER_FAILED_DATASETS__ - - tp_text_file_with_recurring_lines - - __UNZIP_COLLECTION__ - sylph_profile + - deeparg_short_reads + - fastq_paired_end_interlacer - argnorm - - __RELABEL_FROM_FILE__ + - table_pandas_rename_column + - multiqc - 'Removal of the first line because it is not necessary for tooldistillator Remove beginning1' + - tp_text_file_with_recurring_lines + - tooldistillator + - __UNZIP_COLLECTION__ - 'Removal of the first argNorm line that causes a multiQC error Remove beginning1' - - fastq_paired_end_interlacer - - deeparg_short_reads + - __FILTER_FAILED_DATASETS__ + - 'Remove a collection level so that outputs can be taken into account by tooldistillator + + __FLATTEN__' update_time: '2026-05-14' versions: 2 - create_time: '2026-03-13' @@ -102,8 +186,8 @@ deprecated: false doi: null edam_operation: - - Multilocus sequence typing - Data parsing + - Multilocus sequence typing edam_topic: [] id: '2055' keep: true @@ -117,9 +201,9 @@ source: WorkflowHub tags: [] tools: - - coreprofiler_allele_calling - - tooldistillator_summarize - tooldistillator + - tooldistillator_summarize + - coreprofiler_allele_calling update_time: '2026-05-14' versions: 2 - create_time: '2026-01-12' @@ -127,19 +211,19 @@ deprecated: false doi: null edam_operation: - - Phylogenetic tree visualisation - - Sequence alignment - - Validation + - Taxonomic classification - Antimicrobial resistance prediction - - Phylogenetic tree generation - Variant calling - - Sequence analysis - - Local alignment + - Sequence alignment + - Phylogenetic tree visualisation + - Sequencing quality control - Sequence contamination filtering - - Global alignment - Sequence alignment analysis - - Taxonomic classification - - Sequencing quality control + - Phylogenetic tree generation + - Validation + - Global alignment + - Sequence analysis + - Local alignment edam_topic: [] id: '1647' keep: true @@ -157,20 +241,20 @@ - pathogen - tuberculosis tools: - - bcftools_consensus + - fastp - tp_awk_tool - - tb_profiler_profile + - qualimap_bamqc + - 'EMBOSS: seqret84' - kraken2 - - __FLATTEN__ - - multiqc - mosdepth + - __FLATTEN__ + - tp_sed_tool - snippy - - qualimap_bamqc + - multiqc + - bcftools_consensus - tb_variant_filter + - tb_profiler_profile - tbvcfreport - - fastp - - tp_sed_tool - - 'EMBOSS: seqret84' update_time: '2026-01-12' versions: 2 - create_time: '2025-12-22' @@ -178,14 +262,14 @@ deprecated: false doi: null edam_operation: - - Visualisation - Statistical calculation - - Read mapping - - Cross-assembly - - Sequence contamination filtering - - Expression analysis - Taxonomic classification + - Expression analysis - Sequencing quality control + - Sequence contamination filtering + - Read mapping + - Visualisation + - Cross-assembly edam_topic: [] id: '2043' keep: true @@ -203,11 +287,11 @@ - galaxy - sequence-analysis tools: - - falco - - kraken2 - - est_abundance - fastp - recentrifuge + - est_abundance + - kraken2 + - falco update_time: '2025-12-22' versions: 1 - create_time: '2025-12-22' @@ -215,11 +299,11 @@ deprecated: false doi: null edam_operation: - - Visualisation - Statistical calculation - Taxonomic classification - - Genome annotation - Aggregation + - Genome annotation + - Visualisation edam_topic: [] id: '1470' keep: true @@ -236,15 +320,15 @@ - galaxy - microbiome tools: - - interactive_tool_phinch - metaphlan - - kraken2 - taxonomy_krona_chart - krakentools_kreport2krona - - __UNZIP_COLLECTION__ - est_abundance - - interactive_tool_pavian - kraken_biom + - kraken2 + - interactive_tool_phinch + - __UNZIP_COLLECTION__ + - interactive_tool_pavian update_time: '2025-12-22' versions: 2 - create_time: '2025-12-22' @@ -252,10 +336,10 @@ deprecated: false doi: null edam_operation: - - Cross-assembly - Statistical calculation - Taxonomic classification - Expression analysis + - Cross-assembly edam_topic: [] id: '1674' keep: true @@ -272,9 +356,9 @@ - gtn - galaxy tools: - - kraken2 - est_abundance - recentrifuge + - kraken2 update_time: '2025-12-22' versions: 2 - create_time: '2025-12-08' @@ -284,8 +368,8 @@ edam_operation: - Sequence assembly - Read mapping - - Genome annotation - Sequence clustering + - Genome annotation - Read binning edam_topic: [] id: '2028' @@ -306,19 +390,19 @@ - microbiome tools: - bowtie2 - - metabat2 - - __BUILD_LIST__ - concoct_coverage_table - - metabat2_jgi_summarize_bam_contig_depths + - concoct_merge_cut_up_clustering - concoct_extract_fasta_bins - - semibin - - concoct + - concoct_cut_up_fasta - samtools_sort - - maxbin2 - - binette - Fasta_to_Contig2Bin - - concoct_merge_cut_up_clustering - - concoct_cut_up_fasta + - concoct + - __BUILD_LIST__ + - binette + - semibin + - maxbin2 + - metabat2 + - metabat2_jgi_summarize_bam_contig_depths update_time: '2025-12-08' versions: 1 - create_time: '2025-12-04' @@ -329,16 +413,16 @@ deprecated: false doi: null edam_operation: - - Visualisation - - Sequence composition calculation - - Sequence assembly validation - Statistical calculation - - Validation - - Cross-assembly - - Data parsing - - Expression analysis - Taxonomic classification + - Expression analysis + - Sequence assembly validation + - Data parsing - Sequencing quality control + - Validation + - Sequence composition calculation + - Visualisation + - Cross-assembly edam_topic: [] id: '1882' keep: true @@ -352,15 +436,15 @@ source: WorkflowHub tags: [] tools: - - pick_value - - kraken2 - tooldistillator_summarize - - tooldistillator + - recentrifuge + - checkm2 - est_abundance - - quast + - kraken2 + - pick_value - collapse_dataset - - checkm2 - - recentrifuge + - tooldistillator + - quast update_time: '2026-05-13' versions: 3 - create_time: '2026-03-10' @@ -369,19 +453,19 @@ deprecated: false doi: null edam_operation: - - Methylation analysis - - Sequence alignment - - Genome indexing - - SNP detection - - Validation - Read mapping - - Variant calling - - Primer removal - - Sequence contamination filtering - Generation - - Tree-based sequence alignment - Variant classification + - Variant calling + - Tree-based sequence alignment + - Sequence alignment + - Genome indexing - Sequencing quality control + - Sequence contamination filtering + - Validation + - Methylation analysis + - Primer removal + - SNP detection edam_topic: [] id: '155' keep: true @@ -396,21 +480,21 @@ tags: - virology tools: - - ivar_consensus + - fastp + - ivar_variants + - nextclade + - ivar_trim - samtools_view + - ivar_consensus + - qualimap_bamqc - multiqc - __FLATTEN__ - - nextclade + - tp_sed_tool + - snpeff_sars_cov_2 - samtools_stats + - tp_cat - pangolin - bwa_mem - - qualimap_bamqc - - ivar_trim - - fastp - - snpeff_sars_cov_2 - - tp_cat - - tp_sed_tool - - ivar_variants update_time: '2026-05-13' versions: 7 - create_time: '2021-12-21' @@ -420,14 +504,14 @@ doi: null edam_operation: - Formatting + - Generation - Sequence alignment - Genome indexing - - SNP detection + - Sequencing quality control + - Sequence contamination filtering - Validation - Read mapping - - Sequence contamination filtering - - Generation - - Sequencing quality control + - SNP detection edam_topic: [] id: '113' keep: true @@ -445,17 +529,17 @@ - covid19.galaxyproject.org - emergen_validated tools: - - samtools_view - - multiqc - - samtools_stats - - bwa_mem - - lofreq_viterbi - - lofreq_indelqual + - lofreq_filter - fastp - picard_MarkDuplicates + - lofreq_viterbi + - samtools_view - lofreq_call - - lofreq_filter + - multiqc - snpeff_sars_cov_2 + - samtools_stats + - lofreq_indelqual + - bwa_mem update_time: '2026-05-14' versions: 4 - create_time: '2025-12-05' @@ -465,14 +549,14 @@ deprecated: false doi: null edam_operation: - - Sequence alignment - - Genome indexing + - Sequencing quality control + - Sequence contamination filtering + - Generation - Validation - Read mapping + - Sequence alignment - Primer removal - - Sequence contamination filtering - - Generation - - Sequencing quality control + - Genome indexing edam_topic: [] id: '1876' keep: true @@ -487,28 +571,28 @@ tags: - virology tools: + - ivar_variants + - __FLATTEN__ + - snpSift_extractFields + - map_param_value + - collapse_dataset + - tp_cat + - fastp - samtools_view - - __FILTER_FAILED_DATASETS__ - - qualimap_bamqc - - tp_sed_tool - snpEff - - __FLATTEN__ + - tp_find_and_replace + - calculate_numeric_param - samtools_stats - - bwa_mem - lofreq_viterbi - - calculate_numeric_param - - collapse_dataset - - ivar_variants + - snpEff_build_gb - ivar_consensus - - tp_find_and_replace - - map_param_value - - ivar_trim - - fastp - - tp_cat - - snpSift_extractFields - pick_value + - ivar_trim + - qualimap_bamqc - multiqc - - snpEff_build_gb + - tp_sed_tool + - __FILTER_FAILED_DATASETS__ + - bwa_mem update_time: '2026-05-13' versions: 2 - create_time: '2026-02-12' @@ -520,22 +604,22 @@ deprecated: false doi: null edam_operation: + - Data retrieval + - Generation - Multiple sequence alignment - - Sequence alignment - - Genome indexing + - Data handling + - De-novo assembly - Sequence file editing - - Phylogenetic analysis - - Read mapping - - Sequence analysis - - Primer removal + - Sequence alignment - Base position variability plotting + - Genome indexing + - Sequencing quality control - Sequence contamination filtering - - Data retrieval - Sequence alignment analysis - - Data handling - - Generation - - Sequencing quality control - - De-novo assembly + - Sequence analysis + - Read mapping + - Primer removal + - Phylogenetic analysis edam_topic: [] id: '1260' keep: true @@ -550,48 +634,48 @@ tags: - virology tools: - - wc_gnu - - samtools_view - - __FILTER_FAILED_DATASETS__ - - tp_text_file_with_recurring_lines - - qualimap_bamqc + - collection_element_identifiers + - Paste1 + - __FLATTEN__ + - snipit - 'bwa mem will fail if no reference for any segment got suggested by vapor, i.e. the reference genome is empty. In that case, we need to skip further analysis of the sample. __FILTER_FAILED_DATASETS__' - - __HARMONIZELISTS__ - - Show beginning1 - - Filter1 - - __FLATTEN__ - - collection_element_identifiers - - bwa_mem - - __RELABEL_FROM_FILE__ - - __APPLY_RULES__ - - __MERGE_COLLECTION__ - collapse_dataset - - Paste1 - bamtools_split_ref - - snipit - - Grep1 - - ivar_consensus + - tp_cat + - Show beginning1 - param_value_from_file - - tp_find_and_replace - - __UNZIP_COLLECTION__ - - tp_easyjoin_tool - fastp - - tp_cat - - Cut1 + - samtools_view + - tp_find_and_replace - rbc_mafft + - tp_text_file_with_recurring_lines + - __APPLY_RULES__ - __FILTER_FROM_FILE__ - - vapor + - ivar_consensus + - __HARMONIZELISTS__ + - __DUPLICATE_FILE_TO_COLLECTION__ - 'This seemingly no-op transformation will remove samples with no remaining segment results (cases where vapor failed for every segment). __APPLY_RULES__' - - seqtk_subseq + - Grep1 - iqtree - - __DUPLICATE_FILE_TO_COLLECTION__ + - vapor + - __RELABEL_FROM_FILE__ + - wc_gnu + - seqtk_subseq + - tp_easyjoin_tool + - qualimap_bamqc + - __MERGE_COLLECTION__ + - __UNZIP_COLLECTION__ + - __FILTER_FAILED_DATASETS__ + - Filter1 + - Cut1 + - bwa_mem update_time: '2026-05-13' versions: 3 - create_time: '2025-10-11' @@ -601,18 +685,18 @@ deprecated: false doi: null edam_operation: + - Generation - Sequence alignment - Genome indexing + - Sequencing quality control + - Sequence contamination filtering + - Sequence alignment analysis - Validation - - Read mapping + - Global alignment - Sequence analysis + - Read mapping - Primer removal - Local alignment - - Sequence contamination filtering - - Global alignment - - Sequence alignment analysis - - Generation - - Sequencing quality control edam_topic: [] id: '439' keep: true @@ -628,31 +712,31 @@ - virology - pox tools: - - compose_text_param + - collection_element_identifiers + - __FLATTEN__ + - 'EMBOSS: maskseq51' + - tp_cat + - datamash_ops + - param_value_from_file + - fastp - samtools_view - - __FILTER_FAILED_DATASETS__ - - qualimap_bamqc - - tp_sed_tool - - fasta_compute_length - samtools_merge - - __FLATTEN__ - - collection_element_identifiers - samtools_stats - - bwa_mem - __APPLY_RULES__ - __ZIP_COLLECTION__ - - Grep1 - ivar_consensus - - param_value_from_file - - split_file_to_collection - - ivar_trim - - fastp - - tp_cat - - Cut1 - __SORTLIST__ - - 'EMBOSS: maskseq51' + - Grep1 + - fasta_compute_length + - ivar_trim + - qualimap_bamqc - multiqc - - datamash_ops + - split_file_to_collection + - compose_text_param + - tp_sed_tool + - __FILTER_FAILED_DATASETS__ + - Cut1 + - bwa_mem update_time: '2026-05-13' versions: 4 - create_time: '2025-08-11' @@ -661,8 +745,8 @@ doi: null edam_operation: - k-mer counting - - Visualisation - Formatting + - Visualisation - Mapping edam_topic: [] id: '1856' @@ -684,10 +768,10 @@ - name:microgalaxy tools: - '' - - tp_awk_tool - - __FILTER_FROM_FILE__ - bedtools_maskfastabed - mapseq + - tp_awk_tool + - __FILTER_FROM_FILE__ - collection_element_identifiers - taxonomy_krona_chart - biom_convert @@ -699,8 +783,8 @@ deprecated: false doi: null edam_operation: - - Visualisation - Analysis + - Visualisation edam_topic: [] id: '1855' keep: true @@ -717,10 +801,10 @@ - galaxy - microbiome tools: - - collection_column_join - - ampvis2_load - tp_awk_tool + - collection_column_join - collapse_dataset + - ampvis2_load - query_tabular update_time: '2025-08-11' versions: 1 @@ -729,14 +813,14 @@ deprecated: false doi: null edam_operation: - - Sequence trimming - - Sequence composition calculation - - Nucleic acid design - Statistical calculation + - Sequencing quality control + - Sequence contamination filtering + - Sequence trimming - Validation + - Nucleic acid design - Read pre-processing - - Sequence contamination filtering - - Sequencing quality control + - Sequence composition calculation edam_topic: [] id: '1854' keep: true @@ -756,17 +840,17 @@ - mgnify_amplicon - name:microgalaxy tools: + - fastp - cshl_fasta_formatter - tp_find_and_replace - - fastq_to_fasta_python - multiqc + - trimmomatic - fastqc - __UNZIP_COLLECTION__ - - prinseq - mgnify_seqprep - - fastp - - trimmomatic - fastq_filter + - prinseq + - fastq_to_fasta_python update_time: '2025-08-11' versions: 1 - create_time: '2025-08-11' @@ -794,11 +878,11 @@ - name:microgalaxy tools: - '' - - fastq_dl - - CONVERTER_uncompressed_to_gz - tp_awk_tool + - CONVERTER_uncompressed_to_gz - CONVERTER_gz_to_uncompressed - __MERGE_COLLECTION__ + - fastq_dl update_time: '2025-08-11' versions: 1 - create_time: '2025-08-11' @@ -825,9 +909,9 @@ - mgnify_amplicon - name:microgalaxy tools: - - Grouping1 - - collection_column_join - tp_awk_tool + - collection_column_join + - Grouping1 - filter_tabular - query_tabular update_time: '2025-08-11' @@ -837,13 +921,13 @@ deprecated: false doi: null edam_operation: + - Sequencing quality control + - Statistical calculation + - Sequence contamination filtering - Sequence trimming + - Validation - Read pre-processing - Sequence composition calculation - - Sequence contamination filtering - - Statistical calculation - - Validation - - Sequencing quality control edam_topic: [] id: '1850' keep: true @@ -865,12 +949,12 @@ tools: - cshl_fasta_formatter - tp_find_and_replace - - fastq_to_fasta_python - multiqc - - fastqc - - prinseq - trimmomatic + - fastqc - fastq_filter + - prinseq + - fastq_to_fasta_python update_time: '2025-08-11' versions: 1 - create_time: '2025-08-04' @@ -878,13 +962,13 @@ deprecated: false doi: null edam_operation: - - Visualisation - - Alignment - - Formatting - - Mapping - k-mer counting + - Formatting - Comparison + - Mapping + - Alignment - Nucleic acid feature detection + - Visualisation edam_topic: [] id: '1842' keep: true @@ -905,19 +989,19 @@ - name:microgalaxy tools: - '' - - bedtools_getfastabed - - tp_awk_tool - cshl_fasta_formatter - - __FILTER_FROM_FILE__ - - infernal_cmsearch + - tp_awk_tool - mapseq - collection_element_identifiers + - __FILTER_FROM_FILE__ - taxonomy_krona_chart - - cmsearch_deoverlap - biom_convert + - cmsearch_deoverlap + - infernal_cmsearch + - bedtools_getfastabed - gops_concat_1 - - __FILTER_EMPTY_DATASETS__ - query_tabular + - __FILTER_EMPTY_DATASETS__ update_time: '2025-08-11' versions: 1 - create_time: '2025-07-14' @@ -925,8 +1009,8 @@ deprecated: false doi: null edam_operation: - - Species frequency estimation - Taxonomic classification + - Species frequency estimation - Phylogenetic analysis edam_topic: [] id: '1447' @@ -945,15 +1029,15 @@ - galaxy - metagenomics tools: - - Grep1 - humann_rename_table + - humann_regroup_table - tp_find_and_replace - combine_metaphlan2_humann2 - - Cut1 - - humann_renorm_table - - humann_regroup_table - humann_unpack_pathways - humann_split_stratified_table + - humann_renorm_table + - Grep1 + - Cut1 update_time: '2025-07-14' versions: 2 - create_time: '2025-07-07' @@ -961,11 +1045,11 @@ deprecated: false doi: null edam_operation: - - Visualisation - DNA barcoding - - Deposition - Analysis - Variant calling + - Deposition + - Visualisation edam_topic: [] id: '1395' keep: true @@ -982,24 +1066,24 @@ - galaxy - microbiome tools: - - dada2_filterAndTrim + - dada2_dada + - Add_a_column1 + - dada2_makeSequenceTable + - dada2_plotQualityProfile + - collection_element_identifiers + - __SORTLIST__ - dada2_learnErrors + - tp_replace_in_line + - dada2_seqCounts - dada2_assignTaxonomyAddspecies + - cat1 + - dada2_filterAndTrim + - __UNZIP_COLLECTION__ - tp_replace_in_column - - collection_element_identifiers - phyloseq_from_dada2 - - dada2_makeSequenceTable - - dada2_seqCounts - - tp_replace_in_line - - __UNZIP_COLLECTION__ - - dada2_dada - - dada2_mergePairs - - dada2_removeBimeraDenovo - - cat1 - - Add_a_column1 - tp_head_tool - - dada2_plotQualityProfile - - __SORTLIST__ + - dada2_removeBimeraDenovo + - dada2_mergePairs update_time: '2025-07-07' versions: 2 - create_time: '2025-06-23' @@ -1007,25 +1091,25 @@ deprecated: false doi: null edam_operation: - - Sequence comparison - - Phylogenetic tree visualisation - - Visualisation - - Sequence composition calculation - Statistical calculation - Phylogenetic inference - - Validation - - Primer removal - - Sequence alignment analysis + - Conversion - Sequencing quality control + - Sequence alignment analysis + - Sequence comparison + - Sequence composition calculation - Phylogenetic analysis - - Sequence trimming - - Phylogenetic tree editing - - Read pre-processing - - Species frequency estimation - Taxonomic classification - - Sequence similarity search - - Conversion - Aggregation + - Species frequency estimation + - Phylogenetic tree visualisation + - Sequence similarity search + - Phylogenetic tree editing + - Sequence trimming + - Validation + - Read pre-processing + - Primer removal + - Visualisation edam_topic: [] id: '1466' keep: true @@ -1042,28 +1126,28 @@ - galaxy - microbiome tools: - - Grouping1 + - graphlan_annotate + - bg_sortmerna + - cutadapt + - taxonomy_krona_chart + - tp_find_and_replace + - export2graphlan + - humann_split_stratified_table - metaphlan - - fastqc - - tp_sort_header_tool - - humann - - humann_unpack_pathways - - graphlan + - humann_regroup_table + - fastq_paired_end_interlacer + - Grouping1 + - humann_renorm_table - Grep1 + - graphlan + - humann + - tp_sort_header_tool - humann_rename_table - - tp_find_and_replace + - multiqc + - fastqc + - humann_unpack_pathways - combine_metaphlan_humann - Cut1 - - bg_sortmerna - - fastq_paired_end_interlacer - - humann_split_stratified_table - - multiqc - - cutadapt - - taxonomy_krona_chart - - graphlan_annotate - - humann_renorm_table - - humann_regroup_table - - export2graphlan update_time: '2025-06-23' versions: 2 - create_time: '2025-06-23' @@ -1071,12 +1155,12 @@ deprecated: false doi: null edam_operation: - - Phylogenetic tree visualisation - - Visualisation - - Phylogenetic inference - - Phylogenetic tree editing - Taxonomic classification + - Phylogenetic inference - Conversion + - Phylogenetic tree visualisation + - Phylogenetic tree editing + - Visualisation edam_topic: [] id: '1451' keep: true @@ -1094,12 +1178,12 @@ - galaxy - microbiome tools: - - graphlan - metaphlan - - taxonomy_krona_chart - graphlan_annotate - - Cut1 + - taxonomy_krona_chart - export2graphlan + - Cut1 + - graphlan update_time: '2025-06-23' versions: 2 - create_time: '2025-06-23' @@ -1107,16 +1191,16 @@ deprecated: false doi: null edam_operation: - - Sequence trimming - - Sequence composition calculation - Statistical calculation - - Validation - - Primer removal - - Read pre-processing - Sequence similarity search + - Primer removal + - Sequencing quality control + - Sequence trimming - Sequence alignment analysis - Sequence comparison - - Sequencing quality control + - Validation + - Read pre-processing + - Sequence composition calculation edam_topic: [] id: '1444' keep: true @@ -1134,11 +1218,11 @@ - galaxy - microbiome tools: + - fastq_paired_end_interlacer - multiqc - fastqc - - cutadapt - bg_sortmerna - - fastq_paired_end_interlacer + - cutadapt update_time: '2025-06-23' versions: 2 - create_time: '2025-06-23' @@ -1146,8 +1230,8 @@ deprecated: false doi: null edam_operation: - - Species frequency estimation - Taxonomic classification + - Species frequency estimation - Phylogenetic analysis edam_topic: [] id: '1456' @@ -1166,15 +1250,15 @@ - galaxy - microbiome tools: - - Grep1 - humann_rename_table - - humann - - tp_find_and_replace - - humann_renorm_table - - tp_sort_header_tool - humann_regroup_table + - tp_find_and_replace - humann_unpack_pathways - humann_split_stratified_table + - humann_renorm_table + - Grep1 + - humann + - tp_sort_header_tool update_time: '2025-06-23' versions: 2 - create_time: '2025-06-16' @@ -1183,11 +1267,11 @@ doi: null edam_operation: - Visualisation - - Local alignment - - Sequence assembly validation - Read mapping - - Genome assembly + - Sequence assembly validation - Sequence assembly visualisation + - Local alignment + - Genome assembly edam_topic: [] id: '1390' keep: true @@ -1204,15 +1288,15 @@ - galaxy - microbiome tools: - - collection_column_join - bowtie2 - megahit_contig2fastg - - bandage_info - - bandage_image + - collection_column_join - metaspades - - quast - - coverm_contig + - bandage_image + - bandage_info - megahit + - coverm_contig + - quast update_time: '2025-06-16' versions: 2 - create_time: '2025-06-02' @@ -1220,8 +1304,8 @@ deprecated: false doi: null edam_operation: - - Sequence contamination filtering - Sequencing quality control + - Sequence contamination filtering edam_topic: [] id: '1723' keep: true @@ -1238,10 +1322,10 @@ - gtn - galaxy tools: + - fastp + - cshl_fastq_to_fasta - ncbi_blastn_wrapper - Count1 - - cshl_fastq_to_fasta - - fastp update_time: '2025-06-02' versions: 1 - create_time: '2025-06-02' @@ -1249,14 +1333,14 @@ deprecated: false doi: null edam_operation: - - Visualisation - Statistical calculation - - Read mapping - - Cross-assembly - - Sequence contamination filtering - - Expression analysis - Taxonomic classification + - Expression analysis - Sequencing quality control + - Sequence contamination filtering + - Read mapping + - Visualisation + - Cross-assembly edam_topic: [] id: '1644' keep: true @@ -1274,11 +1358,11 @@ - galaxy - sequence-analysis tools: - - falco - - kraken2 - - est_abundance - fastp - recentrifuge + - est_abundance + - kraken2 + - falco update_time: '2025-06-02' versions: 1 - create_time: '2025-06-02' @@ -1286,11 +1370,11 @@ deprecated: false doi: null edam_operation: - - Local alignment - - Sequence alignment - - Global alignment - Sequence alignment analysis + - Global alignment - Sequence analysis + - Sequence alignment + - Local alignment edam_topic: [] id: '1632' keep: true @@ -1307,14 +1391,14 @@ - galaxy - variant-analysis tools: - - Grep1 - - param_value_from_file + - Add_a_column1 - compose_text_param - 'EMBOSS: maskseq51' + - Grep1 - datamash_ops - - Cut1 - fasta_compute_length - - Add_a_column1 + - Cut1 + - param_value_from_file update_time: '2025-06-02' versions: 1 - create_time: '2025-06-02' @@ -1322,16 +1406,16 @@ deprecated: false doi: null edam_operation: + - Pairwise sequence alignment - Aggregation - - Mapping assembly - Antimicrobial resistance prediction - - Sequence analysis - Box-Whisker plot plotting - - Pairwise sequence alignment - - Genome assembly - - Sequence assembly visualisation - - Scatter plot plotting - De-novo assembly + - Scatter plot plotting + - Sequence assembly visualisation + - Sequence analysis + - Mapping assembly + - Genome assembly edam_topic: [] id: '1477' keep: true @@ -1349,14 +1433,14 @@ - microbiome tools: - unicycler - - racon - - staramr_search - - miniasm - - nanoplot - bandage_image + - miniasm + - staramr_search - PlasFlow - - gfa_to_fa + - nanoplot - minimap2 + - racon + - gfa_to_fa update_time: '2025-06-02' versions: 1 - create_time: '2025-06-02' @@ -1364,13 +1448,13 @@ deprecated: false doi: null edam_operation: - - Visualisation - - Sequence clustering - - DNA barcoding - Taxonomic classification + - DNA barcoding - Sequence read processing - Sequencing quality control + - Sequence clustering - Phylogenetic analysis + - Visualisation edam_topic: [] id: '1476' keep: true @@ -1387,21 +1471,21 @@ - galaxy - microbiome tools: - - mothur_pre_cluster - - mothur_make_group + - mothur_unique_seqs + - mothur_cluster_split - mothur_summary_seqs - mothur_count_seqs - - mothur_unique_seqs + - mothur_make_shared + - mothur_make_biom - mothur_merge_files - - mothur_align_seqs - - mothur_filter_seqs - - mothur_cluster_split - mothur_screen_seqs + - mothur_filter_seqs + - mothur_make_group - mothur_classify_seqs - - mothur_make_shared - - krona-text - mothur_classify_otu - - mothur_make_biom + - mothur_align_seqs + - mothur_pre_cluster + - krona-text update_time: '2025-06-02' versions: 1 - create_time: '2025-06-02' @@ -1409,13 +1493,13 @@ deprecated: false doi: null edam_operation: - - Visualisation - - Sequence composition calculation + - Sequencing quality control - Sequence contamination filtering + - Taxonomic classification - Statistical calculation - Validation - - Taxonomic classification - - Sequencing quality control + - Sequence composition calculation + - Visualisation edam_topic: [] id: '1473' keep: true @@ -1432,15 +1516,15 @@ - galaxy - microbiome tools: + - fastp + - datamash_reverse + - taxonomy_krona_chart - multiqc - kraken2 + - tp_replace_in_line - fastqc - - taxonomy_krona_chart - porechop - - tp_replace_in_line - - fastp - Remove beginning1 - - datamash_reverse update_time: '2025-06-02' versions: 1 - create_time: '2025-06-02' @@ -1465,12 +1549,12 @@ - galaxy - microbiome tools: - - humann2 - - taxonomy_krona_chart - metaphlan2krona + - metaphlan2 - humann2_renorm_table + - taxonomy_krona_chart + - humann2 - humann2_regroup_table - - metaphlan2 update_time: '2025-06-02' versions: 1 - create_time: '2025-06-02' @@ -1478,8 +1562,8 @@ deprecated: false doi: null edam_operation: - - Visualisation - Pairwise sequence alignment + - Visualisation edam_topic: [] id: '1469' keep: true @@ -1498,24 +1582,24 @@ - metaplasmidome - name:microgalaxy tools: - - Grouping1 + - Add_a_column1 - CONVERTER_fasta_to_tabular - tp_sorted_uniq - - sort1 - - Filter1 - - MQoutputfilter - - tp_replace_in_column - histogram_rpy - - tp_tail_tool - join1 - - count_gff_features - - tab2fasta - - Cut1 + - Grouping1 - cat1 - - add_column_headers - - Add_a_column1 + - tp_tail_tool + - count_gff_features - ggplot2_histogram - minimap2 + - add_column_headers + - tp_replace_in_column + - Filter1 + - tab2fasta + - Cut1 + - MQoutputfilter + - sort1 update_time: '2025-06-02' versions: 1 - create_time: '2025-06-02' @@ -1523,16 +1607,16 @@ deprecated: false doi: null edam_operation: - - Visualisation - - Phylogenetic tree reconstruction - - Sequence clustering - - Phylogenetic tree generation - - DNA barcoding - - Phylogenetic tree analysis - Taxonomic classification + - DNA barcoding - Sequence read processing - Sequencing quality control + - Phylogenetic tree generation + - Phylogenetic tree reconstruction + - Sequence clustering + - Phylogenetic tree analysis - Phylogenetic analysis + - Visualisation edam_topic: [] id: '1465' keep: true @@ -1549,39 +1633,39 @@ - galaxy - microbiome tools: - - mothur_pre_cluster - - mothur_make_contigs - mothur_count_seqs - - mothur_cluster - - mothur_unique_seqs - - mothur_venn - - mothur_classify_seqs - - mothur_make_shared - - mothur_make_biom - - mothur_summary_seqs - - mothur_cluster_split - mothur_chimera_vsearch + - mothur_get_groups - mothur_screen_seqs - - mothur_remove_lineage - - mothur_summary_single + - mothur_rarefaction_single + - mothur_align_seqs + - newick_display + - mothur_make_shared + - taxonomy_krona_chart + - mothur_cluster - mothur_remove_seqs - - XY_Plot_1 + - mothur_summary_single + - mothur_sub_sample - mothur_remove_groups - - mothur_taxonomy_to_krona + - mothur_classify_seqs + - mothur_seq_error - mothur_count_groups - - mothur_align_seqs - - mothur_filter_seqs - - mothur_dist_shared + - mothur_cluster_split - mothur_tree_shared + - mothur_summary_seqs + - mothur_make_contigs + - mothur_dist_shared - mothur_dist_seqs + - XY_Plot_1 + - mothur_filter_seqs + - mothur_remove_lineage - mothur_classify_otu + - mothur_pre_cluster + - mothur_unique_seqs + - mothur_venn - mothur_heatmap_sim - - mothur_rarefaction_single - - mothur_sub_sample - - newick_display - - taxonomy_krona_chart - - mothur_seq_error - - mothur_get_groups + - mothur_make_biom + - mothur_taxonomy_to_krona update_time: '2025-06-02' versions: 1 - create_time: '2025-06-02' @@ -1589,8 +1673,8 @@ deprecated: false doi: null edam_operation: - - Sequence feature detection - DNA barcoding + - Sequence feature detection edam_topic: [] id: '1460' keep: true @@ -1619,13 +1703,13 @@ deprecated: false doi: null edam_operation: - - Visualisation - - Sequence composition calculation + - Sequencing quality control - Sequence contamination filtering - - Statistical calculation - Taxonomic classification + - Statistical calculation - Aggregation - - Sequencing quality control + - Sequence composition calculation + - Visualisation edam_topic: [] id: '1439' keep: true @@ -1642,13 +1726,13 @@ - galaxy - microbiome tools: - - kraken2 - - Filter1 - - fastqc + - fastp - taxonomy_krona_chart - krakentools_kreport2krona + - kraken2 + - fastqc + - Filter1 - porechop - - fastp update_time: '2025-06-02' versions: 1 - create_time: '2025-06-02' @@ -1656,8 +1740,8 @@ deprecated: false doi: null edam_operation: - - Visualisation - Aggregation + - Visualisation edam_topic: [] id: '1431' keep: true @@ -1683,13 +1767,13 @@ deprecated: false doi: null edam_operation: - - Visualisation - - Sequence clustering - - DNA barcoding - Taxonomic classification + - DNA barcoding - Sequence read processing - Sequencing quality control + - Sequence clustering - Phylogenetic analysis + - Visualisation edam_topic: [] id: '1428' keep: true @@ -1707,9 +1791,9 @@ - galaxy - microbiome tools: + - mothur_remove_lineage - mothur_summary_seqs - mothur_classify_seqs - - mothur_remove_lineage update_time: '2025-06-02' versions: 1 - create_time: '2025-06-02' @@ -1717,13 +1801,13 @@ deprecated: false doi: null edam_operation: - - Visualisation - - Sequence clustering - - DNA barcoding - Taxonomic classification + - DNA barcoding - Sequence read processing - Sequencing quality control + - Sequence clustering - Phylogenetic analysis + - Visualisation edam_topic: [] id: '1422' keep: true @@ -1741,10 +1825,10 @@ - galaxy - microbiome tools: + - mothur_unique_seqs - mothur_summary_seqs - mothur_count_seqs - mothur_screen_seqs - - mothur_unique_seqs update_time: '2025-06-02' versions: 1 - create_time: '2025-06-02' @@ -1752,16 +1836,16 @@ deprecated: false doi: null edam_operation: - - Visualisation - - Phylogenetic tree reconstruction - - Sequence clustering - - Phylogenetic tree generation - - DNA barcoding - - Phylogenetic tree analysis - Taxonomic classification + - DNA barcoding - Sequence read processing - Sequencing quality control + - Phylogenetic tree generation + - Phylogenetic tree reconstruction + - Sequence clustering + - Phylogenetic tree analysis - Phylogenetic analysis + - Visualisation edam_topic: [] id: '1418' keep: true @@ -1778,12 +1862,12 @@ - galaxy - microbiome tools: + - mothur_tree_shared + - mothur_venn - mothur_heatmap_sim - - newick_display - mothur_dist_shared - - mothur_venn - collapse_dataset - - mothur_tree_shared + - newick_display update_time: '2025-06-02' versions: 1 - create_time: '2025-06-02' @@ -1791,13 +1875,13 @@ deprecated: false doi: null edam_operation: - - Visualisation - - Sequence clustering - - DNA barcoding - Taxonomic classification + - DNA barcoding - Sequence read processing - Sequencing quality control + - Sequence clustering - Phylogenetic analysis + - Visualisation edam_topic: [] id: '1412' keep: true @@ -1825,13 +1909,13 @@ deprecated: false doi: null edam_operation: - - Visualisation - - Sequence clustering - - DNA barcoding - Taxonomic classification + - DNA barcoding - Sequence read processing - Sequencing quality control + - Sequence clustering - Phylogenetic analysis + - Visualisation edam_topic: [] id: '1408' keep: true @@ -1849,10 +1933,10 @@ - galaxy - microbiome tools: - - mothur_rarefaction_single + - mothur_cluster - mothur_dist_seqs - mothur_make_shared - - mothur_cluster + - mothur_rarefaction_single update_time: '2025-06-02' versions: 1 - create_time: '2025-06-02' @@ -1860,13 +1944,13 @@ deprecated: false doi: null edam_operation: - - Visualisation - - Sequence clustering - - DNA barcoding - Taxonomic classification + - DNA barcoding - Sequence read processing - Sequencing quality control + - Sequence clustering - Phylogenetic analysis + - Visualisation edam_topic: [] id: '1404' keep: true @@ -1884,12 +1968,12 @@ - galaxy - microbiome tools: - - mothur_remove_groups - - mothur_sub_sample - - mothur_count_groups - mothur_cluster_split - mothur_make_shared + - mothur_sub_sample + - mothur_remove_groups - mothur_classify_otu + - mothur_count_groups update_time: '2025-06-02' versions: 1 - create_time: '2025-06-02' @@ -1897,13 +1981,13 @@ deprecated: false doi: null edam_operation: - - Visualisation - - Sequence clustering - - DNA barcoding - Taxonomic classification + - DNA barcoding - Sequence read processing - Sequencing quality control + - Sequence clustering - Phylogenetic analysis + - Visualisation edam_topic: [] id: '1400' keep: true @@ -1921,13 +2005,13 @@ - galaxy - microbiome tools: - - mothur_pre_cluster - - mothur_summary_seqs - mothur_unique_seqs - - mothur_filter_seqs + - mothur_summary_seqs - mothur_chimera_vsearch - - mothur_screen_seqs - mothur_remove_seqs + - mothur_screen_seqs + - mothur_filter_seqs + - mothur_pre_cluster update_time: '2025-06-02' versions: 1 - create_time: '2025-03-26' @@ -1953,24 +2037,24 @@ source: WorkflowHub tags: [] tools: + - tp_cut_tool + - clair3 + - table_compute + - samtools_depth - bcftools_consensus + - CONVERTER_gz_to_uncompressed - Paste1 - - samtools_coverage - - regexColumn1 - bcftools_norm - - CONVERTER_gz_to_uncompressed - - snpSift_filter - - tp_cut_tool - Cut1 - snpSift_extractFields - - clair3 + - samtools_coverage + - snpSift_filter - collapse_dataset - - Remove beginning1 - - table_compute - - tp_head_tool - - Count1 - - samtools_depth - minimap2 + - Count1 + - tp_head_tool + - Remove beginning1 + - regexColumn1 update_time: '2026-05-14' versions: 5 - create_time: '2025-03-26' @@ -1994,11 +2078,11 @@ tags: [] tools: - '' - - fastq_dl - - CONVERTER_uncompressed_to_gz - tp_awk_tool + - CONVERTER_uncompressed_to_gz - CONVERTER_gz_to_uncompressed - __MERGE_COLLECTION__ + - fastq_dl update_time: '2026-05-14' versions: 2 - create_time: '2025-03-26' @@ -2009,8 +2093,8 @@ doi: null edam_operation: - k-mer counting - - Visualisation - Formatting + - Visualisation - Mapping edam_topic: [] id: '1273' @@ -2026,10 +2110,10 @@ tags: [] tools: - '' - - tp_awk_tool - - __FILTER_FROM_FILE__ - bedtools_maskfastabed - mapseq + - tp_awk_tool + - __FILTER_FROM_FILE__ - collection_element_identifiers - taxonomy_krona_chart - biom_convert @@ -2043,14 +2127,14 @@ deprecated: false doi: null edam_operation: - - Sequence trimming - - Sequence composition calculation - - Nucleic acid design - Statistical calculation + - Sequencing quality control + - Sequence contamination filtering + - Sequence trimming - Validation + - Nucleic acid design - Read pre-processing - - Sequence contamination filtering - - Sequencing quality control + - Sequence composition calculation edam_topic: [] id: '1272' keep: true @@ -2064,17 +2148,17 @@ source: WorkflowHub tags: [] tools: + - fastp - cshl_fasta_formatter - tp_find_and_replace - - fastq_to_fasta_python - multiqc + - trimmomatic - fastqc - __UNZIP_COLLECTION__ - - prinseq - mgnify_seqprep - - fastp - - trimmomatic - fastq_filter + - prinseq + - fastq_to_fasta_python update_time: '2026-05-14' versions: 2 - create_time: '2025-03-26' @@ -2084,13 +2168,13 @@ deprecated: false doi: null edam_operation: + - Sequencing quality control + - Statistical calculation + - Sequence contamination filtering - Sequence trimming + - Validation - Read pre-processing - Sequence composition calculation - - Sequence contamination filtering - - Statistical calculation - - Validation - - Sequencing quality control edam_topic: [] id: '1271' keep: true @@ -2106,12 +2190,12 @@ tools: - cshl_fasta_formatter - tp_find_and_replace - - fastq_to_fasta_python - multiqc - - fastqc - - prinseq - trimmomatic + - fastqc - fastq_filter + - prinseq + - fastq_to_fasta_python update_time: '2026-05-14' versions: 3 - create_time: '2025-03-26' @@ -2121,13 +2205,13 @@ deprecated: false doi: null edam_operation: - - Visualisation - - Alignment - - Formatting - - Mapping - k-mer counting + - Formatting - Comparison + - Mapping + - Alignment - Nucleic acid feature detection + - Visualisation edam_topic: [] id: '1270' keep: true @@ -2142,19 +2226,19 @@ tags: [] tools: - '' - - bedtools_getfastabed - - tp_awk_tool - cshl_fasta_formatter - - __FILTER_FROM_FILE__ - - infernal_cmsearch + - tp_awk_tool - mapseq - collection_element_identifiers + - __FILTER_FROM_FILE__ - taxonomy_krona_chart - - cmsearch_deoverlap - biom_convert + - cmsearch_deoverlap + - infernal_cmsearch + - bedtools_getfastabed - gops_concat_1 - - __FILTER_EMPTY_DATASETS__ - query_tabular + - __FILTER_EMPTY_DATASETS__ update_time: '2026-05-14' versions: 2 - create_time: '2025-03-26' @@ -2176,9 +2260,9 @@ source: WorkflowHub tags: [] tools: - - Grouping1 - - collection_column_join - tp_awk_tool + - collection_column_join + - Grouping1 - filter_tabular - query_tabular update_time: '2026-05-14' @@ -2189,16 +2273,16 @@ deprecated: false doi: null edam_operation: - - Visualisation - - Filtering - - Formatting - Statistical calculation - Imputation - - Standardisation and normalisation + - Formatting - Heat map generation + - Filtering + - Standardisation and normalisation - Protein quantification - - Principal component plotting - Clustering + - Principal component plotting + - Visualisation edam_topic: [] id: '1225' keep: true @@ -2212,23 +2296,23 @@ source: WorkflowHub tags: [] tools: + - query_tabular + - peptide_shaker + - Remove beginning1 + - tp_cat + - search_gui - Grouping1 - - Grep1 - - fasta2tab - - fasta_merge_files_and_filter_unique_sequences - - Filter1 + - fasta_cli - ident_params - - Remove beginning1 + - maxquant - msconvert - - Cut1 - - query_tabular - dbbuilder - - fasta_cli + - Grep1 - filter_tabular - - tp_cat - - search_gui - - peptide_shaker - - maxquant + - Filter1 + - fasta_merge_files_and_filter_unique_sequences + - Cut1 + - fasta2tab update_time: '2026-05-13' versions: 1 - create_time: '2024-12-10' @@ -2238,10 +2322,10 @@ deprecated: false doi: 10.48546/workflowhub.workflow.1199.2 edam_operation: - - Visualisation - Statistical calculation - Taxonomic classification - Aggregation + - Visualisation edam_topic: - Metagenomics - Taxonomy @@ -2261,34 +2345,34 @@ - name:collection - shotgun tools: + - __RELABEL_FROM_FILE__ - collection_column_join - - krakentools_beta_diversity + - cat_multiple - 'Prepare alpha diversity summary file Paste1' - - 'Prepare alpha diversity summary file (paste Simpson and Fisher results) - - Paste1' + - collection_element_identifiers + - krakentools_combine_kreports + - krakentools_kreport2krona + - krakentools_beta_diversity + - est_abundance + - taxonomy_krona_chart - kraken2 - 'Prepare alpha diversity summary file (paste sample identifiers and Simpson results) Paste1' - - taxonomy_krona_chart - - collection_element_identifiers - - krakentools_kreport2krona - - 'Fisher results contains a header line we want to exclude "Fisher''s alpha...loading" + - 'Prepare alpha diversity summary file (paste Simpson and Fisher results) - Show tail1' - - est_abundance - - __RELABEL_FROM_FILE__ + Paste1' - add_line_to_file - - regex1 - krakentools_alpha_diversity - - cat_multiple + - regex1 - 'Extract column name and fraction_total_reads from Bracken report Cut1' - - krakentools_combine_kreports + - 'Fisher results contains a header line we want to exclude "Fisher''s alpha...loading" + + Show tail1' update_time: '2024-12-10' versions: 2 - create_time: '2024-11-26' @@ -2297,8 +2381,8 @@ deprecated: false doi: null edam_operation: - - Visualisation - Prediction and recognition + - Visualisation edam_topic: [] id: '1219' keep: true @@ -2312,8 +2396,8 @@ source: WorkflowHub tags: [] tools: - - Grep1 - msstatstmt + - Grep1 - unipept update_time: '2026-05-13' versions: 1 @@ -2336,17 +2420,17 @@ source: WorkflowHub tags: [] tools: - - Grouping1 - - fasta_merge_files_and_filter_unique_sequences - Filter1 - uniprotxml_downloader + - Grouping1 - Cut1 - - pepquery2 - - tp_cat - - dbbuilder - - Remove beginning1 - collapse_dataset + - dbbuilder - query_tabular + - tp_cat + - fasta_merge_files_and_filter_unique_sequences + - Remove beginning1 + - pepquery2 update_time: '2026-05-13' versions: 1 - create_time: '2024-11-23' @@ -2355,11 +2439,11 @@ deprecated: false doi: null edam_operation: - - Expression analysis - - Protein identification - - Tag-based peptide identification - de Novo sequencing - Target-Decoy + - Expression analysis + - Tag-based peptide identification + - Protein identification edam_topic: [] id: '1216' keep: true @@ -2385,10 +2469,10 @@ deprecated: false doi: null edam_operation: - - Parsing + - Antimicrobial resistance prediction - Data handling + - Parsing - Genome assembly - - Antimicrobial resistance prediction edam_topic: [] id: '1189' keep: true @@ -2407,24 +2491,24 @@ - benchamrking tools: - '' - - hamronize_summarize - - tp_text_file_with_recurring_lines - - cat1 - - hamronize_tool + - cat_multi_datasets + - shovill + - tp_split_on_column + - staramr_search + - collapse_dataset + - datamash_ops - abricate - - addValue + - hamronize_tool + - tp_find_and_replace + - cat1 + - tp_text_file_with_recurring_lines + - cast - __APPLY_RULES__ - - __MERGE_COLLECTION__ - - collapse_dataset - - shovill + - addValue - Grep1 - - cast - - tp_find_and_replace + - hamronize_summarize + - __MERGE_COLLECTION__ - Cut1 - - tp_split_on_column - - datamash_ops - - staramr_search - - cat_multi_datasets update_time: '2026-05-13' versions: 2 - create_time: '2024-10-07' @@ -2433,14 +2517,14 @@ deprecated: false doi: null edam_operation: - - Visualisation - Statistical calculation - Imputation - - Standardisation and normalisation - Heat map generation + - Standardisation and normalisation - Protein quantification - - Principal component plotting - Clustering + - Principal component plotting + - Visualisation edam_topic: [] id: '1177' keep: true @@ -2454,25 +2538,25 @@ source: WorkflowHub tags: [] tools: - - maxquant - - 'Quantified-Proteins + - 'extracting microbial Proteins - Grouping1' + Grep1' - 'extract proteins - Cut1' - - 'extract peptides - Cut1' - 'Quantified-Peptides Grouping1' - - 'extracting microbial Proteins - - Grep1' - 'extracting microbial Peptides Grep1' + - 'Quantified-Proteins + + Grouping1' + - maxquant + - 'extract peptides + + Cut1' update_time: '2026-05-14' versions: 1 - create_time: '2025-12-04' @@ -2484,8 +2568,8 @@ doi: null edam_operation: - Data parsing - - Genome assembly - Sequence assembly visualisation + - Genome assembly edam_topic: [] id: '1043' keep: true @@ -2506,11 +2590,11 @@ - paired-end - quality tools: - - bandage_info - - bandage_image - - tooldistillator - tooldistillator_summarize - shovill + - bandage_image + - bandage_info + - tooldistillator update_time: '2026-05-13' versions: 12 - create_time: '2025-06-19' @@ -2521,13 +2605,13 @@ deprecated: false doi: null edam_operation: - - Cross-assembly - - Data parsing + - Sequencing quality control - Sequence contamination filtering + - Data parsing + - Taxonomic classification - Expression analysis - Statistical calculation - - Taxonomic classification - - Sequencing quality control + - Cross-assembly edam_topic: [] id: '1052' keep: true @@ -2549,14 +2633,14 @@ - taxonomy-assignment - trimming tools: - - kraken2 - - tooldistillator_summarize - - tooldistillator - - __UNZIP_COLLECTION__ - - est_abundance - fastp + - tooldistillator_summarize - recentrifuge - __ZIP_COLLECTION__ + - est_abundance + - kraken2 + - __UNZIP_COLLECTION__ + - tooldistillator update_time: '2026-05-14' versions: 11 - create_time: '2022-11-24' @@ -2564,22 +2648,22 @@ deprecated: false doi: null edam_operation: - - Visualisation - - Multilocus sequence typing - - Sequence alignment - - Genome indexing - - Read mapping + - Genome alignment + - Read binning - Sequence contamination filtering - Clustering - - Genome alignment - - Parsing + - Antimicrobial resistance prediction - Data handling - - Genome assembly + - Sequence alignment + - Parsing + - Genome indexing - RNA-Seq analysis - Sequence trimming - - Antimicrobial resistance prediction - - Read binning - Sequence analysis + - Read mapping + - Multilocus sequence typing + - Visualisation + - Genome assembly edam_topic: [] id: '407' keep: true @@ -2595,17 +2679,17 @@ - bioinformatics - antimicrobial resistance tools: - - kma_map - - hamronize_summarize - seqsero2 - - bbtools_bbduk - - __UNZIP_COLLECTION__ - - srst2 - shovill - - mob_recon + - bbtools_tadpole - hamronize_tool + - bbtools_bbduk - sistr_cmd - - bbtools_tadpole + - mob_recon + - kma_map + - __UNZIP_COLLECTION__ + - hamronize_summarize + - srst2 update_time: '2026-05-13' versions: 1 - create_time: '2023-11-07' @@ -2634,10 +2718,10 @@ deprecated: false doi: null edam_operation: - - Parsing + - Antimicrobial resistance prediction - Data handling + - Parsing - Genome assembly - - Antimicrobial resistance prediction edam_topic: [] id: '470' keep: true @@ -2656,13 +2740,13 @@ - bioinformatics - antimicrobial resistance tools: - - hamronize_summarize - - tp_find_and_replace - abricate - - staramr_search - - collapse_dataset - shovill - hamronize_tool + - tp_find_and_replace + - staramr_search + - collapse_dataset + - hamronize_summarize update_time: '2026-05-13' versions: 1 - create_time: '2023-10-31' @@ -2706,9 +2790,9 @@ source: WorkflowHub tags: [] tools: - - Phylogenetic tree for diversity analysis - - Taxonomic analysis - Rarefaction + - Taxonomic analysis + - Phylogenetic tree for diversity analysis update_time: '2026-05-14' versions: 2 - create_time: '2024-06-26' @@ -2719,15 +2803,15 @@ deprecated: false doi: 10.48546/workflowhub.workflow.1062.1 edam_operation: - - Antimicrobial resistance prediction - Base-calling + - Antimicrobial resistance prediction + - De-novo assembly - Variant calling + - Sequence assembly visualisation + - Sequence assembly - Cross-assembly - Mapping assembly - - Sequence assembly - Genome assembly - - Sequence assembly visualisation - - De-novo assembly edam_topic: [] id: '1062' keep: true @@ -2741,18 +2825,18 @@ source: WorkflowHub tags: [] tools: - - medaka_consensus_pipeline - - param_value_from_file - - compose_text_param - - __BUILD_LIST__ - - tp_find_and_replace - abricate - collection_element_identifiers - bandage_image - - split_file_to_collection - flye - - fasta2tab + - tp_find_and_replace + - split_file_to_collection + - compose_text_param + - __BUILD_LIST__ - tab2fasta + - medaka_consensus_pipeline + - param_value_from_file + - fasta2tab update_time: '2026-05-13' versions: 1 - create_time: '2024-06-26' @@ -2763,14 +2847,12 @@ deprecated: false doi: 10.48546/workflowhub.workflow.1060.1 edam_operation: - - Phylogenetic tree generation (from molecular sequences) + - Phylogenetic tree generation - Visualisation - - Phylogenetic tree generation (maximum likelihood and Bayesian methods) - Multiple sequence alignment - - Mapping - Phylogenetic tree reconstruction - Phylogenetic tree analysis - - Phylogenetic tree generation + - Mapping edam_topic: [] id: '1060' keep: true @@ -2784,28 +2866,28 @@ source: WorkflowHub tags: [] tools: - - Grouping1 - - regexColumn1 - - clustalw - - __FILTER_FAILED_DATASETS__ - - fasta2tab - - tp_sorted_uniq - - fasta_merge_files_and_filter_unique_sequences - - collapse_dataset - - __FILTER_EMPTY_DATASETS__ - - bedtools_getfastabed - - tp_multijoin_tool - - ggplot2_heatmap - - Cut1 - - Remove beginning1 - - fasttree - tp_split_on_column - - collection_column_join + - ggplot2_heatmap + - bedtools_getfastabed + - collapse_dataset + - regex1 - tp_replace_in_column + - fasta_merge_files_and_filter_unique_sequences - newick_display - - regex1 + - regexColumn1 + - tp_multijoin_tool - Count1 + - __FILTER_EMPTY_DATASETS__ + - fasta2tab + - tp_sorted_uniq + - Grouping1 + - fasttree - tab2fasta + - Remove beginning1 + - collection_column_join + - clustalw + - __FILTER_FAILED_DATASETS__ + - Cut1 update_time: '2026-05-13' versions: 1 - create_time: '2024-06-26' @@ -2816,9 +2898,9 @@ deprecated: false doi: 10.48546/workflowhub.workflow.1059.1 edam_operation: - - Visualisation - Taxonomic classification - Aggregation + - Visualisation edam_topic: [] id: '1059' keep: true @@ -2832,9 +2914,9 @@ source: WorkflowHub tags: [] tools: + - krakentools_kreport2krona - kraken2 - taxonomy_krona_chart - - krakentools_kreport2krona update_time: '2026-05-13' versions: 1 - create_time: '2025-12-06' @@ -2846,14 +2928,14 @@ doi: null edam_operation: - Scaffolding - - Multilocus sequence typing - - Structural variation detection - - Sequence motif recognition - Genome annotation + - Nucleic acid feature detection - Data parsing - - Genome assembly - Protein feature detection - - Nucleic acid feature detection + - Structural variation detection + - Sequence motif recognition + - Multilocus sequence typing + - Genome assembly edam_topic: [] id: '1050' keep: true @@ -2873,12 +2955,12 @@ - fasta - genome-annotation tools: + - tooldistillator_summarize + - integron_finder + - plasmidfinder - isescan - bakta - - integron_finder - - tooldistillator_summarize - tooldistillator - - plasmidfinder update_time: '2026-05-13' versions: 13 - create_time: '2025-12-04' @@ -2913,10 +2995,10 @@ - bacterial-genomics - fasta tools: + - tooldistillator_summarize - abricate - amrfinderplus - staramr_search - - tooldistillator_summarize - tooldistillator update_time: '2026-05-13' versions: 9 @@ -2926,19 +3008,19 @@ deprecated: false doi: null edam_operation: - - Phylogenetic tree visualisation - - Sequence alignment - - Validation + - Taxonomic classification - Antimicrobial resistance prediction - - Phylogenetic tree generation - Variant calling - - Sequence analysis - - Local alignment + - Sequence alignment + - Phylogenetic tree visualisation + - Sequencing quality control - Sequence contamination filtering - - Global alignment - Sequence alignment analysis - - Taxonomic classification - - Sequencing quality control + - Phylogenetic tree generation + - Validation + - Global alignment + - Sequence analysis + - Local alignment edam_topic: - Genetic variation - Infectious disease @@ -2959,20 +3041,20 @@ - pathogen - tuberculosis tools: - - bcftools_consensus + - fastp - tp_awk_tool - - tb_profiler_profile + - qualimap_bamqc + - 'EMBOSS: seqret84' - kraken2 - - __FLATTEN__ - - multiqc - mosdepth + - __FLATTEN__ + - tp_sed_tool - snippy - - qualimap_bamqc + - multiqc + - bcftools_consensus - tb_variant_filter + - tb_profiler_profile - tbvcfreport - - fastp - - tp_sed_tool - - 'EMBOSS: seqret84' update_time: '2026-05-13' versions: 1 - create_time: '2025-03-26' @@ -2997,17 +3079,17 @@ tags: - name:amplicon tools: - - dada2_filterAndTrim + - dada2_dada + - dada2_makeSequenceTable + - __APPLY_RULES__ + - dada2_plotQualityProfile - dada2_learnErrors - dada2_assignTaxonomyAddspecies - - dada2_makeSequenceTable - dada2_seqCounts + - dada2_filterAndTrim - __UNZIP_COLLECTION__ - dada2_removeBimeraDenovo - - __APPLY_RULES__ - dada2_mergePairs - - dada2_plotQualityProfile - - dada2_dada update_time: '2026-05-14' versions: 3 - create_time: '2024-02-14' @@ -3031,11 +3113,11 @@ tags: - genome-annotation tools: - - jbrowse - - iframe - create_or_update - - list_organism + - iframe + - jbrowse - create_account + - list_organism update_time: '2025-11-04' versions: 1 - create_time: '2023-10-26' @@ -3047,8 +3129,8 @@ deprecated: false doi: 10.48546/workflowhub.workflow.624.1 edam_operation: - - Visualisation - Taxonomic classification + - Visualisation edam_topic: - Metagenomic sequencing - Metagenomics @@ -3068,14 +3150,14 @@ - shotgun tools: - '' - - humann2 - - taxonomy_krona_chart - metaphlan2krona + - metaphlan2 + - taxonomy_krona_chart - humann2_renorm_table + - merge_metaphlan_tables + - humann2 - humann2_regroup_table - Cut1 - - merge_metaphlan_tables - - metaphlan2 update_time: '2026-05-13' versions: 1 - create_time: '2023-11-09' @@ -3087,16 +3169,16 @@ deprecated: false doi: null edam_operation: - - Visualisation - - Phylogenetic tree reconstruction - - Sequence clustering - - Phylogenetic tree generation - - DNA barcoding - - Phylogenetic tree analysis - Taxonomic classification + - DNA barcoding - Sequence read processing - Sequencing quality control + - Phylogenetic tree generation + - Phylogenetic tree reconstruction + - Sequence clustering + - Phylogenetic tree analysis - Phylogenetic analysis + - Visualisation edam_topic: [] id: '653' keep: true @@ -3111,10 +3193,10 @@ tags: - metagenomics tools: - - mothur_dist_shared - mothur_tree_shared - mothur_heatmap_sim - newick_display + - mothur_dist_shared update_time: '2026-05-13' versions: 1 - create_time: '2023-11-09' @@ -3126,13 +3208,13 @@ deprecated: false doi: null edam_operation: - - Visualisation - - Sequence clustering - - DNA barcoding - Taxonomic classification + - DNA barcoding - Sequence read processing - Sequencing quality control + - Sequence clustering - Phylogenetic analysis + - Visualisation edam_topic: [] id: '652' keep: true @@ -3161,13 +3243,13 @@ deprecated: false doi: null edam_operation: - - Visualisation - - Sequence clustering - - DNA barcoding - Taxonomic classification + - DNA barcoding - Sequence read processing - Sequencing quality control + - Sequence clustering - Phylogenetic analysis + - Visualisation edam_topic: [] id: '651' keep: true @@ -3182,11 +3264,11 @@ tags: - metagenomics tools: - - mothur_sub_sample - - mothur_count_groups - mothur_cluster_split - mothur_make_shared + - mothur_sub_sample - mothur_classify_otu + - mothur_count_groups update_time: '2026-05-13' versions: 1 - create_time: '2023-11-09' @@ -3198,13 +3280,13 @@ deprecated: false doi: null edam_operation: - - Visualisation - - Sequence clustering - - DNA barcoding - Taxonomic classification + - DNA barcoding - Sequence read processing - Sequencing quality control + - Sequence clustering - Phylogenetic analysis + - Visualisation edam_topic: [] id: '650' keep: true @@ -3220,8 +3302,8 @@ tags: - metagenomics tools: - - mothur_classify_seqs - mothur_remove_lineage + - mothur_classify_seqs update_time: '2026-05-13' versions: 1 - create_time: '2023-11-09' @@ -3233,13 +3315,13 @@ deprecated: false doi: null edam_operation: - - Visualisation - - Sequence clustering - - DNA barcoding - Taxonomic classification + - DNA barcoding - Sequence read processing - Sequencing quality control + - Sequence clustering - Phylogenetic analysis + - Visualisation edam_topic: [] id: '648' keep: true @@ -3254,10 +3336,10 @@ tags: - metagenomics tools: + - mothur_unique_seqs - mothur_summary_seqs - mothur_count_seqs - mothur_screen_seqs - - mothur_unique_seqs update_time: '2026-05-13' versions: 1 - create_time: '2023-11-09' @@ -3269,13 +3351,13 @@ deprecated: false doi: null edam_operation: - - Visualisation - - Sequence clustering - - DNA barcoding - Taxonomic classification + - DNA barcoding - Sequence read processing - Sequencing quality control + - Sequence clustering - Phylogenetic analysis + - Visualisation edam_topic: [] id: '649' keep: true @@ -3291,13 +3373,13 @@ tags: - metagenomics tools: - - mothur_pre_cluster - - mothur_summary_seqs - mothur_unique_seqs - - mothur_filter_seqs + - mothur_summary_seqs - mothur_chimera_vsearch - - mothur_screen_seqs - mothur_remove_seqs + - mothur_screen_seqs + - mothur_filter_seqs + - mothur_pre_cluster update_time: '2026-05-13' versions: 1 - create_time: '2021-02-04' @@ -3305,9 +3387,9 @@ deprecated: false doi: null edam_operation: - - Genome assembly - - Sequence contamination filtering - Sequencing quality control + - Sequence contamination filtering + - Genome assembly edam_topic: [] id: '103' keep: true @@ -3333,13 +3415,13 @@ deprecated: false doi: null edam_operation: - - Read pre-processing - - Sequence contamination filtering + - Sequencing quality control - Formatting + - Sequence contamination filtering - Pairwise sequence alignment - - Genome assembly - - Sequencing quality control - Variant calling + - Read pre-processing + - Genome assembly edam_topic: [] id: '102' keep: true @@ -3358,13 +3440,13 @@ - mapping - reads_selection tools: - - fasta_merge_files_and_filter_unique_sequences - ncbi_blastn_wrapper - - samtools_stats - - picard_SamToFastq - shovill + - picard_SamToFastq - ngsutils_bam_filter - minimap2 + - samtools_stats + - fasta_merge_files_and_filter_unique_sequences update_time: '2026-05-13' versions: 1 - create_time: '2022-11-24' @@ -3374,16 +3456,16 @@ deprecated: false doi: null edam_operation: + - Pairwise sequence alignment - Aggregation - - Mapping assembly - Antimicrobial resistance prediction - - Sequence analysis - Box-Whisker plot plotting - - Pairwise sequence alignment - - Genome assembly - - Sequence assembly visualisation - - Scatter plot plotting - De-novo assembly + - Scatter plot plotting + - Sequence assembly visualisation + - Sequence analysis + - Mapping assembly + - Genome assembly edam_topic: - Microbiology id: '406' @@ -3400,14 +3482,14 @@ - metagenomics tools: - unicycler - - racon - - staramr_search - - miniasm - - nanoplot - bandage_image + - miniasm + - staramr_search - PlasFlow - - gfa_to_fa + - nanoplot - minimap2 + - racon + - gfa_to_fa update_time: '2026-05-13' versions: 1 - create_time: '2021-06-17' @@ -3415,8 +3497,8 @@ deprecated: false doi: null edam_operation: - - Visualisation - Taxonomic classification + - Visualisation edam_topic: [] id: '124' keep: true @@ -3432,8 +3514,8 @@ - virology - kraken tools: - - kraken2 - Kraken2Tax + - kraken2 - taxonomy_krona_chart update_time: '2026-05-13' versions: 1 @@ -3442,8 +3524,8 @@ deprecated: false doi: null edam_operation: - - Visualisation - Taxonomic classification + - Visualisation edam_topic: [] id: '101' keep: true @@ -3459,8 +3541,8 @@ - virology - kraken tools: - - kraken2 - Kraken2Tax + - kraken2 - taxonomy_krona_chart update_time: '2026-05-13' versions: 1 @@ -3470,11 +3552,11 @@ deprecated: false doi: '' edam_operation: - - Sequence composition calculation - - Sequence assembly validation - Statistical calculation - - Validation - Sequencing quality control + - Validation + - Sequence composition calculation + - Sequence assembly validation edam_topic: [] id: f0776f7a890b523a keep: true @@ -3489,111 +3571,163 @@ - microbiome - name:microgalaxy tools: + - __RELABEL_FROM_FILE__ + - checkm2 + - collection_element_identifiers - multiqc - __FLATTEN__ - - collection_element_identifiers - - __RELABEL_FROM_FILE__ - __MERGE_COLLECTION__ - regex1 - - checkm2 update_time: '2025-12-08' versions: 1 -- create_time: '2026-04-27' +- create_time: '2025-12-01' creators: [] deprecated: false doi: '' edam_operation: + - Sequencing quality control + - Sequence contamination filtering + - Taxonomic classification + - Statistical calculation + - Validation + - Sequence composition calculation - Visualisation - - Prediction and recognition edam_topic: [] - id: 6ca1b4fe047a03d2 + id: 2a093e63ebf6876b keep: true - latest_version: 1 + latest_version: 3 license: null - link: https://usegalaxy.eu/published/workflow?id=6ca1b4fe047a03d2 - name: Copy of Metaproteomics_GTN shared by user engy.nasr + link: https://usegalaxy.eu/published/workflow?id=2a093e63ebf6876b + name: 'Training: 16S rRNA Analysis with Nanopore Sequencing Reads' number_of_steps: null projects: [] source: https://usegalaxy.eu tags: - - proteomics + - metagenomics - name:microgalaxy tools: - - search_gui - - peptide_shaker - - sqlite_to_tabular - - query_tabular - - unipept - update_time: '2026-04-27' - versions: 1 -- create_time: '2025-12-01' - creators: [] + - fastp + - datamash_reverse + - taxonomy_krona_chart + - multiqc + - kraken2 + - tp_replace_in_line + - fastqc + - porechop + - Remove beginning1 + update_time: '2026-06-12' + versions: 3 +- create_time: '2026-02-10' + creators: + - Subina Mehta deprecated: false doi: '' edam_operation: - - Visualisation - - Sequence composition calculation - - Sequence contamination filtering - Statistical calculation - - Validation - Taxonomic classification + - Genome annotation - Sequencing quality control + - Sequence trimming + - Sequence assembly + - Fold recognition + - Information extraction + - Homology-based gene prediction + - Gene prediction + - Read pre-processing + - Coding region prediction + - Primer removal + - Query and retrieval + - Sequence composition calculation edam_topic: [] - id: 2a093e63ebf6876b + id: 7be08f99f83c927e keep: true - latest_version: 2 - license: null - link: https://usegalaxy.eu/published/workflow?id=2a093e63ebf6876b - name: 'Training: 16S rRNA Analysis with Nanopore Sequencing Reads' + latest_version: 1 + license: CC-BY-4.0 + link: https://usegalaxy.eu/published/workflow?id=7be08f99f83c927e + name: Sadowsky_MetaG-DBgen_02102026 number_of_steps: null projects: [] source: https://usegalaxy.eu tags: - - metagenomics - name:microgalaxy tools: - - multiqc - - kraken2 - - fastqc - - taxonomy_krona_chart - - porechop - - tp_replace_in_line - - fastp + - validate_fasta_database - Remove beginning1 - - datamash_reverse - update_time: '2026-03-16' - versions: 2 -- create_time: '2025-10-01' + - regexColumn1 + - cat_bins + - trim_galore + - fastqc + - eggnog_mapper + - collapse_dataset + - regex1 + - query_tabular + - tp_cat + - tab2fasta + - fasta_merge_files_and_filter_unique_sequences + - maxbin2 + - fasta2tab + - fraggenescan + update_time: '2026-06-09' + versions: 1 +- create_time: '2026-04-27' creators: [] deprecated: false doi: '' edam_operation: + - Prediction and recognition - Visualisation - - Sequence composition calculation - - Formatting + edam_topic: [] + id: 6ca1b4fe047a03d2 + keep: true + latest_version: 1 + license: null + link: https://usegalaxy.eu/published/workflow?id=6ca1b4fe047a03d2 + name: Copy of Metaproteomics_GTN shared by user engy.nasr + number_of_steps: null + projects: [] + source: https://usegalaxy.eu + tags: + - proteomics + - name:microgalaxy + tools: + - peptide_shaker + - unipept + - search_gui + - sqlite_to_tabular + - query_tabular + update_time: '2026-04-27' + versions: 1 +- create_time: '2025-10-01' + creators: [] + deprecated: false + doi: '' + edam_operation: - Statistical calculation - - Validation - - Sequence database search + - Formatting + - Visualisation - Format validation - - Primer removal - - Coding region prediction - - Local alignment - - Sequence assembly - - Database search - - Sequence profile generation + - Conversion + - Probabilistic sequence generation - Sequencing quality control + - Sequence assembly - Protein feature detection - - Sequence trimming - - Multiple sequence alignment - - Sequence assembly validation + - Gene prediction - Sequence motif recognition + - Coding region prediction + - Sequence composition calculation - Sequence generation - - Read pre-processing + - Database search + - Sequence database search - Data retrieval - - Gene prediction - Taxonomic classification - - Conversion - - Probabilistic sequence generation + - Multiple sequence alignment + - Sequence assembly validation + - Sequence trimming + - Sequence profile generation + - Validation + - Read pre-processing + - Primer removal + - Local alignment edam_topic: [] id: 8c91345ed468e22d keep: true @@ -3607,22 +3741,22 @@ tags: - name:microgalaxy tools: + - coverm_genome - fasplit - tp_awk_tool - tp_grep_tool + - sort1 + - cat_bins + - trim_galore - fastqc - checkm_lineage_wf + - coverm_contig - hmmer_hmmscan - - coverm_genome + - interproscan + - tp_cat + - maxbin2 - quast - - coverm_contig - fraggenescan - - maxbin2 - - cat_bins - - tp_cat - - trim_galore - - interproscan - - sort1 update_time: '2026-02-04' versions: 0 - create_time: '2025-11-28' @@ -3633,13 +3767,13 @@ deprecated: false doi: '' edam_operation: - - Visualisation - - Formatting - Statistical calculation - Taxonomic classification - - Conversion - - Aggregation - Standardisation and normalisation + - Formatting + - Aggregation + - Conversion + - Visualisation edam_topic: [] id: 7491883694fff308 keep: true @@ -3657,18 +3791,18 @@ - name:microgalaxy tools: - metaphlan - - kraken2 + - metaphlan2krona - collection_element_identifiers + - sylph_profile - taxonomy_krona_chart - - metaphlan2krona - krakentools_kreport2krona - - taxpasta - est_abundance - - sylph_profile + - kraken2 + - cat1 - add_line_to_file + - taxpasta - datamash_transpose - Remove beginning1 - - cat1 update_time: '2025-12-17' versions: 3 - create_time: '2025-12-01' @@ -3677,11 +3811,11 @@ deprecated: false doi: '' edam_operation: - - Sequence composition calculation - - Sequence assembly validation - Statistical calculation - - Validation - Sequencing quality control + - Validation + - Sequence composition calculation + - Sequence assembly validation edam_topic: [] id: 7371b6918e895e0c keep: true @@ -3696,13 +3830,13 @@ - microbiome - name:microgalaxy tools: + - __RELABEL_FROM_FILE__ + - checkm2 + - collection_element_identifiers - multiqc - __FLATTEN__ - - collection_element_identifiers - - __RELABEL_FROM_FILE__ - __MERGE_COLLECTION__ - regex1 - - checkm2 update_time: '2025-12-08' versions: 16 - create_time: '2023-06-30' @@ -3712,19 +3846,19 @@ deprecated: false doi: '' edam_operation: - - Visualisation - - Sequence feature detection - - Sequence composition calculation - - Filtering - - Formatting - Statistical calculation - - Deposition - - Validation - - Analysis - - Standardisation and normalisation - - Classification + - Formatting - DNA barcoding + - Filtering + - Sequence feature detection - Sequencing quality control + - Standardisation and normalisation + - Analysis + - Validation + - Deposition + - Sequence composition calculation + - Visualisation + - Classification edam_topic: [] id: 466bdd8ba7b67264 keep: true @@ -3741,34 +3875,34 @@ - name:metagenomics - name:pallori tools: - - compose_text_param + - __FLATTEN__ - ampvis2_heatmap - - fastqc - - bg_column_arrange_by_header - - ampvis2_subset_samples - datamash_transpose - - unzip - - biom_convert - - maaslin2 - - volcanoplot - - __FLATTEN__ - - calculate_numeric_param - - mmuphin - - phyloseq_tax_glom + - regex1 - ampvis2_load + - mmuphin + - maaslin2 + - ampvis2_ordinate + - unzip - param_value_from_file + - phyloseq_from_biom - tp_awk_tool + - phyloseq_add_rank_names + - calculate_numeric_param + - ampvis2_export_otu + - bg_column_arrange_by_header + - volcanoplot - tp_cut_tool - - tp_easyjoin_tool + - biom_convert - Remove beginning1 + - tp_easyjoin_tool - multiqc - - ampvis2_ordinate - - phyloseq_from_biom - - phyloseq_add_rank_names - - ampvis2_export_otu - - regex1 - lotus2 + - compose_text_param + - fastqc + - ampvis2_subset_samples - decontam + - phyloseq_tax_glom update_time: '2025-11-18' versions: 193 - create_time: '2024-12-20' @@ -3778,15 +3912,15 @@ deprecated: false doi: '' edam_operation: - - Visualisation - - Formatting - Statistical calculation - - Standardisation and normalisation - - Species frequency estimation - Taxonomic classification - - Conversion + - Formatting - Aggregation + - Species frequency estimation + - Conversion + - Standardisation and normalisation - Phylogenetic analysis + - Visualisation edam_topic: [] id: cb2df493f5e334f7 keep: true @@ -3803,35 +3937,35 @@ - diversity - name:microgalaxy tools: - - metaphlan - - tp_text_file_with_recurring_lines - - est_abundance - - datamash_transpose - - cat1 - - tp_sed_tool - - sort1 - - humann - - kraken2 - collection_element_identifiers - krakentools_kreport2krona - - csv_to_tabular - - collapse_dataset - - humann_unpack_pathways - - humann_rename_table - - tp_awk_tool - tp_replace_in_line - - __UNZIP_COLLECTION__ - - add_line_to_file - - tp_easyjoin_tool - - Remove beginning1 + - collapse_dataset + - datamash_transpose - krakentools_alpha_diversity - - fastq_paired_end_interlacer - - collection_column_join + - tp_awk_tool + - csv_to_tabular - taxonomy_krona_chart + - est_abundance + - kraken2 + - cat1 + - tp_text_file_with_recurring_lines - taxpasta + - metaphlan + - humann_regroup_table - sylph_profile + - fastq_paired_end_interlacer - humann_renorm_table - - humann_regroup_table + - Remove beginning1 + - humann + - sort1 + - humann_rename_table + - collection_column_join + - tp_easyjoin_tool + - tp_sed_tool + - humann_unpack_pathways + - add_line_to_file + - __UNZIP_COLLECTION__ update_time: '2025-11-13' versions: 18 - create_time: '2023-07-02' @@ -3841,13 +3975,13 @@ deprecated: false doi: '' edam_operation: + - Sequencing quality control + - Statistical calculation + - Validation - Read summarisation + - Sequence alignment - Sequence composition calculation - RNA-Seq quantification - - Statistical calculation - - Sequence alignment - - Validation - - Sequencing quality control edam_topic: [] id: ca9d3233b0912765 keep: true @@ -3866,14 +4000,14 @@ - name:barcode - name:transcriptomics tools: + - umi_tools_dedup - collection_column_join + - umi_tools_extract - multiqc - fastqc - - __FILTER_FAILED_DATASETS__ - featurecounts - - umi_tools_dedup + - __FILTER_FAILED_DATASETS__ - rna_star - - umi_tools_extract update_time: '2025-06-26' versions: 48 - create_time: '2024-09-30' @@ -3884,34 +4018,34 @@ deprecated: false doi: '' edam_operation: - - Visualisation - - Sequence composition calculation - - Formatting - Statistical calculation + - Formatting - Gene functional annotation - - Validation - - Sequence database search + - Visualisation - Format validation - - Primer removal - - Coding region prediction - - Local alignment - - Sequence assembly - - Database search - - Sequence profile generation + - Conversion + - Probabilistic sequence generation - Sequencing quality control + - Sequence assembly - Protein feature detection - - Sequence trimming - - Multiple sequence alignment - - Sequence assembly validation + - Gene prediction - Sequence motif recognition + - Coding region prediction + - Sequence composition calculation - Sequence generation - - Sequence analysis - - Read pre-processing + - Database search + - Sequence database search - Data retrieval - - Gene prediction - Taxonomic classification - - Conversion - - Probabilistic sequence generation + - Multiple sequence alignment + - Sequence assembly validation + - Sequence trimming + - Sequence profile generation + - Validation + - Sequence analysis + - Read pre-processing + - Primer removal + - Local alignment edam_topic: [] id: 667bac8d7453e5f1 keep: true @@ -3927,23 +4061,23 @@ - name:microbiome - name:mags tools: + - coverm_genome - fasplit - tp_awk_tool - tp_grep_tool + - sort1 + - cat_bins + - trim_galore - fastqc - checkm_lineage_wf + - interproscan + - coverm_contig - hmmer_hmmscan - - coverm_genome + - kofamscan + - tp_cat + - maxbin2 - quast - - coverm_contig - fraggenescan - - maxbin2 - - tp_cat - - cat_bins - - kofamscan - - trim_galore - - interproscan - - sort1 update_time: '2024-12-21' versions: 14 - create_time: '2024-12-20' @@ -3965,23 +4099,23 @@ deprecated: false doi: '' edam_operation: - - Sequence comparison - - Phylogenetic tree visualisation - - Visualisation - - Sequence composition calculation - - Formatting - Statistical calculation - Phylogenetic inference - - Validation - - Primer removal - - Sequence alignment analysis + - Taxonomic classification + - Formatting + - Conversion + - Phylogenetic tree visualisation + - Sequence similarity search + - Sequence composition calculation + - Phylogenetic tree editing - Sequencing quality control - Sequence trimming - - Phylogenetic tree editing + - Sequence alignment analysis + - Sequence comparison + - Validation - Read pre-processing - - Taxonomic classification - - Sequence similarity search - - Conversion + - Primer removal + - Visualisation edam_topic: [] id: 096b75501c8e0888 keep: true @@ -3999,27 +4133,27 @@ - microbiome - name:microgalaxy tools: - - Grouping1 - - group_humann2_uniref_abundances_to_go - - fastqc + - graphlan_annotate - humann2_renorm_table - - humann2_unpack_pathways - - tp_sort_header_tool - - humann2_genefamilies_genus_level - - humann2 - - metaphlan2krona - - Grep1 - - format_metaphlan2_output - - graphlan - - bg_sortmerna - - fastq_paired_end_interlacer - - multiqc - combine_metaphlan2_humann2 + - bg_sortmerna - cutadapt + - humann2_genefamilies_genus_level - taxonomy_krona_chart - - graphlan_annotate - export2graphlan - metaphlan2 + - fastq_paired_end_interlacer + - group_humann2_uniref_abundances_to_go + - Grouping1 + - Grep1 + - humann2 + - graphlan + - tp_sort_header_tool + - metaphlan2krona + - humann2_unpack_pathways + - format_metaphlan2_output + - multiqc + - fastqc update_time: '2024-12-20' versions: 3 - create_time: '2024-11-21' @@ -4039,16 +4173,16 @@ deprecated: false doi: '' edam_operation: - - Sequence trimming - - Sequence composition calculation - - Statistical calculation - - Gene expression profiling - - Primer removal - - Read pre-processing + - Statistical calculation - Sequence similarity search + - Sequencing quality control + - Gene expression profiling + - Sequence trimming - Sequence alignment analysis - Sequence comparison - - Sequencing quality control + - Read pre-processing + - Primer removal + - Sequence composition calculation edam_topic: [] id: fd90652d475ed739 keep: true @@ -4064,12 +4198,12 @@ - metatranscriptomics - microbiome tools: - - collection_column_join - kallisto_quant - - fastqc - - __UNZIP_COLLECTION__ + - collection_column_join - trim_galore + - fastqc - bg_sortmerna + - __UNZIP_COLLECTION__ update_time: '2024-12-20' versions: 6 - create_time: '2024-12-03' @@ -4079,8 +4213,8 @@ doi: '' edam_operation: - Sequence alignment analysis - - Multiple sequence alignment - Phylogenetic tree generation + - Multiple sequence alignment edam_topic: [] id: a2c46deea34d9d80 keep: true @@ -4095,20 +4229,20 @@ - genome-annotation - name:microgalaxy tools: + - Add_a_column1 + - tab2fasta - tp_split_on_column - - regexColumn1 + - gops_intersect_1 - rbc_mafft - - bg_diamond_view - - Filter1 - - bg_diamond - join1 - - tab2fasta - - collapse_dataset - - Cut1 + - bg_diamond - cat1 + - collapse_dataset - rapidnj - - Add_a_column1 - - gops_intersect_1 + - Filter1 + - bg_diamond_view + - Cut1 + - regexColumn1 update_time: '2024-12-05' versions: 2 - create_time: '2024-11-21' @@ -4121,8 +4255,8 @@ deprecated: false doi: '' edam_operation: - - Visualisation - Prediction and recognition + - Visualisation edam_topic: [] id: cefc49c13ff73231 keep: true @@ -4139,11 +4273,11 @@ - name:massspectrometry - name:microgalaxy tools: - - search_gui - peptide_shaker + - unipept + - search_gui - sqlite_to_tabular - query_tabular - - unipept update_time: '2024-11-21' versions: 40 - create_time: '2024-11-21' @@ -4172,10 +4306,10 @@ - limma-tmm - limma-rle tools: + - __EXTRACT_DATASET__ + - map_param_value - Grep1 - __BUILD_LIST__ - - map_param_value - - __EXTRACT_DATASET__ - __FILTER_EMPTY_DATASETS__ update_time: '2024-11-21' versions: 5 @@ -4189,11 +4323,11 @@ deprecated: false doi: '' edam_operation: - - Visualisation - - Label-free quantification + - Formatting - Prediction and recognition - Filtering - - Formatting + - Visualisation + - Label-free quantification edam_topic: [] id: cd675ab32d3e7833 keep: true @@ -4208,18 +4342,18 @@ - proteomics - name:microgalaxy tools: - - tp_replace_in_column + - peptide_shaker + - search_gui + - unipept - flashlfq - - Filter1 - - msconvert - tp_replace_in_line - Cut1 - regex1 - - Remove beginning1 - - search_gui - - peptide_shaker + - msconvert + - tp_replace_in_column - query_tabular - - unipept + - Filter1 + - Remove beginning1 update_time: '2024-11-21' versions: 1 - create_time: '2024-11-21' @@ -4233,16 +4367,16 @@ deprecated: false doi: '' edam_operation: - - Visualisation - - Statistical inference - Quantification - - Heat map generation - - Query and retrieval - - Indexing - Differential protein expression analysis + - Query and retrieval - Principal component visualisation + - Indexing + - Heat map generation - Filtering - Functional clustering + - Statistical inference + - Visualisation edam_topic: [] id: e5a89ef7b5f1c1d9 keep: true @@ -4257,12 +4391,12 @@ - proteomics - name:microgalaxy tools: - - metaquantome_db - - metaquantome_sample - metaquantome_stat - - metaquantome_filter - - metaquantome_viz - metaquantome_expand + - metaquantome_viz + - metaquantome_db + - metaquantome_filter + - metaquantome_sample update_time: '2024-11-21' versions: 3 - create_time: '2024-11-21' @@ -4274,10 +4408,10 @@ deprecated: false doi: '' edam_operation: - - Cross-assembly - Taxonomic classification - - Read mapping - Expression analysis + - Read mapping + - Cross-assembly edam_topic: [] id: c09159d7aad0f264 keep: true @@ -4294,10 +4428,10 @@ - name:microgalaxy tools: - bowtie2 - - kraken2 + - recentrifuge - fastq_to_tabular + - kraken2 - filter_tabular - - recentrifuge - seq_filter_by_id update_time: '2024-11-21' versions: 2 @@ -4310,11 +4444,11 @@ deprecated: false doi: '' edam_operation: - - Read summarisation - - RNA-Seq quantification + - Sequencing quality control - Validation + - Read summarisation - Read mapping - - Sequencing quality control + - RNA-Seq quantification edam_topic: [] id: 63478edcea3f449a keep: true @@ -4330,8 +4464,8 @@ - metatranscriptomics - name:microgalaxy tools: - - featurecounts - bowtie2 + - featurecounts - multiqc update_time: '2024-11-21' versions: 4 @@ -4344,10 +4478,10 @@ deprecated: false doi: '' edam_operation: - - Sequence composition calculation + - Sequencing quality control - Statistical calculation - Validation - - Sequencing quality control + - Sequence composition calculation edam_topic: [] id: 1ef76b7b86e15792 keep: true @@ -4363,9 +4497,9 @@ - metatranscriptomics - name:microgalaxy tools: - - trimmomatic - fastqc - multiqc + - trimmomatic update_time: '2024-11-21' versions: 6 - create_time: '2023-10-10' @@ -4412,26 +4546,26 @@ - assembly - name:microgalaxy tools: - - mergeCols1 - - bedtools_complementbed - - tp_sort_header_tool - - tp_sed_tool - - cat1 - bedtools_sortbed - - fasta_compute_length - - Filter1 - - addValue - - join1 - collapse_dataset - bedtools_intersectbed - - random_lines1 - - Grep1 - tp_cat - - Cut1 - - fasta_filter_by_length - - tp_grep_tool - datamash_ops + - bedtools_complementbed + - cat1 + - join1 + - mergeCols1 - lastz_wrapper_2 + - tp_grep_tool + - addValue + - fasta_filter_by_length + - Grep1 + - fasta_compute_length + - tp_sort_header_tool + - random_lines1 + - tp_sed_tool + - Filter1 + - Cut1 update_time: '2023-12-14' versions: 0 - create_time: '2023-12-14' @@ -4441,8 +4575,8 @@ doi: '' edam_operation: - Sequence alignment analysis - - Multiple sequence alignment - Phylogenetic tree generation + - Multiple sequence alignment edam_topic: [] id: 86900be4282d4b1d keep: true @@ -4458,20 +4592,20 @@ - genome-annotation - name:microgalaxy tools: + - Add_a_column1 + - tab2fasta - tp_split_on_column - - regexColumn1 + - gops_intersect_1 - rbc_mafft - - bg_diamond_view - - Filter1 - - bg_diamond - join1 - - tab2fasta - - collapse_dataset - - Cut1 + - bg_diamond - cat1 + - collapse_dataset - rapidnj - - Add_a_column1 - - gops_intersect_1 + - Filter1 + - bg_diamond_view + - Cut1 + - regexColumn1 update_time: '2023-12-14' versions: 0 - create_time: '2023-12-14' @@ -4494,11 +4628,11 @@ - genome-annotation - name:microgalaxy tools: - - jbrowse - - iframe - create_or_update - - list_organism + - iframe + - jbrowse - create_account + - list_organism update_time: '2023-12-14' versions: 0 - create_time: '2023-12-14' @@ -4506,24 +4640,24 @@ deprecated: false doi: '' edam_operation: - - Genome assembly + - Base-calling + - Pairwise sequence alignment - Sequence visualisation - - Gene prediction - - Genome annotation - - Sequence analysis + - De-novo assembly - Variant calling - - Base-calling - - Antimicrobial resistance prediction + - Scatter plot plotting + - Genome annotation + - Sequence assembly + - Gene prediction + - Genome visualisation + - Mapping assembly - Coding region prediction - Cross-assembly - - Mapping assembly - - Sequence assembly + - Antimicrobial resistance prediction - Box-Whisker plot plotting - - Genome visualisation - - Pairwise sequence alignment - Sequence assembly visualisation - - Scatter plot plotting - - De-novo assembly + - Sequence analysis + - Genome assembly edam_topic: [] id: 152223c8aed27357 keep: true @@ -4538,42 +4672,42 @@ - wmdi - name:microgalaxy tools: + - circos_wiggle_to_scatter + - tp_split_on_column + - bandage_image + - flye + - deeptools_bam_coverage + - staramr_search + - PlasFlow + - regex1 - jbrowse - - bg_column_arrange_by_header + - tp_cat + - tp_head_tool + - ncbi_blastn_wrapper + - medaka_consensus_pipeline - gff2bed1 - - tp_text_file_with_recurring_lines - - circos_gc_skew + - circos + - tbl2gff3 + - join1 - trimmomatic + - tp_text_file_with_recurring_lines + - prokka + - nanoplot + - bg_column_arrange_by_header - fasta2tab - - fasta_compute_length - Add_a_column1 - - circos_interval_to_tile - - tp_sort_header_tool + - tp_cut_tool - minimap2 - - Filter1 - - bandage_image - - nanoplot - - join1 - - PlasFlow - - circos - - tp_head_tool - - deeptools_bam_coverage - Grep1 - - tp_cut_tool + - tab2fasta + - fasta_compute_length + - tp_sort_header_tool + - circos_interval_to_tile - tp_easyjoin_tool - - tp_cat - regex_replace + - circos_gc_skew + - Filter1 - Cut1 - - tp_split_on_column - - medaka_consensus_pipeline - - circos_wiggle_to_scatter - - ncbi_blastn_wrapper - - staramr_search - - prokka - - regex1 - - flye - - tbl2gff3 - - tab2fasta update_time: '2023-12-14' versions: 0 - create_time: '2023-12-14' @@ -4595,11 +4729,11 @@ - evolution - name:microgalaxy tools: + - snp_dists - bcftools_consensus - - snp_sites - tb_variant_filter + - snp_sites - tp_cat - - snp_dists update_time: '2023-12-14' versions: 0 - create_time: '2023-12-14' @@ -4608,8 +4742,8 @@ doi: '' edam_operation: - Phylogenetic tree visualisation - - Variant calling - Phylogenetic tree generation + - Variant calling edam_topic: [] id: 3a8fde248a4d0383 keep: true @@ -4624,10 +4758,10 @@ - evolution - name:microgalaxy tools: - - trimmomatic - - tb_variant_filter - - __MERGE_COLLECTION__ - snippy + - __MERGE_COLLECTION__ + - tb_variant_filter + - trimmomatic update_time: '2023-12-14' versions: 0 - create_time: '2023-12-14' @@ -4650,14 +4784,14 @@ - evolution - name:microgalaxy tools: + - addName - samtools_view - - tb_profiler_profile - tp_grep_tool + - tp_sed_tool - tp_replace_in_line - __MERGE_COLLECTION__ - tp_cat - - addName - - tp_sed_tool + - tb_profiler_profile update_time: '2023-12-14' versions: 0 - create_time: '2023-12-13' @@ -4683,12 +4817,12 @@ - hpylori tools: - bowtie2 - - bcftools_norm - tp_awk_tool - - snpSift_filter + - bcftools_view + - bcftools_norm - vcf2tsv + - snpSift_filter - freebayes - - bcftools_view update_time: '2023-12-13' versions: 2 - create_time: '2023-10-27' @@ -4714,14 +4848,14 @@ - hpylori tools: - bowtie2 - - samtools_coverage + - collection_element_identifiers + - samtools_depth - bcftools_norm - vcf2tsv - - collection_element_identifiers - - freebayes - - tp_cat - collapse_dataset - - samtools_depth + - samtools_coverage + - tp_cat + - freebayes update_time: '2023-12-13' versions: 13 - create_time: '2025-12-08' @@ -4730,11 +4864,11 @@ deprecated: false doi: '' edam_operation: - - Sequence composition calculation - - Sequence assembly validation - Statistical calculation - - Validation - Sequencing quality control + - Validation + - Sequence composition calculation + - Sequence assembly validation edam_topic: [] id: a8aee61c2cbaf6ea keep: true @@ -4749,13 +4883,13 @@ - microbiome - name:microgalaxy tools: + - __RELABEL_FROM_FILE__ + - checkm2 + - collection_element_identifiers - multiqc - __FLATTEN__ - - collection_element_identifiers - - __RELABEL_FROM_FILE__ - __MERGE_COLLECTION__ - regex1 - - checkm2 update_time: '2025-12-08' versions: 1 - create_time: '2025-02-06' @@ -4782,11 +4916,11 @@ - amplicon - name:microgalaxy tools: - - fastq_dl - - CONVERTER_uncompressed_to_gz - tp_awk_tool + - CONVERTER_uncompressed_to_gz - CONVERTER_gz_to_uncompressed - __MERGE_COLLECTION__ + - fastq_dl update_time: '2025-04-25' versions: 1 - create_time: '2025-02-06' @@ -4798,8 +4932,8 @@ doi: '' edam_operation: - k-mer counting - - Visualisation - Formatting + - Visualisation - Mapping edam_topic: [] id: 45f959d5bf505b15 @@ -4817,10 +4951,10 @@ - metagenomics - name:microgalaxy tools: - - tp_awk_tool - - __FILTER_FROM_FILE__ - bedtools_maskfastabed - mapseq + - tp_awk_tool + - __FILTER_FROM_FILE__ - collection_element_identifiers - taxonomy_krona_chart - biom_convert @@ -4835,14 +4969,14 @@ deprecated: false doi: '' edam_operation: - - Sequence trimming - - Sequence composition calculation - - Nucleic acid design - Statistical calculation + - Sequencing quality control + - Sequence contamination filtering + - Sequence trimming - Validation + - Nucleic acid design - Read pre-processing - - Sequence contamination filtering - - Sequencing quality control + - Sequence composition calculation edam_topic: [] id: a71fcbc60caae8b6 keep: true @@ -4859,17 +4993,17 @@ - metagenomics - name:microgalaxy tools: + - fastp - cshl_fasta_formatter - tp_find_and_replace - - fastq_to_fasta_python - multiqc + - trimmomatic - fastqc - __UNZIP_COLLECTION__ - - prinseq - mgnify_seqprep - - fastp - - trimmomatic - fastq_filter + - prinseq + - fastq_to_fasta_python update_time: '2025-04-25' versions: 1 - create_time: '2025-02-06' @@ -4880,13 +5014,13 @@ deprecated: false doi: '' edam_operation: + - Sequencing quality control + - Statistical calculation + - Sequence contamination filtering - Sequence trimming + - Validation - Read pre-processing - Sequence composition calculation - - Sequence contamination filtering - - Statistical calculation - - Validation - - Sequencing quality control edam_topic: [] id: 5f878c4cc3bff68c keep: true @@ -4905,12 +5039,12 @@ tools: - cshl_fasta_formatter - tp_find_and_replace - - fastq_to_fasta_python - multiqc - - fastqc - - prinseq - trimmomatic + - fastqc - fastq_filter + - prinseq + - fastq_to_fasta_python update_time: '2025-04-25' versions: 1 - create_time: '2025-03-06' @@ -4939,24 +5073,24 @@ - name:pathogfair - name:iwc tools: + - tp_cut_tool + - clair3 + - table_compute + - samtools_depth - bcftools_consensus + - CONVERTER_gz_to_uncompressed - Paste1 - - samtools_coverage - - regexColumn1 - bcftools_norm - - CONVERTER_gz_to_uncompressed - - snpSift_filter - - tp_cut_tool - Cut1 - snpSift_extractFields - - clair3 + - samtools_coverage + - snpSift_filter - collapse_dataset - - Remove beginning1 - - table_compute - - tp_head_tool - - Count1 - - samtools_depth - minimap2 + - Count1 + - tp_head_tool + - Remove beginning1 + - regexColumn1 update_time: '2025-04-25' versions: 1 - create_time: '2025-03-06' @@ -4967,13 +5101,13 @@ deprecated: false doi: '' edam_operation: + - Sequencing quality control + - Statistical calculation + - Sequence contamination filtering - Sequence trimming + - Validation - Read pre-processing - Sequence composition calculation - - Sequence contamination filtering - - Statistical calculation - - Validation - - Sequencing quality control edam_topic: [] id: afb67b4b9952f57d keep: true @@ -4992,12 +5126,12 @@ tools: - cshl_fasta_formatter - tp_find_and_replace - - fastq_to_fasta_python - multiqc - - fastqc - - prinseq - trimmomatic + - fastqc - fastq_filter + - prinseq + - fastq_to_fasta_python update_time: '2025-04-25' versions: 1 - create_time: '2025-03-13' @@ -5026,24 +5160,24 @@ - name:pathogfair - name:iwc tools: + - tp_cut_tool + - clair3 + - table_compute + - samtools_depth - bcftools_consensus + - CONVERTER_gz_to_uncompressed - Paste1 - - samtools_coverage - - regexColumn1 - bcftools_norm - - CONVERTER_gz_to_uncompressed - - snpSift_filter - - tp_cut_tool - Cut1 - snpSift_extractFields - - clair3 + - samtools_coverage + - snpSift_filter - collapse_dataset - - Remove beginning1 - - table_compute - - tp_head_tool - - Count1 - - samtools_depth - minimap2 + - Count1 + - tp_head_tool + - Remove beginning1 + - regexColumn1 update_time: '2025-04-25' versions: 1 - create_time: '2025-03-13' @@ -5070,11 +5204,11 @@ - amplicon - name:microgalaxy tools: - - fastq_dl - - CONVERTER_uncompressed_to_gz - tp_awk_tool + - CONVERTER_uncompressed_to_gz - CONVERTER_gz_to_uncompressed - __MERGE_COLLECTION__ + - fastq_dl update_time: '2025-04-25' versions: 1 - create_time: '2025-03-13' @@ -5086,8 +5220,8 @@ doi: '' edam_operation: - k-mer counting - - Visualisation - Formatting + - Visualisation - Mapping edam_topic: [] id: 8151be18aab3a3c6 @@ -5105,10 +5239,10 @@ - metagenomics - name:microgalaxy tools: - - tp_awk_tool - - __FILTER_FROM_FILE__ - bedtools_maskfastabed - mapseq + - tp_awk_tool + - __FILTER_FROM_FILE__ - collection_element_identifiers - taxonomy_krona_chart - biom_convert @@ -5123,14 +5257,14 @@ deprecated: false doi: '' edam_operation: - - Sequence trimming - - Sequence composition calculation - - Nucleic acid design - Statistical calculation + - Sequencing quality control + - Sequence contamination filtering + - Sequence trimming - Validation + - Nucleic acid design - Read pre-processing - - Sequence contamination filtering - - Sequencing quality control + - Sequence composition calculation edam_topic: [] id: 20b7ae4b517a80fd keep: true @@ -5147,17 +5281,17 @@ - metagenomics - name:microgalaxy tools: + - fastp - cshl_fasta_formatter - tp_find_and_replace - - fastq_to_fasta_python - multiqc + - trimmomatic - fastqc - __UNZIP_COLLECTION__ - - prinseq - mgnify_seqprep - - fastp - - trimmomatic - fastq_filter + - prinseq + - fastq_to_fasta_python update_time: '2025-04-25' versions: 1 - create_time: '2025-03-13' @@ -5168,13 +5302,13 @@ deprecated: false doi: '' edam_operation: + - Sequencing quality control + - Statistical calculation + - Sequence contamination filtering - Sequence trimming + - Validation - Read pre-processing - Sequence composition calculation - - Sequence contamination filtering - - Statistical calculation - - Validation - - Sequencing quality control edam_topic: [] id: 46f184a0e95f3c1c keep: true @@ -5193,12 +5327,12 @@ tools: - cshl_fasta_formatter - tp_find_and_replace - - fastq_to_fasta_python - multiqc - - fastqc - - prinseq - trimmomatic + - fastqc - fastq_filter + - prinseq + - fastq_to_fasta_python update_time: '2025-04-25' versions: 1 - create_time: '2025-03-20' @@ -5209,19 +5343,19 @@ deprecated: false doi: '' edam_operation: - - Visualisation - - Sequence composition calculation - Statistical calculation - - Validation - - Sequence contamination filtering - - Box-Whisker plot plotting - - Sequence alignment analysis - Taxonomic classification - - Data handling - Pairwise sequence alignment + - Box-Whisker plot plotting - Aggregation + - Data handling - Scatter plot plotting - Sequencing quality control + - Sequence contamination filtering + - Sequence alignment analysis + - Validation + - Sequence composition calculation + - Visualisation edam_topic: [] id: a8b9252fad5fe06a keep: true @@ -5239,23 +5373,23 @@ - name:nanopore - name:iwc tools: + - Add_a_column1 + - fastp - collection_column_join - - Grep1 - - samtools_fastx - - regexColumn1 - multiqc - kraken2 + - samtools_fastx - fastqc - - bamtools_split_mapped + - collapse_dataset - nanoplot - - porechop + - minimap2 + - Grep1 - __FILTER_FAILED_DATASETS__ - - krakentools_extract_kraken_reads - - fastp - - collapse_dataset + - bamtools_split_mapped + - porechop - Cut1 - - Add_a_column1 - - minimap2 + - regexColumn1 + - krakentools_extract_kraken_reads update_time: '2025-04-25' versions: 1 - create_time: '2025-12-08' @@ -5264,11 +5398,11 @@ deprecated: false doi: '' edam_operation: - - Sequence composition calculation - - Sequence assembly validation - Statistical calculation - - Validation - Sequencing quality control + - Validation + - Sequence composition calculation + - Sequence assembly validation edam_topic: [] id: f05ed1e5c5dfffa9 keep: true @@ -5283,13 +5417,13 @@ - microbiome - name:microgalaxy tools: + - __RELABEL_FROM_FILE__ + - checkm2 + - collection_element_identifiers - multiqc - __FLATTEN__ - - collection_element_identifiers - - __RELABEL_FROM_FILE__ - __MERGE_COLLECTION__ - regex1 - - checkm2 update_time: '2025-12-08' versions: 1 - create_time: '2025-03-06' @@ -5318,24 +5452,24 @@ - name:pathogfair - name:iwc tools: + - tp_cut_tool + - clair3 + - table_compute + - samtools_depth - bcftools_consensus + - CONVERTER_gz_to_uncompressed - Paste1 - - samtools_coverage - - regexColumn1 - bcftools_norm - - CONVERTER_gz_to_uncompressed - - snpSift_filter - - tp_cut_tool - Cut1 - snpSift_extractFields - - clair3 + - samtools_coverage + - snpSift_filter - collapse_dataset - - Remove beginning1 - - table_compute - - tp_head_tool - - Count1 - - samtools_depth - minimap2 + - Count1 + - tp_head_tool + - Remove beginning1 + - regexColumn1 update_time: '2025-04-25' versions: 1 - create_time: '2025-03-13' @@ -5364,23 +5498,23 @@ - name:pathogfair - name:iwc tools: + - tp_cut_tool + - clair3 + - table_compute + - samtools_depth - bcftools_consensus + - CONVERTER_gz_to_uncompressed - Paste1 - - samtools_coverage - - regexColumn1 - bcftools_norm - - CONVERTER_gz_to_uncompressed - - snpSift_filter - - tp_cut_tool - Cut1 - snpSift_extractFields - - clair3 + - samtools_coverage + - snpSift_filter - collapse_dataset - - Remove beginning1 - - table_compute - - tp_head_tool - - Count1 - - samtools_depth - minimap2 + - Count1 + - tp_head_tool + - Remove beginning1 + - regexColumn1 update_time: '2025-04-25' versions: 1 diff --git a/communities/microgalaxy/resources/tag_filtered_workflows.json b/communities/microgalaxy/resources/tag_filtered_workflows.json index 8f5edb086..a836c9f02 100644 --- a/communities/microgalaxy/resources/tag_filtered_workflows.json +++ b/communities/microgalaxy/resources/tag_filtered_workflows.json @@ -1,4 +1,104 @@ [ + { + "create_time": "2026-06-18", + "creators": [ + "Tristan Reynolds", + "Ammar Aziz" + ], + "deprecated": false, + "doi": "10.48546/workflowhub.workflow.2196.1", + "edam_operation": [ + "Sequencing quality control", + "Phylogenetic analysis" + ], + "edam_topic": [ + "Bioinformatics", + "Biomedical science", + "Genomics", + "Virology" + ], + "id": "2196", + "keep": true, + "latest_version": 1, + "license": "MIT", + "link": "https://workflowhub.eu/workflows/2196?version=1", + "name": "MPXV (Mpox) Phylogenetic Analysis with Squirrel", + "number_of_steps": 3, + "projects": [ + "Melbourne Bioinformatics", + "Galaxy Australia" + ], + "source": "WorkflowHub", + "tags": [ + "amplicon", + "mpox", + "ont", + "virus", + "mpxv", + "phylogeny" + ], + "tools": [ + "squirrel_phylo", + "regex1", + "squirrel_qc" + ], + "update_time": "2026-06-25", + "versions": 1 + }, + { + "create_time": "2026-06-18", + "creators": [ + "Tristan Reynolds", + "Ammar Aziz" + ], + "deprecated": false, + "doi": "10.48546/workflowhub.workflow.2195.1", + "edam_operation": [ + "Sequencing quality control", + "Sequence alignment", + "Validation", + "Mapping" + ], + "edam_topic": [ + "Bioinformatics", + "Biomedical science", + "Genomics", + "Virology" + ], + "id": "2195", + "keep": true, + "latest_version": 1, + "license": "MIT", + "link": "https://workflowhub.eu/workflows/2195?version=1", + "name": "Viral Amplicon Analysis Pipeline for ONT Data", + "number_of_steps": 12, + "projects": [ + "Melbourne Bioinformatics", + "Galaxy Australia" + ], + "source": "WorkflowHub", + "tags": [ + "amplicon", + "mpox", + "ont", + "virus", + "mpxv", + "phylogeny" + ], + "tools": [ + "artic_minion", + "multiqc", + "mosdepth", + "XY_Plot_1", + "regex1", + "__BUILD_LIST__", + "tp_cat", + "fastplong", + "bedtools_makewindowsbed" + ], + "update_time": "2026-06-25", + "versions": 1 + }, { "create_time": "2026-03-02", "creators": [ @@ -8,10 +108,10 @@ "deprecated": false, "doi": "10.48546/workflowhub.workflow.2098.1", "edam_operation": [ - "Visualisation", + "Taxonomic classification", "Formatting", "Demultiplexing", - "Taxonomic classification" + "Visualisation" ], "edam_topic": [ "Taxonomy" @@ -34,20 +134,20 @@ "taxonomic-classification" ], "tools": [ - "qiime2__feature_classifier__classify_sklearn", - "qiime2__feature_table__summarize", - "qiime2_core__tools__import", - "qiime2__taxa__barplot", - "qiime2__feature_classifier__fit_classifier_naive_bayes", "qiime2__feature_table__tabulate_seqs", - "qiime2__feature_classifier__extract_reads", + "biom_convert", "csv_to_tabular", "tp_easyjoin_tool", - "Remove beginning1", - "biom_convert", + "qiime2_core__tools__import", + "qiime2__feature_classifier__classify_sklearn", + "qiime2__feature_table__summarize", + "tabular_to_csv", + "qiime2__taxa__barplot", "qiime_extract_viz", + "qiime2__feature_classifier__fit_classifier_naive_bayes", "qiime2_core__tools__export", - "tabular_to_csv" + "qiime2__feature_classifier__extract_reads", + "Remove beginning1" ], "update_time": "2026-05-13", "versions": 1 @@ -62,11 +162,11 @@ "doi": null, "edam_operation": [ "Data parsing", - "Gene functional annotation", - "Validation", "Taxonomic classification", + "Gene functional annotation", "Sequencing quality control", - "Antimicrobial resistance prediction" + "Antimicrobial resistance prediction", + "Validation" ], "edam_topic": [], "id": "2068", @@ -82,23 +182,23 @@ "source": "WorkflowHub", "tags": [], "tools": [ - "table_pandas_rename_column", - "multiqc", + "tooldistillator_summarize", + "__RELABEL_FROM_FILE__", "groot", "collection_element_identifiers", - "tooldistillator_summarize", - "tooldistillator", - "Remove a collection level so that outputs can be taken into account by tooldistillator\n__FLATTEN__", - "__FILTER_FAILED_DATASETS__", - "tp_text_file_with_recurring_lines", - "__UNZIP_COLLECTION__", "sylph_profile", + "deeparg_short_reads", + "fastq_paired_end_interlacer", "argnorm", - "__RELABEL_FROM_FILE__", + "table_pandas_rename_column", + "multiqc", "Removal of the first line because it is not necessary for tooldistillator\nRemove beginning1", + "tp_text_file_with_recurring_lines", + "tooldistillator", + "__UNZIP_COLLECTION__", "Removal of the first argNorm line that causes a multiQC error\nRemove beginning1", - "fastq_paired_end_interlacer", - "deeparg_short_reads" + "__FILTER_FAILED_DATASETS__", + "Remove a collection level so that outputs can be taken into account by tooldistillator\n__FLATTEN__" ], "update_time": "2026-05-14", "versions": 2 @@ -113,8 +213,8 @@ "deprecated": false, "doi": null, "edam_operation": [ - "Multilocus sequence typing", - "Data parsing" + "Data parsing", + "Multilocus sequence typing" ], "edam_topic": [], "id": "2055", @@ -130,9 +230,9 @@ "source": "WorkflowHub", "tags": [], "tools": [ - "coreprofiler_allele_calling", + "tooldistillator", "tooldistillator_summarize", - "tooldistillator" + "coreprofiler_allele_calling" ], "update_time": "2026-05-14", "versions": 2 @@ -143,19 +243,19 @@ "deprecated": false, "doi": null, "edam_operation": [ - "Phylogenetic tree visualisation", - "Sequence alignment", - "Validation", + "Taxonomic classification", "Antimicrobial resistance prediction", - "Phylogenetic tree generation", "Variant calling", - "Sequence analysis", - "Local alignment", + "Sequence alignment", + "Phylogenetic tree visualisation", + "Sequencing quality control", "Sequence contamination filtering", - "Global alignment", "Sequence alignment analysis", - "Taxonomic classification", - "Sequencing quality control" + "Phylogenetic tree generation", + "Validation", + "Global alignment", + "Sequence analysis", + "Local alignment" ], "edam_topic": [], "id": "1647", @@ -176,20 +276,20 @@ "tuberculosis" ], "tools": [ - "bcftools_consensus", + "fastp", "tp_awk_tool", - "tb_profiler_profile", + "qualimap_bamqc", + "EMBOSS: seqret84", "kraken2", - "__FLATTEN__", - "multiqc", "mosdepth", + "__FLATTEN__", + "tp_sed_tool", "snippy", - "qualimap_bamqc", + "multiqc", + "bcftools_consensus", "tb_variant_filter", - "tbvcfreport", - "fastp", - "tp_sed_tool", - "EMBOSS: seqret84" + "tb_profiler_profile", + "tbvcfreport" ], "update_time": "2026-01-12", "versions": 2 @@ -200,14 +300,14 @@ "deprecated": false, "doi": null, "edam_operation": [ - "Visualisation", "Statistical calculation", - "Read mapping", - "Cross-assembly", - "Sequence contamination filtering", - "Expression analysis", "Taxonomic classification", - "Sequencing quality control" + "Expression analysis", + "Sequencing quality control", + "Sequence contamination filtering", + "Read mapping", + "Visualisation", + "Cross-assembly" ], "edam_topic": [], "id": "2043", @@ -227,11 +327,11 @@ "sequence-analysis" ], "tools": [ - "falco", - "kraken2", - "est_abundance", "fastp", - "recentrifuge" + "recentrifuge", + "est_abundance", + "kraken2", + "falco" ], "update_time": "2025-12-22", "versions": 1 @@ -242,11 +342,11 @@ "deprecated": false, "doi": null, "edam_operation": [ - "Visualisation", "Statistical calculation", "Taxonomic classification", + "Aggregation", "Genome annotation", - "Aggregation" + "Visualisation" ], "edam_topic": [], "id": "1470", @@ -266,15 +366,15 @@ "microbiome" ], "tools": [ - "interactive_tool_phinch", "metaphlan", - "kraken2", "taxonomy_krona_chart", "krakentools_kreport2krona", - "__UNZIP_COLLECTION__", "est_abundance", - "interactive_tool_pavian", - "kraken_biom" + "kraken_biom", + "kraken2", + "interactive_tool_phinch", + "__UNZIP_COLLECTION__", + "interactive_tool_pavian" ], "update_time": "2025-12-22", "versions": 2 @@ -285,10 +385,10 @@ "deprecated": false, "doi": null, "edam_operation": [ - "Cross-assembly", "Statistical calculation", "Taxonomic classification", - "Expression analysis" + "Expression analysis", + "Cross-assembly" ], "edam_topic": [], "id": "1674", @@ -308,9 +408,9 @@ "galaxy" ], "tools": [ - "kraken2", "est_abundance", - "recentrifuge" + "recentrifuge", + "kraken2" ], "update_time": "2025-12-22", "versions": 2 @@ -323,8 +423,8 @@ "edam_operation": [ "Sequence assembly", "Read mapping", - "Genome annotation", "Sequence clustering", + "Genome annotation", "Read binning" ], "edam_topic": [], @@ -348,19 +448,19 @@ ], "tools": [ "bowtie2", - "metabat2", - "__BUILD_LIST__", "concoct_coverage_table", - "metabat2_jgi_summarize_bam_contig_depths", + "concoct_merge_cut_up_clustering", "concoct_extract_fasta_bins", - "semibin", - "concoct", + "concoct_cut_up_fasta", "samtools_sort", - "maxbin2", - "binette", "Fasta_to_Contig2Bin", - "concoct_merge_cut_up_clustering", - "concoct_cut_up_fasta" + "concoct", + "__BUILD_LIST__", + "binette", + "semibin", + "maxbin2", + "metabat2", + "metabat2_jgi_summarize_bam_contig_depths" ], "update_time": "2025-12-08", "versions": 1 @@ -375,16 +475,16 @@ "deprecated": false, "doi": null, "edam_operation": [ - "Visualisation", - "Sequence composition calculation", - "Sequence assembly validation", "Statistical calculation", - "Validation", - "Cross-assembly", - "Data parsing", - "Expression analysis", "Taxonomic classification", - "Sequencing quality control" + "Expression analysis", + "Sequence assembly validation", + "Data parsing", + "Sequencing quality control", + "Validation", + "Sequence composition calculation", + "Visualisation", + "Cross-assembly" ], "edam_topic": [], "id": "1882", @@ -400,15 +500,15 @@ "source": "WorkflowHub", "tags": [], "tools": [ - "pick_value", - "kraken2", "tooldistillator_summarize", - "tooldistillator", + "recentrifuge", + "checkm2", "est_abundance", - "quast", + "kraken2", + "pick_value", "collapse_dataset", - "checkm2", - "recentrifuge" + "tooldistillator", + "quast" ], "update_time": "2026-05-13", "versions": 3 @@ -421,19 +521,19 @@ "deprecated": false, "doi": null, "edam_operation": [ - "Methylation analysis", + "Read mapping", + "Generation", + "Variant classification", + "Variant calling", + "Tree-based sequence alignment", "Sequence alignment", "Genome indexing", - "SNP detection", + "Sequencing quality control", + "Sequence contamination filtering", "Validation", - "Read mapping", - "Variant calling", + "Methylation analysis", "Primer removal", - "Sequence contamination filtering", - "Generation", - "Tree-based sequence alignment", - "Variant classification", - "Sequencing quality control" + "SNP detection" ], "edam_topic": [], "id": "155", @@ -451,21 +551,21 @@ "virology" ], "tools": [ - "ivar_consensus", + "fastp", + "ivar_variants", + "nextclade", + "ivar_trim", "samtools_view", + "ivar_consensus", + "qualimap_bamqc", "multiqc", "__FLATTEN__", - "nextclade", - "samtools_stats", - "pangolin", - "bwa_mem", - "qualimap_bamqc", - "ivar_trim", - "fastp", + "tp_sed_tool", "snpeff_sars_cov_2", + "samtools_stats", "tp_cat", - "tp_sed_tool", - "ivar_variants" + "pangolin", + "bwa_mem" ], "update_time": "2026-05-13", "versions": 7 @@ -479,14 +579,14 @@ "doi": null, "edam_operation": [ "Formatting", + "Generation", "Sequence alignment", "Genome indexing", - "SNP detection", + "Sequencing quality control", + "Sequence contamination filtering", "Validation", "Read mapping", - "Sequence contamination filtering", - "Generation", - "Sequencing quality control" + "SNP detection" ], "edam_topic": [], "id": "113", @@ -507,17 +607,17 @@ "emergen_validated" ], "tools": [ + "lofreq_filter", + "fastp", + "picard_MarkDuplicates", + "lofreq_viterbi", "samtools_view", + "lofreq_call", "multiqc", + "snpeff_sars_cov_2", "samtools_stats", - "bwa_mem", - "lofreq_viterbi", "lofreq_indelqual", - "fastp", - "picard_MarkDuplicates", - "lofreq_call", - "lofreq_filter", - "snpeff_sars_cov_2" + "bwa_mem" ], "update_time": "2026-05-14", "versions": 4 @@ -531,14 +631,14 @@ "deprecated": false, "doi": null, "edam_operation": [ - "Sequence alignment", - "Genome indexing", + "Sequencing quality control", + "Sequence contamination filtering", + "Generation", "Validation", "Read mapping", + "Sequence alignment", "Primer removal", - "Sequence contamination filtering", - "Generation", - "Sequencing quality control" + "Genome indexing" ], "edam_topic": [], "id": "1876", @@ -556,28 +656,28 @@ "virology" ], "tools": [ + "ivar_variants", + "__FLATTEN__", + "snpSift_extractFields", + "map_param_value", + "collapse_dataset", + "tp_cat", + "fastp", "samtools_view", - "__FILTER_FAILED_DATASETS__", - "qualimap_bamqc", - "tp_sed_tool", "snpEff", - "__FLATTEN__", + "tp_find_and_replace", + "calculate_numeric_param", "samtools_stats", - "bwa_mem", "lofreq_viterbi", - "calculate_numeric_param", - "collapse_dataset", - "ivar_variants", + "snpEff_build_gb", "ivar_consensus", - "tp_find_and_replace", - "map_param_value", - "ivar_trim", - "fastp", - "tp_cat", - "snpSift_extractFields", "pick_value", + "ivar_trim", + "qualimap_bamqc", "multiqc", - "snpEff_build_gb" + "tp_sed_tool", + "__FILTER_FAILED_DATASETS__", + "bwa_mem" ], "update_time": "2026-05-13", "versions": 2 @@ -593,22 +693,22 @@ "deprecated": false, "doi": null, "edam_operation": [ + "Data retrieval", + "Generation", "Multiple sequence alignment", - "Sequence alignment", - "Genome indexing", + "Data handling", + "De-novo assembly", "Sequence file editing", - "Phylogenetic analysis", - "Read mapping", - "Sequence analysis", - "Primer removal", + "Sequence alignment", "Base position variability plotting", + "Genome indexing", + "Sequencing quality control", "Sequence contamination filtering", - "Data retrieval", "Sequence alignment analysis", - "Data handling", - "Generation", - "Sequencing quality control", - "De-novo assembly" + "Sequence analysis", + "Read mapping", + "Primer removal", + "Phylogenetic analysis" ], "edam_topic": [], "id": "1260", @@ -626,41 +726,41 @@ "virology" ], "tools": [ - "wc_gnu", - "samtools_view", - "__FILTER_FAILED_DATASETS__", - "tp_text_file_with_recurring_lines", - "qualimap_bamqc", - "bwa mem will fail if no reference for any segment got suggested by vapor, i.e. the reference genome is empty. In that case, we need to skip further analysis of the sample.\n__FILTER_FAILED_DATASETS__", - "__HARMONIZELISTS__", - "Show beginning1", - "Filter1", - "__FLATTEN__", "collection_element_identifiers", - "bwa_mem", - "__RELABEL_FROM_FILE__", - "__APPLY_RULES__", - "__MERGE_COLLECTION__", - "collapse_dataset", "Paste1", - "bamtools_split_ref", + "__FLATTEN__", "snipit", - "Grep1", - "ivar_consensus", + "bwa mem will fail if no reference for any segment got suggested by vapor, i.e. the reference genome is empty. In that case, we need to skip further analysis of the sample.\n__FILTER_FAILED_DATASETS__", + "collapse_dataset", + "bamtools_split_ref", + "tp_cat", + "Show beginning1", "param_value_from_file", - "tp_find_and_replace", - "__UNZIP_COLLECTION__", - "tp_easyjoin_tool", "fastp", - "tp_cat", - "Cut1", + "samtools_view", + "tp_find_and_replace", "rbc_mafft", + "tp_text_file_with_recurring_lines", + "__APPLY_RULES__", "__FILTER_FROM_FILE__", - "vapor", + "ivar_consensus", + "__HARMONIZELISTS__", + "__DUPLICATE_FILE_TO_COLLECTION__", "This seemingly no-op transformation will remove samples with no remaining segment results (cases where vapor failed for every segment).\n__APPLY_RULES__", - "seqtk_subseq", + "Grep1", "iqtree", - "__DUPLICATE_FILE_TO_COLLECTION__" + "vapor", + "__RELABEL_FROM_FILE__", + "wc_gnu", + "seqtk_subseq", + "tp_easyjoin_tool", + "qualimap_bamqc", + "__MERGE_COLLECTION__", + "__UNZIP_COLLECTION__", + "__FILTER_FAILED_DATASETS__", + "Filter1", + "Cut1", + "bwa_mem" ], "update_time": "2026-05-13", "versions": 3 @@ -674,18 +774,18 @@ "deprecated": false, "doi": null, "edam_operation": [ + "Generation", "Sequence alignment", "Genome indexing", + "Sequencing quality control", + "Sequence contamination filtering", + "Sequence alignment analysis", "Validation", - "Read mapping", + "Global alignment", "Sequence analysis", + "Read mapping", "Primer removal", - "Local alignment", - "Sequence contamination filtering", - "Global alignment", - "Sequence alignment analysis", - "Generation", - "Sequencing quality control" + "Local alignment" ], "edam_topic": [], "id": "439", @@ -704,31 +804,31 @@ "pox" ], "tools": [ - "compose_text_param", + "collection_element_identifiers", + "__FLATTEN__", + "EMBOSS: maskseq51", + "tp_cat", + "datamash_ops", + "param_value_from_file", + "fastp", "samtools_view", - "__FILTER_FAILED_DATASETS__", - "qualimap_bamqc", - "tp_sed_tool", - "fasta_compute_length", "samtools_merge", - "__FLATTEN__", - "collection_element_identifiers", "samtools_stats", - "bwa_mem", "__APPLY_RULES__", "__ZIP_COLLECTION__", - "Grep1", "ivar_consensus", - "param_value_from_file", - "split_file_to_collection", - "ivar_trim", - "fastp", - "tp_cat", - "Cut1", "__SORTLIST__", - "EMBOSS: maskseq51", + "Grep1", + "fasta_compute_length", + "ivar_trim", + "qualimap_bamqc", "multiqc", - "datamash_ops" + "split_file_to_collection", + "compose_text_param", + "tp_sed_tool", + "__FILTER_FAILED_DATASETS__", + "Cut1", + "bwa_mem" ], "update_time": "2026-05-13", "versions": 4 @@ -740,8 +840,8 @@ "doi": null, "edam_operation": [ "k-mer counting", - "Visualisation", "Formatting", + "Visualisation", "Mapping" ], "edam_topic": [], @@ -766,10 +866,10 @@ ], "tools": [ "", - "tp_awk_tool", - "__FILTER_FROM_FILE__", "bedtools_maskfastabed", "mapseq", + "tp_awk_tool", + "__FILTER_FROM_FILE__", "collection_element_identifiers", "taxonomy_krona_chart", "biom_convert", @@ -784,8 +884,8 @@ "deprecated": false, "doi": null, "edam_operation": [ - "Visualisation", - "Analysis" + "Analysis", + "Visualisation" ], "edam_topic": [], "id": "1855", @@ -805,10 +905,10 @@ "microbiome" ], "tools": [ - "collection_column_join", - "ampvis2_load", "tp_awk_tool", + "collection_column_join", "collapse_dataset", + "ampvis2_load", "query_tabular" ], "update_time": "2025-08-11", @@ -820,14 +920,14 @@ "deprecated": false, "doi": null, "edam_operation": [ - "Sequence trimming", - "Sequence composition calculation", - "Nucleic acid design", "Statistical calculation", + "Sequencing quality control", + "Sequence contamination filtering", + "Sequence trimming", "Validation", + "Nucleic acid design", "Read pre-processing", - "Sequence contamination filtering", - "Sequencing quality control" + "Sequence composition calculation" ], "edam_topic": [], "id": "1854", @@ -850,17 +950,17 @@ "name:microgalaxy" ], "tools": [ + "fastp", "cshl_fasta_formatter", "tp_find_and_replace", - "fastq_to_fasta_python", "multiqc", + "trimmomatic", "fastqc", "__UNZIP_COLLECTION__", - "prinseq", "mgnify_seqprep", - "fastp", - "trimmomatic", - "fastq_filter" + "fastq_filter", + "prinseq", + "fastq_to_fasta_python" ], "update_time": "2025-08-11", "versions": 1 @@ -893,11 +993,11 @@ ], "tools": [ "", - "fastq_dl", - "CONVERTER_uncompressed_to_gz", "tp_awk_tool", + "CONVERTER_uncompressed_to_gz", "CONVERTER_gz_to_uncompressed", - "__MERGE_COLLECTION__" + "__MERGE_COLLECTION__", + "fastq_dl" ], "update_time": "2025-08-11", "versions": 1 @@ -929,9 +1029,9 @@ "name:microgalaxy" ], "tools": [ - "Grouping1", - "collection_column_join", "tp_awk_tool", + "collection_column_join", + "Grouping1", "filter_tabular", "query_tabular" ], @@ -944,13 +1044,13 @@ "deprecated": false, "doi": null, "edam_operation": [ - "Sequence trimming", - "Read pre-processing", - "Sequence composition calculation", - "Sequence contamination filtering", + "Sequencing quality control", "Statistical calculation", + "Sequence contamination filtering", + "Sequence trimming", "Validation", - "Sequencing quality control" + "Read pre-processing", + "Sequence composition calculation" ], "edam_topic": [], "id": "1850", @@ -975,12 +1075,12 @@ "tools": [ "cshl_fasta_formatter", "tp_find_and_replace", - "fastq_to_fasta_python", "multiqc", + "trimmomatic", "fastqc", + "fastq_filter", "prinseq", - "trimmomatic", - "fastq_filter" + "fastq_to_fasta_python" ], "update_time": "2025-08-11", "versions": 1 @@ -991,13 +1091,13 @@ "deprecated": false, "doi": null, "edam_operation": [ - "Visualisation", - "Alignment", - "Formatting", - "Mapping", "k-mer counting", + "Formatting", "Comparison", - "Nucleic acid feature detection" + "Mapping", + "Alignment", + "Nucleic acid feature detection", + "Visualisation" ], "edam_topic": [], "id": "1842", @@ -1021,19 +1121,19 @@ ], "tools": [ "", - "bedtools_getfastabed", - "tp_awk_tool", "cshl_fasta_formatter", - "__FILTER_FROM_FILE__", - "infernal_cmsearch", + "tp_awk_tool", "mapseq", "collection_element_identifiers", + "__FILTER_FROM_FILE__", "taxonomy_krona_chart", - "cmsearch_deoverlap", "biom_convert", + "cmsearch_deoverlap", + "infernal_cmsearch", + "bedtools_getfastabed", "gops_concat_1", - "__FILTER_EMPTY_DATASETS__", - "query_tabular" + "query_tabular", + "__FILTER_EMPTY_DATASETS__" ], "update_time": "2025-08-11", "versions": 1 @@ -1044,8 +1144,8 @@ "deprecated": false, "doi": null, "edam_operation": [ - "Species frequency estimation", "Taxonomic classification", + "Species frequency estimation", "Phylogenetic analysis" ], "edam_topic": [], @@ -1067,15 +1167,15 @@ "metagenomics" ], "tools": [ - "Grep1", "humann_rename_table", + "humann_regroup_table", "tp_find_and_replace", "combine_metaphlan2_humann2", - "Cut1", - "humann_renorm_table", - "humann_regroup_table", "humann_unpack_pathways", - "humann_split_stratified_table" + "humann_split_stratified_table", + "humann_renorm_table", + "Grep1", + "Cut1" ], "update_time": "2025-07-14", "versions": 2 @@ -1086,11 +1186,11 @@ "deprecated": false, "doi": null, "edam_operation": [ - "Visualisation", "DNA barcoding", - "Deposition", "Analysis", - "Variant calling" + "Variant calling", + "Deposition", + "Visualisation" ], "edam_topic": [], "id": "1395", @@ -1110,24 +1210,24 @@ "microbiome" ], "tools": [ - "dada2_filterAndTrim", + "dada2_dada", + "Add_a_column1", + "dada2_makeSequenceTable", + "dada2_plotQualityProfile", + "collection_element_identifiers", + "__SORTLIST__", "dada2_learnErrors", + "tp_replace_in_line", + "dada2_seqCounts", "dada2_assignTaxonomyAddspecies", + "cat1", + "dada2_filterAndTrim", + "__UNZIP_COLLECTION__", "tp_replace_in_column", - "collection_element_identifiers", "phyloseq_from_dada2", - "dada2_makeSequenceTable", - "dada2_seqCounts", - "tp_replace_in_line", - "__UNZIP_COLLECTION__", - "dada2_dada", - "dada2_mergePairs", - "dada2_removeBimeraDenovo", - "cat1", - "Add_a_column1", "tp_head_tool", - "dada2_plotQualityProfile", - "__SORTLIST__" + "dada2_removeBimeraDenovo", + "dada2_mergePairs" ], "update_time": "2025-07-07", "versions": 2 @@ -1138,25 +1238,25 @@ "deprecated": false, "doi": null, "edam_operation": [ - "Sequence comparison", - "Phylogenetic tree visualisation", - "Visualisation", - "Sequence composition calculation", "Statistical calculation", "Phylogenetic inference", - "Validation", - "Primer removal", - "Sequence alignment analysis", + "Conversion", "Sequencing quality control", + "Sequence alignment analysis", + "Sequence comparison", + "Sequence composition calculation", "Phylogenetic analysis", - "Sequence trimming", - "Phylogenetic tree editing", - "Read pre-processing", - "Species frequency estimation", "Taxonomic classification", + "Aggregation", + "Species frequency estimation", + "Phylogenetic tree visualisation", "Sequence similarity search", - "Conversion", - "Aggregation" + "Phylogenetic tree editing", + "Sequence trimming", + "Validation", + "Read pre-processing", + "Primer removal", + "Visualisation" ], "edam_topic": [], "id": "1466", @@ -1176,28 +1276,28 @@ "microbiome" ], "tools": [ - "Grouping1", - "metaphlan", - "fastqc", - "tp_sort_header_tool", - "humann", - "humann_unpack_pathways", - "graphlan", - "Grep1", - "humann_rename_table", - "tp_find_and_replace", - "combine_metaphlan_humann", - "Cut1", + "graphlan_annotate", "bg_sortmerna", - "fastq_paired_end_interlacer", - "humann_split_stratified_table", - "multiqc", "cutadapt", "taxonomy_krona_chart", - "graphlan_annotate", - "humann_renorm_table", + "tp_find_and_replace", + "export2graphlan", + "humann_split_stratified_table", + "metaphlan", "humann_regroup_table", - "export2graphlan" + "fastq_paired_end_interlacer", + "Grouping1", + "humann_renorm_table", + "Grep1", + "graphlan", + "humann", + "tp_sort_header_tool", + "humann_rename_table", + "multiqc", + "fastqc", + "humann_unpack_pathways", + "combine_metaphlan_humann", + "Cut1" ], "update_time": "2025-06-23", "versions": 2 @@ -1208,12 +1308,12 @@ "deprecated": false, "doi": null, "edam_operation": [ - "Phylogenetic tree visualisation", - "Visualisation", + "Taxonomic classification", "Phylogenetic inference", + "Conversion", + "Phylogenetic tree visualisation", "Phylogenetic tree editing", - "Taxonomic classification", - "Conversion" + "Visualisation" ], "edam_topic": [], "id": "1451", @@ -1233,12 +1333,12 @@ "microbiome" ], "tools": [ - "graphlan", "metaphlan", - "taxonomy_krona_chart", "graphlan_annotate", + "taxonomy_krona_chart", + "export2graphlan", "Cut1", - "export2graphlan" + "graphlan" ], "update_time": "2025-06-23", "versions": 2 @@ -1249,16 +1349,16 @@ "deprecated": false, "doi": null, "edam_operation": [ - "Sequence trimming", - "Sequence composition calculation", "Statistical calculation", - "Validation", - "Primer removal", - "Read pre-processing", "Sequence similarity search", + "Primer removal", + "Sequencing quality control", + "Sequence trimming", "Sequence alignment analysis", "Sequence comparison", - "Sequencing quality control" + "Validation", + "Read pre-processing", + "Sequence composition calculation" ], "edam_topic": [], "id": "1444", @@ -1278,11 +1378,11 @@ "microbiome" ], "tools": [ + "fastq_paired_end_interlacer", "multiqc", "fastqc", - "cutadapt", "bg_sortmerna", - "fastq_paired_end_interlacer" + "cutadapt" ], "update_time": "2025-06-23", "versions": 2 @@ -1293,8 +1393,8 @@ "deprecated": false, "doi": null, "edam_operation": [ - "Species frequency estimation", "Taxonomic classification", + "Species frequency estimation", "Phylogenetic analysis" ], "edam_topic": [], @@ -1315,15 +1415,15 @@ "microbiome" ], "tools": [ - "Grep1", "humann_rename_table", - "humann", - "tp_find_and_replace", - "humann_renorm_table", - "tp_sort_header_tool", "humann_regroup_table", + "tp_find_and_replace", "humann_unpack_pathways", - "humann_split_stratified_table" + "humann_split_stratified_table", + "humann_renorm_table", + "Grep1", + "humann", + "tp_sort_header_tool" ], "update_time": "2025-06-23", "versions": 2 @@ -1335,11 +1435,11 @@ "doi": null, "edam_operation": [ "Visualisation", - "Local alignment", - "Sequence assembly validation", "Read mapping", - "Genome assembly", - "Sequence assembly visualisation" + "Sequence assembly validation", + "Sequence assembly visualisation", + "Local alignment", + "Genome assembly" ], "edam_topic": [], "id": "1390", @@ -1359,15 +1459,15 @@ "microbiome" ], "tools": [ - "collection_column_join", "bowtie2", "megahit_contig2fastg", - "bandage_info", - "bandage_image", + "collection_column_join", "metaspades", - "quast", + "bandage_image", + "bandage_info", + "megahit", "coverm_contig", - "megahit" + "quast" ], "update_time": "2025-06-16", "versions": 2 @@ -1378,8 +1478,8 @@ "deprecated": false, "doi": null, "edam_operation": [ - "Sequence contamination filtering", - "Sequencing quality control" + "Sequencing quality control", + "Sequence contamination filtering" ], "edam_topic": [], "id": "1723", @@ -1399,10 +1499,10 @@ "galaxy" ], "tools": [ - "ncbi_blastn_wrapper", - "Count1", + "fastp", "cshl_fastq_to_fasta", - "fastp" + "ncbi_blastn_wrapper", + "Count1" ], "update_time": "2025-06-02", "versions": 1 @@ -1413,14 +1513,14 @@ "deprecated": false, "doi": null, "edam_operation": [ - "Visualisation", "Statistical calculation", - "Read mapping", - "Cross-assembly", - "Sequence contamination filtering", - "Expression analysis", "Taxonomic classification", - "Sequencing quality control" + "Expression analysis", + "Sequencing quality control", + "Sequence contamination filtering", + "Read mapping", + "Visualisation", + "Cross-assembly" ], "edam_topic": [], "id": "1644", @@ -1440,11 +1540,11 @@ "sequence-analysis" ], "tools": [ - "falco", - "kraken2", - "est_abundance", "fastp", - "recentrifuge" + "recentrifuge", + "est_abundance", + "kraken2", + "falco" ], "update_time": "2025-06-02", "versions": 1 @@ -1455,11 +1555,11 @@ "deprecated": false, "doi": null, "edam_operation": [ - "Local alignment", - "Sequence alignment", - "Global alignment", "Sequence alignment analysis", - "Sequence analysis" + "Global alignment", + "Sequence analysis", + "Sequence alignment", + "Local alignment" ], "edam_topic": [], "id": "1632", @@ -1479,14 +1579,14 @@ "variant-analysis" ], "tools": [ - "Grep1", - "param_value_from_file", + "Add_a_column1", "compose_text_param", "EMBOSS: maskseq51", + "Grep1", "datamash_ops", - "Cut1", "fasta_compute_length", - "Add_a_column1" + "Cut1", + "param_value_from_file" ], "update_time": "2025-06-02", "versions": 1 @@ -1497,16 +1597,16 @@ "deprecated": false, "doi": null, "edam_operation": [ + "Pairwise sequence alignment", "Aggregation", - "Mapping assembly", "Antimicrobial resistance prediction", - "Sequence analysis", "Box-Whisker plot plotting", - "Pairwise sequence alignment", - "Genome assembly", - "Sequence assembly visualisation", + "De-novo assembly", "Scatter plot plotting", - "De-novo assembly" + "Sequence assembly visualisation", + "Sequence analysis", + "Mapping assembly", + "Genome assembly" ], "edam_topic": [], "id": "1477", @@ -1527,14 +1627,14 @@ ], "tools": [ "unicycler", - "racon", - "staramr_search", - "miniasm", - "nanoplot", "bandage_image", + "miniasm", + "staramr_search", "PlasFlow", - "gfa_to_fa", - "minimap2" + "nanoplot", + "minimap2", + "racon", + "gfa_to_fa" ], "update_time": "2025-06-02", "versions": 1 @@ -1545,13 +1645,13 @@ "deprecated": false, "doi": null, "edam_operation": [ - "Visualisation", - "Sequence clustering", - "DNA barcoding", "Taxonomic classification", + "DNA barcoding", "Sequence read processing", "Sequencing quality control", - "Phylogenetic analysis" + "Sequence clustering", + "Phylogenetic analysis", + "Visualisation" ], "edam_topic": [], "id": "1476", @@ -1571,21 +1671,21 @@ "microbiome" ], "tools": [ - "mothur_pre_cluster", - "mothur_make_group", + "mothur_unique_seqs", + "mothur_cluster_split", "mothur_summary_seqs", "mothur_count_seqs", - "mothur_unique_seqs", + "mothur_make_shared", + "mothur_make_biom", "mothur_merge_files", - "mothur_align_seqs", - "mothur_filter_seqs", - "mothur_cluster_split", "mothur_screen_seqs", + "mothur_filter_seqs", + "mothur_make_group", "mothur_classify_seqs", - "mothur_make_shared", - "krona-text", "mothur_classify_otu", - "mothur_make_biom" + "mothur_align_seqs", + "mothur_pre_cluster", + "krona-text" ], "update_time": "2025-06-02", "versions": 1 @@ -1596,13 +1696,13 @@ "deprecated": false, "doi": null, "edam_operation": [ - "Visualisation", - "Sequence composition calculation", + "Sequencing quality control", "Sequence contamination filtering", + "Taxonomic classification", "Statistical calculation", "Validation", - "Taxonomic classification", - "Sequencing quality control" + "Sequence composition calculation", + "Visualisation" ], "edam_topic": [], "id": "1473", @@ -1622,15 +1722,15 @@ "microbiome" ], "tools": [ + "fastp", + "datamash_reverse", + "taxonomy_krona_chart", "multiqc", "kraken2", + "tp_replace_in_line", "fastqc", - "taxonomy_krona_chart", "porechop", - "tp_replace_in_line", - "fastp", - "Remove beginning1", - "datamash_reverse" + "Remove beginning1" ], "update_time": "2025-06-02", "versions": 1 @@ -1661,12 +1761,12 @@ "microbiome" ], "tools": [ - "humann2", - "taxonomy_krona_chart", "metaphlan2krona", + "metaphlan2", "humann2_renorm_table", - "humann2_regroup_table", - "metaphlan2" + "taxonomy_krona_chart", + "humann2", + "humann2_regroup_table" ], "update_time": "2025-06-02", "versions": 1 @@ -1677,8 +1777,8 @@ "deprecated": false, "doi": null, "edam_operation": [ - "Visualisation", - "Pairwise sequence alignment" + "Pairwise sequence alignment", + "Visualisation" ], "edam_topic": [], "id": "1469", @@ -1700,24 +1800,24 @@ "name:microgalaxy" ], "tools": [ - "Grouping1", + "Add_a_column1", "CONVERTER_fasta_to_tabular", "tp_sorted_uniq", - "sort1", - "Filter1", - "MQoutputfilter", - "tp_replace_in_column", "histogram_rpy", - "tp_tail_tool", "join1", + "Grouping1", + "cat1", + "tp_tail_tool", "count_gff_features", + "ggplot2_histogram", + "minimap2", + "add_column_headers", + "tp_replace_in_column", + "Filter1", "tab2fasta", "Cut1", - "cat1", - "add_column_headers", - "Add_a_column1", - "ggplot2_histogram", - "minimap2" + "MQoutputfilter", + "sort1" ], "update_time": "2025-06-02", "versions": 1 @@ -1728,16 +1828,16 @@ "deprecated": false, "doi": null, "edam_operation": [ - "Visualisation", - "Phylogenetic tree reconstruction", - "Sequence clustering", - "Phylogenetic tree generation", - "DNA barcoding", - "Phylogenetic tree analysis", "Taxonomic classification", + "DNA barcoding", "Sequence read processing", "Sequencing quality control", - "Phylogenetic analysis" + "Phylogenetic tree generation", + "Phylogenetic tree reconstruction", + "Sequence clustering", + "Phylogenetic tree analysis", + "Phylogenetic analysis", + "Visualisation" ], "edam_topic": [], "id": "1465", @@ -1757,39 +1857,39 @@ "microbiome" ], "tools": [ - "mothur_pre_cluster", - "mothur_make_contigs", "mothur_count_seqs", - "mothur_cluster", - "mothur_unique_seqs", - "mothur_venn", - "mothur_classify_seqs", - "mothur_make_shared", - "mothur_make_biom", - "mothur_summary_seqs", - "mothur_cluster_split", "mothur_chimera_vsearch", + "mothur_get_groups", "mothur_screen_seqs", - "mothur_remove_lineage", - "mothur_summary_single", + "mothur_rarefaction_single", + "mothur_align_seqs", + "newick_display", + "mothur_make_shared", + "taxonomy_krona_chart", + "mothur_cluster", "mothur_remove_seqs", - "XY_Plot_1", + "mothur_summary_single", + "mothur_sub_sample", "mothur_remove_groups", - "mothur_taxonomy_to_krona", + "mothur_classify_seqs", + "mothur_seq_error", "mothur_count_groups", - "mothur_align_seqs", - "mothur_filter_seqs", - "mothur_dist_shared", + "mothur_cluster_split", "mothur_tree_shared", + "mothur_summary_seqs", + "mothur_make_contigs", + "mothur_dist_shared", "mothur_dist_seqs", + "XY_Plot_1", + "mothur_filter_seqs", + "mothur_remove_lineage", "mothur_classify_otu", - "mothur_heatmap_sim", - "mothur_rarefaction_single", - "mothur_sub_sample", - "newick_display", - "taxonomy_krona_chart", - "mothur_seq_error", - "mothur_get_groups" + "mothur_pre_cluster", + "mothur_unique_seqs", + "mothur_venn", + "mothur_heatmap_sim", + "mothur_make_biom", + "mothur_taxonomy_to_krona" ], "update_time": "2025-06-02", "versions": 1 @@ -1800,8 +1900,8 @@ "deprecated": false, "doi": null, "edam_operation": [ - "Sequence feature detection", - "DNA barcoding" + "DNA barcoding", + "Sequence feature detection" ], "edam_topic": [], "id": "1460", @@ -1835,13 +1935,13 @@ "deprecated": false, "doi": null, "edam_operation": [ - "Visualisation", - "Sequence composition calculation", + "Sequencing quality control", "Sequence contamination filtering", - "Statistical calculation", "Taxonomic classification", + "Statistical calculation", "Aggregation", - "Sequencing quality control" + "Sequence composition calculation", + "Visualisation" ], "edam_topic": [], "id": "1439", @@ -1861,13 +1961,13 @@ "microbiome" ], "tools": [ - "kraken2", - "Filter1", - "fastqc", + "fastp", "taxonomy_krona_chart", "krakentools_kreport2krona", - "porechop", - "fastp" + "kraken2", + "fastqc", + "Filter1", + "porechop" ], "update_time": "2025-06-02", "versions": 1 @@ -1878,8 +1978,8 @@ "deprecated": false, "doi": null, "edam_operation": [ - "Visualisation", - "Aggregation" + "Aggregation", + "Visualisation" ], "edam_topic": [], "id": "1431", @@ -1911,13 +2011,13 @@ "deprecated": false, "doi": null, "edam_operation": [ - "Visualisation", - "Sequence clustering", - "DNA barcoding", "Taxonomic classification", + "DNA barcoding", "Sequence read processing", "Sequencing quality control", - "Phylogenetic analysis" + "Sequence clustering", + "Phylogenetic analysis", + "Visualisation" ], "edam_topic": [], "id": "1428", @@ -1937,9 +2037,9 @@ "microbiome" ], "tools": [ + "mothur_remove_lineage", "mothur_summary_seqs", - "mothur_classify_seqs", - "mothur_remove_lineage" + "mothur_classify_seqs" ], "update_time": "2025-06-02", "versions": 1 @@ -1950,13 +2050,13 @@ "deprecated": false, "doi": null, "edam_operation": [ - "Visualisation", - "Sequence clustering", - "DNA barcoding", "Taxonomic classification", + "DNA barcoding", "Sequence read processing", "Sequencing quality control", - "Phylogenetic analysis" + "Sequence clustering", + "Phylogenetic analysis", + "Visualisation" ], "edam_topic": [], "id": "1422", @@ -1976,10 +2076,10 @@ "microbiome" ], "tools": [ + "mothur_unique_seqs", "mothur_summary_seqs", "mothur_count_seqs", - "mothur_screen_seqs", - "mothur_unique_seqs" + "mothur_screen_seqs" ], "update_time": "2025-06-02", "versions": 1 @@ -1990,16 +2090,16 @@ "deprecated": false, "doi": null, "edam_operation": [ - "Visualisation", - "Phylogenetic tree reconstruction", - "Sequence clustering", - "Phylogenetic tree generation", - "DNA barcoding", - "Phylogenetic tree analysis", "Taxonomic classification", + "DNA barcoding", "Sequence read processing", "Sequencing quality control", - "Phylogenetic analysis" + "Phylogenetic tree generation", + "Phylogenetic tree reconstruction", + "Sequence clustering", + "Phylogenetic tree analysis", + "Phylogenetic analysis", + "Visualisation" ], "edam_topic": [], "id": "1418", @@ -2019,12 +2119,12 @@ "microbiome" ], "tools": [ + "mothur_tree_shared", + "mothur_venn", "mothur_heatmap_sim", - "newick_display", "mothur_dist_shared", - "mothur_venn", "collapse_dataset", - "mothur_tree_shared" + "newick_display" ], "update_time": "2025-06-02", "versions": 1 @@ -2035,13 +2135,13 @@ "deprecated": false, "doi": null, "edam_operation": [ - "Visualisation", - "Sequence clustering", - "DNA barcoding", "Taxonomic classification", + "DNA barcoding", "Sequence read processing", "Sequencing quality control", - "Phylogenetic analysis" + "Sequence clustering", + "Phylogenetic analysis", + "Visualisation" ], "edam_topic": [], "id": "1412", @@ -2074,13 +2174,13 @@ "deprecated": false, "doi": null, "edam_operation": [ - "Visualisation", - "Sequence clustering", - "DNA barcoding", "Taxonomic classification", + "DNA barcoding", "Sequence read processing", "Sequencing quality control", - "Phylogenetic analysis" + "Sequence clustering", + "Phylogenetic analysis", + "Visualisation" ], "edam_topic": [], "id": "1408", @@ -2100,10 +2200,10 @@ "microbiome" ], "tools": [ - "mothur_rarefaction_single", + "mothur_cluster", "mothur_dist_seqs", "mothur_make_shared", - "mothur_cluster" + "mothur_rarefaction_single" ], "update_time": "2025-06-02", "versions": 1 @@ -2114,13 +2214,13 @@ "deprecated": false, "doi": null, "edam_operation": [ - "Visualisation", - "Sequence clustering", - "DNA barcoding", "Taxonomic classification", + "DNA barcoding", "Sequence read processing", "Sequencing quality control", - "Phylogenetic analysis" + "Sequence clustering", + "Phylogenetic analysis", + "Visualisation" ], "edam_topic": [], "id": "1404", @@ -2140,12 +2240,12 @@ "microbiome" ], "tools": [ - "mothur_remove_groups", - "mothur_sub_sample", - "mothur_count_groups", "mothur_cluster_split", "mothur_make_shared", - "mothur_classify_otu" + "mothur_sub_sample", + "mothur_remove_groups", + "mothur_classify_otu", + "mothur_count_groups" ], "update_time": "2025-06-02", "versions": 1 @@ -2156,13 +2256,13 @@ "deprecated": false, "doi": null, "edam_operation": [ - "Visualisation", - "Sequence clustering", - "DNA barcoding", "Taxonomic classification", + "DNA barcoding", "Sequence read processing", "Sequencing quality control", - "Phylogenetic analysis" + "Sequence clustering", + "Phylogenetic analysis", + "Visualisation" ], "edam_topic": [], "id": "1400", @@ -2182,13 +2282,13 @@ "microbiome" ], "tools": [ - "mothur_pre_cluster", - "mothur_summary_seqs", "mothur_unique_seqs", - "mothur_filter_seqs", + "mothur_summary_seqs", "mothur_chimera_vsearch", + "mothur_remove_seqs", "mothur_screen_seqs", - "mothur_remove_seqs" + "mothur_filter_seqs", + "mothur_pre_cluster" ], "update_time": "2025-06-02", "versions": 1 @@ -2220,24 +2320,24 @@ "source": "WorkflowHub", "tags": [], "tools": [ + "tp_cut_tool", + "clair3", + "table_compute", + "samtools_depth", "bcftools_consensus", + "CONVERTER_gz_to_uncompressed", "Paste1", - "samtools_coverage", - "regexColumn1", "bcftools_norm", - "CONVERTER_gz_to_uncompressed", - "snpSift_filter", - "tp_cut_tool", "Cut1", "snpSift_extractFields", - "clair3", + "samtools_coverage", + "snpSift_filter", "collapse_dataset", - "Remove beginning1", - "table_compute", - "tp_head_tool", + "minimap2", "Count1", - "samtools_depth", - "minimap2" + "tp_head_tool", + "Remove beginning1", + "regexColumn1" ], "update_time": "2026-05-14", "versions": 5 @@ -2266,11 +2366,11 @@ "tags": [], "tools": [ "", - "fastq_dl", - "CONVERTER_uncompressed_to_gz", "tp_awk_tool", + "CONVERTER_uncompressed_to_gz", "CONVERTER_gz_to_uncompressed", - "__MERGE_COLLECTION__" + "__MERGE_COLLECTION__", + "fastq_dl" ], "update_time": "2026-05-14", "versions": 2 @@ -2285,8 +2385,8 @@ "doi": null, "edam_operation": [ "k-mer counting", - "Visualisation", "Formatting", + "Visualisation", "Mapping" ], "edam_topic": [], @@ -2304,10 +2404,10 @@ "tags": [], "tools": [ "", - "tp_awk_tool", - "__FILTER_FROM_FILE__", "bedtools_maskfastabed", "mapseq", + "tp_awk_tool", + "__FILTER_FROM_FILE__", "collection_element_identifiers", "taxonomy_krona_chart", "biom_convert", @@ -2325,14 +2425,14 @@ "deprecated": false, "doi": null, "edam_operation": [ - "Sequence trimming", - "Sequence composition calculation", - "Nucleic acid design", "Statistical calculation", + "Sequencing quality control", + "Sequence contamination filtering", + "Sequence trimming", "Validation", + "Nucleic acid design", "Read pre-processing", - "Sequence contamination filtering", - "Sequencing quality control" + "Sequence composition calculation" ], "edam_topic": [], "id": "1272", @@ -2348,17 +2448,17 @@ "source": "WorkflowHub", "tags": [], "tools": [ + "fastp", "cshl_fasta_formatter", "tp_find_and_replace", - "fastq_to_fasta_python", "multiqc", + "trimmomatic", "fastqc", "__UNZIP_COLLECTION__", - "prinseq", "mgnify_seqprep", - "fastp", - "trimmomatic", - "fastq_filter" + "fastq_filter", + "prinseq", + "fastq_to_fasta_python" ], "update_time": "2026-05-14", "versions": 2 @@ -2372,13 +2472,13 @@ "deprecated": false, "doi": null, "edam_operation": [ - "Sequence trimming", - "Read pre-processing", - "Sequence composition calculation", - "Sequence contamination filtering", + "Sequencing quality control", "Statistical calculation", + "Sequence contamination filtering", + "Sequence trimming", "Validation", - "Sequencing quality control" + "Read pre-processing", + "Sequence composition calculation" ], "edam_topic": [], "id": "1271", @@ -2396,12 +2496,12 @@ "tools": [ "cshl_fasta_formatter", "tp_find_and_replace", - "fastq_to_fasta_python", "multiqc", + "trimmomatic", "fastqc", + "fastq_filter", "prinseq", - "trimmomatic", - "fastq_filter" + "fastq_to_fasta_python" ], "update_time": "2026-05-14", "versions": 3 @@ -2415,13 +2515,13 @@ "deprecated": false, "doi": null, "edam_operation": [ - "Visualisation", - "Alignment", - "Formatting", - "Mapping", "k-mer counting", + "Formatting", "Comparison", - "Nucleic acid feature detection" + "Mapping", + "Alignment", + "Nucleic acid feature detection", + "Visualisation" ], "edam_topic": [], "id": "1270", @@ -2438,19 +2538,19 @@ "tags": [], "tools": [ "", - "bedtools_getfastabed", - "tp_awk_tool", "cshl_fasta_formatter", - "__FILTER_FROM_FILE__", - "infernal_cmsearch", + "tp_awk_tool", "mapseq", "collection_element_identifiers", + "__FILTER_FROM_FILE__", "taxonomy_krona_chart", - "cmsearch_deoverlap", "biom_convert", + "cmsearch_deoverlap", + "infernal_cmsearch", + "bedtools_getfastabed", "gops_concat_1", - "__FILTER_EMPTY_DATASETS__", - "query_tabular" + "query_tabular", + "__FILTER_EMPTY_DATASETS__" ], "update_time": "2026-05-14", "versions": 2 @@ -2477,9 +2577,9 @@ "source": "WorkflowHub", "tags": [], "tools": [ - "Grouping1", - "collection_column_join", "tp_awk_tool", + "collection_column_join", + "Grouping1", "filter_tabular", "query_tabular" ], @@ -2494,16 +2594,16 @@ "deprecated": false, "doi": null, "edam_operation": [ - "Visualisation", - "Filtering", - "Formatting", "Statistical calculation", "Imputation", - "Standardisation and normalisation", + "Formatting", "Heat map generation", + "Filtering", + "Standardisation and normalisation", "Protein quantification", + "Clustering", "Principal component plotting", - "Clustering" + "Visualisation" ], "edam_topic": [], "id": "1225", @@ -2519,23 +2619,23 @@ "source": "WorkflowHub", "tags": [], "tools": [ + "query_tabular", + "peptide_shaker", + "Remove beginning1", + "tp_cat", + "search_gui", "Grouping1", - "Grep1", - "fasta2tab", - "fasta_merge_files_and_filter_unique_sequences", - "Filter1", + "fasta_cli", "ident_params", - "Remove beginning1", + "maxquant", "msconvert", - "Cut1", - "query_tabular", "dbbuilder", - "fasta_cli", + "Grep1", "filter_tabular", - "tp_cat", - "search_gui", - "peptide_shaker", - "maxquant" + "Filter1", + "fasta_merge_files_and_filter_unique_sequences", + "Cut1", + "fasta2tab" ], "update_time": "2026-05-13", "versions": 1 @@ -2549,10 +2649,10 @@ "deprecated": false, "doi": "10.48546/workflowhub.workflow.1199.2", "edam_operation": [ - "Visualisation", "Statistical calculation", "Taxonomic classification", - "Aggregation" + "Aggregation", + "Visualisation" ], "edam_topic": [ "Metagenomics", @@ -2576,24 +2676,24 @@ "shotgun" ], "tools": [ + "__RELABEL_FROM_FILE__", "collection_column_join", - "krakentools_beta_diversity", + "cat_multiple", "Prepare alpha diversity summary file\nPaste1", - "Prepare alpha diversity summary file (paste Simpson and Fisher results)\nPaste1", - "kraken2", - "Prepare alpha diversity summary file (paste sample identifiers and Simpson results)\nPaste1", - "taxonomy_krona_chart", "collection_element_identifiers", + "krakentools_combine_kreports", "krakentools_kreport2krona", - "Fisher results contains a header line we want to exclude \"Fisher's alpha...loading\"\nShow tail1", + "krakentools_beta_diversity", "est_abundance", - "__RELABEL_FROM_FILE__", + "taxonomy_krona_chart", + "kraken2", + "Prepare alpha diversity summary file (paste sample identifiers and Simpson results)\nPaste1", + "Prepare alpha diversity summary file (paste Simpson and Fisher results)\nPaste1", "add_line_to_file", - "regex1", "krakentools_alpha_diversity", - "cat_multiple", + "regex1", "Extract column name and fraction_total_reads from Bracken report\nCut1", - "krakentools_combine_kreports" + "Fisher results contains a header line we want to exclude \"Fisher's alpha...loading\"\nShow tail1" ], "update_time": "2024-12-10", "versions": 2 @@ -2606,8 +2706,8 @@ "deprecated": false, "doi": null, "edam_operation": [ - "Visualisation", - "Prediction and recognition" + "Prediction and recognition", + "Visualisation" ], "edam_topic": [], "id": "1219", @@ -2623,8 +2723,8 @@ "source": "WorkflowHub", "tags": [], "tools": [ - "Grep1", "msstatstmt", + "Grep1", "unipept" ], "update_time": "2026-05-13", @@ -2652,17 +2752,17 @@ "source": "WorkflowHub", "tags": [], "tools": [ - "Grouping1", - "fasta_merge_files_and_filter_unique_sequences", "Filter1", "uniprotxml_downloader", + "Grouping1", "Cut1", - "pepquery2", - "tp_cat", - "dbbuilder", - "Remove beginning1", "collapse_dataset", - "query_tabular" + "dbbuilder", + "query_tabular", + "tp_cat", + "fasta_merge_files_and_filter_unique_sequences", + "Remove beginning1", + "pepquery2" ], "update_time": "2026-05-13", "versions": 1 @@ -2675,11 +2775,11 @@ "deprecated": false, "doi": null, "edam_operation": [ + "de Novo sequencing", + "Target-Decoy", "Expression analysis", - "Protein identification", "Tag-based peptide identification", - "de Novo sequencing", - "Target-Decoy" + "Protein identification" ], "edam_topic": [], "id": "1216", @@ -2711,10 +2811,10 @@ "deprecated": false, "doi": null, "edam_operation": [ - "Parsing", + "Antimicrobial resistance prediction", "Data handling", - "Genome assembly", - "Antimicrobial resistance prediction" + "Parsing", + "Genome assembly" ], "edam_topic": [], "id": "1189", @@ -2736,24 +2836,24 @@ ], "tools": [ "", - "hamronize_summarize", - "tp_text_file_with_recurring_lines", - "cat1", - "hamronize_tool", - "abricate", - "addValue", - "__APPLY_RULES__", - "__MERGE_COLLECTION__", - "collapse_dataset", + "cat_multi_datasets", "shovill", - "Grep1", - "cast", - "tp_find_and_replace", - "Cut1", "tp_split_on_column", - "datamash_ops", "staramr_search", - "cat_multi_datasets" + "collapse_dataset", + "datamash_ops", + "abricate", + "hamronize_tool", + "tp_find_and_replace", + "cat1", + "tp_text_file_with_recurring_lines", + "cast", + "__APPLY_RULES__", + "addValue", + "Grep1", + "hamronize_summarize", + "__MERGE_COLLECTION__", + "Cut1" ], "update_time": "2026-05-13", "versions": 2 @@ -2766,14 +2866,14 @@ "deprecated": false, "doi": null, "edam_operation": [ - "Visualisation", "Statistical calculation", "Imputation", - "Standardisation and normalisation", "Heat map generation", + "Standardisation and normalisation", "Protein quantification", + "Clustering", "Principal component plotting", - "Clustering" + "Visualisation" ], "edam_topic": [], "id": "1177", @@ -2789,13 +2889,13 @@ "source": "WorkflowHub", "tags": [], "tools": [ - "maxquant", - "Quantified-Proteins\nGrouping1", + "extracting microbial Proteins\nGrep1", "extract proteins\nCut1", - "extract peptides\nCut1", "Quantified-Peptides\nGrouping1", - "extracting microbial Proteins\nGrep1", - "extracting microbial Peptides\nGrep1" + "extracting microbial Peptides\nGrep1", + "Quantified-Proteins\nGrouping1", + "maxquant", + "extract peptides\nCut1" ], "update_time": "2026-05-14", "versions": 1 @@ -2811,8 +2911,8 @@ "doi": null, "edam_operation": [ "Data parsing", - "Genome assembly", - "Sequence assembly visualisation" + "Sequence assembly visualisation", + "Genome assembly" ], "edam_topic": [], "id": "1043", @@ -2836,11 +2936,11 @@ "quality" ], "tools": [ - "bandage_info", - "bandage_image", - "tooldistillator", "tooldistillator_summarize", - "shovill" + "shovill", + "bandage_image", + "bandage_info", + "tooldistillator" ], "update_time": "2026-05-13", "versions": 12 @@ -2855,13 +2955,13 @@ "deprecated": false, "doi": null, "edam_operation": [ - "Cross-assembly", - "Data parsing", + "Sequencing quality control", "Sequence contamination filtering", + "Data parsing", + "Taxonomic classification", "Expression analysis", "Statistical calculation", - "Taxonomic classification", - "Sequencing quality control" + "Cross-assembly" ], "edam_topic": [], "id": "1052", @@ -2886,14 +2986,14 @@ "trimming" ], "tools": [ - "kraken2", - "tooldistillator_summarize", - "tooldistillator", - "__UNZIP_COLLECTION__", - "est_abundance", "fastp", + "tooldistillator_summarize", "recentrifuge", - "__ZIP_COLLECTION__" + "__ZIP_COLLECTION__", + "est_abundance", + "kraken2", + "__UNZIP_COLLECTION__", + "tooldistillator" ], "update_time": "2026-05-14", "versions": 11 @@ -2904,22 +3004,22 @@ "deprecated": false, "doi": null, "edam_operation": [ - "Visualisation", - "Multilocus sequence typing", - "Sequence alignment", - "Genome indexing", - "Read mapping", + "Genome alignment", + "Read binning", "Sequence contamination filtering", "Clustering", - "Genome alignment", - "Parsing", + "Antimicrobial resistance prediction", "Data handling", - "Genome assembly", + "Sequence alignment", + "Parsing", + "Genome indexing", "RNA-Seq analysis", "Sequence trimming", - "Antimicrobial resistance prediction", - "Read binning", - "Sequence analysis" + "Sequence analysis", + "Read mapping", + "Multilocus sequence typing", + "Visualisation", + "Genome assembly" ], "edam_topic": [], "id": "407", @@ -2938,17 +3038,17 @@ "antimicrobial resistance" ], "tools": [ - "kma_map", - "hamronize_summarize", "seqsero2", - "bbtools_bbduk", - "__UNZIP_COLLECTION__", - "srst2", "shovill", - "mob_recon", + "bbtools_tadpole", "hamronize_tool", + "bbtools_bbduk", "sistr_cmd", - "bbtools_tadpole" + "mob_recon", + "kma_map", + "__UNZIP_COLLECTION__", + "hamronize_summarize", + "srst2" ], "update_time": "2026-05-13", "versions": 1 @@ -2984,10 +3084,10 @@ "deprecated": false, "doi": null, "edam_operation": [ - "Parsing", + "Antimicrobial resistance prediction", "Data handling", - "Genome assembly", - "Antimicrobial resistance prediction" + "Parsing", + "Genome assembly" ], "edam_topic": [], "id": "470", @@ -3009,13 +3109,13 @@ "antimicrobial resistance" ], "tools": [ - "hamronize_summarize", - "tp_find_and_replace", "abricate", + "shovill", + "hamronize_tool", + "tp_find_and_replace", "staramr_search", "collapse_dataset", - "shovill", - "hamronize_tool" + "hamronize_summarize" ], "update_time": "2026-05-13", "versions": 1 @@ -3069,9 +3169,9 @@ "source": "WorkflowHub", "tags": [], "tools": [ - "Phylogenetic tree for diversity analysis", + "Rarefaction", "Taxonomic analysis", - "Rarefaction" + "Phylogenetic tree for diversity analysis" ], "update_time": "2026-05-14", "versions": 2 @@ -3086,15 +3186,15 @@ "deprecated": false, "doi": "10.48546/workflowhub.workflow.1062.1", "edam_operation": [ - "Antimicrobial resistance prediction", "Base-calling", + "Antimicrobial resistance prediction", + "De-novo assembly", "Variant calling", + "Sequence assembly visualisation", + "Sequence assembly", "Cross-assembly", "Mapping assembly", - "Sequence assembly", - "Genome assembly", - "Sequence assembly visualisation", - "De-novo assembly" + "Genome assembly" ], "edam_topic": [], "id": "1062", @@ -3110,18 +3210,18 @@ "source": "WorkflowHub", "tags": [], "tools": [ - "medaka_consensus_pipeline", - "param_value_from_file", - "compose_text_param", - "__BUILD_LIST__", - "tp_find_and_replace", "abricate", "collection_element_identifiers", "bandage_image", - "split_file_to_collection", "flye", - "fasta2tab", - "tab2fasta" + "tp_find_and_replace", + "split_file_to_collection", + "compose_text_param", + "__BUILD_LIST__", + "tab2fasta", + "medaka_consensus_pipeline", + "param_value_from_file", + "fasta2tab" ], "update_time": "2026-05-13", "versions": 1 @@ -3136,14 +3236,12 @@ "deprecated": false, "doi": "10.48546/workflowhub.workflow.1060.1", "edam_operation": [ - "Phylogenetic tree generation (from molecular sequences)", + "Phylogenetic tree generation", "Visualisation", - "Phylogenetic tree generation (maximum likelihood and Bayesian methods)", "Multiple sequence alignment", - "Mapping", "Phylogenetic tree reconstruction", "Phylogenetic tree analysis", - "Phylogenetic tree generation" + "Mapping" ], "edam_topic": [], "id": "1060", @@ -3159,28 +3257,28 @@ "source": "WorkflowHub", "tags": [], "tools": [ - "Grouping1", + "tp_split_on_column", + "ggplot2_heatmap", + "bedtools_getfastabed", + "collapse_dataset", + "regex1", + "tp_replace_in_column", + "fasta_merge_files_and_filter_unique_sequences", + "newick_display", "regexColumn1", - "clustalw", - "__FILTER_FAILED_DATASETS__", + "tp_multijoin_tool", + "Count1", + "__FILTER_EMPTY_DATASETS__", "fasta2tab", "tp_sorted_uniq", - "fasta_merge_files_and_filter_unique_sequences", - "collapse_dataset", - "__FILTER_EMPTY_DATASETS__", - "bedtools_getfastabed", - "tp_multijoin_tool", - "ggplot2_heatmap", - "Cut1", - "Remove beginning1", + "Grouping1", "fasttree", - "tp_split_on_column", + "tab2fasta", + "Remove beginning1", "collection_column_join", - "tp_replace_in_column", - "newick_display", - "regex1", - "Count1", - "tab2fasta" + "clustalw", + "__FILTER_FAILED_DATASETS__", + "Cut1" ], "update_time": "2026-05-13", "versions": 1 @@ -3195,9 +3293,9 @@ "deprecated": false, "doi": "10.48546/workflowhub.workflow.1059.1", "edam_operation": [ - "Visualisation", "Taxonomic classification", - "Aggregation" + "Aggregation", + "Visualisation" ], "edam_topic": [], "id": "1059", @@ -3213,9 +3311,9 @@ "source": "WorkflowHub", "tags": [], "tools": [ + "krakentools_kreport2krona", "kraken2", - "taxonomy_krona_chart", - "krakentools_kreport2krona" + "taxonomy_krona_chart" ], "update_time": "2026-05-13", "versions": 1 @@ -3231,14 +3329,14 @@ "doi": null, "edam_operation": [ "Scaffolding", - "Multilocus sequence typing", - "Structural variation detection", - "Sequence motif recognition", "Genome annotation", + "Nucleic acid feature detection", "Data parsing", - "Genome assembly", "Protein feature detection", - "Nucleic acid feature detection" + "Structural variation detection", + "Sequence motif recognition", + "Multilocus sequence typing", + "Genome assembly" ], "edam_topic": [], "id": "1050", @@ -3261,12 +3359,12 @@ "genome-annotation" ], "tools": [ + "tooldistillator_summarize", + "integron_finder", + "plasmidfinder", "isescan", "bakta", - "integron_finder", - "tooldistillator_summarize", - "tooldistillator", - "plasmidfinder" + "tooldistillator" ], "update_time": "2026-05-13", "versions": 13 @@ -3308,10 +3406,10 @@ "fasta" ], "tools": [ + "tooldistillator_summarize", "abricate", "amrfinderplus", "staramr_search", - "tooldistillator_summarize", "tooldistillator" ], "update_time": "2026-05-13", @@ -3325,19 +3423,19 @@ "deprecated": false, "doi": null, "edam_operation": [ - "Phylogenetic tree visualisation", - "Sequence alignment", - "Validation", + "Taxonomic classification", "Antimicrobial resistance prediction", - "Phylogenetic tree generation", "Variant calling", - "Sequence analysis", - "Local alignment", + "Sequence alignment", + "Phylogenetic tree visualisation", + "Sequencing quality control", "Sequence contamination filtering", - "Global alignment", "Sequence alignment analysis", - "Taxonomic classification", - "Sequencing quality control" + "Phylogenetic tree generation", + "Validation", + "Global alignment", + "Sequence analysis", + "Local alignment" ], "edam_topic": [ "Genetic variation", @@ -3362,20 +3460,20 @@ "tuberculosis" ], "tools": [ - "bcftools_consensus", + "fastp", "tp_awk_tool", - "tb_profiler_profile", + "qualimap_bamqc", + "EMBOSS: seqret84", "kraken2", - "__FLATTEN__", - "multiqc", "mosdepth", + "__FLATTEN__", + "tp_sed_tool", "snippy", - "qualimap_bamqc", + "multiqc", + "bcftools_consensus", "tb_variant_filter", - "tbvcfreport", - "fastp", - "tp_sed_tool", - "EMBOSS: seqret84" + "tb_profiler_profile", + "tbvcfreport" ], "update_time": "2026-05-13", "versions": 1 @@ -3407,17 +3505,17 @@ "name:amplicon" ], "tools": [ - "dada2_filterAndTrim", + "dada2_dada", + "dada2_makeSequenceTable", + "__APPLY_RULES__", + "dada2_plotQualityProfile", "dada2_learnErrors", "dada2_assignTaxonomyAddspecies", - "dada2_makeSequenceTable", "dada2_seqCounts", + "dada2_filterAndTrim", "__UNZIP_COLLECTION__", "dada2_removeBimeraDenovo", - "__APPLY_RULES__", - "dada2_mergePairs", - "dada2_plotQualityProfile", - "dada2_dada" + "dada2_mergePairs" ], "update_time": "2026-05-14", "versions": 3 @@ -3448,11 +3546,11 @@ "genome-annotation" ], "tools": [ - "jbrowse", - "iframe", "create_or_update", - "list_organism", - "create_account" + "iframe", + "jbrowse", + "create_account", + "list_organism" ], "update_time": "2025-11-04", "versions": 1 @@ -3468,8 +3566,8 @@ "deprecated": false, "doi": "10.48546/workflowhub.workflow.624.1", "edam_operation": [ - "Visualisation", - "Taxonomic classification" + "Taxonomic classification", + "Visualisation" ], "edam_topic": [ "Metagenomic sequencing", @@ -3493,14 +3591,14 @@ ], "tools": [ "", - "humann2", - "taxonomy_krona_chart", "metaphlan2krona", + "metaphlan2", + "taxonomy_krona_chart", "humann2_renorm_table", - "humann2_regroup_table", - "Cut1", "merge_metaphlan_tables", - "metaphlan2" + "humann2", + "humann2_regroup_table", + "Cut1" ], "update_time": "2026-05-13", "versions": 1 @@ -3516,16 +3614,16 @@ "deprecated": false, "doi": null, "edam_operation": [ - "Visualisation", - "Phylogenetic tree reconstruction", - "Sequence clustering", - "Phylogenetic tree generation", - "DNA barcoding", - "Phylogenetic tree analysis", "Taxonomic classification", + "DNA barcoding", "Sequence read processing", "Sequencing quality control", - "Phylogenetic analysis" + "Phylogenetic tree generation", + "Phylogenetic tree reconstruction", + "Sequence clustering", + "Phylogenetic tree analysis", + "Phylogenetic analysis", + "Visualisation" ], "edam_topic": [], "id": "653", @@ -3543,10 +3641,10 @@ "metagenomics" ], "tools": [ - "mothur_dist_shared", "mothur_tree_shared", "mothur_heatmap_sim", - "newick_display" + "newick_display", + "mothur_dist_shared" ], "update_time": "2026-05-13", "versions": 1 @@ -3562,13 +3660,13 @@ "deprecated": false, "doi": null, "edam_operation": [ - "Visualisation", - "Sequence clustering", - "DNA barcoding", "Taxonomic classification", + "DNA barcoding", "Sequence read processing", "Sequencing quality control", - "Phylogenetic analysis" + "Sequence clustering", + "Phylogenetic analysis", + "Visualisation" ], "edam_topic": [], "id": "652", @@ -3604,13 +3702,13 @@ "deprecated": false, "doi": null, "edam_operation": [ - "Visualisation", - "Sequence clustering", - "DNA barcoding", "Taxonomic classification", + "DNA barcoding", "Sequence read processing", "Sequencing quality control", - "Phylogenetic analysis" + "Sequence clustering", + "Phylogenetic analysis", + "Visualisation" ], "edam_topic": [], "id": "651", @@ -3628,11 +3726,11 @@ "metagenomics" ], "tools": [ - "mothur_sub_sample", - "mothur_count_groups", "mothur_cluster_split", "mothur_make_shared", - "mothur_classify_otu" + "mothur_sub_sample", + "mothur_classify_otu", + "mothur_count_groups" ], "update_time": "2026-05-13", "versions": 1 @@ -3648,13 +3746,13 @@ "deprecated": false, "doi": null, "edam_operation": [ - "Visualisation", - "Sequence clustering", - "DNA barcoding", "Taxonomic classification", + "DNA barcoding", "Sequence read processing", "Sequencing quality control", - "Phylogenetic analysis" + "Sequence clustering", + "Phylogenetic analysis", + "Visualisation" ], "edam_topic": [], "id": "650", @@ -3672,8 +3770,8 @@ "metagenomics" ], "tools": [ - "mothur_classify_seqs", - "mothur_remove_lineage" + "mothur_remove_lineage", + "mothur_classify_seqs" ], "update_time": "2026-05-13", "versions": 1 @@ -3689,13 +3787,13 @@ "deprecated": false, "doi": null, "edam_operation": [ - "Visualisation", - "Sequence clustering", - "DNA barcoding", "Taxonomic classification", + "DNA barcoding", "Sequence read processing", "Sequencing quality control", - "Phylogenetic analysis" + "Sequence clustering", + "Phylogenetic analysis", + "Visualisation" ], "edam_topic": [], "id": "648", @@ -3713,10 +3811,10 @@ "metagenomics" ], "tools": [ + "mothur_unique_seqs", "mothur_summary_seqs", "mothur_count_seqs", - "mothur_screen_seqs", - "mothur_unique_seqs" + "mothur_screen_seqs" ], "update_time": "2026-05-13", "versions": 1 @@ -3732,13 +3830,13 @@ "deprecated": false, "doi": null, "edam_operation": [ - "Visualisation", - "Sequence clustering", - "DNA barcoding", "Taxonomic classification", + "DNA barcoding", "Sequence read processing", "Sequencing quality control", - "Phylogenetic analysis" + "Sequence clustering", + "Phylogenetic analysis", + "Visualisation" ], "edam_topic": [], "id": "649", @@ -3756,13 +3854,13 @@ "metagenomics" ], "tools": [ - "mothur_pre_cluster", - "mothur_summary_seqs", "mothur_unique_seqs", - "mothur_filter_seqs", + "mothur_summary_seqs", "mothur_chimera_vsearch", + "mothur_remove_seqs", "mothur_screen_seqs", - "mothur_remove_seqs" + "mothur_filter_seqs", + "mothur_pre_cluster" ], "update_time": "2026-05-13", "versions": 1 @@ -3773,9 +3871,9 @@ "deprecated": false, "doi": null, "edam_operation": [ - "Genome assembly", + "Sequencing quality control", "Sequence contamination filtering", - "Sequencing quality control" + "Genome assembly" ], "edam_topic": [], "id": "103", @@ -3807,13 +3905,13 @@ "deprecated": false, "doi": null, "edam_operation": [ - "Read pre-processing", - "Sequence contamination filtering", + "Sequencing quality control", "Formatting", + "Sequence contamination filtering", "Pairwise sequence alignment", - "Genome assembly", - "Sequencing quality control", - "Variant calling" + "Variant calling", + "Read pre-processing", + "Genome assembly" ], "edam_topic": [], "id": "102", @@ -3835,13 +3933,13 @@ "reads_selection" ], "tools": [ - "fasta_merge_files_and_filter_unique_sequences", "ncbi_blastn_wrapper", - "samtools_stats", - "picard_SamToFastq", "shovill", + "picard_SamToFastq", "ngsutils_bam_filter", - "minimap2" + "minimap2", + "samtools_stats", + "fasta_merge_files_and_filter_unique_sequences" ], "update_time": "2026-05-13", "versions": 1 @@ -3855,16 +3953,16 @@ "deprecated": false, "doi": null, "edam_operation": [ + "Pairwise sequence alignment", "Aggregation", - "Mapping assembly", "Antimicrobial resistance prediction", - "Sequence analysis", "Box-Whisker plot plotting", - "Pairwise sequence alignment", - "Genome assembly", - "Sequence assembly visualisation", + "De-novo assembly", "Scatter plot plotting", - "De-novo assembly" + "Sequence assembly visualisation", + "Sequence analysis", + "Mapping assembly", + "Genome assembly" ], "edam_topic": [ "Microbiology" @@ -3885,14 +3983,14 @@ ], "tools": [ "unicycler", - "racon", - "staramr_search", - "miniasm", - "nanoplot", "bandage_image", + "miniasm", + "staramr_search", "PlasFlow", - "gfa_to_fa", - "minimap2" + "nanoplot", + "minimap2", + "racon", + "gfa_to_fa" ], "update_time": "2026-05-13", "versions": 1 @@ -3903,8 +4001,8 @@ "deprecated": false, "doi": null, "edam_operation": [ - "Visualisation", - "Taxonomic classification" + "Taxonomic classification", + "Visualisation" ], "edam_topic": [], "id": "124", @@ -3923,8 +4021,8 @@ "kraken" ], "tools": [ - "kraken2", "Kraken2Tax", + "kraken2", "taxonomy_krona_chart" ], "update_time": "2026-05-13", @@ -3936,8 +4034,8 @@ "deprecated": false, "doi": null, "edam_operation": [ - "Visualisation", - "Taxonomic classification" + "Taxonomic classification", + "Visualisation" ], "edam_topic": [], "id": "101", @@ -3956,8 +4054,8 @@ "kraken" ], "tools": [ - "kraken2", "Kraken2Tax", + "kraken2", "taxonomy_krona_chart" ], "update_time": "2026-05-13", @@ -3971,11 +4069,11 @@ "deprecated": false, "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Sequence assembly validation", "Statistical calculation", + "Sequencing quality control", "Validation", - "Sequencing quality control" + "Sequence composition calculation", + "Sequence assembly validation" ], "edam_topic": [], "id": "f0776f7a890b523a", @@ -3992,91 +4090,149 @@ "name:microgalaxy" ], "tools": [ + "__RELABEL_FROM_FILE__", + "checkm2", + "collection_element_identifiers", "multiqc", "__FLATTEN__", - "collection_element_identifiers", - "__RELABEL_FROM_FILE__", "__MERGE_COLLECTION__", - "regex1", - "checkm2" + "regex1" ], "update_time": "2025-12-08", "versions": 1 }, { - "create_time": "2026-04-27", + "create_time": "2025-12-01", "creators": [], "deprecated": false, "doi": "", "edam_operation": [ - "Visualisation", - "Prediction and recognition" + "Sequencing quality control", + "Sequence contamination filtering", + "Taxonomic classification", + "Statistical calculation", + "Validation", + "Sequence composition calculation", + "Visualisation" ], "edam_topic": [], - "id": "6ca1b4fe047a03d2", + "id": "2a093e63ebf6876b", "keep": true, - "latest_version": 1, + "latest_version": 3, "license": null, - "link": "https://usegalaxy.eu/published/workflow?id=6ca1b4fe047a03d2", - "name": "Copy of Metaproteomics_GTN shared by user engy.nasr", + "link": "https://usegalaxy.eu/published/workflow?id=2a093e63ebf6876b", + "name": "Training: 16S rRNA Analysis with Nanopore Sequencing Reads", "number_of_steps": null, "projects": [], "source": "https://usegalaxy.eu", "tags": [ - "proteomics", + "metagenomics", "name:microgalaxy" ], "tools": [ - "search_gui", - "peptide_shaker", - "sqlite_to_tabular", + "fastp", + "datamash_reverse", + "taxonomy_krona_chart", + "multiqc", + "kraken2", + "tp_replace_in_line", + "fastqc", + "porechop", + "Remove beginning1" + ], + "update_time": "2026-06-12", + "versions": 3 + }, + { + "create_time": "2026-02-10", + "creators": [ + "Subina Mehta" + ], + "deprecated": false, + "doi": "", + "edam_operation": [ + "Statistical calculation", + "Taxonomic classification", + "Genome annotation", + "Sequencing quality control", + "Sequence trimming", + "Sequence assembly", + "Fold recognition", + "Information extraction", + "Homology-based gene prediction", + "Gene prediction", + "Read pre-processing", + "Coding region prediction", + "Primer removal", + "Query and retrieval", + "Sequence composition calculation" + ], + "edam_topic": [], + "id": "7be08f99f83c927e", + "keep": true, + "latest_version": 1, + "license": "CC-BY-4.0", + "link": "https://usegalaxy.eu/published/workflow?id=7be08f99f83c927e", + "name": "Sadowsky_MetaG-DBgen_02102026", + "number_of_steps": null, + "projects": [], + "source": "https://usegalaxy.eu", + "tags": [ + "name:microgalaxy" + ], + "tools": [ + "validate_fasta_database", + "Remove beginning1", + "regexColumn1", + "cat_bins", + "trim_galore", + "fastqc", + "eggnog_mapper", + "collapse_dataset", + "regex1", "query_tabular", - "unipept" + "tp_cat", + "tab2fasta", + "fasta_merge_files_and_filter_unique_sequences", + "maxbin2", + "fasta2tab", + "fraggenescan" ], - "update_time": "2026-04-27", + "update_time": "2026-06-09", "versions": 1 }, { - "create_time": "2025-12-01", + "create_time": "2026-04-27", "creators": [], "deprecated": false, "doi": "", "edam_operation": [ - "Visualisation", - "Sequence composition calculation", - "Sequence contamination filtering", - "Statistical calculation", - "Validation", - "Taxonomic classification", - "Sequencing quality control" + "Prediction and recognition", + "Visualisation" ], "edam_topic": [], - "id": "2a093e63ebf6876b", + "id": "6ca1b4fe047a03d2", "keep": true, - "latest_version": 2, + "latest_version": 1, "license": null, - "link": "https://usegalaxy.eu/published/workflow?id=2a093e63ebf6876b", - "name": "Training: 16S rRNA Analysis with Nanopore Sequencing Reads", + "link": "https://usegalaxy.eu/published/workflow?id=6ca1b4fe047a03d2", + "name": "Copy of Metaproteomics_GTN shared by user engy.nasr", "number_of_steps": null, "projects": [], "source": "https://usegalaxy.eu", "tags": [ - "metagenomics", + "proteomics", "name:microgalaxy" ], "tools": [ - "multiqc", - "kraken2", - "fastqc", - "taxonomy_krona_chart", - "porechop", - "tp_replace_in_line", - "fastp", - "Remove beginning1", - "datamash_reverse" + "peptide_shaker", + "unipept", + "search_gui", + "sqlite_to_tabular", + "query_tabular" ], - "update_time": "2026-03-16", - "versions": 2 + "update_time": "2026-04-27", + "versions": 1 }, { "create_time": "2025-10-01", @@ -4084,32 +4240,32 @@ "deprecated": false, "doi": "", "edam_operation": [ - "Visualisation", - "Sequence composition calculation", - "Formatting", "Statistical calculation", - "Validation", - "Sequence database search", + "Formatting", + "Visualisation", "Format validation", - "Primer removal", - "Coding region prediction", - "Local alignment", - "Sequence assembly", - "Database search", - "Sequence profile generation", + "Conversion", + "Probabilistic sequence generation", "Sequencing quality control", + "Sequence assembly", "Protein feature detection", - "Sequence trimming", - "Multiple sequence alignment", - "Sequence assembly validation", + "Gene prediction", "Sequence motif recognition", + "Coding region prediction", + "Sequence composition calculation", "Sequence generation", + "Database search", + "Sequence database search", + "Data retrieval", + "Taxonomic classification", + "Multiple sequence alignment", + "Sequence assembly validation", + "Sequence trimming", + "Sequence profile generation", + "Validation", "Read pre-processing", - "Data retrieval", - "Gene prediction", - "Taxonomic classification", - "Conversion", - "Probabilistic sequence generation" + "Primer removal", + "Local alignment" ], "edam_topic": [], "id": "8c91345ed468e22d", @@ -4125,22 +4281,22 @@ "name:microgalaxy" ], "tools": [ + "coverm_genome", "fasplit", "tp_awk_tool", "tp_grep_tool", + "sort1", + "cat_bins", + "trim_galore", "fastqc", "checkm_lineage_wf", - "hmmer_hmmscan", - "coverm_genome", - "quast", "coverm_contig", - "fraggenescan", - "maxbin2", - "cat_bins", - "tp_cat", - "trim_galore", + "hmmer_hmmscan", "interproscan", - "sort1" + "tp_cat", + "maxbin2", + "quast", + "fraggenescan" ], "update_time": "2026-02-04", "versions": 0 @@ -4155,13 +4311,13 @@ "deprecated": false, "doi": "", "edam_operation": [ - "Visualisation", - "Formatting", "Statistical calculation", "Taxonomic classification", - "Conversion", + "Standardisation and normalisation", + "Formatting", "Aggregation", - "Standardisation and normalisation" + "Conversion", + "Visualisation" ], "edam_topic": [], "id": "7491883694fff308", @@ -4181,18 +4337,18 @@ ], "tools": [ "metaphlan", - "kraken2", + "metaphlan2krona", "collection_element_identifiers", + "sylph_profile", "taxonomy_krona_chart", - "metaphlan2krona", "krakentools_kreport2krona", - "taxpasta", "est_abundance", - "sylph_profile", + "kraken2", + "cat1", "add_line_to_file", + "taxpasta", "datamash_transpose", - "Remove beginning1", - "cat1" + "Remove beginning1" ], "update_time": "2025-12-17", "versions": 3 @@ -4205,11 +4361,11 @@ "deprecated": false, "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Sequence assembly validation", "Statistical calculation", + "Sequencing quality control", "Validation", - "Sequencing quality control" + "Sequence composition calculation", + "Sequence assembly validation" ], "edam_topic": [], "id": "7371b6918e895e0c", @@ -4226,13 +4382,13 @@ "name:microgalaxy" ], "tools": [ + "__RELABEL_FROM_FILE__", + "checkm2", + "collection_element_identifiers", "multiqc", "__FLATTEN__", - "collection_element_identifiers", - "__RELABEL_FROM_FILE__", "__MERGE_COLLECTION__", - "regex1", - "checkm2" + "regex1" ], "update_time": "2025-12-08", "versions": 16 @@ -4246,19 +4402,19 @@ "deprecated": false, "doi": "", "edam_operation": [ - "Visualisation", - "Sequence feature detection", - "Sequence composition calculation", - "Filtering", - "Formatting", "Statistical calculation", - "Deposition", - "Validation", - "Analysis", - "Standardisation and normalisation", - "Classification", + "Formatting", "DNA barcoding", - "Sequencing quality control" + "Filtering", + "Sequence feature detection", + "Sequencing quality control", + "Standardisation and normalisation", + "Analysis", + "Validation", + "Deposition", + "Sequence composition calculation", + "Visualisation", + "Classification" ], "edam_topic": [], "id": "466bdd8ba7b67264", @@ -4277,34 +4433,34 @@ "name:pallori" ], "tools": [ - "compose_text_param", + "__FLATTEN__", "ampvis2_heatmap", - "fastqc", - "bg_column_arrange_by_header", - "ampvis2_subset_samples", "datamash_transpose", - "unzip", - "biom_convert", - "maaslin2", - "volcanoplot", - "__FLATTEN__", - "calculate_numeric_param", - "mmuphin", - "phyloseq_tax_glom", + "regex1", "ampvis2_load", + "mmuphin", + "maaslin2", + "ampvis2_ordinate", + "unzip", "param_value_from_file", + "phyloseq_from_biom", "tp_awk_tool", + "phyloseq_add_rank_names", + "calculate_numeric_param", + "ampvis2_export_otu", + "bg_column_arrange_by_header", + "volcanoplot", "tp_cut_tool", - "tp_easyjoin_tool", + "biom_convert", "Remove beginning1", + "tp_easyjoin_tool", "multiqc", - "ampvis2_ordinate", - "phyloseq_from_biom", - "phyloseq_add_rank_names", - "ampvis2_export_otu", - "regex1", "lotus2", - "decontam" + "compose_text_param", + "fastqc", + "ampvis2_subset_samples", + "decontam", + "phyloseq_tax_glom" ], "update_time": "2025-11-18", "versions": 193 @@ -4318,15 +4474,15 @@ "deprecated": false, "doi": "", "edam_operation": [ - "Visualisation", - "Formatting", "Statistical calculation", - "Standardisation and normalisation", - "Species frequency estimation", "Taxonomic classification", - "Conversion", + "Formatting", "Aggregation", - "Phylogenetic analysis" + "Species frequency estimation", + "Conversion", + "Standardisation and normalisation", + "Phylogenetic analysis", + "Visualisation" ], "edam_topic": [], "id": "cb2df493f5e334f7", @@ -4345,35 +4501,35 @@ "name:microgalaxy" ], "tools": [ - "metaphlan", - "tp_text_file_with_recurring_lines", - "est_abundance", - "datamash_transpose", - "cat1", - "tp_sed_tool", - "sort1", - "humann", - "kraken2", "collection_element_identifiers", "krakentools_kreport2krona", - "csv_to_tabular", - "collapse_dataset", - "humann_unpack_pathways", - "humann_rename_table", - "tp_awk_tool", "tp_replace_in_line", - "__UNZIP_COLLECTION__", - "add_line_to_file", - "tp_easyjoin_tool", - "Remove beginning1", + "collapse_dataset", + "datamash_transpose", "krakentools_alpha_diversity", - "fastq_paired_end_interlacer", - "collection_column_join", + "tp_awk_tool", + "csv_to_tabular", "taxonomy_krona_chart", + "est_abundance", + "kraken2", + "cat1", + "tp_text_file_with_recurring_lines", "taxpasta", + "metaphlan", + "humann_regroup_table", "sylph_profile", + "fastq_paired_end_interlacer", "humann_renorm_table", - "humann_regroup_table" + "Remove beginning1", + "humann", + "sort1", + "humann_rename_table", + "collection_column_join", + "tp_easyjoin_tool", + "tp_sed_tool", + "humann_unpack_pathways", + "add_line_to_file", + "__UNZIP_COLLECTION__" ], "update_time": "2025-11-13", "versions": 18 @@ -4387,13 +4543,13 @@ "deprecated": false, "doi": "", "edam_operation": [ - "Read summarisation", - "Sequence composition calculation", - "RNA-Seq quantification", + "Sequencing quality control", "Statistical calculation", - "Sequence alignment", "Validation", - "Sequencing quality control" + "Read summarisation", + "Sequence alignment", + "Sequence composition calculation", + "RNA-Seq quantification" ], "edam_topic": [], "id": "ca9d3233b0912765", @@ -4414,14 +4570,14 @@ "name:transcriptomics" ], "tools": [ + "umi_tools_dedup", "collection_column_join", + "umi_tools_extract", "multiqc", "fastqc", - "__FILTER_FAILED_DATASETS__", "featurecounts", - "umi_tools_dedup", - "rna_star", - "umi_tools_extract" + "__FILTER_FAILED_DATASETS__", + "rna_star" ], "update_time": "2025-06-26", "versions": 48 @@ -4442,15 +4598,15 @@ "deprecated": false, "doi": "", "edam_operation": [ - "Sequence composition calculation", "Statistical calculation", - "Validation", - "Read mapping", - "Sequence contamination filtering", "Sequence similarity search", + "Sequencing quality control", + "Sequence contamination filtering", "Sequence alignment analysis", "Sequence comparison", - "Sequencing quality control" + "Validation", + "Read mapping", + "Sequence composition calculation" ], "edam_topic": [], "id": "72e3e5fdc766e24a", @@ -4469,13 +4625,13 @@ "name:preprocessing" ], "tools": [ + "fastp", "bowtie2", "multiqc", "__FLATTEN__", "fastqc", - "__FILTER_FAILED_DATASETS__", - "fastp", - "bg_sortmerna" + "bg_sortmerna", + "__FILTER_FAILED_DATASETS__" ], "update_time": "2025-06-17", "versions": 29 @@ -4489,12 +4645,12 @@ "deprecated": false, "doi": "", "edam_operation": [ - "Phylogenetic tree visualisation", - "Visualisation", + "Taxonomic classification", "Phylogenetic inference", + "Conversion", + "Phylogenetic tree visualisation", "Phylogenetic tree editing", - "Taxonomic classification", - "Conversion" + "Visualisation" ], "edam_topic": [], "id": "05f5f040337786bf", @@ -4513,12 +4669,12 @@ "name:communityprofiling" ], "tools": [ - "graphlan", "metaphlan", - "taxonomy_krona_chart", "graphlan_annotate", + "taxonomy_krona_chart", + "export2graphlan", "Cut1", - "export2graphlan" + "graphlan" ], "update_time": "2025-06-09", "versions": 16 @@ -4539,8 +4695,8 @@ "deprecated": false, "doi": "", "edam_operation": [ - "Species frequency estimation", "Taxonomic classification", + "Species frequency estimation", "Phylogenetic analysis" ], "edam_topic": [], @@ -4560,16 +4716,16 @@ "name:functionalprofiling" ], "tools": [ - "Grep1", "humann_rename_table", - "humann", + "humann_regroup_table", "tp_find_and_replace", "combine_metaphlan2_humann2", - "Cut1", - "humann_renorm_table", - "humann_regroup_table", "humann_unpack_pathways", - "humann_split_stratified_table" + "humann_split_stratified_table", + "humann_renorm_table", + "Grep1", + "Cut1", + "humann" ], "update_time": "2025-06-09", "versions": 6 @@ -4604,24 +4760,24 @@ "name:iwc" ], "tools": [ + "tp_cut_tool", + "clair3", + "table_compute", + "samtools_depth", "bcftools_consensus", + "CONVERTER_gz_to_uncompressed", "Paste1", - "samtools_coverage", - "regexColumn1", "bcftools_norm", - "CONVERTER_gz_to_uncompressed", - "snpSift_filter", - "tp_cut_tool", "Cut1", "snpSift_extractFields", - "clair3", + "samtools_coverage", + "snpSift_filter", "collapse_dataset", - "Remove beginning1", - "table_compute", - "tp_head_tool", + "minimap2", "Count1", - "samtools_depth", - "minimap2" + "tp_head_tool", + "Remove beginning1", + "regexColumn1" ], "update_time": "2025-04-25", "versions": 1 @@ -4656,24 +4812,24 @@ "name:iwc" ], "tools": [ + "tp_cut_tool", + "clair3", + "table_compute", + "samtools_depth", "bcftools_consensus", + "CONVERTER_gz_to_uncompressed", "Paste1", - "samtools_coverage", - "regexColumn1", "bcftools_norm", - "CONVERTER_gz_to_uncompressed", - "snpSift_filter", - "tp_cut_tool", "Cut1", "snpSift_extractFields", - "clair3", + "samtools_coverage", + "snpSift_filter", "collapse_dataset", - "Remove beginning1", - "table_compute", - "tp_head_tool", + "minimap2", "Count1", - "samtools_depth", - "minimap2" + "tp_head_tool", + "Remove beginning1", + "regexColumn1" ], "update_time": "2025-04-25", "versions": 1 @@ -4688,15 +4844,15 @@ "deprecated": false, "doi": "", "edam_operation": [ - "Antimicrobial resistance prediction", "Base-calling", + "Antimicrobial resistance prediction", + "De-novo assembly", "Variant calling", + "Sequence assembly visualisation", + "Sequence assembly", "Cross-assembly", "Mapping assembly", - "Sequence assembly", - "Genome assembly", - "Sequence assembly visualisation", - "De-novo assembly" + "Genome assembly" ], "edam_topic": [], "id": "77e5bbd317750915", @@ -4715,18 +4871,18 @@ "name:microgalaxy" ], "tools": [ - "medaka_consensus_pipeline", - "param_value_from_file", - "compose_text_param", - "__BUILD_LIST__", - "tp_find_and_replace", "abricate", "collection_element_identifiers", "bandage_image", - "split_file_to_collection", "flye", - "fasta2tab", - "tab2fasta" + "tp_find_and_replace", + "split_file_to_collection", + "compose_text_param", + "__BUILD_LIST__", + "tab2fasta", + "medaka_consensus_pipeline", + "param_value_from_file", + "fasta2tab" ], "update_time": "2025-04-25", "versions": 1 @@ -4741,19 +4897,19 @@ "deprecated": false, "doi": "", "edam_operation": [ - "Visualisation", - "Sequence composition calculation", "Statistical calculation", - "Validation", - "Sequence contamination filtering", - "Box-Whisker plot plotting", - "Sequence alignment analysis", "Taxonomic classification", - "Data handling", "Pairwise sequence alignment", + "Box-Whisker plot plotting", "Aggregation", + "Data handling", "Scatter plot plotting", - "Sequencing quality control" + "Sequencing quality control", + "Sequence contamination filtering", + "Sequence alignment analysis", + "Validation", + "Sequence composition calculation", + "Visualisation" ], "edam_topic": [], "id": "344cd3a3c2ce5302", @@ -4773,23 +4929,23 @@ "name:iwc" ], "tools": [ + "Add_a_column1", + "fastp", "collection_column_join", - "Grep1", - "samtools_fastx", - "regexColumn1", "multiqc", "kraken2", + "samtools_fastx", "fastqc", - "bamtools_split_mapped", + "collapse_dataset", "nanoplot", - "porechop", + "minimap2", + "Grep1", "__FILTER_FAILED_DATASETS__", - "krakentools_extract_kraken_reads", - "fastp", - "collapse_dataset", + "bamtools_split_mapped", + "porechop", "Cut1", - "Add_a_column1", - "minimap2" + "regexColumn1", + "krakentools_extract_kraken_reads" ], "update_time": "2025-04-25", "versions": 1 @@ -4804,14 +4960,12 @@ "deprecated": false, "doi": "", "edam_operation": [ - "Phylogenetic tree generation (from molecular sequences)", + "Phylogenetic tree generation", "Visualisation", - "Phylogenetic tree generation (maximum likelihood and Bayesian methods)", "Multiple sequence alignment", - "Mapping", "Phylogenetic tree reconstruction", "Phylogenetic tree analysis", - "Phylogenetic tree generation" + "Mapping" ], "edam_topic": [], "id": "f6a763951d815944", @@ -4830,28 +4984,28 @@ "name:iwc" ], "tools": [ - "Grouping1", + "tp_split_on_column", + "ggplot2_heatmap", + "bedtools_getfastabed", + "collapse_dataset", + "regex1", + "tp_replace_in_column", + "fasta_merge_files_and_filter_unique_sequences", + "newick_display", "regexColumn1", - "clustalw", - "__FILTER_FAILED_DATASETS__", + "tp_multijoin_tool", + "Count1", + "__FILTER_EMPTY_DATASETS__", "fasta2tab", "tp_sorted_uniq", - "fasta_merge_files_and_filter_unique_sequences", - "collapse_dataset", - "__FILTER_EMPTY_DATASETS__", - "bedtools_getfastabed", - "tp_multijoin_tool", - "ggplot2_heatmap", - "Cut1", - "Remove beginning1", + "Grouping1", "fasttree", - "tp_split_on_column", + "tab2fasta", + "Remove beginning1", "collection_column_join", - "tp_replace_in_column", - "newick_display", - "regex1", - "Count1", - "tab2fasta" + "clustalw", + "__FILTER_FAILED_DATASETS__", + "Cut1" ], "update_time": "2025-04-25", "versions": 1 @@ -4866,9 +5020,9 @@ "deprecated": false, "doi": "", "edam_operation": [ - "Visualisation", "Taxonomic classification", - "Aggregation" + "Aggregation", + "Visualisation" ], "edam_topic": [], "id": "ad8b6d73c9654305", @@ -4887,9 +5041,9 @@ "name:iwc" ], "tools": [ + "krakentools_kreport2krona", "kraken2", - "taxonomy_krona_chart", - "krakentools_kreport2krona" + "taxonomy_krona_chart" ], "update_time": "2025-04-25", "versions": 1 @@ -4924,24 +5078,24 @@ "name:iwc" ], "tools": [ + "tp_cut_tool", + "clair3", + "table_compute", + "samtools_depth", "bcftools_consensus", + "CONVERTER_gz_to_uncompressed", "Paste1", - "samtools_coverage", - "regexColumn1", "bcftools_norm", - "CONVERTER_gz_to_uncompressed", - "snpSift_filter", - "tp_cut_tool", "Cut1", "snpSift_extractFields", - "clair3", + "samtools_coverage", + "snpSift_filter", "collapse_dataset", - "Remove beginning1", - "table_compute", - "tp_head_tool", + "minimap2", "Count1", - "samtools_depth", - "minimap2" + "tp_head_tool", + "Remove beginning1", + "regexColumn1" ], "update_time": "2025-04-25", "versions": 1 @@ -4973,11 +5127,11 @@ "name:microgalaxy" ], "tools": [ - "fastq_dl", - "CONVERTER_uncompressed_to_gz", "tp_awk_tool", + "CONVERTER_uncompressed_to_gz", "CONVERTER_gz_to_uncompressed", - "__MERGE_COLLECTION__" + "__MERGE_COLLECTION__", + "fastq_dl" ], "update_time": "2025-04-25", "versions": 1 @@ -4993,8 +5147,8 @@ "doi": "", "edam_operation": [ "k-mer counting", - "Visualisation", "Formatting", + "Visualisation", "Mapping" ], "edam_topic": [], @@ -5014,10 +5168,10 @@ "name:microgalaxy" ], "tools": [ - "tp_awk_tool", - "__FILTER_FROM_FILE__", "bedtools_maskfastabed", "mapseq", + "tp_awk_tool", + "__FILTER_FROM_FILE__", "collection_element_identifiers", "taxonomy_krona_chart", "biom_convert", @@ -5036,14 +5190,14 @@ "deprecated": false, "doi": "", "edam_operation": [ - "Sequence trimming", - "Sequence composition calculation", - "Nucleic acid design", "Statistical calculation", + "Sequencing quality control", + "Sequence contamination filtering", + "Sequence trimming", "Validation", + "Nucleic acid design", "Read pre-processing", - "Sequence contamination filtering", - "Sequencing quality control" + "Sequence composition calculation" ], "edam_topic": [], "id": "0609a4b1941d1a68", @@ -5062,17 +5216,17 @@ "name:microgalaxy" ], "tools": [ + "fastp", "cshl_fasta_formatter", "tp_find_and_replace", - "fastq_to_fasta_python", "multiqc", + "trimmomatic", "fastqc", "__UNZIP_COLLECTION__", - "prinseq", "mgnify_seqprep", - "fastp", - "trimmomatic", - "fastq_filter" + "fastq_filter", + "prinseq", + "fastq_to_fasta_python" ], "update_time": "2025-04-25", "versions": 1 @@ -5087,13 +5241,13 @@ "deprecated": false, "doi": "", "edam_operation": [ - "Sequence trimming", - "Read pre-processing", - "Sequence composition calculation", - "Sequence contamination filtering", + "Sequencing quality control", "Statistical calculation", + "Sequence contamination filtering", + "Sequence trimming", "Validation", - "Sequencing quality control" + "Read pre-processing", + "Sequence composition calculation" ], "edam_topic": [], "id": "d6ff6be33b8bfe85", @@ -5114,12 +5268,12 @@ "tools": [ "cshl_fasta_formatter", "tp_find_and_replace", - "fastq_to_fasta_python", "multiqc", + "trimmomatic", "fastqc", + "fastq_filter", "prinseq", - "trimmomatic", - "fastq_filter" + "fastq_to_fasta_python" ], "update_time": "2025-04-25", "versions": 1 @@ -5134,13 +5288,13 @@ "deprecated": false, "doi": "", "edam_operation": [ - "Sequence trimming", - "Read pre-processing", - "Sequence composition calculation", - "Sequence contamination filtering", + "Sequencing quality control", "Statistical calculation", + "Sequence contamination filtering", + "Sequence trimming", "Validation", - "Sequencing quality control" + "Read pre-processing", + "Sequence composition calculation" ], "edam_topic": [], "id": "76e9cd837ea5e7da", @@ -5161,12 +5315,12 @@ "tools": [ "cshl_fasta_formatter", "tp_find_and_replace", - "fastq_to_fasta_python", "multiqc", + "trimmomatic", "fastqc", + "fastq_filter", "prinseq", - "trimmomatic", - "fastq_filter" + "fastq_to_fasta_python" ], "update_time": "2025-04-25", "versions": 1 @@ -5201,24 +5355,24 @@ "name:iwc" ], "tools": [ + "tp_cut_tool", + "clair3", + "table_compute", + "samtools_depth", "bcftools_consensus", + "CONVERTER_gz_to_uncompressed", "Paste1", - "samtools_coverage", - "regexColumn1", "bcftools_norm", - "CONVERTER_gz_to_uncompressed", - "snpSift_filter", - "tp_cut_tool", "Cut1", "snpSift_extractFields", - "clair3", + "samtools_coverage", + "snpSift_filter", "collapse_dataset", - "Remove beginning1", - "table_compute", - "tp_head_tool", + "minimap2", "Count1", - "samtools_depth", - "minimap2" + "tp_head_tool", + "Remove beginning1", + "regexColumn1" ], "update_time": "2025-04-25", "versions": 1 @@ -5253,24 +5407,24 @@ "name:iwc" ], "tools": [ + "tp_cut_tool", + "clair3", + "table_compute", + "samtools_depth", "bcftools_consensus", + "CONVERTER_gz_to_uncompressed", "Paste1", - "samtools_coverage", - "regexColumn1", "bcftools_norm", - "CONVERTER_gz_to_uncompressed", - "snpSift_filter", - "tp_cut_tool", "Cut1", "snpSift_extractFields", - "clair3", + "samtools_coverage", + "snpSift_filter", "collapse_dataset", - "Remove beginning1", - "table_compute", - "tp_head_tool", + "minimap2", "Count1", - "samtools_depth", - "minimap2" + "tp_head_tool", + "Remove beginning1", + "regexColumn1" ], "update_time": "2025-04-25", "versions": 1 @@ -5302,11 +5456,11 @@ "name:microgalaxy" ], "tools": [ - "fastq_dl", - "CONVERTER_uncompressed_to_gz", "tp_awk_tool", + "CONVERTER_uncompressed_to_gz", "CONVERTER_gz_to_uncompressed", - "__MERGE_COLLECTION__" + "__MERGE_COLLECTION__", + "fastq_dl" ], "update_time": "2025-04-25", "versions": 1 @@ -5322,8 +5476,8 @@ "doi": "", "edam_operation": [ "k-mer counting", - "Visualisation", "Formatting", + "Visualisation", "Mapping" ], "edam_topic": [], @@ -5343,10 +5497,10 @@ "name:microgalaxy" ], "tools": [ - "tp_awk_tool", - "__FILTER_FROM_FILE__", "bedtools_maskfastabed", "mapseq", + "tp_awk_tool", + "__FILTER_FROM_FILE__", "collection_element_identifiers", "taxonomy_krona_chart", "biom_convert", @@ -5365,14 +5519,14 @@ "deprecated": false, "doi": "", "edam_operation": [ - "Sequence trimming", - "Sequence composition calculation", - "Nucleic acid design", "Statistical calculation", + "Sequencing quality control", + "Sequence contamination filtering", + "Sequence trimming", "Validation", + "Nucleic acid design", "Read pre-processing", - "Sequence contamination filtering", - "Sequencing quality control" + "Sequence composition calculation" ], "edam_topic": [], "id": "9fddc44294236e8f", @@ -5391,17 +5545,17 @@ "name:microgalaxy" ], "tools": [ + "fastp", "cshl_fasta_formatter", "tp_find_and_replace", - "fastq_to_fasta_python", "multiqc", + "trimmomatic", "fastqc", "__UNZIP_COLLECTION__", - "prinseq", "mgnify_seqprep", - "fastp", - "trimmomatic", - "fastq_filter" + "fastq_filter", + "prinseq", + "fastq_to_fasta_python" ], "update_time": "2025-04-25", "versions": 1 @@ -5416,13 +5570,13 @@ "deprecated": false, "doi": "", "edam_operation": [ - "Sequence trimming", - "Read pre-processing", - "Sequence composition calculation", - "Sequence contamination filtering", + "Sequencing quality control", "Statistical calculation", + "Sequence contamination filtering", + "Sequence trimming", "Validation", - "Sequencing quality control" + "Read pre-processing", + "Sequence composition calculation" ], "edam_topic": [], "id": "da19c0eaa757fa39", @@ -5443,12 +5597,12 @@ "tools": [ "cshl_fasta_formatter", "tp_find_and_replace", - "fastq_to_fasta_python", "multiqc", + "trimmomatic", "fastqc", + "fastq_filter", "prinseq", - "trimmomatic", - "fastq_filter" + "fastq_to_fasta_python" ], "update_time": "2025-04-25", "versions": 1 @@ -5459,8 +5613,8 @@ "deprecated": false, "doi": "", "edam_operation": [ - "Visualisation", - "Prediction and recognition" + "Prediction and recognition", + "Visualisation" ], "edam_topic": [], "id": "c6b6ba35e5b6500a", @@ -5477,11 +5631,11 @@ "name:microgalaxy" ], "tools": [ - "search_gui", "peptide_shaker", + "unipept", + "search_gui", "sqlite_to_tabular", - "query_tabular", - "unipept" + "query_tabular" ], "update_time": "2025-03-27", "versions": 0 @@ -5495,13 +5649,13 @@ "deprecated": false, "doi": "", "edam_operation": [ - "Antimicrobial resistance prediction", - "Visualisation", - "Sequence composition calculation", + "Sequencing quality control", "Statistical calculation", + "Antimicrobial resistance prediction", "Validation", - "Genome assembly", - "Sequencing quality control" + "Sequence composition calculation", + "Visualisation", + "Genome assembly" ], "edam_topic": [], "id": "4f245ac304ab76d9", @@ -5519,17 +5673,17 @@ "name:wgs" ], "tools": [ - "Grouping1", + "abricate", "collection_column_join", - "regexColumn1", + "shovill", + "ggplot2_heatmap", "multiqc", "__FLATTEN__", + "trimmomatic", "fastqc", - "abricate", - "ggplot2_heatmap", + "Grouping1", "Remove beginning1", - "shovill", - "trimmomatic" + "regexColumn1" ], "update_time": "2025-02-17", "versions": 18 @@ -5544,34 +5698,34 @@ "deprecated": false, "doi": "", "edam_operation": [ - "Visualisation", - "Sequence composition calculation", - "Formatting", "Statistical calculation", + "Formatting", "Gene functional annotation", - "Validation", - "Sequence database search", + "Visualisation", "Format validation", - "Primer removal", - "Coding region prediction", - "Local alignment", + "Conversion", + "Probabilistic sequence generation", + "Sequencing quality control", "Sequence assembly", + "Protein feature detection", + "Gene prediction", + "Sequence motif recognition", + "Coding region prediction", + "Sequence composition calculation", + "Sequence generation", "Database search", - "Sequence profile generation", - "Sequencing quality control", - "Protein feature detection", - "Sequence trimming", + "Sequence database search", + "Data retrieval", + "Taxonomic classification", "Multiple sequence alignment", "Sequence assembly validation", - "Sequence motif recognition", - "Sequence generation", + "Sequence trimming", + "Sequence profile generation", + "Validation", "Sequence analysis", "Read pre-processing", - "Data retrieval", - "Gene prediction", - "Taxonomic classification", - "Conversion", - "Probabilistic sequence generation" + "Primer removal", + "Local alignment" ], "edam_topic": [], "id": "667bac8d7453e5f1", @@ -5589,23 +5743,23 @@ "name:mags" ], "tools": [ + "coverm_genome", "fasplit", "tp_awk_tool", "tp_grep_tool", + "sort1", + "cat_bins", + "trim_galore", "fastqc", "checkm_lineage_wf", - "hmmer_hmmscan", - "coverm_genome", - "quast", + "interproscan", "coverm_contig", - "fraggenescan", - "maxbin2", - "tp_cat", - "cat_bins", + "hmmer_hmmscan", "kofamscan", - "trim_galore", - "interproscan", - "sort1" + "tp_cat", + "maxbin2", + "quast", + "fraggenescan" ], "update_time": "2024-12-21", "versions": 14 @@ -5631,23 +5785,23 @@ "deprecated": false, "doi": "", "edam_operation": [ - "Sequence comparison", - "Phylogenetic tree visualisation", - "Visualisation", - "Sequence composition calculation", - "Formatting", "Statistical calculation", "Phylogenetic inference", - "Validation", - "Primer removal", - "Sequence alignment analysis", + "Taxonomic classification", + "Formatting", + "Conversion", + "Phylogenetic tree visualisation", + "Sequence similarity search", + "Sequence composition calculation", + "Phylogenetic tree editing", "Sequencing quality control", "Sequence trimming", - "Phylogenetic tree editing", + "Sequence alignment analysis", + "Sequence comparison", + "Validation", "Read pre-processing", - "Taxonomic classification", - "Sequence similarity search", - "Conversion" + "Primer removal", + "Visualisation" ], "edam_topic": [], "id": "096b75501c8e0888", @@ -5667,27 +5821,27 @@ "name:microgalaxy" ], "tools": [ - "Grouping1", - "group_humann2_uniref_abundances_to_go", - "fastqc", + "graphlan_annotate", "humann2_renorm_table", - "humann2_unpack_pathways", - "tp_sort_header_tool", + "combine_metaphlan2_humann2", + "bg_sortmerna", + "cutadapt", "humann2_genefamilies_genus_level", + "taxonomy_krona_chart", + "export2graphlan", + "metaphlan2", + "fastq_paired_end_interlacer", + "group_humann2_uniref_abundances_to_go", + "Grouping1", + "Grep1", "humann2", + "graphlan", + "tp_sort_header_tool", "metaphlan2krona", - "Grep1", + "humann2_unpack_pathways", "format_metaphlan2_output", - "graphlan", - "bg_sortmerna", - "fastq_paired_end_interlacer", "multiqc", - "combine_metaphlan2_humann2", - "cutadapt", - "taxonomy_krona_chart", - "graphlan_annotate", - "export2graphlan", - "metaphlan2" + "fastqc" ], "update_time": "2024-12-20", "versions": 3 @@ -5703,23 +5857,23 @@ "deprecated": false, "doi": "", "edam_operation": [ + "Statistical calculation", + "Genome alignment", "Visualisation", + "Genome annotation", + "Read binning", + "Sequencing quality control", + "Sequence assembly", + "Genome comparison", "Sequence composition calculation", + "Query and retrieval", + "Taxonomic classification", "Sequence assembly validation", - "Statistical calculation", "Validation", "Read mapping", - "Genome annotation", "Sequence clustering", - "Read binning", "Local alignment", - "Query and retrieval", - "Sequence assembly", - "Genome comparison", - "Genome alignment", - "Taxonomic classification", - "Genome assembly", - "Sequencing quality control" + "Genome assembly" ], "edam_topic": [], "id": "0563f58718be932d", @@ -5736,31 +5890,31 @@ "name:microgalaxy" ], "tools": [ - "concoct_coverage_table", - "metabat2_jgi_summarize_bam_contig_depths", - "concoct_extract_fasta_bins", + "__FLATTEN__", + "Fasta_to_Contig2Bin", "semibin", + "metabat2_jgi_summarize_bam_contig_depths", + "bowtie2", "coverm_genome", + "gtdbtk_classify_wf", "concoct_merge_cut_up_clustering", "concoct_cut_up_fasta", - "__FLATTEN__", - "maxbin2", - "drep_dereplicate", - "Fasta_to_Contig2Bin", - "metabat2", "checkm_plot", + "concoct_coverage_table", "checkm_lineage_wf", - "__UNZIP_COLLECTION__", + "maxbin2", "quast", - "samtools_sort", - "concoct", - "gtdbtk_classify_wf", + "drep_dereplicate", "fastq_paired_end_joiner", "collection_column_join", - "bowtie2", + "concoct_extract_fasta_bins", "multiqc", + "samtools_sort", + "concoct", "megahit", - "das_tool" + "__UNZIP_COLLECTION__", + "das_tool", + "metabat2" ], "update_time": "2024-12-20", "versions": 1 @@ -5784,16 +5938,16 @@ "deprecated": false, "doi": "", "edam_operation": [ - "Sequence trimming", - "Sequence composition calculation", "Statistical calculation", - "Gene expression profiling", - "Primer removal", - "Read pre-processing", "Sequence similarity search", + "Sequencing quality control", + "Gene expression profiling", + "Sequence trimming", "Sequence alignment analysis", "Sequence comparison", - "Sequencing quality control" + "Read pre-processing", + "Primer removal", + "Sequence composition calculation" ], "edam_topic": [], "id": "fd90652d475ed739", @@ -5811,12 +5965,12 @@ "microbiome" ], "tools": [ - "collection_column_join", "kallisto_quant", - "fastqc", - "__UNZIP_COLLECTION__", + "collection_column_join", "trim_galore", - "bg_sortmerna" + "fastqc", + "bg_sortmerna", + "__UNZIP_COLLECTION__" ], "update_time": "2024-12-20", "versions": 6 @@ -5830,8 +5984,8 @@ "doi": "", "edam_operation": [ "Sequence alignment analysis", - "Multiple sequence alignment", - "Phylogenetic tree generation" + "Phylogenetic tree generation", + "Multiple sequence alignment" ], "edam_topic": [], "id": "a2c46deea34d9d80", @@ -5848,20 +6002,20 @@ "name:microgalaxy" ], "tools": [ + "Add_a_column1", + "tab2fasta", "tp_split_on_column", - "regexColumn1", + "gops_intersect_1", "rbc_mafft", - "bg_diamond_view", - "Filter1", - "bg_diamond", "join1", - "tab2fasta", - "collapse_dataset", - "Cut1", + "bg_diamond", "cat1", + "collapse_dataset", "rapidnj", - "Add_a_column1", - "gops_intersect_1" + "Filter1", + "bg_diamond_view", + "Cut1", + "regexColumn1" ], "update_time": "2024-12-05", "versions": 2 @@ -5878,8 +6032,8 @@ "deprecated": false, "doi": "", "edam_operation": [ - "Visualisation", - "Prediction and recognition" + "Prediction and recognition", + "Visualisation" ], "edam_topic": [], "id": "cefc49c13ff73231", @@ -5898,11 +6052,11 @@ "name:microgalaxy" ], "tools": [ - "search_gui", "peptide_shaker", + "unipept", + "search_gui", "sqlite_to_tabular", - "query_tabular", - "unipept" + "query_tabular" ], "update_time": "2024-11-21", "versions": 40 @@ -5936,10 +6090,10 @@ "limma-rle" ], "tools": [ + "__EXTRACT_DATASET__", + "map_param_value", "Grep1", "__BUILD_LIST__", - "map_param_value", - "__EXTRACT_DATASET__", "__FILTER_EMPTY_DATASETS__" ], "update_time": "2024-11-21", @@ -5957,11 +6111,11 @@ "deprecated": false, "doi": "", "edam_operation": [ - "Visualisation", - "Label-free quantification", + "Formatting", "Prediction and recognition", "Filtering", - "Formatting" + "Visualisation", + "Label-free quantification" ], "edam_topic": [], "id": "cd675ab32d3e7833", @@ -5978,18 +6132,18 @@ "name:microgalaxy" ], "tools": [ - "tp_replace_in_column", + "peptide_shaker", + "search_gui", + "unipept", "flashlfq", - "Filter1", - "msconvert", "tp_replace_in_line", "Cut1", "regex1", - "Remove beginning1", - "search_gui", - "peptide_shaker", + "msconvert", + "tp_replace_in_column", "query_tabular", - "unipept" + "Filter1", + "Remove beginning1" ], "update_time": "2024-11-21", "versions": 1 @@ -6007,16 +6161,16 @@ "deprecated": false, "doi": "", "edam_operation": [ - "Visualisation", - "Statistical inference", "Quantification", - "Heat map generation", - "Query and retrieval", - "Indexing", "Differential protein expression analysis", + "Query and retrieval", "Principal component visualisation", + "Indexing", + "Heat map generation", "Filtering", - "Functional clustering" + "Functional clustering", + "Statistical inference", + "Visualisation" ], "edam_topic": [], "id": "e5a89ef7b5f1c1d9", @@ -6033,12 +6187,12 @@ "name:microgalaxy" ], "tools": [ - "metaquantome_db", - "metaquantome_sample", "metaquantome_stat", - "metaquantome_filter", + "metaquantome_expand", "metaquantome_viz", - "metaquantome_expand" + "metaquantome_db", + "metaquantome_filter", + "metaquantome_sample" ], "update_time": "2024-11-21", "versions": 3 @@ -6054,10 +6208,10 @@ "deprecated": false, "doi": "", "edam_operation": [ - "Cross-assembly", "Taxonomic classification", + "Expression analysis", "Read mapping", - "Expression analysis" + "Cross-assembly" ], "edam_topic": [], "id": "c09159d7aad0f264", @@ -6076,10 +6230,10 @@ ], "tools": [ "bowtie2", - "kraken2", + "recentrifuge", "fastq_to_tabular", + "kraken2", "filter_tabular", - "recentrifuge", "seq_filter_by_id" ], "update_time": "2024-11-21", @@ -6096,11 +6250,11 @@ "deprecated": false, "doi": "", "edam_operation": [ - "Read summarisation", - "RNA-Seq quantification", + "Sequencing quality control", "Validation", + "Read summarisation", "Read mapping", - "Sequencing quality control" + "RNA-Seq quantification" ], "edam_topic": [], "id": "63478edcea3f449a", @@ -6118,8 +6272,8 @@ "name:microgalaxy" ], "tools": [ - "featurecounts", "bowtie2", + "featurecounts", "multiqc" ], "update_time": "2024-11-21", @@ -6136,10 +6290,10 @@ "deprecated": false, "doi": "", "edam_operation": [ - "Sequence composition calculation", + "Sequencing quality control", "Statistical calculation", "Validation", - "Sequencing quality control" + "Sequence composition calculation" ], "edam_topic": [], "id": "1ef76b7b86e15792", @@ -6157,9 +6311,9 @@ "name:microgalaxy" ], "tools": [ - "trimmomatic", "fastqc", - "multiqc" + "multiqc", + "trimmomatic" ], "update_time": "2024-11-21", "versions": 6 @@ -6170,20 +6324,20 @@ "deprecated": false, "doi": "", "edam_operation": [ + "Statistical calculation", "Visualisation", - "Sequence composition calculation", + "Genome annotation", + "Read binning", "Sequence assembly validation", - "Statistical calculation", + "Sequencing quality control", + "Sequence assembly", "Validation", + "Genome comparison", "Read mapping", - "Genome annotation", "Sequence clustering", - "Read binning", + "Sequence composition calculation", "Local alignment", - "Sequence assembly", - "Genome comparison", - "Genome assembly", - "Sequencing quality control" + "Genome assembly" ], "edam_topic": [], "id": "97312d273b6e8bd9", @@ -6199,26 +6353,26 @@ "name:microgalaxy" ], "tools": [ - "concoct_coverage_table", - "metabat2_jgi_summarize_bam_contig_depths", - "concoct_extract_fasta_bins", + "Fasta_to_Contig2Bin", "semibin", + "metabat2_jgi_summarize_bam_contig_depths", + "bowtie2", "coverm_genome", "concoct_merge_cut_up_clustering", "concoct_cut_up_fasta", - "maxbin2", - "drep_dereplicate", - "Fasta_to_Contig2Bin", - "metabat2", + "concoct_coverage_table", + "fastq_paired_end_interlacer", "checkm_lineage_wf", - "__UNZIP_COLLECTION__", + "maxbin2", "quast", + "drep_dereplicate", + "concoct_extract_fasta_bins", "samtools_sort", "concoct", - "fastq_paired_end_interlacer", - "bowtie2", "megahit", - "das_tool" + "__UNZIP_COLLECTION__", + "das_tool", + "metabat2" ], "update_time": "2024-07-11", "versions": 14 @@ -6264,14 +6418,12 @@ "deprecated": false, "doi": "", "edam_operation": [ - "Phylogenetic tree generation (from molecular sequences)", + "Phylogenetic tree generation", "Visualisation", - "Phylogenetic tree generation (maximum likelihood and Bayesian methods)", "Multiple sequence alignment", - "Mapping", "Phylogenetic tree reconstruction", "Phylogenetic tree analysis", - "Phylogenetic tree generation" + "Mapping" ], "edam_topic": [], "id": "376119528377a3ae", @@ -6290,28 +6442,28 @@ "name:iwc" ], "tools": [ - "Grouping1", + "tp_split_on_column", + "ggplot2_heatmap", + "bedtools_getfastabed", + "collapse_dataset", + "regex1", + "tp_replace_in_column", + "fasta_merge_files_and_filter_unique_sequences", + "newick_display", "regexColumn1", - "clustalw", - "__FILTER_FAILED_DATASETS__", + "tp_multijoin_tool", + "Count1", + "__FILTER_EMPTY_DATASETS__", "fasta2tab", "tp_sorted_uniq", - "fasta_merge_files_and_filter_unique_sequences", - "collapse_dataset", - "__FILTER_EMPTY_DATASETS__", - "bedtools_getfastabed", - "tp_multijoin_tool", - "ggplot2_heatmap", - "Cut1", - "Remove beginning1", + "Grouping1", "fasttree", - "tp_split_on_column", + "tab2fasta", + "Remove beginning1", "collection_column_join", - "tp_replace_in_column", - "newick_display", - "regex1", - "Count1", - "tab2fasta" + "clustalw", + "__FILTER_FAILED_DATASETS__", + "Cut1" ], "update_time": "2024-06-24", "versions": 58 @@ -6346,24 +6498,24 @@ "name:iwc" ], "tools": [ + "tp_cut_tool", + "clair3", + "table_compute", + "samtools_depth", "bcftools_consensus", + "CONVERTER_gz_to_uncompressed", "Paste1", - "samtools_coverage", - "regexColumn1", "bcftools_norm", - "CONVERTER_gz_to_uncompressed", - "snpSift_filter", - "tp_cut_tool", "Cut1", "snpSift_extractFields", - "clair3", + "samtools_coverage", + "snpSift_filter", "collapse_dataset", - "Remove beginning1", - "table_compute", - "tp_head_tool", + "minimap2", "Count1", - "samtools_depth", - "minimap2" + "tp_head_tool", + "Remove beginning1", + "regexColumn1" ], "update_time": "2024-06-24", "versions": 72 @@ -6378,19 +6530,19 @@ "deprecated": false, "doi": "", "edam_operation": [ - "Visualisation", - "Sequence composition calculation", "Statistical calculation", - "Validation", - "Sequence contamination filtering", - "Box-Whisker plot plotting", - "Sequence alignment analysis", "Taxonomic classification", - "Data handling", "Pairwise sequence alignment", + "Box-Whisker plot plotting", "Aggregation", + "Data handling", "Scatter plot plotting", - "Sequencing quality control" + "Sequencing quality control", + "Sequence contamination filtering", + "Sequence alignment analysis", + "Validation", + "Sequence composition calculation", + "Visualisation" ], "edam_topic": [], "id": "a705370bc2c13d5c", @@ -6410,23 +6562,23 @@ "name:iwc" ], "tools": [ + "Add_a_column1", + "fastp", "collection_column_join", - "Grep1", - "samtools_fastx", - "regexColumn1", "multiqc", "kraken2", + "samtools_fastx", "fastqc", - "bamtools_split_mapped", + "collapse_dataset", "nanoplot", - "porechop", + "minimap2", + "Grep1", "__FILTER_FAILED_DATASETS__", - "krakentools_extract_kraken_reads", - "fastp", - "collapse_dataset", + "bamtools_split_mapped", + "porechop", "Cut1", - "Add_a_column1", - "minimap2" + "regexColumn1", + "krakentools_extract_kraken_reads" ], "update_time": "2024-06-24", "versions": 190 @@ -6460,9 +6612,9 @@ "name:gtn" ], "tools": [ + "kraken_biom", "kraken2", - "interactive_tool_phinch", - "kraken_biom" + "interactive_tool_phinch" ], "update_time": "2024-06-19", "versions": 8 @@ -6473,11 +6625,11 @@ "deprecated": false, "doi": "", "edam_operation": [ - "Visualisation", - "Label-free quantification", + "Formatting", "Prediction and recognition", "Filtering", - "Formatting" + "Visualisation", + "Label-free quantification" ], "edam_topic": [], "id": "fc42cc9467c6ee8d", @@ -6494,18 +6646,18 @@ "name:microgalaxy" ], "tools": [ - "tp_replace_in_column", + "peptide_shaker", + "search_gui", + "unipept", "flashlfq", - "Filter1", - "msconvert", "tp_replace_in_line", "Cut1", "regex1", - "Remove beginning1", - "search_gui", - "peptide_shaker", + "msconvert", + "tp_replace_in_column", "query_tabular", - "unipept" + "Filter1", + "Remove beginning1" ], "update_time": "2024-06-19", "versions": 0 @@ -6520,15 +6672,15 @@ "deprecated": false, "doi": "", "edam_operation": [ - "Antimicrobial resistance prediction", "Base-calling", + "Antimicrobial resistance prediction", + "De-novo assembly", "Variant calling", + "Sequence assembly visualisation", + "Sequence assembly", "Cross-assembly", "Mapping assembly", - "Sequence assembly", - "Genome assembly", - "Sequence assembly visualisation", - "De-novo assembly" + "Genome assembly" ], "edam_topic": [], "id": "585c21b7b1d864fc", @@ -6547,18 +6699,18 @@ "name:microgalaxy" ], "tools": [ - "medaka_consensus_pipeline", - "param_value_from_file", - "compose_text_param", - "__BUILD_LIST__", - "tp_find_and_replace", "abricate", "collection_element_identifiers", "bandage_image", - "split_file_to_collection", "flye", - "fasta2tab", - "tab2fasta" + "tp_find_and_replace", + "split_file_to_collection", + "compose_text_param", + "__BUILD_LIST__", + "tab2fasta", + "medaka_consensus_pipeline", + "param_value_from_file", + "fasta2tab" ], "update_time": "2024-06-05", "versions": 142 @@ -6573,9 +6725,9 @@ "deprecated": false, "doi": "", "edam_operation": [ - "Visualisation", "Taxonomic classification", - "Aggregation" + "Aggregation", + "Visualisation" ], "edam_topic": [], "id": "10101558b211a782", @@ -6594,9 +6746,9 @@ "name:iwc" ], "tools": [ + "krakentools_kreport2krona", "kraken2", - "taxonomy_krona_chart", - "krakentools_kreport2krona" + "taxonomy_krona_chart" ], "update_time": "2024-06-05", "versions": 58 @@ -6610,14 +6762,12 @@ "deprecated": false, "doi": "", "edam_operation": [ - "Phylogenetic tree generation (from molecular sequences)", + "Phylogenetic tree generation", "Visualisation", - "Phylogenetic tree generation (maximum likelihood and Bayesian methods)", "Multiple sequence alignment", - "Mapping", "Phylogenetic tree reconstruction", "Phylogenetic tree analysis", - "Phylogenetic tree generation" + "Mapping" ], "edam_topic": [], "id": "c8bc4af6dd3b5d02", @@ -6637,29 +6787,29 @@ "name:microgalaxy" ], "tools": [ - "Grouping1", - "regexColumn1", - "clustalw", - "__FILTER_FAILED_DATASETS__", - "fasta2tab", - "tp_sorted_uniq", - "fasta_merge_files_and_filter_unique_sequences", - "collapse_dataset", - "__FILTER_EMPTY_DATASETS__", - "bedtools_getfastabed", - "tp_multijoin_tool", - "ggplot2_heatmap", - "Cut1", - "Remove beginning1", - "fasttree", "tp_split_on_column", - "collection_column_join", + "ggplot2_heatmap", + "bedtools_getfastabed", + "collapse_dataset", + "regex1", "tp_replace_in_column", + "fasta_merge_files_and_filter_unique_sequences", "newick_display", + "regexColumn1", + "tp_multijoin_tool", "interactive_tool_jupyter_notebook", - "regex1", "Count1", - "tab2fasta" + "__FILTER_EMPTY_DATASETS__", + "fasta2tab", + "tp_sorted_uniq", + "Grouping1", + "fasttree", + "tab2fasta", + "Remove beginning1", + "collection_column_join", + "clustalw", + "__FILTER_FAILED_DATASETS__", + "Cut1" ], "update_time": "2024-04-04", "versions": 205 @@ -6710,10 +6860,10 @@ "name:microgalaxy" ], "tools": [ + "__EXTRACT_DATASET__", + "map_param_value", "Grep1", "__BUILD_LIST__", - "map_param_value", - "__EXTRACT_DATASET__", "__FILTER_EMPTY_DATASETS__" ], "update_time": "2024-03-13", @@ -6725,11 +6875,11 @@ "deprecated": false, "doi": "", "edam_operation": [ + "de Novo sequencing", + "Target-Decoy", "Expression analysis", - "Protein identification", "Tag-based peptide identification", - "de Novo sequencing", - "Target-Decoy" + "Protein identification" ], "edam_topic": [], "id": "7cfbf4b7bd3f30d3", @@ -6758,16 +6908,16 @@ "deprecated": false, "doi": "", "edam_operation": [ - "Visualisation", - "Filtering", - "Formatting", "Statistical calculation", "Imputation", - "Standardisation and normalisation", + "Formatting", "Heat map generation", + "Filtering", + "Standardisation and normalisation", "Protein quantification", + "Clustering", "Principal component plotting", - "Clustering" + "Visualisation" ], "edam_topic": [], "id": "8af41219411062ad", @@ -6784,23 +6934,23 @@ "name:clinicalmp" ], "tools": [ + "query_tabular", + "peptide_shaker", + "Remove beginning1", + "tp_cat", + "search_gui", "Grouping1", - "Grep1", - "fasta2tab", - "fasta_merge_files_and_filter_unique_sequences", - "Filter1", + "fasta_cli", "ident_params", - "Remove beginning1", + "maxquant", "msconvert", - "Cut1", - "query_tabular", "dbbuilder", - "fasta_cli", + "Grep1", "filter_tabular", - "tp_cat", - "search_gui", - "peptide_shaker", - "maxquant" + "Filter1", + "fasta_merge_files_and_filter_unique_sequences", + "Cut1", + "fasta2tab" ], "update_time": "2023-12-14", "versions": 1 @@ -6826,17 +6976,17 @@ "name:clinicalmp" ], "tools": [ - "Grouping1", - "fasta_merge_files_and_filter_unique_sequences", "Filter1", "uniprotxml_downloader", + "Grouping1", "Cut1", - "pepquery2", - "tp_cat", + "collapse_dataset", "dbbuilder", + "query_tabular", + "tp_cat", + "fasta_merge_files_and_filter_unique_sequences", "Remove beginning1", - "collapse_dataset", - "query_tabular" + "pepquery2" ], "update_time": "2023-12-14", "versions": 1 @@ -6847,14 +6997,14 @@ "deprecated": false, "doi": "", "edam_operation": [ - "Visualisation", "Statistical calculation", "Imputation", - "Standardisation and normalisation", "Heat map generation", + "Standardisation and normalisation", "Protein quantification", + "Clustering", "Principal component plotting", - "Clustering" + "Visualisation" ], "edam_topic": [], "id": "a49275eb8b2b2ecb", @@ -6871,10 +7021,10 @@ "name:microgalaxy" ], "tools": [ - "Grouping1", - "Grep1", "maxquant", - "Cut1" + "Cut1", + "Grep1", + "Grouping1" ], "update_time": "2023-12-14", "versions": 1 @@ -6885,8 +7035,8 @@ "deprecated": false, "doi": "", "edam_operation": [ - "Visualisation", - "Prediction and recognition" + "Prediction and recognition", + "Visualisation" ], "edam_topic": [], "id": "755ede37d94dc456", @@ -6903,8 +7053,8 @@ "name:clinicalmp" ], "tools": [ - "Grep1", "msstatstmt", + "Grep1", "unipept" ], "update_time": "2023-12-14", @@ -6916,34 +7066,34 @@ "deprecated": false, "doi": "", "edam_operation": [ - "Visualisation", - "Sequence composition calculation", - "Formatting", "Statistical calculation", + "Formatting", "Gene functional annotation", - "Validation", - "Sequence database search", + "Visualisation", "Format validation", - "Primer removal", - "Coding region prediction", - "Local alignment", - "Sequence assembly", - "Database search", - "Sequence profile generation", + "Conversion", + "Probabilistic sequence generation", "Sequencing quality control", + "Sequence assembly", "Protein feature detection", - "Sequence trimming", - "Multiple sequence alignment", - "Sequence assembly validation", + "Gene prediction", "Sequence motif recognition", + "Coding region prediction", + "Sequence composition calculation", "Sequence generation", + "Database search", + "Sequence database search", + "Data retrieval", + "Taxonomic classification", + "Multiple sequence alignment", + "Sequence assembly validation", + "Sequence trimming", + "Sequence profile generation", + "Validation", "Sequence analysis", "Read pre-processing", - "Data retrieval", - "Gene prediction", - "Taxonomic classification", - "Conversion", - "Probabilistic sequence generation" + "Primer removal", + "Local alignment" ], "edam_topic": [], "id": "d57d41e306241396", @@ -6959,23 +7109,23 @@ "name:microgalaxy" ], "tools": [ + "coverm_genome", "fasplit", "tp_awk_tool", "tp_grep_tool", + "sort1", + "cat_bins", + "trim_galore", "fastqc", "checkm_lineage_wf", - "hmmer_hmmscan", - "coverm_genome", - "quast", + "interproscan", "coverm_contig", - "fraggenescan", - "maxbin2", - "cat_bins", - "tp_cat", + "hmmer_hmmscan", "kofamscan", - "trim_galore", - "interproscan", - "sort1" + "tp_cat", + "maxbin2", + "quast", + "fraggenescan" ], "update_time": "2023-12-14", "versions": 1 @@ -6986,16 +7136,16 @@ "deprecated": false, "doi": "", "edam_operation": [ - "Visualisation", - "Statistical inference", "Quantification", - "Heat map generation", - "Query and retrieval", - "Indexing", "Differential protein expression analysis", + "Query and retrieval", "Principal component visualisation", + "Indexing", + "Heat map generation", "Filtering", - "Functional clustering" + "Functional clustering", + "Statistical inference", + "Visualisation" ], "edam_topic": [], "id": "695f7defb516d80d", @@ -7012,12 +7162,12 @@ "name:microgalaxy" ], "tools": [ - "metaquantome_db", - "metaquantome_sample", "metaquantome_stat", - "metaquantome_filter", + "metaquantome_expand", "metaquantome_viz", - "metaquantome_expand" + "metaquantome_db", + "metaquantome_filter", + "metaquantome_sample" ], "update_time": "2023-12-14", "versions": 0 @@ -7028,16 +7178,16 @@ "deprecated": false, "doi": "", "edam_operation": [ - "Visualisation", - "Statistical inference", "Quantification", - "Heat map generation", - "Query and retrieval", - "Indexing", "Differential protein expression analysis", + "Query and retrieval", "Principal component visualisation", + "Indexing", + "Heat map generation", "Filtering", - "Functional clustering" + "Functional clustering", + "Statistical inference", + "Visualisation" ], "edam_topic": [], "id": "4c364c6be27981ba", @@ -7054,12 +7204,12 @@ "name:microgalaxy" ], "tools": [ - "metaquantome_db", - "metaquantome_sample", "metaquantome_stat", - "metaquantome_filter", + "metaquantome_expand", "metaquantome_viz", - "metaquantome_expand" + "metaquantome_db", + "metaquantome_filter", + "metaquantome_sample" ], "update_time": "2023-12-14", "versions": 0 @@ -7070,8 +7220,8 @@ "deprecated": false, "doi": "", "edam_operation": [ - "Visualisation", - "Prediction and recognition" + "Prediction and recognition", + "Visualisation" ], "edam_topic": [], "id": "68967c922de149ae", @@ -7088,11 +7238,11 @@ "name:microgalaxy" ], "tools": [ - "search_gui", "peptide_shaker", + "unipept", + "search_gui", "sqlite_to_tabular", - "query_tabular", - "unipept" + "query_tabular" ], "update_time": "2023-12-14", "versions": 0 @@ -7122,26 +7272,26 @@ "name:microgalaxy" ], "tools": [ - "mergeCols1", - "bedtools_complementbed", - "tp_sort_header_tool", - "tp_sed_tool", - "cat1", "bedtools_sortbed", - "fasta_compute_length", - "Filter1", - "addValue", - "join1", "collapse_dataset", "bedtools_intersectbed", - "random_lines1", - "Grep1", "tp_cat", - "Cut1", - "fasta_filter_by_length", - "tp_grep_tool", "datamash_ops", - "lastz_wrapper_2" + "bedtools_complementbed", + "cat1", + "join1", + "mergeCols1", + "lastz_wrapper_2", + "tp_grep_tool", + "addValue", + "fasta_filter_by_length", + "Grep1", + "fasta_compute_length", + "tp_sort_header_tool", + "random_lines1", + "tp_sed_tool", + "Filter1", + "Cut1" ], "update_time": "2023-12-14", "versions": 0 @@ -7152,13 +7302,13 @@ "deprecated": false, "doi": "", "edam_operation": [ - "Visualisation", - "Sequence composition calculation", + "Sequencing quality control", "Sequence contamination filtering", + "Taxonomic classification", "Statistical calculation", "Validation", - "Taxonomic classification", - "Sequencing quality control" + "Sequence composition calculation", + "Visualisation" ], "edam_topic": [], "id": "08eb5e55109c4d9c", @@ -7175,15 +7325,15 @@ "name:microgalaxy" ], "tools": [ + "fastp", + "datamash_reverse", + "taxonomy_krona_chart", "multiqc", "kraken2", + "tp_replace_in_line", "fastqc", - "taxonomy_krona_chart", "porechop", - "tp_replace_in_line", - "fastp", - "Remove beginning1", - "datamash_reverse" + "Remove beginning1" ], "update_time": "2023-12-14", "versions": 0 @@ -7226,16 +7376,16 @@ "deprecated": false, "doi": "", "edam_operation": [ + "Pairwise sequence alignment", "Aggregation", - "Mapping assembly", "Antimicrobial resistance prediction", - "Sequence analysis", "Box-Whisker plot plotting", - "Pairwise sequence alignment", - "Genome assembly", - "Sequence assembly visualisation", + "De-novo assembly", "Scatter plot plotting", - "De-novo assembly" + "Sequence assembly visualisation", + "Sequence analysis", + "Mapping assembly", + "Genome assembly" ], "edam_topic": [], "id": "44e53ea319e07daa", @@ -7253,14 +7403,14 @@ ], "tools": [ "unicycler", - "racon", - "staramr_search", "bandage_image", "miniasm", - "nanoplot", + "staramr_search", "PlasFlow", - "gfa_to_fa", - "minimap2" + "nanoplot", + "minimap2", + "racon", + "gfa_to_fa" ], "update_time": "2023-12-14", "versions": 0 @@ -7275,13 +7425,13 @@ "deprecated": false, "doi": "", "edam_operation": [ - "Visualisation", - "Sequence composition calculation", + "Sequencing quality control", "Sequence contamination filtering", - "Statistical calculation", "Taxonomic classification", + "Statistical calculation", "Aggregation", - "Sequencing quality control" + "Sequence composition calculation", + "Visualisation" ], "edam_topic": [], "id": "0590554db9794d13", @@ -7298,13 +7448,13 @@ "name:microgalaxy" ], "tools": [ - "kraken2", - "Filter1", - "fastqc", + "fastp", "taxonomy_krona_chart", "krakentools_kreport2krona", - "porechop", - "fastp" + "kraken2", + "fastqc", + "Filter1", + "porechop" ], "update_time": "2023-12-14", "versions": 0 @@ -7315,20 +7465,20 @@ "deprecated": false, "doi": "", "edam_operation": [ - "Sequence trimming", - "Sequence composition calculation", - "Formatting", "Statistical calculation", + "Formatting", + "Data handling", "Sequence file editing", - "Read mapping", - "Primer removal", "Variant calling", - "Read pre-processing", + "Primer removal", + "Sequencing quality control", "Sequence contamination filtering", + "Sequence trimming", "Sequence alignment analysis", - "Data handling", - "Genome assembly", - "Sequencing quality control" + "Read mapping", + "Read pre-processing", + "Sequence composition calculation", + "Genome assembly" ], "edam_topic": [], "id": "ce5c16ac23c4fbb1", @@ -7345,15 +7495,15 @@ ], "tools": [ "bowtie2", - "bamtools", "bg_uniq", - "cutadapt", + "seqtk_subseq", "fastqc", - "tp_cat", + "bamtools", "filter_tabular", - "megahit", "ngsutils_bam_filter", - "seqtk_subseq", + "megahit", + "cutadapt", + "tp_cat", "random_lines1" ], "update_time": "2023-12-14", @@ -7365,11 +7515,11 @@ "deprecated": false, "doi": "", "edam_operation": [ - "Visualisation", - "Sequence assembly validation", "Read mapping", - "Genome assembly", - "Sequence assembly visualisation" + "Sequence assembly validation", + "Sequence assembly visualisation", + "Visualisation", + "Genome assembly" ], "edam_topic": [], "id": "62c47e3c9d4f3aa3", @@ -7385,14 +7535,14 @@ "name:microgalaxy" ], "tools": [ - "collection_column_join", - "bowtie2", "megahit_contig2fastg", - "bandage_info", - "bandage_image", + "bowtie2", + "collection_column_join", "metaspades", - "quast", - "megahit" + "bandage_image", + "bandage_info", + "megahit", + "quast" ], "update_time": "2023-12-14", "versions": 0 @@ -7420,12 +7570,12 @@ "name:microgalaxy" ], "tools": [ - "humann2", - "taxonomy_krona_chart", "metaphlan2krona", + "metaphlan2", "humann2_renorm_table", - "humann2_regroup_table", - "metaphlan2" + "taxonomy_krona_chart", + "humann2", + "humann2_regroup_table" ], "update_time": "2023-12-14", "versions": 0 @@ -7438,11 +7588,11 @@ "deprecated": false, "doi": "", "edam_operation": [ - "Visualisation", "Statistical calculation", "Taxonomic classification", + "Aggregation", "Genome annotation", - "Aggregation" + "Visualisation" ], "edam_topic": [], "id": "4f0daf8e9dd54127", @@ -7459,15 +7609,15 @@ "name:microgalaxy" ], "tools": [ - "interactive_tool_phinch", "metaphlan", - "kraken2", "taxonomy_krona_chart", "krakentools_kreport2krona", - "__UNZIP_COLLECTION__", "est_abundance", - "interactive_tool_pavian", - "kraken_biom" + "kraken_biom", + "kraken2", + "interactive_tool_phinch", + "__UNZIP_COLLECTION__", + "interactive_tool_pavian" ], "update_time": "2023-12-14", "versions": 0 @@ -7478,13 +7628,13 @@ "deprecated": false, "doi": "", "edam_operation": [ - "Visualisation", - "Sequence clustering", - "DNA barcoding", "Taxonomic classification", + "DNA barcoding", "Sequence read processing", "Sequencing quality control", - "Phylogenetic analysis" + "Sequence clustering", + "Phylogenetic analysis", + "Visualisation" ], "edam_topic": [], "id": "565c989730f68362", @@ -7501,21 +7651,21 @@ "name:microgalaxy" ], "tools": [ - "mothur_pre_cluster", - "mothur_make_group", + "mothur_unique_seqs", + "mothur_cluster_split", "mothur_summary_seqs", "mothur_count_seqs", - "mothur_unique_seqs", + "mothur_make_shared", + "mothur_make_biom", "mothur_merge_files", - "mothur_align_seqs", - "mothur_filter_seqs", - "mothur_cluster_split", "mothur_screen_seqs", + "mothur_filter_seqs", + "mothur_make_group", "mothur_classify_seqs", - "mothur_make_shared", - "krona-text", "mothur_classify_otu", - "mothur_make_biom" + "mothur_align_seqs", + "mothur_pre_cluster", + "krona-text" ], "update_time": "2023-12-14", "versions": 0 @@ -7546,8 +7696,8 @@ "name:microgalaxy" ], "tools": [ - "jbrowse", - "snippy" + "snippy", + "jbrowse" ], "update_time": "2023-12-14", "versions": 0 @@ -7558,17 +7708,17 @@ "deprecated": false, "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Formatting", "Statistical calculation", + "Formatting", + "Generation", + "Data handling", + "Variant calling", "Sequence alignment", "Genome indexing", - "Read mapping", - "Variant calling", + "Sequencing quality control", "Sequence alignment analysis", - "Data handling", - "Generation", - "Sequencing quality control" + "Read mapping", + "Sequence composition calculation" ], "edam_topic": [], "id": "291c36e1b18e9deb", @@ -7585,16 +7735,16 @@ "name:microgalaxy" ], "tools": [ + "picard_MarkDuplicates", "vcffilter2", + "picard_MergeSamFiles", + "bamleftalign", "fastqc", "vcf2tsv", "bamFilter", - "freebayes", - "bwa_mem", - "picard_MarkDuplicates", "Cut1", - "picard_MergeSamFiles", - "bamleftalign" + "bwa_mem", + "freebayes" ], "update_time": "2023-12-14", "versions": 0 @@ -7605,16 +7755,16 @@ "deprecated": false, "doi": "", "edam_operation": [ - "Visualisation", - "Phylogenetic tree reconstruction", - "Sequence clustering", - "Phylogenetic tree generation", - "DNA barcoding", - "Phylogenetic tree analysis", "Taxonomic classification", + "DNA barcoding", "Sequence read processing", "Sequencing quality control", - "Phylogenetic analysis" + "Phylogenetic tree generation", + "Phylogenetic tree reconstruction", + "Sequence clustering", + "Phylogenetic tree analysis", + "Phylogenetic analysis", + "Visualisation" ], "edam_topic": [], "id": "c67d2e75eeb4fd19", @@ -7631,39 +7781,39 @@ "name:microgalaxy" ], "tools": [ - "mothur_pre_cluster", - "mothur_make_contigs", "mothur_count_seqs", - "mothur_cluster", - "mothur_unique_seqs", - "mothur_venn", - "mothur_classify_seqs", - "mothur_make_shared", - "mothur_make_biom", - "mothur_summary_seqs", - "mothur_cluster_split", "mothur_chimera_vsearch", + "mothur_get_groups", "mothur_screen_seqs", - "mothur_remove_lineage", - "mothur_summary_single", + "mothur_rarefaction_single", + "mothur_align_seqs", + "newick_display", + "mothur_make_shared", + "taxonomy_krona_chart", + "mothur_cluster", "mothur_remove_seqs", - "XY_Plot_1", + "mothur_summary_single", + "mothur_sub_sample", "mothur_remove_groups", - "mothur_taxonomy_to_krona", + "mothur_classify_seqs", + "mothur_seq_error", "mothur_count_groups", - "mothur_align_seqs", - "mothur_filter_seqs", - "mothur_dist_shared", + "mothur_cluster_split", "mothur_tree_shared", + "mothur_summary_seqs", + "mothur_make_contigs", + "mothur_dist_shared", "mothur_dist_seqs", + "XY_Plot_1", + "mothur_filter_seqs", + "mothur_remove_lineage", "mothur_classify_otu", + "mothur_pre_cluster", + "mothur_unique_seqs", + "mothur_venn", "mothur_heatmap_sim", - "mothur_rarefaction_single", - "mothur_sub_sample", - "newick_display", - "taxonomy_krona_chart", - "mothur_seq_error", - "mothur_get_groups" + "mothur_make_biom", + "mothur_taxonomy_to_krona" ], "update_time": "2023-12-14", "versions": 0 @@ -7677,8 +7827,8 @@ "doi": "", "edam_operation": [ "Sequence alignment analysis", - "Multiple sequence alignment", - "Phylogenetic tree generation" + "Phylogenetic tree generation", + "Multiple sequence alignment" ], "edam_topic": [], "id": "86900be4282d4b1d", @@ -7696,20 +7846,20 @@ "name:microgalaxy" ], "tools": [ + "Add_a_column1", + "tab2fasta", "tp_split_on_column", - "regexColumn1", + "gops_intersect_1", "rbc_mafft", - "bg_diamond_view", - "Filter1", - "bg_diamond", "join1", - "tab2fasta", - "collapse_dataset", - "Cut1", + "bg_diamond", "cat1", + "collapse_dataset", "rapidnj", - "Add_a_column1", - "gops_intersect_1" + "Filter1", + "bg_diamond_view", + "Cut1", + "regexColumn1" ], "update_time": "2023-12-14", "versions": 0 @@ -7720,17 +7870,17 @@ "deprecated": false, "doi": "", "edam_operation": [ - "Visualisation", - "Sequence composition calculation", - "Sequence assembly validation", "Statistical calculation", - "Validation", + "Aggregation", "Genome annotation", - "Coding region prediction", + "Sequence assembly validation", + "Sequencing quality control", "Gene prediction", - "Genome assembly", - "Aggregation", - "Sequencing quality control" + "Validation", + "Coding region prediction", + "Sequence composition calculation", + "Visualisation", + "Genome assembly" ], "edam_topic": [], "id": "8f3ce55d44d9f369", @@ -7779,11 +7929,11 @@ "name:microgalaxy" ], "tools": [ - "jbrowse", - "iframe", "create_or_update", - "list_organism", - "create_account" + "iframe", + "jbrowse", + "create_account", + "list_organism" ], "update_time": "2023-12-14", "versions": 0 @@ -7794,10 +7944,10 @@ "deprecated": false, "doi": "", "edam_operation": [ - "Genome visualisation", "Coding region prediction", - "Genome annotation", - "Gene prediction" + "Gene prediction", + "Genome visualisation", + "Genome annotation" ], "edam_topic": [], "id": "e1894c36f1ab4ab4", @@ -7814,8 +7964,8 @@ "name:microgalaxy" ], "tools": [ - "jbrowse", - "prokka" + "prokka", + "jbrowse" ], "update_time": "2023-12-14", "versions": 0 @@ -7826,24 +7976,24 @@ "deprecated": false, "doi": "", "edam_operation": [ - "Genome assembly", + "Base-calling", + "Pairwise sequence alignment", "Sequence visualisation", - "Gene prediction", - "Genome annotation", - "Sequence analysis", + "De-novo assembly", "Variant calling", - "Base-calling", - "Antimicrobial resistance prediction", + "Scatter plot plotting", + "Genome annotation", + "Sequence assembly", + "Gene prediction", + "Genome visualisation", + "Mapping assembly", "Coding region prediction", "Cross-assembly", - "Mapping assembly", - "Sequence assembly", + "Antimicrobial resistance prediction", "Box-Whisker plot plotting", - "Genome visualisation", - "Pairwise sequence alignment", "Sequence assembly visualisation", - "Scatter plot plotting", - "De-novo assembly" + "Sequence analysis", + "Genome assembly" ], "edam_topic": [], "id": "152223c8aed27357", @@ -7860,42 +8010,42 @@ "name:microgalaxy" ], "tools": [ + "circos_wiggle_to_scatter", + "tp_split_on_column", + "bandage_image", + "flye", + "deeptools_bam_coverage", + "staramr_search", + "PlasFlow", + "regex1", "jbrowse", - "bg_column_arrange_by_header", + "tp_cat", + "tp_head_tool", + "ncbi_blastn_wrapper", + "medaka_consensus_pipeline", "gff2bed1", - "tp_text_file_with_recurring_lines", - "circos_gc_skew", + "circos", + "tbl2gff3", + "join1", "trimmomatic", + "tp_text_file_with_recurring_lines", + "prokka", + "nanoplot", + "bg_column_arrange_by_header", "fasta2tab", - "fasta_compute_length", "Add_a_column1", - "circos_interval_to_tile", - "tp_sort_header_tool", + "tp_cut_tool", "minimap2", - "Filter1", - "bandage_image", - "nanoplot", - "join1", - "PlasFlow", - "circos", - "tp_head_tool", - "deeptools_bam_coverage", "Grep1", - "tp_cut_tool", + "tab2fasta", + "fasta_compute_length", + "tp_sort_header_tool", + "circos_interval_to_tile", "tp_easyjoin_tool", - "tp_cat", "regex_replace", - "Cut1", - "tp_split_on_column", - "medaka_consensus_pipeline", - "circos_wiggle_to_scatter", - "ncbi_blastn_wrapper", - "staramr_search", - "prokka", - "regex1", - "flye", - "tbl2gff3", - "tab2fasta" + "circos_gc_skew", + "Filter1", + "Cut1" ], "update_time": "2023-12-14", "versions": 0 @@ -7924,8 +8074,8 @@ "name:microgalaxy" ], "tools": [ - "raxml", - "interactive_tool_rstudio" + "interactive_tool_rstudio", + "raxml" ], "update_time": "2023-12-14", "versions": 0 @@ -7951,11 +8101,11 @@ "name:microgalaxy" ], "tools": [ + "snp_dists", "bcftools_consensus", - "snp_sites", "tb_variant_filter", - "tp_cat", - "snp_dists" + "snp_sites", + "tp_cat" ], "update_time": "2023-12-14", "versions": 0 @@ -7967,8 +8117,8 @@ "doi": "", "edam_operation": [ "Phylogenetic tree visualisation", - "Variant calling", - "Phylogenetic tree generation" + "Phylogenetic tree generation", + "Variant calling" ], "edam_topic": [], "id": "3a8fde248a4d0383", @@ -7985,10 +8135,10 @@ "name:microgalaxy" ], "tools": [ - "trimmomatic", - "tb_variant_filter", + "snippy", "__MERGE_COLLECTION__", - "snippy" + "tb_variant_filter", + "trimmomatic" ], "update_time": "2023-12-14", "versions": 0 @@ -8016,14 +8166,14 @@ "name:microgalaxy" ], "tools": [ + "addName", "samtools_view", - "tb_profiler_profile", "tp_grep_tool", + "tp_sed_tool", "tp_replace_in_line", "__MERGE_COLLECTION__", "tp_cat", - "addName", - "tp_sed_tool" + "tb_profiler_profile" ], "update_time": "2023-12-14", "versions": 0 @@ -8036,16 +8186,16 @@ "deprecated": false, "doi": "", "edam_operation": [ - "Phylogenetic tree visualisation", - "Sequence composition calculation", "Statistical calculation", - "Validation", + "Taxonomic classification", "Antimicrobial resistance prediction", "Variant calling", + "Phylogenetic tree visualisation", + "Sequencing quality control", "Phylogenetic tree generation", + "Validation", "Genome visualisation", - "Taxonomic classification", - "Sequencing quality control" + "Sequence composition calculation" ], "edam_topic": [], "id": "3ff4dbcc7a602e6b", @@ -8065,13 +8215,13 @@ "tools": [ "multiqc", "kraken2", - "tb_profiler_profile", + "trimmomatic", "fastqc", - "jbrowse", "snippy", - "tbvcfreport", + "jbrowse", "tb_variant_filter", - "trimmomatic" + "tb_profiler_profile", + "tbvcfreport" ], "update_time": "2023-12-14", "versions": 0 @@ -8102,12 +8252,12 @@ ], "tools": [ "bowtie2", - "bcftools_norm", "tp_awk_tool", - "snpSift_filter", + "bcftools_view", + "bcftools_norm", "vcf2tsv", - "freebayes", - "bcftools_view" + "snpSift_filter", + "freebayes" ], "update_time": "2023-12-13", "versions": 2 @@ -8138,14 +8288,14 @@ ], "tools": [ "bowtie2", - "samtools_coverage", + "collection_element_identifiers", + "samtools_depth", "bcftools_norm", "vcf2tsv", - "collection_element_identifiers", - "freebayes", - "tp_cat", "collapse_dataset", - "samtools_depth" + "samtools_coverage", + "tp_cat", + "freebayes" ], "update_time": "2023-12-13", "versions": 13 @@ -8156,13 +8306,13 @@ "deprecated": false, "doi": "", "edam_operation": [ - "Visualisation", - "Alignment", + "k-mer counting", "Formatting", "Mapping", - "k-mer counting", "Comparison", - "Nucleic acid feature detection" + "Alignment", + "Nucleic acid feature detection", + "Visualisation" ], "edam_topic": [], "id": "437704898229dfb6", @@ -8179,14 +8329,14 @@ "name:microgalaxy" ], "tools": [ - "bedtools_getfastabed", + "bedtools_maskfastabed", "tp_awk_tool", - "infernal_cmsearch", "mapseq", - "bedtools_maskfastabed", + "biom_convert", "taxonomy_krona_chart", "cmsearch_deoverlap", - "biom_convert", + "infernal_cmsearch", + "bedtools_getfastabed", "gops_concat_1", "query_tabular" ], @@ -8199,15 +8349,15 @@ "deprecated": false, "doi": "", "edam_operation": [ - "Sequence trimming", - "Sequence composition calculation", "Statistical calculation", - "Validation", - "Read pre-processing", - "Sequence contamination filtering", "Sequence merging", "Data handling", - "Sequencing quality control" + "Sequencing quality control", + "Sequence contamination filtering", + "Sequence trimming", + "Validation", + "Read pre-processing", + "Sequence composition calculation" ], "edam_topic": [], "id": "8f415b0c409f56f7", @@ -8224,17 +8374,17 @@ "name:microgalaxy" ], "tools": [ - "cshl_fasta_formatter", + "fastq_dump", + "fastp", "tp_find_and_replace", - "fastq_to_fasta_python", + "iuc_pear", "multiqc", - "fastq_dump", + "trimmomatic", "fastqc", "__UNZIP_COLLECTION__", + "cshl_fasta_formatter", "prinseq", - "iuc_pear", - "fastp", - "trimmomatic" + "fastq_to_fasta_python" ], "update_time": "2023-12-13", "versions": 1 @@ -8245,11 +8395,11 @@ "deprecated": false, "doi": "", "edam_operation": [ - "Read summarisation", - "RNA-Seq quantification", + "Sequencing quality control", "Validation", + "Read summarisation", "Read mapping", - "Sequencing quality control" + "RNA-Seq quantification" ], "edam_topic": [], "id": "4566262dd0acc8ab", @@ -8267,8 +8417,8 @@ "name:microgalaxy" ], "tools": [ - "featurecounts", "bowtie2", + "featurecounts", "multiqc" ], "update_time": "2023-12-07", @@ -8280,25 +8430,25 @@ "deprecated": false, "doi": "", "edam_operation": [ - "Visualisation", - "Sequence composition calculation", - "Fold recognition", "Statistical calculation", - "Validation", - "Read mapping", + "Gene functional annotation", + "Sequence annotation", "Genome annotation", - "Query and retrieval", - "Sequence alignment analysis", - "Genome assembly", + "Mapping", "Sequencing quality control", + "Sequence alignment analysis", + "Fold recognition", + "Homology-based gene prediction", + "Sequence composition calculation", + "Query and retrieval", "Sequence assembly validation", - "Mapping", + "Validation", "Information extraction", - "Homology-based gene prediction", - "Sequence clustering", "Sequence analysis", - "Sequence annotation", - "Gene functional annotation" + "Read mapping", + "Sequence clustering", + "Visualisation", + "Genome assembly" ], "edam_topic": [], "id": "9b9e1e28f3683f92", @@ -8316,22 +8466,22 @@ "name:microgalaxy" ], "tools": [ - "bedtools_getfastabed", "bowtie2", - "cd_hit", - "eggnog_mapper", - "metaeuk_easy_predict", "multiqc", - "fastqc", - "bg_diamond", - "quast", "bg_diamond_makedb", - "metagene_annotator", - "dbbuilder", - "megahit", + "cd_hit", + "bedtools_getfastabed", + "fastqc", "cat1", + "bg_diamond", + "eggnog_mapper", + "megahit", + "dbbuilder", "kofamscan", - "translate_nucleotides" + "metagene_annotator", + "translate_nucleotides", + "metaeuk_easy_predict", + "quast" ], "update_time": "2023-12-07", "versions": 72 @@ -8342,10 +8492,10 @@ "deprecated": false, "doi": "", "edam_operation": [ - "Sequence composition calculation", + "Sequencing quality control", "Statistical calculation", "Validation", - "Sequencing quality control" + "Sequence composition calculation" ], "edam_topic": [], "id": "bb604ff5e010e7ab", @@ -8363,9 +8513,9 @@ "name:microgalaxy" ], "tools": [ - "trimmomatic", "fastqc", - "multiqc" + "multiqc", + "trimmomatic" ], "update_time": "2023-12-07", "versions": 51 @@ -8376,10 +8526,10 @@ "deprecated": false, "doi": "", "edam_operation": [ - "Cross-assembly", "Taxonomic classification", + "Expression analysis", "Read mapping", - "Expression analysis" + "Cross-assembly" ], "edam_topic": [], "id": "bdc7cfaac0db2eab", @@ -8398,10 +8548,10 @@ ], "tools": [ "bowtie2", - "kraken2", + "recentrifuge", "fastq_to_tabular", + "kraken2", "filter_tabular", - "recentrifuge", "seq_filter_by_id" ], "update_time": "2023-12-07", @@ -8413,14 +8563,14 @@ "deprecated": false, "doi": "", "edam_operation": [ - "Visualisation", - "Filtering", "Statistical calculation", - "Genome annotation", - "Standardisation and normalisation", - "Cross-assembly", "Taxonomic classification", - "Expression analysis" + "Standardisation and normalisation", + "Expression analysis", + "Genome annotation", + "Filtering", + "Visualisation", + "Cross-assembly" ], "edam_topic": [], "id": "e69b555faa6bb962", @@ -8438,11 +8588,11 @@ "name:microgalaxy" ], "tools": [ - "interactive_tool_phinch", - "kraken2", "recentrifuge", - "maaslin2", - "kraken_biom" + "kraken_biom", + "kraken2", + "interactive_tool_phinch", + "maaslin2" ], "update_time": "2023-12-07", "versions": 18 @@ -8453,14 +8603,14 @@ "deprecated": false, "doi": "", "edam_operation": [ - "Visualisation", "Statistical calculation", "Imputation", - "Standardisation and normalisation", "Heat map generation", + "Standardisation and normalisation", "Protein quantification", + "Clustering", "Principal component plotting", - "Clustering" + "Visualisation" ], "edam_topic": [], "id": "96d198ed953449fd", @@ -8487,34 +8637,34 @@ "deprecated": false, "doi": "", "edam_operation": [ - "Visualisation", - "Sequence composition calculation", - "Formatting", "Statistical calculation", + "Formatting", "Gene functional annotation", - "Validation", - "Sequence database search", + "Visualisation", "Format validation", - "Primer removal", - "Coding region prediction", - "Local alignment", - "Sequence assembly", - "Database search", - "Sequence profile generation", + "Conversion", + "Probabilistic sequence generation", "Sequencing quality control", + "Sequence assembly", "Protein feature detection", - "Sequence trimming", - "Multiple sequence alignment", - "Sequence assembly validation", + "Gene prediction", "Sequence motif recognition", + "Coding region prediction", + "Sequence composition calculation", "Sequence generation", - "Sequence analysis", - "Read pre-processing", + "Database search", + "Sequence database search", "Data retrieval", - "Gene prediction", "Taxonomic classification", - "Conversion", - "Probabilistic sequence generation" + "Multiple sequence alignment", + "Sequence assembly validation", + "Sequence trimming", + "Sequence profile generation", + "Validation", + "Sequence analysis", + "Read pre-processing", + "Primer removal", + "Local alignment" ], "edam_topic": [], "id": "6158c3b5fc12044e", @@ -8530,23 +8680,23 @@ "name:microgalaxy" ], "tools": [ + "coverm_genome", "fasplit", "tp_awk_tool", "tp_grep_tool", + "sort1", + "cat_bins", + "trim_galore", "fastqc", "checkm_lineage_wf", - "hmmer_hmmscan", - "coverm_genome", - "quast", + "interproscan", "coverm_contig", - "fraggenescan", - "maxbin2", - "cat_bins", - "tp_cat", + "hmmer_hmmscan", "kofamscan", - "trim_galore", - "interproscan", - "sort1" + "tp_cat", + "maxbin2", + "quast", + "fraggenescan" ], "update_time": "2023-03-16", "versions": 22 @@ -8557,16 +8707,16 @@ "deprecated": false, "doi": "", "edam_operation": [ - "Sequence trimming", - "Sequence composition calculation", "Statistical calculation", - "Gene expression profiling", - "Primer removal", - "Read pre-processing", "Sequence similarity search", + "Sequencing quality control", + "Gene expression profiling", + "Sequence trimming", "Sequence alignment analysis", "Sequence comparison", - "Sequencing quality control" + "Read pre-processing", + "Primer removal", + "Sequence composition calculation" ], "edam_topic": [], "id": "385cc7df70d7916b", @@ -8582,12 +8732,12 @@ "name:microgalaxy" ], "tools": [ - "collection_column_join", "kallisto_quant", - "fastqc", - "__UNZIP_COLLECTION__", + "collection_column_join", "trim_galore", - "bg_sortmerna" + "fastqc", + "bg_sortmerna", + "__UNZIP_COLLECTION__" ], "update_time": "2023-02-27", "versions": 16 @@ -8600,11 +8750,11 @@ "deprecated": false, "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Sequence assembly validation", "Statistical calculation", + "Sequencing quality control", "Validation", - "Sequencing quality control" + "Sequence composition calculation", + "Sequence assembly validation" ], "edam_topic": [], "id": "a8aee61c2cbaf6ea", @@ -8621,13 +8771,13 @@ "name:microgalaxy" ], "tools": [ + "__RELABEL_FROM_FILE__", + "checkm2", + "collection_element_identifiers", "multiqc", "__FLATTEN__", - "collection_element_identifiers", - "__RELABEL_FROM_FILE__", "__MERGE_COLLECTION__", - "regex1", - "checkm2" + "regex1" ], "update_time": "2025-12-08", "versions": 1 @@ -8642,9 +8792,9 @@ "deprecated": false, "doi": "", "edam_operation": [ - "Visualisation", "Taxonomic classification", - "Aggregation" + "Aggregation", + "Visualisation" ], "edam_topic": [], "id": "3011f5dbf884c9bc", @@ -8663,9 +8813,9 @@ "name:iwc" ], "tools": [ + "krakentools_kreport2krona", "kraken2", - "taxonomy_krona_chart", - "krakentools_kreport2krona" + "taxonomy_krona_chart" ], "update_time": "2025-05-23", "versions": 0 @@ -8680,15 +8830,15 @@ "deprecated": false, "doi": "", "edam_operation": [ - "Antimicrobial resistance prediction", "Base-calling", + "Antimicrobial resistance prediction", + "De-novo assembly", "Variant calling", + "Sequence assembly visualisation", + "Sequence assembly", "Cross-assembly", "Mapping assembly", - "Sequence assembly", - "Genome assembly", - "Sequence assembly visualisation", - "De-novo assembly" + "Genome assembly" ], "edam_topic": [], "id": "3f252e077e0bcce5", @@ -8707,18 +8857,18 @@ "name:microgalaxy" ], "tools": [ - "medaka_consensus_pipeline", - "param_value_from_file", - "compose_text_param", - "__BUILD_LIST__", - "tp_find_and_replace", "abricate", "collection_element_identifiers", "bandage_image", - "split_file_to_collection", "flye", - "fasta2tab", - "tab2fasta" + "tp_find_and_replace", + "split_file_to_collection", + "compose_text_param", + "__BUILD_LIST__", + "tab2fasta", + "medaka_consensus_pipeline", + "param_value_from_file", + "fasta2tab" ], "update_time": "2025-04-25", "versions": 1 @@ -8733,14 +8883,12 @@ "deprecated": false, "doi": "", "edam_operation": [ - "Phylogenetic tree generation (from molecular sequences)", + "Phylogenetic tree generation", "Visualisation", - "Phylogenetic tree generation (maximum likelihood and Bayesian methods)", "Multiple sequence alignment", - "Mapping", "Phylogenetic tree reconstruction", "Phylogenetic tree analysis", - "Phylogenetic tree generation" + "Mapping" ], "edam_topic": [], "id": "3ef08553982f6ffc", @@ -8759,28 +8907,28 @@ "name:iwc" ], "tools": [ - "Grouping1", + "tp_split_on_column", + "ggplot2_heatmap", + "bedtools_getfastabed", + "collapse_dataset", + "regex1", + "tp_replace_in_column", + "fasta_merge_files_and_filter_unique_sequences", + "newick_display", "regexColumn1", - "clustalw", - "__FILTER_FAILED_DATASETS__", + "tp_multijoin_tool", + "Count1", + "__FILTER_EMPTY_DATASETS__", "fasta2tab", "tp_sorted_uniq", - "fasta_merge_files_and_filter_unique_sequences", - "collapse_dataset", - "__FILTER_EMPTY_DATASETS__", - "bedtools_getfastabed", - "tp_multijoin_tool", - "ggplot2_heatmap", - "Cut1", - "Remove beginning1", + "Grouping1", "fasttree", - "tp_split_on_column", + "tab2fasta", + "Remove beginning1", "collection_column_join", - "tp_replace_in_column", - "newick_display", - "regex1", - "Count1", - "tab2fasta" + "clustalw", + "__FILTER_FAILED_DATASETS__", + "Cut1" ], "update_time": "2025-04-25", "versions": 1 @@ -8795,9 +8943,9 @@ "deprecated": false, "doi": "", "edam_operation": [ - "Visualisation", "Taxonomic classification", - "Aggregation" + "Aggregation", + "Visualisation" ], "edam_topic": [], "id": "4b5f6b5d4f36e38b", @@ -8816,9 +8964,9 @@ "name:iwc" ], "tools": [ + "krakentools_kreport2krona", "kraken2", - "taxonomy_krona_chart", - "krakentools_kreport2krona" + "taxonomy_krona_chart" ], "update_time": "2025-04-25", "versions": 1 @@ -8853,24 +9001,24 @@ "name:iwc" ], "tools": [ + "tp_cut_tool", + "clair3", + "table_compute", + "samtools_depth", "bcftools_consensus", + "CONVERTER_gz_to_uncompressed", "Paste1", - "samtools_coverage", - "regexColumn1", "bcftools_norm", - "CONVERTER_gz_to_uncompressed", - "snpSift_filter", - "tp_cut_tool", "Cut1", "snpSift_extractFields", - "clair3", + "samtools_coverage", + "snpSift_filter", "collapse_dataset", - "Remove beginning1", - "table_compute", - "tp_head_tool", + "minimap2", "Count1", - "samtools_depth", - "minimap2" + "tp_head_tool", + "Remove beginning1", + "regexColumn1" ], "update_time": "2025-04-25", "versions": 1 @@ -8905,24 +9053,24 @@ "name:iwc" ], "tools": [ + "tp_cut_tool", + "clair3", + "table_compute", + "samtools_depth", "bcftools_consensus", + "CONVERTER_gz_to_uncompressed", "Paste1", - "samtools_coverage", - "regexColumn1", "bcftools_norm", - "CONVERTER_gz_to_uncompressed", - "snpSift_filter", - "tp_cut_tool", "Cut1", "snpSift_extractFields", - "clair3", + "samtools_coverage", + "snpSift_filter", "collapse_dataset", - "Remove beginning1", - "table_compute", - "tp_head_tool", + "minimap2", "Count1", - "samtools_depth", - "minimap2" + "tp_head_tool", + "Remove beginning1", + "regexColumn1" ], "update_time": "2025-04-25", "versions": 1 @@ -8954,11 +9102,11 @@ "name:microgalaxy" ], "tools": [ - "fastq_dl", - "CONVERTER_uncompressed_to_gz", "tp_awk_tool", + "CONVERTER_uncompressed_to_gz", "CONVERTER_gz_to_uncompressed", - "__MERGE_COLLECTION__" + "__MERGE_COLLECTION__", + "fastq_dl" ], "update_time": "2025-04-25", "versions": 1 @@ -8974,8 +9122,8 @@ "doi": "", "edam_operation": [ "k-mer counting", - "Visualisation", "Formatting", + "Visualisation", "Mapping" ], "edam_topic": [], @@ -8995,10 +9143,10 @@ "name:microgalaxy" ], "tools": [ - "tp_awk_tool", - "__FILTER_FROM_FILE__", "bedtools_maskfastabed", "mapseq", + "tp_awk_tool", + "__FILTER_FROM_FILE__", "collection_element_identifiers", "taxonomy_krona_chart", "biom_convert", @@ -9017,14 +9165,14 @@ "deprecated": false, "doi": "", "edam_operation": [ - "Sequence trimming", - "Sequence composition calculation", - "Nucleic acid design", "Statistical calculation", + "Sequencing quality control", + "Sequence contamination filtering", + "Sequence trimming", "Validation", + "Nucleic acid design", "Read pre-processing", - "Sequence contamination filtering", - "Sequencing quality control" + "Sequence composition calculation" ], "edam_topic": [], "id": "a71fcbc60caae8b6", @@ -9043,17 +9191,17 @@ "name:microgalaxy" ], "tools": [ + "fastp", "cshl_fasta_formatter", "tp_find_and_replace", - "fastq_to_fasta_python", "multiqc", + "trimmomatic", "fastqc", "__UNZIP_COLLECTION__", - "prinseq", "mgnify_seqprep", - "fastp", - "trimmomatic", - "fastq_filter" + "fastq_filter", + "prinseq", + "fastq_to_fasta_python" ], "update_time": "2025-04-25", "versions": 1 @@ -9068,13 +9216,13 @@ "deprecated": false, "doi": "", "edam_operation": [ - "Sequence trimming", - "Read pre-processing", - "Sequence composition calculation", - "Sequence contamination filtering", + "Sequencing quality control", "Statistical calculation", + "Sequence contamination filtering", + "Sequence trimming", "Validation", - "Sequencing quality control" + "Read pre-processing", + "Sequence composition calculation" ], "edam_topic": [], "id": "5f878c4cc3bff68c", @@ -9095,12 +9243,12 @@ "tools": [ "cshl_fasta_formatter", "tp_find_and_replace", - "fastq_to_fasta_python", "multiqc", + "trimmomatic", "fastqc", + "fastq_filter", "prinseq", - "trimmomatic", - "fastq_filter" + "fastq_to_fasta_python" ], "update_time": "2025-04-25", "versions": 1 @@ -9135,24 +9283,24 @@ "name:iwc" ], "tools": [ + "tp_cut_tool", + "clair3", + "table_compute", + "samtools_depth", "bcftools_consensus", + "CONVERTER_gz_to_uncompressed", "Paste1", - "samtools_coverage", - "regexColumn1", "bcftools_norm", - "CONVERTER_gz_to_uncompressed", - "snpSift_filter", - "tp_cut_tool", "Cut1", "snpSift_extractFields", - "clair3", + "samtools_coverage", + "snpSift_filter", "collapse_dataset", - "Remove beginning1", - "table_compute", - "tp_head_tool", + "minimap2", "Count1", - "samtools_depth", - "minimap2" + "tp_head_tool", + "Remove beginning1", + "regexColumn1" ], "update_time": "2025-04-25", "versions": 1 @@ -9167,13 +9315,13 @@ "deprecated": false, "doi": "", "edam_operation": [ - "Sequence trimming", - "Read pre-processing", - "Sequence composition calculation", - "Sequence contamination filtering", + "Sequencing quality control", "Statistical calculation", + "Sequence contamination filtering", + "Sequence trimming", "Validation", - "Sequencing quality control" + "Read pre-processing", + "Sequence composition calculation" ], "edam_topic": [], "id": "afb67b4b9952f57d", @@ -9194,12 +9342,12 @@ "tools": [ "cshl_fasta_formatter", "tp_find_and_replace", - "fastq_to_fasta_python", "multiqc", + "trimmomatic", "fastqc", + "fastq_filter", "prinseq", - "trimmomatic", - "fastq_filter" + "fastq_to_fasta_python" ], "update_time": "2025-04-25", "versions": 1 @@ -9234,24 +9382,24 @@ "name:iwc" ], "tools": [ + "tp_cut_tool", + "clair3", + "table_compute", + "samtools_depth", "bcftools_consensus", + "CONVERTER_gz_to_uncompressed", "Paste1", - "samtools_coverage", - "regexColumn1", "bcftools_norm", - "CONVERTER_gz_to_uncompressed", - "snpSift_filter", - "tp_cut_tool", "Cut1", "snpSift_extractFields", - "clair3", + "samtools_coverage", + "snpSift_filter", "collapse_dataset", - "Remove beginning1", - "table_compute", - "tp_head_tool", + "minimap2", "Count1", - "samtools_depth", - "minimap2" + "tp_head_tool", + "Remove beginning1", + "regexColumn1" ], "update_time": "2025-04-25", "versions": 1 @@ -9283,11 +9431,11 @@ "name:microgalaxy" ], "tools": [ - "fastq_dl", - "CONVERTER_uncompressed_to_gz", "tp_awk_tool", + "CONVERTER_uncompressed_to_gz", "CONVERTER_gz_to_uncompressed", - "__MERGE_COLLECTION__" + "__MERGE_COLLECTION__", + "fastq_dl" ], "update_time": "2025-04-25", "versions": 1 @@ -9303,8 +9451,8 @@ "doi": "", "edam_operation": [ "k-mer counting", - "Visualisation", "Formatting", + "Visualisation", "Mapping" ], "edam_topic": [], @@ -9324,10 +9472,10 @@ "name:microgalaxy" ], "tools": [ - "tp_awk_tool", - "__FILTER_FROM_FILE__", "bedtools_maskfastabed", "mapseq", + "tp_awk_tool", + "__FILTER_FROM_FILE__", "collection_element_identifiers", "taxonomy_krona_chart", "biom_convert", @@ -9346,14 +9494,14 @@ "deprecated": false, "doi": "", "edam_operation": [ - "Sequence trimming", - "Sequence composition calculation", - "Nucleic acid design", "Statistical calculation", + "Sequencing quality control", + "Sequence contamination filtering", + "Sequence trimming", "Validation", + "Nucleic acid design", "Read pre-processing", - "Sequence contamination filtering", - "Sequencing quality control" + "Sequence composition calculation" ], "edam_topic": [], "id": "20b7ae4b517a80fd", @@ -9372,17 +9520,17 @@ "name:microgalaxy" ], "tools": [ + "fastp", "cshl_fasta_formatter", "tp_find_and_replace", - "fastq_to_fasta_python", "multiqc", + "trimmomatic", "fastqc", "__UNZIP_COLLECTION__", - "prinseq", "mgnify_seqprep", - "fastp", - "trimmomatic", - "fastq_filter" + "fastq_filter", + "prinseq", + "fastq_to_fasta_python" ], "update_time": "2025-04-25", "versions": 1 @@ -9397,13 +9545,13 @@ "deprecated": false, "doi": "", "edam_operation": [ - "Sequence trimming", - "Read pre-processing", - "Sequence composition calculation", - "Sequence contamination filtering", + "Sequencing quality control", "Statistical calculation", + "Sequence contamination filtering", + "Sequence trimming", "Validation", - "Sequencing quality control" + "Read pre-processing", + "Sequence composition calculation" ], "edam_topic": [], "id": "46f184a0e95f3c1c", @@ -9424,12 +9572,12 @@ "tools": [ "cshl_fasta_formatter", "tp_find_and_replace", - "fastq_to_fasta_python", "multiqc", + "trimmomatic", "fastqc", + "fastq_filter", "prinseq", - "trimmomatic", - "fastq_filter" + "fastq_to_fasta_python" ], "update_time": "2025-04-25", "versions": 1 @@ -9444,19 +9592,19 @@ "deprecated": false, "doi": "", "edam_operation": [ - "Visualisation", - "Sequence composition calculation", "Statistical calculation", - "Validation", - "Sequence contamination filtering", - "Box-Whisker plot plotting", - "Sequence alignment analysis", "Taxonomic classification", - "Data handling", "Pairwise sequence alignment", + "Box-Whisker plot plotting", "Aggregation", + "Data handling", "Scatter plot plotting", - "Sequencing quality control" + "Sequencing quality control", + "Sequence contamination filtering", + "Sequence alignment analysis", + "Validation", + "Sequence composition calculation", + "Visualisation" ], "edam_topic": [], "id": "a8b9252fad5fe06a", @@ -9476,23 +9624,23 @@ "name:iwc" ], "tools": [ + "Add_a_column1", + "fastp", "collection_column_join", - "Grep1", - "samtools_fastx", - "regexColumn1", "multiqc", "kraken2", + "samtools_fastx", "fastqc", - "bamtools_split_mapped", + "collapse_dataset", "nanoplot", - "porechop", + "minimap2", + "Grep1", "__FILTER_FAILED_DATASETS__", - "krakentools_extract_kraken_reads", - "fastp", - "collapse_dataset", + "bamtools_split_mapped", + "porechop", "Cut1", - "Add_a_column1", - "minimap2" + "regexColumn1", + "krakentools_extract_kraken_reads" ], "update_time": "2025-04-25", "versions": 1 @@ -9507,14 +9655,12 @@ "deprecated": false, "doi": "", "edam_operation": [ - "Phylogenetic tree generation (from molecular sequences)", + "Phylogenetic tree generation", "Visualisation", - "Phylogenetic tree generation (maximum likelihood and Bayesian methods)", "Multiple sequence alignment", - "Mapping", "Phylogenetic tree reconstruction", "Phylogenetic tree analysis", - "Phylogenetic tree generation" + "Mapping" ], "edam_topic": [], "id": "2d3063882d8239ff", @@ -9533,28 +9679,28 @@ "name:iwc" ], "tools": [ - "Grouping1", + "tp_split_on_column", + "ggplot2_heatmap", + "bedtools_getfastabed", + "collapse_dataset", + "regex1", + "tp_replace_in_column", + "fasta_merge_files_and_filter_unique_sequences", + "newick_display", "regexColumn1", - "clustalw", - "__FILTER_FAILED_DATASETS__", + "tp_multijoin_tool", + "Count1", + "__FILTER_EMPTY_DATASETS__", "fasta2tab", "tp_sorted_uniq", - "fasta_merge_files_and_filter_unique_sequences", - "collapse_dataset", - "__FILTER_EMPTY_DATASETS__", - "bedtools_getfastabed", - "tp_multijoin_tool", - "ggplot2_heatmap", - "Cut1", - "Remove beginning1", + "Grouping1", "fasttree", - "tp_split_on_column", + "tab2fasta", + "Remove beginning1", "collection_column_join", - "tp_replace_in_column", - "newick_display", - "regex1", - "Count1", - "tab2fasta" + "clustalw", + "__FILTER_FAILED_DATASETS__", + "Cut1" ], "update_time": "2024-07-03", "versions": 1 @@ -9600,9 +9746,9 @@ "deprecated": false, "doi": "", "edam_operation": [ - "Visualisation", "Taxonomic classification", - "Aggregation" + "Aggregation", + "Visualisation" ], "edam_topic": [], "id": "8f5904693b5f74f4", @@ -9621,9 +9767,9 @@ "name:iwc" ], "tools": [ + "krakentools_kreport2krona", "kraken2", - "taxonomy_krona_chart", - "krakentools_kreport2krona" + "taxonomy_krona_chart" ], "update_time": "2024-06-25", "versions": 1 @@ -9638,15 +9784,15 @@ "deprecated": false, "doi": "", "edam_operation": [ - "Antimicrobial resistance prediction", "Base-calling", + "Antimicrobial resistance prediction", + "De-novo assembly", "Variant calling", + "Sequence assembly visualisation", + "Sequence assembly", "Cross-assembly", "Mapping assembly", - "Sequence assembly", - "Genome assembly", - "Sequence assembly visualisation", - "De-novo assembly" + "Genome assembly" ], "edam_topic": [], "id": "cce88bc57b180d09", @@ -9665,18 +9811,18 @@ "name:microgalaxy" ], "tools": [ - "medaka_consensus_pipeline", - "param_value_from_file", - "compose_text_param", - "__BUILD_LIST__", - "tp_find_and_replace", "abricate", "collection_element_identifiers", "bandage_image", - "split_file_to_collection", "flye", - "fasta2tab", - "tab2fasta" + "tp_find_and_replace", + "split_file_to_collection", + "compose_text_param", + "__BUILD_LIST__", + "tab2fasta", + "medaka_consensus_pipeline", + "param_value_from_file", + "fasta2tab" ], "update_time": "2024-06-25", "versions": 1 @@ -9711,24 +9857,24 @@ "name:iwc" ], "tools": [ + "tp_cut_tool", + "clair3", + "table_compute", + "samtools_depth", "bcftools_consensus", + "CONVERTER_gz_to_uncompressed", "Paste1", - "samtools_coverage", - "regexColumn1", "bcftools_norm", - "CONVERTER_gz_to_uncompressed", - "snpSift_filter", - "tp_cut_tool", "Cut1", "snpSift_extractFields", - "clair3", + "samtools_coverage", + "snpSift_filter", "collapse_dataset", - "Remove beginning1", - "table_compute", - "tp_head_tool", + "minimap2", "Count1", - "samtools_depth", - "minimap2" + "tp_head_tool", + "Remove beginning1", + "regexColumn1" ], "update_time": "2024-06-25", "versions": 1 @@ -9743,19 +9889,19 @@ "deprecated": false, "doi": "", "edam_operation": [ - "Visualisation", - "Sequence composition calculation", "Statistical calculation", - "Validation", - "Sequence contamination filtering", - "Box-Whisker plot plotting", - "Sequence alignment analysis", "Taxonomic classification", - "Data handling", "Pairwise sequence alignment", + "Box-Whisker plot plotting", "Aggregation", + "Data handling", "Scatter plot plotting", - "Sequencing quality control" + "Sequencing quality control", + "Sequence contamination filtering", + "Sequence alignment analysis", + "Validation", + "Sequence composition calculation", + "Visualisation" ], "edam_topic": [], "id": "574e42683dc3961b", @@ -9775,23 +9921,23 @@ "name:iwc" ], "tools": [ + "Add_a_column1", + "fastp", "collection_column_join", - "Grep1", - "samtools_fastx", - "regexColumn1", "multiqc", "kraken2", + "samtools_fastx", "fastqc", - "bamtools_split_mapped", + "collapse_dataset", "nanoplot", - "porechop", + "minimap2", + "Grep1", "__FILTER_FAILED_DATASETS__", - "krakentools_extract_kraken_reads", - "fastp", - "collapse_dataset", + "bamtools_split_mapped", + "porechop", "Cut1", - "Add_a_column1", - "minimap2" + "regexColumn1", + "krakentools_extract_kraken_reads" ], "update_time": "2024-06-25", "versions": 1 @@ -9804,11 +9950,11 @@ "deprecated": false, "doi": "", "edam_operation": [ - "Sequence composition calculation", - "Sequence assembly validation", "Statistical calculation", + "Sequencing quality control", "Validation", - "Sequencing quality control" + "Sequence composition calculation", + "Sequence assembly validation" ], "edam_topic": [], "id": "f05ed1e5c5dfffa9", @@ -9825,13 +9971,13 @@ "name:microgalaxy" ], "tools": [ + "__RELABEL_FROM_FILE__", + "checkm2", + "collection_element_identifiers", "multiqc", "__FLATTEN__", - "collection_element_identifiers", - "__RELABEL_FROM_FILE__", "__MERGE_COLLECTION__", - "regex1", - "checkm2" + "regex1" ], "update_time": "2025-12-08", "versions": 1 @@ -9846,15 +9992,15 @@ "deprecated": false, "doi": "", "edam_operation": [ - "Antimicrobial resistance prediction", "Base-calling", + "Antimicrobial resistance prediction", + "De-novo assembly", "Variant calling", + "Sequence assembly visualisation", + "Sequence assembly", "Cross-assembly", "Mapping assembly", - "Sequence assembly", - "Genome assembly", - "Sequence assembly visualisation", - "De-novo assembly" + "Genome assembly" ], "edam_topic": [], "id": "084bb76cf47d7060", @@ -9873,18 +10019,18 @@ "name:microgalaxy" ], "tools": [ - "medaka_consensus_pipeline", - "param_value_from_file", - "compose_text_param", - "__BUILD_LIST__", - "tp_find_and_replace", "abricate", "collection_element_identifiers", "bandage_image", - "split_file_to_collection", "flye", - "fasta2tab", - "tab2fasta" + "tp_find_and_replace", + "split_file_to_collection", + "compose_text_param", + "__BUILD_LIST__", + "tab2fasta", + "medaka_consensus_pipeline", + "param_value_from_file", + "fasta2tab" ], "update_time": "2025-04-25", "versions": 1 @@ -9899,19 +10045,19 @@ "deprecated": false, "doi": "", "edam_operation": [ - "Visualisation", - "Sequence composition calculation", "Statistical calculation", - "Validation", - "Sequence contamination filtering", - "Box-Whisker plot plotting", - "Sequence alignment analysis", "Taxonomic classification", - "Data handling", "Pairwise sequence alignment", + "Box-Whisker plot plotting", "Aggregation", + "Data handling", "Scatter plot plotting", - "Sequencing quality control" + "Sequencing quality control", + "Sequence contamination filtering", + "Sequence alignment analysis", + "Validation", + "Sequence composition calculation", + "Visualisation" ], "edam_topic": [], "id": "69d91340fc7effa2", @@ -9931,23 +10077,23 @@ "name:iwc" ], "tools": [ + "Add_a_column1", + "fastp", "collection_column_join", - "Grep1", - "samtools_fastx", - "regexColumn1", "multiqc", "kraken2", + "samtools_fastx", "fastqc", - "bamtools_split_mapped", + "collapse_dataset", "nanoplot", - "porechop", + "minimap2", + "Grep1", "__FILTER_FAILED_DATASETS__", - "krakentools_extract_kraken_reads", - "fastp", - "collapse_dataset", + "bamtools_split_mapped", + "porechop", "Cut1", - "Add_a_column1", - "minimap2" + "regexColumn1", + "krakentools_extract_kraken_reads" ], "update_time": "2025-04-25", "versions": 1 @@ -9962,14 +10108,12 @@ "deprecated": false, "doi": "", "edam_operation": [ - "Phylogenetic tree generation (from molecular sequences)", + "Phylogenetic tree generation", "Visualisation", - "Phylogenetic tree generation (maximum likelihood and Bayesian methods)", "Multiple sequence alignment", - "Mapping", "Phylogenetic tree reconstruction", "Phylogenetic tree analysis", - "Phylogenetic tree generation" + "Mapping" ], "edam_topic": [], "id": "b60922a253df6654", @@ -9988,28 +10132,28 @@ "name:iwc" ], "tools": [ - "Grouping1", + "tp_split_on_column", + "ggplot2_heatmap", + "bedtools_getfastabed", + "collapse_dataset", + "regex1", + "tp_replace_in_column", + "fasta_merge_files_and_filter_unique_sequences", + "newick_display", "regexColumn1", - "clustalw", - "__FILTER_FAILED_DATASETS__", + "tp_multijoin_tool", + "Count1", + "__FILTER_EMPTY_DATASETS__", "fasta2tab", "tp_sorted_uniq", - "fasta_merge_files_and_filter_unique_sequences", - "collapse_dataset", - "__FILTER_EMPTY_DATASETS__", - "bedtools_getfastabed", - "tp_multijoin_tool", - "ggplot2_heatmap", - "Cut1", - "Remove beginning1", + "Grouping1", "fasttree", - "tp_split_on_column", + "tab2fasta", + "Remove beginning1", "collection_column_join", - "tp_replace_in_column", - "newick_display", - "regex1", - "Count1", - "tab2fasta" + "clustalw", + "__FILTER_FAILED_DATASETS__", + "Cut1" ], "update_time": "2025-04-25", "versions": 1 @@ -10024,9 +10168,9 @@ "deprecated": false, "doi": "", "edam_operation": [ - "Visualisation", "Taxonomic classification", - "Aggregation" + "Aggregation", + "Visualisation" ], "edam_topic": [], "id": "131636a795bac485", @@ -10045,9 +10189,9 @@ "name:iwc" ], "tools": [ + "krakentools_kreport2krona", "kraken2", - "taxonomy_krona_chart", - "krakentools_kreport2krona" + "taxonomy_krona_chart" ], "update_time": "2025-04-25", "versions": 1 @@ -10082,24 +10226,24 @@ "name:iwc" ], "tools": [ + "tp_cut_tool", + "clair3", + "table_compute", + "samtools_depth", "bcftools_consensus", + "CONVERTER_gz_to_uncompressed", "Paste1", - "samtools_coverage", - "regexColumn1", "bcftools_norm", - "CONVERTER_gz_to_uncompressed", - "snpSift_filter", - "tp_cut_tool", "Cut1", "snpSift_extractFields", - "clair3", + "samtools_coverage", + "snpSift_filter", "collapse_dataset", - "Remove beginning1", - "table_compute", - "tp_head_tool", + "minimap2", "Count1", - "samtools_depth", - "minimap2" + "tp_head_tool", + "Remove beginning1", + "regexColumn1" ], "update_time": "2025-04-25", "versions": 1 @@ -10134,24 +10278,24 @@ "name:iwc" ], "tools": [ + "tp_cut_tool", + "clair3", + "table_compute", + "samtools_depth", "bcftools_consensus", + "CONVERTER_gz_to_uncompressed", "Paste1", - "samtools_coverage", - "regexColumn1", "bcftools_norm", - "CONVERTER_gz_to_uncompressed", - "snpSift_filter", - "tp_cut_tool", "Cut1", "snpSift_extractFields", - "clair3", + "samtools_coverage", + "snpSift_filter", "collapse_dataset", - "Remove beginning1", - "table_compute", - "tp_head_tool", + "minimap2", "Count1", - "samtools_depth", - "minimap2" + "tp_head_tool", + "Remove beginning1", + "regexColumn1" ], "update_time": "2025-04-25", "versions": 1 @@ -10186,24 +10330,24 @@ "name:iwc" ], "tools": [ + "tp_cut_tool", + "clair3", + "table_compute", + "samtools_depth", "bcftools_consensus", + "CONVERTER_gz_to_uncompressed", "Paste1", - "samtools_coverage", - "regexColumn1", "bcftools_norm", - "CONVERTER_gz_to_uncompressed", - "snpSift_filter", - "tp_cut_tool", "Cut1", "snpSift_extractFields", - "clair3", + "samtools_coverage", + "snpSift_filter", "collapse_dataset", - "Remove beginning1", - "table_compute", - "tp_head_tool", + "minimap2", "Count1", - "samtools_depth", - "minimap2" + "tp_head_tool", + "Remove beginning1", + "regexColumn1" ], "update_time": "2025-04-25", "versions": 1 @@ -10249,14 +10393,12 @@ "deprecated": false, "doi": "", "edam_operation": [ - "Phylogenetic tree generation (from molecular sequences)", + "Phylogenetic tree generation", "Visualisation", - "Phylogenetic tree generation (maximum likelihood and Bayesian methods)", "Multiple sequence alignment", - "Mapping", "Phylogenetic tree reconstruction", "Phylogenetic tree analysis", - "Phylogenetic tree generation" + "Mapping" ], "edam_topic": [], "id": "eda40b58616a0fe4", @@ -10275,28 +10417,28 @@ "name:iwc" ], "tools": [ - "Grouping1", + "tp_split_on_column", + "ggplot2_heatmap", + "bedtools_getfastabed", + "collapse_dataset", + "regex1", + "tp_replace_in_column", + "fasta_merge_files_and_filter_unique_sequences", + "newick_display", "regexColumn1", - "clustalw", - "__FILTER_FAILED_DATASETS__", + "tp_multijoin_tool", + "Count1", + "__FILTER_EMPTY_DATASETS__", "fasta2tab", "tp_sorted_uniq", - "fasta_merge_files_and_filter_unique_sequences", - "collapse_dataset", - "__FILTER_EMPTY_DATASETS__", - "bedtools_getfastabed", - "tp_multijoin_tool", - "ggplot2_heatmap", - "Cut1", - "Remove beginning1", + "Grouping1", "fasttree", - "tp_split_on_column", + "tab2fasta", + "Remove beginning1", "collection_column_join", - "tp_replace_in_column", - "newick_display", - "regex1", - "Count1", - "tab2fasta" + "clustalw", + "__FILTER_FAILED_DATASETS__", + "Cut1" ], "update_time": "2024-07-03", "versions": 1 @@ -10331,24 +10473,24 @@ "name:iwc" ], "tools": [ + "tp_cut_tool", + "clair3", + "table_compute", + "samtools_depth", "bcftools_consensus", + "CONVERTER_gz_to_uncompressed", "Paste1", - "samtools_coverage", - "regexColumn1", "bcftools_norm", - "CONVERTER_gz_to_uncompressed", - "snpSift_filter", - "tp_cut_tool", "Cut1", "snpSift_extractFields", - "clair3", + "samtools_coverage", + "snpSift_filter", "collapse_dataset", - "Remove beginning1", - "table_compute", - "tp_head_tool", + "minimap2", "Count1", - "samtools_depth", - "minimap2" + "tp_head_tool", + "Remove beginning1", + "regexColumn1" ], "update_time": "2024-06-25", "versions": 1 @@ -10363,15 +10505,15 @@ "deprecated": false, "doi": "", "edam_operation": [ - "Antimicrobial resistance prediction", "Base-calling", + "Antimicrobial resistance prediction", + "De-novo assembly", "Variant calling", + "Sequence assembly visualisation", + "Sequence assembly", "Cross-assembly", "Mapping assembly", - "Sequence assembly", - "Genome assembly", - "Sequence assembly visualisation", - "De-novo assembly" + "Genome assembly" ], "edam_topic": [], "id": "ef8c22c2525063a2", @@ -10390,18 +10532,18 @@ "name:microgalaxy" ], "tools": [ - "medaka_consensus_pipeline", - "param_value_from_file", - "compose_text_param", - "__BUILD_LIST__", - "tp_find_and_replace", "abricate", "collection_element_identifiers", "bandage_image", - "split_file_to_collection", "flye", - "fasta2tab", - "tab2fasta" + "tp_find_and_replace", + "split_file_to_collection", + "compose_text_param", + "__BUILD_LIST__", + "tab2fasta", + "medaka_consensus_pipeline", + "param_value_from_file", + "fasta2tab" ], "update_time": "2024-06-25", "versions": 1 @@ -10416,9 +10558,9 @@ "deprecated": false, "doi": "", "edam_operation": [ - "Visualisation", "Taxonomic classification", - "Aggregation" + "Aggregation", + "Visualisation" ], "edam_topic": [], "id": "d9ba165e6ae55417", @@ -10437,9 +10579,9 @@ "name:iwc" ], "tools": [ + "krakentools_kreport2krona", "kraken2", - "taxonomy_krona_chart", - "krakentools_kreport2krona" + "taxonomy_krona_chart" ], "update_time": "2024-06-25", "versions": 1 @@ -10454,19 +10596,19 @@ "deprecated": false, "doi": "", "edam_operation": [ - "Visualisation", - "Sequence composition calculation", "Statistical calculation", - "Validation", - "Sequence contamination filtering", - "Box-Whisker plot plotting", - "Sequence alignment analysis", "Taxonomic classification", - "Data handling", "Pairwise sequence alignment", + "Box-Whisker plot plotting", "Aggregation", + "Data handling", "Scatter plot plotting", - "Sequencing quality control" + "Sequencing quality control", + "Sequence contamination filtering", + "Sequence alignment analysis", + "Validation", + "Sequence composition calculation", + "Visualisation" ], "edam_topic": [], "id": "25d52afddaa3451b", @@ -10486,23 +10628,23 @@ "name:iwc" ], "tools": [ + "Add_a_column1", + "fastp", "collection_column_join", - "Grep1", - "samtools_fastx", - "regexColumn1", "multiqc", "kraken2", + "samtools_fastx", "fastqc", - "bamtools_split_mapped", + "collapse_dataset", "nanoplot", - "porechop", + "minimap2", + "Grep1", "__FILTER_FAILED_DATASETS__", - "krakentools_extract_kraken_reads", - "fastp", - "collapse_dataset", + "bamtools_split_mapped", + "porechop", "Cut1", - "Add_a_column1", - "minimap2" + "regexColumn1", + "krakentools_extract_kraken_reads" ], "update_time": "2024-06-25", "versions": 1 diff --git a/communities/microgalaxy/resources/tag_filtered_workflows.tsv b/communities/microgalaxy/resources/tag_filtered_workflows.tsv index 1b02bf076..4f0ef2699 100644 --- a/communities/microgalaxy/resources/tag_filtered_workflows.tsv +++ b/communities/microgalaxy/resources/tag_filtered_workflows.tsv @@ -1,244 +1,247 @@ Name Source ID Link Creators Tags Creation time Update time Latest version Versions Number of steps Tools EDAM operations EDAM topics License DOI Projects To keep Deprecated -metagenomic-raw-reads-amr-analysis/main WorkflowHub 2068 https://workflowhub.eu/workflows/2068?version=2 ABRomics None, Hugo Lefeuvre 2026-02-26 2026-05-14 2 2 20.0 "table_pandas_rename_column, multiqc, groot, collection_element_identifiers, tooldistillator_summarize, tooldistillator, Remove a collection level so that outputs can be taken into account by tooldistillator -__FLATTEN__, __FILTER_FAILED_DATASETS__, tp_text_file_with_recurring_lines, __UNZIP_COLLECTION__, sylph_profile, argnorm, __RELABEL_FROM_FILE__, Removal of the first line because it is not necessary for tooldistillator -Remove beginning1, Removal of the first argNorm line that causes a multiQC error -Remove beginning1, fastq_paired_end_interlacer, deeparg_short_reads" Data parsing, Gene functional annotation, Validation, Taxonomic classification, Sequencing quality control, Antimicrobial resistance prediction GPL-3.0-or-later Intergalactic Workflow Commission (IWC) True False -cgmlst-bacterial-genome/main WorkflowHub 2055 https://workflowhub.eu/workflows/2055?version=2 ABRomics None, Clea Siguret, Hugo Lefeuvre 2026-03-13 2026-05-14 2 2 3.0 coreprofiler_allele_calling, tooldistillator_summarize, tooldistillator Multilocus sequence typing, Data parsing GPL-3.0-or-later Intergalactic Workflow Commission (IWC) True False -bacterial-quality-and-contamination-control-post-assembly/main WorkflowHub 1882 https://workflowhub.eu/workflows/1882?version=3 ABRomics None, Pierre Marin, Clea Siguret 2025-12-04 2026-05-13 3 3 14.0 pick_value, kraken2, tooldistillator_summarize, tooldistillator, est_abundance, quast, collapse_dataset, checkm2, recentrifuge Visualisation, Sequence composition calculation, Sequence assembly validation, Statistical calculation, Validation, Cross-assembly, Data parsing, Expression analysis, Taxonomic classification, Sequencing quality control GPL-3.0-or-later Intergalactic Workflow Commission (IWC) True False -sars-cov-2-pe-illumina-artic-ivar-analysis/SARS-COV-2-ILLUMINA-AMPLICON-IVAR-PANGOLIN-NEXTCLADE WorkflowHub 155 https://workflowhub.eu/workflows/155?version=7 Peter van Heusden virology 2026-03-10 2026-05-13 7 7 16.0 ivar_consensus, samtools_view, multiqc, __FLATTEN__, nextclade, samtools_stats, pangolin, bwa_mem, qualimap_bamqc, ivar_trim, fastp, snpeff_sars_cov_2, tp_cat, tp_sed_tool, ivar_variants Methylation analysis, Sequence alignment, Genome indexing, SNP detection, Validation, Read mapping, Variant calling, Primer removal, Sequence contamination filtering, Generation, Tree-based sequence alignment, Variant classification, Sequencing quality control MIT Intergalactic Workflow Commission (IWC) True False -sars-cov-2-pe-illumina-wgs-variant-calling/COVID-19-PE-WGS-ILLUMINA WorkflowHub 113 https://workflowhub.eu/workflows/113?version=4 Wolfgang Maier virology, covid-19, covid19.galaxyproject.org, emergen_validated 2021-12-21 2026-05-14 4 4 11.0 samtools_view, multiqc, samtools_stats, bwa_mem, lofreq_viterbi, lofreq_indelqual, fastp, picard_MarkDuplicates, lofreq_call, lofreq_filter, snpeff_sars_cov_2 Formatting, Sequence alignment, Genome indexing, SNP detection, Validation, Read mapping, Sequence contamination filtering, Generation, Sequencing quality control MIT Intergalactic Workflow Commission (IWC) True False -generic-non-segmented-viral-variant-calling/main WorkflowHub 1876 https://workflowhub.eu/workflows/1876?version=2 Peter van Heusden, Wolfgang Maier virology 2025-12-05 2026-05-13 2 2 23.0 samtools_view, __FILTER_FAILED_DATASETS__, qualimap_bamqc, tp_sed_tool, snpEff, __FLATTEN__, samtools_stats, bwa_mem, lofreq_viterbi, calculate_numeric_param, collapse_dataset, ivar_variants, ivar_consensus, tp_find_and_replace, map_param_value, ivar_trim, fastp, tp_cat, snpSift_extractFields, pick_value, multiqc, snpEff_build_gb Sequence alignment, Genome indexing, Validation, Read mapping, Primer removal, Sequence contamination filtering, Generation, Sequencing quality control AGPL-3.0-or-later Intergalactic Workflow Commission (IWC) True False -influenza-isolates-consensus-and-subtyping/main WorkflowHub 1260 https://workflowhub.eu/workflows/1260?version=3 Viktoria Isabel Schwarz, Wolfgang Maier, Aaron Kolbecher, Saim Momin virology 2026-02-12 2026-05-13 3 3 68.0 "wc_gnu, samtools_view, __FILTER_FAILED_DATASETS__, tp_text_file_with_recurring_lines, qualimap_bamqc, bwa mem will fail if no reference for any segment got suggested by vapor, i.e. the reference genome is empty. In that case, we need to skip further analysis of the sample. -__FILTER_FAILED_DATASETS__, __HARMONIZELISTS__, Show beginning1, Filter1, __FLATTEN__, collection_element_identifiers, bwa_mem, __RELABEL_FROM_FILE__, __APPLY_RULES__, __MERGE_COLLECTION__, collapse_dataset, Paste1, bamtools_split_ref, snipit, Grep1, ivar_consensus, param_value_from_file, tp_find_and_replace, __UNZIP_COLLECTION__, tp_easyjoin_tool, fastp, tp_cat, Cut1, rbc_mafft, __FILTER_FROM_FILE__, vapor, This seemingly no-op transformation will remove samples with no remaining segment results (cases where vapor failed for every segment). -__APPLY_RULES__, seqtk_subseq, iqtree, __DUPLICATE_FILE_TO_COLLECTION__" Multiple sequence alignment, Sequence alignment, Genome indexing, Sequence file editing, Phylogenetic analysis, Read mapping, Sequence analysis, Primer removal, Base position variability plotting, Sequence contamination filtering, Data retrieval, Sequence alignment analysis, Data handling, Generation, Sequencing quality control, De-novo assembly AGPL-3.0-or-later Intergalactic Workflow Commission (IWC) True False -pox-virus-amplicon/main WorkflowHub 439 https://workflowhub.eu/workflows/439?version=4 Viktoria Isabel Schwarz, Wolfgang Maier virology, pox 2025-10-11 2026-05-13 4 4 40.0 compose_text_param, samtools_view, __FILTER_FAILED_DATASETS__, qualimap_bamqc, tp_sed_tool, fasta_compute_length, samtools_merge, __FLATTEN__, collection_element_identifiers, samtools_stats, bwa_mem, __APPLY_RULES__, __ZIP_COLLECTION__, Grep1, ivar_consensus, param_value_from_file, split_file_to_collection, ivar_trim, fastp, tp_cat, Cut1, __SORTLIST__, EMBOSS: maskseq51, multiqc, datamash_ops Sequence alignment, Genome indexing, Validation, Read mapping, Sequence analysis, Primer removal, Local alignment, Sequence contamination filtering, Global alignment, Sequence alignment analysis, Generation, Sequencing quality control MIT Intergalactic Workflow Commission (IWC) True False -allele-based-pathogen-identification/main WorkflowHub 1063 https://workflowhub.eu/workflows/1063?version=5 Engy Nasr, Bérénice Batut, Paul Zierep 2025-03-26 2026-05-14 5 5 23.0 bcftools_consensus, Paste1, samtools_coverage, regexColumn1, bcftools_norm, CONVERTER_gz_to_uncompressed, snpSift_filter, tp_cut_tool, Cut1, snpSift_extractFields, clair3, collapse_dataset, Remove beginning1, table_compute, tp_head_tool, Count1, samtools_depth, minimap2 Pairwise sequence alignment, Variant calling MIT Intergalactic Workflow Commission (IWC) True False -mgnify-amplicon-pipeline-v5-complete/main WorkflowHub 1274 https://workflowhub.eu/workflows/1274?version=2 Rand Zoabi, Paul Zierep 2025-03-26 2026-05-14 2 2 20.0 , fastq_dl, CONVERTER_uncompressed_to_gz, tp_awk_tool, CONVERTER_gz_to_uncompressed, __MERGE_COLLECTION__ Apache-2.0 Intergalactic Workflow Commission (IWC) True False -mgnify-amplicon-pipeline-v5-its/main WorkflowHub 1273 https://workflowhub.eu/workflows/1273?version=2 Rand Zoabi, Paul Zierep 2025-03-26 2026-05-14 2 2 30.0 , tp_awk_tool, __FILTER_FROM_FILE__, bedtools_maskfastabed, mapseq, collection_element_identifiers, taxonomy_krona_chart, biom_convert, __FILTER_EMPTY_DATASETS__ k-mer counting, Visualisation, Formatting, Mapping Apache-2.0 Intergalactic Workflow Commission (IWC) True False -mgnify-amplicon-pipeline-v5-quality-control-paired-end/main WorkflowHub 1272 https://workflowhub.eu/workflows/1272?version=2 Rand Zoabi, Paul Zierep 2025-03-26 2026-05-14 2 2 17.0 cshl_fasta_formatter, tp_find_and_replace, fastq_to_fasta_python, multiqc, fastqc, __UNZIP_COLLECTION__, prinseq, mgnify_seqprep, fastp, trimmomatic, fastq_filter Sequence trimming, Sequence composition calculation, Nucleic acid design, Statistical calculation, Validation, Read pre-processing, Sequence contamination filtering, Sequencing quality control Apache-2.0 Intergalactic Workflow Commission (IWC) True False -mgnify-amplicon-pipeline-v5-quality-control-single-end/main WorkflowHub 1271 https://workflowhub.eu/workflows/1271?version=3 Rand Zoabi, Paul Zierep 2025-03-26 2026-05-14 3 3 14.0 cshl_fasta_formatter, tp_find_and_replace, fastq_to_fasta_python, multiqc, fastqc, prinseq, trimmomatic, fastq_filter Sequence trimming, Read pre-processing, Sequence composition calculation, Sequence contamination filtering, Statistical calculation, Validation, Sequencing quality control Apache-2.0 Intergalactic Workflow Commission (IWC) True False -mgnify-amplicon-pipeline-v5-rrna-prediction/main WorkflowHub 1270 https://workflowhub.eu/workflows/1270?version=2 Rand Zoabi, Paul Zierep 2025-03-26 2026-05-14 2 2 47.0 , bedtools_getfastabed, tp_awk_tool, cshl_fasta_formatter, __FILTER_FROM_FILE__, infernal_cmsearch, mapseq, collection_element_identifiers, taxonomy_krona_chart, cmsearch_deoverlap, biom_convert, gops_concat_1, __FILTER_EMPTY_DATASETS__, query_tabular Visualisation, Alignment, Formatting, Mapping, k-mer counting, Comparison, Nucleic acid feature detection Apache-2.0 Intergalactic Workflow Commission (IWC) True False -mgnify-amplicon-taxonomic-summary-tables/main WorkflowHub 1269 https://workflowhub.eu/workflows/1269?version=2 Rand Zoabi 2025-03-26 2026-05-14 2 2 10.0 Grouping1, collection_column_join, tp_awk_tool, filter_tabular, query_tabular MIT Intergalactic Workflow Commission (IWC) True False -clinicalmp-discovery/main WorkflowHub 1225 https://workflowhub.eu/workflows/1225?version=1 Subina Mehta 2024-12-10 2026-05-13 1 1 24.0 Grouping1, Grep1, fasta2tab, fasta_merge_files_and_filter_unique_sequences, Filter1, ident_params, Remove beginning1, msconvert, Cut1, query_tabular, dbbuilder, fasta_cli, filter_tabular, tp_cat, search_gui, peptide_shaker, maxquant Visualisation, Filtering, Formatting, Statistical calculation, Imputation, Standardisation and normalisation, Heat map generation, Protein quantification, Principal component plotting, Clustering CC-BY-4.0 Intergalactic Workflow Commission (IWC) True False -clinicalmp-data-interpretation/main WorkflowHub 1219 https://workflowhub.eu/workflows/1219?version=1 GalaxyP 2024-11-26 2026-05-13 1 1 6.0 Grep1, msstatstmt, unipept Visualisation, Prediction and recognition CC-BY-4.0 Intergalactic Workflow Commission (IWC) True False -clinicalmp-verification/main WorkflowHub 1218 https://workflowhub.eu/workflows/1218?version=1 Pratik Jagtap 2024-11-26 2026-05-13 1 1 19.0 Grouping1, fasta_merge_files_and_filter_unique_sequences, Filter1, uniprotxml_downloader, Cut1, pepquery2, tp_cat, dbbuilder, Remove beginning1, collapse_dataset, query_tabular CC-BY-4.0 Intergalactic Workflow Commission (IWC) True False -clinicalmp-database-generation/main WorkflowHub 1216 https://workflowhub.eu/workflows/1216?version=1 Subina Mehta 2024-11-23 2026-05-13 1 1 3.0 metanovo, fasta_merge_files_and_filter_unique_sequences Expression analysis, Protein identification, Tag-based peptide identification, de Novo sequencing, Target-Decoy CC-BY-4.0 Intergalactic Workflow Commission (IWC) True False -clinicalmp-quantitation/main WorkflowHub 1177 https://workflowhub.eu/workflows/1177?version=1 GalaxyP 2024-10-07 2026-05-14 1 1 7.0 "maxquant, Quantified-Proteins -Grouping1, extract proteins -Cut1, extract peptides +metagenomic-raw-reads-amr-analysis/main WorkflowHub 2068 https://workflowhub.eu/workflows/2068?version=2 ABRomics None, Hugo Lefeuvre 2026-02-26 2026-05-14 2 2 20.0 "tooldistillator_summarize, __RELABEL_FROM_FILE__, groot, collection_element_identifiers, sylph_profile, deeparg_short_reads, fastq_paired_end_interlacer, argnorm, table_pandas_rename_column, multiqc, Removal of the first line because it is not necessary for tooldistillator +Remove beginning1, tp_text_file_with_recurring_lines, tooldistillator, __UNZIP_COLLECTION__, Removal of the first argNorm line that causes a multiQC error +Remove beginning1, __FILTER_FAILED_DATASETS__, Remove a collection level so that outputs can be taken into account by tooldistillator +__FLATTEN__" Data parsing, Taxonomic classification, Gene functional annotation, Sequencing quality control, Antimicrobial resistance prediction, Validation GPL-3.0-or-later Intergalactic Workflow Commission (IWC) True False +cgmlst-bacterial-genome/main WorkflowHub 2055 https://workflowhub.eu/workflows/2055?version=2 ABRomics None, Clea Siguret, Hugo Lefeuvre 2026-03-13 2026-05-14 2 2 3.0 tooldistillator, tooldistillator_summarize, coreprofiler_allele_calling Data parsing, Multilocus sequence typing GPL-3.0-or-later Intergalactic Workflow Commission (IWC) True False +bacterial-quality-and-contamination-control-post-assembly/main WorkflowHub 1882 https://workflowhub.eu/workflows/1882?version=3 ABRomics None, Pierre Marin, Clea Siguret 2025-12-04 2026-05-13 3 3 14.0 tooldistillator_summarize, recentrifuge, checkm2, est_abundance, kraken2, pick_value, collapse_dataset, tooldistillator, quast Statistical calculation, Taxonomic classification, Expression analysis, Sequence assembly validation, Data parsing, Sequencing quality control, Validation, Sequence composition calculation, Visualisation, Cross-assembly GPL-3.0-or-later Intergalactic Workflow Commission (IWC) True False +sars-cov-2-pe-illumina-artic-ivar-analysis/SARS-COV-2-ILLUMINA-AMPLICON-IVAR-PANGOLIN-NEXTCLADE WorkflowHub 155 https://workflowhub.eu/workflows/155?version=7 Peter van Heusden virology 2026-03-10 2026-05-13 7 7 16.0 fastp, ivar_variants, nextclade, ivar_trim, samtools_view, ivar_consensus, qualimap_bamqc, multiqc, __FLATTEN__, tp_sed_tool, snpeff_sars_cov_2, samtools_stats, tp_cat, pangolin, bwa_mem Read mapping, Generation, Variant classification, Variant calling, Tree-based sequence alignment, Sequence alignment, Genome indexing, Sequencing quality control, Sequence contamination filtering, Validation, Methylation analysis, Primer removal, SNP detection MIT Intergalactic Workflow Commission (IWC) True False +sars-cov-2-pe-illumina-wgs-variant-calling/COVID-19-PE-WGS-ILLUMINA WorkflowHub 113 https://workflowhub.eu/workflows/113?version=4 Wolfgang Maier virology, covid-19, covid19.galaxyproject.org, emergen_validated 2021-12-21 2026-05-14 4 4 11.0 lofreq_filter, fastp, picard_MarkDuplicates, lofreq_viterbi, samtools_view, lofreq_call, multiqc, snpeff_sars_cov_2, samtools_stats, lofreq_indelqual, bwa_mem Formatting, Generation, Sequence alignment, Genome indexing, Sequencing quality control, Sequence contamination filtering, Validation, Read mapping, SNP detection MIT Intergalactic Workflow Commission (IWC) True False +generic-non-segmented-viral-variant-calling/main WorkflowHub 1876 https://workflowhub.eu/workflows/1876?version=2 Peter van Heusden, Wolfgang Maier virology 2025-12-05 2026-05-13 2 2 23.0 ivar_variants, __FLATTEN__, snpSift_extractFields, map_param_value, collapse_dataset, tp_cat, fastp, samtools_view, snpEff, tp_find_and_replace, calculate_numeric_param, samtools_stats, lofreq_viterbi, snpEff_build_gb, ivar_consensus, pick_value, ivar_trim, qualimap_bamqc, multiqc, tp_sed_tool, __FILTER_FAILED_DATASETS__, bwa_mem Sequencing quality control, Sequence contamination filtering, Generation, Validation, Read mapping, Sequence alignment, Primer removal, Genome indexing AGPL-3.0-or-later Intergalactic Workflow Commission (IWC) True False +influenza-isolates-consensus-and-subtyping/main WorkflowHub 1260 https://workflowhub.eu/workflows/1260?version=3 Viktoria Isabel Schwarz, Wolfgang Maier, Aaron Kolbecher, Saim Momin virology 2026-02-12 2026-05-13 3 3 68.0 "collection_element_identifiers, Paste1, __FLATTEN__, snipit, bwa mem will fail if no reference for any segment got suggested by vapor, i.e. the reference genome is empty. In that case, we need to skip further analysis of the sample. +__FILTER_FAILED_DATASETS__, collapse_dataset, bamtools_split_ref, tp_cat, Show beginning1, param_value_from_file, fastp, samtools_view, tp_find_and_replace, rbc_mafft, tp_text_file_with_recurring_lines, __APPLY_RULES__, __FILTER_FROM_FILE__, ivar_consensus, __HARMONIZELISTS__, __DUPLICATE_FILE_TO_COLLECTION__, This seemingly no-op transformation will remove samples with no remaining segment results (cases where vapor failed for every segment). +__APPLY_RULES__, Grep1, iqtree, vapor, __RELABEL_FROM_FILE__, wc_gnu, seqtk_subseq, tp_easyjoin_tool, qualimap_bamqc, __MERGE_COLLECTION__, __UNZIP_COLLECTION__, __FILTER_FAILED_DATASETS__, Filter1, Cut1, bwa_mem" Data retrieval, Generation, Multiple sequence alignment, Data handling, De-novo assembly, Sequence file editing, Sequence alignment, Base position variability plotting, Genome indexing, Sequencing quality control, Sequence contamination filtering, Sequence alignment analysis, Sequence analysis, Read mapping, Primer removal, Phylogenetic analysis AGPL-3.0-or-later Intergalactic Workflow Commission (IWC) True False +pox-virus-amplicon/main WorkflowHub 439 https://workflowhub.eu/workflows/439?version=4 Viktoria Isabel Schwarz, Wolfgang Maier virology, pox 2025-10-11 2026-05-13 4 4 40.0 collection_element_identifiers, __FLATTEN__, EMBOSS: maskseq51, tp_cat, datamash_ops, param_value_from_file, fastp, samtools_view, samtools_merge, samtools_stats, __APPLY_RULES__, __ZIP_COLLECTION__, ivar_consensus, __SORTLIST__, Grep1, fasta_compute_length, ivar_trim, qualimap_bamqc, multiqc, split_file_to_collection, compose_text_param, tp_sed_tool, __FILTER_FAILED_DATASETS__, Cut1, bwa_mem Generation, Sequence alignment, Genome indexing, Sequencing quality control, Sequence contamination filtering, Sequence alignment analysis, Validation, Global alignment, Sequence analysis, Read mapping, Primer removal, Local alignment MIT Intergalactic Workflow Commission (IWC) True False +allele-based-pathogen-identification/main WorkflowHub 1063 https://workflowhub.eu/workflows/1063?version=5 Engy Nasr, Bérénice Batut, Paul Zierep 2025-03-26 2026-05-14 5 5 23.0 tp_cut_tool, clair3, table_compute, samtools_depth, bcftools_consensus, CONVERTER_gz_to_uncompressed, Paste1, bcftools_norm, Cut1, snpSift_extractFields, samtools_coverage, snpSift_filter, collapse_dataset, minimap2, Count1, tp_head_tool, Remove beginning1, regexColumn1 Pairwise sequence alignment, Variant calling MIT Intergalactic Workflow Commission (IWC) True False +mgnify-amplicon-pipeline-v5-complete/main WorkflowHub 1274 https://workflowhub.eu/workflows/1274?version=2 Rand Zoabi, Paul Zierep 2025-03-26 2026-05-14 2 2 20.0 , tp_awk_tool, CONVERTER_uncompressed_to_gz, CONVERTER_gz_to_uncompressed, __MERGE_COLLECTION__, fastq_dl Apache-2.0 Intergalactic Workflow Commission (IWC) True False +mgnify-amplicon-pipeline-v5-its/main WorkflowHub 1273 https://workflowhub.eu/workflows/1273?version=2 Rand Zoabi, Paul Zierep 2025-03-26 2026-05-14 2 2 30.0 , bedtools_maskfastabed, mapseq, tp_awk_tool, __FILTER_FROM_FILE__, collection_element_identifiers, taxonomy_krona_chart, biom_convert, __FILTER_EMPTY_DATASETS__ k-mer counting, Formatting, Visualisation, Mapping Apache-2.0 Intergalactic Workflow Commission (IWC) True False +mgnify-amplicon-pipeline-v5-quality-control-paired-end/main WorkflowHub 1272 https://workflowhub.eu/workflows/1272?version=2 Rand Zoabi, Paul Zierep 2025-03-26 2026-05-14 2 2 17.0 fastp, cshl_fasta_formatter, tp_find_and_replace, multiqc, trimmomatic, fastqc, __UNZIP_COLLECTION__, mgnify_seqprep, fastq_filter, prinseq, fastq_to_fasta_python Statistical calculation, Sequencing quality control, Sequence contamination filtering, Sequence trimming, Validation, Nucleic acid design, Read pre-processing, Sequence composition calculation Apache-2.0 Intergalactic Workflow Commission (IWC) True False +mgnify-amplicon-pipeline-v5-quality-control-single-end/main WorkflowHub 1271 https://workflowhub.eu/workflows/1271?version=3 Rand Zoabi, Paul Zierep 2025-03-26 2026-05-14 3 3 14.0 cshl_fasta_formatter, tp_find_and_replace, multiqc, trimmomatic, fastqc, fastq_filter, prinseq, fastq_to_fasta_python Sequencing quality control, Statistical calculation, Sequence contamination filtering, Sequence trimming, Validation, Read pre-processing, Sequence composition calculation Apache-2.0 Intergalactic Workflow Commission (IWC) True False +mgnify-amplicon-pipeline-v5-rrna-prediction/main WorkflowHub 1270 https://workflowhub.eu/workflows/1270?version=2 Rand Zoabi, Paul Zierep 2025-03-26 2026-05-14 2 2 47.0 , cshl_fasta_formatter, tp_awk_tool, mapseq, collection_element_identifiers, __FILTER_FROM_FILE__, taxonomy_krona_chart, biom_convert, cmsearch_deoverlap, infernal_cmsearch, bedtools_getfastabed, gops_concat_1, query_tabular, __FILTER_EMPTY_DATASETS__ k-mer counting, Formatting, Comparison, Mapping, Alignment, Nucleic acid feature detection, Visualisation Apache-2.0 Intergalactic Workflow Commission (IWC) True False +mgnify-amplicon-taxonomic-summary-tables/main WorkflowHub 1269 https://workflowhub.eu/workflows/1269?version=2 Rand Zoabi 2025-03-26 2026-05-14 2 2 10.0 tp_awk_tool, collection_column_join, Grouping1, filter_tabular, query_tabular MIT Intergalactic Workflow Commission (IWC) True False +clinicalmp-discovery/main WorkflowHub 1225 https://workflowhub.eu/workflows/1225?version=1 Subina Mehta 2024-12-10 2026-05-13 1 1 24.0 query_tabular, peptide_shaker, Remove beginning1, tp_cat, search_gui, Grouping1, fasta_cli, ident_params, maxquant, msconvert, dbbuilder, Grep1, filter_tabular, Filter1, fasta_merge_files_and_filter_unique_sequences, Cut1, fasta2tab Statistical calculation, Imputation, Formatting, Heat map generation, Filtering, Standardisation and normalisation, Protein quantification, Clustering, Principal component plotting, Visualisation CC-BY-4.0 Intergalactic Workflow Commission (IWC) True False +clinicalmp-data-interpretation/main WorkflowHub 1219 https://workflowhub.eu/workflows/1219?version=1 GalaxyP 2024-11-26 2026-05-13 1 1 6.0 msstatstmt, Grep1, unipept Prediction and recognition, Visualisation CC-BY-4.0 Intergalactic Workflow Commission (IWC) True False +clinicalmp-verification/main WorkflowHub 1218 https://workflowhub.eu/workflows/1218?version=1 Pratik Jagtap 2024-11-26 2026-05-13 1 1 19.0 Filter1, uniprotxml_downloader, Grouping1, Cut1, collapse_dataset, dbbuilder, query_tabular, tp_cat, fasta_merge_files_and_filter_unique_sequences, Remove beginning1, pepquery2 CC-BY-4.0 Intergalactic Workflow Commission (IWC) True False +clinicalmp-database-generation/main WorkflowHub 1216 https://workflowhub.eu/workflows/1216?version=1 Subina Mehta 2024-11-23 2026-05-13 1 1 3.0 metanovo, fasta_merge_files_and_filter_unique_sequences de Novo sequencing, Target-Decoy, Expression analysis, Tag-based peptide identification, Protein identification CC-BY-4.0 Intergalactic Workflow Commission (IWC) True False +clinicalmp-quantitation/main WorkflowHub 1177 https://workflowhub.eu/workflows/1177?version=1 GalaxyP 2024-10-07 2026-05-14 1 1 7.0 "extracting microbial Proteins +Grep1, extract proteins Cut1, Quantified-Peptides -Grouping1, extracting microbial Proteins -Grep1, extracting microbial Peptides -Grep1" Visualisation, Statistical calculation, Imputation, Standardisation and normalisation, Heat map generation, Protein quantification, Principal component plotting, Clustering CC-BY-4.0 Intergalactic Workflow Commission (IWC) True False -bacterial-genome-assembly/main WorkflowHub 1043 https://workflowhub.eu/workflows/1043?version=12 Abromics None, Pierre Marin, Clea Siguret abromics, assembly, fastq, genomics, bacterial-genomics, paired-end, quality 2025-12-04 2026-05-13 12 12 5.0 bandage_info, bandage_image, tooldistillator, tooldistillator_summarize, shovill Data parsing, Genome assembly, Sequence assembly visualisation GPL-3.0-or-later Intergalactic Workflow Commission (IWC) True False -quality-and-contamination-control/main WorkflowHub 1052 https://workflowhub.eu/workflows/1052?version=11 ABRomics None, Pierre Marin, Clea Siguret abromics, fastq, genomics, bacterial-genomics, paired-end, quality, taxonomy-assignment, trimming 2025-06-19 2026-05-14 11 11 8.0 kraken2, tooldistillator_summarize, tooldistillator, __UNZIP_COLLECTION__, est_abundance, fastp, recentrifuge, __ZIP_COLLECTION__ Cross-assembly, Data parsing, Sequence contamination filtering, Expression analysis, Statistical calculation, Taxonomic classification, Sequencing quality control GPL-3.0-or-later Intergalactic Workflow Commission (IWC) True False -qiime2-III-VI-downsteam/QIIME2-III-V-Phylogeny-Rarefaction-Taxonomic-Analysis WorkflowHub 1090 https://workflowhub.eu/workflows/1090?version=2 Debjyoti Ghosh 2024-11-26 2026-05-14 2 2 3.0 Phylogenetic tree for diversity analysis, Taxonomic analysis, Rarefaction MIT Intergalactic Workflow Commission (IWC) True False -gene-based-pathogen-identification/main WorkflowHub 1062 https://workflowhub.eu/workflows/1062?version=1 Engy Nasr, Bérénice Batut, Paul Zierep 2024-06-26 2026-05-13 1 1 15.0 medaka_consensus_pipeline, param_value_from_file, compose_text_param, __BUILD_LIST__, tp_find_and_replace, abricate, collection_element_identifiers, bandage_image, split_file_to_collection, flye, fasta2tab, tab2fasta Antimicrobial resistance prediction, Base-calling, Variant calling, Cross-assembly, Mapping assembly, Sequence assembly, Genome assembly, Sequence assembly visualisation, De-novo assembly MIT 10.48546/workflowhub.workflow.1062.1 Intergalactic Workflow Commission (IWC) True False -pathogen-detection-pathogfair-samples-aggregation-and-visualisation/main WorkflowHub 1060 https://workflowhub.eu/workflows/1060?version=1 Engy Nasr, Bérénice Batut, Paul Zierep 2024-06-26 2026-05-13 1 1 60.0 Grouping1, regexColumn1, clustalw, __FILTER_FAILED_DATASETS__, fasta2tab, tp_sorted_uniq, fasta_merge_files_and_filter_unique_sequences, collapse_dataset, __FILTER_EMPTY_DATASETS__, bedtools_getfastabed, tp_multijoin_tool, ggplot2_heatmap, Cut1, Remove beginning1, fasttree, tp_split_on_column, collection_column_join, tp_replace_in_column, newick_display, regex1, Count1, tab2fasta Phylogenetic tree generation (from molecular sequences), Visualisation, Phylogenetic tree generation (maximum likelihood and Bayesian methods), Multiple sequence alignment, Mapping, Phylogenetic tree reconstruction, Phylogenetic tree analysis, Phylogenetic tree generation MIT 10.48546/workflowhub.workflow.1060.1 Intergalactic Workflow Commission (IWC) True False -taxonomy-profiling-and-visualization-with-krona/main WorkflowHub 1059 https://workflowhub.eu/workflows/1059?version=1 Engy Nasr, Bérénice Batut, Paul Zierep 2024-06-26 2026-05-13 1 1 3.0 kraken2, taxonomy_krona_chart, krakentools_kreport2krona Visualisation, Taxonomic classification, Aggregation MIT 10.48546/workflowhub.workflow.1059.1 Intergalactic Workflow Commission (IWC) True False -bacterial_genome_annotation/main WorkflowHub 1050 https://workflowhub.eu/workflows/1050?version=13 ABRomics None, Pierre Marin, Clea Siguret abromics, annotation, genomics, bacterial-genomics, fasta, genome-annotation 2025-12-06 2026-05-13 13 13 6.0 isescan, bakta, integron_finder, tooldistillator_summarize, tooldistillator, plasmidfinder Scaffolding, Multilocus sequence typing, Structural variation detection, Sequence motif recognition, Genome annotation, Data parsing, Genome assembly, Protein feature detection, Nucleic acid feature detection GPL-3.0-or-later Intergalactic Workflow Commission (IWC) True False -amr_gene_detection/main WorkflowHub 1049 https://workflowhub.eu/workflows/1049?version=9 ABRomics None, Pierre Marin, Clea Siguret abromics, amr, amr-detection, genomics, antibiotic-resistance, antimicrobial resistance, antimicrobial-resistance-genes, bacterial-genomics, fasta 2025-12-04 2026-05-13 9 9 5.0 abricate, amrfinderplus, staramr_search, tooldistillator_summarize, tooldistillator Data parsing, Antimicrobial resistance prediction GPL-3.0-or-later Intergalactic Workflow Commission (IWC) True False -dada2/main WorkflowHub 790 https://workflowhub.eu/workflows/790?version=3 Matthias Bernt name:amplicon 2025-03-26 2026-05-14 3 3 14.0 dada2_filterAndTrim, dada2_learnErrors, dada2_assignTaxonomyAddspecies, dada2_makeSequenceTable, dada2_seqCounts, __UNZIP_COLLECTION__, dada2_removeBimeraDenovo, __APPLY_RULES__, dada2_mergePairs, dada2_plotQualityProfile, dada2_dada DNA barcoding, Variant calling MIT Intergalactic Workflow Commission (IWC) True False -Refining Genome Annotations with Apollo (prokaryotes) WorkflowHub 749 https://workflowhub.eu/workflows/749?version=1 Anthony Bretaudeau genome-annotation 2024-02-14 2025-11-04 1 1 5.0 jbrowse, iframe, create_or_update, list_organism, create_account Genome visualisation CC-BY-4.0 10.48546/workflowhub.workflow.749.1 EuroScienceGateway True False -TB Variant Analysis v1.0 WorkflowHub 1647 https://workflowhub.eu/workflows/1647?version=2 gtn, galaxy, pathogen, tuberculosis 2026-01-12 2026-01-12 2 2 15.0 bcftools_consensus, tp_awk_tool, tb_profiler_profile, kraken2, __FLATTEN__, multiqc, mosdepth, snippy, qualimap_bamqc, tb_variant_filter, tbvcfreport, fastp, tp_sed_tool, EMBOSS: seqret84 Phylogenetic tree visualisation, Sequence alignment, Validation, Antimicrobial resistance prediction, Phylogenetic tree generation, Variant calling, Sequence analysis, Local alignment, Sequence contamination filtering, Global alignment, Sequence alignment analysis, Taxonomic classification, Sequencing quality control AGPL-3.0-or-later Galaxy Training Network True False -Quality and contamination control in bacterial isolate using Illumina MiSeq Data WorkflowHub 2043 https://workflowhub.eu/workflows/2043?version=1 gtn, galaxy, sequence-analysis 2025-12-22 2025-12-22 1 1 5.0 falco, kraken2, est_abundance, fastp, recentrifuge Visualisation, Statistical calculation, Read mapping, Cross-assembly, Sequence contamination filtering, Expression analysis, Taxonomic classification, Sequencing quality control GPL-3.0-or-later Galaxy Training Network True False -Taxonomic Profiling and Visualization of Metagenomic Data WorkflowHub 1470 https://workflowhub.eu/workflows/1470?version=2 gtn, galaxy, microbiome 2025-12-22 2025-12-22 2 2 10.0 interactive_tool_phinch, metaphlan, kraken2, taxonomy_krona_chart, krakentools_kreport2krona, __UNZIP_COLLECTION__, est_abundance, interactive_tool_pavian, kraken_biom Visualisation, Statistical calculation, Taxonomic classification, Genome annotation, Aggregation MIT Galaxy Training Network True False -Checking expected species and contamination in bacterial isolate WorkflowHub 1674 https://workflowhub.eu/workflows/1674?version=2 ecology, gtn, galaxy 2025-12-22 2025-12-22 2 2 3.0 kraken2, est_abundance, recentrifuge Cross-assembly, Statistical calculation, Taxonomic classification, Expression analysis GPL-3.0-or-later Galaxy Training Network True False -Metagenomic Binning WorkflowHub 2028 https://workflowhub.eu/workflows/2028?version=1 gtn, galaxy, microgalaxy, binning, microbiome 2025-12-08 2025-12-08 1 1 17.0 bowtie2, metabat2, __BUILD_LIST__, concoct_coverage_table, metabat2_jgi_summarize_bam_contig_depths, concoct_extract_fasta_bins, semibin, concoct, samtools_sort, maxbin2, binette, Fasta_to_Contig2Bin, concoct_merge_cut_up_clustering, concoct_cut_up_fasta Sequence assembly, Read mapping, Genome annotation, Sequence clustering, Read binning MIT Galaxy Training Network True False -MGnify's amplicon pipeline v5.0 - ITS WorkflowHub 1856 https://workflowhub.eu/workflows/1856?version=1 amplicon, gtn, galaxy, metagenomics, mgnify_amplicon, name:microgalaxy 2025-08-11 2025-08-11 1 1 30.0 , tp_awk_tool, __FILTER_FROM_FILE__, bedtools_maskfastabed, mapseq, collection_element_identifiers, taxonomy_krona_chart, biom_convert, __FILTER_EMPTY_DATASETS__ k-mer counting, Visualisation, Formatting, Mapping Apache-2.0 Galaxy Training Network True False -MAPseq to ampvis2 WorkflowHub 1855 https://workflowhub.eu/workflows/1855?version=1 gtn, galaxy, microbiome 2025-08-11 2025-08-11 1 1 9.0 collection_column_join, ampvis2_load, tp_awk_tool, collapse_dataset, query_tabular Visualisation, Analysis MIT Galaxy Training Network True False -MGnify's amplicon pipeline v5.0 - Quality control PE WorkflowHub 1854 https://workflowhub.eu/workflows/1854?version=1 amplicon, gtn, galaxy, metagenomics, mgnify_amplicon, name:microgalaxy 2025-08-11 2025-08-11 1 1 17.0 cshl_fasta_formatter, tp_find_and_replace, fastq_to_fasta_python, multiqc, fastqc, __UNZIP_COLLECTION__, prinseq, mgnify_seqprep, fastp, trimmomatic, fastq_filter Sequence trimming, Sequence composition calculation, Nucleic acid design, Statistical calculation, Validation, Read pre-processing, Sequence contamination filtering, Sequencing quality control Apache-2.0 Galaxy Training Network True False -MGnify's amplicon pipeline v5.0 WorkflowHub 1853 https://workflowhub.eu/workflows/1853?version=1 amplicon, gtn, galaxy, metagenomics, mgnify_amplicon, name:microgalaxy 2025-08-11 2025-08-11 1 1 20.0 , fastq_dl, CONVERTER_uncompressed_to_gz, tp_awk_tool, CONVERTER_gz_to_uncompressed, __MERGE_COLLECTION__ Apache-2.0 Galaxy Training Network True False -MGnify amplicon summary tables WorkflowHub 1851 https://workflowhub.eu/workflows/1851?version=1 amplicon, gtn, galaxy, metagenomics, mgnify_amplicon, name:microgalaxy 2025-08-11 2025-08-11 1 1 10.0 Grouping1, collection_column_join, tp_awk_tool, filter_tabular, query_tabular MIT Galaxy Training Network True False -MGnify's amplicon pipeline v5.0 - Quality control SE WorkflowHub 1850 https://workflowhub.eu/workflows/1850?version=1 amplicon, gtn, galaxy, metagenomics, mgnify_amplicon, name:microgalaxy 2025-08-11 2025-08-11 1 1 14.0 cshl_fasta_formatter, tp_find_and_replace, fastq_to_fasta_python, multiqc, fastqc, prinseq, trimmomatic, fastq_filter Sequence trimming, Read pre-processing, Sequence composition calculation, Sequence contamination filtering, Statistical calculation, Validation, Sequencing quality control Apache-2.0 Galaxy Training Network True False -MGnify's amplicon pipeline v5.0 - rRNA prediction WorkflowHub 1842 https://workflowhub.eu/workflows/1842?version=1 amplicon, gtn, galaxy, metagenomics, mgnify_amplicon, name:microgalaxy 2025-08-04 2025-08-11 1 1 47.0 , bedtools_getfastabed, tp_awk_tool, cshl_fasta_formatter, __FILTER_FROM_FILE__, infernal_cmsearch, mapseq, collection_element_identifiers, taxonomy_krona_chart, cmsearch_deoverlap, biom_convert, gops_concat_1, __FILTER_EMPTY_DATASETS__, query_tabular Visualisation, Alignment, Formatting, Mapping, k-mer counting, Comparison, Nucleic acid feature detection Apache-2.0 Galaxy Training Network True False -Workflow 3: Functional Information (quick) WorkflowHub 1447 https://workflowhub.eu/workflows/1447?version=2 asaim, gtn, galaxy, metagenomics 2025-07-14 2025-07-14 2 2 12.0 Grep1, humann_rename_table, tp_find_and_replace, combine_metaphlan2_humann2, Cut1, humann_renorm_table, humann_regroup_table, humann_unpack_pathways, humann_split_stratified_table Species frequency estimation, Taxonomic classification, Phylogenetic analysis MIT Galaxy Training Network True False -Building an amplicon sequence variant (ASV) table from 16S data using DADA2 WorkflowHub 1395 https://workflowhub.eu/workflows/1395?version=2 gtn, galaxy, microbiome 2025-07-07 2025-07-07 2 2 21.0 dada2_filterAndTrim, dada2_learnErrors, dada2_assignTaxonomyAddspecies, tp_replace_in_column, collection_element_identifiers, phyloseq_from_dada2, dada2_makeSequenceTable, dada2_seqCounts, tp_replace_in_line, __UNZIP_COLLECTION__, dada2_dada, dada2_mergePairs, dada2_removeBimeraDenovo, cat1, Add_a_column1, tp_head_tool, dada2_plotQualityProfile, __SORTLIST__ Visualisation, DNA barcoding, Deposition, Analysis, Variant calling MIT Galaxy Training Network True False -Metatranscriptomics analysis using microbiome RNA-seq data WorkflowHub 1466 https://workflowhub.eu/workflows/1466?version=2 gtn, galaxy, microbiome 2025-06-23 2025-06-23 2 2 33.0 Grouping1, metaphlan, fastqc, tp_sort_header_tool, humann, humann_unpack_pathways, graphlan, Grep1, humann_rename_table, tp_find_and_replace, combine_metaphlan_humann, Cut1, bg_sortmerna, fastq_paired_end_interlacer, humann_split_stratified_table, multiqc, cutadapt, taxonomy_krona_chart, graphlan_annotate, humann_renorm_table, humann_regroup_table, export2graphlan Sequence comparison, Phylogenetic tree visualisation, Visualisation, Sequence composition calculation, Statistical calculation, Phylogenetic inference, Validation, Primer removal, Sequence alignment analysis, Sequencing quality control, Phylogenetic analysis, Sequence trimming, Phylogenetic tree editing, Read pre-processing, Species frequency estimation, Taxonomic classification, Sequence similarity search, Conversion, Aggregation MIT Galaxy Training Network True False -Metatranscriptomics analysis using microbiome RNA-seq data - Workflow 2: Community profile WorkflowHub 1451 https://workflowhub.eu/workflows/1451?version=2 gtn, galaxy, microbiome 2025-06-23 2025-06-23 2 2 6.0 graphlan, metaphlan, taxonomy_krona_chart, graphlan_annotate, Cut1, export2graphlan Phylogenetic tree visualisation, Visualisation, Phylogenetic inference, Phylogenetic tree editing, Taxonomic classification, Conversion MIT Galaxy Training Network True False -Metatranscriptomics analysis using microbiome RNA-seq data - Workflow 1: Preprocessing WorkflowHub 1444 https://workflowhub.eu/workflows/1444?version=2 gtn, galaxy, microbiome 2025-06-23 2025-06-23 2 2 6.0 multiqc, fastqc, cutadapt, bg_sortmerna, fastq_paired_end_interlacer Sequence trimming, Sequence composition calculation, Statistical calculation, Validation, Primer removal, Read pre-processing, Sequence similarity search, Sequence alignment analysis, Sequence comparison, Sequencing quality control MIT Galaxy Training Network True False -Metatranscriptomics analysis using microbiome RNA-seq data - Workflow 3: Functional Information WorkflowHub 1456 https://workflowhub.eu/workflows/1456?version=2 gtn, galaxy, microbiome 2025-06-23 2025-06-23 2 2 18.0 Grep1, humann_rename_table, humann, tp_find_and_replace, humann_renorm_table, tp_sort_header_tool, humann_regroup_table, humann_unpack_pathways, humann_split_stratified_table Species frequency estimation, Taxonomic classification, Phylogenetic analysis MIT Galaxy Training Network True False -Assembly of metagenomic sequencing data WorkflowHub 1390 https://workflowhub.eu/workflows/1390?version=2 gtn, galaxy, microbiome 2025-06-16 2025-06-16 2 2 9.0 collection_column_join, bowtie2, megahit_contig2fastg, bandage_info, bandage_image, metaspades, quast, coverm_contig, megahit Visualisation, Local alignment, Sequence assembly validation, Read mapping, Genome assembly, Sequence assembly visualisation MIT Galaxy Training Network True False -Taxonomic Analysis of eDNA WorkflowHub 1723 https://workflowhub.eu/workflows/1723?version=1 ecology, gtn, galaxy 2025-06-02 2025-06-02 1 1 8.0 ncbi_blastn_wrapper, Count1, cshl_fastq_to_fasta, fastp Sequence contamination filtering, Sequencing quality control CC-BY-4.0 Galaxy Training Network True False -Quality and contamination control in bacterial isolate using Illumina MiSeq Data WorkflowHub 1644 https://workflowhub.eu/workflows/1644?version=1 gtn, galaxy, sequence-analysis 2025-06-02 2025-06-02 1 1 6.0 falco, kraken2, est_abundance, fastp, recentrifuge Visualisation, Statistical calculation, Read mapping, Cross-assembly, Sequence contamination filtering, Expression analysis, Taxonomic classification, Sequencing quality control GPL-3.0-or-later Galaxy Training Network True False -pox-virus-tiled-amplicon-ref-masking WorkflowHub 1632 https://workflowhub.eu/workflows/1632?version=1 gtn, galaxy, variant-analysis 2025-06-02 2025-06-02 1 1 14.0 Grep1, param_value_from_file, compose_text_param, EMBOSS: maskseq51, datamash_ops, Cut1, fasta_compute_length, Add_a_column1 Local alignment, Sequence alignment, Global alignment, Sequence alignment analysis, Sequence analysis MIT Galaxy Training Network True False -Copy Of GTN Training - Antibiotic Resistance Detection WorkflowHub 1477 https://workflowhub.eu/workflows/1477?version=1 gtn, galaxy, microbiome 2025-06-02 2025-06-02 1 1 12.0 unicycler, racon, staramr_search, miniasm, nanoplot, bandage_image, PlasFlow, gfa_to_fa, minimap2 Aggregation, Mapping assembly, Antimicrobial resistance prediction, Sequence analysis, Box-Whisker plot plotting, Pairwise sequence alignment, Genome assembly, Sequence assembly visualisation, Scatter plot plotting, De-novo assembly CC-BY-4.0 Galaxy Training Network True False -Amplicon Tutorial WorkflowHub 1476 https://workflowhub.eu/workflows/1476?version=1 gtn, galaxy, microbiome 2025-06-02 2025-06-02 1 1 17.0 mothur_pre_cluster, mothur_make_group, mothur_summary_seqs, mothur_count_seqs, mothur_unique_seqs, mothur_merge_files, mothur_align_seqs, mothur_filter_seqs, mothur_cluster_split, mothur_screen_seqs, mothur_classify_seqs, mothur_make_shared, krona-text, mothur_classify_otu, mothur_make_biom Visualisation, Sequence clustering, DNA barcoding, Taxonomic classification, Sequence read processing, Sequencing quality control, Phylogenetic analysis CC-BY-4.0 Galaxy Training Network True False -Training: 16S rRNA Analysis with Nanopore Sequencing Reads WorkflowHub 1473 https://workflowhub.eu/workflows/1473?version=1 gtn, galaxy, microbiome 2025-06-02 2025-06-02 1 1 11.0 multiqc, kraken2, fastqc, taxonomy_krona_chart, porechop, tp_replace_in_line, fastp, Remove beginning1, datamash_reverse Visualisation, Sequence composition calculation, Sequence contamination filtering, Statistical calculation, Validation, Taxonomic classification, Sequencing quality control CC-BY-4.0 Galaxy Training Network True False -"WGS Part In ""Analyses Of Metagenomics Data - The Global Picture""" WorkflowHub 1472 https://workflowhub.eu/workflows/1472?version=1 gtn, galaxy, microbiome 2025-06-02 2025-06-02 1 1 7.0 humann2, taxonomy_krona_chart, metaphlan2krona, humann2_renorm_table, humann2_regroup_table, metaphlan2 Visualisation CC-BY-4.0 Galaxy Training Network True False -Query a metaplasmidome database to identify and annotate plasmids in metagenomes WorkflowHub 1469 https://workflowhub.eu/workflows/1469?version=1 gtn, galaxy, metagenomics, metaplasmidome, name:microgalaxy 2025-06-02 2025-06-02 1 1 47.0 Grouping1, CONVERTER_fasta_to_tabular, tp_sorted_uniq, sort1, Filter1, MQoutputfilter, tp_replace_in_column, histogram_rpy, tp_tail_tool, join1, count_gff_features, tab2fasta, Cut1, cat1, add_column_headers, Add_a_column1, ggplot2_histogram, minimap2 Visualisation, Pairwise sequence alignment MIT Galaxy Training Network True False -Training: 16S rRNA Sequencing With Mothur: Main Tutorial WorkflowHub 1465 https://workflowhub.eu/workflows/1465?version=1 gtn, galaxy, microbiome 2025-06-02 2025-06-02 1 1 38.0 mothur_pre_cluster, mothur_make_contigs, mothur_count_seqs, mothur_cluster, mothur_unique_seqs, mothur_venn, mothur_classify_seqs, mothur_make_shared, mothur_make_biom, mothur_summary_seqs, mothur_cluster_split, mothur_chimera_vsearch, mothur_screen_seqs, mothur_remove_lineage, mothur_summary_single, mothur_remove_seqs, XY_Plot_1, mothur_remove_groups, mothur_taxonomy_to_krona, mothur_count_groups, mothur_align_seqs, mothur_filter_seqs, mothur_dist_shared, mothur_tree_shared, mothur_dist_seqs, mothur_classify_otu, mothur_heatmap_sim, mothur_rarefaction_single, mothur_sub_sample, newick_display, taxonomy_krona_chart, mothur_seq_error, mothur_get_groups Visualisation, Phylogenetic tree reconstruction, Sequence clustering, Phylogenetic tree generation, DNA barcoding, Phylogenetic tree analysis, Taxonomic classification, Sequence read processing, Sequencing quality control, Phylogenetic analysis CC-BY-4.0 Galaxy Training Network True False -Workflow for Identifying MF from ITS2 sequencing using LotuS2 - tutorial example run' WorkflowHub 1460 https://workflowhub.eu/workflows/1460?version=1 ecology, fungi, gtn, galaxy, lotus2, metagenomics 2025-06-02 2025-06-02 1 1 1.0 lotus2 Sequence feature detection, DNA barcoding MIT Galaxy Training Network True False -Identification of the micro-organisms in a beer using Nanopore sequencing WorkflowHub 1439 https://workflowhub.eu/workflows/1439?version=1 gtn, galaxy, microbiome 2025-06-02 2025-06-02 1 1 8.0 kraken2, Filter1, fastqc, taxonomy_krona_chart, krakentools_kreport2krona, porechop, fastp Visualisation, Sequence composition calculation, Sequence contamination filtering, Statistical calculation, Taxonomic classification, Aggregation, Sequencing quality control MIT Galaxy Training Network True False -Calculating diversity from microbiome taxonomic data WorkflowHub 1431 https://workflowhub.eu/workflows/1431?version=1 gtn, galaxy, name:gtn 2025-06-02 2025-06-02 1 1 6.0 krakentools_alpha_diversity, krakentools_beta_diversity Visualisation, Aggregation MIT Galaxy Training Network True False -Workflow 3: Classification [Galaxy Training: 16S Microbial Analysis With Mothur] WorkflowHub 1428 https://workflowhub.eu/workflows/1428?version=1 gtn, galaxy, microbiome 2025-06-02 2025-06-02 1 1 3.0 mothur_summary_seqs, mothur_classify_seqs, mothur_remove_lineage Visualisation, Sequence clustering, DNA barcoding, Taxonomic classification, Sequence read processing, Sequencing quality control, Phylogenetic analysis MIT Galaxy Training Network True False -Workflow 1: Quality Control [Galaxy Training: 16S Microbial Analysis With Mothur] WorkflowHub 1422 https://workflowhub.eu/workflows/1422?version=1 gtn, galaxy, microbiome 2025-06-02 2025-06-02 1 1 5.0 mothur_summary_seqs, mothur_count_seqs, mothur_screen_seqs, mothur_unique_seqs Visualisation, Sequence clustering, DNA barcoding, Taxonomic classification, Sequence read processing, Sequencing quality control, Phylogenetic analysis MIT Galaxy Training Network True False -Workflow7: Beta Diversity [Galaxy Training: 16S Microbial Analysis With Mothur] WorkflowHub 1418 https://workflowhub.eu/workflows/1418?version=1 gtn, galaxy, microbiome 2025-06-02 2025-06-02 1 1 6.0 mothur_heatmap_sim, newick_display, mothur_dist_shared, mothur_venn, collapse_dataset, mothur_tree_shared Visualisation, Phylogenetic tree reconstruction, Sequence clustering, Phylogenetic tree generation, DNA barcoding, Phylogenetic tree analysis, Taxonomic classification, Sequence read processing, Sequencing quality control, Phylogenetic analysis MIT Galaxy Training Network True False -Workflow 6: Alpha Diversity [Galaxy Training: 16S Microbial Analysis With Mothur] WorkflowHub 1412 https://workflowhub.eu/workflows/1412?version=1 gtn, galaxy, microbiome 2025-06-02 2025-06-02 1 1 3.0 XY_Plot_1, mothur_rarefaction_single, mothur_summary_single Visualisation, Sequence clustering, DNA barcoding, Taxonomic classification, Sequence read processing, Sequencing quality control, Phylogenetic analysis MIT Galaxy Training Network True False -Workflow 4: Mock OTU Clustering [Galaxy Training: 16S Microbial Analysis With Mothur] WorkflowHub 1408 https://workflowhub.eu/workflows/1408?version=1 gtn, galaxy, microbiome 2025-06-02 2025-06-02 1 1 4.0 mothur_rarefaction_single, mothur_dist_seqs, mothur_make_shared, mothur_cluster Visualisation, Sequence clustering, DNA barcoding, Taxonomic classification, Sequence read processing, Sequencing quality control, Phylogenetic analysis MIT Galaxy Training Network True False -Workflow 5: OTU Clustering [Galaxy Training: 16S Microbial Analysis With Mothur] WorkflowHub 1404 https://workflowhub.eu/workflows/1404?version=1 gtn, galaxy, microbiome 2025-06-02 2025-06-02 1 1 6.0 mothur_remove_groups, mothur_sub_sample, mothur_count_groups, mothur_cluster_split, mothur_make_shared, mothur_classify_otu Visualisation, Sequence clustering, DNA barcoding, Taxonomic classification, Sequence read processing, Sequencing quality control, Phylogenetic analysis MIT Galaxy Training Network True False -Workflow 2: Data Cleaning And Chimera Removal [Galaxy Training: 16S Microbial Analysis With Mothur] WorkflowHub 1400 https://workflowhub.eu/workflows/1400?version=1 gtn, galaxy, microbiome 2025-06-02 2025-06-02 1 1 9.0 mothur_pre_cluster, mothur_summary_seqs, mothur_unique_seqs, mothur_filter_seqs, mothur_chimera_vsearch, mothur_screen_seqs, mothur_remove_seqs Visualisation, Sequence clustering, DNA barcoding, Taxonomic classification, Sequence read processing, Sequencing quality control, Phylogenetic analysis MIT Galaxy Training Network True False -GTN Training - Antibiotic Resistance Detection WorkflowHub 406 https://workflowhub.eu/workflows/406?version=1 Saskia Hiltemann, Willem de Koning metagenomics 2022-11-24 2026-05-13 1 1 12.0 unicycler, racon, staramr_search, miniasm, nanoplot, bandage_image, PlasFlow, gfa_to_fa, minimap2 Aggregation, Mapping assembly, Antimicrobial resistance prediction, Sequence analysis, Box-Whisker plot plotting, Pairwise sequence alignment, Genome assembly, Sequence assembly visualisation, Scatter plot plotting, De-novo assembly Microbiology CC-BY-4.0 Galaxy Training Network True False -3: Plant virus exploration WorkflowHub 103 https://workflowhub.eu/workflows/103?version=1 de_novo, virology, exploration 2021-02-04 2026-05-13 1 1 2.0 fastp, shovill Genome assembly, Sequence contamination filtering, Sequencing quality control Apache-2.0 Integrated and Urban Plant Pathology Laboratory True False -2: Plant virus confirmation WorkflowHub 102 https://workflowhub.eu/workflows/102?version=1 assembly, virology, blast, mapping, reads_selection 2021-02-04 2026-05-13 1 1 7.0 fasta_merge_files_and_filter_unique_sequences, ncbi_blastn_wrapper, samtools_stats, picard_SamToFastq, shovill, ngsutils_bam_filter, minimap2 Read pre-processing, Sequence contamination filtering, Formatting, Pairwise sequence alignment, Genome assembly, Sequencing quality control, Variant calling Apache-2.0 Integrated and Urban Plant Pathology Laboratory True False -1: Plant virus detection with kraken2 (SE) WorkflowHub 124 https://workflowhub.eu/workflows/124?version=1 virology, kraken 2021-06-17 2026-05-13 1 1 3.0 kraken2, Kraken2Tax, taxonomy_krona_chart Visualisation, Taxonomic classification Apache-2.0 Integrated and Urban Plant Pathology Laboratory True False -1: Plant virus detection with kraken2 (PE) WorkflowHub 101 https://workflowhub.eu/workflows/101?version=1 virology, kraken 2021-02-04 2026-05-13 1 1 3.0 kraken2, Kraken2Tax, taxonomy_krona_chart Visualisation, Taxonomic classification Apache-2.0 Integrated and Urban Plant Pathology Laboratory True False -Taxonomy Assignment with QIIME2 WorkflowHub 2098 https://workflowhub.eu/workflows/2098?version=1 Tristan Reynolds, Amy Loughman amplicon, microbiome, taxonomic-classification 2026-03-02 2026-05-13 1 1 19.0 qiime2__feature_classifier__classify_sklearn, qiime2__feature_table__summarize, qiime2_core__tools__import, qiime2__taxa__barplot, qiime2__feature_classifier__fit_classifier_naive_bayes, qiime2__feature_table__tabulate_seqs, qiime2__feature_classifier__extract_reads, csv_to_tabular, tp_easyjoin_tool, Remove beginning1, biom_convert, qiime_extract_viz, qiime2_core__tools__export, tabular_to_csv Visualisation, Formatting, Demultiplexing, Taxonomic classification Taxonomy CC-BY-4.0 10.48546/workflowhub.workflow.2098.1 Melbourne Bioinformatics, Galaxy Australia True False -Taxonomy classification using Kraken2 and Bracken WorkflowHub 1199 https://workflowhub.eu/workflows/1199?version=2 Valentine Murigneux, Mike Thang gucfg2galaxy, metagenomics, name:collection, shotgun 2024-12-10 2024-12-10 2 2 29.0 "collection_column_join, krakentools_beta_diversity, Prepare alpha diversity summary file +Grouping1, extracting microbial Peptides +Grep1, Quantified-Proteins +Grouping1, maxquant, extract peptides +Cut1" Statistical calculation, Imputation, Heat map generation, Standardisation and normalisation, Protein quantification, Clustering, Principal component plotting, Visualisation CC-BY-4.0 Intergalactic Workflow Commission (IWC) True False +bacterial-genome-assembly/main WorkflowHub 1043 https://workflowhub.eu/workflows/1043?version=12 Abromics None, Pierre Marin, Clea Siguret abromics, assembly, fastq, genomics, bacterial-genomics, paired-end, quality 2025-12-04 2026-05-13 12 12 5.0 tooldistillator_summarize, shovill, bandage_image, bandage_info, tooldistillator Data parsing, Sequence assembly visualisation, Genome assembly GPL-3.0-or-later Intergalactic Workflow Commission (IWC) True False +quality-and-contamination-control/main WorkflowHub 1052 https://workflowhub.eu/workflows/1052?version=11 ABRomics None, Pierre Marin, Clea Siguret abromics, fastq, genomics, bacterial-genomics, paired-end, quality, taxonomy-assignment, trimming 2025-06-19 2026-05-14 11 11 8.0 fastp, tooldistillator_summarize, recentrifuge, __ZIP_COLLECTION__, est_abundance, kraken2, __UNZIP_COLLECTION__, tooldistillator Sequencing quality control, Sequence contamination filtering, Data parsing, Taxonomic classification, Expression analysis, Statistical calculation, Cross-assembly GPL-3.0-or-later Intergalactic Workflow Commission (IWC) True False +qiime2-III-VI-downsteam/QIIME2-III-V-Phylogeny-Rarefaction-Taxonomic-Analysis WorkflowHub 1090 https://workflowhub.eu/workflows/1090?version=2 Debjyoti Ghosh 2024-11-26 2026-05-14 2 2 3.0 Rarefaction, Taxonomic analysis, Phylogenetic tree for diversity analysis MIT Intergalactic Workflow Commission (IWC) True False +gene-based-pathogen-identification/main WorkflowHub 1062 https://workflowhub.eu/workflows/1062?version=1 Engy Nasr, Bérénice Batut, Paul Zierep 2024-06-26 2026-05-13 1 1 15.0 abricate, collection_element_identifiers, bandage_image, flye, tp_find_and_replace, split_file_to_collection, compose_text_param, __BUILD_LIST__, tab2fasta, medaka_consensus_pipeline, param_value_from_file, fasta2tab Base-calling, Antimicrobial resistance prediction, De-novo assembly, Variant calling, Sequence assembly visualisation, Sequence assembly, Cross-assembly, Mapping assembly, Genome assembly MIT 10.48546/workflowhub.workflow.1062.1 Intergalactic Workflow Commission (IWC) True False +pathogen-detection-pathogfair-samples-aggregation-and-visualisation/main WorkflowHub 1060 https://workflowhub.eu/workflows/1060?version=1 Engy Nasr, Bérénice Batut, Paul Zierep 2024-06-26 2026-05-13 1 1 60.0 tp_split_on_column, ggplot2_heatmap, bedtools_getfastabed, collapse_dataset, regex1, tp_replace_in_column, fasta_merge_files_and_filter_unique_sequences, newick_display, regexColumn1, tp_multijoin_tool, Count1, __FILTER_EMPTY_DATASETS__, fasta2tab, tp_sorted_uniq, Grouping1, fasttree, tab2fasta, Remove beginning1, collection_column_join, clustalw, __FILTER_FAILED_DATASETS__, Cut1 Phylogenetic tree generation, Visualisation, Multiple sequence alignment, Phylogenetic tree reconstruction, Phylogenetic tree analysis, Mapping MIT 10.48546/workflowhub.workflow.1060.1 Intergalactic Workflow Commission (IWC) True False +taxonomy-profiling-and-visualization-with-krona/main WorkflowHub 1059 https://workflowhub.eu/workflows/1059?version=1 Engy Nasr, Bérénice Batut, Paul Zierep 2024-06-26 2026-05-13 1 1 3.0 krakentools_kreport2krona, kraken2, taxonomy_krona_chart Taxonomic classification, Aggregation, Visualisation MIT 10.48546/workflowhub.workflow.1059.1 Intergalactic Workflow Commission (IWC) True False +bacterial_genome_annotation/main WorkflowHub 1050 https://workflowhub.eu/workflows/1050?version=13 ABRomics None, Pierre Marin, Clea Siguret abromics, annotation, genomics, bacterial-genomics, fasta, genome-annotation 2025-12-06 2026-05-13 13 13 6.0 tooldistillator_summarize, integron_finder, plasmidfinder, isescan, bakta, tooldistillator Scaffolding, Genome annotation, Nucleic acid feature detection, Data parsing, Protein feature detection, Structural variation detection, Sequence motif recognition, Multilocus sequence typing, Genome assembly GPL-3.0-or-later Intergalactic Workflow Commission (IWC) True False +amr_gene_detection/main WorkflowHub 1049 https://workflowhub.eu/workflows/1049?version=9 ABRomics None, Pierre Marin, Clea Siguret abromics, amr, amr-detection, genomics, antibiotic-resistance, antimicrobial resistance, antimicrobial-resistance-genes, bacterial-genomics, fasta 2025-12-04 2026-05-13 9 9 5.0 tooldistillator_summarize, abricate, amrfinderplus, staramr_search, tooldistillator Data parsing, Antimicrobial resistance prediction GPL-3.0-or-later Intergalactic Workflow Commission (IWC) True False +dada2/main WorkflowHub 790 https://workflowhub.eu/workflows/790?version=3 Matthias Bernt name:amplicon 2025-03-26 2026-05-14 3 3 14.0 dada2_dada, dada2_makeSequenceTable, __APPLY_RULES__, dada2_plotQualityProfile, dada2_learnErrors, dada2_assignTaxonomyAddspecies, dada2_seqCounts, dada2_filterAndTrim, __UNZIP_COLLECTION__, dada2_removeBimeraDenovo, dada2_mergePairs DNA barcoding, Variant calling MIT Intergalactic Workflow Commission (IWC) True False +Refining Genome Annotations with Apollo (prokaryotes) WorkflowHub 749 https://workflowhub.eu/workflows/749?version=1 Anthony Bretaudeau genome-annotation 2024-02-14 2025-11-04 1 1 5.0 create_or_update, iframe, jbrowse, create_account, list_organism Genome visualisation CC-BY-4.0 10.48546/workflowhub.workflow.749.1 EuroScienceGateway True False +TB Variant Analysis v1.0 WorkflowHub 1647 https://workflowhub.eu/workflows/1647?version=2 gtn, galaxy, pathogen, tuberculosis 2026-01-12 2026-01-12 2 2 15.0 fastp, tp_awk_tool, qualimap_bamqc, EMBOSS: seqret84, kraken2, mosdepth, __FLATTEN__, tp_sed_tool, snippy, multiqc, bcftools_consensus, tb_variant_filter, tb_profiler_profile, tbvcfreport Taxonomic classification, Antimicrobial resistance prediction, Variant calling, Sequence alignment, Phylogenetic tree visualisation, Sequencing quality control, Sequence contamination filtering, Sequence alignment analysis, Phylogenetic tree generation, Validation, Global alignment, Sequence analysis, Local alignment AGPL-3.0-or-later Galaxy Training Network True False +Quality and contamination control in bacterial isolate using Illumina MiSeq Data WorkflowHub 2043 https://workflowhub.eu/workflows/2043?version=1 gtn, galaxy, sequence-analysis 2025-12-22 2025-12-22 1 1 5.0 fastp, recentrifuge, est_abundance, kraken2, falco Statistical calculation, Taxonomic classification, Expression analysis, Sequencing quality control, Sequence contamination filtering, Read mapping, Visualisation, Cross-assembly GPL-3.0-or-later Galaxy Training Network True False +Taxonomic Profiling and Visualization of Metagenomic Data WorkflowHub 1470 https://workflowhub.eu/workflows/1470?version=2 gtn, galaxy, microbiome 2025-12-22 2025-12-22 2 2 10.0 metaphlan, taxonomy_krona_chart, krakentools_kreport2krona, est_abundance, kraken_biom, kraken2, interactive_tool_phinch, __UNZIP_COLLECTION__, interactive_tool_pavian Statistical calculation, Taxonomic classification, Aggregation, Genome annotation, Visualisation MIT Galaxy Training Network True False +Checking expected species and contamination in bacterial isolate WorkflowHub 1674 https://workflowhub.eu/workflows/1674?version=2 ecology, gtn, galaxy 2025-12-22 2025-12-22 2 2 3.0 est_abundance, recentrifuge, kraken2 Statistical calculation, Taxonomic classification, Expression analysis, Cross-assembly GPL-3.0-or-later Galaxy Training Network True False +Metagenomic Binning WorkflowHub 2028 https://workflowhub.eu/workflows/2028?version=1 gtn, galaxy, microgalaxy, binning, microbiome 2025-12-08 2025-12-08 1 1 17.0 bowtie2, concoct_coverage_table, concoct_merge_cut_up_clustering, concoct_extract_fasta_bins, concoct_cut_up_fasta, samtools_sort, Fasta_to_Contig2Bin, concoct, __BUILD_LIST__, binette, semibin, maxbin2, metabat2, metabat2_jgi_summarize_bam_contig_depths Sequence assembly, Read mapping, Sequence clustering, Genome annotation, Read binning MIT Galaxy Training Network True False +MGnify's amplicon pipeline v5.0 - ITS WorkflowHub 1856 https://workflowhub.eu/workflows/1856?version=1 amplicon, gtn, galaxy, metagenomics, mgnify_amplicon, name:microgalaxy 2025-08-11 2025-08-11 1 1 30.0 , bedtools_maskfastabed, mapseq, tp_awk_tool, __FILTER_FROM_FILE__, collection_element_identifiers, taxonomy_krona_chart, biom_convert, __FILTER_EMPTY_DATASETS__ k-mer counting, Formatting, Visualisation, Mapping Apache-2.0 Galaxy Training Network True False +MAPseq to ampvis2 WorkflowHub 1855 https://workflowhub.eu/workflows/1855?version=1 gtn, galaxy, microbiome 2025-08-11 2025-08-11 1 1 9.0 tp_awk_tool, collection_column_join, collapse_dataset, ampvis2_load, query_tabular Analysis, Visualisation MIT Galaxy Training Network True False +MGnify's amplicon pipeline v5.0 - Quality control PE WorkflowHub 1854 https://workflowhub.eu/workflows/1854?version=1 amplicon, gtn, galaxy, metagenomics, mgnify_amplicon, name:microgalaxy 2025-08-11 2025-08-11 1 1 17.0 fastp, cshl_fasta_formatter, tp_find_and_replace, multiqc, trimmomatic, fastqc, __UNZIP_COLLECTION__, mgnify_seqprep, fastq_filter, prinseq, fastq_to_fasta_python Statistical calculation, Sequencing quality control, Sequence contamination filtering, Sequence trimming, Validation, Nucleic acid design, Read pre-processing, Sequence composition calculation Apache-2.0 Galaxy Training Network True False +MGnify's amplicon pipeline v5.0 WorkflowHub 1853 https://workflowhub.eu/workflows/1853?version=1 amplicon, gtn, galaxy, metagenomics, mgnify_amplicon, name:microgalaxy 2025-08-11 2025-08-11 1 1 20.0 , tp_awk_tool, CONVERTER_uncompressed_to_gz, CONVERTER_gz_to_uncompressed, __MERGE_COLLECTION__, fastq_dl Apache-2.0 Galaxy Training Network True False +MGnify amplicon summary tables WorkflowHub 1851 https://workflowhub.eu/workflows/1851?version=1 amplicon, gtn, galaxy, metagenomics, mgnify_amplicon, name:microgalaxy 2025-08-11 2025-08-11 1 1 10.0 tp_awk_tool, collection_column_join, Grouping1, filter_tabular, query_tabular MIT Galaxy Training Network True False +MGnify's amplicon pipeline v5.0 - Quality control SE WorkflowHub 1850 https://workflowhub.eu/workflows/1850?version=1 amplicon, gtn, galaxy, metagenomics, mgnify_amplicon, name:microgalaxy 2025-08-11 2025-08-11 1 1 14.0 cshl_fasta_formatter, tp_find_and_replace, multiqc, trimmomatic, fastqc, fastq_filter, prinseq, fastq_to_fasta_python Sequencing quality control, Statistical calculation, Sequence contamination filtering, Sequence trimming, Validation, Read pre-processing, Sequence composition calculation Apache-2.0 Galaxy Training Network True False +MGnify's amplicon pipeline v5.0 - rRNA prediction WorkflowHub 1842 https://workflowhub.eu/workflows/1842?version=1 amplicon, gtn, galaxy, metagenomics, mgnify_amplicon, name:microgalaxy 2025-08-04 2025-08-11 1 1 47.0 , cshl_fasta_formatter, tp_awk_tool, mapseq, collection_element_identifiers, __FILTER_FROM_FILE__, taxonomy_krona_chart, biom_convert, cmsearch_deoverlap, infernal_cmsearch, bedtools_getfastabed, gops_concat_1, query_tabular, __FILTER_EMPTY_DATASETS__ k-mer counting, Formatting, Comparison, Mapping, Alignment, Nucleic acid feature detection, Visualisation Apache-2.0 Galaxy Training Network True False +Workflow 3: Functional Information (quick) WorkflowHub 1447 https://workflowhub.eu/workflows/1447?version=2 asaim, gtn, galaxy, metagenomics 2025-07-14 2025-07-14 2 2 12.0 humann_rename_table, humann_regroup_table, tp_find_and_replace, combine_metaphlan2_humann2, humann_unpack_pathways, humann_split_stratified_table, humann_renorm_table, Grep1, Cut1 Taxonomic classification, Species frequency estimation, Phylogenetic analysis MIT Galaxy Training Network True False +Building an amplicon sequence variant (ASV) table from 16S data using DADA2 WorkflowHub 1395 https://workflowhub.eu/workflows/1395?version=2 gtn, galaxy, microbiome 2025-07-07 2025-07-07 2 2 21.0 dada2_dada, Add_a_column1, dada2_makeSequenceTable, dada2_plotQualityProfile, collection_element_identifiers, __SORTLIST__, dada2_learnErrors, tp_replace_in_line, dada2_seqCounts, dada2_assignTaxonomyAddspecies, cat1, dada2_filterAndTrim, __UNZIP_COLLECTION__, tp_replace_in_column, phyloseq_from_dada2, tp_head_tool, dada2_removeBimeraDenovo, dada2_mergePairs DNA barcoding, Analysis, Variant calling, Deposition, Visualisation MIT Galaxy Training Network True False +Metatranscriptomics analysis using microbiome RNA-seq data WorkflowHub 1466 https://workflowhub.eu/workflows/1466?version=2 gtn, galaxy, microbiome 2025-06-23 2025-06-23 2 2 33.0 graphlan_annotate, bg_sortmerna, cutadapt, taxonomy_krona_chart, tp_find_and_replace, export2graphlan, humann_split_stratified_table, metaphlan, humann_regroup_table, fastq_paired_end_interlacer, Grouping1, humann_renorm_table, Grep1, graphlan, humann, tp_sort_header_tool, humann_rename_table, multiqc, fastqc, humann_unpack_pathways, combine_metaphlan_humann, Cut1 Statistical calculation, Phylogenetic inference, Conversion, Sequencing quality control, Sequence alignment analysis, Sequence comparison, Sequence composition calculation, Phylogenetic analysis, Taxonomic classification, Aggregation, Species frequency estimation, Phylogenetic tree visualisation, Sequence similarity search, Phylogenetic tree editing, Sequence trimming, Validation, Read pre-processing, Primer removal, Visualisation MIT Galaxy Training Network True False +Metatranscriptomics analysis using microbiome RNA-seq data - Workflow 2: Community profile WorkflowHub 1451 https://workflowhub.eu/workflows/1451?version=2 gtn, galaxy, microbiome 2025-06-23 2025-06-23 2 2 6.0 metaphlan, graphlan_annotate, taxonomy_krona_chart, export2graphlan, Cut1, graphlan Taxonomic classification, Phylogenetic inference, Conversion, Phylogenetic tree visualisation, Phylogenetic tree editing, Visualisation MIT Galaxy Training Network True False +Metatranscriptomics analysis using microbiome RNA-seq data - Workflow 1: Preprocessing WorkflowHub 1444 https://workflowhub.eu/workflows/1444?version=2 gtn, galaxy, microbiome 2025-06-23 2025-06-23 2 2 6.0 fastq_paired_end_interlacer, multiqc, fastqc, bg_sortmerna, cutadapt Statistical calculation, Sequence similarity search, Primer removal, Sequencing quality control, Sequence trimming, Sequence alignment analysis, Sequence comparison, Validation, Read pre-processing, Sequence composition calculation MIT Galaxy Training Network True False +Metatranscriptomics analysis using microbiome RNA-seq data - Workflow 3: Functional Information WorkflowHub 1456 https://workflowhub.eu/workflows/1456?version=2 gtn, galaxy, microbiome 2025-06-23 2025-06-23 2 2 18.0 humann_rename_table, humann_regroup_table, tp_find_and_replace, humann_unpack_pathways, humann_split_stratified_table, humann_renorm_table, Grep1, humann, tp_sort_header_tool Taxonomic classification, Species frequency estimation, Phylogenetic analysis MIT Galaxy Training Network True False +Assembly of metagenomic sequencing data WorkflowHub 1390 https://workflowhub.eu/workflows/1390?version=2 gtn, galaxy, microbiome 2025-06-16 2025-06-16 2 2 9.0 bowtie2, megahit_contig2fastg, collection_column_join, metaspades, bandage_image, bandage_info, megahit, coverm_contig, quast Visualisation, Read mapping, Sequence assembly validation, Sequence assembly visualisation, Local alignment, Genome assembly MIT Galaxy Training Network True False +Taxonomic Analysis of eDNA WorkflowHub 1723 https://workflowhub.eu/workflows/1723?version=1 ecology, gtn, galaxy 2025-06-02 2025-06-02 1 1 8.0 fastp, cshl_fastq_to_fasta, ncbi_blastn_wrapper, Count1 Sequencing quality control, Sequence contamination filtering CC-BY-4.0 Galaxy Training Network True False +Quality and contamination control in bacterial isolate using Illumina MiSeq Data WorkflowHub 1644 https://workflowhub.eu/workflows/1644?version=1 gtn, galaxy, sequence-analysis 2025-06-02 2025-06-02 1 1 6.0 fastp, recentrifuge, est_abundance, kraken2, falco Statistical calculation, Taxonomic classification, Expression analysis, Sequencing quality control, Sequence contamination filtering, Read mapping, Visualisation, Cross-assembly GPL-3.0-or-later Galaxy Training Network True False +pox-virus-tiled-amplicon-ref-masking WorkflowHub 1632 https://workflowhub.eu/workflows/1632?version=1 gtn, galaxy, variant-analysis 2025-06-02 2025-06-02 1 1 14.0 Add_a_column1, compose_text_param, EMBOSS: maskseq51, Grep1, datamash_ops, fasta_compute_length, Cut1, param_value_from_file Sequence alignment analysis, Global alignment, Sequence analysis, Sequence alignment, Local alignment MIT Galaxy Training Network True False +Copy Of GTN Training - Antibiotic Resistance Detection WorkflowHub 1477 https://workflowhub.eu/workflows/1477?version=1 gtn, galaxy, microbiome 2025-06-02 2025-06-02 1 1 12.0 unicycler, bandage_image, miniasm, staramr_search, PlasFlow, nanoplot, minimap2, racon, gfa_to_fa Pairwise sequence alignment, Aggregation, Antimicrobial resistance prediction, Box-Whisker plot plotting, De-novo assembly, Scatter plot plotting, Sequence assembly visualisation, Sequence analysis, Mapping assembly, Genome assembly CC-BY-4.0 Galaxy Training Network True False +Amplicon Tutorial WorkflowHub 1476 https://workflowhub.eu/workflows/1476?version=1 gtn, galaxy, microbiome 2025-06-02 2025-06-02 1 1 17.0 mothur_unique_seqs, mothur_cluster_split, mothur_summary_seqs, mothur_count_seqs, mothur_make_shared, mothur_make_biom, mothur_merge_files, mothur_screen_seqs, mothur_filter_seqs, mothur_make_group, mothur_classify_seqs, mothur_classify_otu, mothur_align_seqs, mothur_pre_cluster, krona-text Taxonomic classification, DNA barcoding, Sequence read processing, Sequencing quality control, Sequence clustering, Phylogenetic analysis, Visualisation CC-BY-4.0 Galaxy Training Network True False +Training: 16S rRNA Analysis with Nanopore Sequencing Reads WorkflowHub 1473 https://workflowhub.eu/workflows/1473?version=1 gtn, galaxy, microbiome 2025-06-02 2025-06-02 1 1 11.0 fastp, datamash_reverse, taxonomy_krona_chart, multiqc, kraken2, tp_replace_in_line, fastqc, porechop, Remove beginning1 Sequencing quality control, Sequence contamination filtering, Taxonomic classification, Statistical calculation, Validation, Sequence composition calculation, Visualisation CC-BY-4.0 Galaxy Training Network True False +"WGS Part In ""Analyses Of Metagenomics Data - The Global Picture""" WorkflowHub 1472 https://workflowhub.eu/workflows/1472?version=1 gtn, galaxy, microbiome 2025-06-02 2025-06-02 1 1 7.0 metaphlan2krona, metaphlan2, humann2_renorm_table, taxonomy_krona_chart, humann2, humann2_regroup_table Visualisation CC-BY-4.0 Galaxy Training Network True False +Query a metaplasmidome database to identify and annotate plasmids in metagenomes WorkflowHub 1469 https://workflowhub.eu/workflows/1469?version=1 gtn, galaxy, metagenomics, metaplasmidome, name:microgalaxy 2025-06-02 2025-06-02 1 1 47.0 Add_a_column1, CONVERTER_fasta_to_tabular, tp_sorted_uniq, histogram_rpy, join1, Grouping1, cat1, tp_tail_tool, count_gff_features, ggplot2_histogram, minimap2, add_column_headers, tp_replace_in_column, Filter1, tab2fasta, Cut1, MQoutputfilter, sort1 Pairwise sequence alignment, Visualisation MIT Galaxy Training Network True False +Training: 16S rRNA Sequencing With Mothur: Main Tutorial WorkflowHub 1465 https://workflowhub.eu/workflows/1465?version=1 gtn, galaxy, microbiome 2025-06-02 2025-06-02 1 1 38.0 mothur_count_seqs, mothur_chimera_vsearch, mothur_get_groups, mothur_screen_seqs, mothur_rarefaction_single, mothur_align_seqs, newick_display, mothur_make_shared, taxonomy_krona_chart, mothur_cluster, mothur_remove_seqs, mothur_summary_single, mothur_sub_sample, mothur_remove_groups, mothur_classify_seqs, mothur_seq_error, mothur_count_groups, mothur_cluster_split, mothur_tree_shared, mothur_summary_seqs, mothur_make_contigs, mothur_dist_shared, mothur_dist_seqs, XY_Plot_1, mothur_filter_seqs, mothur_remove_lineage, mothur_classify_otu, mothur_pre_cluster, mothur_unique_seqs, mothur_venn, mothur_heatmap_sim, mothur_make_biom, mothur_taxonomy_to_krona Taxonomic classification, DNA barcoding, Sequence read processing, Sequencing quality control, Phylogenetic tree generation, Phylogenetic tree reconstruction, Sequence clustering, Phylogenetic tree analysis, Phylogenetic analysis, Visualisation CC-BY-4.0 Galaxy Training Network True False +Workflow for Identifying MF from ITS2 sequencing using LotuS2 - tutorial example run' WorkflowHub 1460 https://workflowhub.eu/workflows/1460?version=1 ecology, fungi, gtn, galaxy, lotus2, metagenomics 2025-06-02 2025-06-02 1 1 1.0 lotus2 DNA barcoding, Sequence feature detection MIT Galaxy Training Network True False +Identification of the micro-organisms in a beer using Nanopore sequencing WorkflowHub 1439 https://workflowhub.eu/workflows/1439?version=1 gtn, galaxy, microbiome 2025-06-02 2025-06-02 1 1 8.0 fastp, taxonomy_krona_chart, krakentools_kreport2krona, kraken2, fastqc, Filter1, porechop Sequencing quality control, Sequence contamination filtering, Taxonomic classification, Statistical calculation, Aggregation, Sequence composition calculation, Visualisation MIT Galaxy Training Network True False +Calculating diversity from microbiome taxonomic data WorkflowHub 1431 https://workflowhub.eu/workflows/1431?version=1 gtn, galaxy, name:gtn 2025-06-02 2025-06-02 1 1 6.0 krakentools_alpha_diversity, krakentools_beta_diversity Aggregation, Visualisation MIT Galaxy Training Network True False +Workflow 3: Classification [Galaxy Training: 16S Microbial Analysis With Mothur] WorkflowHub 1428 https://workflowhub.eu/workflows/1428?version=1 gtn, galaxy, microbiome 2025-06-02 2025-06-02 1 1 3.0 mothur_remove_lineage, mothur_summary_seqs, mothur_classify_seqs Taxonomic classification, DNA barcoding, Sequence read processing, Sequencing quality control, Sequence clustering, Phylogenetic analysis, Visualisation MIT Galaxy Training Network True False +Workflow 1: Quality Control [Galaxy Training: 16S Microbial Analysis With Mothur] WorkflowHub 1422 https://workflowhub.eu/workflows/1422?version=1 gtn, galaxy, microbiome 2025-06-02 2025-06-02 1 1 5.0 mothur_unique_seqs, mothur_summary_seqs, mothur_count_seqs, mothur_screen_seqs Taxonomic classification, DNA barcoding, Sequence read processing, Sequencing quality control, Sequence clustering, Phylogenetic analysis, Visualisation MIT Galaxy Training Network True False +Workflow7: Beta Diversity [Galaxy Training: 16S Microbial Analysis With Mothur] WorkflowHub 1418 https://workflowhub.eu/workflows/1418?version=1 gtn, galaxy, microbiome 2025-06-02 2025-06-02 1 1 6.0 mothur_tree_shared, mothur_venn, mothur_heatmap_sim, mothur_dist_shared, collapse_dataset, newick_display Taxonomic classification, DNA barcoding, Sequence read processing, Sequencing quality control, Phylogenetic tree generation, Phylogenetic tree reconstruction, Sequence clustering, Phylogenetic tree analysis, Phylogenetic analysis, Visualisation MIT Galaxy Training Network True False +Workflow 6: Alpha Diversity [Galaxy Training: 16S Microbial Analysis With Mothur] WorkflowHub 1412 https://workflowhub.eu/workflows/1412?version=1 gtn, galaxy, microbiome 2025-06-02 2025-06-02 1 1 3.0 XY_Plot_1, mothur_rarefaction_single, mothur_summary_single Taxonomic classification, DNA barcoding, Sequence read processing, Sequencing quality control, Sequence clustering, Phylogenetic analysis, Visualisation MIT Galaxy Training Network True False +Workflow 4: Mock OTU Clustering [Galaxy Training: 16S Microbial Analysis With Mothur] WorkflowHub 1408 https://workflowhub.eu/workflows/1408?version=1 gtn, galaxy, microbiome 2025-06-02 2025-06-02 1 1 4.0 mothur_cluster, mothur_dist_seqs, mothur_make_shared, mothur_rarefaction_single Taxonomic classification, DNA barcoding, Sequence read processing, Sequencing quality control, Sequence clustering, Phylogenetic analysis, Visualisation MIT Galaxy Training Network True False +Workflow 5: OTU Clustering [Galaxy Training: 16S Microbial Analysis With Mothur] WorkflowHub 1404 https://workflowhub.eu/workflows/1404?version=1 gtn, galaxy, microbiome 2025-06-02 2025-06-02 1 1 6.0 mothur_cluster_split, mothur_make_shared, mothur_sub_sample, mothur_remove_groups, mothur_classify_otu, mothur_count_groups Taxonomic classification, DNA barcoding, Sequence read processing, Sequencing quality control, Sequence clustering, Phylogenetic analysis, Visualisation MIT Galaxy Training Network True False +Workflow 2: Data Cleaning And Chimera Removal [Galaxy Training: 16S Microbial Analysis With Mothur] WorkflowHub 1400 https://workflowhub.eu/workflows/1400?version=1 gtn, galaxy, microbiome 2025-06-02 2025-06-02 1 1 9.0 mothur_unique_seqs, mothur_summary_seqs, mothur_chimera_vsearch, mothur_remove_seqs, mothur_screen_seqs, mothur_filter_seqs, mothur_pre_cluster Taxonomic classification, DNA barcoding, Sequence read processing, Sequencing quality control, Sequence clustering, Phylogenetic analysis, Visualisation MIT Galaxy Training Network True False +GTN Training - Antibiotic Resistance Detection WorkflowHub 406 https://workflowhub.eu/workflows/406?version=1 Saskia Hiltemann, Willem de Koning metagenomics 2022-11-24 2026-05-13 1 1 12.0 unicycler, bandage_image, miniasm, staramr_search, PlasFlow, nanoplot, minimap2, racon, gfa_to_fa Pairwise sequence alignment, Aggregation, Antimicrobial resistance prediction, Box-Whisker plot plotting, De-novo assembly, Scatter plot plotting, Sequence assembly visualisation, Sequence analysis, Mapping assembly, Genome assembly Microbiology CC-BY-4.0 Galaxy Training Network True False +3: Plant virus exploration WorkflowHub 103 https://workflowhub.eu/workflows/103?version=1 de_novo, virology, exploration 2021-02-04 2026-05-13 1 1 2.0 fastp, shovill Sequencing quality control, Sequence contamination filtering, Genome assembly Apache-2.0 Integrated and Urban Plant Pathology Laboratory True False +2: Plant virus confirmation WorkflowHub 102 https://workflowhub.eu/workflows/102?version=1 assembly, virology, blast, mapping, reads_selection 2021-02-04 2026-05-13 1 1 7.0 ncbi_blastn_wrapper, shovill, picard_SamToFastq, ngsutils_bam_filter, minimap2, samtools_stats, fasta_merge_files_and_filter_unique_sequences Sequencing quality control, Formatting, Sequence contamination filtering, Pairwise sequence alignment, Variant calling, Read pre-processing, Genome assembly Apache-2.0 Integrated and Urban Plant Pathology Laboratory True False +1: Plant virus detection with kraken2 (SE) WorkflowHub 124 https://workflowhub.eu/workflows/124?version=1 virology, kraken 2021-06-17 2026-05-13 1 1 3.0 Kraken2Tax, kraken2, taxonomy_krona_chart Taxonomic classification, Visualisation Apache-2.0 Integrated and Urban Plant Pathology Laboratory True False +1: Plant virus detection with kraken2 (PE) WorkflowHub 101 https://workflowhub.eu/workflows/101?version=1 virology, kraken 2021-02-04 2026-05-13 1 1 3.0 Kraken2Tax, kraken2, taxonomy_krona_chart Taxonomic classification, Visualisation Apache-2.0 Integrated and Urban Plant Pathology Laboratory True False +MPXV (Mpox) Phylogenetic Analysis with Squirrel WorkflowHub 2196 https://workflowhub.eu/workflows/2196?version=1 Tristan Reynolds, Ammar Aziz amplicon, mpox, ont, virus, mpxv, phylogeny 2026-06-18 2026-06-25 1 1 3.0 squirrel_phylo, regex1, squirrel_qc Sequencing quality control, Phylogenetic analysis Bioinformatics, Biomedical science, Genomics, Virology MIT 10.48546/workflowhub.workflow.2196.1 Melbourne Bioinformatics, Galaxy Australia True False +Viral Amplicon Analysis Pipeline for ONT Data WorkflowHub 2195 https://workflowhub.eu/workflows/2195?version=1 Tristan Reynolds, Ammar Aziz amplicon, mpox, ont, virus, mpxv, phylogeny 2026-06-18 2026-06-25 1 1 12.0 artic_minion, multiqc, mosdepth, XY_Plot_1, regex1, __BUILD_LIST__, tp_cat, fastplong, bedtools_makewindowsbed Sequencing quality control, Sequence alignment, Validation, Mapping Bioinformatics, Biomedical science, Genomics, Virology MIT 10.48546/workflowhub.workflow.2195.1 Melbourne Bioinformatics, Galaxy Australia True False +Taxonomy Assignment with QIIME2 WorkflowHub 2098 https://workflowhub.eu/workflows/2098?version=1 Tristan Reynolds, Amy Loughman amplicon, microbiome, taxonomic-classification 2026-03-02 2026-05-13 1 1 19.0 qiime2__feature_table__tabulate_seqs, biom_convert, csv_to_tabular, tp_easyjoin_tool, qiime2_core__tools__import, qiime2__feature_classifier__classify_sklearn, qiime2__feature_table__summarize, tabular_to_csv, qiime2__taxa__barplot, qiime_extract_viz, qiime2__feature_classifier__fit_classifier_naive_bayes, qiime2_core__tools__export, qiime2__feature_classifier__extract_reads, Remove beginning1 Taxonomic classification, Formatting, Demultiplexing, Visualisation Taxonomy CC-BY-4.0 10.48546/workflowhub.workflow.2098.1 Melbourne Bioinformatics, Galaxy Australia True False +Taxonomy classification using Kraken2 and Bracken WorkflowHub 1199 https://workflowhub.eu/workflows/1199?version=2 Valentine Murigneux, Mike Thang gucfg2galaxy, metagenomics, name:collection, shotgun 2024-12-10 2024-12-10 2 2 29.0 "__RELABEL_FROM_FILE__, collection_column_join, cat_multiple, Prepare alpha diversity summary file +Paste1, collection_element_identifiers, krakentools_combine_kreports, krakentools_kreport2krona, krakentools_beta_diversity, est_abundance, taxonomy_krona_chart, kraken2, Prepare alpha diversity summary file (paste sample identifiers and Simpson results) Paste1, Prepare alpha diversity summary file (paste Simpson and Fisher results) -Paste1, kraken2, Prepare alpha diversity summary file (paste sample identifiers and Simpson results) -Paste1, taxonomy_krona_chart, collection_element_identifiers, krakentools_kreport2krona, Fisher results contains a header line we want to exclude ""Fisher's alpha...loading"" -Show tail1, est_abundance, __RELABEL_FROM_FILE__, add_line_to_file, regex1, krakentools_alpha_diversity, cat_multiple, Extract column name and fraction_total_reads from Bracken report -Cut1, krakentools_combine_kreports" Visualisation, Statistical calculation, Taxonomic classification, Aggregation Metagenomics, Taxonomy CC-BY-4.0 10.48546/workflowhub.workflow.1199.2 QCIF Bioinformatics True False -Analyses of shotgun metagenomics data with MetaPhlAn2 WorkflowHub 624 https://workflowhub.eu/workflows/624?version=1 Valentine Murigneux, Mike Thang, Saskia Hiltemann, Bérénice Batut gucfg2galaxy, metagenomics, shotgun 2023-10-26 2026-05-13 1 1 17.0 , humann2, taxonomy_krona_chart, metaphlan2krona, humann2_renorm_table, humann2_regroup_table, Cut1, merge_metaphlan_tables, metaphlan2 Visualisation, Taxonomic classification Metagenomic sequencing, Metagenomics CC-BY-4.0 10.48546/workflowhub.workflow.624.1 QCIF Bioinformatics True False -Workflow 7 : Beta Diversity [16S Microbial Analysis With Mothur] WorkflowHub 653 https://workflowhub.eu/workflows/653?version=1 Saskia Hiltemann, Bérénice Batut, Dave Clements, Ahmed Mehdi metagenomics 2023-11-09 2026-05-13 1 1 4.0 mothur_dist_shared, mothur_tree_shared, mothur_heatmap_sim, newick_display Visualisation, Phylogenetic tree reconstruction, Sequence clustering, Phylogenetic tree generation, DNA barcoding, Phylogenetic tree analysis, Taxonomic classification, Sequence read processing, Sequencing quality control, Phylogenetic analysis CC-BY-4.0 QCIF Bioinformatics True False -Workflow 6: Alpha Diversity [16S Microbial Analysis With Mothur] WorkflowHub 652 https://workflowhub.eu/workflows/652?version=1 Saskia Hiltemann, Bérénice Batut, Dave Clements, Ahmed Mehdi metagenomics 2023-11-09 2026-05-13 1 1 3.0 XY_Plot_1, mothur_rarefaction_single, mothur_summary_single Visualisation, Sequence clustering, DNA barcoding, Taxonomic classification, Sequence read processing, Sequencing quality control, Phylogenetic analysis CC-BY-4.0 QCIF Bioinformatics True False -Workflow 5: OTU Clustering [16S Microbial Analysis With Mothur] WorkflowHub 651 https://workflowhub.eu/workflows/651?version=1 Saskia Hiltemann, Bérénice Batut, Dave Clements, Ahmed Mehdi metagenomics 2023-11-09 2026-05-13 1 1 5.0 mothur_sub_sample, mothur_count_groups, mothur_cluster_split, mothur_make_shared, mothur_classify_otu Visualisation, Sequence clustering, DNA barcoding, Taxonomic classification, Sequence read processing, Sequencing quality control, Phylogenetic analysis CC-BY-4.0 QCIF Bioinformatics True False -Workflow 3: Classification [Galaxy Training: 16S Microbial Analysis With Mothur] WorkflowHub 650 https://workflowhub.eu/workflows/650?version=1 Saskia Hiltemann, Bérénice Batut, Dave Clements, Ahmed Mehdi metagenomics 2023-11-09 2026-05-13 1 1 2.0 mothur_classify_seqs, mothur_remove_lineage Visualisation, Sequence clustering, DNA barcoding, Taxonomic classification, Sequence read processing, Sequencing quality control, Phylogenetic analysis CC-BY-4.0 QCIF Bioinformatics True False -Workflow 1: Further Quality Control [16S Microbial Analysis With Mothur] WorkflowHub 648 https://workflowhub.eu/workflows/648?version=1 Saskia Hiltemann, Bérénice Batut, Dave Clements, Ahmed Mehdi metagenomics 2023-11-09 2026-05-13 1 1 5.0 mothur_summary_seqs, mothur_count_seqs, mothur_screen_seqs, mothur_unique_seqs Visualisation, Sequence clustering, DNA barcoding, Taxonomic classification, Sequence read processing, Sequencing quality control, Phylogenetic analysis CC-BY-4.0 QCIF Bioinformatics True False -Workflow 2: Data Cleaning And Chimera Removal [16S Microbial Analysis With Mothur] WorkflowHub 649 https://workflowhub.eu/workflows/649?version=1 Saskia Hiltemann, Bérénice Batut, Dave Clements, Ahmed Mehdi metagenomics 2023-11-09 2026-05-13 1 1 9.0 mothur_pre_cluster, mothur_summary_seqs, mothur_unique_seqs, mothur_filter_seqs, mothur_chimera_vsearch, mothur_screen_seqs, mothur_remove_seqs Visualisation, Sequence clustering, DNA barcoding, Taxonomic classification, Sequence read processing, Sequencing quality control, Phylogenetic analysis CC-BY-4.0 QCIF Bioinformatics True False -TB Variant Analysis v1.0 WorkflowHub 1035 https://workflowhub.eu/workflows/1035?version=1 Peter van Heusden pathogen, tuberculosis 2024-06-07 2026-05-13 1 1 15.0 bcftools_consensus, tp_awk_tool, tb_profiler_profile, kraken2, __FLATTEN__, multiqc, mosdepth, snippy, qualimap_bamqc, tb_variant_filter, tbvcfreport, fastp, tp_sed_tool, EMBOSS: seqret84 Phylogenetic tree visualisation, Sequence alignment, Validation, Antimicrobial resistance prediction, Phylogenetic tree generation, Variant calling, Sequence analysis, Local alignment, Sequence contamination filtering, Global alignment, Sequence alignment analysis, Taxonomic classification, Sequencing quality control Genetic variation, Infectious disease, Microbiology, Public health and epidemiology, Sequence assembly AGPL-3.0-or-later SANBI Pathogen Bioinformatics True False -Workflow 3: AMR - SeqSero2/SISTR WorkflowHub 407 https://workflowhub.eu/workflows/407?version=1 bioinformatics, antimicrobial resistance 2022-11-24 2026-05-13 1 1 14.0 kma_map, hamronize_summarize, seqsero2, bbtools_bbduk, __UNZIP_COLLECTION__, srst2, shovill, mob_recon, hamronize_tool, sistr_cmd, bbtools_tadpole Visualisation, Multilocus sequence typing, Sequence alignment, Genome indexing, Read mapping, Sequence contamination filtering, Clustering, Genome alignment, Parsing, Data handling, Genome assembly, RNA-Seq analysis, Sequence trimming, Antimicrobial resistance prediction, Read binning, Sequence analysis GPL-3.0 Seq4AMR True False +Paste1, add_line_to_file, krakentools_alpha_diversity, regex1, Extract column name and fraction_total_reads from Bracken report +Cut1, Fisher results contains a header line we want to exclude ""Fisher's alpha...loading"" +Show tail1" Statistical calculation, Taxonomic classification, Aggregation, Visualisation Metagenomics, Taxonomy CC-BY-4.0 10.48546/workflowhub.workflow.1199.2 QCIF Bioinformatics True False +Analyses of shotgun metagenomics data with MetaPhlAn2 WorkflowHub 624 https://workflowhub.eu/workflows/624?version=1 Valentine Murigneux, Mike Thang, Saskia Hiltemann, Bérénice Batut gucfg2galaxy, metagenomics, shotgun 2023-10-26 2026-05-13 1 1 17.0 , metaphlan2krona, metaphlan2, taxonomy_krona_chart, humann2_renorm_table, merge_metaphlan_tables, humann2, humann2_regroup_table, Cut1 Taxonomic classification, Visualisation Metagenomic sequencing, Metagenomics CC-BY-4.0 10.48546/workflowhub.workflow.624.1 QCIF Bioinformatics True False +Workflow 7 : Beta Diversity [16S Microbial Analysis With Mothur] WorkflowHub 653 https://workflowhub.eu/workflows/653?version=1 Saskia Hiltemann, Bérénice Batut, Dave Clements, Ahmed Mehdi metagenomics 2023-11-09 2026-05-13 1 1 4.0 mothur_tree_shared, mothur_heatmap_sim, newick_display, mothur_dist_shared Taxonomic classification, DNA barcoding, Sequence read processing, Sequencing quality control, Phylogenetic tree generation, Phylogenetic tree reconstruction, Sequence clustering, Phylogenetic tree analysis, Phylogenetic analysis, Visualisation CC-BY-4.0 QCIF Bioinformatics True False +Workflow 6: Alpha Diversity [16S Microbial Analysis With Mothur] WorkflowHub 652 https://workflowhub.eu/workflows/652?version=1 Saskia Hiltemann, Bérénice Batut, Dave Clements, Ahmed Mehdi metagenomics 2023-11-09 2026-05-13 1 1 3.0 XY_Plot_1, mothur_rarefaction_single, mothur_summary_single Taxonomic classification, DNA barcoding, Sequence read processing, Sequencing quality control, Sequence clustering, Phylogenetic analysis, Visualisation CC-BY-4.0 QCIF Bioinformatics True False +Workflow 5: OTU Clustering [16S Microbial Analysis With Mothur] WorkflowHub 651 https://workflowhub.eu/workflows/651?version=1 Saskia Hiltemann, Bérénice Batut, Dave Clements, Ahmed Mehdi metagenomics 2023-11-09 2026-05-13 1 1 5.0 mothur_cluster_split, mothur_make_shared, mothur_sub_sample, mothur_classify_otu, mothur_count_groups Taxonomic classification, DNA barcoding, Sequence read processing, Sequencing quality control, Sequence clustering, Phylogenetic analysis, Visualisation CC-BY-4.0 QCIF Bioinformatics True False +Workflow 3: Classification [Galaxy Training: 16S Microbial Analysis With Mothur] WorkflowHub 650 https://workflowhub.eu/workflows/650?version=1 Saskia Hiltemann, Bérénice Batut, Dave Clements, Ahmed Mehdi metagenomics 2023-11-09 2026-05-13 1 1 2.0 mothur_remove_lineage, mothur_classify_seqs Taxonomic classification, DNA barcoding, Sequence read processing, Sequencing quality control, Sequence clustering, Phylogenetic analysis, Visualisation CC-BY-4.0 QCIF Bioinformatics True False +Workflow 1: Further Quality Control [16S Microbial Analysis With Mothur] WorkflowHub 648 https://workflowhub.eu/workflows/648?version=1 Saskia Hiltemann, Bérénice Batut, Dave Clements, Ahmed Mehdi metagenomics 2023-11-09 2026-05-13 1 1 5.0 mothur_unique_seqs, mothur_summary_seqs, mothur_count_seqs, mothur_screen_seqs Taxonomic classification, DNA barcoding, Sequence read processing, Sequencing quality control, Sequence clustering, Phylogenetic analysis, Visualisation CC-BY-4.0 QCIF Bioinformatics True False +Workflow 2: Data Cleaning And Chimera Removal [16S Microbial Analysis With Mothur] WorkflowHub 649 https://workflowhub.eu/workflows/649?version=1 Saskia Hiltemann, Bérénice Batut, Dave Clements, Ahmed Mehdi metagenomics 2023-11-09 2026-05-13 1 1 9.0 mothur_unique_seqs, mothur_summary_seqs, mothur_chimera_vsearch, mothur_remove_seqs, mothur_screen_seqs, mothur_filter_seqs, mothur_pre_cluster Taxonomic classification, DNA barcoding, Sequence read processing, Sequencing quality control, Sequence clustering, Phylogenetic analysis, Visualisation CC-BY-4.0 QCIF Bioinformatics True False +TB Variant Analysis v1.0 WorkflowHub 1035 https://workflowhub.eu/workflows/1035?version=1 Peter van Heusden pathogen, tuberculosis 2024-06-07 2026-05-13 1 1 15.0 fastp, tp_awk_tool, qualimap_bamqc, EMBOSS: seqret84, kraken2, mosdepth, __FLATTEN__, tp_sed_tool, snippy, multiqc, bcftools_consensus, tb_variant_filter, tb_profiler_profile, tbvcfreport Taxonomic classification, Antimicrobial resistance prediction, Variant calling, Sequence alignment, Phylogenetic tree visualisation, Sequencing quality control, Sequence contamination filtering, Sequence alignment analysis, Phylogenetic tree generation, Validation, Global alignment, Sequence analysis, Local alignment Genetic variation, Infectious disease, Microbiology, Public health and epidemiology, Sequence assembly AGPL-3.0-or-later SANBI Pathogen Bioinformatics True False +Workflow 3: AMR - SeqSero2/SISTR WorkflowHub 407 https://workflowhub.eu/workflows/407?version=1 bioinformatics, antimicrobial resistance 2022-11-24 2026-05-13 1 1 14.0 seqsero2, shovill, bbtools_tadpole, hamronize_tool, bbtools_bbduk, sistr_cmd, mob_recon, kma_map, __UNZIP_COLLECTION__, hamronize_summarize, srst2 Genome alignment, Read binning, Sequence contamination filtering, Clustering, Antimicrobial resistance prediction, Data handling, Sequence alignment, Parsing, Genome indexing, RNA-Seq analysis, Sequence trimming, Sequence analysis, Read mapping, Multilocus sequence typing, Visualisation, Genome assembly GPL-3.0 Seq4AMR True False Workflow 2: Sciensano WorkflowHub 644 https://workflowhub.eu/workflows/644?version=1 2023-11-07 2026-05-13 1 1 1.0 pipeline_stec_1.0 CC-BY-4.0 Seq4AMR True False -Workflow 4: Staramr WorkflowHub 470 https://workflowhub.eu/workflows/470?version=1 10.3390/microorganisms10020292, amr, amr-detection, bioinformatics, antimicrobial resistance 2023-05-11 2026-05-13 1 1 10.0 hamronize_summarize, tp_find_and_replace, abricate, staramr_search, collapse_dataset, shovill, hamronize_tool Parsing, Data handling, Genome assembly, Antimicrobial resistance prediction GPL-3.0 Seq4AMR True False +Workflow 4: Staramr WorkflowHub 470 https://workflowhub.eu/workflows/470?version=1 10.3390/microorganisms10020292, amr, amr-detection, bioinformatics, antimicrobial resistance 2023-05-11 2026-05-13 1 1 10.0 abricate, shovill, hamronize_tool, tp_find_and_replace, staramr_search, collapse_dataset, hamronize_summarize Antimicrobial resistance prediction, Data handling, Parsing, Genome assembly GPL-3.0 Seq4AMR True False Workflow 1: AbritAMR WorkflowHub 634 https://workflowhub.eu/workflows/634?version=1 2023-10-31 2026-05-13 1 1 1.0 abritamr Antimicrobial resistance prediction CC-BY-4.0 Seq4AMR True False -AMR-Pathfinder WorkflowHub 1189 https://workflowhub.eu/workflows/1189?version=2 Helena Rasche, Dennis Dollée, Birgit Rijvers amr, amr-detection, benchamrking 2024-11-14 2026-05-13 2 2 36.0 , hamronize_summarize, tp_text_file_with_recurring_lines, cat1, hamronize_tool, abricate, addValue, __APPLY_RULES__, __MERGE_COLLECTION__, collapse_dataset, shovill, Grep1, cast, tp_find_and_replace, Cut1, tp_split_on_column, datamash_ops, staramr_search, cat_multi_datasets Parsing, Data handling, Genome assembly, Antimicrobial resistance prediction MIT Seq4AMR, ErasmusMC Clinical Bioinformatics True False -Copy of Metaproteomics_GTN shared by user engy.nasr https://usegalaxy.eu 6ca1b4fe047a03d2 https://usegalaxy.eu/published/workflow?id=6ca1b4fe047a03d2 proteomics, name:microgalaxy 2026-04-27 2026-04-27 1 1 search_gui, peptide_shaker, sqlite_to_tabular, query_tabular, unipept Visualisation, Prediction and recognition True False -Training: 16S rRNA Analysis with Nanopore Sequencing Reads https://usegalaxy.eu 2a093e63ebf6876b https://usegalaxy.eu/published/workflow?id=2a093e63ebf6876b metagenomics, name:microgalaxy 2025-12-01 2026-03-16 2 2 multiqc, kraken2, fastqc, taxonomy_krona_chart, porechop, tp_replace_in_line, fastp, Remove beginning1, datamash_reverse Visualisation, Sequence composition calculation, Sequence contamination filtering, Statistical calculation, Validation, Taxonomic classification, Sequencing quality control True False -MetaG_extended https://usegalaxy.eu 8c91345ed468e22d https://usegalaxy.eu/published/workflow?id=8c91345ed468e22d name:microgalaxy 2025-10-01 2026-02-04 0 0 fasplit, tp_awk_tool, tp_grep_tool, fastqc, checkm_lineage_wf, hmmer_hmmscan, coverm_genome, quast, coverm_contig, fraggenescan, maxbin2, cat_bins, tp_cat, trim_galore, interproscan, sort1 Visualisation, Sequence composition calculation, Formatting, Statistical calculation, Validation, Sequence database search, Format validation, Primer removal, Coding region prediction, Local alignment, Sequence assembly, Database search, Sequence profile generation, Sequencing quality control, Protein feature detection, Sequence trimming, Multiple sequence alignment, Sequence assembly validation, Sequence motif recognition, Sequence generation, Read pre-processing, Data retrieval, Gene prediction, Taxonomic classification, Conversion, Probabilistic sequence generation True False -Metagenomic Taxonomy Analysis https://usegalaxy.eu 7491883694fff308 https://usegalaxy.eu/published/workflow?id=7491883694fff308 Bérénice Batut, Géraldine Piot, Mina Hojat Ansari name:metagenomics, microbiome, diversity, name:microgalaxy 2025-11-28 2025-12-17 3 3 metaphlan, kraken2, collection_element_identifiers, taxonomy_krona_chart, metaphlan2krona, krakentools_kreport2krona, taxpasta, est_abundance, sylph_profile, add_line_to_file, datamash_transpose, Remove beginning1, cat1 Visualisation, Formatting, Statistical calculation, Taxonomic classification, Conversion, Aggregation, Standardisation and normalisation MIT True False -Quality control of bins generated by MetaBAT2, MaxBin2, SemiBin, and CONCOCT https://usegalaxy.eu 7371b6918e895e0c https://usegalaxy.eu/published/workflow?id=7371b6918e895e0c Bérénice Batut microbiome, name:microgalaxy 2025-12-01 2025-12-08 16 16 multiqc, __FLATTEN__, collection_element_identifiers, __RELABEL_FROM_FILE__, __MERGE_COLLECTION__, regex1, checkm2 Sequence composition calculation, Sequence assembly validation, Statistical calculation, Validation, Sequencing quality control MIT True False -pAllori Amplicon 16S Pre-Processing and Taxonomy Classification https://usegalaxy.eu 466bdd8ba7b67264 https://usegalaxy.eu/published/workflow?id=466bdd8ba7b67264 Engy Nasr, Paul Zierep name:microgalaxy, name:16s, name:metagenomics, name:pallori 2023-06-30 2025-11-18 193 193 compose_text_param, ampvis2_heatmap, fastqc, bg_column_arrange_by_header, ampvis2_subset_samples, datamash_transpose, unzip, biom_convert, maaslin2, volcanoplot, __FLATTEN__, calculate_numeric_param, mmuphin, phyloseq_tax_glom, ampvis2_load, param_value_from_file, tp_awk_tool, tp_cut_tool, tp_easyjoin_tool, Remove beginning1, multiqc, ampvis2_ordinate, phyloseq_from_biom, phyloseq_add_rank_names, ampvis2_export_otu, regex1, lotus2, decontam Visualisation, Sequence feature detection, Sequence composition calculation, Filtering, Formatting, Statistical calculation, Deposition, Validation, Analysis, Standardisation and normalisation, Classification, DNA barcoding, Sequencing quality control MIT True False -Metagenomic Taxonomy and Functional Analysis https://usegalaxy.eu cb2df493f5e334f7 https://usegalaxy.eu/published/workflow?id=cb2df493f5e334f7 Bérénice Batut, Géraldine Piot name:metagenomics, microbiome, diversity, name:microgalaxy 2024-12-20 2025-11-13 18 18 metaphlan, tp_text_file_with_recurring_lines, est_abundance, datamash_transpose, cat1, tp_sed_tool, sort1, humann, kraken2, collection_element_identifiers, krakentools_kreport2krona, csv_to_tabular, collapse_dataset, humann_unpack_pathways, humann_rename_table, tp_awk_tool, tp_replace_in_line, __UNZIP_COLLECTION__, add_line_to_file, tp_easyjoin_tool, Remove beginning1, krakentools_alpha_diversity, fastq_paired_end_interlacer, collection_column_join, taxonomy_krona_chart, taxpasta, sylph_profile, humann_renorm_table, humann_regroup_table Visualisation, Formatting, Statistical calculation, Standardisation and normalisation, Species frequency estimation, Taxonomic classification, Conversion, Aggregation, Phylogenetic analysis MIT True False -pAllori Blood RNA https://usegalaxy.eu ca9d3233b0912765 https://usegalaxy.eu/published/workflow?id=ca9d3233b0912765 Engy Nasr, Paul Zierep name:microgalaxy, name:pallori, name:bloodrna, name:umi, name:barcode, name:transcriptomics 2023-07-02 2025-06-26 48 48 collection_column_join, multiqc, fastqc, __FILTER_FAILED_DATASETS__, featurecounts, umi_tools_dedup, rna_star, umi_tools_extract Read summarisation, Sequence composition calculation, RNA-Seq quantification, Statistical calculation, Sequence alignment, Validation, Sequencing quality control MIT True False - pAllori ASiam Preprocessing MT https://usegalaxy.eu 72e3e5fdc766e24a https://usegalaxy.eu/published/workflow?id=72e3e5fdc766e24a Bérénice Batut, Pratik Jagtap, Subina Mehta, Ray Sajulga, Emma Leith, Praveen Kumar, Saskia Hiltemann, Paul Zierep, Engy Nasr name:microgalaxy, name:adaptedasiam, name:metatranscriptomics, name:preprocessing 2023-06-30 2025-06-17 29 29 bowtie2, multiqc, __FLATTEN__, fastqc, __FILTER_FAILED_DATASETS__, fastp, bg_sortmerna Sequence composition calculation, Statistical calculation, Validation, Read mapping, Sequence contamination filtering, Sequence similarity search, Sequence alignment analysis, Sequence comparison, Sequencing quality control MIT False False - pAllori ASiam Community Profile MT https://usegalaxy.eu 05f5f040337786bf https://usegalaxy.eu/published/workflow?id=05f5f040337786bf Engy Nasr, Bérénice Batut name:microgalaxy, name:metatranscriptomics, name:adaptedasiam, name:communityprofiling 2023-06-30 2025-06-09 16 16 graphlan, metaphlan, taxonomy_krona_chart, graphlan_annotate, Cut1, export2graphlan Phylogenetic tree visualisation, Visualisation, Phylogenetic inference, Phylogenetic tree editing, Taxonomic classification, Conversion MIT False False -pAllori ASiam Functional Information MT https://usegalaxy.eu a7a6d8ecc2795f58 https://usegalaxy.eu/published/workflow?id=a7a6d8ecc2795f58 Bérénice Batut, Pratik Jagtap, Subina Mehta, Ray Sajulga, Emma Leith, Praveen Kumar, Saskia Hiltemann, Paul Zierep, Engy Nasr name:microgalaxy, name:metatranscriptomics, name:adaptedasiam, name:functionalprofiling 2023-07-07 2025-06-09 6 6 Grep1, humann_rename_table, humann, tp_find_and_replace, combine_metaphlan2_humann2, Cut1, humann_renorm_table, humann_regroup_table, humann_unpack_pathways, humann_split_stratified_table Species frequency estimation, Taxonomic classification, Phylogenetic analysis MIT False False -Allele-based Pathogen Identification (release v0.1.1) https://usegalaxy.eu cdf2f02428f5f83f https://usegalaxy.eu/published/workflow?id=cdf2f02428f5f83f Engy Nasr, Bérénice Batut, Paul Zierep name:collection, name:microgalaxy, name:pathogfair, name:iwc 2024-09-19 2025-04-25 1 1 bcftools_consensus, Paste1, samtools_coverage, regexColumn1, bcftools_norm, CONVERTER_gz_to_uncompressed, snpSift_filter, tp_cut_tool, Cut1, snpSift_extractFields, clair3, collapse_dataset, Remove beginning1, table_compute, tp_head_tool, Count1, samtools_depth, minimap2 Pairwise sequence alignment, Variant calling MIT False False -Allele-based Pathogen Identification (release v0.1) https://usegalaxy.eu d215a2e554fd83bc https://usegalaxy.eu/published/workflow?id=d215a2e554fd83bc Engy Nasr, Bérénice Batut, Paul Zierep name:collection, name:microgalaxy, name:pathogfair, name:iwc 2024-09-19 2025-04-25 1 1 bcftools_consensus, Paste1, samtools_coverage, regexColumn1, bcftools_norm, CONVERTER_gz_to_uncompressed, snpSift_filter, tp_cut_tool, Cut1, snpSift_extractFields, clair3, collapse_dataset, Remove beginning1, table_compute, tp_head_tool, Count1, samtools_depth, minimap2 Pairwise sequence alignment, Variant calling MIT False False -Gene-based Pathogen Identification (release v0.1) https://usegalaxy.eu 77e5bbd317750915 https://usegalaxy.eu/published/workflow?id=77e5bbd317750915 Engy Nasr, Bérénice Batut, Paul Zierep name:collection, name:pathogfair, name:iwc, name:microgalaxy 2024-09-19 2025-04-25 1 1 medaka_consensus_pipeline, param_value_from_file, compose_text_param, __BUILD_LIST__, tp_find_and_replace, abricate, collection_element_identifiers, bandage_image, split_file_to_collection, flye, fasta2tab, tab2fasta Antimicrobial resistance prediction, Base-calling, Variant calling, Cross-assembly, Mapping assembly, Sequence assembly, Genome assembly, Sequence assembly visualisation, De-novo assembly MIT False False -Nanopore Preprocessing (release v0.1) https://usegalaxy.eu 344cd3a3c2ce5302 https://usegalaxy.eu/published/workflow?id=344cd3a3c2ce5302 Bérénice Batut, Engy Nasr, Paul Zierep name:collection, name:microgalaxy, name:pathogfair, name:nanopore, name:iwc 2024-09-19 2025-04-25 1 1 collection_column_join, Grep1, samtools_fastx, regexColumn1, multiqc, kraken2, fastqc, bamtools_split_mapped, nanoplot, porechop, __FILTER_FAILED_DATASETS__, krakentools_extract_kraken_reads, fastp, collapse_dataset, Cut1, Add_a_column1, minimap2 Visualisation, Sequence composition calculation, Statistical calculation, Validation, Sequence contamination filtering, Box-Whisker plot plotting, Sequence alignment analysis, Taxonomic classification, Data handling, Pairwise sequence alignment, Aggregation, Scatter plot plotting, Sequencing quality control MIT False False -Pathogen Detection PathoGFAIR Samples Aggregation and Visualisation (release v0.1) https://usegalaxy.eu f6a763951d815944 https://usegalaxy.eu/published/workflow?id=f6a763951d815944 Engy Nasr, Bérénice Batut, Paul Zierep name:collection, name:microgalaxy, name:pathogfair, name:iwc 2024-09-19 2025-04-25 1 1 Grouping1, regexColumn1, clustalw, __FILTER_FAILED_DATASETS__, fasta2tab, tp_sorted_uniq, fasta_merge_files_and_filter_unique_sequences, collapse_dataset, __FILTER_EMPTY_DATASETS__, bedtools_getfastabed, tp_multijoin_tool, ggplot2_heatmap, Cut1, Remove beginning1, fasttree, tp_split_on_column, collection_column_join, tp_replace_in_column, newick_display, regex1, Count1, tab2fasta Phylogenetic tree generation (from molecular sequences), Visualisation, Phylogenetic tree generation (maximum likelihood and Bayesian methods), Multiple sequence alignment, Mapping, Phylogenetic tree reconstruction, Phylogenetic tree analysis, Phylogenetic tree generation MIT False False -Taxonomy Profiling and Visualization with Kron (release v0.1) https://usegalaxy.eu ad8b6d73c9654305 https://usegalaxy.eu/published/workflow?id=ad8b6d73c9654305 Engy Nasr, Bérénice Batut, Paul Zierep name:collection, name:microgalaxy, name:pathogfair, name:iwc 2024-09-19 2025-04-25 1 1 kraken2, taxonomy_krona_chart, krakentools_kreport2krona Visualisation, Taxonomic classification, Aggregation MIT False False -Allele-based Pathogen Identification (release v0.1.2) https://usegalaxy.eu 64abcddeb516a712 https://usegalaxy.eu/published/workflow?id=64abcddeb516a712 Engy Nasr, Bérénice Batut, Paul Zierep name:collection, name:microgalaxy, name:pathogfair, name:iwc 2024-10-31 2025-04-25 1 1 bcftools_consensus, Paste1, samtools_coverage, regexColumn1, bcftools_norm, CONVERTER_gz_to_uncompressed, snpSift_filter, tp_cut_tool, Cut1, snpSift_extractFields, clair3, collapse_dataset, Remove beginning1, table_compute, tp_head_tool, Count1, samtools_depth, minimap2 Pairwise sequence alignment, Variant calling MIT False False -MGnify's amplicon pipeline v5.0 (release v0.1) https://usegalaxy.eu c8d70d4402852fb5 https://usegalaxy.eu/published/workflow?id=c8d70d4402852fb5 EMBL's European Bioinformatics Institute, Rand Zoabi, Paul Zierep mgnify_amplicon, metagenomics, amplicon, name:microgalaxy 2025-02-06 2025-04-25 1 1 fastq_dl, CONVERTER_uncompressed_to_gz, tp_awk_tool, CONVERTER_gz_to_uncompressed, __MERGE_COLLECTION__ Apache-2.0 False False -MGnify's amplicon pipeline v5.0 - ITS (release v0.1) https://usegalaxy.eu 08e25b733cd796e6 https://usegalaxy.eu/published/workflow?id=08e25b733cd796e6 EMBL's European Bioinformatics Institute, Rand Zoabi, Paul Zierep mgnify_amplicon, amplicon, metagenomics, name:microgalaxy 2025-02-06 2025-04-25 1 1 tp_awk_tool, __FILTER_FROM_FILE__, bedtools_maskfastabed, mapseq, collection_element_identifiers, taxonomy_krona_chart, biom_convert, __FILTER_EMPTY_DATASETS__ k-mer counting, Visualisation, Formatting, Mapping Apache-2.0 False False -MGnify's amplicon pipeline v5.0 - Quality control PE (release v0.1) https://usegalaxy.eu 0609a4b1941d1a68 https://usegalaxy.eu/published/workflow?id=0609a4b1941d1a68 EMBL's European Bioinformatics Institute, Rand Zoabi, Paul Zierep mgnify_amplicon, amplicon, metagenomics, name:microgalaxy 2025-02-06 2025-04-25 1 1 cshl_fasta_formatter, tp_find_and_replace, fastq_to_fasta_python, multiqc, fastqc, __UNZIP_COLLECTION__, prinseq, mgnify_seqprep, fastp, trimmomatic, fastq_filter Sequence trimming, Sequence composition calculation, Nucleic acid design, Statistical calculation, Validation, Read pre-processing, Sequence contamination filtering, Sequencing quality control Apache-2.0 False False -MGnify's amplicon pipeline v5.0 - Quality control SE (release v0.1) https://usegalaxy.eu d6ff6be33b8bfe85 https://usegalaxy.eu/published/workflow?id=d6ff6be33b8bfe85 MGnify - EMBL, Rand Zoabi, Paul Zierep mgnify_amplicon, amplicon, metagenomics, name:microgalaxy 2025-02-06 2025-04-25 1 1 cshl_fasta_formatter, tp_find_and_replace, fastq_to_fasta_python, multiqc, fastqc, prinseq, trimmomatic, fastq_filter Sequence trimming, Read pre-processing, Sequence composition calculation, Sequence contamination filtering, Statistical calculation, Validation, Sequencing quality control Apache-2.0 False False -MGnify's amplicon pipeline v5.0 - Quality control SE (release v0.2) https://usegalaxy.eu 76e9cd837ea5e7da https://usegalaxy.eu/published/workflow?id=76e9cd837ea5e7da MGnify - EMBL, Rand Zoabi, Paul Zierep mgnify_amplicon, amplicon, metagenomics, name:microgalaxy 2025-02-27 2025-04-25 1 1 cshl_fasta_formatter, tp_find_and_replace, fastq_to_fasta_python, multiqc, fastqc, prinseq, trimmomatic, fastq_filter Sequence trimming, Read pre-processing, Sequence composition calculation, Sequence contamination filtering, Statistical calculation, Validation, Sequencing quality control Apache-2.0 False False -Allele-based Pathogen Identification (release v0.1.3) https://usegalaxy.eu 6aa2891bd2b41f32 https://usegalaxy.eu/published/workflow?id=6aa2891bd2b41f32 Engy Nasr, Bérénice Batut, Paul Zierep name:collection, name:microgalaxy, name:pathogfair, name:iwc 2025-03-06 2025-04-25 1 1 bcftools_consensus, Paste1, samtools_coverage, regexColumn1, bcftools_norm, CONVERTER_gz_to_uncompressed, snpSift_filter, tp_cut_tool, Cut1, snpSift_extractFields, clair3, collapse_dataset, Remove beginning1, table_compute, tp_head_tool, Count1, samtools_depth, minimap2 Pairwise sequence alignment, Variant calling MIT False False -Allele-based Pathogen Identification (release v0.1.4) https://usegalaxy.eu 60e0b2a28a900178 https://usegalaxy.eu/published/workflow?id=60e0b2a28a900178 Engy Nasr, Bérénice Batut, Paul Zierep name:collection, name:microgalaxy, name:pathogfair, name:iwc 2025-03-13 2025-04-25 1 1 bcftools_consensus, Paste1, samtools_coverage, regexColumn1, bcftools_norm, CONVERTER_gz_to_uncompressed, snpSift_filter, tp_cut_tool, Cut1, snpSift_extractFields, clair3, collapse_dataset, Remove beginning1, table_compute, tp_head_tool, Count1, samtools_depth, minimap2 Pairwise sequence alignment, Variant calling MIT False False -MGnify's amplicon pipeline v5.0 (release v0.2) https://usegalaxy.eu 32219131f48494bf https://usegalaxy.eu/published/workflow?id=32219131f48494bf EMBL's European Bioinformatics Institute, Rand Zoabi, Paul Zierep mgnify_amplicon, metagenomics, amplicon, name:microgalaxy 2025-03-13 2025-04-25 1 1 fastq_dl, CONVERTER_uncompressed_to_gz, tp_awk_tool, CONVERTER_gz_to_uncompressed, __MERGE_COLLECTION__ Apache-2.0 False False -MGnify's amplicon pipeline v5.0 - ITS (release v0.2) https://usegalaxy.eu fb806b88850f3427 https://usegalaxy.eu/published/workflow?id=fb806b88850f3427 EMBL's European Bioinformatics Institute, Rand Zoabi, Paul Zierep mgnify_amplicon, amplicon, metagenomics, name:microgalaxy 2025-03-13 2025-04-25 1 1 tp_awk_tool, __FILTER_FROM_FILE__, bedtools_maskfastabed, mapseq, collection_element_identifiers, taxonomy_krona_chart, biom_convert, __FILTER_EMPTY_DATASETS__ k-mer counting, Visualisation, Formatting, Mapping Apache-2.0 False False -MGnify's amplicon pipeline v5.0 - Quality control PE (release v0.2) https://usegalaxy.eu 9fddc44294236e8f https://usegalaxy.eu/published/workflow?id=9fddc44294236e8f EMBL's European Bioinformatics Institute, Rand Zoabi, Paul Zierep mgnify_amplicon, amplicon, metagenomics, name:microgalaxy 2025-03-13 2025-04-25 1 1 cshl_fasta_formatter, tp_find_and_replace, fastq_to_fasta_python, multiqc, fastqc, __UNZIP_COLLECTION__, prinseq, mgnify_seqprep, fastp, trimmomatic, fastq_filter Sequence trimming, Sequence composition calculation, Nucleic acid design, Statistical calculation, Validation, Read pre-processing, Sequence contamination filtering, Sequencing quality control Apache-2.0 False False -MGnify's amplicon pipeline v5.0 - Quality control SE (release v0.3) https://usegalaxy.eu da19c0eaa757fa39 https://usegalaxy.eu/published/workflow?id=da19c0eaa757fa39 MGnify - EMBL, Rand Zoabi, Paul Zierep mgnify_amplicon, amplicon, metagenomics, name:microgalaxy 2025-03-13 2025-04-25 1 1 cshl_fasta_formatter, tp_find_and_replace, fastq_to_fasta_python, multiqc, fastqc, prinseq, trimmomatic, fastq_filter Sequence trimming, Read pre-processing, Sequence composition calculation, Sequence contamination filtering, Statistical calculation, Validation, Sequencing quality control Apache-2.0 False False -Copy of Metaproteomics_GTN shared by user engy.nasr https://usegalaxy.eu c6b6ba35e5b6500a https://usegalaxy.eu/published/workflow?id=c6b6ba35e5b6500a proteomics, name:microgalaxy 2025-02-14 2025-03-27 0 0 search_gui, peptide_shaker, sqlite_to_tabular, query_tabular, unipept Visualisation, Prediction and recognition False False -pAllori WGS https://usegalaxy.eu 4f245ac304ab76d9 https://usegalaxy.eu/published/workflow?id=4f245ac304ab76d9 Engy Nasr, Paul Zierep name:pallori, name:microgalaxy, name:wgs 2024-07-16 2025-02-17 18 18 Grouping1, collection_column_join, regexColumn1, multiqc, __FLATTEN__, fastqc, abricate, ggplot2_heatmap, Remove beginning1, shovill, trimmomatic Antimicrobial resistance prediction, Visualisation, Sequence composition calculation, Statistical calculation, Validation, Genome assembly, Sequencing quality control MIT False False -MetaG: Preparation, Building and Annotation of Metagenomics Assembled Genomes https://usegalaxy.eu 667bac8d7453e5f1 https://usegalaxy.eu/published/workflow?id=667bac8d7453e5f1 Valerie C. Schiml, Magnus Ø. Arntzen, Bérénice Batut name:microgalaxy, name:microbiome, name:mags 2024-09-30 2024-12-21 14 14 fasplit, tp_awk_tool, tp_grep_tool, fastqc, checkm_lineage_wf, hmmer_hmmscan, coverm_genome, quast, coverm_contig, fraggenescan, maxbin2, tp_cat, cat_bins, kofamscan, trim_galore, interproscan, sort1 Visualisation, Sequence composition calculation, Formatting, Statistical calculation, Gene functional annotation, Validation, Sequence database search, Format validation, Primer removal, Coding region prediction, Local alignment, Sequence assembly, Database search, Sequence profile generation, Sequencing quality control, Protein feature detection, Sequence trimming, Multiple sequence alignment, Sequence assembly validation, Sequence motif recognition, Sequence generation, Sequence analysis, Read pre-processing, Data retrieval, Gene prediction, Taxonomic classification, Conversion, Probabilistic sequence generation MIT True False -ASaiM-MT: Metatranscriptomics Analysis of Microbes https://usegalaxy.eu 096b75501c8e0888 https://usegalaxy.eu/published/workflow?id=096b75501c8e0888 Subina Mehta, Marie Crane, Emma Leith, Bérénice Batut, Saskia Hiltemann, Magnus Ø Arntzen, Benoit J. Kunath, Phillip B. Pope, Francesco Delogu, Ray Sajulga, Praveen Kumar, James E. Johnson, Timothy J. Griffin, Pratik D. Jagtap asaim, metatranscriptomics, rna-seq, microbiome, name:microgalaxy 2024-12-20 2024-12-20 3 3 Grouping1, group_humann2_uniref_abundances_to_go, fastqc, humann2_renorm_table, humann2_unpack_pathways, tp_sort_header_tool, humann2_genefamilies_genus_level, humann2, metaphlan2krona, Grep1, format_metaphlan2_output, graphlan, bg_sortmerna, fastq_paired_end_interlacer, multiqc, combine_metaphlan2_humann2, cutadapt, taxonomy_krona_chart, graphlan_annotate, export2graphlan, metaphlan2 Sequence comparison, Phylogenetic tree visualisation, Visualisation, Sequence composition calculation, Formatting, Statistical calculation, Phylogenetic inference, Validation, Primer removal, Sequence alignment analysis, Sequencing quality control, Sequence trimming, Phylogenetic tree editing, Read pre-processing, Taxonomic classification, Sequence similarity search, Conversion MIT True False -MAGs building with individual assembly https://usegalaxy.eu 0563f58718be932d https://usegalaxy.eu/published/workflow?id=0563f58718be932d Bérénice Batut, Paul Zierep, Mina Hojat Ansari, Patrick Bühler name:fairymags, name:microgalaxy 2024-12-20 2024-12-20 1 1 concoct_coverage_table, metabat2_jgi_summarize_bam_contig_depths, concoct_extract_fasta_bins, semibin, coverm_genome, concoct_merge_cut_up_clustering, concoct_cut_up_fasta, __FLATTEN__, maxbin2, drep_dereplicate, Fasta_to_Contig2Bin, metabat2, checkm_plot, checkm_lineage_wf, __UNZIP_COLLECTION__, quast, samtools_sort, concoct, gtdbtk_classify_wf, fastq_paired_end_joiner, collection_column_join, bowtie2, multiqc, megahit, das_tool Visualisation, Sequence composition calculation, Sequence assembly validation, Statistical calculation, Validation, Read mapping, Genome annotation, Sequence clustering, Read binning, Local alignment, Query and retrieval, Sequence assembly, Genome comparison, Genome alignment, Taxonomic classification, Genome assembly, Sequencing quality control MIT False False -MetaT: Metatranscriptomics data analysis https://usegalaxy.eu fd90652d475ed739 https://usegalaxy.eu/published/workflow?id=fd90652d475ed739 Valerie C. Schiml, Magnus Ø. Arntzen, Francesco Delogu, Praveen Kumar, Benoit Kunath, Bérénice Batut, Subina Mehta, James E. Johnson, Björn Grüning, Phillip B. Pope, Pratik D. Jagtap, Timothy J. Griffin name:microgalaxy, metatranscriptomics, microbiome 2024-11-21 2024-12-20 6 6 collection_column_join, kallisto_quant, fastqc, __UNZIP_COLLECTION__, trim_galore, bg_sortmerna Sequence trimming, Sequence composition calculation, Statistical calculation, Gene expression profiling, Primer removal, Read pre-processing, Sequence similarity search, Sequence alignment analysis, Sequence comparison, Sequencing quality control MIT True False -Halophiles workup of Comparative gene analysis https://usegalaxy.eu a2c46deea34d9d80 https://usegalaxy.eu/published/workflow?id=a2c46deea34d9d80 Anton Nekrutenko genome-annotation, name:microgalaxy 2024-12-03 2024-12-05 2 2 tp_split_on_column, regexColumn1, rbc_mafft, bg_diamond_view, Filter1, bg_diamond, join1, tab2fasta, collapse_dataset, Cut1, cat1, rapidnj, Add_a_column1, gops_intersect_1 Sequence alignment analysis, Multiple sequence alignment, Phylogenetic tree generation True False -Metaproteomics workflow https://usegalaxy.eu cefc49c13ff73231 https://usegalaxy.eu/published/workflow?id=cefc49c13ff73231 Timothy Griffin, Pratik Jagtap, James Johnson, Clemens Blank, Subina Mehta name:metaproteomics, name:galaxyp, name:massspectrometry, name:microgalaxy 2024-11-21 2024-11-21 40 40 search_gui, peptide_shaker, sqlite_to_tabular, query_tabular, unipept Visualisation, Prediction and recognition MIT True False -Feature-Count Table Normalization https://usegalaxy.eu 6239178d7cc4ac68 https://usegalaxy.eu/published/workflow?id=6239178d7cc4ac68 Johannes Effenberger name:microgalaxy, normalization, softmax, relative-abundance, sigmoid, css, limma-tmm, limma-rle 2024-11-21 2024-11-21 5 5 Grep1, __BUILD_LIST__, map_param_value, __EXTRACT_DATASET__, __FILTER_EMPTY_DATASETS__ MIT True False -metaQuantome_datacreation_workflow https://usegalaxy.eu cd675ab32d3e7833 https://usegalaxy.eu/published/workflow?id=cd675ab32d3e7833 Subina Metha, Timothy J. Griffin, Pratik Jagtap, Emma Leith, Marie Crane proteomics, name:microgalaxy 2024-11-21 2024-11-21 1 1 tp_replace_in_column, flashlfq, Filter1, msconvert, tp_replace_in_line, Cut1, regex1, Remove beginning1, search_gui, peptide_shaker, query_tabular, unipept Visualisation, Label-free quantification, Prediction and recognition, Filtering, Formatting MIT True False -metaquantome-function-worklow https://usegalaxy.eu e5a89ef7b5f1c1d9 https://usegalaxy.eu/published/workflow?id=e5a89ef7b5f1c1d9 Subina Mehta, Timothy J. Griffin, Pratik Jagtap, Emma Leith, Marie Crane, Praveen Kumar proteomics, name:microgalaxy 2024-11-21 2024-11-21 3 3 metaquantome_db, metaquantome_sample, metaquantome_stat, metaquantome_filter, metaquantome_viz, metaquantome_expand Visualisation, Statistical inference, Quantification, Heat map generation, Query and retrieval, Indexing, Differential protein expression analysis, Principal component visualisation, Filtering, Functional clustering MIT True False -Cloud Aerosol MT-MG Contamination Filtering https://usegalaxy.eu c09159d7aad0f264 https://usegalaxy.eu/published/workflow?id=c09159d7aad0f264 Engy Nasr , Bérénice Batut, Raphaëlle Péguilhan, Pierre Amato metagenomics, metatranscriptomics, name:microgalaxy 2024-11-21 2024-11-21 2 2 bowtie2, kraken2, fastq_to_tabular, filter_tabular, recentrifuge, seq_filter_by_id Cross-assembly, Taxonomic classification, Read mapping, Expression analysis MIT True False - Cloud-Aerosole MT-MG Functional Profiling https://usegalaxy.eu 63478edcea3f449a https://usegalaxy.eu/published/workflow?id=63478edcea3f449a Engy Nasr, Bérénice Batut, Raphaëlle Péguilhan, Pierre Amato metagenomics, metatranscriptomics, name:microgalaxy 2024-11-21 2024-11-21 4 4 featurecounts, bowtie2, multiqc Read summarisation, RNA-Seq quantification, Validation, Read mapping, Sequencing quality control MIT True False -Cloud-Aerosole MT-MG Pre-Processing https://usegalaxy.eu 1ef76b7b86e15792 https://usegalaxy.eu/published/workflow?id=1ef76b7b86e15792 Engy Nasr, Bérénice Batut, Raphaëlle Péguilhan, Pierre Amato metagenomics, metatranscriptomics, name:microgalaxy 2024-11-21 2024-11-21 6 6 trimmomatic, fastqc, multiqc Sequence composition calculation, Statistical calculation, Validation, Sequencing quality control MIT True False -MAGs workflow https://usegalaxy.eu 97312d273b6e8bd9 https://usegalaxy.eu/published/workflow?id=97312d273b6e8bd9 name:microgalaxy 2023-11-15 2024-07-11 14 14 concoct_coverage_table, metabat2_jgi_summarize_bam_contig_depths, concoct_extract_fasta_bins, semibin, coverm_genome, concoct_merge_cut_up_clustering, concoct_cut_up_fasta, maxbin2, drep_dereplicate, Fasta_to_Contig2Bin, metabat2, checkm_lineage_wf, __UNZIP_COLLECTION__, quast, samtools_sort, concoct, fastq_paired_end_interlacer, bowtie2, megahit, das_tool Visualisation, Sequence composition calculation, Sequence assembly validation, Statistical calculation, Validation, Read mapping, Genome annotation, Sequence clustering, Read binning, Local alignment, Sequence assembly, Genome comparison, Genome assembly, Sequencing quality control False False +AMR-Pathfinder WorkflowHub 1189 https://workflowhub.eu/workflows/1189?version=2 Helena Rasche, Dennis Dollée, Birgit Rijvers amr, amr-detection, benchamrking 2024-11-14 2026-05-13 2 2 36.0 , cat_multi_datasets, shovill, tp_split_on_column, staramr_search, collapse_dataset, datamash_ops, abricate, hamronize_tool, tp_find_and_replace, cat1, tp_text_file_with_recurring_lines, cast, __APPLY_RULES__, addValue, Grep1, hamronize_summarize, __MERGE_COLLECTION__, Cut1 Antimicrobial resistance prediction, Data handling, Parsing, Genome assembly MIT Seq4AMR, ErasmusMC Clinical Bioinformatics True False +Training: 16S rRNA Analysis with Nanopore Sequencing Reads https://usegalaxy.eu 2a093e63ebf6876b https://usegalaxy.eu/published/workflow?id=2a093e63ebf6876b metagenomics, name:microgalaxy 2025-12-01 2026-06-12 3 3 fastp, datamash_reverse, taxonomy_krona_chart, multiqc, kraken2, tp_replace_in_line, fastqc, porechop, Remove beginning1 Sequencing quality control, Sequence contamination filtering, Taxonomic classification, Statistical calculation, Validation, Sequence composition calculation, Visualisation True False +Sadowsky_MetaG-DBgen_02102026 https://usegalaxy.eu 7be08f99f83c927e https://usegalaxy.eu/published/workflow?id=7be08f99f83c927e Subina Mehta name:microgalaxy 2026-02-10 2026-06-09 1 1 validate_fasta_database, Remove beginning1, regexColumn1, cat_bins, trim_galore, fastqc, eggnog_mapper, collapse_dataset, regex1, query_tabular, tp_cat, tab2fasta, fasta_merge_files_and_filter_unique_sequences, maxbin2, fasta2tab, fraggenescan Statistical calculation, Taxonomic classification, Genome annotation, Sequencing quality control, Sequence trimming, Sequence assembly, Fold recognition, Information extraction, Homology-based gene prediction, Gene prediction, Read pre-processing, Coding region prediction, Primer removal, Query and retrieval, Sequence composition calculation CC-BY-4.0 True False +Copy of Metaproteomics_GTN shared by user engy.nasr https://usegalaxy.eu 6ca1b4fe047a03d2 https://usegalaxy.eu/published/workflow?id=6ca1b4fe047a03d2 proteomics, name:microgalaxy 2026-04-27 2026-04-27 1 1 peptide_shaker, unipept, search_gui, sqlite_to_tabular, query_tabular Prediction and recognition, Visualisation True False +MetaG_extended https://usegalaxy.eu 8c91345ed468e22d https://usegalaxy.eu/published/workflow?id=8c91345ed468e22d name:microgalaxy 2025-10-01 2026-02-04 0 0 coverm_genome, fasplit, tp_awk_tool, tp_grep_tool, sort1, cat_bins, trim_galore, fastqc, checkm_lineage_wf, coverm_contig, hmmer_hmmscan, interproscan, tp_cat, maxbin2, quast, fraggenescan Statistical calculation, Formatting, Visualisation, Format validation, Conversion, Probabilistic sequence generation, Sequencing quality control, Sequence assembly, Protein feature detection, Gene prediction, Sequence motif recognition, Coding region prediction, Sequence composition calculation, Sequence generation, Database search, Sequence database search, Data retrieval, Taxonomic classification, Multiple sequence alignment, Sequence assembly validation, Sequence trimming, Sequence profile generation, Validation, Read pre-processing, Primer removal, Local alignment True False +Metagenomic Taxonomy Analysis https://usegalaxy.eu 7491883694fff308 https://usegalaxy.eu/published/workflow?id=7491883694fff308 Bérénice Batut, Géraldine Piot, Mina Hojat Ansari name:metagenomics, microbiome, diversity, name:microgalaxy 2025-11-28 2025-12-17 3 3 metaphlan, metaphlan2krona, collection_element_identifiers, sylph_profile, taxonomy_krona_chart, krakentools_kreport2krona, est_abundance, kraken2, cat1, add_line_to_file, taxpasta, datamash_transpose, Remove beginning1 Statistical calculation, Taxonomic classification, Standardisation and normalisation, Formatting, Aggregation, Conversion, Visualisation MIT True False +Quality control of bins generated by MetaBAT2, MaxBin2, SemiBin, and CONCOCT https://usegalaxy.eu 7371b6918e895e0c https://usegalaxy.eu/published/workflow?id=7371b6918e895e0c Bérénice Batut microbiome, name:microgalaxy 2025-12-01 2025-12-08 16 16 __RELABEL_FROM_FILE__, checkm2, collection_element_identifiers, multiqc, __FLATTEN__, __MERGE_COLLECTION__, regex1 Statistical calculation, Sequencing quality control, Validation, Sequence composition calculation, Sequence assembly validation MIT True False +pAllori Amplicon 16S Pre-Processing and Taxonomy Classification https://usegalaxy.eu 466bdd8ba7b67264 https://usegalaxy.eu/published/workflow?id=466bdd8ba7b67264 Engy Nasr, Paul Zierep name:microgalaxy, name:16s, name:metagenomics, name:pallori 2023-06-30 2025-11-18 193 193 __FLATTEN__, ampvis2_heatmap, datamash_transpose, regex1, ampvis2_load, mmuphin, maaslin2, ampvis2_ordinate, unzip, param_value_from_file, phyloseq_from_biom, tp_awk_tool, phyloseq_add_rank_names, calculate_numeric_param, ampvis2_export_otu, bg_column_arrange_by_header, volcanoplot, tp_cut_tool, biom_convert, Remove beginning1, tp_easyjoin_tool, multiqc, lotus2, compose_text_param, fastqc, ampvis2_subset_samples, decontam, phyloseq_tax_glom Statistical calculation, Formatting, DNA barcoding, Filtering, Sequence feature detection, Sequencing quality control, Standardisation and normalisation, Analysis, Validation, Deposition, Sequence composition calculation, Visualisation, Classification MIT True False +Metagenomic Taxonomy and Functional Analysis https://usegalaxy.eu cb2df493f5e334f7 https://usegalaxy.eu/published/workflow?id=cb2df493f5e334f7 Bérénice Batut, Géraldine Piot name:metagenomics, microbiome, diversity, name:microgalaxy 2024-12-20 2025-11-13 18 18 collection_element_identifiers, krakentools_kreport2krona, tp_replace_in_line, collapse_dataset, datamash_transpose, krakentools_alpha_diversity, tp_awk_tool, csv_to_tabular, taxonomy_krona_chart, est_abundance, kraken2, cat1, tp_text_file_with_recurring_lines, taxpasta, metaphlan, humann_regroup_table, sylph_profile, fastq_paired_end_interlacer, humann_renorm_table, Remove beginning1, humann, sort1, humann_rename_table, collection_column_join, tp_easyjoin_tool, tp_sed_tool, humann_unpack_pathways, add_line_to_file, __UNZIP_COLLECTION__ Statistical calculation, Taxonomic classification, Formatting, Aggregation, Species frequency estimation, Conversion, Standardisation and normalisation, Phylogenetic analysis, Visualisation MIT True False +pAllori Blood RNA https://usegalaxy.eu ca9d3233b0912765 https://usegalaxy.eu/published/workflow?id=ca9d3233b0912765 Engy Nasr, Paul Zierep name:microgalaxy, name:pallori, name:bloodrna, name:umi, name:barcode, name:transcriptomics 2023-07-02 2025-06-26 48 48 umi_tools_dedup, collection_column_join, umi_tools_extract, multiqc, fastqc, featurecounts, __FILTER_FAILED_DATASETS__, rna_star Sequencing quality control, Statistical calculation, Validation, Read summarisation, Sequence alignment, Sequence composition calculation, RNA-Seq quantification MIT True False + pAllori ASiam Preprocessing MT https://usegalaxy.eu 72e3e5fdc766e24a https://usegalaxy.eu/published/workflow?id=72e3e5fdc766e24a Bérénice Batut, Pratik Jagtap, Subina Mehta, Ray Sajulga, Emma Leith, Praveen Kumar, Saskia Hiltemann, Paul Zierep, Engy Nasr name:microgalaxy, name:adaptedasiam, name:metatranscriptomics, name:preprocessing 2023-06-30 2025-06-17 29 29 fastp, bowtie2, multiqc, __FLATTEN__, fastqc, bg_sortmerna, __FILTER_FAILED_DATASETS__ Statistical calculation, Sequence similarity search, Sequencing quality control, Sequence contamination filtering, Sequence alignment analysis, Sequence comparison, Validation, Read mapping, Sequence composition calculation MIT False False + pAllori ASiam Community Profile MT https://usegalaxy.eu 05f5f040337786bf https://usegalaxy.eu/published/workflow?id=05f5f040337786bf Engy Nasr, Bérénice Batut name:microgalaxy, name:metatranscriptomics, name:adaptedasiam, name:communityprofiling 2023-06-30 2025-06-09 16 16 metaphlan, graphlan_annotate, taxonomy_krona_chart, export2graphlan, Cut1, graphlan Taxonomic classification, Phylogenetic inference, Conversion, Phylogenetic tree visualisation, Phylogenetic tree editing, Visualisation MIT False False +pAllori ASiam Functional Information MT https://usegalaxy.eu a7a6d8ecc2795f58 https://usegalaxy.eu/published/workflow?id=a7a6d8ecc2795f58 Bérénice Batut, Pratik Jagtap, Subina Mehta, Ray Sajulga, Emma Leith, Praveen Kumar, Saskia Hiltemann, Paul Zierep, Engy Nasr name:microgalaxy, name:metatranscriptomics, name:adaptedasiam, name:functionalprofiling 2023-07-07 2025-06-09 6 6 humann_rename_table, humann_regroup_table, tp_find_and_replace, combine_metaphlan2_humann2, humann_unpack_pathways, humann_split_stratified_table, humann_renorm_table, Grep1, Cut1, humann Taxonomic classification, Species frequency estimation, Phylogenetic analysis MIT False False +Allele-based Pathogen Identification (release v0.1.1) https://usegalaxy.eu cdf2f02428f5f83f https://usegalaxy.eu/published/workflow?id=cdf2f02428f5f83f Engy Nasr, Bérénice Batut, Paul Zierep name:collection, name:microgalaxy, name:pathogfair, name:iwc 2024-09-19 2025-04-25 1 1 tp_cut_tool, clair3, table_compute, samtools_depth, bcftools_consensus, CONVERTER_gz_to_uncompressed, Paste1, bcftools_norm, Cut1, snpSift_extractFields, samtools_coverage, snpSift_filter, collapse_dataset, minimap2, Count1, tp_head_tool, Remove beginning1, regexColumn1 Pairwise sequence alignment, Variant calling MIT False False +Allele-based Pathogen Identification (release v0.1) https://usegalaxy.eu d215a2e554fd83bc https://usegalaxy.eu/published/workflow?id=d215a2e554fd83bc Engy Nasr, Bérénice Batut, Paul Zierep name:collection, name:microgalaxy, name:pathogfair, name:iwc 2024-09-19 2025-04-25 1 1 tp_cut_tool, clair3, table_compute, samtools_depth, bcftools_consensus, CONVERTER_gz_to_uncompressed, Paste1, bcftools_norm, Cut1, snpSift_extractFields, samtools_coverage, snpSift_filter, collapse_dataset, minimap2, Count1, tp_head_tool, Remove beginning1, regexColumn1 Pairwise sequence alignment, Variant calling MIT False False +Gene-based Pathogen Identification (release v0.1) https://usegalaxy.eu 77e5bbd317750915 https://usegalaxy.eu/published/workflow?id=77e5bbd317750915 Engy Nasr, Bérénice Batut, Paul Zierep name:collection, name:pathogfair, name:iwc, name:microgalaxy 2024-09-19 2025-04-25 1 1 abricate, collection_element_identifiers, bandage_image, flye, tp_find_and_replace, split_file_to_collection, compose_text_param, __BUILD_LIST__, tab2fasta, medaka_consensus_pipeline, param_value_from_file, fasta2tab Base-calling, Antimicrobial resistance prediction, De-novo assembly, Variant calling, Sequence assembly visualisation, Sequence assembly, Cross-assembly, Mapping assembly, Genome assembly MIT False False +Nanopore Preprocessing (release v0.1) https://usegalaxy.eu 344cd3a3c2ce5302 https://usegalaxy.eu/published/workflow?id=344cd3a3c2ce5302 Bérénice Batut, Engy Nasr, Paul Zierep name:collection, name:microgalaxy, name:pathogfair, name:nanopore, name:iwc 2024-09-19 2025-04-25 1 1 Add_a_column1, fastp, collection_column_join, multiqc, kraken2, samtools_fastx, fastqc, collapse_dataset, nanoplot, minimap2, Grep1, __FILTER_FAILED_DATASETS__, bamtools_split_mapped, porechop, Cut1, regexColumn1, krakentools_extract_kraken_reads Statistical calculation, Taxonomic classification, Pairwise sequence alignment, Box-Whisker plot plotting, Aggregation, Data handling, Scatter plot plotting, Sequencing quality control, Sequence contamination filtering, Sequence alignment analysis, Validation, Sequence composition calculation, Visualisation MIT False False +Pathogen Detection PathoGFAIR Samples Aggregation and Visualisation (release v0.1) https://usegalaxy.eu f6a763951d815944 https://usegalaxy.eu/published/workflow?id=f6a763951d815944 Engy Nasr, Bérénice Batut, Paul Zierep name:collection, name:microgalaxy, name:pathogfair, name:iwc 2024-09-19 2025-04-25 1 1 tp_split_on_column, ggplot2_heatmap, bedtools_getfastabed, collapse_dataset, regex1, tp_replace_in_column, fasta_merge_files_and_filter_unique_sequences, newick_display, regexColumn1, tp_multijoin_tool, Count1, __FILTER_EMPTY_DATASETS__, fasta2tab, tp_sorted_uniq, Grouping1, fasttree, tab2fasta, Remove beginning1, collection_column_join, clustalw, __FILTER_FAILED_DATASETS__, Cut1 Phylogenetic tree generation, Visualisation, Multiple sequence alignment, Phylogenetic tree reconstruction, Phylogenetic tree analysis, Mapping MIT False False +Taxonomy Profiling and Visualization with Kron (release v0.1) https://usegalaxy.eu ad8b6d73c9654305 https://usegalaxy.eu/published/workflow?id=ad8b6d73c9654305 Engy Nasr, Bérénice Batut, Paul Zierep name:collection, name:microgalaxy, name:pathogfair, name:iwc 2024-09-19 2025-04-25 1 1 krakentools_kreport2krona, kraken2, taxonomy_krona_chart Taxonomic classification, Aggregation, Visualisation MIT False False +Allele-based Pathogen Identification (release v0.1.2) https://usegalaxy.eu 64abcddeb516a712 https://usegalaxy.eu/published/workflow?id=64abcddeb516a712 Engy Nasr, Bérénice Batut, Paul Zierep name:collection, name:microgalaxy, name:pathogfair, name:iwc 2024-10-31 2025-04-25 1 1 tp_cut_tool, clair3, table_compute, samtools_depth, bcftools_consensus, CONVERTER_gz_to_uncompressed, Paste1, bcftools_norm, Cut1, snpSift_extractFields, samtools_coverage, snpSift_filter, collapse_dataset, minimap2, Count1, tp_head_tool, Remove beginning1, regexColumn1 Pairwise sequence alignment, Variant calling MIT False False +MGnify's amplicon pipeline v5.0 (release v0.1) https://usegalaxy.eu c8d70d4402852fb5 https://usegalaxy.eu/published/workflow?id=c8d70d4402852fb5 EMBL's European Bioinformatics Institute, Rand Zoabi, Paul Zierep mgnify_amplicon, metagenomics, amplicon, name:microgalaxy 2025-02-06 2025-04-25 1 1 tp_awk_tool, CONVERTER_uncompressed_to_gz, CONVERTER_gz_to_uncompressed, __MERGE_COLLECTION__, fastq_dl Apache-2.0 False False +MGnify's amplicon pipeline v5.0 - ITS (release v0.1) https://usegalaxy.eu 08e25b733cd796e6 https://usegalaxy.eu/published/workflow?id=08e25b733cd796e6 EMBL's European Bioinformatics Institute, Rand Zoabi, Paul Zierep mgnify_amplicon, amplicon, metagenomics, name:microgalaxy 2025-02-06 2025-04-25 1 1 bedtools_maskfastabed, mapseq, tp_awk_tool, __FILTER_FROM_FILE__, collection_element_identifiers, taxonomy_krona_chart, biom_convert, __FILTER_EMPTY_DATASETS__ k-mer counting, Formatting, Visualisation, Mapping Apache-2.0 False False +MGnify's amplicon pipeline v5.0 - Quality control PE (release v0.1) https://usegalaxy.eu 0609a4b1941d1a68 https://usegalaxy.eu/published/workflow?id=0609a4b1941d1a68 EMBL's European Bioinformatics Institute, Rand Zoabi, Paul Zierep mgnify_amplicon, amplicon, metagenomics, name:microgalaxy 2025-02-06 2025-04-25 1 1 fastp, cshl_fasta_formatter, tp_find_and_replace, multiqc, trimmomatic, fastqc, __UNZIP_COLLECTION__, mgnify_seqprep, fastq_filter, prinseq, fastq_to_fasta_python Statistical calculation, Sequencing quality control, Sequence contamination filtering, Sequence trimming, Validation, Nucleic acid design, Read pre-processing, Sequence composition calculation Apache-2.0 False False +MGnify's amplicon pipeline v5.0 - Quality control SE (release v0.1) https://usegalaxy.eu d6ff6be33b8bfe85 https://usegalaxy.eu/published/workflow?id=d6ff6be33b8bfe85 MGnify - EMBL, Rand Zoabi, Paul Zierep mgnify_amplicon, amplicon, metagenomics, name:microgalaxy 2025-02-06 2025-04-25 1 1 cshl_fasta_formatter, tp_find_and_replace, multiqc, trimmomatic, fastqc, fastq_filter, prinseq, fastq_to_fasta_python Sequencing quality control, Statistical calculation, Sequence contamination filtering, Sequence trimming, Validation, Read pre-processing, Sequence composition calculation Apache-2.0 False False +MGnify's amplicon pipeline v5.0 - Quality control SE (release v0.2) https://usegalaxy.eu 76e9cd837ea5e7da https://usegalaxy.eu/published/workflow?id=76e9cd837ea5e7da MGnify - EMBL, Rand Zoabi, Paul Zierep mgnify_amplicon, amplicon, metagenomics, name:microgalaxy 2025-02-27 2025-04-25 1 1 cshl_fasta_formatter, tp_find_and_replace, multiqc, trimmomatic, fastqc, fastq_filter, prinseq, fastq_to_fasta_python Sequencing quality control, Statistical calculation, Sequence contamination filtering, Sequence trimming, Validation, Read pre-processing, Sequence composition calculation Apache-2.0 False False +Allele-based Pathogen Identification (release v0.1.3) https://usegalaxy.eu 6aa2891bd2b41f32 https://usegalaxy.eu/published/workflow?id=6aa2891bd2b41f32 Engy Nasr, Bérénice Batut, Paul Zierep name:collection, name:microgalaxy, name:pathogfair, name:iwc 2025-03-06 2025-04-25 1 1 tp_cut_tool, clair3, table_compute, samtools_depth, bcftools_consensus, CONVERTER_gz_to_uncompressed, Paste1, bcftools_norm, Cut1, snpSift_extractFields, samtools_coverage, snpSift_filter, collapse_dataset, minimap2, Count1, tp_head_tool, Remove beginning1, regexColumn1 Pairwise sequence alignment, Variant calling MIT False False +Allele-based Pathogen Identification (release v0.1.4) https://usegalaxy.eu 60e0b2a28a900178 https://usegalaxy.eu/published/workflow?id=60e0b2a28a900178 Engy Nasr, Bérénice Batut, Paul Zierep name:collection, name:microgalaxy, name:pathogfair, name:iwc 2025-03-13 2025-04-25 1 1 tp_cut_tool, clair3, table_compute, samtools_depth, bcftools_consensus, CONVERTER_gz_to_uncompressed, Paste1, bcftools_norm, Cut1, snpSift_extractFields, samtools_coverage, snpSift_filter, collapse_dataset, minimap2, Count1, tp_head_tool, Remove beginning1, regexColumn1 Pairwise sequence alignment, Variant calling MIT False False +MGnify's amplicon pipeline v5.0 (release v0.2) https://usegalaxy.eu 32219131f48494bf https://usegalaxy.eu/published/workflow?id=32219131f48494bf EMBL's European Bioinformatics Institute, Rand Zoabi, Paul Zierep mgnify_amplicon, metagenomics, amplicon, name:microgalaxy 2025-03-13 2025-04-25 1 1 tp_awk_tool, CONVERTER_uncompressed_to_gz, CONVERTER_gz_to_uncompressed, __MERGE_COLLECTION__, fastq_dl Apache-2.0 False False +MGnify's amplicon pipeline v5.0 - ITS (release v0.2) https://usegalaxy.eu fb806b88850f3427 https://usegalaxy.eu/published/workflow?id=fb806b88850f3427 EMBL's European Bioinformatics Institute, Rand Zoabi, Paul Zierep mgnify_amplicon, amplicon, metagenomics, name:microgalaxy 2025-03-13 2025-04-25 1 1 bedtools_maskfastabed, mapseq, tp_awk_tool, __FILTER_FROM_FILE__, collection_element_identifiers, taxonomy_krona_chart, biom_convert, __FILTER_EMPTY_DATASETS__ k-mer counting, Formatting, Visualisation, Mapping Apache-2.0 False False +MGnify's amplicon pipeline v5.0 - Quality control PE (release v0.2) https://usegalaxy.eu 9fddc44294236e8f https://usegalaxy.eu/published/workflow?id=9fddc44294236e8f EMBL's European Bioinformatics Institute, Rand Zoabi, Paul Zierep mgnify_amplicon, amplicon, metagenomics, name:microgalaxy 2025-03-13 2025-04-25 1 1 fastp, cshl_fasta_formatter, tp_find_and_replace, multiqc, trimmomatic, fastqc, __UNZIP_COLLECTION__, mgnify_seqprep, fastq_filter, prinseq, fastq_to_fasta_python Statistical calculation, Sequencing quality control, Sequence contamination filtering, Sequence trimming, Validation, Nucleic acid design, Read pre-processing, Sequence composition calculation Apache-2.0 False False +MGnify's amplicon pipeline v5.0 - Quality control SE (release v0.3) https://usegalaxy.eu da19c0eaa757fa39 https://usegalaxy.eu/published/workflow?id=da19c0eaa757fa39 MGnify - EMBL, Rand Zoabi, Paul Zierep mgnify_amplicon, amplicon, metagenomics, name:microgalaxy 2025-03-13 2025-04-25 1 1 cshl_fasta_formatter, tp_find_and_replace, multiqc, trimmomatic, fastqc, fastq_filter, prinseq, fastq_to_fasta_python Sequencing quality control, Statistical calculation, Sequence contamination filtering, Sequence trimming, Validation, Read pre-processing, Sequence composition calculation Apache-2.0 False False +Copy of Metaproteomics_GTN shared by user engy.nasr https://usegalaxy.eu c6b6ba35e5b6500a https://usegalaxy.eu/published/workflow?id=c6b6ba35e5b6500a proteomics, name:microgalaxy 2025-02-14 2025-03-27 0 0 peptide_shaker, unipept, search_gui, sqlite_to_tabular, query_tabular Prediction and recognition, Visualisation False False +pAllori WGS https://usegalaxy.eu 4f245ac304ab76d9 https://usegalaxy.eu/published/workflow?id=4f245ac304ab76d9 Engy Nasr, Paul Zierep name:pallori, name:microgalaxy, name:wgs 2024-07-16 2025-02-17 18 18 abricate, collection_column_join, shovill, ggplot2_heatmap, multiqc, __FLATTEN__, trimmomatic, fastqc, Grouping1, Remove beginning1, regexColumn1 Sequencing quality control, Statistical calculation, Antimicrobial resistance prediction, Validation, Sequence composition calculation, Visualisation, Genome assembly MIT False False +MetaG: Preparation, Building and Annotation of Metagenomics Assembled Genomes https://usegalaxy.eu 667bac8d7453e5f1 https://usegalaxy.eu/published/workflow?id=667bac8d7453e5f1 Valerie C. Schiml, Magnus Ø. Arntzen, Bérénice Batut name:microgalaxy, name:microbiome, name:mags 2024-09-30 2024-12-21 14 14 coverm_genome, fasplit, tp_awk_tool, tp_grep_tool, sort1, cat_bins, trim_galore, fastqc, checkm_lineage_wf, interproscan, coverm_contig, hmmer_hmmscan, kofamscan, tp_cat, maxbin2, quast, fraggenescan Statistical calculation, Formatting, Gene functional annotation, Visualisation, Format validation, Conversion, Probabilistic sequence generation, Sequencing quality control, Sequence assembly, Protein feature detection, Gene prediction, Sequence motif recognition, Coding region prediction, Sequence composition calculation, Sequence generation, Database search, Sequence database search, Data retrieval, Taxonomic classification, Multiple sequence alignment, Sequence assembly validation, Sequence trimming, Sequence profile generation, Validation, Sequence analysis, Read pre-processing, Primer removal, Local alignment MIT True False +ASaiM-MT: Metatranscriptomics Analysis of Microbes https://usegalaxy.eu 096b75501c8e0888 https://usegalaxy.eu/published/workflow?id=096b75501c8e0888 Subina Mehta, Marie Crane, Emma Leith, Bérénice Batut, Saskia Hiltemann, Magnus Ø Arntzen, Benoit J. Kunath, Phillip B. Pope, Francesco Delogu, Ray Sajulga, Praveen Kumar, James E. Johnson, Timothy J. Griffin, Pratik D. Jagtap asaim, metatranscriptomics, rna-seq, microbiome, name:microgalaxy 2024-12-20 2024-12-20 3 3 graphlan_annotate, humann2_renorm_table, combine_metaphlan2_humann2, bg_sortmerna, cutadapt, humann2_genefamilies_genus_level, taxonomy_krona_chart, export2graphlan, metaphlan2, fastq_paired_end_interlacer, group_humann2_uniref_abundances_to_go, Grouping1, Grep1, humann2, graphlan, tp_sort_header_tool, metaphlan2krona, humann2_unpack_pathways, format_metaphlan2_output, multiqc, fastqc Statistical calculation, Phylogenetic inference, Taxonomic classification, Formatting, Conversion, Phylogenetic tree visualisation, Sequence similarity search, Sequence composition calculation, Phylogenetic tree editing, Sequencing quality control, Sequence trimming, Sequence alignment analysis, Sequence comparison, Validation, Read pre-processing, Primer removal, Visualisation MIT True False +MAGs building with individual assembly https://usegalaxy.eu 0563f58718be932d https://usegalaxy.eu/published/workflow?id=0563f58718be932d Bérénice Batut, Paul Zierep, Mina Hojat Ansari, Patrick Bühler name:fairymags, name:microgalaxy 2024-12-20 2024-12-20 1 1 __FLATTEN__, Fasta_to_Contig2Bin, semibin, metabat2_jgi_summarize_bam_contig_depths, bowtie2, coverm_genome, gtdbtk_classify_wf, concoct_merge_cut_up_clustering, concoct_cut_up_fasta, checkm_plot, concoct_coverage_table, checkm_lineage_wf, maxbin2, quast, drep_dereplicate, fastq_paired_end_joiner, collection_column_join, concoct_extract_fasta_bins, multiqc, samtools_sort, concoct, megahit, __UNZIP_COLLECTION__, das_tool, metabat2 Statistical calculation, Genome alignment, Visualisation, Genome annotation, Read binning, Sequencing quality control, Sequence assembly, Genome comparison, Sequence composition calculation, Query and retrieval, Taxonomic classification, Sequence assembly validation, Validation, Read mapping, Sequence clustering, Local alignment, Genome assembly MIT False False +MetaT: Metatranscriptomics data analysis https://usegalaxy.eu fd90652d475ed739 https://usegalaxy.eu/published/workflow?id=fd90652d475ed739 Valerie C. Schiml, Magnus Ø. Arntzen, Francesco Delogu, Praveen Kumar, Benoit Kunath, Bérénice Batut, Subina Mehta, James E. Johnson, Björn Grüning, Phillip B. Pope, Pratik D. Jagtap, Timothy J. Griffin name:microgalaxy, metatranscriptomics, microbiome 2024-11-21 2024-12-20 6 6 kallisto_quant, collection_column_join, trim_galore, fastqc, bg_sortmerna, __UNZIP_COLLECTION__ Statistical calculation, Sequence similarity search, Sequencing quality control, Gene expression profiling, Sequence trimming, Sequence alignment analysis, Sequence comparison, Read pre-processing, Primer removal, Sequence composition calculation MIT True False +Halophiles workup of Comparative gene analysis https://usegalaxy.eu a2c46deea34d9d80 https://usegalaxy.eu/published/workflow?id=a2c46deea34d9d80 Anton Nekrutenko genome-annotation, name:microgalaxy 2024-12-03 2024-12-05 2 2 Add_a_column1, tab2fasta, tp_split_on_column, gops_intersect_1, rbc_mafft, join1, bg_diamond, cat1, collapse_dataset, rapidnj, Filter1, bg_diamond_view, Cut1, regexColumn1 Sequence alignment analysis, Phylogenetic tree generation, Multiple sequence alignment True False +Metaproteomics workflow https://usegalaxy.eu cefc49c13ff73231 https://usegalaxy.eu/published/workflow?id=cefc49c13ff73231 Timothy Griffin, Pratik Jagtap, James Johnson, Clemens Blank, Subina Mehta name:metaproteomics, name:galaxyp, name:massspectrometry, name:microgalaxy 2024-11-21 2024-11-21 40 40 peptide_shaker, unipept, search_gui, sqlite_to_tabular, query_tabular Prediction and recognition, Visualisation MIT True False +Feature-Count Table Normalization https://usegalaxy.eu 6239178d7cc4ac68 https://usegalaxy.eu/published/workflow?id=6239178d7cc4ac68 Johannes Effenberger name:microgalaxy, normalization, softmax, relative-abundance, sigmoid, css, limma-tmm, limma-rle 2024-11-21 2024-11-21 5 5 __EXTRACT_DATASET__, map_param_value, Grep1, __BUILD_LIST__, __FILTER_EMPTY_DATASETS__ MIT True False +metaQuantome_datacreation_workflow https://usegalaxy.eu cd675ab32d3e7833 https://usegalaxy.eu/published/workflow?id=cd675ab32d3e7833 Subina Metha, Timothy J. Griffin, Pratik Jagtap, Emma Leith, Marie Crane proteomics, name:microgalaxy 2024-11-21 2024-11-21 1 1 peptide_shaker, search_gui, unipept, flashlfq, tp_replace_in_line, Cut1, regex1, msconvert, tp_replace_in_column, query_tabular, Filter1, Remove beginning1 Formatting, Prediction and recognition, Filtering, Visualisation, Label-free quantification MIT True False +metaquantome-function-worklow https://usegalaxy.eu e5a89ef7b5f1c1d9 https://usegalaxy.eu/published/workflow?id=e5a89ef7b5f1c1d9 Subina Mehta, Timothy J. Griffin, Pratik Jagtap, Emma Leith, Marie Crane, Praveen Kumar proteomics, name:microgalaxy 2024-11-21 2024-11-21 3 3 metaquantome_stat, metaquantome_expand, metaquantome_viz, metaquantome_db, metaquantome_filter, metaquantome_sample Quantification, Differential protein expression analysis, Query and retrieval, Principal component visualisation, Indexing, Heat map generation, Filtering, Functional clustering, Statistical inference, Visualisation MIT True False +Cloud Aerosol MT-MG Contamination Filtering https://usegalaxy.eu c09159d7aad0f264 https://usegalaxy.eu/published/workflow?id=c09159d7aad0f264 Engy Nasr , Bérénice Batut, Raphaëlle Péguilhan, Pierre Amato metagenomics, metatranscriptomics, name:microgalaxy 2024-11-21 2024-11-21 2 2 bowtie2, recentrifuge, fastq_to_tabular, kraken2, filter_tabular, seq_filter_by_id Taxonomic classification, Expression analysis, Read mapping, Cross-assembly MIT True False + Cloud-Aerosole MT-MG Functional Profiling https://usegalaxy.eu 63478edcea3f449a https://usegalaxy.eu/published/workflow?id=63478edcea3f449a Engy Nasr, Bérénice Batut, Raphaëlle Péguilhan, Pierre Amato metagenomics, metatranscriptomics, name:microgalaxy 2024-11-21 2024-11-21 4 4 bowtie2, featurecounts, multiqc Sequencing quality control, Validation, Read summarisation, Read mapping, RNA-Seq quantification MIT True False +Cloud-Aerosole MT-MG Pre-Processing https://usegalaxy.eu 1ef76b7b86e15792 https://usegalaxy.eu/published/workflow?id=1ef76b7b86e15792 Engy Nasr, Bérénice Batut, Raphaëlle Péguilhan, Pierre Amato metagenomics, metatranscriptomics, name:microgalaxy 2024-11-21 2024-11-21 6 6 fastqc, multiqc, trimmomatic Sequencing quality control, Statistical calculation, Validation, Sequence composition calculation MIT True False +MAGs workflow https://usegalaxy.eu 97312d273b6e8bd9 https://usegalaxy.eu/published/workflow?id=97312d273b6e8bd9 name:microgalaxy 2023-11-15 2024-07-11 14 14 Fasta_to_Contig2Bin, semibin, metabat2_jgi_summarize_bam_contig_depths, bowtie2, coverm_genome, concoct_merge_cut_up_clustering, concoct_cut_up_fasta, concoct_coverage_table, fastq_paired_end_interlacer, checkm_lineage_wf, maxbin2, quast, drep_dereplicate, concoct_extract_fasta_bins, samtools_sort, concoct, megahit, __UNZIP_COLLECTION__, das_tool, metabat2 Statistical calculation, Visualisation, Genome annotation, Read binning, Sequence assembly validation, Sequencing quality control, Sequence assembly, Validation, Genome comparison, Read mapping, Sequence clustering, Sequence composition calculation, Local alignment, Genome assembly False False PathoGFAIR https://usegalaxy.eu 0dce37adb369492c https://usegalaxy.eu/published/workflow?id=0dce37adb369492c Engy Nasr, Bérénice Batut, Paul Zierep name:microgalaxy, name:iwc, name:pathogfair, name:nanopore, name:collection 2024-05-31 2024-07-03 93 93 MIT False False -Pathogen Detection PathoGFAIR Samples Aggregation and Visualisation https://usegalaxy.eu 376119528377a3ae https://usegalaxy.eu/published/workflow?id=376119528377a3ae Engy Nasr, Bérénice Batut, Paul Zierep name:collection, name:microgalaxy, name:pathogfair, name:iwc 2024-04-03 2024-06-24 58 58 Grouping1, regexColumn1, clustalw, __FILTER_FAILED_DATASETS__, fasta2tab, tp_sorted_uniq, fasta_merge_files_and_filter_unique_sequences, collapse_dataset, __FILTER_EMPTY_DATASETS__, bedtools_getfastabed, tp_multijoin_tool, ggplot2_heatmap, Cut1, Remove beginning1, fasttree, tp_split_on_column, collection_column_join, tp_replace_in_column, newick_display, regex1, Count1, tab2fasta Phylogenetic tree generation (from molecular sequences), Visualisation, Phylogenetic tree generation (maximum likelihood and Bayesian methods), Multiple sequence alignment, Mapping, Phylogenetic tree reconstruction, Phylogenetic tree analysis, Phylogenetic tree generation MIT False False -Allele-based Pathogen Identification https://usegalaxy.eu 09c7069ae409c362 https://usegalaxy.eu/published/workflow?id=09c7069ae409c362 Engy Nasr, Bérénice Batut, Paul Zierep name:collection, name:microgalaxy, name:pathogfair, name:iwc 2023-04-12 2024-06-24 72 72 bcftools_consensus, Paste1, samtools_coverage, regexColumn1, bcftools_norm, CONVERTER_gz_to_uncompressed, snpSift_filter, tp_cut_tool, Cut1, snpSift_extractFields, clair3, collapse_dataset, Remove beginning1, table_compute, tp_head_tool, Count1, samtools_depth, minimap2 Pairwise sequence alignment, Variant calling MIT False False -Nanopore Preprocessing https://usegalaxy.eu a705370bc2c13d5c https://usegalaxy.eu/published/workflow?id=a705370bc2c13d5c Bérénice Batut, Engy Nasr, Paul Zierep name:collection, name:microgalaxy, name:pathogfair, name:nanopore, name:iwc 2023-04-12 2024-06-24 190 190 collection_column_join, Grep1, samtools_fastx, regexColumn1, multiqc, kraken2, fastqc, bamtools_split_mapped, nanoplot, porechop, __FILTER_FAILED_DATASETS__, krakentools_extract_kraken_reads, fastp, collapse_dataset, Cut1, Add_a_column1, minimap2 Visualisation, Sequence composition calculation, Statistical calculation, Validation, Sequence contamination filtering, Box-Whisker plot plotting, Sequence alignment analysis, Taxonomic classification, Data handling, Pairwise sequence alignment, Aggregation, Scatter plot plotting, Sequencing quality control MIT False False -Taxonomy Profiling and Visualization with Phinch https://usegalaxy.eu b67b5ecd3305f830 https://usegalaxy.eu/published/workflow?id=b67b5ecd3305f830 Engy Nasr, Bérénice Batut, Paul Zierep name:collection, name:microgalaxy, name:gtn 2023-04-12 2024-06-19 8 8 kraken2, interactive_tool_phinch, kraken_biom Taxonomic classification, Genome annotation MIT False False -metaQuantome_datacreation_workflow https://usegalaxy.eu fc42cc9467c6ee8d https://usegalaxy.eu/published/workflow?id=fc42cc9467c6ee8d proteomics, name:microgalaxy 2023-12-14 2024-06-19 0 0 tp_replace_in_column, flashlfq, Filter1, msconvert, tp_replace_in_line, Cut1, regex1, Remove beginning1, search_gui, peptide_shaker, query_tabular, unipept Visualisation, Label-free quantification, Prediction and recognition, Filtering, Formatting False False -Gene-based Pathogen Identification https://usegalaxy.eu 585c21b7b1d864fc https://usegalaxy.eu/published/workflow?id=585c21b7b1d864fc Engy Nasr, Bérénice Batut, Paul Zierep name:collection, name:pathogfair, name:iwc, name:microgalaxy 2023-04-13 2024-06-05 142 142 medaka_consensus_pipeline, param_value_from_file, compose_text_param, __BUILD_LIST__, tp_find_and_replace, abricate, collection_element_identifiers, bandage_image, split_file_to_collection, flye, fasta2tab, tab2fasta Antimicrobial resistance prediction, Base-calling, Variant calling, Cross-assembly, Mapping assembly, Sequence assembly, Genome assembly, Sequence assembly visualisation, De-novo assembly MIT False False -Taxonomy Profiling and Visualization with Krona https://usegalaxy.eu 10101558b211a782 https://usegalaxy.eu/published/workflow?id=10101558b211a782 Engy Nasr, Bérénice Batut, Paul Zierep name:collection, name:microgalaxy, name:pathogfair, name:iwc 2023-05-11 2024-06-05 58 58 kraken2, taxonomy_krona_chart, krakentools_kreport2krona Visualisation, Taxonomic classification, Aggregation MIT False False -Pathogen-Detection-Nanopore-All-Samples-Analysis-Juyptool https://usegalaxy.eu c8bc4af6dd3b5d02 https://usegalaxy.eu/published/workflow?id=c8bc4af6dd3b5d02 Engy Nasr, Bérénice Batut microbiome, nanopore, iwc, name:collection, name:microgalaxy 2022-11-29 2024-04-04 205 205 Grouping1, regexColumn1, clustalw, __FILTER_FAILED_DATASETS__, fasta2tab, tp_sorted_uniq, fasta_merge_files_and_filter_unique_sequences, collapse_dataset, __FILTER_EMPTY_DATASETS__, bedtools_getfastabed, tp_multijoin_tool, ggplot2_heatmap, Cut1, Remove beginning1, fasttree, tp_split_on_column, collection_column_join, tp_replace_in_column, newick_display, interactive_tool_jupyter_notebook, regex1, Count1, tab2fasta Phylogenetic tree generation (from molecular sequences), Visualisation, Phylogenetic tree generation (maximum likelihood and Bayesian methods), Multiple sequence alignment, Mapping, Phylogenetic tree reconstruction, Phylogenetic tree analysis, Phylogenetic tree generation MIT False False +Pathogen Detection PathoGFAIR Samples Aggregation and Visualisation https://usegalaxy.eu 376119528377a3ae https://usegalaxy.eu/published/workflow?id=376119528377a3ae Engy Nasr, Bérénice Batut, Paul Zierep name:collection, name:microgalaxy, name:pathogfair, name:iwc 2024-04-03 2024-06-24 58 58 tp_split_on_column, ggplot2_heatmap, bedtools_getfastabed, collapse_dataset, regex1, tp_replace_in_column, fasta_merge_files_and_filter_unique_sequences, newick_display, regexColumn1, tp_multijoin_tool, Count1, __FILTER_EMPTY_DATASETS__, fasta2tab, tp_sorted_uniq, Grouping1, fasttree, tab2fasta, Remove beginning1, collection_column_join, clustalw, __FILTER_FAILED_DATASETS__, Cut1 Phylogenetic tree generation, Visualisation, Multiple sequence alignment, Phylogenetic tree reconstruction, Phylogenetic tree analysis, Mapping MIT False False +Allele-based Pathogen Identification https://usegalaxy.eu 09c7069ae409c362 https://usegalaxy.eu/published/workflow?id=09c7069ae409c362 Engy Nasr, Bérénice Batut, Paul Zierep name:collection, name:microgalaxy, name:pathogfair, name:iwc 2023-04-12 2024-06-24 72 72 tp_cut_tool, clair3, table_compute, samtools_depth, bcftools_consensus, CONVERTER_gz_to_uncompressed, Paste1, bcftools_norm, Cut1, snpSift_extractFields, samtools_coverage, snpSift_filter, collapse_dataset, minimap2, Count1, tp_head_tool, Remove beginning1, regexColumn1 Pairwise sequence alignment, Variant calling MIT False False +Nanopore Preprocessing https://usegalaxy.eu a705370bc2c13d5c https://usegalaxy.eu/published/workflow?id=a705370bc2c13d5c Bérénice Batut, Engy Nasr, Paul Zierep name:collection, name:microgalaxy, name:pathogfair, name:nanopore, name:iwc 2023-04-12 2024-06-24 190 190 Add_a_column1, fastp, collection_column_join, multiqc, kraken2, samtools_fastx, fastqc, collapse_dataset, nanoplot, minimap2, Grep1, __FILTER_FAILED_DATASETS__, bamtools_split_mapped, porechop, Cut1, regexColumn1, krakentools_extract_kraken_reads Statistical calculation, Taxonomic classification, Pairwise sequence alignment, Box-Whisker plot plotting, Aggregation, Data handling, Scatter plot plotting, Sequencing quality control, Sequence contamination filtering, Sequence alignment analysis, Validation, Sequence composition calculation, Visualisation MIT False False +Taxonomy Profiling and Visualization with Phinch https://usegalaxy.eu b67b5ecd3305f830 https://usegalaxy.eu/published/workflow?id=b67b5ecd3305f830 Engy Nasr, Bérénice Batut, Paul Zierep name:collection, name:microgalaxy, name:gtn 2023-04-12 2024-06-19 8 8 kraken_biom, kraken2, interactive_tool_phinch Taxonomic classification, Genome annotation MIT False False +metaQuantome_datacreation_workflow https://usegalaxy.eu fc42cc9467c6ee8d https://usegalaxy.eu/published/workflow?id=fc42cc9467c6ee8d proteomics, name:microgalaxy 2023-12-14 2024-06-19 0 0 peptide_shaker, search_gui, unipept, flashlfq, tp_replace_in_line, Cut1, regex1, msconvert, tp_replace_in_column, query_tabular, Filter1, Remove beginning1 Formatting, Prediction and recognition, Filtering, Visualisation, Label-free quantification False False +Gene-based Pathogen Identification https://usegalaxy.eu 585c21b7b1d864fc https://usegalaxy.eu/published/workflow?id=585c21b7b1d864fc Engy Nasr, Bérénice Batut, Paul Zierep name:collection, name:pathogfair, name:iwc, name:microgalaxy 2023-04-13 2024-06-05 142 142 abricate, collection_element_identifiers, bandage_image, flye, tp_find_and_replace, split_file_to_collection, compose_text_param, __BUILD_LIST__, tab2fasta, medaka_consensus_pipeline, param_value_from_file, fasta2tab Base-calling, Antimicrobial resistance prediction, De-novo assembly, Variant calling, Sequence assembly visualisation, Sequence assembly, Cross-assembly, Mapping assembly, Genome assembly MIT False False +Taxonomy Profiling and Visualization with Krona https://usegalaxy.eu 10101558b211a782 https://usegalaxy.eu/published/workflow?id=10101558b211a782 Engy Nasr, Bérénice Batut, Paul Zierep name:collection, name:microgalaxy, name:pathogfair, name:iwc 2023-05-11 2024-06-05 58 58 krakentools_kreport2krona, kraken2, taxonomy_krona_chart Taxonomic classification, Aggregation, Visualisation MIT False False +Pathogen-Detection-Nanopore-All-Samples-Analysis-Juyptool https://usegalaxy.eu c8bc4af6dd3b5d02 https://usegalaxy.eu/published/workflow?id=c8bc4af6dd3b5d02 Engy Nasr, Bérénice Batut microbiome, nanopore, iwc, name:collection, name:microgalaxy 2022-11-29 2024-04-04 205 205 tp_split_on_column, ggplot2_heatmap, bedtools_getfastabed, collapse_dataset, regex1, tp_replace_in_column, fasta_merge_files_and_filter_unique_sequences, newick_display, regexColumn1, tp_multijoin_tool, interactive_tool_jupyter_notebook, Count1, __FILTER_EMPTY_DATASETS__, fasta2tab, tp_sorted_uniq, Grouping1, fasttree, tab2fasta, Remove beginning1, collection_column_join, clustalw, __FILTER_FAILED_DATASETS__, Cut1 Phylogenetic tree generation, Visualisation, Multiple sequence alignment, Phylogenetic tree reconstruction, Phylogenetic tree analysis, Mapping MIT False False Mgnify ML https://usegalaxy.eu 011f701c5a55bfdf https://usegalaxy.eu/published/workflow?id=011f701c5a55bfdf name:microgalaxy 2023-10-10 2024-03-15 128 128 interactive_tool_jupyter_notebook, __BUILD_LIST__ True False -Normalization https://usegalaxy.eu 0603f0898211f806 https://usegalaxy.eu/published/workflow?id=0603f0898211f806 name:microgalaxy 2023-09-25 2024-03-13 80 80 Grep1, __BUILD_LIST__, map_param_value, __EXTRACT_DATASET__, __FILTER_EMPTY_DATASETS__ False False -WF1_Database_Generation_Workflow https://usegalaxy.eu 7cfbf4b7bd3f30d3 https://usegalaxy.eu/published/workflow?id=7cfbf4b7bd3f30d3 name:clinicalmp, name:microgalaxy 2023-12-14 2023-12-14 1 1 metanovo, fasta_merge_files_and_filter_unique_sequences Expression analysis, Protein identification, Tag-based peptide identification, de Novo sequencing, Target-Decoy False False -WF2_Discovery-Workflow https://usegalaxy.eu 8af41219411062ad https://usegalaxy.eu/published/workflow?id=8af41219411062ad name:microgalaxy, name:clinicalmp 2023-12-14 2023-12-14 1 1 Grouping1, Grep1, fasta2tab, fasta_merge_files_and_filter_unique_sequences, Filter1, ident_params, Remove beginning1, msconvert, Cut1, query_tabular, dbbuilder, fasta_cli, filter_tabular, tp_cat, search_gui, peptide_shaker, maxquant Visualisation, Filtering, Formatting, Statistical calculation, Imputation, Standardisation and normalisation, Heat map generation, Protein quantification, Principal component plotting, Clustering False False -WF3_VERIFICATION_WORKFLOW https://usegalaxy.eu d87fc6685e47d27d https://usegalaxy.eu/published/workflow?id=d87fc6685e47d27d name:microgalaxy, name:clinicalmp 2023-12-14 2023-12-14 1 1 Grouping1, fasta_merge_files_and_filter_unique_sequences, Filter1, uniprotxml_downloader, Cut1, pepquery2, tp_cat, dbbuilder, Remove beginning1, collapse_dataset, query_tabular False False -WF4_Quantitation_Workflow https://usegalaxy.eu a49275eb8b2b2ecb https://usegalaxy.eu/published/workflow?id=a49275eb8b2b2ecb name:clinicalmp, name:microgalaxy 2023-12-14 2023-12-14 1 1 Grouping1, Grep1, maxquant, Cut1 Visualisation, Statistical calculation, Imputation, Standardisation and normalisation, Heat map generation, Protein quantification, Principal component plotting, Clustering False False -WF5_Data_Interpretation_Worklow https://usegalaxy.eu 755ede37d94dc456 https://usegalaxy.eu/published/workflow?id=755ede37d94dc456 name:microgalaxy, name:clinicalmp 2023-12-14 2023-12-14 1 1 Grep1, msstatstmt, unipept Visualisation, Prediction and recognition False False -MetaG_extended https://usegalaxy.eu d57d41e306241396 https://usegalaxy.eu/published/workflow?id=d57d41e306241396 name:microgalaxy 2023-12-14 2023-12-14 1 1 fasplit, tp_awk_tool, tp_grep_tool, fastqc, checkm_lineage_wf, hmmer_hmmscan, coverm_genome, quast, coverm_contig, fraggenescan, maxbin2, cat_bins, tp_cat, kofamscan, trim_galore, interproscan, sort1 Visualisation, Sequence composition calculation, Formatting, Statistical calculation, Gene functional annotation, Validation, Sequence database search, Format validation, Primer removal, Coding region prediction, Local alignment, Sequence assembly, Database search, Sequence profile generation, Sequencing quality control, Protein feature detection, Sequence trimming, Multiple sequence alignment, Sequence assembly validation, Sequence motif recognition, Sequence generation, Sequence analysis, Read pre-processing, Data retrieval, Gene prediction, Taxonomic classification, Conversion, Probabilistic sequence generation False False -metaquantome-taxonomy-workflow https://usegalaxy.eu 695f7defb516d80d https://usegalaxy.eu/published/workflow?id=695f7defb516d80d proteomics, name:microgalaxy 2023-12-14 2023-12-14 0 0 metaquantome_db, metaquantome_sample, metaquantome_stat, metaquantome_filter, metaquantome_viz, metaquantome_expand Visualisation, Statistical inference, Quantification, Heat map generation, Query and retrieval, Indexing, Differential protein expression analysis, Principal component visualisation, Filtering, Functional clustering False False -metaquantome-function-worklow https://usegalaxy.eu 4c364c6be27981ba https://usegalaxy.eu/published/workflow?id=4c364c6be27981ba proteomics, name:microgalaxy 2023-12-14 2023-12-14 0 0 metaquantome_db, metaquantome_sample, metaquantome_stat, metaquantome_filter, metaquantome_viz, metaquantome_expand Visualisation, Statistical inference, Quantification, Heat map generation, Query and retrieval, Indexing, Differential protein expression analysis, Principal component visualisation, Filtering, Functional clustering False False -Metaproteomics_GTN https://usegalaxy.eu 68967c922de149ae https://usegalaxy.eu/published/workflow?id=68967c922de149ae proteomics, name:microgalaxy 2023-12-14 2023-12-14 0 0 search_gui, peptide_shaker, sqlite_to_tabular, query_tabular, unipept Visualisation, Prediction and recognition False False -Ecoli Comparison https://usegalaxy.eu 0e492839192d26e0 https://usegalaxy.eu/published/workflow?id=0e492839192d26e0 assembly, name:microgalaxy 2023-12-14 2023-12-14 0 0 mergeCols1, bedtools_complementbed, tp_sort_header_tool, tp_sed_tool, cat1, bedtools_sortbed, fasta_compute_length, Filter1, addValue, join1, collapse_dataset, bedtools_intersectbed, random_lines1, Grep1, tp_cat, Cut1, fasta_filter_by_length, tp_grep_tool, datamash_ops, lastz_wrapper_2 Read mapping, Sequence alignment, Mapping True False -Training: 16S rRNA Analysis with Nanopore Sequencing Reads https://usegalaxy.eu 08eb5e55109c4d9c https://usegalaxy.eu/published/workflow?id=08eb5e55109c4d9c metagenomics, name:microgalaxy 2023-12-14 2023-12-14 0 0 multiqc, kraken2, fastqc, taxonomy_krona_chart, porechop, tp_replace_in_line, fastp, Remove beginning1, datamash_reverse Visualisation, Sequence composition calculation, Sequence contamination filtering, Statistical calculation, Validation, Taxonomic classification, Sequencing quality control False False +Normalization https://usegalaxy.eu 0603f0898211f806 https://usegalaxy.eu/published/workflow?id=0603f0898211f806 name:microgalaxy 2023-09-25 2024-03-13 80 80 __EXTRACT_DATASET__, map_param_value, Grep1, __BUILD_LIST__, __FILTER_EMPTY_DATASETS__ False False +WF1_Database_Generation_Workflow https://usegalaxy.eu 7cfbf4b7bd3f30d3 https://usegalaxy.eu/published/workflow?id=7cfbf4b7bd3f30d3 name:clinicalmp, name:microgalaxy 2023-12-14 2023-12-14 1 1 metanovo, fasta_merge_files_and_filter_unique_sequences de Novo sequencing, Target-Decoy, Expression analysis, Tag-based peptide identification, Protein identification False False +WF2_Discovery-Workflow https://usegalaxy.eu 8af41219411062ad https://usegalaxy.eu/published/workflow?id=8af41219411062ad name:microgalaxy, name:clinicalmp 2023-12-14 2023-12-14 1 1 query_tabular, peptide_shaker, Remove beginning1, tp_cat, search_gui, Grouping1, fasta_cli, ident_params, maxquant, msconvert, dbbuilder, Grep1, filter_tabular, Filter1, fasta_merge_files_and_filter_unique_sequences, Cut1, fasta2tab Statistical calculation, Imputation, Formatting, Heat map generation, Filtering, Standardisation and normalisation, Protein quantification, Clustering, Principal component plotting, Visualisation False False +WF3_VERIFICATION_WORKFLOW https://usegalaxy.eu d87fc6685e47d27d https://usegalaxy.eu/published/workflow?id=d87fc6685e47d27d name:microgalaxy, name:clinicalmp 2023-12-14 2023-12-14 1 1 Filter1, uniprotxml_downloader, Grouping1, Cut1, collapse_dataset, dbbuilder, query_tabular, tp_cat, fasta_merge_files_and_filter_unique_sequences, Remove beginning1, pepquery2 False False +WF4_Quantitation_Workflow https://usegalaxy.eu a49275eb8b2b2ecb https://usegalaxy.eu/published/workflow?id=a49275eb8b2b2ecb name:clinicalmp, name:microgalaxy 2023-12-14 2023-12-14 1 1 maxquant, Cut1, Grep1, Grouping1 Statistical calculation, Imputation, Heat map generation, Standardisation and normalisation, Protein quantification, Clustering, Principal component plotting, Visualisation False False +WF5_Data_Interpretation_Worklow https://usegalaxy.eu 755ede37d94dc456 https://usegalaxy.eu/published/workflow?id=755ede37d94dc456 name:microgalaxy, name:clinicalmp 2023-12-14 2023-12-14 1 1 msstatstmt, Grep1, unipept Prediction and recognition, Visualisation False False +MetaG_extended https://usegalaxy.eu d57d41e306241396 https://usegalaxy.eu/published/workflow?id=d57d41e306241396 name:microgalaxy 2023-12-14 2023-12-14 1 1 coverm_genome, fasplit, tp_awk_tool, tp_grep_tool, sort1, cat_bins, trim_galore, fastqc, checkm_lineage_wf, interproscan, coverm_contig, hmmer_hmmscan, kofamscan, tp_cat, maxbin2, quast, fraggenescan Statistical calculation, Formatting, Gene functional annotation, Visualisation, Format validation, Conversion, Probabilistic sequence generation, Sequencing quality control, Sequence assembly, Protein feature detection, Gene prediction, Sequence motif recognition, Coding region prediction, Sequence composition calculation, Sequence generation, Database search, Sequence database search, Data retrieval, Taxonomic classification, Multiple sequence alignment, Sequence assembly validation, Sequence trimming, Sequence profile generation, Validation, Sequence analysis, Read pre-processing, Primer removal, Local alignment False False +metaquantome-taxonomy-workflow https://usegalaxy.eu 695f7defb516d80d https://usegalaxy.eu/published/workflow?id=695f7defb516d80d proteomics, name:microgalaxy 2023-12-14 2023-12-14 0 0 metaquantome_stat, metaquantome_expand, metaquantome_viz, metaquantome_db, metaquantome_filter, metaquantome_sample Quantification, Differential protein expression analysis, Query and retrieval, Principal component visualisation, Indexing, Heat map generation, Filtering, Functional clustering, Statistical inference, Visualisation False False +metaquantome-function-worklow https://usegalaxy.eu 4c364c6be27981ba https://usegalaxy.eu/published/workflow?id=4c364c6be27981ba proteomics, name:microgalaxy 2023-12-14 2023-12-14 0 0 metaquantome_stat, metaquantome_expand, metaquantome_viz, metaquantome_db, metaquantome_filter, metaquantome_sample Quantification, Differential protein expression analysis, Query and retrieval, Principal component visualisation, Indexing, Heat map generation, Filtering, Functional clustering, Statistical inference, Visualisation False False +Metaproteomics_GTN https://usegalaxy.eu 68967c922de149ae https://usegalaxy.eu/published/workflow?id=68967c922de149ae proteomics, name:microgalaxy 2023-12-14 2023-12-14 0 0 peptide_shaker, unipept, search_gui, sqlite_to_tabular, query_tabular Prediction and recognition, Visualisation False False +Ecoli Comparison https://usegalaxy.eu 0e492839192d26e0 https://usegalaxy.eu/published/workflow?id=0e492839192d26e0 assembly, name:microgalaxy 2023-12-14 2023-12-14 0 0 bedtools_sortbed, collapse_dataset, bedtools_intersectbed, tp_cat, datamash_ops, bedtools_complementbed, cat1, join1, mergeCols1, lastz_wrapper_2, tp_grep_tool, addValue, fasta_filter_by_length, Grep1, fasta_compute_length, tp_sort_header_tool, random_lines1, tp_sed_tool, Filter1, Cut1 Read mapping, Sequence alignment, Mapping True False +Training: 16S rRNA Analysis with Nanopore Sequencing Reads https://usegalaxy.eu 08eb5e55109c4d9c https://usegalaxy.eu/published/workflow?id=08eb5e55109c4d9c metagenomics, name:microgalaxy 2023-12-14 2023-12-14 0 0 fastp, datamash_reverse, taxonomy_krona_chart, multiqc, kraken2, tp_replace_in_line, fastqc, porechop, Remove beginning1 Sequencing quality control, Sequence contamination filtering, Taxonomic classification, Statistical calculation, Validation, Sequence composition calculation, Visualisation False False Main Metatranscriptomics Analysis https://usegalaxy.eu 7a08ecdf23e0c7a3 https://usegalaxy.eu/published/workflow?id=7a08ecdf23e0c7a3 Bérénice Batut, Pratik Jagtap, Subina Mehta, Ray Sajulga, Emma Leith, Praveen Kumar, Saskia Hiltemann, Paul Zierep name:microgalaxy 2023-12-14 2023-12-14 0 0 MIT False False -Copy Of GTN Training - Antibiotic Resistance Detection https://usegalaxy.eu 44e53ea319e07daa https://usegalaxy.eu/published/workflow?id=44e53ea319e07daa metagenomics, name:microgalaxy 2023-12-14 2023-12-14 0 0 unicycler, racon, staramr_search, bandage_image, miniasm, nanoplot, PlasFlow, gfa_to_fa, minimap2 Aggregation, Mapping assembly, Antimicrobial resistance prediction, Sequence analysis, Box-Whisker plot plotting, Pairwise sequence alignment, Genome assembly, Sequence assembly visualisation, Scatter plot plotting, De-novo assembly False False -Identification of the micro-organisms in a beer using Nanopore sequencing https://usegalaxy.eu 0590554db9794d13 https://usegalaxy.eu/published/workflow?id=0590554db9794d13 Bérénice Batut, Teresa Müller, Polina Polunina metagenomics, name:microgalaxy 2023-12-14 2023-12-14 0 0 kraken2, Filter1, fastqc, taxonomy_krona_chart, krakentools_kreport2krona, porechop, fastp Visualisation, Sequence composition calculation, Sequence contamination filtering, Statistical calculation, Taxonomic classification, Aggregation, Sequencing quality control MIT False False -workflow-generate-dataset-for-assembly-tutorial https://usegalaxy.eu ce5c16ac23c4fbb1 https://usegalaxy.eu/published/workflow?id=ce5c16ac23c4fbb1 name:microgalaxy 2023-12-14 2023-12-14 0 0 bowtie2, bamtools, bg_uniq, cutadapt, fastqc, tp_cat, filter_tabular, megahit, ngsutils_bam_filter, seqtk_subseq, random_lines1 Sequence trimming, Sequence composition calculation, Formatting, Statistical calculation, Sequence file editing, Read mapping, Primer removal, Variant calling, Read pre-processing, Sequence contamination filtering, Sequence alignment analysis, Data handling, Genome assembly, Sequencing quality control False False -Metagenomics assembly tutorial workflow https://usegalaxy.eu 62c47e3c9d4f3aa3 https://usegalaxy.eu/published/workflow?id=62c47e3c9d4f3aa3 name:microgalaxy 2023-12-14 2023-12-14 0 0 collection_column_join, bowtie2, megahit_contig2fastg, bandage_info, bandage_image, metaspades, quast, megahit Visualisation, Sequence assembly validation, Read mapping, Genome assembly, Sequence assembly visualisation False False -"WGS Part In ""Analyses Of Metagenomics Data - The Global Picture""" https://usegalaxy.eu c2b7ec5aacfc6107 https://usegalaxy.eu/published/workflow?id=c2b7ec5aacfc6107 metagenomics, name:microgalaxy 2023-12-14 2023-12-14 0 0 humann2, taxonomy_krona_chart, metaphlan2krona, humann2_renorm_table, humann2_regroup_table, metaphlan2 Visualisation False False -Taxonomic Profiling and Visualization of Metagenomic Data https://usegalaxy.eu 4f0daf8e9dd54127 https://usegalaxy.eu/published/workflow?id=4f0daf8e9dd54127 Bérénice Batut metagenomics, name:microgalaxy 2023-12-14 2023-12-14 0 0 interactive_tool_phinch, metaphlan, kraken2, taxonomy_krona_chart, krakentools_kreport2krona, __UNZIP_COLLECTION__, est_abundance, interactive_tool_pavian, kraken_biom Visualisation, Statistical calculation, Taxonomic classification, Genome annotation, Aggregation MIT False False -Amplicon Tutorial https://usegalaxy.eu 565c989730f68362 https://usegalaxy.eu/published/workflow?id=565c989730f68362 metagenomics, name:microgalaxy 2023-12-14 2023-12-14 0 0 mothur_pre_cluster, mothur_make_group, mothur_summary_seqs, mothur_count_seqs, mothur_unique_seqs, mothur_merge_files, mothur_align_seqs, mothur_filter_seqs, mothur_cluster_split, mothur_screen_seqs, mothur_classify_seqs, mothur_make_shared, krona-text, mothur_classify_otu, mothur_make_biom Visualisation, Sequence clustering, DNA barcoding, Taxonomic classification, Sequence read processing, Sequencing quality control, Phylogenetic analysis False False -Microbial Variant Calling https://usegalaxy.eu 515ef1601bc24a6c https://usegalaxy.eu/published/workflow?id=515ef1601bc24a6c variant-analysis, name:microgalaxy 2023-12-14 2023-12-14 0 0 jbrowse, snippy Genome visualisation, Phylogenetic tree visualisation, Phylogenetic tree generation, Variant calling False False -Calling variants in non-diploid systems https://usegalaxy.eu 291c36e1b18e9deb https://usegalaxy.eu/published/workflow?id=291c36e1b18e9deb variant-analysis, name:microgalaxy 2023-12-14 2023-12-14 0 0 vcffilter2, fastqc, vcf2tsv, bamFilter, freebayes, bwa_mem, picard_MarkDuplicates, Cut1, picard_MergeSamFiles, bamleftalign Sequence composition calculation, Formatting, Statistical calculation, Sequence alignment, Genome indexing, Read mapping, Variant calling, Sequence alignment analysis, Data handling, Generation, Sequencing quality control False False -Training: 16S rRNA Sequencing With Mothur: Main Tutorial https://usegalaxy.eu c67d2e75eeb4fd19 https://usegalaxy.eu/published/workflow?id=c67d2e75eeb4fd19 metagenomics, name:microgalaxy 2023-12-14 2023-12-14 0 0 mothur_pre_cluster, mothur_make_contigs, mothur_count_seqs, mothur_cluster, mothur_unique_seqs, mothur_venn, mothur_classify_seqs, mothur_make_shared, mothur_make_biom, mothur_summary_seqs, mothur_cluster_split, mothur_chimera_vsearch, mothur_screen_seqs, mothur_remove_lineage, mothur_summary_single, mothur_remove_seqs, XY_Plot_1, mothur_remove_groups, mothur_taxonomy_to_krona, mothur_count_groups, mothur_align_seqs, mothur_filter_seqs, mothur_dist_shared, mothur_tree_shared, mothur_dist_seqs, mothur_classify_otu, mothur_heatmap_sim, mothur_rarefaction_single, mothur_sub_sample, newick_display, taxonomy_krona_chart, mothur_seq_error, mothur_get_groups Visualisation, Phylogenetic tree reconstruction, Sequence clustering, Phylogenetic tree generation, DNA barcoding, Phylogenetic tree analysis, Taxonomic classification, Sequence read processing, Sequencing quality control, Phylogenetic analysis False False -Comparative gene analysis https://usegalaxy.eu 86900be4282d4b1d https://usegalaxy.eu/published/workflow?id=86900be4282d4b1d Anton Nekrutenko vgp, genome-annotation, name:microgalaxy 2023-12-14 2023-12-14 0 0 tp_split_on_column, regexColumn1, rbc_mafft, bg_diamond_view, Filter1, bg_diamond, join1, tab2fasta, collapse_dataset, Cut1, cat1, rapidnj, Add_a_column1, gops_intersect_1 Sequence alignment analysis, Multiple sequence alignment, Phylogenetic tree generation True False -Unicycler training https://usegalaxy.eu 8f3ce55d44d9f369 https://usegalaxy.eu/published/workflow?id=8f3ce55d44d9f369 assembly, name:microgalaxy 2023-12-14 2023-12-14 0 0 unicycler, multiqc, fastqc, prokka, quast Visualisation, Sequence composition calculation, Sequence assembly validation, Statistical calculation, Validation, Genome annotation, Coding region prediction, Gene prediction, Genome assembly, Aggregation, Sequencing quality control False False -Apollo Load Test https://usegalaxy.eu 3c233cc56d4df8b0 https://usegalaxy.eu/published/workflow?id=3c233cc56d4df8b0 genome-annotation, name:microgalaxy 2023-12-14 2023-12-14 0 0 jbrowse, iframe, create_or_update, list_organism, create_account Genome visualisation True False -Genome Annotation with Prokka [Feb 2020] https://usegalaxy.eu e1894c36f1ab4ab4 https://usegalaxy.eu/published/workflow?id=e1894c36f1ab4ab4 genome-annotation, name:microgalaxy 2023-12-14 2023-12-14 0 0 jbrowse, prokka Genome visualisation, Coding region prediction, Genome annotation, Gene prediction False False -Flye-AMR workflow EMC/WMDI - v3.5 (imported from URL) https://usegalaxy.eu 152223c8aed27357 https://usegalaxy.eu/published/workflow?id=152223c8aed27357 wmdi, name:microgalaxy 2023-12-14 2023-12-14 0 0 jbrowse, bg_column_arrange_by_header, gff2bed1, tp_text_file_with_recurring_lines, circos_gc_skew, trimmomatic, fasta2tab, fasta_compute_length, Add_a_column1, circos_interval_to_tile, tp_sort_header_tool, minimap2, Filter1, bandage_image, nanoplot, join1, PlasFlow, circos, tp_head_tool, deeptools_bam_coverage, Grep1, tp_cut_tool, tp_easyjoin_tool, tp_cat, regex_replace, Cut1, tp_split_on_column, medaka_consensus_pipeline, circos_wiggle_to_scatter, ncbi_blastn_wrapper, staramr_search, prokka, regex1, flye, tbl2gff3, tab2fasta Genome assembly, Sequence visualisation, Gene prediction, Genome annotation, Sequence analysis, Variant calling, Base-calling, Antimicrobial resistance prediction, Coding region prediction, Cross-assembly, Mapping assembly, Sequence assembly, Box-Whisker plot plotting, Genome visualisation, Pairwise sequence alignment, Sequence assembly visualisation, Scatter plot plotting, De-novo assembly True False -Mtb phylogeny https://usegalaxy.eu 875b3ca170ac12a1 https://usegalaxy.eu/published/workflow?id=875b3ca170ac12a1 evolution, name:microgalaxy 2023-12-14 2023-12-14 0 0 raxml, interactive_tool_rstudio Phylogenetic tree analysis, Sequence analysis False False -From VCFs to SNP distance matrix https://usegalaxy.eu 6d333ed886aab471 https://usegalaxy.eu/published/workflow?id=6d333ed886aab471 evolution, name:microgalaxy 2023-12-14 2023-12-14 0 0 bcftools_consensus, snp_sites, tb_variant_filter, tp_cat, snp_dists True False -From Fastqs to VCFs and BAMs https://usegalaxy.eu 3a8fde248a4d0383 https://usegalaxy.eu/published/workflow?id=3a8fde248a4d0383 evolution, name:microgalaxy 2023-12-14 2023-12-14 0 0 trimmomatic, tb_variant_filter, __MERGE_COLLECTION__, snippy Phylogenetic tree visualisation, Variant calling, Phylogenetic tree generation True False -From BAMs to drug resistance prediction with TB-profiler https://usegalaxy.eu d0d6dae0d1eecc21 https://usegalaxy.eu/published/workflow?id=d0d6dae0d1eecc21 evolution, name:microgalaxy 2023-12-14 2023-12-14 0 0 samtools_view, tb_profiler_profile, tp_grep_tool, tp_replace_in_line, __MERGE_COLLECTION__, tp_cat, addName, tp_sed_tool Antimicrobial resistance prediction True False -M. tuberculosis Variant Analysis tutorial https://usegalaxy.eu 3ff4dbcc7a602e6b https://usegalaxy.eu/published/workflow?id=3ff4dbcc7a602e6b Peter van Heusden variant-analysis, prokaryote, name:microgalaxy 2023-12-14 2023-12-14 0 0 multiqc, kraken2, tb_profiler_profile, fastqc, jbrowse, snippy, tbvcfreport, tb_variant_filter, trimmomatic Phylogenetic tree visualisation, Sequence composition calculation, Statistical calculation, Validation, Antimicrobial resistance prediction, Variant calling, Phylogenetic tree generation, Genome visualisation, Taxonomic classification, Sequencing quality control MIT False False -Compute Allel Frequency Table from paired reads https://usegalaxy.eu 21a39ac4c1becb31 https://usegalaxy.eu/published/workflow?id=21a39ac4c1becb31 name:microgalaxy, hpylori 2023-12-13 2023-12-13 2 2 bowtie2, bcftools_norm, tp_awk_tool, snpSift_filter, vcf2tsv, freebayes, bcftools_view Read mapping, Statistical calculation, Variant calling True False -Reference genome choice (indels, coverage, depth) for short reads https://usegalaxy.eu 61fe08fb3d5e83f8 https://usegalaxy.eu/published/workflow?id=61fe08fb3d5e83f8 name:microgalaxy, hpylori 2023-10-27 2023-12-13 13 13 bowtie2, samtools_coverage, bcftools_norm, vcf2tsv, collection_element_identifiers, freebayes, tp_cat, collapse_dataset, samtools_depth Read mapping, Statistical calculation, Variant calling True False -MGnify amplicon rRNA-prediction + ITS https://usegalaxy.eu 437704898229dfb6 https://usegalaxy.eu/published/workflow?id=437704898229dfb6 mgnify_amplicon_showcase, name:microgalaxy 2023-12-12 2023-12-13 1 1 bedtools_getfastabed, tp_awk_tool, infernal_cmsearch, mapseq, bedtools_maskfastabed, taxonomy_krona_chart, cmsearch_deoverlap, biom_convert, gops_concat_1, query_tabular Visualisation, Alignment, Formatting, Mapping, k-mer counting, Comparison, Nucleic acid feature detection False False -MGnify amplicon QC https://usegalaxy.eu 8f415b0c409f56f7 https://usegalaxy.eu/published/workflow?id=8f415b0c409f56f7 mgnify_amplicon_showcase, name:microgalaxy 2023-12-13 2023-12-13 1 1 cshl_fasta_formatter, tp_find_and_replace, fastq_to_fasta_python, multiqc, fastq_dump, fastqc, __UNZIP_COLLECTION__, prinseq, iuc_pear, fastp, trimmomatic Sequence trimming, Sequence composition calculation, Statistical calculation, Validation, Read pre-processing, Sequence contamination filtering, Sequence merging, Data handling, Sequencing quality control False False - Cloud-Aerosole MT-MG Functional Profiling https://usegalaxy.eu 4566262dd0acc8ab https://usegalaxy.eu/published/workflow?id=4566262dd0acc8ab metagenomics, metatranscriptomics, name:microgalaxy 2021-11-10 2023-12-07 2 2 featurecounts, bowtie2, multiqc Read summarisation, RNA-Seq quantification, Validation, Read mapping, Sequencing quality control False False -Cloud-Aerosole MT-MG Reference Gene Catalog Building https://usegalaxy.eu 9b9e1e28f3683f92 https://usegalaxy.eu/published/workflow?id=9b9e1e28f3683f92 metagenomics, metatranscriptomics, name:microgalaxy 2021-11-01 2023-12-07 72 72 bedtools_getfastabed, bowtie2, cd_hit, eggnog_mapper, metaeuk_easy_predict, multiqc, fastqc, bg_diamond, quast, bg_diamond_makedb, metagene_annotator, dbbuilder, megahit, cat1, kofamscan, translate_nucleotides Visualisation, Sequence composition calculation, Fold recognition, Statistical calculation, Validation, Read mapping, Genome annotation, Query and retrieval, Sequence alignment analysis, Genome assembly, Sequencing quality control, Sequence assembly validation, Mapping, Information extraction, Homology-based gene prediction, Sequence clustering, Sequence analysis, Sequence annotation, Gene functional annotation False False -Cloud-Aerosole MT-MG Pre-Processing https://usegalaxy.eu bb604ff5e010e7ab https://usegalaxy.eu/published/workflow?id=bb604ff5e010e7ab metagenomics, metatranscriptomics, name:microgalaxy 2021-11-01 2023-12-07 51 51 trimmomatic, fastqc, multiqc Sequence composition calculation, Statistical calculation, Validation, Sequencing quality control False False -Cloud Aerosol MT-MG Contamination Filtering https://usegalaxy.eu bdc7cfaac0db2eab https://usegalaxy.eu/published/workflow?id=bdc7cfaac0db2eab metagenomics, metatranscriptomics, name:microgalaxy 2022-06-29 2023-12-07 28 28 bowtie2, kraken2, fastq_to_tabular, filter_tabular, recentrifuge, seq_filter_by_id Cross-assembly, Taxonomic classification, Read mapping, Expression analysis False False -Cloud-Aerosole MT-MG Taxonomic Profiling https://usegalaxy.eu e69b555faa6bb962 https://usegalaxy.eu/published/workflow?id=e69b555faa6bb962 metagenomics, metatranscriptomics, name:microgalaxy 2022-09-03 2023-12-07 18 18 interactive_tool_phinch, kraken2, recentrifuge, maaslin2, kraken_biom Visualisation, Filtering, Statistical calculation, Genome annotation, Standardisation and normalisation, Cross-assembly, Taxonomic classification, Expression analysis False False -MetaP https://usegalaxy.eu 96d198ed953449fd https://usegalaxy.eu/published/workflow?id=96d198ed953449fd name:microgalaxy 2020-01-30 2023-03-16 2 2 maxquant Visualisation, Statistical calculation, Imputation, Standardisation and normalisation, Heat map generation, Protein quantification, Principal component plotting, Clustering False False -MetaG_extended https://usegalaxy.eu 6158c3b5fc12044e https://usegalaxy.eu/published/workflow?id=6158c3b5fc12044e name:microgalaxy 2023-02-10 2023-03-16 22 22 fasplit, tp_awk_tool, tp_grep_tool, fastqc, checkm_lineage_wf, hmmer_hmmscan, coverm_genome, quast, coverm_contig, fraggenescan, maxbin2, cat_bins, tp_cat, kofamscan, trim_galore, interproscan, sort1 Visualisation, Sequence composition calculation, Formatting, Statistical calculation, Gene functional annotation, Validation, Sequence database search, Format validation, Primer removal, Coding region prediction, Local alignment, Sequence assembly, Database search, Sequence profile generation, Sequencing quality control, Protein feature detection, Sequence trimming, Multiple sequence alignment, Sequence assembly validation, Sequence motif recognition, Sequence generation, Sequence analysis, Read pre-processing, Data retrieval, Gene prediction, Taxonomic classification, Conversion, Probabilistic sequence generation False False -MetaT https://usegalaxy.eu 385cc7df70d7916b https://usegalaxy.eu/published/workflow?id=385cc7df70d7916b name:microgalaxy 2020-01-27 2023-02-27 16 16 collection_column_join, kallisto_quant, fastqc, __UNZIP_COLLECTION__, trim_galore, bg_sortmerna Sequence trimming, Sequence composition calculation, Statistical calculation, Gene expression profiling, Primer removal, Read pre-processing, Sequence similarity search, Sequence alignment analysis, Sequence comparison, Sequencing quality control False False -Quality control of bins generated by MetaBAT2, MaxBin2, SemiBin, and CONCOCT https://usegalaxy.fr f0776f7a890b523a https://usegalaxy.fr/published/workflow?id=f0776f7a890b523a Bérénice Batut microbiome, name:microgalaxy 2025-12-08 2025-12-08 1 1 multiqc, __FLATTEN__, collection_element_identifiers, __RELABEL_FROM_FILE__, __MERGE_COLLECTION__, regex1, checkm2 Sequence composition calculation, Sequence assembly validation, Statistical calculation, Validation, Sequencing quality control MIT True False -Quality control of bins generated by MetaBAT2, MaxBin2, SemiBin, and CONCOCT https://usegalaxy.org a8aee61c2cbaf6ea https://usegalaxy.org/published/workflow?id=a8aee61c2cbaf6ea Bérénice Batut microbiome, name:microgalaxy 2025-12-08 2025-12-08 1 1 multiqc, __FLATTEN__, collection_element_identifiers, __RELABEL_FROM_FILE__, __MERGE_COLLECTION__, regex1, checkm2 Sequence composition calculation, Sequence assembly validation, Statistical calculation, Validation, Sequencing quality control MIT True False -Copy of Taxonomy Profiling and Visualization with Krona shared by user engy.nasr https://usegalaxy.org 3011f5dbf884c9bc https://usegalaxy.org/published/workflow?id=3011f5dbf884c9bc Engy Nasr, Bérénice Batut, Paul Zierep name:collection, name:microgalaxy, name:pathogfair, name:iwc 2025-04-12 2025-05-23 0 0 kraken2, taxonomy_krona_chart, krakentools_kreport2krona Visualisation, Taxonomic classification, Aggregation MIT False False -Gene-based Pathogen Identification (release v0.1) https://usegalaxy.org 3f252e077e0bcce5 https://usegalaxy.org/published/workflow?id=3f252e077e0bcce5 Engy Nasr, Bérénice Batut, Paul Zierep name:collection, name:pathogfair, name:iwc, name:microgalaxy 2024-09-19 2025-04-25 1 1 medaka_consensus_pipeline, param_value_from_file, compose_text_param, __BUILD_LIST__, tp_find_and_replace, abricate, collection_element_identifiers, bandage_image, split_file_to_collection, flye, fasta2tab, tab2fasta Antimicrobial resistance prediction, Base-calling, Variant calling, Cross-assembly, Mapping assembly, Sequence assembly, Genome assembly, Sequence assembly visualisation, De-novo assembly MIT False False -Pathogen Detection PathoGFAIR Samples Aggregation and Visualisation (release v0.1) https://usegalaxy.org 3ef08553982f6ffc https://usegalaxy.org/published/workflow?id=3ef08553982f6ffc Engy Nasr, Bérénice Batut, Paul Zierep name:collection, name:microgalaxy, name:pathogfair, name:iwc 2024-09-19 2025-04-25 1 1 Grouping1, regexColumn1, clustalw, __FILTER_FAILED_DATASETS__, fasta2tab, tp_sorted_uniq, fasta_merge_files_and_filter_unique_sequences, collapse_dataset, __FILTER_EMPTY_DATASETS__, bedtools_getfastabed, tp_multijoin_tool, ggplot2_heatmap, Cut1, Remove beginning1, fasttree, tp_split_on_column, collection_column_join, tp_replace_in_column, newick_display, regex1, Count1, tab2fasta Phylogenetic tree generation (from molecular sequences), Visualisation, Phylogenetic tree generation (maximum likelihood and Bayesian methods), Multiple sequence alignment, Mapping, Phylogenetic tree reconstruction, Phylogenetic tree analysis, Phylogenetic tree generation MIT False False -Taxonomy Profiling and Visualization with Kron (release v0.1) https://usegalaxy.org 4b5f6b5d4f36e38b https://usegalaxy.org/published/workflow?id=4b5f6b5d4f36e38b Engy Nasr, Bérénice Batut, Paul Zierep name:collection, name:microgalaxy, name:pathogfair, name:iwc 2024-09-19 2025-04-25 1 1 kraken2, taxonomy_krona_chart, krakentools_kreport2krona Visualisation, Taxonomic classification, Aggregation MIT False False -Allele-based Pathogen Identification (release v0.1.2) https://usegalaxy.org 6d778eeb176d563c https://usegalaxy.org/published/workflow?id=6d778eeb176d563c Engy Nasr, Bérénice Batut, Paul Zierep name:collection, name:microgalaxy, name:pathogfair, name:iwc 2024-10-31 2025-04-25 1 1 bcftools_consensus, Paste1, samtools_coverage, regexColumn1, bcftools_norm, CONVERTER_gz_to_uncompressed, snpSift_filter, tp_cut_tool, Cut1, snpSift_extractFields, clair3, collapse_dataset, Remove beginning1, table_compute, tp_head_tool, Count1, samtools_depth, minimap2 Pairwise sequence alignment, Variant calling MIT False False -Allele-based Pathogen Identification (release v0.1.1) https://usegalaxy.org 29ba77708cdafe0f https://usegalaxy.org/published/workflow?id=29ba77708cdafe0f Engy Nasr, Bérénice Batut, Paul Zierep name:collection, name:microgalaxy, name:pathogfair, name:iwc 2024-11-28 2025-04-25 1 1 bcftools_consensus, Paste1, samtools_coverage, regexColumn1, bcftools_norm, CONVERTER_gz_to_uncompressed, snpSift_filter, tp_cut_tool, Cut1, snpSift_extractFields, clair3, collapse_dataset, Remove beginning1, table_compute, tp_head_tool, Count1, samtools_depth, minimap2 Pairwise sequence alignment, Variant calling MIT False False -MGnify's amplicon pipeline v5.0 (release v0.1) https://usegalaxy.org 8e863bbef37cc36b https://usegalaxy.org/published/workflow?id=8e863bbef37cc36b EMBL's European Bioinformatics Institute, Rand Zoabi, Paul Zierep mgnify_amplicon, metagenomics, amplicon, name:microgalaxy 2025-02-06 2025-04-25 1 1 fastq_dl, CONVERTER_uncompressed_to_gz, tp_awk_tool, CONVERTER_gz_to_uncompressed, __MERGE_COLLECTION__ Apache-2.0 True False -MGnify's amplicon pipeline v5.0 - ITS (release v0.1) https://usegalaxy.org 45f959d5bf505b15 https://usegalaxy.org/published/workflow?id=45f959d5bf505b15 EMBL's European Bioinformatics Institute, Rand Zoabi, Paul Zierep mgnify_amplicon, amplicon, metagenomics, name:microgalaxy 2025-02-06 2025-04-25 1 1 tp_awk_tool, __FILTER_FROM_FILE__, bedtools_maskfastabed, mapseq, collection_element_identifiers, taxonomy_krona_chart, biom_convert, __FILTER_EMPTY_DATASETS__ k-mer counting, Visualisation, Formatting, Mapping Apache-2.0 True False -MGnify's amplicon pipeline v5.0 - Quality control PE (release v0.1) https://usegalaxy.org a71fcbc60caae8b6 https://usegalaxy.org/published/workflow?id=a71fcbc60caae8b6 EMBL's European Bioinformatics Institute, Rand Zoabi, Paul Zierep mgnify_amplicon, amplicon, metagenomics, name:microgalaxy 2025-02-06 2025-04-25 1 1 cshl_fasta_formatter, tp_find_and_replace, fastq_to_fasta_python, multiqc, fastqc, __UNZIP_COLLECTION__, prinseq, mgnify_seqprep, fastp, trimmomatic, fastq_filter Sequence trimming, Sequence composition calculation, Nucleic acid design, Statistical calculation, Validation, Read pre-processing, Sequence contamination filtering, Sequencing quality control Apache-2.0 True False -MGnify's amplicon pipeline v5.0 - Quality control SE (release v0.1) https://usegalaxy.org 5f878c4cc3bff68c https://usegalaxy.org/published/workflow?id=5f878c4cc3bff68c MGnify - EMBL, Rand Zoabi, Paul Zierep mgnify_amplicon, amplicon, metagenomics, name:microgalaxy 2025-02-06 2025-04-25 1 1 cshl_fasta_formatter, tp_find_and_replace, fastq_to_fasta_python, multiqc, fastqc, prinseq, trimmomatic, fastq_filter Sequence trimming, Read pre-processing, Sequence composition calculation, Sequence contamination filtering, Statistical calculation, Validation, Sequencing quality control Apache-2.0 True False -Allele-based Pathogen Identification (release v0.1.3) https://usegalaxy.org 3e703abaeb870f6f https://usegalaxy.org/published/workflow?id=3e703abaeb870f6f Engy Nasr, Bérénice Batut, Paul Zierep name:collection, name:microgalaxy, name:pathogfair, name:iwc 2025-03-06 2025-04-25 1 1 bcftools_consensus, Paste1, samtools_coverage, regexColumn1, bcftools_norm, CONVERTER_gz_to_uncompressed, snpSift_filter, tp_cut_tool, Cut1, snpSift_extractFields, clair3, collapse_dataset, Remove beginning1, table_compute, tp_head_tool, Count1, samtools_depth, minimap2 Pairwise sequence alignment, Variant calling MIT True False -MGnify's amplicon pipeline v5.0 - Quality control SE (release v0.2) https://usegalaxy.org afb67b4b9952f57d https://usegalaxy.org/published/workflow?id=afb67b4b9952f57d MGnify - EMBL, Rand Zoabi, Paul Zierep mgnify_amplicon, amplicon, metagenomics, name:microgalaxy 2025-03-06 2025-04-25 1 1 cshl_fasta_formatter, tp_find_and_replace, fastq_to_fasta_python, multiqc, fastqc, prinseq, trimmomatic, fastq_filter Sequence trimming, Read pre-processing, Sequence composition calculation, Sequence contamination filtering, Statistical calculation, Validation, Sequencing quality control Apache-2.0 True False -Allele-based Pathogen Identification (release v0.1.4) https://usegalaxy.org cb810cdaa4915f4b https://usegalaxy.org/published/workflow?id=cb810cdaa4915f4b Engy Nasr, Bérénice Batut, Paul Zierep name:collection, name:microgalaxy, name:pathogfair, name:iwc 2025-03-13 2025-04-25 1 1 bcftools_consensus, Paste1, samtools_coverage, regexColumn1, bcftools_norm, CONVERTER_gz_to_uncompressed, snpSift_filter, tp_cut_tool, Cut1, snpSift_extractFields, clair3, collapse_dataset, Remove beginning1, table_compute, tp_head_tool, Count1, samtools_depth, minimap2 Pairwise sequence alignment, Variant calling MIT True False -MGnify's amplicon pipeline v5.0 (release v0.2) https://usegalaxy.org 77de7101effbff3d https://usegalaxy.org/published/workflow?id=77de7101effbff3d EMBL's European Bioinformatics Institute, Rand Zoabi, Paul Zierep mgnify_amplicon, metagenomics, amplicon, name:microgalaxy 2025-03-13 2025-04-25 1 1 fastq_dl, CONVERTER_uncompressed_to_gz, tp_awk_tool, CONVERTER_gz_to_uncompressed, __MERGE_COLLECTION__ Apache-2.0 True False -MGnify's amplicon pipeline v5.0 - ITS (release v0.2) https://usegalaxy.org 8151be18aab3a3c6 https://usegalaxy.org/published/workflow?id=8151be18aab3a3c6 EMBL's European Bioinformatics Institute, Rand Zoabi, Paul Zierep mgnify_amplicon, amplicon, metagenomics, name:microgalaxy 2025-03-13 2025-04-25 1 1 tp_awk_tool, __FILTER_FROM_FILE__, bedtools_maskfastabed, mapseq, collection_element_identifiers, taxonomy_krona_chart, biom_convert, __FILTER_EMPTY_DATASETS__ k-mer counting, Visualisation, Formatting, Mapping Apache-2.0 True False -MGnify's amplicon pipeline v5.0 - Quality control PE (release v0.2) https://usegalaxy.org 20b7ae4b517a80fd https://usegalaxy.org/published/workflow?id=20b7ae4b517a80fd EMBL's European Bioinformatics Institute, Rand Zoabi, Paul Zierep mgnify_amplicon, amplicon, metagenomics, name:microgalaxy 2025-03-13 2025-04-25 1 1 cshl_fasta_formatter, tp_find_and_replace, fastq_to_fasta_python, multiqc, fastqc, __UNZIP_COLLECTION__, prinseq, mgnify_seqprep, fastp, trimmomatic, fastq_filter Sequence trimming, Sequence composition calculation, Nucleic acid design, Statistical calculation, Validation, Read pre-processing, Sequence contamination filtering, Sequencing quality control Apache-2.0 True False -MGnify's amplicon pipeline v5.0 - Quality control SE (release v0.3) https://usegalaxy.org 46f184a0e95f3c1c https://usegalaxy.org/published/workflow?id=46f184a0e95f3c1c MGnify - EMBL, Rand Zoabi, Paul Zierep mgnify_amplicon, amplicon, metagenomics, name:microgalaxy 2025-03-13 2025-04-25 1 1 cshl_fasta_formatter, tp_find_and_replace, fastq_to_fasta_python, multiqc, fastqc, prinseq, trimmomatic, fastq_filter Sequence trimming, Read pre-processing, Sequence composition calculation, Sequence contamination filtering, Statistical calculation, Validation, Sequencing quality control Apache-2.0 True False -Nanopore Preprocessing (release v0.1) https://usegalaxy.org a8b9252fad5fe06a https://usegalaxy.org/published/workflow?id=a8b9252fad5fe06a Bérénice Batut, Engy Nasr, Paul Zierep name:collection, name:microgalaxy, name:pathogfair, name:nanopore, name:iwc 2025-03-20 2025-04-25 1 1 collection_column_join, Grep1, samtools_fastx, regexColumn1, multiqc, kraken2, fastqc, bamtools_split_mapped, nanoplot, porechop, __FILTER_FAILED_DATASETS__, krakentools_extract_kraken_reads, fastp, collapse_dataset, Cut1, Add_a_column1, minimap2 Visualisation, Sequence composition calculation, Statistical calculation, Validation, Sequence contamination filtering, Box-Whisker plot plotting, Sequence alignment analysis, Taxonomic classification, Data handling, Pairwise sequence alignment, Aggregation, Scatter plot plotting, Sequencing quality control MIT True False -Pathogen Detection PathoGFAIR Samples Aggregation and Visualisation https://usegalaxy.org 2d3063882d8239ff https://usegalaxy.org/published/workflow?id=2d3063882d8239ff Engy Nasr, Bérénice Batut, Paul Zierep name:collection, name:microgalaxy, name:pathogfair, name:iwc 2024-07-03 2024-07-03 1 1 Grouping1, regexColumn1, clustalw, __FILTER_FAILED_DATASETS__, fasta2tab, tp_sorted_uniq, fasta_merge_files_and_filter_unique_sequences, collapse_dataset, __FILTER_EMPTY_DATASETS__, bedtools_getfastabed, tp_multijoin_tool, ggplot2_heatmap, Cut1, Remove beginning1, fasttree, tp_split_on_column, collection_column_join, tp_replace_in_column, newick_display, regex1, Count1, tab2fasta Phylogenetic tree generation (from molecular sequences), Visualisation, Phylogenetic tree generation (maximum likelihood and Bayesian methods), Multiple sequence alignment, Mapping, Phylogenetic tree reconstruction, Phylogenetic tree analysis, Phylogenetic tree generation MIT False False +Copy Of GTN Training - Antibiotic Resistance Detection https://usegalaxy.eu 44e53ea319e07daa https://usegalaxy.eu/published/workflow?id=44e53ea319e07daa metagenomics, name:microgalaxy 2023-12-14 2023-12-14 0 0 unicycler, bandage_image, miniasm, staramr_search, PlasFlow, nanoplot, minimap2, racon, gfa_to_fa Pairwise sequence alignment, Aggregation, Antimicrobial resistance prediction, Box-Whisker plot plotting, De-novo assembly, Scatter plot plotting, Sequence assembly visualisation, Sequence analysis, Mapping assembly, Genome assembly False False +Identification of the micro-organisms in a beer using Nanopore sequencing https://usegalaxy.eu 0590554db9794d13 https://usegalaxy.eu/published/workflow?id=0590554db9794d13 Bérénice Batut, Teresa Müller, Polina Polunina metagenomics, name:microgalaxy 2023-12-14 2023-12-14 0 0 fastp, taxonomy_krona_chart, krakentools_kreport2krona, kraken2, fastqc, Filter1, porechop Sequencing quality control, Sequence contamination filtering, Taxonomic classification, Statistical calculation, Aggregation, Sequence composition calculation, Visualisation MIT False False +workflow-generate-dataset-for-assembly-tutorial https://usegalaxy.eu ce5c16ac23c4fbb1 https://usegalaxy.eu/published/workflow?id=ce5c16ac23c4fbb1 name:microgalaxy 2023-12-14 2023-12-14 0 0 bowtie2, bg_uniq, seqtk_subseq, fastqc, bamtools, filter_tabular, ngsutils_bam_filter, megahit, cutadapt, tp_cat, random_lines1 Statistical calculation, Formatting, Data handling, Sequence file editing, Variant calling, Primer removal, Sequencing quality control, Sequence contamination filtering, Sequence trimming, Sequence alignment analysis, Read mapping, Read pre-processing, Sequence composition calculation, Genome assembly False False +Metagenomics assembly tutorial workflow https://usegalaxy.eu 62c47e3c9d4f3aa3 https://usegalaxy.eu/published/workflow?id=62c47e3c9d4f3aa3 name:microgalaxy 2023-12-14 2023-12-14 0 0 megahit_contig2fastg, bowtie2, collection_column_join, metaspades, bandage_image, bandage_info, megahit, quast Read mapping, Sequence assembly validation, Sequence assembly visualisation, Visualisation, Genome assembly False False +"WGS Part In ""Analyses Of Metagenomics Data - The Global Picture""" https://usegalaxy.eu c2b7ec5aacfc6107 https://usegalaxy.eu/published/workflow?id=c2b7ec5aacfc6107 metagenomics, name:microgalaxy 2023-12-14 2023-12-14 0 0 metaphlan2krona, metaphlan2, humann2_renorm_table, taxonomy_krona_chart, humann2, humann2_regroup_table Visualisation False False +Taxonomic Profiling and Visualization of Metagenomic Data https://usegalaxy.eu 4f0daf8e9dd54127 https://usegalaxy.eu/published/workflow?id=4f0daf8e9dd54127 Bérénice Batut metagenomics, name:microgalaxy 2023-12-14 2023-12-14 0 0 metaphlan, taxonomy_krona_chart, krakentools_kreport2krona, est_abundance, kraken_biom, kraken2, interactive_tool_phinch, __UNZIP_COLLECTION__, interactive_tool_pavian Statistical calculation, Taxonomic classification, Aggregation, Genome annotation, Visualisation MIT False False +Amplicon Tutorial https://usegalaxy.eu 565c989730f68362 https://usegalaxy.eu/published/workflow?id=565c989730f68362 metagenomics, name:microgalaxy 2023-12-14 2023-12-14 0 0 mothur_unique_seqs, mothur_cluster_split, mothur_summary_seqs, mothur_count_seqs, mothur_make_shared, mothur_make_biom, mothur_merge_files, mothur_screen_seqs, mothur_filter_seqs, mothur_make_group, mothur_classify_seqs, mothur_classify_otu, mothur_align_seqs, mothur_pre_cluster, krona-text Taxonomic classification, DNA barcoding, Sequence read processing, Sequencing quality control, Sequence clustering, Phylogenetic analysis, Visualisation False False +Microbial Variant Calling https://usegalaxy.eu 515ef1601bc24a6c https://usegalaxy.eu/published/workflow?id=515ef1601bc24a6c variant-analysis, name:microgalaxy 2023-12-14 2023-12-14 0 0 snippy, jbrowse Genome visualisation, Phylogenetic tree visualisation, Phylogenetic tree generation, Variant calling False False +Calling variants in non-diploid systems https://usegalaxy.eu 291c36e1b18e9deb https://usegalaxy.eu/published/workflow?id=291c36e1b18e9deb variant-analysis, name:microgalaxy 2023-12-14 2023-12-14 0 0 picard_MarkDuplicates, vcffilter2, picard_MergeSamFiles, bamleftalign, fastqc, vcf2tsv, bamFilter, Cut1, bwa_mem, freebayes Statistical calculation, Formatting, Generation, Data handling, Variant calling, Sequence alignment, Genome indexing, Sequencing quality control, Sequence alignment analysis, Read mapping, Sequence composition calculation False False +Training: 16S rRNA Sequencing With Mothur: Main Tutorial https://usegalaxy.eu c67d2e75eeb4fd19 https://usegalaxy.eu/published/workflow?id=c67d2e75eeb4fd19 metagenomics, name:microgalaxy 2023-12-14 2023-12-14 0 0 mothur_count_seqs, mothur_chimera_vsearch, mothur_get_groups, mothur_screen_seqs, mothur_rarefaction_single, mothur_align_seqs, newick_display, mothur_make_shared, taxonomy_krona_chart, mothur_cluster, mothur_remove_seqs, mothur_summary_single, mothur_sub_sample, mothur_remove_groups, mothur_classify_seqs, mothur_seq_error, mothur_count_groups, mothur_cluster_split, mothur_tree_shared, mothur_summary_seqs, mothur_make_contigs, mothur_dist_shared, mothur_dist_seqs, XY_Plot_1, mothur_filter_seqs, mothur_remove_lineage, mothur_classify_otu, mothur_pre_cluster, mothur_unique_seqs, mothur_venn, mothur_heatmap_sim, mothur_make_biom, mothur_taxonomy_to_krona Taxonomic classification, DNA barcoding, Sequence read processing, Sequencing quality control, Phylogenetic tree generation, Phylogenetic tree reconstruction, Sequence clustering, Phylogenetic tree analysis, Phylogenetic analysis, Visualisation False False +Comparative gene analysis https://usegalaxy.eu 86900be4282d4b1d https://usegalaxy.eu/published/workflow?id=86900be4282d4b1d Anton Nekrutenko vgp, genome-annotation, name:microgalaxy 2023-12-14 2023-12-14 0 0 Add_a_column1, tab2fasta, tp_split_on_column, gops_intersect_1, rbc_mafft, join1, bg_diamond, cat1, collapse_dataset, rapidnj, Filter1, bg_diamond_view, Cut1, regexColumn1 Sequence alignment analysis, Phylogenetic tree generation, Multiple sequence alignment True False +Unicycler training https://usegalaxy.eu 8f3ce55d44d9f369 https://usegalaxy.eu/published/workflow?id=8f3ce55d44d9f369 assembly, name:microgalaxy 2023-12-14 2023-12-14 0 0 unicycler, multiqc, fastqc, prokka, quast Statistical calculation, Aggregation, Genome annotation, Sequence assembly validation, Sequencing quality control, Gene prediction, Validation, Coding region prediction, Sequence composition calculation, Visualisation, Genome assembly False False +Apollo Load Test https://usegalaxy.eu 3c233cc56d4df8b0 https://usegalaxy.eu/published/workflow?id=3c233cc56d4df8b0 genome-annotation, name:microgalaxy 2023-12-14 2023-12-14 0 0 create_or_update, iframe, jbrowse, create_account, list_organism Genome visualisation True False +Genome Annotation with Prokka [Feb 2020] https://usegalaxy.eu e1894c36f1ab4ab4 https://usegalaxy.eu/published/workflow?id=e1894c36f1ab4ab4 genome-annotation, name:microgalaxy 2023-12-14 2023-12-14 0 0 prokka, jbrowse Coding region prediction, Gene prediction, Genome visualisation, Genome annotation False False +Flye-AMR workflow EMC/WMDI - v3.5 (imported from URL) https://usegalaxy.eu 152223c8aed27357 https://usegalaxy.eu/published/workflow?id=152223c8aed27357 wmdi, name:microgalaxy 2023-12-14 2023-12-14 0 0 circos_wiggle_to_scatter, tp_split_on_column, bandage_image, flye, deeptools_bam_coverage, staramr_search, PlasFlow, regex1, jbrowse, tp_cat, tp_head_tool, ncbi_blastn_wrapper, medaka_consensus_pipeline, gff2bed1, circos, tbl2gff3, join1, trimmomatic, tp_text_file_with_recurring_lines, prokka, nanoplot, bg_column_arrange_by_header, fasta2tab, Add_a_column1, tp_cut_tool, minimap2, Grep1, tab2fasta, fasta_compute_length, tp_sort_header_tool, circos_interval_to_tile, tp_easyjoin_tool, regex_replace, circos_gc_skew, Filter1, Cut1 Base-calling, Pairwise sequence alignment, Sequence visualisation, De-novo assembly, Variant calling, Scatter plot plotting, Genome annotation, Sequence assembly, Gene prediction, Genome visualisation, Mapping assembly, Coding region prediction, Cross-assembly, Antimicrobial resistance prediction, Box-Whisker plot plotting, Sequence assembly visualisation, Sequence analysis, Genome assembly True False +Mtb phylogeny https://usegalaxy.eu 875b3ca170ac12a1 https://usegalaxy.eu/published/workflow?id=875b3ca170ac12a1 evolution, name:microgalaxy 2023-12-14 2023-12-14 0 0 interactive_tool_rstudio, raxml Phylogenetic tree analysis, Sequence analysis False False +From VCFs to SNP distance matrix https://usegalaxy.eu 6d333ed886aab471 https://usegalaxy.eu/published/workflow?id=6d333ed886aab471 evolution, name:microgalaxy 2023-12-14 2023-12-14 0 0 snp_dists, bcftools_consensus, tb_variant_filter, snp_sites, tp_cat True False +From Fastqs to VCFs and BAMs https://usegalaxy.eu 3a8fde248a4d0383 https://usegalaxy.eu/published/workflow?id=3a8fde248a4d0383 evolution, name:microgalaxy 2023-12-14 2023-12-14 0 0 snippy, __MERGE_COLLECTION__, tb_variant_filter, trimmomatic Phylogenetic tree visualisation, Phylogenetic tree generation, Variant calling True False +From BAMs to drug resistance prediction with TB-profiler https://usegalaxy.eu d0d6dae0d1eecc21 https://usegalaxy.eu/published/workflow?id=d0d6dae0d1eecc21 evolution, name:microgalaxy 2023-12-14 2023-12-14 0 0 addName, samtools_view, tp_grep_tool, tp_sed_tool, tp_replace_in_line, __MERGE_COLLECTION__, tp_cat, tb_profiler_profile Antimicrobial resistance prediction True False +M. tuberculosis Variant Analysis tutorial https://usegalaxy.eu 3ff4dbcc7a602e6b https://usegalaxy.eu/published/workflow?id=3ff4dbcc7a602e6b Peter van Heusden variant-analysis, prokaryote, name:microgalaxy 2023-12-14 2023-12-14 0 0 multiqc, kraken2, trimmomatic, fastqc, snippy, jbrowse, tb_variant_filter, tb_profiler_profile, tbvcfreport Statistical calculation, Taxonomic classification, Antimicrobial resistance prediction, Variant calling, Phylogenetic tree visualisation, Sequencing quality control, Phylogenetic tree generation, Validation, Genome visualisation, Sequence composition calculation MIT False False +Compute Allel Frequency Table from paired reads https://usegalaxy.eu 21a39ac4c1becb31 https://usegalaxy.eu/published/workflow?id=21a39ac4c1becb31 name:microgalaxy, hpylori 2023-12-13 2023-12-13 2 2 bowtie2, tp_awk_tool, bcftools_view, bcftools_norm, vcf2tsv, snpSift_filter, freebayes Read mapping, Statistical calculation, Variant calling True False +Reference genome choice (indels, coverage, depth) for short reads https://usegalaxy.eu 61fe08fb3d5e83f8 https://usegalaxy.eu/published/workflow?id=61fe08fb3d5e83f8 name:microgalaxy, hpylori 2023-10-27 2023-12-13 13 13 bowtie2, collection_element_identifiers, samtools_depth, bcftools_norm, vcf2tsv, collapse_dataset, samtools_coverage, tp_cat, freebayes Read mapping, Statistical calculation, Variant calling True False +MGnify amplicon rRNA-prediction + ITS https://usegalaxy.eu 437704898229dfb6 https://usegalaxy.eu/published/workflow?id=437704898229dfb6 mgnify_amplicon_showcase, name:microgalaxy 2023-12-12 2023-12-13 1 1 bedtools_maskfastabed, tp_awk_tool, mapseq, biom_convert, taxonomy_krona_chart, cmsearch_deoverlap, infernal_cmsearch, bedtools_getfastabed, gops_concat_1, query_tabular k-mer counting, Formatting, Mapping, Comparison, Alignment, Nucleic acid feature detection, Visualisation False False +MGnify amplicon QC https://usegalaxy.eu 8f415b0c409f56f7 https://usegalaxy.eu/published/workflow?id=8f415b0c409f56f7 mgnify_amplicon_showcase, name:microgalaxy 2023-12-13 2023-12-13 1 1 fastq_dump, fastp, tp_find_and_replace, iuc_pear, multiqc, trimmomatic, fastqc, __UNZIP_COLLECTION__, cshl_fasta_formatter, prinseq, fastq_to_fasta_python Statistical calculation, Sequence merging, Data handling, Sequencing quality control, Sequence contamination filtering, Sequence trimming, Validation, Read pre-processing, Sequence composition calculation False False + Cloud-Aerosole MT-MG Functional Profiling https://usegalaxy.eu 4566262dd0acc8ab https://usegalaxy.eu/published/workflow?id=4566262dd0acc8ab metagenomics, metatranscriptomics, name:microgalaxy 2021-11-10 2023-12-07 2 2 bowtie2, featurecounts, multiqc Sequencing quality control, Validation, Read summarisation, Read mapping, RNA-Seq quantification False False +Cloud-Aerosole MT-MG Reference Gene Catalog Building https://usegalaxy.eu 9b9e1e28f3683f92 https://usegalaxy.eu/published/workflow?id=9b9e1e28f3683f92 metagenomics, metatranscriptomics, name:microgalaxy 2021-11-01 2023-12-07 72 72 bowtie2, multiqc, bg_diamond_makedb, cd_hit, bedtools_getfastabed, fastqc, cat1, bg_diamond, eggnog_mapper, megahit, dbbuilder, kofamscan, metagene_annotator, translate_nucleotides, metaeuk_easy_predict, quast Statistical calculation, Gene functional annotation, Sequence annotation, Genome annotation, Mapping, Sequencing quality control, Sequence alignment analysis, Fold recognition, Homology-based gene prediction, Sequence composition calculation, Query and retrieval, Sequence assembly validation, Validation, Information extraction, Sequence analysis, Read mapping, Sequence clustering, Visualisation, Genome assembly False False +Cloud-Aerosole MT-MG Pre-Processing https://usegalaxy.eu bb604ff5e010e7ab https://usegalaxy.eu/published/workflow?id=bb604ff5e010e7ab metagenomics, metatranscriptomics, name:microgalaxy 2021-11-01 2023-12-07 51 51 fastqc, multiqc, trimmomatic Sequencing quality control, Statistical calculation, Validation, Sequence composition calculation False False +Cloud Aerosol MT-MG Contamination Filtering https://usegalaxy.eu bdc7cfaac0db2eab https://usegalaxy.eu/published/workflow?id=bdc7cfaac0db2eab metagenomics, metatranscriptomics, name:microgalaxy 2022-06-29 2023-12-07 28 28 bowtie2, recentrifuge, fastq_to_tabular, kraken2, filter_tabular, seq_filter_by_id Taxonomic classification, Expression analysis, Read mapping, Cross-assembly False False +Cloud-Aerosole MT-MG Taxonomic Profiling https://usegalaxy.eu e69b555faa6bb962 https://usegalaxy.eu/published/workflow?id=e69b555faa6bb962 metagenomics, metatranscriptomics, name:microgalaxy 2022-09-03 2023-12-07 18 18 recentrifuge, kraken_biom, kraken2, interactive_tool_phinch, maaslin2 Statistical calculation, Taxonomic classification, Standardisation and normalisation, Expression analysis, Genome annotation, Filtering, Visualisation, Cross-assembly False False +MetaP https://usegalaxy.eu 96d198ed953449fd https://usegalaxy.eu/published/workflow?id=96d198ed953449fd name:microgalaxy 2020-01-30 2023-03-16 2 2 maxquant Statistical calculation, Imputation, Heat map generation, Standardisation and normalisation, Protein quantification, Clustering, Principal component plotting, Visualisation False False +MetaG_extended https://usegalaxy.eu 6158c3b5fc12044e https://usegalaxy.eu/published/workflow?id=6158c3b5fc12044e name:microgalaxy 2023-02-10 2023-03-16 22 22 coverm_genome, fasplit, tp_awk_tool, tp_grep_tool, sort1, cat_bins, trim_galore, fastqc, checkm_lineage_wf, interproscan, coverm_contig, hmmer_hmmscan, kofamscan, tp_cat, maxbin2, quast, fraggenescan Statistical calculation, Formatting, Gene functional annotation, Visualisation, Format validation, Conversion, Probabilistic sequence generation, Sequencing quality control, Sequence assembly, Protein feature detection, Gene prediction, Sequence motif recognition, Coding region prediction, Sequence composition calculation, Sequence generation, Database search, Sequence database search, Data retrieval, Taxonomic classification, Multiple sequence alignment, Sequence assembly validation, Sequence trimming, Sequence profile generation, Validation, Sequence analysis, Read pre-processing, Primer removal, Local alignment False False +MetaT https://usegalaxy.eu 385cc7df70d7916b https://usegalaxy.eu/published/workflow?id=385cc7df70d7916b name:microgalaxy 2020-01-27 2023-02-27 16 16 kallisto_quant, collection_column_join, trim_galore, fastqc, bg_sortmerna, __UNZIP_COLLECTION__ Statistical calculation, Sequence similarity search, Sequencing quality control, Gene expression profiling, Sequence trimming, Sequence alignment analysis, Sequence comparison, Read pre-processing, Primer removal, Sequence composition calculation False False +Quality control of bins generated by MetaBAT2, MaxBin2, SemiBin, and CONCOCT https://usegalaxy.fr f0776f7a890b523a https://usegalaxy.fr/published/workflow?id=f0776f7a890b523a Bérénice Batut microbiome, name:microgalaxy 2025-12-08 2025-12-08 1 1 __RELABEL_FROM_FILE__, checkm2, collection_element_identifiers, multiqc, __FLATTEN__, __MERGE_COLLECTION__, regex1 Statistical calculation, Sequencing quality control, Validation, Sequence composition calculation, Sequence assembly validation MIT True False +Quality control of bins generated by MetaBAT2, MaxBin2, SemiBin, and CONCOCT https://usegalaxy.org a8aee61c2cbaf6ea https://usegalaxy.org/published/workflow?id=a8aee61c2cbaf6ea Bérénice Batut microbiome, name:microgalaxy 2025-12-08 2025-12-08 1 1 __RELABEL_FROM_FILE__, checkm2, collection_element_identifiers, multiqc, __FLATTEN__, __MERGE_COLLECTION__, regex1 Statistical calculation, Sequencing quality control, Validation, Sequence composition calculation, Sequence assembly validation MIT True False +Copy of Taxonomy Profiling and Visualization with Krona shared by user engy.nasr https://usegalaxy.org 3011f5dbf884c9bc https://usegalaxy.org/published/workflow?id=3011f5dbf884c9bc Engy Nasr, Bérénice Batut, Paul Zierep name:collection, name:microgalaxy, name:pathogfair, name:iwc 2025-04-12 2025-05-23 0 0 krakentools_kreport2krona, kraken2, taxonomy_krona_chart Taxonomic classification, Aggregation, Visualisation MIT False False +Gene-based Pathogen Identification (release v0.1) https://usegalaxy.org 3f252e077e0bcce5 https://usegalaxy.org/published/workflow?id=3f252e077e0bcce5 Engy Nasr, Bérénice Batut, Paul Zierep name:collection, name:pathogfair, name:iwc, name:microgalaxy 2024-09-19 2025-04-25 1 1 abricate, collection_element_identifiers, bandage_image, flye, tp_find_and_replace, split_file_to_collection, compose_text_param, __BUILD_LIST__, tab2fasta, medaka_consensus_pipeline, param_value_from_file, fasta2tab Base-calling, Antimicrobial resistance prediction, De-novo assembly, Variant calling, Sequence assembly visualisation, Sequence assembly, Cross-assembly, Mapping assembly, Genome assembly MIT False False +Pathogen Detection PathoGFAIR Samples Aggregation and Visualisation (release v0.1) https://usegalaxy.org 3ef08553982f6ffc https://usegalaxy.org/published/workflow?id=3ef08553982f6ffc Engy Nasr, Bérénice Batut, Paul Zierep name:collection, name:microgalaxy, name:pathogfair, name:iwc 2024-09-19 2025-04-25 1 1 tp_split_on_column, ggplot2_heatmap, bedtools_getfastabed, collapse_dataset, regex1, tp_replace_in_column, fasta_merge_files_and_filter_unique_sequences, newick_display, regexColumn1, tp_multijoin_tool, Count1, __FILTER_EMPTY_DATASETS__, fasta2tab, tp_sorted_uniq, Grouping1, fasttree, tab2fasta, Remove beginning1, collection_column_join, clustalw, __FILTER_FAILED_DATASETS__, Cut1 Phylogenetic tree generation, Visualisation, Multiple sequence alignment, Phylogenetic tree reconstruction, Phylogenetic tree analysis, Mapping MIT False False +Taxonomy Profiling and Visualization with Kron (release v0.1) https://usegalaxy.org 4b5f6b5d4f36e38b https://usegalaxy.org/published/workflow?id=4b5f6b5d4f36e38b Engy Nasr, Bérénice Batut, Paul Zierep name:collection, name:microgalaxy, name:pathogfair, name:iwc 2024-09-19 2025-04-25 1 1 krakentools_kreport2krona, kraken2, taxonomy_krona_chart Taxonomic classification, Aggregation, Visualisation MIT False False +Allele-based Pathogen Identification (release v0.1.2) https://usegalaxy.org 6d778eeb176d563c https://usegalaxy.org/published/workflow?id=6d778eeb176d563c Engy Nasr, Bérénice Batut, Paul Zierep name:collection, name:microgalaxy, name:pathogfair, name:iwc 2024-10-31 2025-04-25 1 1 tp_cut_tool, clair3, table_compute, samtools_depth, bcftools_consensus, CONVERTER_gz_to_uncompressed, Paste1, bcftools_norm, Cut1, snpSift_extractFields, samtools_coverage, snpSift_filter, collapse_dataset, minimap2, Count1, tp_head_tool, Remove beginning1, regexColumn1 Pairwise sequence alignment, Variant calling MIT False False +Allele-based Pathogen Identification (release v0.1.1) https://usegalaxy.org 29ba77708cdafe0f https://usegalaxy.org/published/workflow?id=29ba77708cdafe0f Engy Nasr, Bérénice Batut, Paul Zierep name:collection, name:microgalaxy, name:pathogfair, name:iwc 2024-11-28 2025-04-25 1 1 tp_cut_tool, clair3, table_compute, samtools_depth, bcftools_consensus, CONVERTER_gz_to_uncompressed, Paste1, bcftools_norm, Cut1, snpSift_extractFields, samtools_coverage, snpSift_filter, collapse_dataset, minimap2, Count1, tp_head_tool, Remove beginning1, regexColumn1 Pairwise sequence alignment, Variant calling MIT False False +MGnify's amplicon pipeline v5.0 (release v0.1) https://usegalaxy.org 8e863bbef37cc36b https://usegalaxy.org/published/workflow?id=8e863bbef37cc36b EMBL's European Bioinformatics Institute, Rand Zoabi, Paul Zierep mgnify_amplicon, metagenomics, amplicon, name:microgalaxy 2025-02-06 2025-04-25 1 1 tp_awk_tool, CONVERTER_uncompressed_to_gz, CONVERTER_gz_to_uncompressed, __MERGE_COLLECTION__, fastq_dl Apache-2.0 True False +MGnify's amplicon pipeline v5.0 - ITS (release v0.1) https://usegalaxy.org 45f959d5bf505b15 https://usegalaxy.org/published/workflow?id=45f959d5bf505b15 EMBL's European Bioinformatics Institute, Rand Zoabi, Paul Zierep mgnify_amplicon, amplicon, metagenomics, name:microgalaxy 2025-02-06 2025-04-25 1 1 bedtools_maskfastabed, mapseq, tp_awk_tool, __FILTER_FROM_FILE__, collection_element_identifiers, taxonomy_krona_chart, biom_convert, __FILTER_EMPTY_DATASETS__ k-mer counting, Formatting, Visualisation, Mapping Apache-2.0 True False +MGnify's amplicon pipeline v5.0 - Quality control PE (release v0.1) https://usegalaxy.org a71fcbc60caae8b6 https://usegalaxy.org/published/workflow?id=a71fcbc60caae8b6 EMBL's European Bioinformatics Institute, Rand Zoabi, Paul Zierep mgnify_amplicon, amplicon, metagenomics, name:microgalaxy 2025-02-06 2025-04-25 1 1 fastp, cshl_fasta_formatter, tp_find_and_replace, multiqc, trimmomatic, fastqc, __UNZIP_COLLECTION__, mgnify_seqprep, fastq_filter, prinseq, fastq_to_fasta_python Statistical calculation, Sequencing quality control, Sequence contamination filtering, Sequence trimming, Validation, Nucleic acid design, Read pre-processing, Sequence composition calculation Apache-2.0 True False +MGnify's amplicon pipeline v5.0 - Quality control SE (release v0.1) https://usegalaxy.org 5f878c4cc3bff68c https://usegalaxy.org/published/workflow?id=5f878c4cc3bff68c MGnify - EMBL, Rand Zoabi, Paul Zierep mgnify_amplicon, amplicon, metagenomics, name:microgalaxy 2025-02-06 2025-04-25 1 1 cshl_fasta_formatter, tp_find_and_replace, multiqc, trimmomatic, fastqc, fastq_filter, prinseq, fastq_to_fasta_python Sequencing quality control, Statistical calculation, Sequence contamination filtering, Sequence trimming, Validation, Read pre-processing, Sequence composition calculation Apache-2.0 True False +Allele-based Pathogen Identification (release v0.1.3) https://usegalaxy.org 3e703abaeb870f6f https://usegalaxy.org/published/workflow?id=3e703abaeb870f6f Engy Nasr, Bérénice Batut, Paul Zierep name:collection, name:microgalaxy, name:pathogfair, name:iwc 2025-03-06 2025-04-25 1 1 tp_cut_tool, clair3, table_compute, samtools_depth, bcftools_consensus, CONVERTER_gz_to_uncompressed, Paste1, bcftools_norm, Cut1, snpSift_extractFields, samtools_coverage, snpSift_filter, collapse_dataset, minimap2, Count1, tp_head_tool, Remove beginning1, regexColumn1 Pairwise sequence alignment, Variant calling MIT True False +MGnify's amplicon pipeline v5.0 - Quality control SE (release v0.2) https://usegalaxy.org afb67b4b9952f57d https://usegalaxy.org/published/workflow?id=afb67b4b9952f57d MGnify - EMBL, Rand Zoabi, Paul Zierep mgnify_amplicon, amplicon, metagenomics, name:microgalaxy 2025-03-06 2025-04-25 1 1 cshl_fasta_formatter, tp_find_and_replace, multiqc, trimmomatic, fastqc, fastq_filter, prinseq, fastq_to_fasta_python Sequencing quality control, Statistical calculation, Sequence contamination filtering, Sequence trimming, Validation, Read pre-processing, Sequence composition calculation Apache-2.0 True False +Allele-based Pathogen Identification (release v0.1.4) https://usegalaxy.org cb810cdaa4915f4b https://usegalaxy.org/published/workflow?id=cb810cdaa4915f4b Engy Nasr, Bérénice Batut, Paul Zierep name:collection, name:microgalaxy, name:pathogfair, name:iwc 2025-03-13 2025-04-25 1 1 tp_cut_tool, clair3, table_compute, samtools_depth, bcftools_consensus, CONVERTER_gz_to_uncompressed, Paste1, bcftools_norm, Cut1, snpSift_extractFields, samtools_coverage, snpSift_filter, collapse_dataset, minimap2, Count1, tp_head_tool, Remove beginning1, regexColumn1 Pairwise sequence alignment, Variant calling MIT True False +MGnify's amplicon pipeline v5.0 (release v0.2) https://usegalaxy.org 77de7101effbff3d https://usegalaxy.org/published/workflow?id=77de7101effbff3d EMBL's European Bioinformatics Institute, Rand Zoabi, Paul Zierep mgnify_amplicon, metagenomics, amplicon, name:microgalaxy 2025-03-13 2025-04-25 1 1 tp_awk_tool, CONVERTER_uncompressed_to_gz, CONVERTER_gz_to_uncompressed, __MERGE_COLLECTION__, fastq_dl Apache-2.0 True False +MGnify's amplicon pipeline v5.0 - ITS (release v0.2) https://usegalaxy.org 8151be18aab3a3c6 https://usegalaxy.org/published/workflow?id=8151be18aab3a3c6 EMBL's European Bioinformatics Institute, Rand Zoabi, Paul Zierep mgnify_amplicon, amplicon, metagenomics, name:microgalaxy 2025-03-13 2025-04-25 1 1 bedtools_maskfastabed, mapseq, tp_awk_tool, __FILTER_FROM_FILE__, collection_element_identifiers, taxonomy_krona_chart, biom_convert, __FILTER_EMPTY_DATASETS__ k-mer counting, Formatting, Visualisation, Mapping Apache-2.0 True False +MGnify's amplicon pipeline v5.0 - Quality control PE (release v0.2) https://usegalaxy.org 20b7ae4b517a80fd https://usegalaxy.org/published/workflow?id=20b7ae4b517a80fd EMBL's European Bioinformatics Institute, Rand Zoabi, Paul Zierep mgnify_amplicon, amplicon, metagenomics, name:microgalaxy 2025-03-13 2025-04-25 1 1 fastp, cshl_fasta_formatter, tp_find_and_replace, multiqc, trimmomatic, fastqc, __UNZIP_COLLECTION__, mgnify_seqprep, fastq_filter, prinseq, fastq_to_fasta_python Statistical calculation, Sequencing quality control, Sequence contamination filtering, Sequence trimming, Validation, Nucleic acid design, Read pre-processing, Sequence composition calculation Apache-2.0 True False +MGnify's amplicon pipeline v5.0 - Quality control SE (release v0.3) https://usegalaxy.org 46f184a0e95f3c1c https://usegalaxy.org/published/workflow?id=46f184a0e95f3c1c MGnify - EMBL, Rand Zoabi, Paul Zierep mgnify_amplicon, amplicon, metagenomics, name:microgalaxy 2025-03-13 2025-04-25 1 1 cshl_fasta_formatter, tp_find_and_replace, multiqc, trimmomatic, fastqc, fastq_filter, prinseq, fastq_to_fasta_python Sequencing quality control, Statistical calculation, Sequence contamination filtering, Sequence trimming, Validation, Read pre-processing, Sequence composition calculation Apache-2.0 True False +Nanopore Preprocessing (release v0.1) https://usegalaxy.org a8b9252fad5fe06a https://usegalaxy.org/published/workflow?id=a8b9252fad5fe06a Bérénice Batut, Engy Nasr, Paul Zierep name:collection, name:microgalaxy, name:pathogfair, name:nanopore, name:iwc 2025-03-20 2025-04-25 1 1 Add_a_column1, fastp, collection_column_join, multiqc, kraken2, samtools_fastx, fastqc, collapse_dataset, nanoplot, minimap2, Grep1, __FILTER_FAILED_DATASETS__, bamtools_split_mapped, porechop, Cut1, regexColumn1, krakentools_extract_kraken_reads Statistical calculation, Taxonomic classification, Pairwise sequence alignment, Box-Whisker plot plotting, Aggregation, Data handling, Scatter plot plotting, Sequencing quality control, Sequence contamination filtering, Sequence alignment analysis, Validation, Sequence composition calculation, Visualisation MIT True False +Pathogen Detection PathoGFAIR Samples Aggregation and Visualisation https://usegalaxy.org 2d3063882d8239ff https://usegalaxy.org/published/workflow?id=2d3063882d8239ff Engy Nasr, Bérénice Batut, Paul Zierep name:collection, name:microgalaxy, name:pathogfair, name:iwc 2024-07-03 2024-07-03 1 1 tp_split_on_column, ggplot2_heatmap, bedtools_getfastabed, collapse_dataset, regex1, tp_replace_in_column, fasta_merge_files_and_filter_unique_sequences, newick_display, regexColumn1, tp_multijoin_tool, Count1, __FILTER_EMPTY_DATASETS__, fasta2tab, tp_sorted_uniq, Grouping1, fasttree, tab2fasta, Remove beginning1, collection_column_join, clustalw, __FILTER_FAILED_DATASETS__, Cut1 Phylogenetic tree generation, Visualisation, Multiple sequence alignment, Phylogenetic tree reconstruction, Phylogenetic tree analysis, Mapping MIT False False PathoGFAIR (imported from uploaded file) https://usegalaxy.org e55593af91337a05 https://usegalaxy.org/published/workflow?id=e55593af91337a05 Engy Nasr, Bérénice Batut, Paul Zierep name:microgalaxy, name:iwc, name:pathogfair, name:nanopore, name:collection 2024-07-03 2024-07-03 0 0 MIT False False -Taxonomy Profiling and Visualization with Krona https://usegalaxy.org 8f5904693b5f74f4 https://usegalaxy.org/published/workflow?id=8f5904693b5f74f4 Engy Nasr, Bérénice Batut, Paul Zierep name:collection, name:microgalaxy, name:pathogfair, name:iwc 2024-06-25 2024-06-25 1 1 kraken2, taxonomy_krona_chart, krakentools_kreport2krona Visualisation, Taxonomic classification, Aggregation MIT False False -Gene-based Pathogen Identification https://usegalaxy.org cce88bc57b180d09 https://usegalaxy.org/published/workflow?id=cce88bc57b180d09 Engy Nasr, Bérénice Batut, Paul Zierep name:collection, name:pathogfair, name:iwc, name:microgalaxy 2024-06-25 2024-06-25 1 1 medaka_consensus_pipeline, param_value_from_file, compose_text_param, __BUILD_LIST__, tp_find_and_replace, abricate, collection_element_identifiers, bandage_image, split_file_to_collection, flye, fasta2tab, tab2fasta Antimicrobial resistance prediction, Base-calling, Variant calling, Cross-assembly, Mapping assembly, Sequence assembly, Genome assembly, Sequence assembly visualisation, De-novo assembly MIT False False -Allele-based Pathogen Identification https://usegalaxy.org 38911ba6f66d80f6 https://usegalaxy.org/published/workflow?id=38911ba6f66d80f6 Engy Nasr, Bérénice Batut, Paul Zierep name:collection, name:microgalaxy, name:pathogfair, name:iwc 2024-06-25 2024-06-25 1 1 bcftools_consensus, Paste1, samtools_coverage, regexColumn1, bcftools_norm, CONVERTER_gz_to_uncompressed, snpSift_filter, tp_cut_tool, Cut1, snpSift_extractFields, clair3, collapse_dataset, Remove beginning1, table_compute, tp_head_tool, Count1, samtools_depth, minimap2 Pairwise sequence alignment, Variant calling MIT False False -Nanopore Preprocessing https://usegalaxy.org 574e42683dc3961b https://usegalaxy.org/published/workflow?id=574e42683dc3961b Bérénice Batut, Engy Nasr, Paul Zierep name:collection, name:microgalaxy, name:pathogfair, name:nanopore, name:iwc 2024-06-25 2024-06-25 1 1 collection_column_join, Grep1, samtools_fastx, regexColumn1, multiqc, kraken2, fastqc, bamtools_split_mapped, nanoplot, porechop, __FILTER_FAILED_DATASETS__, krakentools_extract_kraken_reads, fastp, collapse_dataset, Cut1, Add_a_column1, minimap2 Visualisation, Sequence composition calculation, Statistical calculation, Validation, Sequence contamination filtering, Box-Whisker plot plotting, Sequence alignment analysis, Taxonomic classification, Data handling, Pairwise sequence alignment, Aggregation, Scatter plot plotting, Sequencing quality control MIT False False -Quality control of bins generated by MetaBAT2, MaxBin2, SemiBin, and CONCOCT https://usegalaxy.org.au f05ed1e5c5dfffa9 https://usegalaxy.org.au/published/workflow?id=f05ed1e5c5dfffa9 Bérénice Batut microbiome, name:microgalaxy 2025-12-08 2025-12-08 1 1 multiqc, __FLATTEN__, collection_element_identifiers, __RELABEL_FROM_FILE__, __MERGE_COLLECTION__, regex1, checkm2 Sequence composition calculation, Sequence assembly validation, Statistical calculation, Validation, Sequencing quality control MIT True False -Gene-based Pathogen Identification (release v0.1) https://usegalaxy.org.au 084bb76cf47d7060 https://usegalaxy.org.au/published/workflow?id=084bb76cf47d7060 Engy Nasr, Bérénice Batut, Paul Zierep name:collection, name:pathogfair, name:iwc, name:microgalaxy 2024-09-19 2025-04-25 1 1 medaka_consensus_pipeline, param_value_from_file, compose_text_param, __BUILD_LIST__, tp_find_and_replace, abricate, collection_element_identifiers, bandage_image, split_file_to_collection, flye, fasta2tab, tab2fasta Antimicrobial resistance prediction, Base-calling, Variant calling, Cross-assembly, Mapping assembly, Sequence assembly, Genome assembly, Sequence assembly visualisation, De-novo assembly MIT False False -Nanopore Preprocessing (release v0.1) https://usegalaxy.org.au 69d91340fc7effa2 https://usegalaxy.org.au/published/workflow?id=69d91340fc7effa2 Bérénice Batut, Engy Nasr, Paul Zierep name:collection, name:microgalaxy, name:pathogfair, name:nanopore, name:iwc 2024-09-19 2025-04-25 1 1 collection_column_join, Grep1, samtools_fastx, regexColumn1, multiqc, kraken2, fastqc, bamtools_split_mapped, nanoplot, porechop, __FILTER_FAILED_DATASETS__, krakentools_extract_kraken_reads, fastp, collapse_dataset, Cut1, Add_a_column1, minimap2 Visualisation, Sequence composition calculation, Statistical calculation, Validation, Sequence contamination filtering, Box-Whisker plot plotting, Sequence alignment analysis, Taxonomic classification, Data handling, Pairwise sequence alignment, Aggregation, Scatter plot plotting, Sequencing quality control MIT False False -Pathogen Detection PathoGFAIR Samples Aggregation and Visualisation (release v0.1) https://usegalaxy.org.au b60922a253df6654 https://usegalaxy.org.au/published/workflow?id=b60922a253df6654 Engy Nasr, Bérénice Batut, Paul Zierep name:collection, name:microgalaxy, name:pathogfair, name:iwc 2024-09-19 2025-04-25 1 1 Grouping1, regexColumn1, clustalw, __FILTER_FAILED_DATASETS__, fasta2tab, tp_sorted_uniq, fasta_merge_files_and_filter_unique_sequences, collapse_dataset, __FILTER_EMPTY_DATASETS__, bedtools_getfastabed, tp_multijoin_tool, ggplot2_heatmap, Cut1, Remove beginning1, fasttree, tp_split_on_column, collection_column_join, tp_replace_in_column, newick_display, regex1, Count1, tab2fasta Phylogenetic tree generation (from molecular sequences), Visualisation, Phylogenetic tree generation (maximum likelihood and Bayesian methods), Multiple sequence alignment, Mapping, Phylogenetic tree reconstruction, Phylogenetic tree analysis, Phylogenetic tree generation MIT False False -Taxonomy Profiling and Visualization with Kron (release v0.1) https://usegalaxy.org.au 131636a795bac485 https://usegalaxy.org.au/published/workflow?id=131636a795bac485 Engy Nasr, Bérénice Batut, Paul Zierep name:collection, name:microgalaxy, name:pathogfair, name:iwc 2024-09-19 2025-04-25 1 1 kraken2, taxonomy_krona_chart, krakentools_kreport2krona Visualisation, Taxonomic classification, Aggregation MIT False False -Allele-based Pathogen Identification (release v0.1.2) https://usegalaxy.org.au 857e482acfcb2dba https://usegalaxy.org.au/published/workflow?id=857e482acfcb2dba Engy Nasr, Bérénice Batut, Paul Zierep name:collection, name:microgalaxy, name:pathogfair, name:iwc 2024-10-31 2025-04-25 1 1 bcftools_consensus, Paste1, samtools_coverage, regexColumn1, bcftools_norm, CONVERTER_gz_to_uncompressed, snpSift_filter, tp_cut_tool, Cut1, snpSift_extractFields, clair3, collapse_dataset, Remove beginning1, table_compute, tp_head_tool, Count1, samtools_depth, minimap2 Pairwise sequence alignment, Variant calling MIT False False -Allele-based Pathogen Identification (release v0.1.3) https://usegalaxy.org.au 0e11619979c2830c https://usegalaxy.org.au/published/workflow?id=0e11619979c2830c Engy Nasr, Bérénice Batut, Paul Zierep name:collection, name:microgalaxy, name:pathogfair, name:iwc 2025-03-06 2025-04-25 1 1 bcftools_consensus, Paste1, samtools_coverage, regexColumn1, bcftools_norm, CONVERTER_gz_to_uncompressed, snpSift_filter, tp_cut_tool, Cut1, snpSift_extractFields, clair3, collapse_dataset, Remove beginning1, table_compute, tp_head_tool, Count1, samtools_depth, minimap2 Pairwise sequence alignment, Variant calling MIT True False -Allele-based Pathogen Identification (release v0.1.4) https://usegalaxy.org.au 76a0a3af8de11622 https://usegalaxy.org.au/published/workflow?id=76a0a3af8de11622 Engy Nasr, Bérénice Batut, Paul Zierep name:collection, name:microgalaxy, name:pathogfair, name:iwc 2025-03-13 2025-04-25 1 1 bcftools_consensus, Paste1, samtools_coverage, regexColumn1, bcftools_norm, CONVERTER_gz_to_uncompressed, snpSift_filter, tp_cut_tool, Cut1, snpSift_extractFields, clair3, collapse_dataset, Remove beginning1, table_compute, tp_head_tool, Count1, samtools_depth, minimap2 Pairwise sequence alignment, Variant calling MIT True False +Taxonomy Profiling and Visualization with Krona https://usegalaxy.org 8f5904693b5f74f4 https://usegalaxy.org/published/workflow?id=8f5904693b5f74f4 Engy Nasr, Bérénice Batut, Paul Zierep name:collection, name:microgalaxy, name:pathogfair, name:iwc 2024-06-25 2024-06-25 1 1 krakentools_kreport2krona, kraken2, taxonomy_krona_chart Taxonomic classification, Aggregation, Visualisation MIT False False +Gene-based Pathogen Identification https://usegalaxy.org cce88bc57b180d09 https://usegalaxy.org/published/workflow?id=cce88bc57b180d09 Engy Nasr, Bérénice Batut, Paul Zierep name:collection, name:pathogfair, name:iwc, name:microgalaxy 2024-06-25 2024-06-25 1 1 abricate, collection_element_identifiers, bandage_image, flye, tp_find_and_replace, split_file_to_collection, compose_text_param, __BUILD_LIST__, tab2fasta, medaka_consensus_pipeline, param_value_from_file, fasta2tab Base-calling, Antimicrobial resistance prediction, De-novo assembly, Variant calling, Sequence assembly visualisation, Sequence assembly, Cross-assembly, Mapping assembly, Genome assembly MIT False False +Allele-based Pathogen Identification https://usegalaxy.org 38911ba6f66d80f6 https://usegalaxy.org/published/workflow?id=38911ba6f66d80f6 Engy Nasr, Bérénice Batut, Paul Zierep name:collection, name:microgalaxy, name:pathogfair, name:iwc 2024-06-25 2024-06-25 1 1 tp_cut_tool, clair3, table_compute, samtools_depth, bcftools_consensus, CONVERTER_gz_to_uncompressed, Paste1, bcftools_norm, Cut1, snpSift_extractFields, samtools_coverage, snpSift_filter, collapse_dataset, minimap2, Count1, tp_head_tool, Remove beginning1, regexColumn1 Pairwise sequence alignment, Variant calling MIT False False +Nanopore Preprocessing https://usegalaxy.org 574e42683dc3961b https://usegalaxy.org/published/workflow?id=574e42683dc3961b Bérénice Batut, Engy Nasr, Paul Zierep name:collection, name:microgalaxy, name:pathogfair, name:nanopore, name:iwc 2024-06-25 2024-06-25 1 1 Add_a_column1, fastp, collection_column_join, multiqc, kraken2, samtools_fastx, fastqc, collapse_dataset, nanoplot, minimap2, Grep1, __FILTER_FAILED_DATASETS__, bamtools_split_mapped, porechop, Cut1, regexColumn1, krakentools_extract_kraken_reads Statistical calculation, Taxonomic classification, Pairwise sequence alignment, Box-Whisker plot plotting, Aggregation, Data handling, Scatter plot plotting, Sequencing quality control, Sequence contamination filtering, Sequence alignment analysis, Validation, Sequence composition calculation, Visualisation MIT False False +Quality control of bins generated by MetaBAT2, MaxBin2, SemiBin, and CONCOCT https://usegalaxy.org.au f05ed1e5c5dfffa9 https://usegalaxy.org.au/published/workflow?id=f05ed1e5c5dfffa9 Bérénice Batut microbiome, name:microgalaxy 2025-12-08 2025-12-08 1 1 __RELABEL_FROM_FILE__, checkm2, collection_element_identifiers, multiqc, __FLATTEN__, __MERGE_COLLECTION__, regex1 Statistical calculation, Sequencing quality control, Validation, Sequence composition calculation, Sequence assembly 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https://workflowhub.eu/workflows/2046?version=1, https://workflowhub.eu/workflows/2047?version=1, https://workflowhub.eu/workflows/2048?version=1, https://workflowhub.eu/workflows/221?version=3, https://workflowhub.eu/workflows/225?version=1, https://workflowhub.eu/workflows/406?version=1, https://workflowhub.eu/workflows/52?version=1, https://workflowhub.eu/workflows/605?version=2, https://workflowhub.eu/workflows/612?version=26, https://workflowhub.eu/workflows/641?version=33, https://workflowhub.eu/workflows/642?version=25, https://workflowhub.eu/workflows/750?version=4, https://workflowhub.eu/workflows/788?version=1, https://workflowhub.eu/workflows/789?version=1 - assembly/ERGA-post-assembly-QC, assembly/assembly-with-preprocessing, assembly/chloroplast-assembly, assembly/debruijn-graph-assembly, assembly/largegenome, assembly/metagenomics-assembly, assembly/mrsa-illumina, assembly/mrsa-nanopore, microbiome/metagenomics-assembly, microbiome/pathogen-detection-from-nanopore-foodborne-data, microbiome/plasmid-metagenomics-nanopore True False @@ -1693,11 +1651,13 @@ Genetics, Evolutionary biology, Statistics and probability, DNA polymorphism iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/bayescan - https://github.com/galaxyproject/tools-iuc/tree/main/tools/bayescan + https://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan bayescan BayeScan BAYEsian genome SCAN for outliers, aims at identifying candidate loci under natural selection from genetic data, using differences in allele frequencies between populations. 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BiG-SCAPE does this by rapidly calculating a distance matrix between gene clusters based on a comparison of their protein domain content, order, copy number and sequence identity.It defines a distance metric between Gene Clusters using a combination of three indices (Jaccard Index of domain types, Domain Sequence Similarity the Adjacency...BiG-SCAPE and CORASON provide a set of tools to explore the diversity of biosynthetic gene clusters (BGCs) across large numbers of genomes, by constructing BGC sequence similarity networks, grouping BGCs into gene cluster families, and exploring gene cluster diversity linked to enzyme phylogenies. + + 0 0 1 @@ -1878,8 +1834,6 @@ 0 0 0 - 0 - 0 95 95 2449 @@ -1900,8 +1854,6 @@ 2449 95 95 - - True False @@ -1913,10 +1865,10 @@ Binning refinement tool 2025-01-14 https://github.com/genotoul-bioinfo/Binette - 1.2.1 + @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ binette 1.2.1 - Up-to-date + To update Metagenomics Read binning Read binning @@ -1924,11 +1876,13 @@ Metagenomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/binette - https://github.com/galaxyproject/tools-iuc/tree/main/tools/binette + https://github.com/galaxyproject/tools-iuc/tree/master/tools/binette binette Binette Binette is a fast and accurate binning refinement tool to constructs high quality MAGs from the output of multiple binning tools. + https://usegalaxy.eu/published/workflow?id=00f15824c7a9b196, https://usegalaxy.eu/published/workflow?id=7ecd92cb382d8168, https://usegalaxy.eu/published/workflow?id=ce5c9287a67e6085, https://usegalaxy.org/published/workflow?id=7251c6e0dad8f927, https://workflowhub.eu/workflows/1352?version=4, https://workflowhub.eu/workflows/2028?version=1, https://workflowhub.eu/workflows/2100?version=2 + microbiome/metagenomics-binning 1 1 1 @@ -1939,7 +1893,6 @@ 0 0 0 - 0 1 0 0 @@ -1952,7 +1905,6 @@ 0 0 0 - 0 1 1 0 @@ -1977,8 +1929,6 @@ 425 20 20 - https://usegalaxy.eu/published/workflow?id=00f15824c7a9b196, https://usegalaxy.eu/published/workflow?id=7ecd92cb382d8168, https://usegalaxy.eu/published/workflow?id=ce5c9287a67e6085, https://usegalaxy.org/published/workflow?id=7251c6e0dad8f927, https://workflowhub.eu/workflows/1352?version=4, https://workflowhub.eu/workflows/2028?version=1, https://workflowhub.eu/workflows/2100?version=2 - microbiome/metagenomics-binning True False @@ -2001,11 +1951,13 @@ Metagenomics, Sequence assembly, Microbial ecology iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/binning_refiner - https://github.com/galaxyproject/tools-iuc/tree/main/tools/binning_refiner + https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner binning_refiner Binning_refiner Improving genome bins through the combination of different binning programs + + 0 0 1 @@ -2016,7 +1968,6 @@ 0 0 0 - 0 1 0 0 @@ -2030,7 +1981,6 @@ 0 0 0 - 0 1 0 0 @@ -2054,8 +2004,6 @@ 236 64 64 - - True False @@ -2078,11 +2026,13 @@ Whole genome sequencing, DNA polymorphism, Genotype and phenotype, Infectious disease, Agricultural science iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/hansel - https://github.com/galaxyproject/tools-iuc/tree/main/tools/hansel + https://github.com/galaxyproject/tools-iuc/tree/master/tools/hansel Biohansel BioHansel BioHansel is a tool for performing high-resolution genotyping of bacterial isolates by identifying phylogenetically informative single nucleotide polymorphisms (SNPs), also known as canonical SNPs, in whole genome sequencing (WGS) data. The application uses a fast k-mer matching algorithm to map pathogen WGS data to canonical SNPs contained in hierarchically structured schemas and assigns genotypes based on the detected SNP profile. + + 1 0 1 @@ -2105,8 +2055,6 @@ 0 0 0 - 0 - 0 1 1 1 @@ -2131,8 +2079,6 @@ 850 102 93 - - True False @@ -2160,6 +2106,8 @@ + + 0 0 0 @@ -2206,10 +2154,6 @@ 0 0 0 - 0 - 0 - - True False @@ -2232,11 +2176,13 @@ Laboratory information management, Sequence analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/biom_format - https://github.com/galaxyproject/tools-iuc/tree/main/tools/biom_format + https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format biomformat biomformat This package includes basic tools for reading biom-format files, accessing and subsetting data tables from a biom object, as well as limited support for writing a biom-object back to a biom-format file. 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genome-annotation/comparison-braker-helixer-annotation, genome-annotation/funannotate, genome-annotation/helixer True False @@ -2848,11 +2776,13 @@ Metagenomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/cami_amber - https://github.com/galaxyproject/tools-iuc/tree/main/tools/cami_amber + https://github.com/galaxyproject/tools-iuc/tree/master/tools/cami_amber cami-amber AMBER AMBER is an evaluation package for the comparative assessment of genome reconstructions and taxonomic assignments from metagenome benchmark datasets. It provides performance metrics, results rankings, and comparative visualizations for assessing multiple programs or parameter effects. The provided metrics were used in the first community benchmarking challenge of the initiative for the Critical Assessment of Metagenomic Interpretation. + https://usegalaxy.eu/published/workflow?id=00f15824c7a9b196, https://usegalaxy.eu/published/workflow?id=17d2e76147fc940c, https://usegalaxy.eu/published/workflow?id=43098b8afe78b071, https://usegalaxy.eu/published/workflow?id=ce5c9287a67e6085, https://usegalaxy.eu/published/workflow?id=e4dabaf57668dbd1, https://workflowhub.eu/workflows/2100?version=2 + 4 4 4 @@ -2876,8 +2806,6 @@ 0 0 0 - 0 - 0 3 0 0 @@ -2901,8 +2829,6 @@ 10522 8 8 - https://usegalaxy.eu/published/workflow?id=00f15824c7a9b196, https://usegalaxy.eu/published/workflow?id=17d2e76147fc940c, https://usegalaxy.eu/published/workflow?id=43098b8afe78b071, https://usegalaxy.eu/published/workflow?id=ce5c9287a67e6085, https://usegalaxy.eu/published/workflow?id=e4dabaf57668dbd1, https://workflowhub.eu/workflows/2100?version=2 - True False @@ -2914,10 +2840,10 @@ Canu is a hierarchical assembly pipeline designed for high-noise single-molecule sequencing (such as the PacBio RS II/Sequel or Oxford Nanopore MinION). 2018-06-07 https://github.com/marbl/canu - 2.3 + @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ canu 2.3 - Up-to-date + To update Assembly De-novo assembly De-novo assembly @@ -2930,6 +2856,8 @@ CANU De-novo assembly tool for long read chemistry like Nanopore data and PacBio data. + https://usegalaxy.eu/published/workflow?id=93d7a5704ec1d82d, https://usegalaxy.org.au/published/workflow?id=344b2ad2604939bc + 0 1 1 @@ -2938,7 +2866,6 @@ 0 0 0 - 0 1 0 1 @@ -2954,7 +2881,6 @@ 0 0 0 - 0 1 1 0 @@ -2978,8 +2904,6 @@ 17992 2365 2135 - https://usegalaxy.eu/published/workflow?id=93d7a5704ec1d82d - True False @@ -3002,7 +2926,9 @@ iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/cawlign - https://github.com/galaxyproject/tools-iuc/tree/main/tools/cawlign + https://github.com/galaxyproject/tools-iuc/tree/master/tools/cawlign + + @@ -3019,7 +2945,6 @@ 0 0 0 - 0 1 0 0 @@ -3031,7 +2956,6 @@ 0 0 0 - 0 1 0 0 @@ -3055,8 +2979,6 @@ 0 0 0 - - True False @@ -3079,11 +3001,13 @@ Sequencing iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/cdhit - https://github.com/galaxyproject/tools-iuc/tree/main/tools/cdhit + https://github.com/galaxyproject/tools-iuc/tree/master/tools/cdhit cd-hit cd-hit Cluster a nucleotide dataset into representative sequences. + https://usegalaxy.eu/published/workflow?id=2ee0eb74e839b476, https://usegalaxy.eu/published/workflow?id=974cc681d07ec788, https://usegalaxy.eu/published/workflow?id=9b9e1e28f3683f92, https://usegalaxy.eu/published/workflow?id=bebcbd6f0ffa55c5 + 0 0 1 @@ -3092,7 +3016,6 @@ 0 0 0 - 0 1 0 1 @@ -3107,7 +3030,6 @@ 0 0 0 - 0 1 1 1 @@ -3132,8 +3054,6 @@ 21326 958 958 - https://usegalaxy.eu/published/workflow?id=2ee0eb74e839b476, https://usegalaxy.eu/published/workflow?id=974cc681d07ec788, https://usegalaxy.eu/published/workflow?id=9b9e1e28f3683f92, https://usegalaxy.eu/published/workflow?id=bebcbd6f0ffa55c5 - True False @@ -3156,11 +3076,13 @@ devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/cd_hit_dup - https://github.com/galaxyproject/tools-devteam/tree/main/tools/cd_hit_dup + https://github.com/galaxyproject/tools-devteam/tree/master/tools/cd_hit_dup + https://usegalaxy.org/published/workflow?id=35c2626849348f2c + 1 0 0 @@ -3171,7 +3093,6 @@ 0 0 0 - 0 1 0 0 @@ -3192,7 +3113,6 @@ 0 0 0 - 0 501 770 7542 @@ -3209,8 +3129,6 @@ 7542 770 501 - https://usegalaxy.org/published/workflow?id=35c2626849348f2c - True False @@ -3233,11 +3151,13 @@ Transcriptomics, Microarray experiment iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/cemitool - https://github.com/galaxyproject/tools-iuc/tree/main/tools/cemitool + https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool cemitool CEMiTool It unifies the discovery and the analysis of coexpression gene modules in a fully automatic manner, while providing a user-friendly html report with high quality graphs. Our tool evaluates if modules contain genes that are over-represented by specific pathways or that are altered in a specific sample group. Additionally, CEMiTool is able to integrate transcriptomic data with interactome information, identifying the potential hubs on each network. + + 1 1 1 @@ -3261,8 +3181,6 @@ 0 0 0 - 0 - 0 1 0 0 @@ -3286,8 +3204,6 @@ 1092 138 138 - - True False @@ -3310,11 +3226,13 @@ Phylogenomics, Phylogenetics, Taxonomy, Metagenomics, Data quality management iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/checkm - https://github.com/galaxyproject/tools-iuc/tree/main/tools/checkm + https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm checkm CheckM CheckM provides a set of tools for assessing the quality of genomes recovered from isolates, single cells, or metagenomes. + https://usegalaxy.eu/published/workflow?id=0563f58718be932d, https://usegalaxy.eu/published/workflow?id=1e5f1d9a51032e44, https://usegalaxy.eu/published/workflow?id=3eaa913306c16146, https://usegalaxy.eu/published/workflow?id=5b940b283d91d99d, https://usegalaxy.eu/published/workflow?id=6158c3b5fc12044e, https://usegalaxy.eu/published/workflow?id=6416cfdbd5273063, https://usegalaxy.eu/published/workflow?id=667bac8d7453e5f1, https://usegalaxy.eu/published/workflow?id=8c91345ed468e22d, https://usegalaxy.eu/published/workflow?id=8deb08d4f228e198, https://usegalaxy.eu/published/workflow?id=97312d273b6e8bd9, https://usegalaxy.eu/published/workflow?id=d57d41e306241396, https://usegalaxy.org.au/published/workflow?id=2120112358db8e01, https://usegalaxy.org.au/published/workflow?id=41331c03339e2b19, https://usegalaxy.org.au/published/workflow?id=92fcdd490831c6c5, https://usegalaxy.org/published/workflow?id=7251c6e0dad8f927, https://usegalaxy.org/published/workflow?id=80565301ada0d3eb, https://workflowhub.eu/workflows/1352?version=4 + microbiome/mags-building, microbiome/metagenomics-binning 10 10 10 @@ -3325,7 +3243,6 @@ 0 0 0 - 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genome-annotation/bacterial-genome-quality-control True False @@ -3453,9 +3365,9 @@ Assess quality of single-contig viral genomes 2024-09-13 https://bitbucket.org/berkeleylab/checkv/ - 1.0.3 + @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ checkv - 1.1.0 + 1.1.1 To update Metagenomics Sequence assembly, Validation, Read mapping @@ -3464,11 +3376,13 @@ Metagenomics, Sequence assembly, Metagenomic sequencing, Mapping ufz https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/checkv/ - https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/checkv + https://github.com/Helmholtz-UFZ/galaxy-tools/tree/master/tools/checkv checkv CheckV CheckV is a fully automated command-line pipeline for assessing the quality of single-contig viral genomes, including identification of host contamination for integrated proviruses, estimating completeness for genome fragments, and identification of closed genomes. + https://usegalaxy.eu/published/workflow?id=36de05d50c703164, https://usegalaxy.eu/published/workflow?id=62392daea25a3980, https://usegalaxy.eu/published/workflow?id=87231a6a7938cb95, https://usegalaxy.eu/published/workflow?id=c62d65832377e376 + 1 0 1 @@ -3495,8 +3409,6 @@ 0 0 0 - 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0 1 0 0 @@ -3573,7 +3484,6 @@ 0 0 0 - 0 6 6 10 @@ -3594,8 +3504,6 @@ 10 6 6 - https://usegalaxy.eu/published/workflow?id=4eb9dfe91fc2dc67, https://usegalaxy.eu/published/workflow?id=93d7a5704ec1d82d, https://usegalaxy.eu/published/workflow?id=ece3ffe0800e6880 - True False @@ -3618,11 +3526,13 @@ iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign - https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign + https://github.com/galaxyproject/tools-iuc/tree/master/tools/cialign + https://usegalaxy.eu/published/workflow?id=93d7a5704ec1d82d + 0 0 1 @@ -3633,7 +3543,6 @@ 0 0 0 - 0 1 0 0 @@ -3650,7 +3559,6 @@ 0 0 0 - 0 3 3 6 @@ -3671,8 +3579,6 @@ 6 3 3 - https://usegalaxy.eu/published/workflow?id=93d7a5704ec1d82d - True False @@ -3684,9 +3590,9 @@ Symphonizing pileup and full-alignment for high-performance long-read variant calling 2022-06-15 https://github.com/HKU-BAL/Clair3 - 1.0.10 + @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ clair3 - 2.0.1 + 2.0.2 To update Sequence Analysis, Variant Analysis Variant calling @@ -3695,11 +3601,13 @@ Molecular genetics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/clair3 - https://github.com/galaxyproject/tools-iuc/tree/main/tools/clair3 + https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 clair3 Clair3 Clair3 is a germline small variant caller for long-reads. Clair3 makes the best of two major method categories: pileup calling handles most variant candidates with speed, and full-alignment tackles complicated candidates to maximize precision and recall. Clair3 runs fast and has superior performance, especially at lower coverage. Clair3 is simple and modular for easy deployment and integration. + https://usegalaxy.eu/published/workflow?id=09c7069ae409c362, https://usegalaxy.eu/published/workflow?id=3f0b104a74acf869, https://usegalaxy.eu/published/workflow?id=60e0b2a28a900178, https://usegalaxy.eu/published/workflow?id=64abcddeb516a712, https://usegalaxy.eu/published/workflow?id=6aa2891bd2b41f32, https://usegalaxy.eu/published/workflow?id=cb54883452a73019, https://usegalaxy.eu/published/workflow?id=cdf2f02428f5f83f, https://usegalaxy.eu/published/workflow?id=d215a2e554fd83bc, https://usegalaxy.org.au/published/workflow?id=0e11619979c2830c, https://usegalaxy.org.au/published/workflow?id=244ea5e94237ebad, https://usegalaxy.org.au/published/workflow?id=76a0a3af8de11622, https://usegalaxy.org.au/published/workflow?id=857e482acfcb2dba, https://usegalaxy.org/published/workflow?id=29ba77708cdafe0f, https://usegalaxy.org/published/workflow?id=38911ba6f66d80f6, https://usegalaxy.org/published/workflow?id=3e703abaeb870f6f, https://usegalaxy.org/published/workflow?id=6d778eeb176d563c, https://usegalaxy.org/published/workflow?id=cb810cdaa4915f4b, https://workflowhub.eu/workflows/1063?version=5, https://workflowhub.eu/workflows/1479?version=1 + microbiome/pathogen-detection-from-nanopore-foodborne-data 1 1 1 @@ -3710,7 +3618,6 @@ 0 0 0 - 0 1 0 0 @@ -3723,7 +3630,6 @@ 0 0 0 - 0 1 1 0 @@ -3748,8 +3654,6 @@ 7427 395 395 - https://usegalaxy.eu/published/workflow?id=09c7069ae409c362, https://usegalaxy.eu/published/workflow?id=3f0b104a74acf869, https://usegalaxy.eu/published/workflow?id=60e0b2a28a900178, https://usegalaxy.eu/published/workflow?id=64abcddeb516a712, https://usegalaxy.eu/published/workflow?id=6aa2891bd2b41f32, https://usegalaxy.eu/published/workflow?id=cb54883452a73019, https://usegalaxy.eu/published/workflow?id=cdf2f02428f5f83f, https://usegalaxy.eu/published/workflow?id=d215a2e554fd83bc, https://usegalaxy.org.au/published/workflow?id=0e11619979c2830c, https://usegalaxy.org.au/published/workflow?id=244ea5e94237ebad, https://usegalaxy.org.au/published/workflow?id=76a0a3af8de11622, https://usegalaxy.org.au/published/workflow?id=857e482acfcb2dba, https://usegalaxy.org/published/workflow?id=29ba77708cdafe0f, https://usegalaxy.org/published/workflow?id=38911ba6f66d80f6, https://usegalaxy.org/published/workflow?id=3e703abaeb870f6f, https://usegalaxy.org/published/workflow?id=6d778eeb176d563c, https://usegalaxy.org/published/workflow?id=cb810cdaa4915f4b, https://workflowhub.eu/workflows/1063?version=5, https://workflowhub.eu/workflows/1479?version=1 - microbiome/pathogen-detection-from-nanopore-foodborne-data True False @@ -3777,6 +3681,8 @@ clinod The command line NoD predictor (clinod) can be run from the command line to predict Nucleolar localization sequences (NoLSs) that are short targeting sequences responsible for the localization of proteins to the nucleolus.The predictor accepts a list of FASTA formatted sequences as an input and outputs the NOLS predictions as a result.Please note that currently, JPred secondary structure predictions are not supported by clinod. However, we are working on it. + + 1 0 0 @@ -3807,8 +3713,6 @@ 0 0 0 - 0 - 0 31 31 585 @@ -3825,8 +3729,6 @@ 585 31 31 - - True False @@ -3849,11 +3751,13 @@ Phylogeny, Sequence analysis devteam https://github.com/galaxyproject/tools-iuc/tree/main/tools/clustalw - https://github.com/galaxyproject/tools-iuc/tree/main/tools/clustalw + https://github.com/galaxyproject/tools-iuc/tree/master/tools/clustalw clustal2 Clustal 2 (Clustal W, Clustal X) Multiple sequence alignment program with a command-line interface (Clustal W) and a graphical user interface (Clustal X). The display colours allow conserved features to be highlighted for easy viewing in the alignment. It is available for several platforms, including Windows, Macintosh PowerMac, Linux and Solaris.Names occassionally spelled also as Clustal W2, ClustalW2, ClustalW, ClustalX, Clustal2. + https://usegalaxy.eu/published/workflow?id=36de05d50c703164, https://usegalaxy.eu/published/workflow?id=376119528377a3ae, https://usegalaxy.eu/published/workflow?id=3e0246389fb70340, https://usegalaxy.eu/published/workflow?id=974cc681d07ec788, https://usegalaxy.eu/published/workflow?id=c8bc4af6dd3b5d02, https://usegalaxy.eu/published/workflow?id=f6a763951d815944, https://usegalaxy.org.au/published/workflow?id=b60922a253df6654, https://usegalaxy.org.au/published/workflow?id=eda40b58616a0fe4, https://usegalaxy.org/published/workflow?id=042758b8a8c5ac80, https://usegalaxy.org/published/workflow?id=07f7198b63108131, https://usegalaxy.org/published/workflow?id=18e7a954c0b6e4bc, https://usegalaxy.org/published/workflow?id=2d3063882d8239ff, https://usegalaxy.org/published/workflow?id=3d7baebefa7c9b81, https://usegalaxy.org/published/workflow?id=3ef08553982f6ffc, https://usegalaxy.org/published/workflow?id=603e5c61c57bcf3f, https://usegalaxy.org/published/workflow?id=6a1eb7e7bececba1, https://usegalaxy.org/published/workflow?id=75c2cf36253194c2, https://usegalaxy.org/published/workflow?id=7b68f97bf88f99b9, https://usegalaxy.org/published/workflow?id=87685c6247521b54, https://usegalaxy.org/published/workflow?id=8b7e03f09b0183d9, https://usegalaxy.org/published/workflow?id=a484a1e1a7335696, https://usegalaxy.org/published/workflow?id=b2fb90873471f4e7, https://usegalaxy.org/published/workflow?id=be9bd7286d38c210, https://usegalaxy.org/published/workflow?id=f7bf58d66cafcf1f, https://workflowhub.eu/workflows/1060?version=1, https://workflowhub.eu/workflows/1487?version=2, https://workflowhub.eu/workflows/1541?version=1, https://workflowhub.eu/workflows/1656?version=1, https://workflowhub.eu/workflows/358?version=1 + ecology/phylogeny-data-prep, genome-annotation/hpc-for-lsgc, microbiome/pathogen-detection-from-nanopore-foodborne-data 1 1 1 @@ -3862,7 +3766,6 @@ 0 0 0 - 0 1 1 1 @@ -3877,7 +3780,6 @@ 0 0 0 - 0 1 1 1 @@ -3902,8 +3804,6 @@ 180847 11778 7113 - https://usegalaxy.eu/published/workflow?id=36de05d50c703164, https://usegalaxy.eu/published/workflow?id=376119528377a3ae, https://usegalaxy.eu/published/workflow?id=3e0246389fb70340, https://usegalaxy.eu/published/workflow?id=974cc681d07ec788, https://usegalaxy.eu/published/workflow?id=c8bc4af6dd3b5d02, https://usegalaxy.eu/published/workflow?id=f6a763951d815944, https://usegalaxy.org.au/published/workflow?id=b60922a253df6654, https://usegalaxy.org.au/published/workflow?id=eda40b58616a0fe4, https://usegalaxy.org/published/workflow?id=042758b8a8c5ac80, https://usegalaxy.org/published/workflow?id=07f7198b63108131, https://usegalaxy.org/published/workflow?id=18e7a954c0b6e4bc, https://usegalaxy.org/published/workflow?id=2d3063882d8239ff, https://usegalaxy.org/published/workflow?id=3d7baebefa7c9b81, https://usegalaxy.org/published/workflow?id=3ef08553982f6ffc, https://usegalaxy.org/published/workflow?id=603e5c61c57bcf3f, https://usegalaxy.org/published/workflow?id=6a1eb7e7bececba1, https://usegalaxy.org/published/workflow?id=75c2cf36253194c2, https://usegalaxy.org/published/workflow?id=7b68f97bf88f99b9, https://usegalaxy.org/published/workflow?id=87685c6247521b54, https://usegalaxy.org/published/workflow?id=8b7e03f09b0183d9, https://usegalaxy.org/published/workflow?id=a484a1e1a7335696, https://usegalaxy.org/published/workflow?id=b2fb90873471f4e7, https://usegalaxy.org/published/workflow?id=be9bd7286d38c210, https://workflowhub.eu/workflows/1060?version=1, https://workflowhub.eu/workflows/1487?version=2, https://workflowhub.eu/workflows/1541?version=1, https://workflowhub.eu/workflows/1656?version=1, https://workflowhub.eu/workflows/358?version=1 - ecology/phylogeny-data-prep, genome-annotation/hpc-for-lsgc, microbiome/pathogen-detection-from-nanopore-foodborne-data True False @@ -3926,11 +3826,13 @@ Phylogenetics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/codeml - https://github.com/galaxyproject/tools-iuc/tree/main/tools/codeml + https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml paml PAML Package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood. + + 0 0 1 @@ -3953,8 +3855,6 @@ 0 0 0 - 0 - 0 1 1 1 @@ -3979,8 +3879,6 @@ 62891 84 72 - - True False @@ -4003,11 +3901,13 @@ Genetic variation iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/cojac - https://github.com/galaxyproject/tools-iuc/tree/main/tools/cojac + https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac cojac COJAC CoOccurrence adJusted Analysis and Calling - The cojac package comprises a set of command-line tools to analyse co-occurrence of mutations on amplicons. It is useful, for example, for early detection of viral variants of concern (e.g. Alpha, Delta, Omicron) in environmental samples, and has been designed to scan for multiple SARS-CoV-2 variants in wastewater samples, as analyzed jointly by ETH Zurich, EPFL and Eawag. + https://usegalaxy.eu/published/workflow?id=d88145e7475e0b7b + 2 0 3 @@ -4031,8 +3931,6 @@ 0 0 0 - 0 - 0 3 0 0 @@ -4056,8 +3954,6 @@ 2783 20 20 - https://usegalaxy.eu/published/workflow?id=d88145e7475e0b7b - True False @@ -4085,6 +3981,8 @@ Combine Metaphlan and HUMAnN This tool combine MetaPhlAn outputs and HUMANnN outputs + https://usegalaxy.eu/published/workflow?id=69eddfde874af35b, https://usegalaxy.eu/published/workflow?id=9472be79da012999, https://usegalaxy.fr/published/workflow?id=c4f6062e51d0f45e, https://workflowhub.eu/workflows/1466?version=2 + microbiome/metatranscriptomics 1 0 1 @@ -4107,8 +4005,6 @@ 0 0 0 - 0 - 0 1 1 0 @@ -4133,8 +4029,6 @@ 2125 155 155 - https://usegalaxy.eu/published/workflow?id=69eddfde874af35b, https://usegalaxy.eu/published/workflow?id=9472be79da012999, https://usegalaxy.fr/published/workflow?id=c4f6062e51d0f45e, https://workflowhub.eu/workflows/1466?version=2 - microbiome/metatranscriptomics True False @@ -4157,7 +4051,9 @@ iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/comebin - https://github.com/galaxyproject/tools-iuc/tree/main/tools/comebin + https://github.com/galaxyproject/tools-iuc/tree/master/tools/comebin + + @@ -4172,7 +4068,6 @@ 0 0 0 - 0 1 0 0 @@ -4189,7 +4084,6 @@ 0 0 0 - 0 1 1 2 @@ -4210,8 +4104,6 @@ 2 1 1 - - True False @@ -4234,7 +4126,9 @@ iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/comebin_bam/ - https://github.com/galaxyproject/tools-iuc/tree/main/tools/comebin_bam + https://github.com/galaxyproject/tools-iuc/tree/master/tools/comebin_bam + + @@ -4249,7 +4143,6 @@ 0 0 0 - 0 1 0 0 @@ -4286,9 +4179,6 @@ 0 0 0 - 0 - - True False @@ -4316,8 +4206,8 @@ Compare HUMAnN2 outputs This tool compare HUMANnN2 outputs with gene families or pathways and their relative abundances between several samples - 0 - 0 + + 0 0 0 @@ -4364,8 +4254,6 @@ 248 32 23 - - True False @@ -4379,7 +4267,7 @@ https://github.com/huangnengCSU/compleasm 0.2.6 compleasm - 0.2.7 + 0.2.8 To update Sequence Analysis Sequence assembly validation @@ -4388,11 +4276,13 @@ Sequence assembly, Transcriptomics, Sequence analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/compleasm - https://github.com/galaxyproject/tools-iuc/tree/main/tools/compleasm + https://github.com/galaxyproject/tools-iuc/tree/master/tools/compleasm compleasm Compleasm Compleasm: a faster and more accurate reimplementation of BUSCO.It provides measures for quantitative assessment of genome assembly, gene set, and transcriptome completeness based on evolutionarily informed expectations of gene content from near-universal single-copy orthologs. + 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computational framework that simplifies the reconstruction, analysis, and visualization of phylogenetic trees and multiple sequence alignments. Here, we present ETE v3, featuring numerous improvements in the underlying library of methods, and providing a novel set of standalone tools to perform common tasks in comparative genomics and phylogenetics. The new features include (i) building gene-based and supermatrix-based phylogenies using a single command, (ii) testing and visualizing evolutionary models, (iii) calculating distances between trees of different size or including duplications, and (iv) providing seamless integration with the NCBI taxonomy database. ETE is freely available at http://etetoolkit.org + + 0 0 7 @@ -6110,8 +5956,6 @@ 0 0 0 - 0 - 0 7 7 0 @@ -6135,8 +5979,6 @@ 292 41 32 - - True False @@ -6148,7 +5990,7 @@ A toolkit for the analysis and visualization of trees. 2024-11-25 http://etetoolkit.org - 3.1.3 + @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ curl To update @@ -6159,11 +6001,13 @@ Phylogenetics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/ete-toolkit - https://github.com/galaxyproject/tools-iuc/tree/main/tools/ete-toolkit + https://github.com/galaxyproject/tools-iuc/tree/master/tools/ete-toolkit ete ete The Environment for Tree Exploration (ETE) is a computational framework that simplifies the reconstruction, analysis, and visualization of phylogenetic trees and multiple sequence alignments. Here, we present ETE v3, featuring numerous improvements in the underlying library of methods, and providing a novel set of standalone tools to perform common tasks in comparative genomics and phylogenetics. The new features include (i) building gene-based and supermatrix-based phylogenies using a single command, (ii) testing and visualizing evolutionary models, (iii) calculating distances between trees of different size or including duplications, and (iv) providing seamless integration with the NCBI taxonomy database. 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Any non-numeric columns will be filtered out. Your first column may contains row names, but it will also work if your first column already corresponds to the numeric values of a variable. - 0 + + 0 0 0 @@ -6519,9 +6354,6 @@ 0 0 0 - 0 - - True False @@ -6544,11 +6376,13 @@ Metagenomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/fairy - https://github.com/galaxyproject/tools-iuc/tree/main/tools/fairy + https://github.com/galaxyproject/tools-iuc/tree/master/tools/fairy fairy fairy fast approximate contig coverage for metagenomic binningFairy computes multi-sample contig coverage for metagenome-assembled genome (MAG) binning.Fairy is used after metagenomic assembly and before binning. 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assembly/mrsa-illumina, ecology/ENA_Biodiv_submission, epigenetics/cut_and_run, epigenetics/methylation-seq, galaxy-interface/workflow-automation, galaxy-interface/workflow-fairification, sequence-analysis/quality-contamination-control, single-cell/scatac-preprocessing-tenx, transcriptomics/mirna-target-finder, transcriptomics/ref-based, variant-analysis/exome-seq, variant-analysis/somatic-variant-discovery, variant-analysis/somatic-variants True False @@ -6698,11 +6526,13 @@ Metagenomics, Microbiology, Public health and epidemiology iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/fargene - https://github.com/galaxyproject/tools-iuc/tree/main/tools/fargene + https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene fargene fARGene fARGene (Fragmented Antibiotic Resistance Gene iENntifiEr ) is a tool that takes either fragmented metagenomic data or longer sequences as input and predicts and delivers full-length antiobiotic resistance genes as output. + + 1 0 1 @@ -6713,7 +6543,6 @@ 0 0 0 - 0 1 0 0 @@ -6726,7 +6555,6 @@ 0 0 0 - 0 1 1 1 @@ -6751,8 +6579,6 @@ 2100 448 414 - - True False @@ -6775,11 +6601,13 @@ Microbiology, Genetic variation iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastani - https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastani + https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastani fastani FastANI FastANI is developed for fast alignment-free computation of whole-genome Average Nucleotide Identity (ANI). 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Main functions are to create a DIAMOND database from the GTDB taxonomy data or create a NCBI taxdump format out of this data. This tool can also create a mapping between the taxonomy classification between GTDB and NCBI. + https://usegalaxy.eu/published/workflow?id=cf0159c14418525e, https://usegalaxy.eu/published/workflow?id=e4dabaf57668dbd1, https://workflowhub.eu/workflows/2099?version=2 + 1 1 1 @@ -9344,8 +9106,6 @@ 0 0 0 - 0 - 0 1 0 0 @@ -9369,8 +9129,6 @@ 1127 27 27 - https://usegalaxy.eu/published/workflow?id=cf0159c14418525e, https://usegalaxy.eu/published/workflow?id=e4dabaf57668dbd1, https://workflowhub.eu/workflows/2099?version=1 - True False @@ -9393,11 +9151,13 @@ Metagenomics, Taxonomy, Phylogenetics, Database management, Proteins iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/gtdbtk - https://github.com/galaxyproject/tools-iuc/tree/main/tools/gtdbtk + https://github.com/galaxyproject/tools-iuc/tree/master/tools/gtdbtk GTDB-Tk GTDB-Tk a toolkit to classify genomes with the Genome Taxonomy Database.GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.GTDB-Tk is a software toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes based on the Genome Database Taxonomy GTDB. It is designed to work with recent advances that allow hundreds or thousands of metagenome-assembled genomes (MAGs) to be obtained directly from environmental samples. It can also be applied to isolate and single-cell genomes. The GTDB-Tk is open source and released under the GNU General Public License (Version 3). + https://usegalaxy.eu/published/workflow?id=0563f58718be932d, https://usegalaxy.eu/published/workflow?id=17d2e76147fc940c, https://usegalaxy.eu/published/workflow?id=1e5f1d9a51032e44, https://usegalaxy.eu/published/workflow?id=2c992e509aa5dd9d, https://usegalaxy.eu/published/workflow?id=7ecd92cb382d8168, https://usegalaxy.eu/published/workflow?id=c62d65832377e376, https://usegalaxy.eu/published/workflow?id=e4dabaf57668dbd1, https://usegalaxy.org/published/workflow?id=33d90e718ce500ef, https://usegalaxy.org/published/workflow?id=84233173d92fa506, https://usegalaxy.org/published/workflow?id=8d229c0f58a07ebe, https://usegalaxy.org/published/workflow?id=9b589bc76208fb1e, https://workflowhub.eu/workflows/1352?version=4, https://workflowhub.eu/workflows/2099?version=2 + 1 1 1 @@ -9408,7 +9168,6 @@ 0 0 0 - 0 1 0 0 @@ -9422,7 +9181,6 @@ 0 0 0 - 0 1 1 0 @@ -9446,8 +9204,6 @@ 8082 959 959 - https://usegalaxy.eu/published/workflow?id=0563f58718be932d, https://usegalaxy.eu/published/workflow?id=17d2e76147fc940c, https://usegalaxy.eu/published/workflow?id=1e5f1d9a51032e44, https://usegalaxy.eu/published/workflow?id=2c992e509aa5dd9d, https://usegalaxy.eu/published/workflow?id=7ecd92cb382d8168, https://usegalaxy.eu/published/workflow?id=c62d65832377e376, https://usegalaxy.eu/published/workflow?id=e4dabaf57668dbd1, https://usegalaxy.org/published/workflow?id=33d90e718ce500ef, https://usegalaxy.org/published/workflow?id=8d229c0f58a07ebe, https://usegalaxy.org/published/workflow?id=9b589bc76208fb1e, https://workflowhub.eu/workflows/1352?version=4, https://workflowhub.eu/workflows/2099?version=1 - True False @@ -9459,7 +9215,7 @@ Gubbins - bacterial recombination detection 2017-06-22 - 3.2.1 + @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ gubbins 3.4.3 To update @@ -9470,11 +9226,13 @@ Phylogeny, Genotype and phenotype, Whole genome sequencing iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/gubbins - https://github.com/galaxyproject/tools-iuc/tree/main/tools/gubbins + https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins gubbins Gubbins Gubbins is a tool for rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences. + + 1 1 1 @@ -9485,7 +9243,6 @@ 0 0 0 - 0 1 0 0 @@ -9498,7 +9255,6 @@ 0 0 0 - 0 1 1 1 @@ -9523,8 +9279,6 @@ 10555 1033 920 - - True False @@ -9536,7 +9290,7 @@ A wrapper for the guppy basecaller tool from Oxford Nanopore Technologies 2020-11-18 http://artbio.fr - 6.5.7+galaxy0 + 6.5.7 To update @@ -9547,13 +9301,13 @@ artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/guppy - https://github.com/ARTbio/tools-artbio/tree/main/tools/guppy + https://github.com/ARTbio/tools-artbio/tree/master/tools/guppy + + - 0 - 0 0 0 0 @@ -9600,8 +9354,6 @@ 7 1 1 - - True False @@ -9613,10 +9365,10 @@ Hierarchical All-against-All association 2025-11-05 https://github.com/biobakery/halla - 0.8.40 + @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ halla 0.8.40 - Up-to-date + To update Metagenomics Statistical calculation, Gene expression profiling, Essential dynamics Statistical calculation, Gene expression profiling, Essential dynamics @@ -9624,11 +9376,13 @@ Microbial ecology, Microarray experiment, Metabolomics, Phylogeny, Epigenetics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/halla - https://github.com/galaxyproject/tools-iuc/tree/main/tools/halla + https://github.com/galaxyproject/tools-iuc/tree/master/tools/halla halla HAllA High-sensitivity pattern discovery in large, paired multi-omic datasets. + + 0 0 1 @@ -9675,10 +9429,6 @@ 0 0 0 - 0 - 0 - - True False @@ -9701,11 +9451,13 @@ Public health and epidemiology, Microbiology, Bioinformatics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/hamronization - https://github.com/galaxyproject/tools-iuc/tree/main/tools/hamronization + https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization hamronization hAMRonization Parse multiple Antimicrobial Resistance Analysis Reports into a common data structure + https://usegalaxy.eu/published/workflow?id=eb5ab8bc82569eee, https://workflowhub.eu/workflows/1189?version=2, https://workflowhub.eu/workflows/407?version=1, https://workflowhub.eu/workflows/470?version=1 + 0 0 2 @@ -9714,7 +9466,6 @@ 0 0 0 - 0 2 0 0 @@ -9730,7 +9481,6 @@ 0 0 0 - 0 2 0 0 @@ -9754,8 +9504,6 @@ 18691 262 262 - https://usegalaxy.eu/published/workflow?id=eb5ab8bc82569eee, https://workflowhub.eu/workflows/1189?version=2, https://workflowhub.eu/workflows/407?version=1, https://workflowhub.eu/workflows/470?version=1 - True False @@ -9778,11 +9526,13 @@ Sequence assembly, Metagenomics galaxy-australia https://github.com/galaxyproject/tools-iuc/tree/main/tools/hifiasm_meta - https://github.com/galaxyproject/tools-iuc/tree/main/tools/hifiasm_meta + https://github.com/galaxyproject/tools-iuc/tree/master/tools/hifiasm_meta hifiasm-meta Hifiasm-meta Hifiasm_meta - de novo metagenome assembler, based on hifiasm, a haplotype-resolved de novo assembler for PacBio Hifi reads. + + 0 1 1 @@ -9793,7 +9543,6 @@ 0 0 0 - 0 1 0 0 @@ -9807,7 +9556,6 @@ 0 0 0 - 0 1 0 0 @@ -9831,8 +9579,6 @@ 597 56 56 - - True False @@ -9860,6 +9606,8 @@ + + 0 0 0 @@ -9906,10 +9654,6 @@ 0 0 0 - 0 - 0 - - True False @@ -9932,11 +9676,13 @@ Sequence analysis, Sequence sites, features and motifs, Gene and protein families iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/hmmer3 - https://github.com/galaxyproject/tools-iuc/tree/main/tools/hmmer3 + https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 hmmer3 HMMER3 This tool is used for searching sequence databases for homologs of protein sequences, and for making protein sequence alignments. It implements methods using probabilistic models called profile hidden Markov models. The new HMMER3 project, HMMER is now as fast as BLAST for protein search. + https://usegalaxy.eu/published/workflow?id=02631612a43a4d9b, https://usegalaxy.eu/published/workflow?id=0ab3e47ebd3b520e, https://usegalaxy.eu/published/workflow?id=24eaa682897379c8, https://usegalaxy.eu/published/workflow?id=3eaa913306c16146, https://usegalaxy.eu/published/workflow?id=58955868b504c60d, https://usegalaxy.eu/published/workflow?id=5be158931abca947, https://usegalaxy.eu/published/workflow?id=6158c3b5fc12044e, https://usegalaxy.eu/published/workflow?id=6416cfdbd5273063, https://usegalaxy.eu/published/workflow?id=667bac8d7453e5f1, https://usegalaxy.eu/published/workflow?id=8c91345ed468e22d, https://usegalaxy.eu/published/workflow?id=8deb08d4f228e198, https://usegalaxy.eu/published/workflow?id=9a60ecf98d4f8134, https://usegalaxy.eu/published/workflow?id=d57d41e306241396, https://usegalaxy.fr/published/workflow?id=5ec6d378e60f7ccc, https://usegalaxy.fr/published/workflow?id=7ebb54181b404733, https://usegalaxy.fr/published/workflow?id=b131218bec7eacb4, https://usegalaxy.fr/published/workflow?id=d425a77157cae2ee, https://usegalaxy.org/published/workflow?id=84b447be2f1c5870, https://workflowhub.eu/workflows/100?version=1, https://workflowhub.eu/workflows/37?version=1, https://workflowhub.eu/workflows/38?version=1, https://workflowhub.eu/workflows/39?version=1, https://workflowhub.eu/workflows/40?version=1 + 12 12 12 @@ -9945,7 +9691,6 @@ 0 0 0 - 0 12 12 0 @@ -9960,7 +9705,6 @@ 0 0 0 - 0 12 12 12 @@ -9985,8 +9729,6 @@ 41573 584 560 - https://usegalaxy.eu/published/workflow?id=02631612a43a4d9b, https://usegalaxy.eu/published/workflow?id=0ab3e47ebd3b520e, https://usegalaxy.eu/published/workflow?id=24eaa682897379c8, https://usegalaxy.eu/published/workflow?id=3eaa913306c16146, https://usegalaxy.eu/published/workflow?id=58955868b504c60d, https://usegalaxy.eu/published/workflow?id=5be158931abca947, https://usegalaxy.eu/published/workflow?id=6158c3b5fc12044e, https://usegalaxy.eu/published/workflow?id=6416cfdbd5273063, https://usegalaxy.eu/published/workflow?id=667bac8d7453e5f1, https://usegalaxy.eu/published/workflow?id=8c91345ed468e22d, https://usegalaxy.eu/published/workflow?id=8deb08d4f228e198, https://usegalaxy.eu/published/workflow?id=9a60ecf98d4f8134, https://usegalaxy.eu/published/workflow?id=d57d41e306241396, https://usegalaxy.fr/published/workflow?id=5ec6d378e60f7ccc, https://usegalaxy.fr/published/workflow?id=7ebb54181b404733, https://usegalaxy.fr/published/workflow?id=b131218bec7eacb4, https://usegalaxy.fr/published/workflow?id=d425a77157cae2ee, https://workflowhub.eu/workflows/100?version=1, https://workflowhub.eu/workflows/37?version=1, https://workflowhub.eu/workflows/38?version=1, https://workflowhub.eu/workflows/39?version=1, https://workflowhub.eu/workflows/40?version=1 - True False @@ -10009,11 +9751,13 @@ Metagenomics, Phylogenomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/humann - https://github.com/galaxyproject/tools-iuc/tree/main/tools/humann + https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann humann humann HUMAnN is a pipeline for efficiently and accurately profiling the presence/absence and abundance of microbial pathways in a community from metagenomic or metatranscriptomic sequencing data (typically millions of short DNA/RNA reads). This process, referred to as functional profiling, aims to describe the metabolic potential of a microbial community and its members. More generally, functional profiling answers the question “What are the microbes in my community-of-interest doing (or are capable of doing)?” + https://usegalaxy.eu/published/workflow?id=21a17d6c473a88c0, https://usegalaxy.eu/published/workflow?id=23dd2253da51e22e, https://usegalaxy.eu/published/workflow?id=3118d383c81cf805, https://usegalaxy.eu/published/workflow?id=4d32b1b3ac0a7161, https://usegalaxy.eu/published/workflow?id=5ce8a472e6e95c60, https://usegalaxy.eu/published/workflow?id=5f0faac42b0a5062, https://usegalaxy.eu/published/workflow?id=69eddfde874af35b, https://usegalaxy.eu/published/workflow?id=713a5485e2007f90, https://usegalaxy.eu/published/workflow?id=87cc0cd143a12c41, https://usegalaxy.eu/published/workflow?id=9472be79da012999, https://usegalaxy.eu/published/workflow?id=a7a6d8ecc2795f58, https://usegalaxy.eu/published/workflow?id=a8f829deb69b30ab, https://usegalaxy.eu/published/workflow?id=b14845359b702444, https://usegalaxy.eu/published/workflow?id=cb2df493f5e334f7, https://usegalaxy.eu/published/workflow?id=d7e532d13a7f1ea6, https://usegalaxy.eu/published/workflow?id=fdca6c9d394986bf, https://usegalaxy.fr/published/workflow?id=c4f6062e51d0f45e, https://usegalaxy.fr/published/workflow?id=fd733565098d76c9, https://workflowhub.eu/workflows/1447?version=2, https://workflowhub.eu/workflows/1456?version=2, https://workflowhub.eu/workflows/1466?version=2 + microbiome/metatranscriptomics, microbiome/metatranscriptomics-short 6 10 10 @@ -10022,7 +9766,6 @@ 0 0 0 - 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for counting k-mers in DNA sequence. + https://usegalaxy.eu/published/workflow?id=342169b55bdc2993, https://usegalaxy.eu/published/workflow?id=bc32937d505135ab + 0 1 1 @@ -11333,7 +11043,6 @@ 0 0 0 - 0 1 0 0 @@ -11347,7 +11056,6 @@ 0 0 0 - 0 1 1 0 @@ -11371,8 +11079,6 @@ 7912 491 491 - https://usegalaxy.eu/published/workflow?id=342169b55bdc2993, https://usegalaxy.eu/published/workflow?id=bc32937d505135ab - True False @@ -11395,11 +11101,13 @@ Metagenomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/kaiju - https://github.com/galaxyproject/tools-iuc/tree/main/tools/kaiju + https://github.com/galaxyproject/tools-iuc/tree/master/tools/kaiju kaiju Kaiju Program for the taxonomic assignment of high-throughput sequencing reads, e.g., Illumina or Roche/454, from whole-genome sequencing of metagenomic DNA. Reads are directly assigned to taxa using the NCBI taxonomy and a reference database of protein sequences from Bacteria, Archaea, Fungi, microbial eukaryotes and viruses. + + 0 0 5 @@ -11426,8 +11134,6 @@ 0 0 0 - 0 - 0 2 2 2 @@ -11448,8 +11154,6 @@ 2 2 2 - - True False @@ -11477,6 +11181,8 @@ + + 0 0 0 @@ -11523,10 +11229,6 @@ 0 0 0 - 0 - 0 - - True False @@ -11549,11 +11251,13 @@ Sequence assembly iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/khmer - https://github.com/galaxyproject/tools-iuc/tree/main/tools/khmer + https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer khmer khmer khmer is a set of command-line tools for working with DNA shotgun sequencing data from genomes, transcriptomes, metagenomes, and single cells. khmer can make de novo assemblies faster, and sometimes better. khmer can also identify (and fix) problems with shotgun data. + + 8 8 8 @@ -11563,7 +11267,6 @@ 0 0 0 - 0 1 0 0 @@ -11577,7 +11280,6 @@ 0 0 0 - 0 8 8 8 @@ -11602,8 +11304,6 @@ 4930 326 292 - - True False @@ -11615,7 +11315,7 @@ Screen genome assemblies of Klebsiella pneumoniae and the Klebsiella pneumoniae species complex (KpSC) 2022-09-09 https://github.com/katholt/Kleborate - 2.3.2 + @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ kleborate 3.2.4 To update @@ -11626,11 +11326,13 @@ Public health and epidemiology, Metagenomics, Population genomics, Sequence assembly, Whole genome sequencing iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/kleborate - https://github.com/galaxyproject/tools-iuc/tree/main/tools/kleborate + https://github.com/galaxyproject/tools-iuc/tree/master/tools/kleborate kleborate Kleborate Genomic surveillance framework and global population structure for Klebsiella pneumoniae.Kleborate is a tool to screen genome assemblies of Klebsiella pneumoniae and the Klebsiella pneumoniae species complex (KpSC) for:.A manuscript describing the Kleborate software in full is currently in preparation. In the meantime, if you use Kleborate, please cite the preprint: Lam, MMC. et al. Genomic surveillance framework and global population structure for Klebsiella pneumoniae. bioRxiv (2020). + + 0 0 1 @@ -11641,7 +11343,6 @@ 0 0 0 - 0 1 0 0 @@ -11655,7 +11356,6 @@ 0 0 0 - 0 1 0 0 @@ -11679,8 +11379,6 @@ 1479 123 123 - - True False @@ -11692,7 +11390,7 @@ A tool for creating data files for statistics based on kmers 2025-04-16 https://github.com/SantaMcCloud/kmer2stats - 1.0.1 + @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ kmer2stats 1.0.3 To update @@ -11703,10 +11401,12 @@ iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/kmer2stats - https://github.com/galaxyproject/tools-iuc/tree/main/tools/kmer2stats + https://github.com/galaxyproject/tools-iuc/tree/master/tools/kmer2stats + + https://usegalaxy.eu/published/workflow?id=342169b55bdc2993 0 0 @@ -11734,8 +11434,6 @@ 0 0 0 - 0 - 0 8 8 310 @@ -11756,8 +11454,6 @@ 310 8 8 - https://usegalaxy.eu/published/workflow?id=342169b55bdc2993 - True False @@ -11769,10 +11465,10 @@ an alignment-free taxonomic classifier based on k-mer/minimizer counting 2025-12-18 https://github.com/gdefazio/kMetaShot - 2.0 + @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ kmetashot 2.0 - Up-to-date + To update Metagenomics @@ -11785,10 +11481,11 @@ kMetaShot The application of 2nd and 3rd generation High Throughput Sequencing (HTS) technologies has deeply reshaped experimental method to investigate microbial communities and obtain a taxonomic and functional profile of the invetigated community. Shotgun Metagenomics allow to quickly obtain a representation of microorganisms genomes characterizing a particular environment. In order to obtain a fast e reliable taxonomic classification of microorganisms genomes we present kMetaShot, an alignment-free taxonomic classifier based on k-mer/minimizer counting. - 0 - 0 + + microbiome/mags-building 1 0 + 1 0 0 0 @@ -11809,6 +11506,7 @@ 0 0 0 + 1 0 0 0 @@ -11831,10 +11529,6 @@ 0 0 0 - 0 - 0 - - True False @@ -11857,11 +11551,13 @@ iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/kmindex - https://github.com/galaxyproject/tools-iuc/tree/main/tools/kmindex + https://github.com/galaxyproject/tools-iuc/tree/master/tools/kmindex kmindex kmindex kmindex is a tool for indexing and querying sequencing samples. It is built on top of kmtricks. + + 0 0 2 @@ -11908,10 +11604,81 @@ 0 0 0 - 0 - 0 + True + False + + + + kneaddata + kneaddata + txt + Quality control and contaminant removal for metagenomic data + 2026-02-04 + https://github.com/biobakery/kneaddata + 0.12.1 + kneaddata + 0.12.4 + To update + Metagenomics, Sequence Analysis + + + iuc + https://github.com/galaxyproject/tools-iuc/tree/main/tools/kneaddata + https://github.com/galaxyproject/tools-iuc/tree/master/tools/kneaddata + + + + + https://usegalaxy.eu/published/workflow?id=8e13c87e751e88d8 + + 0 + 0 + 1 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 1 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 True False @@ -11923,10 +11690,10 @@ Gene function annotation tool based on KEGG Orthology and hidden Markov model 2020-11-12 https://github.com/takaram/kofam_scan - 1.3.0 + @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ kofamscan 1.3.0 - Up-to-date + To update Sequence Analysis Sequence analysis, Gene functional annotation Sequence analysis, Gene functional annotation @@ -11934,11 +11701,13 @@ Genomics, Structure analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/kofamscan - https://github.com/galaxyproject/tools-iuc/tree/main/tools/kofamscan + https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan kofamscan kofamscan KofamScan is a gene function annotation tool based on KEGG Orthology and hidden Markov model. 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Previous attempts by otherbioinformatics software to accomplish this task have often used sequence alignmentor machine learning techniques that were quite slow, leading to the developmentof less sensitive but much faster abundance estimation programs. Kraken aims toachieve high sensitivity and high speed by utilizing exact alignments of k-mersand a novel classification algorithm. 2017-01-24 http://ccb.jhu.edu/software/kraken/ - + 1.3.1 kraken 1.1.1 To update @@ -12011,11 +11776,13 @@ Taxonomy, Metagenomics devteam https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/kraken - https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/kraken + https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/kraken kraken Kraken System for assigning taxonomic labels to short DNA sequences, usually obtained through metagenomic studies. Previous attempts by other bioinformatics software to accomplish this task have often used sequence alignment or machine learning techniques that were quite slow, leading to the development of less sensitive but much faster abundance estimation programs. It aims to achieve high sensitivity and high speed by utilizing exact alignments of k-mers and a novel classification algorithm. + https://usegalaxy.org.au/published/workflow?id=b6bad1f167257248, https://usegalaxy.org/published/workflow?id=074a0b1bc8273c16, https://usegalaxy.org/published/workflow?id=2ec3e326c51d3147, https://usegalaxy.org/published/workflow?id=33d90e718ce500ef, https://usegalaxy.org/published/workflow?id=7321c6ad5425d347, https://usegalaxy.org/published/workflow?id=87b3305ea433b4e2, https://usegalaxy.org/published/workflow?id=a89e1018a00b883c, https://usegalaxy.org/published/workflow?id=e0c33057ac2670ba, https://usegalaxy.org/published/workflow?id=fb01e1a49793c8be + 5 5 5 @@ -12024,7 +11791,6 @@ 0 0 0 - 0 1 0 0 @@ -12038,7 +11804,6 @@ 0 0 0 - 2 0 5 5 @@ -12064,8 +11829,6 @@ 176166 6929 5005 - https://usegalaxy.org.au/published/workflow?id=b6bad1f167257248, https://usegalaxy.org/published/workflow?id=074a0b1bc8273c16, https://usegalaxy.org/published/workflow?id=2ec3e326c51d3147, https://usegalaxy.org/published/workflow?id=33d90e718ce500ef, https://usegalaxy.org/published/workflow?id=7321c6ad5425d347, https://usegalaxy.org/published/workflow?id=87b3305ea433b4e2, https://usegalaxy.org/published/workflow?id=a89e1018a00b883c, https://usegalaxy.org/published/workflow?id=e0c33057ac2670ba, https://usegalaxy.org/published/workflow?id=fb01e1a49793c8be - True False @@ -12088,11 +11851,13 @@ Taxonomy, Metagenomics, Microbial ecology iuc https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/kraken2/kraken2 - https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/kraken2/kraken2 + https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/kraken2/kraken2 kraken2 kraken2 Kraken 2 is the newest version of Kraken, a taxonomic classification system using exact k-mer matches to achieve high accuracy and fast classification speeds. 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0 @@ -13219,8 +13029,6 @@ 930 18 18 - - True False @@ -13232,7 +13040,7 @@ LotuS2 OTU processing pipeline 2021-05-13 https://lotus2.earlham.ac.uk/ - 2.32 + @VERSION@ lotus2 2.34.1 To update @@ -13243,11 +13051,13 @@ Metagenomics, Taxonomy, Microbial ecology earlhaminst https://github.com/EarlhamInst/earlham-galaxytools/tree/main/tools/lotus2 - https://github.com/EarlhamInst/earlham-galaxytools/tree/main/tools/lotus2 + https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 lotus2 lotus2 LotuS2 is a lightweight and user-friendly pipeline that is fast, precise, and streamlined, using extensive pre- and post-ASV/OTU clustering steps to further increase data quality. High data usage rates and reliability enable high-throughput microbiome analysis in minutes. + https://usegalaxy.eu/published/workflow?id=466bdd8ba7b67264, https://workflowhub.eu/workflows/1460?version=1 + microbiome/lotus2-identifying-fungi, microbiome/mgnify-amplicon 0 1 1 @@ -13270,8 +13080,6 @@ 0 0 0 - 0 - 0 1 1 0 @@ -13296,8 +13104,6 @@ 2401 273 273 - https://usegalaxy.eu/published/workflow?id=466bdd8ba7b67264, https://workflowhub.eu/workflows/1460?version=1 - microbiome/lotus2-identifying-fungi, microbiome/mgnify-amplicon True False @@ -13309,10 +13115,10 @@ m6anet to detect m6A RNA modifications from nanopore data 2023-10-25 https://m6anet.readthedocs.io/en/latest - 2.1.0 + @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ m6anet 2.1.0 - Up-to-date + To update Sequence Analysis Quantification, Imputation, Gene expression profiling Quantification, Imputation, Gene expression profiling @@ -13320,11 +13126,13 @@ RNA-Seq, Transcriptomics, RNA, Machine learning iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/m6anet - https://github.com/galaxyproject/tools-iuc/tree/main/tools/m6anet + https://github.com/galaxyproject/tools-iuc/tree/master/tools/m6anet m6Anet m6Anet Detection of m6A from direct RNA sequencing using a Multiple Instance Learning framework. + + 0 0 1 @@ -13349,8 +13157,6 @@ 0 0 0 - 0 - 0 1 0 12 @@ -13373,8 +13179,6 @@ 47 12 12 - - True False @@ -13397,11 +13201,13 @@ Metagenomics, Statistics and probability iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/maaslin2 - https://github.com/galaxyproject/tools-iuc/tree/main/tools/maaslin2 + https://github.com/galaxyproject/tools-iuc/tree/master/tools/maaslin2 maaslin2 MaAsLin2 MaAsLin2 is comprehensive R package for efficiently determining multivariable association between phenotypes, environments, exposures, covariates and microbial meta’omic features. 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All rights reserved.This tool is a short Python script intended to be run prior to calling the NCBI BLAST+ command line tool makeblastdb or in other settings where you want to collapse duplicated sequences in a FASTA file to a single representative. + + 0 0 0 @@ -13679,10 +13479,6 @@ 0 0 0 - 0 - 0 - - True False @@ -13705,11 +13501,13 @@ Genomics, DNA, Sequence analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/maker - https://github.com/galaxyproject/tools-iuc/tree/main/tools/maker + https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker maker MAKER Portable and easily configurable genome annotation pipeline. 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genome-annotation/annotation-with-maker, genome-annotation/annotation-with-maker-short True False @@ -13771,7 +13565,7 @@ fast and accurate sequence read classification tool designed to assign taxonomy and OTU classifications to ribosomal RNA sequences. 2023-08-02 https://github.com/jfmrod/MAPseq - 2.1.1b + @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ perl To update @@ -13782,11 +13576,13 @@ Functional, regulatory and non-coding RNA, Sequence analysis, Sequence sites, features and motifs iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/mapseq - https://github.com/galaxyproject/tools-iuc/tree/main/tools/mapseq + https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq mapseq MAPseq Highly efficient k-mer search with confidence estimates, for rRNA sequence analysis . + https://usegalaxy.eu/published/workflow?id=08e25b733cd796e6, https://usegalaxy.eu/published/workflow?id=437704898229dfb6, https://usegalaxy.eu/published/workflow?id=fb806b88850f3427, https://usegalaxy.org/published/workflow?id=45f959d5bf505b15, https://usegalaxy.org/published/workflow?id=8151be18aab3a3c6, https://workflowhub.eu/workflows/1270?version=2, https://workflowhub.eu/workflows/1273?version=2, https://workflowhub.eu/workflows/1842?version=1, https://workflowhub.eu/workflows/1856?version=1 + microbiome/mgnify-amplicon 1 0 1 @@ -13797,7 +13593,6 @@ 0 0 0 - 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Metaeuk combines the fast andsensitive homology search capabilities of MMseqs2 with a dynamic programmingprocedure to recover optimal exons sets. It reduces redundancies in multiplediscoveries of the same gene and resolves conflicting gene predictions onthe same strand. 2020-08-04 https://github.com/soedinglab/metaeuk - 7.bba0d80 + @TOOL_VERSION@ metaeuk 6.a5d39d9 To update @@ -14937,11 +14701,13 @@ Metagenomics, Gene and protein families iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/metaeuk - https://github.com/galaxyproject/tools-iuc/tree/main/tools/metaeuk + https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk MetaEuk MetaEuk MetaEuk - sensitive, high-throughput gene discovery and annotation for large-scale eukaryotic metagenomics + https://usegalaxy.eu/published/workflow?id=9b9e1e28f3683f92 + 0 0 1 @@ -14964,8 +14730,6 @@ 0 0 0 - 0 - 0 1 1 1 @@ -14990,8 +14754,6 @@ 507 58 57 - https://usegalaxy.eu/published/workflow?id=9b9e1e28f3683f92 - True False @@ -15003,10 +14765,10 @@ MetaGeneAnnotator gene-finding program for prokaryote and phage 2018-03-21 http://metagene.nig.ac.jp/ - 1.0 + @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ metagene_annotator 1.0 - Up-to-date + To update Sequence Analysis Sequence annotation Sequence annotation @@ -15019,6 +14781,8 @@ MetaGeneAnnotator Prokaryotic gene finding program from environmental genome shotgun sequences or metagenomic sequences. + https://usegalaxy.eu/published/workflow?id=3dcf09e75d707573, https://usegalaxy.eu/published/workflow?id=799b924edd3c401b, https://usegalaxy.eu/published/workflow?id=9b9e1e28f3683f92, https://usegalaxy.eu/published/workflow?id=a644e6b450dabca8 + 0 0 1 @@ -15027,7 +14791,6 @@ 0 0 0 - 0 1 0 1 @@ -15043,7 +14806,6 @@ 0 0 0 - 0 1 1 0 @@ -15067,8 +14829,6 @@ 20971 457 439 - https://usegalaxy.eu/published/workflow?id=3dcf09e75d707573, https://usegalaxy.eu/published/workflow?id=799b924edd3c401b, https://usegalaxy.eu/published/workflow?id=9b9e1e28f3683f92, https://usegalaxy.eu/published/workflow?id=a644e6b450dabca8 - True False @@ -15091,11 +14851,13 @@ Metagenomics, Sequencing iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/metagenomeseq - https://github.com/galaxyproject/tools-iuc/tree/main/tools/metagenomeseq + https://github.com/galaxyproject/tools-iuc/tree/master/tools/metagenomeseq metagenomeseq metagenomeSeq Designed to determine features (be it Operational Taxanomic Unit (OTU), species, etc.) that are differentially abundant between two or more groups of multiple samples. It is designed to address the effects of both normalization and under-sampling of microbial communities on disease association detection and the testing of feature correlations. + + 1 0 1 @@ -15118,8 +14880,6 @@ 0 0 0 - 0 - 0 1 1 1 @@ -15144,8 +14904,6 @@ 782 79 43 - - True False @@ -15168,11 +14926,13 @@ Metagenomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/metamdbg - https://github.com/galaxyproject/tools-iuc/tree/main/tools/metamdbg + https://github.com/galaxyproject/tools-iuc/tree/master/tools/metamdbg metamdbg metaMDBG MetaMDBG is a fast and low-memory assembler for long and accurate metagenomics reads (e.g. PacBio HiFi, Nanopore r10.4). It is based on the minimizer de-Brujin graph (MDBG), which have been reimplemetend specifically for metagenomics assembly. MetaMDBG combines an efficient multi-k approach in minimizer-space for dealing with uneven species coverages, and a novel abundance-based filtering method for simplifying strain complexity. + + 2 0 2 @@ -15219,10 +14979,6 @@ 0 0 0 - 0 - 0 - - True False @@ -15234,10 +14990,10 @@ Produce targeted databases for mass spectrometry analysis. 2022-03-29 https://github.com/uct-cbio/proteomics-pipelines - 1.9.4 + @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ metanovo 1.9.4 - Up-to-date + To update Proteomics Target-Decoy, de Novo sequencing, Tag-based peptide identification, Protein identification, Expression analysis Target-Decoy, de Novo sequencing, Tag-based peptide identification, Protein identification, Expression analysis @@ -15250,6 +15006,8 @@ MetaNovo An open-source pipeline for probabilistic peptide discovery in complex metaproteomic datasets. + https://usegalaxy.eu/published/workflow?id=2f7e13eb26c8cd18, https://usegalaxy.eu/published/workflow?id=7cfbf4b7bd3f30d3, https://usegalaxy.eu/published/workflow?id=c6aecbdbeb27585f, https://usegalaxy.eu/published/workflow?id=d7c7a4d6c8072167, https://usegalaxy.eu/published/workflow?id=f2b45a7ff4f449e6, https://usegalaxy.org.au/published/workflow?id=351f3fab960c013b, https://usegalaxy.org/published/workflow?id=2be8ecd5922d23d1, https://workflowhub.eu/workflows/1216?version=1, https://workflowhub.eu/workflows/1461?version=1, https://workflowhub.eu/workflows/1474?version=1 + microbiome/clinical-mp-1-database-generation, proteomics/clinical-mp-1-database-generation 1 1 1 @@ -15272,8 +15030,6 @@ 0 0 0 - 0 - 0 1 1 0 @@ -15298,8 +15054,6 @@ 5126 49 49 - https://usegalaxy.eu/published/workflow?id=2f7e13eb26c8cd18, https://usegalaxy.eu/published/workflow?id=7cfbf4b7bd3f30d3, https://usegalaxy.eu/published/workflow?id=c6aecbdbeb27585f, https://usegalaxy.eu/published/workflow?id=d7c7a4d6c8072167, https://usegalaxy.eu/published/workflow?id=f2b45a7ff4f449e6, https://usegalaxy.org.au/published/workflow?id=351f3fab960c013b, https://usegalaxy.org/published/workflow?id=2be8ecd5922d23d1, https://workflowhub.eu/workflows/1216?version=1, https://workflowhub.eu/workflows/1461?version=1, https://workflowhub.eu/workflows/1474?version=1 - microbiome/clinical-mp-1-database-generation, proteomics/clinical-mp-1-database-generation True False @@ -15322,17 +15076,18 @@ Metagenomics, Phylogenomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/metaphlan - https://github.com/galaxyproject/tools-iuc/tree/main/tools/metaphlan + https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan metaphlan MetaPhlAn Computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data. + https://usegalaxy.eu/published/workflow?id=052f35a526798020, https://usegalaxy.eu/published/workflow?id=05f5f040337786bf, https://usegalaxy.eu/published/workflow?id=19de5cbae7f48103, https://usegalaxy.eu/published/workflow?id=21a17d6c473a88c0, https://usegalaxy.eu/published/workflow?id=39d36a7ce0ef268d, https://usegalaxy.eu/published/workflow?id=4d32b1b3ac0a7161, https://usegalaxy.eu/published/workflow?id=4f0daf8e9dd54127, https://usegalaxy.eu/published/workflow?id=4f21205e71cabd37, https://usegalaxy.eu/published/workflow?id=5f0faac42b0a5062, https://usegalaxy.eu/published/workflow?id=69eddfde874af35b, https://usegalaxy.eu/published/workflow?id=713a5485e2007f90, https://usegalaxy.eu/published/workflow?id=7491883694fff308, https://usegalaxy.eu/published/workflow?id=79b4ae4403772098, https://usegalaxy.eu/published/workflow?id=87cc0cd143a12c41, https://usegalaxy.eu/published/workflow?id=9472be79da012999, https://usegalaxy.eu/published/workflow?id=a8f829deb69b30ab, https://usegalaxy.eu/published/workflow?id=b14845359b702444, https://usegalaxy.eu/published/workflow?id=cb2df493f5e334f7, https://usegalaxy.eu/published/workflow?id=fdca6c9d394986bf, https://usegalaxy.fr/published/workflow?id=09e8293456ee6d99, https://usegalaxy.fr/published/workflow?id=c4f6062e51d0f45e, https://usegalaxy.org.au/published/workflow?id=6b7e565258a9da2a, https://workflowhub.eu/workflows/1451?version=2, https://workflowhub.eu/workflows/1466?version=2, https://workflowhub.eu/workflows/1470?version=2, https://workflowhub.eu/workflows/624?version=1 + microbiome/metatranscriptomics, microbiome/metatranscriptomics-short, microbiome/taxonomic-profiling 1 2 4 4 0 - 1 0 0 0 @@ -15350,7 +15105,6 @@ 0 0 0 - 0 1 4 4 @@ -15375,8 +15129,6 @@ 57513 3016 3016 - https://usegalaxy.eu/published/workflow?id=05f5f040337786bf, https://usegalaxy.eu/published/workflow?id=19de5cbae7f48103, https://usegalaxy.eu/published/workflow?id=21a17d6c473a88c0, https://usegalaxy.eu/published/workflow?id=39d36a7ce0ef268d, https://usegalaxy.eu/published/workflow?id=4d32b1b3ac0a7161, https://usegalaxy.eu/published/workflow?id=4f0daf8e9dd54127, https://usegalaxy.eu/published/workflow?id=4f21205e71cabd37, https://usegalaxy.eu/published/workflow?id=5f0faac42b0a5062, https://usegalaxy.eu/published/workflow?id=69eddfde874af35b, https://usegalaxy.eu/published/workflow?id=713a5485e2007f90, https://usegalaxy.eu/published/workflow?id=7491883694fff308, https://usegalaxy.eu/published/workflow?id=79b4ae4403772098, https://usegalaxy.eu/published/workflow?id=87cc0cd143a12c41, https://usegalaxy.eu/published/workflow?id=9472be79da012999, https://usegalaxy.eu/published/workflow?id=a8f829deb69b30ab, https://usegalaxy.eu/published/workflow?id=b14845359b702444, https://usegalaxy.eu/published/workflow?id=cb2df493f5e334f7, https://usegalaxy.eu/published/workflow?id=fdca6c9d394986bf, https://usegalaxy.fr/published/workflow?id=09e8293456ee6d99, https://usegalaxy.fr/published/workflow?id=c4f6062e51d0f45e, https://usegalaxy.org.au/published/workflow?id=6b7e565258a9da2a, https://workflowhub.eu/workflows/1451?version=2, https://workflowhub.eu/workflows/1466?version=2, https://workflowhub.eu/workflows/1470?version=2, https://workflowhub.eu/workflows/624?version=1 - microbiome/metatranscriptomics, microbiome/metatranscriptomics-short, microbiome/taxonomic-profiling True False @@ -15404,6 +15156,8 @@ metaQuantome metaQuantome software suite analyzes the state of a microbiome by leveraging complex taxonomic and functional hierarchies to summarize peptide-level quantitative information. metaQuantome offers differential abundance analysis, principal components analysis, and clustered heat map visualizations, as well as exploratory analysis for a single sample or experimental condition. + https://usegalaxy.eu/published/workflow?id=4c364c6be27981ba, https://usegalaxy.eu/published/workflow?id=695f7defb516d80d, https://usegalaxy.eu/published/workflow?id=ce7f7c6eef526d67, https://usegalaxy.eu/published/workflow?id=dc438d4ae1866df8, https://usegalaxy.eu/published/workflow?id=e5a89ef7b5f1c1d9, https://usegalaxy.org.au/published/workflow?id=cada735fa0716570, https://usegalaxy.org.au/published/workflow?id=f8183bba3a1d150d, https://workflowhub.eu/workflows/1453?version=1, https://workflowhub.eu/workflows/1459?version=1 + proteomics/metaquantome-function, proteomics/metaquantome-taxonomy 0 6 6 @@ -15426,8 +15180,6 @@ 0 0 0 - 0 - 0 6 6 6 @@ -15452,8 +15204,6 @@ 4600 116 107 - https://usegalaxy.eu/published/workflow?id=4c364c6be27981ba, https://usegalaxy.eu/published/workflow?id=695f7defb516d80d, https://usegalaxy.eu/published/workflow?id=ce7f7c6eef526d67, https://usegalaxy.eu/published/workflow?id=dc438d4ae1866df8, https://usegalaxy.eu/published/workflow?id=e5a89ef7b5f1c1d9, https://usegalaxy.org.au/published/workflow?id=cada735fa0716570, https://usegalaxy.org.au/published/workflow?id=f8183bba3a1d150d, https://workflowhub.eu/workflows/1453?version=1, https://workflowhub.eu/workflows/1459?version=1 - proteomics/metaquantome-function, proteomics/metaquantome-taxonomy True False @@ -15476,7 +15226,9 @@ iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/metasbt - https://github.com/galaxyproject/tools-iuc/tree/main/tools/metasbt + https://github.com/galaxyproject/tools-iuc/tree/master/tools/metasbt + + @@ -15527,10 +15279,6 @@ 0 0 0 - 0 - 0 - - True False @@ -15540,7 +15288,7 @@ metawrapmg_binning, metawrapmg_bin_refinement A flexible pipeline for genome-resolved metagenomic data analysis - 2024-04-11 + 2024-04-12 https://github.com/bxlab/metaWRAP 1.3.0 metawrap-mg @@ -15553,11 +15301,13 @@ Whole genome sequencing, Metagenomic sequencing, Metagenomics galaxy-australia https://github.com/galaxyproject/tools-iuc/tree/main/tools/metawrapmg - https://github.com/galaxyproject/tools-iuc/tree/main/tools/metawrapmg + https://github.com/galaxyproject/tools-iuc/tree/master/tools/metawrapmg metawrap MetaWRAP MetaWRAP aims to be an easy-to-use metagenomic wrapper suite that accomplishes the core tasks of metagenomic analysis from start to finish: read quality control, assembly, visualization, taxonomic profiling, extracting draft genomes (binning), and functional annotation. + + 0 2 2 @@ -15568,7 +15318,6 @@ 0 0 0 - 0 2 0 0 @@ -15585,7 +15334,6 @@ 0 0 0 - 0 100 100 1596 @@ -15606,8 +15354,6 @@ 2183 167 167 - - True False @@ -15630,11 +15376,13 @@ Metagenomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/mg_toolkit - https://github.com/galaxyproject/tools-iuc/tree/main/tools/mg_toolkit + https://github.com/galaxyproject/tools-iuc/tree/master/tools/mg_toolkit mg-toolkit mg-toolkit Metagenomics toolkit enables scientists to download all of the sample metadata for a given study or sequence to a single csv file. + + 0 0 2 @@ -15661,8 +15409,6 @@ 0 0 0 - 0 - 0 10 10 21 @@ -15683,8 +15429,156 @@ 21 10 10 + True + False + + + + mgnify_genome_search + mgnify_genome_search + tabular + Queue genomes against registered genome from MGnify Database + 2026-01-26 + https://github.com/SantaMcCloud/MGnify-genome-search + @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ + mgnify-genome-search + 1.0.0 + To update + Metagenomics + + + + + iuc + https://github.com/galaxyproject/tools-iuc/tree/main/tools/mgnify_genome_search + https://github.com/galaxyproject/tools-iuc/tree/master/tools/mgnify_genome_search + + + + + + + 0 + 0 + 1 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + True + False + + + + mgnify_pipelines_toolkit + mgnify_pipelines_toolkit_classify_var_regions, mgnify_pipelines_toolkit_make_asv_count_table, mgnify_pipelines_toolkit_mapseq_to_asv_table, mgnify_pipelines_toolkit_permute_primers, mgnify_pipelines_toolkit_primer_val_classification, mgnify_pipelines_toolkit_rev_comp_se_primers + json, tabular, txt, tsv, fasta + Utilities for use in the MGnify pipelines + 2026-04-22 + https://github.com/EBI-Metagenomics/mgnify-pipelines-toolkit + 1.5.1 + mgnify-pipelines-toolkit + 1.5.2 + To update + Metagenomics + + + iuc + https://github.com/galaxyproject/tools-iuc/tree/main/tools/mgnify_pipelines_toolkit + https://github.com/galaxyproject/tools-iuc/tree/master/tools/mgnify_pipelines_toolkit + + + + + + + 0 + 0 + 6 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 True False @@ -15712,6 +15606,8 @@ SeqPrep Strips adapters and optionally merges overlapping paired-end (or paired-end contamination in mate-pair libraries) illumina style reads. + https://usegalaxy.eu/published/workflow?id=0609a4b1941d1a68, https://usegalaxy.eu/published/workflow?id=9fddc44294236e8f, https://usegalaxy.org/published/workflow?id=20b7ae4b517a80fd, https://usegalaxy.org/published/workflow?id=a71fcbc60caae8b6, https://workflowhub.eu/workflows/1272?version=2, https://workflowhub.eu/workflows/1854?version=1 + microbiome/mgnify-amplicon 1 0 0 @@ -15734,8 +15630,6 @@ 0 0 0 - 0 - 0 1 1 0 @@ -15760,8 +15654,6 @@ 1792 115 115 - https://usegalaxy.eu/published/workflow?id=0609a4b1941d1a68, https://usegalaxy.eu/published/workflow?id=9fddc44294236e8f, https://usegalaxy.org/published/workflow?id=20b7ae4b517a80fd, https://usegalaxy.org/published/workflow?id=a71fcbc60caae8b6, https://workflowhub.eu/workflows/1272?version=2, https://workflowhub.eu/workflows/1854?version=1 - microbiome/mgnify-amplicon True False @@ -15784,7 +15676,9 @@ iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/micro_decon - https://github.com/galaxyproject/tools-iuc/tree/main/tools/micro_decon + https://github.com/galaxyproject/tools-iuc/tree/master/tools/micro_decon + + @@ -15835,10 +15729,6 @@ 0 0 0 - 0 - 0 - - True False @@ -15850,10 +15740,10 @@ Short-read assembler based on a de Bruijn graph 2020-04-08 https://gatb.inria.fr/software/minia/ - 3.2.6 + @TOOL_VERSION@ minia 3.2.6 - Up-to-date + To update Assembly Genome assembly Genome assembly @@ -15861,11 +15751,13 @@ Sequence assembly iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/minia - https://github.com/galaxyproject/tools-iuc/tree/main/tools/minia + https://github.com/galaxyproject/tools-iuc/tree/master/tools/minia minia Minia Short-read assembler based on a de Bruijn graph, capable of assembling a human genome on a desktop computer in a day. + https://usegalaxy.eu/published/workflow?id=9ba580ba8b01db40 + 0 1 1 @@ -15876,7 +15768,6 @@ 0 0 0 - 0 1 0 0 @@ -15889,7 +15780,6 @@ 0 0 0 - 0 1 1 1 @@ -15914,8 +15804,6 @@ 7115 364 349 - https://usegalaxy.eu/published/workflow?id=9ba580ba8b01db40 - True False @@ -15927,7 +15815,7 @@ Miniasm - Ultrafast de novo assembly for long noisy reads (though having no consensus step) 2019-06-18 https://github.com/lh3/miniasm - 0.3_r179 + @TOOL_VERSION@ miniasm 0.3 To update @@ -15938,11 +15826,13 @@ Genomics, Sequence assembly iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/miniasm - https://github.com/galaxyproject/tools-iuc/tree/main/tools/miniasm + https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniasm miniasm miniasm Miniasm is a very fast OLC-based de novo assembler for noisy long reads. It takes all-vs-all read self-mappings (typically by minimap) as input and outputs an assembly graph in the GFA format. + https://usegalaxy.eu/published/workflow?id=249c115413f17f28, https://usegalaxy.eu/published/workflow?id=32d2f5340098bcbd, https://usegalaxy.eu/published/workflow?id=39837ca09374598b, https://usegalaxy.eu/published/workflow?id=44e53ea319e07daa, https://usegalaxy.eu/published/workflow?id=b4de76c0a4d0e23a, https://usegalaxy.eu/published/workflow?id=c48807045e258dd8, https://usegalaxy.eu/published/workflow?id=dc7107896a3f2964, https://usegalaxy.org.au/published/workflow?id=d9571b3dfef34e5e, https://workflowhub.eu/workflows/1477?version=1, https://workflowhub.eu/workflows/406?version=1 + microbiome/plasmid-metagenomics-nanopore 1 1 1 @@ -15951,7 +15841,6 @@ 0 0 0 - 0 1 0 1 @@ -15966,7 +15855,6 @@ 0 0 0 - 0 1 1 1 @@ -15991,8 +15879,6 @@ 22031 1337 1149 - https://usegalaxy.eu/published/workflow?id=249c115413f17f28, https://usegalaxy.eu/published/workflow?id=32d2f5340098bcbd, https://usegalaxy.eu/published/workflow?id=39837ca09374598b, https://usegalaxy.eu/published/workflow?id=44e53ea319e07daa, https://usegalaxy.eu/published/workflow?id=b4de76c0a4d0e23a, https://usegalaxy.eu/published/workflow?id=c48807045e258dd8, https://usegalaxy.eu/published/workflow?id=dc7107896a3f2964, https://usegalaxy.org.au/published/workflow?id=d9571b3dfef34e5e, https://workflowhub.eu/workflows/1477?version=1, https://workflowhub.eu/workflows/406?version=1 - microbiome/plasmid-metagenomics-nanopore True False @@ -16020,6 +15906,8 @@ minipolish A tool that bridges the output of miniasm (long-read assembly) and racon (assembly polishing) together to polish a draft assembly. It also provides read depth information in contigs. + + 0 0 1 @@ -16030,7 +15918,6 @@ 0 0 0 - 0 1 0 0 @@ -16044,7 +15931,6 @@ 0 0 0 - 0 1 0 0 @@ -16068,8 +15954,6 @@ 278 43 43 - - True False @@ -16092,11 +15976,13 @@ Sequence sites, features and motifs, Sequence analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/miniprot - https://github.com/galaxyproject/tools-iuc/tree/main/tools/miniprot + https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot miniprot miniprot Miniprot aligns a protein sequence against a genome with affine gap penalty, splicing and frameshift. It is primarily intended for annotating protein-coding genes in a new species using known genes from other species. + https://usegalaxy.eu/published/workflow?id=0c92c3c322c3effe + 2 0 2 @@ -16120,8 +16006,6 @@ 0 0 0 - 0 - 0 2 0 0 @@ -16145,8 +16029,81 @@ 5685 167 167 - https://usegalaxy.eu/published/workflow?id=0c92c3c322c3effe + True + False + + + + mist_typing + mist_call, mist_dists + tabular, json + Wrappers for Minimap2-inferred Sequence Typing (MiST). + 2026-01-08 + https://github.com/BioinformaticsPlatformWIV-ISP/MiST + 1.2.0 + mist_typing + 1.2.0 + Up-to-date + Sequence Analysis, Phylogenetics + + + + + iuc + https://github.com/galaxyproject/tools-iuc/tree/main/tools/mist_typing + https://github.com/galaxyproject/tools-iuc/tree/master/tools/mist_typing + + + + + + 0 + 0 + 2 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 True False @@ -16158,7 +16115,7 @@ de-novo annotation of metazoan mitochondrial genomes 2020-02-18 http://mitos.bioinf.uni-leipzig.de/ - 1.1.7 + @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ mitos 2.1.10 To update @@ -16169,11 +16126,13 @@ Zoology, Whole genome sequencing iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/mitos - https://github.com/galaxyproject/tools-iuc/tree/main/tools/mitos + https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos mitos MITOS De novo metazoan mitochondrial genome annotation. + https://usegalaxy.eu/published/workflow?id=0de5fcc38ef1501d, https://usegalaxy.eu/published/workflow?id=2d0400b5d05c6c10, https://usegalaxy.org/published/workflow?id=110ad20060b03e02 + 1 1 2 @@ -16196,9 +16155,7 @@ 0 0 0 - 0 - 0 - 2 + 1 2 1 0 @@ -16222,8 +16179,6 @@ 367835 2265 2255 - https://usegalaxy.eu/published/workflow?id=0de5fcc38ef1501d, https://usegalaxy.eu/published/workflow?id=2d0400b5d05c6c10, https://usegalaxy.org/published/workflow?id=110ad20060b03e02 - True False @@ -16233,11 +16188,11 @@ mlst, mlst_list tabular, fasta, txt Scan contig files against PubMLST typing schemes - 2016-12-12 + 2016-12-13 https://github.com/tseemann/mlst 2.22.0 mlst - 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assembly/hybrid_denovo_assembly, assembly/largegenome, assembly/unicycler-assembly, contributing/create-new-tutorial-content, ecology/ENA_Biodiv_submission, ecology/ref-based-rad-seq, epigenetics/cut_and_run, galaxy-interface/workflow-automation, galaxy-interface/workflow-fairification, genome-annotation/crispr-screen, introduction/galaxy-intro-ngs-data-managment, introduction/vsi_qc, microbiome/host-removal, microbiome/mags-building, microbiome/metatranscriptomics, microbiome/metatranscriptomics-short, microbiome/mgnify-amplicon, microbiome/nanopore-16S-metagenomics, microbiome/pathogen-detection-from-nanopore-foodborne-data, sequence-analysis/mapping, sequence-analysis/quality-control, single-cell/scrna-preprocessing, single-cell/scrna-preprocessing-tenx, transcriptomics/differential-isoform-expression, transcriptomics/full-de-novo, transcriptomics/minerva-pathways, transcriptomics/mirna-target-finder, transcriptomics/ref-based, transcriptomics/rna-seq-reads-to-counts, variant-analysis/exome-seq, variant-analysis/sars-cov-2, variant-analysis/somatic-variant-discovery, variant-analysis/somatic-variants, variant-analysis/tb-variant-analysis True False @@ -17170,11 +17176,13 @@ Whole genome sequencing, Genotype and phenotype, Probes and primers, Genetic variation, Metagenomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/mykrobe - https://github.com/galaxyproject/tools-iuc/tree/main/tools/mykrobe + https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe Mykrobe Mykrobe Antibiotic resistance prediction for Mycobacterium tuberculosis from genome sequence data with Mykrobe.Antibiotic resistance prediction in minutes.Table of Contents generated with DocToc.AMR prediction (Mykrobe predictor).Before attempting to install with bioconda, please ensure you have your channels set up as specified in the documentation. If you don't, you may run into issues with an older version of mykrobe being installed + + 0 0 1 @@ -17185,7 +17193,6 @@ 0 0 0 - 0 1 0 0 @@ -17222,9 +17229,6 @@ 0 0 0 - 0 - - True False @@ -17236,7 +17240,7 @@ RScript to parse the results of mykrobe predictor. 2018-09-28 https://github.com/phac-nml/mykrobe-parser - 0.1.4.1 + @VERSION@ r-base To update @@ -17252,7 +17256,8 @@ - 0 + + 0 0 0 @@ -17299,9 +17304,6 @@ 0 0 0 - 0 - - True False @@ -17313,10 +17315,10 @@ Creates a SQLite database for proteomics data 2015-06-01 https://github.com/galaxyproteomics/mzToSQLite - 2.1.1+galaxy0 + 2.1.1 mztosqlite 2.1.1 - To update + Up-to-date Proteomics Conversion, Peptide database search Conversion, Peptide database search @@ -17329,6 +17331,8 @@ mzToSQLite Convert proteomics data files into a SQLite databaseExtract data from proteomics mzIdentML and mass spec scan files: mzML, MGF, etc and store in a SQLite database.The intended purpose is to provide a Galaxy dataset that can support an interactive Galaxy visualization plugin. + https://usegalaxy.eu/published/workflow?id=03e52c8c71710cae, https://usegalaxy.eu/published/workflow?id=0aee7ffa5f6384bd, https://usegalaxy.eu/published/workflow?id=2a7e63d1cc583002, https://usegalaxy.eu/published/workflow?id=41d096891bada138, https://usegalaxy.eu/published/workflow?id=41e9882300fa2386, https://usegalaxy.eu/published/workflow?id=6e5f0d05c91876c2, https://usegalaxy.eu/published/workflow?id=8a85663218676b59, https://usegalaxy.eu/published/workflow?id=9a8b5e99ca9500e3, https://usegalaxy.eu/published/workflow?id=b89cf3cb6a25c999, https://usegalaxy.eu/published/workflow?id=eb54512829d8509c, https://usegalaxy.eu/published/workflow?id=edea08c943ff9c5e, https://usegalaxy.org.au/published/workflow?id=1b9bfe7ce484fdc2, https://usegalaxy.org/published/workflow?id=f4486159b08900a4, https://workflowhub.eu/workflows/1429?version=2 + proteomics/proteogenomics-dbsearch 1 1 1 @@ -17351,8 +17355,6 @@ 0 0 0 - 0 - 0 1 1 1 @@ -17377,8 +17379,6 @@ 1287 181 171 - https://usegalaxy.eu/published/workflow?id=03e52c8c71710cae, https://usegalaxy.eu/published/workflow?id=0aee7ffa5f6384bd, https://usegalaxy.eu/published/workflow?id=2a7e63d1cc583002, https://usegalaxy.eu/published/workflow?id=41d096891bada138, https://usegalaxy.eu/published/workflow?id=41e9882300fa2386, https://usegalaxy.eu/published/workflow?id=6e5f0d05c91876c2, https://usegalaxy.eu/published/workflow?id=8a85663218676b59, https://usegalaxy.eu/published/workflow?id=9a8b5e99ca9500e3, https://usegalaxy.eu/published/workflow?id=b89cf3cb6a25c999, https://usegalaxy.eu/published/workflow?id=eb54512829d8509c, https://usegalaxy.eu/published/workflow?id=edea08c943ff9c5e, https://usegalaxy.org.au/published/workflow?id=1b9bfe7ce484fdc2, https://usegalaxy.org/published/workflow?id=f4486159b08900a4, https://workflowhub.eu/workflows/1429?version=2 - proteomics/proteogenomics-dbsearch True False @@ -17388,7 +17388,7 @@ nanocompore_db, nanocompore_sampcomp tabular, tar, txt Nanocompore compares 2 ONT nanopore direct RNA sequencing datasets from different experimental conditions expected to have a significant impact on RNA modifications. It is recommended to have at least 2 replicates per condition. For example one can use a control condition with a significantly reduced number of modifications such as a cell line for which a modification writing enzyme was knocked-down or knocked-out. Alternatively, on a smaller scale transcripts of interests could be synthesized in-vitro. - 2020-04-27 + 2020-04-28 https://nanocompore.rna.rocks/ 1.0.0rc3.post2 nanocompore @@ -17401,11 +17401,13 @@ Functional, regulatory and non-coding RNA, RNA-Seq, Gene transcripts, Transcriptomics, Transcription factors and regulatory sites iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanocompore - https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanocompore + https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore Nanocompore Nanocompore RNA modifications detection by comparative Nanopore direct RNA sequencing.RNA modifications detection from Nanopore dRNA-Seq data.Nanocompore identifies differences in ONT nanopore sequencing raw signal corresponding to RNA modifications by comparing 2 samples.Analyses performed for the nanocompore paper.Nanocompore compares 2 ONT nanopore direct RNA sequencing datasets from different experimental conditions expected to have a significant impact on RNA modifications. It is recommended to have at least 2 replicates per condition. For example one can use a control condition with a significantly reduced number of modifications such as a cell line for which a modification writing enzyme was knocked-down or knocked-out. Alternatively, on a smaller scale transcripts of interests could be synthesized in-vitro + https://usegalaxy.eu/published/workflow?id=778923dd04996e07, https://usegalaxy.eu/published/workflow?id=77db45ad90b4033d + 0 1 2 @@ -17428,8 +17430,6 @@ 0 0 0 - 0 - 0 2 2 2 @@ -17454,8 +17454,6 @@ 392 12 10 - https://usegalaxy.eu/published/workflow?id=778923dd04996e07, https://usegalaxy.eu/published/workflow?id=77db45ad90b4033d - True False @@ -17467,10 +17465,10 @@ Plotting tool for long read sequencing data and alignments 2018-09-24 https://github.com/wdecoster/NanoPlot - 1.46.2 + @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ nanoplot - 1.46.2 - Up-to-date + 1.47.1 + To update Visualization Scatter plot plotting, Box-Whisker plot plotting Scatter plot plotting, Box-Whisker plot plotting @@ -17478,11 +17476,13 @@ Genomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanoplot - https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanoplot + 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variant-analysis/sars-cov-2-variant-discovery True False @@ -18017,11 +18001,13 @@ iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/nonpareil - https://github.com/galaxyproject/tools-iuc/tree/main/tools/nonpareil + https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil nonpareil nonpareil Estimate metagenomic coverage and sequence diversity + + 1 0 1 @@ -18030,7 +18016,6 @@ 0 0 0 - 0 1 0 1 @@ -18045,7 +18030,6 @@ 0 0 0 - 0 1 1 1 @@ -18070,8 +18054,6 @@ 227 45 39 - - True False @@ -18094,11 +18076,13 @@ Sequencing, Genomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/nugen_nudup - https://github.com/galaxyproject/tools-iuc/tree/main/tools/nugen_nudup + https://github.com/galaxyproject/tools-iuc/tree/master/tools/nugen_nudup nudup NuDup Marks/removes duplicate molecules based on the molecular tagging technology used in Tecan products. + + 0 0 1 @@ -18145,24 +18129,20 @@ 0 0 0 - 0 - 0 - - True False obitools - obi_annotate, obi_clean, obi_convert, obi_grep, obi_multiplex, obi_pairing, obi_uniq - fasta + obi_annotate, obi_clean, obi_complement, obi_convert, obi_grep, obi_multiplex, obi_pairing, obi_pcr, obi_refidx, obi_tag, obi_taxonomy, obi_uniq + csv, fasta OBITools is a set of programs developed to simplify the manipulation of sequence files 2017-03-22 https://github.com/metabarcoding/obitools4 - 4.4.42 + 4.4.45 obitools4 - 4.4.42 + 4.4.45 Up-to-date Sequence Analysis @@ -18171,17 +18151,17 @@ iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/obitools - https://github.com/galaxyproject/tools-iuc/tree/main/tools/obitools + https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools + https://usegalaxy.eu/published/workflow?id=513389e1a8c6bba9, https://usegalaxy.eu/published/workflow?id=afad9a17a80bb26d, https://usegalaxy.eu/published/workflow?id=edf7e2128f5aef8d, https://usegalaxy.org.au/published/workflow?id=470eb26144325590, https://workflowhub.eu/workflows/1702?version=1, https://workflowhub.eu/workflows/655?version=1 + ecology/Obitools-metabarcoding 0 5 - 7 - 5 - 0 - 0 + 12 + 12 0 0 0 @@ -18224,8 +18204,6 @@ 32975 391 389 - https://usegalaxy.eu/published/workflow?id=513389e1a8c6bba9, https://usegalaxy.eu/published/workflow?id=afad9a17a80bb26d, https://usegalaxy.eu/published/workflow?id=edf7e2128f5aef8d, https://usegalaxy.org.au/published/workflow?id=470eb26144325590, https://workflowhub.eu/workflows/1702?version=1, https://workflowhub.eu/workflows/655?version=1 - ecology/Obitools-metabarcoding True False @@ -18248,11 +18226,13 @@ Proteomics, Sequence analysis, Statistics and probability iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/omark - https://github.com/galaxyproject/tools-iuc/tree/main/tools/omark + https://github.com/galaxyproject/tools-iuc/tree/master/tools/omark omark OMArk OMArk is a software for proteome (protein-coding gene repertoire) quality assessment. It provides measures of proteome completeness, characterizes the consistency of all protein coding genes with regard to their homologs, and identifies the presence of contamination from other species. OMArk relies on the OMA orthology database, from which it exploits orthology relationships, and on the OMAmer software for fast placement of all proteins into gene families. + https://usegalaxy.eu/published/workflow?id=31bc2a44fb89aa89, https://usegalaxy.eu/published/workflow?id=327beb1edda305ff, https://usegalaxy.eu/published/workflow?id=3d604dad4f1f5b3d, https://usegalaxy.eu/published/workflow?id=4077e77b6af919c4, https://usegalaxy.eu/published/workflow?id=6550f72070b24082, https://usegalaxy.eu/published/workflow?id=8976041ef89e4548, https://usegalaxy.org.au/published/workflow?id=dd9272826e6dd98d, https://usegalaxy.org.au/published/workflow?id=e263fcb6c98e231b, https://usegalaxy.org.au/published/workflow?id=ec7efff3d3249177, https://usegalaxy.org/published/workflow?id=4605309321799e9b, https://usegalaxy.org/published/workflow?id=80a7124c40438cc9, https://usegalaxy.org/published/workflow?id=f4111a169255535c, https://workflowhub.eu/workflows/1096?version=2, https://workflowhub.eu/workflows/1255?version=3, https://workflowhub.eu/workflows/1500?version=1, https://workflowhub.eu/workflows/1746?version=1, https://workflowhub.eu/workflows/2029?version=1 + genome-annotation/braker3, genome-annotation/comparison-braker-helixer-annotation, genome-annotation/helixer 1 1 1 @@ -18275,8 +18255,6 @@ 0 0 0 - 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Other popular ORF searching tools are OrfM and getorf. Compared to OrfM and getorf, orfipy provides the most options to fine tune ORF searches. orfipy uses multiple CPU cores and is particularly faster for data containing multiple smaller fasta sequences such as de-novo transcriptome assemblies. Please read the preprint here. + https://usegalaxy.eu/published/workflow?id=30dc526dcfa500df + genome-annotation/gene-centric 1 0 1 @@ -18430,8 +18406,6 @@ 0 0 0 - 0 - 0 1 0 0 @@ -18455,8 +18429,6 @@ 4285 515 515 - https://usegalaxy.eu/published/workflow?id=30dc526dcfa500df - genome-annotation/gene-centric True False @@ -18470,7 +18442,7 @@ https://github.com/davidemms/OrthoFinder 2.5.5 orthofinder - 3.1.4 + 3.1.5 To update Phylogenetics, Sequence Analysis Genome comparison, Phylogenetic tree generation (from molecular sequences), Phylogenetic tree analysis, Genome alignment @@ -18479,11 +18451,13 @@ Phylogenetics, Phylogenomics, Bioinformatics, Comparative genomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/orthofinder - https://github.com/galaxyproject/tools-iuc/tree/main/tools/orthofinder + https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder OrthoFinder OrthoFinder OrthoFinder is a fast, accurate and comprehensive platform for comparative genomics. 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0 - 0 1 1 0 @@ -19071,8 +19029,6 @@ 8949 323 323 - https://usegalaxy.eu/published/workflow?id=11eba1b28ec87963, https://usegalaxy.eu/published/workflow?id=1f9a9a7998ef5ab3, https://usegalaxy.eu/published/workflow?id=47a0407867a90f95, https://usegalaxy.eu/published/workflow?id=87231a6a7938cb95, https://usegalaxy.eu/published/workflow?id=9b025479fade745d, https://usegalaxy.eu/published/workflow?id=b7a3cbcd32734e8b, https://usegalaxy.org.au/published/workflow?id=6e1e24f9e0326930, https://workflowhub.eu/workflows/1688?version=1 - transcriptomics/differential-isoform-expression True False @@ -19095,11 +19051,13 @@ Metagenomics, Microbial ecology, Sequence assembly, Taxonomy ufz https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox - https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/phabox + https://github.com/Helmholtz-UFZ/galaxy-tools/tree/master/tools/phabox phabox PhaBOX Web server for identifying and characterizing phage contigs in metagenomic data. + + 0 0 0 @@ -19146,10 +19104,6 @@ 0 0 0 - 0 - 0 - - True False @@ -19172,11 +19126,13 @@ Metagenomics, Sequence sites, features and motifs, Workflows, Functional, regulatory and non-coding RNA iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/pharokka - https://github.com/galaxyproject/tools-iuc/tree/main/tools/pharokka + https://github.com/galaxyproject/tools-iuc/tree/master/tools/pharokka pharokka Pharokka Pharokka is a rapid standardised annotation tool for bacteriophage genomes and metagenomes. + https://usegalaxy.eu/published/workflow?id=46ef864fe9468894, https://usegalaxy.eu/published/workflow?id=62392daea25a3980 + 0 1 1 @@ -19187,7 +19143,6 @@ 0 0 0 - 0 1 0 0 @@ -19199,7 +19154,6 @@ 0 0 0 - 1 0 0 1 @@ -19225,8 +19179,6 @@ 18156 884 884 - https://usegalaxy.eu/published/workflow?id=46ef864fe9468894, https://usegalaxy.eu/published/workflow?id=62392daea25a3980 - True False @@ -19238,7 +19190,7 @@ Phage host interaction toolkit report generator 2025-06-04 https://git.ufz.de/borimcor/phage-host-analysis - 0.3.0 + @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ bioconductor-biostrings 2.78.0 To update @@ -19249,11 +19201,13 @@ ufz https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phi-toolkit - https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/phi-toolkit + https://github.com/Helmholtz-UFZ/galaxy-tools/tree/master/tools/phi-toolkit + https://usegalaxy.eu/published/workflow?id=c62d65832377e376 + 1 0 1 @@ -19300,10 +19254,6 @@ 0 0 0 - 0 - 0 - https://usegalaxy.eu/published/workflow?id=c62d65832377e376 - True False @@ -19326,11 +19276,13 @@ Microbiology, Sequence analysis, Metagenomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/phyloseq - https://github.com/galaxyproject/tools-iuc/tree/main/tools/phyloseq + https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq phyloseq phyloseq Provides a set of classes and tools to facilitate the import, storage, analysis, and graphical display of microbiome census data. + https://usegalaxy.eu/published/workflow?id=466bdd8ba7b67264, https://usegalaxy.eu/published/workflow?id=e3918808605cf8cd, https://usegalaxy.org/published/workflow?id=4faff660f6defa10, https://workflowhub.eu/workflows/1395?version=2 + microbiome/dada-16S 4 1 7 @@ -19339,7 +19291,6 @@ 0 0 0 - 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https://github.com/galaxyproject/tools-iuc/tree/main/tools/picrust2 + https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust2 picrust2 PICRUSt2 PICRUSt2 (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) is a software for predicting functional abundances based only on marker gene sequences. + https://usegalaxy.eu/published/workflow?id=be9ff4159593cc34 + 0 7 7 @@ -19585,8 +19531,6 @@ 0 0 0 - 0 - 0 7 0 0 @@ -19610,8 +19554,6 @@ 9321 392 392 - https://usegalaxy.eu/published/workflow?id=be9ff4159593cc34 - True False @@ -19634,7 +19576,9 @@ iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/pimento - https://github.com/galaxyproject/tools-iuc/tree/main/tools/pimento + https://github.com/galaxyproject/tools-iuc/tree/master/tools/pimento + + @@ -19665,8 +19609,6 @@ 0 0 0 - 0 - 0 1 1 2 @@ -19687,8 +19629,6 @@ 2 1 1 - - True False @@ -19711,7 +19651,9 @@ iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/pirate - https://github.com/galaxyproject/tools-iuc/tree/main/tools/pirate + https://github.com/galaxyproject/tools-iuc/tree/master/tools/pirate + + @@ -19762,10 +19704,6 @@ 0 0 0 - 0 - 0 - - True False @@ -19777,10 +19715,10 @@ PlasClass is a tool to classify sequences of plasmid or chromosomal origin 2025-07-31 https://github.com/Shamir-Lab/PlasClass - 0.1.1 + @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ plasclass 0.1.1 - Up-to-date + To update Sequence Analysis Sequence classification, Sequence assembly, k-mer counting Sequence classification, Sequence assembly, k-mer counting @@ -19788,11 +19726,13 @@ Metagenomics, Sequence assembly, DNA, Metagenomic sequencing iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/plasclass - https://github.com/galaxyproject/tools-iuc/tree/main/tools/plasclass + https://github.com/galaxyproject/tools-iuc/tree/master/tools/plasclass PlasClass PlasClass PlasClass is a tool for easy classification of sequences as either plasmid or chromosomal. For example, it can be used to classify the contigs in a (metagenomic) assembly. + https://usegalaxy.eu/published/workflow?id=d0339e4a794f4922 + 0 0 1 @@ -19839,10 +19779,6 @@ 0 0 0 - 0 - 0 - https://usegalaxy.eu/published/workflow?id=d0339e4a794f4922 - True False @@ -19854,10 +19790,10 @@ PlasFlow - Prediction of plasmid sequences in metagenomic contigs. 2018-09-05 https://github.com/smaegol/PlasFlow - 1.1.0 + @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ plasflow 1.1.0 - Up-to-date + To update Sequence Analysis Sequence analysis Sequence analysis @@ -19865,11 +19801,13 @@ Metagenomics, Sequence assembly, Mobile genetic elements, Machine learning iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/plasflow - https://github.com/galaxyproject/tools-iuc/tree/main/tools/plasflow + https://github.com/galaxyproject/tools-iuc/tree/master/tools/plasflow plasflow PlasFlow PlasFlow is a set of scripts used for prediction of plasmid sequences in metagenomic contigs. + https://usegalaxy.eu/published/workflow?id=152223c8aed27357, https://usegalaxy.eu/published/workflow?id=249c115413f17f28, https://usegalaxy.eu/published/workflow?id=3081569659a45b9e, https://usegalaxy.eu/published/workflow?id=32d2f5340098bcbd, https://usegalaxy.eu/published/workflow?id=39837ca09374598b, https://usegalaxy.eu/published/workflow?id=44e53ea319e07daa, https://usegalaxy.eu/published/workflow?id=9219557de92e0203, https://usegalaxy.eu/published/workflow?id=b4de76c0a4d0e23a, https://usegalaxy.eu/published/workflow?id=c48807045e258dd8, https://usegalaxy.eu/published/workflow?id=dc7107896a3f2964, https://usegalaxy.org.au/published/workflow?id=d9571b3dfef34e5e, https://usegalaxy.org/published/workflow?id=33d90e718ce500ef, https://workflowhub.eu/workflows/1477?version=1, https://workflowhub.eu/workflows/406?version=1 + microbiome/plasmid-metagenomics-nanopore 1 1 1 @@ -19878,7 +19816,6 @@ 0 0 0 - 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genome-annotation/bacterial-genome-annotation True False @@ -20010,7 +19942,7 @@ 1.1 spades - 4.2.0 + 4.3.0 To update Assembly @@ -20024,7 +19956,8 @@ - 0 + + 0 0 0 @@ -20071,9 +20004,6 @@ 0 0 0 - 0 - - True False @@ -20096,11 +20026,13 @@ Sequence assembly, Sequence composition, complexity and repeats, Mapping iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/polypolish - https://github.com/galaxyproject/tools-iuc/tree/main/tools/polypolish + https://github.com/galaxyproject/tools-iuc/tree/master/tools/polypolish Polypolish Polypolish Polypolish is a tool for polishing genome assemblies with short reads. Unlike other tools in this category, Polypolish uses SAM files where each read has been aligned to all possible locations (not just a single best location). This allows it to repair errors in repeat regions that other alignment-based polishers cannot fix. + https://usegalaxy.eu/published/workflow?id=2c992e509aa5dd9d, https://workflowhub.eu/workflows/1613?version=2 + assembly/mrsa-nanopore 0 1 1 @@ -20109,7 +20041,6 @@ 0 0 0 - 0 1 0 1 @@ -20124,7 +20055,6 @@ 0 0 0 - 0 1 1 0 @@ -20149,8 +20079,6 @@ 1760 183 183 - https://usegalaxy.eu/published/workflow?id=2c992e509aa5dd9d, https://workflowhub.eu/workflows/1613?version=2 - assembly/mrsa-nanopore True False @@ -20173,11 +20101,13 @@ Metagenomics, Gene and protein families, Model organisms, Public health and epidemiology, Mapping iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/ppanggolin - https://github.com/galaxyproject/tools-iuc/tree/main/tools/ppanggolin + https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin ppanggolin PPanGGOLiN PPanGGOLiN is a software suite used to create and manipulate prokaryotic pangenomes from a set of either genomic DNA sequences or provided genome annotations. 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It generates summary statistics of the input in graphical and tabular formats that can be used for quality control steps. PRINSEQ is available as both standalone and web-based versions. + + https://usegalaxy.eu/published/workflow?id=0609a4b1941d1a68, https://usegalaxy.eu/published/workflow?id=76e9cd837ea5e7da, https://usegalaxy.eu/published/workflow?id=8f415b0c409f56f7, https://usegalaxy.eu/published/workflow?id=9fddc44294236e8f, https://usegalaxy.eu/published/workflow?id=d6ff6be33b8bfe85, https://usegalaxy.eu/published/workflow?id=da19c0eaa757fa39, https://usegalaxy.org/published/workflow?id=20b7ae4b517a80fd, https://usegalaxy.org/published/workflow?id=46f184a0e95f3c1c, https://usegalaxy.org/published/workflow?id=5f878c4cc3bff68c, https://usegalaxy.org/published/workflow?id=a71fcbc60caae8b6, https://usegalaxy.org/published/workflow?id=afb67b4b9952f57d, https://workflowhub.eu/workflows/1271?version=3, https://workflowhub.eu/workflows/1272?version=2, https://workflowhub.eu/workflows/1850?version=1, https://workflowhub.eu/workflows/1854?version=1 + microbiome/mgnify-amplicon + 1 + 0 + 1 + 1 + 0 + 0 + 0 + 0 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qiime2__cutadapt__trim_single qza - 2022-08-26 - https://github.com/qiime2/q2-quality-filter + 2022-08-25 + https://github.com/qiime2/q2-cutadapt 2026.1.0+q2galaxy.2026.1.0 @@ -20942,23 +21000,23 @@ Microbial ecology, Metatranscriptomics, Metagenomics Microbial ecology, Metatranscriptomics, Metagenomics q2d2 - https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_filter - https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_filter + https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt + https://github.com/qiime2/galaxy-tools/tree/master/tools/suite_qiime2__cutadapt qiime2 QIIME 2 QIIME 2 is an AI-ready microbiome multi-omics data science platform that is trusted, free, open source, extensible, and community developed and supported bioinformatics. - 1 - 1 - 1 - 1 - 0 - 0 + + + 4 + 4 + 4 + 4 0 0 0 - 1 0 + 4 0 0 0 @@ -20973,43 +21031,41 @@ 0 0 0 - 1 + 4 0 0 - 25 - 25 - 55 - 55 - 16 - 16 - 39 - 39 + 73 + 73 + 364 + 364 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qiime2__rescript__get_pr2_data, qiime2__rescript__get_silva_data, qiime2__rescript__get_unite_data, qiime2__rescript__merge_taxa, qiime2__rescript__orient_reads, qiime2__rescript__orient_seqs, qiime2__rescript__parse_silva_taxonomy, qiime2__rescript__reverse_transcribe, qiime2__rescript__subsample_fasta, qiime2__rescript__trim_alignment + qiime2__composition__add_pseudocount, qiime2__composition__ancom, qiime2__composition__ancombc, qiime2__composition__ancombc2, qiime2__composition__ancombc2_visualizer, qiime2__composition__da_barplot, qiime2__composition__tabulate qza, qzv - 2024-04-25 - https://github.com/nbokulich/RESCRIPt - 2026.1.0+q2galaxy.2026.1.0 + 2022-08-25 + https://github.com/qiime2/q2-composition + 2026.1.0+0.g4b3aa86.dirty-q2galaxy.2026.1.0 To update @@ -21019,22 +21075,25 @@ Microbial ecology, Metatranscriptomics, Metagenomics Microbial ecology, Metatranscriptomics, Metagenomics q2d2 - https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript - https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript + https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition + https://github.com/qiime2/galaxy-tools/tree/master/tools/suite_qiime2__composition qiime2 QIIME 2 QIIME 2 is an AI-ready microbiome multi-omics data science platform that is trusted, free, open source, extensible, and community developed and supported bioinformatics. - 0 - 0 - 3 + + + 4 + 6 + 4 + 2 0 0 0 0 + 4 0 0 - 3 0 0 0 @@ -21047,45 +21106,40 @@ 0 0 0 + 4 0 0 - 0 - 0 - 0 - 0 - 6 - 6 - 18 - 18 - 0 - 0 - 0 - 0 - 0 - 0 - 0 - 0 - 0 - 0 - 0 - 0 - 18 - 18 - 6 - 6 - - + 26 + 26 + 388 + 388 + 31 + 31 + 256 + 256 + 8 + 8 + 325 + 325 + 9 + 9 + 89 + 89 + 1058 + 1058 + 74 + 74 True False qiime2 - qiime2__sample_classifier__classify_samples, qiime2__sample_classifier__classify_samples_from_dist, qiime2__sample_classifier__classify_samples_ncv, qiime2__sample_classifier__confusion_matrix, qiime2__sample_classifier__fit_classifier, qiime2__sample_classifier__fit_regressor, qiime2__sample_classifier__heatmap, qiime2__sample_classifier__metatable, qiime2__sample_classifier__predict_classification, qiime2__sample_classifier__predict_regression, qiime2__sample_classifier__regress_samples, qiime2__sample_classifier__regress_samples_ncv, qiime2__sample_classifier__scatterplot, qiime2__sample_classifier__split_table, qiime2__sample_classifier__summarize + qiime2__boots__alpha, qiime2__boots__alpha_average, qiime2__boots__alpha_collection, qiime2__boots__beta, qiime2__boots__beta_average, qiime2__boots__beta_collection, qiime2__boots__core_metrics, qiime2__boots__kmer_diversity, qiime2__boots__resample qza, qzv - 2022-08-26 - https://github.com/qiime2/q2-sample-classifier + 2025-11-01 + https://library.qiime2.org/plugins/caporaso-lab/q2-boots 2026.1.0+q2galaxy.2026.1.0 @@ -21096,99 +21150,19 @@ Microbial ecology, Metatranscriptomics, Metagenomics Microbial ecology, Metatranscriptomics, Metagenomics q2d2 - 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-21204,68 +21178,13 @@ 0 0 0 - 12 0 0 - 167 - 167 - 880 - 880 - 93 - 93 - 338 - 338 - 66 - 66 - 373 - 373 - 13 - 13 - 91 - 91 - 1682 - 1682 - 339 - 339 - https://usegalaxy.eu/published/workflow?id=7c07e87c77dcee05 - - True - False - - - - qiime2 - qiime2__metadata__distance_matrix, qiime2__metadata__merge, qiime2__metadata__shuffle_groups, qiime2__metadata__tabulate - qza, qzv - - 2022-08-26 - https://github.com/qiime2/q2-metadata - 2026.1.0+q2galaxy.2026.1.0 - - - To update - Metagenomics, Sequence Analysis, Statistics - Demultiplexing, Visualisation, Taxonomic classification - Demultiplexing, Visualisation, Taxonomic classification - Microbial ecology, Metatranscriptomics, Metagenomics - Microbial ecology, Metatranscriptomics, Metagenomics - q2d2 - https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__metadata - https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__metadata - qiime2 - QIIME 2 - QIIME 2 is an AI-ready microbiome multi-omics data science 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@@ Microbial ecology, Metatranscriptomics, Metagenomics Microbial ecology, Metatranscriptomics, Metagenomics q2d2 - https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__stats - https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__stats + https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch + https://github.com/qiime2/galaxy-tools/tree/master/tools/suite_qiime2__vsearch qiime2 QIIME 2 QIIME 2 is an AI-ready microbiome multi-omics data science platform that is trusted, free, open source, extensible, and community developed and supported bioinformatics. - 0 - 0 - 9 - 0 - 0 - 0 - 0 - 0 - 0 - 6 - 0 - 0 - 0 - 0 - 0 - 0 - 0 - 0 - 0 - 0 - 0 - 0 - 0 - 0 - 0 - 0 - 0 - 0 + + + 8 + 8 + 8 + 8 0 0 0 0 + 8 0 0 0 @@ -21379,21 +21256,40 @@ 0 0 0 + 8 0 0 - - + 31 + 31 + 409 + 409 + 18 + 18 + 280 + 280 + 5 + 5 + 24 + 24 + 10 + 10 + 77 + 77 + 790 + 790 + 64 + 64 True False qiime2 - qiime2__quality_control__bowtie2_build, 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https://usegalaxy.org/published/workflow?id=b335f75495dab9b4, https://usegalaxy.org/published/workflow?id=b92e0ee710d167b2, https://workflowhub.eu/workflows/893?version=3 + 6 6 6 @@ -21418,7 +21316,6 @@ 0 0 0 - 0 6 0 0 @@ -21434,43 +21331,40 @@ 0 0 0 - 0 6 0 0 - 4 - 4 - 6 - 6 - 11 - 11 - 105 - 105 - 4 - 4 - 11 - 11 - 0 - 0 - 0 - 0 - 122 - 122 - 19 - 19 - - + 289 + 289 + 1358 + 1358 + 251 + 251 + 1071 + 1071 + 91 + 91 + 1146 + 1146 + 28 + 28 + 127 + 127 + 3702 + 3702 + 659 + 659 True False qiime2 - qiime2__diversity_lib__alpha_passthrough, qiime2__diversity_lib__beta_passthrough, qiime2__diversity_lib__beta_phylogenetic_meta_passthrough, qiime2__diversity_lib__beta_phylogenetic_passthrough, qiime2__diversity_lib__bray_curtis, qiime2__diversity_lib__faith_pd, qiime2__diversity_lib__jaccard, qiime2__diversity_lib__observed_features, qiime2__diversity_lib__pielou_evenness, qiime2__diversity_lib__shannon_entropy, qiime2__diversity_lib__unweighted_unifrac, qiime2__diversity_lib__weighted_unifrac - qza + qiime2__deblur__denoise_16S, qiime2__deblur__denoise_other, qiime2__deblur__visualize_stats + qza, qzv - 2022-08-26 - https://github.com/qiime2/q2-diversity-lib + 2022-08-25 + https://github.com/biocore/deblur 2026.1.0+q2galaxy.2026.1.0 @@ -21481,23 +21375,23 @@ Microbial ecology, Metatranscriptomics, Metagenomics Microbial ecology, Metatranscriptomics, Metagenomics q2d2 - https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib - https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib + https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__deblur + https://github.com/qiime2/galaxy-tools/tree/master/tools/suite_qiime2__deblur qiime2 QIIME 2 QIIME 2 is an AI-ready microbiome multi-omics data science platform that is trusted, free, open source, extensible, and community developed and supported bioinformatics. - 12 - 12 - 12 - 12 - 0 - 0 + + + 3 + 3 + 3 + 3 0 0 0 - 12 0 + 2 0 0 0 @@ -21512,42 +21406,40 @@ 0 0 0 - 12 + 3 0 0 - 4 - 4 - 33 - 33 + 40 + 40 + 225 + 225 + 24 + 24 + 78 + 78 + 9 + 9 + 177 + 177 + 1 + 1 8 8 - 47 - 47 - 6 - 6 - 2850 - 2850 - 2 - 2 - 3 - 3 - 2933 - 2933 - 20 - 20 - https://usegalaxy.org/published/workflow?id=7251c6e0dad8f927 - + 488 + 488 + 74 + 74 True False qiime2 - qiime2__alignment__mafft, qiime2__alignment__mafft_add, qiime2__alignment__mask - qza + qiime2__diversity__adonis, qiime2__diversity__alpha, qiime2__diversity__alpha_correlation, qiime2__diversity__alpha_group_significance, qiime2__diversity__alpha_phylogenetic, qiime2__diversity__alpha_rarefaction, qiime2__diversity__beta, qiime2__diversity__beta_correlation, qiime2__diversity__beta_group_significance, qiime2__diversity__beta_phylogenetic, qiime2__diversity__beta_rarefaction, qiime2__diversity__bioenv, qiime2__diversity__core_metrics, qiime2__diversity__core_metrics_phylogenetic, qiime2__diversity__filter_alpha_diversity, qiime2__diversity__filter_distance_matrix, qiime2__diversity__mantel, qiime2__diversity__partial_procrustes, qiime2__diversity__pcoa, qiime2__diversity__pcoa_biplot, qiime2__diversity__procrustes_analysis, qiime2__diversity__tsne, qiime2__diversity__umap + qzv, qza - 2022-08-26 - https://github.com/qiime2/q2-alignment + 2022-08-25 + https://github.com/qiime2/q2-diversity 2026.1.0+q2galaxy.2026.1.0 @@ -21558,23 +21450,23 @@ Microbial ecology, Metatranscriptomics, Metagenomics Microbial ecology, Metatranscriptomics, Metagenomics q2d2 - https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment - https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment + https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity + https://github.com/qiime2/galaxy-tools/tree/master/tools/suite_qiime2__diversity qiime2 QIIME 2 QIIME 2 is an AI-ready microbiome multi-omics data science platform that is trusted, free, open source, extensible, and community developed and supported bioinformatics. - 3 - 3 - 3 - 3 - 0 - 0 + https://usegalaxy.eu/published/workflow?id=457a3de5c1512707, https://usegalaxy.eu/published/workflow?id=6e5fad1de09af683, https://usegalaxy.eu/published/workflow?id=a91c46b9e0c1d635, https://usegalaxy.org.au/published/workflow?id=543001c51567b438, https://usegalaxy.org/published/workflow?id=7251c6e0dad8f927, https://usegalaxy.org/published/workflow?id=c6b6524108f53688, https://usegalaxy.org/published/workflow?id=ef28b1c267b5a318 + + 21 + 22 + 22 + 21 0 0 0 - 3 0 + 22 0 0 0 @@ -21589,42 +21481,40 @@ 0 0 0 - 3 + 21 0 0 - 67 - 67 - 390 - 390 - 35 - 35 - 78 - 78 - 16 - 16 - 114 - 114 - 14 - 14 - 69 - 69 - 651 - 651 - 132 - 132 - - + 135 + 135 + 3770 + 3770 + 88 + 88 + 2286 + 2286 + 60 + 60 + 1211 + 1211 + 26 + 26 + 360 + 360 + 7627 + 7627 + 309 + 309 True False qiime2 - qiime2__vizard__boxplot, qiime2__vizard__heatmap, qiime2__vizard__lineplot, qiime2__vizard__scatterplot_2d + qiime2__emperor__biplot, qiime2__emperor__plot, qiime2__emperor__procrustes_plot qzv - 2024-10-30 - https://github.com/qiime2/q2-vizard + 2022-08-25 + http://biocore.github.io/emperor/build/html/index.html 2026.1.0+q2galaxy.2026.1.0 @@ -21635,44 +21525,27 @@ Microbial ecology, Metatranscriptomics, Metagenomics Microbial ecology, Metatranscriptomics, Metagenomics q2d2 - https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vizard - https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vizard + https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__emperor + https://github.com/qiime2/galaxy-tools/tree/master/tools/suite_qiime2__emperor qiime2 QIIME 2 QIIME 2 is an AI-ready microbiome multi-omics data science platform that is trusted, free, open source, extensible, and community developed and supported bioinformatics. - 0 - 0 - 4 - 0 - 0 - 0 - 0 - 0 - 0 - 1 - 0 - 0 - 0 - 0 - 0 - 0 - 0 - 0 - 0 - 0 + + + 3 + 3 + 3 + 3 0 0 0 0 + 3 0 0 0 0 - 5 - 5 - 20 - 20 0 0 0 @@ -21683,26 +21556,41 @@ 0 0 0 + 3 0 0 - 20 - 20 - 5 - 5 - - + 42 + 42 + 142 + 142 + 34 + 34 + 198 + 198 + 15 + 15 + 195 + 195 + 9 + 9 + 27 + 27 + 562 + 562 + 100 + 100 True False qiime2 - qiime2__diversity__adonis, qiime2__diversity__alpha, qiime2__diversity__alpha_correlation, qiime2__diversity__alpha_group_significance, qiime2__diversity__alpha_phylogenetic, qiime2__diversity__alpha_rarefaction, qiime2__diversity__beta, qiime2__diversity__beta_correlation, qiime2__diversity__beta_group_significance, qiime2__diversity__beta_phylogenetic, qiime2__diversity__beta_rarefaction, qiime2__diversity__bioenv, qiime2__diversity__core_metrics, qiime2__diversity__core_metrics_phylogenetic, qiime2__diversity__filter_alpha_diversity, qiime2__diversity__filter_distance_matrix, qiime2__diversity__mantel, qiime2__diversity__partial_procrustes, qiime2__diversity__pcoa, qiime2__diversity__pcoa_biplot, qiime2__diversity__procrustes_analysis, qiime2__diversity__tsne, qiime2__diversity__umap - qzv, qza + qiime2_core__tools__export, qiime2_core__tools__import, qiime2_core__tools__import_fastq + qza - 2022-08-26 - https://github.com/qiime2/q2-diversity - 2026.1.0+q2galaxy.2026.1.0 + 2022-08-25 + https://qiime2.org + 2026.1.0+dist.h02a552c2 To update @@ -21712,23 +21600,23 @@ Microbial ecology, Metatranscriptomics, Metagenomics Microbial ecology, Metatranscriptomics, Metagenomics q2d2 - https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity - https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity + https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2_core__tools + https://github.com/qiime2/galaxy-tools/tree/master/tools/suite_qiime2_core__tools qiime2 QIIME 2 QIIME 2 is an AI-ready microbiome multi-omics data science platform that is trusted, free, open source, extensible, and community developed and supported bioinformatics. - 21 - 22 - 22 - 21 - 0 - 0 + https://usegalaxy.eu/published/workflow?id=3d0039098a87642c, https://usegalaxy.eu/published/workflow?id=457a3de5c1512707, https://usegalaxy.eu/published/workflow?id=5528702f49c33d83, https://usegalaxy.eu/published/workflow?id=5d401d357500617f, https://usegalaxy.eu/published/workflow?id=6e5fad1de09af683, https://usegalaxy.eu/published/workflow?id=86b31ac8a7720e41, https://usegalaxy.eu/published/workflow?id=a91c46b9e0c1d635, https://usegalaxy.eu/published/workflow?id=b1f68ff8158d0b85, https://usegalaxy.eu/published/workflow?id=b2975bb705d3e851, https://usegalaxy.eu/published/workflow?id=be9ff4159593cc34, https://usegalaxy.eu/published/workflow?id=c0b5b499b149005f, https://usegalaxy.eu/published/workflow?id=c58941443cec9380, https://usegalaxy.eu/published/workflow?id=ca5da5179cefec8b, https://usegalaxy.eu/published/workflow?id=fb96000c99db2fa8, https://usegalaxy.org.au/published/workflow?id=19b0f96df6d09b4e, https://usegalaxy.org.au/published/workflow?id=3c1bf73067334071, https://usegalaxy.org.au/published/workflow?id=543001c51567b438, https://usegalaxy.org.au/published/workflow?id=57aa23f4f0418a07, https://usegalaxy.org.au/published/workflow?id=cddd668a29b1488a, https://usegalaxy.org.au/published/workflow?id=f946d722f7c27479, https://usegalaxy.org/published/workflow?id=0dc387dc861bdb61, https://usegalaxy.org/published/workflow?id=4ca9319c98be08f8, https://usegalaxy.org/published/workflow?id=685b0de4c31f6695, https://usegalaxy.org/published/workflow?id=76b2c4762dd61d03, https://usegalaxy.org/published/workflow?id=7aa87e7f9cfdae78, https://usegalaxy.org/published/workflow?id=a7cc1038b14f2201, https://usegalaxy.org/published/workflow?id=b335f75495dab9b4, https://usegalaxy.org/published/workflow?id=b92e0ee710d167b2, https://usegalaxy.org/published/workflow?id=c6b6524108f53688, https://usegalaxy.org/published/workflow?id=ef28b1c267b5a318, https://workflowhub.eu/workflows/2098?version=1, https://workflowhub.eu/workflows/893?version=3 + + 3 + 3 + 3 + 3 0 0 0 - 22 0 + 3 0 0 0 @@ -21743,42 +21631,40 @@ 0 0 0 - 21 + 2 0 0 - 135 - 135 - 3770 - 3770 - 88 - 88 - 2286 - 2286 - 60 - 60 - 1211 - 1211 - 26 - 26 - 360 - 360 - 7627 - 7627 - 309 - 309 - https://usegalaxy.eu/published/workflow?id=457a3de5c1512707, https://usegalaxy.eu/published/workflow?id=6e5fad1de09af683, https://usegalaxy.eu/published/workflow?id=a91c46b9e0c1d635, https://usegalaxy.org.au/published/workflow?id=543001c51567b438, https://usegalaxy.org/published/workflow?id=7251c6e0dad8f927, https://usegalaxy.org/published/workflow?id=c6b6524108f53688, https://usegalaxy.org/published/workflow?id=ef28b1c267b5a318 - + 636 + 636 + 61165 + 61165 + 813 + 813 + 58124 + 58124 + 228 + 228 + 10152 + 10152 + 62 + 62 + 2237 + 2237 + 131678 + 131678 + 1739 + 1739 True False qiime2 - qiime2__demux__emp_paired, qiime2__demux__emp_single, qiime2__demux__filter_samples, qiime2__demux__partition_samples_paired, qiime2__demux__partition_samples_single, qiime2__demux__subsample_paired, qiime2__demux__subsample_single, qiime2__demux__summarize, qiime2__demux__tabulate_read_counts - qza, qzv + qiime2__taxa__barplot, qiime2__taxa__barplot2, qiime2__taxa__collapse, qiime2__taxa__filter_seqs, qiime2__taxa__filter_table + qzv, qza - 2022-08-26 - https://github.com/qiime2/q2-demux + 2022-08-25 + https://github.com/qiime2/q2-taxa 2026.1.0+q2galaxy.2026.1.0 @@ -21789,23 +21675,23 @@ Microbial ecology, Metatranscriptomics, Metagenomics Microbial ecology, Metatranscriptomics, Metagenomics q2d2 - https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__demux - https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__demux + https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa + https://github.com/qiime2/galaxy-tools/tree/master/tools/suite_qiime2__taxa qiime2 QIIME 2 QIIME 2 is an AI-ready microbiome multi-omics data science platform that is trusted, free, open source, extensible, and community developed and supported bioinformatics. - 6 - 6 - 6 - 6 - 0 - 0 + https://usegalaxy.eu/published/workflow?id=be9ff4159593cc34, https://usegalaxy.eu/published/workflow?id=e2af8c661e98f4f4, https://workflowhub.eu/workflows/2098?version=1 + + 4 + 4 + 4 + 4 0 0 0 - 6 0 + 4 0 0 0 @@ -21820,42 +21706,40 @@ 0 0 0 - 6 + 4 0 0 - 289 - 289 - 1358 - 1358 - 251 - 251 - 1071 - 1071 - 91 - 91 - 1146 - 1146 - 28 - 28 - 127 - 127 - 3702 - 3702 - 659 - 659 - https://usegalaxy.eu/published/workflow?id=3d0039098a87642c, https://usegalaxy.eu/published/workflow?id=5528702f49c33d83, https://usegalaxy.eu/published/workflow?id=5d401d357500617f, https://usegalaxy.eu/published/workflow?id=86b31ac8a7720e41, https://usegalaxy.eu/published/workflow?id=b1f68ff8158d0b85, https://usegalaxy.eu/published/workflow?id=b2975bb705d3e851, https://usegalaxy.eu/published/workflow?id=be9ff4159593cc34, https://usegalaxy.eu/published/workflow?id=c0b5b499b149005f, https://usegalaxy.eu/published/workflow?id=c58941443cec9380, https://usegalaxy.eu/published/workflow?id=ca5da5179cefec8b, https://usegalaxy.eu/published/workflow?id=fb96000c99db2fa8, https://usegalaxy.org.au/published/workflow?id=19b0f96df6d09b4e, https://usegalaxy.org.au/published/workflow?id=3c1bf73067334071, https://usegalaxy.org.au/published/workflow?id=57aa23f4f0418a07, https://usegalaxy.org.au/published/workflow?id=cddd668a29b1488a, https://usegalaxy.org.au/published/workflow?id=f946d722f7c27479, https://usegalaxy.org/published/workflow?id=0dc387dc861bdb61, https://usegalaxy.org/published/workflow?id=4ca9319c98be08f8, https://usegalaxy.org/published/workflow?id=685b0de4c31f6695, https://usegalaxy.org/published/workflow?id=76b2c4762dd61d03, https://usegalaxy.org/published/workflow?id=7aa87e7f9cfdae78, https://usegalaxy.org/published/workflow?id=a7cc1038b14f2201, https://usegalaxy.org/published/workflow?id=b335f75495dab9b4, https://usegalaxy.org/published/workflow?id=b92e0ee710d167b2, https://workflowhub.eu/workflows/893?version=3 - + 266 + 266 + 2747 + 2747 + 159 + 159 + 1008 + 1008 + 78 + 78 + 690 + 690 + 22 + 22 + 236 + 236 + 4681 + 4681 + 525 + 525 True False qiime2 - qiime2__deblur__denoise_16S, qiime2__deblur__denoise_other, qiime2__deblur__visualize_stats - qza, qzv + qiime2__diversity_lib__alpha_passthrough, qiime2__diversity_lib__beta_passthrough, qiime2__diversity_lib__beta_phylogenetic_meta_passthrough, qiime2__diversity_lib__beta_phylogenetic_passthrough, qiime2__diversity_lib__bray_curtis, qiime2__diversity_lib__faith_pd, qiime2__diversity_lib__jaccard, qiime2__diversity_lib__observed_features, qiime2__diversity_lib__pielou_evenness, qiime2__diversity_lib__shannon_entropy, qiime2__diversity_lib__unweighted_unifrac, qiime2__diversity_lib__weighted_unifrac + qza - 2022-08-26 - https://github.com/biocore/deblur + 2022-08-25 + https://github.com/qiime2/q2-diversity-lib 2026.1.0+q2galaxy.2026.1.0 @@ -21866,23 +21750,23 @@ Microbial ecology, Metatranscriptomics, Metagenomics Microbial ecology, Metatranscriptomics, Metagenomics q2d2 - https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__deblur - https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__deblur + https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib + https://github.com/qiime2/galaxy-tools/tree/master/tools/suite_qiime2__diversity_lib qiime2 QIIME 2 QIIME 2 is an AI-ready microbiome multi-omics data science platform that is trusted, free, open source, extensible, and community developed and supported bioinformatics. - 3 - 3 - 3 - 3 - 0 - 0 + https://usegalaxy.org/published/workflow?id=7251c6e0dad8f927 + + 12 + 12 + 12 + 12 0 0 0 - 2 0 + 12 0 0 0 @@ -21897,42 +21781,40 @@ 0 0 0 - 3 + 12 0 0 - 40 - 40 - 225 - 225 - 24 - 24 - 78 - 78 - 9 - 9 - 177 - 177 - 1 - 1 + 4 + 4 + 33 + 33 8 8 - 488 - 488 - 74 - 74 - - + 47 + 47 + 6 + 6 + 2850 + 2850 + 2 + 2 + 3 + 3 + 2933 + 2933 + 20 + 20 True False qiime2 - qiime2__dada2__denoise_ccs, qiime2__dada2__denoise_paired, qiime2__dada2__denoise_pyro, qiime2__dada2__denoise_single, qiime2__dada2__plot_base_transitions + qiime2__stats__alpha_group_significance, qiime2__stats__collate_stats, qiime2__stats__facet_across, qiime2__stats__facet_within, qiime2__stats__mann_whitney_u, qiime2__stats__mann_whitney_u_facet, qiime2__stats__plot_rainclouds, qiime2__stats__prep_alpha_distribution, qiime2__stats__wilcoxon_srt, qiime2__stats__wilcoxon_srt_facet qza, qzv - 2022-08-26 - http://benjjneb.github.io/dada2/ + 2024-10-30 + https://github.com/qiime2/q2-stats 2026.1.0+q2galaxy.2026.1.0 @@ -21943,22 +21825,43 @@ Microbial ecology, Metatranscriptomics, Metagenomics Microbial ecology, Metatranscriptomics, Metagenomics q2d2 - https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 - https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 + https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__stats + https://github.com/qiime2/galaxy-tools/tree/master/tools/suite_qiime2__stats qiime2 QIIME 2 QIIME 2 is an AI-ready microbiome multi-omics data science platform that is trusted, free, open source, extensible, and community developed and supported bioinformatics. - 4 - 4 - 4 - 4 + + + 0 + 9 + 9 + 0 + 0 + 0 + 0 + 0 + 6 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 0 0 0 0 0 - 4 0 0 0 @@ -21974,42 +21877,19 @@ 0 0 0 - 4 0 0 - 319 - 319 - 2670 - 2670 - 253 - 253 - 1230 - 1230 - 79 - 79 - 843 - 843 - 29 - 29 - 182 - 182 - 4925 - 4925 - 680 - 680 - https://usegalaxy.eu/published/workflow?id=3d0039098a87642c, https://usegalaxy.eu/published/workflow?id=5223c9554718114d, https://usegalaxy.eu/published/workflow?id=851b97ea3d1de9f7, https://usegalaxy.eu/published/workflow?id=b3d48f81329926fc, https://usegalaxy.eu/published/workflow?id=be9ff4159593cc34, https://usegalaxy.eu/published/workflow?id=da17a4d690eb0ff3, https://usegalaxy.eu/published/workflow?id=e1f08a63fbc8e173, https://usegalaxy.org.au/published/workflow?id=2d16ed86414f23b3, https://usegalaxy.org.au/published/workflow?id=fb517ec08b571a2d, https://usegalaxy.org/published/workflow?id=517f307db25e4715, https://usegalaxy.org/published/workflow?id=8bb471c28e1a30a3, https://usegalaxy.org/published/workflow?id=a382adce80293f0d, https://usegalaxy.org/published/workflow?id=d32392a39c4d6fbf, https://workflowhub.eu/workflows/892?version=3 - True False qiime2 - qiime2__cutadapt__demux_paired, qiime2__cutadapt__demux_single, qiime2__cutadapt__trim_paired, qiime2__cutadapt__trim_single - qza + qiime2__sample_classifier__classify_samples, qiime2__sample_classifier__classify_samples_from_dist, qiime2__sample_classifier__classify_samples_ncv, qiime2__sample_classifier__confusion_matrix, qiime2__sample_classifier__fit_classifier, qiime2__sample_classifier__fit_regressor, qiime2__sample_classifier__heatmap, qiime2__sample_classifier__metatable, qiime2__sample_classifier__predict_classification, qiime2__sample_classifier__predict_regression, qiime2__sample_classifier__regress_samples, qiime2__sample_classifier__regress_samples_ncv, qiime2__sample_classifier__scatterplot, qiime2__sample_classifier__split_table, qiime2__sample_classifier__summarize + qza, qzv - 2022-08-26 - https://github.com/qiime2/q2-cutadapt + 2022-08-25 + https://github.com/qiime2/q2-sample-classifier 2026.1.0+q2galaxy.2026.1.0 @@ -22020,22 +21900,24 @@ Microbial ecology, Metatranscriptomics, Metagenomics Microbial ecology, Metatranscriptomics, Metagenomics q2d2 - https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt - https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt + https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier + https://github.com/qiime2/galaxy-tools/tree/master/tools/suite_qiime2__sample_classifier qiime2 QIIME 2 QIIME 2 is an AI-ready microbiome multi-omics data science platform that is trusted, free, open source, extensible, and community developed and supported bioinformatics. - 4 - 4 - 4 - 4 + + + 15 + 15 + 15 + 15 0 0 0 0 + 15 0 - 4 0 0 0 @@ -22049,45 +21931,41 @@ 0 0 0 + 15 0 0 + 5 + 5 + 30 + 30 + 17 + 17 + 47 + 47 + 5 + 5 + 6 + 6 + 1 + 1 4 - 0 - 0 - 73 - 73 - 364 - 364 - 69 - 69 - 273 - 273 - 7 - 7 - 213 - 213 - 3 - 3 - 31 - 31 - 881 - 881 - 152 - 152 - - + 4 + 87 + 87 + 28 + 28 True False qiime2 - qiime2__composition__add_pseudocount, qiime2__composition__ancom, qiime2__composition__ancombc, qiime2__composition__ancombc2, qiime2__composition__ancombc2_visualizer, qiime2__composition__da_barplot, qiime2__composition__tabulate + qiime2__rescript__cull_seqs, qiime2__rescript__degap_seqs, qiime2__rescript__dereplicate, qiime2__rescript__edit_taxonomy, qiime2__rescript__evaluate_classifications, qiime2__rescript__evaluate_cross_validate, qiime2__rescript__evaluate_fit_classifier, qiime2__rescript__evaluate_seqs, qiime2__rescript__evaluate_taxonomy, qiime2__rescript__extract_seq_segments, qiime2__rescript__filter_seqs_length, qiime2__rescript__filter_seqs_length_by_taxon, qiime2__rescript__filter_taxa, qiime2__rescript__get_bv_brc_genome_features, qiime2__rescript__get_bv_brc_genomes, qiime2__rescript__get_bv_brc_metadata, qiime2__rescript__get_eukaryome_data, qiime2__rescript__get_gtdb_data, qiime2__rescript__get_midori2_data, qiime2__rescript__get_ncbi_data, qiime2__rescript__get_ncbi_data_protein, qiime2__rescript__get_ncbi_genomes, qiime2__rescript__get_pr2_data, qiime2__rescript__get_silva_data, qiime2__rescript__get_unite_data, qiime2__rescript__merge_taxa, qiime2__rescript__orient_reads, qiime2__rescript__orient_seqs, qiime2__rescript__parse_silva_taxonomy, qiime2__rescript__reverse_transcribe, qiime2__rescript__subsample_fasta, qiime2__rescript__trim_alignment qza, qzv - 2022-08-26 - https://github.com/qiime2/q2-composition - 2026.1.0+0.g4b3aa86.dirty-q2galaxy.2026.1.0 + 2024-04-25 + https://github.com/nbokulich/RESCRIPt + 2026.1.0+q2galaxy.2026.1.0 To update @@ -22097,23 +21975,23 @@ Microbial ecology, Metatranscriptomics, Metagenomics Microbial ecology, Metatranscriptomics, Metagenomics q2d2 - https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition - https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition + https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript + https://github.com/qiime2/galaxy-tools/tree/master/tools/suite_qiime2__rescript qiime2 QIIME 2 QIIME 2 is an AI-ready microbiome multi-omics data science platform that is trusted, free, open source, extensible, and community developed and supported bioinformatics. - 4 - 4 - 4 - 2 + + 0 + 3 + 3 0 0 0 0 - 4 0 + 3 0 0 0 @@ -22128,42 +22006,40 @@ 0 0 0 - 4 0 0 - 26 - 26 - 388 - 388 - 31 - 31 - 256 - 256 - 8 - 8 - 325 - 325 - 9 - 9 - 89 - 89 - 1058 - 1058 - 74 - 74 - - + 0 + 6 + 6 + 18 + 18 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 18 + 18 + 6 + 6 True False qiime2 - qiime2__taxa__barplot, qiime2__taxa__barplot2, qiime2__taxa__collapse, qiime2__taxa__filter_seqs, qiime2__taxa__filter_table - qzv, qza + qiime2__quality_filter__q_score + qza - 2022-08-26 - https://github.com/qiime2/q2-taxa + 2022-08-25 + https://github.com/qiime2/q2-quality-filter 2026.1.0+q2galaxy.2026.1.0 @@ -22174,23 +22050,23 @@ Microbial ecology, Metatranscriptomics, Metagenomics Microbial ecology, Metatranscriptomics, Metagenomics q2d2 - https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa - https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa + https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_filter + https://github.com/qiime2/galaxy-tools/tree/master/tools/suite_qiime2__quality_filter qiime2 QIIME 2 QIIME 2 is an AI-ready microbiome multi-omics data science platform that is trusted, free, open source, extensible, and community developed and supported bioinformatics. - 4 - 4 - 4 - 4 - 0 - 0 + + + 1 + 1 + 1 + 1 0 0 0 - 4 0 + 1 0 0 0 @@ -22205,42 +22081,40 @@ 0 0 0 - 4 + 1 0 0 - 266 - 266 - 2747 - 2747 - 159 - 159 - 1008 - 1008 - 78 - 78 - 690 - 690 - 22 - 22 - 236 - 236 - 4681 - 4681 - 525 - 525 - https://usegalaxy.eu/published/workflow?id=be9ff4159593cc34, https://usegalaxy.eu/published/workflow?id=e2af8c661e98f4f4, https://workflowhub.eu/workflows/2098?version=1 - + 25 + 25 + 55 + 55 + 16 + 16 + 39 + 39 + 7 + 7 + 90 + 90 + 13 + 13 + 21 + 21 + 205 + 205 + 61 + 61 True False qiime2 - qiime2__boots__alpha, qiime2__boots__alpha_average, qiime2__boots__alpha_collection, qiime2__boots__beta, qiime2__boots__beta_average, qiime2__boots__beta_collection, qiime2__boots__core_metrics, qiime2__boots__kmer_diversity, qiime2__boots__resample - qza, qzv + qiime2__vizard__boxplot, qiime2__vizard__heatmap, qiime2__vizard__lineplot, qiime2__vizard__scatterplot_2d + qzv - 2025-11-01 - https://library.qiime2.org/plugins/caporaso-lab/q2-boots + 2024-10-30 + https://github.com/qiime2/q2-vizard 2026.1.0+q2galaxy.2026.1.0 @@ -22251,12 +22125,24 @@ Microbial ecology, Metatranscriptomics, Metagenomics Microbial ecology, Metatranscriptomics, Metagenomics q2d2 - https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__boots - https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__boots + https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vizard + https://github.com/qiime2/galaxy-tools/tree/master/tools/suite_qiime2__vizard qiime2 QIIME 2 QIIME 2 is an AI-ready microbiome multi-omics data science platform that is trusted, free, open source, extensible, and community developed and supported bioinformatics. + + + 0 + 4 + 4 + 0 + 0 + 0 + 0 + 0 + 1 + 0 0 0 0 @@ -22273,6 +22159,10 @@ 0 0 0 + 5 + 5 + 20 + 20 0 0 0 @@ -22285,10 +22175,48 @@ 0 0 0 + 20 + 20 + 5 + 5 + True + False + + + + qiime2 + qiime2__alignment__mafft, qiime2__alignment__mafft_add, qiime2__alignment__mask + qza + + 2022-08-25 + https://github.com/qiime2/q2-alignment + 2026.1.0+q2galaxy.2026.1.0 + + + To update + Metagenomics, Sequence Analysis, Statistics + Demultiplexing, Visualisation, Taxonomic classification + Demultiplexing, Visualisation, Taxonomic classification + Microbial ecology, Metatranscriptomics, Metagenomics + Microbial ecology, Metatranscriptomics, Metagenomics + q2d2 + https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment + https://github.com/qiime2/galaxy-tools/tree/master/tools/suite_qiime2__alignment + qiime2 + QIIME 2 + QIIME 2 is an AI-ready microbiome multi-omics data science platform that is trusted, free, open source, extensible, and community developed and supported bioinformatics. + + + + 3 + 3 + 3 + 3 0 0 0 0 + 3 0 0 0 @@ -22303,21 +22231,40 @@ 0 0 0 + 3 0 0 - - + 67 + 67 + 390 + 390 + 35 + 35 + 78 + 78 + 16 + 16 + 114 + 114 + 14 + 14 + 69 + 69 + 651 + 651 + 132 + 132 True False qiime2 - qiime2__vsearch__cluster_features_closed_reference, qiime2__vsearch__cluster_features_de_novo, qiime2__vsearch__cluster_features_open_reference, qiime2__vsearch__dereplicate_sequences, qiime2__vsearch__fastq_stats, qiime2__vsearch__merge_pairs, qiime2__vsearch__uchime_denovo, qiime2__vsearch__uchime_ref - qza, qzv + qiime2__phylogeny__align_to_tree_mafft_fasttree, qiime2__phylogeny__align_to_tree_mafft_iqtree, qiime2__phylogeny__align_to_tree_mafft_raxml, qiime2__phylogeny__fasttree, qiime2__phylogeny__filter_table, qiime2__phylogeny__filter_tree, qiime2__phylogeny__iqtree, qiime2__phylogeny__iqtree_ultrafast_bootstrap, qiime2__phylogeny__midpoint_root, qiime2__phylogeny__raxml, qiime2__phylogeny__raxml_rapid_bootstrap, qiime2__phylogeny__robinson_foulds + qza - 2022-08-26 - https://github.com/qiime2/q2-vsearch + 2022-08-25 + https://github.com/qiime2/q2-phylogeny 2026.1.0+q2galaxy.2026.1.0 @@ -22328,23 +22275,23 @@ Microbial ecology, Metatranscriptomics, Metagenomics Microbial ecology, Metatranscriptomics, Metagenomics q2d2 - https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch - https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch + https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__phylogeny + https://github.com/qiime2/galaxy-tools/tree/master/tools/suite_qiime2__phylogeny qiime2 QIIME 2 QIIME 2 is an AI-ready microbiome multi-omics data science platform that is trusted, free, open source, extensible, and community developed and supported bioinformatics. - 8 - 8 - 8 - 8 - 0 - 0 + https://usegalaxy.eu/published/workflow?id=7c07e87c77dcee05 + + 12 + 12 + 12 + 12 0 0 0 - 8 0 + 12 0 0 0 @@ -22359,42 +22306,40 @@ 0 0 0 - 8 + 12 0 0 - 31 - 31 - 409 - 409 - 18 - 18 - 280 - 280 - 5 - 5 - 24 - 24 - 10 - 10 - 77 - 77 - 790 - 790 - 64 - 64 - - + 167 + 167 + 880 + 880 + 93 + 93 + 338 + 338 + 66 + 66 + 373 + 373 + 13 + 13 + 91 + 91 + 1682 + 1682 + 339 + 339 True False qiime2 - qiime2__emperor__biplot, qiime2__emperor__plot, qiime2__emperor__procrustes_plot - qzv + qiime2__fragment_insertion__classify_otus_experimental, qiime2__fragment_insertion__filter_features, qiime2__fragment_insertion__sepp + qza - 2022-08-26 - http://biocore.github.io/emperor/build/html/index.html + 2022-08-25 + https://github.com/qiime2/q2-fragment-insertion 2026.1.0+q2galaxy.2026.1.0 @@ -22405,12 +22350,14 @@ Microbial ecology, Metatranscriptomics, Metagenomics Microbial ecology, Metatranscriptomics, Metagenomics q2d2 - https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__emperor - https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__emperor + https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__fragment_insertion + https://github.com/qiime2/galaxy-tools/tree/master/tools/suite_qiime2__fragment_insertion qiime2 QIIME 2 QIIME 2 is an AI-ready microbiome multi-omics data science platform that is trusted, free, open source, extensible, and community developed and supported bioinformatics. + https://usegalaxy.eu/published/workflow?id=6ad6d87618c4e405 + 3 3 3 @@ -22419,7 +22366,6 @@ 0 0 0 - 0 3 0 0 @@ -22427,40 +22373,37 @@ 0 0 0 - 0 - 0 - 0 - 0 - 0 - 0 - 0 - 0 - 0 - 3 - 0 - 0 - 42 - 42 - 142 - 142 - 34 - 34 - 198 - 198 - 15 - 15 - 195 - 195 - 9 - 9 - 27 - 27 - 562 - 562 - 100 - 100 - - + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 3 + 0 + 0 + 16 + 16 + 81 + 81 + 7 + 7 + 59 + 59 + 1 + 1 + 6 + 6 + 2 + 2 + 2 + 2 + 148 + 148 + 26 + 26 True False @@ -22470,7 +22413,7 @@ qiime2__feature_classifier__blast, qiime2__feature_classifier__classify_consensus_blast, qiime2__feature_classifier__classify_consensus_vsearch, qiime2__feature_classifier__classify_hybrid_vsearch_sklearn, qiime2__feature_classifier__classify_sklearn, qiime2__feature_classifier__extract_reads, qiime2__feature_classifier__find_consensus_annotation, qiime2__feature_classifier__fit_classifier_naive_bayes, qiime2__feature_classifier__fit_classifier_sklearn, qiime2__feature_classifier__makeblastdb, qiime2__feature_classifier__vsearch_global qza - 2022-08-26 + 2022-08-25 https://github.com/qiime2/q2-feature-classifier 2026.1.0+q2galaxy.2026.1.0 @@ -22483,11 +22426,13 @@ Microbial ecology, Metatranscriptomics, Metagenomics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_classifier - https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_classifier + https://github.com/qiime2/galaxy-tools/tree/master/tools/suite_qiime2__feature_classifier qiime2 QIIME 2 QIIME 2 is an AI-ready microbiome multi-omics data science platform that is trusted, free, open source, extensible, and community developed and supported bioinformatics. + https://usegalaxy.eu/published/workflow?id=be9ff4159593cc34, https://usegalaxy.eu/published/workflow?id=e2af8c661e98f4f4, https://usegalaxy.org/published/workflow?id=7251c6e0dad8f927, https://workflowhub.eu/workflows/2098?version=1 + 10 10 10 @@ -22496,7 +22441,6 @@ 0 0 0 - 0 10 0 0 @@ -22512,7 +22456,6 @@ 0 0 0 - 0 10 0 0 @@ -22536,8 +22479,81 @@ 5762 673 673 - https://usegalaxy.eu/published/workflow?id=be9ff4159593cc34, https://usegalaxy.eu/published/workflow?id=e2af8c661e98f4f4, https://usegalaxy.org/published/workflow?id=7251c6e0dad8f927, https://workflowhub.eu/workflows/2098?version=1 + True + False + + + + qiime2 + qiime2__longitudinal__anova, qiime2__longitudinal__feature_volatility, qiime2__longitudinal__first_differences, qiime2__longitudinal__first_distances, qiime2__longitudinal__linear_mixed_effects, qiime2__longitudinal__maturity_index, qiime2__longitudinal__nmit, qiime2__longitudinal__pairwise_differences, qiime2__longitudinal__pairwise_distances, qiime2__longitudinal__plot_feature_volatility, qiime2__longitudinal__volatility + qzv, qza + + 2022-08-25 + https://github.com/qiime2/q2-longitudinal + 2026.1.0+q2galaxy.2026.1.0 + + To update + Metagenomics, Sequence Analysis, Statistics + Demultiplexing, Visualisation, Taxonomic classification + Demultiplexing, Visualisation, Taxonomic classification + Microbial ecology, Metatranscriptomics, Metagenomics + Microbial ecology, Metatranscriptomics, Metagenomics + q2d2 + https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal + https://github.com/qiime2/galaxy-tools/tree/master/tools/suite_qiime2__longitudinal + qiime2 + QIIME 2 + QIIME 2 is an AI-ready microbiome multi-omics data science platform that is trusted, free, open source, extensible, and community developed and supported bioinformatics. + + + + 11 + 11 + 11 + 11 + 0 + 0 + 0 + 0 + 11 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 11 + 0 + 0 + 12 + 12 + 63 + 63 + 7 + 7 + 60 + 60 + 6 + 6 + 142 + 142 + 2 + 2 + 8 + 8 + 273 + 273 + 27 + 27 True False @@ -22547,7 +22563,7 @@ qiime2__feature_table___summarize, qiime2__feature_table__core_features, qiime2__feature_table__filter_features, qiime2__feature_table__filter_features_conditionally, qiime2__feature_table__filter_samples, qiime2__feature_table__filter_seqs, qiime2__feature_table__group, qiime2__feature_table__heatmap, qiime2__feature_table__merge, qiime2__feature_table__merge_seqs, qiime2__feature_table__merge_taxa, qiime2__feature_table__normalize, qiime2__feature_table__presence_absence, qiime2__feature_table__rarefy, qiime2__feature_table__relative_frequency, qiime2__feature_table__rename_ids, qiime2__feature_table__split, qiime2__feature_table__subsample_ids, qiime2__feature_table__summarize, qiime2__feature_table__tabulate_feature_frequencies, qiime2__feature_table__tabulate_sample_frequencies, qiime2__feature_table__tabulate_seqs, qiime2__feature_table__transpose qzv, qza - 2022-08-26 + 2022-08-25 https://github.com/qiime2/q2-feature-table 2026.1.0+q2galaxy.2026.1.0 @@ -22560,11 +22576,13 @@ Microbial ecology, Metatranscriptomics, Metagenomics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table - https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table + https://github.com/qiime2/galaxy-tools/tree/master/tools/suite_qiime2__feature_table qiime2 QIIME 2 QIIME 2 is an AI-ready microbiome multi-omics data science platform that is trusted, free, open source, extensible, and community developed and supported bioinformatics. + https://usegalaxy.eu/published/workflow?id=3d0039098a87642c, https://usegalaxy.eu/published/workflow?id=5223c9554718114d, https://usegalaxy.eu/published/workflow?id=851b97ea3d1de9f7, https://usegalaxy.eu/published/workflow?id=b3d48f81329926fc, https://usegalaxy.eu/published/workflow?id=be9ff4159593cc34, https://usegalaxy.eu/published/workflow?id=da17a4d690eb0ff3, https://usegalaxy.eu/published/workflow?id=e1f08a63fbc8e173, https://usegalaxy.org.au/published/workflow?id=2d16ed86414f23b3, https://usegalaxy.org.au/published/workflow?id=fb517ec08b571a2d, https://usegalaxy.org/published/workflow?id=517f307db25e4715, https://usegalaxy.org/published/workflow?id=8bb471c28e1a30a3, https://usegalaxy.org/published/workflow?id=a382adce80293f0d, https://usegalaxy.org/published/workflow?id=d32392a39c4d6fbf, https://workflowhub.eu/workflows/2098?version=1, https://workflowhub.eu/workflows/892?version=3 + 17 17 17 @@ -22573,7 +22591,6 @@ 0 0 0 - 0 17 0 0 @@ -22589,7 +22606,6 @@ 0 0 0 - 0 17 0 0 @@ -22613,19 +22629,17 @@ 10796 624 624 - https://usegalaxy.eu/published/workflow?id=3d0039098a87642c, https://usegalaxy.eu/published/workflow?id=5223c9554718114d, https://usegalaxy.eu/published/workflow?id=851b97ea3d1de9f7, https://usegalaxy.eu/published/workflow?id=b3d48f81329926fc, https://usegalaxy.eu/published/workflow?id=be9ff4159593cc34, https://usegalaxy.eu/published/workflow?id=da17a4d690eb0ff3, https://usegalaxy.eu/published/workflow?id=e1f08a63fbc8e173, https://usegalaxy.org.au/published/workflow?id=2d16ed86414f23b3, https://usegalaxy.org.au/published/workflow?id=fb517ec08b571a2d, https://usegalaxy.org/published/workflow?id=517f307db25e4715, https://usegalaxy.org/published/workflow?id=8bb471c28e1a30a3, https://usegalaxy.org/published/workflow?id=a382adce80293f0d, https://usegalaxy.org/published/workflow?id=d32392a39c4d6fbf, https://workflowhub.eu/workflows/2098?version=1, https://workflowhub.eu/workflows/892?version=3 - True False qiime2 - qiime2__fondue___get_sequences, qiime2__fondue__combine_seqs, qiime2__fondue__get_all, qiime2__fondue__get_ids_from_query, qiime2__fondue__get_metadata, qiime2__fondue__get_sequences, qiime2__fondue__merge_metadata, qiime2__fondue__scrape_collection - qza + qiime2__quality_control__bowtie2_build, qiime2__quality_control__decontam_identify, qiime2__quality_control__decontam_identify_batches, qiime2__quality_control__decontam_score_viz, qiime2__quality_control__evaluate_composition, qiime2__quality_control__evaluate_seqs, qiime2__quality_control__evaluate_taxonomy, qiime2__quality_control__exclude_seqs, qiime2__quality_control__filter_reads + qza, qzv - 2025-11-01 - https://github.com/bokulich-lab/q2-fondue + 2022-08-25 + https://github.com/qiime2/q2-quality-control 2026.1.0+q2galaxy.2026.1.0 @@ -22636,16 +22650,23 @@ Microbial ecology, Metatranscriptomics, Metagenomics Microbial ecology, Metatranscriptomics, Metagenomics q2d2 - https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__fondue - https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__fondue + https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control + https://github.com/qiime2/galaxy-tools/tree/master/tools/suite_qiime2__quality_control qiime2 QIIME 2 QIIME 2 is an AI-ready microbiome multi-omics data science platform that is trusted, free, open source, extensible, and community developed and supported bioinformatics. + + + 6 + 6 + 6 + 6 0 0 0 0 + 6 0 0 0 @@ -22660,49 +22681,40 @@ 0 0 0 + 6 0 0 + 4 + 4 + 6 + 6 + 11 + 11 + 105 + 105 + 4 + 4 + 11 + 11 0 0 0 0 - 0 - 0 - 0 - 0 - 0 - 0 - 0 - 0 - 0 - 0 - 0 - 0 - 0 - 0 - 0 - 0 - 0 - 0 - 0 - 0 - 0 - 0 - 0 - 0 - - + 122 + 122 + 19 + 19 True False qiime2 - qiime2__fragment_insertion__classify_otus_experimental, 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assembly/largegenome, microbiome/plasmid-metagenomics-nanopore True False @@ -23473,10 +23465,10 @@ Randomly subsample sequencing reads to a specified coverage 2024-02-16 https://github.com/mbhall88/rasusa - 4.1.0 + @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ rasusa 4.1.0 - Up-to-date + To update Sequence Analysis Sequence assembly validation, Sequencing quality control Sequence assembly validation @@ -23484,11 +23476,13 @@ Genomics, Sequence analysis, Sequence assembly, RNA-Seq iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/rasusa - https://github.com/galaxyproject/tools-iuc/tree/main/tools/rasusa + https://github.com/galaxyproject/tools-iuc/tree/master/tools/rasusa rasusa rasusa Rasusa: Randomly subsample sequencing reads to aspecified coverageProduces an unbiased subsample of your reads + + 0 0 1 @@ -23499,7 +23493,6 @@ 0 0 0 - 0 1 0 0 @@ -23516,7 +23509,6 @@ 0 0 0 - 0 24 24 104 @@ -23537,8 +23529,6 @@ 104 24 24 - - True False @@ -23550,7 +23540,7 @@ RAxML - A Maximum Likelihood based phylogenetic inference 2015-11-05 http://www.exelixis-lab.org/web/software/raxml/ - 8.2.12 + @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ raxml 8.2.13 To update @@ -23561,11 +23551,13 @@ Phylogenetics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml - https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml + https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml raxml RAxML A tool for Phylogenetic Analysis and Post-Analysis of Large Phylogenies. + https://usegalaxy.eu/published/workflow?id=470656ef317c9dd5, https://usegalaxy.eu/published/workflow?id=875b3ca170ac12a1, https://usegalaxy.org/published/workflow?id=7251c6e0dad8f927, https://usegalaxy.org/published/workflow?id=d4f0a7ccb09f1e55, https://workflowhub.eu/workflows/1577?version=1 + evolution/mtb_phylogeny 1 1 1 @@ -23574,7 +23566,6 @@ 0 0 0 - 0 1 0 1 @@ -23589,7 +23580,6 @@ 0 0 0 - 0 1 1 1 @@ -23614,8 +23604,6 @@ 41266 3663 3318 - https://usegalaxy.eu/published/workflow?id=470656ef317c9dd5, https://usegalaxy.eu/published/workflow?id=875b3ca170ac12a1, https://usegalaxy.org/published/workflow?id=7251c6e0dad8f927, https://usegalaxy.org/published/workflow?id=d4f0a7ccb09f1e55, https://workflowhub.eu/workflows/1577?version=1 - evolution/mtb_phylogeny True False @@ -23627,9 +23615,9 @@ RAxML-NG - A Maximum Likelihood based phylogenetic tree inference 2025-12-20 http://www.exelixis-lab.org/web/software/raxml-ng/ - 2.0.1 + 2.0.2 raxml-ng - 2.0.1 + 2.0.2 Up-to-date Phylogenetics Phylogenetic tree generation (maximum likelihood and Bayesian methods), Phylogenetic tree bootstrapping @@ -23638,11 +23626,13 @@ Phylogenetics, Agricultural science, Phylogenomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxmlng - https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxmlng + https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxmlng RAxML-NG RAxML-NG Phylogenetic tree inference tool which uses maximum-likelihood (ML) optimality criterion. + + 0 0 1 @@ -23689,10 +23679,6 @@ 0 0 0 - 0 - 0 - - True False @@ -23704,10 +23690,10 @@ Infer a species tree from sequencing reads. 2025-11-23 https://github.com/DessimozLab/read2tree - 2.0.1 + @TOOL_VERSION@ read2tree 2.0.1 - Up-to-date + To update Phylogenetics @@ -23715,11 +23701,13 @@ Phylogenomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/read2tree - https://github.com/galaxyproject/tools-iuc/tree/main/tools/read2tree + https://github.com/galaxyproject/tools-iuc/tree/master/tools/read2tree read2tree read2tree read2tree is a software tool for generating alignment matrices and performing tree inference directly from sequencing reads. It leverages the OMA database and a set of input reads, bypassing many of the standard steps typically required in phylogenomic analysis. In particular, it avoids for read filtering, assembly, gene prediction, gene annotation, all-vs-all comparison, orthology prediction, alignment, and concatenation. + + 0 0 1 @@ -23766,10 +23754,6 @@ 0 0 0 - 0 - 0 - - True False @@ -23781,7 +23765,7 @@ Rapid decontamination of SARS-CoV-2 sequencing reads 2022-01-28 https://github.com/GenomePathogenAnalysisService/read-it-and-keep - 0.2.2 + @TOOL_VERSION@ read-it-and-keep 0.3.0 To update @@ -23792,11 +23776,13 @@ Pathology, Genomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/read_it_and_keep - https://github.com/galaxyproject/tools-iuc/tree/main/tools/read_it_and_keep + https://github.com/galaxyproject/tools-iuc/tree/master/tools/read_it_and_keep read_it_and_keep read_it_and_keep Read-it-and-keep is a bioinformatics tool designed to filter and extract sequencing reads according to user-defined criteria, such as the presence of specific motifs or coverage of regions of interest. This type of filtering can be particularly useful for targeted analyses, where only relevant sequences are retained for further study, optimising computing and storage resources. + https://usegalaxy.eu/published/workflow?id=3fb550d7c2bc390a, https://usegalaxy.eu/published/workflow?id=4a764275d4bf9f31, https://usegalaxy.eu/published/workflow?id=629e57958afed44c, https://usegalaxy.eu/published/workflow?id=7c986f4d14c6a539, https://usegalaxy.eu/published/workflow?id=d88145e7475e0b7b, https://usegalaxy.eu/published/workflow?id=d967194ca51ff11e, https://workflowhub.eu/workflows/519?version=1, https://workflowhub.eu/workflows/521?version=1 + 1 0 1 @@ -23820,8 +23806,6 @@ 0 0 0 - 0 - 0 1 0 0 @@ -23845,8 +23829,6 @@ 3790 89 89 - https://usegalaxy.eu/published/workflow?id=3fb550d7c2bc390a, https://usegalaxy.eu/published/workflow?id=4a764275d4bf9f31, https://usegalaxy.eu/published/workflow?id=629e57958afed44c, https://usegalaxy.eu/published/workflow?id=7c986f4d14c6a539, https://usegalaxy.eu/published/workflow?id=d88145e7475e0b7b, https://usegalaxy.eu/published/workflow?id=d967194ca51ff11e, https://workflowhub.eu/workflows/519?version=1, https://workflowhub.eu/workflows/521?version=1 - True False @@ -23858,10 +23840,10 @@ Reago is tool to assembly 16S ribosomal RNA recovery from metagenomic data. 2015-12-09 https://github.com/chengyuan/reago-1.1 - 1.1 + @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ reago 1.1 - Up-to-date + To update Metagenomics, RNA Sequence assembly Sequence assembly @@ -23874,6 +23856,8 @@ REAGO This is an assembly tool for 16S ribosomal RNA recovery from metagenomic data. + + 0 0 1 @@ -23900,8 +23884,6 @@ 0 0 0 - 0 - 0 7 7 18 @@ -23922,8 +23904,6 @@ 18 7 7 - - True False @@ -23946,11 +23926,13 @@ Metagenomics, Microbial ecology, Metagenomic sequencing iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/recentrifuge - https://github.com/galaxyproject/tools-iuc/tree/main/tools/recentrifuge + https://github.com/galaxyproject/tools-iuc/tree/master/tools/recentrifuge Recentrifuge Recentrifuge Robust comparative analysis and contamination removal for metagenomics. + https://usegalaxy.eu/published/workflow?id=0a82eb8b44d9d502, https://usegalaxy.eu/published/workflow?id=0abd32dbc5207b88, https://usegalaxy.eu/published/workflow?id=0c47571d20535426, https://usegalaxy.eu/published/workflow?id=2fa2f67603772413, https://usegalaxy.eu/published/workflow?id=47e14222073e7192, https://usegalaxy.eu/published/workflow?id=884a4415b669690c, https://usegalaxy.eu/published/workflow?id=aafcfcb585c5ca75, https://usegalaxy.eu/published/workflow?id=bb63b5bb983fd49c, https://usegalaxy.eu/published/workflow?id=bdc7cfaac0db2eab, https://usegalaxy.eu/published/workflow?id=c09159d7aad0f264, https://usegalaxy.eu/published/workflow?id=c14d2e8b3c191bc4, https://usegalaxy.eu/published/workflow?id=c930a54a30dcc7e3, https://usegalaxy.eu/published/workflow?id=e69b555faa6bb962, https://usegalaxy.eu/published/workflow?id=ebb131f2a6172081, https://usegalaxy.fr/published/workflow?id=3d3b40398d1cd1ae, https://usegalaxy.org/published/workflow?id=1be5c982c2d36a6c, https://usegalaxy.org/published/workflow?id=2a782ad24271f570, https://usegalaxy.org/published/workflow?id=323c651ca583c9e5, https://usegalaxy.org/published/workflow?id=4f698eaeef30e364, https://usegalaxy.org/published/workflow?id=623fc80c7f91a33a, https://usegalaxy.org/published/workflow?id=9f68718f025bed30, https://usegalaxy.org/published/workflow?id=b6a795834009ce06, https://usegalaxy.org/published/workflow?id=de9bf4c1024f8d53, https://usegalaxy.org/published/workflow?id=dfd73857c0eb2a21, https://usegalaxy.org/published/workflow?id=f378960ee55f567e, https://workflowhub.eu/workflows/1052?version=11, https://workflowhub.eu/workflows/1644?version=1, https://workflowhub.eu/workflows/1674?version=2, https://workflowhub.eu/workflows/1881?version=2, https://workflowhub.eu/workflows/1882?version=3, https://workflowhub.eu/workflows/2043?version=1 + ecology/bacterial-isolate-species-contamination-checking, sequence-analysis/quality-contamination-control 1 1 1 @@ -23959,7 +23941,6 @@ 0 0 0 - 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ecology/bacterial-isolate-species-contamination-checking, sequence-analysis/quality-contamination-control True False @@ -24012,7 +23990,7 @@ Remove terminal stop codons from coding sequences 2025-12-04 https://github.com/veg/CAPHEINE - 1.0.0 + @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ biopython 1.70 To update @@ -24023,7 +24001,9 @@ iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/remove_terminal_stop_codons - https://github.com/galaxyproject/tools-iuc/tree/main/tools/remove_terminal_stop_codons + https://github.com/galaxyproject/tools-iuc/tree/master/tools/remove_terminal_stop_codons + + @@ -24040,7 +24020,6 @@ 0 0 0 - 0 1 0 0 @@ -24052,7 +24031,6 @@ 0 0 0 - 0 1 0 0 @@ -24076,8 +24054,6 @@ 0 0 0 - - True False @@ -24105,6 +24081,8 @@ + + 0 0 1 @@ -24131,8 +24109,6 @@ 0 0 0 - 0 - 0 83 83 369 @@ -24153,8 +24129,6 @@ 369 83 83 - - True False @@ -24166,10 +24140,10 @@ Roary the pangenome pipeline 2017-06-21 https://sanger-pathogens.github.io/Roary/ - 3.13.0 + @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ roary 3.13.0 - Up-to-date + To update Sequence Analysis Genome assembly Genome assembly @@ -24177,11 +24151,13 @@ DNA, Genomics, Mapping iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/roary - https://github.com/galaxyproject/tools-iuc/tree/main/tools/roary + https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary roary Roary A high speed stand alone pan genome pipeline, which takes annotated assemblies in GFF3 format (produced by Prokka (Seemann, 2014)) and calculates the pan genome. + https://usegalaxy.eu/published/workflow?id=46ef864fe9468894, https://usegalaxy.eu/published/workflow?id=628062a8cf93261f, https://usegalaxy.eu/published/workflow?id=94c3d329c31c712f, https://usegalaxy.eu/published/workflow?id=b1a799497c366eef, https://usegalaxy.eu/published/workflow?id=e16e524c557d7928, https://usegalaxy.org.au/published/workflow?id=05f3abecd4ddd4a1, https://usegalaxy.org.au/published/workflow?id=3fd2195b6928d5e0, https://usegalaxy.org/published/workflow?id=23a87246c646eb8a, https://usegalaxy.org/published/workflow?id=78d8b738f5715a8a, https://usegalaxy.org/published/workflow?id=80565301ada0d3eb + 1 1 1 @@ -24190,7 +24166,6 @@ 0 0 0 - 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transcriptomics/differential-isoform-expression, transcriptomics/minerva-pathways, transcriptomics/ref-based, transcriptomics/rna-seq-reads-to-counts + True + False + + + + samestr + samestr_compare, samestr_convert, samestr_extract, samestr_filter, samestr_merge, samestr_stats, samestr_summarize + tabular, fasta, fasta.gz, npz + Strain-level analysis and comparison of metagenomic samples + 2026-04-15 + https://github.com/danielpodlesny/samestr + 1.2025.111 + samestr + 1.2025.111 + Up-to-date + Metagenomics + + + + + iuc + https://github.com/galaxyproject/tools-iuc/tree/main/tools/samestr + https://github.com/galaxyproject/tools-iuc/tree/master/tools/samestr + + + + + https://usegalaxy.eu/published/workflow?id=052f35a526798020 + + 0 + 0 + 7 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 True False @@ -24320,10 +24365,10 @@ Scoary calculates the assocations between all genes in the accessory genome and the traits. 2021-03-18 https://github.com/AdmiralenOla/Scoary - 1.6.16 + @TOOL_VERSION@ scoary 1.6.16 - Up-to-date + To update Metagenomics Analysis Analysis @@ -24331,11 +24376,13 @@ Genotype and phenotype, Model organisms, GWAS study, Functional genomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/scoary - https://github.com/galaxyproject/tools-iuc/tree/main/tools/scoary + https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary scoary Scoary Pan-genome wide association studies and  is designed to take the gene_presence_absence.csv file from Roary as well as a traits file created by the user and calculate the assocations between all genes in the accessory genome (all genes that are present in i genomes where 1 < i < N) and the traits. It reports a list of genes sorted by strength of association per trait. + + 0 0 1 @@ -24359,8 +24406,6 @@ 0 0 0 - 0 - 0 1 0 0 @@ -24384,8 +24429,6 @@ 1366 113 113 - - True False @@ -24399,7 +24442,7 @@ https://semibin.readthedocs.io/en/latest/ 2.1.0 semibin - 2.2.1 + 2.3.0 To update Metagenomics Sequence assembly, Read binning @@ -24408,11 +24451,13 @@ Metagenomics, Machine learning, Microbial ecology, Sequence assembly iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin - https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin + https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin semibin SemiBin Command tool for metagenomic binning with semi-supervised deep learning using information from reference genomes. + https://usegalaxy.eu/published/workflow?id=00f15824c7a9b196, https://usegalaxy.eu/published/workflow?id=0563f58718be932d, https://usegalaxy.eu/published/workflow?id=1e5f1d9a51032e44, https://usegalaxy.eu/published/workflow?id=43098b8afe78b071, https://usegalaxy.eu/published/workflow?id=7ecd92cb382d8168, https://usegalaxy.eu/published/workflow?id=97312d273b6e8bd9, https://usegalaxy.eu/published/workflow?id=ce5c9287a67e6085, https://workflowhub.eu/workflows/1352?version=4, https://workflowhub.eu/workflows/2028?version=1, https://workflowhub.eu/workflows/2100?version=2 + microbiome/metagenomics-binning 1 6 6 @@ -24423,7 +24468,6 @@ 0 0 0 - 0 1 0 0 @@ -24436,7 +24480,6 @@ 0 0 0 - 0 1 6 0 @@ -24461,8 +24504,6 @@ 2872 64 64 - https://usegalaxy.eu/published/workflow?id=00f15824c7a9b196, https://usegalaxy.eu/published/workflow?id=0563f58718be932d, https://usegalaxy.eu/published/workflow?id=1e5f1d9a51032e44, https://usegalaxy.eu/published/workflow?id=43098b8afe78b071, https://usegalaxy.eu/published/workflow?id=7ecd92cb382d8168, https://usegalaxy.eu/published/workflow?id=97312d273b6e8bd9, https://usegalaxy.eu/published/workflow?id=ce5c9287a67e6085, https://workflowhub.eu/workflows/1352?version=4, https://workflowhub.eu/workflows/2028?version=1, https://workflowhub.eu/workflows/2100?version=2 - microbiome/metagenomics-binning True False @@ -24485,11 +24526,13 @@ Database management, Sequence analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqkit - https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqkit + https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit seqkit seqkit FASTA and FASTQ are basic and ubiquitous formats for storing nucleotide and protein sequences. Common manipulations of FASTA/Q file include converting, searching, filtering, deduplication, splitting, shuffling, and sampling. Existing tools only implement some of these manipulations, and not particularly efficiently, and some are only available for certain operating systems. Furthermore, the complicated installation process of required packages and running environments can render these programs less user friendly. SeqKit demonstrates competitive performance in execution time and memory usage compared to similar tools. 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Your result will be stored in 'SeqSero_result.txt' in that directory. And the assembled alleles can also be found in the directory if using "-m a" (allele mode) + https://usegalaxy.eu/published/workflow?id=fde21b5f5c169114, https://workflowhub.eu/workflows/407?version=1 + 0 0 1 @@ -24654,7 +24693,6 @@ 0 0 0 - 0 1 0 0 @@ -24671,7 +24709,6 @@ 0 0 0 - 0 116 116 14011 @@ -24692,8 +24729,6 @@ 14013 118 118 - https://usegalaxy.eu/published/workflow?id=fde21b5f5c169114, https://workflowhub.eu/workflows/407?version=1 - True False @@ -24705,10 +24740,10 @@ Faster de novo assembly pipeline based around Spades 2017-10-24 https://github.com/tseemann/shovill - 1.4.2 + @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ shovill 1.4.2 - Up-to-date + To update Assembly Genome assembly Genome assembly @@ -24716,11 +24751,13 @@ Genomics, Microbiology, Sequence assembly iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/shovill - https://github.com/galaxyproject/tools-iuc/tree/main/tools/shovill + https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill shovill shovill Shovill is a pipeline for assembly of bacterial isolate genomes from Illumina paired-end reads.  Shovill uses SPAdes at its core, but alters the steps before and after the primary assembly step to get similar results in less time. 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assembly/mrsa-illumina True False @@ -24782,10 +24815,10 @@ SISTR in silico serotyping tool 2017-02-20 https://github.com/phac-nml/sistr_cmd - 1.1.3 + @VERSION@ sistr_cmd 1.1.3 - Up-to-date + To update Sequence Analysis Genome assembly, Visualisation, Multilocus sequence typing Genome assembly, Visualisation, Multilocus sequence typing @@ -24798,6 +24831,8 @@ SISTR The Salmonella In Silico Typing Resource (SISTR) is an open-source and freely available web application for rapid in silico typing and serovar prediction from Salmonella genome assemblies using cgMLST and O and H antigen gene searching. + https://usegalaxy.eu/published/workflow?id=628062a8cf93261f, https://usegalaxy.eu/published/workflow?id=94c3d329c31c712f, https://usegalaxy.eu/published/workflow?id=cbe3769f1abb9fa5, https://usegalaxy.eu/published/workflow?id=fde21b5f5c169114, https://usegalaxy.org.au/published/workflow?id=2120112358db8e01, https://usegalaxy.org.au/published/workflow?id=41331c03339e2b19, https://usegalaxy.org.au/published/workflow?id=92fcdd490831c6c5, https://workflowhub.eu/workflows/407?version=1 + 0 1 1 @@ -24808,7 +24843,6 @@ 0 0 0 - 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assembly/debruijn-graph-assembly, assembly/metagenomics-assembly, microbiome/metagenomics-assembly True False @@ -25396,7 +25413,7 @@ spotyping txt, excel.xls, pdf SpoTyping allows fast and accurate in silico Mycobacterium spoligotyping from sequence reads - 2018-05-07 + 2018-05-08 https://github.com/xiaeryu/SpoTyping-v2.0 2.1 spotyping @@ -25409,11 +25426,13 @@ Microbiology, Sequencing, Sequence composition, complexity and repeats, Genetic variation iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/spotyping - https://github.com/galaxyproject/tools-iuc/tree/main/tools/spotyping + https://github.com/galaxyproject/tools-iuc/tree/master/tools/spotyping spotyping SpoTyping Fast and accurate in silico Mycobacterium spoligotyping from sequence reads. + + 0 0 1 @@ -25437,8 +25456,6 @@ 0 0 0 - 0 - 0 1 0 0 @@ -25462,8 +25479,6 @@ 2042 34 34 - - True False @@ -25486,11 +25501,13 @@ Virology iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/squirrel - https://github.com/galaxyproject/tools-iuc/tree/main/tools/squirrel + https://github.com/galaxyproject/tools-iuc/tree/master/tools/squirrel squirrel squirrel Some QUIck Reconstruction to Resolve Evolutionary LinksSquirrel provides a rapid way of producing reliable alignments for MPXV and also enable maximum-likelihood phylogenetics pipeline tree estimation. + https://usegalaxy.org.au/published/workflow?id=b9fd488b0938d323, https://workflowhub.eu/workflows/2196?version=1 + 0 2 2 @@ -25517,8 +25534,6 @@ 0 0 0 - 0 - 0 2 2 7 @@ -25539,8 +25554,6 @@ 200 43 43 - https://usegalaxy.org.au/published/workflow?id=b9fd488b0938d323 - True False @@ -25563,12 +25576,13 @@ Microbiology artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie - https://github.com/ARTbio/tools-artbio/tree/main/tools/sr_bowtie + https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie sr_bowtie sr_bowtie Bowtie_ is a short read aligner designed to be ultrafast and memory-efficient. It is developed by Ben Langmead and Cole Trapnell. Please cite: Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biology 10:R25... _Bowtie: http://bowtie-bio.sourceforge.net/index.shtmlA generic "Map with Bowtie for Illumina" Galaxy tool is available in the main Galaxy distribution.However, this Bowtie wrapper tool only takes FASTQ files as inputs.The sRbowtie wrapper works with short (-v bowtie mode) reads inputs, in fasta or fastq format, and proposes a simplified set of configurations suited to small RNA analysis. - 0 + + 0 0 0 @@ -25599,7 +25613,6 @@ 0 0 0 - 0 2 2 98 @@ -25616,8 +25629,6 @@ 98 2 2 - - True False @@ -25625,25 +25636,27 @@ srst2 srst2 - tabular, fasta - SRST2 Short Read Sequence Typing for Bacterial Pathogens - 2022-08-22 - http://katholt.github.io/srst2/ + bam, tabular, fasta + Short Read Sequence Typing for Bacterial Pathogens + 2015-12-02 + + 0.3.7 + srst2 0.2.0 - samtools - 1.23.1 To update - Metagenomics - Multilocus sequence typing - Multilocus sequence typing - Whole genome sequencing, Public health and epidemiology, Comparative genomics - Whole genome sequencing, Public health and epidemiology, Comparative genomics - iuc - https://github.com/galaxyproject/tools-iuc/tree/main/tools/srst2 - https://github.com/galaxyproject/tools-iuc/tree/main/tools/srst2 - srst2 - srst2 - Short Read Sequence Typing for Bacterial Pathogens + Sequence Analysis + + + + + nml + + https://github.com/phac-nml/galaxy_tools/tree/master/tools/srst2 + + + + + https://workflowhub.eu/workflows/407?version=1 0 0 @@ -25655,7 +25668,6 @@ 0 0 0 - 0 1 0 0 @@ -25669,7 +25681,6 @@ 0 0 0 - 0 1 0 0 @@ -25693,8 +25704,6 @@ 478 69 69 - https://workflowhub.eu/workflows/407?version=1 - True False @@ -25702,25 +25711,27 @@ srst2 srst2 - bam, tabular, fasta - Short Read Sequence Typing for Bacterial Pathogens - 2015-12-02 - - 0.3.7 - srst2 + tabular, fasta + SRST2 Short Read Sequence Typing for Bacterial Pathogens + 2022-08-22 + http://katholt.github.io/srst2/ 0.2.0 + samtools + 1.23.1 To update - Sequence Analysis - - - - - nml - - https://github.com/phac-nml/galaxy_tools/tree/master/tools/srst2 - - + Metagenomics + Multilocus sequence typing + Multilocus sequence typing + Whole genome sequencing, Public health and epidemiology, Comparative genomics + Whole genome sequencing, Public health and epidemiology, Comparative genomics + iuc + https://github.com/galaxyproject/tools-iuc/tree/main/tools/srst2 + https://github.com/galaxyproject/tools-iuc/tree/master/tools/srst2 + srst2 + srst2 + Short Read Sequence Typing for Bacterial Pathogens + https://workflowhub.eu/workflows/407?version=1 0 0 @@ -25732,7 +25743,6 @@ 0 0 0 - 0 1 0 0 @@ -25746,7 +25756,6 @@ 0 0 0 - 0 1 0 0 @@ -25770,8 +25779,6 @@ 478 69 69 - https://workflowhub.eu/workflows/407?version=1 - True False @@ -25783,10 +25790,10 @@ Scan genome contigs against the ResFinder, PlasmidFinder, and PointFinder antimicrobial resistance databases. 2024-09-19 https://github.com/phac-nml/staramr - 0.12.2 + @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ staramr - 0.12.2 - Up-to-date + 0.12.3 + To update Sequence Analysis Antimicrobial resistance prediction Antimicrobial resistance prediction @@ -25794,11 +25801,13 @@ Microbiology, Public health and epidemiology, Infectious disease iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/staramr - https://github.com/galaxyproject/tools-iuc/tree/main/tools/staramr + https://github.com/galaxyproject/tools-iuc/tree/master/tools/staramr staramr staramr staramr (*AMR) scans bacterial genome contigs against the ResFinder, PointFinder, and PlasmidFinder databases (used by the ResFinder webservice and other webservices offered by the Center for Genomic Epidemiology) and compiles a summary report of detected antimicrobial resistance genes. 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genome-annotation/amr-gene-detection, microbiome/plasmid-metagenomics-nanopore True False @@ -25876,7 +25881,8 @@ - 0 + + 0 0 0 @@ -25923,9 +25929,6 @@ 0 0 0 - 0 - - True False @@ -25937,10 +25940,10 @@ for using multi-locus genotype data to investigate population structure. 2017-09-22 https://web.stanford.edu/group/pritchardlab/structure.html - 2.3.4 + @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ structure 2.3.4 - Up-to-date + To update Phylogenetics, Variant Analysis Genetic variation analysis Genetic variation analysis @@ -25948,11 +25951,13 @@ Population genetics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/structure - https://github.com/galaxyproject/tools-iuc/tree/main/tools/structure + https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure structure Structure The program structureis a free software package for using multi-locus genotype data to investigate population structure. Its uses include inferring the presence of distinct populations, assigning individuals to populations, studying hybrid zones, identifying migrants and admixed individuals, and estimating population allele frequencies in situations where many individuals are migrants or admixed. + + 0 1 1 @@ -25975,8 +25980,6 @@ 0 0 0 - 0 - 0 1 1 1 @@ -26001,8 +26004,6 @@ 4233 158 141 - - True False @@ -26025,7 +26026,9 @@ q2d2 - https://github.com/qiime2/galaxy-tools/tree/main/tool_collections/suite_qiime2_core + https://github.com/qiime2/galaxy-tools/tree/master/tool_collections/suite_qiime2_core + + @@ -26076,10 +26079,6 @@ 0 0 0 - 0 - 0 - - True False @@ -26107,11 +26106,12 @@ sylph fast and precise species-level metagenomic profiling with ANIs + https://usegalaxy.eu/published/workflow?id=7491883694fff308, https://usegalaxy.eu/published/workflow?id=cb2df493f5e334f7, https://workflowhub.eu/workflows/2068?version=2 + + 2 2 - 0 2 2 - 0 0 0 0 @@ -26131,7 +26131,6 @@ 0 0 0 - 0 1 0 0 @@ -26155,8 +26154,6 @@ 270 11 11 - https://usegalaxy.eu/published/workflow?id=7491883694fff308, https://usegalaxy.eu/published/workflow?id=cb2df493f5e334f7, https://workflowhub.eu/workflows/2068?version=2 - True False @@ -26179,11 +26176,13 @@ DNA polymorphism, Sequence assembly, Mapping, Sequencing iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/syri - https://github.com/galaxyproject/tools-iuc/tree/main/tools/syri + https://github.com/galaxyproject/tools-iuc/tree/master/tools/syri SyRI SyRI SyRI is tool for finding genomic rearrangements and local sequence differences from whole-genome assemblies.Genomic differences range from single nucleotide differences to complex structural variations. Current methods typically annotate sequence differences ranging from SNPs to large indels accurately but do not unravel the full complexity of structural rearrangements, including inversions, translocations, and duplications, where highly similar sequence changes in location, orientation, or copy number. Here, we present SyRI, a pairwise whole-genome comparison tool for chromosome-level assemblies. SyRI starts by finding rearranged regions and then searches for differences in the sequences, which are distinguished for residing in syntenic or rearranged regions. This distinction is important as rearranged regions are inherited differently compared to syntenic regions. + https://usegalaxy.fr/published/workflow?id=356dced9687596b7, https://usegalaxy.fr/published/workflow?id=ce4acd38084ee9ef + 0 0 1 @@ -26210,8 +26209,6 @@ 0 0 0 - 0 - 0 22 22 84 @@ -26232,8 +26229,6 @@ 160 27 27 - https://usegalaxy.fr/published/workflow?id=356dced9687596b7, https://usegalaxy.fr/published/workflow?id=ce4acd38084ee9ef - True False @@ -26256,11 +26251,13 @@ Phylogenomics devteam https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/t2ps - https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/t2ps + https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/t2ps t2ps Draw phylogeny "Given taxonomy representation (produced by *Fetch taxonomic representation* tool) this utility produces a graphical representations of phylogenetic tree in PDF format." - Galaxy tool wrapper + 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standardise taxonomic profiles created by a range of bioinformatics tools. 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assembly/debruijn-graph-assembly, assembly/general-introduction True False @@ -28016,10 +28040,10 @@ Virus Identification By iteRative ANnoTation 2024-09-11 https://github.com/AnantharamanLab/VIBRANT - 1.2.1 + @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ vibrant 1.2.1 - Up-to-date + To update Metagenomics Sequence trimming, Scaffolding, Genome annotation Sequence trimming, Scaffolding, Genome annotation @@ -28027,11 +28051,13 @@ Metagenomics, Microbial ecology, Sequence assembly, Molecular interactions, pathways and networks, Endocrinology and metabolism ufz https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant - https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/vibrant + https://github.com/Helmholtz-UFZ/galaxy-tools/tree/master/tools/vibrant VIBRANT VIBRANT Automated recovery, annotation and curation of microbial viruses, and evaluation of virome function from genomic sequences.Virus Identification By iteRative ANnoTation.Discovery Environment Applications List.Created by upendra_35, last modified on Nov 04, 2019.If you find VIBRANT useful please consider citing our preprint on bioRxiv:.Kieft, K., Zhou, Z., and Anantharaman, K. (2019). VIBRANT: Automated recovery, annotation and curation of microbial viruses, and evaluation of virome function from genomic sequences. BioRxiv 855387.VIBRANT is a tool for automated recovery and annotation of bacterial and archaeal viruses, determination of genome completeness, and characterization of virome function from metagenomic assemblies.The QuickStart tutorial provides an introduction to basic DE functionality and navigation.Please work through the tutorial and use the intercom button on the bottom right of this page if you have any questions + https://usegalaxy.eu/published/workflow?id=87231a6a7938cb95, https://usegalaxy.eu/published/workflow?id=c62d65832377e376 + 1 0 1 @@ -28058,8 +28084,6 @@ 0 0 0 - 0 - 0 65 65 1586 @@ -28080,8 +28104,6 @@ 1586 65 65 - https://usegalaxy.eu/published/workflow?id=87231a6a7938cb95, https://usegalaxy.eu/published/workflow?id=c62d65832377e376 - True False @@ -28093,10 +28115,10 @@ Contigs prediction as viral, chromosomal, plasmidic or uncertain. 2025-07-04 https://github.com/ablab/viralVerify - 1.1 + @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ viralverify 1.1 - Up-to-date + To update Sequence Analysis, Metagenomics @@ -28104,7 +28126,9 @@ iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/viralverify - https://github.com/galaxyproject/tools-iuc/tree/main/tools/viralverify + https://github.com/galaxyproject/tools-iuc/tree/master/tools/viralverify + + @@ -28119,7 +28143,6 @@ 0 0 0 - 0 1 0 0 @@ -28156,9 +28179,6 @@ 0 0 0 - 0 - - True False @@ -28181,11 +28201,13 @@ Metagenomics, Virology, Microbial ecology iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/virannot - https://github.com/galaxyproject/tools-iuc/tree/main/tools/virannot + https://github.com/galaxyproject/tools-iuc/tree/master/tools/virannot virannot virAnnot VirAnnot was build to ease the assembly, blast search, taxonomic annotation and OTUs assignation of viral metagenomic HTS data. It is used in Virologie team of UMR1332 BFP laboratory at INRAE. VirAnnot also takes part of the Euphresco project "Plant Health Bioinformatics Network". See more.It is designed to identify viruses in plant metagenomic data but it can be used to assemble and annotate any sequences with the NCBI taxonomy. + https://usegalaxy.eu/published/workflow?id=17f73aba442315e6, https://usegalaxy.eu/published/workflow?id=86465932556bc96c + 0 0 3 @@ -28212,8 +28234,6 @@ 0 0 0 - 0 - 0 16 16 336 @@ -28234,8 +28254,6 @@ 350 18 18 - https://usegalaxy.eu/published/workflow?id=17f73aba442315e6, https://usegalaxy.eu/published/workflow?id=86465932556bc96c - True False @@ -28247,10 +28265,10 @@ VirSorter2 applies a multi-classifier, expert-guided approach to detect diverse DNA and RNA virus genomes. 2024-06-20 https://github.com/jiarong/VirSorter2/ - 2.2.4 + @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ virsorter 2.2.4 - Up-to-date + To update Metagenomics Taxonomic classification Taxonomic classification @@ -28258,11 +28276,13 @@ Metagenomics ufz https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/virsorter - https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/virsorter + https://github.com/Helmholtz-UFZ/galaxy-tools/tree/master/tools/virsorter virsorter virsorter Identify DNA and RNA virus sequences. + https://usegalaxy.eu/published/workflow?id=62392daea25a3980, https://usegalaxy.eu/published/workflow?id=87231a6a7938cb95 + 0 0 1 @@ -28289,8 +28309,6 @@ 0 0 0 - 0 - 0 144 144 2379 @@ -28311,8 +28329,6 @@ 2379 144 144 - https://usegalaxy.eu/published/workflow?id=62392daea25a3980, https://usegalaxy.eu/published/workflow?id=87231a6a7938cb95 - True False @@ -28340,6 +28356,8 @@ vRhyme vRhyme enables binning of viral genomes from metagenomes. + https://usegalaxy.eu/published/workflow?id=62392daea25a3980 + 0 0 1 @@ -28366,8 +28384,6 @@ 0 0 0 - 0 - 0 6 6 47 @@ -28388,8 +28404,6 @@ 47 6 6 - https://usegalaxy.eu/published/workflow?id=62392daea25a3980 - True False @@ -28412,11 +28426,13 @@ Metagenomics, Sequence analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/vsearch - https://github.com/galaxyproject/tools-iuc/tree/main/tools/vsearch + https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch vsearch VSEARCH High-throughput search and clustering sequence analysis tool. It supports de novo and reference based chimera detection, clustering, full-length and prefix dereplication, reverse complementation, masking, all-vs-all pairwise global alignment, exact and global alignment searching, shuffling, subsampling and sorting. It also supports FASTQ file analysis, filtering and conversion. + https://usegalaxy.eu/published/workflow?id=1ae9a523ef719a3d, https://usegalaxy.eu/published/workflow?id=401746888e8b3aa8, https://usegalaxy.eu/published/workflow?id=4eb9dfe91fc2dc67, https://usegalaxy.eu/published/workflow?id=8a7caaa658744441, https://usegalaxy.eu/published/workflow?id=9382f9bbbdddb5ad, https://usegalaxy.eu/published/workflow?id=9cbba5de2cbeeb0f, https://usegalaxy.eu/published/workflow?id=a8417c63e9e22afb, https://usegalaxy.eu/published/workflow?id=c3aa516e78ca4191, https://usegalaxy.org.au/published/workflow?id=14e80b7f9f68ec2a, https://usegalaxy.org.au/published/workflow?id=869440d35a618836, https://workflowhub.eu/workflows/232?version=1, https://workflowhub.eu/workflows/233?version=1 + 8 8 8 @@ -28425,7 +28441,6 @@ 0 0 0 - 0 8 8 8 @@ -28440,7 +28455,6 @@ 0 0 0 - 0 8 8 8 @@ -28465,8 +28479,6 @@ 35354 1010 642 - https://usegalaxy.eu/published/workflow?id=401746888e8b3aa8, https://usegalaxy.eu/published/workflow?id=4eb9dfe91fc2dc67, https://usegalaxy.eu/published/workflow?id=8a7caaa658744441, https://usegalaxy.eu/published/workflow?id=9382f9bbbdddb5ad, https://usegalaxy.eu/published/workflow?id=9cbba5de2cbeeb0f, https://usegalaxy.eu/published/workflow?id=a8417c63e9e22afb, https://usegalaxy.eu/published/workflow?id=c3aa516e78ca4191, https://usegalaxy.org.au/published/workflow?id=14e80b7f9f68ec2a, https://usegalaxy.org.au/published/workflow?id=869440d35a618836, https://workflowhub.eu/workflows/232?version=1, https://workflowhub.eu/workflows/233?version=1 - True False diff --git a/communities/microgalaxy/resources/tools_filtered_by_ts_categories.json b/communities/microgalaxy/resources/tools_filtered_by_ts_categories.json index 3093e32c7..660986f94 100644 --- a/communities/microgalaxy/resources/tools_filtered_by_ts_categories.json +++ b/communities/microgalaxy/resources/tools_filtered_by_ts_categories.json @@ -29,12 +29,13 @@ "bio.tool name": null, "bio.tool description": null, "biii ID": null, + "Related Workflows": [], + "Related Tutorials": [], "Number of tools on UseGalaxy.org (Main)": 0, "Number of tools on UseGalaxy.org.au": 0, "Number of tools on UseGalaxy.eu": 0, "Number of tools on UseGalaxy.fr": 0, "Number of tools on APOSTL": 0, - "Number of tools on MBAC Metabiome Portal": 0, "Number of tools on ChemFlow": 0, "Number of tools on CIRM-CFBP": 0, "Number of tools on Coloc-stats": 0, @@ -51,7 +52,6 @@ "Number of tools on MISSISSIPPI": 0, "Number of tools on Oqtans": 0, "Number of tools on Palfinder": 0, - "Number of tools on PepSimili": 0, "Number of tools on PhagePromotor": 0, "Number of tools on UseGalaxy.be": 0, "Number of tools on UseGalaxy.cz": 0, @@ -77,8 +77,6 @@ "Suite runs (last 5 years) on main servers": 0, "Suite users on main servers": 0, "Suite users (last 5 years) on main servers": 0, - "Related Workflows": [], - "Related Tutorials": [], "To keep": true, "Deprecated": false }, @@ -117,17 +115,18 @@ ], "Suite owner": "earlhaminst", "Suite source": "https://github.com/EarlhamInst/earlham-galaxytools/tree/main/tools/TreeBest", - "Suite parsed folder": "https://github.com/EarlhamInst/earlham-galaxytools/tree/main/tools/TreeBest", + "Suite parsed folder": "https://github.com/TGAC/earlham-galaxytools/tree/master/tools/TreeBest", "bio.tool ID": "treebest", "bio.tool name": "TreeBeST", "bio.tool description": "TreeBeST, which stands for (gene) Tree Building guided by Species Tree, is a versatile program that builds, manipulates and displays phylogenetic trees. It is particularly designed for building gene trees with a known species tree and is highly efficient and accurate.TreeBeST is previously known as NJTREE. It has been largely used in the TreeFam database, Ensembl Compara and OPTIC database of Chris Ponting group.", "biii ID": null, + "Related Workflows": [], + "Related Tutorials": [], "Number of tools on UseGalaxy.org (Main)": 0, "Number of tools on UseGalaxy.org.au": 0, "Number of tools on UseGalaxy.eu": 1, "Number of tools on UseGalaxy.fr": 1, "Number of tools on APOSTL": 0, - "Number of tools on MBAC Metabiome Portal": 0, "Number of tools on ChemFlow": 0, "Number of tools on CIRM-CFBP": 0, "Number of tools on Coloc-stats": 0, @@ -144,7 +143,6 @@ "Number of tools on MISSISSIPPI": 0, "Number of tools on Oqtans": 0, "Number of tools on Palfinder": 0, - "Number of tools on PepSimili": 0, "Number of tools on PhagePromotor": 0, "Number of tools on UseGalaxy.be": 0, "Number of tools on UseGalaxy.cz": 1, @@ -170,8 +168,6 @@ "Suite runs (last 5 years) on main servers": 967, "Suite users on main servers": 59, "Suite users (last 5 years) on main servers": 46, - "Related Workflows": [], - "Related Tutorials": [], "To keep": true, "Deprecated": false }, @@ -217,17 +213,18 @@ ], "Suite owner": "earlhaminst", "Suite source": "https://github.com/EarlhamInst/earlham-galaxytools/tree/main/tools/ete", - "Suite parsed folder": "https://github.com/EarlhamInst/earlham-galaxytools/tree/main/tools/ete", + "Suite parsed folder": "https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete", "bio.tool ID": "ete", "bio.tool name": "ete", "bio.tool description": "The Environment for Tree Exploration (ETE) is a computational framework that simplifies the reconstruction, analysis, and visualization of phylogenetic trees and multiple sequence alignments. Here, we present ETE v3, featuring numerous improvements in the underlying library of methods, and providing a novel set of standalone tools to perform common tasks in comparative genomics and phylogenetics. The new features include (i) building gene-based and supermatrix-based phylogenies using a single command, (ii) testing and visualizing evolutionary models, (iii) calculating distances between trees of different size or including duplications, and (iv) providing seamless integration with the NCBI taxonomy database. ETE is freely available at http://etetoolkit.org", "biii ID": null, + "Related Workflows": [], + "Related Tutorials": [], "Number of tools on UseGalaxy.org (Main)": 0, "Number of tools on UseGalaxy.org.au": 0, "Number of tools on UseGalaxy.eu": 7, "Number of tools on UseGalaxy.fr": 7, "Number of tools on APOSTL": 0, - "Number of tools on MBAC Metabiome Portal": 0, "Number of tools on ChemFlow": 0, "Number of tools on CIRM-CFBP": 0, "Number of tools on Coloc-stats": 0, @@ -244,7 +241,6 @@ "Number of tools on MISSISSIPPI": 0, "Number of tools on Oqtans": 0, "Number of tools on Palfinder": 0, - "Number of tools on PepSimili": 0, "Number of tools on PhagePromotor": 0, "Number of tools on UseGalaxy.be": 0, "Number of tools on UseGalaxy.cz": 7, @@ -270,8 +266,6 @@ "Suite runs (last 5 years) on main servers": 292, "Suite users on main servers": 41, "Suite users (last 5 years) on main servers": 32, - "Related Workflows": [], - "Related Tutorials": [], "To keep": true, "Deprecated": false }, @@ -290,7 +284,7 @@ "Description": "LotuS2 OTU processing pipeline", "Suite first commit date": "2021-05-13", "Homepage": "https://lotus2.earlham.ac.uk/", - "Suite version": "2.32", + "Suite version": "@VERSION@", "Suite conda package": "lotus2", "Latest suite conda package version": "2.34.1", "Suite version status": "To update", @@ -317,17 +311,24 @@ ], "Suite owner": "earlhaminst", "Suite source": "https://github.com/EarlhamInst/earlham-galaxytools/tree/main/tools/lotus2", - "Suite parsed folder": "https://github.com/EarlhamInst/earlham-galaxytools/tree/main/tools/lotus2", + "Suite parsed folder": "https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2", "bio.tool ID": "lotus2", "bio.tool name": "lotus2", "bio.tool description": "LotuS2 is a lightweight and user-friendly pipeline that is fast, precise, and streamlined, using extensive pre- and post-ASV/OTU clustering steps to further increase data quality. High data usage rates and reliability enable high-throughput microbiome analysis in minutes.", "biii ID": null, + "Related Workflows": [ + "https://usegalaxy.eu/published/workflow?id=466bdd8ba7b67264", + "https://workflowhub.eu/workflows/1460?version=1" + ], + "Related Tutorials": [ + "microbiome/lotus2-identifying-fungi", + "microbiome/mgnify-amplicon" + ], "Number of tools on UseGalaxy.org (Main)": 0, "Number of tools on UseGalaxy.org.au": 1, "Number of tools on UseGalaxy.eu": 1, "Number of tools on UseGalaxy.fr": 1, "Number of tools on APOSTL": 0, - "Number of tools on MBAC Metabiome Portal": 0, "Number of tools on ChemFlow": 0, "Number of tools on CIRM-CFBP": 0, "Number of tools on Coloc-stats": 0, @@ -344,7 +345,6 @@ "Number of tools on MISSISSIPPI": 0, "Number of tools on Oqtans": 0, "Number of tools on Palfinder": 0, - "Number of tools on PepSimili": 0, "Number of tools on PhagePromotor": 0, "Number of tools on UseGalaxy.be": 1, "Number of tools on UseGalaxy.cz": 1, @@ -370,14 +370,6 @@ "Suite runs (last 5 years) on main servers": 2401, "Suite users on main servers": 273, "Suite users (last 5 years) on main servers": 273, - "Related Workflows": [ - "https://usegalaxy.eu/published/workflow?id=466bdd8ba7b67264", - "https://workflowhub.eu/workflows/1460?version=1" - ], - "Related Tutorials": [ - "microbiome/lotus2-identifying-fungi", - "microbiome/mgnify-amplicon" - ], "To keep": true, "Deprecated": false }, @@ -399,7 +391,7 @@ "Description": "T-Coffee", "Suite first commit date": "2016-12-13", "Homepage": "https://tcoffee.org/", - "Suite version": "13.45.0.4846264", + "Suite version": "@TOOL_VERSION@", "Suite conda package": "t-coffee", "Latest suite conda package version": "13.46.0.919e8c6b", "Suite version status": "To update", @@ -412,17 +404,18 @@ "EDAM reduced topics": [], "Suite owner": "earlhaminst", "Suite source": "https://github.com/EarlhamInst/earlham-galaxytools/tree/main/tools/t_coffee", - "Suite parsed folder": "https://github.com/EarlhamInst/earlham-galaxytools/tree/main/tools/t_coffee", + "Suite parsed folder": "https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee", "bio.tool ID": null, "bio.tool name": null, "bio.tool description": null, "biii ID": null, + "Related Workflows": [], + "Related Tutorials": [], "Number of tools on UseGalaxy.org (Main)": 0, "Number of tools on UseGalaxy.org.au": 0, "Number of tools on UseGalaxy.eu": 1, "Number of tools on UseGalaxy.fr": 0, "Number of tools on APOSTL": 0, - "Number of tools on MBAC Metabiome Portal": 0, "Number of tools on ChemFlow": 0, "Number of tools on CIRM-CFBP": 0, "Number of tools on Coloc-stats": 0, @@ -439,7 +432,6 @@ "Number of tools on MISSISSIPPI": 0, "Number of tools on Oqtans": 0, "Number of tools on Palfinder": 0, - "Number of tools on PepSimili": 0, "Number of tools on PhagePromotor": 0, "Number of tools on UseGalaxy.be": 0, "Number of tools on UseGalaxy.cz": 1, @@ -465,8 +457,6 @@ "Suite runs (last 5 years) on main servers": 3959, "Suite users on main servers": 312, "Suite users (last 5 years) on main servers": 275, - "Related Workflows": [], - "Related Tutorials": [], "To keep": true, "Deprecated": false }, @@ -500,12 +490,13 @@ "bio.tool name": null, "bio.tool description": null, "biii ID": null, + "Related Workflows": [], + "Related Tutorials": [], "Number of tools on UseGalaxy.org (Main)": 0, "Number of tools on UseGalaxy.org.au": 0, "Number of tools on UseGalaxy.eu": 0, "Number of tools on UseGalaxy.fr": 1, "Number of tools on APOSTL": 0, - "Number of tools on MBAC Metabiome Portal": 0, "Number of tools on ChemFlow": 0, "Number of tools on CIRM-CFBP": 0, "Number of tools on Coloc-stats": 0, @@ -522,7 +513,6 @@ "Number of tools on MISSISSIPPI": 0, "Number of tools on Oqtans": 0, "Number of tools on Palfinder": 0, - "Number of tools on PepSimili": 0, "Number of tools on PhagePromotor": 0, "Number of tools on UseGalaxy.be": 0, "Number of tools on UseGalaxy.cz": 0, @@ -548,8 +538,6 @@ "Suite runs (last 5 years) on main servers": 3, "Suite users on main servers": 2, "Suite users (last 5 years) on main servers": 2, - "Related Workflows": [], - "Related Tutorials": [], "To keep": true, "Deprecated": false }, @@ -584,12 +572,13 @@ "bio.tool name": null, "bio.tool description": null, "biii ID": null, + "Related Workflows": [], + "Related Tutorials": [], "Number of tools on UseGalaxy.org (Main)": 0, "Number of tools on UseGalaxy.org.au": 0, "Number of tools on UseGalaxy.eu": 0, "Number of tools on UseGalaxy.fr": 0, "Number of tools on APOSTL": 0, - "Number of tools on MBAC Metabiome Portal": 0, "Number of tools on ChemFlow": 0, "Number of tools on CIRM-CFBP": 0, "Number of tools on Coloc-stats": 0, @@ -606,7 +595,6 @@ "Number of tools on MISSISSIPPI": 0, "Number of tools on Oqtans": 0, "Number of tools on Palfinder": 0, - "Number of tools on PepSimili": 0, "Number of tools on PhagePromotor": 0, "Number of tools on UseGalaxy.be": 0, "Number of tools on UseGalaxy.cz": 0, @@ -632,8 +620,6 @@ "Suite runs (last 5 years) on main servers": 0, "Suite users on main servers": 0, "Suite users (last 5 years) on main servers": 0, - "Related Workflows": [], - "Related Tutorials": [], "To keep": true, "Deprecated": false }, @@ -667,12 +653,13 @@ "bio.tool name": null, "bio.tool description": null, "biii ID": null, + "Related Workflows": [], + "Related Tutorials": [], "Number of tools on UseGalaxy.org (Main)": 0, "Number of tools on UseGalaxy.org.au": 0, "Number of tools on UseGalaxy.eu": 0, "Number of tools on UseGalaxy.fr": 0, "Number of tools on APOSTL": 0, - "Number of tools on MBAC Metabiome Portal": 0, "Number of tools on ChemFlow": 0, "Number of tools on CIRM-CFBP": 0, "Number of tools on Coloc-stats": 0, @@ -689,7 +676,6 @@ "Number of tools on MISSISSIPPI": 0, "Number of tools on Oqtans": 0, "Number of tools on Palfinder": 0, - "Number of tools on PepSimili": 0, "Number of tools on PhagePromotor": 0, "Number of tools on UseGalaxy.be": 0, "Number of tools on UseGalaxy.cz": 0, @@ -715,8 +701,6 @@ "Suite runs (last 5 years) on main servers": 0, "Suite users on main servers": 0, "Suite users (last 5 years) on main servers": 0, - "Related Workflows": [], - "Related Tutorials": [], "To keep": true, "Deprecated": false }, @@ -731,12 +715,12 @@ "txt" ], "Description": "CryptoGenotyper is a standalone tool to *in-silico* determine species and subtype based on SSU rRNA (18S) and gp60 markers.", - "Suite first commit date": "2020-10-14", + "Suite first commit date": "2020-10-13", "Homepage": "https://github.com/phac-nml/CryptoGenotyper", - "Suite version": "1.5.0", + "Suite version": "@VERSION@", "Suite conda package": "cryptogenotyper", "Latest suite conda package version": "1.5.0", - "Suite version status": "Up-to-date", + "Suite version status": "To update", "ToolShed categories": [ "Sequence Analysis" ], @@ -751,12 +735,20 @@ "bio.tool name": null, "bio.tool description": null, "biii ID": null, + "Related Workflows": [ + "https://usegalaxy.eu/published/workflow?id=07865c770825c54a", + "https://usegalaxy.eu/published/workflow?id=280877e42b09f49f", + "https://usegalaxy.eu/published/workflow?id=3d7659452e3af984", + "https://usegalaxy.eu/published/workflow?id=4ba4da05a7696923", + "https://usegalaxy.eu/published/workflow?id=aefe927f13bc9374", + "https://usegalaxy.eu/published/workflow?id=f7558edf450e781f" + ], + "Related Tutorials": [], "Number of tools on UseGalaxy.org (Main)": 0, "Number of tools on UseGalaxy.org.au": 0, "Number of tools on UseGalaxy.eu": 1, "Number of tools on UseGalaxy.fr": 0, "Number of tools on APOSTL": 0, - "Number of tools on MBAC Metabiome Portal": 0, "Number of tools on ChemFlow": 0, "Number of tools on CIRM-CFBP": 0, "Number of tools on Coloc-stats": 0, @@ -773,7 +765,6 @@ "Number of tools on MISSISSIPPI": 0, "Number of tools on Oqtans": 0, "Number of tools on Palfinder": 0, - "Number of tools on PepSimili": 0, "Number of tools on PhagePromotor": 0, "Number of tools on UseGalaxy.be": 0, "Number of tools on UseGalaxy.cz": 1, @@ -799,15 +790,6 @@ "Suite runs (last 5 years) on main servers": 12430, "Suite users on main servers": 31, "Suite users (last 5 years) on main servers": 31, - "Related Workflows": [ - "https://usegalaxy.eu/published/workflow?id=07865c770825c54a", - "https://usegalaxy.eu/published/workflow?id=280877e42b09f49f", - "https://usegalaxy.eu/published/workflow?id=3d7659452e3af984", - "https://usegalaxy.eu/published/workflow?id=4ba4da05a7696923", - "https://usegalaxy.eu/published/workflow?id=aefe927f13bc9374", - "https://usegalaxy.eu/published/workflow?id=f7558edf450e781f" - ], - "Related Tutorials": [], "To keep": true, "Deprecated": false }, @@ -823,10 +805,10 @@ "Description": "EC-Typer - in silico serotyping of Escherichia coli species", "Suite first commit date": "2018-12-21", "Homepage": "https://github.com/phac-nml/ecoli_serotyping", - "Suite version": "2.0.0", + "Suite version": "@VERSION@", "Suite conda package": "ectyper", "Latest suite conda package version": "2.0.0", - "Suite version status": "Up-to-date", + "Suite version status": "To update", "ToolShed categories": [ "Sequence Analysis" ], @@ -861,12 +843,15 @@ "bio.tool name": "ECTyper", "bio.tool description": "Ectyper is a standalone serotyping module for Escherichia coli. It supports fasta and fastq file formats. (Galaxy Version 1.0.0)", "biii ID": null, + "Related Workflows": [ + "https://usegalaxy.eu/published/workflow?id=b90585626a793502" + ], + "Related Tutorials": [], "Number of tools on UseGalaxy.org (Main)": 0, "Number of tools on UseGalaxy.org.au": 1, "Number of tools on UseGalaxy.eu": 1, "Number of tools on UseGalaxy.fr": 0, "Number of tools on APOSTL": 0, - "Number of tools on MBAC Metabiome Portal": 0, "Number of tools on ChemFlow": 0, "Number of tools on CIRM-CFBP": 0, "Number of tools on Coloc-stats": 0, @@ -883,7 +868,6 @@ "Number of tools on MISSISSIPPI": 0, "Number of tools on Oqtans": 0, "Number of tools on Palfinder": 0, - "Number of tools on PepSimili": 0, "Number of tools on PhagePromotor": 0, "Number of tools on UseGalaxy.be": 0, "Number of tools on UseGalaxy.cz": 1, @@ -909,10 +893,6 @@ "Suite runs (last 5 years) on main servers": 30473, "Suite users on main servers": 219, "Suite users (last 5 years) on main servers": 219, - "Related Workflows": [ - "https://usegalaxy.eu/published/workflow?id=b90585626a793502" - ], - "Related Tutorials": [], "To keep": true, "Deprecated": false }, @@ -946,12 +926,13 @@ "bio.tool name": null, "bio.tool description": null, "biii ID": null, + "Related Workflows": [], + "Related Tutorials": [], "Number of tools on UseGalaxy.org (Main)": 0, "Number of tools on UseGalaxy.org.au": 0, "Number of tools on UseGalaxy.eu": 0, "Number of tools on UseGalaxy.fr": 0, "Number of tools on APOSTL": 0, - "Number of tools on MBAC Metabiome Portal": 0, "Number of tools on ChemFlow": 0, "Number of tools on CIRM-CFBP": 0, "Number of tools on Coloc-stats": 0, @@ -968,7 +949,6 @@ "Number of tools on MISSISSIPPI": 0, "Number of tools on Oqtans": 0, "Number of tools on Palfinder": 0, - "Number of tools on PepSimili": 0, "Number of tools on PhagePromotor": 0, "Number of tools on UseGalaxy.be": 0, "Number of tools on UseGalaxy.cz": 0, @@ -994,8 +974,6 @@ "Suite runs (last 5 years) on main servers": 0, "Suite users on main servers": 0, "Suite users (last 5 years) on main servers": 0, - "Related Workflows": [], - "Related Tutorials": [], "To keep": true, "Deprecated": false }, @@ -1029,12 +1007,13 @@ "bio.tool name": null, "bio.tool description": null, "biii ID": null, + "Related Workflows": [], + "Related Tutorials": [], "Number of tools on UseGalaxy.org (Main)": 0, "Number of tools on UseGalaxy.org.au": 0, "Number of tools on UseGalaxy.eu": 0, "Number of tools on UseGalaxy.fr": 0, "Number of tools on APOSTL": 0, - "Number of tools on MBAC Metabiome Portal": 0, "Number of tools on ChemFlow": 0, "Number of tools on CIRM-CFBP": 0, "Number of tools on Coloc-stats": 0, @@ -1051,7 +1030,6 @@ "Number of tools on MISSISSIPPI": 0, "Number of tools on Oqtans": 0, "Number of tools on Palfinder": 0, - "Number of tools on PepSimili": 0, "Number of tools on PhagePromotor": 0, "Number of tools on UseGalaxy.be": 0, "Number of tools on UseGalaxy.cz": 0, @@ -1077,8 +1055,6 @@ "Suite runs (last 5 years) on main servers": 0, "Suite users on main servers": 0, "Suite users (last 5 years) on main servers": 0, - "Related Workflows": [], - "Related Tutorials": [], "To keep": true, "Deprecated": false }, @@ -1111,12 +1087,13 @@ "bio.tool name": null, "bio.tool description": null, "biii ID": null, + "Related Workflows": [], + "Related Tutorials": [], "Number of tools on UseGalaxy.org (Main)": 0, "Number of tools on UseGalaxy.org.au": 0, "Number of tools on UseGalaxy.eu": 0, "Number of tools on UseGalaxy.fr": 0, "Number of tools on APOSTL": 0, - "Number of tools on MBAC Metabiome Portal": 0, "Number of tools on ChemFlow": 0, "Number of tools on CIRM-CFBP": 0, "Number of tools on Coloc-stats": 0, @@ -1133,7 +1110,6 @@ "Number of tools on MISSISSIPPI": 0, "Number of tools on Oqtans": 0, "Number of tools on Palfinder": 0, - "Number of tools on PepSimili": 0, "Number of tools on PhagePromotor": 0, "Number of tools on UseGalaxy.be": 0, "Number of tools on UseGalaxy.cz": 0, @@ -1159,8 +1135,6 @@ "Suite runs (last 5 years) on main servers": 0, "Suite users on main servers": 0, "Suite users (last 5 years) on main servers": 0, - "Related Workflows": [], - "Related Tutorials": [], "To keep": true, "Deprecated": false }, @@ -1194,12 +1168,13 @@ "bio.tool name": null, "bio.tool description": null, "biii ID": null, + "Related Workflows": [], + "Related Tutorials": [], "Number of tools on UseGalaxy.org (Main)": 0, "Number of tools on UseGalaxy.org.au": 0, "Number of tools on UseGalaxy.eu": 0, "Number of tools on UseGalaxy.fr": 0, "Number of tools on APOSTL": 0, - "Number of tools on MBAC Metabiome Portal": 0, "Number of tools on ChemFlow": 0, "Number of tools on CIRM-CFBP": 0, "Number of tools on Coloc-stats": 0, @@ -1216,7 +1191,6 @@ "Number of tools on MISSISSIPPI": 0, "Number of tools on Oqtans": 0, "Number of tools on Palfinder": 0, - "Number of tools on PepSimili": 0, "Number of tools on PhagePromotor": 0, "Number of tools on UseGalaxy.be": 0, "Number of tools on UseGalaxy.cz": 0, @@ -1242,8 +1216,6 @@ "Suite runs (last 5 years) on main servers": 0, "Suite users on main servers": 0, "Suite users (last 5 years) on main servers": 0, - "Related Workflows": [], - "Related Tutorials": [], "To keep": true, "Deprecated": false }, @@ -1295,12 +1267,17 @@ "bio.tool name": "mob_suite", "bio.tool description": "MOB-suite: Software tools for clustering, reconstruction and typing of plasmids from draft assembliesThe MOB-suite depends on a series of databases which are too large to be hosted in git-hub. They can be downloaded or updated by running mob_init or if running any of the tools for the first time, the databases will download and initialize automatically if you do not specify an alternate database location.", "biii ID": null, + "Related Workflows": [ + "https://usegalaxy.eu/published/workflow?id=2c992e509aa5dd9d", + "https://usegalaxy.eu/published/workflow?id=d0339e4a794f4922", + "https://workflowhub.eu/workflows/407?version=1" + ], + "Related Tutorials": [], "Number of tools on UseGalaxy.org (Main)": 0, "Number of tools on UseGalaxy.org.au": 2, "Number of tools on UseGalaxy.eu": 2, "Number of tools on UseGalaxy.fr": 2, "Number of tools on APOSTL": 0, - "Number of tools on MBAC Metabiome Portal": 0, "Number of tools on ChemFlow": 0, "Number of tools on CIRM-CFBP": 0, "Number of tools on Coloc-stats": 0, @@ -1317,7 +1294,6 @@ "Number of tools on MISSISSIPPI": 0, "Number of tools on Oqtans": 0, "Number of tools on Palfinder": 0, - "Number of tools on PepSimili": 0, "Number of tools on PhagePromotor": 0, "Number of tools on UseGalaxy.be": 0, "Number of tools on UseGalaxy.cz": 2, @@ -1343,12 +1319,6 @@ "Suite runs (last 5 years) on main servers": 229082, "Suite users on main servers": 832, "Suite users (last 5 years) on main servers": 832, - "Related Workflows": [ - "https://usegalaxy.eu/published/workflow?id=2c992e509aa5dd9d", - "https://usegalaxy.eu/published/workflow?id=d0339e4a794f4922", - "https://workflowhub.eu/workflows/407?version=1" - ], - "Related Tutorials": [], "To keep": true, "Deprecated": false }, @@ -1381,12 +1351,15 @@ "bio.tool name": null, "bio.tool description": null, "biii ID": null, + "Related Workflows": [ + "https://usegalaxy.eu/published/workflow?id=93d7a5704ec1d82d" + ], + "Related Tutorials": [], "Number of tools on UseGalaxy.org (Main)": 0, "Number of tools on UseGalaxy.org.au": 0, "Number of tools on UseGalaxy.eu": 1, "Number of tools on UseGalaxy.fr": 0, "Number of tools on APOSTL": 0, - "Number of tools on MBAC Metabiome Portal": 0, "Number of tools on ChemFlow": 0, "Number of tools on CIRM-CFBP": 0, "Number of tools on Coloc-stats": 0, @@ -1403,7 +1376,6 @@ "Number of tools on MISSISSIPPI": 0, "Number of tools on Oqtans": 0, "Number of tools on Palfinder": 0, - "Number of tools on PepSimili": 0, "Number of tools on PhagePromotor": 0, "Number of tools on UseGalaxy.be": 0, "Number of tools on UseGalaxy.cz": 0, @@ -1429,10 +1401,6 @@ "Suite runs (last 5 years) on main servers": 18, "Suite users on main servers": 4, "Suite users (last 5 years) on main servers": 4, - "Related Workflows": [ - "https://usegalaxy.eu/published/workflow?id=93d7a5704ec1d82d" - ], - "Related Tutorials": [], "To keep": true, "Deprecated": false }, @@ -1447,7 +1415,7 @@ "Description": "RScript to parse the results of mykrobe predictor.", "Suite first commit date": "2018-09-28", "Homepage": "https://github.com/phac-nml/mykrobe-parser", - "Suite version": "0.1.4.1", + "Suite version": "@VERSION@", "Suite conda package": "r-base", "Latest suite conda package version": null, "Suite version status": "To update", @@ -1465,12 +1433,13 @@ "bio.tool name": null, "bio.tool description": null, "biii ID": null, + "Related Workflows": [], + "Related Tutorials": [], "Number of tools on UseGalaxy.org (Main)": 0, "Number of tools on UseGalaxy.org.au": 0, "Number of tools on UseGalaxy.eu": 0, "Number of tools on UseGalaxy.fr": 0, "Number of tools on APOSTL": 0, - "Number of tools on MBAC Metabiome Portal": 0, "Number of tools on ChemFlow": 0, "Number of tools on CIRM-CFBP": 0, "Number of tools on Coloc-stats": 0, @@ -1487,7 +1456,6 @@ "Number of tools on MISSISSIPPI": 0, "Number of tools on Oqtans": 0, "Number of tools on Palfinder": 0, - "Number of tools on PepSimili": 0, "Number of tools on PhagePromotor": 0, "Number of tools on UseGalaxy.be": 0, "Number of tools on UseGalaxy.cz": 0, @@ -1513,8 +1481,6 @@ "Suite runs (last 5 years) on main servers": 0, "Suite users on main servers": 0, "Suite users (last 5 years) on main servers": 0, - "Related Workflows": [], - "Related Tutorials": [], "To keep": true, "Deprecated": false }, @@ -1533,7 +1499,7 @@ "Homepage": null, "Suite version": "1.1", "Suite conda package": "spades", - "Latest suite conda package version": "4.2.0", + "Latest suite conda package version": "4.3.0", "Suite version status": "To update", "ToolShed categories": [ "Assembly" @@ -1549,12 +1515,13 @@ "bio.tool name": null, "bio.tool description": null, "biii ID": null, + "Related Workflows": [], + "Related Tutorials": [], "Number of tools on UseGalaxy.org (Main)": 0, "Number of tools on UseGalaxy.org.au": 0, "Number of tools on UseGalaxy.eu": 0, "Number of tools on UseGalaxy.fr": 0, "Number of tools on APOSTL": 0, - "Number of tools on MBAC Metabiome Portal": 0, "Number of tools on ChemFlow": 0, "Number of tools on CIRM-CFBP": 0, "Number of tools on Coloc-stats": 0, @@ -1571,7 +1538,6 @@ "Number of tools on MISSISSIPPI": 0, "Number of tools on Oqtans": 0, "Number of tools on Palfinder": 0, - "Number of tools on PepSimili": 0, "Number of tools on PhagePromotor": 0, "Number of tools on UseGalaxy.be": 0, "Number of tools on UseGalaxy.cz": 0, @@ -1597,8 +1563,6 @@ "Suite runs (last 5 years) on main servers": 0, "Suite users on main servers": 0, "Suite users (last 5 years) on main servers": 0, - "Related Workflows": [], - "Related Tutorials": [], "To keep": true, "Deprecated": false }, @@ -1632,12 +1596,13 @@ "bio.tool name": null, "bio.tool description": null, "biii ID": null, + "Related Workflows": [], + "Related Tutorials": [], "Number of tools on UseGalaxy.org (Main)": 0, "Number of tools on UseGalaxy.org.au": 0, "Number of tools on UseGalaxy.eu": 0, "Number of tools on UseGalaxy.fr": 0, "Number of tools on APOSTL": 0, - "Number of tools on MBAC Metabiome Portal": 0, "Number of tools on ChemFlow": 0, "Number of tools on CIRM-CFBP": 0, "Number of tools on Coloc-stats": 0, @@ -1654,7 +1619,6 @@ "Number of tools on MISSISSIPPI": 0, "Number of tools on Oqtans": 0, "Number of tools on Palfinder": 0, - "Number of tools on PepSimili": 0, "Number of tools on PhagePromotor": 0, "Number of tools on UseGalaxy.be": 0, "Number of tools on UseGalaxy.cz": 0, @@ -1680,8 +1644,6 @@ "Suite runs (last 5 years) on main servers": 0, "Suite users on main servers": 0, "Suite users (last 5 years) on main servers": 0, - "Related Workflows": [], - "Related Tutorials": [], "To keep": true, "Deprecated": false }, @@ -1699,10 +1661,10 @@ "Description": "SISTR in silico serotyping tool", "Suite first commit date": "2017-02-20", "Homepage": "https://github.com/phac-nml/sistr_cmd", - "Suite version": "1.1.3", + "Suite version": "@VERSION@", "Suite conda package": "sistr_cmd", "Latest suite conda package version": "1.1.3", - "Suite version status": "Up-to-date", + "Suite version status": "To update", "ToolShed categories": [ "Sequence Analysis" ], @@ -1737,12 +1699,22 @@ "bio.tool name": "SISTR", "bio.tool description": "The Salmonella In Silico Typing Resource (SISTR) is an open-source and freely available web application for rapid in silico typing and serovar prediction from Salmonella genome assemblies using cgMLST and O and H antigen gene searching.", "biii ID": null, + "Related Workflows": [ + "https://usegalaxy.eu/published/workflow?id=628062a8cf93261f", + "https://usegalaxy.eu/published/workflow?id=94c3d329c31c712f", + "https://usegalaxy.eu/published/workflow?id=cbe3769f1abb9fa5", + "https://usegalaxy.eu/published/workflow?id=fde21b5f5c169114", + "https://usegalaxy.org.au/published/workflow?id=2120112358db8e01", + "https://usegalaxy.org.au/published/workflow?id=41331c03339e2b19", + "https://usegalaxy.org.au/published/workflow?id=92fcdd490831c6c5", + "https://workflowhub.eu/workflows/407?version=1" + ], + "Related Tutorials": [], "Number of tools on UseGalaxy.org (Main)": 0, "Number of tools on UseGalaxy.org.au": 1, "Number of tools on UseGalaxy.eu": 1, "Number of tools on UseGalaxy.fr": 0, "Number of tools on APOSTL": 0, - "Number of tools on MBAC Metabiome Portal": 0, "Number of tools on ChemFlow": 0, "Number of tools on CIRM-CFBP": 0, "Number of tools on Coloc-stats": 0, @@ -1759,7 +1731,6 @@ "Number of tools on MISSISSIPPI": 0, "Number of tools on Oqtans": 0, "Number of tools on Palfinder": 0, - "Number of tools on PepSimili": 0, "Number of tools on PhagePromotor": 0, "Number of tools on UseGalaxy.be": 0, "Number of tools on UseGalaxy.cz": 1, @@ -1785,16 +1756,6 @@ "Suite runs (last 5 years) on main servers": 6252, "Suite users on main servers": 492, "Suite users (last 5 years) on main servers": 486, - "Related Workflows": [ - "https://usegalaxy.eu/published/workflow?id=628062a8cf93261f", - "https://usegalaxy.eu/published/workflow?id=94c3d329c31c712f", - "https://usegalaxy.eu/published/workflow?id=cbe3769f1abb9fa5", - "https://usegalaxy.eu/published/workflow?id=fde21b5f5c169114", - "https://usegalaxy.org.au/published/workflow?id=2120112358db8e01", - "https://usegalaxy.org.au/published/workflow?id=92fcdd490831c6c5", - "https://workflowhub.eu/workflows/407?version=1" - ], - "Related Tutorials": [], "To keep": true, "Deprecated": false }, @@ -1809,10 +1770,10 @@ "Description": "SMALT aligns DNA sequencing reads with a reference genome.", "Suite first commit date": "2017-09-19", "Homepage": "http://www.sanger.ac.uk/science/tools/smalt-0", - "Suite version": "0.7.6", + "Suite version": "@VERSION@", "Suite conda package": "smalt", "Latest suite conda package version": "0.7.6", - "Suite version status": "Up-to-date", + "Suite version status": "To update", "ToolShed categories": [ "Sequence Analysis" ], @@ -1827,12 +1788,13 @@ "bio.tool name": null, "bio.tool description": null, "biii ID": null, + "Related Workflows": [], + "Related Tutorials": [], "Number of tools on UseGalaxy.org (Main)": 0, "Number of tools on UseGalaxy.org.au": 0, "Number of tools on UseGalaxy.eu": 0, "Number of tools on UseGalaxy.fr": 0, "Number of tools on APOSTL": 0, - "Number of tools on MBAC Metabiome Portal": 0, "Number of tools on ChemFlow": 0, "Number of tools on CIRM-CFBP": 0, "Number of tools on Coloc-stats": 0, @@ -1849,7 +1811,6 @@ "Number of tools on MISSISSIPPI": 0, "Number of tools on Oqtans": 0, "Number of tools on Palfinder": 0, - "Number of tools on PepSimili": 0, "Number of tools on PhagePromotor": 0, "Number of tools on UseGalaxy.be": 0, "Number of tools on UseGalaxy.cz": 0, @@ -1875,8 +1836,6 @@ "Suite runs (last 5 years) on main servers": 0, "Suite users on main servers": 0, "Suite users (last 5 years) on main servers": 0, - "Related Workflows": [], - "Related Tutorials": [], "To keep": true, "Deprecated": false }, @@ -1911,12 +1870,15 @@ "bio.tool name": null, "bio.tool description": null, "biii ID": null, + "Related Workflows": [ + "https://workflowhub.eu/workflows/407?version=1" + ], + "Related Tutorials": [], "Number of tools on UseGalaxy.org (Main)": 0, "Number of tools on UseGalaxy.org.au": 0, "Number of tools on UseGalaxy.eu": 1, "Number of tools on UseGalaxy.fr": 0, "Number of tools on APOSTL": 0, - "Number of tools on MBAC Metabiome Portal": 0, "Number of tools on ChemFlow": 0, "Number of tools on CIRM-CFBP": 0, "Number of tools on Coloc-stats": 0, @@ -1933,7 +1895,6 @@ "Number of tools on MISSISSIPPI": 0, "Number of tools on Oqtans": 0, "Number of tools on Palfinder": 0, - "Number of tools on PepSimili": 0, "Number of tools on PhagePromotor": 0, "Number of tools on UseGalaxy.be": 0, "Number of tools on UseGalaxy.cz": 1, @@ -1959,10 +1920,6 @@ "Suite runs (last 5 years) on main servers": 478, "Suite users on main servers": 69, "Suite users (last 5 years) on main servers": 69, - "Related Workflows": [ - "https://workflowhub.eu/workflows/407?version=1" - ], - "Related Tutorials": [], "To keep": true, "Deprecated": false }, @@ -1997,12 +1954,13 @@ "bio.tool name": null, "bio.tool description": null, "biii ID": null, + "Related Workflows": [], + "Related Tutorials": [], "Number of tools on UseGalaxy.org (Main)": 0, "Number of tools on UseGalaxy.org.au": 0, "Number of tools on UseGalaxy.eu": 0, "Number of tools on UseGalaxy.fr": 0, "Number of tools on APOSTL": 0, - "Number of tools on MBAC Metabiome Portal": 0, "Number of tools on ChemFlow": 0, "Number of tools on CIRM-CFBP": 0, "Number of tools on Coloc-stats": 0, @@ -2019,7 +1977,6 @@ "Number of tools on MISSISSIPPI": 0, "Number of tools on Oqtans": 0, "Number of tools on Palfinder": 0, - "Number of tools on PepSimili": 0, "Number of tools on PhagePromotor": 0, "Number of tools on UseGalaxy.be": 0, "Number of tools on UseGalaxy.cz": 0, @@ -2045,8 +2002,6 @@ "Suite runs (last 5 years) on main servers": 0, "Suite users on main servers": 0, "Suite users (last 5 years) on main servers": 0, - "Related Workflows": [], - "Related Tutorials": [], "To keep": true, "Deprecated": false }, @@ -2079,12 +2034,13 @@ "bio.tool name": null, "bio.tool description": null, "biii ID": null, + "Related Workflows": [], + "Related Tutorials": [], "Number of tools on UseGalaxy.org (Main)": 0, "Number of tools on UseGalaxy.org.au": 0, "Number of tools on UseGalaxy.eu": 1, "Number of tools on UseGalaxy.fr": 0, "Number of tools on APOSTL": 0, - "Number of tools on MBAC Metabiome Portal": 0, "Number of tools on ChemFlow": 0, "Number of tools on CIRM-CFBP": 0, "Number of tools on Coloc-stats": 0, @@ -2101,7 +2057,6 @@ "Number of tools on MISSISSIPPI": 0, "Number of tools on Oqtans": 0, "Number of tools on Palfinder": 0, - "Number of tools on PepSimili": 0, "Number of tools on PhagePromotor": 0, "Number of tools on UseGalaxy.be": 0, "Number of tools on UseGalaxy.cz": 0, @@ -2127,8 +2082,6 @@ "Suite runs (last 5 years) on main servers": 369, "Suite users on main servers": 83, "Suite users (last 5 years) on main servers": 83, - "Related Workflows": [], - "Related Tutorials": [], "To keep": true, "Deprecated": false }, @@ -2147,7 +2100,7 @@ "Description": "Eukaryotic Genome Annotation Pipeline - External (EGAPx)", "Suite first commit date": "2024-08-19", "Homepage": "https://github.com/ncbi/egapx", - "Suite version": "0.5.0", + "Suite version": "0.5.2", "Suite conda package": null, "Latest suite conda package version": null, "Suite version status": "To update", @@ -2160,17 +2113,23 @@ "EDAM reduced topics": [], "Suite owner": "richard-burhans", "Suite source": "https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_egapx", - "Suite parsed folder": "https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_egapx", + "Suite parsed folder": "https://github.com/richard-burhans/galaxytools/tree/master/tools/ncbi_egapx", "bio.tool ID": null, "bio.tool name": null, "bio.tool description": null, "biii ID": null, + "Related Workflows": [ + "https://usegalaxy.org/published/workflow?id=7251c6e0dad8f927", + "https://usegalaxy.org/published/workflow?id=951575e9a352301c", + "https://usegalaxy.org/published/workflow?id=ce488732866ba48f", + "https://usegalaxy.org/published/workflow?id=e93a0522ec3a35e6" + ], + "Related Tutorials": [], "Number of tools on UseGalaxy.org (Main)": 3, "Number of tools on UseGalaxy.org.au": 0, "Number of tools on UseGalaxy.eu": 1, "Number of tools on UseGalaxy.fr": 0, "Number of tools on APOSTL": 0, - "Number of tools on MBAC Metabiome Portal": 0, "Number of tools on ChemFlow": 0, "Number of tools on CIRM-CFBP": 0, "Number of tools on Coloc-stats": 0, @@ -2187,7 +2146,6 @@ "Number of tools on MISSISSIPPI": 0, "Number of tools on Oqtans": 0, "Number of tools on Palfinder": 0, - "Number of tools on PepSimili": 0, "Number of tools on PhagePromotor": 0, "Number of tools on UseGalaxy.be": 0, "Number of tools on UseGalaxy.cz": 0, @@ -2213,13 +2171,6 @@ "Suite runs (last 5 years) on main servers": 1044, "Suite users on main servers": 51, "Suite users (last 5 years) on main servers": 51, - "Related Workflows": [ - "https://usegalaxy.org/published/workflow?id=7251c6e0dad8f927", - "https://usegalaxy.org/published/workflow?id=951575e9a352301c", - "https://usegalaxy.org/published/workflow?id=ce488732866ba48f", - "https://usegalaxy.org/published/workflow?id=e93a0522ec3a35e6" - ], - "Related Tutorials": [], "To keep": true, "Deprecated": false }, @@ -2234,7 +2185,7 @@ "qza" ], "Description": null, - "Suite first commit date": "2022-08-26", + "Suite first commit date": "2022-08-25", "Homepage": "https://github.com/qiime2/q2-alignment", "Suite version": "2026.1.0+q2galaxy.2026.1.0", "Suite conda package": null, @@ -2267,17 +2218,18 @@ ], "Suite owner": "q2d2", "Suite source": "https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment", - "Suite parsed folder": "https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment", + "Suite parsed folder": "https://github.com/qiime2/galaxy-tools/tree/master/tools/suite_qiime2__alignment", "bio.tool ID": "qiime2", "bio.tool name": "QIIME 2", "bio.tool description": "QIIME 2 is an AI-ready microbiome multi-omics data science platform that is trusted, free, open source, extensible, and community developed and supported bioinformatics.", "biii ID": null, + "Related Workflows": [], + "Related Tutorials": [], "Number of tools on UseGalaxy.org (Main)": 3, "Number of tools on UseGalaxy.org.au": 3, "Number of tools on UseGalaxy.eu": 3, "Number of tools on UseGalaxy.fr": 3, "Number of tools on APOSTL": 0, - 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"Suite parsed folder": "https://github.com/qiime2/galaxy-tools/tree/main/tool_collections/suite_qiime2_core", + "Suite parsed folder": "https://github.com/qiime2/galaxy-tools/tree/master/tool_collections/suite_qiime2_core", "bio.tool ID": null, "bio.tool name": null, "bio.tool description": null, "biii ID": null, + "Related Workflows": [], + "Related Tutorials": [], "Number of tools on UseGalaxy.org (Main)": 0, "Number of tools on UseGalaxy.org.au": 0, "Number of tools on UseGalaxy.eu": 0, "Number of tools on UseGalaxy.fr": 0, "Number of tools on APOSTL": 0, - "Number of tools on MBAC Metabiome Portal": 0, "Number of tools on ChemFlow": 0, "Number of tools on CIRM-CFBP": 0, "Number of tools on Coloc-stats": 0, @@ -5328,7 +5226,6 @@ "Number of tools on MISSISSIPPI": 0, "Number of tools on Oqtans": 0, "Number of tools on Palfinder": 0, - "Number of tools on PepSimili": 0, "Number of tools on PhagePromotor": 0, "Number of tools on UseGalaxy.be": 0, "Number of tools on UseGalaxy.cz": 0, @@ -5354,8 +5251,6 @@ "Suite runs (last 5 years) on main servers": 0, "Suite users on main servers": 0, "Suite users (last 5 years) on main servers": 0, - 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"Number of tools on MBAC Metabiome Portal": 0, "Number of tools on ChemFlow": 0, "Number of tools on CIRM-CFBP": 0, "Number of tools on Coloc-stats": 0, @@ -5506,7 +5410,6 @@ "Number of tools on MISSISSIPPI": 0, "Number of tools on Oqtans": 0, "Number of tools on Palfinder": 0, - "Number of tools on PepSimili": 0, "Number of tools on PhagePromotor": 0, "Number of tools on UseGalaxy.be": 1, "Number of tools on UseGalaxy.cz": 1, @@ -5532,18 +5435,6 @@ "Suite runs (last 5 years) on main servers": 357, "Suite users on main servers": 1915, "Suite users (last 5 years) on main servers": 85, - "Related Workflows": [ - "https://usegalaxy.org/published/workflow?id=19c9c8cc3c813bda", - "https://usegalaxy.org/published/workflow?id=2f7638035fb889ac", - "https://usegalaxy.org/published/workflow?id=55aa743125c2465d", - "https://usegalaxy.org/published/workflow?id=59347cc210c4cdbc", - "https://usegalaxy.org/published/workflow?id=7294f75ad01ca7ed", - "https://usegalaxy.org/published/workflow?id=7b67ffcf1b7c2232", - 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"Number of tools on MBAC Metabiome Portal": 0, "Number of tools on ChemFlow": 0, "Number of tools on CIRM-CFBP": 0, "Number of tools on Coloc-stats": 0, @@ -5598,7 +5509,6 @@ "Number of tools on MISSISSIPPI": 0, "Number of tools on Oqtans": 0, "Number of tools on Palfinder": 0, - "Number of tools on PepSimili": 0, "Number of tools on PhagePromotor": 0, "Number of tools on UseGalaxy.be": 1, "Number of tools on UseGalaxy.cz": 1, @@ -5624,27 +5534,6 @@ "Suite runs (last 5 years) on main servers": 71178, "Suite users on main servers": 4507, "Suite users (last 5 years) on main servers": 3821, - "Related Workflows": [ - "https://usegalaxy.eu/published/workflow?id=0bafeb17c21ebc9c", - "https://usegalaxy.eu/published/workflow?id=2e0075791f7fa384", - "https://usegalaxy.eu/published/workflow?id=2ee0eb74e839b476", - "https://usegalaxy.eu/published/workflow?id=4a764275d4bf9f31", - "https://usegalaxy.eu/published/workflow?id=628062a8cf93261f", - "https://usegalaxy.eu/published/workflow?id=a459c311f461adce", - 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"Suite parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/lca_wrapper", + "Suite parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/lca_wrapper", "bio.tool ID": null, "bio.tool name": null, "bio.tool description": null, "biii ID": null, + "Related Workflows": [ + "https://usegalaxy.org/published/workflow?id=19c9c8cc3c813bda", + "https://usegalaxy.org/published/workflow?id=2f7638035fb889ac", + "https://usegalaxy.org/published/workflow?id=55aa743125c2465d", + "https://usegalaxy.org/published/workflow?id=59347cc210c4cdbc", + "https://usegalaxy.org/published/workflow?id=7294f75ad01ca7ed", + "https://usegalaxy.org/published/workflow?id=7b67ffcf1b7c2232", + "https://usegalaxy.org/published/workflow?id=85d825931edf4a64", + "https://usegalaxy.org/published/workflow?id=896d29573ea3e574", + "https://usegalaxy.org/published/workflow?id=d851f8436497dd1c" + ], + "Related Tutorials": [], "Number of tools on UseGalaxy.org (Main)": 0, "Number of tools on UseGalaxy.org.au": 0, "Number of tools on UseGalaxy.eu": 1, "Number of tools on UseGalaxy.fr": 0, "Number of tools on APOSTL": 0, - "Number of tools on MBAC Metabiome Portal": 0, "Number of tools on ChemFlow": 0, "Number of tools on CIRM-CFBP": 0, "Number of tools on Coloc-stats": 0, @@ -5699,7 +5599,6 @@ "Number of tools on MISSISSIPPI": 0, "Number of tools on Oqtans": 0, "Number of tools on Palfinder": 0, - "Number of tools on PepSimili": 0, "Number of tools on PhagePromotor": 0, "Number of tools on UseGalaxy.be": 1, "Number of tools on UseGalaxy.cz": 1, @@ -5725,18 +5624,6 @@ "Suite runs (last 5 years) on main servers": 123, "Suite users on main servers": 1132, "Suite users (last 5 years) on main servers": 17, - "Related Workflows": [ - "https://usegalaxy.org/published/workflow?id=19c9c8cc3c813bda", - "https://usegalaxy.org/published/workflow?id=2f7638035fb889ac", - "https://usegalaxy.org/published/workflow?id=55aa743125c2465d", - "https://usegalaxy.org/published/workflow?id=59347cc210c4cdbc", - "https://usegalaxy.org/published/workflow?id=7294f75ad01ca7ed", - "https://usegalaxy.org/published/workflow?id=7b67ffcf1b7c2232", - 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"Number of tools on MBAC Metabiome Portal": 0, "Number of tools on ChemFlow": 0, "Number of tools on CIRM-CFBP": 0, "Number of tools on Coloc-stats": 0, @@ -5799,7 +5697,6 @@ "Number of tools on MISSISSIPPI": 0, "Number of tools on Oqtans": 0, "Number of tools on Palfinder": 0, - "Number of tools on PepSimili": 0, "Number of tools on PhagePromotor": 0, "Number of tools on UseGalaxy.be": 1, "Number of tools on UseGalaxy.cz": 1, @@ -5825,18 +5722,6 @@ "Suite runs (last 5 years) on main servers": 507, "Suite users on main servers": 1333, "Suite users (last 5 years) on main servers": 77, - "Related Workflows": [ - "https://usegalaxy.org/published/workflow?id=19c9c8cc3c813bda", - "https://usegalaxy.org/published/workflow?id=2f7638035fb889ac", - "https://usegalaxy.org/published/workflow?id=55aa743125c2465d", - "https://usegalaxy.org/published/workflow?id=59347cc210c4cdbc", - "https://usegalaxy.org/published/workflow?id=7294f75ad01ca7ed", - "https://usegalaxy.org/published/workflow?id=7b67ffcf1b7c2232", - 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"Number of tools on MBAC Metabiome Portal": 0, "Number of tools on ChemFlow": 0, "Number of tools on CIRM-CFBP": 0, "Number of tools on Coloc-stats": 0, @@ -5891,7 +5786,6 @@ "Number of tools on MISSISSIPPI": 0, "Number of tools on Oqtans": 0, "Number of tools on Palfinder": 0, - "Number of tools on PepSimili": 0, "Number of tools on PhagePromotor": 0, "Number of tools on UseGalaxy.be": 1, "Number of tools on UseGalaxy.cz": 1, @@ -5917,17 +5811,6 @@ "Suite runs (last 5 years) on main servers": 863, "Suite users on main servers": 1225, "Suite users (last 5 years) on main servers": 71, - "Related Workflows": [ - "https://usegalaxy.org/published/workflow?id=19c9c8cc3c813bda", - "https://usegalaxy.org/published/workflow?id=2f7638035fb889ac", - "https://usegalaxy.org/published/workflow?id=55aa743125c2465d", - "https://usegalaxy.org/published/workflow?id=59347cc210c4cdbc", - "https://usegalaxy.org/published/workflow?id=7b67ffcf1b7c2232", - "https://usegalaxy.org/published/workflow?id=85d825931edf4a64", - 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It integrates and cross-links with a large number of in silico secondary metabolite analysis tools that have been published earlier.", "biii ID": null, + "Related Workflows": [ + "https://usegalaxy.eu/published/workflow?id=0461bbd1f96292e2", + "https://usegalaxy.eu/published/workflow?id=0ab3e47ebd3b520e", + "https://usegalaxy.eu/published/workflow?id=24eaa682897379c8", + "https://usegalaxy.eu/published/workflow?id=33312e5643279e8a", + "https://usegalaxy.eu/published/workflow?id=5be158931abca947", + "https://usegalaxy.eu/published/workflow?id=6984990d0ac2e1e6", + "https://usegalaxy.eu/published/workflow?id=6a5c39c1d38a10c2", + "https://usegalaxy.eu/published/workflow?id=6d87481be47902e1", + "https://usegalaxy.eu/published/workflow?id=9a60ecf98d4f8134", + "https://usegalaxy.eu/published/workflow?id=a448400f69594135", + "https://usegalaxy.eu/published/workflow?id=bf48b0eb15e8ff75", + "https://usegalaxy.eu/published/workflow?id=cc59ae1a9878942c", + "https://usegalaxy.eu/published/workflow?id=edbaf66c1e97ebdb", + "https://usegalaxy.eu/published/workflow?id=f141db5179ea8422", + "https://usegalaxy.org.au/published/workflow?id=35f39173f0ac9179", + "https://usegalaxy.org/published/workflow?id=84233173d92fa506", + "https://usegalaxy.org/published/workflow?id=c451e4dca9981ed0", + "https://workflowhub.eu/workflows/1558?version=1", + "https://workflowhub.eu/workflows/37?version=1", + "https://workflowhub.eu/workflows/38?version=1", + "https://workflowhub.eu/workflows/39?version=1", + "https://workflowhub.eu/workflows/40?version=1" + ], + "Related Tutorials": [ + "genome-annotation/secondary-metabolite-discovery" + ], "Number of tools on UseGalaxy.org (Main)": 1, "Number of tools on UseGalaxy.org.au": 1, "Number of tools on UseGalaxy.eu": 1, "Number of tools on UseGalaxy.fr": 1, "Number of tools on APOSTL": 0, - "Number of tools on MBAC Metabiome Portal": 0, "Number of tools on ChemFlow": 0, "Number of tools on CIRM-CFBP": 0, "Number of tools on Coloc-stats": 0, @@ -5997,7 +5906,6 @@ "Number of tools on MISSISSIPPI": 0, "Number of tools on Oqtans": 0, "Number of tools on Palfinder": 0, - "Number of tools on PepSimili": 0, "Number of tools on PhagePromotor": 0, "Number of tools on UseGalaxy.be": 1, "Number of tools on UseGalaxy.cz": 1, @@ -6023,32 +5931,6 @@ "Suite runs (last 5 years) on main servers": 52560, "Suite users on main servers": 2539, "Suite users (last 5 years) on main servers": 2386, - "Related Workflows": [ - "https://usegalaxy.eu/published/workflow?id=0461bbd1f96292e2", - "https://usegalaxy.eu/published/workflow?id=0ab3e47ebd3b520e", - "https://usegalaxy.eu/published/workflow?id=24eaa682897379c8", - "https://usegalaxy.eu/published/workflow?id=33312e5643279e8a", - "https://usegalaxy.eu/published/workflow?id=5be158931abca947", - "https://usegalaxy.eu/published/workflow?id=6984990d0ac2e1e6", - "https://usegalaxy.eu/published/workflow?id=6a5c39c1d38a10c2", - "https://usegalaxy.eu/published/workflow?id=6d87481be47902e1", - "https://usegalaxy.eu/published/workflow?id=9a60ecf98d4f8134", - "https://usegalaxy.eu/published/workflow?id=a448400f69594135", - "https://usegalaxy.eu/published/workflow?id=bf48b0eb15e8ff75", - "https://usegalaxy.eu/published/workflow?id=cc59ae1a9878942c", - "https://usegalaxy.eu/published/workflow?id=edbaf66c1e97ebdb", - "https://usegalaxy.eu/published/workflow?id=f141db5179ea8422", - "https://usegalaxy.org.au/published/workflow?id=35f39173f0ac9179", - "https://usegalaxy.org/published/workflow?id=c451e4dca9981ed0", - "https://workflowhub.eu/workflows/1558?version=1", - "https://workflowhub.eu/workflows/37?version=1", - "https://workflowhub.eu/workflows/38?version=1", - "https://workflowhub.eu/workflows/39?version=1", - "https://workflowhub.eu/workflows/40?version=1" - ], - "Related Tutorials": [ - "genome-annotation/secondary-metabolite-discovery" - ], "To keep": true, "Deprecated": false }, @@ -6065,10 +5947,10 @@ "Description": "Canu is a hierarchical assembly pipeline designed for high-noise single-molecule sequencing (such as the PacBio RS II/Sequel or Oxford Nanopore MinION).", "Suite first commit date": "2018-06-07", "Homepage": "https://github.com/marbl/canu", - "Suite version": "2.3", + "Suite version": "@TOOL_VERSION@+galaxy@VERSION_SUFFIX@", "Suite conda package": "canu", "Latest suite conda package version": "2.3", - "Suite version status": "Up-to-date", + "Suite version status": "To update", "ToolShed categories": [ "Assembly" ], @@ -6091,12 +5973,16 @@ "bio.tool name": "CANU", "bio.tool description": "De-novo assembly tool for long read chemistry like Nanopore data and PacBio data.", "biii ID": null, + "Related Workflows": [ + "https://usegalaxy.eu/published/workflow?id=93d7a5704ec1d82d", + "https://usegalaxy.org.au/published/workflow?id=344b2ad2604939bc" + ], + "Related Tutorials": [], "Number of tools on UseGalaxy.org (Main)": 0, "Number of tools on UseGalaxy.org.au": 1, "Number of tools on UseGalaxy.eu": 1, "Number of tools on UseGalaxy.fr": 1, "Number of tools on APOSTL": 0, - "Number of tools on MBAC Metabiome Portal": 0, "Number of tools on ChemFlow": 0, "Number of tools on CIRM-CFBP": 0, "Number of tools on Coloc-stats": 0, @@ -6113,7 +5999,6 @@ "Number of tools on MISSISSIPPI": 0, "Number of tools on Oqtans": 0, "Number of tools on Palfinder": 0, - "Number of tools on PepSimili": 0, "Number of tools on PhagePromotor": 0, "Number of tools on UseGalaxy.be": 0, "Number of tools on UseGalaxy.cz": 1, @@ -6139,10 +6024,6 @@ "Suite runs (last 5 years) on main servers": 17992, "Suite users on main servers": 2365, "Suite users (last 5 years) on main servers": 2135, - "Related Workflows": [ - "https://usegalaxy.eu/published/workflow?id=93d7a5704ec1d82d" - ], - "Related Tutorials": [], "To keep": true, "Deprecated": false }, @@ -6185,12 +6066,20 @@ "bio.tool name": "Combine Metaphlan and HUMAnN", "bio.tool description": "This tool combine MetaPhlAn outputs and HUMANnN outputs", "biii ID": null, + "Related Workflows": [ + "https://usegalaxy.eu/published/workflow?id=69eddfde874af35b", + "https://usegalaxy.eu/published/workflow?id=9472be79da012999", + "https://usegalaxy.fr/published/workflow?id=c4f6062e51d0f45e", + "https://workflowhub.eu/workflows/1466?version=2" + ], + "Related Tutorials": [ + "microbiome/metatranscriptomics" + ], "Number of tools on UseGalaxy.org (Main)": 1, "Number of tools on UseGalaxy.org.au": 0, "Number of tools on UseGalaxy.eu": 1, "Number of tools on UseGalaxy.fr": 1, "Number of tools on APOSTL": 0, - "Number of tools on MBAC Metabiome Portal": 0, "Number of tools on ChemFlow": 0, "Number of tools on CIRM-CFBP": 0, "Number of tools on Coloc-stats": 0, @@ -6207,7 +6096,6 @@ "Number of tools on MISSISSIPPI": 0, "Number of tools on Oqtans": 0, "Number of tools on Palfinder": 0, - "Number of tools on PepSimili": 0, "Number of tools on PhagePromotor": 0, "Number of tools on UseGalaxy.be": 1, "Number of tools on UseGalaxy.cz": 1, @@ -6233,15 +6121,6 @@ "Suite runs (last 5 years) on main servers": 2125, "Suite users on main servers": 155, "Suite users (last 5 years) on main servers": 155, - "Related Workflows": [ - "https://usegalaxy.eu/published/workflow?id=69eddfde874af35b", - "https://usegalaxy.eu/published/workflow?id=9472be79da012999", - "https://usegalaxy.fr/published/workflow?id=c4f6062e51d0f45e", - "https://workflowhub.eu/workflows/1466?version=2" - ], - "Related Tutorials": [ - "microbiome/metatranscriptomics" - ], "To keep": true, "Deprecated": false }, @@ -6285,12 +6164,13 @@ "bio.tool name": "Compare HUMAnN2 outputs", "bio.tool description": "This tool compare HUMANnN2 outputs with gene families or pathways and their relative abundances between several samples", "biii ID": null, + "Related Workflows": [], + "Related Tutorials": [], "Number of tools on UseGalaxy.org (Main)": 0, "Number of tools on UseGalaxy.org.au": 0, "Number of tools on UseGalaxy.eu": 0, "Number of tools on UseGalaxy.fr": 0, "Number of tools on APOSTL": 0, - "Number of tools on MBAC Metabiome Portal": 0, "Number of tools on ChemFlow": 0, "Number of tools on CIRM-CFBP": 0, "Number of tools on Coloc-stats": 0, @@ -6307,7 +6187,6 @@ "Number of tools on MISSISSIPPI": 0, "Number of tools on Oqtans": 0, "Number of tools on Palfinder": 0, - "Number of tools on PepSimili": 0, "Number of tools on PhagePromotor": 0, "Number of tools on UseGalaxy.be": 0, "Number of tools on UseGalaxy.cz": 1, @@ -6333,8 +6212,6 @@ "Suite runs (last 5 years) on main servers": 248, "Suite users on main servers": 32, "Suite users (last 5 years) on main servers": 23, - "Related Workflows": [], - "Related Tutorials": [], "To keep": true, "Deprecated": false }, @@ -6390,54 +6267,6 @@ "bio.tool name": "Flye", "bio.tool description": "Flye is a de novo assembler for single molecule sequencing reads, such as those produced by PacBio and Oxford Nanopore Technologies. 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"Number of tools on MBAC Metabiome Portal": 0, "Number of tools on ChemFlow": 0, "Number of tools on CIRM-CFBP": 0, "Number of tools on Coloc-stats": 0, @@ -6596,7 +6489,6 @@ "Number of tools on MISSISSIPPI": 0, "Number of tools on Oqtans": 0, "Number of tools on Palfinder": 0, - "Number of tools on PepSimili": 0, "Number of tools on PhagePromotor": 0, "Number of tools on UseGalaxy.be": 1, "Number of tools on UseGalaxy.cz": 1, @@ -6622,21 +6514,6 @@ "Suite runs (last 5 years) on main servers": 6485, "Suite users on main servers": 731, "Suite users (last 5 years) on main servers": 555, - "Related Workflows": [ - "https://usegalaxy.eu/published/workflow?id=096b75501c8e0888", - "https://usegalaxy.eu/published/workflow?id=2cf09adb1ed6c3ec", - "https://usegalaxy.eu/published/workflow?id=7ab70660e6235cf0", - "https://usegalaxy.eu/published/workflow?id=994e5ff1df7d6c9e", - "https://usegalaxy.eu/published/workflow?id=9cbba5de2cbeeb0f", - "https://usegalaxy.eu/published/workflow?id=a8f829deb69b30ab", - 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"Number of tools on MBAC Metabiome Portal": 0, "Number of tools on ChemFlow": 0, "Number of tools on CIRM-CFBP": 0, "Number of tools on Coloc-stats": 0, @@ -7652,10 +7565,9 @@ "Number of tools on MISSISSIPPI": 0, "Number of tools on Oqtans": 0, "Number of tools on Palfinder": 0, - "Number of tools on PepSimili": 0, "Number of tools on PhagePromotor": 0, "Number of tools on UseGalaxy.be": 1, - "Number of tools on UseGalaxy.cz": 0, + "Number of tools on UseGalaxy.cz": 1, "Number of tools on UseGalaxy.no": 0, "Number of tools on Viral Variant Visualizer (VVV)": 0, "Suite users (last 5 years) (usegalaxy.eu)": 626, @@ -7678,42 +7590,6 @@ "Suite runs (last 5 years) on main servers": 5616, "Suite users on main servers": 1070, "Suite users (last 5 years) on main servers": 1070, - "Related Workflows": [ - "https://usegalaxy.eu/published/workflow?id=07c92110c3fffcf8", - "https://usegalaxy.eu/published/workflow?id=1ce406de61de8492", - "https://usegalaxy.eu/published/workflow?id=2cd5670f075704ab", - 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"Suite version": "2.0", + "Suite version": "@TOOL_VERSION@+galaxy@VERSION_SUFFIX@", "Suite conda package": "kmetashot", "Latest suite conda package version": "2.0", - "Suite version status": "Up-to-date", + "Suite version status": "To update", "ToolShed categories": [ "Metagenomics" ], @@ -7750,12 +7626,15 @@ "bio.tool name": "kMetaShot", "bio.tool description": "The application of 2nd and 3rd generation High Throughput Sequencing (HTS) technologies has deeply reshaped experimental method to investigate microbial communities and obtain a taxonomic and functional profile of the invetigated community. Shotgun Metagenomics allow to quickly obtain a representation of microorganisms genomes characterizing a particular environment. In order to obtain a fast e reliable taxonomic classification of microorganisms genomes we present kMetaShot, an alignment-free taxonomic classifier based on k-mer/minimizer counting.", "biii ID": null, - "Number of tools on UseGalaxy.org (Main)": 0, + "Related Workflows": [], + "Related Tutorials": [ + "microbiome/mags-building" + ], + "Number of tools on UseGalaxy.org (Main)": 1, "Number of tools on UseGalaxy.org.au": 0, "Number of tools on UseGalaxy.eu": 1, "Number of tools on UseGalaxy.fr": 0, "Number of tools on APOSTL": 0, - "Number of tools on MBAC Metabiome Portal": 0, "Number of tools on ChemFlow": 0, "Number of tools on CIRM-CFBP": 0, "Number of tools on Coloc-stats": 0, @@ -7772,10 +7651,9 @@ "Number of tools on MISSISSIPPI": 0, "Number of tools on Oqtans": 0, "Number of tools on Palfinder": 0, - "Number of tools on PepSimili": 0, "Number of tools on PhagePromotor": 0, "Number of tools on UseGalaxy.be": 0, - "Number of tools on UseGalaxy.cz": 0, + "Number of tools on UseGalaxy.cz": 1, "Number of tools on UseGalaxy.no": 0, "Number of tools on Viral Variant Visualizer (VVV)": 0, "Suite users (last 5 years) (usegalaxy.eu)": 0, @@ -7798,8 +7676,6 @@ "Suite runs (last 5 years) on main servers": 0, "Suite users on main servers": 0, "Suite users (last 5 years) on main servers": 0, - "Related Workflows": [], - "Related Tutorials": [], "To keep": true, "Deprecated": false }, @@ -7850,12 +7726,13 @@ "bio.tool name": "Lighter", "bio.tool description": "Kmer-based error correction method for whole genome sequencing data. Lighter uses sampling (rather than counting) to obtain a set of kmers that are likely from the genome. Using this information, Lighter can correct the reads containing sequence errors.", "biii ID": null, + "Related Workflows": [], + "Related Tutorials": [], "Number of tools on UseGalaxy.org (Main)": 0, "Number of tools on UseGalaxy.org.au": 0, "Number of tools on UseGalaxy.eu": 1, "Number of tools on UseGalaxy.fr": 1, "Number of tools on APOSTL": 0, - "Number of tools on MBAC Metabiome Portal": 0, "Number of tools on ChemFlow": 0, "Number of tools on CIRM-CFBP": 0, "Number of tools on Coloc-stats": 0, @@ -7872,7 +7749,6 @@ "Number of tools on MISSISSIPPI": 0, "Number of tools on Oqtans": 0, "Number of tools on Palfinder": 0, - "Number of tools on PepSimili": 0, "Number of tools on PhagePromotor": 0, "Number of tools on UseGalaxy.be": 0, "Number of tools on UseGalaxy.cz": 1, @@ -7898,8 +7774,6 @@ "Suite runs (last 5 years) on main servers": 106, "Suite users on main servers": 37, "Suite users (last 5 years) on main servers": 31, - "Related Workflows": [], - "Related Tutorials": [], "To keep": true, "Deprecated": false }, @@ -7943,58 +7817,11 @@ "bio.tool name": "MAFFT", "bio.tool description": "MAFFT (Multiple Alignment using Fast Fourier Transform) is a high speed multiple sequence alignment program.", "biii ID": null, - 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"Number of tools on MBAC Metabiome Portal": 0, "Number of tools on ChemFlow": 0, "Number of tools on CIRM-CFBP": 0, "Number of tools on Coloc-stats": 0, @@ -8135,7 +8018,6 @@ "Number of tools on MISSISSIPPI": 0, "Number of tools on Oqtans": 0, "Number of tools on Palfinder": 0, - "Number of tools on PepSimili": 0, "Number of tools on PhagePromotor": 0, "Number of tools on UseGalaxy.be": 1, "Number of tools on UseGalaxy.cz": 1, @@ -8161,17 +8043,6 @@ "Suite runs (last 5 years) on main servers": 1792, "Suite users on main servers": 115, "Suite users (last 5 years) on main servers": 115, - "Related Workflows": [ - "https://usegalaxy.eu/published/workflow?id=0609a4b1941d1a68", - "https://usegalaxy.eu/published/workflow?id=9fddc44294236e8f", - "https://usegalaxy.org/published/workflow?id=20b7ae4b517a80fd", - "https://usegalaxy.org/published/workflow?id=a71fcbc60caae8b6", - "https://workflowhub.eu/workflows/1272?version=2", - "https://workflowhub.eu/workflows/1854?version=1" - ], - "Related Tutorials": [ - "microbiome/mgnify-amplicon" - ], "To keep": true, "Deprecated": false }, @@ -8216,12 +8087,13 @@ "bio.tool name": "minipolish", "bio.tool description": "A tool that bridges the output of miniasm (long-read assembly) and racon (assembly polishing) together to polish a draft assembly. It also provides read depth information in contigs.", "biii ID": null, + "Related Workflows": [], + "Related Tutorials": [], "Number of tools on UseGalaxy.org (Main)": 0, "Number of tools on UseGalaxy.org.au": 0, "Number of tools on UseGalaxy.eu": 1, "Number of tools on UseGalaxy.fr": 0, "Number of tools on APOSTL": 0, - "Number of tools on MBAC Metabiome Portal": 0, "Number of tools on ChemFlow": 0, "Number of tools on CIRM-CFBP": 0, "Number of tools on Coloc-stats": 0, @@ -8238,7 +8110,6 @@ "Number of tools on MISSISSIPPI": 0, "Number of tools on Oqtans": 0, "Number of tools on Palfinder": 0, - "Number of tools on PepSimili": 0, "Number of tools on PhagePromotor": 0, "Number of tools on UseGalaxy.be": 0, "Number of tools on UseGalaxy.cz": 1, @@ -8264,8 +8135,6 @@ "Suite runs (last 5 years) on main servers": 278, "Suite users on main servers": 43, "Suite users (last 5 years) on main servers": 43, - "Related Workflows": [], - "Related Tutorials": [], "To keep": true, "Deprecated": false }, @@ -8310,12 +8179,13 @@ "bio.tool name": "Metagenomic operational taxonomic units (mOTUs)", "bio.tool description": "Metagenomic operational taxonomic units (mOTUs) enable high-accuracy taxonomic profiling of known (sequenced) and unknown microorganisms at species-level resolution from shotgun metagenomic or metatranscriptomic data. The method clusters single-copy phylogenetic marker gene sequences from metagenomes and reference genomes into mOTUs to quantify their abundances in meta-omics data with very high precision and recall.", "biii ID": null, + "Related Workflows": [], + "Related Tutorials": [], "Number of tools on UseGalaxy.org (Main)": 0, "Number of tools on UseGalaxy.org.au": 0, "Number of tools on UseGalaxy.eu": 3, "Number of tools on UseGalaxy.fr": 3, "Number of tools on APOSTL": 0, - "Number of tools on MBAC Metabiome Portal": 0, "Number of tools on ChemFlow": 0, "Number of tools on CIRM-CFBP": 0, "Number of tools on Coloc-stats": 0, @@ -8332,7 +8202,6 @@ "Number of tools on MISSISSIPPI": 0, "Number of tools on Oqtans": 0, "Number of tools on Palfinder": 0, - "Number of tools on PepSimili": 0, "Number of tools on PhagePromotor": 0, "Number of tools on UseGalaxy.be": 0, "Number of tools on UseGalaxy.cz": 0, @@ -8358,8 +8227,6 @@ "Suite runs (last 5 years) on main servers": 377, "Suite users on main servers": 40, "Suite users (last 5 years) on main servers": 40, - "Related Workflows": [], - "Related Tutorials": [], "To keep": true, "Deprecated": false }, @@ -8549,54 +8416,6 @@ "bio.tool name": null, "bio.tool description": null, "biii ID": null, - "Number of tools on UseGalaxy.org (Main)": 7, - "Number of tools on UseGalaxy.org.au": 34, - "Number of tools on UseGalaxy.eu": 135, - "Number of tools on UseGalaxy.fr": 0, - "Number of tools on APOSTL": 0, - "Number of tools on MBAC Metabiome Portal": 0, - "Number of tools on ChemFlow": 0, - "Number of tools on CIRM-CFBP": 0, - "Number of tools on Coloc-stats": 0, - "Number of tools on Galaxy@AuBi": 0, - "Number of tools on Galaxy@Pasteur": 0, - "Number of tools on GalaxyTrakr": 0, - "Number of tools on GASLINI": 0, - "Number of tools on HyPhy HIV NGS Tools": 0, - "Number of tools on ImmPort Galaxy": 0, - "Number of tools on InteractoMIX": 0, - "Number of tools on IPK Galaxy Blast Suite": 0, - "Number of tools on Lebanese University Galaxy": 0, - "Number of tools on Mandoiu Lab": 0, - "Number of tools on MISSISSIPPI": 0, - 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"Suite version": "1.6", + "Suite version": "@TOOL_VERSION@+galaxy@VERSION_SUFFIX@", "Suite conda package": "pfam_scan", "Latest suite conda package version": "1.6", - "Suite version status": "Up-to-date", + "Suite version status": "To update", "ToolShed categories": [ "Sequence Analysis" ], @@ -8685,12 +8550,24 @@ "bio.tool name": "PfamScan", "bio.tool description": "This tool is used to search a FASTA sequence against a library of Pfam HMM.", "biii ID": null, + "Related Workflows": [ + "https://usegalaxy.eu/published/workflow?id=11eba1b28ec87963", + "https://usegalaxy.eu/published/workflow?id=1f9a9a7998ef5ab3", + "https://usegalaxy.eu/published/workflow?id=47a0407867a90f95", + "https://usegalaxy.eu/published/workflow?id=87231a6a7938cb95", + "https://usegalaxy.eu/published/workflow?id=9b025479fade745d", + "https://usegalaxy.eu/published/workflow?id=b7a3cbcd32734e8b", + "https://usegalaxy.org.au/published/workflow?id=6e1e24f9e0326930", + "https://workflowhub.eu/workflows/1688?version=1" + ], + "Related Tutorials": [ + "transcriptomics/differential-isoform-expression" + ], "Number of tools on UseGalaxy.org (Main)": 1, "Number of tools on UseGalaxy.org.au": 1, "Number of tools on UseGalaxy.eu": 1, "Number of tools on UseGalaxy.fr": 1, "Number of tools on APOSTL": 0, - "Number of tools on MBAC Metabiome Portal": 0, "Number of tools on ChemFlow": 0, "Number of tools on CIRM-CFBP": 0, "Number of tools on Coloc-stats": 0, @@ -8707,7 +8584,6 @@ "Number of tools on MISSISSIPPI": 0, "Number of tools on Oqtans": 0, "Number of tools on Palfinder": 0, - "Number of tools on PepSimili": 0, "Number of tools on PhagePromotor": 0, "Number of tools on UseGalaxy.be": 1, "Number of tools on UseGalaxy.cz": 1, @@ -8733,19 +8609,6 @@ "Suite runs (last 5 years) on main servers": 8949, "Suite users on main servers": 323, "Suite users (last 5 years) on main servers": 323, - "Related Workflows": [ - "https://usegalaxy.eu/published/workflow?id=11eba1b28ec87963", - "https://usegalaxy.eu/published/workflow?id=1f9a9a7998ef5ab3", - "https://usegalaxy.eu/published/workflow?id=47a0407867a90f95", - "https://usegalaxy.eu/published/workflow?id=87231a6a7938cb95", - "https://usegalaxy.eu/published/workflow?id=9b025479fade745d", - "https://usegalaxy.eu/published/workflow?id=b7a3cbcd32734e8b", - "https://usegalaxy.org.au/published/workflow?id=6e1e24f9e0326930", - "https://workflowhub.eu/workflows/1688?version=1" - ], - "Related Tutorials": [ - "transcriptomics/differential-isoform-expression" - ], "To keep": true, "Deprecated": false }, @@ -8760,7 +8623,7 @@ "Description": "q2-dbotu is a Qiime 2 plugin for performing OTU clustering", "Suite first commit date": "2025-03-20", "Homepage": "https://github.com/cduvallet/q2-dbotu/tree/master", - "Suite version": "2022.11.1+galaxy0", + "Suite version": "2022.11.1", "Suite conda package": null, "Latest suite conda package version": null, "Suite version status": "To update", @@ -8794,12 +8657,13 @@ "bio.tool name": "QIIME 2", "bio.tool description": "QIIME 2 is an AI-ready microbiome multi-omics data science platform that is trusted, free, open source, extensible, and community developed and supported bioinformatics.", "biii ID": null, + "Related Workflows": [], + "Related Tutorials": [], "Number of tools on UseGalaxy.org (Main)": 0, "Number of tools on UseGalaxy.org.au": 0, "Number of tools on UseGalaxy.eu": 1, "Number of tools on UseGalaxy.fr": 0, "Number of tools on APOSTL": 0, - "Number of tools on MBAC Metabiome Portal": 0, "Number of tools on ChemFlow": 0, "Number of tools on CIRM-CFBP": 0, "Number of tools on Coloc-stats": 0, @@ -8816,7 +8680,6 @@ "Number of tools on MISSISSIPPI": 0, "Number of tools on Oqtans": 0, "Number of tools on Palfinder": 0, - "Number of tools on PepSimili": 0, "Number of tools on PhagePromotor": 0, "Number of tools on UseGalaxy.be": 0, "Number of tools on UseGalaxy.cz": 0, @@ -8842,8 +8705,6 @@ "Suite runs (last 5 years) on main servers": 13, "Suite users on main servers": 7, "Suite users (last 5 years) on main servers": 7, - "Related Workflows": [], - "Related Tutorials": [], "To keep": true, "Deprecated": false }, @@ -8888,12 +8749,45 @@ "bio.tool name": "Racon", "bio.tool description": "Consensus module for raw de novo DNA assembly of long uncorrected readsRacon is intended as a standalone consensus module to correct raw contigs generated by rapid assembly methods which do not include a consensus step. The goal of Racon is to generate genomic consensus which is of similar or better quality compared to the output generated by assembly methods which employ both error correction and consensus steps, while providing a speedup of several times compared to those methods. 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"Number of tools on MBAC Metabiome Portal": 0, "Number of tools on ChemFlow": 0, "Number of tools on CIRM-CFBP": 0, "Number of tools on Coloc-stats": 0, @@ -9038,7 +8899,6 @@ "Number of tools on MISSISSIPPI": 0, "Number of tools on Oqtans": 0, "Number of tools on Palfinder": 0, - "Number of tools on PepSimili": 0, "Number of tools on PhagePromotor": 0, "Number of tools on UseGalaxy.be": 0, "Number of tools on UseGalaxy.cz": 0, @@ -9064,8 +8924,6 @@ "Suite runs (last 5 years) on main servers": 18, "Suite users on main servers": 7, "Suite users (last 5 years) on main servers": 7, - "Related Workflows": [], - "Related Tutorials": [], "To keep": true, "Deprecated": false }, @@ -9113,12 +8971,46 @@ "bio.tool name": "SortMeRNA", "bio.tool description": "Sequence analysis tool for filtering, mapping and OTU-picking NGS reads.", "biii ID": null, + "Related Workflows": [ + "https://usegalaxy.eu/published/workflow?id=096b75501c8e0888", + "https://usegalaxy.eu/published/workflow?id=2cf09adb1ed6c3ec", + "https://usegalaxy.eu/published/workflow?id=385cc7df70d7916b", + "https://usegalaxy.eu/published/workflow?id=401746888e8b3aa8", + "https://usegalaxy.eu/published/workflow?id=4d32b1b3ac0a7161", + "https://usegalaxy.eu/published/workflow?id=5f0faac42b0a5062", + "https://usegalaxy.eu/published/workflow?id=69eddfde874af35b", + "https://usegalaxy.eu/published/workflow?id=72e3e5fdc766e24a", + "https://usegalaxy.eu/published/workflow?id=7ab70660e6235cf0", + "https://usegalaxy.eu/published/workflow?id=87cc0cd143a12c41", + "https://usegalaxy.eu/published/workflow?id=9382f9bbbdddb5ad", + "https://usegalaxy.eu/published/workflow?id=9472be79da012999", + "https://usegalaxy.eu/published/workflow?id=994e5ff1df7d6c9e", + "https://usegalaxy.eu/published/workflow?id=9cbba5de2cbeeb0f", + "https://usegalaxy.eu/published/workflow?id=a8417c63e9e22afb", + "https://usegalaxy.eu/published/workflow?id=a8f829deb69b30ab", + "https://usegalaxy.eu/published/workflow?id=c3aa516e78ca4191", + "https://usegalaxy.eu/published/workflow?id=d05c6f0f3205fbd2", + "https://usegalaxy.eu/published/workflow?id=dfc2c53ac3103eff", + "https://usegalaxy.eu/published/workflow?id=e423c80058601e78", + "https://usegalaxy.eu/published/workflow?id=f6e8a63283262518", + "https://usegalaxy.eu/published/workflow?id=f9175e670d8dfaa1", + "https://usegalaxy.eu/published/workflow?id=fd90652d475ed739", + "https://usegalaxy.eu/published/workflow?id=fdca6c9d394986bf", + "https://usegalaxy.fr/published/workflow?id=c4f6062e51d0f45e", + "https://usegalaxy.fr/published/workflow?id=e6991d64e851b09e", + "https://usegalaxy.org.au/published/workflow?id=408a31694e9c85e6", + "https://workflowhub.eu/workflows/1444?version=2", + "https://workflowhub.eu/workflows/1466?version=2" + ], + "Related Tutorials": [ + "microbiome/metatranscriptomics", + "microbiome/metatranscriptomics-short" + ], "Number of tools on UseGalaxy.org (Main)": 1, "Number of tools on UseGalaxy.org.au": 1, "Number of tools on UseGalaxy.eu": 1, "Number of tools on UseGalaxy.fr": 1, "Number of tools on APOSTL": 0, - "Number of tools on MBAC Metabiome Portal": 0, "Number of tools on ChemFlow": 0, "Number of tools on CIRM-CFBP": 0, "Number of tools on Coloc-stats": 0, @@ -9135,7 +9027,6 @@ "Number of tools on MISSISSIPPI": 0, "Number of tools on Oqtans": 0, "Number of tools on Palfinder": 0, - "Number of tools on PepSimili": 0, "Number of tools on PhagePromotor": 0, "Number of tools on UseGalaxy.be": 1, "Number of tools on UseGalaxy.cz": 1, @@ -9161,41 +9052,6 @@ "Suite runs (last 5 years) on main servers": 34715, "Suite users on main servers": 2274, "Suite users (last 5 years) on main servers": 2051, - "Related Workflows": [ - "https://usegalaxy.eu/published/workflow?id=096b75501c8e0888", - "https://usegalaxy.eu/published/workflow?id=2cf09adb1ed6c3ec", - "https://usegalaxy.eu/published/workflow?id=385cc7df70d7916b", - "https://usegalaxy.eu/published/workflow?id=401746888e8b3aa8", - "https://usegalaxy.eu/published/workflow?id=4d32b1b3ac0a7161", - "https://usegalaxy.eu/published/workflow?id=5f0faac42b0a5062", - 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"https://usegalaxy.eu/published/workflow?id=fd90652d475ed739", - "https://usegalaxy.eu/published/workflow?id=fdca6c9d394986bf", - "https://usegalaxy.fr/published/workflow?id=c4f6062e51d0f45e", - "https://usegalaxy.fr/published/workflow?id=e6991d64e851b09e", - "https://usegalaxy.org.au/published/workflow?id=408a31694e9c85e6", - "https://workflowhub.eu/workflows/1444?version=2", - "https://workflowhub.eu/workflows/1466?version=2" - ], - "Related Tutorials": [ - "microbiome/metatranscriptomics", - "microbiome/metatranscriptomics-short" - ], "To keep": true, "Deprecated": false }, @@ -9237,12 +9093,17 @@ "bio.tool name": "sylph", "bio.tool description": "fast and precise species-level metagenomic profiling with ANIs", "biii ID": null, + "Related Workflows": [ + "https://usegalaxy.eu/published/workflow?id=7491883694fff308", + "https://usegalaxy.eu/published/workflow?id=cb2df493f5e334f7", + "https://workflowhub.eu/workflows/2068?version=2" + ], + "Related Tutorials": [], "Number of tools on UseGalaxy.org (Main)": 2, - "Number of tools on UseGalaxy.org.au": 0, + "Number of tools on UseGalaxy.org.au": 2, "Number of tools on UseGalaxy.eu": 2, "Number of tools on UseGalaxy.fr": 2, "Number of tools on APOSTL": 0, - "Number of tools on MBAC Metabiome Portal": 0, "Number of tools on ChemFlow": 0, "Number of tools on CIRM-CFBP": 0, "Number of tools on Coloc-stats": 0, @@ -9259,7 +9120,6 @@ "Number of tools on MISSISSIPPI": 0, "Number of tools on Oqtans": 0, "Number of tools on Palfinder": 0, - "Number of tools on PepSimili": 0, "Number of tools on PhagePromotor": 0, "Number of tools on UseGalaxy.be": 0, "Number of tools on UseGalaxy.cz": 1, @@ -9285,12 +9145,6 @@ "Suite runs (last 5 years) on main servers": 270, "Suite users on main servers": 11, "Suite users (last 5 years) on main servers": 11, - "Related Workflows": [ - "https://usegalaxy.eu/published/workflow?id=7491883694fff308", - "https://usegalaxy.eu/published/workflow?id=cb2df493f5e334f7", - "https://workflowhub.eu/workflows/2068?version=2" - ], - "Related Tutorials": [], "To keep": true, "Deprecated": false }, @@ -9346,12 +9200,13 @@ "bio.tool name": "TIARA", "bio.tool description": "Total Integrated Archive of Short-Read and Array (TIARA) database, contains personal genomic information obtained from next generation sequencing (NGS) techniques and ultra-high-resolution comparative genomic hybridization (CGH) arrays. This database improves the accuracy of detecting personal genomic variations, such as SNPs, short indels and structural variants (SVs).", "biii ID": null, + "Related Workflows": [], + "Related Tutorials": [], "Number of tools on UseGalaxy.org (Main)": 0, "Number of tools on UseGalaxy.org.au": 0, "Number of tools on UseGalaxy.eu": 1, "Number of tools on UseGalaxy.fr": 0, "Number of tools on APOSTL": 0, - "Number of tools on MBAC Metabiome Portal": 0, "Number of tools on ChemFlow": 0, "Number of tools on CIRM-CFBP": 0, "Number of tools on Coloc-stats": 0, @@ -9368,7 +9223,6 @@ "Number of tools on MISSISSIPPI": 0, "Number of tools on Oqtans": 0, "Number of tools on Palfinder": 0, - "Number of tools on PepSimili": 0, "Number of tools on PhagePromotor": 0, "Number of tools on UseGalaxy.be": 0, "Number of tools on UseGalaxy.cz": 0, @@ -9394,8 +9248,6 @@ "Suite runs (last 5 years) on main servers": 365, "Suite users on main servers": 33, "Suite users (last 5 years) on main servers": 33, - "Related Workflows": [], - "Related Tutorials": [], "To keep": true, "Deprecated": false }, @@ -9412,7 +9264,7 @@ "Homepage": "http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/", "Suite version": "0.6.10", "Suite conda package": "trim-galore", - "Latest suite conda package version": "2.2.0", + "Latest suite conda package version": "2.3.0", "Suite version status": "To update", "ToolShed categories": [ "Sequence Analysis", @@ -9441,54 +9293,6 @@ "bio.tool name": "Trim Galore", "bio.tool description": "A wrapper tool around Cutadapt and FastQC to consistently apply quality and adapter trimming to FastQ files, with some extra functionality for MspI-digested RRBS-type (Reduced Representation Bisufite-Seq) libraries.", "biii ID": null, - "Number of tools on UseGalaxy.org (Main)": 1, - "Number of tools on UseGalaxy.org.au": 1, - "Number of tools on UseGalaxy.eu": 1, - "Number of tools on UseGalaxy.fr": 1, - "Number of tools on APOSTL": 0, - "Number of tools on MBAC Metabiome Portal": 0, - "Number of tools on ChemFlow": 0, - 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"Suite version": "1.2.0", + "Suite version": "@TOOL_VERSION@+galaxy@VERSION_SUFFIX@", "Suite conda package": "abritamr", - "Latest suite conda package version": "1.2.0", - "Suite version status": "Up-to-date", + "Latest suite conda package version": "1.3.0", + "Suite version status": "To update", "ToolShed categories": [ "Sequence Analysis" ], @@ -10161,17 +10009,22 @@ ], "Suite owner": "iuc", "Suite source": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/abritamr", - "Suite parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/abritamr", + "Suite parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/abritamr", "bio.tool ID": "abritamr", "bio.tool name": "abriTAMR", "bio.tool description": "an AMR gene detection pipeline that runs AMRFinderPlus on a single (or list ) of given isolates and collates the results into a table, separating genes identified into functionally relevant groups.", "biii ID": null, + "Related Workflows": [ + "https://usegalaxy.eu/published/workflow?id=eb5ab8bc82569eee", + "https://usegalaxy.org.au/published/workflow?id=7a0c4804e4d4c905", + "https://workflowhub.eu/workflows/634?version=1" + ], + "Related Tutorials": [], "Number of tools on UseGalaxy.org (Main)": 0, "Number of tools on UseGalaxy.org.au": 1, "Number of tools on UseGalaxy.eu": 1, "Number of tools on UseGalaxy.fr": 1, "Number of tools on APOSTL": 0, - "Number of tools on MBAC Metabiome Portal": 0, "Number of tools on ChemFlow": 0, "Number of tools on CIRM-CFBP": 0, "Number of tools on Coloc-stats": 0, @@ -10188,7 +10041,6 @@ "Number of tools on MISSISSIPPI": 0, "Number of tools on Oqtans": 0, "Number of tools on Palfinder": 0, - "Number of tools on PepSimili": 0, "Number of tools on PhagePromotor": 0, "Number of tools on UseGalaxy.be": 0, "Number of tools on UseGalaxy.cz": 0, @@ -10214,12 +10066,6 @@ "Suite runs (last 5 years) on main servers": 3518, "Suite users on main servers": 419, "Suite users (last 5 years) on main servers": 419, - "Related Workflows": [ - "https://usegalaxy.eu/published/workflow?id=eb5ab8bc82569eee", - "https://usegalaxy.org.au/published/workflow?id=7a0c4804e4d4c905", - "https://workflowhub.eu/workflows/634?version=1" - ], - "Related Tutorials": [], "To keep": true, "Deprecated": false }, @@ -10235,10 +10081,10 @@ "Description": "Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler", "Suite first commit date": "2015-04-14", "Homepage": "https://github.com/bcgsc/abyss", - "Suite version": "2.3.10", + "Suite version": "@TOOL_VERSION@+galaxy@VERSION_SUFFIX@", "Suite conda package": "abyss", "Latest suite conda package version": "2.3.10", - "Suite version status": "Up-to-date", + "Suite version status": "To update", "ToolShed categories": [ "Assembly" ], @@ -10260,17 +10106,18 @@ ], "Suite owner": "iuc", "Suite source": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/abyss", - "Suite parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/abyss", + "Suite parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss", "bio.tool ID": "abyss", "bio.tool name": "ABySS", "bio.tool description": "De novo genome sequence assembler using short reads.", "biii ID": null, + "Related Workflows": [], + "Related Tutorials": [], "Number of tools on UseGalaxy.org (Main)": 0, "Number of tools on UseGalaxy.org.au": 1, "Number of tools on UseGalaxy.eu": 1, "Number of tools on UseGalaxy.fr": 1, "Number of tools on APOSTL": 0, - "Number of tools on MBAC Metabiome Portal": 0, "Number of tools on ChemFlow": 0, "Number of tools on CIRM-CFBP": 0, "Number of tools on Coloc-stats": 0, @@ -10287,7 +10134,6 @@ "Number of tools on MISSISSIPPI": 1, "Number of tools on Oqtans": 0, "Number of tools on Palfinder": 0, - "Number of tools on PepSimili": 0, "Number of tools on PhagePromotor": 0, "Number of tools on UseGalaxy.be": 1, "Number of tools on UseGalaxy.cz": 1, @@ -10313,8 +10159,6 @@ "Suite runs (last 5 years) on main servers": 10277, "Suite users on main servers": 2191, "Suite users (last 5 years) on main servers": 1850, - "Related Workflows": [], - "Related Tutorials": [], "To keep": true, "Deprecated": false }, @@ -10354,17 +10198,18 @@ ], "Suite owner": "iuc", "Suite source": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/aldex2", - "Suite parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/aldex2", + "Suite parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2", "bio.tool ID": "aldex2", "bio.tool name": "ALDEx2", "bio.tool description": "A differential abundance analysis for the comparison of two or more conditions. 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Reports both P and fdr values calculated by the Benjamini Hochberg correction.", "biii ID": null, + "Related Workflows": [], + "Related Tutorials": [], "Number of tools on UseGalaxy.org (Main)": 0, "Number of tools on UseGalaxy.org.au": 0, "Number of tools on UseGalaxy.eu": 1, "Number of tools on UseGalaxy.fr": 0, "Number of tools on APOSTL": 0, - "Number of tools on MBAC Metabiome Portal": 0, "Number of tools on ChemFlow": 0, "Number of tools on CIRM-CFBP": 0, "Number of tools on Coloc-stats": 0, @@ -10381,7 +10226,6 @@ "Number of tools on MISSISSIPPI": 0, "Number of tools on Oqtans": 0, "Number of tools on Palfinder": 0, - "Number of tools on PepSimili": 0, "Number of tools on PhagePromotor": 0, "Number of tools on UseGalaxy.be": 0, "Number of tools on UseGalaxy.cz": 1, @@ -10407,8 +10251,6 @@ "Suite runs (last 5 years) on main servers": 356, "Suite users on main servers": 64, "Suite users (last 5 years) on main servers": 64, - "Related Workflows": [], - "Related Tutorials": [], "To keep": true, "Deprecated": false }, @@ -10457,17 +10299,18 @@ ], "Suite owner": "iuc", "Suite source": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/amas", - "Suite parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/amas", + "Suite parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/amas", "bio.tool ID": "amas", "bio.tool name": "AMAS", "bio.tool description": "AMAS (Alignment Manipulation And Summary), a tool that works on amino acid and nucleotide alignments and combines capabilities of sequence manipulation with a function that calculates basic statistics.", "biii ID": null, + "Related Workflows": [], + "Related Tutorials": [], "Number of tools on UseGalaxy.org (Main)": 0, "Number of tools on UseGalaxy.org.au": 0, "Number of tools on UseGalaxy.eu": 5, "Number of tools on UseGalaxy.fr": 0, "Number of tools on APOSTL": 0, - "Number of tools on MBAC Metabiome Portal": 0, "Number of tools on ChemFlow": 0, "Number of tools on CIRM-CFBP": 0, "Number of tools on Coloc-stats": 0, @@ -10484,7 +10327,6 @@ "Number of tools on MISSISSIPPI": 0, "Number of tools on Oqtans": 0, "Number of tools on Palfinder": 0, - "Number of tools on PepSimili": 0, "Number of tools on PhagePromotor": 0, "Number of tools on UseGalaxy.be": 0, "Number of tools on UseGalaxy.cz": 0, @@ -10510,8 +10352,6 @@ "Suite runs (last 5 years) on main servers": 0, "Suite users on main servers": 0, "Suite users (last 5 years) on main servers": 0, - "Related Workflows": [], - "Related Tutorials": [], "To keep": true, "Deprecated": false }, @@ -10556,17 +10396,18 @@ ], "Suite owner": "iuc", "Suite source": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/amplican", - "Suite parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/amplican", + "Suite parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican", "bio.tool ID": "amplican", "bio.tool name": "amplican", "bio.tool description": "It performs alignment of the amplicon reads, normalizes gathered data, calculates multiple statistics (e.g. cut rates, frameshifts) and presents results in form of aggregated reports. Data and statistics can be broken down by experiments, barcodes, user defined groups, guides and amplicons allowing for quick identification of potential problems.", "biii ID": null, + "Related Workflows": [], + "Related Tutorials": [], "Number of tools on UseGalaxy.org (Main)": 0, "Number of tools on UseGalaxy.org.au": 0, "Number of tools on UseGalaxy.eu": 1, "Number of tools on UseGalaxy.fr": 0, "Number of tools on APOSTL": 0, - "Number of tools on MBAC Metabiome Portal": 0, "Number of tools on ChemFlow": 0, "Number of tools on CIRM-CFBP": 0, "Number of tools on Coloc-stats": 0, @@ -10583,7 +10424,6 @@ "Number of tools on MISSISSIPPI": 0, "Number of tools on Oqtans": 0, "Number of tools on Palfinder": 0, - "Number of tools on PepSimili": 0, "Number of tools on PhagePromotor": 0, "Number of tools on UseGalaxy.be": 0, "Number of tools on UseGalaxy.cz": 1, @@ -10609,8 +10449,6 @@ "Suite runs (last 5 years) on main servers": 85, "Suite users on main servers": 18, "Suite users (last 5 years) on main servers": 18, - "Related Workflows": [], - "Related Tutorials": [], "To keep": true, "Deprecated": false }, @@ -10626,7 +10464,7 @@ "Description": "AmpliGone is a tool which accurately finds and removes primer sequences from NGS reads in an amplicon experiment. ", "Suite first commit date": "2025-07-29", "Homepage": "https://rivm-bioinformatics.github.io/AmpliGone/latest/", - "Suite version": "2.0.1", + "Suite version": "@TOOL_VERSION@+galaxy@VERSION_SUFFIX@", "Suite conda package": "AmpliGone", "Latest suite conda package version": "2.0.2", "Suite version status": "To update", @@ -10640,17 +10478,18 @@ "EDAM reduced topics": [], "Suite owner": "iuc", "Suite source": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/ampligone", - "Suite parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/ampligone", + "Suite parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampligone", "bio.tool ID": null, "bio.tool name": null, "bio.tool description": null, "biii ID": null, + "Related Workflows": [], + "Related Tutorials": [], "Number of tools on UseGalaxy.org (Main)": 0, "Number of tools on UseGalaxy.org.au": 0, "Number of tools on UseGalaxy.eu": 1, "Number of tools on UseGalaxy.fr": 0, "Number of tools on APOSTL": 0, - "Number of tools on MBAC Metabiome Portal": 0, "Number of tools on ChemFlow": 0, "Number of tools on CIRM-CFBP": 0, "Number of tools on Coloc-stats": 0, @@ -10667,7 +10506,6 @@ "Number of tools on MISSISSIPPI": 0, "Number of tools on Oqtans": 0, "Number of tools on Palfinder": 0, - "Number of tools on PepSimili": 0, "Number of tools on PhagePromotor": 0, "Number of tools on UseGalaxy.be": 0, "Number of tools on UseGalaxy.cz": 0, @@ -10693,8 +10531,6 @@ "Suite runs (last 5 years) on main servers": 0, "Suite users on main servers": 0, "Suite users (last 5 years) on main servers": 0, - "Related Workflows": [], - "Related Tutorials": [], "To keep": true, "Deprecated": false }, @@ -10710,10 +10546,10 @@ "Description": "\"AMRFinderPlus is designed to find acquired antimicrobial resistance genes and point mutations in protein and/or assembled nucleotide sequences.It can also search \"plus\", stress, heat, and biocide resistance and virulence factors for some organisms.", "Suite first commit date": "2023-05-12", "Homepage": "https://github.com/ncbi/amr", - 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"Number of tools on MBAC Metabiome Portal": 0, "Number of tools on ChemFlow": 0, "Number of tools on CIRM-CFBP": 0, "Number of tools on Coloc-stats": 0, @@ -10762,7 +10633,6 @@ "Number of tools on MISSISSIPPI": 0, "Number of tools on Oqtans": 0, "Number of tools on Palfinder": 0, - "Number of tools on PepSimili": 0, "Number of tools on PhagePromotor": 0, "Number of tools on UseGalaxy.be": 0, "Number of tools on UseGalaxy.cz": 1, @@ -10788,41 +10658,6 @@ "Suite runs (last 5 years) on main servers": 64355, "Suite users on main servers": 1670, "Suite users (last 5 years) on main servers": 1670, - "Related Workflows": [ - "https://usegalaxy.eu/published/workflow?id=1ce523ef51f47134", - "https://usegalaxy.eu/published/workflow?id=2c992e509aa5dd9d", - "https://usegalaxy.eu/published/workflow?id=309fc4fc2e0da89c", - "https://usegalaxy.eu/published/workflow?id=32de10b9de8a999a", - "https://usegalaxy.eu/published/workflow?id=3439bd061fafcf12", - "https://usegalaxy.eu/published/workflow?id=34df701aa23a9fb3", - 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"Number of tools on MBAC Metabiome Portal": 0, "Number of tools on ChemFlow": 0, "Number of tools on CIRM-CFBP": 0, "Number of tools on Coloc-stats": 0, @@ -10973,7 +10810,6 @@ "Number of tools on MISSISSIPPI": 0, "Number of tools on Oqtans": 0, "Number of tools on Palfinder": 0, - "Number of tools on PepSimili": 0, "Number of tools on PhagePromotor": 0, "Number of tools on UseGalaxy.be": 0, "Number of tools on UseGalaxy.cz": 1, @@ -10999,11 +10835,6 @@ "Suite runs (last 5 years) on main servers": 302, "Suite users on main servers": 51, "Suite users (last 5 years) on main servers": 51, - "Related Workflows": [ - "https://workflowhub.eu/workflows/2024?version=4", - "https://workflowhub.eu/workflows/2068?version=2" - ], - "Related Tutorials": [], "To keep": true, "Deprecated": false }, @@ -11025,7 +10856,7 @@ "Homepage": "https://github.com/artic-network/fieldbioinformatics", "Suite version": "1.7.3", "Suite conda package": "artic", - "Latest suite conda package version": "1.10.1", + "Latest suite conda package version": "1.11.0", "Suite version status": "To update", "ToolShed categories": [ "Sequence Analysis" @@ -11044,17 +10875,22 @@ ], "Suite owner": "iuc", "Suite source": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/artic", - "Suite parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/artic", + "Suite parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic", "bio.tool ID": "artic", "bio.tool name": "ARTIC", "bio.tool description": "A bioinformatics pipeline for working with virus sequencing data sequenced with nanopore", "biii ID": null, + "Related Workflows": [ + "https://usegalaxy.org.au/published/workflow?id=aa1d123c0a0929f3", + "https://workflowhub.eu/workflows/2195?version=1", + "https://workflowhub.eu/workflows/521?version=1" + ], + "Related Tutorials": [], "Number of tools on UseGalaxy.org (Main)": 0, "Number of tools on UseGalaxy.org.au": 2, "Number of tools on UseGalaxy.eu": 2, "Number of tools on UseGalaxy.fr": 0, "Number of tools on APOSTL": 0, - "Number of tools on MBAC Metabiome Portal": 0, "Number of tools on ChemFlow": 0, "Number of tools on CIRM-CFBP": 0, "Number of tools on Coloc-stats": 0, @@ -11071,7 +10907,6 @@ "Number of tools on MISSISSIPPI": 0, "Number of tools on Oqtans": 0, "Number of tools on Palfinder": 0, - "Number of tools on PepSimili": 0, "Number of tools on PhagePromotor": 0, "Number of tools on UseGalaxy.be": 1, "Number of tools on UseGalaxy.cz": 2, @@ -11097,11 +10932,6 @@ "Suite runs (last 5 years) on main servers": 15256, "Suite users on main servers": 240, "Suite users (last 5 years) on main servers": 240, - "Related Workflows": [ - "https://usegalaxy.org.au/published/workflow?id=aa1d123c0a0929f3", - "https://workflowhub.eu/workflows/521?version=1" - ], - "Related Tutorials": [], "To keep": true, "Deprecated": false }, @@ -11129,17 +10959,18 @@ "EDAM reduced topics": [], "Suite owner": "iuc", "Suite source": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/assembly-stats", - "Suite parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/assembly-stats", + "Suite parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/assembly-stats", "bio.tool ID": null, "bio.tool name": null, "bio.tool description": null, "biii ID": null, + "Related Workflows": [], + "Related Tutorials": [], "Number of tools on UseGalaxy.org (Main)": 0, "Number of tools on UseGalaxy.org.au": 0, "Number of tools on UseGalaxy.eu": 1, "Number of tools on UseGalaxy.fr": 1, "Number of tools on APOSTL": 0, - "Number of tools on MBAC Metabiome Portal": 0, "Number of tools on ChemFlow": 0, "Number of tools on CIRM-CFBP": 0, "Number of tools on Coloc-stats": 0, @@ -11156,7 +10987,6 @@ "Number of tools on MISSISSIPPI": 0, "Number of tools on Oqtans": 0, "Number of tools on Palfinder": 0, - "Number of tools on PepSimili": 0, "Number of tools on PhagePromotor": 0, "Number of tools on UseGalaxy.be": 0, "Number of tools on UseGalaxy.cz": 0, @@ -11182,8 +11012,6 @@ "Suite runs (last 5 years) on main servers": 32, "Suite users on main servers": 18, "Suite users (last 5 years) on main servers": 18, - "Related Workflows": [], - "Related Tutorials": [], "To keep": true, "Deprecated": true }, @@ -11198,7 +11026,7 @@ "Description": "Automated MLST typing from PubMLST and InstitutPasteur.", "Suite first commit date": "2025-02-24", "Homepage": "https://github.com/Syph-and-VPD-Lab/autoBIGS.cli", - "Suite version": "0.6.2", + "Suite version": "@TOOL_VERSION@+galaxy@VERSION_SUFFIX@", "Suite conda package": "autobigs-cli", "Latest suite conda package version": "0.6.5", "Suite version status": "To update", @@ -11211,17 +11039,18 @@ "EDAM reduced topics": [], "Suite owner": "iuc", "Suite source": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/autobigs", - 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Capable of querying a variety of MLST databases from both Institut Pasteur and PubMLST.", "biii ID": null, + "Related Workflows": [], + "Related Tutorials": [], "Number of tools on UseGalaxy.org (Main)": 0, "Number of tools on UseGalaxy.org.au": 0, "Number of tools on UseGalaxy.eu": 1, "Number of tools on UseGalaxy.fr": 0, "Number of tools on APOSTL": 0, - "Number of tools on MBAC Metabiome Portal": 0, "Number of tools on ChemFlow": 0, "Number of tools on CIRM-CFBP": 0, "Number of tools on Coloc-stats": 0, @@ -11238,7 +11067,6 @@ "Number of tools on MISSISSIPPI": 0, "Number of tools on Oqtans": 0, "Number of tools on Palfinder": 0, - "Number of tools on PepSimili": 0, "Number of tools on PhagePromotor": 0, "Number of tools on UseGalaxy.be": 0, "Number of tools on UseGalaxy.cz": 0, @@ -11264,8 +11092,6 @@ "Suite runs (last 5 years) on main servers": 53, "Suite users on main servers": 31, "Suite users (last 5 years) on main servers": 31, - "Related Workflows": [], - "Related Tutorials": [], "To keep": true, "Deprecated": false }, @@ -11310,59 +11136,11 @@ ], "Suite owner": "iuc", "Suite source": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/bakta", - 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It is faster than almost all short-read aligners, yet retains unrivaled sensitivity and specificity, particularly for reads with many errors and indels.", "biii ID": null, + "Related Workflows": [ + "https://usegalaxy.eu/published/workflow?id=d967194ca51ff11e", + "https://usegalaxy.org.au/published/workflow?id=25f65a29ce3c3ee0", + "https://workflowhub.eu/workflows/407?version=1", + "https://workflowhub.eu/workflows/519?version=1" + ], + "Related Tutorials": [], "Number of tools on UseGalaxy.org (Main)": 6, - "Number of tools on UseGalaxy.org.au": 3, + "Number of tools on UseGalaxy.org.au": 4, "Number of tools on UseGalaxy.eu": 6, "Number of tools on UseGalaxy.fr": 6, "Number of tools on APOSTL": 0, - "Number of tools on MBAC Metabiome Portal": 0, "Number of tools on ChemFlow": 0, "Number of tools on CIRM-CFBP": 0, "Number of tools on Coloc-stats": 0, @@ -12094,7 +11928,6 @@ "Number of tools on MISSISSIPPI": 0, "Number of tools on Oqtans": 0, "Number of tools on Palfinder": 0, - "Number of tools on PepSimili": 0, "Number of tools on PhagePromotor": 0, "Number of tools on UseGalaxy.be": 0, "Number of tools on UseGalaxy.cz": 4, @@ -12120,13 +11953,6 @@ "Suite runs (last 5 years) on main servers": 39445, "Suite users on main servers": 1152, "Suite users (last 5 years) on main servers": 1152, - "Related Workflows": [ - "https://usegalaxy.eu/published/workflow?id=d967194ca51ff11e", - "https://usegalaxy.org.au/published/workflow?id=25f65a29ce3c3ee0", - "https://workflowhub.eu/workflows/407?version=1", - "https://workflowhub.eu/workflows/519?version=1" - ], - "Related Tutorials": [], "To keep": true, "Deprecated": false }, @@ -12142,7 +11968,7 @@ "Description": "Construct sequence similarity networks of BGCs and groups them into GCF", "Suite first commit date": "2024-02-18", "Homepage": "https://github.com/medema-group/BiG-SCAPE", - "Suite version": "1.1.9", + "Suite version": "@TOOL_VERSION@+galaxy@VERSION_SUFFIX@", "Suite conda package": "bigscape", "Latest suite conda package version": "2.0.3", "Suite version status": "To update", @@ -12177,17 +12003,18 @@ ], "Suite owner": "iuc", "Suite source": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/bigscape", - "Suite parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/bigscape", + "Suite parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape", "bio.tool ID": "BiG-SCAPE", "bio.tool name": "BiG-SCAPE", "bio.tool description": "A computational framework to explore large-scale biosynthetic diversity.BiG-SCAPE (Biosynthetic Gene Similarity Clustering and Prospecting Engine) is a software package, written in Python, that constructs sequence similarity networks of Biosynthetic Gene Clusters (BGCs) and groups them into Gene Cluster Families (GCFs). 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"Number of tools on PepSimili": 0, "Number of tools on PhagePromotor": 0, "Number of tools on UseGalaxy.be": 0, "Number of tools on UseGalaxy.cz": 0, @@ -12230,8 +12056,6 @@ "Suite runs (last 5 years) on main servers": 2449, "Suite users on main servers": 95, "Suite users (last 5 years) on main servers": 95, - "Related Workflows": [], - "Related Tutorials": [], "To keep": true, "Deprecated": false }, @@ -12246,10 +12070,10 @@ "Description": "Binning refinement tool", "Suite first commit date": "2025-01-14", "Homepage": "https://github.com/genotoul-bioinfo/Binette", - "Suite version": "1.2.1", + "Suite version": "@TOOL_VERSION@+galaxy@VERSION_SUFFIX@", "Suite conda package": "binette", "Latest suite conda package version": "1.2.1", - "Suite version status": "Up-to-date", + "Suite version status": "To update", "ToolShed categories": [ "Metagenomics" ], @@ -12267,17 +12091,28 @@ ], "Suite owner": "iuc", "Suite source": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/binette", - 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Our tool evaluates if modules contain genes that are over-represented by specific pathways or that are altered in a specific sample group. 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"Number of tools on MBAC Metabiome Portal": 0, "Number of tools on ChemFlow": 0, "Number of tools on CIRM-CFBP": 0, "Number of tools on Coloc-stats": 0, @@ -14018,7 +13846,6 @@ "Number of tools on MISSISSIPPI": 0, "Number of tools on Oqtans": 0, "Number of tools on Palfinder": 0, - "Number of tools on PepSimili": 0, "Number of tools on PhagePromotor": 0, "Number of tools on UseGalaxy.be": 1, "Number of tools on UseGalaxy.cz": 10, @@ -14044,28 +13871,6 @@ "Suite runs (last 5 years) on main servers": 17422, "Suite users on main servers": 1042, "Suite users (last 5 years) on main servers": 1042, - "Related Workflows": [ - "https://usegalaxy.eu/published/workflow?id=0563f58718be932d", - "https://usegalaxy.eu/published/workflow?id=1e5f1d9a51032e44", - "https://usegalaxy.eu/published/workflow?id=3eaa913306c16146", - "https://usegalaxy.eu/published/workflow?id=5b940b283d91d99d", - "https://usegalaxy.eu/published/workflow?id=6158c3b5fc12044e", - "https://usegalaxy.eu/published/workflow?id=6416cfdbd5273063", - 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"Suite parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign", + "Suite parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/cialign", "bio.tool ID": null, "bio.tool name": null, "bio.tool description": null, "biii ID": null, + "Related Workflows": [ + "https://usegalaxy.eu/published/workflow?id=93d7a5704ec1d82d" + ], + "Related Tutorials": [], "Number of tools on UseGalaxy.org (Main)": 0, "Number of tools on UseGalaxy.org.au": 0, "Number of tools on UseGalaxy.eu": 1, "Number of tools on UseGalaxy.fr": 0, "Number of tools on APOSTL": 0, - "Number of tools on MBAC Metabiome Portal": 0, "Number of tools on ChemFlow": 0, "Number of tools on CIRM-CFBP": 0, "Number of tools on Coloc-stats": 0, @@ -14332,7 +14138,6 @@ "Number of tools on MISSISSIPPI": 0, "Number of tools on Oqtans": 0, "Number of tools on Palfinder": 0, - "Number of tools on PepSimili": 0, "Number of tools on PhagePromotor": 0, "Number of tools on UseGalaxy.be": 0, "Number of tools on UseGalaxy.cz": 0, @@ -14358,10 +14163,6 @@ "Suite runs (last 5 years) on main servers": 6, "Suite users on main servers": 3, "Suite users (last 5 years) on main servers": 3, - 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It is available for several platforms, including Windows, Macintosh PowerMac, Linux and Solaris.Names occassionally spelled also as Clustal W2, ClustalW2, ClustalW, ClustalX, Clustal2.", "biii ID": null, + "Related Workflows": [ + "https://usegalaxy.eu/published/workflow?id=36de05d50c703164", + "https://usegalaxy.eu/published/workflow?id=376119528377a3ae", + "https://usegalaxy.eu/published/workflow?id=3e0246389fb70340", + "https://usegalaxy.eu/published/workflow?id=974cc681d07ec788", + "https://usegalaxy.eu/published/workflow?id=c8bc4af6dd3b5d02", + "https://usegalaxy.eu/published/workflow?id=f6a763951d815944", + "https://usegalaxy.org.au/published/workflow?id=b60922a253df6654", + "https://usegalaxy.org.au/published/workflow?id=eda40b58616a0fe4", + "https://usegalaxy.org/published/workflow?id=042758b8a8c5ac80", + "https://usegalaxy.org/published/workflow?id=07f7198b63108131", + "https://usegalaxy.org/published/workflow?id=18e7a954c0b6e4bc", + "https://usegalaxy.org/published/workflow?id=2d3063882d8239ff", + "https://usegalaxy.org/published/workflow?id=3d7baebefa7c9b81", + "https://usegalaxy.org/published/workflow?id=3ef08553982f6ffc", + "https://usegalaxy.org/published/workflow?id=603e5c61c57bcf3f", + "https://usegalaxy.org/published/workflow?id=6a1eb7e7bececba1", + "https://usegalaxy.org/published/workflow?id=75c2cf36253194c2", + "https://usegalaxy.org/published/workflow?id=7b68f97bf88f99b9", + "https://usegalaxy.org/published/workflow?id=87685c6247521b54", + "https://usegalaxy.org/published/workflow?id=8b7e03f09b0183d9", + "https://usegalaxy.org/published/workflow?id=a484a1e1a7335696", + "https://usegalaxy.org/published/workflow?id=b2fb90873471f4e7", + "https://usegalaxy.org/published/workflow?id=be9bd7286d38c210", + "https://usegalaxy.org/published/workflow?id=f7bf58d66cafcf1f", + "https://workflowhub.eu/workflows/1060?version=1", + "https://workflowhub.eu/workflows/1487?version=2", + "https://workflowhub.eu/workflows/1541?version=1", + "https://workflowhub.eu/workflows/1656?version=1", + "https://workflowhub.eu/workflows/358?version=1" + ], + "Related Tutorials": [ + "ecology/phylogeny-data-prep", + "genome-annotation/hpc-for-lsgc", + "microbiome/pathogen-detection-from-nanopore-foodborne-data" + ], "Number of tools on UseGalaxy.org (Main)": 1, "Number of tools on UseGalaxy.org.au": 1, "Number of tools on UseGalaxy.eu": 1, "Number of tools on UseGalaxy.fr": 1, "Number of tools on APOSTL": 0, - "Number of tools on MBAC Metabiome Portal": 0, "Number of tools on ChemFlow": 0, "Number of tools on CIRM-CFBP": 0, "Number of tools on Coloc-stats": 0, @@ -14541,7 +14375,6 @@ "Number of tools on MISSISSIPPI": 0, "Number of tools on Oqtans": 0, "Number of tools on Palfinder": 0, - "Number of tools on PepSimili": 0, "Number of tools on PhagePromotor": 0, "Number of tools on UseGalaxy.be": 1, "Number of tools on UseGalaxy.cz": 1, @@ -14567,41 +14400,6 @@ "Suite runs (last 5 years) on main servers": 180847, "Suite users on main servers": 11778, "Suite users (last 5 years) on main servers": 7113, - "Related Workflows": [ - "https://usegalaxy.eu/published/workflow?id=36de05d50c703164", - "https://usegalaxy.eu/published/workflow?id=376119528377a3ae", - "https://usegalaxy.eu/published/workflow?id=3e0246389fb70340", - "https://usegalaxy.eu/published/workflow?id=974cc681d07ec788", - "https://usegalaxy.eu/published/workflow?id=c8bc4af6dd3b5d02", - "https://usegalaxy.eu/published/workflow?id=f6a763951d815944", - 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"Number of tools on MBAC Metabiome Portal": 0, "Number of tools on ChemFlow": 0, "Number of tools on CIRM-CFBP": 0, "Number of tools on Coloc-stats": 0, @@ -14667,7 +14466,6 @@ "Number of tools on MISSISSIPPI": 0, "Number of tools on Oqtans": 0, "Number of tools on Palfinder": 0, - "Number of tools on PepSimili": 0, "Number of tools on PhagePromotor": 0, "Number of tools on UseGalaxy.be": 1, "Number of tools on UseGalaxy.cz": 1, @@ -14693,8 +14491,6 @@ "Suite runs (last 5 years) on main servers": 62891, "Suite users on main servers": 84, "Suite users (last 5 years) on main servers": 72, - "Related Workflows": [], - "Related Tutorials": [], "To keep": true, "Deprecated": false }, @@ -14734,17 +14530,20 @@ ], "Suite owner": "iuc", "Suite source": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/cojac", - "Suite parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/cojac", + "Suite parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac", "bio.tool ID": "cojac", "bio.tool name": "COJAC", "bio.tool description": "CoOccurrence adJusted Analysis and Calling - 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], - "Related Tutorials": [ - "genome-annotation/bacterial-genome-quality-control", - "microbiome/mags-building", - "microbiome/metagenomics-binning" - ], "To keep": true, "Deprecated": false }, @@ -18026,17 +17804,18 @@ ], "Suite owner": "iuc", "Suite source": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/emboss", - "Suite parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/emboss", + "Suite parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss", "bio.tool ID": "emboss", "bio.tool name": "EMBOSS", "bio.tool description": "Diverse suite of tools for sequence analysis; many programs analagous to GCG; context-sensitive help for each tool.", "biii ID": null, + "Related Workflows": [], + "Related Tutorials": [], "Number of tools on UseGalaxy.org (Main)": 0, "Number of tools on UseGalaxy.org.au": 0, "Number of tools on UseGalaxy.eu": 2, "Number of tools on UseGalaxy.fr": 0, "Number of tools on APOSTL": 0, - "Number of tools on MBAC Metabiome Portal": 0, "Number of tools on ChemFlow": 0, "Number of tools on CIRM-CFBP": 0, "Number of tools on Coloc-stats": 0, @@ -18053,7 +17832,6 @@ "Number of tools on MISSISSIPPI": 0, "Number of tools on Oqtans": 0, "Number of tools on Palfinder": 0, - 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FastANI supports pairwise comparison of both complete and draft genome assemblies.", "biii ID": null, + "Related Workflows": [ + "https://usegalaxy.eu/published/workflow?id=2a1dc58e51d5f01a", + "https://usegalaxy.eu/published/workflow?id=bf48b0eb15e8ff75" + ], + "Related Tutorials": [], "Number of tools on UseGalaxy.org (Main)": 0, "Number of tools on UseGalaxy.org.au": 1, "Number of tools on UseGalaxy.eu": 1, "Number of tools on UseGalaxy.fr": 1, "Number of tools on APOSTL": 0, - "Number of tools on MBAC Metabiome Portal": 0, "Number of tools on ChemFlow": 0, "Number of tools on CIRM-CFBP": 0, "Number of tools on Coloc-stats": 0, @@ -19143,7 +18922,6 @@ "Number of tools on MISSISSIPPI": 0, "Number of tools on Oqtans": 0, "Number of tools on Palfinder": 0, - "Number of tools on PepSimili": 0, "Number of tools on PhagePromotor": 0, "Number of tools on UseGalaxy.be": 1, "Number of tools on UseGalaxy.cz": 1, @@ -19169,11 +18947,6 @@ "Suite runs (last 5 years) on main servers": 32202, "Suite users on main servers": 1403, "Suite users (last 5 years) on main servers": 1380, - 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"Number of tools on MBAC Metabiome Portal": 0, "Number of tools on ChemFlow": 0, "Number of tools on CIRM-CFBP": 0, "Number of tools on Coloc-stats": 0, @@ -20059,7 +19836,6 @@ "Number of tools on MISSISSIPPI": 0, "Number of tools on Oqtans": 0, "Number of tools on Palfinder": 0, - "Number of tools on PepSimili": 0, "Number of tools on PhagePromotor": 0, "Number of tools on UseGalaxy.be": 0, "Number of tools on UseGalaxy.cz": 0, @@ -20085,10 +19861,6 @@ "Suite runs (last 5 years) on main servers": 526, "Suite users on main servers": 48, "Suite users (last 5 years) on main servers": 48, - "Related Workflows": [ - "https://usegalaxy.org.au/published/workflow?id=aa1d123c0a0929f3" - ], - "Related Tutorials": [], "To keep": true, "Deprecated": false }, @@ -20103,7 +19875,7 @@ "Description": "FASTQE", "Suite first commit date": "2020-07-13", "Homepage": "https://fastqe.com/", - "Suite version": "0.3.1+galaxy0", + "Suite version": "0.3.1", "Suite conda package": "fastqe", "Latest suite conda package version": "0.5.2", "Suite version status": "To update", @@ -20126,17 +19898,50 @@ ], "Suite owner": "iuc", "Suite source": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastqe", - 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"Related Workflows": [], - "Related Tutorials": [], "To keep": true, "Deprecated": false }, @@ -21676,10 +21438,10 @@ "Description": "Performs GO Enrichment analysis.", "Suite first commit date": "2018-12-28", "Homepage": "https://github.com/DanFaria/GOEnrichment", - "Suite version": "2.0.1", + "Suite version": "@TOOL_VERSION@+galaxy@VERSION_SUFFIX@", "Suite conda package": "goenrichment", "Latest suite conda package version": "2.0.1", - "Suite version status": "Up-to-date", + "Suite version status": "To update", "ToolShed categories": [ "Genome annotation" ], @@ -21697,17 +21459,27 @@ ], "Suite owner": "iuc", "Suite source": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/goenrichment", - "Suite parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/goenrichment", + "Suite parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment", "bio.tool ID": "goenrichment", "bio.tool name": "GOEnrichment", "bio.tool description": "GOEnrichment is a tool for performing GO enrichment analysis of gene sets, such as those obtained from RNA-seq or Microarray experiments, to help characterize them at the functional level. 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"Number of tools on MBAC Metabiome Portal": 0, "Number of tools on ChemFlow": 0, "Number of tools on CIRM-CFBP": 0, "Number of tools on Coloc-stats": 0, @@ -23087,7 +22855,6 @@ "Number of tools on MISSISSIPPI": 0, "Number of tools on Oqtans": 0, "Number of tools on Palfinder": 0, - "Number of tools on PepSimili": 0, "Number of tools on PhagePromotor": 0, "Number of tools on UseGalaxy.be": 6, "Number of tools on UseGalaxy.cz": 10, @@ -23113,33 +22880,6 @@ "Suite runs (last 5 years) on main servers": 61453, "Suite users on main servers": 1057, "Suite users (last 5 years) on main servers": 1057, - "Related Workflows": [ - "https://usegalaxy.eu/published/workflow?id=21a17d6c473a88c0", - "https://usegalaxy.eu/published/workflow?id=23dd2253da51e22e", - "https://usegalaxy.eu/published/workflow?id=3118d383c81cf805", - "https://usegalaxy.eu/published/workflow?id=4d32b1b3ac0a7161", - "https://usegalaxy.eu/published/workflow?id=5ce8a472e6e95c60", - "https://usegalaxy.eu/published/workflow?id=5f0faac42b0a5062", - 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"Number of tools on MBAC Metabiome Portal": 0, "Number of tools on ChemFlow": 0, "Number of tools on CIRM-CFBP": 0, "Number of tools on Coloc-stats": 0, @@ -24827,10 +24580,9 @@ "Number of tools on MISSISSIPPI": 0, "Number of tools on Oqtans": 0, "Number of tools on Palfinder": 0, - "Number of tools on PepSimili": 0, "Number of tools on PhagePromotor": 0, "Number of tools on UseGalaxy.be": 1, - "Number of tools on UseGalaxy.cz": 0, + "Number of tools on UseGalaxy.cz": 1, "Number of tools on UseGalaxy.no": 0, "Number of tools on Viral Variant Visualizer (VVV)": 0, "Suite users (last 5 years) (usegalaxy.eu)": 626, @@ -24853,42 +24605,6 @@ "Suite runs (last 5 years) on main servers": 5616, "Suite users on main servers": 1070, "Suite users (last 5 years) on main servers": 1070, - "Related Workflows": [ - "https://usegalaxy.eu/published/workflow?id=07c92110c3fffcf8", - "https://usegalaxy.eu/published/workflow?id=1ce406de61de8492", - "https://usegalaxy.eu/published/workflow?id=2cd5670f075704ab", - 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"Suite version": null, + "Suite version": "@WRAPPER_VERSION@+@VERSION_SUFFIX@", "Suite conda package": "kmer-jellyfish", "Latest suite conda package version": "2.3.1", "Suite version status": "To update", @@ -24929,17 +24645,21 @@ ], "Suite owner": "iuc", "Suite source": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/jellyfish", - "Suite parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/jellyfish", + "Suite parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish", "bio.tool ID": "Jellyfish", "bio.tool name": "Jellyfish", "bio.tool description": "A command-line algorithm for counting k-mers in DNA sequence.", "biii ID": null, + "Related Workflows": [ + "https://usegalaxy.eu/published/workflow?id=342169b55bdc2993", + "https://usegalaxy.eu/published/workflow?id=bc32937d505135ab" + ], + "Related Tutorials": [], "Number of tools on UseGalaxy.org (Main)": 0, "Number of tools on UseGalaxy.org.au": 1, "Number of tools on UseGalaxy.eu": 1, "Number of tools on UseGalaxy.fr": 1, "Number of tools on APOSTL": 0, - "Number of tools on MBAC Metabiome Portal": 0, "Number of tools on ChemFlow": 0, "Number of tools on CIRM-CFBP": 0, "Number of tools on Coloc-stats": 0, @@ -24956,7 +24676,6 @@ "Number of tools on MISSISSIPPI": 0, "Number of tools on Oqtans": 0, "Number of tools on Palfinder": 0, - "Number of tools on PepSimili": 0, "Number of tools on PhagePromotor": 0, "Number of tools on UseGalaxy.be": 0, "Number of tools on UseGalaxy.cz": 1, @@ -24982,11 +24701,6 @@ "Suite runs (last 5 years) on main servers": 7912, "Suite users on main servers": 491, "Suite users (last 5 years) on main servers": 491, - "Related Workflows": [ - "https://usegalaxy.eu/published/workflow?id=342169b55bdc2993", - "https://usegalaxy.eu/published/workflow?id=bc32937d505135ab" - ], - "Related Tutorials": [], "To keep": true, "Deprecated": false }, @@ -25026,17 +24740,18 @@ ], "Suite owner": "iuc", "Suite source": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/kaiju", - "Suite parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/kaiju", + "Suite parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/kaiju", "bio.tool ID": "kaiju", "bio.tool name": "Kaiju", "bio.tool description": "Program for the taxonomic assignment of high-throughput sequencing reads, e.g., Illumina or Roche/454, from whole-genome sequencing of metagenomic DNA. Reads are directly assigned to taxa using the NCBI taxonomy and a reference database of protein sequences from Bacteria, Archaea, Fungi, microbial eukaryotes and viruses.", "biii ID": null, + "Related Workflows": [], + "Related Tutorials": [], "Number of tools on UseGalaxy.org (Main)": 0, "Number of tools on UseGalaxy.org.au": 0, "Number of tools on UseGalaxy.eu": 5, "Number of tools on UseGalaxy.fr": 0, "Number of tools on APOSTL": 0, - "Number of tools on MBAC Metabiome Portal": 0, "Number of tools on ChemFlow": 0, "Number of tools on CIRM-CFBP": 0, "Number of tools on Coloc-stats": 0, @@ -25053,7 +24768,6 @@ "Number of tools on MISSISSIPPI": 0, "Number of tools on Oqtans": 0, "Number of tools on Palfinder": 0, - "Number of tools on PepSimili": 0, "Number of tools on PhagePromotor": 0, "Number of tools on UseGalaxy.be": 0, "Number of tools on UseGalaxy.cz": 0, @@ -25079,8 +24793,6 @@ "Suite runs (last 5 years) on main servers": 2, "Suite users on main servers": 2, "Suite users (last 5 years) on main servers": 2, - "Related Workflows": [], - "Related Tutorials": [], "To keep": true, "Deprecated": false }, @@ -25128,17 +24840,18 @@ ], "Suite owner": "iuc", "Suite source": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/khmer", - "Suite parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/khmer", + "Suite parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer", "bio.tool ID": "khmer", "bio.tool name": "khmer", "bio.tool description": "khmer is a set of command-line tools for working with DNA shotgun sequencing data from genomes, transcriptomes, metagenomes, and single cells. khmer can make de novo assemblies faster, and sometimes better. khmer can also identify (and fix) problems with shotgun data.", "biii ID": null, + "Related Workflows": [], + "Related Tutorials": [], "Number of tools on UseGalaxy.org (Main)": 8, "Number of tools on UseGalaxy.org.au": 8, "Number of tools on UseGalaxy.eu": 8, "Number of tools on UseGalaxy.fr": 0, "Number of tools on APOSTL": 0, - "Number of tools on MBAC Metabiome Portal": 0, "Number of tools on ChemFlow": 0, "Number of tools on CIRM-CFBP": 0, "Number of tools on Coloc-stats": 0, @@ -25155,7 +24868,6 @@ "Number of tools on MISSISSIPPI": 1, "Number of tools on Oqtans": 0, "Number of tools on Palfinder": 0, - "Number of tools on PepSimili": 0, "Number of tools on PhagePromotor": 0, "Number of tools on UseGalaxy.be": 8, "Number of tools on UseGalaxy.cz": 8, @@ -25181,8 +24893,6 @@ "Suite runs (last 5 years) on main servers": 4930, "Suite users on main servers": 326, "Suite users (last 5 years) on main servers": 292, - "Related Workflows": [], - "Related Tutorials": [], "To keep": true, "Deprecated": false }, @@ -25197,7 +24907,7 @@ "Description": "Screen genome assemblies of Klebsiella pneumoniae and the Klebsiella pneumoniae species complex (KpSC)", "Suite first commit date": "2022-09-09", "Homepage": "https://github.com/katholt/Kleborate", - "Suite version": "2.3.2", + "Suite version": "@TOOL_VERSION@+galaxy@VERSION_SUFFIX@", "Suite conda package": "kleborate", "Latest suite conda package version": "3.2.4", "Suite version status": "To update", @@ -25230,17 +24940,18 @@ ], "Suite owner": "iuc", "Suite source": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/kleborate", - "Suite parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/kleborate", + "Suite parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/kleborate", "bio.tool ID": "kleborate", "bio.tool name": "Kleborate", "bio.tool description": "Genomic surveillance framework and global population structure for Klebsiella pneumoniae.Kleborate is a tool to screen genome assemblies of Klebsiella pneumoniae and the Klebsiella pneumoniae species complex (KpSC) for:.A manuscript describing the Kleborate software in full is currently in preparation. In the meantime, if you use Kleborate, please cite the preprint: Lam, MMC. et al. Genomic surveillance framework and global population structure for Klebsiella pneumoniae. bioRxiv (2020).", "biii ID": null, + "Related Workflows": [], + "Related Tutorials": [], "Number of tools on UseGalaxy.org (Main)": 0, "Number of tools on UseGalaxy.org.au": 0, "Number of tools on UseGalaxy.eu": 1, "Number of tools on UseGalaxy.fr": 0, "Number of tools on APOSTL": 0, - "Number of tools on MBAC Metabiome Portal": 0, "Number of tools on ChemFlow": 0, "Number of tools on CIRM-CFBP": 0, "Number of tools on Coloc-stats": 0, @@ -25257,7 +24968,6 @@ "Number of tools on MISSISSIPPI": 0, "Number of tools on Oqtans": 0, "Number of tools on Palfinder": 0, - "Number of tools on PepSimili": 0, "Number of tools on PhagePromotor": 0, "Number of tools on UseGalaxy.be": 0, "Number of tools on UseGalaxy.cz": 1, @@ -25283,8 +24993,6 @@ "Suite runs (last 5 years) on main servers": 1479, "Suite users on main servers": 123, "Suite users (last 5 years) on main servers": 123, - "Related Workflows": [], - "Related Tutorials": [], "To keep": true, "Deprecated": false }, @@ -25299,7 +25007,7 @@ "Description": "A tool for creating data files for statistics based on kmers", "Suite first commit date": "2025-04-16", "Homepage": "https://github.com/SantaMcCloud/kmer2stats", - "Suite version": "1.0.1", + "Suite version": "@TOOL_VERSION@+galaxy@VERSION_SUFFIX@", "Suite conda package": "kmer2stats", "Latest suite conda package version": "1.0.3", "Suite version status": "To update", @@ -25312,17 +25020,20 @@ "EDAM reduced topics": [], "Suite owner": "iuc", "Suite source": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/kmer2stats", - "Suite parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/kmer2stats", + "Suite parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/kmer2stats", "bio.tool ID": null, "bio.tool name": null, "bio.tool description": null, "biii ID": null, + "Related Workflows": [ + "https://usegalaxy.eu/published/workflow?id=342169b55bdc2993" + ], + "Related Tutorials": [], "Number of tools on UseGalaxy.org (Main)": 0, "Number of tools on UseGalaxy.org.au": 0, "Number of tools on UseGalaxy.eu": 1, "Number of tools on UseGalaxy.fr": 1, "Number of tools on APOSTL": 0, - "Number of tools on MBAC Metabiome Portal": 0, "Number of tools on ChemFlow": 0, "Number of tools on CIRM-CFBP": 0, "Number of tools on Coloc-stats": 0, @@ -25339,7 +25050,6 @@ "Number of tools on MISSISSIPPI": 0, "Number of tools on Oqtans": 0, "Number of tools on Palfinder": 0, - "Number of tools on PepSimili": 0, "Number of tools on PhagePromotor": 0, "Number of tools on UseGalaxy.be": 0, "Number of tools on UseGalaxy.cz": 0, @@ -25365,10 +25075,6 @@ "Suite runs (last 5 years) on main servers": 310, "Suite users on main servers": 8, "Suite users (last 5 years) on main servers": 8, - "Related Workflows": [ - "https://usegalaxy.eu/published/workflow?id=342169b55bdc2993" - ], - "Related Tutorials": [], "To keep": true, "Deprecated": false }, @@ -25397,17 +25103,18 @@ "EDAM reduced topics": [], "Suite owner": "iuc", "Suite source": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/kmindex", - "Suite parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/kmindex", + "Suite parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/kmindex", "bio.tool ID": "kmindex", "bio.tool name": "kmindex", "bio.tool description": "kmindex is a tool for indexing and querying sequencing samples. It is built on top of kmtricks.", "biii ID": null, + "Related Workflows": [], + "Related Tutorials": [], "Number of tools on UseGalaxy.org (Main)": 0, "Number of tools on UseGalaxy.org.au": 0, "Number of tools on UseGalaxy.eu": 2, "Number of tools on UseGalaxy.fr": 0, "Number of tools on APOSTL": 0, - "Number of tools on MBAC Metabiome Portal": 0, "Number of tools on ChemFlow": 0, "Number of tools on CIRM-CFBP": 0, "Number of tools on Coloc-stats": 0, @@ -25424,7 +25131,6 @@ "Number of tools on MISSISSIPPI": 0, "Number of tools on Oqtans": 0, "Number of tools on Palfinder": 0, - "Number of tools on PepSimili": 0, "Number of tools on PhagePromotor": 0, "Number of tools on UseGalaxy.be": 0, "Number of tools on UseGalaxy.cz": 0, @@ -25450,8 +25156,89 @@ "Suite runs (last 5 years) on main servers": 0, "Suite users on main servers": 0, "Suite users (last 5 years) on main servers": 0, - "Related Workflows": [], + "To keep": true, + "Deprecated": false + }, + { + "Suite ID": "kneaddata", + "Tool IDs": [ + "kneaddata" + ], + "Tool output formats": [ + "txt" + ], + "Description": "Quality control and contaminant removal for metagenomic data", + "Suite first commit date": "2026-02-04", + "Homepage": "https://github.com/biobakery/kneaddata", + "Suite version": "0.12.1", + "Suite conda package": "kneaddata", + "Latest suite conda package version": "0.12.4", + "Suite version status": "To update", + "ToolShed categories": [ + "Metagenomics", + "Sequence Analysis" + ], + "EDAM operations": [], + "EDAM reduced operations": [], + "EDAM topics": [], + "EDAM reduced topics": [], + "Suite owner": "iuc", + "Suite source": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/kneaddata", + "Suite parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/kneaddata", + "bio.tool ID": null, + "bio.tool name": null, + "bio.tool description": null, + "biii ID": null, + "Related Workflows": [ + "https://usegalaxy.eu/published/workflow?id=8e13c87e751e88d8" + ], "Related Tutorials": [], + "Number of tools on UseGalaxy.org (Main)": 0, + "Number of tools on UseGalaxy.org.au": 0, + "Number of tools on UseGalaxy.eu": 1, + "Number of tools on UseGalaxy.fr": 0, + "Number of tools on APOSTL": 0, + "Number of tools on ChemFlow": 0, + "Number of tools on CIRM-CFBP": 0, + "Number of tools on Coloc-stats": 0, + "Number of tools on Galaxy@AuBi": 0, + "Number of tools on Galaxy@Pasteur": 0, + "Number of tools on GalaxyTrakr": 1, + "Number of tools on GASLINI": 0, + "Number of tools on HyPhy HIV NGS Tools": 0, + "Number of tools on ImmPort Galaxy": 0, + "Number of tools on InteractoMIX": 0, + "Number of tools on IPK Galaxy Blast Suite": 0, + "Number of tools on Lebanese University Galaxy": 0, + "Number of tools on Mandoiu Lab": 0, + "Number of tools on MISSISSIPPI": 0, + "Number of tools on Oqtans": 0, + "Number of tools on Palfinder": 0, + "Number of tools on PhagePromotor": 0, + "Number of tools on UseGalaxy.be": 0, + "Number of tools on UseGalaxy.cz": 0, + "Number of tools on UseGalaxy.no": 0, + "Number of tools on Viral Variant Visualizer (VVV)": 0, + "Suite users (last 5 years) (usegalaxy.eu)": 0, + "Suite users (usegalaxy.eu)": 0, + "Suite runs (last 5 years) (usegalaxy.eu)": 0, + "Suite runs (usegalaxy.eu)": 0, + "Suite users (last 5 years) (usegalaxy.org)": 0, + "Suite users (usegalaxy.org)": 0, + "Suite runs (last 5 years) (usegalaxy.org)": 0, + "Suite runs (usegalaxy.org)": 0, + "Suite users (last 5 years) (usegalaxy.org.au)": 0, + "Suite users (usegalaxy.org.au)": 0, + "Suite runs (last 5 years) (usegalaxy.org.au)": 0, + "Suite runs (usegalaxy.org.au)": 0, + "Suite users (last 5 years) (usegalaxy.fr)": 0, + "Suite users (usegalaxy.fr)": 0, + "Suite runs (last 5 years) (usegalaxy.fr)": 0, + "Suite runs (usegalaxy.fr)": 0, + "Suite runs on main servers": 0, + "Suite runs (last 5 years) on main servers": 0, + "Suite users on main servers": 0, + "Suite users (last 5 years) on main servers": 0, "To keep": true, "Deprecated": false }, @@ -25467,10 +25254,10 @@ "Description": "Gene function annotation tool based on KEGG Orthology and hidden Markov model", "Suite first commit date": "2020-11-12", "Homepage": "https://github.com/takaram/kofam_scan", - "Suite version": "1.3.0", + "Suite version": "@TOOL_VERSION@+galaxy@VERSION_SUFFIX@", "Suite conda package": "kofamscan", "Latest suite conda package version": "1.3.0", - "Suite version status": "Up-to-date", + "Suite version status": "To update", "ToolShed categories": [ "Sequence Analysis" ], @@ -25492,17 +25279,26 @@ ], "Suite owner": "iuc", "Suite source": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/kofamscan", - "Suite parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/kofamscan", + "Suite parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan", "bio.tool ID": "kofamscan", "bio.tool name": "kofamscan", "bio.tool description": "KofamScan is a gene function annotation tool based on KEGG Orthology and hidden Markov model. You need KOfam database to use this tool.", "biii ID": null, + "Related Workflows": [ + "https://usegalaxy.eu/published/workflow?id=3eaa913306c16146", + "https://usegalaxy.eu/published/workflow?id=6158c3b5fc12044e", + "https://usegalaxy.eu/published/workflow?id=6416cfdbd5273063", + "https://usegalaxy.eu/published/workflow?id=667bac8d7453e5f1", + "https://usegalaxy.eu/published/workflow?id=8deb08d4f228e198", + "https://usegalaxy.eu/published/workflow?id=9b9e1e28f3683f92", + "https://usegalaxy.eu/published/workflow?id=d57d41e306241396" + ], + "Related Tutorials": [], "Number of tools on UseGalaxy.org (Main)": 0, "Number of tools on UseGalaxy.org.au": 0, "Number of tools on UseGalaxy.eu": 1, "Number of tools on UseGalaxy.fr": 1, "Number of tools on APOSTL": 0, - "Number of tools on MBAC Metabiome Portal": 0, "Number of tools on ChemFlow": 0, "Number of tools on CIRM-CFBP": 0, "Number of tools on Coloc-stats": 0, @@ -25519,7 +25315,6 @@ "Number of tools on MISSISSIPPI": 0, "Number of tools 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"https://github.com/galaxyproject/tools-iuc/tree/main/tools/kraken_biom", - "Suite parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/kraken_biom", + "Suite parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/kraken_biom", "bio.tool ID": "kraken-biom", "bio.tool name": "kraken-biom", "bio.tool description": "Create BIOM-format tables from Kraken output", "biii ID": null, + "Related Workflows": [ + "https://usegalaxy.eu/published/workflow?id=39d36a7ce0ef268d", + "https://usegalaxy.eu/published/workflow?id=4f0daf8e9dd54127", + "https://usegalaxy.eu/published/workflow?id=a0ea6fc756dd17ea", + "https://usegalaxy.eu/published/workflow?id=b67b5ecd3305f830", + "https://usegalaxy.eu/published/workflow?id=e69b555faa6bb962", + "https://workflowhub.eu/workflows/1470?version=2" + ], + "Related Tutorials": [ + "microbiome/taxonomic-profiling" + ], "Number of tools on UseGalaxy.org (Main)": 1, "Number of tools on UseGalaxy.org.au": 1, "Number of tools on UseGalaxy.eu": 1, "Number of tools on UseGalaxy.fr": 1, "Number of tools on APOSTL": 0, - "Number of tools on MBAC Metabiome Portal": 0, "Number of tools on ChemFlow": 0, "Number of tools on CIRM-CFBP": 0, "Number of tools on Coloc-stats": 0, @@ -25622,7 +25417,6 @@ "Number of tools on MISSISSIPPI": 0, "Number of tools on Oqtans": 0, "Number of tools on Palfinder": 0, - "Number of tools on PepSimili": 0, "Number of tools on PhagePromotor": 0, "Number of tools on UseGalaxy.be": 1, "Number of tools on UseGalaxy.cz": 1, @@ -25648,17 +25442,6 @@ "Suite runs (last 5 years) on main servers": 5877, "Suite users on main servers": 1008, "Suite users (last 5 years) on main servers": 1008, - "Related Workflows": [ - "https://usegalaxy.eu/published/workflow?id=39d36a7ce0ef268d", - "https://usegalaxy.eu/published/workflow?id=4f0daf8e9dd54127", - "https://usegalaxy.eu/published/workflow?id=a0ea6fc756dd17ea", - "https://usegalaxy.eu/published/workflow?id=b67b5ecd3305f830", - "https://usegalaxy.eu/published/workflow?id=e69b555faa6bb962", - "https://workflowhub.eu/workflows/1470?version=2" - ], - "Related Tutorials": [ - "microbiome/taxonomic-profiling" - ], "To keep": true, "Deprecated": false }, @@ -25674,7 +25457,7 @@ "Description": "Kraken taxonomy report", "Suite first commit date": "2016-06-01", "Homepage": "https://github.com/blankenberg/Kraken-Taxonomy-Report", - "Suite version": "0.0.3", + "Suite version": "@TOOL_VERSION@+galaxy@VERSION_SUFFIX@", "Suite conda package": "biopython", "Latest suite conda package version": "1.70", "Suite version status": "To update", @@ -25699,17 +25482,21 @@ ], "Suite owner": "iuc", "Suite source": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/kraken_taxonomy_report", - "Suite parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/kraken_taxonomy_report", + "Suite parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/kraken_taxonomy_report", "bio.tool ID": "Kraken-Taxonomy-Report", "bio.tool name": "Kraken-Taxonomy-Report", "bio.tool description": "view report of classification for multiple samples", "biii ID": null, + "Related Workflows": [ + "https://usegalaxy.eu/published/workflow?id=2e5e6291cd112225", + "https://usegalaxy.eu/published/workflow?id=b659069edd9b1d4e" + ], + "Related Tutorials": [], "Number of tools on UseGalaxy.org (Main)": 1, "Number of tools on UseGalaxy.org.au": 1, "Number of tools on UseGalaxy.eu": 1, "Number of tools on UseGalaxy.fr": 1, "Number of tools on APOSTL": 0, - "Number of tools on MBAC Metabiome Portal": 0, "Number of tools on ChemFlow": 0, "Number of tools on CIRM-CFBP": 0, "Number of tools on Coloc-stats": 0, @@ -25726,7 +25513,6 @@ "Number of tools on MISSISSIPPI": 0, "Number of tools on Oqtans": 0, "Number of tools on Palfinder": 0, - "Number of tools on PepSimili": 0, "Number of tools on PhagePromotor": 0, "Number of tools on UseGalaxy.be": 1, "Number of tools on UseGalaxy.cz": 1, @@ -25752,11 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0, "Number of tools on Coloc-stats": 0, @@ -26518,7 +26393,6 @@ "Number of tools on MISSISSIPPI": 0, "Number of tools on Oqtans": 0, "Number of tools on Palfinder": 0, - "Number of tools on PepSimili": 0, "Number of tools on PhagePromotor": 0, "Number of tools on UseGalaxy.be": 0, "Number of tools on UseGalaxy.cz": 1, @@ -26544,8 +26418,6 @@ "Suite runs (last 5 years) on main servers": 930, "Suite users on main servers": 18, "Suite users (last 5 years) on main servers": 18, - "Related Workflows": [], - "Related Tutorials": [], "To keep": true, "Deprecated": false }, @@ -26560,10 +26432,10 @@ "Description": "m6anet to detect m6A RNA modifications from nanopore data", "Suite first commit date": "2023-10-25", "Homepage": "https://m6anet.readthedocs.io/en/latest", - "Suite version": "2.1.0", + "Suite version": "@TOOL_VERSION@+galaxy@VERSION_SUFFIX@", "Suite conda package": "m6anet", "Latest suite conda package version": "2.1.0", - "Suite version status": "Up-to-date", + "Suite version 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MaAsLin2 relies on general linear models to accommodate most modern epidemiological study designs, including cross-sectional and longitudinal, and offers a variety of data exploration, normalization, and transformation methods.", "biii ID": null, + "Related Workflows": [ + "https://usegalaxy.eu/published/workflow?id=466bdd8ba7b67264", + "https://usegalaxy.eu/published/workflow?id=4ddf2ec5c460d622", + "https://usegalaxy.eu/published/workflow?id=e1296dbcf34499b0", + "https://usegalaxy.eu/published/workflow?id=e69b555faa6bb962" + ], + "Related Tutorials": [], "Number of tools on UseGalaxy.org (Main)": 0, "Number of tools on UseGalaxy.org.au": 0, "Number of tools on UseGalaxy.eu": 1, "Number of tools on UseGalaxy.fr": 1, "Number of tools on APOSTL": 0, - "Number of tools on MBAC Metabiome Portal": 0, "Number of tools on ChemFlow": 0, "Number of tools on CIRM-CFBP": 0, "Number of tools on Coloc-stats": 0, @@ -26718,7 +26594,6 @@ "Number of tools on MISSISSIPPI": 0, "Number of tools on Oqtans": 0, "Number of tools on Palfinder": 0, - "Number of tools on PepSimili": 0, "Number of tools on PhagePromotor": 0, "Number of tools on UseGalaxy.be": 0, "Number of tools on UseGalaxy.cz": 1, @@ -26744,13 +26619,6 @@ "Suite runs (last 5 years) on main servers": 3680, "Suite users on main servers": 102, "Suite users (last 5 years) on main servers": 102, - "Related Workflows": [ - "https://usegalaxy.eu/published/workflow?id=466bdd8ba7b67264", - "https://usegalaxy.eu/published/workflow?id=4ddf2ec5c460d622", - "https://usegalaxy.eu/published/workflow?id=e1296dbcf34499b0", - "https://usegalaxy.eu/published/workflow?id=e69b555faa6bb962" - ], - "Related Tutorials": [], "To keep": true, "Deprecated": false }, @@ -26780,17 +26648,18 @@ "EDAM reduced topics": [], "Suite owner": "iuc", "Suite source": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/maaslin3", - "Suite parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/maaslin3", + "Suite parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/maaslin3", "bio.tool ID": null, "bio.tool name": null, "bio.tool description": null, "biii ID": null, + "Related Workflows": [], + "Related Tutorials": [], "Number of tools on UseGalaxy.org (Main)": 0, "Number of tools on UseGalaxy.org.au": 0, "Number of tools on UseGalaxy.eu": 1, "Number of tools on UseGalaxy.fr": 0, "Number of tools on APOSTL": 0, - "Number of tools on MBAC Metabiome Portal": 0, "Number of tools on ChemFlow": 0, "Number of tools on CIRM-CFBP": 0, "Number of tools on Coloc-stats": 0, @@ -26807,7 +26676,6 @@ "Number of tools on MISSISSIPPI": 0, "Number of tools on Oqtans": 0, "Number of tools on Palfinder": 0, - "Number of tools on PepSimili": 0, "Number of tools on PhagePromotor": 0, "Number of tools on UseGalaxy.be": 0, "Number of tools on UseGalaxy.cz": 0, @@ -26833,8 +26701,6 @@ "Suite runs (last 5 years) on main servers": 0, "Suite users on main servers": 0, "Suite users (last 5 years) on main servers": 0, - "Related Workflows": [], - "Related Tutorials": [], "To keep": true, "Deprecated": false }, @@ -26877,17 +26743,32 @@ ], "Suite owner": "iuc", "Suite source": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/maker", - "Suite parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/maker", + "Suite parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker", "bio.tool ID": "maker", "bio.tool name": "MAKER", "bio.tool description": "Portable and easily configurable genome annotation pipeline. 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"Number of tools on MBAC Metabiome Portal": 0, "Number of tools on ChemFlow": 0, "Number of tools on CIRM-CFBP": 0, "Number of tools on Coloc-stats": 0, @@ -26904,7 +26785,6 @@ "Number of tools on MISSISSIPPI": 0, "Number of tools on Oqtans": 0, "Number of tools on Palfinder": 0, - "Number of tools on PepSimili": 0, "Number of tools on PhagePromotor": 0, "Number of tools on UseGalaxy.be": 2, "Number of tools on UseGalaxy.cz": 2, @@ -26930,22 +26810,6 @@ "Suite runs (last 5 years) on main servers": 22047, "Suite users on main servers": 4200, "Suite users (last 5 years) on main servers": 3961, - "Related Workflows": [ - "https://usegalaxy.eu/published/workflow?id=26ad77bc07a7e512", - "https://usegalaxy.eu/published/workflow?id=6ca20e710f4f3ffb", - "https://usegalaxy.org.au/published/workflow?id=7a87dfe5bdd30040", - "https://usegalaxy.org.au/published/workflow?id=7e40485d1ed45b7c", - "https://usegalaxy.org/published/workflow?id=65b4051e722228b8", - "https://usegalaxy.org/published/workflow?id=c42c66d1b627c5a5", - 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"Number of tools on MBAC Metabiome Portal": 0, "Number of tools on ChemFlow": 0, "Number of tools on CIRM-CFBP": 0, "Number of tools on Coloc-stats": 0, @@ -27012,7 +26889,6 @@ "Number of tools on MISSISSIPPI": 0, "Number of tools on Oqtans": 0, "Number of tools on Palfinder": 0, - "Number of tools on PepSimili": 0, "Number of tools on PhagePromotor": 0, "Number of tools on UseGalaxy.be": 1, "Number of tools on UseGalaxy.cz": 1, @@ -27038,20 +26914,6 @@ "Suite runs (last 5 years) on main servers": 10046, "Suite users on main servers": 88, "Suite users (last 5 years) on main servers": 88, - "Related Workflows": [ - "https://usegalaxy.eu/published/workflow?id=08e25b733cd796e6", - "https://usegalaxy.eu/published/workflow?id=437704898229dfb6", - "https://usegalaxy.eu/published/workflow?id=fb806b88850f3427", - "https://usegalaxy.org/published/workflow?id=45f959d5bf505b15", - "https://usegalaxy.org/published/workflow?id=8151be18aab3a3c6", - "https://workflowhub.eu/workflows/1270?version=2", - 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"Number of tools on MBAC Metabiome Portal": 0, "Number of tools on ChemFlow": 0, "Number of tools on CIRM-CFBP": 0, "Number of tools on Coloc-stats": 0, @@ -27223,7 +27105,6 @@ "Number of tools on MISSISSIPPI": 0, "Number of tools on Oqtans": 0, "Number of tools on Palfinder": 0, - "Number of tools on PepSimili": 1, "Number of tools on PhagePromotor": 0, "Number of tools on UseGalaxy.be": 1, "Number of tools on UseGalaxy.cz": 1, @@ -27249,28 +27130,6 @@ "Suite runs (last 5 years) on main servers": 9721, "Suite users on main servers": 1222, "Suite users (last 5 years) on main servers": 1154, - "Related Workflows": [ - "https://usegalaxy.eu/published/workflow?id=00f15824c7a9b196", - "https://usegalaxy.eu/published/workflow?id=02631612a43a4d9b", - "https://usegalaxy.eu/published/workflow?id=0563f58718be932d", - "https://usegalaxy.eu/published/workflow?id=1e5f1d9a51032e44", - "https://usegalaxy.eu/published/workflow?id=6158c3b5fc12044e", - "https://usegalaxy.eu/published/workflow?id=667bac8d7453e5f1", - 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"Suite version status": "Up-to-date", + "Suite version status": "To update", "ToolShed categories": [ "Sequence Analysis" ], @@ -27309,17 +27168,18 @@ ], "Suite owner": "iuc", "Suite source": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/mcl", - "Suite parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/mcl", + "Suite parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/mcl", "bio.tool ID": "mcl", "bio.tool name": "MCL", "bio.tool description": "MCL is a clustering algorithm widely used in bioinformatics and gaining traction in other fields.", "biii ID": null, + "Related Workflows": [], + "Related Tutorials": [], "Number of tools on UseGalaxy.org (Main)": 0, "Number of tools on UseGalaxy.org.au": 0, "Number of tools on UseGalaxy.eu": 1, "Number of tools on UseGalaxy.fr": 0, "Number of tools on APOSTL": 0, - "Number of tools on MBAC Metabiome Portal": 0, "Number of tools on ChemFlow": 0, "Number of tools on CIRM-CFBP": 0, "Number of tools on Coloc-stats": 0, @@ -27336,7 +27196,6 @@ "Number of tools on MISSISSIPPI": 0, "Number of tools on Oqtans": 0, "Number of tools on Palfinder": 0, - 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"Number of tools on MBAC Metabiome Portal": 0, "Number of tools on ChemFlow": 0, "Number of tools on CIRM-CFBP": 0, "Number of tools on Coloc-stats": 0, @@ -28772,7 +28618,6 @@ "Number of tools on MISSISSIPPI": 0, "Number of tools on Oqtans": 0, "Number of tools on Palfinder": 0, - "Number of tools on PepSimili": 0, "Number of tools on PhagePromotor": 0, "Number of tools on UseGalaxy.be": 0, "Number of tools on UseGalaxy.cz": 0, @@ -28798,8 +28643,6 @@ "Suite runs (last 5 years) on main servers": 0, "Suite users on main servers": 0, "Suite users (last 5 years) on main servers": 0, - "Related Workflows": [], - "Related Tutorials": [], "To keep": true, "Deprecated": false }, @@ -28815,7 +28658,7 @@ "Description": "MetaEuk is a modular toolkit designed for large-scale gene discovery andannotation in eukaryotic metagenomic contigs. 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It is designed to address the effects of both normalization and under-sampling of microbial communities on disease association detection and the testing of feature correlations.", "biii ID": null, + "Related Workflows": [], + "Related Tutorials": [], "Number of tools on UseGalaxy.org (Main)": 1, "Number of tools on UseGalaxy.org.au": 0, "Number of tools on UseGalaxy.eu": 1, "Number of tools on UseGalaxy.fr": 1, "Number of tools on APOSTL": 0, - "Number of tools on MBAC Metabiome Portal": 0, "Number of tools on ChemFlow": 0, "Number of tools on CIRM-CFBP": 0, "Number of tools on Coloc-stats": 0, @@ -28963,7 +28805,6 @@ "Number of tools on MISSISSIPPI": 0, "Number of tools on Oqtans": 0, "Number of tools on Palfinder": 0, - "Number of tools on PepSimili": 0, "Number of tools on PhagePromotor": 0, "Number of tools on UseGalaxy.be": 1, "Number of tools on UseGalaxy.cz": 1, @@ -28989,8 +28830,6 @@ "Suite runs (last 5 years) on main servers": 782, "Suite users on main servers": 79, "Suite users (last 5 years) on main servers": 43, - "Related Workflows": [], - "Related Tutorials": [], "To keep": true, "Deprecated": false }, @@ -29031,17 +28870,18 @@ ], "Suite owner": "iuc", "Suite source": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/metamdbg", - "Suite parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/metamdbg", + "Suite parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/metamdbg", "bio.tool ID": "metamdbg", "bio.tool name": "metaMDBG", "bio.tool description": "MetaMDBG is a fast and low-memory assembler for long and accurate metagenomics reads (e.g. PacBio HiFi, Nanopore r10.4). 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MetaMDBG combines an efficient multi-k approach in minimizer-space for dealing with uneven species coverages, and a novel abundance-based filtering method for simplifying strain complexity.", "biii ID": null, + "Related Workflows": [], + "Related Tutorials": [], "Number of tools on UseGalaxy.org (Main)": 2, "Number of tools on UseGalaxy.org.au": 0, "Number of tools on UseGalaxy.eu": 2, "Number of tools on UseGalaxy.fr": 0, "Number of tools on APOSTL": 0, - "Number of tools on MBAC Metabiome Portal": 0, "Number of tools on ChemFlow": 0, "Number of tools on CIRM-CFBP": 0, "Number of tools on Coloc-stats": 0, @@ -29058,7 +28898,6 @@ "Number of tools on MISSISSIPPI": 0, "Number of tools on Oqtans": 0, "Number of tools on Palfinder": 0, - "Number of tools on PepSimili": 0, "Number of tools on PhagePromotor": 0, "Number of tools on UseGalaxy.be": 0, "Number of tools on UseGalaxy.cz": 0, @@ -29084,8 +28923,6 @@ "Suite runs (last 5 years) on main servers": 0, "Suite users on main servers": 0, 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OMArk relies on the OMA orthology database, from which it exploits orthology relationships, and on the OMAmer software for fast placement of all proteins into gene families.", "biii ID": null, + "Related Workflows": [ + "https://usegalaxy.eu/published/workflow?id=31bc2a44fb89aa89", + "https://usegalaxy.eu/published/workflow?id=327beb1edda305ff", + "https://usegalaxy.eu/published/workflow?id=3d604dad4f1f5b3d", + "https://usegalaxy.eu/published/workflow?id=4077e77b6af919c4", + "https://usegalaxy.eu/published/workflow?id=6550f72070b24082", + "https://usegalaxy.eu/published/workflow?id=8976041ef89e4548", + "https://usegalaxy.org.au/published/workflow?id=dd9272826e6dd98d", + "https://usegalaxy.org.au/published/workflow?id=e263fcb6c98e231b", + "https://usegalaxy.org.au/published/workflow?id=ec7efff3d3249177", + "https://usegalaxy.org/published/workflow?id=4605309321799e9b", + "https://usegalaxy.org/published/workflow?id=80a7124c40438cc9", + "https://usegalaxy.org/published/workflow?id=f4111a169255535c", + "https://workflowhub.eu/workflows/1096?version=2", + "https://workflowhub.eu/workflows/1255?version=3", + "https://workflowhub.eu/workflows/1500?version=1", + "https://workflowhub.eu/workflows/1746?version=1", + "https://workflowhub.eu/workflows/2029?version=1" + ], + "Related Tutorials": [ + "genome-annotation/braker3", + "genome-annotation/comparison-braker-helixer-annotation", + "genome-annotation/helixer" + ], "Number of tools on UseGalaxy.org (Main)": 1, "Number of tools on UseGalaxy.org.au": 1, "Number of tools on UseGalaxy.eu": 1, "Number of tools on UseGalaxy.fr": 1, "Number of tools on APOSTL": 0, - "Number of tools on MBAC Metabiome Portal": 0, "Number of tools on ChemFlow": 0, "Number of tools on CIRM-CFBP": 0, "Number of tools on Coloc-stats": 0, @@ -33996,7 +34173,6 @@ "Number of tools on MISSISSIPPI": 0, "Number of tools on Oqtans": 0, "Number of tools on Palfinder": 0, - "Number of tools on PepSimili": 0, "Number of tools on PhagePromotor": 0, "Number of tools on UseGalaxy.be": 1, "Number of tools on UseGalaxy.cz": 1, @@ -34022,30 +34198,6 @@ "Suite runs (last 5 years) on main servers": 1109, "Suite users on main servers": 127, "Suite users (last 5 years) on main servers": 127, - "Related Workflows": [ - "https://usegalaxy.eu/published/workflow?id=31bc2a44fb89aa89", - "https://usegalaxy.eu/published/workflow?id=327beb1edda305ff", - "https://usegalaxy.eu/published/workflow?id=3d604dad4f1f5b3d", - "https://usegalaxy.eu/published/workflow?id=4077e77b6af919c4", - "https://usegalaxy.eu/published/workflow?id=6550f72070b24082", - "https://usegalaxy.eu/published/workflow?id=8976041ef89e4548", - "https://usegalaxy.org.au/published/workflow?id=dd9272826e6dd98d", - "https://usegalaxy.org.au/published/workflow?id=e263fcb6c98e231b", - "https://usegalaxy.org.au/published/workflow?id=ec7efff3d3249177", - "https://usegalaxy.org/published/workflow?id=4605309321799e9b", - "https://usegalaxy.org/published/workflow?id=80a7124c40438cc9", - "https://usegalaxy.org/published/workflow?id=f4111a169255535c", - "https://workflowhub.eu/workflows/1096?version=2", - "https://workflowhub.eu/workflows/1255?version=3", - "https://workflowhub.eu/workflows/1500?version=1", - "https://workflowhub.eu/workflows/1746?version=1", - "https://workflowhub.eu/workflows/2029?version=1" - ], - "Related Tutorials": [ - "genome-annotation/braker3", - "genome-annotation/comparison-braker-helixer-annotation", - "genome-annotation/helixer" - ], "To keep": true, "Deprecated": false }, @@ -34095,17 +34247,22 @@ ], "Suite owner": "iuc", "Suite source": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/orfipy", - "Suite parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/orfipy", + "Suite parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy", "bio.tool ID": "orfipy", "bio.tool name": "orfipy", "bio.tool description": "A fast and flexible tool for extracting ORFs.orfipy is a tool written in python/cython to extract ORFs in extremely an fast and flexible manner. Other popular ORF searching tools are OrfM and getorf. Compared to OrfM and getorf, orfipy provides the most options to fine tune ORF searches. orfipy uses multiple CPU cores and is particularly faster for data containing multiple smaller fasta sequences such as de-novo transcriptome assemblies. Please read the preprint here.", "biii ID": null, + "Related Workflows": [ + "https://usegalaxy.eu/published/workflow?id=30dc526dcfa500df" + ], + "Related Tutorials": [ + "genome-annotation/gene-centric" + ], "Number of tools on UseGalaxy.org (Main)": 1, "Number of tools on UseGalaxy.org.au": 0, "Number of tools on UseGalaxy.eu": 1, "Number of tools on UseGalaxy.fr": 0, "Number of tools on APOSTL": 0, - "Number of tools on MBAC Metabiome Portal": 0, "Number of tools on ChemFlow": 0, "Number of tools on CIRM-CFBP": 0, "Number of tools on Coloc-stats": 0, @@ -34122,7 +34279,6 @@ "Number of tools on MISSISSIPPI": 0, "Number of tools on Oqtans": 0, "Number of tools on Palfinder": 0, - "Number of tools on PepSimili": 0, "Number of tools on PhagePromotor": 0, "Number of tools on UseGalaxy.be": 0, "Number of tools on UseGalaxy.cz": 1, @@ -34148,12 +34304,6 @@ "Suite runs (last 5 years) on main servers": 4285, "Suite users on main servers": 515, "Suite users (last 5 years) on main servers": 515, - "Related Workflows": [ - "https://usegalaxy.eu/published/workflow?id=30dc526dcfa500df" - ], - "Related Tutorials": [ - "genome-annotation/gene-centric" - ], "To keep": true, "Deprecated": false }, @@ -34172,7 +34322,7 @@ "Homepage": "https://github.com/davidemms/OrthoFinder", "Suite version": "2.5.5", "Suite conda package": "orthofinder", - "Latest suite conda package version": "3.1.4", + "Latest suite conda package version": "3.1.5", "Suite version status": "To update", "ToolShed categories": [ "Phylogenetics", @@ -34203,17 +34353,23 @@ ], "Suite owner": "iuc", "Suite source": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/orthofinder", - "Suite parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/orthofinder", + "Suite parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder", "bio.tool ID": "OrthoFinder", "bio.tool name": "OrthoFinder", "bio.tool description": "OrthoFinder is a fast, accurate and comprehensive platform for comparative genomics. 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OrthoFinder also provides comprehensive statistics for comparative genomic analyses.", "biii ID": null, + "Related Workflows": [ + "https://usegalaxy.eu/published/workflow?id=d8492b49aed84d4f", + "https://usegalaxy.eu/published/workflow?id=e0c709127e9a42ae", + "https://usegalaxy.eu/published/workflow?id=e5becc6d66b2568c", + "https://usegalaxy.org/published/workflow?id=84b447be2f1c5870" + ], + "Related Tutorials": [], "Number of tools on UseGalaxy.org (Main)": 1, "Number of tools on UseGalaxy.org.au": 1, "Number of tools on UseGalaxy.eu": 1, "Number of tools on UseGalaxy.fr": 1, "Number of tools on APOSTL": 0, - "Number of tools on MBAC Metabiome Portal": 0, "Number of tools on ChemFlow": 0, "Number of tools on CIRM-CFBP": 0, "Number of tools on Coloc-stats": 0, @@ -34230,7 +34386,6 @@ "Number of tools on MISSISSIPPI": 0, "Number of tools on Oqtans": 0, "Number of tools on Palfinder": 0, - "Number of tools on PepSimili": 0, "Number of tools on PhagePromotor": 0, "Number of tools on UseGalaxy.be": 1, "Number of tools on UseGalaxy.cz": 1, @@ -34256,11 +34411,6 @@ "Suite runs (last 5 years) on main servers": 5541, "Suite users on main servers": 970, "Suite users (last 5 years) on main servers": 970, - "Related Workflows": [ - "https://usegalaxy.eu/published/workflow?id=d8492b49aed84d4f", - "https://usegalaxy.eu/published/workflow?id=e5becc6d66b2568c" - ], - "Related Tutorials": [], "To keep": true, "Deprecated": false }, @@ -34300,17 +34450,18 @@ ], "Suite owner": "iuc", "Suite source": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/pacu", - "Suite parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/pacu", + "Suite parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/pacu", "bio.tool ID": "pacu", "bio.tool name": "PACU", "bio.tool description": "PACU is a workflow for whole genome sequencing based phylogeny of Illumina and ONT R9/R10 data.PACU stands for the Prokaryotic Awesome variant Calling Utility and is named after an omnivorous fish (that eats both Illumina and ONT reads).", "biii ID": null, + "Related Workflows": [], + "Related Tutorials": [], "Number of tools on UseGalaxy.org (Main)": 0, "Number of tools on UseGalaxy.org.au": 0, "Number of tools on UseGalaxy.eu": 2, "Number of tools on UseGalaxy.fr": 0, "Number of tools on APOSTL": 0, - "Number of tools on MBAC Metabiome Portal": 0, "Number of tools on ChemFlow": 0, "Number of tools on CIRM-CFBP": 0, "Number of tools on Coloc-stats": 0, @@ -34327,7 +34478,6 @@ "Number of tools on MISSISSIPPI": 0, "Number of tools on Oqtans": 0, "Number of tools on Palfinder": 0, - "Number of tools on PepSimili": 0, "Number of tools on PhagePromotor": 0, "Number of tools on UseGalaxy.be": 0, "Number of tools on UseGalaxy.cz": 0, @@ -34353,8 +34503,6 @@ "Suite runs (last 5 years) on main servers": 223, "Suite users on main servers": 19, "Suite users (last 5 years) on main servers": 19, - "Related Workflows": [], - "Related Tutorials": [], "To keep": true, "Deprecated": false }, @@ -34370,7 +34518,7 @@ "Description": "Wraps PAL2NAL to convert protein alignments and nucleotide FASTA into codon-aware alignments.", "Suite first commit date": "2025-11-09", "Homepage": "http://www.bork.embl.de/pal2nal", - "Suite version": null, + "Suite version": "@TOOL_VERSION@+galaxy@WRAPPER_VERSION@", "Suite conda package": "pal2nal", "Latest suite conda package version": "14.1", "Suite version status": "To update", @@ -34384,17 +34532,18 @@ "EDAM reduced topics": [], "Suite owner": "iuc", "Suite source": "https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal", - "Suite parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/pal2nal", + "Suite parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/pal2nal", "bio.tool ID": null, "bio.tool name": null, "bio.tool description": null, "biii ID": null, + "Related Workflows": [], + "Related Tutorials": [], "Number of tools on UseGalaxy.org (Main)": 0, "Number of tools on UseGalaxy.org.au": 0, "Number of tools on UseGalaxy.eu": 1, "Number of tools on UseGalaxy.fr": 0, "Number of tools on APOSTL": 0, - "Number of tools on MBAC Metabiome Portal": 0, "Number of tools on ChemFlow": 0, "Number of tools on CIRM-CFBP": 0, "Number of tools on Coloc-stats": 0, @@ -34411,7 +34560,6 @@ "Number of tools on MISSISSIPPI": 0, "Number of tools on Oqtans": 0, "Number of tools on Palfinder": 0, - "Number of tools on PepSimili": 0, "Number of tools on PhagePromotor": 0, "Number of tools on UseGalaxy.be": 0, "Number of tools on UseGalaxy.cz": 0, @@ -34437,8 +34585,6 @@ "Suite runs (last 5 years) on main servers": 0, "Suite users on main servers": 0, "Suite users (last 5 years) on main servers": 0, - "Related Workflows": [], - "Related Tutorials": [], "To keep": true, "Deprecated": false }, @@ -34453,9 +34599,9 @@ "Description": "A Bacterial Pangenome Analysis Pipeline", "Suite first commit date": "2025-02-28", "Homepage": "https://github.com/gtonkinhill/panaroo/releases", - "Suite version": "1.6.0", + "Suite version": "1.7.0", "Suite conda package": "panaroo", - "Latest suite conda package version": "1.6.0", + "Latest suite conda package version": "1.7.0", "Suite version status": "Up-to-date", "ToolShed categories": [ "Sequence Analysis" @@ -34486,17 +34632,18 @@ ], "Suite owner": "galaxy-australia", "Suite source": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/panaroo", - "Suite parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/panaroo", + "Suite parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/panaroo", "bio.tool ID": "panaroo", "bio.tool name": "Panaroo", "bio.tool description": "Producing Polished Prokaryotic Pangenomes with the Panaroo Pipeline.", "biii ID": null, + "Related Workflows": [], + "Related Tutorials": [], "Number of tools on UseGalaxy.org (Main)": 0, "Number of tools on UseGalaxy.org.au": 1, "Number of tools on UseGalaxy.eu": 1, "Number of tools on UseGalaxy.fr": 0, "Number of tools on APOSTL": 0, - "Number of tools on MBAC Metabiome Portal": 0, "Number of tools on ChemFlow": 0, "Number of tools on CIRM-CFBP": 0, "Number of tools on Coloc-stats": 0, @@ -34513,7 +34660,6 @@ "Number of tools on MISSISSIPPI": 0, "Number of tools on Oqtans": 0, "Number of tools on Palfinder": 0, - "Number of tools on PepSimili": 0, "Number of tools on PhagePromotor": 0, "Number of tools on UseGalaxy.be": 0, "Number of tools on UseGalaxy.cz": 0, @@ -34539,8 +34685,6 @@ "Suite runs (last 5 years) on main servers": 609, "Suite users on main servers": 106, "Suite users (last 5 years) on main servers": 106, - "Related Workflows": [], - "Related Tutorials": [], "To keep": true, "Deprecated": false }, @@ -34573,17 +34717,18 @@ "EDAM reduced topics": [], "Suite owner": "iuc", "Suite source": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta", - "Suite parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta", + "Suite parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/panta", "bio.tool ID": null, "bio.tool name": null, "bio.tool description": null, "biii ID": null, + "Related Workflows": [], + "Related Tutorials": [], "Number of tools on UseGalaxy.org (Main)": 0, "Number of tools on UseGalaxy.org.au": 0, "Number of tools on UseGalaxy.eu": 1, "Number of tools on UseGalaxy.fr": 0, "Number of tools on APOSTL": 0, - "Number of tools on MBAC Metabiome Portal": 0, "Number of tools on ChemFlow": 0, "Number of tools on CIRM-CFBP": 0, "Number of tools on Coloc-stats": 0, @@ -34600,7 +34745,6 @@ "Number of tools on MISSISSIPPI": 0, "Number of tools on Oqtans": 0, "Number of tools on Palfinder": 0, - "Number of tools on PepSimili": 0, "Number of tools on PhagePromotor": 0, "Number of tools on UseGalaxy.be": 0, "Number of tools on UseGalaxy.cz": 0, @@ -34626,8 +34770,6 @@ "Suite runs (last 5 years) on main servers": 0, "Suite users on main servers": 0, "Suite users (last 5 years) on main servers": 0, - "Related Workflows": [], - "Related Tutorials": [], "To keep": true, "Deprecated": false }, @@ -34679,17 +34821,21 @@ ], "Suite owner": "iuc", "Suite source": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/pharokka", - "Suite parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/pharokka", + "Suite parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/pharokka", "bio.tool ID": "pharokka", "bio.tool name": "Pharokka", "bio.tool description": "Pharokka is a rapid standardised annotation tool for bacteriophage genomes and metagenomes.", "biii ID": null, + "Related Workflows": [ + "https://usegalaxy.eu/published/workflow?id=46ef864fe9468894", + "https://usegalaxy.eu/published/workflow?id=62392daea25a3980" + ], + "Related Tutorials": [], "Number of tools on UseGalaxy.org (Main)": 0, "Number of tools on UseGalaxy.org.au": 1, "Number of tools on UseGalaxy.eu": 1, "Number of tools on UseGalaxy.fr": 1, "Number of tools on APOSTL": 0, - "Number of tools on MBAC Metabiome Portal": 0, "Number of tools on ChemFlow": 0, "Number of tools on CIRM-CFBP": 0, "Number of tools on Coloc-stats": 0, @@ -34706,7 +34852,6 @@ "Number of tools on MISSISSIPPI": 0, "Number of tools on Oqtans": 0, "Number of tools on Palfinder": 0, - "Number of tools on PepSimili": 1, "Number of tools on PhagePromotor": 0, "Number of tools on UseGalaxy.be": 0, "Number of tools on UseGalaxy.cz": 1, @@ -34732,11 +34877,6 @@ "Suite runs (last 5 years) on main servers": 18156, "Suite users on main servers": 884, "Suite users (last 5 years) on main servers": 884, - "Related Workflows": [ - "https://usegalaxy.eu/published/workflow?id=46ef864fe9468894", - "https://usegalaxy.eu/published/workflow?id=62392daea25a3980" - ], - "Related Tutorials": [], "To keep": true, "Deprecated": false }, @@ -34788,17 +34928,25 @@ ], "Suite owner": "iuc", "Suite source": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/phyloseq", - "Suite parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/phyloseq", + "Suite parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq", "bio.tool ID": "phyloseq", "bio.tool name": "phyloseq", "bio.tool description": "Provides a set of classes and tools to facilitate the import, storage, analysis, and graphical display of microbiome census data.", "biii ID": null, + "Related Workflows": [ + "https://usegalaxy.eu/published/workflow?id=466bdd8ba7b67264", + "https://usegalaxy.eu/published/workflow?id=e3918808605cf8cd", + "https://usegalaxy.org/published/workflow?id=4faff660f6defa10", + "https://workflowhub.eu/workflows/1395?version=2" + ], + "Related Tutorials": [ + "microbiome/dada-16S" + ], "Number of tools on UseGalaxy.org (Main)": 4, "Number of tools on UseGalaxy.org.au": 1, "Number of tools on UseGalaxy.eu": 7, "Number of tools on UseGalaxy.fr": 6, "Number of tools on APOSTL": 0, - "Number of tools on MBAC Metabiome Portal": 0, "Number of tools on ChemFlow": 0, "Number of tools on CIRM-CFBP": 0, "Number of tools on Coloc-stats": 0, @@ -34815,7 +34963,6 @@ "Number of tools on MISSISSIPPI": 0, "Number of tools on Oqtans": 0, "Number of tools on Palfinder": 0, - "Number of tools on PepSimili": 0, "Number of tools on PhagePromotor": 0, "Number of tools on UseGalaxy.be": 1, "Number of tools on UseGalaxy.cz": 3, @@ -34841,15 +34988,6 @@ "Suite runs (last 5 years) on main servers": 4536, "Suite users on main servers": 456, "Suite users (last 5 years) on main servers": 456, - "Related Workflows": [ - "https://usegalaxy.eu/published/workflow?id=466bdd8ba7b67264", - "https://usegalaxy.eu/published/workflow?id=e3918808605cf8cd", - "https://usegalaxy.org/published/workflow?id=4faff660f6defa10", - "https://workflowhub.eu/workflows/1395?version=2" - ], - "Related Tutorials": [ - "microbiome/dada-16S" - ], "To keep": true, "Deprecated": false }, @@ -34865,10 +35003,10 @@ "Description": "PhyML is a phylogeny software based on the maximum-likelihood principle.", "Suite first commit date": "2019-05-27", "Homepage": "http://www.atgc-montpellier.fr/phyml/", - 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"Number of tools on MBAC Metabiome Portal": 0, "Number of tools on ChemFlow": 0, "Number of tools on CIRM-CFBP": 0, "Number of tools on Coloc-stats": 0, @@ -34915,7 +35057,6 @@ "Number of tools on MISSISSIPPI": 0, "Number of tools on Oqtans": 0, "Number of tools on Palfinder": 0, - "Number of tools on PepSimili": 0, "Number of tools on PhagePromotor": 0, "Number of tools on UseGalaxy.be": 1, "Number of tools on UseGalaxy.cz": 1, @@ -34941,11 +35082,6 @@ "Suite runs (last 5 years) on main servers": 4261, "Suite users on main servers": 654, "Suite users (last 5 years) on main servers": 580, - "Related Workflows": [ - "https://usegalaxy.fr/published/workflow?id=63b49f322ec366b5", - "https://usegalaxy.fr/published/workflow?id=894143d81af8dff0" - ], - "Related Tutorials": [], "To keep": true, "Deprecated": false }, @@ -34999,17 +35135,18 @@ ], "Suite owner": "iuc", "Suite source": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/picrust", - "Suite parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/picrust", + "Suite parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust", "bio.tool ID": "picrust", "bio.tool name": "PICRUSt", "bio.tool description": "PICRUSt (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) is a bioinformatics software package designed to predict metagenome functional content from marker gene (e.g., 16S rRNA) surveys and full genomes.", "biii ID": null, + "Related Workflows": [], + "Related Tutorials": [], "Number of tools on UseGalaxy.org (Main)": 0, "Number of tools on UseGalaxy.org.au": 6, "Number of tools on UseGalaxy.eu": 6, "Number of tools on UseGalaxy.fr": 6, "Number of tools on APOSTL": 0, - "Number of tools on MBAC Metabiome Portal": 0, "Number of tools on ChemFlow": 0, "Number of tools on CIRM-CFBP": 0, "Number of tools on Coloc-stats": 0, @@ -35026,7 +35163,6 @@ "Number of tools on MISSISSIPPI": 0, "Number of tools on Oqtans": 0, "Number of tools on Palfinder": 0, - "Number of tools on PepSimili": 0, "Number of tools on PhagePromotor": 0, "Number of tools on UseGalaxy.be": 0, "Number of tools on UseGalaxy.cz": 5, @@ -35052,8 +35188,6 @@ "Suite runs (last 5 years) on main servers": 3352, "Suite users on main servers": 124, "Suite users (last 5 years) on main servers": 102, - "Related Workflows": [], - "Related Tutorials": [], "To keep": true, "Deprecated": false }, @@ -35107,17 +35241,20 @@ ], "Suite owner": "iuc", "Suite source": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/picrust2", - "Suite parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/picrust2", + "Suite parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust2", "bio.tool ID": "picrust2", "bio.tool name": "PICRUSt2", "bio.tool description": "PICRUSt2 (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) is a software for predicting functional abundances based only on marker gene sequences.", "biii ID": null, + "Related Workflows": [ + "https://usegalaxy.eu/published/workflow?id=be9ff4159593cc34" + ], + "Related Tutorials": [], "Number of tools on UseGalaxy.org (Main)": 0, "Number of tools on UseGalaxy.org.au": 7, "Number of tools on UseGalaxy.eu": 7, "Number of tools on UseGalaxy.fr": 0, "Number of tools on APOSTL": 0, - "Number of tools on MBAC Metabiome Portal": 0, "Number of tools on ChemFlow": 0, "Number of tools on CIRM-CFBP": 0, "Number of tools on Coloc-stats": 0, @@ -35134,7 +35271,6 @@ "Number of tools on MISSISSIPPI": 0, "Number of tools on Oqtans": 0, "Number of tools on Palfinder": 0, - "Number of tools on PepSimili": 0, "Number of tools on PhagePromotor": 0, "Number of tools on UseGalaxy.be": 0, "Number of tools on UseGalaxy.cz": 7, @@ -35160,10 +35296,6 @@ "Suite runs (last 5 years) on main servers": 9321, "Suite users on main servers": 392, "Suite users (last 5 years) on main servers": 392, - "Related Workflows": [ - "https://usegalaxy.eu/published/workflow?id=be9ff4159593cc34" - ], - "Related Tutorials": [], "To keep": true, "Deprecated": false }, @@ -35198,17 +35330,18 @@ "EDAM reduced topics": [], "Suite owner": "iuc", "Suite source": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/pimento", - "Suite parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/pimento", + "Suite parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/pimento", "bio.tool ID": null, "bio.tool name": null, "bio.tool description": null, "biii ID": null, + "Related Workflows": [], + "Related Tutorials": [], "Number of tools on UseGalaxy.org (Main)": 0, "Number of tools on UseGalaxy.org.au": 0, "Number of tools on UseGalaxy.eu": 6, "Number of tools on UseGalaxy.fr": 0, "Number of tools on APOSTL": 0, - "Number of tools on MBAC Metabiome Portal": 0, "Number of tools on ChemFlow": 0, "Number of tools on CIRM-CFBP": 0, "Number of tools on Coloc-stats": 0, @@ -35225,7 +35358,6 @@ "Number of tools on MISSISSIPPI": 0, "Number of tools on Oqtans": 0, "Number of tools on Palfinder": 0, - "Number of tools on PepSimili": 0, "Number of tools on PhagePromotor": 0, "Number of tools on UseGalaxy.be": 0, "Number of tools on UseGalaxy.cz": 0, @@ -35251,8 +35383,6 @@ "Suite runs (last 5 years) on main servers": 2, "Suite users on main servers": 1, "Suite users (last 5 years) on main servers": 1, - "Related Workflows": [], - "Related Tutorials": [], "To keep": true, "Deprecated": false }, @@ -35287,17 +35417,18 @@ "EDAM reduced topics": [], "Suite owner": "iuc", "Suite source": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/pirate", - "Suite parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/pirate", + "Suite parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/pirate", "bio.tool ID": null, "bio.tool name": null, "bio.tool description": null, "biii ID": null, + "Related Workflows": [], + "Related Tutorials": [], "Number of tools on UseGalaxy.org (Main)": 0, "Number of tools on UseGalaxy.org.au": 0, "Number of tools on UseGalaxy.eu": 1, "Number of tools on UseGalaxy.fr": 0, "Number of tools on APOSTL": 0, - "Number of tools on MBAC Metabiome Portal": 0, "Number of tools on ChemFlow": 0, "Number of tools on CIRM-CFBP": 0, "Number of tools on Coloc-stats": 0, @@ -35314,7 +35445,6 @@ "Number of tools on MISSISSIPPI": 0, "Number of tools on Oqtans": 0, "Number of tools on Palfinder": 0, - "Number of tools on PepSimili": 0, "Number of tools on PhagePromotor": 0, "Number of tools on UseGalaxy.be": 0, "Number of tools on UseGalaxy.cz": 0, @@ -35340,8 +35470,6 @@ "Suite runs (last 5 years) on main servers": 0, "Suite users on main servers": 0, "Suite users (last 5 years) on main servers": 0, - "Related Workflows": [], - "Related Tutorials": [], "To keep": true, "Deprecated": false }, @@ -35356,10 +35484,10 @@ "Description": "PlasClass is a tool to classify sequences of plasmid or chromosomal origin", "Suite first commit date": "2025-07-31", "Homepage": "https://github.com/Shamir-Lab/PlasClass", - "Suite version": "0.1.1", + "Suite version": "@TOOL_VERSION@+galaxy@VERSION_SUFFIX@", "Suite conda package": "plasclass", "Latest suite conda package version": "0.1.1", - "Suite version status": "Up-to-date", + "Suite version status": "To update", "ToolShed categories": [ "Sequence Analysis" ], @@ -35387,17 +35515,20 @@ ], "Suite owner": "iuc", "Suite source": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/plasclass", - "Suite parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/plasclass", + "Suite parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/plasclass", "bio.tool ID": "PlasClass", "bio.tool name": "PlasClass", "bio.tool description": "PlasClass is a tool for easy classification of sequences as either plasmid or chromosomal. For example, it can be used to classify the contigs in a (metagenomic) assembly.", "biii ID": null, + "Related Workflows": [ + "https://usegalaxy.eu/published/workflow?id=d0339e4a794f4922" + ], + "Related Tutorials": [], "Number of tools on UseGalaxy.org (Main)": 0, "Number of tools on UseGalaxy.org.au": 0, "Number of tools on UseGalaxy.eu": 1, "Number of tools on UseGalaxy.fr": 0, "Number of tools on APOSTL": 0, - "Number of tools on MBAC Metabiome Portal": 0, "Number of tools on ChemFlow": 0, "Number of tools on CIRM-CFBP": 0, "Number of tools on Coloc-stats": 0, @@ -35414,7 +35545,6 @@ "Number of tools on MISSISSIPPI": 0, "Number of tools on Oqtans": 0, "Number of tools on Palfinder": 0, - "Number of tools on PepSimili": 0, "Number of tools on PhagePromotor": 0, "Number of tools on UseGalaxy.be": 0, "Number of tools on UseGalaxy.cz": 0, @@ -35440,10 +35570,6 @@ "Suite runs (last 5 years) on main servers": 0, "Suite users on main servers": 0, "Suite users (last 5 years) on main servers": 0, - 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"Number of tools on MBAC Metabiome Portal": 0, "Number of tools on ChemFlow": 0, "Number of tools on CIRM-CFBP": 0, "Number of tools on Coloc-stats": 0, @@ -35513,7 +35657,6 @@ "Number of tools on MISSISSIPPI": 0, "Number of tools on Oqtans": 0, "Number of tools on Palfinder": 0, - "Number of tools on PepSimili": 0, "Number of tools on PhagePromotor": 0, "Number of tools on UseGalaxy.be": 1, "Number of tools on UseGalaxy.cz": 1, @@ -35539,25 +35682,6 @@ "Suite runs (last 5 years) on main servers": 66494, "Suite users on main servers": 1888, "Suite users (last 5 years) on main servers": 1720, - "Related Workflows": [ - "https://usegalaxy.eu/published/workflow?id=152223c8aed27357", - "https://usegalaxy.eu/published/workflow?id=249c115413f17f28", - "https://usegalaxy.eu/published/workflow?id=3081569659a45b9e", - "https://usegalaxy.eu/published/workflow?id=32d2f5340098bcbd", - "https://usegalaxy.eu/published/workflow?id=39837ca09374598b", - "https://usegalaxy.eu/published/workflow?id=44e53ea319e07daa", - 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"Number of tools on MBAC Metabiome Portal": 0, "Number of tools on ChemFlow": 0, "Number of tools on CIRM-CFBP": 0, "Number of tools on Coloc-stats": 0, @@ -35633,7 +35792,6 @@ "Number of tools on MISSISSIPPI": 0, "Number of tools on Oqtans": 0, "Number of tools on Palfinder": 0, - "Number of tools on PepSimili": 0, "Number of tools on PhagePromotor": 0, "Number of tools on UseGalaxy.be": 1, "Number of tools on UseGalaxy.cz": 1, @@ -35659,42 +35817,6 @@ "Suite runs (last 5 years) on main servers": 61941, "Suite users on main servers": 1897, "Suite users (last 5 years) on main servers": 1897, - "Related Workflows": [ - "https://usegalaxy.eu/published/workflow?id=1306ed083d91a852", - "https://usegalaxy.eu/published/workflow?id=2a1dc58e51d5f01a", - "https://usegalaxy.eu/published/workflow?id=2c1a6da84d891cf2", - "https://usegalaxy.eu/published/workflow?id=36ea584e0f60893e", - "https://usegalaxy.eu/published/workflow?id=3f5fe28793ed0c6c", - "https://usegalaxy.eu/published/workflow?id=4a218fb93d78ba67", - 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Unlike other tools in this category, Polypolish uses SAM files where each read has been aligned to all possible locations (not just a single best location). 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"quickmerge", "Latest suite conda package version": "0.3", - "Suite version status": "Up-to-date", + "Suite version status": "To update", "ToolShed categories": [ "Assembly" ], @@ -37514,17 +37823,18 @@ ], "Suite owner": "iuc", "Suite source": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/quickmerge", - "Suite parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/quickmerge", + "Suite parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge", "bio.tool ID": "quickmerge", "bio.tool name": "quickmerge", "bio.tool description": "Quickmerge is a program that uses complementary information from genomes assembled with long reads in order to improve contiguity, and works with assemblies derived from both Pacific Biosciences or Oxford Nanopore. Quickmerge will even work with hybrid assemblies made by combining long reads and Illumina short reads.", "biii ID": null, + "Related Workflows": [], + "Related Tutorials": [], "Number of tools on UseGalaxy.org (Main)": 0, "Number of tools on UseGalaxy.org.au": 0, "Number of tools on UseGalaxy.eu": 1, "Number of tools on UseGalaxy.fr": 0, "Number of tools on APOSTL": 0, - "Number of tools on MBAC Metabiome Portal": 0, "Number of tools on ChemFlow": 0, "Number of tools on CIRM-CFBP": 0, "Number of tools on Coloc-stats": 0, @@ -37541,7 +37851,6 @@ "Number of tools on MISSISSIPPI": 0, "Number of tools on Oqtans": 0, "Number of tools on Palfinder": 0, - "Number of tools on PepSimili": 0, "Number of tools on PhagePromotor": 0, "Number of tools on UseGalaxy.be": 0, "Number of tools on UseGalaxy.cz": 0, @@ -37567,8 +37876,6 @@ "Suite runs (last 5 years) on main servers": 0, "Suite users on main servers": 0, "Suite users (last 5 years) on main servers": 0, - "Related Workflows": [], - "Related Tutorials": [], "To keep": true, "Deprecated": false }, @@ -37583,10 +37890,10 @@ "Description": "neighbour-joining phylogenetic inference", "Suite first commit date": "2024-11-21", "Homepage": "https://github.com/khowe/quicktree", - 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"Number of tools on MBAC Metabiome Portal": 0, "Number of tools on ChemFlow": 0, "Number of tools on CIRM-CFBP": 0, "Number of tools on Coloc-stats": 0, @@ -37631,7 +37943,6 @@ "Number of tools on MISSISSIPPI": 0, "Number of tools on Oqtans": 0, "Number of tools on Palfinder": 0, - "Number of tools on PepSimili": 0, "Number of tools on PhagePromotor": 0, "Number of tools on UseGalaxy.be": 1, "Number of tools on UseGalaxy.cz": 0, @@ -37657,12 +37968,6 @@ "Suite runs (last 5 years) on main servers": 466, "Suite users on main servers": 69, "Suite users (last 5 years) on main servers": 69, - "Related Workflows": [ - "https://workflowhub.eu/workflows/1650?version=1" - ], - "Related Tutorials": [ - "sequence-analysis/tapscan-streptophyte-algae" - ], "To keep": true, "Deprecated": false }, @@ -37677,10 +37982,10 @@ "Description": "Randomly subsample sequencing reads to a specified coverage", "Suite first commit date": "2024-02-16", "Homepage": "https://github.com/mbhall88/rasusa", - "Suite version": "4.1.0", + "Suite version": "@TOOL_VERSION@+galaxy@VERSION_SUFFIX@", "Suite conda package": "rasusa", "Latest suite conda package version": "4.1.0", - "Suite version status": "Up-to-date", + "Suite version status": "To update", "ToolShed categories": [ "Sequence Analysis" ], @@ -37706,17 +38011,18 @@ ], "Suite owner": "iuc", "Suite source": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/rasusa", - "Suite parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/rasusa", + "Suite parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/rasusa", "bio.tool ID": "rasusa", "bio.tool name": "rasusa", "bio.tool description": "Rasusa: Randomly subsample sequencing reads to aspecified coverageProduces an unbiased subsample of your reads", "biii ID": null, + "Related Workflows": [], + "Related Tutorials": [], "Number of tools on UseGalaxy.org (Main)": 0, "Number of tools on UseGalaxy.org.au": 0, "Number of tools on UseGalaxy.eu": 1, "Number of tools on UseGalaxy.fr": 1, "Number of tools on APOSTL": 0, - "Number of tools on MBAC Metabiome Portal": 0, "Number of tools on ChemFlow": 0, "Number of tools on CIRM-CFBP": 0, "Number of tools on Coloc-stats": 0, @@ -37733,7 +38039,6 @@ "Number of tools on MISSISSIPPI": 0, "Number of tools on Oqtans": 0, "Number of tools on Palfinder": 0, - 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A Maximum Likelihood based phylogenetic tree inference", "Suite first commit date": "2025-12-20", "Homepage": "http://www.exelixis-lab.org/web/software/raxml-ng/", - "Suite version": "2.0.1", + "Suite version": "2.0.2", "Suite conda package": "raxml-ng", - "Latest suite conda package version": "2.0.1", + "Latest suite conda package version": "2.0.2", "Suite version status": "Up-to-date", "ToolShed categories": [ "Phylogenetics" @@ -37904,17 +38205,18 @@ ], "Suite owner": "iuc", "Suite source": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxmlng", - "Suite parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxmlng", + "Suite parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxmlng", "bio.tool ID": "RAxML-NG", "bio.tool name": "RAxML-NG", "bio.tool description": "Phylogenetic tree inference tool which uses maximum-likelihood (ML) optimality criterion.", "biii ID": null, + "Related Workflows": [], + "Related Tutorials": [], "Number of tools on UseGalaxy.org (Main)": 0, "Number of tools on UseGalaxy.org.au": 0, "Number of tools on UseGalaxy.eu": 1, "Number of tools on UseGalaxy.fr": 0, "Number of tools on APOSTL": 0, - "Number of tools on MBAC Metabiome Portal": 0, "Number of tools on ChemFlow": 0, "Number of tools on CIRM-CFBP": 0, "Number of tools on Coloc-stats": 0, @@ -37931,7 +38233,6 @@ "Number of tools on MISSISSIPPI": 0, "Number of tools on Oqtans": 0, "Number of tools on Palfinder": 0, - "Number of tools on PepSimili": 0, "Number of tools on PhagePromotor": 0, "Number of tools on UseGalaxy.be": 0, "Number of tools on UseGalaxy.cz": 0, @@ -37957,8 +38258,6 @@ "Suite runs (last 5 years) on main servers": 0, "Suite users on main servers": 0, "Suite users (last 5 years) on main servers": 0, - "Related Workflows": [], - "Related Tutorials": [], "To keep": true, "Deprecated": false }, @@ -37973,10 +38272,10 @@ "Description": "Infer a species tree from sequencing reads.", "Suite first commit date": "2025-11-23", "Homepage": "https://github.com/DessimozLab/read2tree", - "Suite version": "2.0.1", + "Suite version": "@TOOL_VERSION@", "Suite conda package": "read2tree", "Latest suite conda package version": "2.0.1", - "Suite version status": "Up-to-date", + "Suite version status": "To update", "ToolShed categories": [ "Phylogenetics" ], @@ -37990,17 +38289,18 @@ ], "Suite owner": "iuc", "Suite source": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/read2tree", - "Suite parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/read2tree", + "Suite parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/read2tree", "bio.tool ID": "read2tree", "bio.tool name": "read2tree", "bio.tool description": "read2tree is a software tool for generating alignment matrices and performing tree inference directly from sequencing reads. 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In particular, it avoids for read filtering, assembly, gene prediction, gene annotation, all-vs-all comparison, orthology prediction, alignment, and concatenation.", "biii ID": null, + "Related Workflows": [], + "Related Tutorials": [], "Number of tools on UseGalaxy.org (Main)": 0, "Number of tools on UseGalaxy.org.au": 0, "Number of tools on UseGalaxy.eu": 1, "Number of tools on UseGalaxy.fr": 0, "Number of tools on APOSTL": 0, - "Number of tools on MBAC Metabiome Portal": 0, "Number of tools on ChemFlow": 0, "Number of tools on CIRM-CFBP": 0, "Number of tools on Coloc-stats": 0, @@ -38017,7 +38317,6 @@ "Number of tools on MISSISSIPPI": 0, "Number of tools on Oqtans": 0, "Number of tools on Palfinder": 0, - "Number of tools on PepSimili": 0, "Number of tools on PhagePromotor": 0, "Number of tools on UseGalaxy.be": 0, "Number of tools on UseGalaxy.cz": 0, @@ -38043,8 +38342,6 @@ "Suite runs (last 5 years) on main servers": 0, "Suite users on main servers": 0, "Suite users (last 5 years) on main servers": 0, - "Related Workflows": [], - "Related Tutorials": [], "To keep": true, "Deprecated": false }, @@ -38057,7 +38354,7 @@ "Description": "Rapid decontamination of SARS-CoV-2 sequencing reads", "Suite first commit date": "2022-01-28", "Homepage": "https://github.com/GenomePathogenAnalysisService/read-it-and-keep", - "Suite version": "0.2.2", + "Suite version": "@TOOL_VERSION@", "Suite conda package": "read-it-and-keep", "Latest suite conda package version": "0.3.0", "Suite version status": "To update", @@ -38082,17 +38379,27 @@ ], "Suite owner": "iuc", "Suite source": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/read_it_and_keep", - "Suite parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/read_it_and_keep", + "Suite parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/read_it_and_keep", "bio.tool ID": "read_it_and_keep", "bio.tool name": "read_it_and_keep", "bio.tool description": "Read-it-and-keep is a bioinformatics tool designed to filter and extract sequencing reads according to user-defined criteria, such as the presence of specific motifs or coverage of regions of interest. This type of filtering can be particularly useful for targeted analyses, where only relevant sequences are retained for further study, optimising computing and storage resources.", "biii ID": null, + "Related Workflows": [ + "https://usegalaxy.eu/published/workflow?id=3fb550d7c2bc390a", + "https://usegalaxy.eu/published/workflow?id=4a764275d4bf9f31", + "https://usegalaxy.eu/published/workflow?id=629e57958afed44c", + "https://usegalaxy.eu/published/workflow?id=7c986f4d14c6a539", + "https://usegalaxy.eu/published/workflow?id=d88145e7475e0b7b", + "https://usegalaxy.eu/published/workflow?id=d967194ca51ff11e", + "https://workflowhub.eu/workflows/519?version=1", + "https://workflowhub.eu/workflows/521?version=1" + ], + "Related Tutorials": [], "Number of tools on UseGalaxy.org (Main)": 1, "Number of tools on UseGalaxy.org.au": 0, "Number of tools on UseGalaxy.eu": 1, "Number of tools on UseGalaxy.fr": 0, "Number of tools on APOSTL": 0, - "Number of tools on MBAC Metabiome Portal": 0, "Number of tools on ChemFlow": 0, "Number of tools on CIRM-CFBP": 0, "Number of tools on Coloc-stats": 0, @@ -38109,7 +38416,6 @@ "Number of tools on MISSISSIPPI": 0, "Number of tools on Oqtans": 0, "Number of tools on Palfinder": 0, - 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"Number of tools on MBAC Metabiome Portal": 0, "Number of tools on ChemFlow": 0, "Number of tools on CIRM-CFBP": 0, "Number of tools on Coloc-stats": 0, @@ -38219,7 +38550,6 @@ "Number of tools on MISSISSIPPI": 0, "Number of tools on Oqtans": 0, "Number of tools on Palfinder": 0, - "Number of tools on PepSimili": 0, "Number of tools on PhagePromotor": 0, "Number of tools on UseGalaxy.be": 1, "Number of tools on UseGalaxy.cz": 1, @@ -38245,43 +38575,6 @@ "Suite runs (last 5 years) on main servers": 5641, "Suite users on main servers": 530, "Suite users (last 5 years) on main servers": 530, - "Related Workflows": [ - "https://usegalaxy.eu/published/workflow?id=0a82eb8b44d9d502", - "https://usegalaxy.eu/published/workflow?id=0abd32dbc5207b88", - "https://usegalaxy.eu/published/workflow?id=0c47571d20535426", - "https://usegalaxy.eu/published/workflow?id=2fa2f67603772413", - "https://usegalaxy.eu/published/workflow?id=47e14222073e7192", - "https://usegalaxy.eu/published/workflow?id=884a4415b669690c", - 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It reports a list of genes sorted by strength of association per trait.", "biii ID": null, + "Related Workflows": [], + "Related Tutorials": [], "Number of tools on UseGalaxy.org (Main)": 0, "Number of tools on UseGalaxy.org.au": 0, "Number of tools on UseGalaxy.eu": 1, "Number of tools on UseGalaxy.fr": 0, "Number of tools on APOSTL": 0, - "Number of tools on MBAC Metabiome Portal": 0, "Number of tools on ChemFlow": 0, "Number of tools on CIRM-CFBP": 0, "Number of tools on Coloc-stats": 0, @@ -38729,7 +39107,6 @@ "Number of tools on MISSISSIPPI": 0, "Number of tools on Oqtans": 0, "Number of tools on Palfinder": 0, - "Number of tools on PepSimili": 0, "Number of tools on PhagePromotor": 0, "Number of tools on UseGalaxy.be": 0, "Number of tools on UseGalaxy.cz": 1, @@ -38755,8 +39132,6 @@ "Suite runs (last 5 years) on main servers": 1366, "Suite users on main servers": 113, "Suite users (last 5 years) on main servers": 113, - "Related Workflows": [], - "Related Tutorials": [], "To keep": true, "Deprecated": false }, @@ -38779,7 +39154,7 @@ "Homepage": "https://semibin.readthedocs.io/en/latest/", "Suite version": "2.1.0", "Suite conda package": "semibin", - "Latest suite conda package version": "2.2.1", + "Latest suite conda package version": "2.3.0", "Suite version status": "To update", "ToolShed categories": [ "Metagenomics" @@ -38806,17 +39181,31 @@ ], "Suite owner": "iuc", "Suite source": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin", - "Suite parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin", + "Suite parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin", "bio.tool ID": "semibin", "bio.tool name": "SemiBin", "bio.tool description": "Command tool for metagenomic binning with semi-supervised deep learning using information from reference genomes.", "biii ID": null, + "Related Workflows": [ + "https://usegalaxy.eu/published/workflow?id=00f15824c7a9b196", + "https://usegalaxy.eu/published/workflow?id=0563f58718be932d", + "https://usegalaxy.eu/published/workflow?id=1e5f1d9a51032e44", + "https://usegalaxy.eu/published/workflow?id=43098b8afe78b071", + "https://usegalaxy.eu/published/workflow?id=7ecd92cb382d8168", + "https://usegalaxy.eu/published/workflow?id=97312d273b6e8bd9", + "https://usegalaxy.eu/published/workflow?id=ce5c9287a67e6085", + "https://workflowhub.eu/workflows/1352?version=4", + "https://workflowhub.eu/workflows/2028?version=1", + "https://workflowhub.eu/workflows/2100?version=2" + ], + "Related Tutorials": [ + "microbiome/metagenomics-binning" + ], "Number of tools on UseGalaxy.org (Main)": 1, "Number of tools on UseGalaxy.org.au": 6, "Number of tools on UseGalaxy.eu": 6, "Number of tools on UseGalaxy.fr": 1, "Number of tools on APOSTL": 0, - "Number of tools on MBAC Metabiome Portal": 0, "Number of tools on ChemFlow": 0, "Number of tools on CIRM-CFBP": 0, "Number of tools on Coloc-stats": 0, @@ -38833,7 +39222,6 @@ "Number of tools on MISSISSIPPI": 0, "Number of tools on Oqtans": 0, "Number of tools on Palfinder": 0, - "Number of tools on PepSimili": 0, "Number of tools on PhagePromotor": 0, "Number of tools on UseGalaxy.be": 1, "Number of tools on UseGalaxy.cz": 6, @@ -38859,21 +39247,6 @@ "Suite runs (last 5 years) on main servers": 2872, "Suite users on main servers": 64, "Suite users (last 5 years) on main servers": 64, - "Related Workflows": [ - "https://usegalaxy.eu/published/workflow?id=00f15824c7a9b196", - "https://usegalaxy.eu/published/workflow?id=0563f58718be932d", - "https://usegalaxy.eu/published/workflow?id=1e5f1d9a51032e44", - "https://usegalaxy.eu/published/workflow?id=43098b8afe78b071", - "https://usegalaxy.eu/published/workflow?id=7ecd92cb382d8168", - "https://usegalaxy.eu/published/workflow?id=97312d273b6e8bd9", - "https://usegalaxy.eu/published/workflow?id=ce5c9287a67e6085", - "https://workflowhub.eu/workflows/1352?version=4", - "https://workflowhub.eu/workflows/2028?version=1", - "https://workflowhub.eu/workflows/2100?version=2" - ], - "Related Tutorials": [ - "microbiome/metagenomics-binning" - ], "To keep": true, "Deprecated": false }, @@ -38924,17 +39297,30 @@ ], "Suite owner": "iuc", "Suite source": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqkit", - "Suite parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqkit", + "Suite parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit", "bio.tool ID": "seqkit", "bio.tool name": "seqkit", "bio.tool description": "FASTA and FASTQ are basic and ubiquitous formats for storing nucleotide and protein sequences. Common manipulations of FASTA/Q file include converting, searching, filtering, deduplication, splitting, shuffling, and sampling. Existing tools only implement some of these manipulations, and not particularly efficiently, and some are only available for certain operating systems. Furthermore, the complicated installation process of required packages and running environments can render these programs less user friendly. SeqKit demonstrates competitive performance in execution time and memory usage compared to similar tools. The efficiency and usability of SeqKit enable researchers to rapidly accomplish common FASTA/Q file manipulations.", "biii ID": null, + "Related Workflows": [ + "https://usegalaxy.eu/published/workflow?id=8ee6213aec38e4cc", + "https://usegalaxy.eu/published/workflow?id=e0c709127e9a42ae", + "https://usegalaxy.org.au/published/workflow?id=7559224fc32dce3a", + "https://usegalaxy.org.au/published/workflow?id=7a0c4804e4d4c905", + "https://usegalaxy.org.au/published/workflow?id=ed3e48a73b5aaa56", + "https://workflowhub.eu/workflows/2024?version=4", + "https://workflowhub.eu/workflows/2036?version=1", + "https://workflowhub.eu/workflows/2038?version=1", + "https://workflowhub.eu/workflows/601?version=2", + "https://workflowhub.eu/workflows/602?version=2", + "https://workflowhub.eu/workflows/697?version=1" + ], + "Related Tutorials": [], "Number of tools on UseGalaxy.org (Main)": 3, "Number of tools on UseGalaxy.org.au": 6, "Number of tools on UseGalaxy.eu": 8, "Number of tools on UseGalaxy.fr": 5, "Number of tools on APOSTL": 0, - "Number of tools on MBAC Metabiome Portal": 0, "Number of tools on ChemFlow": 0, "Number of tools on CIRM-CFBP": 0, "Number of tools on Coloc-stats": 0, @@ -38951,7 +39337,6 @@ "Number of tools on MISSISSIPPI": 0, "Number of tools on Oqtans": 0, "Number of tools on Palfinder": 0, - "Number of tools on PepSimili": 0, "Number of tools on PhagePromotor": 0, "Number of tools on UseGalaxy.be": 0, "Number of tools on UseGalaxy.cz": 4, @@ -38977,18 +39362,6 @@ "Suite runs (last 5 years) on main servers": 16764, "Suite users on main servers": 585, "Suite users (last 5 years) on main servers": 585, - "Related Workflows": [ - "https://usegalaxy.org.au/published/workflow?id=7559224fc32dce3a", - "https://usegalaxy.org.au/published/workflow?id=7a0c4804e4d4c905", - "https://usegalaxy.org.au/published/workflow?id=ed3e48a73b5aaa56", - "https://workflowhub.eu/workflows/2024?version=4", - "https://workflowhub.eu/workflows/2036?version=1", - "https://workflowhub.eu/workflows/2038?version=1", - "https://workflowhub.eu/workflows/601?version=2", - "https://workflowhub.eu/workflows/602?version=2", - "https://workflowhub.eu/workflows/697?version=1" - ], - "Related Tutorials": [], "To keep": true, "Deprecated": false }, @@ -39031,17 +39404,20 @@ ], "Suite owner": "iuc", "Suite source": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqprep", - "Suite parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqprep", + "Suite parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep", "bio.tool ID": "seqprep", "bio.tool name": "SeqPrep", "bio.tool description": "Strips adapters and optionally merges overlapping paired-end (or paired-end contamination in mate-pair libraries) illumina style reads.", "biii ID": null, + "Related Workflows": [], + "Related Tutorials": [ + "microbiome/mgnify-amplicon" + ], "Number of tools on UseGalaxy.org (Main)": 0, "Number of tools on UseGalaxy.org.au": 0, "Number of tools on UseGalaxy.eu": 1, "Number of tools on UseGalaxy.fr": 0, "Number of tools on APOSTL": 0, - "Number of tools on MBAC Metabiome Portal": 0, "Number of tools on ChemFlow": 0, "Number of tools on CIRM-CFBP": 0, "Number of tools on Coloc-stats": 0, @@ -39058,7 +39434,6 @@ "Number of tools on MISSISSIPPI": 0, "Number of tools on Oqtans": 0, "Number of tools on Palfinder": 0, - "Number of tools on PepSimili": 0, "Number of tools on PhagePromotor": 0, "Number of tools on UseGalaxy.be": 0, "Number of tools on UseGalaxy.cz": 0, @@ -39084,10 +39459,6 @@ "Suite runs (last 5 years) on main servers": 3602, "Suite users on main servers": 227, "Suite users (last 5 years) on main servers": 227, - "Related Workflows": [], - "Related Tutorials": [ - "microbiome/mgnify-amplicon" - ], "To keep": true, "Deprecated": false }, @@ -39132,17 +39503,21 @@ ], "Suite owner": "iuc", "Suite source": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqsero2", - "Suite parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqsero2", + "Suite parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2", "bio.tool ID": "seqsero2", "bio.tool name": "SeqSero2", "bio.tool description": "rapid and improved Salmonella serotype determination using whole genome sequencing data | SeqSero-Salmonella Serotyping by Whole Genome Sequencing | Salmonella Serotyping by Whole Genome Sequencing | Online version: http://www.denglab.info/SeqSero2 | Salmonella serotype prediction from genome sequencing data | Citation: SeqSero, Zhang et al. 2015; SeqSero2, Zhang et al. 2019 | Salmonella serotype derterminants databases | Upon executing the command, a directory named 'SeqSero_result_Time_your_run' will be created. Your result will be stored in 'SeqSero_result.txt' in that directory. And the assembled alleles can also be found in the directory if using \"-m a\" (allele mode)", "biii ID": null, + "Related Workflows": [ + "https://usegalaxy.eu/published/workflow?id=fde21b5f5c169114", + "https://workflowhub.eu/workflows/407?version=1" + ], + "Related Tutorials": [], "Number of tools on UseGalaxy.org (Main)": 0, "Number of tools on UseGalaxy.org.au": 0, "Number of tools on UseGalaxy.eu": 1, "Number of tools on UseGalaxy.fr": 1, "Number of tools on APOSTL": 0, - "Number of tools on MBAC Metabiome Portal": 0, "Number of tools on ChemFlow": 0, "Number of tools on CIRM-CFBP": 0, "Number of tools on Coloc-stats": 0, @@ -39159,7 +39534,6 @@ "Number of tools on MISSISSIPPI": 0, "Number of tools on Oqtans": 0, "Number of tools on Palfinder": 0, - "Number of tools on PepSimili": 0, "Number of tools on PhagePromotor": 0, "Number of tools on UseGalaxy.be": 0, "Number of tools on UseGalaxy.cz": 0, @@ -39185,11 +39559,6 @@ "Suite runs (last 5 years) on main servers": 14013, "Suite users on main servers": 118, "Suite users (last 5 years) on main servers": 118, - "Related Workflows": [ - "https://usegalaxy.eu/published/workflow?id=fde21b5f5c169114", - "https://workflowhub.eu/workflows/407?version=1" - ], - "Related Tutorials": [], "To keep": true, "Deprecated": false }, @@ -39207,10 +39576,10 @@ "Description": "Faster de novo assembly pipeline based around Spades", "Suite first commit date": "2017-10-24", "Homepage": "https://github.com/tseemann/shovill", - "Suite version": "1.4.2", + "Suite version": "@TOOL_VERSION@+galaxy@VERSION_SUFFIX@", "Suite conda package": "shovill", "Latest suite conda package version": "1.4.2", - "Suite version status": "Up-to-date", + "Suite version status": "To update", "ToolShed categories": [ "Assembly" ], @@ -39232,59 +39601,11 @@ ], "Suite owner": "iuc", "Suite source": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/shovill", - "Suite parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/shovill", + "Suite parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill", "bio.tool ID": "shovill", "bio.tool name": "shovill", "bio.tool description": "Shovill is a pipeline for assembly of bacterial isolate genomes from Illumina paired-end reads. Shovill uses SPAdes at its core, but alters the steps before and after the primary assembly step to get similar results in less time. Shovill also supports other assemblers like SKESA, Velvet and Megahit, so you can take advantage of the pre- and post-processing the Shovill provides with those too.", "biii ID": null, - "Number of tools on UseGalaxy.org (Main)": 1, - "Number of tools on UseGalaxy.org.au": 1, - "Number of tools on UseGalaxy.eu": 1, - "Number of tools on UseGalaxy.fr": 1, - "Number of tools on APOSTL": 0, - "Number of tools on MBAC Metabiome Portal": 0, - "Number of tools on ChemFlow": 0, - "Number of tools on CIRM-CFBP": 0, - "Number of tools on Coloc-stats": 0, - "Number of tools on Galaxy@AuBi": 1, - "Number of tools on Galaxy@Pasteur": 1, - "Number of tools on GalaxyTrakr": 1, - "Number of tools on GASLINI": 0, - "Number of tools on HyPhy HIV NGS Tools": 0, - "Number of tools on ImmPort Galaxy": 0, - "Number of tools on InteractoMIX": 0, - "Number of tools on IPK Galaxy Blast Suite": 0, - "Number of tools on Lebanese University Galaxy": 0, - "Number of tools on Mandoiu Lab": 0, - "Number of tools on MISSISSIPPI": 0, - 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"Suite parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/smallgenomeutilities", + "Suite parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities", "bio.tool ID": "v-pipe", "bio.tool name": "V-pipe", "bio.tool description": "Bioinformatics pipeline for the analysis of next-generation sequencing data derived from intra-host viral populations.", "biii ID": null, + "Related Workflows": [], + "Related Tutorials": [], "Number of tools on UseGalaxy.org (Main)": 0, "Number of tools on UseGalaxy.org.au": 0, "Number of tools on UseGalaxy.eu": 1, "Number of tools on UseGalaxy.fr": 0, "Number of tools on APOSTL": 0, - "Number of tools on MBAC Metabiome Portal": 0, "Number of tools on ChemFlow": 0, "Number of tools on CIRM-CFBP": 0, "Number of tools on Coloc-stats": 0, @@ -39425,7 +39795,6 @@ "Number of tools on MISSISSIPPI": 0, "Number of tools on Oqtans": 0, "Number of tools on Palfinder": 0, - "Number of tools on PepSimili": 0, "Number of tools on PhagePromotor": 0, "Number of tools on UseGalaxy.be": 0, "Number of tools on UseGalaxy.cz": 1, @@ -39451,8 +39820,6 @@ "Suite runs (last 5 years) on main servers": 168, "Suite users on main servers": 15, "Suite users (last 5 years) on main servers": 15, - 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"Number of tools on MBAC Metabiome Portal": 0, "Number of tools on ChemFlow": 0, "Number of tools on CIRM-CFBP": 0, "Number of tools on Coloc-stats": 0, @@ -39521,7 +39898,6 @@ "Number of tools on MISSISSIPPI": 0, "Number of tools on Oqtans": 0, "Number of tools on Palfinder": 0, - "Number of tools on PepSimili": 0, "Number of tools on PhagePromotor": 0, "Number of tools on UseGalaxy.be": 1, "Number of tools on UseGalaxy.cz": 1, @@ -39547,17 +39923,6 @@ "Suite runs (last 5 years) on main servers": 2834, "Suite users on main servers": 803, "Suite users (last 5 years) on main servers": 706, - "Related Workflows": [ - "https://usegalaxy.eu/published/workflow?id=26ad77bc07a7e512", - "https://usegalaxy.eu/published/workflow?id=6ca20e710f4f3ffb", - "https://usegalaxy.org.au/published/workflow?id=7a87dfe5bdd30040", - "https://usegalaxy.org.au/published/workflow?id=7e40485d1ed45b7c", - "https://usegalaxy.org/published/workflow?id=c42c66d1b627c5a5", - "https://workflowhub.eu/workflows/1504?version=1" - 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"Suite version": "2.3.4", + "Suite version": "@TOOL_VERSION@+galaxy@VERSION_SUFFIX@", "Suite conda package": "structure", "Latest suite conda package version": "2.3.4", - "Suite version status": "Up-to-date", + "Suite version status": "To update", "ToolShed categories": [ "Phylogenetics", "Variant Analysis" @@ -40471,17 +40827,18 @@ ], "Suite owner": "iuc", "Suite source": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/structure", - "Suite parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/structure", + "Suite parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure", "bio.tool ID": "structure", "bio.tool name": "Structure", "bio.tool description": "The program structureis a free software package for using multi-locus genotype data to investigate population structure. Its uses include inferring the presence of distinct populations, assigning individuals to populations, studying hybrid zones, identifying migrants and admixed individuals, and estimating population allele frequencies in situations where many individuals are migrants or admixed.", "biii ID": null, + "Related Workflows": [], + "Related Tutorials": [], "Number of tools on UseGalaxy.org (Main)": 0, "Number of tools on UseGalaxy.org.au": 1, "Number of tools on UseGalaxy.eu": 1, "Number of tools on UseGalaxy.fr": 1, "Number of tools on APOSTL": 0, - "Number of tools on MBAC Metabiome Portal": 0, "Number of tools on ChemFlow": 0, "Number of tools on CIRM-CFBP": 0, "Number of tools on Coloc-stats": 0, @@ -40498,7 +40855,6 @@ "Number of tools on MISSISSIPPI": 0, "Number of tools on Oqtans": 0, "Number of tools on Palfinder": 0, - "Number of tools on PepSimili": 0, "Number of tools on PhagePromotor": 0, "Number of tools on UseGalaxy.be": 1, "Number of tools on UseGalaxy.cz": 1, @@ -40524,8 +40880,6 @@ "Suite runs (last 5 years) on main servers": 4233, "Suite users on main servers": 158, "Suite users (last 5 years) on main servers": 141, - "Related Workflows": [], - "Related Tutorials": [], "To keep": true, "Deprecated": false }, @@ -40577,17 +40931,21 @@ ], "Suite owner": "iuc", "Suite source": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/syri", - "Suite parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/syri", + "Suite parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/syri", "bio.tool ID": "SyRI", "bio.tool name": "SyRI", "bio.tool description": "SyRI is tool for finding genomic rearrangements and local sequence differences from whole-genome assemblies.Genomic differences range from single nucleotide differences to complex structural variations. Current methods typically annotate sequence differences ranging from SNPs to large indels accurately but do not unravel the full complexity of structural rearrangements, including inversions, translocations, and duplications, where highly similar sequence changes in location, orientation, or copy number. Here, we present SyRI, a pairwise whole-genome comparison tool for chromosome-level assemblies. SyRI starts by finding rearranged regions and then searches for differences in the sequences, which are distinguished for residing in syntenic or rearranged regions. This distinction is important as rearranged regions are inherited differently compared to syntenic regions.", "biii ID": null, + "Related Workflows": [ + "https://usegalaxy.fr/published/workflow?id=356dced9687596b7", + "https://usegalaxy.fr/published/workflow?id=ce4acd38084ee9ef" + ], + "Related Tutorials": [], "Number of tools on UseGalaxy.org (Main)": 0, "Number of tools on UseGalaxy.org.au": 0, "Number of tools on UseGalaxy.eu": 1, "Number of tools on UseGalaxy.fr": 1, "Number of tools on APOSTL": 0, - "Number of tools on MBAC Metabiome Portal": 0, "Number of tools on ChemFlow": 0, "Number of tools on CIRM-CFBP": 0, "Number of tools on Coloc-stats": 0, @@ -40604,7 +40962,6 @@ "Number of tools on MISSISSIPPI": 0, "Number of tools on Oqtans": 0, "Number of tools on Palfinder": 0, - "Number of tools on PepSimili": 0, "Number of tools on PhagePromotor": 0, "Number of tools on UseGalaxy.be": 0, "Number of tools on UseGalaxy.cz": 0, @@ -40630,11 +40987,6 @@ "Suite runs (last 5 years) on main servers": 160, "Suite users on main servers": 27, "Suite users (last 5 years) on main servers": 27, - 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"Number of tools on MBAC Metabiome Portal": 0, "Number of tools on ChemFlow": 0, "Number of tools on CIRM-CFBP": 0, "Number of tools on Coloc-stats": 0, @@ -40705,7 +41062,6 @@ "Number of tools on MISSISSIPPI": 0, "Number of tools on Oqtans": 0, "Number of tools on Palfinder": 0, - "Number of tools on PepSimili": 0, "Number of tools on PhagePromotor": 0, "Number of tools on UseGalaxy.be": 0, "Number of tools on UseGalaxy.cz": 1, @@ -40731,12 +41087,6 @@ "Suite runs (last 5 years) on main servers": 1094, "Suite users on main servers": 12, "Suite users (last 5 years) on main servers": 12, - "Related Workflows": [ - "https://usegalaxy.eu/published/workflow?id=cf0159c14418525e", - "https://usegalaxy.eu/published/workflow?id=e4dabaf57668dbd1", - "https://workflowhub.eu/workflows/2099?version=1" - ], - "Related Tutorials": [], "To keep": true, "Deprecated": false }, @@ -40751,7 +41101,7 @@ "Description": "Krona pie chart from taxonomic profile", "Suite first commit date": "2015-08-06", "Homepage": "http://sourceforge.net/projects/krona/", - "Suite version": "2.7.1+galaxy0", + "Suite version": "2.7.1", "Suite conda package": "krona", "Latest suite conda package version": "2.8.1", "Suite version status": "To update", @@ -40772,59 +41122,11 @@ ], "Suite owner": "crs4", "Suite source": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/taxonomy_krona_chart", - "Suite parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/taxonomy_krona_chart", + "Suite parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/taxonomy_krona_chart", "bio.tool ID": "krona", "bio.tool name": "Krona", "bio.tool description": "Krona creates interactive HTML5 charts of hierarchical data (such as taxonomic abundance in a metagenome).", "biii ID": null, - "Number of tools on UseGalaxy.org (Main)": 1, - "Number of tools on UseGalaxy.org.au": 1, - "Number of tools on UseGalaxy.eu": 1, - "Number of tools on UseGalaxy.fr": 1, - "Number of tools on APOSTL": 0, - "Number of tools on MBAC Metabiome Portal": 0, - 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"Suite version": "0.7.0", + "Suite version": "@TOOL_VERSION@+galaxy@VERSION_SUFFIX@", "Suite conda package": "taxpasta", "Latest suite conda package version": "0.7.0", - "Suite version status": "Up-to-date", + "Suite version status": "To update", "ToolShed categories": [ "Sequence Analysis" ], @@ -41012,17 +41360,22 @@ ], "Suite owner": "iuc", "Suite source": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/taxpasta", - "Suite parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/taxpasta", + "Suite parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/taxpasta", "bio.tool ID": "taxpasta", "bio.tool name": "taxpasta", "bio.tool description": "TAXonomic Profile Aggregation and STAndardisationThe main purpose of taxpasta is to standardise taxonomic profiles created by a range of bioinformatics tools. We call those tools taxonomic profilers. They each come with their own particular tabular output format. Across the profilers, relative abundances can be reported in read counts, fractions, or percentages, as well as any number of additional columns with extra information. We therefore decided to take the lessons learnt to heart and provide our own solution to deal with this pasticcio. With taxpasta you can ingest all of those formats and, at a minimum, output taxonomy identifiers and their integer counts. Taxpasta can not only standardise profiles but also merge them across samples for the same profiler into a single table.", "biii ID": null, + "Related Workflows": [ + "https://usegalaxy.eu/published/workflow?id=7491883694fff308", + "https://usegalaxy.eu/published/workflow?id=b14845359b702444", + "https://usegalaxy.eu/published/workflow?id=cb2df493f5e334f7" + ], + "Related Tutorials": [], "Number of tools on UseGalaxy.org (Main)": 0, "Number of tools on UseGalaxy.org.au": 0, "Number of tools on UseGalaxy.eu": 1, "Number of tools on UseGalaxy.fr": 1, "Number of tools on APOSTL": 0, - "Number of tools on MBAC Metabiome Portal": 0, "Number of tools on ChemFlow": 0, "Number of tools on CIRM-CFBP": 0, "Number of tools on Coloc-stats": 0, @@ -41039,7 +41392,6 @@ "Number of tools on MISSISSIPPI": 0, "Number of tools on Oqtans": 0, "Number of tools on Palfinder": 0, - "Number of tools on PepSimili": 0, "Number of tools on PhagePromotor": 0, "Number of tools on UseGalaxy.be": 0, "Number of tools on UseGalaxy.cz": 0, @@ -41065,12 +41417,6 @@ "Suite runs (last 5 years) on main servers": 341, "Suite users on main servers": 52, "Suite users (last 5 years) on main servers": 52, - "Related Workflows": [ - "https://usegalaxy.eu/published/workflow?id=7491883694fff308", - "https://usegalaxy.eu/published/workflow?id=b14845359b702444", - "https://usegalaxy.eu/published/workflow?id=cb2df493f5e334f7" - ], - "Related Tutorials": [], "To keep": true, "Deprecated": false }, @@ -41109,17 +41455,36 @@ "EDAM reduced topics": [], "Suite owner": "iuc", "Suite source": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/tb-profiler", - "Suite parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/tb-profiler", + "Suite parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/tb-profiler", "bio.tool ID": "tb-profiler", "bio.tool name": "tb-profiler", "bio.tool description": "A tool for drug resistance prediction from _M. tuberculosis_ genomic data 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], "To keep": true, "Deprecated": false }, @@ -42943,17 +43359,18 @@ ], "Suite owner": "iuc", "Suite source": "https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/biotradis", - "Suite parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/biotradis", + "Suite parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis", "bio.tool ID": "biotradis", "bio.tool name": "biotradis", "bio.tool description": "The Bio::TraDIS pipeline provides software utilities for the processing, mapping, and analysis of transposon insertion sequencing data. The pipeline was designed with the data from the TraDIS sequencing protocol in mind, but should work with a variety of transposon insertion sequencing protocols as long as they produce data in the expected format.", "biii ID": null, + "Related Workflows": [], + "Related Tutorials": [], "Number of tools on UseGalaxy.org (Main)": 3, "Number of tools on UseGalaxy.org.au": 0, "Number of tools on UseGalaxy.eu": 0, "Number of tools on UseGalaxy.fr": 0, "Number of tools on APOSTL": 0, - "Number of tools on MBAC Metabiome Portal": 0, "Number of tools on ChemFlow": 0, "Number of tools on CIRM-CFBP": 0, "Number of tools on Coloc-stats": 0, @@ -42970,7 +43387,6 @@ "Number of tools on MISSISSIPPI": 0, "Number of tools on Oqtans": 0, "Number of tools on Palfinder": 0, - "Number of tools on PepSimili": 0, "Number of tools on PhagePromotor": 0, "Number of tools on UseGalaxy.be": 0, "Number of tools on UseGalaxy.cz": 0, @@ -42996,8 +43412,6 @@ "Suite runs (last 5 years) on main servers": 6369, "Suite users on main servers": 176, "Suite users (last 5 years) on main servers": 165, - "Related Workflows": [], - "Related Tutorials": [], "To keep": true, "Deprecated": false }, @@ -43016,7 +43430,7 @@ "Description": "Kraken is a system for assigning taxonomic labels to short DNAsequences, usually obtained through metagenomic studies. 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It aims to achieve high sensitivity and high speed by utilizing exact alignments of k-mers and a novel classification algorithm.", "biii ID": null, + "Related Workflows": [ + "https://usegalaxy.org.au/published/workflow?id=b6bad1f167257248", + "https://usegalaxy.org/published/workflow?id=074a0b1bc8273c16", + "https://usegalaxy.org/published/workflow?id=2ec3e326c51d3147", + "https://usegalaxy.org/published/workflow?id=33d90e718ce500ef", + "https://usegalaxy.org/published/workflow?id=7321c6ad5425d347", + "https://usegalaxy.org/published/workflow?id=87b3305ea433b4e2", + "https://usegalaxy.org/published/workflow?id=a89e1018a00b883c", + "https://usegalaxy.org/published/workflow?id=e0c33057ac2670ba", + "https://usegalaxy.org/published/workflow?id=fb01e1a49793c8be" + ], + "Related Tutorials": [], "Number of tools on UseGalaxy.org (Main)": 5, "Number of tools on UseGalaxy.org.au": 5, "Number of tools on UseGalaxy.eu": 5, "Number of tools on UseGalaxy.fr": 5, "Number of tools on APOSTL": 0, - "Number of tools on MBAC Metabiome Portal": 0, "Number of tools on ChemFlow": 0, "Number of tools on CIRM-CFBP": 0, "Number of tools on Coloc-stats": 0, @@ -43066,7 +43491,6 @@ "Number of tools on MISSISSIPPI": 0, "Number of tools on Oqtans": 0, "Number of tools on Palfinder": 0, - "Number of tools on PepSimili": 2, "Number of tools on PhagePromotor": 0, "Number of tools on UseGalaxy.be": 5, "Number of tools on UseGalaxy.cz": 5, @@ -43092,18 +43516,6 @@ "Suite runs (last 5 years) on main servers": 176166, "Suite users on main servers": 6929, "Suite users (last 5 years) on main servers": 5005, - "Related Workflows": [ - "https://usegalaxy.org.au/published/workflow?id=b6bad1f167257248", - "https://usegalaxy.org/published/workflow?id=074a0b1bc8273c16", - "https://usegalaxy.org/published/workflow?id=2ec3e326c51d3147", - "https://usegalaxy.org/published/workflow?id=33d90e718ce500ef", - "https://usegalaxy.org/published/workflow?id=7321c6ad5425d347", - "https://usegalaxy.org/published/workflow?id=87b3305ea433b4e2", - "https://usegalaxy.org/published/workflow?id=a89e1018a00b883c", - "https://usegalaxy.org/published/workflow?id=e0c33057ac2670ba", - "https://usegalaxy.org/published/workflow?id=fb01e1a49793c8be" - ], - "Related Tutorials": [], "To keep": true, "Deprecated": false }, @@ -43144,59 +43556,11 @@ ], "Suite owner": "iuc", "Suite source": "https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/kraken2/kraken2", - "Suite parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/kraken2/kraken2", + "Suite parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/kraken2/kraken2", "bio.tool ID": "kraken2", "bio.tool name": "kraken2", "bio.tool description": "Kraken 2 is the newest version of Kraken, a taxonomic classification system using exact k-mer matches to achieve high accuracy and fast classification speeds. 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"Number of tools on MBAC Metabiome Portal": 0, "Number of tools on ChemFlow": 0, "Number of tools on CIRM-CFBP": 0, "Number of tools on Coloc-stats": 0, @@ -43605,7 +44024,6 @@ "Number of tools on MISSISSIPPI": 0, "Number of tools on Oqtans": 0, "Number of tools on Palfinder": 0, - "Number of tools on PepSimili": 0, "Number of tools on PhagePromotor": 0, "Number of tools on UseGalaxy.be": 1, "Number of tools on UseGalaxy.cz": 1, @@ -43631,16 +44049,6 @@ "Suite runs (last 5 years) on main servers": 732, "Suite users on main servers": 75, "Suite users (last 5 years) on main servers": 63, - "Related Workflows": [ - "https://usegalaxy.eu/published/workflow?id=ba3a5d59b3879764", - "https://usegalaxy.eu/published/workflow?id=cd675ab32d3e7833", - "https://usegalaxy.eu/published/workflow?id=d0e062aee910086a", - "https://usegalaxy.eu/published/workflow?id=fc42cc9467c6ee8d", - "https://workflowhub.eu/workflows/1450?version=1" - ], - "Related Tutorials": [ - "proteomics/metaquantome-data-creation" - ], "To keep": true, "Deprecated": false }, @@ -43677,12 +44085,23 @@ "bio.tool name": null, "bio.tool description": null, "biii ID": null, + "Related Workflows": [ + "https://usegalaxy.eu/published/workflow?id=4c7fabcb345f5990", + "https://usegalaxy.eu/published/workflow?id=8ef3379dded2490a", + "https://usegalaxy.eu/published/workflow?id=bee2a7669a7dea5b", + "https://usegalaxy.org.au/published/workflow?id=9365a7de314c9f85", + "https://usegalaxy.org/published/workflow?id=e3a30c0583183c1e", + "https://workflowhub.eu/workflows/1410?version=1", + "https://workflowhub.eu/workflows/1793?version=1" + ], + "Related Tutorials": [ + "proteomics/neoantigen-fragpipe-discovery" + ], "Number of tools on UseGalaxy.org (Main)": 2, "Number of tools on UseGalaxy.org.au": 2, "Number of tools on UseGalaxy.eu": 2, "Number of tools on UseGalaxy.fr": 0, "Number of tools on APOSTL": 0, - "Number of tools on MBAC Metabiome Portal": 0, "Number of tools on ChemFlow": 0, "Number of tools on CIRM-CFBP": 0, "Number of tools on Coloc-stats": 0, @@ -43699,7 +44118,6 @@ "Number of tools on MISSISSIPPI": 0, "Number of tools on Oqtans": 0, "Number of tools on Palfinder": 0, - "Number of tools on PepSimili": 0, "Number of tools on PhagePromotor": 0, "Number of tools on UseGalaxy.be": 0, "Number of tools on UseGalaxy.cz": 0, @@ -43725,18 +44143,6 @@ "Suite runs (last 5 years) on main servers": 505, "Suite users on main servers": 64, "Suite users (last 5 years) on main servers": 64, - "Related Workflows": [ - "https://usegalaxy.eu/published/workflow?id=4c7fabcb345f5990", - "https://usegalaxy.eu/published/workflow?id=8ef3379dded2490a", - "https://usegalaxy.eu/published/workflow?id=bee2a7669a7dea5b", - "https://usegalaxy.org.au/published/workflow?id=9365a7de314c9f85", - "https://usegalaxy.org/published/workflow?id=e3a30c0583183c1e", - "https://workflowhub.eu/workflows/1410?version=1", - "https://workflowhub.eu/workflows/1793?version=1" - ], - "Related Tutorials": [ - "proteomics/neoantigen-fragpipe-discovery" - ], "To keep": true, "Deprecated": false }, @@ -43748,7 +44154,7 @@ ], "Tool output formats": [], "Description": "wrapper for MaxQuant", - "Suite first commit date": "2015-01-24", + "Suite first commit date": "2015-01-23", "Homepage": "https://www.maxquant.org/", "Suite version": "2.0.3.0", "Suite conda package": "maxquant", @@ -43792,12 +44198,50 @@ "bio.tool name": "MaxQuant", "bio.tool description": "Quantitative proteomics software package designed for analyzing large mass-spectrometric data sets. 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"Suite version status": "Up-to-date", + "Suite version status": "To update", "ToolShed categories": [ "Sequence Analysis" ], @@ -43925,12 +44329,18 @@ "bio.tool name": "MetaGeneAnnotator", "bio.tool description": "Prokaryotic gene finding program from environmental genome shotgun sequences or metagenomic sequences.", "biii ID": null, + "Related Workflows": [ + "https://usegalaxy.eu/published/workflow?id=3dcf09e75d707573", + "https://usegalaxy.eu/published/workflow?id=799b924edd3c401b", + "https://usegalaxy.eu/published/workflow?id=9b9e1e28f3683f92", + "https://usegalaxy.eu/published/workflow?id=a644e6b450dabca8" + ], + "Related Tutorials": [], "Number of tools on UseGalaxy.org (Main)": 0, "Number of tools on UseGalaxy.org.au": 0, "Number of tools on UseGalaxy.eu": 1, "Number of tools on UseGalaxy.fr": 0, "Number of tools on APOSTL": 0, - "Number of tools on MBAC Metabiome Portal": 0, "Number of tools on ChemFlow": 0, "Number of tools on CIRM-CFBP": 0, "Number of tools on Coloc-stats": 0, @@ -43947,7 +44357,6 @@ "Number of tools on MISSISSIPPI": 0, "Number of tools on Oqtans": 0, "Number of tools on Palfinder": 0, - "Number of tools on PepSimili": 0, "Number of tools on PhagePromotor": 0, "Number of tools on UseGalaxy.be": 0, "Number of tools on UseGalaxy.cz": 1, @@ -43973,13 +44382,6 @@ "Suite runs (last 5 years) on main servers": 20971, "Suite users on main servers": 457, "Suite users (last 5 years) on main servers": 439, - "Related Workflows": [ - "https://usegalaxy.eu/published/workflow?id=3dcf09e75d707573", - "https://usegalaxy.eu/published/workflow?id=799b924edd3c401b", - "https://usegalaxy.eu/published/workflow?id=9b9e1e28f3683f92", - "https://usegalaxy.eu/published/workflow?id=a644e6b450dabca8" - ], - "Related Tutorials": [], "To keep": true, "Deprecated": false }, @@ -43995,10 +44397,10 @@ "Description": "Produce targeted databases for mass spectrometry analysis.", "Suite first commit date": "2022-03-29", "Homepage": "https://github.com/uct-cbio/proteomics-pipelines", - "Suite version": "1.9.4", + "Suite version": "@TOOL_VERSION@+galaxy@VERSION_SUFFIX@", "Suite conda package": "metanovo", "Latest suite conda package version": "1.9.4", - "Suite version status": "Up-to-date", + "Suite version status": "To update", "ToolShed categories": [ "Proteomics" ], @@ -44037,12 +44439,27 @@ "bio.tool name": "MetaNovo", "bio.tool description": "An open-source pipeline for probabilistic peptide discovery in complex metaproteomic datasets.", "biii ID": null, + "Related Workflows": [ + "https://usegalaxy.eu/published/workflow?id=2f7e13eb26c8cd18", + "https://usegalaxy.eu/published/workflow?id=7cfbf4b7bd3f30d3", + "https://usegalaxy.eu/published/workflow?id=c6aecbdbeb27585f", + "https://usegalaxy.eu/published/workflow?id=d7c7a4d6c8072167", + "https://usegalaxy.eu/published/workflow?id=f2b45a7ff4f449e6", + "https://usegalaxy.org.au/published/workflow?id=351f3fab960c013b", + "https://usegalaxy.org/published/workflow?id=2be8ecd5922d23d1", + "https://workflowhub.eu/workflows/1216?version=1", + "https://workflowhub.eu/workflows/1461?version=1", + "https://workflowhub.eu/workflows/1474?version=1" + ], + "Related Tutorials": [ + "microbiome/clinical-mp-1-database-generation", + "proteomics/clinical-mp-1-database-generation" + ], "Number of tools on UseGalaxy.org (Main)": 1, "Number of tools on UseGalaxy.org.au": 1, "Number of tools on UseGalaxy.eu": 1, "Number of tools on UseGalaxy.fr": 0, "Number of tools on APOSTL": 0, - "Number of tools on MBAC Metabiome Portal": 0, "Number of tools on ChemFlow": 0, "Number of tools on CIRM-CFBP": 0, "Number of tools on Coloc-stats": 0, @@ -44059,7 +44476,6 @@ "Number of tools on MISSISSIPPI": 0, "Number of tools on Oqtans": 0, "Number of tools on Palfinder": 0, - "Number of tools on PepSimili": 0, "Number of tools on PhagePromotor": 0, "Number of tools on UseGalaxy.be": 1, "Number of tools on UseGalaxy.cz": 1, @@ -44085,22 +44501,6 @@ "Suite runs (last 5 years) on main servers": 5126, "Suite users on main servers": 49, "Suite users (last 5 years) on main servers": 49, - "Related Workflows": [ - "https://usegalaxy.eu/published/workflow?id=2f7e13eb26c8cd18", - "https://usegalaxy.eu/published/workflow?id=7cfbf4b7bd3f30d3", - "https://usegalaxy.eu/published/workflow?id=c6aecbdbeb27585f", - "https://usegalaxy.eu/published/workflow?id=d7c7a4d6c8072167", - "https://usegalaxy.eu/published/workflow?id=f2b45a7ff4f449e6", - "https://usegalaxy.org.au/published/workflow?id=351f3fab960c013b", - 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"Number of tools on MBAC Metabiome Portal": 0, "Number of tools on ChemFlow": 0, "Number of tools on CIRM-CFBP": 0, "Number of tools on Coloc-stats": 0, @@ -44194,7 +44608,6 @@ "Number of tools on MISSISSIPPI": 0, "Number of tools on Oqtans": 0, "Number of tools on Palfinder": 0, - "Number of tools on PepSimili": 0, "Number of tools on PhagePromotor": 0, "Number of tools on UseGalaxy.be": 6, "Number of tools on UseGalaxy.cz": 6, @@ -44220,21 +44633,6 @@ "Suite runs (last 5 years) on main servers": 4600, "Suite users on main servers": 116, "Suite users (last 5 years) on main servers": 107, - "Related Workflows": [ - "https://usegalaxy.eu/published/workflow?id=4c364c6be27981ba", - "https://usegalaxy.eu/published/workflow?id=695f7defb516d80d", - "https://usegalaxy.eu/published/workflow?id=ce7f7c6eef526d67", - "https://usegalaxy.eu/published/workflow?id=dc438d4ae1866df8", - "https://usegalaxy.eu/published/workflow?id=e5a89ef7b5f1c1d9", - "https://usegalaxy.org.au/published/workflow?id=cada735fa0716570", - 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peptides and proteins in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling", "biii ID": null, + "Related Workflows": [ + "https://usegalaxy.org.au/published/workflow?id=1727d16fa4dec19c", + "https://workflowhub.eu/workflows/1426?version=1", + "https://workflowhub.eu/workflows/1458?version=1", + "https://workflowhub.eu/workflows/1462?version=1" + ], + "Related Tutorials": [ + "proteomics/DIA_Analysis_MSstats", + "proteomics/maxquant-label-free", + "proteomics/maxquant-msstats-dda-lfq" + ], "Number of tools on UseGalaxy.org (Main)": 1, "Number of tools on UseGalaxy.org.au": 1, "Number of tools on UseGalaxy.eu": 1, "Number of tools on UseGalaxy.fr": 0, "Number of tools on APOSTL": 0, - "Number of tools on MBAC Metabiome Portal": 0, "Number of tools on ChemFlow": 0, "Number of tools on CIRM-CFBP": 0, "Number of tools on Coloc-stats": 0, @@ -44460,7 +44866,6 @@ "Number of tools on MISSISSIPPI": 0, "Number of tools on Oqtans": 0, "Number of tools on 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version": "3.4.4", + "Suite version": "@TOOL_VERSION@+galaxy@VERSION_SUFFIX@", "Suite conda package": "r-ggplot2", "Latest suite conda package version": "2.2.1", "Suite version status": "To update", @@ -45189,17 +45573,18 @@ ], "Suite owner": "artbio", "Suite source": "https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms", - "Suite parsed folder": "https://github.com/ARTbio/tools-artbio/tree/main/tools/ez_histograms", + "Suite parsed folder": "https://github.com/ARTbio/tools-artbio/tree/master/tools/ez_histograms", "bio.tool ID": "ez_histograms", "bio.tool name": "ez_histograms", "bio.tool description": "This tool produces histograms or density plots from any tabular datasets, using ggplot2.You may provide headerless tables as well as tables with column headers. Any non-numeric columns will be filtered out. Your first column may contains row names, but it will also work if your first column already corresponds to the numeric values of a variable.", "biii ID": null, + "Related Workflows": [], + "Related Tutorials": [], "Number of tools on UseGalaxy.org (Main)": 0, "Number of tools on UseGalaxy.org.au": 0, "Number of tools on UseGalaxy.eu": 0, "Number of tools on UseGalaxy.fr": 0, "Number of tools on APOSTL": 0, - "Number of tools on MBAC Metabiome Portal": 0, "Number of tools on ChemFlow": 0, "Number of tools on CIRM-CFBP": 0, "Number of tools on Coloc-stats": 0, @@ -45216,7 +45601,6 @@ "Number of tools on MISSISSIPPI": 1, "Number of tools on Oqtans": 0, "Number of tools on Palfinder": 0, - "Number of tools on PepSimili": 0, "Number of tools on PhagePromotor": 0, "Number of tools on UseGalaxy.be": 0, "Number of tools on UseGalaxy.cz": 0, @@ -45242,8 +45626,6 @@ "Suite runs (last 5 years) on main servers": 0, "Suite users on main servers": 0, "Suite users (last 5 years) on main servers": 0, - "Related Workflows": [], - "Related Tutorials": [], "To keep": true, "Deprecated": false }, @@ -45259,7 +45641,7 @@ "Description": "A wrapper for the guppy basecaller tool from Oxford Nanopore Technologies", "Suite first commit date": "2020-11-18", "Homepage": "http://artbio.fr", - "Suite version": "6.5.7+galaxy0", + "Suite version": "6.5.7", "Suite conda package": null, "Latest suite conda package version": null, "Suite version status": "To update", @@ -45272,17 +45654,18 @@ "EDAM reduced topics": [], "Suite owner": "artbio", "Suite source": "https://github.com/ARTbio/tools-artbio/tree/main/tools/guppy", - "Suite parsed folder": "https://github.com/ARTbio/tools-artbio/tree/main/tools/guppy", + "Suite parsed folder": "https://github.com/ARTbio/tools-artbio/tree/master/tools/guppy", "bio.tool ID": null, "bio.tool name": null, "bio.tool description": null, "biii ID": null, + "Related Workflows": [], + "Related Tutorials": [], "Number of tools on UseGalaxy.org (Main)": 0, "Number of tools on UseGalaxy.org.au": 0, "Number of tools on UseGalaxy.eu": 0, "Number of tools on UseGalaxy.fr": 0, "Number of tools on APOSTL": 0, - "Number of tools on MBAC Metabiome Portal": 0, "Number of tools on ChemFlow": 0, "Number of tools on CIRM-CFBP": 0, "Number of tools on Coloc-stats": 0, @@ -45299,7 +45682,6 @@ "Number of tools on MISSISSIPPI": 0, "Number of tools on Oqtans": 0, "Number of tools on Palfinder": 0, - "Number of tools on PepSimili": 0, "Number of tools on PhagePromotor": 0, "Number of tools on UseGalaxy.be": 0, "Number of tools on UseGalaxy.cz": 0, @@ -45325,8 +45707,6 @@ "Suite runs (last 5 years) on main servers": 7, "Suite users on main servers": 1, "Suite users (last 5 years) on main servers": 1, - "Related Workflows": [], - "Related Tutorials": [], "To keep": true, "Deprecated": false }, @@ -45360,17 +45740,18 @@ ], "Suite owner": "artbio", "Suite source": "https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie", - "Suite parsed folder": "https://github.com/ARTbio/tools-artbio/tree/main/tools/sr_bowtie", + "Suite parsed folder": "https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie", "bio.tool ID": "sr_bowtie", "bio.tool name": "sr_bowtie", "bio.tool description": "Bowtie_ is a short read aligner designed to be ultrafast and memory-efficient. It is developed by Ben Langmead and Cole Trapnell. Please cite: Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biology 10:R25... _Bowtie: http://bowtie-bio.sourceforge.net/index.shtmlA generic \"Map with Bowtie for Illumina\" Galaxy tool is available in the main Galaxy distribution.However, this Bowtie wrapper tool only takes FASTQ files as inputs.The sRbowtie wrapper works with short (-v bowtie mode) reads inputs, in fasta or fastq format, and proposes a simplified set of configurations suited to small RNA analysis.", "biii ID": null, + "Related Workflows": [], + "Related Tutorials": [], "Number of tools on UseGalaxy.org (Main)": 0, "Number of tools on UseGalaxy.org.au": 0, "Number of tools on UseGalaxy.eu": 0, "Number of tools on UseGalaxy.fr": 0, "Number of tools on APOSTL": 0, - "Number of tools on MBAC Metabiome Portal": 0, "Number of tools on ChemFlow": 0, "Number of tools on CIRM-CFBP": 0, "Number of tools on Coloc-stats": 0, @@ -45387,7 +45768,6 @@ "Number of tools on MISSISSIPPI": 1, "Number of tools on Oqtans": 0, "Number of tools on Palfinder": 0, - "Number of tools on PepSimili": 0, "Number of tools on PhagePromotor": 0, "Number of tools on UseGalaxy.be": 0, "Number of tools on UseGalaxy.cz": 0, @@ -45413,8 +45793,6 @@ "Suite runs (last 5 years) on main servers": 98, "Suite users on main servers": 2, "Suite users (last 5 years) on main servers": 2, - "Related Workflows": [], - "Related Tutorials": [], "To keep": true, "Deprecated": false }, @@ -45452,12 +45830,20 @@ "bio.tool name": null, "bio.tool description": null, "biii ID": null, + "Related Workflows": [ + "https://usegalaxy.eu/published/workflow?id=428be4c7d1fd828f", + "https://usegalaxy.eu/published/workflow?id=7c45c90fffe40aca", + "https://usegalaxy.eu/published/workflow?id=d33ab07e4cf44f8c", + "https://workflowhub.eu/workflows/1696?version=1" + ], + "Related Tutorials": [ + "ecology/PAMPA-toolsuite-tutorial" + ], "Number of tools on UseGalaxy.org (Main)": 0, "Number of tools on UseGalaxy.org.au": 5, "Number of tools on UseGalaxy.eu": 5, "Number of tools on UseGalaxy.fr": 5, "Number of tools on APOSTL": 0, - "Number of tools on MBAC Metabiome Portal": 0, "Number of tools on ChemFlow": 0, "Number of tools on CIRM-CFBP": 0, "Number of tools on Coloc-stats": 0, @@ -45474,7 +45860,6 @@ "Number of tools on MISSISSIPPI": 0, "Number of tools on Oqtans": 0, "Number of tools on Palfinder": 0, - "Number of tools on PepSimili": 0, "Number of tools on PhagePromotor": 0, "Number of tools on UseGalaxy.be": 5, "Number of tools on UseGalaxy.cz": 5, @@ -45500,15 +45885,6 @@ "Suite runs (last 5 years) on main servers": 3139, "Suite users on main servers": 80, "Suite users (last 5 years) on main servers": 77, - "Related Workflows": [ - "https://usegalaxy.eu/published/workflow?id=428be4c7d1fd828f", - "https://usegalaxy.eu/published/workflow?id=7c45c90fffe40aca", - "https://usegalaxy.eu/published/workflow?id=d33ab07e4cf44f8c", - "https://workflowhub.eu/workflows/1696?version=1" - ], - "Related Tutorials": [ - "ecology/PAMPA-toolsuite-tutorial" - ], "To keep": true, "Deprecated": false }, @@ -45524,7 +45900,7 @@ "Description": "The Sanntis tool identify biosynthetic gene clusters (BGCs) in genomic & metagenomic data", "Suite first commit date": "2024-07-26", "Homepage": "https://github.com/Finn-Lab/SanntiS", - "Suite version": "0.9.3.5", + "Suite version": "@TOOL_VERSION@+galaxy@VERSION_SUFFIX@", "Suite conda package": "sanntis", "Latest suite conda package version": "0.9.4.1", "Suite version status": "To update", @@ -45542,12 +45918,20 @@ "bio.tool name": null, "bio.tool description": null, "biii ID": null, + "Related Workflows": [ + "https://usegalaxy.eu/published/workflow?id=a448400f69594135", + "https://usegalaxy.eu/published/workflow?id=b9c938d1af08124b", + "https://usegalaxy.eu/published/workflow?id=cc59ae1a9878942c", + "https://workflowhub.eu/workflows/1663?version=1" + ], + "Related Tutorials": [ + "ecology/marine_omics_bgc" + ], "Number of tools on UseGalaxy.org (Main)": 0, "Number of tools on UseGalaxy.org.au": 1, "Number of tools on UseGalaxy.eu": 1, - "Number of tools on UseGalaxy.fr": 0, + "Number of tools on UseGalaxy.fr": 1, "Number of tools on APOSTL": 0, - "Number of tools on MBAC Metabiome Portal": 0, "Number of tools on ChemFlow": 0, "Number of tools on CIRM-CFBP": 0, "Number of tools on Coloc-stats": 0, @@ -45564,7 +45948,6 @@ "Number of tools on MISSISSIPPI": 0, "Number of tools on Oqtans": 0, "Number of tools on Palfinder": 0, - "Number of tools on PepSimili": 0, "Number of tools on PhagePromotor": 0, "Number of tools on UseGalaxy.be": 1, "Number of tools on UseGalaxy.cz": 0, @@ -45590,15 +45973,6 @@ "Suite runs (last 5 years) on main servers": 310, "Suite users on main servers": 27, "Suite users (last 5 years) on main servers": 27, - "Related Workflows": [ - "https://usegalaxy.eu/published/workflow?id=a448400f69594135", - "https://usegalaxy.eu/published/workflow?id=b9c938d1af08124b", - "https://usegalaxy.eu/published/workflow?id=cc59ae1a9878942c", - "https://workflowhub.eu/workflows/1663?version=1" - ], - "Related Tutorials": [ - "ecology/marine_omics_bgc" - ], "To keep": true, "Deprecated": false }, @@ -45631,12 +46005,13 @@ "bio.tool name": null, "bio.tool description": null, "biii ID": null, + "Related Workflows": [], + "Related Tutorials": [], "Number of tools on UseGalaxy.org (Main)": 0, "Number of tools on UseGalaxy.org.au": 0, "Number of tools on UseGalaxy.eu": 1, "Number of tools on UseGalaxy.fr": 0, "Number of tools on APOSTL": 0, - "Number of tools on MBAC Metabiome Portal": 0, "Number of tools on ChemFlow": 0, "Number of tools on CIRM-CFBP": 0, "Number of tools on Coloc-stats": 0, @@ -45653,7 +46028,6 @@ "Number of tools on MISSISSIPPI": 0, "Number of tools on Oqtans": 0, "Number of tools on Palfinder": 0, - "Number of tools on PepSimili": 0, "Number of tools on PhagePromotor": 0, "Number of tools on UseGalaxy.be": 0, "Number of tools on UseGalaxy.cz": 0, @@ -45679,8 +46053,6 @@ "Suite runs (last 5 years) on main servers": 0, "Suite users on main servers": 0, "Suite users (last 5 years) on main servers": 0, - "Related Workflows": [], - "Related Tutorials": [], "To keep": true, "Deprecated": false }, @@ -45722,12 +46094,15 @@ "bio.tool name": "Blast2GO", "bio.tool description": "Bioinformatics platform for high-quality functional annotation and analysis of genomic datasets. It allows analyzing and visualizing newly sequenced genomes by combining state-of-the-art methodologies, standard resources and algorithms. It allows to gain biological insights fast and easy even for completely novel genomes. Perform out-of-the-box the entire workflow of functional annotation of your transcriptomic datasets including its analysis and biological interpretation.", "biii ID": null, + "Related Workflows": [ + "https://usegalaxy.eu/published/workflow?id=33312e5643279e8a" + ], + "Related Tutorials": [], "Number of tools on UseGalaxy.org (Main)": 0, "Number of tools on UseGalaxy.org.au": 0, "Number of tools on UseGalaxy.eu": 0, "Number of tools on UseGalaxy.fr": 0, "Number of tools on APOSTL": 0, - "Number of tools on MBAC Metabiome Portal": 0, "Number of tools on ChemFlow": 0, "Number of tools on CIRM-CFBP": 0, "Number of tools on Coloc-stats": 0, @@ -45744,7 +46119,6 @@ "Number of tools on MISSISSIPPI": 0, "Number of tools on Oqtans": 0, "Number of tools on Palfinder": 0, - "Number of tools on PepSimili": 0, "Number of tools on PhagePromotor": 0, "Number of tools on UseGalaxy.be": 0, "Number of tools on UseGalaxy.cz": 1, @@ -45770,10 +46144,6 @@ "Suite runs (last 5 years) on main servers": 851, "Suite users on main servers": 304, "Suite users (last 5 years) on main servers": 205, - "Related Workflows": [ - "https://usegalaxy.eu/published/workflow?id=33312e5643279e8a" - ], - "Related Tutorials": [], "To keep": true, "Deprecated": false }, @@ -45817,12 +46187,15 @@ "bio.tool name": "blast_rbh", "bio.tool description": "This tool is a short Python script to run reciprocal BLAST searches on a pair of sequence files, and extract the reciprocal best hits.", "biii ID": null, + "Related Workflows": [ + "https://usegalaxy.eu/published/workflow?id=7f6950394a8c9c4a" + ], + "Related Tutorials": [], "Number of tools on UseGalaxy.org (Main)": 0, "Number of tools on UseGalaxy.org.au": 0, "Number of tools on UseGalaxy.eu": 1, "Number of tools on UseGalaxy.fr": 0, "Number of tools on APOSTL": 0, - "Number of tools on MBAC Metabiome Portal": 0, "Number of tools on ChemFlow": 0, "Number of tools on CIRM-CFBP": 0, "Number of tools on Coloc-stats": 0, @@ -45839,7 +46212,6 @@ "Number of tools on MISSISSIPPI": 0, "Number of tools on Oqtans": 0, "Number of tools on Palfinder": 0, - "Number of tools on PepSimili": 0, "Number of tools on PhagePromotor": 0, "Number of tools on UseGalaxy.be": 0, "Number of tools on UseGalaxy.cz": 1, @@ -45865,10 +46237,6 @@ "Suite runs (last 5 years) on main servers": 25833, "Suite users on main servers": 502, "Suite users (last 5 years) on main servers": 413, - "Related Workflows": [ - "https://usegalaxy.eu/published/workflow?id=7f6950394a8c9c4a" - ], - "Related Tutorials": [], "To keep": true, "Deprecated": false }, @@ -45913,12 +46281,18 @@ "bio.tool name": "blastxml_to_top_descr", "bio.tool description": "This tool is a short Python script to parse a BLAST XML file, and extract the identifiers with description for the top matches (by default the top 3), and output these as a simple tabular file along with the query identifiers.", "biii ID": null, + "Related Workflows": [ + "https://usegalaxy.eu/published/workflow?id=33312e5643279e8a", + "https://usegalaxy.eu/published/workflow?id=8f747dbff3216993", + "https://usegalaxy.eu/published/workflow?id=bebcbd6f0ffa55c5", + "https://usegalaxy.eu/published/workflow?id=e14b81a8c0b1b7a4" + ], + "Related Tutorials": [], "Number of tools on UseGalaxy.org (Main)": 0, "Number of tools on UseGalaxy.org.au": 0, "Number of tools on UseGalaxy.eu": 1, "Number of tools on UseGalaxy.fr": 0, "Number of tools on APOSTL": 0, - "Number of tools on MBAC Metabiome Portal": 0, "Number of tools on ChemFlow": 0, "Number of tools on CIRM-CFBP": 0, "Number of tools on Coloc-stats": 0, @@ -45935,7 +46309,6 @@ "Number of tools on MISSISSIPPI": 0, "Number of tools on Oqtans": 0, "Number of tools on Palfinder": 0, - "Number of tools on PepSimili": 0, "Number of tools on PhagePromotor": 0, "Number of tools on UseGalaxy.be": 0, "Number of tools on UseGalaxy.cz": 1, @@ -45961,13 +46334,6 @@ "Suite runs (last 5 years) on main servers": 263613, "Suite users on main servers": 653, "Suite users (last 5 years) on main servers": 530, - "Related Workflows": [ - "https://usegalaxy.eu/published/workflow?id=33312e5643279e8a", - "https://usegalaxy.eu/published/workflow?id=8f747dbff3216993", - "https://usegalaxy.eu/published/workflow?id=bebcbd6f0ffa55c5", - "https://usegalaxy.eu/published/workflow?id=e14b81a8c0b1b7a4" - ], - "Related Tutorials": [], "To keep": true, "Deprecated": false }, @@ -46013,12 +46379,13 @@ "bio.tool name": "make_nr", "bio.tool description": "Make a FASTA file non-redundant, with a Galaxy wrapperThis tool is copyright 2018 by Peter Cock, The James Hutton Institute, UK. All rights reserved.This tool is a short Python script intended to be run prior to calling the NCBI BLAST+ command line tool makeblastdb or in other settings where you want to collapse duplicated sequences in a FASTA file to a single representative.", "biii ID": null, + "Related Workflows": [], + "Related Tutorials": [], "Number of tools on UseGalaxy.org (Main)": 0, "Number of tools on UseGalaxy.org.au": 0, "Number of tools on UseGalaxy.eu": 0, "Number of tools on UseGalaxy.fr": 0, "Number of tools on APOSTL": 0, - "Number of tools on MBAC Metabiome Portal": 0, "Number of tools on ChemFlow": 0, "Number of tools on CIRM-CFBP": 0, "Number of tools on Coloc-stats": 0, @@ -46035,7 +46402,6 @@ "Number of tools on MISSISSIPPI": 0, "Number of tools on Oqtans": 0, "Number of tools on Palfinder": 0, - "Number of tools on PepSimili": 0, "Number of tools on PhagePromotor": 0, "Number of tools on UseGalaxy.be": 0, "Number of tools on UseGalaxy.cz": 0, @@ -46061,8 +46427,6 @@ "Suite runs (last 5 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"https://usegalaxy.eu/published/workflow?id=0b9071d5dfa38559", + "https://usegalaxy.eu/published/workflow?id=0ec71ca86af5cbb3", "https://usegalaxy.eu/published/workflow?id=0f044c9f62773a88", "https://usegalaxy.eu/published/workflow?id=10150b1a188f6d07", "https://usegalaxy.eu/published/workflow?id=12a018217ee146ca", "https://usegalaxy.eu/published/workflow?id=152223c8aed27357", "https://usegalaxy.eu/published/workflow?id=17f73aba442315e6", "https://usegalaxy.eu/published/workflow?id=1860e02bcb894a64", + "https://usegalaxy.eu/published/workflow?id=1ae9a523ef719a3d", "https://usegalaxy.eu/published/workflow?id=1b43449ed8481892", "https://usegalaxy.eu/published/workflow?id=2497292e98937a5f", "https://usegalaxy.eu/published/workflow?id=24eaa682897379c8", @@ -46247,6 +46566,8 @@ "https://usegalaxy.org.au/published/workflow?id=3d47e0de658b3304", "https://usegalaxy.org.au/published/workflow?id=4047f9f242542716", "https://usegalaxy.org.au/published/workflow?id=470eb26144325590", + "https://usegalaxy.org.au/published/workflow?id=586a218c9b29d99a", + "https://usegalaxy.org.au/published/workflow?id=58f97e4a249796cb", "https://usegalaxy.org.au/published/workflow?id=5cf5334877cc1297", "https://usegalaxy.org.au/published/workflow?id=5fb44f257e445f56", "https://usegalaxy.org.au/published/workflow?id=762791e094457bf2", @@ -46256,12 +46577,14 @@ "https://usegalaxy.org.au/published/workflow?id=897a1255cef5c310", "https://usegalaxy.org.au/published/workflow?id=94c7fdcbbc7b428a", "https://usegalaxy.org.au/published/workflow?id=97e55a900db3863b", + "https://usegalaxy.org.au/published/workflow?id=a5b356c8baef01cf", "https://usegalaxy.org.au/published/workflow?id=c049ae8f729b2d7e", "https://usegalaxy.org.au/published/workflow?id=c92fead7c30c7497", "https://usegalaxy.org.au/published/workflow?id=d2dcd3b54e5082a6", "https://usegalaxy.org.au/published/workflow?id=d417e920ff97e4c1", "https://usegalaxy.org.au/published/workflow?id=d720c98f7227b6d5", "https://usegalaxy.org.au/published/workflow?id=dccc8fb49d61ac33", + "https://usegalaxy.org.au/published/workflow?id=dce03a1f302668c5", "https://usegalaxy.org/published/workflow?id=1473cdcbd664d147", "https://usegalaxy.org/published/workflow?id=1b80302437db5937", "https://usegalaxy.org/published/workflow?id=529b410bd03b66aa", @@ -46320,6 +46643,52 @@ "sequence-analysis/ncbi-blast-against-the-madland", "sequence-analysis/viral_primer_design" ], + "Number of tools on UseGalaxy.org (Main)": 16, + "Number of tools on UseGalaxy.org.au": 16, + "Number of tools on UseGalaxy.eu": 16, + "Number of tools on UseGalaxy.fr": 16, + "Number of tools on APOSTL": 0, + "Number of tools on ChemFlow": 0, + "Number of tools on CIRM-CFBP": 0, + "Number of tools on Coloc-stats": 0, + "Number of tools on Galaxy@AuBi": 16, + "Number of tools on Galaxy@Pasteur": 16, + "Number of tools on GalaxyTrakr": 16, + "Number of tools on GASLINI": 0, + "Number of tools on HyPhy HIV NGS Tools": 0, + "Number of tools on ImmPort Galaxy": 0, + "Number of tools on InteractoMIX": 0, + "Number of tools on IPK Galaxy Blast Suite": 16, + "Number of tools on Lebanese University Galaxy": 0, + "Number of tools on Mandoiu Lab": 0, + "Number of tools on MISSISSIPPI": 16, + "Number of tools on Oqtans": 0, + "Number of tools on Palfinder": 0, + "Number of tools on PhagePromotor": 15, + "Number of tools on UseGalaxy.be": 16, + "Number of tools on UseGalaxy.cz": 16, + "Number of tools on UseGalaxy.no": 15, + "Number of tools on Viral Variant Visualizer (VVV)": 0, + "Suite users (last 5 years) (usegalaxy.eu)": 4564, + "Suite users (usegalaxy.eu)": 5012, + "Suite runs (last 5 years) (usegalaxy.eu)": 608297, + "Suite runs (usegalaxy.eu)": 687163, + "Suite users (last 5 years) (usegalaxy.org)": 5091, + "Suite users (usegalaxy.org)": 6262, + "Suite runs (last 5 years) (usegalaxy.org)": 690841, + "Suite runs (usegalaxy.org)": 770815, + "Suite users (last 5 years) (usegalaxy.org.au)": 1316, + "Suite users (usegalaxy.org.au)": 1731, + "Suite runs (last 5 years) (usegalaxy.org.au)": 262398, + "Suite runs (usegalaxy.org.au)": 287817, + "Suite users (last 5 years) (usegalaxy.fr)": 159, + "Suite users (usegalaxy.fr)": 164, + "Suite runs (last 5 years) (usegalaxy.fr)": 12993, + "Suite runs (usegalaxy.fr)": 13154, + "Suite runs on main servers": 1758949, + "Suite runs (last 5 years) on main servers": 1574529, + "Suite users on main servers": 13169, + "Suite users (last 5 years) on main servers": 11130, "To keep": true, "Deprecated": false }, @@ -46351,12 +46720,13 @@ "bio.tool name": null, "bio.tool description": null, "biii ID": null, + "Related Workflows": [], + "Related Tutorials": [], "Number of tools on UseGalaxy.org (Main)": 0, "Number of tools on UseGalaxy.org.au": 0, "Number of tools on UseGalaxy.eu": 0, "Number of tools on UseGalaxy.fr": 2, "Number of tools on APOSTL": 0, - "Number of tools on MBAC Metabiome Portal": 0, "Number of tools on ChemFlow": 0, "Number of tools on CIRM-CFBP": 0, "Number of tools on Coloc-stats": 0, @@ -46373,7 +46743,6 @@ "Number of tools on MISSISSIPPI": 0, "Number of tools on Oqtans": 0, "Number of tools on Palfinder": 0, - "Number of tools on PepSimili": 0, "Number of tools on PhagePromotor": 0, "Number of tools on UseGalaxy.be": 0, "Number of tools on UseGalaxy.cz": 0, @@ -46399,8 +46768,6 @@ "Suite runs (last 5 years) on main servers": 0, "Suite users on main servers": 0, "Suite users (last 5 years) on main servers": 0, - "Related Workflows": [], - "Related Tutorials": [], "To keep": true, "Deprecated": false }, @@ -46431,12 +46798,13 @@ "bio.tool name": null, "bio.tool description": null, "biii ID": null, + "Related Workflows": [], + "Related Tutorials": [], "Number of tools on UseGalaxy.org (Main)": 0, "Number of tools on UseGalaxy.org.au": 0, "Number of tools on UseGalaxy.eu": 0, "Number of tools on UseGalaxy.fr": 1, "Number of tools on APOSTL": 0, - "Number of tools on MBAC Metabiome Portal": 0, "Number of tools on ChemFlow": 0, "Number of tools on CIRM-CFBP": 0, "Number of tools on Coloc-stats": 0, @@ -46453,7 +46821,6 @@ "Number of tools on MISSISSIPPI": 0, "Number of tools on Oqtans": 0, "Number of tools on Palfinder": 0, - "Number of tools on PepSimili": 0, "Number of tools on PhagePromotor": 0, "Number of tools on UseGalaxy.be": 0, "Number of tools on UseGalaxy.cz": 0, @@ -46479,8 +46846,6 @@ "Suite runs (last 5 years) on main servers": 0, "Suite users on main servers": 0, "Suite users (last 5 years) on main servers": 0, - "Related Workflows": [], - "Related Tutorials": [], "To keep": true, "Deprecated": false }, @@ -46511,12 +46876,13 @@ "bio.tool name": null, "bio.tool description": null, "biii ID": null, + "Related Workflows": [], + "Related Tutorials": [], "Number of tools on UseGalaxy.org (Main)": 0, "Number of tools on UseGalaxy.org.au": 0, "Number of tools on UseGalaxy.eu": 0, "Number of tools on UseGalaxy.fr": 1, "Number of tools on APOSTL": 0, - "Number of tools on MBAC Metabiome Portal": 0, "Number of tools on ChemFlow": 0, "Number of tools on CIRM-CFBP": 0, "Number of tools on Coloc-stats": 0, @@ -46533,7 +46899,6 @@ "Number of tools on MISSISSIPPI": 0, "Number of tools on Oqtans": 0, "Number of tools on Palfinder": 0, - "Number of tools on PepSimili": 0, "Number of tools on PhagePromotor": 0, "Number of tools on UseGalaxy.be": 0, "Number of tools on UseGalaxy.cz": 0, @@ -46559,8 +46924,6 @@ "Suite runs (last 5 years) on main servers": 0, "Suite users on main servers": 0, "Suite users (last 5 years) on main servers": 0, - "Related Workflows": [], - "Related Tutorials": [], "To keep": true, "Deprecated": false }, @@ -46576,9 +46939,9 @@ "Description": "Assess quality of single-contig viral genomes", "Suite first commit date": "2024-09-13", "Homepage": "https://bitbucket.org/berkeleylab/checkv/", - "Suite version": "1.0.3", + "Suite version": "@TOOL_VERSION@+galaxy@VERSION_SUFFIX@", "Suite conda package": "checkv", - "Latest suite conda package version": "1.1.0", + "Latest suite conda package version": "1.1.1", "Suite version status": "To update", "ToolShed categories": [ "Metagenomics" @@ -46607,17 +46970,23 @@ ], "Suite owner": "ufz", "Suite source": "https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/checkv/", - "Suite parsed folder": "https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/checkv", + "Suite parsed folder": "https://github.com/Helmholtz-UFZ/galaxy-tools/tree/master/tools/checkv", "bio.tool ID": "checkv", "bio.tool name": "CheckV", "bio.tool description": "CheckV is a fully automated command-line pipeline for assessing the quality of single-contig viral genomes, including identification of host contamination for integrated proviruses, estimating completeness for genome fragments, and identification of closed genomes.", "biii ID": null, + "Related Workflows": [ + "https://usegalaxy.eu/published/workflow?id=36de05d50c703164", + "https://usegalaxy.eu/published/workflow?id=62392daea25a3980", + "https://usegalaxy.eu/published/workflow?id=87231a6a7938cb95", + "https://usegalaxy.eu/published/workflow?id=c62d65832377e376" + ], + "Related Tutorials": [], "Number of tools on UseGalaxy.org (Main)": 1, "Number of tools on UseGalaxy.org.au": 0, "Number of tools on UseGalaxy.eu": 1, "Number of tools on UseGalaxy.fr": 0, "Number of tools on APOSTL": 0, - "Number of tools on MBAC Metabiome Portal": 0, "Number of tools on ChemFlow": 0, "Number of tools on CIRM-CFBP": 0, "Number of tools on Coloc-stats": 0, @@ -46634,7 +47003,6 @@ "Number of tools on MISSISSIPPI": 0, "Number of tools on Oqtans": 0, "Number of tools on Palfinder": 0, - "Number of tools on PepSimili": 0, "Number of tools on PhagePromotor": 0, "Number of tools on UseGalaxy.be": 0, "Number of tools on UseGalaxy.cz": 0, @@ -46660,13 +47028,6 @@ "Suite runs (last 5 years) on main servers": 4548, "Suite users on main servers": 84, "Suite users (last 5 years) on main servers": 84, - "Related Workflows": [ - "https://usegalaxy.eu/published/workflow?id=36de05d50c703164", - "https://usegalaxy.eu/published/workflow?id=62392daea25a3980", - "https://usegalaxy.eu/published/workflow?id=87231a6a7938cb95", - "https://usegalaxy.eu/published/workflow?id=c62d65832377e376" - ], - "Related Tutorials": [], "To keep": true, "Deprecated": false }, @@ -46686,9 +47047,9 @@ "Description": "Prokaryotic genome annotation", "Suite first commit date": "2025-04-16", "Homepage": "https://github.com/nigyta/dfast_core/", - "Suite version": "1.3.6", + "Suite version": "@TOOL_VERSION@+galaxy@VERSION_SUFFIX@", "Suite conda package": "dfast", - "Latest suite conda package version": "1.3.9", + "Latest suite conda package version": "1.4.0", "Suite version status": "To update", "ToolShed categories": [ "Genome annotation" @@ -46711,17 +47072,18 @@ ], "Suite owner": "ufz", "Suite source": "https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/dfast/", - "Suite parsed folder": "https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/dfast", + "Suite parsed folder": "https://github.com/Helmholtz-UFZ/galaxy-tools/tree/master/tools/dfast", "bio.tool ID": "dfast", "bio.tool name": "DFAST", "bio.tool description": "Flexible prokaryotic genome annotation pipeline for faster genome publication.", "biii ID": null, + "Related Workflows": [], + "Related Tutorials": [], "Number of tools on UseGalaxy.org (Main)": 0, "Number of tools on UseGalaxy.org.au": 0, "Number of tools on UseGalaxy.eu": 0, "Number of tools on UseGalaxy.fr": 0, "Number of tools on APOSTL": 0, - "Number of tools on MBAC Metabiome Portal": 0, "Number of tools on ChemFlow": 0, "Number of tools on CIRM-CFBP": 0, "Number of tools on Coloc-stats": 0, @@ -46738,7 +47100,6 @@ "Number of tools on MISSISSIPPI": 0, "Number of tools on Oqtans": 0, "Number of tools on Palfinder": 0, - "Number of tools on PepSimili": 0, "Number of tools on PhagePromotor": 0, "Number of tools on UseGalaxy.be": 0, "Number of tools on UseGalaxy.cz": 0, @@ -46764,8 +47125,6 @@ "Suite runs (last 5 years) on main servers": 0, "Suite users on main servers": 0, "Suite users (last 5 years) on main servers": 0, - "Related Workflows": [], - "Related Tutorials": [], "To keep": true, "Deprecated": false }, @@ -46801,17 +47160,18 @@ ], "Suite owner": "ufz", "Suite source": "https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/eukcc", - "Suite parsed folder": "https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/eukcc", + "Suite parsed folder": "https://github.com/Helmholtz-UFZ/galaxy-tools/tree/master/tools/eukcc", "bio.tool ID": "eukcc", "bio.tool name": "EukCC", "bio.tool description": "EukCC is a completeness and contamination estimator for metagenomic assembled microbial eukaryotic genomes.", "biii ID": null, + "Related Workflows": [], + "Related Tutorials": [], "Number of tools on UseGalaxy.org (Main)": 0, "Number of tools on UseGalaxy.org.au": 0, "Number of tools on UseGalaxy.eu": 0, "Number of tools on UseGalaxy.fr": 0, "Number of tools on APOSTL": 0, - "Number of tools on MBAC Metabiome Portal": 0, "Number of tools on ChemFlow": 0, "Number of tools on CIRM-CFBP": 0, "Number of tools on Coloc-stats": 0, @@ -46828,7 +47188,6 @@ "Number of tools on MISSISSIPPI": 0, "Number of tools on Oqtans": 0, "Number of tools on Palfinder": 0, - "Number of tools on PepSimili": 0, "Number of tools on PhagePromotor": 0, "Number of tools on UseGalaxy.be": 0, "Number of tools on UseGalaxy.cz": 0, @@ -46854,8 +47213,6 @@ "Suite runs (last 5 years) on main servers": 0, "Suite users on main servers": 0, "Suite users (last 5 years) on main servers": 0, - "Related Workflows": [], - "Related Tutorials": [], "To keep": true, "Deprecated": false }, @@ -46868,10 +47225,10 @@ "Description": "Identify virus and plasmid genomes from nucleotide sequences", "Suite first commit date": "2024-06-17", "Homepage": "https://github.com/apcamargo/genomad/", - "Suite version": "1.12.0", + "Suite version": "@TOOL_VERSION@+galaxy@VERSION_SUFFIX@", "Suite conda package": "genomad", "Latest suite conda package version": "1.12.0", - "Suite version status": "Up-to-date", + "Suite version status": "To update", "ToolShed categories": [ "Metagenomics" ], @@ -46891,17 +47248,25 @@ ], "Suite owner": "ufz", "Suite source": "https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/genomad/", - "Suite parsed folder": "https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/genomad", + "Suite parsed folder": "https://github.com/Helmholtz-UFZ/galaxy-tools/tree/master/tools/genomad", "bio.tool ID": "genomad", "bio.tool name": "geNomad", "bio.tool description": "geNomad is a tool that identifies virus and plasmid genomes from nucleotide sequences. It provides state-of-the-art classification performance and can be used to quickly find mobile genetic elements from genomes, metagenomes, or metatranscriptomes.", "biii ID": null, + "Related Workflows": [ + "https://usegalaxy.eu/published/workflow?id=36de05d50c703164", + "https://usegalaxy.eu/published/workflow?id=62392daea25a3980", + "https://usegalaxy.eu/published/workflow?id=c62d65832377e376", + "https://usegalaxy.eu/published/workflow?id=d0339e4a794f4922", + "https://usegalaxy.org/published/workflow?id=5729beda978a9c8e", + "https://usegalaxy.org/published/workflow?id=e0bd6b062a2239ae" + ], + "Related Tutorials": [], "Number of tools on UseGalaxy.org (Main)": 1, "Number of tools on UseGalaxy.org.au": 0, "Number of tools on UseGalaxy.eu": 1, "Number of tools on UseGalaxy.fr": 1, "Number of tools on APOSTL": 0, - "Number of tools on MBAC Metabiome Portal": 0, "Number of tools on ChemFlow": 0, "Number of tools on CIRM-CFBP": 0, "Number of tools on Coloc-stats": 0, @@ -46918,7 +47283,6 @@ "Number of tools on MISSISSIPPI": 0, "Number of tools on Oqtans": 0, "Number of tools on Palfinder": 0, - "Number of tools on PepSimili": 0, "Number of tools on PhagePromotor": 0, "Number of tools on UseGalaxy.be": 0, "Number of tools on UseGalaxy.cz": 0, @@ -46944,14 +47308,6 @@ "Suite runs (last 5 years) on main servers": 2647, "Suite users on main servers": 139, "Suite users (last 5 years) on main servers": 139, - "Related Workflows": [ - "https://usegalaxy.eu/published/workflow?id=36de05d50c703164", - "https://usegalaxy.eu/published/workflow?id=62392daea25a3980", - "https://usegalaxy.eu/published/workflow?id=c62d65832377e376", - "https://usegalaxy.eu/published/workflow?id=d0339e4a794f4922", - "https://usegalaxy.org/published/workflow?id=e0bd6b062a2239ae" - ], - "Related Tutorials": [], "To keep": true, "Deprecated": false }, @@ -46966,10 +47322,10 @@ "Description": "Integrated Phage Host Prediction", "Suite first commit date": "2024-10-14", "Homepage": "https://bitbucket.org/srouxjgi/iphop/", - "Suite version": "1.4.2", + "Suite version": "@TOOL_VERSION@+galaxy@VERSION_SUFFIX@", "Suite conda package": "iphop", "Latest suite conda package version": "1.4.2", - "Suite version status": "Up-to-date", + "Suite version status": "To update", "ToolShed categories": [ "Metagenomics" ], @@ -46983,17 +47339,21 @@ "EDAM reduced topics": [], "Suite owner": "ufz", "Suite source": "https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/iphop/", - "Suite parsed folder": "https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/iphop", + "Suite parsed folder": "https://github.com/Helmholtz-UFZ/galaxy-tools/tree/master/tools/iphop", "bio.tool ID": "iphop", "bio.tool name": "iPHoP", "bio.tool description": "An automated command-line pipeline for predicting host genus of novel bacteriophages and archaeoviruses based on their genome sequences.", "biii ID": null, + "Related Workflows": [ + "https://usegalaxy.eu/published/workflow?id=62392daea25a3980", + "https://usegalaxy.eu/published/workflow?id=c62d65832377e376" + ], + "Related Tutorials": [], "Number of tools on UseGalaxy.org (Main)": 1, "Number of tools on UseGalaxy.org.au": 0, "Number of tools on UseGalaxy.eu": 1, "Number of tools on UseGalaxy.fr": 0, "Number of tools on APOSTL": 0, - "Number of tools on MBAC Metabiome Portal": 0, "Number of tools on ChemFlow": 0, "Number of tools on CIRM-CFBP": 0, "Number of tools on Coloc-stats": 0, @@ -47010,7 +47370,6 @@ "Number of tools on MISSISSIPPI": 0, "Number of tools on Oqtans": 0, "Number of tools on Palfinder": 0, - "Number of tools on PepSimili": 0, "Number of tools on PhagePromotor": 0, "Number of tools on UseGalaxy.be": 0, "Number of tools on UseGalaxy.cz": 0, @@ -47036,11 +47395,6 @@ "Suite runs (last 5 years) on main servers": 26, "Suite users on main servers": 9, "Suite users (last 5 years) on main servers": 9, - "Related Workflows": [ - "https://usegalaxy.eu/published/workflow?id=62392daea25a3980", - "https://usegalaxy.eu/published/workflow?id=c62d65832377e376" - ], - "Related Tutorials": [], "To keep": true, "Deprecated": false }, @@ -47069,17 +47423,18 @@ "EDAM reduced topics": [], "Suite owner": "mbernt", "Suite source": "https://github.com/bernt-matthias/mb-galaxy-tools/blob/master/tools/longorf/", - "Suite parsed folder": "https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/longorf", + "Suite parsed folder": "https://github.com/Helmholtz-UFZ/galaxy-tools/tree/master/tools/longorf", "bio.tool ID": null, "bio.tool name": null, "bio.tool description": null, "biii ID": null, + "Related Workflows": [], + "Related Tutorials": [], "Number of tools on UseGalaxy.org (Main)": 0, "Number of tools on UseGalaxy.org.au": 0, "Number of tools on UseGalaxy.eu": 0, "Number of tools on UseGalaxy.fr": 0, "Number of tools on APOSTL": 0, - "Number of tools on MBAC Metabiome Portal": 0, "Number of tools on ChemFlow": 0, "Number of tools on CIRM-CFBP": 0, "Number of tools on Coloc-stats": 0, @@ -47096,7 +47451,6 @@ "Number of tools on MISSISSIPPI": 0, "Number of tools on Oqtans": 0, "Number of tools on Palfinder": 0, - "Number of tools on PepSimili": 0, "Number of tools on PhagePromotor": 0, "Number of tools on UseGalaxy.be": 0, "Number of tools on UseGalaxy.cz": 0, @@ -47122,8 +47476,6 @@ "Suite runs (last 5 years) on main servers": 0, "Suite users on main servers": 0, "Suite users (last 5 years) on main servers": 0, - "Related Workflows": [], - "Related Tutorials": [], "To keep": true, "Deprecated": false }, @@ -47177,17 +47529,18 @@ ], "Suite owner": "ufz", "Suite source": "https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox", - "Suite parsed folder": "https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/phabox", + "Suite parsed folder": "https://github.com/Helmholtz-UFZ/galaxy-tools/tree/master/tools/phabox", "bio.tool ID": "phabox", "bio.tool name": "PhaBOX", "bio.tool description": "Web server for identifying and characterizing phage contigs in metagenomic data.", "biii ID": null, + "Related Workflows": [], + "Related Tutorials": [], "Number of tools on UseGalaxy.org (Main)": 0, "Number of tools on UseGalaxy.org.au": 0, "Number of tools on UseGalaxy.eu": 0, "Number of tools on UseGalaxy.fr": 0, "Number of tools on APOSTL": 0, - "Number of tools on MBAC Metabiome Portal": 0, "Number of tools on ChemFlow": 0, "Number of tools on CIRM-CFBP": 0, "Number of tools on Coloc-stats": 0, @@ -47204,7 +47557,6 @@ "Number of tools on MISSISSIPPI": 0, "Number of tools on Oqtans": 0, "Number of tools on Palfinder": 0, - "Number of tools on PepSimili": 0, "Number of tools on PhagePromotor": 0, "Number of tools on UseGalaxy.be": 0, "Number of tools on UseGalaxy.cz": 0, @@ -47230,8 +47582,6 @@ "Suite runs (last 5 years) on main servers": 0, "Suite users on main servers": 0, "Suite users (last 5 years) on main servers": 0, - "Related Workflows": [], - "Related Tutorials": [], "To keep": true, "Deprecated": false }, @@ -47247,7 +47597,7 @@ "Description": "Phage host interaction toolkit report generator", "Suite first commit date": "2025-06-04", "Homepage": "https://git.ufz.de/borimcor/phage-host-analysis", - "Suite version": "0.3.0", + "Suite version": "@TOOL_VERSION@+galaxy@VERSION_SUFFIX@", "Suite conda package": "bioconductor-biostrings", "Latest suite conda package version": "2.78.0", "Suite version status": "To update", @@ -47260,17 +47610,20 @@ "EDAM reduced topics": [], "Suite owner": "ufz", "Suite source": "https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phi-toolkit", - "Suite parsed folder": "https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/phi-toolkit", + "Suite parsed folder": "https://github.com/Helmholtz-UFZ/galaxy-tools/tree/master/tools/phi-toolkit", "bio.tool ID": null, "bio.tool name": null, "bio.tool description": null, "biii ID": null, + "Related Workflows": [ + "https://usegalaxy.eu/published/workflow?id=c62d65832377e376" + ], + "Related Tutorials": [], "Number of tools on UseGalaxy.org (Main)": 1, "Number of tools on UseGalaxy.org.au": 0, "Number of tools on UseGalaxy.eu": 1, "Number of tools on UseGalaxy.fr": 0, "Number of tools on APOSTL": 0, - "Number of tools on MBAC Metabiome Portal": 0, "Number of tools on ChemFlow": 0, "Number of tools on CIRM-CFBP": 0, "Number of tools on Coloc-stats": 0, @@ -47287,7 +47640,6 @@ "Number of tools on MISSISSIPPI": 0, "Number of tools on Oqtans": 0, "Number of tools on Palfinder": 0, - "Number of tools on PepSimili": 0, "Number of tools on PhagePromotor": 0, "Number of tools on UseGalaxy.be": 0, "Number of tools on UseGalaxy.cz": 0, @@ -47313,10 +47665,6 @@ "Suite runs (last 5 years) on main servers": 0, "Suite users on main servers": 0, "Suite users (last 5 years) on main servers": 0, - "Related Workflows": [ - "https://usegalaxy.eu/published/workflow?id=c62d65832377e376" - ], - "Related Tutorials": [], "To keep": true, "Deprecated": false }, @@ -47332,7 +47680,7 @@ "Description": "A tool for analyzing and visualizing the relationship between various doses and their corresponding biological responses", "Suite first commit date": "2024-04-06", "Homepage": "https://github.com/bernt-matthias/mb-galaxy-tools", - "Suite version": "3.0.1", + "Suite version": "@TOOL_VERSION@+galaxy@VERSION_SUFFIX@", "Suite conda package": "r-drc", "Latest suite conda package version": "3.0_1", "Suite version status": "To update", @@ -47345,17 +47693,18 @@ "EDAM reduced topics": [], "Suite owner": "ufz", "Suite source": "https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/tox_tools/dose_responses", - "Suite parsed folder": "https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/tox_tools/dose_responses", + "Suite parsed folder": "https://github.com/Helmholtz-UFZ/galaxy-tools/tree/master/tools/tox_tools/dose_responses", "bio.tool ID": null, "bio.tool name": null, "bio.tool description": null, "biii ID": null, + "Related Workflows": [], + "Related Tutorials": [], "Number of tools on UseGalaxy.org (Main)": 0, "Number of tools on UseGalaxy.org.au": 0, "Number of tools on UseGalaxy.eu": 0, "Number of tools on UseGalaxy.fr": 0, "Number of tools on APOSTL": 0, - "Number of tools on MBAC Metabiome Portal": 0, "Number of tools on ChemFlow": 0, "Number of tools on CIRM-CFBP": 0, "Number of tools on Coloc-stats": 0, @@ -47372,7 +47721,6 @@ "Number of tools on MISSISSIPPI": 0, "Number of tools on Oqtans": 0, "Number of tools on Palfinder": 0, - "Number of tools on PepSimili": 0, "Number of tools on PhagePromotor": 0, "Number of tools on UseGalaxy.be": 0, "Number of tools on UseGalaxy.cz": 0, @@ -47398,8 +47746,6 @@ "Suite runs (last 5 years) on main servers": 0, "Suite users on main servers": 0, "Suite users (last 5 years) on main servers": 0, - "Related Workflows": [], - "Related Tutorials": [], "To keep": true, "Deprecated": false }, @@ -47417,10 +47763,10 @@ "Description": "Virus Identification By iteRative ANnoTation", "Suite first commit date": "2024-09-11", "Homepage": "https://github.com/AnantharamanLab/VIBRANT", - "Suite version": "1.2.1", + "Suite version": "@TOOL_VERSION@+galaxy@VERSION_SUFFIX@", "Suite conda package": "vibrant", "Latest suite conda package version": "1.2.1", - "Suite version status": "Up-to-date", + "Suite version status": "To update", "ToolShed categories": [ "Metagenomics" ], @@ -47450,17 +47796,21 @@ ], "Suite owner": "ufz", "Suite source": "https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant", - "Suite parsed folder": "https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/vibrant", + "Suite parsed folder": "https://github.com/Helmholtz-UFZ/galaxy-tools/tree/master/tools/vibrant", "bio.tool ID": "VIBRANT", "bio.tool name": "VIBRANT", "bio.tool description": "Automated recovery, annotation and curation of microbial viruses, and evaluation of virome function from genomic sequences.Virus Identification By iteRative ANnoTation.Discovery Environment Applications List.Created by upendra_35, last modified on Nov 04, 2019.If you find VIBRANT useful please consider citing our preprint on bioRxiv:.Kieft, K., Zhou, Z., and Anantharaman, K. (2019). VIBRANT: Automated recovery, annotation and curation of microbial viruses, and evaluation of virome function from genomic sequences. BioRxiv 855387.VIBRANT is a tool for automated recovery and annotation of bacterial and archaeal viruses, determination of genome completeness, and characterization of virome function from metagenomic assemblies.The QuickStart tutorial provides an introduction to basic DE functionality and navigation.Please work through the tutorial and use the intercom button on the bottom right of this page if you have any questions", "biii ID": null, + "Related Workflows": [ + "https://usegalaxy.eu/published/workflow?id=87231a6a7938cb95", + "https://usegalaxy.eu/published/workflow?id=c62d65832377e376" + ], + "Related Tutorials": [], "Number of tools on UseGalaxy.org (Main)": 1, "Number of tools on UseGalaxy.org.au": 0, "Number of tools on UseGalaxy.eu": 1, "Number of tools on UseGalaxy.fr": 0, "Number of tools on APOSTL": 0, - "Number of tools on MBAC Metabiome Portal": 0, "Number of tools on ChemFlow": 0, "Number of tools on CIRM-CFBP": 0, "Number of tools on Coloc-stats": 0, @@ -47477,7 +47827,6 @@ "Number of tools on MISSISSIPPI": 0, "Number of tools on Oqtans": 0, "Number of tools on Palfinder": 0, - "Number of tools on PepSimili": 0, "Number of tools on PhagePromotor": 0, "Number of tools on UseGalaxy.be": 0, "Number of tools on UseGalaxy.cz": 0, @@ -47503,11 +47852,6 @@ "Suite runs (last 5 years) on main servers": 1586, "Suite users on main servers": 65, "Suite users (last 5 years) on main servers": 65, - "Related Workflows": [ - "https://usegalaxy.eu/published/workflow?id=87231a6a7938cb95", - "https://usegalaxy.eu/published/workflow?id=c62d65832377e376" - ], - "Related Tutorials": [], "To keep": true, "Deprecated": false }, @@ -47524,10 +47868,10 @@ "Description": "VirSorter2 applies a multi-classifier, expert-guided approach to detect diverse DNA and RNA virus genomes.", "Suite first commit date": "2024-06-20", "Homepage": "https://github.com/jiarong/VirSorter2/", - "Suite version": "2.2.4", + "Suite version": "@TOOL_VERSION@+galaxy@VERSION_SUFFIX@", "Suite conda package": "virsorter", "Latest suite conda package version": "2.2.4", - "Suite version status": "Up-to-date", + "Suite version status": "To update", "ToolShed categories": [ "Metagenomics" ], @@ -47545,17 +47889,21 @@ ], "Suite owner": "ufz", "Suite source": "https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/virsorter", - "Suite parsed folder": "https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/virsorter", + "Suite parsed folder": "https://github.com/Helmholtz-UFZ/galaxy-tools/tree/master/tools/virsorter", "bio.tool ID": "virsorter", "bio.tool name": "virsorter", "bio.tool description": "Identify DNA and RNA virus sequences.", "biii ID": null, + "Related Workflows": [ + "https://usegalaxy.eu/published/workflow?id=62392daea25a3980", + "https://usegalaxy.eu/published/workflow?id=87231a6a7938cb95" + ], + "Related Tutorials": [], "Number of tools on UseGalaxy.org (Main)": 0, "Number of tools on UseGalaxy.org.au": 0, "Number of tools on UseGalaxy.eu": 1, "Number 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assembly, Whole genome sequencing, Public health and epidemiology, Genomics, Microbiology, Antimicrobial resistance + Filtering, Mapping assembly, Sequence assembly visualisation, Sequencing quality control, Statistical calculation, Genome assembly, Sequence assembly validation, Sequence contamination filtering, Visualisation, Sequencing error detection, Sequence composition calculation, Sequence alignment, De-novo assembly, Cross-assembly, Scatter plot plotting, Read mapping, Box-Whisker plot plotting + 2021-03-24 + 2026-01-05 + 16 + True + False + False + True + polypolish, bandage_image, bwa_mem2, porechop, upload1, __EXTRACT_DATASET__, nanoplot, __FLATTEN__, quast, fastp, CONVERTER_bz2_to_uncompressed, fastqc, flye, filtlong + UseGalaxy.be, UseGalaxy.eu + UseGalaxy.cz, UseGalaxy.fr + 0 + + 11648 + 17299 + 7.766667 + 0 + Assembly Making sense of a newly assembled genome https://training.galaxyproject.org//topics/assembly/tutorials/ecoli_comparison/tutorial.html Sequence assembly, Genomics, Microbiology - Sequence visualisation, Read mapping, Mapping, Sequence alignment, Genome visualisation + Sequence alignment, Mapping, Genome visualisation, Read mapping, Sequence visualisation 2018-06-14 2026-04-13 30 @@ -95,14 +119,14 @@ False False True - jbrowse, cat1, collapse_dataset, tp_replace_in_column, random_lines1, tp_replace_in_line, join1, fasta_filter_by_length, circos_interval_to_tiles, tp_sort_header_tool, Filter1, fasta_compute_length, addValue, tp_cat, bedtools_intersectbed, circos, tp_sed_tool, datamash_ops, tp_grep_tool, mergeCols1, Cut1, bedtools_sortbed, upload1, Grep1, circos_aln_to_links, lastz_wrapper_2, bedtools_complementbed + Filter1, collapse_dataset, join1, tp_sort_header_tool, bedtools_intersectbed, addValue, datamash_ops, circos, circos_interval_to_tiles, upload1, cat1, tp_replace_in_column, bedtools_sortbed, random_lines1, fasta_compute_length, circos_aln_to_links, tp_cat, tp_replace_in_line, mergeCols1, bedtools_complementbed, jbrowse, Grep1, fasta_filter_by_length, tp_grep_tool, lastz_wrapper_2, tp_sed_tool, Cut1 0 - 6969 - 13261 - 8.116667 + 7029 + 13334 + 8.166667 0 @@ -111,7 +135,7 @@ Unicycler Assembly https://training.galaxyproject.org//topics/assembly/tutorials/unicycler-assembly/tutorial.html Sequence assembly, Genomics, Microbiology - Statistical calculation, Genome assembly, Coding region prediction, Visualisation, Sequence assembly validation, Validation, Gene prediction, Sequence composition calculation, Aggregation, Genome annotation, Sequencing quality control + Statistical calculation, Sequencing quality control, Genome assembly, Sequence assembly validation, Visualisation, Genome annotation, Sequence composition calculation, Aggregation, Validation, Gene prediction, Coding region prediction 2017-10-11 2026-01-23 25 @@ -119,86 +143,62 @@ True False True - multiqc, fastqc, unicycler, quast, prokka + unicycler, quast, prokka, fastqc, multiqc UseGalaxy.org.au, UseGalaxy.eu, UseGalaxy.org (Main) Galaxy@AuBi, GalaxyTrakr, MISSISSIPPI, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no 0 - 3823772 - 9058168 + 3931702 + 9259758 7.083333 0 - - - Assembly - Genome Assembly of a bacterial genome (MRSA) sequenced using Illumina MiSeq Data - https://training.galaxyproject.org//topics/assembly/tutorials/mrsa-illumina/tutorial.html - Sequence assembly, Whole genome sequencing, Public health and epidemiology, Genomics, Microbiology - Sequence assembly visualisation, Read mapping, Genome assembly, Visualisation, Sequence assembly validation, Sequence contamination filtering, Sequencing quality control - 2021-03-24 - 2026-01-05 - 18 - True - False - True - True - upload1, shovill, bandage_image, fastp, bandage_info, quast, falco - UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main) - - 0 - - 11568 - 17594 - 9.533333 - 0 - Assembly Assembly of metagenomic sequencing data https://training.galaxyproject.org//topics/assembly/tutorials/metagenomics-assembly/tutorial.html Metagenomics, Sequence assembly - Sequence alignment analysis, Statistical calculation, Primer removal, Genome assembly, Visualisation, Local alignment, Sequence composition calculation, Formatting, Variant calling, Sequence file editing, Sequence assembly visualisation, Read mapping, Sequence assembly validation, Data handling, Read pre-processing, Sequence contamination filtering, Sequence trimming, Sequencing quality control - 2026-05-21 - 2026-05-21 + Variant calling, Sequence assembly validation, Primer removal, Visualisation, Sequence composition calculation, Local alignment, Read mapping, Sequence assembly visualisation, Sequencing quality control, Statistical calculation, Genome assembly, Sequence contamination filtering, Data handling, Sequence trimming, Sequence alignment analysis, Sequence file editing, Formatting, Read pre-processing + 2026-07-01 + 2026-07-01 0 True False True True - metaspades, collection_column_join, bandage_image, filter_tabular, coverm_contig, megahit_contig2fastg, bamtools, fastqc, bandage_info, megahit, bowtie2, tp_cat, quast, ngsutils_bam_filter, seqtk_subseq, random_lines1, cutadapt, bg_uniq + bandage_info, bowtie2, megahit, cutadapt, bandage_image, tp_cat, bamtools, collection_column_join, bg_uniq, coverm_contig, ngsutils_bam_filter, random_lines1, quast, seqtk_subseq, metaspades, fastqc, filter_tabular, megahit_contig2fastg UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main) 0 - 6 - 7 - 11.666667 + 3 + 3 + 27.166667 0 Assembly - Genome Assembly of MRSA from Oxford Nanopore MinION data (and optionally Illumina data) - https://training.galaxyproject.org//topics/assembly/tutorials/mrsa-nanopore/tutorial.html - Sequence assembly, Whole genome sequencing, Public health and epidemiology, Genomics, Microbiology, Antimicrobial resistance - Scatter plot plotting, De-novo assembly, Sequence assembly visualisation, Statistical calculation, Genome assembly, Sequencing error detection, Read mapping, Visualisation, Filtering, Sequence assembly validation, Sequence alignment, Box-Whisker plot plotting, Sequence composition calculation, Cross-assembly, Mapping assembly, Sequence contamination filtering, Sequencing quality control + Genome Assembly of a bacterial genome (MRSA) sequenced using Illumina MiSeq Data + https://training.galaxyproject.org//topics/assembly/tutorials/mrsa-illumina/tutorial.html + Sequence assembly, Whole genome sequencing, Public health and epidemiology, Genomics, Microbiology + Sequence assembly visualisation, Sequencing quality control, Genome assembly, Sequence assembly validation, Visualisation, Read mapping, Sequence contamination filtering 2021-03-24 2026-01-05 - 16 + 18 True False - False True - upload1, bandage_image, nanoplot, porechop, filtlong, fastqc, flye, __EXTRACT_DATASET__, fastp, polypolish, quast, __FLATTEN__, CONVERTER_bz2_to_uncompressed, bwa_mem2 - UseGalaxy.be, UseGalaxy.eu - UseGalaxy.cz, UseGalaxy.fr + True + bandage_info, bandage_image, upload1, quast, fastp, falco, shovill + UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main) + 0 - 11438 - 16929 - 7.583333 + 11970 + 18118 + 9.583333 0 @@ -207,7 +207,7 @@ Checking expected species and contamination in bacterial isolate https://training.galaxyproject.org//topics/ecology/tutorials/bacterial-isolate-species-contamination-checking/tutorial.html Whole genome sequencing, Genomics, Microbiology, Microbial ecology - Cross-assembly, Expression analysis, Taxonomic classification, Statistical calculation + Expression analysis, Cross-assembly, Statistical calculation, Taxonomic classification 2024-03-04 2026-04-08 6 @@ -215,14 +215,14 @@ False False True - recentrifuge, upload1, kraken2, est_abundance + upload1, est_abundance, recentrifuge, kraken2 UseGalaxy.eu, UseGalaxy.fr Galaxy@AuBi, GalaxyTrakr, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.org (Main) 0 - 1036 - 1378 - 8.266667 + 1067 + 1415 + 8.516667 0 @@ -244,8 +244,8 @@ 0 - 2502 - 3565 + 2636 + 3732 8.050000 0 @@ -255,7 +255,7 @@ Identifying tuberculosis transmission links: from SNPs to transmission clusters https://training.galaxyproject.org//topics/evolution/tutorials/mtb_transmission/tutorial.html Genomics, Microbiology, Infectious disease, DNA polymorphism - Phylogenetic tree visualisation, Antimicrobial resistance prediction, Variant calling, Phylogenetic tree generation + Variant calling, Phylogenetic tree visualisation, Antimicrobial resistance prediction, Phylogenetic tree generation 2022-03-16 2025-05-26 13 @@ -263,14 +263,14 @@ False False True - addName, __MERGE_COLLECTION__, trimmomatic, collapse_dataset, tp_replace_in_line, snippy, samtools_view, tp_cat, tp_sed_tool, tb_variant_filter, bcftools_consensus, snp_sites, tp_grep_tool, tb_profiler_profile, upload1, Grep1, clustering_from_distmat, snp_dists, tp_easyjoin_tool + bcftools_consensus, tp_easyjoin_tool, __MERGE_COLLECTION__, snp_dists, collapse_dataset, tb_profiler_profile, tb_variant_filter, samtools_view, snippy, snp_sites, addName, upload1, tp_cat, tp_replace_in_line, trimmomatic, Grep1, tp_grep_tool, tp_sed_tool, clustering_from_distmat UseGalaxy.eu 0 - 3555 - 5077 - 7.800000 + 3741 + 5323 + 7.750000 0 @@ -279,7 +279,7 @@ Phylogenetic analysis for bacterial comparative genomics https://training.galaxyproject.org//topics/evolution/tutorials/bacterial-comparative-genomics/tutorial.html Genomics, Microbiology, Phylogeny - Phylogenetic tree generation (maximum likelihood and Bayesian methods), Phylogenetic tree generation (from molecular sequences) + 2025-03-14 2025-03-14 1 @@ -292,9 +292,9 @@ GalaxyTrakr 0 - 198 - 239 - 10.266667 + 220 + 261 + 12.266667 0 @@ -303,7 +303,7 @@ Genome annotation with Prokka https://training.galaxyproject.org//topics/genome-annotation/tutorials/annotation-with-prokka/tutorial.html Genomics, Microbiology, Gene and protein families, Sequence analysis - Coding region prediction, Gene prediction, Genome annotation, Genome visualisation + Genome annotation, Gene prediction, Genome visualisation, Coding region prediction 2018-03-06 2026-01-23 27 @@ -311,62 +311,62 @@ True True True - jbrowse, prokka + prokka, jbrowse UseGalaxy.be, UseGalaxy.eu, UseGalaxy.org (Main) Galaxy@AuBi, GalaxyTrakr, MISSISSIPPI, UseGalaxy.org.au, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no 0 - 3829962 - 9068268 + 3937916 + 9269864 7.166667 0 Genome Annotation - Refining Genome Annotations with Apollo (prokaryotes) - https://training.galaxyproject.org//topics/genome-annotation/tutorials/apollo/tutorial.html - Genomics, Microbiology, Gene and protein families, Sequence analysis - Genome visualisation - 2021-06-04 - 2025-05-15 - 22 - True + Bacterial Genome Annotation + https://training.galaxyproject.org//topics/genome-annotation/tutorials/bacterial-genome-annotation/tutorial.html + Genomics, Microbiology, Gene and protein families, Sequence analysis, Whole genome sequencing, Functional genomics, Mobile genetic elements + Structural variation detection, Genome visualisation, Genome assembly, Multilocus sequence typing, Genome annotation, Nucleic acid feature detection, Scaffolding, Sequence motif recognition, Protein feature detection + 2024-02-01 + 2024-10-15 + 6 True + False True True - jbrowse, iframe, list_organism, create_account, create_or_update - - UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.no + jbrowse, Grouping1, bakta, plasmidfinder, upload1, tp_replace_in_column, tbl2gff3, isescan, integron_finder, tp_tail_tool + UseGalaxy.eu, UseGalaxy.fr + Galaxy@AuBi, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.org (Main) 0 - 3585787 - 8259740 - 13.183333 + 8849 + 12131 + 7.933333 0 Genome Annotation - Bacterial Genome Annotation - https://training.galaxyproject.org//topics/genome-annotation/tutorials/bacterial-genome-annotation/tutorial.html - Genomics, Microbiology, Gene and protein families, Sequence analysis, Whole genome sequencing, Functional genomics, Mobile genetic elements - Protein feature detection, Structural variation detection, Genome assembly, Scaffolding, Multilocus sequence typing, Genome visualisation, Nucleic acid feature detection, Sequence motif recognition, Genome annotation - 2024-02-01 - 2024-10-15 - 6 + Refining Genome Annotations with Apollo (prokaryotes) + https://training.galaxyproject.org//topics/genome-annotation/tutorials/apollo/tutorial.html + Genomics, Microbiology, Gene and protein families, Sequence analysis + Genome visualisation + 2021-06-04 + 2025-05-15 + 22 True - False True True - isescan, upload1, Grouping1, plasmidfinder, integron_finder, tbl2gff3, jbrowse, tp_tail_tool, tp_replace_in_column, bakta - UseGalaxy.eu, UseGalaxy.fr - Galaxy@AuBi, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.org (Main) + True + list_organism, jbrowse, create_or_update, create_account, iframe + + UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.no 0 - 8485 - 11611 - 7.716667 + 3693456 + 8460925 + 13.216667 0 @@ -375,7 +375,7 @@ Identification of AMR genes in an assembled bacterial genome https://training.galaxyproject.org//topics/genome-annotation/tutorials/amr-gene-detection/tutorial.html Whole genome sequencing, Public health and epidemiology, Genomics, Microbiology, Sequence analysis, Infectious disease, Antimicrobial resistance - Genome annotation, Antimicrobial resistance prediction, Genome visualisation, Read mapping + Antimicrobial resistance prediction, Genome annotation, Genome visualisation, Read mapping 2024-01-23 2025-12-18 10 @@ -383,62 +383,62 @@ False True True - upload1, Grep1, tbl2gff3, jbrowse, bowtie2, staramr_search, bakta + bowtie2, jbrowse, bakta, staramr_search, upload1, Grep1, tbl2gff3 Galaxy@AuBi, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr UseGalaxy.org (Main) 0 - 4294 - 5838 - 9.300000 + 4562 + 6177 + 9.133333 0 Genome Annotation - Bacterial genome quality control - https://training.galaxyproject.org//topics/genome-annotation/tutorials/bacterial-genome-quality-control/tutorial.html + Dataset construction for bacterial comparative genomics + https://training.galaxyproject.org//topics/genome-annotation/tutorials/bacterial-comparative-genomics-dataset-construction/tutorial.html Genomics, Microbiology - Validation, Genome comparison, Sequence composition calculation, Statistical calculation, Sequence assembly validation, Sequencing quality control - 2025-03-14 + Sequence database search, Data retrieval, Data handling 2025-03-14 - 1 + 2026-04-13 + 2 True False False False - checkm2, drep_dereplicate, upload1 - UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main) - GalaxyTrakr, UseGalaxy.cz + sort1, datasets_download_genome, Remove beginning1, upload1, cat1, bg_uniq, Cut1 + UseGalaxy.fr + UseGalaxy.cz 0 - 195 - 233 - 7.733333 + 134 + 152 + 12.733333 0 Genome Annotation - Dataset construction for bacterial comparative genomics - https://training.galaxyproject.org//topics/genome-annotation/tutorials/bacterial-comparative-genomics-dataset-construction/tutorial.html + Bacterial genome quality control + https://training.galaxyproject.org//topics/genome-annotation/tutorials/bacterial-genome-quality-control/tutorial.html Genomics, Microbiology - Data handling, Data retrieval, Sequence database search + Statistical calculation, Sequencing quality control, Sequence assembly validation, Genome comparison, Validation, Sequence composition calculation 2025-03-14 - 2026-04-13 - 2 + 2025-03-14 + 1 True False False False - upload1, sort1, Remove beginning1, cat1, Cut1, datasets_download_genome, bg_uniq - UseGalaxy.fr - UseGalaxy.cz + upload1, drep_dereplicate, checkm2 + UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main) + GalaxyTrakr, UseGalaxy.cz 0 - 115 - 133 - 11.683333 + 223 + 263 + 12.216667 0 @@ -447,7 +447,7 @@ Comparative gene analysis in unannotated genomes https://training.galaxyproject.org//topics/genome-annotation/tutorials/gene-centric/tutorial.html Genomics, Gene and protein families, Sequence analysis, Phylogeny, Comparative genomics - Sequence alignment analysis, Multiple sequence alignment, Database search, De-novo assembly, Transcriptome assembly, Coding region prediction, Phylogenetic tree generation + De-novo assembly, Sequence alignment analysis, Multiple sequence alignment, Database search, Transcriptome assembly, Phylogenetic tree generation, Coding region prediction 2022-09-08 2025-06-03 10 @@ -455,14 +455,14 @@ False False True - bg_diamond_makedb, gops_intersect_1, bg_diamond_view, tp_split_on_column, bg_diamond, Filter1, cat1, Add_a_column1, orfipy, tab2fasta, rbc_mafft, collapse_dataset, Cut1, rapidnj, regexColumn1, join1 + bg_diamond_view, bg_diamond, gops_intersect_1, cat1, Filter1, rapidnj, regexColumn1, tab2fasta, join1, collapse_dataset, orfipy, Add_a_column1, tp_split_on_column, rbc_mafft, bg_diamond_makedb, Cut1 UseGalaxy.eu, UseGalaxy.org (Main) UseGalaxy.cz 0 - 2056 - 2827 - 9.833333 + 2094 + 2869 + 9.950000 0 @@ -471,7 +471,7 @@ Essential genes detection with Transposon insertion sequencing https://training.galaxyproject.org//topics/genome-annotation/tutorials/tnseq/tutorial.html Genomics, Microbiology, Sequence analysis, Mobile genetic elements - Primer removal, Sequence trimming, Transposon prediction, Read pre-processing + Sequence trimming, Transposon prediction, Primer removal, Read pre-processing 2019-07-02 2024-03-18 12 @@ -479,14 +479,14 @@ True False True - transit_gumbel, __EXTRACT_DATASET__, tp_sort_header_tool, Filter1, Add_a_column1, gff_to_prot, Cut1, deeptools_bam_coverage, tp_easyjoin_tool, cutadapt, bowtie_wrapper, bg_find_subsequences + gff_to_prot, cutadapt, bowtie_wrapper, tp_easyjoin_tool, deeptools_bam_coverage, Filter1, __EXTRACT_DATASET__, bg_find_subsequences, Add_a_column1, transit_gumbel, tp_sort_header_tool, Cut1 UseGalaxy.org.au, UseGalaxy.be, UseGalaxy.no UseGalaxy.cz, UseGalaxy.eu 0 - 3819196 - 9051236 - 5.700000 + 3926930 + 9252504 + 5.750000 0 @@ -495,7 +495,7 @@ Microbial Variant Calling https://training.galaxyproject.org//topics/variant-analysis/tutorials/microbial-variants/tutorial.html Genomics, Sequence assembly, DNA polymorphism, Microbiology, Sequence analysis, Genetic variation - Phylogenetic tree visualisation, Variant calling, Genome visualisation, Phylogenetic tree generation + Variant calling, Phylogenetic tree visualisation, Genome visualisation, Phylogenetic tree generation 2018-02-26 2026-01-23 25 @@ -503,14 +503,14 @@ False False True - jbrowse, snippy + snippy, jbrowse UseGalaxy.be, UseGalaxy.eu, UseGalaxy.org (Main) GalaxyTrakr, UseGalaxy.org.au, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no 0 - 16133 - 25453 - 5.000000 + 16380 + 25775 + 5.033333 0 @@ -519,7 +519,7 @@ Analyses of metagenomics data - The global picture https://training.galaxyproject.org//topics/microbiome/tutorials/general-tutorial/tutorial.html Metagenomics, Microbial ecology, Taxonomy, Sequence analysis, Metabarcoding - Phylogenetic analysis, Taxonomic classification, Sequencing quality control, Visualisation, Sequence read processing, Sequence clustering, DNA barcoding + Sequencing quality control, Phylogenetic analysis, Visualisation, Sequence read processing, Taxonomic classification, Sequence clustering, DNA barcoding 2017-06-22 2024-08-09 4 @@ -527,38 +527,38 @@ False False True - mothur_filter_seqs, humann2_renorm_table, mothur_pre_cluster, humann2, mothur_cluster_split, metaphlan2, mothur_align_seqs, mothur_screen_seqs, mothur_make_biom, mothur_make_group, mothur_classify_otu, mothur_make_shared, mothur_summary_seqs, taxonomy_krona_chart, krona-text, mothur_merge_files, metaphlan2krona, mothur_unique_seqs, mothur_classify_seqs, humann2_regroup_table, mothur_count_seqs + mothur_classify_seqs, humann2, mothur_merge_files, mothur_classify_otu, krona-text, mothur_filter_seqs, taxonomy_krona_chart, mothur_pre_cluster, metaphlan2, mothur_summary_seqs, mothur_align_seqs, mothur_make_biom, mothur_screen_seqs, humann2_renorm_table, humann2_regroup_table, mothur_unique_seqs, mothur_count_seqs, mothur_make_shared, mothur_cluster_split, metaphlan2krona, mothur_make_group UseGalaxy.org.au, UseGalaxy.fr, UseGalaxy.no 0 - 11137 - 14970 + 11493 + 15412 5.733333 0 Microbiome - Metatranscriptomics analysis using microbiome RNA-seq data (short) - https://training.galaxyproject.org//topics/microbiome/tutorials/metatranscriptomics-short/tutorial.html - Metatranscriptomics, Microbial ecology, Taxonomy, Function analysis, Sequence analysis - Sequence alignment analysis, Phylogenetic tree visualisation, Statistical calculation, Primer removal, Phylogenetic inference, Visualisation, Species frequency estimation, Sequence composition calculation, Sequence comparison, Phylogenetic tree editing, Phylogenetic analysis, Taxonomic classification, Conversion, Validation, Sequence similarity search, Read pre-processing, Sequence trimming, Sequencing quality control - 2020-02-13 - 2025-06-16 - 6 + Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition + https://training.galaxyproject.org//topics/microbiome/tutorials/pathogen-detection-from-nanopore-foodborne-data/tutorial.html + Metagenomics, Public health and epidemiology, Taxonomy, Sequence assembly, Pathology, Sequence analysis + Variant calling, Phylogenetic tree reconstruction, Mapping assembly, Multiple sequence alignment, Base-calling, Visualisation, Sequence composition calculation, Aggregation, Phylogenetic tree generation, Phylogenetic tree analysis, De-novo assembly, Pairwise sequence alignment, Mapping, Scatter plot plotting, Sequence assembly, Box-Whisker plot plotting, Sequence assembly visualisation, Sequencing quality control, Statistical calculation, Genome assembly, Multilocus sequence typing, Sequence contamination filtering, Antimicrobial resistance prediction, Data handling, Sequence alignment analysis, Cross-assembly, Taxonomic classification, Validation + 2023-01-26 + 2025-11-18 + 12 True False True True - graphlan_annotate, tp_find_and_replace, graphlan, multiqc, bg_sortmerna, tp_sort_header_tool, export2graphlan, cutadapt, fastq_paired_end_interlacer, fastqc, Cut1, humann_renorm_table, humann, Grep1, taxonomy_krona_chart, metaphlan, combine_metaphlan2_humann2, humann_rename_table, humann_regroup_table, humann_unpack_pathways, humann_split_stratified_table - UseGalaxy.org.au, UseGalaxy.be, UseGalaxy.org (Main) - UseGalaxy.cz, UseGalaxy.no + __FILTER_EMPTY_DATASETS__, abricate, bcftools_consensus, __FILTER_FAILED_DATASETS__, bandage_image, collection_column_join, clair3, Remove beginning1, ggplot2_heatmap, Count1, collapse_dataset, collection_element_identifiers, regex1, tp_head_tool, fasta2tab, fasta_merge_files_and_filter_unique_sequences, bamtools_split_mapped, porechop, bedtools_getfastabed, samtools_depth, medaka_consensus_pipeline, minimap2, taxonomy_krona_chart, krakentools_kreport2krona, samtools_fastx, flye, mlst, kraken2, bcftools_norm, split_file_to_collection, clustalw, Cut1, snpSift_extractFields, Grouping1, samtools_coverage, tp_replace_in_column, param_value_from_file, tp_multijoin_tool, newick_display, fastp, barchart_gnuplot, Add_a_column1, tp_find_and_replace, krakentools_extract_kraken_reads, Paste1, nanoplot, tp_sorted_uniq, snpSift_filter, tp_cut_tool, Grep1, tab2fasta, __BUILD_LIST__, regexColumn1, table_compute, compose_text_param, add_line_to_file, fastqc, fasttree, tp_split_on_column, multiqc, CONVERTER_gz_to_uncompressed + UseGalaxy.eu + UseGalaxy.org.au, UseGalaxy.be, UseGalaxy.cz 0 - 1036 - 1323 - 9.983333 + 5895 + 8528 + 8.633333 0 @@ -567,7 +567,7 @@ Taxonomic Profiling and Visualization of Metagenomic Data https://training.galaxyproject.org//topics/microbiome/tutorials/taxonomic-profiling/tutorial.html Metagenomics, Microbial ecology, Taxonomy, Sequence analysis - Taxonomic classification, Aggregation, Statistical calculation, Visualisation, Genome annotation + Statistical calculation, Taxonomic classification, Visualisation, Genome annotation, Aggregation 2023-05-03 2026-05-11 8 @@ -575,14 +575,38 @@ False True True - taxonomy_krona_chart, interactive_tool_phinch, est_abundance, kraken_biom, metaphlan, __UNZIP_COLLECTION__, krakentools_kreport2krona, interactive_tool_pavian, kraken2 + metaphlan, __UNZIP_COLLECTION__, interactive_tool_pavian, interactive_tool_phinch, taxonomy_krona_chart, krakentools_kreport2krona, est_abundance, kraken_biom, kraken2 UseGalaxy.org.au, UseGalaxy.be, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main) 0 - 14694 - 19544 - 5.583333 + 15278 + 20295 + 5.650000 + 0 + + + + Microbiome + Metatranscriptomics analysis using microbiome RNA-seq data + https://training.galaxyproject.org//topics/microbiome/tutorials/metatranscriptomics/tutorial.html + Metatranscriptomics, Microbial ecology, Taxonomy, Function analysis, Sequence analysis + Phylogenetic tree visualisation, Primer removal, Visualisation, Sequence composition calculation, Aggregation, Phylogenetic tree editing, Phylogenetic inference, Statistical calculation, Sequencing quality control, Phylogenetic analysis, Conversion, Sequence trimming, Taxonomic classification, Species frequency estimation, Sequence alignment analysis, Sequence comparison, Validation, Read pre-processing, Sequence similarity search + 2019-11-21 + 2025-06-16 + 6 + True + True + True + True + metaphlan, cutadapt, fastq_paired_end_interlacer, humann_rename_table, combine_metaphlan_humann, graphlan, bg_sortmerna, humann_regroup_table, tp_sort_header_tool, taxonomy_krona_chart, humann, Grouping1, tp_find_and_replace, humann_renorm_table, humann_split_stratified_table, Grep1, export2graphlan, humann_unpack_pathways, fastqc, graphlan_annotate, multiqc, Cut1 + UseGalaxy.be, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.org (Main) + UseGalaxy.eu + 0 + + 3926230 + 9247565 + 6.883333 0 @@ -591,7 +615,7 @@ Antibiotic resistance detection https://training.galaxyproject.org//topics/microbiome/tutorials/plasmid-metagenomics-nanopore/tutorial.html Metagenomic sequencing, Public health and epidemiology, Metagenomics, Microbiology, Infectious disease, Sequence analysis, Antimicrobial resistance - Scatter plot plotting, De-novo assembly, Sequence assembly visualisation, Sequence analysis, Genome assembly, Pairwise sequence alignment, Antimicrobial resistance prediction, Box-Whisker plot plotting, Aggregation, Mapping assembly + Mapping assembly, Sequence assembly visualisation, Genome assembly, Antimicrobial resistance prediction, Aggregation, De-novo assembly, Pairwise sequence alignment, Scatter plot plotting, Sequence analysis, Box-Whisker plot plotting 2019-06-25 2024-06-14 4 @@ -599,14 +623,14 @@ False True True - PlasFlow, bandage_image, nanoplot, miniasm, unicycler, racon, staramr_search, gfa_to_fa, minimap2 + PlasFlow, bandage_image, minimap2, staramr_search, unicycler, racon, gfa_to_fa, miniasm, nanoplot UseGalaxy.eu UseGalaxy.org.au, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org (Main) 0 - 4171 - 5713 - 6.783333 + 4331 + 5886 + 6.900000 0 @@ -615,7 +639,7 @@ 16S Microbial analysis with Nanopore data https://training.galaxyproject.org//topics/microbiome/tutorials/nanopore-16S-metagenomics/tutorial.html Microbial ecology, Taxonomy, Sequence analysis, Metabarcoding - Sequence contamination filtering, Validation, Sequence composition calculation, Taxonomic classification, Statistical calculation, Visualisation, Sequencing quality control + Sequencing quality control, Statistical calculation, Taxonomic classification, Sequence contamination filtering, Visualisation, Validation, Sequence composition calculation 2020-11-24 2024-07-31 5 @@ -623,110 +647,110 @@ False False True - taxonomy_krona_chart, porechop, datamash_reverse, multiqc, Remove beginning1, fastqc, fastp, tp_replace_in_line, kraken2 + tp_replace_in_line, Remove beginning1, datamash_reverse, taxonomy_krona_chart, fastp, fastqc, porechop, multiqc, kraken2 UseGalaxy.org.au, UseGalaxy.be, UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org (Main) GalaxyTrakr, UseGalaxy.cz, UseGalaxy.fr 0 - 10045 - 13873 - 5.433333 + 10366 + 14282 + 5.450000 0 Microbiome - Binning of metagenomic sequencing data - https://training.galaxyproject.org//topics/microbiome/tutorials/metagenomics-binning/tutorial.html - Metagenomics, Sequence assembly - Read mapping, Statistical calculation, Sequencing quality control, Sequence assembly validation, Read binning, Validation, Genome comparison, Sequence composition calculation, Sequence clustering, Genome annotation, Sequence assembly - 2023-12-05 - 2026-04-09 - 9 + Identification of the micro-organisms in a beer using Nanopore sequencing + https://training.galaxyproject.org//topics/microbiome/tutorials/beer-data-analysis/tutorial.html + Metagenomics, Microbial ecology, Taxonomy, Sequence analysis + Sequencing quality control, Statistical calculation, Taxonomic classification, Sequence contamination filtering, Visualisation, Sequence composition calculation, Aggregation + 2022-09-29 + 2024-11-29 + 5 True False True True - concoct, concoct_cut_up_fasta, __BUILD_LIST__, Fasta_to_Contig2Bin, concoct_coverage_table, das_tool, metabat2_jgi_summarize_bam_contig_depths, bowtie2, samtools_sort, drep_dereplicate, maxbin2, metabat2, concoct_merge_cut_up_clustering, semibin, binette, checkm_lineage_wf, concoct_extract_fasta_bins - UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr - GalaxyTrakr, UseGalaxy.org.au, UseGalaxy.org (Main) + Filter1, taxonomy_krona_chart, fastp, fastqc, krakentools_kreport2krona, porechop, kraken2 + UseGalaxy.org.au, UseGalaxy.be, UseGalaxy.eu, UseGalaxy.org (Main) + GalaxyTrakr, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no 0 - 7203 - 8810 - 5.333333 + 3516 + 5095 + 8.383333 0 Microbiome - Remove contamination and host reads - https://training.galaxyproject.org//topics/microbiome/tutorials/host-removal/tutorial.html - - Validation, Sequencing quality control, Read mapping - 2025-12-18 - 2026-05-12 - 3 + Metatranscriptomics analysis using microbiome RNA-seq data (short) + https://training.galaxyproject.org//topics/microbiome/tutorials/metatranscriptomics-short/tutorial.html + Metatranscriptomics, Microbial ecology, Taxonomy, Function analysis, Sequence analysis + Phylogenetic tree visualisation, Primer removal, Visualisation, Sequence composition calculation, Phylogenetic tree editing, Phylogenetic inference, Statistical calculation, Sequencing quality control, Phylogenetic analysis, Conversion, Sequence trimming, Taxonomic classification, Species frequency estimation, Sequence alignment analysis, Sequence comparison, Validation, Read pre-processing, Sequence similarity search + 2020-02-13 + 2025-06-16 + 6 True False True True - bowtie2, __ZIP_COLLECTION__, multiqc - Galaxy@AuBi, UseGalaxy.org.au, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main) - GalaxyTrakr, MISSISSIPPI, UseGalaxy.no + metaphlan, cutadapt, fastq_paired_end_interlacer, humann_rename_table, graphlan, bg_sortmerna, humann_regroup_table, tp_sort_header_tool, combine_metaphlan2_humann2, taxonomy_krona_chart, humann, tp_find_and_replace, humann_renorm_table, humann_split_stratified_table, Grep1, export2graphlan, humann_unpack_pathways, fastqc, graphlan_annotate, multiqc, Cut1 + UseGalaxy.org.au, UseGalaxy.be, UseGalaxy.org (Main) + UseGalaxy.cz, UseGalaxy.no 0 - 355 - 431 - 6.166667 + 1094 + 1386 + 9.866667 0 Microbiome - Metatranscriptomics analysis using microbiome RNA-seq data - https://training.galaxyproject.org//topics/microbiome/tutorials/metatranscriptomics/tutorial.html - Metatranscriptomics, Microbial ecology, Taxonomy, Function analysis, Sequence analysis - Sequence alignment analysis, Phylogenetic tree visualisation, Statistical calculation, Primer removal, Phylogenetic inference, Visualisation, Species frequency estimation, Sequence composition calculation, Sequence comparison, Phylogenetic tree editing, Phylogenetic analysis, Taxonomic classification, Conversion, Validation, Sequence similarity search, Aggregation, Read pre-processing, Sequence trimming, Sequencing quality control - 2019-11-21 - 2025-06-16 - 6 - True + Remove contamination and host reads + https://training.galaxyproject.org//topics/microbiome/tutorials/host-removal/tutorial.html + + Sequencing quality control, Validation, Read mapping + 2025-12-18 + 2026-05-12 + 3 True + False True True - graphlan_annotate, tp_find_and_replace, graphlan, multiqc, bg_sortmerna, tp_sort_header_tool, export2graphlan, cutadapt, fastq_paired_end_interlacer, Grouping1, fastqc, combine_metaphlan_humann, Cut1, humann_renorm_table, humann, Grep1, taxonomy_krona_chart, metaphlan, humann_rename_table, humann_regroup_table, humann_unpack_pathways, humann_split_stratified_table - UseGalaxy.be, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.org (Main) - UseGalaxy.eu + __ZIP_COLLECTION__, bowtie2, multiqc + Galaxy@AuBi, UseGalaxy.org.au, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main) + GalaxyTrakr, MISSISSIPPI, UseGalaxy.no 0 - 3818338 - 9046054 - 6.816667 + 471 + 573 + 9.583333 0 Microbiome - Building an amplicon sequence variant (ASV) table from 16S data using DADA2 - https://training.galaxyproject.org//topics/microbiome/tutorials/dada-16S/tutorial.html - Microbial ecology, Taxonomy, Sequence analysis, Metabarcoding - Analysis, Deposition, Visualisation, Variant calling, DNA barcoding - 2024-06-05 - 2026-04-13 - 12 + Binning of metagenomic sequencing data + https://training.galaxyproject.org//topics/microbiome/tutorials/metagenomics-binning/tutorial.html + Metagenomics, Sequence assembly + Statistical calculation, Sequencing quality control, Read binning, Sequence assembly validation, Genome annotation, Sequence composition calculation, Sequence assembly, Sequence clustering, Genome comparison, Validation, Read mapping + 2023-12-05 + 2026-04-09 + 9 True False True True - dada2_plotQualityProfile, dada2_mergePairs, cat1, tp_replace_in_column, tp_replace_in_line, __UNZIP_COLLECTION__, tp_head_tool, phyloseq_from_dada2, Grouping1, dada2_makeSequenceTable, __SORTLIST__, dada2_removeBimeraDenovo, collection_element_identifiers, dada2_assignTaxonomyAddspecies, dada2_filterAndTrim, Add_a_column1, dada2_seqCounts, interactive_tool_phyloseq, dada2_dada, dada2_learnErrors - UseGalaxy.org.au, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main) - + concoct_cut_up_fasta, bowtie2, maxbin2, concoct_coverage_table, metabat2, concoct, concoct_extract_fasta_bins, binette, checkm_lineage_wf, drep_dereplicate, __BUILD_LIST__, Fasta_to_Contig2Bin, samtools_sort, concoct_merge_cut_up_clustering, das_tool, semibin, metabat2_jgi_summarize_bam_contig_depths + UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr + GalaxyTrakr, UseGalaxy.org.au, UseGalaxy.org (Main) 0 - 9282 - 13212 - 5.466667 + 7493 + 9145 + 5.450000 0 @@ -735,7 +759,7 @@ Assembly of metagenomic sequencing data https://training.galaxyproject.org//topics/microbiome/tutorials/metagenomics-assembly/tutorial.html Metagenomics, Sequence assembly - Sequence alignment analysis, Statistical calculation, Primer removal, Genome assembly, Visualisation, Local alignment, Sequence composition calculation, Formatting, Variant calling, Sequence file editing, Sequence assembly visualisation, Read mapping, Sequence assembly validation, Data handling, Read pre-processing, Sequence contamination filtering, Sequence trimming, Sequencing quality control + Variant calling, Sequence assembly validation, Primer removal, Visualisation, Sequence composition calculation, Local alignment, Read mapping, Sequence assembly visualisation, Sequencing quality control, Statistical calculation, Genome assembly, Sequence contamination filtering, Data handling, Sequence trimming, Sequence alignment analysis, Sequence file editing, Formatting, Read pre-processing 2022-12-05 2026-05-11 11 @@ -743,86 +767,62 @@ False True True - metaspades, collection_column_join, bandage_image, filter_tabular, coverm_contig, megahit_contig2fastg, bamtools, fastqc, bandage_info, megahit, bowtie2, tp_cat, quast, ngsutils_bam_filter, seqtk_subseq, random_lines1, cutadapt, bg_uniq + bandage_info, bowtie2, megahit, cutadapt, bandage_image, tp_cat, bamtools, collection_column_join, bg_uniq, coverm_contig, ngsutils_bam_filter, random_lines1, quast, seqtk_subseq, metaspades, fastqc, filter_tabular, megahit_contig2fastg UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main) 0 - 5414 - 7491 - 10.150000 + 5645 + 7763 + 10.383333 0 Microbiome - Identification of the micro-organisms in a beer using Nanopore sequencing - https://training.galaxyproject.org//topics/microbiome/tutorials/beer-data-analysis/tutorial.html - Metagenomics, Microbial ecology, Taxonomy, Sequence analysis - Sequence contamination filtering, Sequence composition calculation, Aggregation, Statistical calculation, Taxonomic classification, Visualisation, Sequencing quality control - 2022-09-29 - 2024-11-29 - 5 - True - False - True - True - taxonomy_krona_chart, porechop, fastqc, Filter1, fastp, krakentools_kreport2krona, kraken2 - UseGalaxy.org.au, UseGalaxy.be, UseGalaxy.eu, UseGalaxy.org (Main) - GalaxyTrakr, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no - 0 - - 3449 - 5021 - 8.383333 - 0 - - - - Microbiome - Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition - https://training.galaxyproject.org//topics/microbiome/tutorials/pathogen-detection-from-nanopore-foodborne-data/tutorial.html - Metagenomics, Public health and epidemiology, Taxonomy, Sequence assembly, Pathology, Sequence analysis - Sequence alignment analysis, Statistical calculation, Genome assembly, Visualisation, Antimicrobial resistance prediction, Mapping, Phylogenetic tree generation (maximum likelihood and Bayesian methods), Box-Whisker plot plotting, Sequence composition calculation, Phylogenetic tree generation (from molecular sequences), Base-calling, Phylogenetic tree analysis, Variant calling, Sequence assembly, Phylogenetic tree reconstruction, Phylogenetic tree generation, Scatter plot plotting, De-novo assembly, Taxonomic classification, Sequence assembly visualisation, Pairwise sequence alignment, Multilocus sequence typing, Data handling, Validation, Multiple sequence alignment, Aggregation, Cross-assembly, Mapping assembly, Sequence contamination filtering, Sequencing quality control - 2023-01-26 - 2025-11-18 + Building an amplicon sequence variant (ASV) table from 16S data using DADA2 + https://training.galaxyproject.org//topics/microbiome/tutorials/dada-16S/tutorial.html + Microbial ecology, Taxonomy, Sequence analysis, Metabarcoding + Variant calling, Analysis, Visualisation, DNA barcoding, Deposition + 2024-06-05 + 2026-04-13 12 True False True True - ggplot2_heatmap, Count1, Paste1, tp_find_and_replace, abricate, multiqc, fastp, table_compute, collapse_dataset, barchart_gnuplot, tp_replace_in_column, compose_text_param, minimap2, regexColumn1, mlst, __FILTER_FAILED_DATASETS__, CONVERTER_gz_to_uncompressed, __BUILD_LIST__, clair3, tp_split_on_column, krakentools_extract_kraken_reads, bamtools_split_mapped, samtools_fastx, tab2fasta, krakentools_kreport2krona, tp_head_tool, bedtools_getfastabed, fasta_merge_files_and_filter_unique_sequences, medaka_consensus_pipeline, Grouping1, split_file_to_collection, bcftools_consensus, tp_cut_tool, __FILTER_EMPTY_DATASETS__, samtools_coverage, snpSift_filter, Remove beginning1, fastqc, flye, fasta2tab, newick_display, regex1, Cut1, snpSift_extractFields, bcftools_norm, Grep1, tp_multijoin_tool, param_value_from_file, taxonomy_krona_chart, bandage_image, collection_element_identifiers, fasttree, nanoplot, tp_sorted_uniq, porechop, Add_a_column1, add_line_to_file, clustalw, samtools_depth, collection_column_join, kraken2 - UseGalaxy.eu - UseGalaxy.org.au, UseGalaxy.be, UseGalaxy.cz + dada2_removeBimeraDenovo, __SORTLIST__, collection_element_identifiers, interactive_tool_phyloseq, tp_head_tool, __UNZIP_COLLECTION__, dada2_filterAndTrim, dada2_learnErrors, dada2_plotQualityProfile, dada2_seqCounts, phyloseq_from_dada2, Grouping1, cat1, tp_replace_in_column, Add_a_column1, dada2_dada, tp_replace_in_line, dada2_assignTaxonomyAddspecies, dada2_mergePairs, dada2_makeSequenceTable + UseGalaxy.org.au, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main) + 0 - 5672 - 8267 - 8.566667 + 9857 + 14019 + 5.516667 0 Microbiome - Building and Annotating Metagenome-Assembled Genomes (MAGs) from Short Metagenomics Paired Reads - https://training.galaxyproject.org//topics/microbiome/tutorials/mags-building/tutorial.html - Metagenomics, Sequence assembly - Data handling, Validation, Genome comparison, Sequence composition calculation, Statistical calculation, Genome annotation, Sequence assembly validation, Sequencing quality control - 2025-12-18 - 2026-05-18 - 6 - True + QIIME 2 Moving Pictures + https://training.galaxyproject.org//topics/microbiome/tutorials/qiime2-moving-pictures/tutorial.html + Microbial ecology, Taxonomy, Sequence analysis, Metabarcoding + + 2024-03-14 + 2026-02-18 + 2 + external False - True False - Summary_Statistics1, Grouping1, multiqc, Remove beginning1, __EXTRACT_DATASET__, tp_sort_header_tool, checkm_lineage_wf, cat1, fasterq_dump, drep_dereplicate, collapse_dataset, Cut1, kmetashot, tp_replace_in_column, collection_column_join, join1, bakta - UseGalaxy.eu + False + + UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr, UseGalaxy.ca 0 - 1022 - 1315 - 5.666667 + 810 + 1215 + 7.550000 0 @@ -841,36 +841,36 @@ False - UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr + UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr, UseGalaxy.ca 0 - 518 - 857 - 10.133333 + 544 + 887 + 10.066667 0 Microbiome - QIIME 2 Moving Pictures - https://training.galaxyproject.org//topics/microbiome/tutorials/qiime2-moving-pictures/tutorial.html - Microbial ecology, Taxonomy, Sequence analysis, Metabarcoding - - 2024-03-14 - 2026-02-18 - 2 - external - False + Building and Annotating Metagenome-Assembled Genomes (MAGs) from Short Metagenomics Paired Reads + https://training.galaxyproject.org//topics/microbiome/tutorials/mags-building/tutorial.html + Metagenomics, Sequence assembly + Statistical calculation, Sequencing quality control, Sequence assembly validation, Data handling, Genome annotation, Sequence composition calculation, Genome comparison, Validation + 2025-12-18 + 2026-05-18 + 6 + True False + True False - - - UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr + collection_column_join, Remove beginning1, Grouping1, bakta, cat1, fasterq_dump, tp_replace_in_column, drep_dereplicate, __EXTRACT_DATASET__, checkm_lineage_wf, join1, multiqc, collapse_dataset, Summary_Statistics1, tp_sort_header_tool, kmetashot, Cut1 + UseGalaxy.eu, UseGalaxy.org (Main) + UseGalaxy.cz 0 - 771 - 1141 - 7.250000 + 1247 + 1579 + 6.550000 0 @@ -879,7 +879,7 @@ 16S Microbial Analysis with mothur (extended) https://training.galaxyproject.org//topics/microbiome/tutorials/mothur-miseq-sop/tutorial.html Microbial ecology, Taxonomy, Sequence analysis, Metabarcoding - Phylogenetic analysis, Taxonomic classification, Sequencing quality control, Visualisation, Phylogenetic tree generation, Sequence read processing, Phylogenetic tree analysis, Phylogenetic tree reconstruction, Sequence clustering, DNA barcoding + Phylogenetic tree reconstruction, Sequencing quality control, Phylogenetic analysis, Visualisation, Phylogenetic tree generation, Sequence read processing, Phylogenetic tree analysis, Taxonomic classification, Sequence clustering, DNA barcoding 2017-02-12 2025-12-18 5 @@ -887,14 +887,14 @@ False False True - mothur_dist_shared, mothur_filter_seqs, mothur_count_seqs, mothur_tree_shared, mothur_rarefaction_single, mothur_dist_seqs, mothur_summary_single, mothur_chimera_vsearch, XY_Plot_1, mothur_pre_cluster, mothur_cluster, mothur_cluster_split, mothur_align_seqs, mothur_sub_sample, mothur_screen_seqs, mothur_taxonomy_to_krona, mothur_make_biom, mothur_remove_groups, mothur_classify_otu, mothur_count_groups, mothur_make_shared, newick_display, mothur_get_groups, mothur_summary_seqs, mothur_venn, taxonomy_krona_chart, mothur_seq_error, mothur_remove_lineage, mothur_unique_seqs, mothur_classify_seqs, mothur_make_contigs, mothur_remove_seqs, mothur_heatmap_sim + mothur_sub_sample, mothur_classify_seqs, mothur_classify_otu, mothur_get_groups, mothur_dist_shared, mothur_cluster, mothur_summary_single, mothur_filter_seqs, mothur_heatmap_sim, taxonomy_krona_chart, mothur_tree_shared, mothur_chimera_vsearch, mothur_pre_cluster, mothur_make_contigs, mothur_summary_seqs, XY_Plot_1, mothur_align_seqs, mothur_make_biom, mothur_screen_seqs, mothur_count_groups, newick_display, mothur_remove_seqs, mothur_unique_seqs, mothur_count_seqs, mothur_venn, mothur_make_shared, mothur_rarefaction_single, mothur_taxonomy_to_krona, mothur_cluster_split, mothur_dist_seqs, mothur_remove_groups, mothur_remove_lineage, mothur_seq_error UseGalaxy.be, UseGalaxy.eu UseGalaxy.org.au, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org (Main) 0 - 14146 - 20833 - 5.016667 + 14424 + 21194 + 5.000000 0 @@ -903,7 +903,7 @@ 16S Microbial Analysis with mothur (short) https://training.galaxyproject.org//topics/microbiome/tutorials/mothur-miseq-sop-short/tutorial.html Microbial ecology, Taxonomy, Sequence analysis, Metabarcoding - Phylogenetic analysis, Taxonomic classification, Sequencing quality control, Visualisation, Phylogenetic tree generation, Sequence read processing, Phylogenetic tree analysis, Phylogenetic tree reconstruction, Sequence clustering, DNA barcoding + Phylogenetic tree reconstruction, Sequencing quality control, Phylogenetic analysis, Visualisation, Phylogenetic tree generation, Sequence read processing, Phylogenetic tree analysis, Taxonomic classification, Sequence clustering, DNA barcoding 2019-05-13 2025-12-18 6 @@ -911,14 +911,14 @@ False True True - mothur_dist_shared, mothur_filter_seqs, mothur_count_seqs, mothur_tree_shared, mothur_rarefaction_single, mothur_dist_seqs, mothur_summary_single, collapse_dataset, mothur_chimera_vsearch, XY_Plot_1, mothur_pre_cluster, mothur_cluster, mothur_cluster_split, mothur_sub_sample, mothur_screen_seqs, mothur_remove_groups, mothur_classify_otu, mothur_count_groups, mothur_make_shared, newick_display, mothur_summary_seqs, mothur_venn, mothur_remove_lineage, mothur_unique_seqs, mothur_classify_seqs, mothur_remove_seqs, mothur_heatmap_sim + mothur_sub_sample, mothur_classify_seqs, mothur_classify_otu, collapse_dataset, mothur_dist_shared, mothur_cluster, mothur_summary_single, mothur_filter_seqs, mothur_heatmap_sim, mothur_tree_shared, mothur_chimera_vsearch, mothur_pre_cluster, mothur_summary_seqs, XY_Plot_1, mothur_screen_seqs, mothur_count_groups, newick_display, mothur_remove_seqs, mothur_unique_seqs, mothur_count_seqs, mothur_venn, mothur_make_shared, mothur_rarefaction_single, mothur_cluster_split, mothur_dist_seqs, mothur_remove_groups, mothur_remove_lineage UseGalaxy.org.au, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org (Main) UseGalaxy.fr 0 - 6699 - 11212 - 7.700000 + 6785 + 11364 + 7.750000 0 @@ -927,7 +927,7 @@ M. tuberculosis Variant Analysis https://training.galaxyproject.org//topics/variant-analysis/tutorials/tb-variant-analysis/tutorial.html Genomics, Microbiology, Sequence assembly, Genetic variation, Public health and epidemiology, Infectious disease - Sequence alignment analysis, Phylogenetic tree visualisation, Taxonomic classification, Sequence analysis, Statistical calculation, Sequence alignment, Global alignment, Genome visualisation, Local alignment, Antimicrobial resistance prediction, Validation, Sequence composition calculation, Sequence contamination filtering, Variant calling, Sequencing quality control, Phylogenetic tree generation + Variant calling, Phylogenetic tree visualisation, Global alignment, Sequencing quality control, Statistical calculation, Genome visualisation, Sequence contamination filtering, Antimicrobial resistance prediction, Sequence composition calculation, Phylogenetic tree generation, Sequence alignment, Sequence alignment analysis, Taxonomic classification, Local alignment, Validation, Sequence analysis 2020-07-25 2026-01-06 32 @@ -935,71 +935,71 @@ False True True - kraken2, multiqc, jbrowse, qualimap_bamqc, fastp, samtools_stats, EMBOSS: seqret84, jvarkit_wgscoverageplotter, mosdepth, snippy, EMBOSS:%20seqret84, __FLATTEN__, tp_sed_tool, tb_variant_filter, bcftools_consensus, tp_awk_tool, fastqc, tb_profiler_profile, upload1, tbvcfreport + bcftools_consensus, tbvcfreport, tb_profiler_profile, tb_variant_filter, jvarkit_wgscoverageplotter, snippy, __FLATTEN__, EMBOSS:%20seqret84, tp_awk_tool, kraken2, samtools_stats, qualimap_bamqc, upload1, EMBOSS: seqret84, fastp, jbrowse, mosdepth, fastqc, tp_sed_tool, multiqc 0 - 8399 - 12705 - 7.716667 + 8651 + 13093 + 7.800000 0 Proteomics - metaQuantome 1: Data creation - https://training.galaxyproject.org//topics/proteomics/tutorials/metaquantome-data-creation/tutorial.html - Proteomics, Proteogenomics, Biodiversity, Taxonomy - Prediction and recognition, Label-free quantification, Visualisation, Formatting, Filtering - 2020-10-16 - 2024-03-14 - 20 + metaQuantome 3: Taxonomy + https://training.galaxyproject.org//topics/proteomics/tutorials/metaquantome-taxonomy/tutorial.html + Proteomics, Proteogenomics, Metatranscriptomics, Microbial ecology, Metagenomics, Taxonomy + Filtering, Differential protein expression analysis, Principal component visualisation, Visualisation, Indexing, Functional clustering, Quantification, Query and retrieval, Statistical inference, Heat map generation + 2020-10-29 + 2024-03-15 + 14 True False False True - Grep1, msconvert, peptide_shaker, Remove beginning1, flashlfq, query_tabular, Filter1, unipept, regex1, tp_replace_in_column, Cut1, tp_replace_in_line, search_gui - UseGalaxy.eu - UseGalaxy.org.au, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.no + metaquantome_expand, metaquantome_viz, metaquantome_filter, metaquantome_db, metaquantome_sample, metaquantome_stat + UseGalaxy.be, UseGalaxy.eu + UseGalaxy.org.au, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no 0 - 937 - 1558 - 9.366667 + 501 + 642 + 14.800000 0 Proteomics - Metaproteomics tutorial - https://training.galaxyproject.org//topics/proteomics/tutorials/metaproteomics/tutorial.html + metaQuantome 1: Data creation + https://training.galaxyproject.org//topics/proteomics/tutorials/metaquantome-data-creation/tutorial.html Proteomics, Proteogenomics, Biodiversity, Taxonomy - Visualisation, Prediction and recognition - 2017-06-28 - 2026-05-11 - 42 + Filtering, Label-free quantification, Prediction and recognition, Formatting, Visualisation + 2020-10-16 + 2024-03-14 + 20 True False + False True - True - sqlite_to_tabular, query_tabular, unipept, peptide_shaker, search_gui - UseGalaxy.org.au, UseGalaxy.eu, UseGalaxy.org (Main) - UseGalaxy.be, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no + peptide_shaker, query_tabular, tp_replace_in_line, Remove beginning1, unipept, Filter1, tp_replace_in_column, Grep1, msconvert, regex1, flashlfq, search_gui, Cut1 + UseGalaxy.eu + UseGalaxy.org.au, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.no 0 - 3109 - 4879 - 9.833333 + 958 + 1579 + 9.483333 0 Proteomics - metaQuantome 3: Taxonomy - https://training.galaxyproject.org//topics/proteomics/tutorials/metaquantome-taxonomy/tutorial.html - Proteomics, Proteogenomics, Metatranscriptomics, Microbial ecology, Metagenomics, Taxonomy - Statistical inference, Functional clustering, Visualisation, Differential protein expression analysis, Principal component visualisation, Heat map generation, Quantification, Query and retrieval, Filtering, Indexing + metaQuantome 2: Function + https://training.galaxyproject.org//topics/proteomics/tutorials/metaquantome-function/tutorial.html + Proteomics, Proteogenomics, Metatranscriptomics, Microbial ecology, Metagenomics + Filtering, Differential protein expression analysis, Principal component visualisation, Visualisation, Indexing, Functional clustering, Quantification, Query and retrieval, Statistical inference, Heat map generation 2020-10-29 2024-03-15 14 @@ -1007,38 +1007,38 @@ False False True - metaquantome_viz, metaquantome_expand, metaquantome_db, metaquantome_sample, metaquantome_filter, metaquantome_stat + metaquantome_expand, metaquantome_viz, metaquantome_filter, metaquantome_db, metaquantome_sample, metaquantome_stat UseGalaxy.be, UseGalaxy.eu UseGalaxy.org.au, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no 0 - 485 - 626 - 14.650000 + 471 + 646 + 15.133333 0 Proteomics - metaQuantome 2: Function - https://training.galaxyproject.org//topics/proteomics/tutorials/metaquantome-function/tutorial.html - Proteomics, Proteogenomics, Metatranscriptomics, Microbial ecology, Metagenomics - Statistical inference, Functional clustering, Visualisation, Differential protein expression analysis, Principal component visualisation, Heat map generation, Quantification, Query and retrieval, Filtering, Indexing - 2020-10-29 - 2024-03-15 - 14 + Metaproteomics tutorial + https://training.galaxyproject.org//topics/proteomics/tutorials/metaproteomics/tutorial.html + Proteomics, Proteogenomics, Biodiversity, Taxonomy + Visualisation, Prediction and recognition + 2017-06-28 + 2026-05-11 + 42 True False - False True - metaquantome_viz, metaquantome_expand, metaquantome_db, metaquantome_sample, metaquantome_filter, metaquantome_stat - UseGalaxy.be, UseGalaxy.eu - UseGalaxy.org.au, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no + True + query_tabular, peptide_shaker, unipept, sqlite_to_tabular, search_gui + UseGalaxy.org.au, UseGalaxy.eu, UseGalaxy.org (Main) + UseGalaxy.be, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no 0 - 452 - 626 - 15.466667 + 3191 + 4985 + 10.183333 0 @@ -1047,7 +1047,7 @@ Quality and contamination control in bacterial isolate using Illumina MiSeq Data https://training.galaxyproject.org//topics/sequence-analysis/tutorials/quality-contamination-control/tutorial.html Whole genome sequencing, Genomics, Microbiology, Microbial ecology - Expression analysis, Taxonomic classification, Statistical calculation, Read mapping, Visualisation, Cross-assembly, Sequence contamination filtering, Sequencing quality control + Expression analysis, Sequencing quality control, Statistical calculation, Sequence contamination filtering, Visualisation, Cross-assembly, Taxonomic classification, Read mapping 2024-07-15 2025-12-18 5 @@ -1055,14 +1055,14 @@ False True True - upload1, est_abundance, fastp, falco, recentrifuge, kraken2 + upload1, recentrifuge, fastp, falco, est_abundance, kraken2 GalaxyTrakr, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main) 0 - 2057 - 2730 - 10.500000 + 2176 + 2857 + 10.350000 0 @@ -1071,7 +1071,7 @@ Calling variants in non-diploid systems https://training.galaxyproject.org//topics/variant-analysis/tutorials/non-dip/tutorial.html Genomics, Sequence assembly, DNA polymorphism, Microbiology, Sequence analysis, Genetic variation - Sequence alignment analysis, Statistical calculation, Read mapping, Generation, Data handling, Genome indexing, Sequence composition calculation, Sequence alignment, Formatting, Variant calling, Sequencing quality control + Variant calling, Statistical calculation, Sequencing quality control, Data handling, Sequence composition calculation, Genome indexing, Sequence alignment, Sequence alignment analysis, Generation, Formatting, Read mapping 2017-02-16 2024-03-15 23 @@ -1079,14 +1079,14 @@ False False True - bamFilter, freebayes, bamleftalign, vcffilter2, picard_MarkDuplicates, fastqc, picard_MergeSamFiles, vcf2tsv, Cut1, bwa_mem + bamleftalign, freebayes, vcffilter2, picard_MarkDuplicates, bamFilter, fastqc, vcf2tsv, picard_MergeSamFiles, bwa_mem, Cut1 UseGalaxy.be, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main) UseGalaxy.org.au, UseGalaxy.cz, UseGalaxy.no 0 - 9869 - 16898 - 5.550000 + 10064 + 17198 + 5.716667 0 diff --git a/communities/microgalaxy/resources/tutorials.tsv b/communities/microgalaxy/resources/tutorials.tsv index 744ac1df0..71a49f39a 100644 --- a/communities/microgalaxy/resources/tutorials.tsv +++ b/communities/microgalaxy/resources/tutorials.tsv @@ -1,43 +1,43 @@ Topic Title Link EDAM topic EDAM operation Creation Last modification Version Tutorial Slides Video Workflows Tools Servers with precise tool versions Servers with tool but different versions Feedback number Feedback mean note Visitors Page views Visit duration Video views -Assembly Making sense of a newly assembled genome https://training.galaxyproject.org//topics/assembly/tutorials/ecoli_comparison/tutorial.html Sequence assembly, Genomics, Microbiology Sequence visualisation, Read mapping, Mapping, Sequence alignment, Genome visualisation 2018-06-14 2026-04-13 30 True False False True jbrowse, cat1, collapse_dataset, tp_replace_in_column, random_lines1, tp_replace_in_line, join1, fasta_filter_by_length, circos_interval_to_tiles, tp_sort_header_tool, Filter1, fasta_compute_length, addValue, tp_cat, bedtools_intersectbed, circos, tp_sed_tool, datamash_ops, tp_grep_tool, mergeCols1, Cut1, bedtools_sortbed, upload1, Grep1, circos_aln_to_links, lastz_wrapper_2, bedtools_complementbed 0 6969 13261 8.116666666666667 0 -Assembly Unicycler Assembly https://training.galaxyproject.org//topics/assembly/tutorials/unicycler-assembly/tutorial.html Sequence assembly, Genomics, Microbiology Statistical calculation, Genome assembly, Coding region prediction, Visualisation, Sequence assembly validation, Validation, Gene prediction, Sequence composition calculation, Aggregation, Genome annotation, Sequencing quality control 2017-10-11 2026-01-23 25 True True False True multiqc, fastqc, unicycler, quast, prokka UseGalaxy.org.au, UseGalaxy.eu, UseGalaxy.org (Main) Galaxy@AuBi, GalaxyTrakr, MISSISSIPPI, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no 0 3823772 9058168 7.083333333333333 0 -Assembly Genome Assembly of a bacterial genome (MRSA) sequenced using Illumina MiSeq Data https://training.galaxyproject.org//topics/assembly/tutorials/mrsa-illumina/tutorial.html Sequence assembly, Whole genome sequencing, Public health and epidemiology, Genomics, Microbiology Sequence assembly visualisation, Read mapping, Genome assembly, Visualisation, Sequence assembly validation, Sequence contamination filtering, Sequencing quality control 2021-03-24 2026-01-05 18 True False True True upload1, shovill, bandage_image, fastp, bandage_info, quast, falco UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main) 0 11568 17594 9.533333333333333 0 -Assembly Assembly of metagenomic sequencing data https://training.galaxyproject.org//topics/assembly/tutorials/metagenomics-assembly/tutorial.html Metagenomics, Sequence assembly Sequence alignment analysis, Statistical calculation, Primer removal, Genome assembly, Visualisation, Local alignment, Sequence composition calculation, Formatting, Variant calling, Sequence file editing, Sequence assembly visualisation, Read mapping, Sequence assembly validation, Data handling, Read pre-processing, Sequence contamination filtering, Sequence trimming, Sequencing quality control 2026-05-21 2026-05-21 0 True False True True metaspades, collection_column_join, bandage_image, filter_tabular, coverm_contig, megahit_contig2fastg, bamtools, fastqc, bandage_info, megahit, bowtie2, tp_cat, quast, ngsutils_bam_filter, seqtk_subseq, random_lines1, cutadapt, bg_uniq UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main) 0 6 7 11.666666666666666 0 -Assembly Genome Assembly of MRSA from Oxford Nanopore MinION data (and optionally Illumina data) https://training.galaxyproject.org//topics/assembly/tutorials/mrsa-nanopore/tutorial.html Sequence assembly, Whole genome sequencing, Public health and epidemiology, Genomics, Microbiology, Antimicrobial resistance Scatter plot plotting, De-novo assembly, Sequence assembly visualisation, Statistical calculation, Genome assembly, Sequencing error detection, Read mapping, Visualisation, Filtering, Sequence assembly validation, Sequence alignment, Box-Whisker plot plotting, Sequence composition calculation, Cross-assembly, Mapping assembly, Sequence contamination filtering, Sequencing quality control 2021-03-24 2026-01-05 16 True False False True upload1, bandage_image, nanoplot, porechop, filtlong, fastqc, flye, __EXTRACT_DATASET__, fastp, polypolish, quast, __FLATTEN__, CONVERTER_bz2_to_uncompressed, bwa_mem2 UseGalaxy.be, UseGalaxy.eu UseGalaxy.cz, UseGalaxy.fr 0 11438 16929 7.583333333333333 0 -Ecology Checking expected species and contamination in bacterial isolate https://training.galaxyproject.org//topics/ecology/tutorials/bacterial-isolate-species-contamination-checking/tutorial.html Whole genome sequencing, Genomics, Microbiology, Microbial ecology Cross-assembly, Expression analysis, Taxonomic classification, Statistical calculation 2024-03-04 2026-04-08 6 True False False True recentrifuge, upload1, kraken2, est_abundance UseGalaxy.eu, UseGalaxy.fr Galaxy@AuBi, GalaxyTrakr, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.org (Main) 0 1036 1378 8.266666666666667 0 -Evolution Tree thinking for tuberculosis evolution and epidemiology https://training.galaxyproject.org//topics/evolution/tutorials/mtb_phylogeny/tutorial.html Genomics, Microbiology, Phylogeny, Infectious disease Phylogenetic tree analysis, Sequence analysis 2022-03-16 2025-06-04 12 True False False True upload1, raxml, interactive_tool_rstudio UseGalaxy.eu 0 2502 3565 8.05 0 -Evolution Identifying tuberculosis transmission links: from SNPs to transmission clusters https://training.galaxyproject.org//topics/evolution/tutorials/mtb_transmission/tutorial.html Genomics, Microbiology, Infectious disease, DNA polymorphism Phylogenetic tree visualisation, Antimicrobial resistance prediction, Variant calling, Phylogenetic tree generation 2022-03-16 2025-05-26 13 True False False True addName, __MERGE_COLLECTION__, trimmomatic, collapse_dataset, tp_replace_in_line, snippy, samtools_view, tp_cat, tp_sed_tool, tb_variant_filter, bcftools_consensus, snp_sites, tp_grep_tool, tb_profiler_profile, upload1, Grep1, clustering_from_distmat, snp_dists, tp_easyjoin_tool UseGalaxy.eu 0 3555 5077 7.8 0 -Evolution Phylogenetic analysis for bacterial comparative genomics https://training.galaxyproject.org//topics/evolution/tutorials/bacterial-comparative-genomics/tutorial.html Genomics, Microbiology, Phylogeny Phylogenetic tree generation (maximum likelihood and Bayesian methods), Phylogenetic tree generation (from molecular sequences) 2025-03-14 2025-03-14 1 True False False False upload1, fasttree Galaxy@AuBi, MISSISSIPPI, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org (Main) GalaxyTrakr 0 198 239 10.266666666666667 0 -Genome Annotation Genome annotation with Prokka https://training.galaxyproject.org//topics/genome-annotation/tutorials/annotation-with-prokka/tutorial.html Genomics, Microbiology, Gene and protein families, Sequence analysis Coding region prediction, Gene prediction, Genome annotation, Genome visualisation 2018-03-06 2026-01-23 27 True True True True jbrowse, prokka UseGalaxy.be, UseGalaxy.eu, UseGalaxy.org (Main) Galaxy@AuBi, GalaxyTrakr, MISSISSIPPI, UseGalaxy.org.au, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no 0 3829962 9068268 7.166666666666667 0 -Genome Annotation Refining Genome Annotations with Apollo (prokaryotes) https://training.galaxyproject.org//topics/genome-annotation/tutorials/apollo/tutorial.html Genomics, Microbiology, Gene and protein families, Sequence analysis Genome visualisation 2021-06-04 2025-05-15 22 True True True True jbrowse, iframe, list_organism, create_account, create_or_update UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.no 0 3585787 8259740 13.183333333333334 0 -Genome Annotation Bacterial Genome Annotation https://training.galaxyproject.org//topics/genome-annotation/tutorials/bacterial-genome-annotation/tutorial.html Genomics, Microbiology, Gene and protein families, Sequence analysis, Whole genome sequencing, Functional genomics, Mobile genetic elements Protein feature detection, Structural variation detection, Genome assembly, Scaffolding, Multilocus sequence typing, Genome visualisation, Nucleic acid feature detection, Sequence motif recognition, Genome annotation 2024-02-01 2024-10-15 6 True False True True isescan, upload1, Grouping1, plasmidfinder, integron_finder, tbl2gff3, jbrowse, tp_tail_tool, tp_replace_in_column, bakta UseGalaxy.eu, UseGalaxy.fr Galaxy@AuBi, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.org (Main) 0 8485 11611 7.716666666666667 0 -Genome Annotation Identification of AMR genes in an assembled bacterial genome https://training.galaxyproject.org//topics/genome-annotation/tutorials/amr-gene-detection/tutorial.html Whole genome sequencing, Public health and epidemiology, Genomics, Microbiology, Sequence analysis, Infectious disease, Antimicrobial resistance Genome annotation, Antimicrobial resistance prediction, Genome visualisation, Read mapping 2024-01-23 2025-12-18 10 True False True True upload1, Grep1, tbl2gff3, jbrowse, bowtie2, staramr_search, bakta Galaxy@AuBi, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr UseGalaxy.org (Main) 0 4294 5838 9.3 0 -Genome Annotation Bacterial genome quality control https://training.galaxyproject.org//topics/genome-annotation/tutorials/bacterial-genome-quality-control/tutorial.html Genomics, Microbiology Validation, Genome comparison, Sequence composition calculation, Statistical calculation, Sequence assembly validation, Sequencing quality control 2025-03-14 2025-03-14 1 True False False False checkm2, drep_dereplicate, upload1 UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main) GalaxyTrakr, UseGalaxy.cz 0 195 233 7.733333333333333 0 -Genome Annotation Dataset construction for bacterial comparative genomics https://training.galaxyproject.org//topics/genome-annotation/tutorials/bacterial-comparative-genomics-dataset-construction/tutorial.html Genomics, Microbiology Data handling, Data retrieval, Sequence database search 2025-03-14 2026-04-13 2 True False False False upload1, sort1, Remove beginning1, cat1, Cut1, datasets_download_genome, bg_uniq UseGalaxy.fr UseGalaxy.cz 0 115 133 11.683333333333334 0 -Genome Annotation Comparative gene analysis in unannotated genomes https://training.galaxyproject.org//topics/genome-annotation/tutorials/gene-centric/tutorial.html Genomics, Gene and protein families, Sequence analysis, Phylogeny, Comparative genomics Sequence alignment analysis, Multiple sequence alignment, Database search, De-novo assembly, Transcriptome assembly, Coding region prediction, Phylogenetic tree generation 2022-09-08 2025-06-03 10 True False False True bg_diamond_makedb, gops_intersect_1, bg_diamond_view, tp_split_on_column, bg_diamond, Filter1, cat1, Add_a_column1, orfipy, tab2fasta, rbc_mafft, collapse_dataset, Cut1, rapidnj, regexColumn1, join1 UseGalaxy.eu, UseGalaxy.org (Main) UseGalaxy.cz 0 2056 2827 9.833333333333334 0 -Genome Annotation Essential genes detection with Transposon insertion sequencing https://training.galaxyproject.org//topics/genome-annotation/tutorials/tnseq/tutorial.html Genomics, Microbiology, Sequence analysis, Mobile genetic elements Primer removal, Sequence trimming, Transposon prediction, Read pre-processing 2019-07-02 2024-03-18 12 True True False True transit_gumbel, __EXTRACT_DATASET__, tp_sort_header_tool, Filter1, Add_a_column1, gff_to_prot, Cut1, deeptools_bam_coverage, tp_easyjoin_tool, cutadapt, bowtie_wrapper, bg_find_subsequences UseGalaxy.org.au, UseGalaxy.be, UseGalaxy.no UseGalaxy.cz, UseGalaxy.eu 0 3819196 9051236 5.7 0 -Variant Analysis Microbial Variant Calling https://training.galaxyproject.org//topics/variant-analysis/tutorials/microbial-variants/tutorial.html Genomics, Sequence assembly, DNA polymorphism, Microbiology, Sequence analysis, Genetic variation Phylogenetic tree visualisation, Variant calling, Genome visualisation, Phylogenetic tree generation 2018-02-26 2026-01-23 25 True False False True jbrowse, snippy UseGalaxy.be, UseGalaxy.eu, UseGalaxy.org (Main) GalaxyTrakr, UseGalaxy.org.au, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no 0 16133 25453 5.0 0 -Microbiome Analyses of metagenomics data - The global picture https://training.galaxyproject.org//topics/microbiome/tutorials/general-tutorial/tutorial.html Metagenomics, Microbial ecology, Taxonomy, Sequence analysis, Metabarcoding Phylogenetic analysis, Taxonomic classification, Sequencing quality control, Visualisation, Sequence read processing, Sequence clustering, DNA barcoding 2017-06-22 2024-08-09 4 True False False True mothur_filter_seqs, humann2_renorm_table, mothur_pre_cluster, humann2, mothur_cluster_split, metaphlan2, mothur_align_seqs, mothur_screen_seqs, mothur_make_biom, mothur_make_group, mothur_classify_otu, mothur_make_shared, mothur_summary_seqs, taxonomy_krona_chart, krona-text, mothur_merge_files, metaphlan2krona, mothur_unique_seqs, mothur_classify_seqs, humann2_regroup_table, mothur_count_seqs UseGalaxy.org.au, UseGalaxy.fr, UseGalaxy.no 0 11137 14970 5.733333333333333 0 -Microbiome Metatranscriptomics analysis using microbiome RNA-seq data (short) https://training.galaxyproject.org//topics/microbiome/tutorials/metatranscriptomics-short/tutorial.html Metatranscriptomics, Microbial ecology, Taxonomy, Function analysis, Sequence analysis Sequence alignment analysis, Phylogenetic tree visualisation, Statistical calculation, Primer removal, Phylogenetic inference, Visualisation, Species frequency estimation, Sequence composition calculation, Sequence comparison, Phylogenetic tree editing, Phylogenetic analysis, Taxonomic classification, Conversion, Validation, Sequence similarity search, Read pre-processing, Sequence trimming, Sequencing quality control 2020-02-13 2025-06-16 6 True False True True graphlan_annotate, tp_find_and_replace, graphlan, multiqc, bg_sortmerna, tp_sort_header_tool, export2graphlan, cutadapt, fastq_paired_end_interlacer, fastqc, Cut1, humann_renorm_table, humann, Grep1, taxonomy_krona_chart, metaphlan, combine_metaphlan2_humann2, humann_rename_table, humann_regroup_table, humann_unpack_pathways, humann_split_stratified_table UseGalaxy.org.au, UseGalaxy.be, UseGalaxy.org (Main) UseGalaxy.cz, UseGalaxy.no 0 1036 1323 9.983333333333333 0 -Microbiome Taxonomic Profiling and Visualization of Metagenomic Data https://training.galaxyproject.org//topics/microbiome/tutorials/taxonomic-profiling/tutorial.html Metagenomics, Microbial ecology, Taxonomy, Sequence analysis Taxonomic classification, Aggregation, Statistical calculation, Visualisation, Genome annotation 2023-05-03 2026-05-11 8 True False True True taxonomy_krona_chart, interactive_tool_phinch, est_abundance, kraken_biom, metaphlan, __UNZIP_COLLECTION__, krakentools_kreport2krona, interactive_tool_pavian, kraken2 UseGalaxy.org.au, UseGalaxy.be, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main) 0 14694 19544 5.583333333333333 0 -Microbiome Antibiotic resistance detection https://training.galaxyproject.org//topics/microbiome/tutorials/plasmid-metagenomics-nanopore/tutorial.html Metagenomic sequencing, Public health and epidemiology, Metagenomics, Microbiology, Infectious disease, Sequence analysis, Antimicrobial resistance Scatter plot plotting, De-novo assembly, Sequence assembly visualisation, Sequence analysis, Genome assembly, Pairwise sequence alignment, Antimicrobial resistance prediction, Box-Whisker plot plotting, Aggregation, Mapping assembly 2019-06-25 2024-06-14 4 True False True True PlasFlow, bandage_image, nanoplot, miniasm, unicycler, racon, staramr_search, gfa_to_fa, minimap2 UseGalaxy.eu UseGalaxy.org.au, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org (Main) 0 4171 5713 6.783333333333333 0 -Microbiome 16S Microbial analysis with Nanopore data https://training.galaxyproject.org//topics/microbiome/tutorials/nanopore-16S-metagenomics/tutorial.html Microbial ecology, Taxonomy, Sequence analysis, Metabarcoding Sequence contamination filtering, Validation, Sequence composition calculation, Taxonomic classification, Statistical calculation, Visualisation, Sequencing quality control 2020-11-24 2024-07-31 5 True False False True taxonomy_krona_chart, porechop, datamash_reverse, multiqc, Remove beginning1, fastqc, fastp, tp_replace_in_line, kraken2 UseGalaxy.org.au, UseGalaxy.be, UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org (Main) GalaxyTrakr, UseGalaxy.cz, UseGalaxy.fr 0 10045 13873 5.433333333333334 0 -Microbiome Binning of metagenomic sequencing data https://training.galaxyproject.org//topics/microbiome/tutorials/metagenomics-binning/tutorial.html Metagenomics, Sequence assembly Read mapping, Statistical calculation, Sequencing quality control, Sequence assembly validation, Read binning, Validation, Genome comparison, Sequence composition calculation, Sequence clustering, Genome annotation, Sequence assembly 2023-12-05 2026-04-09 9 True False True True concoct, concoct_cut_up_fasta, __BUILD_LIST__, Fasta_to_Contig2Bin, concoct_coverage_table, das_tool, metabat2_jgi_summarize_bam_contig_depths, bowtie2, samtools_sort, drep_dereplicate, maxbin2, metabat2, concoct_merge_cut_up_clustering, semibin, binette, checkm_lineage_wf, concoct_extract_fasta_bins UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr GalaxyTrakr, UseGalaxy.org.au, UseGalaxy.org (Main) 0 7203 8810 5.333333333333333 0 -Microbiome Remove contamination and host reads https://training.galaxyproject.org//topics/microbiome/tutorials/host-removal/tutorial.html Validation, Sequencing quality control, Read mapping 2025-12-18 2026-05-12 3 True False True True bowtie2, __ZIP_COLLECTION__, multiqc Galaxy@AuBi, UseGalaxy.org.au, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main) GalaxyTrakr, MISSISSIPPI, UseGalaxy.no 0 355 431 6.166666666666667 0 -Microbiome Metatranscriptomics analysis using microbiome RNA-seq data https://training.galaxyproject.org//topics/microbiome/tutorials/metatranscriptomics/tutorial.html Metatranscriptomics, Microbial ecology, Taxonomy, Function analysis, Sequence analysis Sequence alignment analysis, Phylogenetic tree visualisation, Statistical calculation, Primer removal, Phylogenetic inference, Visualisation, Species frequency estimation, Sequence composition calculation, Sequence comparison, Phylogenetic tree editing, Phylogenetic analysis, Taxonomic classification, Conversion, Validation, Sequence similarity search, Aggregation, Read pre-processing, Sequence trimming, Sequencing quality control 2019-11-21 2025-06-16 6 True True True True graphlan_annotate, tp_find_and_replace, graphlan, multiqc, bg_sortmerna, tp_sort_header_tool, export2graphlan, cutadapt, fastq_paired_end_interlacer, Grouping1, fastqc, combine_metaphlan_humann, Cut1, humann_renorm_table, humann, Grep1, taxonomy_krona_chart, metaphlan, humann_rename_table, humann_regroup_table, humann_unpack_pathways, humann_split_stratified_table UseGalaxy.be, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.org (Main) UseGalaxy.eu 0 3818338 9046054 6.816666666666666 0 -Microbiome Building an amplicon sequence variant (ASV) table from 16S data using DADA2 https://training.galaxyproject.org//topics/microbiome/tutorials/dada-16S/tutorial.html Microbial ecology, Taxonomy, Sequence analysis, Metabarcoding Analysis, Deposition, Visualisation, Variant calling, DNA barcoding 2024-06-05 2026-04-13 12 True False True True dada2_plotQualityProfile, dada2_mergePairs, cat1, tp_replace_in_column, tp_replace_in_line, __UNZIP_COLLECTION__, tp_head_tool, phyloseq_from_dada2, Grouping1, dada2_makeSequenceTable, __SORTLIST__, dada2_removeBimeraDenovo, collection_element_identifiers, dada2_assignTaxonomyAddspecies, dada2_filterAndTrim, Add_a_column1, dada2_seqCounts, interactive_tool_phyloseq, dada2_dada, dada2_learnErrors UseGalaxy.org.au, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main) 0 9282 13212 5.466666666666667 0 -Microbiome Assembly of metagenomic sequencing data https://training.galaxyproject.org//topics/microbiome/tutorials/metagenomics-assembly/tutorial.html Metagenomics, Sequence assembly Sequence alignment analysis, Statistical calculation, Primer removal, Genome assembly, Visualisation, Local alignment, Sequence composition calculation, Formatting, Variant calling, Sequence file editing, Sequence assembly visualisation, Read mapping, Sequence assembly validation, Data handling, Read pre-processing, Sequence contamination filtering, Sequence trimming, Sequencing quality control 2022-12-05 2026-05-11 11 True False True True metaspades, collection_column_join, bandage_image, filter_tabular, coverm_contig, megahit_contig2fastg, bamtools, fastqc, bandage_info, megahit, bowtie2, tp_cat, quast, ngsutils_bam_filter, seqtk_subseq, random_lines1, cutadapt, bg_uniq UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main) 0 5414 7491 10.15 0 -Microbiome Identification of the micro-organisms in a beer using Nanopore sequencing https://training.galaxyproject.org//topics/microbiome/tutorials/beer-data-analysis/tutorial.html Metagenomics, Microbial ecology, Taxonomy, Sequence analysis Sequence contamination filtering, Sequence composition calculation, Aggregation, Statistical calculation, Taxonomic classification, Visualisation, Sequencing quality control 2022-09-29 2024-11-29 5 True False True True taxonomy_krona_chart, porechop, fastqc, Filter1, fastp, krakentools_kreport2krona, kraken2 UseGalaxy.org.au, UseGalaxy.be, UseGalaxy.eu, UseGalaxy.org (Main) GalaxyTrakr, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no 0 3449 5021 8.383333333333333 0 -Microbiome Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition https://training.galaxyproject.org//topics/microbiome/tutorials/pathogen-detection-from-nanopore-foodborne-data/tutorial.html Metagenomics, Public health and epidemiology, Taxonomy, Sequence assembly, Pathology, Sequence analysis Sequence alignment analysis, Statistical calculation, Genome assembly, Visualisation, Antimicrobial resistance prediction, Mapping, Phylogenetic tree generation (maximum likelihood and Bayesian methods), Box-Whisker plot plotting, Sequence composition calculation, Phylogenetic tree generation (from molecular sequences), Base-calling, Phylogenetic tree analysis, Variant calling, Sequence assembly, Phylogenetic tree reconstruction, Phylogenetic tree generation, Scatter plot plotting, De-novo assembly, Taxonomic classification, Sequence assembly visualisation, Pairwise sequence alignment, Multilocus sequence typing, Data handling, Validation, Multiple sequence alignment, Aggregation, Cross-assembly, Mapping assembly, Sequence contamination filtering, Sequencing quality control 2023-01-26 2025-11-18 12 True False True True ggplot2_heatmap, Count1, Paste1, tp_find_and_replace, abricate, multiqc, fastp, table_compute, collapse_dataset, barchart_gnuplot, tp_replace_in_column, compose_text_param, minimap2, regexColumn1, mlst, __FILTER_FAILED_DATASETS__, CONVERTER_gz_to_uncompressed, __BUILD_LIST__, clair3, tp_split_on_column, krakentools_extract_kraken_reads, bamtools_split_mapped, samtools_fastx, tab2fasta, krakentools_kreport2krona, tp_head_tool, bedtools_getfastabed, fasta_merge_files_and_filter_unique_sequences, medaka_consensus_pipeline, Grouping1, split_file_to_collection, bcftools_consensus, tp_cut_tool, __FILTER_EMPTY_DATASETS__, samtools_coverage, snpSift_filter, Remove beginning1, fastqc, flye, fasta2tab, newick_display, regex1, Cut1, snpSift_extractFields, bcftools_norm, Grep1, tp_multijoin_tool, param_value_from_file, taxonomy_krona_chart, bandage_image, collection_element_identifiers, fasttree, nanoplot, tp_sorted_uniq, porechop, Add_a_column1, add_line_to_file, clustalw, samtools_depth, collection_column_join, kraken2 UseGalaxy.eu UseGalaxy.org.au, UseGalaxy.be, UseGalaxy.cz 0 5672 8267 8.566666666666666 0 -Microbiome Building and Annotating Metagenome-Assembled Genomes (MAGs) from Short Metagenomics Paired Reads https://training.galaxyproject.org//topics/microbiome/tutorials/mags-building/tutorial.html Metagenomics, Sequence assembly Data handling, Validation, Genome comparison, Sequence composition calculation, Statistical calculation, Genome annotation, Sequence assembly validation, Sequencing quality control 2025-12-18 2026-05-18 6 True False True False Summary_Statistics1, Grouping1, multiqc, Remove beginning1, __EXTRACT_DATASET__, tp_sort_header_tool, checkm_lineage_wf, cat1, fasterq_dump, drep_dereplicate, collapse_dataset, Cut1, kmetashot, tp_replace_in_column, collection_column_join, join1, bakta UseGalaxy.eu 0 1022 1315 5.666666666666667 0 -Microbiome QIIME 2 Cancer Microbiome Intervention https://training.galaxyproject.org//topics/microbiome/tutorials/qiime2-cancer-microbiome-intervention/tutorial.html Microbial ecology, Taxonomy, Sequence analysis, Metabarcoding 2024-02-12 2024-03-14 3 external False False False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 0 518 857 10.133333333333333 0 -Microbiome QIIME 2 Moving Pictures https://training.galaxyproject.org//topics/microbiome/tutorials/qiime2-moving-pictures/tutorial.html Microbial ecology, Taxonomy, Sequence analysis, Metabarcoding 2024-03-14 2026-02-18 2 external False False False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 0 771 1141 7.25 0 -Microbiome 16S Microbial Analysis with mothur (extended) https://training.galaxyproject.org//topics/microbiome/tutorials/mothur-miseq-sop/tutorial.html Microbial ecology, Taxonomy, Sequence analysis, Metabarcoding Phylogenetic analysis, Taxonomic classification, Sequencing quality control, Visualisation, Phylogenetic tree generation, Sequence read processing, Phylogenetic tree analysis, Phylogenetic tree reconstruction, Sequence clustering, DNA barcoding 2017-02-12 2025-12-18 5 True False False True mothur_dist_shared, mothur_filter_seqs, mothur_count_seqs, mothur_tree_shared, mothur_rarefaction_single, mothur_dist_seqs, mothur_summary_single, mothur_chimera_vsearch, XY_Plot_1, mothur_pre_cluster, mothur_cluster, mothur_cluster_split, mothur_align_seqs, mothur_sub_sample, mothur_screen_seqs, mothur_taxonomy_to_krona, mothur_make_biom, mothur_remove_groups, mothur_classify_otu, mothur_count_groups, mothur_make_shared, newick_display, mothur_get_groups, mothur_summary_seqs, mothur_venn, taxonomy_krona_chart, mothur_seq_error, mothur_remove_lineage, mothur_unique_seqs, mothur_classify_seqs, mothur_make_contigs, mothur_remove_seqs, mothur_heatmap_sim UseGalaxy.be, UseGalaxy.eu UseGalaxy.org.au, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org (Main) 0 14146 20833 5.016666666666667 0 -Microbiome 16S Microbial Analysis with mothur (short) https://training.galaxyproject.org//topics/microbiome/tutorials/mothur-miseq-sop-short/tutorial.html Microbial ecology, Taxonomy, Sequence analysis, Metabarcoding Phylogenetic analysis, Taxonomic classification, Sequencing quality control, Visualisation, Phylogenetic tree generation, Sequence read processing, Phylogenetic tree analysis, Phylogenetic tree reconstruction, Sequence clustering, DNA barcoding 2019-05-13 2025-12-18 6 True False True True mothur_dist_shared, mothur_filter_seqs, mothur_count_seqs, mothur_tree_shared, mothur_rarefaction_single, mothur_dist_seqs, mothur_summary_single, collapse_dataset, mothur_chimera_vsearch, XY_Plot_1, mothur_pre_cluster, mothur_cluster, mothur_cluster_split, mothur_sub_sample, mothur_screen_seqs, mothur_remove_groups, mothur_classify_otu, mothur_count_groups, mothur_make_shared, newick_display, mothur_summary_seqs, mothur_venn, mothur_remove_lineage, mothur_unique_seqs, mothur_classify_seqs, mothur_remove_seqs, mothur_heatmap_sim UseGalaxy.org.au, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org (Main) UseGalaxy.fr 0 6699 11212 7.7 0 -Variant Analysis M. tuberculosis Variant Analysis https://training.galaxyproject.org//topics/variant-analysis/tutorials/tb-variant-analysis/tutorial.html Genomics, Microbiology, Sequence assembly, Genetic variation, Public health and epidemiology, Infectious disease Sequence alignment analysis, Phylogenetic tree visualisation, Taxonomic classification, Sequence analysis, Statistical calculation, Sequence alignment, Global alignment, Genome visualisation, Local alignment, Antimicrobial resistance prediction, Validation, Sequence composition calculation, Sequence contamination filtering, Variant calling, Sequencing quality control, Phylogenetic tree generation 2020-07-25 2026-01-06 32 True False True True kraken2, multiqc, jbrowse, qualimap_bamqc, fastp, samtools_stats, EMBOSS: seqret84, jvarkit_wgscoverageplotter, mosdepth, snippy, EMBOSS:%20seqret84, __FLATTEN__, tp_sed_tool, tb_variant_filter, bcftools_consensus, tp_awk_tool, fastqc, tb_profiler_profile, upload1, tbvcfreport 0 8399 12705 7.716666666666667 0 -Proteomics metaQuantome 1: Data creation https://training.galaxyproject.org//topics/proteomics/tutorials/metaquantome-data-creation/tutorial.html Proteomics, Proteogenomics, Biodiversity, Taxonomy Prediction and recognition, Label-free quantification, Visualisation, Formatting, Filtering 2020-10-16 2024-03-14 20 True False False True Grep1, msconvert, peptide_shaker, Remove beginning1, flashlfq, query_tabular, Filter1, unipept, regex1, tp_replace_in_column, Cut1, tp_replace_in_line, search_gui UseGalaxy.eu UseGalaxy.org.au, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.no 0 937 1558 9.366666666666667 0 -Proteomics Metaproteomics tutorial https://training.galaxyproject.org//topics/proteomics/tutorials/metaproteomics/tutorial.html Proteomics, Proteogenomics, Biodiversity, Taxonomy Visualisation, Prediction and recognition 2017-06-28 2026-05-11 42 True False True True sqlite_to_tabular, query_tabular, unipept, peptide_shaker, search_gui UseGalaxy.org.au, UseGalaxy.eu, UseGalaxy.org (Main) UseGalaxy.be, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no 0 3109 4879 9.833333333333334 0 -Proteomics metaQuantome 3: Taxonomy https://training.galaxyproject.org//topics/proteomics/tutorials/metaquantome-taxonomy/tutorial.html Proteomics, Proteogenomics, Metatranscriptomics, Microbial ecology, Metagenomics, Taxonomy Statistical inference, Functional clustering, Visualisation, Differential protein expression analysis, Principal component visualisation, Heat map generation, Quantification, Query and retrieval, Filtering, Indexing 2020-10-29 2024-03-15 14 True False False True metaquantome_viz, metaquantome_expand, metaquantome_db, metaquantome_sample, metaquantome_filter, metaquantome_stat UseGalaxy.be, UseGalaxy.eu UseGalaxy.org.au, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no 0 485 626 14.65 0 -Proteomics metaQuantome 2: Function https://training.galaxyproject.org//topics/proteomics/tutorials/metaquantome-function/tutorial.html Proteomics, Proteogenomics, Metatranscriptomics, Microbial ecology, Metagenomics Statistical inference, Functional clustering, Visualisation, Differential protein expression analysis, Principal component visualisation, Heat map generation, Quantification, Query and retrieval, Filtering, Indexing 2020-10-29 2024-03-15 14 True False False True metaquantome_viz, metaquantome_expand, metaquantome_db, metaquantome_sample, metaquantome_filter, metaquantome_stat UseGalaxy.be, UseGalaxy.eu UseGalaxy.org.au, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no 0 452 626 15.466666666666667 0 -Sequence analysis Quality and contamination control in bacterial isolate using Illumina MiSeq Data https://training.galaxyproject.org//topics/sequence-analysis/tutorials/quality-contamination-control/tutorial.html Whole genome sequencing, Genomics, Microbiology, Microbial ecology Expression analysis, Taxonomic classification, Statistical calculation, Read mapping, Visualisation, Cross-assembly, Sequence contamination filtering, Sequencing quality control 2024-07-15 2025-12-18 5 True False True True upload1, est_abundance, fastp, falco, recentrifuge, kraken2 GalaxyTrakr, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main) 0 2057 2730 10.5 0 -Variant Analysis Calling variants in non-diploid systems https://training.galaxyproject.org//topics/variant-analysis/tutorials/non-dip/tutorial.html Genomics, Sequence assembly, DNA polymorphism, Microbiology, Sequence analysis, Genetic variation Sequence alignment analysis, Statistical calculation, Read mapping, Generation, Data handling, Genome indexing, Sequence composition calculation, Sequence alignment, Formatting, Variant calling, Sequencing quality control 2017-02-16 2024-03-15 23 True False False True bamFilter, freebayes, bamleftalign, vcffilter2, picard_MarkDuplicates, fastqc, picard_MergeSamFiles, vcf2tsv, Cut1, bwa_mem UseGalaxy.be, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main) UseGalaxy.org.au, UseGalaxy.cz, UseGalaxy.no 0 9869 16898 5.55 0 +Assembly Genome Assembly of MRSA from Oxford Nanopore MinION data (and optionally Illumina data) https://training.galaxyproject.org//topics/assembly/tutorials/mrsa-nanopore/tutorial.html Sequence assembly, Whole genome sequencing, Public health and epidemiology, Genomics, Microbiology, Antimicrobial resistance Filtering, Mapping assembly, Sequence assembly visualisation, Sequencing quality control, Statistical calculation, Genome assembly, Sequence assembly validation, Sequence contamination filtering, Visualisation, Sequencing error detection, Sequence composition calculation, Sequence alignment, De-novo assembly, Cross-assembly, Scatter plot plotting, Read mapping, Box-Whisker plot plotting 2021-03-24 2026-01-05 16 True False False True polypolish, bandage_image, bwa_mem2, porechop, upload1, __EXTRACT_DATASET__, nanoplot, __FLATTEN__, quast, fastp, CONVERTER_bz2_to_uncompressed, fastqc, flye, filtlong UseGalaxy.be, UseGalaxy.eu UseGalaxy.cz, UseGalaxy.fr 0 11648 17299 7.766666666666667 0 +Assembly Making sense of a newly assembled genome https://training.galaxyproject.org//topics/assembly/tutorials/ecoli_comparison/tutorial.html Sequence assembly, Genomics, Microbiology Sequence alignment, Mapping, Genome visualisation, Read mapping, Sequence visualisation 2018-06-14 2026-04-13 30 True False False True Filter1, collapse_dataset, join1, tp_sort_header_tool, bedtools_intersectbed, addValue, datamash_ops, circos, circos_interval_to_tiles, upload1, cat1, tp_replace_in_column, bedtools_sortbed, random_lines1, fasta_compute_length, circos_aln_to_links, tp_cat, tp_replace_in_line, mergeCols1, bedtools_complementbed, jbrowse, Grep1, fasta_filter_by_length, tp_grep_tool, lastz_wrapper_2, tp_sed_tool, Cut1 0 7029 13334 8.166666666666666 0 +Assembly Unicycler Assembly https://training.galaxyproject.org//topics/assembly/tutorials/unicycler-assembly/tutorial.html Sequence assembly, Genomics, Microbiology Statistical calculation, Sequencing quality control, Genome assembly, Sequence assembly validation, Visualisation, Genome annotation, Sequence composition calculation, Aggregation, Validation, Gene prediction, Coding region prediction 2017-10-11 2026-01-23 25 True True False True unicycler, quast, prokka, fastqc, multiqc UseGalaxy.org.au, UseGalaxy.eu, UseGalaxy.org (Main) Galaxy@AuBi, GalaxyTrakr, MISSISSIPPI, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no 0 3931702 9259758 7.083333333333333 0 +Assembly Assembly of metagenomic sequencing data https://training.galaxyproject.org//topics/assembly/tutorials/metagenomics-assembly/tutorial.html Metagenomics, Sequence assembly Variant calling, Sequence assembly validation, Primer removal, Visualisation, Sequence composition calculation, Local alignment, Read mapping, Sequence assembly visualisation, Sequencing quality control, Statistical calculation, Genome assembly, Sequence contamination filtering, Data handling, Sequence trimming, Sequence alignment analysis, Sequence file editing, Formatting, Read pre-processing 2026-07-01 2026-07-01 0 True False True True bandage_info, bowtie2, megahit, cutadapt, bandage_image, tp_cat, bamtools, collection_column_join, bg_uniq, coverm_contig, ngsutils_bam_filter, random_lines1, quast, seqtk_subseq, metaspades, fastqc, filter_tabular, megahit_contig2fastg UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main) 0 3 3 27.166666666666668 0 +Assembly Genome Assembly of a bacterial genome (MRSA) sequenced using Illumina MiSeq Data https://training.galaxyproject.org//topics/assembly/tutorials/mrsa-illumina/tutorial.html Sequence assembly, Whole genome sequencing, Public health and epidemiology, Genomics, Microbiology Sequence assembly visualisation, Sequencing quality control, Genome assembly, Sequence assembly validation, Visualisation, Read mapping, Sequence contamination filtering 2021-03-24 2026-01-05 18 True False True True bandage_info, bandage_image, upload1, quast, fastp, falco, shovill UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main) 0 11970 18118 9.583333333333334 0 +Ecology Checking expected species and contamination in bacterial isolate https://training.galaxyproject.org//topics/ecology/tutorials/bacterial-isolate-species-contamination-checking/tutorial.html Whole genome sequencing, Genomics, Microbiology, Microbial ecology Expression analysis, Cross-assembly, Statistical calculation, Taxonomic classification 2024-03-04 2026-04-08 6 True False False True upload1, est_abundance, recentrifuge, kraken2 UseGalaxy.eu, UseGalaxy.fr Galaxy@AuBi, GalaxyTrakr, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.org (Main) 0 1067 1415 8.516666666666667 0 +Evolution Tree thinking for tuberculosis evolution and epidemiology https://training.galaxyproject.org//topics/evolution/tutorials/mtb_phylogeny/tutorial.html Genomics, Microbiology, Phylogeny, Infectious disease Phylogenetic tree analysis, Sequence analysis 2022-03-16 2025-06-04 12 True False False True upload1, raxml, interactive_tool_rstudio UseGalaxy.eu 0 2636 3732 8.05 0 +Evolution Identifying tuberculosis transmission links: from SNPs to transmission clusters https://training.galaxyproject.org//topics/evolution/tutorials/mtb_transmission/tutorial.html Genomics, Microbiology, Infectious disease, DNA polymorphism Variant calling, Phylogenetic tree visualisation, Antimicrobial resistance prediction, Phylogenetic tree generation 2022-03-16 2025-05-26 13 True False False True bcftools_consensus, tp_easyjoin_tool, __MERGE_COLLECTION__, snp_dists, collapse_dataset, tb_profiler_profile, tb_variant_filter, samtools_view, snippy, snp_sites, addName, upload1, tp_cat, tp_replace_in_line, trimmomatic, Grep1, tp_grep_tool, tp_sed_tool, clustering_from_distmat UseGalaxy.eu 0 3741 5323 7.75 0 +Evolution Phylogenetic analysis for bacterial comparative genomics https://training.galaxyproject.org//topics/evolution/tutorials/bacterial-comparative-genomics/tutorial.html Genomics, Microbiology, Phylogeny 2025-03-14 2025-03-14 1 True False False False upload1, fasttree Galaxy@AuBi, MISSISSIPPI, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org (Main) GalaxyTrakr 0 220 261 12.266666666666667 0 +Genome Annotation Genome annotation with Prokka https://training.galaxyproject.org//topics/genome-annotation/tutorials/annotation-with-prokka/tutorial.html Genomics, Microbiology, Gene and protein families, Sequence analysis Genome annotation, Gene prediction, Genome visualisation, Coding region prediction 2018-03-06 2026-01-23 27 True True True True prokka, jbrowse UseGalaxy.be, UseGalaxy.eu, UseGalaxy.org (Main) Galaxy@AuBi, GalaxyTrakr, MISSISSIPPI, UseGalaxy.org.au, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no 0 3937916 9269864 7.166666666666667 0 +Genome Annotation Bacterial Genome Annotation https://training.galaxyproject.org//topics/genome-annotation/tutorials/bacterial-genome-annotation/tutorial.html Genomics, Microbiology, Gene and protein families, Sequence analysis, Whole genome sequencing, Functional genomics, Mobile genetic elements Structural variation detection, Genome visualisation, Genome assembly, Multilocus sequence typing, Genome annotation, Nucleic acid feature detection, Scaffolding, Sequence motif recognition, Protein feature detection 2024-02-01 2024-10-15 6 True False True True jbrowse, Grouping1, bakta, plasmidfinder, upload1, tp_replace_in_column, tbl2gff3, isescan, integron_finder, tp_tail_tool UseGalaxy.eu, UseGalaxy.fr Galaxy@AuBi, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.org (Main) 0 8849 12131 7.933333333333334 0 +Genome Annotation Refining Genome Annotations with Apollo (prokaryotes) https://training.galaxyproject.org//topics/genome-annotation/tutorials/apollo/tutorial.html Genomics, Microbiology, Gene and protein families, Sequence analysis Genome visualisation 2021-06-04 2025-05-15 22 True True True True list_organism, jbrowse, create_or_update, create_account, iframe UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.no 0 3693456 8460925 13.216666666666667 0 +Genome Annotation Identification of AMR genes in an assembled bacterial genome https://training.galaxyproject.org//topics/genome-annotation/tutorials/amr-gene-detection/tutorial.html Whole genome sequencing, Public health and epidemiology, Genomics, Microbiology, Sequence analysis, Infectious disease, Antimicrobial resistance Antimicrobial resistance prediction, Genome annotation, Genome visualisation, Read mapping 2024-01-23 2025-12-18 10 True False True True bowtie2, jbrowse, bakta, staramr_search, upload1, Grep1, tbl2gff3 Galaxy@AuBi, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr UseGalaxy.org (Main) 0 4562 6177 9.133333333333333 0 +Genome Annotation Dataset construction for bacterial comparative genomics https://training.galaxyproject.org//topics/genome-annotation/tutorials/bacterial-comparative-genomics-dataset-construction/tutorial.html Genomics, Microbiology Sequence database search, Data retrieval, Data handling 2025-03-14 2026-04-13 2 True False False False sort1, datasets_download_genome, Remove beginning1, upload1, cat1, bg_uniq, Cut1 UseGalaxy.fr UseGalaxy.cz 0 134 152 12.733333333333333 0 +Genome Annotation Bacterial genome quality control https://training.galaxyproject.org//topics/genome-annotation/tutorials/bacterial-genome-quality-control/tutorial.html Genomics, Microbiology Statistical calculation, Sequencing quality control, Sequence assembly validation, Genome comparison, Validation, Sequence composition calculation 2025-03-14 2025-03-14 1 True False False False upload1, drep_dereplicate, checkm2 UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main) GalaxyTrakr, UseGalaxy.cz 0 223 263 12.216666666666667 0 +Genome Annotation Comparative gene analysis in unannotated genomes https://training.galaxyproject.org//topics/genome-annotation/tutorials/gene-centric/tutorial.html Genomics, Gene and protein families, Sequence analysis, Phylogeny, Comparative genomics De-novo assembly, Sequence alignment analysis, Multiple sequence alignment, Database search, Transcriptome assembly, Phylogenetic tree generation, Coding region prediction 2022-09-08 2025-06-03 10 True False False True bg_diamond_view, bg_diamond, gops_intersect_1, cat1, Filter1, rapidnj, regexColumn1, tab2fasta, join1, collapse_dataset, orfipy, Add_a_column1, tp_split_on_column, rbc_mafft, bg_diamond_makedb, Cut1 UseGalaxy.eu, UseGalaxy.org (Main) UseGalaxy.cz 0 2094 2869 9.95 0 +Genome Annotation Essential genes detection with Transposon insertion sequencing https://training.galaxyproject.org//topics/genome-annotation/tutorials/tnseq/tutorial.html Genomics, Microbiology, Sequence analysis, Mobile genetic elements Sequence trimming, Transposon prediction, Primer removal, Read pre-processing 2019-07-02 2024-03-18 12 True True False True gff_to_prot, cutadapt, bowtie_wrapper, tp_easyjoin_tool, deeptools_bam_coverage, Filter1, __EXTRACT_DATASET__, bg_find_subsequences, Add_a_column1, transit_gumbel, tp_sort_header_tool, Cut1 UseGalaxy.org.au, UseGalaxy.be, UseGalaxy.no UseGalaxy.cz, UseGalaxy.eu 0 3926930 9252504 5.75 0 +Variant Analysis Microbial Variant Calling https://training.galaxyproject.org//topics/variant-analysis/tutorials/microbial-variants/tutorial.html Genomics, Sequence assembly, DNA polymorphism, Microbiology, Sequence analysis, Genetic variation Variant calling, Phylogenetic tree visualisation, Genome visualisation, Phylogenetic tree generation 2018-02-26 2026-01-23 25 True False False True snippy, jbrowse UseGalaxy.be, UseGalaxy.eu, UseGalaxy.org (Main) GalaxyTrakr, UseGalaxy.org.au, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no 0 16380 25775 5.033333333333333 0 +Microbiome Analyses of metagenomics data - The global picture https://training.galaxyproject.org//topics/microbiome/tutorials/general-tutorial/tutorial.html Metagenomics, Microbial ecology, Taxonomy, Sequence analysis, Metabarcoding Sequencing quality control, Phylogenetic analysis, Visualisation, Sequence read processing, Taxonomic classification, Sequence clustering, DNA barcoding 2017-06-22 2024-08-09 4 True False False True mothur_classify_seqs, humann2, mothur_merge_files, mothur_classify_otu, krona-text, mothur_filter_seqs, taxonomy_krona_chart, mothur_pre_cluster, metaphlan2, mothur_summary_seqs, mothur_align_seqs, mothur_make_biom, mothur_screen_seqs, humann2_renorm_table, humann2_regroup_table, mothur_unique_seqs, mothur_count_seqs, mothur_make_shared, mothur_cluster_split, metaphlan2krona, mothur_make_group UseGalaxy.org.au, UseGalaxy.fr, UseGalaxy.no 0 11493 15412 5.733333333333333 0 +Microbiome Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition https://training.galaxyproject.org//topics/microbiome/tutorials/pathogen-detection-from-nanopore-foodborne-data/tutorial.html Metagenomics, Public health and epidemiology, Taxonomy, Sequence assembly, Pathology, Sequence analysis Variant calling, Phylogenetic tree reconstruction, Mapping assembly, Multiple sequence alignment, Base-calling, Visualisation, Sequence composition calculation, Aggregation, Phylogenetic tree generation, Phylogenetic tree analysis, De-novo assembly, Pairwise sequence alignment, Mapping, Scatter plot plotting, Sequence assembly, Box-Whisker plot plotting, Sequence assembly visualisation, Sequencing quality control, Statistical calculation, Genome assembly, Multilocus sequence typing, Sequence contamination filtering, Antimicrobial resistance prediction, Data handling, Sequence alignment analysis, Cross-assembly, Taxonomic classification, Validation 2023-01-26 2025-11-18 12 True False True True __FILTER_EMPTY_DATASETS__, abricate, bcftools_consensus, __FILTER_FAILED_DATASETS__, bandage_image, collection_column_join, clair3, Remove beginning1, ggplot2_heatmap, Count1, collapse_dataset, collection_element_identifiers, regex1, tp_head_tool, fasta2tab, fasta_merge_files_and_filter_unique_sequences, bamtools_split_mapped, porechop, bedtools_getfastabed, samtools_depth, medaka_consensus_pipeline, minimap2, taxonomy_krona_chart, krakentools_kreport2krona, samtools_fastx, flye, mlst, kraken2, bcftools_norm, split_file_to_collection, clustalw, Cut1, snpSift_extractFields, Grouping1, samtools_coverage, tp_replace_in_column, param_value_from_file, tp_multijoin_tool, newick_display, fastp, barchart_gnuplot, Add_a_column1, tp_find_and_replace, krakentools_extract_kraken_reads, Paste1, nanoplot, tp_sorted_uniq, snpSift_filter, tp_cut_tool, Grep1, tab2fasta, __BUILD_LIST__, regexColumn1, table_compute, compose_text_param, add_line_to_file, fastqc, fasttree, tp_split_on_column, multiqc, CONVERTER_gz_to_uncompressed UseGalaxy.eu UseGalaxy.org.au, UseGalaxy.be, UseGalaxy.cz 0 5895 8528 8.633333333333333 0 +Microbiome Taxonomic Profiling and Visualization of Metagenomic Data https://training.galaxyproject.org//topics/microbiome/tutorials/taxonomic-profiling/tutorial.html Metagenomics, Microbial ecology, Taxonomy, Sequence analysis Statistical calculation, Taxonomic classification, Visualisation, Genome annotation, Aggregation 2023-05-03 2026-05-11 8 True False True True metaphlan, __UNZIP_COLLECTION__, interactive_tool_pavian, interactive_tool_phinch, taxonomy_krona_chart, krakentools_kreport2krona, est_abundance, kraken_biom, kraken2 UseGalaxy.org.au, UseGalaxy.be, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main) 0 15278 20295 5.65 0 +Microbiome Metatranscriptomics analysis using microbiome RNA-seq data https://training.galaxyproject.org//topics/microbiome/tutorials/metatranscriptomics/tutorial.html Metatranscriptomics, Microbial ecology, Taxonomy, Function analysis, Sequence analysis Phylogenetic tree visualisation, Primer removal, Visualisation, Sequence composition calculation, Aggregation, Phylogenetic tree editing, Phylogenetic inference, Statistical calculation, Sequencing quality control, Phylogenetic analysis, Conversion, Sequence trimming, Taxonomic classification, Species frequency estimation, Sequence alignment analysis, Sequence comparison, Validation, Read pre-processing, Sequence similarity search 2019-11-21 2025-06-16 6 True True True True metaphlan, cutadapt, fastq_paired_end_interlacer, humann_rename_table, combine_metaphlan_humann, graphlan, bg_sortmerna, humann_regroup_table, tp_sort_header_tool, taxonomy_krona_chart, humann, Grouping1, tp_find_and_replace, humann_renorm_table, humann_split_stratified_table, Grep1, export2graphlan, humann_unpack_pathways, fastqc, graphlan_annotate, multiqc, Cut1 UseGalaxy.be, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.org (Main) UseGalaxy.eu 0 3926230 9247565 6.883333333333334 0 +Microbiome Antibiotic resistance detection https://training.galaxyproject.org//topics/microbiome/tutorials/plasmid-metagenomics-nanopore/tutorial.html Metagenomic sequencing, Public health and epidemiology, Metagenomics, Microbiology, Infectious disease, Sequence analysis, Antimicrobial resistance Mapping assembly, Sequence assembly visualisation, Genome assembly, Antimicrobial resistance prediction, Aggregation, De-novo assembly, Pairwise sequence alignment, Scatter plot plotting, Sequence analysis, Box-Whisker plot plotting 2019-06-25 2024-06-14 4 True False True True PlasFlow, bandage_image, minimap2, staramr_search, unicycler, racon, gfa_to_fa, miniasm, nanoplot UseGalaxy.eu UseGalaxy.org.au, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org (Main) 0 4331 5886 6.9 0 +Microbiome 16S Microbial analysis with Nanopore data https://training.galaxyproject.org//topics/microbiome/tutorials/nanopore-16S-metagenomics/tutorial.html Microbial ecology, Taxonomy, Sequence analysis, Metabarcoding Sequencing quality control, Statistical calculation, Taxonomic classification, Sequence contamination filtering, Visualisation, Validation, Sequence composition calculation 2020-11-24 2024-07-31 5 True False False True tp_replace_in_line, Remove beginning1, datamash_reverse, taxonomy_krona_chart, fastp, fastqc, porechop, multiqc, kraken2 UseGalaxy.org.au, UseGalaxy.be, UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org (Main) GalaxyTrakr, UseGalaxy.cz, UseGalaxy.fr 0 10366 14282 5.45 0 +Microbiome Identification of the micro-organisms in a beer using Nanopore sequencing https://training.galaxyproject.org//topics/microbiome/tutorials/beer-data-analysis/tutorial.html Metagenomics, Microbial ecology, Taxonomy, Sequence analysis Sequencing quality control, Statistical calculation, Taxonomic classification, Sequence contamination filtering, Visualisation, Sequence composition calculation, Aggregation 2022-09-29 2024-11-29 5 True False True True Filter1, taxonomy_krona_chart, fastp, fastqc, krakentools_kreport2krona, porechop, kraken2 UseGalaxy.org.au, UseGalaxy.be, UseGalaxy.eu, UseGalaxy.org (Main) GalaxyTrakr, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no 0 3516 5095 8.383333333333333 0 +Microbiome Metatranscriptomics analysis using microbiome RNA-seq data (short) https://training.galaxyproject.org//topics/microbiome/tutorials/metatranscriptomics-short/tutorial.html Metatranscriptomics, Microbial ecology, Taxonomy, Function analysis, Sequence analysis Phylogenetic tree visualisation, Primer removal, Visualisation, Sequence composition calculation, Phylogenetic tree editing, Phylogenetic inference, Statistical calculation, Sequencing quality control, Phylogenetic analysis, Conversion, Sequence trimming, Taxonomic classification, Species frequency estimation, Sequence alignment analysis, Sequence comparison, Validation, Read pre-processing, Sequence similarity search 2020-02-13 2025-06-16 6 True False True True metaphlan, cutadapt, fastq_paired_end_interlacer, humann_rename_table, graphlan, bg_sortmerna, humann_regroup_table, tp_sort_header_tool, combine_metaphlan2_humann2, taxonomy_krona_chart, humann, tp_find_and_replace, humann_renorm_table, humann_split_stratified_table, Grep1, export2graphlan, humann_unpack_pathways, fastqc, graphlan_annotate, multiqc, Cut1 UseGalaxy.org.au, UseGalaxy.be, UseGalaxy.org (Main) UseGalaxy.cz, UseGalaxy.no 0 1094 1386 9.866666666666667 0 +Microbiome Remove contamination and host reads https://training.galaxyproject.org//topics/microbiome/tutorials/host-removal/tutorial.html Sequencing quality control, Validation, Read mapping 2025-12-18 2026-05-12 3 True False True True __ZIP_COLLECTION__, bowtie2, multiqc Galaxy@AuBi, UseGalaxy.org.au, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main) GalaxyTrakr, MISSISSIPPI, UseGalaxy.no 0 471 573 9.583333333333334 0 +Microbiome Binning of metagenomic sequencing data https://training.galaxyproject.org//topics/microbiome/tutorials/metagenomics-binning/tutorial.html Metagenomics, Sequence assembly Statistical calculation, Sequencing quality control, Read binning, Sequence assembly validation, Genome annotation, Sequence composition calculation, Sequence assembly, Sequence clustering, Genome comparison, Validation, Read mapping 2023-12-05 2026-04-09 9 True False True True concoct_cut_up_fasta, bowtie2, maxbin2, concoct_coverage_table, metabat2, concoct, concoct_extract_fasta_bins, binette, checkm_lineage_wf, drep_dereplicate, __BUILD_LIST__, Fasta_to_Contig2Bin, samtools_sort, concoct_merge_cut_up_clustering, das_tool, semibin, metabat2_jgi_summarize_bam_contig_depths UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr GalaxyTrakr, UseGalaxy.org.au, UseGalaxy.org (Main) 0 7493 9145 5.45 0 +Microbiome Assembly of metagenomic sequencing data https://training.galaxyproject.org//topics/microbiome/tutorials/metagenomics-assembly/tutorial.html Metagenomics, Sequence assembly Variant calling, Sequence assembly validation, Primer removal, Visualisation, Sequence composition calculation, Local alignment, Read mapping, Sequence assembly visualisation, Sequencing quality control, Statistical calculation, Genome assembly, Sequence contamination filtering, Data handling, Sequence trimming, Sequence alignment analysis, Sequence file editing, Formatting, Read pre-processing 2022-12-05 2026-05-11 11 True False True True bandage_info, bowtie2, megahit, cutadapt, bandage_image, tp_cat, bamtools, collection_column_join, bg_uniq, coverm_contig, ngsutils_bam_filter, random_lines1, quast, seqtk_subseq, metaspades, fastqc, filter_tabular, megahit_contig2fastg UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main) 0 5645 7763 10.383333333333333 0 +Microbiome Building an amplicon sequence variant (ASV) table from 16S data using DADA2 https://training.galaxyproject.org//topics/microbiome/tutorials/dada-16S/tutorial.html Microbial ecology, Taxonomy, Sequence analysis, Metabarcoding Variant calling, Analysis, Visualisation, DNA barcoding, Deposition 2024-06-05 2026-04-13 12 True False True True dada2_removeBimeraDenovo, __SORTLIST__, collection_element_identifiers, interactive_tool_phyloseq, tp_head_tool, __UNZIP_COLLECTION__, dada2_filterAndTrim, dada2_learnErrors, dada2_plotQualityProfile, dada2_seqCounts, phyloseq_from_dada2, Grouping1, cat1, tp_replace_in_column, Add_a_column1, dada2_dada, tp_replace_in_line, dada2_assignTaxonomyAddspecies, dada2_mergePairs, dada2_makeSequenceTable UseGalaxy.org.au, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main) 0 9857 14019 5.516666666666667 0 +Microbiome QIIME 2 Moving Pictures https://training.galaxyproject.org//topics/microbiome/tutorials/qiime2-moving-pictures/tutorial.html Microbial ecology, Taxonomy, Sequence analysis, Metabarcoding 2024-03-14 2026-02-18 2 external False False False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr, UseGalaxy.ca 0 810 1215 7.55 0 +Microbiome QIIME 2 Cancer Microbiome Intervention https://training.galaxyproject.org//topics/microbiome/tutorials/qiime2-cancer-microbiome-intervention/tutorial.html Microbial ecology, Taxonomy, Sequence analysis, Metabarcoding 2024-02-12 2024-03-14 3 external False False False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr, UseGalaxy.ca 0 544 887 10.066666666666666 0 +Microbiome Building and Annotating Metagenome-Assembled Genomes (MAGs) from Short Metagenomics Paired Reads https://training.galaxyproject.org//topics/microbiome/tutorials/mags-building/tutorial.html Metagenomics, Sequence assembly Statistical calculation, Sequencing quality control, Sequence assembly validation, Data handling, Genome annotation, Sequence composition calculation, Genome comparison, Validation 2025-12-18 2026-05-18 6 True False True False collection_column_join, Remove beginning1, Grouping1, bakta, cat1, fasterq_dump, tp_replace_in_column, drep_dereplicate, __EXTRACT_DATASET__, checkm_lineage_wf, join1, multiqc, collapse_dataset, Summary_Statistics1, tp_sort_header_tool, kmetashot, Cut1 UseGalaxy.eu, UseGalaxy.org (Main) UseGalaxy.cz 0 1247 1579 6.55 0 +Microbiome 16S Microbial Analysis with mothur (extended) https://training.galaxyproject.org//topics/microbiome/tutorials/mothur-miseq-sop/tutorial.html Microbial ecology, Taxonomy, Sequence analysis, Metabarcoding Phylogenetic tree reconstruction, Sequencing quality control, Phylogenetic analysis, Visualisation, Phylogenetic tree generation, Sequence read processing, Phylogenetic tree analysis, Taxonomic classification, Sequence clustering, DNA barcoding 2017-02-12 2025-12-18 5 True False False True mothur_sub_sample, mothur_classify_seqs, mothur_classify_otu, mothur_get_groups, mothur_dist_shared, mothur_cluster, mothur_summary_single, mothur_filter_seqs, mothur_heatmap_sim, taxonomy_krona_chart, mothur_tree_shared, mothur_chimera_vsearch, mothur_pre_cluster, mothur_make_contigs, mothur_summary_seqs, XY_Plot_1, mothur_align_seqs, mothur_make_biom, mothur_screen_seqs, mothur_count_groups, newick_display, mothur_remove_seqs, mothur_unique_seqs, mothur_count_seqs, mothur_venn, mothur_make_shared, mothur_rarefaction_single, mothur_taxonomy_to_krona, mothur_cluster_split, mothur_dist_seqs, mothur_remove_groups, mothur_remove_lineage, mothur_seq_error UseGalaxy.be, UseGalaxy.eu UseGalaxy.org.au, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org (Main) 0 14424 21194 5.0 0 +Microbiome 16S Microbial Analysis with mothur (short) https://training.galaxyproject.org//topics/microbiome/tutorials/mothur-miseq-sop-short/tutorial.html Microbial ecology, Taxonomy, Sequence analysis, Metabarcoding Phylogenetic tree reconstruction, Sequencing quality control, Phylogenetic analysis, Visualisation, Phylogenetic tree generation, Sequence read processing, Phylogenetic tree analysis, Taxonomic classification, Sequence clustering, DNA barcoding 2019-05-13 2025-12-18 6 True False True True mothur_sub_sample, mothur_classify_seqs, mothur_classify_otu, collapse_dataset, mothur_dist_shared, mothur_cluster, mothur_summary_single, mothur_filter_seqs, mothur_heatmap_sim, mothur_tree_shared, mothur_chimera_vsearch, mothur_pre_cluster, mothur_summary_seqs, XY_Plot_1, mothur_screen_seqs, mothur_count_groups, newick_display, mothur_remove_seqs, mothur_unique_seqs, mothur_count_seqs, mothur_venn, mothur_make_shared, mothur_rarefaction_single, mothur_cluster_split, mothur_dist_seqs, mothur_remove_groups, mothur_remove_lineage UseGalaxy.org.au, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org (Main) UseGalaxy.fr 0 6785 11364 7.75 0 +Variant Analysis M. tuberculosis Variant Analysis https://training.galaxyproject.org//topics/variant-analysis/tutorials/tb-variant-analysis/tutorial.html Genomics, Microbiology, Sequence assembly, Genetic variation, Public health and epidemiology, Infectious disease Variant calling, Phylogenetic tree visualisation, Global alignment, Sequencing quality control, Statistical calculation, Genome visualisation, Sequence contamination filtering, Antimicrobial resistance prediction, Sequence composition calculation, Phylogenetic tree generation, Sequence alignment, Sequence alignment analysis, Taxonomic classification, Local alignment, Validation, Sequence analysis 2020-07-25 2026-01-06 32 True False True True bcftools_consensus, tbvcfreport, tb_profiler_profile, tb_variant_filter, jvarkit_wgscoverageplotter, snippy, __FLATTEN__, EMBOSS:%20seqret84, tp_awk_tool, kraken2, samtools_stats, qualimap_bamqc, upload1, EMBOSS: seqret84, fastp, jbrowse, mosdepth, fastqc, tp_sed_tool, multiqc 0 8651 13093 7.8 0 +Proteomics metaQuantome 3: Taxonomy https://training.galaxyproject.org//topics/proteomics/tutorials/metaquantome-taxonomy/tutorial.html Proteomics, Proteogenomics, Metatranscriptomics, Microbial ecology, Metagenomics, Taxonomy Filtering, Differential protein expression analysis, Principal component visualisation, Visualisation, Indexing, Functional clustering, Quantification, Query and retrieval, Statistical inference, Heat map generation 2020-10-29 2024-03-15 14 True False False True metaquantome_expand, metaquantome_viz, metaquantome_filter, metaquantome_db, metaquantome_sample, metaquantome_stat UseGalaxy.be, UseGalaxy.eu UseGalaxy.org.au, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no 0 501 642 14.8 0 +Proteomics metaQuantome 1: Data creation https://training.galaxyproject.org//topics/proteomics/tutorials/metaquantome-data-creation/tutorial.html Proteomics, Proteogenomics, Biodiversity, Taxonomy Filtering, Label-free quantification, Prediction and recognition, Formatting, Visualisation 2020-10-16 2024-03-14 20 True False False True peptide_shaker, query_tabular, tp_replace_in_line, Remove beginning1, unipept, Filter1, tp_replace_in_column, Grep1, msconvert, regex1, flashlfq, search_gui, Cut1 UseGalaxy.eu UseGalaxy.org.au, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.no 0 958 1579 9.483333333333333 0 +Proteomics metaQuantome 2: Function https://training.galaxyproject.org//topics/proteomics/tutorials/metaquantome-function/tutorial.html Proteomics, Proteogenomics, Metatranscriptomics, Microbial ecology, Metagenomics Filtering, Differential protein expression analysis, Principal component visualisation, Visualisation, Indexing, Functional clustering, Quantification, Query and retrieval, Statistical inference, Heat map generation 2020-10-29 2024-03-15 14 True False False True metaquantome_expand, metaquantome_viz, metaquantome_filter, metaquantome_db, metaquantome_sample, metaquantome_stat UseGalaxy.be, UseGalaxy.eu UseGalaxy.org.au, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no 0 471 646 15.133333333333333 0 +Proteomics Metaproteomics tutorial https://training.galaxyproject.org//topics/proteomics/tutorials/metaproteomics/tutorial.html Proteomics, Proteogenomics, Biodiversity, Taxonomy Visualisation, Prediction and recognition 2017-06-28 2026-05-11 42 True False True True query_tabular, peptide_shaker, unipept, sqlite_to_tabular, search_gui UseGalaxy.org.au, UseGalaxy.eu, UseGalaxy.org (Main) UseGalaxy.be, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no 0 3191 4985 10.183333333333334 0 +Sequence analysis Quality and contamination control in bacterial isolate using Illumina MiSeq Data https://training.galaxyproject.org//topics/sequence-analysis/tutorials/quality-contamination-control/tutorial.html Whole genome sequencing, Genomics, Microbiology, Microbial ecology Expression analysis, Sequencing quality control, Statistical calculation, Sequence contamination filtering, Visualisation, Cross-assembly, Taxonomic classification, Read mapping 2024-07-15 2025-12-18 5 True False True True upload1, recentrifuge, fastp, falco, est_abundance, kraken2 GalaxyTrakr, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main) 0 2176 2857 10.35 0 +Variant Analysis Calling variants in non-diploid systems https://training.galaxyproject.org//topics/variant-analysis/tutorials/non-dip/tutorial.html Genomics, Sequence assembly, DNA polymorphism, Microbiology, Sequence analysis, Genetic variation Variant calling, Statistical calculation, Sequencing quality control, Data handling, Sequence composition calculation, Genome indexing, Sequence alignment, Sequence alignment analysis, Generation, Formatting, Read mapping 2017-02-16 2024-03-15 23 True False False True bamleftalign, freebayes, vcffilter2, picard_MarkDuplicates, bamFilter, fastqc, vcf2tsv, picard_MergeSamFiles, bwa_mem, Cut1 UseGalaxy.be, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main) UseGalaxy.org.au, UseGalaxy.cz, UseGalaxy.no 0 10064 17198 5.716666666666667 0 diff --git a/communities/microgalaxy/resources/tutorials.yml b/communities/microgalaxy/resources/tutorials.yml index 6a227139f..a2dde5137 100644 --- a/communities/microgalaxy/resources/tutorials.yml +++ b/communities/microgalaxy/resources/tutorials.yml @@ -1,183 +1,383 @@ -- admin_install: +- abbreviations: + SVs: Structural Variations + admin_install: install_repository_dependencies: true install_resolver_dependencies: true install_tool_dependencies: true tools: - - name: text_processing - owner: bgruening - revisions: ddf54b12c295 - tool_panel_section_label: Text Manipulation - tool_shed_url: https://toolshed.g2.bx.psu.edu/ - - name: text_processing - owner: bgruening - revisions: d698c222f354 - tool_panel_section_label: Text Manipulation - tool_shed_url: https://toolshed.g2.bx.psu.edu/ - - name: text_processing - owner: bgruening - revisions: d698c222f354 - tool_panel_section_label: Text Manipulation - tool_shed_url: https://toolshed.g2.bx.psu.edu/ - - name: text_processing - owner: bgruening - revisions: d698c222f354 - tool_panel_section_label: Text Manipulation - tool_shed_url: https://toolshed.g2.bx.psu.edu/ - - name: text_processing - owner: bgruening - revisions: d698c222f354 - tool_panel_section_label: Text Manipulation - tool_shed_url: https://toolshed.g2.bx.psu.edu/ - - name: text_processing + - name: flye owner: bgruening - revisions: d698c222f354 - tool_panel_section_label: Text Manipulation - tool_shed_url: https://toolshed.g2.bx.psu.edu/ - - name: add_value - owner: devteam - revisions: 745871c0b055 - tool_panel_section_label: Text Manipulation - tool_shed_url: https://toolshed.g2.bx.psu.edu/ - - name: fasta_compute_length - owner: devteam - revisions: de2db1bdfbf8 - tool_panel_section_label: FASTA/FASTQ + revisions: cb8dfd28c16f + tool_panel_section_label: Assembly tool_shed_url: https://toolshed.g2.bx.psu.edu/ - - name: fasta_filter_by_length + - name: fastqc owner: devteam - revisions: e626b3ff9922 + revisions: 5ec9f6bceaee tool_panel_section_label: FASTA/FASTQ tool_shed_url: https://toolshed.g2.bx.psu.edu/ - - name: fasta_filter_by_length - owner: devteam - revisions: 8cacfcf96a52 - tool_panel_section_label: FASTA/FASTQ + - name: bandage + owner: iuc + revisions: 86ec2f06de3c + tool_panel_section_label: Graph/Display Data tool_shed_url: https://toolshed.g2.bx.psu.edu/ - - name: lastz - owner: devteam - revisions: e7f19d6a9af8 + - name: bwa_mem2 + owner: iuc + revisions: d3e88507ee64 tool_panel_section_label: Mapping tool_shed_url: https://toolshed.g2.bx.psu.edu/ - - name: merge_cols - owner: devteam - revisions: f2aac0c5c60d - tool_panel_section_label: Text Manipulation - tool_shed_url: https://toolshed.g2.bx.psu.edu/ - - name: bedtools + - name: fastp owner: iuc - revisions: e19bebe96cd2 - tool_panel_section_label: BED + revisions: f875da9d433c + tool_panel_section_label: FASTA/FASTQ tool_shed_url: https://toolshed.g2.bx.psu.edu/ - - name: bedtools + - name: filtlong owner: iuc - revisions: e19bebe96cd2 - tool_panel_section_label: BED + revisions: 8880fb74ef56 + tool_panel_section_label: FASTA/FASTQ tool_shed_url: https://toolshed.g2.bx.psu.edu/ - - name: bedtools + - name: filtlong owner: iuc - revisions: e19bebe96cd2 - tool_panel_section_label: BED + revisions: 1f296803dfa3 + tool_panel_section_label: FASTA/FASTQ tool_shed_url: https://toolshed.g2.bx.psu.edu/ - - name: circos + - name: nanoplot owner: iuc - revisions: df7356989ac1 - tool_panel_section_label: Graph/Display Data + revisions: 0f1c34698076 + tool_panel_section_label: Nanopore tool_shed_url: https://toolshed.g2.bx.psu.edu/ - - name: circos + - name: polypolish owner: iuc - revisions: df7356989ac1 - tool_panel_section_label: Graph/Display Data + revisions: f355085dd2aa + tool_panel_section_label: Metagenomic Analysis tool_shed_url: https://toolshed.g2.bx.psu.edu/ - - name: datamash_ops + - name: porechop owner: iuc - revisions: 562f3c677828 - tool_panel_section_label: Join, Subtract and Group + revisions: 93d623d9979c + tool_panel_section_label: Nanopore tool_shed_url: https://toolshed.g2.bx.psu.edu/ - - name: jbrowse + - name: quast owner: iuc - revisions: fd5dbf0f732e - tool_panel_section_label: Graph/Display Data - tool_shed_url: https://toolshed.g2.bx.psu.edu/ - - name: collapse_collections - owner: nml - revisions: 25136a2b0cfe - tool_panel_section_label: Collection Operations - 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https://training.galaxyproject.org/training-material/api/topics/assembly/tutorials/ecoli_comparison/tutorial.json + \ true\ninstall_resolver_dependencies: true\ntools:\n- name: flye\n owner: bgruening\n\ + \ revisions: cb8dfd28c16f\n tool_panel_section_label: Assembly\n tool_shed_url:\ + \ https://toolshed.g2.bx.psu.edu/\n- name: fastqc\n owner: devteam\n revisions:\ + \ 5ec9f6bceaee\n tool_panel_section_label: FASTA/FASTQ\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n\ + - name: bandage\n owner: iuc\n revisions: 86ec2f06de3c\n tool_panel_section_label:\ + \ Graph/Display Data\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name:\ + \ bwa_mem2\n owner: iuc\n revisions: d3e88507ee64\n tool_panel_section_label:\ + \ Mapping\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fastp\n \ + \ owner: iuc\n revisions: f875da9d433c\n tool_panel_section_label: FASTA/FASTQ\n\ + \ tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: filtlong\n owner:\ + \ iuc\n revisions: 8880fb74ef56\n tool_panel_section_label: FASTA/FASTQ\n tool_shed_url:\ + \ https://toolshed.g2.bx.psu.edu/\n- name: filtlong\n owner: iuc\n revisions:\ + \ 1f296803dfa3\n tool_panel_section_label: FASTA/FASTQ\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n\ + - name: nanoplot\n owner: iuc\n revisions: 0f1c34698076\n tool_panel_section_label:\ + \ Nanopore\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: polypolish\n\ + \ owner: iuc\n revisions: f355085dd2aa\n tool_panel_section_label: Metagenomic\ + \ Analysis\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: porechop\n\ + \ owner: iuc\n revisions: 93d623d9979c\n tool_panel_section_label: Nanopore\n\ + \ tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: quast\n owner: iuc\n\ + \ revisions: 72472698a2df\n tool_panel_section_label: Assembly\n tool_shed_url:\ + \ https://toolshed.g2.bx.psu.edu/\n" + api: https://training.galaxyproject.org/training-material/api/topics/assembly/tutorials/mrsa-nanopore/tutorial.json + contributions: + authorship: + - bazante1 + - bebatut + editing: + - hexylena + - bazante1 + - shiltemann + - miaomiaozhou88 + - tflowers15 + funding: + - avans-atgm + - abromics + - unimelb + - melbournebioinformatics + - AustralianBioCommons + reviewing: + - abretaud + - gallardoalba + - bgruening + - shiltemann + - hexylena + - bebatut + - matuskalas contributors: - - email: anton@nekrut.org - id: nekrut - joined: 2017-09 - name: Anton Nekrutenko - page: https://training.galaxyproject.org/training-material/hall-of-fame/nekrut/ - url: https://training.galaxyproject.org/training-material/api/contributors/nekrut.json - - email: delphine.lariviere@galaxy.org - id: delphine-l + - affiliations: + - avans-atgm + id: bazante1 + joined: 2020-12 + name: Bazante Sanders + page: https://training.galaxyproject.org/training-material/hall-of-fame/bazante1/ + url: https://training.galaxyproject.org/training-material/api/contributors/bazante1.json + - affiliations: + - gallantries + - ifb + - elixir-europe + contact_for_training: true + elixir_node: fr + email: berenice.batut@gmail.com + fediverse: https://piaille.fr/@bebatut + fediverse_flavor: mastodon + former_affiliations: + - uni-freiburg + - deNBI + id: bebatut joined: 2017-09 - name: Delphine Lariviere - orcid: 0000-0001-6421-3484 - page: https://training.galaxyproject.org/training-material/hall-of-fame/delphine-l/ - url: https://training.galaxyproject.org/training-material/api/contributors/delphine-l.json + linkedin: berenicebatut + location: + country: FR + lat: 45.77 + lon: 3.08 + matrix: bebatut:matrix.org + name: "B\xE9r\xE9nice Batut" + orcid: 0000-0001-9852-1987 + page: https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/ + twitter: bebatut + url: https://training.galaxyproject.org/training-material/api/contributors/bebatut.json - affiliations: + - elixir-europe + contact_for_training: false + elixir_node: nl + former_affiliations: + - deNBI + - avans-atgm + - uni-freiburg - erasmusmc - gallantries - by-covid + - elixir-converge + id: hexylena + joined: 2017-09 + location: + country: NL + lat: 51.91 + lon: 4.46 + maintainer_contact: gitter + matrix: hexylena:matrix.org + name: Helena Rasche + orcid: 0000-0001-9760-8992 + page: https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/ + url: https://training.galaxyproject.org/training-material/api/contributors/hexylena.json + - affiliations: + - avans-atgm + id: bazante1 + joined: 2020-12 + name: Bazante Sanders + page: https://training.galaxyproject.org/training-material/hall-of-fame/bazante1/ + url: https://training.galaxyproject.org/training-material/api/contributors/bazante1.json + - affiliations: + - uni-freiburg + - nfdi4plants + - elixir-europe + bio: Researcher at Erasmus Medical Center + bluesky: shiltemann.bsky.social + contact_for_training: true + elixir_node: nl + email: saskia.hiltemann@gmail.com + fediverse: https://mstdn.science/@shiltemann + fediverse_flavor: mastodon + former_affiliations: + - CINECA-Project + - gallantries + - erasmusmc + id: shiltemann + joined: 2017-09 + linkedin: shiltemann + location: + country: NL + lat: 51.912 + lon: 4.462 + maintainer_contact: gitter + matrix: shiltemann:matrix.org + name: Saskia Hiltemann + orcid: 0000-0003-3803-468X + page: https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/ + url: https://training.galaxyproject.org/training-material/api/contributors/shiltemann.json + - email: m.zhou1@avans.nl + id: miaomiaozhou88 + joined: 2020-12 + name: Miaomiao Zhou + orcid: 0000-0003-4426-1758 + page: https://training.galaxyproject.org/training-material/hall-of-fame/miaomiaozhou88/ + url: https://training.galaxyproject.org/training-material/api/contributors/miaomiaozhou88.json + - affiliations: + - AustralianBioCommons + - unimelb + - melbournebioinformatics + email: treynolds@unimelb.edu.au + id: tflowers15 + joined: 2025-03 + name: Tristan Reynolds + orcid: 0000-0002-6606-5953 + page: https://training.galaxyproject.org/training-material/hall-of-fame/tflowers15/ + url: https://training.galaxyproject.org/training-material/api/contributors/tflowers15.json + - avatar: /training-material/shared/images/logo-avans.png + former_members: + - dirowa + - hexylena + id: avans-atgm + joined: 2020-11 + members: + - bazante1 + name: Avans Hogeschool + page: https://training.galaxyproject.org/training-material/hall-of-fame/avans-atgm/ + ror: 015d5s513 + short_name: Avans + url: https://training.galaxyproject.org/training-material/api/organisations/avans-atgm.json + - avatar: /training-material/assets/images/abromics.png + github: false + id: abromics + joined: 2024-01 + name: ABRomics + page: https://training.galaxyproject.org/training-material/hall-of-fame/abromics/ + url: https://training.galaxyproject.org/training-material/api/organisations/abromics.json + - avatar: /training-material/shared/images/unimelb_Logo_RGB.png + id: unimelb + members: + - annasyme + - cat-bro + - GraceAHall + - supernord + - tflowers15 + - uwwint + - vinisalazar + name: The University of Melbourne + page: https://training.galaxyproject.org/training-material/hall-of-fame/unimelb/ + url: https://training.galaxyproject.org/training-material/api/organisations/unimelb.json + - avatar: /training-material/shared/images/Melbourne-Bioinformatics-logo.png + former_members: + - annasyme + id: melbournebioinformatics + members: + - GraceAHall + - tflowers15 + - vinisalazar + name: Melbourne Bioinformatics + page: https://training.galaxyproject.org/training-material/hall-of-fame/melbournebioinformatics/ + url: https://training.galaxyproject.org/training-material/api/organisations/melbournebioinformatics.json + - avatar: /training-material/shared/images/Australian-Biocommons-Favicon-RGB.png + id: AustralianBioCommons + members: + - annasyme + - burkemlou + - cat-bro + - igormakunin + - mthang + - PatCapon39 + - supernord + - tflowers15 + - uwwint + name: Australian BioCommons + page: https://training.galaxyproject.org/training-material/hall-of-fame/AustralianBioCommons/ + url: https://training.galaxyproject.org/training-material/api/organisations/AustralianBioCommons.json + - affiliations: + - elixir-europe + bluesky: abretaud.bsky.social + contact_for_training: true + elixir_node: fr + email: anthony.bretaudeau@irisa.fr + fediverse: https://genomic.social/@abretaud + fediverse_flavor: mastodon + former_affiliations: + - eurosciencegateway + - gallantries + id: abretaud + joined: 2017-09 + location: + country: FR + lat: 48.11 + lon: -1.64 + matrix: abretaud:matrix.org + name: Anthony Bretaudeau + orcid: 0000-0003-0914-2470 + page: https://training.galaxyproject.org/training-material/hall-of-fame/abretaud/ + url: https://training.galaxyproject.org/training-material/api/contributors/abretaud.json + - elixir_node: de + former_affiliations: + - uni-freiburg + - elixir-europe + id: gallardoalba + joined: 2020-11 + name: "Crist\xF3bal Gallardo" + orcid: 0000-0002-5752-2155 + page: https://training.galaxyproject.org/training-material/hall-of-fame/gallardoalba/ + url: https://training.galaxyproject.org/training-material/api/contributors/gallardoalba.json + - affiliations: + - deNBI + - mwk + - uni-freiburg - elixir-europe + - materialvitaldigital + contact_for_training: true + elixir_node: de + email: bjoern.gruening@gmail.com + fediverse: https://fosstodon.org/@bgruening + fediverse_flavor: mastodon + former_affiliations: + - eurosciencegateway + - eosc-life + - by-covid + - crc992 - elixir-converge + id: bgruening + joined: 2017-09 + linkedin: bgruening + location: + country: DE + lat: 47.997791 + lon: 7.842609 + matrix: bgruening:matrix.org + name: "Bj\xF6rn Gr\xFCning" + orcid: 0000-0002-3079-6586 + page: https://training.galaxyproject.org/training-material/hall-of-fame/bgruening/ + twitter: bjoerngruening + url: https://training.galaxyproject.org/training-material/api/contributors/bgruening.json + - affiliations: + - uni-freiburg + - nfdi4plants + - elixir-europe + bio: Researcher at Erasmus Medical Center + bluesky: shiltemann.bsky.social + contact_for_training: true + elixir_node: nl + email: saskia.hiltemann@gmail.com + fediverse: https://mstdn.science/@shiltemann + fediverse_flavor: mastodon + former_affiliations: + - CINECA-Project + - gallantries + - erasmusmc + id: shiltemann + joined: 2017-09 + linkedin: shiltemann + location: + country: NL + lat: 51.912 + lon: 4.462 + maintainer_contact: gitter + matrix: shiltemann:matrix.org + name: Saskia Hiltemann + orcid: 0000-0003-3803-468X + page: https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/ + url: https://training.galaxyproject.org/training-material/api/contributors/shiltemann.json + - affiliations: + - elixir-europe contact_for_training: false elixir_node: nl former_affiliations: - deNBI - avans-atgm - uni-freiburg + - erasmusmc + - gallantries + - by-covid + - elixir-converge id: hexylena joined: 2017-09 location: @@ -190,88 +390,144 @@ orcid: 0000-0001-9760-8992 page: https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/ url: https://training.galaxyproject.org/training-material/api/contributors/hexylena.json - dir: topics/assembly/tutorials/ecoli_comparison + - affiliations: + - gallantries + - ifb + - elixir-europe + contact_for_training: true + elixir_node: fr + email: berenice.batut@gmail.com + fediverse: https://piaille.fr/@bebatut + fediverse_flavor: mastodon + former_affiliations: + - uni-freiburg + - deNBI + id: bebatut + joined: 2017-09 + linkedin: berenicebatut + location: + country: FR + lat: 45.77 + lon: 3.08 + matrix: bebatut:matrix.org + name: "B\xE9r\xE9nice Batut" + orcid: 0000-0001-9852-1987 + page: https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/ + twitter: bebatut + url: https://training.galaxyproject.org/training-material/api/contributors/bebatut.json + - id: matuskalas + joined: 2024-06 + name: "Mat\xFA\u0161 Kala\u0161" + page: https://training.galaxyproject.org/training-material/hall-of-fame/matuskalas/ + url: https://training.galaxyproject.org/training-material/api/contributors/matuskalas.json + dir: topics/assembly/tutorials/mrsa-nanopore edam_ontology: - topic_0196 + - topic_3673 + - topic_3305 - topic_0622 - topic_3301 + - topic_4013 edam_operation: - - Sequence visualisation - - Read mapping - - Mapping + - Filtering + - Mapping assembly + - Sequence assembly visualisation + - Sequencing quality control + - Statistical calculation + - Genome assembly + - Sequence assembly validation + - Sequence contamination filtering + - Visualisation + - Sequencing error detection + - Sequence composition calculation - Sequence alignment - - Genome visualisation + - De-novo assembly + - Cross-assembly + - Scatter plot plotting + - Read mapping + - Box-Whisker plot plotting edam_topic: - Sequence assembly + - Whole genome sequencing + - Public health and epidemiology - Genomics - Microbiology - exact_supported_servers: [] + - Antimicrobial resistance + exact_supported_servers: + - UseGalaxy.be + - UseGalaxy.eu feedback_mean_note: null feedback_number: 0 + follow_up_training: + - topic_name: genome-annotation + tutorials: + - amr-gene-detection + type: internal + - topic_name: galaxy-interface + tutorials: + - history-to-workflow + type: internal hands_on: true - id: assembly/ecoli_comparison - inexact_supported_servers: [] + id: assembly/mrsa-nanopore + inexact_supported_servers: + - UseGalaxy.cz + - UseGalaxy.fr js_requirements: - mathjax: null + mathjax: 12631 mermaid: false key_points: - - We learned how to download large sets of completed genomes from NCBI - - We learned how to use Galaxy's rule-based collection builder - - We learned how to use a combination of Galaxy tools to create complex views of - genome comparisons - - We learned about idiosyncrasies of data formats and how to deal with them using - Galaxy tools + - Nanopore produces fantastic assemblies but with low quality data + - Annotation with Prokka is very easy layout: tutorial_hands_on + level: Introductory license: CC-BY-4.0 - mod_date: '2026-04-13' + mod_date: '2026-01-05' objectives: - - Identification of the most closely related genome to my new assembly - - Perform sequence comparison to locate rearrangements - - Identify genes located in deletions - pageviews: 13261 - pub_date: '2018-06-14' + - Run tools to evaluate sequencing data on quality and quantity + - Process the output of quality control tools + - Improve the quality of sequencing data + - Run a tool to assemble a bacterial genome using short reads + - Run tools to assess the quality of an assembly + - Understand the outputs of tools to assess the quality of an assembly + pageviews: 17299 + pub_date: '2021-03-24' questions: - - I just assembled a genome. How does it compare with already sequenced genomes? - - How do I find rearranged, inserted, or deleted regions? - requirements: - - topic_name: assembly - tutorials: - - unicycler-assembly - type: internal - short_id: T00032 + - How to check the quality of the MinION data (together with Illumina data)? + - How to perform an assembly of a bacterial genome with MinION data? + - How to check the quality of an assembly? + short_id: T00037 short_tools: - - jbrowse - - cat1 - - collapse_dataset - - tp_replace_in_column - - random_lines1 - - tp_replace_in_line - - join1 - - fasta_filter_by_length - - circos_interval_to_tiles - - tp_sort_header_tool - - Filter1 - - fasta_compute_length - - addValue - - tp_cat - - bedtools_intersectbed - - circos - - tp_sed_tool - - datamash_ops - - tp_grep_tool - - mergeCols1 - - Cut1 - - bedtools_sortbed + - polypolish + - bandage_image + - bwa_mem2 + - porechop - upload1 - - Grep1 - - circos_aln_to_links - - lastz_wrapper_2 - - bedtools_complementbed + - __EXTRACT_DATASET__ + - nanoplot + - __FLATTEN__ + - quast + - fastp + - CONVERTER_bz2_to_uncompressed + - fastqc + - flye + - filtlong slides: false slides_recordings: false supported_servers: - exact: [] - inexact: [] + exact: + - name: UseGalaxy.be + url: https://usegalaxy.be/ + usegalaxy: false + - name: UseGalaxy.eu + url: https://usegalaxy.eu + usegalaxy: true + inexact: + - name: UseGalaxy.cz + url: https://usegalaxy.cz/ + usegalaxy: false + - name: UseGalaxy.fr + url: https://usegalaxy.fr/ + usegalaxy: true supported_servers_matrix: servers: - name: APOSTL @@ -313,9 +569,6 @@ - name: IPK Galaxy Blast Suite url: https://galaxy-web.ipk-gatersleben.de usegalaxy: false - - name: Lebanese University Galaxy - url: http://galaxy.ul.edu.lb/ - usegalaxy: false - name: Mandoiu Lab url: https://neo.engr.uconn.edu/ usegalaxy: false @@ -331,9 +584,6 @@ - name: PepSimili url: http://pepsimili.e-nios.com:8080/ usegalaxy: false - - name: PhagePromotor - url: https://galaxy.bio.di.uminho.pt/ - usegalaxy: false - name: UseGalaxy.org.au url: https://usegalaxy.org.au usegalaxy: true @@ -359,18 +609,18 @@ url: https://viralvariant.anses.fr/ usegalaxy: false tools: - - id: Cut1 + - id: CONVERTER_bz2_to_uncompressed servers: - server: http://apostl.moffitt.org/ - state: local + state: missing - server: http://mbac.gmu.edu:8080/ - state: local + state: missing - server: https://vm-chemflow-francegrille.eu/ state: missing - server: https://iris.angers.inra.fr/galaxypub-cfbp - state: missing - - server: https://hyperbrowser.uio.no/coloc-stats state: local + - server: https://hyperbrowser.uio.no/coloc-stats + state: missing - server: https://galaxy.mesocentre.uca.fr state: local - server: https://galaxy.pasteur.fr/ @@ -378,7 +628,7 @@ - server: https://galaxytrakr.org/ state: local - server: http://igg.cloud.ba.infn.it/galaxy - state: local + state: missing - server: https://galaxy.hyphy.org/ state: local - server: https://www.immportgalaxy.org/ @@ -386,20 +636,16 @@ - server: http://galaxy.interactomix.com/ state: missing - server: https://galaxy-web.ipk-gatersleben.de - state: missing - - server: http://galaxy.ul.edu.lb/ state: local - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr state: local - server: http://galaxy.inf.ethz.ch - state: local - - server: https://palfinder.ls.manchester.ac.uk/ state: missing - - server: http://pepsimili.e-nios.com:8080/ + - server: https://palfinder.ls.manchester.ac.uk/ state: local - - server: https://galaxy.bio.di.uminho.pt/ + - server: http://pepsimili.e-nios.com:8080/ state: local - server: https://usegalaxy.org.au state: local @@ -418,22 +664,22 @@ - server: https://viralvariant.anses.fr/ state: local version: local - - id: Filter1 + - id: __EXTRACT_DATASET__ servers: - server: http://apostl.moffitt.org/ - state: local + state: missing - server: http://mbac.gmu.edu:8080/ - state: local + state: missing - server: https://vm-chemflow-francegrille.eu/ state: missing - server: https://iris.angers.inra.fr/galaxypub-cfbp state: missing - server: https://hyperbrowser.uio.no/coloc-stats - state: local + state: missing - server: https://galaxy.mesocentre.uca.fr state: local - server: https://galaxy.pasteur.fr/ - state: local + state: missing - server: https://galaxytrakr.org/ state: local - server: http://igg.cloud.ba.infn.it/galaxy @@ -443,23 +689,19 @@ - server: https://www.immportgalaxy.org/ state: missing - server: http://galaxy.interactomix.com/ - state: missing + state: local - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: local - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr state: local - server: http://galaxy.inf.ethz.ch - state: local + state: missing - server: https://palfinder.ls.manchester.ac.uk/ state: missing - server: http://pepsimili.e-nios.com:8080/ state: local - - server: https://galaxy.bio.di.uminho.pt/ - state: local - server: https://usegalaxy.org.au state: local - server: https://usegalaxy.be/ @@ -477,22 +719,22 @@ - server: https://viralvariant.anses.fr/ state: local version: local - - id: Grep1 + - id: __FLATTEN__ servers: - server: http://apostl.moffitt.org/ - state: local + state: missing - server: http://mbac.gmu.edu:8080/ - state: local + state: missing - server: https://vm-chemflow-francegrille.eu/ state: missing - server: https://iris.angers.inra.fr/galaxypub-cfbp state: missing - server: https://hyperbrowser.uio.no/coloc-stats - state: local + state: missing - server: https://galaxy.mesocentre.uca.fr state: local - server: https://galaxy.pasteur.fr/ - state: local + state: missing - server: https://galaxytrakr.org/ state: local - server: http://igg.cloud.ba.infn.it/galaxy @@ -502,23 +744,19 @@ - server: https://www.immportgalaxy.org/ state: missing - server: http://galaxy.interactomix.com/ - state: missing + state: local - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: local - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr state: local - server: http://galaxy.inf.ethz.ch - state: local + state: missing - server: https://palfinder.ls.manchester.ac.uk/ state: missing - server: http://pepsimili.e-nios.com:8080/ state: local - - server: https://galaxy.bio.di.uminho.pt/ - state: local - server: https://usegalaxy.org.au state: local - server: https://usegalaxy.be/ @@ -536,184 +774,225 @@ - server: https://viralvariant.anses.fr/ state: local version: local - - id: cat1 + - id: toolshed.g2.bx.psu.edu/repos/bgruening/flye/flye/2.9.1+galaxy0 servers: - server: http://apostl.moffitt.org/ - state: local + state: missing - server: http://mbac.gmu.edu:8080/ - state: local + state: missing - server: https://vm-chemflow-francegrille.eu/ state: missing - server: https://iris.angers.inra.fr/galaxypub-cfbp state: missing - server: https://hyperbrowser.uio.no/coloc-stats - state: local + state: missing - server: https://galaxy.mesocentre.uca.fr - state: local + state: exact + version: 2.9.1+galaxy0 - server: https://galaxy.pasteur.fr/ - state: local + state: inexact + versions: + - 2.9.4+galaxy0 - server: https://galaxytrakr.org/ - state: local + state: inexact + versions: + - 2.9.5+galaxy1 - server: http://igg.cloud.ba.infn.it/galaxy - state: local + state: missing - server: https://galaxy.hyphy.org/ - state: local + state: missing - server: https://www.immportgalaxy.org/ state: missing - server: http://galaxy.interactomix.com/ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: local - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr - state: local + state: missing - server: http://galaxy.inf.ethz.ch - state: local + state: missing - server: https://palfinder.ls.manchester.ac.uk/ state: missing - server: http://pepsimili.e-nios.com:8080/ - state: local - - server: https://galaxy.bio.di.uminho.pt/ - state: local + state: missing - server: https://usegalaxy.org.au - state: local + state: exact + version: 2.9.1+galaxy0 - server: https://usegalaxy.be/ - state: local + state: exact + version: 2.9.1+galaxy0 - server: https://usegalaxy.cz/ - state: local + state: exact + version: 2.9.1+galaxy0 - server: https://usegalaxy.eu - state: local + state: exact + version: 2.9.1+galaxy0 - server: https://usegalaxy.fr/ - state: local + state: exact + version: 2.9.1+galaxy0 - server: https://usegalaxy.no/ - state: local + state: inexact + versions: + - 2.9+galaxy0 + - 2.9.6+galaxy0 + - 2.8.3+galaxy0 + - 2.9.3+galaxy0 + - '2.6' + - 2.6+galaxy0 - server: https://usegalaxy.org - state: local + state: exact + version: 2.9.1+galaxy0 - server: https://viralvariant.anses.fr/ - state: local - version: local - - id: join1 + state: missing + version: 2.9.1+galaxy0 + - id: toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy0 servers: - server: http://apostl.moffitt.org/ - state: local + state: missing - server: http://mbac.gmu.edu:8080/ - state: local + state: missing - server: https://vm-chemflow-francegrille.eu/ state: missing - server: https://iris.angers.inra.fr/galaxypub-cfbp state: missing - server: https://hyperbrowser.uio.no/coloc-stats - state: local + state: missing - server: https://galaxy.mesocentre.uca.fr - state: local + state: inexact + versions: + - '0.72' + - 0.72+galaxy1 + - 0.73+galaxy0 - server: https://galaxy.pasteur.fr/ - state: local + state: exact + version: 0.74+galaxy0 - server: https://galaxytrakr.org/ - state: local + state: inexact + versions: + - 0.74+galaxy1 - server: http://igg.cloud.ba.infn.it/galaxy - state: local + state: missing - server: https://galaxy.hyphy.org/ - state: local + state: missing - server: https://www.immportgalaxy.org/ state: missing - server: http://galaxy.interactomix.com/ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: local - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr - state: local + state: inexact + versions: + - 0.74+galaxy1 - server: http://galaxy.inf.ethz.ch - state: local - - server: https://palfinder.ls.manchester.ac.uk/ state: missing + - server: https://palfinder.ls.manchester.ac.uk/ + state: inexact + versions: + - '0.72' + - 0.72+galaxy1 + - '0.65' + - '0.71' - server: http://pepsimili.e-nios.com:8080/ - state: local - - server: https://galaxy.bio.di.uminho.pt/ - state: local + state: exact + version: 0.74+galaxy0 - server: https://usegalaxy.org.au - state: local + state: exact + version: 0.74+galaxy0 - server: https://usegalaxy.be/ - state: local + state: exact + version: 0.74+galaxy0 - server: https://usegalaxy.cz/ - state: local + state: exact + version: 0.74+galaxy0 - server: https://usegalaxy.eu - state: local + state: exact + version: 0.74+galaxy0 - server: https://usegalaxy.fr/ - state: local + state: exact + version: 0.74+galaxy0 - server: https://usegalaxy.no/ - state: local + state: inexact + versions: + - 0.72+galaxy1 + - 0.73+galaxy0 - server: https://usegalaxy.org - state: local + state: exact + version: 0.74+galaxy0 - server: https://viralvariant.anses.fr/ - state: local - version: local - - id: random_lines1 + state: missing + version: 0.74+galaxy0 + - id: toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/2022.09+galaxy4 servers: - server: http://apostl.moffitt.org/ - state: local + state: missing - server: http://mbac.gmu.edu:8080/ - state: local + state: missing - server: https://vm-chemflow-francegrille.eu/ state: missing - server: https://iris.angers.inra.fr/galaxypub-cfbp state: missing - server: https://hyperbrowser.uio.no/coloc-stats - state: local + state: missing - server: https://galaxy.mesocentre.uca.fr - state: local + state: exact + version: 2022.09+galaxy4 - server: https://galaxy.pasteur.fr/ - state: local + state: inexact + versions: + - 0.8.1+galaxy3 - server: https://galaxytrakr.org/ - state: local + state: missing - server: http://igg.cloud.ba.infn.it/galaxy - state: local + state: missing - server: https://galaxy.hyphy.org/ - state: local + state: missing - server: https://www.immportgalaxy.org/ state: missing - server: http://galaxy.interactomix.com/ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: local - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr - state: local + state: exact + version: 2022.09+galaxy4 - server: http://galaxy.inf.ethz.ch - state: local + state: missing - server: https://palfinder.ls.manchester.ac.uk/ state: missing - server: http://pepsimili.e-nios.com:8080/ - state: local - - server: https://galaxy.bio.di.uminho.pt/ - state: local + state: missing - server: https://usegalaxy.org.au - state: local + state: exact + version: 2022.09+galaxy4 - server: https://usegalaxy.be/ - state: local + state: exact + version: 2022.09+galaxy4 - server: https://usegalaxy.cz/ - state: local + state: exact + version: 2022.09+galaxy4 - server: https://usegalaxy.eu - state: local + state: exact + version: 2022.09+galaxy4 - server: https://usegalaxy.fr/ - state: local + state: exact + version: 2022.09+galaxy4 - server: https://usegalaxy.no/ - state: local + state: exact + version: 2022.09+galaxy4 - server: https://usegalaxy.org - state: local + state: exact + version: 2022.09+galaxy4 - server: https://viralvariant.anses.fr/ - state: local - version: local - - id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.0 + state: missing + version: 2022.09+galaxy4 + - id: toolshed.g2.bx.psu.edu/repos/iuc/bwa_mem2/bwa_mem2/2.2.1+galaxy1 servers: - server: http://apostl.moffitt.org/ state: missing @@ -727,65 +1006,60 @@ state: missing - server: https://galaxy.mesocentre.uca.fr state: exact - version: 0.1.0 + version: 2.2.1+galaxy1 - server: https://galaxy.pasteur.fr/ state: missing - server: https://galaxytrakr.org/ - state: exact - version: 0.1.0 + state: inexact + versions: + - 2.3+galaxy0 - server: http://igg.cloud.ba.infn.it/galaxy state: missing - server: https://galaxy.hyphy.org/ - state: inexact - versions: - - 9.5+galaxy3 + state: missing - server: https://www.immportgalaxy.org/ state: missing - server: http://galaxy.interactomix.com/ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr - state: inexact - versions: - - 9.5+galaxy3 + state: exact + version: 2.2.1+galaxy1 - server: http://galaxy.inf.ethz.ch state: missing - server: https://palfinder.ls.manchester.ac.uk/ state: missing - server: http://pepsimili.e-nios.com:8080/ state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - server: https://usegalaxy.org.au state: exact - version: 0.1.0 + version: 2.2.1+galaxy1 - server: https://usegalaxy.be/ state: exact - version: 0.1.0 + version: 2.2.1+galaxy1 - server: https://usegalaxy.cz/ state: exact - version: 0.1.0 + version: 2.2.1+galaxy1 - server: https://usegalaxy.eu state: exact - version: 0.1.0 + version: 2.2.1+galaxy1 - server: https://usegalaxy.fr/ state: exact - version: 0.1.0 + version: 2.2.1+galaxy1 - server: https://usegalaxy.no/ - state: exact - version: 0.1.0 + state: missing - server: https://usegalaxy.org state: exact - version: 0.1.0 + version: 2.2.1+galaxy1 - server: https://viralvariant.anses.fr/ - state: missing - version: 0.1.0 - - id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/1.1.1 + state: inexact + versions: + - 2.3+galaxy0 + version: 2.2.1+galaxy1 + - id: toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/1.0.1+galaxy3 servers: - server: http://apostl.moffitt.org/ state: missing @@ -799,65 +1073,67 @@ state: missing - server: https://galaxy.mesocentre.uca.fr state: exact - version: 1.1.1 + version: 1.0.1+galaxy3 - server: https://galaxy.pasteur.fr/ - state: missing + state: inexact + versions: + - 0.23.2+galaxy0 - server: https://galaxytrakr.org/ state: exact - version: 1.1.1 + version: 1.0.1+galaxy3 - server: http://igg.cloud.ba.infn.it/galaxy state: missing - server: https://galaxy.hyphy.org/ - state: inexact - versions: - - 9.5+galaxy3 + state: missing - server: https://www.immportgalaxy.org/ state: missing - server: http://galaxy.interactomix.com/ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr state: inexact versions: - - 9.5+galaxy3 + - 1.3.3+galaxy0 - server: http://galaxy.inf.ethz.ch state: missing - server: https://palfinder.ls.manchester.ac.uk/ state: missing - server: http://pepsimili.e-nios.com:8080/ state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - server: https://usegalaxy.org.au state: exact - version: 1.1.1 + version: 1.0.1+galaxy3 - server: https://usegalaxy.be/ state: exact - version: 1.1.1 + version: 1.0.1+galaxy3 - server: https://usegalaxy.cz/ state: exact - version: 1.1.1 + version: 1.0.1+galaxy3 - server: https://usegalaxy.eu state: exact - version: 1.1.1 + version: 1.0.1+galaxy3 - server: https://usegalaxy.fr/ state: exact - version: 1.1.1 + version: 1.0.1+galaxy3 - server: https://usegalaxy.no/ - state: exact - version: 1.1.1 + state: inexact + versions: + - 0.20.1+galaxy0 + - 0.23.2+galaxy0 + - 0.19.5+galaxy1 - server: https://usegalaxy.org state: exact - version: 1.1.1 + version: 1.0.1+galaxy3 - server: https://viralvariant.anses.fr/ - state: missing - version: 1.1.1 - - id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/1.1.3 + state: inexact + versions: + - 0.23.2+galaxy0 + - 1.0.1+galaxy2 + version: 1.0.1+galaxy3 + - id: toolshed.g2.bx.psu.edu/repos/iuc/filtlong/filtlong/0.2.0 servers: - server: http://apostl.moffitt.org/ state: missing @@ -870,66 +1146,70 @@ - server: https://hyperbrowser.uio.no/coloc-stats state: missing - server: https://galaxy.mesocentre.uca.fr - state: exact - version: 1.1.3 + state: inexact + versions: + - 0.3.0+galaxy0 + - 0.3.1+galaxy0 + - 0.2.1+galaxy0 - server: https://galaxy.pasteur.fr/ - state: missing + state: inexact + versions: + - 0.2.1+galaxy0 - server: https://galaxytrakr.org/ - state: exact - version: 1.1.3 + state: inexact + versions: + - 0.2.1+galaxy0 - server: http://igg.cloud.ba.infn.it/galaxy state: missing - server: https://galaxy.hyphy.org/ - state: inexact - versions: - - 9.5+galaxy3 + state: missing - server: https://www.immportgalaxy.org/ state: missing - server: http://galaxy.interactomix.com/ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr - state: inexact - versions: - - 9.5+galaxy3 + state: missing - server: http://galaxy.inf.ethz.ch state: missing - server: https://palfinder.ls.manchester.ac.uk/ state: missing - server: http://pepsimili.e-nios.com:8080/ state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - server: https://usegalaxy.org.au state: exact - version: 1.1.3 + version: 0.2.0 - server: https://usegalaxy.be/ state: exact - version: 1.1.3 + version: 0.2.0 - server: https://usegalaxy.cz/ - state: exact - version: 1.1.3 + state: inexact + versions: + - 0.3.0+galaxy0 + - 0.3.1+galaxy0 + - 0.2.1+galaxy0 - server: https://usegalaxy.eu state: exact - version: 1.1.3 + version: 0.2.0 - server: https://usegalaxy.fr/ - state: exact - version: 1.1.3 + state: inexact + versions: + - 0.3.0+galaxy0 + - 0.3.1+galaxy0 + - 0.2.1+galaxy0 - server: https://usegalaxy.no/ state: exact - version: 1.1.3 + version: 0.2.0 - server: https://usegalaxy.org state: exact - version: 1.1.3 + version: 0.2.0 - server: https://viralvariant.anses.fr/ state: missing - version: 1.1.3 - - id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/1.1.2 + version: 0.2.0 + - id: toolshed.g2.bx.psu.edu/repos/iuc/filtlong/filtlong/0.2.1+galaxy0 servers: - server: http://apostl.moffitt.org/ state: missing @@ -943,65 +1223,58 @@ state: missing - server: https://galaxy.mesocentre.uca.fr state: exact - version: 1.1.2 + version: 0.2.1+galaxy0 - server: https://galaxy.pasteur.fr/ - state: missing + state: exact + version: 0.2.1+galaxy0 - server: https://galaxytrakr.org/ state: exact - version: 1.1.2 + version: 0.2.1+galaxy0 - server: http://igg.cloud.ba.infn.it/galaxy state: missing - server: https://galaxy.hyphy.org/ - state: inexact - versions: - - 9.5+galaxy3 + state: missing - server: https://www.immportgalaxy.org/ state: missing - server: http://galaxy.interactomix.com/ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr - state: inexact - versions: - - 9.5+galaxy3 + state: missing - server: http://galaxy.inf.ethz.ch state: missing - server: https://palfinder.ls.manchester.ac.uk/ state: missing - server: http://pepsimili.e-nios.com:8080/ state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - server: https://usegalaxy.org.au state: exact - version: 1.1.2 + version: 0.2.1+galaxy0 - server: https://usegalaxy.be/ state: exact - version: 1.1.2 + version: 0.2.1+galaxy0 - server: https://usegalaxy.cz/ state: exact - version: 1.1.2 + version: 0.2.1+galaxy0 - server: https://usegalaxy.eu state: exact - version: 1.1.2 + version: 0.2.1+galaxy0 - server: https://usegalaxy.fr/ state: exact - version: 1.1.2 + version: 0.2.1+galaxy0 - server: https://usegalaxy.no/ state: exact - version: 1.1.2 + version: 0.2.1+galaxy0 - server: https://usegalaxy.org state: exact - version: 1.1.2 + version: 0.2.1+galaxy0 - server: https://viralvariant.anses.fr/ state: missing - version: 1.1.2 - - id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/1.1.1 + version: 0.2.1+galaxy0 + - id: toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.41.0+galaxy0 servers: - server: http://apostl.moffitt.org/ state: missing @@ -1015,137 +1288,65 @@ state: missing - server: https://galaxy.mesocentre.uca.fr state: exact - version: 1.1.1 + version: 1.41.0+galaxy0 - server: https://galaxy.pasteur.fr/ - state: missing - - server: https://galaxytrakr.org/ - state: exact - version: 1.1.1 - - server: http://igg.cloud.ba.infn.it/galaxy - state: missing - - server: https://galaxy.hyphy.org/ state: inexact versions: - - 9.5+galaxy3 - - server: https://www.immportgalaxy.org/ - state: missing - - server: http://galaxy.interactomix.com/ - state: missing - - server: https://galaxy-web.ipk-gatersleben.de - state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - - server: https://neo.engr.uconn.edu/ - state: missing - - server: https://mississippi.sorbonne-universite.fr + - 1.43.0+galaxy0 + - server: https://galaxytrakr.org/ state: inexact versions: - - 9.5+galaxy3 - - server: http://galaxy.inf.ethz.ch - state: missing - - server: https://palfinder.ls.manchester.ac.uk/ - state: missing - - server: http://pepsimili.e-nios.com:8080/ - state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - - server: https://usegalaxy.org.au - state: exact - version: 1.1.1 - - server: https://usegalaxy.be/ - state: exact - version: 1.1.1 - - server: https://usegalaxy.cz/ - state: exact - version: 1.1.1 - - server: https://usegalaxy.eu - state: exact - version: 1.1.1 - - server: https://usegalaxy.fr/ - state: exact - version: 1.1.1 - - server: https://usegalaxy.no/ - state: exact - version: 1.1.1 - - server: https://usegalaxy.org - state: exact - version: 1.1.1 - - server: https://viralvariant.anses.fr/ - state: missing - version: 1.1.1 - - id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/1.1.1 - servers: - - server: http://apostl.moffitt.org/ - state: missing - - server: http://mbac.gmu.edu:8080/ - state: missing - - server: https://vm-chemflow-francegrille.eu/ - state: missing - - server: https://iris.angers.inra.fr/galaxypub-cfbp - state: missing - - server: https://hyperbrowser.uio.no/coloc-stats - state: missing - - server: https://galaxy.mesocentre.uca.fr - state: exact - version: 1.1.1 - - server: https://galaxy.pasteur.fr/ - state: missing - - server: https://galaxytrakr.org/ - state: exact - version: 1.1.1 + - 1.28.2+galaxy1 - server: http://igg.cloud.ba.infn.it/galaxy state: missing - server: https://galaxy.hyphy.org/ - state: inexact - versions: - - 9.5+galaxy3 + state: missing - server: https://www.immportgalaxy.org/ state: missing - server: http://galaxy.interactomix.com/ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr state: inexact versions: - - 9.5+galaxy3 + - 1.46.2+galaxy0 - server: http://galaxy.inf.ethz.ch state: missing - server: https://palfinder.ls.manchester.ac.uk/ state: missing - server: http://pepsimili.e-nios.com:8080/ state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - server: https://usegalaxy.org.au state: exact - version: 1.1.1 + version: 1.41.0+galaxy0 - server: https://usegalaxy.be/ state: exact - version: 1.1.1 + version: 1.41.0+galaxy0 - server: https://usegalaxy.cz/ state: exact - version: 1.1.1 + version: 1.41.0+galaxy0 - server: https://usegalaxy.eu state: exact - version: 1.1.1 + version: 1.41.0+galaxy0 - server: https://usegalaxy.fr/ state: exact - version: 1.1.1 + version: 1.41.0+galaxy0 - server: https://usegalaxy.no/ - state: exact - version: 1.1.1 + state: inexact + versions: + - 1.28.2+galaxy1 + - 1.36.2+galaxy1 + - 1.25.0+galaxy1 - server: https://usegalaxy.org state: exact - version: 1.1.1 + version: 1.41.0+galaxy0 - server: https://viralvariant.anses.fr/ state: missing - version: 1.1.1 - - id: toolshed.g2.bx.psu.edu/repos/devteam/add_value/addValue/1.0.0 + version: 1.41.0+galaxy0 + - id: toolshed.g2.bx.psu.edu/repos/iuc/polypolish/polypolish/0.5.0+galaxy2 servers: - server: http://apostl.moffitt.org/ state: missing @@ -1158,12 +1359,16 @@ - server: https://hyperbrowser.uio.no/coloc-stats state: missing - server: https://galaxy.mesocentre.uca.fr - state: missing + state: inexact + versions: + - 0.6.1+galaxy0 + - 0.5.0+galaxy0 - server: https://galaxy.pasteur.fr/ state: missing - server: https://galaxytrakr.org/ - state: exact - version: 1.0.0 + state: inexact + versions: + - 0.6.1+galaxy0 - server: http://igg.cloud.ba.infn.it/galaxy state: missing - server: https://galaxy.hyphy.org/ @@ -1174,46 +1379,42 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr - state: inexact - versions: - - 1.0.1 + state: missing - server: http://galaxy.inf.ethz.ch state: missing - server: https://palfinder.ls.manchester.ac.uk/ state: missing - server: http://pepsimili.e-nios.com:8080/ state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - server: https://usegalaxy.org.au state: exact - version: 1.0.0 + version: 0.5.0+galaxy2 - server: https://usegalaxy.be/ state: exact - version: 1.0.0 + version: 0.5.0+galaxy2 - server: https://usegalaxy.cz/ - state: exact - version: 1.0.0 + state: inexact + versions: + - 0.6.1+galaxy0 + - 0.5.0+galaxy0 + - 0.6.0+galaxy0 - server: https://usegalaxy.eu state: exact - version: 1.0.0 + version: 0.5.0+galaxy2 - server: https://usegalaxy.fr/ state: exact - version: 1.0.0 + version: 0.5.0+galaxy2 - server: https://usegalaxy.no/ state: missing - server: https://usegalaxy.org - state: exact - version: 1.0.0 + state: missing - server: https://viralvariant.anses.fr/ state: missing - version: 1.0.0 - - id: toolshed.g2.bx.psu.edu/repos/devteam/fasta_compute_length/fasta_compute_length/1.0.1 + version: 0.5.0+galaxy2 + - id: toolshed.g2.bx.psu.edu/repos/iuc/porechop/porechop/0.2.3 servers: - server: http://apostl.moffitt.org/ state: missing @@ -1228,12 +1429,14 @@ - server: https://galaxy.mesocentre.uca.fr state: missing - server: https://galaxy.pasteur.fr/ - state: missing + state: inexact + versions: + - 0.2.4+galaxy0 - server: https://galaxytrakr.org/ state: inexact versions: - - 1.0.4 - - 1.0.3 + - 0.2.4+galaxy0 + - 0.2.4+galaxy1 - server: http://igg.cloud.ba.infn.it/galaxy state: missing - server: https://galaxy.hyphy.org/ @@ -1244,130 +1447,44 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr - state: inexact - versions: - - 1.0.4 - - 1.0.2 + state: missing - server: http://galaxy.inf.ethz.ch state: missing - server: https://palfinder.ls.manchester.ac.uk/ state: missing - server: http://pepsimili.e-nios.com:8080/ state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - server: https://usegalaxy.org.au state: exact - version: 1.0.1 + version: 0.2.3 - server: https://usegalaxy.be/ state: exact - version: 1.0.1 + version: 0.2.3 - server: https://usegalaxy.cz/ state: inexact versions: - - 1.0.4 - - 1.0.3 + - 0.2.4+galaxy0 + - 0.2.4+galaxy1 - server: https://usegalaxy.eu state: exact - version: 1.0.1 + version: 0.2.3 - server: https://usegalaxy.fr/ state: inexact versions: - - 1.0.4 - - 1.0.3 - - 1.0.2 - - server: https://usegalaxy.no/ - state: inexact - versions: - - 1.0.3 - - server: https://usegalaxy.org - state: inexact - versions: - - 1.0.4 - - 1.0.3 - - 1.0.2 - - 1.0.0 - - server: https://viralvariant.anses.fr/ - state: missing - version: 1.0.1 - - id: toolshed.g2.bx.psu.edu/repos/devteam/fasta_filter_by_length/fasta_filter_by_length/1.1 - servers: - - server: http://apostl.moffitt.org/ - state: missing - - server: http://mbac.gmu.edu:8080/ - state: missing - - server: https://vm-chemflow-francegrille.eu/ - state: missing - - server: https://iris.angers.inra.fr/galaxypub-cfbp - state: missing - - server: https://hyperbrowser.uio.no/coloc-stats - state: missing - - server: https://galaxy.mesocentre.uca.fr - state: inexact - versions: - - '1.2' - - server: https://galaxy.pasteur.fr/ - state: missing - - server: https://galaxytrakr.org/ - state: missing - - server: http://igg.cloud.ba.infn.it/galaxy - state: missing - - server: https://galaxy.hyphy.org/ - state: missing - - server: https://www.immportgalaxy.org/ - state: missing - - server: http://galaxy.interactomix.com/ - state: missing - - server: https://galaxy-web.ipk-gatersleben.de - state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - - server: https://neo.engr.uconn.edu/ - state: missing - - server: https://mississippi.sorbonne-universite.fr - state: inexact - versions: - - '1.2' - - server: http://galaxy.inf.ethz.ch - state: missing - - server: https://palfinder.ls.manchester.ac.uk/ - state: missing - - server: http://pepsimili.e-nios.com:8080/ - state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - - server: https://usegalaxy.org.au - state: inexact - versions: - - '1.2' - - server: https://usegalaxy.be/ - state: exact - version: '1.1' - - server: https://usegalaxy.cz/ - state: inexact - versions: - - '1.2' - - server: https://usegalaxy.eu - state: exact - version: '1.1' - - server: https://usegalaxy.fr/ - state: exact - version: '1.1' + - 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page: https://training.galaxyproject.org/training-material/hall-of-fame/nekrut/ - url: https://training.galaxyproject.org/training-material/api/contributors/nekrut.json - - email: delphine.lariviere@galaxy.org - id: delphine-l - joined: 2017-09 - name: Delphine Lariviere - orcid: 0000-0001-6421-3484 - page: https://training.galaxyproject.org/training-material/hall-of-fame/delphine-l/ - url: https://training.galaxyproject.org/training-material/api/contributors/delphine-l.json - - elixir_node: au - email: simon.gladman@unimelb.edu.au - id: slugger70 - in_memoriam: "Simon\ - \ Gladman, system administrator of UseGalaxy.org.au, passed away on November\ - \ 26, 2022\n\nHe was a fantastic teacher, tutorial author, system administrator, and warm\ - \ and welcoming friend. He contributed heavily to the Galaxy Training Network\ - \ and especially the Galaxy Administration community over the years, we will\ - \ miss him dearly. The GTN and GAT would not be what they are today, without\ - \ him.\n\n\u201CHave I told you about my watch?\u201D" - joined: 2017-09 - name: Simon Gladman - orcid: 0000-0002-6100-4385 - page: https://training.galaxyproject.org/training-material/hall-of-fame/slugger70/ - url: https://training.galaxyproject.org/training-material/api/contributors/slugger70.json - - avatar: /training-material/shared/images/unimelb_Logo_RGB.png - id: unimelb - members: - - annasyme - - cat-bro - - GraceAHall - - supernord - - tflowers15 - - uwwint - - vinisalazar - name: The University of Melbourne - page: https://training.galaxyproject.org/training-material/hall-of-fame/unimelb/ - url: https://training.galaxyproject.org/training-material/api/organisations/unimelb.json - - avatar: /training-material/shared/images/Melbourne-Bioinformatics-logo.png - former_members: - - annasyme - id: melbournebioinformatics - members: - - GraceAHall - - tflowers15 - - vinisalazar - name: Melbourne Bioinformatics - page: https://training.galaxyproject.org/training-material/hall-of-fame/melbournebioinformatics/ - 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matrix: bgruening:matrix.org - name: "Bj\xF6rn Gr\xFCning" - orcid: 0000-0002-3079-6586 - page: https://training.galaxyproject.org/training-material/hall-of-fame/bgruening/ - twitter: bjoerngruening - url: https://training.galaxyproject.org/training-material/api/contributors/bgruening.json - - affiliations: - - elixir-europe - bluesky: abretaud.bsky.social - contact_for_training: true - elixir_node: fr - email: anthony.bretaudeau@irisa.fr - fediverse: https://genomic.social/@abretaud - fediverse_flavor: mastodon - former_affiliations: - - eurosciencegateway - - gallantries - id: abretaud - joined: 2017-09 - location: - country: FR - lat: 48.11 - lon: -1.64 - matrix: abretaud:matrix.org - name: Anthony Bretaudeau - orcid: 0000-0003-0914-2470 - page: https://training.galaxyproject.org/training-material/hall-of-fame/abretaud/ - url: https://training.galaxyproject.org/training-material/api/contributors/abretaud.json - - affiliations: - - gallantries - - ifb - - elixir-europe - contact_for_training: true - 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url: https://training.galaxyproject.org/training-material/api/contributors/njall.json - dir: topics/assembly/tutorials/unicycler-assembly - edam_ontology: - - topic_0196 - - topic_0622 - - topic_3301 - edam_operation: - - Statistical calculation - - Genome assembly - - Coding region prediction - - Visualisation - - Sequence assembly validation - - Validation - - Gene prediction - - Sequence composition calculation - - Aggregation - - Genome annotation - - Sequencing quality control - edam_topic: - - Sequence assembly - - Genomics - - Microbiology - exact_supported_servers: - - UseGalaxy.org.au - - UseGalaxy.eu - - UseGalaxy.org (Main) - feedback_mean_note: null - feedback_number: 0 - follow_up_training: - - topic_name: assembly - tutorials: - - ecoli_comparison - type: internal - hands_on: true - id: assembly/unicycler-assembly - inexact_supported_servers: - - Galaxy@AuBi - - GalaxyTrakr - - MISSISSIPPI - - UseGalaxy.be - - UseGalaxy.cz - - UseGalaxy.fr - - UseGalaxy.no - js_requirements: - mathjax: null - mermaid: false - key_points: - - We learned about the strategies used by assemblers for hybrid assemblies - - We performed an hybrid assembly of a bacterial genome and its annotation - - Unicycler is a pipeline bases on Spades and Pilon dedicated to hybrid assembly - of Small genomes - - Combination of short and long reads helped us produce an almost perfect assembly - layout: tutorial_hands_on - level: Introductory - license: CC-BY-4.0 - mod_date: '2026-01-23' - objectives: - - Perform Quality Control on your reads - - Perform a Small genome Assembly with Unicycler - - Evaluate the Quality of the Assembly with Quast - - Annotate the assembly with Prokka - pageviews: 9058168 - pub_date: '2017-10-11' - questions: - - I have short reads and long reads. 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]\n 3 -> 6 [label=\"contigs_graph\"]\n k99656c96011a4ce0bb5b8ee1e4541eb1[color=lightseagreen,label=\"\ - Output\\nbandage_info_output\"]\n 6 -> k99656c96011a4ce0bb5b8ee1e4541eb1\n}" - history: - - hash: c2bf6f178fef000d5cb44eb66371b894ed1a8d9e - message: Update workflow and workflow tests - num: 8 - short_hash: c2bf6f178 - unix: '1766097170' - - hash: 597f8ce954083c7cd4e43765b6c4709619637e6a - message: Add Bazante's ORCID - num: 7 - short_hash: 597f8ce95 - unix: '1706018263' - - hash: 03e4290900ade23b2dffb3f61ea2875a64f2c396 - message: Fix workflows - num: 6 - short_hash: 03e429090 - unix: '1706004257' - - hash: c88bcbb6f04ad1847e0747f7fb9256ee0ec858de - message: Add license and creator to workflows - num: 5 - short_hash: c88bcbb6f - unix: '1705678137' - - hash: 5fbcc03b0d2408af8c03f0c7867791b47b4cceff - message: Update the MRSA short-read assembly tutorial - num: 4 - short_hash: 5fbcc03b0 - unix: '1705072112' - - hash: 31848c0ae9109d020ddee510ad5a1c374c3df96e - message: fix linting issues - num: 3 - short_hash: 31848c0ae - unix: '1610039782' - - hash: 9c83730d5b61b1ed51890ee8c00dbf73834d7b54 - message: Finish illumina version - num: 2 - short_hash: 9c83730d5 - unix: '1610038238' - - hash: c1175777fc34b261481e16516de8fde7c890c4ae - message: Add Illumina version of tutorial - num: 1 - short_hash: c1175777f - unix: '1608293515' - inputs: - - annotation: '' - content_id: null - errors: null - id: 0 - input_connections: {} - inputs: - - description: '' - name: Input Paired End Collection - label: Input Paired End Collection - name: Input dataset collection - outputs: [] - position: - left: 0.0 - top: 293.93356048202895 - tool_id: null - tool_state: '{"optional": false, "tag": null, "collection_type": "list:paired", - "fields": null}' - tool_version: null - type: data_collection_input - uuid: 52f613fe-2dac-4144-b467-c0a8d85795ee - when: null - workflow_outputs: [] - license: MIT - mermaid: "flowchart TD\n 0[\"\u2139\uFE0F Input Collection\\nInput Paired End\ - \ Collection\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"fastp\"\ - 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name: "B\xE9r\xE9nice Batut" - description: Assembly of metagenomic sequencing data - features: - comments: false - parameters: false - report: - markdown: ' - - # Workflow Execution Report - - - ## Workflow Inputs - - ```galaxy - - invocation_inputs() - - ``` - - - ## Workflow Outputs - - ```galaxy - - invocation_outputs() - - ``` - - - ## Workflow - - ```galaxy - - workflow_display() - - ``` - - ' - subworkflows: false - graph_dot: "digraph main {\n node [fontname=\"Atkinson Hyperlegible\", shape=box,\ - \ color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n edge [fontname=\"\ - Atkinson Hyperlegible\"];\n 0[color=lightblue,label=\"\u2139\uFE0F Input Collection\\\ - nQC controlled reads\"]\n 1[label=\"metaSPAdes\"]\n 0 -> 1 [label=\"output\"\ - ]\n kba8ef041cea5479a8aab38b3d6f0af60[color=lightseagreen,label=\"Output\\\ - nout_ag\"]\n 1 -> kba8ef041cea5479a8aab38b3d6f0af60\n kc3b9a23494d245798eba895e7e49e129[color=lightseagreen,label=\"\ - Output\\nout_ags\"]\n 1 -> kc3b9a23494d245798eba895e7e49e129\n 2[label=\"\ - MEGAHIT\"]\n 0 -> 2 [label=\"output\"]\n k759ce084a80b4a04b74e6e387357e25a[color=lightseagreen,label=\"\ - Output\\noutput\"]\n 2 -> k759ce084a80b4a04b74e6e387357e25a\n 3[label=\"Bowtie2\"\ - ]\n 0 -> 3 [label=\"output\"]\n 2 -> 3 [label=\"output\"]\n k95b806c753ee4a788e24a5794c9c220a[color=lightseagreen,label=\"\ - Output\\nmapping_stats\"]\n 3 -> k95b806c753ee4a788e24a5794c9c220a\n 4[label=\"\ - CoverM contig\"]\n 0 -> 4 [label=\"output\"]\n 2 -> 4 [label=\"output\"]\n\ - \ k51a8a5a9b3bb43b980e57ec7b84a6cd5[color=lightseagreen,label=\"Output\\noutput\"\ - ]\n 4 -> k51a8a5a9b3bb43b980e57ec7b84a6cd5\n 5[label=\"Quast\"]\n 2 -> 5\ - \ [label=\"output\"]\n 0 -> 5 [label=\"output\"]\n k5553b6a6863d4846944f7ed609a3734a[color=lightseagreen,label=\"\ - Output\\nreport_html_meta\"]\n 5 -> k5553b6a6863d4846944f7ed609a3734a\n 6[label=\"\ - megahit contig2fastg\"]\n 2 -> 6 [label=\"output\"]\n 7[label=\"Bandage Image\"\ - ]\n 6 -> 7 [label=\"fastg\"]\n k63861d0be0a64604bd091b0f7ee9d54b[color=lightseagreen,label=\"\ - Output\\noutfile\"]\n 7 -> k63861d0be0a64604bd091b0f7ee9d54b\n 8[label=\"\ - Bandage Info\"]\n 6 -> 8 [label=\"fastg\"]\n 9[label=\"Column join\"]\n 8\ - \ -> 9 [label=\"outfile\"]\n kc882d313508440d48c979552fb7b35ad[color=lightseagreen,label=\"\ - Output\\ntabular_output\"]\n 9 -> kc882d313508440d48c979552fb7b35ad\n}" - history: [] - inputs: - - annotation: Metagenomics reads that have been controlled for quality - content_id: null - errors: null - id: 0 - input_connections: {} - inputs: - - description: Metagenomics reads that have been controlled for quality - name: QC controlled reads - label: QC controlled reads - name: Input dataset collection - outputs: [] - position: - left: 0 - top: 434.0193226947046 - tool_id: null - tool_state: '{"optional": false, "tag": null, "collection_type": "list:paired"}' - tool_version: null - type: data_collection_input - uuid: 768bd692-5d23-4394-b236-03d68f086b6f - when: null - workflow_outputs: [] - license: MIT - mermaid: "flowchart TD\n 0[\"\u2139\uFE0F Input Collection\\nQC controlled reads\"\ - 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url: https://training.galaxyproject.org/training-material/api/contributors/bazante1.json - - affiliations: - - uni-freiburg - - nfdi4plants - - elixir-europe - bio: Researcher at Erasmus Medical Center - bluesky: shiltemann.bsky.social - contact_for_training: true - elixir_node: nl - email: saskia.hiltemann@gmail.com - fediverse: https://mstdn.science/@shiltemann - fediverse_flavor: mastodon - former_affiliations: - - CINECA-Project - - gallantries - - erasmusmc - id: shiltemann - joined: 2017-09 - linkedin: shiltemann - location: - country: NL - lat: 51.912 - lon: 4.462 - maintainer_contact: gitter - matrix: shiltemann:matrix.org - name: Saskia Hiltemann - orcid: 0000-0003-3803-468X - page: https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/ - url: https://training.galaxyproject.org/training-material/api/contributors/shiltemann.json - - email: m.zhou1@avans.nl - id: miaomiaozhou88 - joined: 2020-12 - name: Miaomiao Zhou - orcid: 0000-0003-4426-1758 - page: https://training.galaxyproject.org/training-material/hall-of-fame/miaomiaozhou88/ - 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state: local - version: local - symlink: null - tags: - - nanopore - - assembly - - amr - - microgalaxy - time: null - time_estimation: 2h - title: Genome Assembly of MRSA from Oxford Nanopore MinION data (and optionally - Illumina data) - tools: - - CONVERTER_bz2_to_uncompressed - - __EXTRACT_DATASET__ - - __FLATTEN__ - - toolshed.g2.bx.psu.edu/repos/bgruening/flye/flye/2.9.1+galaxy0 - - toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy0 - - toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/2022.09+galaxy4 - - toolshed.g2.bx.psu.edu/repos/iuc/bwa_mem2/bwa_mem2/2.2.1+galaxy1 - - toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/1.0.1+galaxy3 - - toolshed.g2.bx.psu.edu/repos/iuc/filtlong/filtlong/0.2.0 - - toolshed.g2.bx.psu.edu/repos/iuc/filtlong/filtlong/0.2.1+galaxy0 - - toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.41.0+galaxy0 - - toolshed.g2.bx.psu.edu/repos/iuc/polypolish/polypolish/0.5.0+galaxy2 - - toolshed.g2.bx.psu.edu/repos/iuc/porechop/porechop/0.2.3 - - toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.2.0+galaxy1 - - upload1 - topic_name: assembly - topic_name_human: Assembly - tours: false - translations: - slides: [] - tutorial: [] - video: false - tutorial_name: mrsa-nanopore - type: tutorial - url: https://training.galaxyproject.org//topics/assembly/tutorials/mrsa-nanopore/tutorial.html - urls: - hands_on: https://training.galaxyproject.org/training-material/api/topics/assembly/tutorials/mrsa-nanopore/tutorial.json - slides: https://training.galaxyproject.org/training-material/api/topics/assembly/tutorials/mrsa-nanopore/tutorial.json - version: 16 - video: false - video_versions: 0 - video_view: 0 - visit_duration: 455 - visitors: 11438 - workflows: - - creators: - - class: Person - identifier: https://orcid.org/0000-0003-2255-1631 - name: Bazante Sanders - - class: Person - identifier: https://orcid.org/0000-0001-9852-1987 - name: "B\xE9r\xE9nice Batut" - - class: Person - identifier: 0000-0002-6606-5953 - name: Tristan Reynolds - description: Genome Assembly of MRSA from Oxford Nanopore MinION data (and optionally - Illumina data) - features: - comments: false - parameters: false - report: - markdown: ' - - # Workflow Execution Report - - - ## Workflow Inputs - - ```galaxy - - invocation_inputs() - - ``` - - - ## Workflow Outputs - - ```galaxy - - invocation_outputs() - - ``` - - - ## Workflow - - ```galaxy - - workflow_display() - - ``` - - ' - subworkflows: false - graph_dot: "digraph main {\n node [fontname=\"Atkinson Hyperlegible\", shape=box,\ - \ color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n edge [fontname=\"\ - Atkinson Hyperlegible\"];\n 0[color=lightblue,label=\"\u2139\uFE0F Input Dataset\\\ - nNanopore raw reads\"]\n 1[color=lightblue,label=\"\u2139\uFE0F Input Collection\\\ - nInput Paired End Collection\"]\n 2[label=\"FastQC\"]\n 0 -> 2 [label=\"output\"\ - ]\n 3[label=\"Convert compressed file to uncompressed.\"]\n 0 -> 3 [label=\"\ - output\"]\n 4[label=\"fastp\"]\n 1 -> 4 [label=\"output\"]\n kf172ab83f29740b3adc0beb1dbec99ab[color=lightseagreen,label=\"\ - Output\\nreport_json\"]\n 4 -> kf172ab83f29740b3adc0beb1dbec99ab\n 5[label=\"\ - 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consensus\"]\n 13[label=\"Quast\"]\n 11 -> 13 [label=\"consensus\"]\n kdabfb8fd87914959a9dc9b3c1e57a69c[color=lightseagreen,label=\"\ - Output\\nquast_report_before_polishing\"]\n 13 -> kdabfb8fd87914959a9dc9b3c1e57a69c\n\ - \ 14[label=\"Bandage Image\"]\n 11 -> 14 [label=\"assembly_gfa\"]\n 15[label=\"\ - BWA-MEM2\"]\n 8 -> 15 [label=\"output\"]\n 11 -> 15 [label=\"consensus\"]\n\ - \ 16[label=\"Polypolish\"]\n 11 -> 16 [label=\"consensus\"]\n 12 -> 16 [label=\"\ - bam_output\"]\n 15 -> 16 [label=\"bam_output\"]\n 17[label=\"Quast\"]\n 11\ - \ -> 17 [label=\"consensus\"]\n 16 -> 17 [label=\"polished_fasta\"]\n k4e465b5168bf42039a7c897f46c70277[color=lightseagreen,label=\"\ - Output\\nquast_report_after_polishing\"]\n 17 -> k4e465b5168bf42039a7c897f46c70277\n\ - }" - history: - - hash: de24119db10356969b4a079fb05ca176372ea330 - message: Update workflow and workflow tests - num: 2 - short_hash: de24119db - unix: '1766110919' - - hash: 96393a7fcb4d6dc37d86866cf8a61c931293502f - message: Add MRSA Nanopore assembly tutorial to AMR learning pathway - num: 1 - short_hash: 96393a7fc - unix: '1709135526' - inputs: - - annotation: Nanopore raw reads - content_id: null - errors: null - id: 0 - input_connections: {} - inputs: - - description: Nanopore raw reads - name: Nanopore raw reads - label: Nanopore raw reads - name: Input dataset - outputs: [] - position: - left: 20.534814361006397 - top: 589.9124911241256 - tool_id: null - tool_state: '{"optional": false, "tag": null}' - tool_version: null - type: data_input - uuid: cd4fd302-af94-4771-9b80-7c7acb6619d4 - when: null - workflow_outputs: [] - - annotation: '' - content_id: null - errors: null - id: 1 - input_connections: {} - inputs: - - description: '' - name: Input Paired End Collection - label: Input Paired End Collection - name: Input dataset collection - outputs: [] - position: - left: 0.0 - top: 968.6942909141043 - tool_id: null - tool_state: '{"optional": false, "tag": null, "collection_type": "list:paired", - "fields": null}' - tool_version: null - type: data_collection_input - 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\ Forward Reads\"];\n 6 -->|output| 7;\n 8[\"Extract Reverse Reads\"];\n \ - \ 6 -->|output| 8;\n 9[\"filtlong\"];\n 7 -->|output| 9;\n 8 -->|output|\ - \ 9;\n 0 -->|output| 9;\n 10[\"NanoPlot\"];\n 9 -->|outfile| 10;\n 89524090-f590-434d-89e2-66f0b1a23c7c[\"\ - Output\\nnanoplot_after_filtering\"];\n 10 --> 89524090-f590-434d-89e2-66f0b1a23c7c;\n\ - \ style 89524090-f590-434d-89e2-66f0b1a23c7c stroke:#2c3143,stroke-width:4px;\n\ - \ 11[\"Flye\"];\n 9 -->|outfile| 11;\n f12e718f-1bd5-490d-bd41-f0747aaa41a6[\"\ - Output\\nflye_assembly_info\"];\n 11 --> f12e718f-1bd5-490d-bd41-f0747aaa41a6;\n\ - \ style f12e718f-1bd5-490d-bd41-f0747aaa41a6 stroke:#2c3143,stroke-width:4px;\n\ - \ 12[\"BWA-MEM2\"];\n 7 -->|output| 12;\n 11 -->|consensus| 12;\n 13[\"\ - Quast\"];\n 11 -->|consensus| 13;\n dabfb8fd-8791-4959-a9dc-9b3c1e57a69c[\"\ - Output\\nquast_report_before_polishing\"];\n 13 --> dabfb8fd-8791-4959-a9dc-9b3c1e57a69c;\n\ - \ style dabfb8fd-8791-4959-a9dc-9b3c1e57a69c stroke:#2c3143,stroke-width:4px;\n\ - \ 14[\"Bandage Image\"];\n 11 -->|assembly_gfa| 14;\n 15[\"BWA-MEM2\"];\n\ - \ 8 -->|output| 15;\n 11 -->|consensus| 15;\n 16[\"Polypolish\"];\n 11 -->|consensus|\ - \ 16;\n 12 -->|bam_output| 16;\n 15 -->|bam_output| 16;\n 17[\"Quast\"];\n\ - \ 11 -->|consensus| 17;\n 16 -->|polished_fasta| 17;\n 4e465b51-68bf-4203-9a7c-897f46c70277[\"\ - Output\\nquast_report_after_polishing\"];\n 17 --> 4e465b51-68bf-4203-9a7c-897f46c70277;\n\ - \ style 4e465b51-68bf-4203-9a7c-897f46c70277 stroke:#2c3143,stroke-width:4px;" - modified: 2026-05-21 00:30:23 +0000 - name: Genome Assembly of MRSA using Oxford Nanopore MinION (and Illumina data - if available) - outputs: - - annotation: '' - content_id: toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/1.0.1+galaxy3 - errors: null - id: 4 - input_connections: - single_paired|paired_input: - id: 1 - output_name: output - inputs: - - description: runtime parameter for tool fastp - name: single_paired - label: null - name: fastp - outputs: - - name: output_paired_coll - 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- server: https://galaxy.pasteur.fr/ - state: local - - server: https://galaxytrakr.org/ - state: local - - server: http://igg.cloud.ba.infn.it/galaxy - state: local - - server: https://galaxy.hyphy.org/ - state: local - - server: https://www.immportgalaxy.org/ - state: local - - server: http://galaxy.interactomix.com/ - state: local - - server: https://galaxy-web.ipk-gatersleben.de - state: local - - server: http://galaxy.ul.edu.lb/ - state: local - - server: https://neo.engr.uconn.edu/ - state: local - - server: https://mississippi.sorbonne-universite.fr - state: local - - server: http://galaxy.inf.ethz.ch - state: local - - server: https://palfinder.ls.manchester.ac.uk/ - state: local - - server: http://pepsimili.e-nios.com:8080/ - state: local - - server: https://galaxy.bio.di.uminho.pt/ - state: local - - server: https://usegalaxy.org.au - state: missing - - server: https://usegalaxy.be/ - state: local - - server: https://usegalaxy.cz/ - state: local - - server: https://usegalaxy.eu - 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urls: - hands_on: https://training.galaxyproject.org/training-material/api/topics/ecology/tutorials/bacterial-isolate-species-contamination-checking/tutorial.json - slides: https://training.galaxyproject.org/training-material/api/topics/ecology/tutorials/bacterial-isolate-species-contamination-checking/tutorial.json - version: 6 - video: false - video_versions: 0 - video_view: 0 - visit_duration: 496 - visitors: 1036 - workflows: - - creators: - - alternateName: pimarin - class: Person - email: mailto:pierre.marin@france-bioinformatique.fr - familyName: MARIN - identifier: 0000-0002-8304-138X - name: Pierre - - class: Person - identifier: https://orcid.org/0000-0001-9852-1987 - name: "B\xE9r\xE9nice Batut" - - class: Person - identifier: 0000-0002-6606-5953 - name: Tristan Reynolds - description: Checking expected species and contamination in bacterial isolate - features: - comments: false - parameters: false - report: - markdown: ' - - # Workflow Execution Report - - - ## Workflow Inputs - - ```galaxy - - invocation_inputs() - - ``` - - - ## Workflow Outputs - - ```galaxy - - invocation_outputs() - - ``` - - - ## Workflow - - ```galaxy - - workflow_display() - - ``` - - ' - subworkflows: false - graph_dot: "digraph main {\n node [fontname=\"Atkinson Hyperlegible\", shape=box,\ - \ color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n edge [fontname=\"\ - Atkinson Hyperlegible\"];\n 0[color=lightblue,label=\"\u2139\uFE0F Input Collection\\\ - nInput Paired End Reads Collection\"]\n 1[label=\"Kraken2\"]\n 0 -> 1 [label=\"\ - output\"]\n ka408a64458cd4f5eaf2515b5ea63aa76[color=lightseagreen,label=\"\ - Output\\nkraken_report_reads\"]\n 1 -> ka408a64458cd4f5eaf2515b5ea63aa76\n\ - \ k54b85a5372ee4b73b1867fd55e8aab9b[color=lightseagreen,label=\"Output\\nkraken_report_tabular\"\ - ]\n 1 -> k54b85a5372ee4b73b1867fd55e8aab9b\n 2[label=\"Bracken\"]\n 1 ->\ - \ 2 [label=\"report_output\"]\n kae6c6464f5f54e5bb616d38166fc0133[color=lightseagreen,label=\"\ - Output\\nbracken_report_tsv\"]\n 2 -> kae6c6464f5f54e5bb616d38166fc0133\n \ - \ k8ca52af9f83942b6aa74f1a6a1dfbbc8[color=lightseagreen,label=\"Output\\nbracken_kraken_report\"\ - ]\n 2 -> k8ca52af9f83942b6aa74f1a6a1dfbbc8\n 3[label=\"Recentrifuge\"]\n \ - \ 1 -> 3 [label=\"output\"]\n kb5694f2dc8cd4460bfff74fd0792ecb3[color=lightseagreen,label=\"\ - Output\\nrecentrifuge_stats_tabular\"]\n 3 -> kb5694f2dc8cd4460bfff74fd0792ecb3\n\ - \ kbd947a1d0443465f86585d76d9ce69f8[color=lightseagreen,label=\"Output\\nrecentrifuge_report_html\"\ - ]\n 3 -> kbd947a1d0443465f86585d76d9ce69f8\n kc7457acb41bc4191b3fb6716e15fbe57[color=lightseagreen,label=\"\ - Output\\nrecentrifuge_data_tabular\"]\n 3 -> kc7457acb41bc4191b3fb6716e15fbe57\n\ - \ k94f6ff070e0647ad88f8a058d0808537[color=lightseagreen,label=\"Output\\nrecentrifuge_logfile\"\ - ]\n 3 -> k94f6ff070e0647ad88f8a058d0808537\n}" - history: - - hash: ecc2e2e411eb58e2349f8d3d61e067d02b4aa218 - message: Update workflow and workflow tests - num: 4 - short_hash: ecc2e2e41 - unix: '1765506765' - - hash: 4854483dab21555869c5c49b91fa3113146c07dc - message: Update Bracken version toolshed - num: 3 - short_hash: 4854483da - unix: '1712233925' - - hash: 96c80b0ad7e5179b3d43364e789efee1adeea130 - message: Update workflow creators - num: 2 - short_hash: 96c80b0ad - unix: '1706542936' - - hash: 96df58f868367e22ade2e451a1d9ecacba822bcc - message: Create new tutorial for checking expected species and contamination - in bacterial isolate - num: 1 - short_hash: 96df58f86 - unix: '1706542439' - inputs: - - annotation: '' - content_id: null - errors: null - id: 0 - input_connections: {} - inputs: - - description: '' - name: Input Paired End Reads Collection - label: Input Paired End Reads Collection - name: Input dataset collection - outputs: [] - position: - left: 0 - top: 77.19660790675707 - tool_id: null - tool_state: '{"optional": false, "tag": null, "collection_type": "list:paired", - "fields": null}' - tool_version: null - type: data_collection_input - uuid: a6b78808-bb96-4dda-9fe5-e984ee46de00 - when: null - workflow_outputs: [] - license: GPL-3.0-or-later - 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\ stroke:#2c3143,stroke-width:4px;\n 3[\"Recentrifuge\"];\n 1 -->|output|\ - \ 3;\n b5694f2d-c8cd-4460-bfff-74fd0792ecb3[\"Output\\nrecentrifuge_stats_tabular\"\ - ];\n 3 --> b5694f2d-c8cd-4460-bfff-74fd0792ecb3;\n style b5694f2d-c8cd-4460-bfff-74fd0792ecb3\ - \ stroke:#2c3143,stroke-width:4px;\n bd947a1d-0443-465f-8658-5d76d9ce69f8[\"\ - Output\\nrecentrifuge_report_html\"];\n 3 --> bd947a1d-0443-465f-8658-5d76d9ce69f8;\n\ - \ style bd947a1d-0443-465f-8658-5d76d9ce69f8 stroke:#2c3143,stroke-width:4px;\n\ - \ c7457acb-41bc-4191-b3fb-6716e15fbe57[\"Output\\nrecentrifuge_data_tabular\"\ - ];\n 3 --> c7457acb-41bc-4191-b3fb-6716e15fbe57;\n style c7457acb-41bc-4191-b3fb-6716e15fbe57\ - \ stroke:#2c3143,stroke-width:4px;\n 94f6ff07-0e06-47ad-88f8-a058d0808537[\"\ - Output\\nrecentrifuge_logfile\"];\n 3 --> 94f6ff07-0e06-47ad-88f8-a058d0808537;\n\ - \ style 94f6ff07-0e06-47ad-88f8-a058d0808537 stroke:#2c3143,stroke-width:4px;" - modified: 2026-05-21 00:30:23 +0000 - name: Checking expected species and contamination in bacterial isolate - 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Lower sampling proportions and - shorter sampling timeframes lead to lower clustering rates that shoud not be confounded - with lack of transmission. - layout: tutorial_hands_on - level: Intermediate - license: CC-BY-4.0 - mod_date: '2025-05-26' - objectives: - - Create a SNP alignment - - Calculate pairwise SNP distances between MTB samples - - Identify transmission clusters based on SNP distances - - Study the emergence and spread of drug resistance based on transmission analysis. - pageviews: 5077 - pub_date: '2022-03-16' - requirements: - - topic_name: galaxy-interface - tutorials: - - collections - type: internal - - topic_name: variant-analysis - tutorials: - - tb-variant-analysis - type: internal - short_id: T00145 - short_tools: - - addName - - __MERGE_COLLECTION__ - - trimmomatic - - collapse_dataset - - tp_replace_in_line - - snippy - - samtools_view - - tp_cat - - tp_sed_tool - - tb_variant_filter - - bcftools_consensus - - snp_sites - - tp_grep_tool - - tb_profiler_profile - 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\ revisions: 2c749ed310da\n tool_panel_section_label: Apollo\n tool_shed_url:\ - \ https://toolshed.g2.bx.psu.edu/\n- name: jbrowse\n owner: iuc\n revisions:\ - \ a6e57ff585c0\n tool_panel_section_label: Graph/Display Data\n tool_shed_url:\ - \ https://toolshed.g2.bx.psu.edu/\n" - api: https://training.galaxyproject.org/training-material/api/topics/genome-annotation/tutorials/apollo/tutorial.json - contributions: - authorship: - - abretaud - - hexylena - - nathandunn - - mboudet - funding: - - gallantries - - eurosciencegateway - reviewing: - - abretaud - - bgruening - - shiltemann - - hexylena - - bebatut - - stephanierobin - - simonbray - contributors: - - affiliations: - - elixir-europe - bluesky: abretaud.bsky.social - contact_for_training: true - elixir_node: fr - email: anthony.bretaudeau@irisa.fr - fediverse: https://genomic.social/@abretaud - fediverse_flavor: mastodon - former_affiliations: - - eurosciencegateway - - gallantries - id: abretaud - joined: 2017-09 - location: - country: FR - lat: 48.11 - lon: -1.64 - matrix: abretaud:matrix.org - name: Anthony Bretaudeau - orcid: 0000-0003-0914-2470 - page: https://training.galaxyproject.org/training-material/hall-of-fame/abretaud/ - url: https://training.galaxyproject.org/training-material/api/contributors/abretaud.json - - affiliations: - - erasmusmc - - gallantries - - by-covid - - elixir-europe - - elixir-converge - contact_for_training: false - elixir_node: nl - former_affiliations: - - deNBI - - avans-atgm - - uni-freiburg - id: hexylena - joined: 2017-09 - location: - country: NL - lat: 51.91 - lon: 4.46 - maintainer_contact: gitter - matrix: hexylena:matrix.org - name: Helena Rasche - orcid: 0000-0001-9760-8992 - page: https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/ - url: https://training.galaxyproject.org/training-material/api/contributors/hexylena.json - - email: nathandunn@lbl.gov - id: nathandunn - joined: 2019-07 - name: Nathan Dunn - page: https://training.galaxyproject.org/training-material/hall-of-fame/nathandunn/ - twitter: precogincog - url: https://training.galaxyproject.org/training-material/api/contributors/nathandunn.json - - affiliations: - - elixir-europe - elixir_node: fr - email: mateo.boudet@inrae.fr - id: mboudet - joined: 2021-05 - name: Mateo Boudet - orcid: 0000-0002-7028-7620 - page: https://training.galaxyproject.org/training-material/hall-of-fame/mboudet/ - url: https://training.galaxyproject.org/training-material/api/contributors/mboudet.json - - avatar: https://gallantries.github.io/assets/images/gallantries-logo.png - end_date: '2023-09-30' - former_members: - - abretaud - - shiltemann - funder_name: Erasmus+ Programme - funding_database: erasmusplus - funding_id: 2020-1-NL01-KA203-064717 - funding_statement: 'This project (2020-1-NL01-KA203-064717) - is funded with the support of the Erasmus+ programme of the European Union. - Their funding has supported a large number of tutorials within the GTN across - a wide array of topics. - - eu flag with the text: with the support of the erasmus programme of the - european union - - erasmus plus - logo' - github: false - id: gallantries - joined: 2020-09 - members: - - bebatut - - colineroyaux - - fpsom - - hexylena - - yvanlebras - name: 'Gallantries: Bridging Training Communities in Life Science, Environment - and Health' - page: https://training.galaxyproject.org/training-material/hall-of-fame/gallantries/ - short_name: Gallantries - start_date: '2020-09-01' - url: https://training.galaxyproject.org/training-material/api/grants/gallantries.json - - avatar: /training-material/assets/images/eurosciencegateway.png - former_members: - - abretaud - - abdulrahmanazab - - bgruening - - B0r1sD - - dadrasarmin - - elichad - - ElectronicBlueberry - - erxleben - - kysrpex - - leandro-liborio - - lopiola - - martenson - - mira-miracoli - - patrick-austin - - pauldg - - rlibouba - - SaimMomin12 - - sanjaysrikakulam - - sebastian-schaaf - - stain - - torfinnnome - - wm75 - funding_database: cordis - funding_id: '101057388' - funding_statement: "EuroScienceGateway was funded by the European Union programme\ - \ Horizon Europe (HORIZON-INFRA-2021-EOSC-01-04) under grant agreement number\ - \ 101057388 and by UK Research and Innovation (UKRI) under the UK government\u2019\ - s Horizon Europe funding guarantee grant number 10038963." - github: false - id: eurosciencegateway - joined: 2023-10 - members: - - davelopez - name: EuroScienceGateway - page: https://training.galaxyproject.org/training-material/hall-of-fame/eurosciencegateway/ - url: https://training.galaxyproject.org/training-material/api/grants/eurosciencegateway.json - - affiliations: - - elixir-europe - bluesky: abretaud.bsky.social - contact_for_training: true - elixir_node: fr - email: anthony.bretaudeau@irisa.fr - fediverse: https://genomic.social/@abretaud - fediverse_flavor: mastodon - former_affiliations: - - eurosciencegateway - - gallantries - id: abretaud - joined: 2017-09 - location: - country: FR - lat: 48.11 - lon: -1.64 - matrix: abretaud:matrix.org - name: Anthony Bretaudeau - orcid: 0000-0003-0914-2470 - page: https://training.galaxyproject.org/training-material/hall-of-fame/abretaud/ - url: https://training.galaxyproject.org/training-material/api/contributors/abretaud.json - - affiliations: - - deNBI - - mwk - - uni-freiburg - - elixir-europe - - materialvitaldigital - contact_for_training: true - elixir_node: de - email: bjoern.gruening@gmail.com - fediverse: https://fosstodon.org/@bgruening - fediverse_flavor: mastodon - former_affiliations: - - eurosciencegateway - - eosc-life - - by-covid - - crc992 - - elixir-converge - id: bgruening - joined: 2017-09 - linkedin: bgruening - location: - country: DE - lat: 47.997791 - lon: 7.842609 - matrix: bgruening:matrix.org - name: "Bj\xF6rn Gr\xFCning" - orcid: 0000-0002-3079-6586 - page: https://training.galaxyproject.org/training-material/hall-of-fame/bgruening/ - twitter: bjoerngruening - url: https://training.galaxyproject.org/training-material/api/contributors/bgruening.json - - affiliations: - - uni-freiburg - - nfdi4plants - - elixir-europe - bio: Researcher at Erasmus Medical Center - bluesky: shiltemann.bsky.social - contact_for_training: true - elixir_node: nl - email: saskia.hiltemann@gmail.com - fediverse: https://mstdn.science/@shiltemann - fediverse_flavor: mastodon - former_affiliations: - - CINECA-Project - - gallantries - - erasmusmc - id: shiltemann - joined: 2017-09 - linkedin: shiltemann - location: - country: NL - lat: 51.912 - lon: 4.462 - maintainer_contact: gitter - matrix: shiltemann:matrix.org - name: Saskia Hiltemann - orcid: 0000-0003-3803-468X - page: https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/ - url: https://training.galaxyproject.org/training-material/api/contributors/shiltemann.json - - affiliations: - - erasmusmc - - gallantries - - by-covid - - elixir-europe - - elixir-converge - contact_for_training: false - elixir_node: nl - former_affiliations: - - deNBI - - avans-atgm - - uni-freiburg - id: hexylena - joined: 2017-09 - location: - country: NL - lat: 51.91 - lon: 4.46 - maintainer_contact: gitter - matrix: hexylena:matrix.org - name: Helena Rasche - orcid: 0000-0001-9760-8992 - page: https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/ - url: https://training.galaxyproject.org/training-material/api/contributors/hexylena.json - - affiliations: - - gallantries - - ifb - - elixir-europe - contact_for_training: true - elixir_node: fr - email: berenice.batut@gmail.com - fediverse: https://piaille.fr/@bebatut - fediverse_flavor: mastodon - former_affiliations: - - uni-freiburg - - deNBI - id: bebatut - joined: 2017-09 - linkedin: berenicebatut - location: - country: FR - lat: 45.77 - lon: 3.08 - matrix: bebatut:matrix.org - name: "B\xE9r\xE9nice Batut" - orcid: 0000-0001-9852-1987 - page: https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/ - twitter: bebatut - url: https://training.galaxyproject.org/training-material/api/contributors/bebatut.json - - email: stephanie.robin@inrae.fr - id: stephanierobin - joined: 2021-11 - name: "St\xE9phanie Robin" - orcid: 0000-0001-7379-9173 - page: https://training.galaxyproject.org/training-material/hall-of-fame/stephanierobin/ - 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\ -> 6 [label=\"out_file1\"]\n 7[label=\"JBrowse\"]\n 0 -> 7 [label=\"output\"\ - ]\n 3 -> 7 [label=\"annotation_gff3\"]\n 6 -> 7 [label=\"output\"]\n 4 ->\ - \ 7 [label=\"output\"]\n kc4e08c514520483ab48a99adc9a5d09f[color=lightseagreen,label=\"\ - Output\\njbrowse_output\"]\n 7 -> kc4e08c514520483ab48a99adc9a5d09f\n}" - history: - - hash: f52ead1fa4d239d06e53378776f7a78ee02dae8c - message: Correct creator names - num: 6 - short_hash: f52ead1fa - unix: '1765497330' - - hash: 8f5019e24f767aedb7863e58784f1f826feef711 - message: Updated workflow and workflow tests - num: 5 - short_hash: 8f5019e24 - unix: '1765326710' - - hash: 597f8ce954083c7cd4e43765b6c4709619637e6a - message: Add Bazante's ORCID - num: 4 - short_hash: 597f8ce95 - unix: '1706018263' - - hash: 03e4290900ade23b2dffb3f61ea2875a64f2c396 - message: Fix workflows - num: 3 - short_hash: 03e429090 - unix: '1706004257' - - hash: c88bcbb6f04ad1847e0747f7fb9256ee0ec858de - message: Add license and creator to workflows - num: 2 - short_hash: c88bcbb6f - 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tutorial_name: bacterial-genome-quality-control + tutorial_name: mrsa-nanopore type: tutorial - url: https://training.galaxyproject.org//topics/genome-annotation/tutorials/bacterial-genome-quality-control/tutorial.html + url: https://training.galaxyproject.org//topics/assembly/tutorials/mrsa-nanopore/tutorial.html urls: - hands_on: https://training.galaxyproject.org/training-material/api/topics/genome-annotation/tutorials/bacterial-genome-quality-control/tutorial.json - slides: https://training.galaxyproject.org/training-material/api/topics/genome-annotation/tutorials/bacterial-genome-quality-control/tutorial.json - version: 1 + hands_on: https://training.galaxyproject.org/training-material/api/topics/assembly/tutorials/mrsa-nanopore/tutorial.json + slides: https://training.galaxyproject.org/training-material/api/topics/assembly/tutorials/mrsa-nanopore/tutorial.json + version: 16 video: false video_versions: 0 video_view: 0 - visit_duration: 464 - visitors: 195 - zenodo_link: https://zenodo.org/records/1 + visit_duration: 466 + visitors: 11648 + workflows: + - creators: + - class: Person + identifier: https://orcid.org/0000-0003-2255-1631 + name: Bazante Sanders + - class: Person + identifier: https://orcid.org/0000-0001-9852-1987 + name: "B\xE9r\xE9nice Batut" + - class: Person + identifier: 0000-0002-6606-5953 + name: Tristan Reynolds + description: Genome Assembly of MRSA from Oxford Nanopore MinION data (and optionally + Illumina data) + features: + comments: false + parameters: false + report: + markdown: ' + + # Workflow Execution Report + + + ## Workflow Inputs + + ```galaxy + + invocation_inputs() + + ``` + + + ## Workflow Outputs + + ```galaxy + + invocation_outputs() + + ``` + + + ## Workflow + + ```galaxy + + workflow_display() + + ``` + + ' + subworkflows: false + graph_dot: "digraph main {\n node [fontname=\"Atkinson Hyperlegible\", shape=box,\ + \ color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n edge [fontname=\"\ + Atkinson Hyperlegible\"];\n 0[color=lightblue,label=\"\u2139\uFE0F Input Dataset\\\ + nNanopore raw reads\"]\n 1[color=lightblue,label=\"\u2139\uFE0F Input Collection\\\ + nInput Paired End Collection\"]\n 2[label=\"FastQC\"]\n 0 -> 2 [label=\"output\"\ + ]\n 3[label=\"Convert compressed file to uncompressed.\"]\n 0 -> 3 [label=\"\ + output\"]\n 4[label=\"fastp\"]\n 1 -> 4 [label=\"output\"]\n kf172ab83f29740b3adc0beb1dbec99ab[color=lightseagreen,label=\"\ + Output\\nreport_json\"]\n 4 -> kf172ab83f29740b3adc0beb1dbec99ab\n 5[label=\"\ + NanoPlot\"]\n 3 -> 5 [label=\"output1\"]\n ka97e6f3381824a3386dd6cfbb83a842d[color=lightseagreen,label=\"\ + Output\\nnanoplot_before_filtering\"]\n 5 -> ka97e6f3381824a3386dd6cfbb83a842d\n\ + \ 6[label=\"Flatten collection\"]\n 4 -> 6 [label=\"output_paired_coll\"]\n\ + \ 7[label=\"Extract Forward Reads\"]\n 6 -> 7 [label=\"output\"]\n 8[label=\"\ + Extract Reverse Reads\"]\n 6 -> 8 [label=\"output\"]\n 9[label=\"filtlong\"\ + ]\n 7 -> 9 [label=\"output\"]\n 8 -> 9 [label=\"output\"]\n 0 -> 9 [label=\"\ + output\"]\n 10[label=\"NanoPlot\"]\n 9 -> 10 [label=\"outfile\"]\n k89524090f590434d89e266f0b1a23c7c[color=lightseagreen,label=\"\ + Output\\nnanoplot_after_filtering\"]\n 10 -> k89524090f590434d89e266f0b1a23c7c\n\ + \ 11[label=\"Flye\"]\n 9 -> 11 [label=\"outfile\"]\n kf12e718f1bd5490dbd41f0747aaa41a6[color=lightseagreen,label=\"\ + Output\\nflye_assembly_info\"]\n 11 -> kf12e718f1bd5490dbd41f0747aaa41a6\n\ + \ 12[label=\"BWA-MEM2\"]\n 7 -> 12 [label=\"output\"]\n 11 -> 12 [label=\"\ + consensus\"]\n 13[label=\"Quast\"]\n 11 -> 13 [label=\"consensus\"]\n kdabfb8fd87914959a9dc9b3c1e57a69c[color=lightseagreen,label=\"\ + Output\\nquast_report_before_polishing\"]\n 13 -> kdabfb8fd87914959a9dc9b3c1e57a69c\n\ + \ 14[label=\"Bandage Image\"]\n 11 -> 14 [label=\"assembly_gfa\"]\n 15[label=\"\ + BWA-MEM2\"]\n 8 -> 15 [label=\"output\"]\n 11 -> 15 [label=\"consensus\"]\n\ + \ 16[label=\"Polypolish\"]\n 11 -> 16 [label=\"consensus\"]\n 12 -> 16 [label=\"\ + bam_output\"]\n 15 -> 16 [label=\"bam_output\"]\n 17[label=\"Quast\"]\n 11\ + \ -> 17 [label=\"consensus\"]\n 16 -> 17 [label=\"polished_fasta\"]\n k4e465b5168bf42039a7c897f46c70277[color=lightseagreen,label=\"\ + Output\\nquast_report_after_polishing\"]\n 17 -> k4e465b5168bf42039a7c897f46c70277\n\ + }" + history: + - hash: de24119db10356969b4a079fb05ca176372ea330 + message: Update workflow and workflow tests + num: 2 + short_hash: de24119db + unix: '1766110919' + - hash: 96393a7fcb4d6dc37d86866cf8a61c931293502f + message: Add MRSA Nanopore assembly tutorial to AMR learning pathway + num: 1 + short_hash: 96393a7fc + unix: '1709135526' + inputs: + - annotation: Nanopore raw reads + content_id: null + errors: null + id: 0 + input_connections: {} + inputs: + - description: Nanopore raw reads + name: Nanopore raw reads + label: Nanopore raw reads + name: Input dataset + outputs: [] + position: + left: 20.534814361006397 + top: 589.9124911241256 + tool_id: null + tool_state: '{"optional": false, "tag": null}' + tool_version: null + type: data_input + uuid: cd4fd302-af94-4771-9b80-7c7acb6619d4 + when: null + workflow_outputs: [] + - annotation: '' + content_id: null + errors: null + id: 1 + input_connections: {} + inputs: + - description: '' + name: Input Paired End Collection + label: Input Paired End Collection + name: Input dataset collection + outputs: [] + position: + left: 0.0 + top: 968.6942909141043 + tool_id: null + tool_state: '{"optional": false, "tag": null, "collection_type": "list:paired", + "fields": null}' + tool_version: null + type: data_collection_input + uuid: b0940b0b-a1fb-4e9f-a4d0-e88f4fc8e51e + when: null + workflow_outputs: [] + license: MIT + mermaid: "flowchart TD\n 0[\"\u2139\uFE0F Input Dataset\\nNanopore raw reads\"\ + ];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"\u2139\uFE0F Input Collection\\\ + nInput Paired End Collection\"];\n style 1 stroke:#2c3143,stroke-width:4px;\n\ + \ 2[\"FastQC\"];\n 0 -->|output| 2;\n 3[\"Convert compressed file to uncompressed.\"\ + ];\n 0 -->|output| 3;\n 4[\"fastp\"];\n 1 -->|output| 4;\n f172ab83-f297-40b3-adc0-beb1dbec99ab[\"\ + Output\\nreport_json\"];\n 4 --> f172ab83-f297-40b3-adc0-beb1dbec99ab;\n style\ + \ f172ab83-f297-40b3-adc0-beb1dbec99ab stroke:#2c3143,stroke-width:4px;\n 5[\"\ + NanoPlot\"];\n 3 -->|output1| 5;\n a97e6f33-8182-4a33-86dd-6cfbb83a842d[\"\ + Output\\nnanoplot_before_filtering\"];\n 5 --> a97e6f33-8182-4a33-86dd-6cfbb83a842d;\n\ + \ style a97e6f33-8182-4a33-86dd-6cfbb83a842d stroke:#2c3143,stroke-width:4px;\n\ + \ 6[\"Flatten collection\"];\n 4 -->|output_paired_coll| 6;\n 7[\"Extract\ + \ Forward Reads\"];\n 6 -->|output| 7;\n 8[\"Extract Reverse Reads\"];\n \ + \ 6 -->|output| 8;\n 9[\"filtlong\"];\n 7 -->|output| 9;\n 8 -->|output|\ + \ 9;\n 0 -->|output| 9;\n 10[\"NanoPlot\"];\n 9 -->|outfile| 10;\n 89524090-f590-434d-89e2-66f0b1a23c7c[\"\ + Output\\nnanoplot_after_filtering\"];\n 10 --> 89524090-f590-434d-89e2-66f0b1a23c7c;\n\ + \ style 89524090-f590-434d-89e2-66f0b1a23c7c stroke:#2c3143,stroke-width:4px;\n\ + \ 11[\"Flye\"];\n 9 -->|outfile| 11;\n f12e718f-1bd5-490d-bd41-f0747aaa41a6[\"\ + Output\\nflye_assembly_info\"];\n 11 --> f12e718f-1bd5-490d-bd41-f0747aaa41a6;\n\ + \ style f12e718f-1bd5-490d-bd41-f0747aaa41a6 stroke:#2c3143,stroke-width:4px;\n\ + \ 12[\"BWA-MEM2\"];\n 7 -->|output| 12;\n 11 -->|consensus| 12;\n 13[\"\ + Quast\"];\n 11 -->|consensus| 13;\n dabfb8fd-8791-4959-a9dc-9b3c1e57a69c[\"\ + Output\\nquast_report_before_polishing\"];\n 13 --> dabfb8fd-8791-4959-a9dc-9b3c1e57a69c;\n\ + \ style dabfb8fd-8791-4959-a9dc-9b3c1e57a69c stroke:#2c3143,stroke-width:4px;\n\ + \ 14[\"Bandage Image\"];\n 11 -->|assembly_gfa| 14;\n 15[\"BWA-MEM2\"];\n\ + \ 8 -->|output| 15;\n 11 -->|consensus| 15;\n 16[\"Polypolish\"];\n 11 -->|consensus|\ + \ 16;\n 12 -->|bam_output| 16;\n 15 -->|bam_output| 16;\n 17[\"Quast\"];\n\ + \ 11 -->|consensus| 17;\n 16 -->|polished_fasta| 17;\n 4e465b51-68bf-4203-9a7c-897f46c70277[\"\ + Output\\nquast_report_after_polishing\"];\n 17 --> 4e465b51-68bf-4203-9a7c-897f46c70277;\n\ + \ style 4e465b51-68bf-4203-9a7c-897f46c70277 stroke:#2c3143,stroke-width:4px;" + modified: 2026-07-01 00:31:37 +0000 + name: Genome Assembly of MRSA using Oxford Nanopore MinION (and Illumina data + if available) + outputs: + - annotation: '' + content_id: toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/1.0.1+galaxy3 + errors: null + id: 4 + input_connections: + single_paired|paired_input: + id: 1 + output_name: output + inputs: + - description: runtime parameter for tool fastp + name: single_paired + label: null + name: fastp + outputs: + - name: output_paired_coll + type: input + - name: report_html + type: html + - name: report_json + type: json + position: + left: 331.55158575828335 + top: 935.7727448543545 + post_job_actions: + ChangeDatatypeActionout1: + action_arguments: + newtype: fastqsanger.gz + action_type: ChangeDatatypeAction + output_name: out1 + ChangeDatatypeActionout2: + action_arguments: + newtype: fastqsanger.gz + action_type: ChangeDatatypeAction + output_name: out2 + tool_id: toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/1.0.1+galaxy3 + tool_shed_repository: + changeset_revision: f875da9d433c + name: fastp + owner: iuc + tool_shed: toolshed.g2.bx.psu.edu + tool_state: '{"duplicated_reads": {"handling_options": {"eval_dups": "--dont_eval_duplication", + "__current_case__": 0}}, "filter_options": {"quality_filtering_options": {"disable_quality_filtering": + false, "qualified_quality_phred": "30", "unqualified_percent_limit": null, + "n_base_limit": null}, "length_filtering_options": {"disable_length_filtering": + false, "length_required": null, "length_limit": null}, "low_complexity_filter": + {"enable_low_complexity_filter": false, "complexity_threshold": null}}, "output_options": + {"report_html": true, "report_json": true}, "overrepresented_sequence_analysis": + {"overrepresentation_analysis": false, "overrepresentation_sampling": null}, + "read_mod_options": {"polyg_tail_trimming": {"trimming_select": "", "__current_case__": + 1, "poly_g_min_len": null}, "polyx_tail_trimming": {"polyx_trimming_select": + "", "__current_case__": 1}, "umi_processing": {"umi": false, "umi_loc": null, + "umi_len": null, "umi_prefix": null}, "cutting_by_quality_options": {"cut_front_select": + {"cut_front": "", "__current_case__": 1}, "cut_tail_select": {"cut_tail": + "", "__current_case__": 1}, "cut_right_select": {"cut_right": "", "__current_case__": + 1}}, "base_correction_options": {"correction": false}}, "single_paired": {"single_paired_selector": + "paired_collection", "__current_case__": 1, "paired_input": {"__class__": + "RuntimeValue"}, "merge_reads": {"merge": "", "__current_case__": 1}, "adapter_trimming_options": + {"disable_adapter_trimming": false, "adapter_sequence1": null, "adapter_sequence2": + null, "detect_adapter_for_pe": false}, "global_trimming_options": {"trim_front1": + null, "trim_tail1": null, "trim_front2": null, "trim_tail2": null}}, "__page__": + 0, "__rerun_remap_job_id__": null}' + tool_version: 1.0.1+galaxy3 + type: tool + uuid: feeaf946-2ca5-4ec3-bb2a-b0aa9b6d3395 + when: null + workflow_outputs: + - label: report_json + output_name: report_json + uuid: f172ab83-f297-40b3-adc0-beb1dbec99ab + - annotation: '' + content_id: toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.41.0+galaxy0 + errors: null + id: 5 + input_connections: + mode|reads|files: + id: 3 + output_name: output1 + inputs: [] + label: null + name: NanoPlot + outputs: + - name: output_html + type: html + - name: nanostats + type: tabular + - name: nanostats_post_filtering + type: tabular + - name: read_length + type: png + - name: log_read_length + type: png + position: + left: 877.4782234964777 + top: 254.30721900676204 + post_job_actions: {} + tool_id: toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.41.0+galaxy0 + tool_shed_repository: + changeset_revision: 0f1c34698076 + name: nanoplot + owner: iuc + tool_shed: toolshed.g2.bx.psu.edu + tool_state: '{"__input_ext": "input", "chromInfo": "/shared/ifbstor1/galaxy/mutable-config/tool-data/shared/ucsc/chrom/?.len", + "customization": {"color": null, "plots": null, "N50": true}, "filter": {"maxlength": + null, "minlength": null, "drop_outliers": false, "downsample": null, "loglength": + false, "percentqual": false, "alength": false, "minqual": null, "runtime_until": + null, "readtype": null, "barcoded": false, "no_supplementary": false}, "mode": + {"choice": "batch", "__current_case__": 0, "reads": {"type": "fastq", "__current_case__": + 0, "files": {"__class__": "ConnectedValue"}}}, "__page__": null, "__rerun_remap_job_id__": + null}' + tool_version: 1.41.0+galaxy0 + type: tool + uuid: ad46f297-04f2-4959-aa09-db88cd91cc27 + when: null + workflow_outputs: + - 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- elixir_node: fr - id: hchiapello - joined: 2025-03 - name: "H\xE9l\xE8ne Chiapello" - page: https://training.galaxyproject.org/training-material/hall-of-fame/hchiapello/ - url: https://training.galaxyproject.org/training-material/api/contributors/hchiapello.json - - affiliations: - - gallantries - - ifb - - elixir-europe - contact_for_training: true - elixir_node: fr - email: berenice.batut@gmail.com - fediverse: https://piaille.fr/@bebatut - fediverse_flavor: mastodon - former_affiliations: - - uni-freiburg - - deNBI - id: bebatut + - email: anton@nekrut.org + id: nekrut joined: 2017-09 - linkedin: berenicebatut - location: - country: FR - lat: 45.77 - lon: 3.08 - matrix: bebatut:matrix.org - name: "B\xE9r\xE9nice Batut" - orcid: 0000-0001-9852-1987 - page: https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/ - twitter: bebatut - url: https://training.galaxyproject.org/training-material/api/contributors/bebatut.json - - id: vloux - joined: 2019-04 - name: Valentin Loux - page: https://training.galaxyproject.org/training-material/hall-of-fame/vloux/ - url: https://training.galaxyproject.org/training-material/api/contributors/vloux.json - - affiliations: - - elixir-europe - bluesky: abretaud.bsky.social - contact_for_training: true - elixir_node: fr - email: anthony.bretaudeau@irisa.fr - fediverse: https://genomic.social/@abretaud - fediverse_flavor: mastodon - former_affiliations: - - eurosciencegateway - - gallantries - id: abretaud + name: Anton Nekrutenko + page: https://training.galaxyproject.org/training-material/hall-of-fame/nekrut/ + url: https://training.galaxyproject.org/training-material/api/contributors/nekrut.json + - email: delphine.lariviere@galaxy.org + id: delphine-l joined: 2017-09 - location: - country: FR - lat: 48.11 - lon: -1.64 - matrix: abretaud:matrix.org - name: Anthony Bretaudeau - orcid: 0000-0003-0914-2470 - page: https://training.galaxyproject.org/training-material/hall-of-fame/abretaud/ - url: https://training.galaxyproject.org/training-material/api/contributors/abretaud.json + name: Delphine Lariviere + orcid: 0000-0001-6421-3484 + page: https://training.galaxyproject.org/training-material/hall-of-fame/delphine-l/ + url: https://training.galaxyproject.org/training-material/api/contributors/delphine-l.json - affiliations: - - uni-freiburg - - nfdi4plants - elixir-europe - bio: Researcher at Erasmus Medical Center - bluesky: shiltemann.bsky.social - contact_for_training: true + contact_for_training: false elixir_node: nl - email: saskia.hiltemann@gmail.com - fediverse: https://mstdn.science/@shiltemann - fediverse_flavor: mastodon former_affiliations: - - CINECA-Project - - gallantries + - deNBI + - avans-atgm + - uni-freiburg - erasmusmc - id: shiltemann + - gallantries + - by-covid + - elixir-converge + id: hexylena joined: 2017-09 - linkedin: shiltemann location: country: NL - lat: 51.912 - lon: 4.462 + lat: 51.91 + lon: 4.46 maintainer_contact: gitter - matrix: shiltemann:matrix.org - name: Saskia Hiltemann - orcid: 0000-0003-3803-468X - page: https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/ - url: https://training.galaxyproject.org/training-material/api/contributors/shiltemann.json - dir: topics/genome-annotation/tutorials/bacterial-comparative-genomics-dataset-construction - draft: true + matrix: hexylena:matrix.org + name: Helena Rasche + orcid: 0000-0001-9760-8992 + page: https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/ + url: https://training.galaxyproject.org/training-material/api/contributors/hexylena.json + dir: topics/assembly/tutorials/ecoli_comparison edam_ontology: + - topic_0196 - topic_0622 - topic_3301 edam_operation: - - Data handling - - Data retrieval - - Sequence database search + - Sequence alignment + - Mapping + - Genome visualisation + - Read mapping + - Sequence visualisation edam_topic: + - Sequence assembly - Genomics - Microbiology - exact_supported_servers: - - UseGalaxy.fr + exact_supported_servers: [] feedback_mean_note: null feedback_number: 0 hands_on: true - id: genome-annotation/bacterial-comparative-genomics-dataset-construction - inexact_supported_servers: - - UseGalaxy.cz + id: assembly/ecoli_comparison + inexact_supported_servers: [] js_requirements: mathjax: null mermaid: false key_points: - - to do - - to do + - We learned how to download large sets of completed genomes from NCBI + - We learned how to use Galaxy's rule-based collection builder + - We learned how to use a combination of Galaxy tools to create complex views of + genome comparisons + - We learned about idiosyncrasies of data formats and how to deal with them using + Galaxy tools layout: tutorial_hands_on - level: Introductory license: CC-BY-4.0 mod_date: '2026-04-13' objectives: - - to do - - to do - pageviews: 133 - pub_date: '2025-03-14' + - Identification of the most closely related genome to my new assembly + - Perform sequence comparison to locate rearrangements + - Identify genes located in deletions + pageviews: 13334 + pub_date: '2018-06-14' questions: - - to do - - to do - short_id: T00494 + - I just assembled a genome. How does it compare with already sequenced genomes? + - How do I find rearranged, inserted, or deleted regions? + requirements: + - topic_name: assembly + tutorials: + - unicycler-assembly + type: internal + short_id: T00032 short_tools: + - Filter1 + - collapse_dataset + - join1 + - tp_sort_header_tool + - bedtools_intersectbed + - addValue + - datamash_ops + - circos + - circos_interval_to_tiles - upload1 - - sort1 - - Remove beginning1 - cat1 + - tp_replace_in_column + - bedtools_sortbed + - random_lines1 + - fasta_compute_length + - circos_aln_to_links + - tp_cat + - tp_replace_in_line + - mergeCols1 + - bedtools_complementbed + - jbrowse + - Grep1 + - fasta_filter_by_length + - tp_grep_tool + - lastz_wrapper_2 + - tp_sed_tool - Cut1 - - datasets_download_genome - - bg_uniq slides: false slides_recordings: false supported_servers: - exact: - - name: UseGalaxy.fr - url: https://usegalaxy.fr/ - usegalaxy: true - inexact: - - name: UseGalaxy.cz - url: https://usegalaxy.cz/ - usegalaxy: false + exact: [] + inexact: [] supported_servers_matrix: servers: - name: APOSTL @@ -23871,9 +2470,6 @@ - name: IPK Galaxy Blast Suite url: https://galaxy-web.ipk-gatersleben.de usegalaxy: false - - name: Lebanese University Galaxy - url: http://galaxy.ul.edu.lb/ - usegalaxy: false - name: Mandoiu Lab url: https://neo.engr.uconn.edu/ usegalaxy: false @@ -23889,9 +2485,6 @@ - name: PepSimili url: http://pepsimili.e-nios.com:8080/ usegalaxy: false - - name: PhagePromotor - url: https://galaxy.bio.di.uminho.pt/ - usegalaxy: false - name: UseGalaxy.org.au url: https://usegalaxy.org.au usegalaxy: true @@ -23945,8 +2538,6 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: local - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr @@ -23957,8 +2548,6 @@ state: missing - server: http://pepsimili.e-nios.com:8080/ state: local - - server: https://galaxy.bio.di.uminho.pt/ - state: local - server: https://usegalaxy.org.au state: local - server: https://usegalaxy.be/ @@ -23976,7 +2565,62 @@ - server: https://viralvariant.anses.fr/ state: local version: local - - id: Remove beginning1 + - id: Filter1 + servers: + - server: http://apostl.moffitt.org/ + state: local + - server: http://mbac.gmu.edu:8080/ + state: local + - server: https://vm-chemflow-francegrille.eu/ + state: missing + - server: https://iris.angers.inra.fr/galaxypub-cfbp + state: missing + - server: https://hyperbrowser.uio.no/coloc-stats + state: local + - server: https://galaxy.mesocentre.uca.fr + state: local + - server: https://galaxy.pasteur.fr/ + state: local + - server: https://galaxytrakr.org/ + state: local + - server: http://igg.cloud.ba.infn.it/galaxy + state: local + - server: https://galaxy.hyphy.org/ + state: local + - server: https://www.immportgalaxy.org/ + state: missing + - server: http://galaxy.interactomix.com/ + state: missing + - server: https://galaxy-web.ipk-gatersleben.de + state: missing + - server: https://neo.engr.uconn.edu/ + state: missing + - server: https://mississippi.sorbonne-universite.fr + state: local + - server: http://galaxy.inf.ethz.ch + state: local + - server: https://palfinder.ls.manchester.ac.uk/ + state: missing + - server: http://pepsimili.e-nios.com:8080/ + state: local + - server: https://usegalaxy.org.au + state: local + - server: https://usegalaxy.be/ + state: local + - server: https://usegalaxy.cz/ + state: local + - server: https://usegalaxy.eu + state: local + - server: https://usegalaxy.fr/ + state: local + - server: https://usegalaxy.no/ + state: local + - server: https://usegalaxy.org + state: local + - server: https://viralvariant.anses.fr/ + state: local + version: local + - id: Grep1 servers: - server: http://apostl.moffitt.org/ state: local @@ -24004,8 +2648,6 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: local - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr @@ -24016,8 +2658,6 @@ state: missing - server: http://pepsimili.e-nios.com:8080/ state: local - - server: https://galaxy.bio.di.uminho.pt/ - state: local - server: https://usegalaxy.org.au state: local - server: https://usegalaxy.be/ @@ -24063,8 +2703,6 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: local - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr @@ -24075,8 +2713,6 @@ state: missing - server: http://pepsimili.e-nios.com:8080/ state: local - - server: https://galaxy.bio.di.uminho.pt/ - state: local - server: https://usegalaxy.org.au state: local - server: https://usegalaxy.be/ @@ -24094,7 +2730,7 @@ - server: https://viralvariant.anses.fr/ state: local version: local - - id: sort1 + - id: join1 servers: - server: http://apostl.moffitt.org/ state: local @@ -24122,8 +2758,61 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ + - 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state: local + state: exact + version: 2.27.0.2 - server: https://viralvariant.anses.fr/ - state: local - version: local - - id: toolshed.g2.bx.psu.edu/repos/bgruening/diamond/bg_diamond/2.0.15+galaxy0 + state: missing + version: 2.27.0.2 + - id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_sortbed/2.27.0.0 servers: - server: http://apostl.moffitt.org/ state: missing @@ -24934,12 +3835,15 @@ state: missing - server: https://galaxy.mesocentre.uca.fr state: exact - version: 2.0.15+galaxy0 + version: 2.27.0.0 - server: https://galaxy.pasteur.fr/ - state: exact - version: 2.0.15+galaxy0 + state: inexact + versions: + - 2.31.1+galaxy0 - server: https://galaxytrakr.org/ - state: missing + state: inexact + versions: + - 2.31.1+galaxy0 - server: http://igg.cloud.ba.infn.it/galaxy state: missing - server: https://galaxy.hyphy.org/ @@ -24949,47 +3853,60 @@ - server: http://galaxy.interactomix.com/ state: missing - server: https://galaxy-web.ipk-gatersleben.de - state: exact - version: 2.0.15+galaxy0 - - server: http://galaxy.ul.edu.lb/ state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr - state: missing + state: inexact + versions: + - 2.31.1+galaxy0 - server: http://galaxy.inf.ethz.ch state: missing - server: https://palfinder.ls.manchester.ac.uk/ state: missing - server: http://pepsimili.e-nios.com:8080/ state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - server: https://usegalaxy.org.au state: exact - version: 2.0.15+galaxy0 + version: 2.27.0.0 - server: https://usegalaxy.be/ state: exact - version: 2.0.15+galaxy0 + version: 2.27.0.0 - server: https://usegalaxy.cz/ - state: exact - version: 2.0.15+galaxy0 + state: inexact + versions: + - 2.27.1 + - 2.31.1+galaxy0 + - 2.30.0+galaxy2 + - 2.29.2 + - 2.29.0 + - 2.30.0+galaxy1 + - 2.30.0 + - 2.19.0 - server: https://usegalaxy.eu state: exact - version: 2.0.15+galaxy0 + version: 2.27.0.0 - server: https://usegalaxy.fr/ - state: exact - version: 2.0.15+galaxy0 + state: inexact + versions: + - 2.31.1+galaxy0 + - 2.30.0+galaxy2 + - 2.29.2 + - 2.29.0 + - 2.30.0 - server: https://usegalaxy.no/ - state: exact - version: 2.0.15+galaxy0 + state: inexact + versions: + - 2.29.2 + - 2.30.0 + - 2.19.0 - server: https://usegalaxy.org state: exact - version: 2.0.15+galaxy0 + version: 2.27.0.0 - server: https://viralvariant.anses.fr/ state: missing - version: 2.0.15+galaxy0 - - id: toolshed.g2.bx.psu.edu/repos/bgruening/diamond/bg_diamond_makedb/2.0.15+galaxy0 + version: 2.27.0.0 + - id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos/0.69.8+galaxy7 servers: - server: http://apostl.moffitt.org/ state: missing @@ -25002,13 +3919,16 @@ - server: https://hyperbrowser.uio.no/coloc-stats state: missing - server: https://galaxy.mesocentre.uca.fr - state: exact - version: 2.0.15+galaxy0 + state: inexact + versions: + - 0.69.8+galaxy12 - server: https://galaxy.pasteur.fr/ - state: exact - version: 2.0.15+galaxy0 + state: inexact + versions: + - 0.69.8+galaxy12 - server: https://galaxytrakr.org/ - state: missing + state: exact + version: 0.69.8+galaxy7 - server: http://igg.cloud.ba.infn.it/galaxy state: missing - server: https://galaxy.hyphy.org/ @@ -25019,45 +3939,47 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr - state: missing + state: inexact + versions: + - 0.69.8+galaxy12 - server: http://galaxy.inf.ethz.ch state: missing - server: https://palfinder.ls.manchester.ac.uk/ state: missing - server: http://pepsimili.e-nios.com:8080/ state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - server: https://usegalaxy.org.au state: exact - version: 2.0.15+galaxy0 + version: 0.69.8+galaxy7 - server: https://usegalaxy.be/ state: exact - version: 2.0.15+galaxy0 + version: 0.69.8+galaxy7 - server: https://usegalaxy.cz/ - state: exact - version: 2.0.15+galaxy0 + state: inexact + versions: + - 0.69.8+galaxy12 + - 0.69.8+galaxy9 - server: https://usegalaxy.eu - state: exact - version: 2.0.15+galaxy0 + state: inexact + versions: + - 0.69.8+galaxy12 + - 0.69.8+galaxy10 - server: https://usegalaxy.fr/ state: exact - version: 2.0.15+galaxy0 + version: 0.69.8+galaxy7 - server: https://usegalaxy.no/ state: exact - version: 2.0.15+galaxy0 + version: 0.69.8+galaxy7 - server: https://usegalaxy.org state: exact - version: 2.0.15+galaxy0 + version: 0.69.8+galaxy7 - server: https://viralvariant.anses.fr/ state: missing - version: 2.0.15+galaxy0 - - id: toolshed.g2.bx.psu.edu/repos/bgruening/diamond/bg_diamond_view/2.0.15+galaxy0 + version: 0.69.8+galaxy7 + - id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_aln_to_links/0.69.8+galaxy7 servers: - server: http://apostl.moffitt.org/ state: missing @@ -25070,13 +3992,16 @@ - server: https://hyperbrowser.uio.no/coloc-stats state: missing - server: https://galaxy.mesocentre.uca.fr - state: exact - version: 2.0.15+galaxy0 + state: inexact + versions: + - 0.69.8+galaxy12 - server: https://galaxy.pasteur.fr/ - state: exact - version: 2.0.15+galaxy0 + state: inexact + versions: + - 0.69.8+galaxy12 - server: https://galaxytrakr.org/ - state: missing + state: exact + version: 0.69.8+galaxy7 - server: http://igg.cloud.ba.infn.it/galaxy state: missing - server: https://galaxy.hyphy.org/ @@ -25087,45 +4012,45 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr - state: missing + state: inexact + versions: + - 0.69.8+galaxy12 - server: http://galaxy.inf.ethz.ch state: missing - server: https://palfinder.ls.manchester.ac.uk/ state: missing - server: http://pepsimili.e-nios.com:8080/ state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - server: https://usegalaxy.org.au state: exact - version: 2.0.15+galaxy0 + version: 0.69.8+galaxy7 - server: https://usegalaxy.be/ state: exact - version: 2.0.15+galaxy0 + version: 0.69.8+galaxy7 - server: https://usegalaxy.cz/ - state: exact - version: 2.0.15+galaxy0 + state: inexact + versions: + - 0.69.8+galaxy12 + - 0.69.8+galaxy9 - server: https://usegalaxy.eu state: exact - version: 2.0.15+galaxy0 + version: 0.69.8+galaxy7 - server: https://usegalaxy.fr/ state: exact - version: 2.0.15+galaxy0 + version: 0.69.8+galaxy7 - server: https://usegalaxy.no/ state: exact - version: 2.0.15+galaxy0 + version: 0.69.8+galaxy7 - server: https://usegalaxy.org state: exact - version: 2.0.15+galaxy0 + version: 0.69.8+galaxy7 - server: https://viralvariant.anses.fr/ state: missing - version: 2.0.15+galaxy0 - - id: toolshed.g2.bx.psu.edu/repos/bgruening/split_file_on_column/tp_split_on_column/0.4 + version: 0.69.8+galaxy7 + - id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_interval_to_tiles/0.69.8+galaxy7 servers: - server: http://apostl.moffitt.org/ state: missing @@ -25153,8 +4078,6 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr @@ -25165,34 +4088,93 @@ state: missing - server: http://pepsimili.e-nios.com:8080/ state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - server: https://usegalaxy.org.au + state: missing + - server: https://usegalaxy.be/ + state: missing + - server: https://usegalaxy.cz/ + state: missing + - server: https://usegalaxy.eu + state: missing + - server: https://usegalaxy.fr/ + state: missing + - server: https://usegalaxy.no/ + state: missing + - server: https://usegalaxy.org + state: missing + - server: https://viralvariant.anses.fr/ + state: missing + version: 0.69.8+galaxy7 + - id: toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.1.0 + servers: + - server: http://apostl.moffitt.org/ + state: missing + - server: http://mbac.gmu.edu:8080/ + state: missing + - server: https://vm-chemflow-francegrille.eu/ + state: missing + - 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server: https://usegalaxy.org.au + state: exact + version: 1.1.0 - server: https://usegalaxy.be/ state: exact - version: '0.4' + version: 1.1.0 - server: https://usegalaxy.cz/ state: exact - version: '0.4' + version: 1.1.0 - server: https://usegalaxy.eu state: exact - version: '0.4' + version: 1.1.0 - server: https://usegalaxy.fr/ state: exact - version: '0.4' + version: 1.1.0 - server: https://usegalaxy.no/ state: exact - version: '0.4' + version: 1.1.0 - server: https://usegalaxy.org state: exact - version: '0.4' + version: 1.1.0 - server: https://viralvariant.anses.fr/ state: missing - version: '0.4' - - id: toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/1.6 + version: 1.1.0 + - id: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.8+galaxy1 servers: - server: http://apostl.moffitt.org/ state: missing @@ -25205,13 +4187,18 @@ - server: https://hyperbrowser.uio.no/coloc-stats state: missing - server: https://galaxy.mesocentre.uca.fr - state: exact - version: '1.6' + state: inexact + versions: + - 1.16.9+galaxy0 + - 1.16.11+galaxy1 - server: https://galaxy.pasteur.fr/ - state: missing + state: inexact + versions: + - 1.16.11+galaxy1 - server: https://galaxytrakr.org/ - state: exact - version: '1.6' + state: inexact + versions: + - 1.16.11+galaxy1 - server: http://igg.cloud.ba.infn.it/galaxy state: missing - server: https://galaxy.hyphy.org/ @@ -25222,48 +4209,47 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr state: inexact versions: - - '2.0' - - 2.1+galaxy0 + - 1.16.11+galaxy1 - server: http://galaxy.inf.ethz.ch state: missing - server: https://palfinder.ls.manchester.ac.uk/ state: missing - server: http://pepsimili.e-nios.com:8080/ state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - server: https://usegalaxy.org.au state: exact - version: '1.6' + version: 1.16.8+galaxy1 - server: https://usegalaxy.be/ state: exact - version: '1.6' + version: 1.16.8+galaxy1 - server: https://usegalaxy.cz/ - state: exact - version: '1.6' + state: inexact + versions: + - 1.16.11+galaxy1 - server: https://usegalaxy.eu state: exact - version: '1.6' + version: 1.16.8+galaxy1 - server: https://usegalaxy.fr/ state: exact - version: '1.6' + version: 1.16.8+galaxy1 - server: https://usegalaxy.no/ - state: exact - version: '1.6' + state: inexact + versions: + - 1.16.9+galaxy0 + - 1.16.11+galaxy1 + - 1.16.10+galaxy0 - server: https://usegalaxy.org state: exact - version: '1.6' + version: 1.16.8+galaxy1 - server: https://viralvariant.anses.fr/ state: missing - version: '1.6' - - id: toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.0 + version: 1.16.8+galaxy1 + - id: toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/4.0 servers: - server: http://apostl.moffitt.org/ state: missing @@ -25276,66 +4262,76 @@ - server: https://hyperbrowser.uio.no/coloc-stats state: missing - server: https://galaxy.mesocentre.uca.fr - state: exact - version: '2.0' + state: inexact + versions: + - '4.1' + - 5.1.0 + - '4.2' - server: https://galaxy.pasteur.fr/ - state: missing + state: inexact + versions: + - 5.1.0 - server: https://galaxytrakr.org/ state: inexact versions: - - '1.6' - - '2.1' - - 2.1+galaxy0 + - 5.1.0 - server: http://igg.cloud.ba.infn.it/galaxy state: missing - server: https://galaxy.hyphy.org/ - state: missing + state: inexact + versions: + - 5.1.0 - server: https://www.immportgalaxy.org/ state: missing - server: http://galaxy.interactomix.com/ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr - state: exact - version: '2.0' + state: inexact + versions: + - 5.1.0 - server: http://galaxy.inf.ethz.ch state: missing - server: https://palfinder.ls.manchester.ac.uk/ state: missing - server: http://pepsimili.e-nios.com:8080/ state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - server: https://usegalaxy.org.au state: exact - version: '2.0' + version: '4.0' - server: https://usegalaxy.be/ state: exact - version: '2.0' + version: '4.0' - server: https://usegalaxy.cz/ - state: exact - version: '2.0' + state: inexact + versions: + - 5.1.0 + - '4.2' + - '1.0' - server: https://usegalaxy.eu state: exact - version: '2.0' + version: '4.0' - server: https://usegalaxy.fr/ - state: exact - version: '2.0' + state: inexact + versions: + - '4.1' + - 5.1.0 - server: https://usegalaxy.no/ - state: exact - version: '2.0' + state: inexact + versions: + - '4.1' + - 5.1.0 + - '4.2' - server: https://usegalaxy.org state: exact - version: '2.0' + version: '4.0' - server: https://viralvariant.anses.fr/ state: missing - version: '2.0' - - id: toolshed.g2.bx.psu.edu/repos/devteam/intersect/gops_intersect_1/1.0.0 + version: '4.0' + - id: toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/4.2 servers: - 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email: delphine.lariviere@galaxy.org + id: delphine-l + joined: 2017-09 + name: Delphine Lariviere + orcid: 0000-0001-6421-3484 + page: https://training.galaxyproject.org/training-material/hall-of-fame/delphine-l/ + url: https://training.galaxyproject.org/training-material/api/contributors/delphine-l.json + - elixir_node: au + email: simon.gladman@unimelb.edu.au + id: slugger70 + in_memoriam: "Simon\ + \ Gladman, system administrator of UseGalaxy.org.au, passed away on November\ + \ 26, 2022\n\nHe was a fantastic teacher, tutorial author, system administrator, and warm\ + \ and welcoming friend. He contributed heavily to the Galaxy Training Network\ + \ and especially the Galaxy Administration community over the years, we will\ + \ miss him dearly. The GTN and GAT would not be what they are today, without\ + \ him.\n\n\u201CHave I told you about my watch?\u201D" + joined: 2017-09 + name: Simon Gladman + orcid: 0000-0002-6100-4385 + page: https://training.galaxyproject.org/training-material/hall-of-fame/slugger70/ + url: https://training.galaxyproject.org/training-material/api/contributors/slugger70.json + - avatar: /training-material/shared/images/unimelb_Logo_RGB.png + id: unimelb + members: + - annasyme + - cat-bro + - GraceAHall + - supernord + - tflowers15 + - uwwint + - vinisalazar + name: The University of Melbourne + page: https://training.galaxyproject.org/training-material/hall-of-fame/unimelb/ + url: https://training.galaxyproject.org/training-material/api/organisations/unimelb.json + - avatar: /training-material/shared/images/Melbourne-Bioinformatics-logo.png + former_members: + - annasyme + id: melbournebioinformatics + members: + - GraceAHall + - tflowers15 + - vinisalazar + name: Melbourne Bioinformatics + page: https://training.galaxyproject.org/training-material/hall-of-fame/melbournebioinformatics/ + url: https://training.galaxyproject.org/training-material/api/organisations/melbournebioinformatics.json + - avatar: /training-material/shared/images/Australian-Biocommons-Favicon-RGB.png + id: AustralianBioCommons + members: + - annasyme + - burkemlou + - cat-bro + - igormakunin + - mthang + - PatCapon39 + - supernord + - tflowers15 + - uwwint + name: Australian BioCommons + page: https://training.galaxyproject.org/training-material/hall-of-fame/AustralianBioCommons/ + url: https://training.galaxyproject.org/training-material/api/organisations/AustralianBioCommons.json + - affiliations: + - uni-freiburg + - nfdi4plants + - elixir-europe + bio: Researcher at Erasmus Medical Center + bluesky: shiltemann.bsky.social + contact_for_training: true + elixir_node: nl + email: saskia.hiltemann@gmail.com + fediverse: https://mstdn.science/@shiltemann + fediverse_flavor: mastodon + former_affiliations: + - CINECA-Project + - gallantries + - erasmusmc + id: shiltemann + joined: 2017-09 + linkedin: shiltemann + location: + country: NL + lat: 51.912 + lon: 4.462 + maintainer_contact: gitter + matrix: shiltemann:matrix.org + name: Saskia Hiltemann + orcid: 0000-0003-3803-468X + page: https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/ + url: https://training.galaxyproject.org/training-material/api/contributors/shiltemann.json + - affiliations: + - biofair + - earlham + - elixir-europe + - elixir-steers + bluesky: nsoranzo.bsky.social + elixir_node: uk + fediverse: https://mstdn.science/@nsoranzo + fediverse_flavor: mastodon + id: nsoranzo + joined: 2017-09 + linkedin: nicola-soranzo-7884125 + location: + country: UK + lat: 52.62188 + lon: 1.21899 + matrix: nsoranzo:matrix.org + name: Nicola Soranzo + orcid: 0000-0003-3627-5340 + page: https://training.galaxyproject.org/training-material/hall-of-fame/nsoranzo/ + twitter: NicolaSoranzo + url: https://training.galaxyproject.org/training-material/api/contributors/nsoranzo.json + - affiliations: + - elixir-europe + contact_for_training: false + elixir_node: nl + former_affiliations: + - deNBI + - avans-atgm + - uni-freiburg + - erasmusmc + - gallantries + - by-covid + - elixir-converge + id: hexylena + joined: 2017-09 + location: + country: NL + lat: 51.91 + lon: 4.46 + maintainer_contact: gitter + matrix: hexylena:matrix.org + name: Helena Rasche + orcid: 0000-0001-9760-8992 + page: https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/ + url: https://training.galaxyproject.org/training-material/api/contributors/hexylena.json + - affiliations: + - deNBI + - mwk + - uni-freiburg + - elixir-europe + - materialvitaldigital + contact_for_training: true + elixir_node: de + email: bjoern.gruening@gmail.com + fediverse: https://fosstodon.org/@bgruening + fediverse_flavor: mastodon + former_affiliations: + - eurosciencegateway + - eosc-life + - by-covid + - crc992 + - elixir-converge + id: bgruening + joined: 2017-09 + linkedin: bgruening + location: + country: DE + lat: 47.997791 + lon: 7.842609 + matrix: bgruening:matrix.org + name: "Bj\xF6rn Gr\xFCning" + orcid: 0000-0002-3079-6586 + page: https://training.galaxyproject.org/training-material/hall-of-fame/bgruening/ + twitter: bjoerngruening + url: https://training.galaxyproject.org/training-material/api/contributors/bgruening.json + - affiliations: + - elixir-europe + bluesky: abretaud.bsky.social + contact_for_training: true + elixir_node: fr + email: anthony.bretaudeau@irisa.fr + fediverse: https://genomic.social/@abretaud + fediverse_flavor: mastodon + former_affiliations: + - eurosciencegateway + - gallantries + id: abretaud + joined: 2017-09 + location: + country: FR + lat: 48.11 + lon: -1.64 + matrix: abretaud:matrix.org + name: Anthony Bretaudeau + orcid: 0000-0003-0914-2470 + page: https://training.galaxyproject.org/training-material/hall-of-fame/abretaud/ + url: https://training.galaxyproject.org/training-material/api/contributors/abretaud.json + - affiliations: + - gallantries + - ifb + - elixir-europe + contact_for_training: true + elixir_node: fr + email: berenice.batut@gmail.com + fediverse: https://piaille.fr/@bebatut + fediverse_flavor: mastodon + former_affiliations: + - uni-freiburg + - deNBI + id: bebatut + joined: 2017-09 + linkedin: berenicebatut + location: + country: FR + lat: 45.77 + lon: 3.08 + matrix: bebatut:matrix.org + name: "B\xE9r\xE9nice Batut" + orcid: 0000-0001-9852-1987 + page: https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/ + twitter: bebatut + url: https://training.galaxyproject.org/training-material/api/contributors/bebatut.json + - affiliations: + - elixir-europe + elixir_node: fr + id: lecorguille + joined: 2017-09 + name: "Gildas Le Corguill\xE9" + page: https://training.galaxyproject.org/training-material/hall-of-fame/lecorguille/ + url: https://training.galaxyproject.org/training-material/api/contributors/lecorguille.json + - id: afgane + joined: 2018-06 + name: Enis Afgan + page: https://training.galaxyproject.org/training-material/hall-of-fame/afgane/ + url: https://training.galaxyproject.org/training-material/api/contributors/afgane.json + - id: willdurand + joined: 2017-09 + name: William Durand + page: https://training.galaxyproject.org/training-material/hall-of-fame/willdurand/ + url: https://training.galaxyproject.org/training-material/api/contributors/willdurand.json + - email: anton@nekrut.org + id: nekrut + joined: 2017-09 + name: Anton Nekrutenko + page: https://training.galaxyproject.org/training-material/hall-of-fame/nekrut/ + url: https://training.galaxyproject.org/training-material/api/contributors/nekrut.json + - email: delphine.lariviere@galaxy.org + id: delphine-l + joined: 2017-09 + name: Delphine Lariviere + orcid: 0000-0001-6421-3484 + page: https://training.galaxyproject.org/training-material/hall-of-fame/delphine-l/ + url: https://training.galaxyproject.org/training-material/api/contributors/delphine-l.json + - id: njall + joined: 2019-02 + name: Niall Beard + page: https://training.galaxyproject.org/training-material/hall-of-fame/njall/ + url: https://training.galaxyproject.org/training-material/api/contributors/njall.json + dir: topics/assembly/tutorials/unicycler-assembly + edam_ontology: + - topic_0196 + - topic_0622 + - topic_3301 + edam_operation: + - Statistical calculation + - Sequencing quality control + - Genome assembly + - Sequence assembly validation + - Visualisation + - Genome annotation + - Sequence composition calculation + - Aggregation + - Validation + - Gene prediction + - Coding region prediction + edam_topic: + - Sequence assembly + - Genomics + - Microbiology + exact_supported_servers: + - UseGalaxy.org.au + - UseGalaxy.eu + - UseGalaxy.org (Main) + feedback_mean_note: null + feedback_number: 0 + follow_up_training: + - topic_name: assembly + tutorials: + - ecoli_comparison + type: internal + hands_on: true + id: assembly/unicycler-assembly + inexact_supported_servers: + - Galaxy@AuBi + - GalaxyTrakr + - MISSISSIPPI + - UseGalaxy.be + - UseGalaxy.cz + - UseGalaxy.fr + - UseGalaxy.no + js_requirements: + mathjax: null + mermaid: false + key_points: + - We learned about the strategies used by assemblers for hybrid assemblies + - We performed an hybrid assembly of a bacterial genome and its annotation + - Unicycler is a pipeline bases on Spades and Pilon dedicated to hybrid assembly + of Small genomes + - Combination of short and long reads helped us produce an almost perfect assembly + layout: tutorial_hands_on + level: Introductory + license: CC-BY-4.0 + mod_date: '2026-01-23' + objectives: + - Perform Quality Control on your reads + - Perform a Small genome Assembly with Unicycler + - Evaluate the Quality of the Assembly with Quast + - Annotate the assembly with Prokka + pageviews: 9259758 + pub_date: '2017-10-11' + questions: + - I have short reads and long reads. How do I assemble a genome? + short_id: T00038 + short_tools: + - unicycler + - quast + - prokka + - fastqc + - multiqc + slides: true + slides_recordings: false + supported_servers: + exact: + - name: UseGalaxy.org.au + url: https://usegalaxy.org.au + usegalaxy: true + - name: UseGalaxy.eu + url: https://usegalaxy.eu + usegalaxy: true + - name: UseGalaxy.org (Main) + url: https://usegalaxy.org + usegalaxy: true + inexact: + - name: Galaxy@AuBi + url: https://galaxy.mesocentre.uca.fr + usegalaxy: false + - name: GalaxyTrakr + url: https://galaxytrakr.org/ + usegalaxy: false + - name: MISSISSIPPI + url: https://mississippi.sorbonne-universite.fr + usegalaxy: false + - name: UseGalaxy.be + url: https://usegalaxy.be/ + usegalaxy: false + - name: UseGalaxy.cz + url: https://usegalaxy.cz/ + usegalaxy: false + - name: UseGalaxy.fr + url: https://usegalaxy.fr/ + usegalaxy: true + - name: UseGalaxy.no + url: https://usegalaxy.no/ + usegalaxy: false + supported_servers_matrix: + servers: + - name: APOSTL + url: http://apostl.moffitt.org/ + usegalaxy: false + - name: MBAC Metabiome Portal + url: http://mbac.gmu.edu:8080/ + usegalaxy: false + - name: ChemFlow + url: https://vm-chemflow-francegrille.eu/ + usegalaxy: false + - name: CIRM-CFBP + url: https://iris.angers.inra.fr/galaxypub-cfbp + usegalaxy: false + - name: Coloc-stats + url: https://hyperbrowser.uio.no/coloc-stats + usegalaxy: false + - name: Galaxy@AuBi + url: https://galaxy.mesocentre.uca.fr + usegalaxy: false + - name: Galaxy@Pasteur + url: https://galaxy.pasteur.fr/ + usegalaxy: false + - name: GalaxyTrakr + url: https://galaxytrakr.org/ + usegalaxy: false + - name: GASLINI + url: http://igg.cloud.ba.infn.it/galaxy + usegalaxy: false + - name: HyPhy HIV NGS Tools + url: https://galaxy.hyphy.org/ + usegalaxy: false + - name: ImmPort Galaxy + url: https://www.immportgalaxy.org/ + usegalaxy: false + - name: InteractoMIX + url: http://galaxy.interactomix.com/ + usegalaxy: false + - name: IPK Galaxy Blast Suite + url: https://galaxy-web.ipk-gatersleben.de + usegalaxy: false + - name: Mandoiu Lab + url: https://neo.engr.uconn.edu/ + usegalaxy: false + - name: MISSISSIPPI + url: https://mississippi.sorbonne-universite.fr + usegalaxy: false + - name: Oqtans + url: http://galaxy.inf.ethz.ch + usegalaxy: false + - name: Palfinder + url: https://palfinder.ls.manchester.ac.uk/ + usegalaxy: false + - name: PepSimili + url: http://pepsimili.e-nios.com:8080/ + usegalaxy: false + - name: UseGalaxy.org.au + url: https://usegalaxy.org.au + usegalaxy: true + - name: UseGalaxy.be + url: https://usegalaxy.be/ + usegalaxy: false + - name: UseGalaxy.cz + url: https://usegalaxy.cz/ + usegalaxy: false + - name: UseGalaxy.eu + url: https://usegalaxy.eu + usegalaxy: true + - name: UseGalaxy.fr + url: https://usegalaxy.fr/ + usegalaxy: true + - name: UseGalaxy.no + url: https://usegalaxy.no/ + usegalaxy: false + - name: UseGalaxy.org (Main) + url: https://usegalaxy.org + usegalaxy: true + - name: Viral Variant Visualizer (VVV) + url: https://viralvariant.anses.fr/ + usegalaxy: false + tools: + - id: toolshed.g2.bx.psu.edu/repos/crs4/prokka/prokka/1.14.5 servers: - 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server: https://palfinder.ls.manchester.ac.uk/ state: missing - server: http://pepsimili.e-nios.com:8080/ state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - server: https://usegalaxy.org.au state: exact - version: 2.3.2 + version: '1.7' - server: https://usegalaxy.be/ - state: exact - version: 2.3.2 + state: inexact + versions: + - 1.27+galaxy3 + - 1.27+galaxy4 + - 1.11+galaxy1 + - 1.24.1+galaxy0 + - 1.33+galaxy0 + - '1.6' + - 1.11+galaxy0 + - 1.35+galaxy1 + - 1.33+galaxy3 + - 1.34+galaxy0 + - 1.8+galaxy0 + - 1.9+galaxy1 + - 1.8+galaxy1 + - '1.9' + - 1.35+galaxy0 + - 1.33+galaxy2 - server: https://usegalaxy.cz/ state: exact - version: 2.3.2 + version: '1.7' - server: https://usegalaxy.eu state: exact - version: 2.3.2 + version: '1.7' - server: https://usegalaxy.fr/ state: exact - version: 2.3.2 + version: '1.7' - server: https://usegalaxy.no/ - state: missing + state: exact + version: '1.7' - server: https://usegalaxy.org state: exact - version: 2.3.2 + version: '1.7' - 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state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr - state: exact - version: 5.1.0 + state: inexact + versions: + - 5.3.0+galaxy1 + - 5.2.0+galaxy1 - server: http://galaxy.inf.ethz.ch state: missing - server: https://palfinder.ls.manchester.ac.uk/ state: missing - server: http://pepsimili.e-nios.com:8080/ state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - server: https://usegalaxy.org.au state: exact - version: 5.1.0 + version: 5.0.2+galaxy0 - server: https://usegalaxy.be/ state: exact - version: 5.1.0 + version: 5.0.2+galaxy0 - server: https://usegalaxy.cz/ state: exact - version: 5.1.0 + version: 5.0.2+galaxy0 - server: https://usegalaxy.eu state: exact - version: 5.1.0 + version: 5.0.2+galaxy0 - server: https://usegalaxy.fr/ state: exact - version: 5.1.0 + version: 5.0.2+galaxy0 - server: https://usegalaxy.no/ - state: exact - version: 5.1.0 + state: inexact + versions: + - 5.2.0+galaxy1 + - 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- server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr state: inexact versions: - - 7.526+galaxy2 + - 0.5.1+galaxy0 - server: http://galaxy.inf.ethz.ch state: missing - server: https://palfinder.ls.manchester.ac.uk/ state: missing - server: http://pepsimili.e-nios.com:8080/ state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - server: https://usegalaxy.org.au state: exact - version: 7.489+galaxy0 + version: 0.4.8.0 - server: https://usegalaxy.be/ state: exact - version: 7.489+galaxy0 + version: 0.4.8.0 - server: https://usegalaxy.cz/ - state: exact - version: 7.489+galaxy0 + state: inexact + versions: + - 0.5.1+galaxy0 + - 0.5.0+galaxy1 - server: https://usegalaxy.eu state: exact - version: 7.489+galaxy0 + version: 0.4.8.0 - server: https://usegalaxy.fr/ state: exact - version: 7.489+galaxy0 + version: 0.4.8.0 - server: https://usegalaxy.no/ state: exact - version: 7.489+galaxy0 + version: 0.4.8.0 - 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- toolshed.g2.bx.psu.edu/repos/devteam/tabular_to_fasta/tab2fasta/1.1.1 - - toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regexColumn1/1.0.1 - - toolshed.g2.bx.psu.edu/repos/iuc/orfipy/orfipy/0.0.4+galaxy0 - - toolshed.g2.bx.psu.edu/repos/iuc/rapidnj/rapidnj/2.3.2 - - toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0 - - toolshed.g2.bx.psu.edu/repos/rnateam/mafft/rbc_mafft/7.489+galaxy0 - topic_name: genome-annotation - topic_name_human: Genome Annotation + - toolshed.g2.bx.psu.edu/repos/crs4/prokka/prokka/1.14.5 + - toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1 + - toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.7 + - toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.0.2+galaxy0 + - toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.4.8.0 + topic_name: assembly + topic_name_human: Assembly tours: false translations: slides: [] tutorial: [] video: false - tutorial_name: gene-centric + tutorial_name: unicycler-assembly type: tutorial - url: https://training.galaxyproject.org//topics/genome-annotation/tutorials/gene-centric/tutorial.html + url: https://training.galaxyproject.org//topics/assembly/tutorials/unicycler-assembly/tutorial.html urls: - hands_on: https://training.galaxyproject.org/training-material/api/topics/genome-annotation/tutorials/gene-centric/tutorial.json - slides: https://training.galaxyproject.org/training-material/api/topics/genome-annotation/tutorials/gene-centric/tutorial.json - version: 10 + hands_on: https://training.galaxyproject.org/training-material/api/topics/assembly/tutorials/unicycler-assembly/tutorial.json + slides: https://training.galaxyproject.org/training-material/api/topics/assembly/tutorials/unicycler-assembly/tutorial.json + version: 25 video: false video_versions: 0 video_view: 0 - visit_duration: 590 - visitors: 2056 + visit_duration: 425 + visitors: 3931702 workflows: - - creators: - - class: Person - identifier: 0000-0002-5987-8032 - name: Anton Nekrutenko - description: Workflows for comparison of genes in annotated genomes + - creators: [] + description: Unicycler Assembly features: comments: false parameters: false @@ -25883,330 +5705,760 @@ graph_dot: "digraph main {\n node [fontname=\"Atkinson Hyperlegible\", shape=box,\ \ color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n edge [fontname=\"\ Atkinson Hyperlegible\"];\n 0[color=lightblue,label=\"\u2139\uFE0F Input Dataset\\\ - nExons\"]\n 1[color=lightblue,label=\"\u2139\uFE0F Input Collection\\nDiamond\ - \ makedb\"]\n 2[color=lightblue,label=\"\u2139\uFE0F Input Collection\\nORFipy\ - \ BED\"]\n 3[label=\"Diamond: Find hits in ORFs\"]\n 0 -> 3 [label=\"output\"\ - ]\n 1 -> 3 [label=\"output\"]\n 4[label=\"Column Regex Find And Replace\"\ - ]\n 2 -> 4 [label=\"output\"]\n 5[label=\"Alignments\"]\n 3 -> 5 [label=\"\ - daa_output\"]\n 6[label=\"Cut\"]\n 4 -> 6 [label=\"out_file1\"]\n 7[label=\"\ - Alignments + BED\"]\n 6 -> 7 [label=\"out_file1\"]\n 5 -> 7 [label=\"blast_tabular\"\ - ]\n 8[label=\"Cut\"]\n 7 -> 8 [label=\"out_file1\"]\n 9[label=\"Collapse\ - 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- hash: 476d3d57ff2b0ce249879b60aa03500ab62685d6 - message: workflow update + - hash: 232ce03723ab9acbd124828954705c1cd2679abd + message: removed name label bit + num: 9 + short_hash: 232ce0372 + unix: '1581615057' + - hash: cccd85216e3d9baaca787eb7ae8808bd5f3fa2dc + message: minor tweaks and files unhidden + num: 8 + short_hash: cccd85216 + unix: '1581613998' + - hash: 2a2b6329ed96aaaf214703eae87459c58d6e8702 + message: name fixed + num: 7 + short_hash: 2a2b6329e + unix: '1581095735' + - hash: 3d424d5e65326cf45c1e4d34851998ab29e6e85c + message: annotation fixed + num: 6 + short_hash: 3d424d5e6 + unix: '1581014437' + - hash: 2eade3cbf7b99b8252c3a53ac6cac59e0cacd432 + message: tags added + num: 5 + short_hash: 2eade3cbf + unix: '1581004807' + - hash: 07642064759cb13fda345ab9a687aa96b80b3004 + message: workflows updated with newer tools, added missing + num: 4 + short_hash: '076420647' + unix: '1580135207' + - hash: 667ff3de9c4e13d341a6d864bd6dc826ef15ca04 + message: annotation + num: 3 + short_hash: 667ff3de9 + unix: '1579690769' + - 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label: null + output_name: output + uuid: e14afa81-ce6c-4577-b17e-90ef2b75c885 + - annotation: '' content_id: null errors: null id: 1 input_connections: {} inputs: - - description: Diamond DB created from ORF predicted from genomes used in the - analysis - name: Diamond makedb - label: Diamond makedb - name: Input dataset collection + - description: '' + name: Reverse Reads + label: Reverse Reads + name: Input dataset outputs: [] position: - left: 0.0 - top: 185.71875 + left: 187.359375 + top: 656.765625 tool_id: null - tool_state: '{"optional": false, "tag": "", "collection_type": "list"}' + tool_state: '{"optional": false}' tool_version: null - type: data_collection_input - uuid: 0acc2c20-91fb-4470-80ac-2eeb7e2f32ae - workflow_outputs: [] - - annotation: BED dataset containing information about ORFs predicted in genomes - of interest + type: data_input + uuid: 25209075-9248-4e70-9396-87e6e28995e1 + workflow_outputs: + - label: null + output_name: output + uuid: 4cade8d2-87ae-4bae-8795-b1f64c5c3cab + - 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annotation: '' + content_id: null + errors: null + id: 0 + input_connections: {} + inputs: + - description: '' + name: Forward reads + label: Forward reads + name: Input dataset + outputs: [] + position: + left: 230.140625 + top: 404.015625 + tool_id: null + tool_state: '{"optional": false}' + tool_version: null + type: data_input + uuid: 5152d41f-3523-496e-afa2-8d4b0af89b2a + workflow_outputs: + - label: null + output_name: output + uuid: e14afa81-ce6c-4577-b17e-90ef2b75c885 + - annotation: '' + content_id: null + errors: null + id: 1 + input_connections: {} + inputs: + - description: '' + name: Reverse Reads + label: Reverse Reads + name: Input dataset + outputs: [] + position: + left: 187.359375 + top: 656.765625 + tool_id: null + tool_state: '{"optional": false}' + tool_version: null + type: data_input + uuid: 25209075-9248-4e70-9396-87e6e28995e1 + workflow_outputs: + - label: null + output_name: output + uuid: 4cade8d2-87ae-4bae-8795-b1f64c5c3cab + - annotation: '' content_id: null errors: null id: 2 input_connections: {} inputs: - - description: BED dataset containing information about ORFs predicted in genomes - of interest - name: ORFipy BED - label: ORFipy BED - name: Input dataset collection + - description: '' + name: Long Reads + label: Long Reads + name: Input dataset outputs: [] position: - left: 1.90625 - top: 313.203125 + left: 186.65625 + top: 803.734375 tool_id: null - tool_state: '{"optional": false, "format": ["bed"], "tag": "", "collection_type": - "list"}' + tool_state: '{"optional": false}' tool_version: null - type: data_collection_input - uuid: 329b3c07-f0ee-4882-abf7-1215062a0fec - workflow_outputs: [] - license: null - mermaid: "flowchart TD\n 0[\"\u2139\uFE0F Input Dataset\\nExons\"];\n style\ - \ 0 stroke:#2c3143,stroke-width:4px;\n 1[\"\u2139\uFE0F Input Collection\\\ - nDiamond makedb\"];\n style 1 stroke:#2c3143,stroke-width:4px;\n 2[\"\u2139\ - \uFE0F Input Collection\\nORFipy BED\"];\n style 2 stroke:#2c3143,stroke-width:4px;\n\ - \ 3[\"Diamond: Find hits in ORFs\"];\n 0 -->|output| 3;\n 1 -->|output| 3;\n\ - \ 4[\"Column Regex Find And Replace\"];\n 2 -->|output| 4;\n 5[\"Alignments\"\ - ];\n 3 -->|daa_output| 5;\n 6[\"Cut\"];\n 4 -->|out_file1| 6;\n 7[\"Alignments\ - \ + BED\"];\n 6 -->|out_file1| 7;\n 5 -->|blast_tabular| 7;\n 8[\"Cut\"];\n\ - \ 7 -->|out_file1| 8;\n 9[\"Collapse Collection\"];\n 7 -->|out_file1| 9;\n\ - \ 10[\"Intersect\"];\n 6 -->|out_file1| 10;\n 8 -->|out_file1| 10;\n 11[\"\ - Filter\"];\n 9 -->|output| 11;\n 12[\"Overlapping ORFs\"];\n 10 -->|output|\ - \ 12;\n 13[\"Cut\"];\n 11 -->|out_file1| 13;\n 14[\"Compute\"];\n 12 -->|output|\ - \ 14;\n 15[\"Compute\"];\n 13 -->|out_file1| 15;\n 16[\"Split file\"];\n\ - \ 15 -->|out_file1| 16;\n 17[\"Report\"];\n 15 -->|out_file1| 17;\n 18[\"\ - Tabular-to-FASTA\"];\n 16 -->|split_output| 18;\n 19[\"Cut\"];\n 17 -->|out_file1|\ - \ 19;\n 20[\"MAFFT\"];\n 18 -->|output| 20;\n 21[\"Filter: Plus strand matches\"\ - ];\n 19 -->|out_file1| 21;\n 22[\"Filter: Minus strand matches\"];\n 19 -->|out_file1|\ - \ 22;\n 23[\"Join neighbors\"];\n 20 -->|outputAlignment| 23;\n 54ea37cc-63d1-422a-9f5e-124b8d39e6bd[\"\ - Output\\nJoin neighbors on input dataset(s): Calculated distances\"];\n 23\ - \ --> 54ea37cc-63d1-422a-9f5e-124b8d39e6bd;\n style 54ea37cc-63d1-422a-9f5e-124b8d39e6bd\ - \ stroke:#2c3143,stroke-width:4px;\n 24[\"Compute\"];\n 21 -->|out_file1|\ - \ 24;\n 25[\"Compute\"];\n 22 -->|out_file1| 25;\n 26[\"Concatenate datasets\"\ - ];\n 24 -->|out_file1| 26;\n 25 -->|out_file1| 26;\n 27[\"Compute\"];\n \ - \ 26 -->|out_file1| 27;\n 28[\"Cut\"];\n 27 -->|out_file1| 28;\n 29[\"Compute\"\ - ];\n 28 -->|out_file1| 29;\n 30[\"Join two Datasets\"];\n 14 -->|out_file1|\ - \ 30;\n 29 -->|out_file1| 30;\n 31[\"Mapping report\"];\n 30 -->|out_file1|\ - \ 31;" - modified: 2026-05-21 00:30:24 +0000 - name: Comparative gene analysis - outputs: - - annotation: Compute NJ phylogenetic trees - content_id: toolshed.g2.bx.psu.edu/repos/iuc/rapidnj/rapidnj/2.3.2 + type: data_input + uuid: c1cfa6a5-2c17-4cd7-b582-ce85ff552b67 + workflow_outputs: + - label: null + output_name: output + uuid: bf7b5353-30b6-471b-91b7-5fd2143bf981 + - 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plushz + - bebatut + - vinisalazar + - paulzierep + funding: + - gallantries contributors: - - email: delphine.lariviere@galaxy.org - id: delphine-l - joined: 2017-09 - name: Delphine Lariviere - orcid: 0000-0001-6421-3484 - page: https://training.galaxyproject.org/training-material/hall-of-fame/delphine-l/ - url: https://training.galaxyproject.org/training-material/api/contributors/delphine-l.json + - affiliations: + - uni-freiburg + id: plushz + joined: 2022-03 + name: Polina Polunina + orcid: 0000-0002-0507-4602 + page: https://training.galaxyproject.org/training-material/hall-of-fame/plushz/ + url: https://training.galaxyproject.org/training-material/api/contributors/plushz.json - affiliations: - gallantries - ifb @@ -26232,85 +6484,174 @@ page: https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/ twitter: bebatut url: https://training.galaxyproject.org/training-material/api/contributors/bebatut.json - dir: topics/genome-annotation/tutorials/tnseq + - affiliations: + - unimelb + - melbournebioinformatics + id: vinisalazar + joined: 2025-10 + name: Vini Salazar + orcid: 0000-0002-8362-3195 + page: https://training.galaxyproject.org/training-material/hall-of-fame/vinisalazar/ + url: https://training.galaxyproject.org/training-material/api/contributors/vinisalazar.json + - affiliations: + - uni-freiburg + - elixir-europe + - deNBI + - mwk + - materialvitaldigital + email: zierep@informatik.uni-freiburg.de + id: paulzierep + joined: 2023-02 + name: Paul Zierep + orcid: 0000-0003-2982-388X + page: https://training.galaxyproject.org/training-material/hall-of-fame/paulzierep/ + url: https://training.galaxyproject.org/training-material/api/contributors/paulzierep.json + - avatar: https://gallantries.github.io/assets/images/gallantries-logo.png + end_date: '2023-09-30' + former_members: + - abretaud + - hexylena + - shiltemann + funder_name: Erasmus+ Programme + funding_database: erasmusplus + funding_id: 2020-1-NL01-KA203-064717 + funding_statement: 'This project (2020-1-NL01-KA203-064717) + is funded with the support of the Erasmus+ programme of the European Union. + Their funding has supported a large number of tutorials within the GTN across + a wide array of topics. + + eu flag with the text: with the support of the erasmus programme of the + european union + + erasmus plus + logo' + github: false + id: gallantries + joined: 2020-09 + members: + - bebatut + - colineroyaux + - fpsom + - yvanlebras + name: 'Gallantries: Bridging Training Communities in Life Science, Environment + and Health' + page: https://training.galaxyproject.org/training-material/hall-of-fame/gallantries/ + short_name: Gallantries + start_date: '2020-09-01' + url: https://training.galaxyproject.org/training-material/api/grants/gallantries.json + dir: topics/assembly/tutorials/metagenomics-assembly edam_ontology: - - topic_0622 - - topic_3301 - - topic_0080 - - topic_0798 + - topic_3174 + - topic_0196 edam_operation: + - Variant calling + - Sequence assembly validation - Primer removal + - Visualisation + - Sequence composition calculation + - Local alignment + - Read mapping + - Sequence assembly visualisation + - Sequencing quality control + - Statistical calculation + - Genome assembly + - Sequence contamination filtering + - Data handling - Sequence trimming - - Transposon prediction + - Sequence alignment analysis + - Sequence file editing + - Formatting - Read pre-processing edam_topic: - - Genomics - - Microbiology - - Sequence analysis - - Mobile genetic elements - exact_supported_servers: - - UseGalaxy.org.au - - UseGalaxy.be - - UseGalaxy.no + - Metagenomics + - Sequence assembly + exact_supported_servers: [] feedback_mean_note: null feedback_number: 0 hands_on: true - id: genome-annotation/tnseq + id: assembly/metagenomics-assembly inexact_supported_servers: - UseGalaxy.cz - UseGalaxy.eu + - UseGalaxy.fr + - UseGalaxy.org (Main) js_requirements: - mathjax: null + mathjax: 27693 mermaid: false key_points: - - TnSeq is a useful analysis to detect essential genes and conditional essential - genes - - The saturation of the library must be sufficient so that every gene must have - been impacted at least once - - Be sure you have removed every transposon sequence before starting your analysis - - Verify the results manually do separate domain essential and essential genes + - Assembly groups reads into contigs and scaffolds. + - de Brujin Graphs use k-mers to assembly reads. + - MetaSPAdes and MEGAHIT are short-read assemblers. + - MetaQUAST is a tool to assess metagenomic assembly quality. layout: tutorial_hands_on + level: Introductory license: CC-BY-4.0 - mod_date: '2024-03-18' + mod_date: '2026-07-01' objectives: - - Understand the read structure of TnSeq analyses - - Predict Essential genes with Transit - - Compare gene essentiality in control sample and an different experimental condition - pageviews: 9051236 - priority: 4 - pub_date: '2019-07-02' + - Describe what an assembly is. + - Explain the difference between co-assembly and individual assembly. + - Explain the difference between reads, contigs and scaffolds. + - Explain how tools based on de Bruijn graph work. + - Evaluate the quality of the Assembly with QUAST, Bowtie2, and CoverM-Contig. + - Construct and apply simple assembly pipelines on short read data. + pageviews: 3 + pub_date: '2026-07-01' questions: - - What is Transposon insertion Sequencing? - - 'How to get TA sites Coverage ? ' - - How to predict essential genes ? - short_id: T00179 + - Why metagenomic data should be assembled? + - What is the difference between co-assembly and individual assembly? + - What is the difference between reads, contigs and scaffolds? + - How tools based on De Bruijn graph work? + - How to assess the quality of metagenomic data assembly? + recordings: + - captioners: + - bebatut + - sophia120199 + date: '2023-05-02' + galaxy_version: '23.01' + length: 1H + speakers: + - bebatut + youtube_id: 1ZYGy85Im7w + - captioners: + - gdefazio + - natalie-wa + date: '2026-03-26' + galaxy_version: 25.1.2.dev0 + length: 1H15M + speakers: + - gdefazio + youtube_id: KzqLR4btsic + redirect_from: + - /topics/metagenomics/tutorials/metagenomics-assembly/tutorial + - /short/assembly/metagenomics-assembly + - /short/T00035 + short_id: T00035 short_tools: - - transit_gumbel - - __EXTRACT_DATASET__ - - tp_sort_header_tool - - Filter1 - - Add_a_column1 - - gff_to_prot - - Cut1 - - deeptools_bam_coverage - 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- server: https://galaxy.bio.di.uminho.pt/ - state: missing - server: https://usegalaxy.org.au state: exact - version: '0.2' + version: 1.1.3+galaxy1 - server: https://usegalaxy.be/ state: exact - version: '0.2' + version: 1.1.3+galaxy1 - server: https://usegalaxy.cz/ state: exact - version: '0.2' + version: 1.1.3+galaxy1 - server: https://usegalaxy.eu state: exact - version: '0.2' + version: 1.1.3+galaxy1 - server: https://usegalaxy.fr/ - state: missing + state: exact + version: 1.1.3+galaxy1 - server: https://usegalaxy.no/ state: exact - version: '0.2' + version: 1.1.3+galaxy1 - server: https://usegalaxy.org state: exact - version: '0.2' + version: 1.1.3+galaxy1 - server: https://viralvariant.anses.fr/ state: missing - version: '0.2' - - id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.2 + version: 1.1.3+galaxy1 + - id: toolshed.g2.bx.psu.edu/repos/iuc/megahit_contig2fastg/megahit_contig2fastg/1.1.3+galaxy10 servers: - server: http://apostl.moffitt.org/ state: missing @@ -26735,66 +7792,65 @@ - server: https://hyperbrowser.uio.no/coloc-stats state: missing - server: https://galaxy.mesocentre.uca.fr - state: exact - version: 1.1.2 + state: missing - server: https://galaxy.pasteur.fr/ state: missing - server: https://galaxytrakr.org/ - state: exact - version: 1.1.2 + state: missing - server: http://igg.cloud.ba.infn.it/galaxy state: missing - server: https://galaxy.hyphy.org/ - state: inexact - versions: - - 9.5+galaxy3 + state: missing - server: https://www.immportgalaxy.org/ state: missing - server: http://galaxy.interactomix.com/ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr state: inexact versions: - - 9.5+galaxy3 + - 1.1.3+galaxy1 - server: http://galaxy.inf.ethz.ch state: missing - server: https://palfinder.ls.manchester.ac.uk/ state: missing - server: http://pepsimili.e-nios.com:8080/ state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - server: https://usegalaxy.org.au - state: exact - version: 1.1.2 + state: inexact + versions: + - 1.1.3+galaxy1 - server: https://usegalaxy.be/ - state: exact - version: 1.1.2 + state: inexact + versions: + - 1.1.3+galaxy1 - server: https://usegalaxy.cz/ - state: exact - version: 1.1.2 + state: inexact + versions: + - 1.1.3+galaxy1 - server: https://usegalaxy.eu - state: exact - version: 1.1.2 + state: inexact + versions: + - 1.1.3+galaxy1 - server: https://usegalaxy.fr/ - state: exact - version: 1.1.2 + state: inexact + versions: + - 1.1.3+galaxy1 - server: https://usegalaxy.no/ - state: exact - version: 1.1.2 + state: inexact + versions: + - 1.1.3+galaxy1 - server: https://usegalaxy.org - state: exact - version: 1.1.2 + state: inexact + versions: + - 1.1.3+galaxy1 - server: https://viralvariant.anses.fr/ state: missing - version: 1.1.2 - - id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/1.1.1 + version: 1.1.3+galaxy10 + - id: toolshed.g2.bx.psu.edu/repos/iuc/ngsutils_bam_filter/ngsutils_bam_filter/0.5.9 servers: - server: http://apostl.moffitt.org/ state: missing @@ -26807,66 +7863,56 @@ - server: https://hyperbrowser.uio.no/coloc-stats state: missing - server: https://galaxy.mesocentre.uca.fr - state: exact - version: 1.1.1 + state: missing - server: https://galaxy.pasteur.fr/ state: missing - server: https://galaxytrakr.org/ - state: exact - version: 1.1.1 + state: missing - server: http://igg.cloud.ba.infn.it/galaxy state: missing - server: https://galaxy.hyphy.org/ - state: inexact - versions: - - 9.5+galaxy3 + state: missing - server: https://www.immportgalaxy.org/ state: missing - server: http://galaxy.interactomix.com/ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr - state: inexact - versions: - - 9.5+galaxy3 + state: missing - server: http://galaxy.inf.ethz.ch state: missing - server: https://palfinder.ls.manchester.ac.uk/ state: missing - server: http://pepsimili.e-nios.com:8080/ state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - server: https://usegalaxy.org.au state: exact - version: 1.1.1 + version: 0.5.9 - server: https://usegalaxy.be/ state: exact - version: 1.1.1 + version: 0.5.9 - server: https://usegalaxy.cz/ state: exact - version: 1.1.1 + version: 0.5.9 - server: https://usegalaxy.eu state: exact - version: 1.1.1 + version: 0.5.9 - server: https://usegalaxy.fr/ state: exact - version: 1.1.1 + version: 0.5.9 - server: https://usegalaxy.no/ state: exact - version: 1.1.1 + version: 0.5.9 - server: https://usegalaxy.org state: exact - version: 1.1.1 + version: 0.5.9 - server: https://viralvariant.anses.fr/ state: missing - version: 1.1.1 - - id: toolshed.g2.bx.psu.edu/repos/devteam/bowtie_wrappers/bowtie_wrapper/1.2.0 + version: 0.5.9 + - id: toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.2.0+galaxy1 servers: - server: http://apostl.moffitt.org/ state: missing @@ -26879,11 +7925,13 @@ - server: https://hyperbrowser.uio.no/coloc-stats state: missing - server: https://galaxy.mesocentre.uca.fr - state: missing + state: exact + version: 5.2.0+galaxy1 - server: https://galaxy.pasteur.fr/ state: missing - server: https://galaxytrakr.org/ - state: missing + state: exact + version: 5.2.0+galaxy1 - server: http://igg.cloud.ba.infn.it/galaxy state: missing - server: https://galaxy.hyphy.org/ @@ -26894,44 +7942,42 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr state: exact - version: 1.2.0 + version: 5.2.0+galaxy1 - server: http://galaxy.inf.ethz.ch state: missing - server: https://palfinder.ls.manchester.ac.uk/ state: missing - server: http://pepsimili.e-nios.com:8080/ state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - server: https://usegalaxy.org.au state: exact - version: 1.2.0 + version: 5.2.0+galaxy1 - server: https://usegalaxy.be/ state: exact - version: 1.2.0 + version: 5.2.0+galaxy1 - server: https://usegalaxy.cz/ state: exact - version: 1.2.0 + version: 5.2.0+galaxy1 - server: https://usegalaxy.eu state: exact - version: 1.2.0 + version: 5.2.0+galaxy1 - server: https://usegalaxy.fr/ - state: missing + state: exact + version: 5.2.0+galaxy1 - server: https://usegalaxy.no/ state: exact - version: 1.2.0 + version: 5.2.0+galaxy1 - server: https://usegalaxy.org - state: missing + state: exact + version: 5.2.0+galaxy1 - server: https://viralvariant.anses.fr/ state: missing - version: 1.2.0 - - id: toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/1.3.0 + version: 5.2.0+galaxy1 + - id: toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.3.0+galaxy0 servers: - server: http://apostl.moffitt.org/ state: missing @@ -26944,16 +7990,19 @@ - server: https://hyperbrowser.uio.no/coloc-stats state: missing - server: https://galaxy.mesocentre.uca.fr - state: exact - version: 1.3.0 + state: inexact + versions: + - 5.3.0+galaxy1 + - 5.0.2+galaxy0 + - 5.2.0+galaxy1 - server: https://galaxy.pasteur.fr/ state: missing - server: https://galaxytrakr.org/ state: inexact versions: - - '1.6' - - '2.1' - - 2.1+galaxy0 + - 5.3.0+galaxy1 + - 5.2.0+galaxy1 + - '4.5' - server: http://igg.cloud.ba.infn.it/galaxy state: missing - server: https://galaxy.hyphy.org/ @@ -26964,52 +8013,51 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr state: inexact versions: - - '2.0' - - 2.1+galaxy0 + - 5.3.0+galaxy1 + - 5.2.0+galaxy1 - server: http://galaxy.inf.ethz.ch state: missing - server: https://palfinder.ls.manchester.ac.uk/ state: missing - server: http://pepsimili.e-nios.com:8080/ state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - server: https://usegalaxy.org.au state: exact - version: 1.3.0 + version: 5.3.0+galaxy0 - server: https://usegalaxy.be/ state: exact - version: 1.3.0 + version: 5.3.0+galaxy0 - server: https://usegalaxy.cz/ - state: inexact - versions: - - '1.4' - - '2.0' - - '1.6' - - 1.1.0 + state: exact + version: 5.3.0+galaxy0 - server: https://usegalaxy.eu state: exact - version: 1.3.0 + version: 5.3.0+galaxy0 - server: https://usegalaxy.fr/ state: exact - version: 1.3.0 + version: 5.3.0+galaxy0 - server: https://usegalaxy.no/ - state: exact - version: 1.3.0 + state: inexact + versions: + - 5.2.0+galaxy1 + - 5.2.0+galaxy0 + - 5.0.2+galaxy3 + - 5.0.2+galaxy2 + - 5.0.2+galaxy4 + - 5.0.2+galaxy1 + - 5.0.2+galaxy5 - server: https://usegalaxy.org state: exact - version: 1.3.0 + version: 5.3.0+galaxy0 - server: https://viralvariant.anses.fr/ state: missing - version: 1.3.0 - - id: toolshed.g2.bx.psu.edu/repos/iuc/gff_to_prot/gff_to_prot/3.0.2+galaxy0 + version: 5.3.0+galaxy0 + - id: toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_subseq/1.3.1 servers: - server: http://apostl.moffitt.org/ state: missing @@ -27022,11 +8070,13 @@ - server: https://hyperbrowser.uio.no/coloc-stats state: missing - server: https://galaxy.mesocentre.uca.fr - state: missing + state: exact + version: 1.3.1 - server: https://galaxy.pasteur.fr/ state: missing - server: https://galaxytrakr.org/ - state: missing + state: exact + version: 1.3.1 - server: http://igg.cloud.ba.infn.it/galaxy state: missing - server: https://galaxy.hyphy.org/ @@ -27037,44 +8087,43 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr - state: missing + state: inexact + versions: + - 1.5+galaxy0 - server: http://galaxy.inf.ethz.ch state: missing - server: https://palfinder.ls.manchester.ac.uk/ state: missing - server: http://pepsimili.e-nios.com:8080/ state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - server: https://usegalaxy.org.au state: exact - version: 3.0.2+galaxy0 + version: 1.3.1 - server: https://usegalaxy.be/ state: exact - version: 3.0.2+galaxy0 + version: 1.3.1 - server: https://usegalaxy.cz/ state: exact - version: 3.0.2+galaxy0 + version: 1.3.1 - server: https://usegalaxy.eu state: exact - version: 3.0.2+galaxy0 + version: 1.3.1 - server: https://usegalaxy.fr/ - state: missing + state: exact + version: 1.3.1 - server: https://usegalaxy.no/ state: exact - version: 3.0.2+galaxy0 + version: 1.3.1 - server: https://usegalaxy.org state: exact - version: 3.0.2+galaxy0 + version: 1.3.1 - server: https://viralvariant.anses.fr/ state: missing - version: 3.0.2+galaxy0 - - id: toolshed.g2.bx.psu.edu/repos/iuc/transit_gumbel/transit_gumbel/3.0.2+galaxy0 + version: 1.3.1 + - id: toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.0+galaxy0 servers: - server: http://apostl.moffitt.org/ state: missing @@ -27087,11 +8136,16 @@ - server: https://hyperbrowser.uio.no/coloc-stats state: missing - server: https://galaxy.mesocentre.uca.fr - state: missing + state: exact + version: 4.0+galaxy0 - server: https://galaxy.pasteur.fr/ - state: missing + state: inexact + versions: + - 4.9+galaxy1 - server: https://galaxytrakr.org/ - state: missing + state: inexact + versions: + - 1.16.9 - server: http://igg.cloud.ba.infn.it/galaxy state: missing - server: https://galaxy.hyphy.org/ @@ -27102,46 +8156,52 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr - state: missing + state: inexact + versions: + - 4.8+galaxy1 + - 5.2+galaxy2 - server: http://galaxy.inf.ethz.ch state: missing - server: https://palfinder.ls.manchester.ac.uk/ state: missing - server: http://pepsimili.e-nios.com:8080/ state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - server: https://usegalaxy.org.au state: exact - version: 3.0.2+galaxy0 + version: 4.0+galaxy0 - server: https://usegalaxy.be/ state: exact - version: 3.0.2+galaxy0 + version: 4.0+galaxy0 - server: https://usegalaxy.cz/ state: inexact versions: - - 3.0.2+galaxy1 - - 3.2.3+galaxy0 + - 5.1+galaxy0 + - 5.0+galaxy0 + - 4.9+galaxy1 + - 5.2+galaxy2 + - 5.2+galaxy0 + - 5.2+galaxy1 + - 4.4+galaxy0 - server: https://usegalaxy.eu state: exact - version: 3.0.2+galaxy0 + version: 4.0+galaxy0 - server: https://usegalaxy.fr/ - state: missing - - server: https://usegalaxy.no/ state: exact - version: 3.0.2+galaxy0 + version: 4.0+galaxy0 + - server: https://usegalaxy.no/ + state: inexact + versions: + - 1.16.5 - server: https://usegalaxy.org state: exact - version: 3.0.2+galaxy0 + version: 4.0+galaxy0 - server: https://viralvariant.anses.fr/ state: missing - version: 3.0.2+galaxy0 - - id: toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/1.16.5 + version: 4.0+galaxy0 + - id: toolshed.g2.bx.psu.edu/repos/nml/metaspades/metaspades/4.2.0+galaxy0 servers: - server: http://apostl.moffitt.org/ state: missing @@ -27154,21 +8214,12 @@ - server: https://hyperbrowser.uio.no/coloc-stats state: missing - server: https://galaxy.mesocentre.uca.fr - state: inexact - versions: - - 4.9+galaxy1 - - 4.8+galaxy1 - - 5.0+galaxy0 - - 4.0+galaxy0 - - 5.1+galaxy0 + state: exact + version: 4.2.0+galaxy0 - server: https://galaxy.pasteur.fr/ - state: inexact - versions: - - 4.9+galaxy1 + state: missing - server: https://galaxytrakr.org/ - state: inexact - versions: - - 1.16.9 + state: missing - server: http://igg.cloud.ba.infn.it/galaxy state: missing - server: https://galaxy.hyphy.org/ @@ -27179,1838 +8230,1620 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr - state: inexact - versions: - - 4.8+galaxy1 - - 5.2+galaxy2 + state: exact + version: 4.2.0+galaxy0 - server: http://galaxy.inf.ethz.ch state: missing - server: https://palfinder.ls.manchester.ac.uk/ state: missing - server: http://pepsimili.e-nios.com:8080/ state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: inexact - versions: - - 4.4+galaxy0 - server: https://usegalaxy.org.au state: exact - version: 1.16.5 + version: 4.2.0+galaxy0 - server: https://usegalaxy.be/ state: exact - version: 1.16.5 + version: 4.2.0+galaxy0 - server: https://usegalaxy.cz/ - state: inexact - versions: - - 4.9+galaxy1 - - 5.0+galaxy0 - - 5.1+galaxy0 - - 5.2+galaxy2 - - 4.4+galaxy0 - - 5.2+galaxy1 - - 5.2+galaxy0 + state: exact + version: 4.2.0+galaxy0 - server: https://usegalaxy.eu - state: inexact - versions: - - 4.9+galaxy1 - - 4.8+galaxy1 - - 5.0+galaxy0 - - 4.0+galaxy0 - - 5.1+galaxy0 - - 5.2+galaxy2 - - 4.4+galaxy0 - - 1.16.3 - - 3.5+galaxy2 - - 3.5+galaxy0 - - 5.2+galaxy1 - - '1.16' - - 4.0+galaxy1 - - 3.4+galaxy2 - - 5.2+galaxy0 - - 3.7+galaxy0 - - 3.5+galaxy1 - - 4.8+galaxy0 - - 3.4+galaxy0 - - 4.6+galaxy1 - - 3.4+galaxy1 - - '1.6' - - 1.16.1 - - 4.7+galaxy0 - - 1.1.a - - 4.6+galaxy0 - - 4.9+galaxy0 + state: exact + version: 4.2.0+galaxy0 - server: https://usegalaxy.fr/ + state: exact + version: 4.2.0+galaxy0 + - server: https://usegalaxy.no/ state: inexact versions: - - 4.9+galaxy1 - - 4.8+galaxy1 - - 5.0+galaxy0 - - 4.0+galaxy0 - - 5.1+galaxy0 - - 5.2+galaxy2 - - 4.4+galaxy0 - - 3.5+galaxy2 - - 3.5+galaxy0 - - 1.16.8 - - 5.2+galaxy1 - - 4.0+galaxy1 - - 3.4+galaxy2 - - 5.2+galaxy0 - - 3.7+galaxy0 - - 3.5+galaxy1 - - 4.8+galaxy0 - - 3.4+galaxy0 - - 1.16.6 - - 4.6+galaxy1 - - 3.4+galaxy1 - - 4.7+galaxy0 - - 4.6+galaxy0 - - 4.9+galaxy0 - - server: https://usegalaxy.no/ - state: exact - version: 1.16.5 + - 3.9.0 + - 3.15.4+galaxy2 + - 3.15.3+galaxy1 + - 3.9.0.1 + - 3.15.4+galaxy0 + - 3.15.3+galaxy2 + - 3.15.4+galaxy1 - server: https://usegalaxy.org state: exact - version: 1.16.5 + version: 4.2.0+galaxy0 - server: https://viralvariant.anses.fr/ state: missing - version: 1.16.5 - symlink: null + version: 4.2.0+galaxy0 + symlink: true tags: - - bacteria - - tnseq - - essential genes + - assembly + - metagenomics - microgalaxy - time_estimation: 7H - title: Essential genes detection with Transposon insertion sequencing + time: null + time_estimation: 2H + title: Assembly of metagenomic sequencing data tools: - - Cut1 - - Filter1 - - __EXTRACT_DATASET__ - - toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/deeptools_bam_coverage/3.3.2.0.0 - - toolshed.g2.bx.psu.edu/repos/bgruening/find_subsequences/bg_find_subsequences/0.2 - - toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.2 - - toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/1.1.1 - - toolshed.g2.bx.psu.edu/repos/devteam/bowtie_wrappers/bowtie_wrapper/1.2.0 - - toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/1.3.0 - - toolshed.g2.bx.psu.edu/repos/iuc/gff_to_prot/gff_to_prot/3.0.2+galaxy0 - - toolshed.g2.bx.psu.edu/repos/iuc/transit_gumbel/transit_gumbel/3.0.2+galaxy0 - - toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/1.16.5 - topic_name: genome-annotation - topic_name_human: Genome Annotation + - random_lines1 + - toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.1 + - toolshed.g2.bx.psu.edu/repos/bgruening/unique/bg_uniq/0.3 + - toolshed.g2.bx.psu.edu/repos/devteam/bamtools/bamtools/2.5.1+galaxy0 + - toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.4.5+galaxy1 + - toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.5.3+galaxy1 + - toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.73+galaxy0 + - toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/0.8.1+galaxy4 + - toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_info/0.8.1+galaxy2 + - toolshed.g2.bx.psu.edu/repos/iuc/collection_column_join/collection_column_join/0.0.3 + - toolshed.g2.bx.psu.edu/repos/iuc/coverm_contig/coverm_contig/0.7.0+galaxy0 + - toolshed.g2.bx.psu.edu/repos/iuc/filter_tabular/filter_tabular/2.0.0 + - toolshed.g2.bx.psu.edu/repos/iuc/megahit/megahit/1.2.9+galaxy0 + - toolshed.g2.bx.psu.edu/repos/iuc/megahit/megahit/1.2.9+galaxy2 + - 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tool_version: null - type: data_input - uuid: 7af899e7-676b-46ef-8c15-ff7b73b0fe76 - workflow_outputs: - - label: null - output_name: output - uuid: e850fc22-c77f-4bbe-968f-ba44dea4caaf - - annotation: '' - content_id: null - errors: null - id: 3 - input_connections: {} - inputs: - - description: '' - name: staph_aur.fasta - label: staph_aur.fasta - name: staph_aur.fasta - outputs: [] - position: - left: 183 - top: 550 - tool_id: null - tool_state: '{"name": "staph_aur.fasta"}' - tool_version: null - type: data_input - uuid: b522e8dc-3f8f-4e6d-9a2d-c970e25bf6f9 - workflow_outputs: - - label: null - output_name: output - uuid: 793cf25f-49a3-4afa-8165-c5c54e581864 - - annotation: '' + report: + markdown: ' + + # Workflow Execution Report + + + ## Workflow Inputs + + ```galaxy + + invocation_inputs() + + ``` + + + ## Workflow Outputs + + ```galaxy + + invocation_outputs() + + ``` + + + ## Workflow + + ```galaxy + + workflow_display() + + ``` + + ' + subworkflows: false + graph_dot: "digraph main {\n node [fontname=\"Atkinson Hyperlegible\", shape=box,\ + \ color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n edge [fontname=\"\ + Atkinson Hyperlegible\"];\n 0[color=lightblue,label=\"\u2139\uFE0F Input Collection\\\ + nQC controlled reads\"]\n 1[label=\"metaSPAdes\"]\n 0 -> 1 [label=\"output\"\ + ]\n kba8ef041cea5479a8aab38b3d6f0af60[color=lightseagreen,label=\"Output\\\ + nout_ag\"]\n 1 -> kba8ef041cea5479a8aab38b3d6f0af60\n kc3b9a23494d245798eba895e7e49e129[color=lightseagreen,label=\"\ + Output\\nout_ags\"]\n 1 -> kc3b9a23494d245798eba895e7e49e129\n 2[label=\"\ + MEGAHIT\"]\n 0 -> 2 [label=\"output\"]\n k759ce084a80b4a04b74e6e387357e25a[color=lightseagreen,label=\"\ + Output\\noutput\"]\n 2 -> k759ce084a80b4a04b74e6e387357e25a\n 3[label=\"Bowtie2\"\ + ]\n 0 -> 3 [label=\"output\"]\n 2 -> 3 [label=\"output\"]\n k95b806c753ee4a788e24a5794c9c220a[color=lightseagreen,label=\"\ + Output\\nmapping_stats\"]\n 3 -> k95b806c753ee4a788e24a5794c9c220a\n 4[label=\"\ + CoverM contig\"]\n 0 -> 4 [label=\"output\"]\n 2 -> 4 [label=\"output\"]\n\ + \ k51a8a5a9b3bb43b980e57ec7b84a6cd5[color=lightseagreen,label=\"Output\\noutput\"\ + ]\n 4 -> k51a8a5a9b3bb43b980e57ec7b84a6cd5\n 5[label=\"Quast\"]\n 2 -> 5\ + \ [label=\"output\"]\n 0 -> 5 [label=\"output\"]\n k5553b6a6863d4846944f7ed609a3734a[color=lightseagreen,label=\"\ + Output\\nreport_html_meta\"]\n 5 -> k5553b6a6863d4846944f7ed609a3734a\n 6[label=\"\ + megahit contig2fastg\"]\n 2 -> 6 [label=\"output\"]\n 7[label=\"Bandage Image\"\ + ]\n 6 -> 7 [label=\"fastg\"]\n k63861d0be0a64604bd091b0f7ee9d54b[color=lightseagreen,label=\"\ + Output\\noutfile\"]\n 7 -> k63861d0be0a64604bd091b0f7ee9d54b\n 8[label=\"\ + Bandage Info\"]\n 6 -> 8 [label=\"fastg\"]\n 9[label=\"Column join\"]\n 8\ + \ -> 9 [label=\"outfile\"]\n kc882d313508440d48c979552fb7b35ad[color=lightseagreen,label=\"\ + Output\\ntabular_output\"]\n 9 -> kc882d313508440d48c979552fb7b35ad\n}" + history: [] + inputs: + - annotation: Metagenomics reads that have been controlled for quality content_id: null errors: null - id: 4 + id: 0 input_connections: {} inputs: - - description: '' - name: staph_aur.gff3 - label: staph_aur.gff3 - name: staph_aur.gff3 + - description: Metagenomics reads that have been controlled for quality + name: QC controlled reads + label: QC controlled reads + name: Input dataset collection outputs: [] position: - left: 183 - top: 694 + left: 0 + top: 434.0193226947046 tool_id: null - tool_state: '{"name": "staph_aur.gff3"}' + tool_state: '{"optional": false, "tag": null, "collection_type": "list:paired"}' tool_version: null - type: data_input - uuid: e523846f-d4bf-43a8-a6f6-5763dba67f8f - workflow_outputs: - - label: null - output_name: output - uuid: 2e39f099-2536-4a11-add0-9cf3576f1d68 + type: data_collection_input + uuid: 768bd692-5d23-4394-b236-03d68f086b6f + when: null + workflow_outputs: [] + license: MIT + mermaid: "flowchart TD\n 0[\"\u2139\uFE0F Input Collection\\nQC controlled reads\"\ + ];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"metaSPAdes\"];\n 0 -->|output|\ + \ 1;\n ba8ef041-cea5-479a-8aab-38b3d6f0af60[\"Output\\nout_ag\"];\n 1 -->\ + \ ba8ef041-cea5-479a-8aab-38b3d6f0af60;\n style ba8ef041-cea5-479a-8aab-38b3d6f0af60\ + \ stroke:#2c3143,stroke-width:4px;\n c3b9a234-94d2-4579-8eba-895e7e49e129[\"\ + Output\\nout_ags\"];\n 1 --> c3b9a234-94d2-4579-8eba-895e7e49e129;\n style\ + \ c3b9a234-94d2-4579-8eba-895e7e49e129 stroke:#2c3143,stroke-width:4px;\n 2[\"\ + MEGAHIT\"];\n 0 -->|output| 2;\n 759ce084-a80b-4a04-b74e-6e387357e25a[\"Output\\\ + noutput\"];\n 2 --> 759ce084-a80b-4a04-b74e-6e387357e25a;\n style 759ce084-a80b-4a04-b74e-6e387357e25a\ + \ stroke:#2c3143,stroke-width:4px;\n 3[\"Bowtie2\"];\n 0 -->|output| 3;\n\ + \ 2 -->|output| 3;\n 95b806c7-53ee-4a78-8e24-a5794c9c220a[\"Output\\nmapping_stats\"\ + ];\n 3 --> 95b806c7-53ee-4a78-8e24-a5794c9c220a;\n style 95b806c7-53ee-4a78-8e24-a5794c9c220a\ + \ stroke:#2c3143,stroke-width:4px;\n 4[\"CoverM contig\"];\n 0 -->|output|\ + \ 4;\n 2 -->|output| 4;\n 51a8a5a9-b3bb-43b9-80e5-7ec7b84a6cd5[\"Output\\\ + noutput\"];\n 4 --> 51a8a5a9-b3bb-43b9-80e5-7ec7b84a6cd5;\n style 51a8a5a9-b3bb-43b9-80e5-7ec7b84a6cd5\ + \ stroke:#2c3143,stroke-width:4px;\n 5[\"Quast\"];\n 2 -->|output| 5;\n 0\ + \ -->|output| 5;\n 5553b6a6-863d-4846-944f-7ed609a3734a[\"Output\\nreport_html_meta\"\ + ];\n 5 --> 5553b6a6-863d-4846-944f-7ed609a3734a;\n style 5553b6a6-863d-4846-944f-7ed609a3734a\ + \ stroke:#2c3143,stroke-width:4px;\n 6[\"megahit contig2fastg\"];\n 2 -->|output|\ + \ 6;\n 7[\"Bandage Image\"];\n 6 -->|fastg| 7;\n 63861d0b-e0a6-4604-bd09-1b0f7ee9d54b[\"\ + Output\\noutfile\"];\n 7 --> 63861d0b-e0a6-4604-bd09-1b0f7ee9d54b;\n style\ + \ 63861d0b-e0a6-4604-bd09-1b0f7ee9d54b stroke:#2c3143,stroke-width:4px;\n 8[\"\ + Bandage Info\"];\n 6 -->|fastg| 8;\n 9[\"Column join\"];\n 8 -->|outfile|\ + \ 9;\n c882d313-5084-40d4-8c97-9552fb7b35ad[\"Output\\ntabular_output\"];\n\ + \ 9 --> c882d313-5084-40d4-8c97-9552fb7b35ad;\n style c882d313-5084-40d4-8c97-9552fb7b35ad\ + \ stroke:#2c3143,stroke-width:4px;" + modified: 2026-07-01 00:31:39 +0000 + name: Assembly of metagenomic sequencing data + outputs: - 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id: VerenaMoo + joined: 2024-12 + name: Verena Moosmann + page: https://training.galaxyproject.org/training-material/hall-of-fame/VerenaMoo/ + url: https://training.galaxyproject.org/training-material/api/contributors/VerenaMoo.json - affiliations: - - elixir-europe - elixir_node: au - id: tseemann - joined: 2018-06 - name: Torsten Seemann - page: https://training.galaxyproject.org/training-material/hall-of-fame/tseemann/ - url: https://training.galaxyproject.org/training-material/api/contributors/tseemann.json + - AustralianBioCommons + - unimelb + - melbournebioinformatics + email: treynolds@unimelb.edu.au + id: tflowers15 + joined: 2025-03 + name: Tristan Reynolds + orcid: 0000-0002-6606-5953 + page: https://training.galaxyproject.org/training-material/hall-of-fame/tflowers15/ + url: https://training.galaxyproject.org/training-material/api/contributors/tflowers15.json + - avatar: /training-material/shared/images/logo-avans.png + former_members: + - dirowa + - hexylena + id: avans-atgm + joined: 2020-11 + members: + - bazante1 + name: Avans Hogeschool + page: https://training.galaxyproject.org/training-material/hall-of-fame/avans-atgm/ + ror: 015d5s513 + short_name: Avans + url: https://training.galaxyproject.org/training-material/api/organisations/avans-atgm.json + - avatar: /training-material/assets/images/abromics.png + github: false + id: abromics + joined: 2024-01 + name: ABRomics + page: https://training.galaxyproject.org/training-material/hall-of-fame/abromics/ + url: https://training.galaxyproject.org/training-material/api/organisations/abromics.json - avatar: /training-material/shared/images/unimelb_Logo_RGB.png id: unimelb members: @@ -29050,46 +9883,66 @@ name: Australian BioCommons page: https://training.galaxyproject.org/training-material/hall-of-fame/AustralianBioCommons/ url: https://training.galaxyproject.org/training-material/api/organisations/AustralianBioCommons.json - - contact_for_training: true - email: jen@galaxyproject.org - id: jennaj - joined: 2018-06 - linkedin: jennifer.hillman.jackson - location: - country: US - lat: 36.969918 - lon: -122.0226576 - maintainer_contact: https://help.galaxyproject.org/ - matrix: jennaj:matrix.org - name: Jennifer Hillman-Jackson - orcid: 0000-0003-4012-8116 - page: https://training.galaxyproject.org/training-material/hall-of-fame/jennaj/ - twitter: jennaj_io - url: https://training.galaxyproject.org/training-material/api/contributors/jennaj.json - affiliations: - - erasmusmc - - gallantries - - by-covid + - uni-freiburg - elixir-europe - - elixir-converge - contact_for_training: false - elixir_node: nl - former_affiliations: - deNBI - - avans-atgm + - mwk + - biont + contact_for_training: true + elixir_node: de + email: muellert@informatik.uni-freibrug.de + id: teresa-m + joined: 2022-09 + linkedin: teresamueller87 + matrix: teresa-m:matrix.org + name: "Teresa M\xFCller" + orcid: 0000-0003-1252-9684 + page: https://training.galaxyproject.org/training-material/hall-of-fame/teresa-m/ + url: https://training.galaxyproject.org/training-material/api/contributors/teresa-m.json + - affiliations: - uni-freiburg - id: hexylena + - elixir-europe + bluesky: dvarshney.bsky.social + email: varshney@informatik.uni-freiburg.de + id: deeptivarshney + joined: 2022-12 + name: Deepti Varshney + orcid: 0000-0003-0419-6832 + page: https://training.galaxyproject.org/training-material/hall-of-fame/deeptivarshney/ + url: https://training.galaxyproject.org/training-material/api/contributors/deeptivarshney.json + - affiliations: + - elixir-europe + bluesky: abretaud.bsky.social + contact_for_training: true + elixir_node: fr + email: anthony.bretaudeau@irisa.fr + fediverse: https://genomic.social/@abretaud + fediverse_flavor: mastodon + former_affiliations: + - eurosciencegateway + - gallantries + id: abretaud joined: 2017-09 location: - country: NL - lat: 51.91 - lon: 4.46 - maintainer_contact: gitter - matrix: hexylena:matrix.org - name: Helena Rasche - orcid: 0000-0001-9760-8992 - page: https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/ - url: https://training.galaxyproject.org/training-material/api/contributors/hexylena.json + country: FR + lat: 48.11 + lon: -1.64 + matrix: abretaud:matrix.org + name: Anthony Bretaudeau + orcid: 0000-0003-0914-2470 + page: https://training.galaxyproject.org/training-material/hall-of-fame/abretaud/ + url: https://training.galaxyproject.org/training-material/api/contributors/abretaud.json + - elixir_node: de + former_affiliations: + - uni-freiburg + - elixir-europe + id: gallardoalba + joined: 2020-11 + name: "Crist\xF3bal Gallardo" + orcid: 0000-0002-5752-2155 + page: https://training.galaxyproject.org/training-material/hall-of-fame/gallardoalba/ + url: https://training.galaxyproject.org/training-material/api/contributors/gallardoalba.json - affiliations: - deNBI - mwk @@ -29148,6 +10001,34 @@ orcid: 0000-0003-3803-468X page: https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/ url: https://training.galaxyproject.org/training-material/api/contributors/shiltemann.json + - affiliations: + - elixir-europe + contact_for_training: false + elixir_node: nl + former_affiliations: + - deNBI + - avans-atgm + - uni-freiburg + - erasmusmc + - gallantries + - by-covid + - elixir-converge + id: hexylena + joined: 2017-09 + location: + country: NL + lat: 51.91 + lon: 4.46 + maintainer_contact: gitter + matrix: hexylena:matrix.org + name: Helena Rasche + orcid: 0000-0001-9760-8992 + page: https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/ + url: https://training.galaxyproject.org/training-material/api/contributors/hexylena.json + - id: pimarin + name: pimarin + page: https://training.galaxyproject.org/training-material/hall-of-fame/pimarin/ + url: https://training.galaxyproject.org/training-material/api/contributors/pimarin.json - affiliations: - gallantries - ifb @@ -29173,176 +10054,148 @@ page: https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/ twitter: bebatut url: https://training.galaxyproject.org/training-material/api/contributors/bebatut.json + - email: nate@bx.psu.edu + id: natefoo + joined: 2017-12 + matrix: natefoo:matrix.org + name: Nate Coraor + orcid: 0000-0001-8083-2963 + page: https://training.galaxyproject.org/training-material/hall-of-fame/natefoo/ + twitter: natefoo + url: https://training.galaxyproject.org/training-material/api/contributors/natefoo.json - affiliations: + - by-covid + - uni-freiburg - elixir-europe - bluesky: abretaud.bsky.social - contact_for_training: true - elixir_node: fr - email: anthony.bretaudeau@irisa.fr - fediverse: https://genomic.social/@abretaud + - deNBI + - mwk + elixir_node: de + fediverse: https://fediscience.org/@zerodivision fediverse_flavor: mastodon former_affiliations: - eurosciencegateway - - gallantries - id: abretaud + id: wm75 joined: 2017-09 - location: - country: FR - lat: 48.11 - lon: -1.64 - matrix: abretaud:matrix.org - name: Anthony Bretaudeau - orcid: 0000-0003-0914-2470 - page: https://training.galaxyproject.org/training-material/hall-of-fame/abretaud/ - url: https://training.galaxyproject.org/training-material/api/contributors/abretaud.json + matrix: wm75:matrix.org + name: Wolfgang Maier + orcid: 0000-0002-9464-6640 + page: https://training.galaxyproject.org/training-material/hall-of-fame/wm75/ + url: https://training.galaxyproject.org/training-material/api/contributors/wm75.json - affiliations: - - biofair - - earlham + - uni-freiburg - elixir-europe - - elixir-steers - bluesky: nsoranzo.bsky.social - elixir_node: uk - fediverse: https://mstdn.science/@nsoranzo - fediverse_flavor: mastodon - id: nsoranzo - joined: 2017-09 - linkedin: nicola-soranzo-7884125 - location: - country: UK - lat: 52.62188 - lon: 1.21899 - matrix: nsoranzo:matrix.org - name: Nicola Soranzo - orcid: 0000-0003-3627-5340 - page: https://training.galaxyproject.org/training-material/hall-of-fame/nsoranzo/ - twitter: NicolaSoranzo - url: https://training.galaxyproject.org/training-material/api/contributors/nsoranzo.json - - elixir_node: au - email: simon.gladman@unimelb.edu.au - id: slugger70 - in_memoriam: "Simon\ - \ Gladman, system administrator of UseGalaxy.org.au, passed away on November\ - \ 26, 2022\n\nHe was a fantastic teacher, tutorial author, system administrator, and warm\ - \ and welcoming friend. He contributed heavily to the Galaxy Training Network\ - \ and especially the Galaxy Administration community over the years, we will\ - \ miss him dearly. The GTN and GAT would not be what they are today, without\ - \ him.\n\n\u201CHave I told you about my watch?\u201D" - joined: 2017-09 - name: Simon Gladman - orcid: 0000-0002-6100-4385 - page: https://training.galaxyproject.org/training-material/hall-of-fame/slugger70/ - url: https://training.galaxyproject.org/training-material/api/contributors/slugger70.json - - bio: Research at the South African National Bioinformatics Institute - id: pvanheus - joined: 2017-09 - name: Peter van Heusden - orcid: 0000-0001-6553-5274 - page: https://training.galaxyproject.org/training-material/hall-of-fame/pvanheus/ - twitter: pvanheus - url: https://training.galaxyproject.org/training-material/api/contributors/pvanheus.json - - id: njall - joined: 2019-02 - name: Niall Beard - page: https://training.galaxyproject.org/training-material/hall-of-fame/njall/ - url: https://training.galaxyproject.org/training-material/api/contributors/njall.json - - id: mblue9 - joined: 2018-09 - name: Maria Doyle - orcid: 0000-0003-4847-8436 - page: https://training.galaxyproject.org/training-material/hall-of-fame/mblue9/ - url: https://training.galaxyproject.org/training-material/api/contributors/mblue9.json - dir: topics/variant-analysis/tutorials/microbial-variants + - deNBI + - mwk + - materialvitaldigital + email: zierep@informatik.uni-freiburg.de + id: paulzierep + joined: 2023-02 + name: Paul Zierep + orcid: 0000-0003-2982-388X + page: https://training.galaxyproject.org/training-material/hall-of-fame/paulzierep/ + url: https://training.galaxyproject.org/training-material/api/contributors/paulzierep.json + dir: topics/assembly/tutorials/mrsa-illumina edam_ontology: - - topic_0622 - topic_0196 - - topic_2885 + - topic_3673 + - topic_3305 + - topic_0622 - topic_3301 - - topic_0080 - - topic_0199 edam_operation: - - Phylogenetic tree visualisation - - Variant calling - - Genome visualisation - - Phylogenetic tree generation + - Sequence assembly visualisation + - Sequencing quality control + - Genome assembly + - Sequence assembly validation + - Visualisation + - Read mapping + - Sequence contamination filtering edam_topic: - - Genomics - Sequence assembly - - DNA polymorphism + - Whole genome sequencing + - Public health and epidemiology + - Genomics - Microbiology - - Sequence analysis - - Genetic variation exact_supported_servers: - UseGalaxy.be + - UseGalaxy.cz - UseGalaxy.eu + - UseGalaxy.fr - UseGalaxy.org (Main) feedback_mean_note: null feedback_number: 0 + follow_up_training: + - topic_name: genome-annotation + tutorials: + - amr-gene-detection + type: internal + - topic_name: galaxy-interface + tutorials: + - history-to-workflow + type: internal hands_on: true - id: variant-analysis/microbial-variants - inexact_supported_servers: - - GalaxyTrakr - - UseGalaxy.org.au - - UseGalaxy.cz - - UseGalaxy.fr - - UseGalaxy.no + id: assembly/mrsa-illumina + inexact_supported_servers: [] js_requirements: mathjax: null mermaid: false key_points: - - We used a tool called Snippy to call variants between our reads and our reference - genome. - - As our reference genome had annotations, we could see what effect the changes - have on the features as annotated in the reference and therefore make inferences - on the possible changes to the phenotype. - - We used the JBrowse genome browser to visualise what these changes look like. + - Illumina assemblies can be done with Shovill + - It is hard to get the genome in one contig layout: tutorial_hands_on license: CC-BY-4.0 - mod_date: '2026-01-23' + mod_date: '2026-01-05' objectives: - - Find variants between a reference genome and a set of reads - - Visualise the SNP in context of the reads aligned to the genome - - Determine the effect of those variants on genomic features - - Understand if the SNP is potentially affecting the phenotype - pageviews: 25453 - pub_date: '2018-02-26' + - Run tools to evaluate sequencing data on quality and quantity + - Process the output of quality control tools + - Improve the quality of sequencing data + - Run a tool to assemble a bacterial genome using short reads + - Run tools to assess the quality of an assembly + - Understand the outputs of tools to assess the quality of an assembly + pageviews: 18118 + pub_date: '2021-03-24' questions: - - How do we detect differences between a set of reads from a microorganism and a - reference genome - short_id: T00313 + - How to check the quality of the MiSeq data? + - How to perform an assembly of a bacterial genome with MiSeq data? + - How to check the quality of an assembly? + recordings: + - bot-timestamp: 1725486412 + captioners: + - meltemktn + date: '2024-09-04' + galaxy_version: 24.1.2.dev0 + length: 39M + speakers: + - meltemktn + youtube_id: rRHH77qtZHg + short_id: T00036 short_tools: - - jbrowse - - snippy + - bandage_info + - bandage_image + - upload1 + - quast + - fastp + - falco + - shovill slides: false slides_recordings: false - subtopic: introduction supported_servers: exact: - name: UseGalaxy.be url: https://usegalaxy.be/ usegalaxy: false - - name: UseGalaxy.eu - url: https://usegalaxy.eu - usegalaxy: true - - name: UseGalaxy.org (Main) - url: https://usegalaxy.org - usegalaxy: true - inexact: - - name: GalaxyTrakr - url: https://galaxytrakr.org/ - usegalaxy: false - - name: UseGalaxy.org.au - url: https://usegalaxy.org.au - usegalaxy: true - name: UseGalaxy.cz url: https://usegalaxy.cz/ usegalaxy: false + - name: UseGalaxy.eu + url: https://usegalaxy.eu + usegalaxy: true - name: UseGalaxy.fr url: https://usegalaxy.fr/ usegalaxy: true - - name: UseGalaxy.no - url: https://usegalaxy.no/ - usegalaxy: false + - name: UseGalaxy.org (Main) + url: https://usegalaxy.org + usegalaxy: true + inexact: [] supported_servers_matrix: servers: - name: APOSTL @@ -29384,9 +10237,6 @@ - name: IPK Galaxy Blast Suite url: https://galaxy-web.ipk-gatersleben.de usegalaxy: false - - name: Lebanese University Galaxy - url: http://galaxy.ul.edu.lb/ - usegalaxy: false - name: Mandoiu Lab url: https://neo.engr.uconn.edu/ usegalaxy: false @@ -29402,9 +10252,6 @@ - name: PepSimili url: http://pepsimili.e-nios.com:8080/ usegalaxy: false - 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server: https://hyperbrowser.uio.no/coloc-stats + state: missing + - server: https://galaxy.mesocentre.uca.fr + state: exact + version: 0.23.2+galaxy0 + - server: https://galaxy.pasteur.fr/ + state: exact + version: 0.23.2+galaxy0 - server: https://galaxytrakr.org/ state: inexact versions: - - 1.16.11+galaxy1 + - 1.0.1+galaxy3 + - 1.3.3+galaxy0 + - 1.0.1+galaxy0 - server: http://igg.cloud.ba.infn.it/galaxy state: missing - server: https://galaxy.hyphy.org/ @@ -29465,56 +10505,118 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr state: inexact versions: - - 1.16.11+galaxy1 + - 1.3.3+galaxy0 - server: http://galaxy.inf.ethz.ch state: missing - server: https://palfinder.ls.manchester.ac.uk/ state: missing - server: http://pepsimili.e-nios.com:8080/ state: missing - - server: https://galaxy.bio.di.uminho.pt/ - 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server: https://iris.angers.inra.fr/galaxypub-cfbp + state: missing + - server: https://hyperbrowser.uio.no/coloc-stats + state: missing + - server: https://galaxy.mesocentre.uca.fr + state: exact + version: 1.0.1+galaxy3 + - server: https://galaxy.pasteur.fr/ state: inexact versions: - - 1.16.11+galaxy1 - - 1.16.9+galaxy0 - - 1.16.8+galaxy1 - - 1.16.10+galaxy0 - - 1.16.5+galaxy7 + - 0.23.2+galaxy0 + - server: https://galaxytrakr.org/ + state: exact + version: 1.0.1+galaxy3 + - server: http://igg.cloud.ba.infn.it/galaxy + state: missing + - server: https://galaxy.hyphy.org/ + state: missing + - server: https://www.immportgalaxy.org/ + state: missing + - server: http://galaxy.interactomix.com/ + state: missing + - server: https://galaxy-web.ipk-gatersleben.de + state: missing + - server: https://neo.engr.uconn.edu/ + state: missing + - server: https://mississippi.sorbonne-universite.fr + state: inexact + versions: + - 1.3.3+galaxy0 + - server: http://galaxy.inf.ethz.ch + state: missing + - server: https://palfinder.ls.manchester.ac.uk/ + state: missing + - server: http://pepsimili.e-nios.com:8080/ + state: missing + - server: https://usegalaxy.org.au + state: exact + version: 1.0.1+galaxy3 + - server: https://usegalaxy.be/ + state: exact + version: 1.0.1+galaxy3 + - server: https://usegalaxy.cz/ + state: exact + version: 1.0.1+galaxy3 + - server: https://usegalaxy.eu + state: exact + version: 1.0.1+galaxy3 + - server: https://usegalaxy.fr/ + state: exact + version: 1.0.1+galaxy3 - server: https://usegalaxy.no/ state: inexact versions: - - 1.16.11+galaxy1 - - 1.16.9+galaxy0 - - 1.16.10+galaxy0 + - 0.20.1+galaxy0 + - 0.23.2+galaxy0 + - 0.19.5+galaxy1 - server: https://usegalaxy.org state: exact - version: 0.7.0.3 + version: 1.0.1+galaxy3 - server: https://viralvariant.anses.fr/ - state: missing - version: 0.7.0.3 - - id: toolshed.g2.bx.psu.edu/repos/iuc/snippy/snippy/3.2 + state: inexact + versions: + - 0.23.2+galaxy0 + - 1.0.1+galaxy2 + version: 1.0.1+galaxy3 + - id: toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.2.0+galaxy1 servers: - server: http://apostl.moffitt.org/ state: missing @@ -29527,13 +10629,80 @@ - server: https://hyperbrowser.uio.no/coloc-stats state: missing - server: https://galaxy.mesocentre.uca.fr - state: missing + state: exact + version: 5.2.0+galaxy1 - server: https://galaxy.pasteur.fr/ state: missing - server: https://galaxytrakr.org/ + state: exact + version: 5.2.0+galaxy1 + - server: http://igg.cloud.ba.infn.it/galaxy + state: missing + - server: https://galaxy.hyphy.org/ + state: missing + - server: https://www.immportgalaxy.org/ + state: missing + - server: http://galaxy.interactomix.com/ + state: missing + - server: https://galaxy-web.ipk-gatersleben.de + state: missing + - server: https://neo.engr.uconn.edu/ + state: missing + - server: https://mississippi.sorbonne-universite.fr + state: exact + version: 5.2.0+galaxy1 + - server: http://galaxy.inf.ethz.ch + state: missing + - server: https://palfinder.ls.manchester.ac.uk/ + state: missing + - server: http://pepsimili.e-nios.com:8080/ + state: missing + - server: https://usegalaxy.org.au + state: exact + version: 5.2.0+galaxy1 + - server: https://usegalaxy.be/ + state: exact + version: 5.2.0+galaxy1 + - server: https://usegalaxy.cz/ + state: exact + version: 5.2.0+galaxy1 + - server: https://usegalaxy.eu + state: exact + version: 5.2.0+galaxy1 + - server: https://usegalaxy.fr/ + state: exact + version: 5.2.0+galaxy1 + - server: https://usegalaxy.no/ + state: exact + version: 5.2.0+galaxy1 + - server: https://usegalaxy.org + state: exact + version: 5.2.0+galaxy1 + - server: https://viralvariant.anses.fr/ + state: missing + version: 5.2.0+galaxy1 + - id: toolshed.g2.bx.psu.edu/repos/iuc/shovill/shovill/1.1.0+galaxy1 + servers: + - server: http://apostl.moffitt.org/ + state: missing + - server: http://mbac.gmu.edu:8080/ + state: missing + - server: https://vm-chemflow-francegrille.eu/ + state: missing + - server: https://iris.angers.inra.fr/galaxypub-cfbp + state: missing + - server: https://hyperbrowser.uio.no/coloc-stats + state: missing + - server: https://galaxy.mesocentre.uca.fr + state: exact + version: 1.1.0+galaxy1 + - server: https://galaxy.pasteur.fr/ state: inexact versions: - - 4.6.0+galaxy0 + - 1.4.2+galaxy0 + - server: https://galaxytrakr.org/ + state: exact + version: 1.1.0+galaxy1 - server: http://igg.cloud.ba.infn.it/galaxy state: missing - server: https://galaxy.hyphy.org/ @@ -29544,8 +10713,6 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr @@ -29556,116 +10723,295 @@ state: missing - server: http://pepsimili.e-nios.com:8080/ state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - server: https://usegalaxy.org.au - state: inexact - versions: - - 4.6.0+galaxy0 - - 4.5.0 - - 4.5.0+galaxy1 + state: exact + version: 1.1.0+galaxy1 - server: https://usegalaxy.be/ state: exact - version: '3.2' + version: 1.1.0+galaxy1 - server: https://usegalaxy.cz/ - state: inexact - versions: - - 4.6.0+galaxy0 + state: exact + version: 1.1.0+galaxy1 - server: https://usegalaxy.eu state: exact - version: '3.2' + version: 1.1.0+galaxy1 - server: https://usegalaxy.fr/ + state: exact + version: 1.1.0+galaxy1 + - server: https://usegalaxy.no/ + state: exact + version: 1.1.0+galaxy1 + - server: https://usegalaxy.org + state: exact + version: 1.1.0+galaxy1 + - server: https://viralvariant.anses.fr/ + state: missing + version: 1.1.0+galaxy1 + - id: toolshed.g2.bx.psu.edu/repos/iuc/shovill/shovill/1.1.0+galaxy2 + servers: + - server: http://apostl.moffitt.org/ + state: missing + - server: http://mbac.gmu.edu:8080/ + state: missing + - server: https://vm-chemflow-francegrille.eu/ + state: missing + - server: https://iris.angers.inra.fr/galaxypub-cfbp + state: missing + - server: https://hyperbrowser.uio.no/coloc-stats + state: missing + - server: https://galaxy.mesocentre.uca.fr + state: exact + version: 1.1.0+galaxy2 + - server: https://galaxy.pasteur.fr/ state: inexact versions: - - 4.6.0+galaxy0 - - server: https://usegalaxy.no/ + - 1.4.2+galaxy0 + - server: https://galaxytrakr.org/ state: inexact versions: - - 4.6.0+galaxy0 + - 1.1.0+galaxy1 + - 1.4.2+galaxy0 + - server: http://igg.cloud.ba.infn.it/galaxy + state: missing + - server: https://galaxy.hyphy.org/ + state: missing + - server: https://www.immportgalaxy.org/ + state: missing + - server: http://galaxy.interactomix.com/ + state: missing + - server: https://galaxy-web.ipk-gatersleben.de + state: missing + - server: https://neo.engr.uconn.edu/ + state: missing + - server: https://mississippi.sorbonne-universite.fr + state: missing + - server: http://galaxy.inf.ethz.ch + state: missing + - server: https://palfinder.ls.manchester.ac.uk/ + state: missing + - server: http://pepsimili.e-nios.com:8080/ + state: missing + - server: https://usegalaxy.org.au + state: exact + version: 1.1.0+galaxy2 + - server: https://usegalaxy.be/ + state: exact + version: 1.1.0+galaxy2 + - server: https://usegalaxy.cz/ + state: exact + version: 1.1.0+galaxy2 + - server: https://usegalaxy.eu + state: exact + version: 1.1.0+galaxy2 + - server: https://usegalaxy.fr/ + state: exact + version: 1.1.0+galaxy2 + - server: https://usegalaxy.no/ + state: exact + version: 1.1.0+galaxy2 - server: https://usegalaxy.org state: exact - version: '3.2' + version: 1.1.0+galaxy2 - server: https://viralvariant.anses.fr/ state: missing - version: '3.2' + version: 1.1.0+galaxy2 + - id: upload1 + servers: + - server: http://apostl.moffitt.org/ + state: local + - server: http://mbac.gmu.edu:8080/ + state: local + - server: https://vm-chemflow-francegrille.eu/ + state: local + - server: https://iris.angers.inra.fr/galaxypub-cfbp + state: local + - server: https://hyperbrowser.uio.no/coloc-stats + state: local + - server: https://galaxy.mesocentre.uca.fr + state: local + - server: https://galaxy.pasteur.fr/ + state: local + - server: https://galaxytrakr.org/ + state: local + - server: http://igg.cloud.ba.infn.it/galaxy + state: local + - server: https://galaxy.hyphy.org/ + state: local + - server: https://www.immportgalaxy.org/ + state: local + - server: http://galaxy.interactomix.com/ + state: local + - server: https://galaxy-web.ipk-gatersleben.de + state: local + - server: https://neo.engr.uconn.edu/ + state: local + - server: https://mississippi.sorbonne-universite.fr + state: local + - server: http://galaxy.inf.ethz.ch + state: local + - server: https://palfinder.ls.manchester.ac.uk/ + state: local + - server: http://pepsimili.e-nios.com:8080/ + state: local + - server: https://usegalaxy.org.au + state: missing + - server: https://usegalaxy.be/ + state: local + - server: https://usegalaxy.cz/ + state: local + - server: https://usegalaxy.eu + state: local + - server: https://usegalaxy.fr/ + state: local + - server: https://usegalaxy.no/ + state: local + - server: https://usegalaxy.org + state: local + - server: https://viralvariant.anses.fr/ + state: local + version: local symlink: null tags: - - prokaryote + - illumina + - assembly - microgalaxy - - gmod - - jbrowse1 - time_estimation: 45m - title: Microbial Variant Calling + time: null + time_estimation: 2h + title: Genome Assembly of a bacterial genome (MRSA) sequenced using Illumina MiSeq + Data tools: - - toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/0.7.0.3 - - toolshed.g2.bx.psu.edu/repos/iuc/snippy/snippy/3.2 - topic_name: variant-analysis - topic_name_human: Variant Analysis + - toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/2022.09+galaxy4 + - toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_info/2022.09+galaxy2 + - toolshed.g2.bx.psu.edu/repos/iuc/falco/falco/1.2.4+galaxy0 + - toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.2+galaxy0 + - toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/1.0.1+galaxy3 + - toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.2.0+galaxy1 + - toolshed.g2.bx.psu.edu/repos/iuc/shovill/shovill/1.1.0+galaxy1 + - toolshed.g2.bx.psu.edu/repos/iuc/shovill/shovill/1.1.0+galaxy2 + - upload1 + topic_name: assembly + topic_name_human: Assembly tours: false translations: slides: [] tutorial: [] video: false - tutorial_name: microbial-variants + tutorial_name: mrsa-illumina type: tutorial - url: https://training.galaxyproject.org//topics/variant-analysis/tutorials/microbial-variants/tutorial.html + url: https://training.galaxyproject.org//topics/assembly/tutorials/mrsa-illumina/tutorial.html urls: - hands_on: https://training.galaxyproject.org/training-material/api/topics/variant-analysis/tutorials/microbial-variants/tutorial.json - slides: https://training.galaxyproject.org/training-material/api/topics/variant-analysis/tutorials/microbial-variants/tutorial.json - version: 25 - video: false - video_versions: 0 + hands_on: https://training.galaxyproject.org/training-material/api/topics/assembly/tutorials/mrsa-illumina/tutorial.json + slides: https://training.galaxyproject.org/training-material/api/topics/assembly/tutorials/mrsa-illumina/tutorial.json + version: 18 + video: true + video_versions: 1 video_view: 0 - visit_duration: 300 - visitors: 16133 + visit_duration: 575 + visitors: 11970 workflows: - - creators: [] - description: Microbial Variant Calling + - creators: + - class: Person + identifier: https://orcid.org/0000-0003-2255-1631 + name: Bazante Sanders + - class: Person + identifier: https://orcid.org/0000-0001-9852-1987 + name: "B\xE9r\xE9nice Batut" + - class: Person + identifier: 0000-0002-6606-5953 + name: Tristan Reynolds + description: Genome Assembly of MRSA using Illumina MiSeq Data features: comments: false parameters: false - report: null + report: + markdown: ' + + # Workflow Execution Report + + + ## Workflow Inputs + + ```galaxy + + invocation_inputs() + + ``` + + + ## Workflow Outputs + + ```galaxy + + invocation_outputs() + + ``` + + + ## Workflow + + ```galaxy + + workflow_display() + + ``` + + ' subworkflows: false graph_dot: "digraph main {\n node [fontname=\"Atkinson Hyperlegible\", shape=box,\ \ color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n edge [fontname=\"\ - Atkinson Hyperlegible\"];\n 0[color=lightblue,label=\"\u2139\uFE0F Input Dataset\\\ - nInput dataset\"]\n 1[color=lightblue,label=\"\u2139\uFE0F Input Dataset\\\ - nInput dataset\"]\n 2[color=lightblue,label=\"\u2139\uFE0F Input Dataset\\\ - nInput dataset\"]\n 3[color=lightblue,label=\"\u2139\uFE0F Input Dataset\\\ - nInput dataset\"]\n 4[color=lightblue,label=\"\u2139\uFE0F Input Dataset\\\ - nInput dataset\"]\n 5[label=\"snippy\"]\n 0 -> 5 [label=\"output\"]\n 1 ->\ - \ 5 [label=\"output\"]\n 3 -> 5 [label=\"output\"]\n k01897a3305344731ad5b8cbc4a3974a3[color=lightseagreen,label=\"\ - Output\\nsnippy_fasta\"]\n 5 -> k01897a3305344731ad5b8cbc4a3974a3\n kf02fec14e3fb46e68dbd9a47ed4eedf6[color=lightseagreen,label=\"\ - Output\\nsnippy_tabular\"]\n 5 -> kf02fec14e3fb46e68dbd9a47ed4eedf6\n 6[label=\"\ - JBrowse\"]\n 5 -> 6 [label=\"snpgff\"]\n 4 -> 6 [label=\"output\"]\n 5 ->\ - \ 6 [label=\"snpsbam\"]\n 2 -> 6 [label=\"output\"]\n k9e5db34752354e8387830e91835ad7f3[color=lightseagreen,label=\"\ - Output\\njbrowse_html\"]\n 6 -> k9e5db34752354e8387830e91835ad7f3\n}" + Atkinson Hyperlegible\"];\n 0[color=lightblue,label=\"\u2139\uFE0F Input Collection\\\ + nInput Paired End Collection\"]\n 1[label=\"fastp\"]\n 0 -> 1 [label=\"output\"\ + ]\n k33eb25c09f2f4cbf8646db053deec7a4[color=lightseagreen,label=\"Output\\\ + nfastp_json\"]\n 1 -> k33eb25c09f2f4cbf8646db053deec7a4\n 2[label=\"Falco\"\ + ]\n 0 -> 2 [label=\"output\"]\n 3[label=\"Shovill\"]\n 1 -> 3 [label=\"output_paired_coll\"\ + ]\n k225015a77ccc4d68a8680e826069dfca[color=lightseagreen,label=\"Output\\\ + nshovill_log\"]\n 3 -> k225015a77ccc4d68a8680e826069dfca\n 4[label=\"Quast\"\ + ]\n 3 -> 4 [label=\"contigs\"]\n k2c7b1b247ac548429d14be65e433e787[color=lightseagreen,label=\"\ + Output\\nquast_output\"]\n 4 -> k2c7b1b247ac548429d14be65e433e787\n 5[label=\"\ + Bandage Image\"]\n 3 -> 5 [label=\"contigs_graph\"]\n 6[label=\"Bandage Info\"\ + ]\n 3 -> 6 [label=\"contigs_graph\"]\n k99656c96011a4ce0bb5b8ee1e4541eb1[color=lightseagreen,label=\"\ + Output\\nbandage_info_output\"]\n 6 -> k99656c96011a4ce0bb5b8ee1e4541eb1\n}" history: - - hash: 667ff3de9c4e13d341a6d864bd6dc826ef15ca04 - message: annotation + - hash: c2bf6f178fef000d5cb44eb66371b894ed1a8d9e + message: Update workflow and workflow tests + num: 8 + short_hash: c2bf6f178 + unix: '1766097170' + - hash: 597f8ce954083c7cd4e43765b6c4709619637e6a + message: Add Bazante's ORCID + num: 7 + short_hash: 597f8ce95 + unix: '1706018263' + - hash: 03e4290900ade23b2dffb3f61ea2875a64f2c396 + message: Fix workflows + num: 6 + short_hash: 03e429090 + unix: '1706004257' + - hash: c88bcbb6f04ad1847e0747f7fb9256ee0ec858de + message: Add license and creator to workflows num: 5 - short_hash: 667ff3de9 - unix: '1579690769' - - hash: eb4d724e0064c77beb20efa626a0f28fd0500676 - message: Workflow renaming + short_hash: c88bcbb6f + unix: '1705678137' + - hash: 5fbcc03b0d2408af8c03f0c7867791b47b4cceff + message: Update the MRSA short-read assembly tutorial num: 4 - short_hash: eb4d724e0 - unix: '1579084895' - - hash: dfb97360348d32210f7c4bae68f1154a2336e520 - message: annotate workflow outputs + short_hash: 5fbcc03b0 + unix: '1705072112' + - hash: 31848c0ae9109d020ddee510ad5a1c374c3df96e + message: fix linting issues num: 3 - short_hash: dfb973603 - unix: '1526109637' - - hash: 8803cca01f5e6e62243a1cefbe21e701e89151af - message: pretty'fy workflow + short_hash: 31848c0ae + unix: '1610039782' + - hash: 9c83730d5b61b1ed51890ee8c00dbf73834d7b54 + message: Finish illumina version num: 2 - short_hash: 8803cca01 - unix: '1526109452' - - hash: 5a1bff42297572d14d33b4e41de89694a6957676 - message: Add some love to microbial variant calling tutorial (#732) + short_hash: 9c83730d5 + unix: '1610038238' + - hash: c1175777fc34b261481e16516de8fde7c890c4ae + message: Add Illumina version of tutorial num: 1 - short_hash: 5a1bff422 - unix: '1523043969' + short_hash: c1175777f + unix: '1608293515' inputs: - annotation: '' content_id: null @@ -29674,440 +11020,454 @@ input_connections: {} inputs: - description: '' - name: mutant_R1 - label: null - name: Input dataset + name: Input Paired End Collection + label: Input Paired End Collection + name: Input dataset collection outputs: [] position: - left: 10 - top: 10 + left: 0.0 + top: 293.93356048202895 tool_id: null - tool_state: '{"name": "mutant_R1"}' + tool_state: '{"optional": false, "tag": null, "collection_type": "list:paired", + "fields": null}' tool_version: null - type: data_input - uuid: f78a5562-288a-49fa-a8e4-a6facf09bffe + type: data_collection_input + uuid: 52f613fe-2dac-4144-b467-c0a8d85795ee + when: null workflow_outputs: [] + license: MIT + mermaid: "flowchart TD\n 0[\"\u2139\uFE0F Input Collection\\nInput Paired End\ + \ Collection\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"fastp\"\ + ];\n 0 -->|output| 1;\n 33eb25c0-9f2f-4cbf-8646-db053deec7a4[\"Output\\nfastp_json\"\ + ];\n 1 --> 33eb25c0-9f2f-4cbf-8646-db053deec7a4;\n style 33eb25c0-9f2f-4cbf-8646-db053deec7a4\ + \ stroke:#2c3143,stroke-width:4px;\n 2[\"Falco\"];\n 0 -->|output| 2;\n 3[\"\ + Shovill\"];\n 1 -->|output_paired_coll| 3;\n 225015a7-7ccc-4d68-a868-0e826069dfca[\"\ + Output\\nshovill_log\"];\n 3 --> 225015a7-7ccc-4d68-a868-0e826069dfca;\n style\ + \ 225015a7-7ccc-4d68-a868-0e826069dfca stroke:#2c3143,stroke-width:4px;\n 4[\"\ + Quast\"];\n 3 -->|contigs| 4;\n 2c7b1b24-7ac5-4842-9d14-be65e433e787[\"Output\\\ + nquast_output\"];\n 4 --> 2c7b1b24-7ac5-4842-9d14-be65e433e787;\n style 2c7b1b24-7ac5-4842-9d14-be65e433e787\ + \ stroke:#2c3143,stroke-width:4px;\n 5[\"Bandage Image\"];\n 3 -->|contigs_graph|\ + \ 5;\n 6[\"Bandage Info\"];\n 3 -->|contigs_graph| 6;\n 99656c96-011a-4ce0-bb5b-8ee1e4541eb1[\"\ + Output\\nbandage_info_output\"];\n 6 --> 99656c96-011a-4ce0-bb5b-8ee1e4541eb1;\n\ + \ style 99656c96-011a-4ce0-bb5b-8ee1e4541eb1 stroke:#2c3143,stroke-width:4px;" + modified: 2026-07-01 00:31:37 +0000 + name: Genome Assembly of MRSA using Illumina MiSeq Data + outputs: - 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bebatut + editing: + - clsiguret + - tflowers15 + funding: + - abromics + - unimelb + - melbournebioinformatics + - AustralianBioCommons + reviewing: + - hexylena + - shiltemann contributors: + - affiliations: + - gallantries + - ifb + - elixir-europe + contact_for_training: true + elixir_node: fr + email: berenice.batut@gmail.com + fediverse: https://piaille.fr/@bebatut + fediverse_flavor: mastodon + former_affiliations: + - uni-freiburg + - deNBI + id: bebatut + joined: 2017-09 + linkedin: berenicebatut + location: + country: FR + lat: 45.77 + lon: 3.08 + matrix: bebatut:matrix.org + name: "B\xE9r\xE9nice Batut" + orcid: 0000-0001-9852-1987 + page: https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/ + twitter: bebatut + url: https://training.galaxyproject.org/training-material/api/contributors/bebatut.json + - affiliations: + - ifb + - elixir-europe + elixir_node: fr + email: clea.siguret@gmail.com + id: clsiguret + joined: 2024-04 + linkedin: "cl\xE9a-siguret-58423b107" + matrix: clsiguret:matrix.org + name: Clea Siguret + orcid: 0009-0005-6140-0379 + page: https://training.galaxyproject.org/training-material/hall-of-fame/clsiguret/ + url: https://training.galaxyproject.org/training-material/api/contributors/clsiguret.json + - affiliations: + - AustralianBioCommons + - unimelb + - melbournebioinformatics + email: treynolds@unimelb.edu.au + id: tflowers15 + joined: 2025-03 + name: Tristan Reynolds + orcid: 0000-0002-6606-5953 + page: https://training.galaxyproject.org/training-material/hall-of-fame/tflowers15/ + url: https://training.galaxyproject.org/training-material/api/contributors/tflowers15.json + - avatar: /training-material/assets/images/abromics.png + github: false + id: abromics + joined: 2024-01 + name: ABRomics + page: https://training.galaxyproject.org/training-material/hall-of-fame/abromics/ + url: https://training.galaxyproject.org/training-material/api/organisations/abromics.json + - avatar: /training-material/shared/images/unimelb_Logo_RGB.png + id: unimelb + members: + - annasyme + - cat-bro + - GraceAHall + - supernord + - tflowers15 + - uwwint + - vinisalazar + name: The University of Melbourne + page: https://training.galaxyproject.org/training-material/hall-of-fame/unimelb/ + url: https://training.galaxyproject.org/training-material/api/organisations/unimelb.json + - avatar: /training-material/shared/images/Melbourne-Bioinformatics-logo.png + former_members: + - annasyme + id: melbournebioinformatics + members: + - GraceAHall + - tflowers15 + - vinisalazar + name: Melbourne Bioinformatics + page: https://training.galaxyproject.org/training-material/hall-of-fame/melbournebioinformatics/ + url: https://training.galaxyproject.org/training-material/api/organisations/melbournebioinformatics.json + - avatar: /training-material/shared/images/Australian-Biocommons-Favicon-RGB.png + id: AustralianBioCommons + members: + - annasyme + - burkemlou + - cat-bro + - igormakunin + - mthang + - PatCapon39 + - supernord + - tflowers15 + - uwwint + name: Australian BioCommons + page: https://training.galaxyproject.org/training-material/hall-of-fame/AustralianBioCommons/ + url: https://training.galaxyproject.org/training-material/api/organisations/AustralianBioCommons.json + - affiliations: + - elixir-europe + contact_for_training: false + elixir_node: nl + former_affiliations: + - deNBI + - avans-atgm + - uni-freiburg + - erasmusmc + - gallantries + - by-covid + - elixir-converge + id: hexylena + joined: 2017-09 + location: + country: NL + lat: 51.91 + lon: 4.46 + maintainer_contact: gitter + matrix: hexylena:matrix.org + name: Helena Rasche + orcid: 0000-0001-9760-8992 + page: https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/ + url: https://training.galaxyproject.org/training-material/api/contributors/hexylena.json - affiliations: - uni-freiburg - nfdi4plants @@ -30136,128 +11496,86 @@ orcid: 0000-0003-3803-468X page: https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/ url: https://training.galaxyproject.org/training-material/api/contributors/shiltemann.json - - affiliations: - - gallantries - - ifb - - elixir-europe - contact_for_training: true - elixir_node: fr - email: berenice.batut@gmail.com - fediverse: https://piaille.fr/@bebatut - fediverse_flavor: mastodon - former_affiliations: - - uni-freiburg - - deNBI - id: bebatut - joined: 2017-09 - linkedin: berenicebatut - location: - country: FR - lat: 45.77 - lon: 3.08 - matrix: bebatut:matrix.org - name: "B\xE9r\xE9nice Batut" - orcid: 0000-0001-9852-1987 - page: https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/ - twitter: bebatut - url: https://training.galaxyproject.org/training-material/api/contributors/bebatut.json - dir: topics/microbiome/tutorials/general-tutorial + dir: topics/ecology/tutorials/bacterial-isolate-species-contamination-checking edam_ontology: - - topic_3174 + - topic_3673 + - topic_0622 + - topic_3301 - topic_3697 - - topic_0637 - - topic_0080 - - topic_4038 edam_operation: - - Phylogenetic analysis + - Expression analysis + - Cross-assembly + - Statistical calculation - Taxonomic classification - - Sequencing quality control - - Visualisation - - Sequence read processing - - Sequence clustering - - DNA barcoding edam_topic: - - Metagenomics + - Whole genome sequencing + - Genomics + - Microbiology - Microbial ecology - - Taxonomy - - Sequence analysis - - Metabarcoding - exact_supported_servers: [] + exact_supported_servers: + - UseGalaxy.eu + - UseGalaxy.fr feedback_mean_note: null feedback_number: 0 hands_on: true - id: microbiome/general-tutorial + id: ecology/bacterial-isolate-species-contamination-checking inexact_supported_servers: - - UseGalaxy.org.au - - UseGalaxy.fr - - UseGalaxy.no + - Galaxy@AuBi + - GalaxyTrakr + - UseGalaxy.be + - UseGalaxy.cz + - UseGalaxy.org (Main) js_requirements: mathjax: null mermaid: false key_points: - - With amplicon data, we can extract information about the studied community structure - - With shotgun data, we can extract information about the studied community structure - and also the functions realised by the community - - The tools used to analyze amplicon and shotgun data are different, except for - the visualisation - - Metagenomics data analyses are complex and time-consuming + - Kraken assigns taxons to sequences + - Bracken extracts species from Kraken assignations + - Recentrifuge extracts stats and creates visualization from Kraken report layout: tutorial_hands_on + level: Introductory license: CC-BY-4.0 - mod_date: '2024-08-09' + mod_date: '2026-04-08' objectives: - - Choosing the best approach to analyze metagenomics data - - Selection of tools to analyze amplicon data or shotgun data - - Visualisation of a community structure - pageviews: 14970 - pub_date: '2017-06-22' + - Run a series of tool to identify species in bacterial isolate sequencing data + - Visualize the species abundance + pageviews: 1415 + pub_date: '2024-03-04' questions: - - How to analyze metagenomics data? - - What information can be extracted of metagenomics data? - - What is the difference between amplicon and shotgun data? - - What are the difference in the analyses of amplicon and shotgun data? - redirect_from: - - /topics/metagenomics/tutorials/general-tutorial/tutorial - - /short/microbiome/general-tutorial - - /short/T00201 - - /short/T00385 - short_id: T00385 + - What are the species in bacterial isolate sequencing data? + short_id: T00423 short_tools: - 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name: UseGalaxy.be + url: https://usegalaxy.be/ + usegalaxy: false + - name: UseGalaxy.cz + url: https://usegalaxy.cz/ + usegalaxy: false + - name: UseGalaxy.eu + url: https://usegalaxy.eu + usegalaxy: true + - name: UseGalaxy.fr + url: https://usegalaxy.fr/ + usegalaxy: true + - name: UseGalaxy.no + url: https://usegalaxy.no/ + usegalaxy: false + - name: UseGalaxy.org (Main) + url: https://usegalaxy.org + usegalaxy: true + - name: Viral Variant Visualizer (VVV) + url: https://viralvariant.anses.fr/ + usegalaxy: false + tools: + - id: toolshed.g2.bx.psu.edu/repos/iuc/bracken/est_abundance/2.9+galaxy0 servers: - server: http://apostl.moffitt.org/ state: missing @@ -30852,83 +11672,17 @@ - server: https://galaxy.mesocentre.uca.fr state: inexact versions: - - 1.39.5.0 + - 3.0+galaxy0 + - 2.8+galaxy0 + - 2.7+galaxy1 + - 3.1+galaxy0 + - 2.6.1+galaxy0 - server: https://galaxy.pasteur.fr/ state: missing - server: https://galaxytrakr.org/ - state: missing - - server: http://igg.cloud.ba.infn.it/galaxy - 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state: inexact - versions: - - 1.39.5.0 - - server: https://usegalaxy.no/ - state: inexact - versions: - - 1.39.5.0 - - server: https://usegalaxy.org - state: exact - version: 1.36.1.0 - - server: https://viralvariant.anses.fr/ - state: missing - version: 1.36.1.0 - - id: toolshed.g2.bx.psu.edu/repos/iuc/mothur_classify_seqs/mothur_classify_seqs/1.36.1.0 - servers: - - server: http://apostl.moffitt.org/ - state: missing - - server: http://mbac.gmu.edu:8080/ - state: missing - - server: https://vm-chemflow-francegrille.eu/ - state: missing - - server: https://iris.angers.inra.fr/galaxypub-cfbp - state: missing - - server: https://hyperbrowser.uio.no/coloc-stats - state: missing - - server: https://galaxy.mesocentre.uca.fr state: inexact versions: - - 1.39.5.0 - - server: https://galaxy.pasteur.fr/ - state: missing - - server: https://galaxytrakr.org/ - state: missing + - 3.1+galaxy0 - server: http://igg.cloud.ba.infn.it/galaxy state: missing - server: https://galaxy.hyphy.org/ @@ -30939,8 +11693,6 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr @@ -30951,37 +11703,37 @@ state: missing - server: http://pepsimili.e-nios.com:8080/ state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - server: https://usegalaxy.org.au + state: exact + version: 2.9+galaxy0 + - server: https://usegalaxy.be/ state: inexact versions: - - 1.39.5.0 - - server: https://usegalaxy.be/ - state: exact - version: 1.36.1.0 + - 2.8+galaxy0 + - 3.1+galaxy0 - server: https://usegalaxy.cz/ state: inexact versions: - - 1.39.5.0 + - 2.8+galaxy0 + - 3.1+galaxy0 - server: https://usegalaxy.eu state: exact - version: 1.36.1.0 + version: 2.9+galaxy0 - server: https://usegalaxy.fr/ - state: inexact - versions: - - 1.39.5.0 + state: exact + version: 2.9+galaxy0 - server: https://usegalaxy.no/ state: inexact versions: - - 1.39.5.0 + - 2.6.1+galaxy0 + - 2.7+galaxy0 - server: https://usegalaxy.org state: exact - version: 1.36.1.0 + version: 2.9+galaxy0 - server: https://viralvariant.anses.fr/ state: missing - version: 1.36.1.0 - - id: toolshed.g2.bx.psu.edu/repos/iuc/mothur_cluster_split/mothur_cluster_split/1.36.1.0 + version: 2.9+galaxy0 + - id: toolshed.g2.bx.psu.edu/repos/iuc/bracken/est_abundance/3.1+galaxy0 servers: - server: http://apostl.moffitt.org/ state: missing @@ -30994,13 +11746,13 @@ - server: https://hyperbrowser.uio.no/coloc-stats state: missing - server: https://galaxy.mesocentre.uca.fr - state: inexact - versions: - - 1.39.5.0 + state: exact + version: 3.1+galaxy0 - server: https://galaxy.pasteur.fr/ state: missing - server: https://galaxytrakr.org/ - state: missing + state: exact + version: 3.1+galaxy0 - server: http://igg.cloud.ba.infn.it/galaxy state: missing - server: https://galaxy.hyphy.org/ @@ -31011,8 +11763,6 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr @@ -31023,37 +11773,33 @@ state: missing - server: http://pepsimili.e-nios.com:8080/ state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - server: https://usegalaxy.org.au - state: inexact - versions: - - 1.39.5.0 + state: exact + version: 3.1+galaxy0 - server: https://usegalaxy.be/ state: exact - version: 1.36.1.0 + version: 3.1+galaxy0 - server: https://usegalaxy.cz/ - state: inexact - versions: - - 1.39.5.0 + state: exact + version: 3.1+galaxy0 - server: https://usegalaxy.eu state: exact - version: 1.36.1.0 + version: 3.1+galaxy0 - server: https://usegalaxy.fr/ - state: inexact - versions: - - 1.39.5.0 + state: exact + version: 3.1+galaxy0 - server: https://usegalaxy.no/ state: inexact versions: - - 1.39.5.0 + - 2.6.1+galaxy0 + - 2.7+galaxy0 - server: https://usegalaxy.org state: exact - version: 1.36.1.0 + version: 3.1+galaxy0 - server: https://viralvariant.anses.fr/ state: missing - version: 1.36.1.0 - - id: toolshed.g2.bx.psu.edu/repos/iuc/mothur_count_seqs/mothur_count_seqs/1.36.1.0 + version: 3.1+galaxy0 + - id: toolshed.g2.bx.psu.edu/repos/iuc/kraken2/kraken2/2.1.3+galaxy2 servers: - server: http://apostl.moffitt.org/ state: missing @@ -31066,13 +11812,13 @@ - server: https://hyperbrowser.uio.no/coloc-stats state: missing - server: https://galaxy.mesocentre.uca.fr - state: inexact - versions: - - 1.39.5.0 + state: exact + version: 2.1.3+galaxy2 - server: https://galaxy.pasteur.fr/ state: missing - server: https://galaxytrakr.org/ - state: missing + state: exact + version: 2.1.3+galaxy2 - server: http://igg.cloud.ba.infn.it/galaxy state: missing - server: https://galaxy.hyphy.org/ @@ -31083,8 +11829,6 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr @@ -31094,38 +11838,37 @@ - server: https://palfinder.ls.manchester.ac.uk/ state: missing - server: http://pepsimili.e-nios.com:8080/ - state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - - server: https://usegalaxy.org.au state: inexact versions: - - 1.39.5.0 + - 2.1.1+galaxy1 + - server: https://usegalaxy.org.au + state: exact + version: 2.1.3+galaxy2 - server: https://usegalaxy.be/ state: exact - version: 1.36.1.0 + version: 2.1.3+galaxy2 - server: https://usegalaxy.cz/ - state: inexact - versions: - - 1.39.5.0 + state: exact + version: 2.1.3+galaxy2 - server: https://usegalaxy.eu state: exact - version: 1.36.1.0 + version: 2.1.3+galaxy2 - server: https://usegalaxy.fr/ - state: inexact - versions: - - 1.39.5.0 + state: exact + version: 2.1.3+galaxy2 - server: https://usegalaxy.no/ state: inexact versions: - - 1.39.5.0 + - 2.1.1+galaxy0 + - 2.1.1+galaxy1 + - 2.0.8_beta+galaxy0 - server: https://usegalaxy.org state: exact - version: 1.36.1.0 + version: 2.1.3+galaxy2 - server: https://viralvariant.anses.fr/ state: missing - version: 1.36.1.0 - - id: toolshed.g2.bx.psu.edu/repos/iuc/mothur_filter_seqs/mothur_filter_seqs/1.36.1.0 + version: 2.1.3+galaxy2 + - id: toolshed.g2.bx.psu.edu/repos/iuc/recentrifuge/recentrifuge/1.12.1+galaxy0 servers: - server: http://apostl.moffitt.org/ state: missing @@ -31138,13 +11881,14 @@ - server: https://hyperbrowser.uio.no/coloc-stats state: missing - server: https://galaxy.mesocentre.uca.fr - state: inexact - versions: - - 1.39.5.0 + state: exact + version: 1.12.1+galaxy0 - server: https://galaxy.pasteur.fr/ state: missing - server: https://galaxytrakr.org/ - state: missing + state: inexact + versions: + - 1.16.1+galaxy0 - server: http://igg.cloud.ba.infn.it/galaxy state: missing - server: https://galaxy.hyphy.org/ @@ -31155,8 +11899,6 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr @@ -31167,37 +11909,41 @@ state: missing - server: http://pepsimili.e-nios.com:8080/ state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - server: https://usegalaxy.org.au state: inexact versions: - - 1.39.5.0 + - 1.16.1+galaxy0 + - 1.15.0+galaxy0 + - 1.14.1+galaxy0 + - 1.15.1+galaxy0 + - 1.16.0+galaxy0 - server: https://usegalaxy.be/ state: exact - version: 1.36.1.0 + version: 1.12.1+galaxy0 - server: https://usegalaxy.cz/ - state: inexact - versions: - - 1.39.5.0 + state: exact + version: 1.12.1+galaxy0 - server: https://usegalaxy.eu state: exact - version: 1.36.1.0 + version: 1.12.1+galaxy0 - server: https://usegalaxy.fr/ - state: inexact - versions: - - 1.39.5.0 + state: exact + version: 1.12.1+galaxy0 - server: https://usegalaxy.no/ + state: missing + - server: https://usegalaxy.org state: inexact versions: - - 1.39.5.0 - - server: https://usegalaxy.org - state: exact - version: 1.36.1.0 + - 1.16.1+galaxy0 + - 1.15.0+galaxy0 + - 1.14.1+galaxy0 + - 1.15.1+galaxy0 + - 1.16.0+galaxy0 + - 1.14.0+galaxy0 - server: https://viralvariant.anses.fr/ state: missing - version: 1.36.1.0 - - id: toolshed.g2.bx.psu.edu/repos/iuc/mothur_make_biom/mothur_make_biom/1.36.1.0 + version: 1.12.1+galaxy0 + - id: toolshed.g2.bx.psu.edu/repos/iuc/recentrifuge/recentrifuge/1.16.1+galaxy0 servers: - server: http://apostl.moffitt.org/ state: missing @@ -31210,13 +11956,13 @@ - server: https://hyperbrowser.uio.no/coloc-stats state: missing - server: https://galaxy.mesocentre.uca.fr - state: inexact - versions: - - 1.39.5.0 + state: exact + version: 1.16.1+galaxy0 - server: https://galaxy.pasteur.fr/ state: missing - server: https://galaxytrakr.org/ - state: missing + state: exact + version: 1.16.1+galaxy0 - server: http://igg.cloud.ba.infn.it/galaxy state: missing - server: https://galaxy.hyphy.org/ @@ -31227,8 +11973,6 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr @@ -31239,109 +11983,796 @@ state: missing - server: http://pepsimili.e-nios.com:8080/ state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - server: https://usegalaxy.org.au - state: inexact - versions: - - 1.39.5.0 + state: exact + version: 1.16.1+galaxy0 - server: https://usegalaxy.be/ state: exact - version: 1.36.1.0 + version: 1.16.1+galaxy0 - server: https://usegalaxy.cz/ - state: inexact - versions: - - 1.39.5.0 + state: exact + version: 1.16.1+galaxy0 - server: https://usegalaxy.eu state: exact - version: 1.36.1.0 + version: 1.16.1+galaxy0 - server: https://usegalaxy.fr/ - state: inexact - versions: - - 1.39.5.0 + state: exact + version: 1.16.1+galaxy0 - server: https://usegalaxy.no/ - state: inexact - versions: - - 1.39.5.0 + state: missing - server: https://usegalaxy.org state: exact - version: 1.36.1.0 + version: 1.16.1+galaxy0 - server: https://viralvariant.anses.fr/ state: missing - version: 1.36.1.0 - - id: toolshed.g2.bx.psu.edu/repos/iuc/mothur_make_group/mothur_make_group/1.36.1.0 + version: 1.16.1+galaxy0 + - id: upload1 servers: - server: http://apostl.moffitt.org/ - state: missing + state: local - server: http://mbac.gmu.edu:8080/ - state: missing + state: local - server: https://vm-chemflow-francegrille.eu/ - state: missing + state: local - server: https://iris.angers.inra.fr/galaxypub-cfbp - state: missing + state: local - server: https://hyperbrowser.uio.no/coloc-stats - state: missing + state: local - server: https://galaxy.mesocentre.uca.fr - state: inexact - versions: - - 1.39.5.0 + state: local - server: https://galaxy.pasteur.fr/ - state: missing + state: local - server: https://galaxytrakr.org/ - state: missing + state: local - server: http://igg.cloud.ba.infn.it/galaxy - state: missing + state: local - server: https://galaxy.hyphy.org/ - state: missing + state: local - server: https://www.immportgalaxy.org/ - state: missing + state: local - server: http://galaxy.interactomix.com/ - state: missing + state: local - server: https://galaxy-web.ipk-gatersleben.de - state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing + state: local - server: https://neo.engr.uconn.edu/ - state: missing + state: local - server: https://mississippi.sorbonne-universite.fr - state: missing + state: local - server: http://galaxy.inf.ethz.ch - state: missing + state: local - server: https://palfinder.ls.manchester.ac.uk/ - state: missing + state: local - server: http://pepsimili.e-nios.com:8080/ - state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing + state: local - server: https://usegalaxy.org.au - state: inexact - versions: - - 1.39.5.0 + state: missing - server: https://usegalaxy.be/ - state: exact - version: 1.36.1.0 + state: local - server: https://usegalaxy.cz/ - state: inexact - versions: - - 1.39.5.0 + state: local - server: https://usegalaxy.eu - state: exact - version: 1.36.1.0 + state: local - server: https://usegalaxy.fr/ - state: inexact - versions: - - 1.39.5.0 + state: local - server: https://usegalaxy.no/ - state: inexact - versions: - - 1.39.5.0 + state: local - server: https://usegalaxy.org - state: exact - version: 1.36.1.0 + state: local - server: https://viralvariant.anses.fr/ - state: missing - version: 1.36.1.0 - - id: toolshed.g2.bx.psu.edu/repos/iuc/mothur_make_shared/mothur_make_shared/1.36.1.0 + state: local + version: local + symlink: null + tags: + - illumina + - bacteria + - microgalaxy + time_estimation: 1H + title: Checking expected species and contamination in bacterial isolate + tools: + - toolshed.g2.bx.psu.edu/repos/iuc/bracken/est_abundance/2.9+galaxy0 + - toolshed.g2.bx.psu.edu/repos/iuc/bracken/est_abundance/3.1+galaxy0 + - toolshed.g2.bx.psu.edu/repos/iuc/kraken2/kraken2/2.1.3+galaxy2 + - toolshed.g2.bx.psu.edu/repos/iuc/recentrifuge/recentrifuge/1.12.1+galaxy0 + - toolshed.g2.bx.psu.edu/repos/iuc/recentrifuge/recentrifuge/1.16.1+galaxy0 + - upload1 + topic_name: ecology + topic_name_human: Ecology + tours: false + translations: + slides: [] + tutorial: [] + video: false + tutorial_name: bacterial-isolate-species-contamination-checking + type: tutorial + url: https://training.galaxyproject.org//topics/ecology/tutorials/bacterial-isolate-species-contamination-checking/tutorial.html + urls: + hands_on: https://training.galaxyproject.org/training-material/api/topics/ecology/tutorials/bacterial-isolate-species-contamination-checking/tutorial.json + slides: https://training.galaxyproject.org/training-material/api/topics/ecology/tutorials/bacterial-isolate-species-contamination-checking/tutorial.json + version: 6 + video: false + video_versions: 0 + video_view: 0 + visit_duration: 511 + visitors: 1067 + workflows: + - creators: + - alternateName: pimarin + class: Person + email: mailto:pierre.marin@france-bioinformatique.fr + familyName: MARIN + identifier: 0000-0002-8304-138X + name: Pierre + - class: Person + identifier: https://orcid.org/0000-0001-9852-1987 + name: "B\xE9r\xE9nice Batut" + - class: Person + identifier: 0000-0002-6606-5953 + name: Tristan Reynolds + description: Checking expected species and contamination in bacterial isolate + features: + comments: false + parameters: false + report: + markdown: ' + + # Workflow Execution Report + + + ## Workflow Inputs + + ```galaxy + + invocation_inputs() + + ``` + + + ## Workflow Outputs + + ```galaxy + + invocation_outputs() + + ``` + + + ## Workflow + + ```galaxy + + workflow_display() + + ``` + + ' + subworkflows: false + graph_dot: "digraph main {\n node [fontname=\"Atkinson Hyperlegible\", shape=box,\ + \ color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n edge [fontname=\"\ + Atkinson Hyperlegible\"];\n 0[color=lightblue,label=\"\u2139\uFE0F Input Collection\\\ + nInput Paired End Reads Collection\"]\n 1[label=\"Kraken2\"]\n 0 -> 1 [label=\"\ + output\"]\n ka408a64458cd4f5eaf2515b5ea63aa76[color=lightseagreen,label=\"\ + Output\\nkraken_report_reads\"]\n 1 -> ka408a64458cd4f5eaf2515b5ea63aa76\n\ + \ k54b85a5372ee4b73b1867fd55e8aab9b[color=lightseagreen,label=\"Output\\nkraken_report_tabular\"\ + ]\n 1 -> k54b85a5372ee4b73b1867fd55e8aab9b\n 2[label=\"Bracken\"]\n 1 ->\ + \ 2 [label=\"report_output\"]\n kae6c6464f5f54e5bb616d38166fc0133[color=lightseagreen,label=\"\ + Output\\nbracken_report_tsv\"]\n 2 -> kae6c6464f5f54e5bb616d38166fc0133\n \ + \ k8ca52af9f83942b6aa74f1a6a1dfbbc8[color=lightseagreen,label=\"Output\\nbracken_kraken_report\"\ + ]\n 2 -> k8ca52af9f83942b6aa74f1a6a1dfbbc8\n 3[label=\"Recentrifuge\"]\n \ + \ 1 -> 3 [label=\"output\"]\n kb5694f2dc8cd4460bfff74fd0792ecb3[color=lightseagreen,label=\"\ + Output\\nrecentrifuge_stats_tabular\"]\n 3 -> kb5694f2dc8cd4460bfff74fd0792ecb3\n\ + \ kbd947a1d0443465f86585d76d9ce69f8[color=lightseagreen,label=\"Output\\nrecentrifuge_report_html\"\ + ]\n 3 -> kbd947a1d0443465f86585d76d9ce69f8\n kc7457acb41bc4191b3fb6716e15fbe57[color=lightseagreen,label=\"\ + Output\\nrecentrifuge_data_tabular\"]\n 3 -> kc7457acb41bc4191b3fb6716e15fbe57\n\ + \ k94f6ff070e0647ad88f8a058d0808537[color=lightseagreen,label=\"Output\\nrecentrifuge_logfile\"\ + ]\n 3 -> k94f6ff070e0647ad88f8a058d0808537\n}" + history: + - hash: ecc2e2e411eb58e2349f8d3d61e067d02b4aa218 + message: Update workflow and workflow tests + num: 4 + short_hash: ecc2e2e41 + unix: '1765506765' + - hash: 4854483dab21555869c5c49b91fa3113146c07dc + message: Update Bracken version toolshed + num: 3 + short_hash: 4854483da + unix: '1712233925' + - hash: 96c80b0ad7e5179b3d43364e789efee1adeea130 + message: Update workflow creators + num: 2 + short_hash: 96c80b0ad + unix: '1706542936' + - hash: 96df58f868367e22ade2e451a1d9ecacba822bcc + message: Create new tutorial for checking expected species and contamination + in bacterial isolate + num: 1 + short_hash: 96df58f86 + unix: '1706542439' + inputs: + - annotation: '' + content_id: null + errors: null + id: 0 + input_connections: {} + inputs: + - description: '' + name: Input Paired End Reads Collection + label: Input Paired End Reads Collection + name: Input dataset collection + outputs: [] + position: + left: 0 + top: 77.19660790675707 + tool_id: null + tool_state: '{"optional": false, "tag": null, "collection_type": "list:paired", + "fields": null}' + tool_version: null + type: data_collection_input + uuid: a6b78808-bb96-4dda-9fe5-e984ee46de00 + when: null + workflow_outputs: [] + license: GPL-3.0-or-later + mermaid: "flowchart TD\n 0[\"\u2139\uFE0F Input Collection\\nInput Paired End\ + \ Reads Collection\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"Kraken2\"\ + ];\n 0 -->|output| 1;\n a408a644-58cd-4f5e-af25-15b5ea63aa76[\"Output\\nkraken_report_reads\"\ + ];\n 1 --> a408a644-58cd-4f5e-af25-15b5ea63aa76;\n style a408a644-58cd-4f5e-af25-15b5ea63aa76\ + \ stroke:#2c3143,stroke-width:4px;\n 54b85a53-72ee-4b73-b186-7fd55e8aab9b[\"\ + Output\\nkraken_report_tabular\"];\n 1 --> 54b85a53-72ee-4b73-b186-7fd55e8aab9b;\n\ + \ style 54b85a53-72ee-4b73-b186-7fd55e8aab9b stroke:#2c3143,stroke-width:4px;\n\ + \ 2[\"Bracken\"];\n 1 -->|report_output| 2;\n ae6c6464-f5f5-4e5b-b616-d38166fc0133[\"\ + Output\\nbracken_report_tsv\"];\n 2 --> ae6c6464-f5f5-4e5b-b616-d38166fc0133;\n\ + \ style ae6c6464-f5f5-4e5b-b616-d38166fc0133 stroke:#2c3143,stroke-width:4px;\n\ + \ 8ca52af9-f839-42b6-aa74-f1a6a1dfbbc8[\"Output\\nbracken_kraken_report\"];\n\ + \ 2 --> 8ca52af9-f839-42b6-aa74-f1a6a1dfbbc8;\n style 8ca52af9-f839-42b6-aa74-f1a6a1dfbbc8\ + \ stroke:#2c3143,stroke-width:4px;\n 3[\"Recentrifuge\"];\n 1 -->|output|\ + \ 3;\n b5694f2d-c8cd-4460-bfff-74fd0792ecb3[\"Output\\nrecentrifuge_stats_tabular\"\ + ];\n 3 --> b5694f2d-c8cd-4460-bfff-74fd0792ecb3;\n style b5694f2d-c8cd-4460-bfff-74fd0792ecb3\ + \ stroke:#2c3143,stroke-width:4px;\n bd947a1d-0443-465f-8658-5d76d9ce69f8[\"\ + Output\\nrecentrifuge_report_html\"];\n 3 --> bd947a1d-0443-465f-8658-5d76d9ce69f8;\n\ + \ style bd947a1d-0443-465f-8658-5d76d9ce69f8 stroke:#2c3143,stroke-width:4px;\n\ + \ c7457acb-41bc-4191-b3fb-6716e15fbe57[\"Output\\nrecentrifuge_data_tabular\"\ + ];\n 3 --> c7457acb-41bc-4191-b3fb-6716e15fbe57;\n style c7457acb-41bc-4191-b3fb-6716e15fbe57\ + \ stroke:#2c3143,stroke-width:4px;\n 94f6ff07-0e06-47ad-88f8-a058d0808537[\"\ + Output\\nrecentrifuge_logfile\"];\n 3 --> 94f6ff07-0e06-47ad-88f8-a058d0808537;\n\ + \ style 94f6ff07-0e06-47ad-88f8-a058d0808537 stroke:#2c3143,stroke-width:4px;" + modified: 2026-07-01 00:31:38 +0000 + name: Checking expected species and contamination in bacterial isolate + outputs: + - annotation: '' + content_id: toolshed.g2.bx.psu.edu/repos/iuc/kraken2/kraken2/2.1.3+galaxy2 + errors: null + id: 1 + input_connections: + single_paired|input_pair: + id: 0 + output_name: output + inputs: + - description: runtime parameter for tool Kraken2 + name: single_paired + label: null + name: Kraken2 + outputs: + - name: report_output + type: tabular + - name: output + type: tabular + position: + left: 322.6153124569796 + top: 96.22518458429411 + post_job_actions: {} + tool_id: toolshed.g2.bx.psu.edu/repos/iuc/kraken2/kraken2/2.1.3+galaxy2 + tool_shed_repository: + changeset_revision: e150ae930235 + name: kraken2 + owner: iuc + tool_shed: toolshed.g2.bx.psu.edu + tool_state: '{"confidence": "0.0", "kraken2_database": "k2_pluspf_20210517", + "min_base_quality": "10", "minimum_hit_groups": "2", "quick": false, "report": + {"create_report": true, "use_mpa_style": false, "report_zero_counts": false, + "report_minimizer_data": false}, "single_paired": {"single_paired_selector": + "collection", "__current_case__": 0, "input_pair": {"__class__": "ConnectedValue"}}, + "split_reads": false, "use_names": false, "__page__": 0, "__rerun_remap_job_id__": + null}' + tool_version: 2.1.3+galaxy2 + type: tool + uuid: 75b7f2b8-2b63-4f1a-a877-4babef16a08b + when: null + workflow_outputs: + - label: kraken_report_reads + output_name: output + uuid: a408a644-58cd-4f5e-af25-15b5ea63aa76 + - label: kraken_report_tabular + output_name: report_output + uuid: 54b85a53-72ee-4b73-b186-7fd55e8aab9b + - annotation: '' + content_id: toolshed.g2.bx.psu.edu/repos/iuc/bracken/est_abundance/3.1+galaxy0 + errors: null + id: 2 + input_connections: + input: + id: 1 + output_name: report_output + inputs: [] + label: null + name: Bracken + outputs: + - name: report + type: tabular + - name: kraken_report + type: tabular + position: + left: 618.0787322325853 + top: 0 + post_job_actions: + RenameDatasetActionkraken_report: + action_arguments: + newname: bracken_kraken_report + action_type: RenameDatasetAction + output_name: kraken_report + RenameDatasetActionreport: + action_arguments: + newname: bracken_report_tsv + action_type: RenameDatasetAction + output_name: report + tool_id: toolshed.g2.bx.psu.edu/repos/iuc/bracken/est_abundance/3.1+galaxy0 + tool_shed_repository: + changeset_revision: 4d350ac5148e + name: bracken + owner: iuc + tool_shed: toolshed.g2.bx.psu.edu + tool_state: '{"input": {"__class__": "ConnectedValue"}, "kmer_distr": "16S_SILVA138_k2db", + "level": "S", "logfile_output": false, "out_report": true, "threshold": "10", + "__page__": null, "__rerun_remap_job_id__": null}' + tool_version: 3.1+galaxy0 + type: tool + uuid: 53b9c80b-f5f4-4fee-9778-fb4fd6b76165 + when: null + workflow_outputs: + - label: bracken_report_tsv + output_name: report + uuid: ae6c6464-f5f5-4e5b-b616-d38166fc0133 + - label: bracken_kraken_report + output_name: kraken_report + uuid: 8ca52af9-f839-42b6-aa74-f1a6a1dfbbc8 + - annotation: '' + content_id: toolshed.g2.bx.psu.edu/repos/iuc/recentrifuge/recentrifuge/1.16.1+galaxy0 + errors: null + id: 3 + input_connections: + input_file: + id: 1 + output_name: output + inputs: [] + label: null + name: Recentrifuge + outputs: + - name: html_report + type: html + - name: logfile + type: txt + - name: data_tsv + type: tabular + - name: stat_tsv + type: tabular + position: + left: 618.0753303964757 + top: 289.00103504332145 + post_job_actions: + RenameDatasetActiondata_tsv: + action_arguments: + newname: recentrifuge_data_tabular + action_type: RenameDatasetAction + output_name: data_tsv + RenameDatasetActionhtml_report: + action_arguments: + newname: recentrifuge_report_html + action_type: RenameDatasetAction + output_name: html_report + RenameDatasetActionlogfile: + action_arguments: + newname: recentrifuge_logfile + action_type: RenameDatasetAction + output_name: logfile + RenameDatasetActionstat_tsv: + action_arguments: + newname: recentrifuge_stats_tabular + action_type: RenameDatasetAction + output_name: stat_tsv + tool_id: toolshed.g2.bx.psu.edu/repos/iuc/recentrifuge/recentrifuge/1.16.1+galaxy0 + tool_shed_repository: + changeset_revision: 613ee22af97c + name: recentrifuge + owner: iuc + tool_shed: toolshed.g2.bx.psu.edu + tool_state: '{"advanced_option": {"controls": "0", "scoring": null, "minscore_value": + "0", "mintaxa": "0", "exclude_taxa_name": null, "include_taxa_name": null, + "avoidcross": false}, "database": {"database_name": "2020-12-03"}, "file_type": + {"filetype": "kraken", "__current_case__": 3}, "input_file": {"__class__": + "ConnectedValue"}, "more_advanced_option": {"ctrlminscore": "0", "ctrlmintaxa": + "0", "summary": "ADD", "takeoutroot": false, "nokollapse": false, "strain": + true, "sequential": false}, "output_option": {"extra": "TSV", "nohtml": false, + "no_logfile": false}, "__page__": null, "__rerun_remap_job_id__": null}' + tool_version: 1.16.1+galaxy0 + type: tool + uuid: 4b3b34ad-2352-4e93-abbc-69da3ab9ee3a + when: null + workflow_outputs: + - label: recentrifuge_stats_tabular + output_name: stat_tsv + uuid: b5694f2d-c8cd-4460-bfff-74fd0792ecb3 + - label: recentrifuge_report_html + output_name: html_report + uuid: bd947a1d-0443-465f-8658-5d76d9ce69f8 + - label: recentrifuge_data_tabular + output_name: data_tsv + uuid: c7457acb-41bc-4191-b3fb-6716e15fbe57 + - label: recentrifuge_logfile + output_name: logfile + uuid: 94f6ff07-0e06-47ad-88f8-a058d0808537 + parent_id: ecology/bacterial-isolate-species-contamination-checking + path: topics/ecology/tutorials/bacterial-isolate-species-contamination-checking/workflows/Checking-expected-species-and-contamination-in-bacterial-isolate.ga + tags: + - ecology + test_results: null + tests: true + title: Checking expected species and contamination in bacterial isolate + topic_id: ecology + trs_endpoint: https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/ecology-bacterial-isolate-species-contamination-checking/versions/checking-expected-species-and-contamination-in-bacterial-isolate + tutorial_id: bacterial-isolate-species-contamination-checking + url: https://training.galaxyproject.org/training-material/topics/ecology/tutorials/bacterial-isolate-species-contamination-checking/workflows/Checking-expected-species-and-contamination-in-bacterial-isolate.ga + url_html: https://training.galaxyproject.org/training-material/topics/ecology/tutorials/bacterial-isolate-species-contamination-checking/workflows/Checking-expected-species-and-contamination-in-bacterial-isolate.html + version: 3 + wfid: ecology-bacterial-isolate-species-contamination-checking + wfname: checking-expected-species-and-contamination-in-bacterial-isolate + workflow: Checking-expected-species-and-contamination-in-bacterial-isolate.ga + workflow_tools: + - 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cstritt + - dbrites + - GaloGS + editing: + - wm75 + reviewing: + - hexylena + - pvanheus + - cstritt + - shiltemann + - bebatut + - wm75 + - bgruening + contributors: + - id: cstritt + joined: 2022-03 + name: Christoph Stritt + page: https://training.galaxyproject.org/training-material/hall-of-fame/cstritt/ + url: https://training.galaxyproject.org/training-material/api/contributors/cstritt.json + - id: dbrites + joined: 2022-03 + name: Daniela Brites + page: https://training.galaxyproject.org/training-material/hall-of-fame/dbrites/ + url: https://training.galaxyproject.org/training-material/api/contributors/dbrites.json + - id: GaloGS + joined: 2022-03 + name: Galo A. Goig + page: https://training.galaxyproject.org/training-material/hall-of-fame/GaloGS/ + url: https://training.galaxyproject.org/training-material/api/contributors/GaloGS.json + - affiliations: + - by-covid + - uni-freiburg + - elixir-europe + - deNBI + - mwk + elixir_node: de + fediverse: https://fediscience.org/@zerodivision + fediverse_flavor: mastodon + former_affiliations: + - eurosciencegateway + id: wm75 + joined: 2017-09 + matrix: wm75:matrix.org + name: Wolfgang Maier + orcid: 0000-0002-9464-6640 + page: https://training.galaxyproject.org/training-material/hall-of-fame/wm75/ + url: https://training.galaxyproject.org/training-material/api/contributors/wm75.json + - affiliations: + - elixir-europe + contact_for_training: false + elixir_node: nl + former_affiliations: + - deNBI + - avans-atgm + - uni-freiburg + - erasmusmc + - gallantries + - by-covid + - elixir-converge + id: hexylena + joined: 2017-09 + location: + country: NL + lat: 51.91 + lon: 4.46 + maintainer_contact: gitter + matrix: hexylena:matrix.org + name: Helena Rasche + orcid: 0000-0001-9760-8992 + page: https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/ + url: https://training.galaxyproject.org/training-material/api/contributors/hexylena.json + - bio: Research at the South African National Bioinformatics Institute + id: pvanheus + joined: 2017-09 + name: Peter van Heusden + orcid: 0000-0001-6553-5274 + page: https://training.galaxyproject.org/training-material/hall-of-fame/pvanheus/ + twitter: pvanheus + url: https://training.galaxyproject.org/training-material/api/contributors/pvanheus.json + - id: cstritt + joined: 2022-03 + name: Christoph Stritt + page: https://training.galaxyproject.org/training-material/hall-of-fame/cstritt/ + url: https://training.galaxyproject.org/training-material/api/contributors/cstritt.json + - affiliations: + - uni-freiburg + - nfdi4plants + - elixir-europe + bio: Researcher at Erasmus Medical Center + bluesky: shiltemann.bsky.social + contact_for_training: true + elixir_node: nl + email: saskia.hiltemann@gmail.com + fediverse: https://mstdn.science/@shiltemann + fediverse_flavor: mastodon + former_affiliations: + - CINECA-Project + - gallantries + - erasmusmc + id: shiltemann + joined: 2017-09 + linkedin: shiltemann + location: + country: NL + lat: 51.912 + lon: 4.462 + maintainer_contact: gitter + matrix: shiltemann:matrix.org + name: Saskia Hiltemann + orcid: 0000-0003-3803-468X + page: https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/ + url: https://training.galaxyproject.org/training-material/api/contributors/shiltemann.json + - affiliations: + - gallantries + - ifb + - elixir-europe + contact_for_training: true + elixir_node: fr + email: berenice.batut@gmail.com + fediverse: https://piaille.fr/@bebatut + fediverse_flavor: mastodon + former_affiliations: + - uni-freiburg + - deNBI + id: bebatut + joined: 2017-09 + linkedin: berenicebatut + location: + country: FR + lat: 45.77 + lon: 3.08 + matrix: bebatut:matrix.org + name: "B\xE9r\xE9nice Batut" + orcid: 0000-0001-9852-1987 + page: https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/ + twitter: bebatut + url: https://training.galaxyproject.org/training-material/api/contributors/bebatut.json + - affiliations: + - by-covid + - uni-freiburg + - elixir-europe + - deNBI + - mwk + elixir_node: de + fediverse: https://fediscience.org/@zerodivision + fediverse_flavor: mastodon + former_affiliations: + - eurosciencegateway + id: wm75 + joined: 2017-09 + matrix: wm75:matrix.org + name: Wolfgang Maier + orcid: 0000-0002-9464-6640 + page: https://training.galaxyproject.org/training-material/hall-of-fame/wm75/ + url: https://training.galaxyproject.org/training-material/api/contributors/wm75.json + - affiliations: + - deNBI + - mwk + - uni-freiburg + - elixir-europe + - materialvitaldigital + contact_for_training: true + elixir_node: de + email: bjoern.gruening@gmail.com + fediverse: https://fosstodon.org/@bgruening + fediverse_flavor: mastodon + former_affiliations: + - eurosciencegateway + - eosc-life + - by-covid + - crc992 + - elixir-converge + id: bgruening + joined: 2017-09 + linkedin: bgruening + location: + country: DE + lat: 47.997791 + lon: 7.842609 + matrix: bgruening:matrix.org + name: "Bj\xF6rn Gr\xFCning" + orcid: 0000-0002-3079-6586 + page: https://training.galaxyproject.org/training-material/hall-of-fame/bgruening/ + twitter: bjoerngruening + url: https://training.galaxyproject.org/training-material/api/contributors/bgruening.json + dir: topics/evolution/tutorials/mtb_phylogeny + edam_ontology: + - topic_0622 + - topic_3301 + - topic_0084 + - topic_3324 + edam_operation: + - Phylogenetic tree analysis + - Sequence analysis + edam_topic: + - Genomics + - Microbiology + - 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slides: https://training.galaxyproject.org/training-material/api/topics/microbiome/tutorials/general-tutorial/tutorial.json - version: 4 + hands_on: https://training.galaxyproject.org/training-material/api/topics/evolution/tutorials/mtb_phylogeny/tutorial.json + slides: https://training.galaxyproject.org/training-material/api/topics/evolution/tutorials/mtb_phylogeny/tutorial.json + version: 12 video: false video_versions: 0 video_view: 0 - visit_duration: 344 - visitors: 11137 + visit_duration: 483 + visitors: 2636 workflows: - creators: [] - description: Analyses of metagenomics data - The global picture + description: Estimate a phylogenetic tree from whole genome sequencing data for + M. tuberculosis features: comments: false parameters: false @@ -31900,338 +12999,167 @@ graph_dot: "digraph main {\n node [fontname=\"Atkinson Hyperlegible\", shape=box,\ \ color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n edge [fontname=\"\ Atkinson Hyperlegible\"];\n 0[color=lightblue,label=\"\u2139\uFE0F Input Dataset\\\ - 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name: WGS Part In "Analyses Of Metagenomics Data - The Global Picture" - outputs: [] - parent_id: microbiome/general-tutorial - path: topics/microbiome/tutorials/general-tutorial/workflows/wgs-worklow.ga + - label: Best-scoring ML Tree + output_name: bestTree + uuid: 9f8ae577-c583-4a2d-b64d-14c25fb859d9 + - label: Info + output_name: info + uuid: bdb8cf2f-b553-4a96-8b55-38b4b499ab88 + parent_id: evolution/mtb_phylogeny + path: topics/evolution/tutorials/mtb_phylogeny/workflows/main_workflow.ga tags: - - microbiome + - evolution test_results: null tests: false - title: WGS Part In "Analyses Of Metagenomics Data - The Global Picture" - topic_id: microbiome - trs_endpoint: https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/microbiome-general-tutorial/versions/wgs-worklow - tutorial_id: general-tutorial - url: https://training.galaxyproject.org/training-material/topics/microbiome/tutorials/general-tutorial/workflows/wgs-worklow.ga - url_html: https://training.galaxyproject.org/training-material/topics/microbiome/tutorials/general-tutorial/workflows/wgs-worklow.html + title: Mtb phylogeny + topic_id: evolution + trs_endpoint: https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/evolution-mtb_phylogeny/versions/main-workflow + tutorial_id: mtb_phylogeny + url: https://training.galaxyproject.org/training-material/topics/evolution/tutorials/mtb_phylogeny/workflows/main_workflow.ga + url_html: https://training.galaxyproject.org/training-material/topics/evolution/tutorials/mtb_phylogeny/workflows/main_workflow.html version: 1 - 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linkedin: subinamehta - matrix: subinamehta:matrix.org - name: Subina Mehta - orcid: 0000-0001-9818-0537 - page: https://training.galaxyproject.org/training-material/hall-of-fame/subinamehta/ - twitter: Subina_Mehta - url: https://training.galaxyproject.org/training-material/api/contributors/subinamehta.json - - email: rsajulga@umn.edu - id: jraysajulga - joined: 2018-11 - name: Ray Sajulga - page: https://training.galaxyproject.org/training-material/hall-of-fame/jraysajulga/ - url: https://training.galaxyproject.org/training-material/api/contributors/jraysajulga.json + - id: GaloGS + joined: 2022-03 + name: Galo A. Goig + page: https://training.galaxyproject.org/training-material/hall-of-fame/GaloGS/ + url: https://training.galaxyproject.org/training-material/api/contributors/GaloGS.json + - id: dbrites + joined: 2022-03 + name: Daniela Brites + page: https://training.galaxyproject.org/training-material/hall-of-fame/dbrites/ + url: https://training.galaxyproject.org/training-material/api/contributors/dbrites.json + - id: cstritt + joined: 2022-03 + name: Christoph Stritt + page: https://training.galaxyproject.org/training-material/hall-of-fame/cstritt/ + url: https://training.galaxyproject.org/training-material/api/contributors/cstritt.json - affiliations: - - gallantries - - ifb + - by-covid + - uni-freiburg - elixir-europe - contact_for_training: true - elixir_node: fr - email: berenice.batut@gmail.com - fediverse: https://piaille.fr/@bebatut + - deNBI + - mwk + elixir_node: de + fediverse: https://fediscience.org/@zerodivision fediverse_flavor: mastodon former_affiliations: - - uni-freiburg - - deNBI - id: bebatut + - eurosciencegateway + id: wm75 joined: 2017-09 - linkedin: berenicebatut - location: - country: FR - lat: 45.77 - lon: 3.08 - matrix: bebatut:matrix.org - name: "B\xE9r\xE9nice Batut" - orcid: 0000-0001-9852-1987 - page: https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/ - twitter: bebatut - url: https://training.galaxyproject.org/training-material/api/contributors/bebatut.json - - email: leith023@umn.edu - id: emmaleith - joined: 2019-07 - name: Emma Leith - page: https://training.galaxyproject.org/training-material/hall-of-fame/emmaleith/ - url: https://training.galaxyproject.org/training-material/api/contributors/emmaleith.json - - email: kumar207@umn.edu - id: pravs3683 - joined: 2019-04 - name: Praveen Kumar - page: https://training.galaxyproject.org/training-material/hall-of-fame/pravs3683/ - url: https://training.galaxyproject.org/training-material/api/contributors/pravs3683.json + matrix: wm75:matrix.org + name: Wolfgang Maier + orcid: 0000-0002-9464-6640 + page: https://training.galaxyproject.org/training-material/hall-of-fame/wm75/ + url: https://training.galaxyproject.org/training-material/api/contributors/wm75.json - affiliations: - uni-freiburg - nfdi4plants @@ -32480,73 +13384,17 @@ page: https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/ url: https://training.galaxyproject.org/training-material/api/contributors/shiltemann.json - affiliations: - - uni-freiburg - - elixir-europe - - deNBI - - mwk - - materialvitaldigital - email: zierep@informatik.uni-freiburg.de - id: paulzierep - joined: 2023-02 - name: Paul Zierep - orcid: 0000-0003-2982-388X - page: https://training.galaxyproject.org/training-material/hall-of-fame/paulzierep/ - url: https://training.galaxyproject.org/training-material/api/contributors/paulzierep.json - - affiliations: - - uni-freiburg - - elixir-europe - elixir_node: de - email: engynasr94@gmail.com - id: EngyNasr - joined: 2021-05 - matrix: EngyNasr:matrix.org - name: Engy Nasr - orcid: 0000-0001-9047-4215 - page: https://training.galaxyproject.org/training-material/hall-of-fame/EngyNasr/ - url: https://training.galaxyproject.org/training-material/api/contributors/EngyNasr.json - - elixir_node: fr - id: ogerdfx - joined: 2025-06 - name: Christine Oger - page: https://training.galaxyproject.org/training-material/hall-of-fame/ogerdfx/ - url: https://training.galaxyproject.org/training-material/api/contributors/ogerdfx.json - - affiliations: - - gallantries - - ifb - - elixir-europe - contact_for_training: true - elixir_node: fr - email: berenice.batut@gmail.com - fediverse: https://piaille.fr/@bebatut - fediverse_flavor: mastodon - former_affiliations: - - uni-freiburg - - deNBI - id: bebatut - joined: 2017-09 - linkedin: berenicebatut - location: - country: FR - lat: 45.77 - lon: 3.08 - matrix: bebatut:matrix.org - name: "B\xE9r\xE9nice Batut" - orcid: 0000-0001-9852-1987 - page: https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/ - twitter: bebatut - url: https://training.galaxyproject.org/training-material/api/contributors/bebatut.json - - affiliations: - - erasmusmc - - gallantries - - by-covid - elixir-europe - - elixir-converge contact_for_training: false elixir_node: nl former_affiliations: - deNBI - avans-atgm - uni-freiburg + - erasmusmc + - gallantries + - by-covid + - elixir-converge id: hexylena joined: 2017-09 location: @@ -32559,47 +13407,11 @@ orcid: 0000-0001-9760-8992 page: https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/ url: https://training.galaxyproject.org/training-material/api/contributors/hexylena.json - - affiliations: - - uni-freiburg - - nfdi4plants - - elixir-europe - bio: Researcher at Erasmus Medical Center - bluesky: shiltemann.bsky.social - contact_for_training: true - elixir_node: nl - email: saskia.hiltemann@gmail.com - fediverse: https://mstdn.science/@shiltemann - fediverse_flavor: mastodon - former_affiliations: - - CINECA-Project - - gallantries - - erasmusmc - id: shiltemann - joined: 2017-09 - linkedin: shiltemann - location: - country: NL - lat: 51.912 - lon: 4.462 - maintainer_contact: gitter - matrix: shiltemann:matrix.org - name: Saskia Hiltemann - orcid: 0000-0003-3803-468X - page: https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/ - url: https://training.galaxyproject.org/training-material/api/contributors/shiltemann.json - - affiliations: - - uni-freiburg - - elixir-europe - - deNBI - - mwk - - materialvitaldigital - email: zierep@informatik.uni-freiburg.de - id: paulzierep - joined: 2023-02 - name: Paul Zierep - orcid: 0000-0003-2982-388X - page: https://training.galaxyproject.org/training-material/hall-of-fame/paulzierep/ - url: https://training.galaxyproject.org/training-material/api/contributors/paulzierep.json + - id: GaloGS + joined: 2022-03 + name: Galo A. Goig + page: https://training.galaxyproject.org/training-material/hall-of-fame/GaloGS/ + url: https://training.galaxyproject.org/training-material/api/contributors/GaloGS.json - affiliations: - deNBI - mwk @@ -32630,145 +13442,139 @@ page: https://training.galaxyproject.org/training-material/hall-of-fame/bgruening/ twitter: bjoerngruening url: https://training.galaxyproject.org/training-material/api/contributors/bgruening.json - dir: topics/microbiome/tutorials/metatranscriptomics-short + - bio: Research at the South African National Bioinformatics Institute + id: pvanheus + joined: 2017-09 + name: Peter van Heusden + orcid: 0000-0001-6553-5274 + page: https://training.galaxyproject.org/training-material/hall-of-fame/pvanheus/ + twitter: pvanheus + url: https://training.galaxyproject.org/training-material/api/contributors/pvanheus.json + - id: cstritt + joined: 2022-03 + name: Christoph Stritt + page: https://training.galaxyproject.org/training-material/hall-of-fame/cstritt/ + url: https://training.galaxyproject.org/training-material/api/contributors/cstritt.json + - affiliations: + - elixir-europe + contact_for_training: true + elixir_node: ch + email: lucille.delisle@unige.ch + id: lldelisle + joined: 2019-08 + location: + country: CH + lat: 46.19 + lon: 6.15 + maintainer_contact: matrix + matrix: lldelisle:matrix.org + name: Lucille Delisle + orcid: 0000-0002-1964-4960 + page: https://training.galaxyproject.org/training-material/hall-of-fame/lldelisle/ + url: https://training.galaxyproject.org/training-material/api/contributors/lldelisle.json + - affiliations: + - by-covid + - uni-freiburg + - elixir-europe + - deNBI + - mwk + elixir_node: de + fediverse: https://fediscience.org/@zerodivision + fediverse_flavor: mastodon + former_affiliations: + - eurosciencegateway + id: wm75 + joined: 2017-09 + matrix: wm75:matrix.org + name: Wolfgang Maier + orcid: 0000-0002-9464-6640 + page: https://training.galaxyproject.org/training-material/hall-of-fame/wm75/ + url: https://training.galaxyproject.org/training-material/api/contributors/wm75.json + dir: topics/evolution/tutorials/mtb_transmission edam_ontology: - - topic_3941 - - topic_3697 - - topic_0637 - - topic_1775 - - topic_0080 + - topic_0622 + - topic_3301 + - topic_3324 + - topic_2885 edam_operation: - - Sequence alignment analysis + - Variant calling - Phylogenetic tree visualisation - - Statistical calculation - - Primer removal - - Phylogenetic inference - - Visualisation - - Species frequency estimation - - Sequence composition calculation - - Sequence comparison - - Phylogenetic tree editing - - Phylogenetic analysis - - Taxonomic classification - - Conversion - - Validation - - Sequence similarity search - - Read pre-processing - - Sequence trimming - - Sequencing quality control + - Antimicrobial resistance prediction + - Phylogenetic tree generation edam_topic: - - Metatranscriptomics - - Microbial ecology - - Taxonomy - - Function analysis - - Sequence analysis + - Genomics + - Microbiology + - Infectious disease + - DNA polymorphism exact_supported_servers: - - UseGalaxy.org.au - - UseGalaxy.be - - UseGalaxy.org (Main) + - UseGalaxy.eu feedback_mean_note: null feedback_number: 0 hands_on: true - id: microbiome/metatranscriptomics-short - inexact_supported_servers: - - UseGalaxy.cz - - UseGalaxy.no + id: evolution/mtb_transmission + inexact_supported_servers: [] js_requirements: mathjax: null mermaid: false key_points: - - Metatranscriptomics data have the same QC profile that RNA-seq data - - A lot of metatranscriptomics sequences are identified as rRNA sequences - - With shotgun data, we can extract information about the studied community structure - and also the functions realised by the community - - Metatranscriptomics data analyses are complex and must be careful done, specially - when they are done without combination to metagenomics data analyses + - Clustering is a useful tool to detect transmission links between patients and + oubreak investigation. + - Clustering can be used to investigate the transmission of certain traits, like + drug resistance. + - Clustering does not provide information about particular transmission events nor + their directionality (who infected whom). + - Clustering is very much influenced by sampling. Lower sampling proportions and + shorter sampling timeframes lead to lower clustering rates that shoud not be confounded + with lack of transmission. layout: tutorial_hands_on - level: Introductory + level: Intermediate license: CC-BY-4.0 - mod_date: '2025-06-16' + mod_date: '2025-05-26' objectives: - - Choose the best approach to analyze metatranscriptomics data - - Understand the functional microbiome characterization using metatranscriptomic - results - - Understand where metatranscriptomics fits in 'multi-omic' analysis of microbiomes - - Visualise a community structure - pageviews: 1323 - pub_date: '2020-02-13' - questions: - - How to analyze metatranscriptomics data?" - - What information can be extracted of metatranscriptomics data? - - How to assign taxa and function to the identified sequences? - recordings: - - captioners: - - paulzierep - date: '2023-05-17' - galaxy_version: '23.01' - length: 1H5M - speakers: - - paulzierep - youtube_id: HNYop3vLpoM - - captioners: - - EngyNasr - - shiltemann - date: '2021-02-15' - galaxy_version: '21.01' - length: 1H30M - speakers: - - pratikdjagtap - - timothygriffin - - subinamehta - - shiltemann - youtube_id: EMaos5u1_a8 - redirect_from: - - /topics/metagenomics/tutorials/metatranscriptomics-short/tutorial - - /short/microbiome/metatranscriptomics-short - - /short/T00204 - - /short/T00389 - short_id: T00389 + - Create a SNP alignment + - Calculate pairwise SNP distances between MTB samples + - Identify transmission clusters based on SNP distances + - Study the emergence and spread of drug resistance based on transmission analysis. + pageviews: 5323 + pub_date: '2022-03-16' + requirements: + - topic_name: galaxy-interface + tutorials: + - collections + type: internal + - topic_name: variant-analysis + tutorials: + - tb-variant-analysis + type: internal + short_id: T00145 short_tools: - - graphlan_annotate - - tp_find_and_replace - - graphlan - - multiqc - - bg_sortmerna - - tp_sort_header_tool - - export2graphlan - - cutadapt - - fastq_paired_end_interlacer - - fastqc - - Cut1 - - humann_renorm_table - - humann + - bcftools_consensus + - tp_easyjoin_tool + - __MERGE_COLLECTION__ + - snp_dists + - collapse_dataset + - tb_profiler_profile + - tb_variant_filter + - samtools_view + - snippy + - snp_sites + - addName + - upload1 + - tp_cat + - tp_replace_in_line + - trimmomatic - Grep1 - - taxonomy_krona_chart - - metaphlan - - combine_metaphlan2_humann2 - - humann_rename_table - - humann_regroup_table - - humann_unpack_pathways - - humann_split_stratified_table + - tp_grep_tool + - tp_sed_tool + - clustering_from_distmat slides: false slides_recordings: false - subtopic: metatranscriptomics supported_servers: exact: - - name: UseGalaxy.org.au - url: https://usegalaxy.org.au - usegalaxy: true - - name: UseGalaxy.be - url: https://usegalaxy.be/ - usegalaxy: false - - name: UseGalaxy.org (Main) - url: https://usegalaxy.org + - name: UseGalaxy.eu + url: https://usegalaxy.eu usegalaxy: true - inexact: - - name: UseGalaxy.cz - url: https://usegalaxy.cz/ - usegalaxy: false - - name: UseGalaxy.no - url: https://usegalaxy.no/ - usegalaxy: false + inexact: [] supported_servers_matrix: servers: - name: APOSTL @@ -32810,9 +13616,6 @@ - name: IPK Galaxy Blast Suite url: https://galaxy-web.ipk-gatersleben.de usegalaxy: false - - name: Lebanese University Galaxy - url: http://galaxy.ul.edu.lb/ - usegalaxy: false - name: Mandoiu Lab url: https://neo.engr.uconn.edu/ usegalaxy: false @@ -32828,9 +13631,6 @@ - name: PepSimili url: http://pepsimili.e-nios.com:8080/ usegalaxy: false - - name: PhagePromotor - url: https://galaxy.bio.di.uminho.pt/ - usegalaxy: false - name: UseGalaxy.org.au url: https://usegalaxy.org.au usegalaxy: true @@ -32856,7 +13656,7 @@ url: https://viralvariant.anses.fr/ usegalaxy: false tools: - - id: Cut1 + - id: Grep1 servers: - server: http://apostl.moffitt.org/ state: local @@ -32884,8 +13684,6 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: local - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr @@ -32896,8 +13694,6 @@ state: missing - server: http://pepsimili.e-nios.com:8080/ state: local - - server: https://galaxy.bio.di.uminho.pt/ - state: local - server: https://usegalaxy.org.au state: local - server: https://usegalaxy.be/ @@ -32915,22 +13711,22 @@ - server: https://viralvariant.anses.fr/ state: local version: local - - id: Grep1 + - id: __MERGE_COLLECTION__ servers: - server: http://apostl.moffitt.org/ - state: local + state: missing - server: http://mbac.gmu.edu:8080/ - state: local + state: missing - server: https://vm-chemflow-francegrille.eu/ state: missing - server: https://iris.angers.inra.fr/galaxypub-cfbp state: missing - server: https://hyperbrowser.uio.no/coloc-stats - state: local + state: missing - server: https://galaxy.mesocentre.uca.fr state: local - server: https://galaxy.pasteur.fr/ - state: local + state: missing - server: https://galaxytrakr.org/ state: local - server: http://igg.cloud.ba.infn.it/galaxy @@ -32940,23 +13736,19 @@ - server: https://www.immportgalaxy.org/ state: missing - server: http://galaxy.interactomix.com/ - state: missing + state: local - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: local - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr state: local - server: http://galaxy.inf.ethz.ch - state: local + state: missing - server: https://palfinder.ls.manchester.ac.uk/ state: missing - server: http://pepsimili.e-nios.com:8080/ state: local - - server: https://galaxy.bio.di.uminho.pt/ - state: local - server: https://usegalaxy.org.au state: local - server: https://usegalaxy.be/ @@ -32974,7 +13766,7 @@ - server: https://viralvariant.anses.fr/ state: local version: local - - id: toolshed.g2.bx.psu.edu/repos/bebatut/combine_metaphlan2_humann2/combine_metaphlan2_humann2/0.2.0 + - id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.1 servers: - server: http://apostl.moffitt.org/ state: missing @@ -32987,59 +13779,62 @@ - server: https://hyperbrowser.uio.no/coloc-stats state: missing - server: https://galaxy.mesocentre.uca.fr - state: missing + state: exact + version: 0.1.1 - server: https://galaxy.pasteur.fr/ state: missing - server: https://galaxytrakr.org/ - state: missing + state: exact + version: 0.1.1 - server: http://igg.cloud.ba.infn.it/galaxy state: missing - server: https://galaxy.hyphy.org/ - state: missing + state: inexact + versions: + - 9.5+galaxy3 - server: https://www.immportgalaxy.org/ state: missing - server: http://galaxy.interactomix.com/ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr - state: missing + state: inexact + versions: + - 9.5+galaxy3 - server: http://galaxy.inf.ethz.ch state: missing - server: https://palfinder.ls.manchester.ac.uk/ state: missing - server: http://pepsimili.e-nios.com:8080/ state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - server: https://usegalaxy.org.au state: exact - version: 0.2.0 + version: 0.1.1 - server: https://usegalaxy.be/ state: exact - version: 0.2.0 + version: 0.1.1 - server: https://usegalaxy.cz/ - state: inexact - versions: - - 0.1.0 + state: exact + version: 0.1.1 - server: https://usegalaxy.eu - state: missing + state: exact + version: 0.1.1 - server: https://usegalaxy.fr/ - state: missing + state: exact + version: 0.1.1 - server: https://usegalaxy.no/ state: exact - version: 0.2.0 + version: 0.1.1 - server: https://usegalaxy.org state: exact - version: 0.2.0 + version: 0.1.1 - server: https://viralvariant.anses.fr/ state: missing - version: 0.2.0 - - id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.4 + version: 0.1.1 + - id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.2 servers: - server: http://apostl.moffitt.org/ state: missing @@ -33053,15 +13848,12 @@ state: missing - server: https://galaxy.mesocentre.uca.fr state: exact - version: 1.1.4 + version: 1.1.2 - server: https://galaxy.pasteur.fr/ state: missing - server: https://galaxytrakr.org/ - state: inexact - versions: - - 9.5+galaxy3 - - 1.1.3 - - 9.5+galaxy2 + state: exact + version: 1.1.2 - server: http://igg.cloud.ba.infn.it/galaxy state: missing - server: https://galaxy.hyphy.org/ @@ -33074,8 +13866,6 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr @@ -33088,36 +13878,31 @@ state: missing - server: http://pepsimili.e-nios.com:8080/ state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - server: https://usegalaxy.org.au state: exact - version: 1.1.4 + version: 1.1.2 - server: https://usegalaxy.be/ state: exact - version: 1.1.4 + version: 1.1.2 - server: https://usegalaxy.cz/ state: exact - version: 1.1.4 + version: 1.1.2 - server: https://usegalaxy.eu state: exact - version: 1.1.4 + version: 1.1.2 - server: https://usegalaxy.fr/ state: exact - version: 1.1.4 + version: 1.1.2 - server: https://usegalaxy.no/ - state: inexact - versions: - - 1.1.3 - - 1.1.1 - - 1.1.0 + state: exact + version: 1.1.2 - server: https://usegalaxy.org state: exact - version: 1.1.4 + version: 1.1.2 - server: https://viralvariant.anses.fr/ state: missing - version: 1.1.4 - - id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.5+galaxy2 + version: 1.1.2 + - id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/1.1.1 servers: - server: http://apostl.moffitt.org/ state: missing @@ -33130,16 +13915,13 @@ - server: https://hyperbrowser.uio.no/coloc-stats state: missing - server: https://galaxy.mesocentre.uca.fr - state: inexact - versions: - - 9.5+galaxy3 - - 1.1.3 - - 1.1.4 + state: exact + version: 1.1.1 - server: https://galaxy.pasteur.fr/ state: missing - server: https://galaxytrakr.org/ state: exact - version: 9.5+galaxy2 + version: 1.1.1 - server: http://igg.cloud.ba.infn.it/galaxy state: missing - server: https://galaxy.hyphy.org/ @@ -33152,8 +13934,6 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr @@ -33166,36 +13946,31 @@ state: missing - server: http://pepsimili.e-nios.com:8080/ state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - server: https://usegalaxy.org.au state: exact - version: 9.5+galaxy2 + version: 1.1.1 - server: https://usegalaxy.be/ state: exact - version: 9.5+galaxy2 + version: 1.1.1 - server: https://usegalaxy.cz/ state: exact - version: 9.5+galaxy2 + version: 1.1.1 - server: https://usegalaxy.eu state: exact - version: 9.5+galaxy2 + version: 1.1.1 - server: https://usegalaxy.fr/ state: exact - version: 9.5+galaxy2 + version: 1.1.1 - server: https://usegalaxy.no/ - state: inexact - versions: - - 1.1.3 - - 1.1.1 - - 1.1.0 + state: exact + version: 1.1.1 - server: https://usegalaxy.org state: exact - version: 9.5+galaxy2 + version: 1.1.1 - server: https://viralvariant.anses.fr/ state: missing - version: 9.5+galaxy2 - - id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/9.5+galaxy2 + version: 1.1.1 + - id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/1.1.2 servers: - server: http://apostl.moffitt.org/ state: missing @@ -33208,15 +13983,13 @@ - server: https://hyperbrowser.uio.no/coloc-stats state: missing - server: https://galaxy.mesocentre.uca.fr - state: inexact - versions: - - 1.1.1 - - 9.5+galaxy3 + state: exact + version: 1.1.2 - server: https://galaxy.pasteur.fr/ state: missing - server: https://galaxytrakr.org/ state: exact - version: 9.5+galaxy2 + version: 1.1.2 - server: http://igg.cloud.ba.infn.it/galaxy state: missing - server: https://galaxy.hyphy.org/ @@ -33229,8 +14002,6 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr @@ -33243,35 +14014,31 @@ state: missing - server: http://pepsimili.e-nios.com:8080/ state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - server: https://usegalaxy.org.au state: exact - version: 9.5+galaxy2 + version: 1.1.2 - server: https://usegalaxy.be/ state: exact - version: 9.5+galaxy2 + version: 1.1.2 - server: https://usegalaxy.cz/ state: exact - version: 9.5+galaxy2 + version: 1.1.2 - server: https://usegalaxy.eu state: exact - version: 9.5+galaxy2 + version: 1.1.2 - server: https://usegalaxy.fr/ state: exact - version: 9.5+galaxy2 + version: 1.1.2 - server: https://usegalaxy.no/ - state: inexact - versions: - - 1.1.1 - - 1.1.0 + state: exact + version: 1.1.2 - server: https://usegalaxy.org state: exact - version: 9.5+galaxy2 + version: 1.1.2 - server: https://viralvariant.anses.fr/ state: missing - version: 9.5+galaxy2 - - id: toolshed.g2.bx.psu.edu/repos/crs4/taxonomy_krona_chart/taxonomy_krona_chart/2.7.1+galaxy0 + version: 1.1.2 + - id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/1.1.1 servers: - server: http://apostl.moffitt.org/ state: missing @@ -33285,64 +14052,61 @@ state: missing - server: https://galaxy.mesocentre.uca.fr state: exact - version: 2.7.1+galaxy0 + version: 1.1.1 - server: https://galaxy.pasteur.fr/ - state: exact - version: 2.7.1+galaxy0 + state: missing - server: https://galaxytrakr.org/ state: exact - version: 2.7.1+galaxy0 + version: 1.1.1 - server: http://igg.cloud.ba.infn.it/galaxy state: missing - server: https://galaxy.hyphy.org/ - state: missing + state: inexact + versions: + - 9.5+galaxy3 - server: https://www.immportgalaxy.org/ state: missing - server: http://galaxy.interactomix.com/ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr - state: missing + state: inexact + versions: + - 9.5+galaxy3 - server: http://galaxy.inf.ethz.ch state: missing - server: https://palfinder.ls.manchester.ac.uk/ state: missing - server: http://pepsimili.e-nios.com:8080/ - state: exact - version: 2.7.1+galaxy0 - - server: https://galaxy.bio.di.uminho.pt/ state: missing - server: https://usegalaxy.org.au state: exact - version: 2.7.1+galaxy0 + version: 1.1.1 - server: https://usegalaxy.be/ state: exact - version: 2.7.1+galaxy0 + version: 1.1.1 - server: https://usegalaxy.cz/ state: exact - version: 2.7.1+galaxy0 + version: 1.1.1 - server: https://usegalaxy.eu state: exact - version: 2.7.1+galaxy0 + version: 1.1.1 - server: https://usegalaxy.fr/ state: exact - version: 2.7.1+galaxy0 + version: 1.1.1 - server: https://usegalaxy.no/ - state: inexact - versions: - - 2.7.1 + state: exact + version: 1.1.1 - server: https://usegalaxy.org state: exact - version: 2.7.1+galaxy0 + version: 1.1.1 - server: https://viralvariant.anses.fr/ state: missing - version: 2.7.1+galaxy0 - - id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_paired_end_interlacer/fastq_paired_end_interlacer/1.2.0.1+galaxy0 + version: 1.1.1 + - id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_consensus/bcftools_consensus/1.15.1+galaxy3 servers: - server: http://apostl.moffitt.org/ state: missing @@ -33355,14 +14119,15 @@ - server: https://hyperbrowser.uio.no/coloc-stats state: missing - server: https://galaxy.mesocentre.uca.fr - state: exact - version: 1.2.0.1+galaxy0 + state: missing - server: https://galaxy.pasteur.fr/ state: exact - version: 1.2.0.1+galaxy0 + version: 1.15.1+galaxy3 - server: https://galaxytrakr.org/ - state: exact - version: 1.2.0.1+galaxy0 + state: inexact + versions: + - 1.15.1+galaxy4 + - 1.22+galaxy0 - server: http://igg.cloud.ba.infn.it/galaxy state: missing - server: https://galaxy.hyphy.org/ @@ -33373,45 +14138,47 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr - state: missing + state: exact + version: 1.15.1+galaxy3 - server: http://galaxy.inf.ethz.ch state: missing - server: https://palfinder.ls.manchester.ac.uk/ state: missing - server: http://pepsimili.e-nios.com:8080/ state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - server: https://usegalaxy.org.au state: exact - version: 1.2.0.1+galaxy0 + version: 1.15.1+galaxy3 - server: https://usegalaxy.be/ state: exact - version: 1.2.0.1+galaxy0 + version: 1.15.1+galaxy3 - server: https://usegalaxy.cz/ state: exact - version: 1.2.0.1+galaxy0 + version: 1.15.1+galaxy3 - server: https://usegalaxy.eu state: exact - version: 1.2.0.1+galaxy0 + version: 1.15.1+galaxy3 - server: https://usegalaxy.fr/ state: exact - version: 1.2.0.1+galaxy0 + version: 1.15.1+galaxy3 - server: https://usegalaxy.no/ - state: exact - version: 1.2.0.1+galaxy0 + state: inexact + versions: + - 1.10+galaxy1 + - '1.10' + - 1.9+galaxy1 - server: https://usegalaxy.org state: exact - version: 1.2.0.1+galaxy0 + version: 1.15.1+galaxy3 - server: https://viralvariant.anses.fr/ - state: missing - version: 1.2.0.1+galaxy0 - - id: toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy1 + state: inexact + versions: + - 1.15.1+galaxy4 + version: 1.15.1+galaxy3 + - id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_consensus/bcftools_consensus/1.9+galaxy2 servers: - server: http://apostl.moffitt.org/ state: missing @@ -33424,18 +14191,16 @@ - server: https://hyperbrowser.uio.no/coloc-stats state: missing - server: https://galaxy.mesocentre.uca.fr - state: inexact - versions: - - '0.72' - - 0.73+galaxy0 - - 0.72+galaxy1 + state: missing - server: https://galaxy.pasteur.fr/ state: inexact versions: - - 0.74+galaxy0 + - 1.15.1+galaxy3 - server: https://galaxytrakr.org/ - state: exact - version: 0.74+galaxy1 + state: inexact + versions: + - 1.15.1+galaxy4 + - 1.22+galaxy0 - server: http://igg.cloud.ba.infn.it/galaxy state: missing - server: https://galaxy.hyphy.org/ @@ -33446,57 +14211,203 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr - state: exact - version: 0.74+galaxy1 + state: inexact + versions: + - 1.15.1+galaxy3 + - 1.22+galaxy0 + - 1.10+galaxy1 - server: http://galaxy.inf.ethz.ch state: missing - server: https://palfinder.ls.manchester.ac.uk/ + state: missing + - server: http://pepsimili.e-nios.com:8080/ + state: missing + - server: https://usegalaxy.org.au state: inexact versions: - - '0.72' - - 0.72+galaxy1 - - '0.71' - - '0.65' + - 1.15.1+galaxy3 + - 1.15.1+galaxy4 + - 1.22+galaxy0 + - 1.10+galaxy1 + - '1.10' + - '1.9' + - 1.4.0 + - 1.15.1+galaxy2 + - 1.15.1+galaxy0 + - server: https://usegalaxy.be/ + state: exact + version: 1.9+galaxy2 + - server: https://usegalaxy.cz/ + state: inexact + versions: + - 1.15.1+galaxy3 + - 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server: https://galaxy.mesocentre.uca.fr + state: missing + - server: https://galaxy.pasteur.fr/ + state: missing + - server: https://galaxytrakr.org/ + state: missing + - server: http://igg.cloud.ba.infn.it/galaxy + state: missing + - server: https://galaxy.hyphy.org/ + state: missing + - server: https://www.immportgalaxy.org/ + state: missing + - server: http://galaxy.interactomix.com/ + state: missing + - server: https://galaxy-web.ipk-gatersleben.de + state: missing + - server: https://neo.engr.uconn.edu/ + state: missing + - server: https://mississippi.sorbonne-universite.fr + state: missing + - server: http://galaxy.inf.ethz.ch + state: missing + - server: https://palfinder.ls.manchester.ac.uk/ + state: missing - server: http://pepsimili.e-nios.com:8080/ + state: missing + - server: https://usegalaxy.org.au + state: missing + - server: https://usegalaxy.be/ + state: missing + - server: https://usegalaxy.cz/ + state: missing + - server: https://usegalaxy.eu + state: exact + version: 1.1.1 + - server: https://usegalaxy.fr/ + state: missing + - server: https://usegalaxy.no/ + state: missing + - server: https://usegalaxy.org + state: missing + - server: https://viralvariant.anses.fr/ + state: missing + version: 1.1.1 + - id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.13+galaxy2 + servers: + - server: http://apostl.moffitt.org/ + state: missing + - server: http://mbac.gmu.edu:8080/ + state: missing + - server: https://vm-chemflow-francegrille.eu/ + state: missing + - server: https://iris.angers.inra.fr/galaxypub-cfbp + state: missing + - server: https://hyperbrowser.uio.no/coloc-stats + state: missing + - server: https://galaxy.mesocentre.uca.fr state: inexact versions: - - 0.74+galaxy0 - - server: https://galaxy.bio.di.uminho.pt/ + - '1.9' + - 1.22+galaxy1 + - 1.21+galaxy0 + - 1.15.1+galaxy2 + - 1.20+galaxy3 + - server: https://galaxy.pasteur.fr/ + state: missing + - server: https://galaxytrakr.org/ state: inexact versions: - - 0.74+galaxy0 + - 1.22+galaxy1 + - 1.21+galaxy0 + - 1.22+galaxy2 + - server: http://igg.cloud.ba.infn.it/galaxy + state: missing + - server: https://galaxy.hyphy.org/ + state: inexact + versions: + - 1.22+galaxy1 + - server: https://www.immportgalaxy.org/ + state: missing + - server: http://galaxy.interactomix.com/ + state: missing + - server: https://galaxy-web.ipk-gatersleben.de + state: missing + - server: https://neo.engr.uconn.edu/ + state: missing + - server: https://mississippi.sorbonne-universite.fr + state: inexact + versions: + - 1.22+galaxy2 + - server: http://galaxy.inf.ethz.ch + state: missing + - server: https://palfinder.ls.manchester.ac.uk/ + state: missing + - server: http://pepsimili.e-nios.com:8080/ + state: missing - server: https://usegalaxy.org.au state: exact - version: 0.74+galaxy1 + version: 1.13+galaxy2 - server: https://usegalaxy.be/ state: exact - version: 0.74+galaxy1 + version: 1.13+galaxy2 - server: https://usegalaxy.cz/ state: exact - version: 0.74+galaxy1 + version: 1.13+galaxy2 - server: https://usegalaxy.eu state: exact - version: 0.74+galaxy1 + version: 1.13+galaxy2 - server: https://usegalaxy.fr/ state: exact - version: 0.74+galaxy1 + version: 1.13+galaxy2 - server: https://usegalaxy.no/ - state: inexact - versions: - - 0.73+galaxy0 - - 0.72+galaxy1 + state: exact + version: 1.13+galaxy2 - server: https://usegalaxy.org state: exact - version: 0.74+galaxy1 + version: 1.13+galaxy2 - server: https://viralvariant.anses.fr/ state: missing - version: 0.74+galaxy1 - - id: toolshed.g2.bx.psu.edu/repos/iuc/export2graphlan/export2graphlan/0.20+galaxy0 + version: 1.13+galaxy2 + - id: toolshed.g2.bx.psu.edu/repos/iuc/snippy/snippy/3.2 servers: - server: http://apostl.moffitt.org/ state: missing @@ -33509,12 +14420,13 @@ - server: https://hyperbrowser.uio.no/coloc-stats state: missing - server: https://galaxy.mesocentre.uca.fr - state: exact - version: 0.20+galaxy0 + state: missing - server: https://galaxy.pasteur.fr/ state: missing - server: https://galaxytrakr.org/ - state: missing + state: inexact + versions: + - 4.6.0+galaxy0 - server: http://igg.cloud.ba.infn.it/galaxy state: missing - server: https://galaxy.hyphy.org/ @@ -33525,8 +14437,6 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr @@ -33537,33 +14447,37 @@ state: missing - server: http://pepsimili.e-nios.com:8080/ state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - server: https://usegalaxy.org.au - state: exact - version: 0.20+galaxy0 + state: inexact + versions: + - 4.6.0+galaxy0 + - 4.5.0+galaxy1 + - 4.5.0 - server: https://usegalaxy.be/ state: exact - version: 0.20+galaxy0 + version: '3.2' - server: https://usegalaxy.cz/ - state: exact - version: 0.20+galaxy0 + state: inexact + versions: + - 4.6.0+galaxy0 - server: https://usegalaxy.eu state: exact - version: 0.20+galaxy0 + version: '3.2' - server: https://usegalaxy.fr/ - state: exact - version: 0.20+galaxy0 + state: inexact + versions: + - 4.6.0+galaxy0 - server: https://usegalaxy.no/ - state: exact - version: 0.20+galaxy0 + state: inexact + versions: + - 4.6.0+galaxy0 - server: https://usegalaxy.org state: exact - version: 0.20+galaxy0 + version: '3.2' - server: https://viralvariant.anses.fr/ state: missing - version: 0.20+galaxy0 - - id: toolshed.g2.bx.psu.edu/repos/iuc/graphlan/graphlan/1.1.3 + version: '3.2' + - id: toolshed.g2.bx.psu.edu/repos/iuc/snippy/snippy/4.6.0+galaxy0 servers: - server: http://apostl.moffitt.org/ state: missing @@ -33576,13 +14490,12 @@ - server: https://hyperbrowser.uio.no/coloc-stats state: missing - server: https://galaxy.mesocentre.uca.fr - state: exact - version: 1.1.3 + state: missing - server: https://galaxy.pasteur.fr/ state: missing - server: https://galaxytrakr.org/ state: exact - version: 1.1.3 + version: 4.6.0+galaxy0 - server: http://igg.cloud.ba.infn.it/galaxy state: missing - server: https://galaxy.hyphy.org/ @@ -33593,8 +14506,6 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr @@ -33605,33 +14516,31 @@ state: missing - server: http://pepsimili.e-nios.com:8080/ state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - server: https://usegalaxy.org.au state: exact - version: 1.1.3 + version: 4.6.0+galaxy0 - server: https://usegalaxy.be/ state: exact - version: 1.1.3 + version: 4.6.0+galaxy0 - server: https://usegalaxy.cz/ state: exact - version: 1.1.3 + version: 4.6.0+galaxy0 - server: https://usegalaxy.eu state: exact - version: 1.1.3 + version: 4.6.0+galaxy0 - server: https://usegalaxy.fr/ state: exact - version: 1.1.3 + version: 4.6.0+galaxy0 - server: https://usegalaxy.no/ state: exact - version: 1.1.3 + version: 4.6.0+galaxy0 - server: https://usegalaxy.org state: exact - version: 1.1.3 + version: 4.6.0+galaxy0 - server: https://viralvariant.anses.fr/ state: missing - version: 1.1.3 - - id: toolshed.g2.bx.psu.edu/repos/iuc/graphlan_annotate/graphlan_annotate/1.1.3 + version: 4.6.0+galaxy0 + - id: toolshed.g2.bx.psu.edu/repos/iuc/snp_dists/snp_dists/0.6.3+galaxy0 servers: - server: http://apostl.moffitt.org/ state: missing @@ -33644,13 +14553,13 @@ - server: https://hyperbrowser.uio.no/coloc-stats state: missing - server: https://galaxy.mesocentre.uca.fr - state: exact - version: 1.1.3 + state: missing - server: https://galaxy.pasteur.fr/ state: missing - server: https://galaxytrakr.org/ - state: exact - version: 1.1.3 + state: inexact + versions: + - 0.8.2+galaxy0 - server: http://igg.cloud.ba.infn.it/galaxy state: missing - server: https://galaxy.hyphy.org/ @@ -33661,8 +14570,6 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr @@ -33673,33 +14580,32 @@ state: missing - server: http://pepsimili.e-nios.com:8080/ state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - server: https://usegalaxy.org.au - state: exact - version: 1.1.3 + state: inexact + versions: + - 0.8.2+galaxy0 - server: https://usegalaxy.be/ state: exact - version: 1.1.3 + version: 0.6.3+galaxy0 - server: https://usegalaxy.cz/ state: exact - version: 1.1.3 + version: 0.6.3+galaxy0 - server: https://usegalaxy.eu state: exact - version: 1.1.3 + version: 0.6.3+galaxy0 - server: https://usegalaxy.fr/ - state: exact - version: 1.1.3 + state: missing - server: https://usegalaxy.no/ state: exact - version: 1.1.3 + version: 0.6.3+galaxy0 - server: https://usegalaxy.org - state: exact - version: 1.1.3 + state: inexact + versions: + - 0.8.2+galaxy0 - server: https://viralvariant.anses.fr/ state: missing - version: 1.1.3 - - id: toolshed.g2.bx.psu.edu/repos/iuc/humann/humann/3.9+galaxy0 + version: 0.6.3+galaxy0 + - id: toolshed.g2.bx.psu.edu/repos/iuc/snp_dists/snp_dists/0.8.2+galaxy0 servers: - server: http://apostl.moffitt.org/ state: missing @@ -33712,13 +14618,12 @@ - server: https://hyperbrowser.uio.no/coloc-stats state: missing - server: https://galaxy.mesocentre.uca.fr - state: exact - version: 3.9+galaxy0 + state: missing - server: https://galaxy.pasteur.fr/ state: missing - server: https://galaxytrakr.org/ state: exact - version: 3.9+galaxy0 + version: 0.8.2+galaxy0 - server: http://igg.cloud.ba.infn.it/galaxy state: missing - server: https://galaxy.hyphy.org/ @@ -33729,8 +14634,6 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr @@ -33741,35 +14644,30 @@ state: missing - server: http://pepsimili.e-nios.com:8080/ state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - server: https://usegalaxy.org.au state: exact - version: 3.9+galaxy0 + version: 0.8.2+galaxy0 - server: https://usegalaxy.be/ state: exact - version: 3.9+galaxy0 + version: 0.8.2+galaxy0 - server: https://usegalaxy.cz/ state: exact - version: 3.9+galaxy0 + version: 0.8.2+galaxy0 - server: https://usegalaxy.eu state: exact - version: 3.9+galaxy0 + version: 0.8.2+galaxy0 - server: https://usegalaxy.fr/ - state: exact - version: 3.9+galaxy0 + state: missing - server: https://usegalaxy.no/ - state: inexact - versions: - - 3.0.0+galaxy1 - - 3.6.0+galaxy0 + state: exact + version: 0.8.2+galaxy0 - server: https://usegalaxy.org state: exact - version: 3.9+galaxy0 + version: 0.8.2+galaxy0 - server: https://viralvariant.anses.fr/ state: missing - version: 3.9+galaxy0 - - id: toolshed.g2.bx.psu.edu/repos/iuc/humann_regroup_table/humann_regroup_table/3.9+galaxy0 + version: 0.8.2+galaxy0 + - id: toolshed.g2.bx.psu.edu/repos/iuc/snp_sites/snp_sites/2.5.1+galaxy0 servers: - server: http://apostl.moffitt.org/ state: missing @@ -33782,13 +14680,12 @@ - server: https://hyperbrowser.uio.no/coloc-stats state: missing - server: https://galaxy.mesocentre.uca.fr - state: exact - version: 3.9+galaxy0 + state: missing - server: https://galaxy.pasteur.fr/ state: missing - server: https://galaxytrakr.org/ state: exact - version: 3.9+galaxy0 + version: 2.5.1+galaxy0 - server: http://igg.cloud.ba.infn.it/galaxy state: missing - server: https://galaxy.hyphy.org/ @@ -33799,8 +14696,6 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr @@ -33811,41 +14706,30 @@ state: missing - server: http://pepsimili.e-nios.com:8080/ state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - server: https://usegalaxy.org.au state: exact - version: 3.9+galaxy0 + version: 2.5.1+galaxy0 - server: https://usegalaxy.be/ state: exact - version: 3.9+galaxy0 + version: 2.5.1+galaxy0 - server: https://usegalaxy.cz/ state: exact - version: 3.9+galaxy0 + version: 2.5.1+galaxy0 - server: https://usegalaxy.eu - state: inexact - versions: - - 3.7+galaxy0 - - 3.6.0+galaxy0 - - 3.0.0+galaxy1 - - 3.8+galaxy0 - - 3.0.0+galaxy0 - - 3.6.1+galaxy0 - - server: https://usegalaxy.fr/ state: exact - version: 3.9+galaxy0 + version: 2.5.1+galaxy0 + - server: https://usegalaxy.fr/ + state: missing - server: https://usegalaxy.no/ - state: inexact - versions: - - 3.6.0+galaxy0 - - 3.0.0+galaxy1 + state: exact + version: 2.5.1+galaxy0 - server: https://usegalaxy.org state: exact - version: 3.9+galaxy0 + version: 2.5.1+galaxy0 - server: https://viralvariant.anses.fr/ state: missing - version: 3.9+galaxy0 - - id: toolshed.g2.bx.psu.edu/repos/iuc/humann_rename_table/humann_rename_table/3.9+galaxy0 + version: 2.5.1+galaxy0 + - id: toolshed.g2.bx.psu.edu/repos/iuc/tb_variant_filter/tb_variant_filter/0.1.3+galaxy0 servers: - server: http://apostl.moffitt.org/ state: missing @@ -33858,13 +14742,11 @@ - server: https://hyperbrowser.uio.no/coloc-stats state: missing - server: https://galaxy.mesocentre.uca.fr - state: exact - version: 3.9+galaxy0 + state: missing - server: https://galaxy.pasteur.fr/ state: missing - server: https://galaxytrakr.org/ - state: exact - version: 3.9+galaxy0 + state: missing - server: http://igg.cloud.ba.infn.it/galaxy state: missing - server: https://galaxy.hyphy.org/ @@ -33875,8 +14757,6 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr @@ -33887,34 +14767,34 @@ state: missing - server: http://pepsimili.e-nios.com:8080/ state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - server: https://usegalaxy.org.au state: exact - version: 3.9+galaxy0 + version: 0.1.3+galaxy0 - server: https://usegalaxy.be/ state: exact - version: 3.9+galaxy0 + version: 0.1.3+galaxy0 - server: https://usegalaxy.cz/ - state: exact - version: 3.9+galaxy0 + state: inexact + versions: + - 0.3.6+galaxy0 + - 0.4.0+galaxy0 - server: https://usegalaxy.eu state: exact - version: 3.9+galaxy0 + version: 0.1.3+galaxy0 - server: https://usegalaxy.fr/ - state: exact - version: 3.9+galaxy0 - - server: https://usegalaxy.no/ state: inexact versions: - - 3.6.0+galaxy0 + - 0.4.0+galaxy0 + - server: https://usegalaxy.no/ + state: exact + version: 0.1.3+galaxy0 - server: https://usegalaxy.org state: exact - version: 3.9+galaxy0 + version: 0.1.3+galaxy0 - server: https://viralvariant.anses.fr/ state: missing - version: 3.9+galaxy0 - - id: toolshed.g2.bx.psu.edu/repos/iuc/humann_renorm_table/humann_renorm_table/3.9+galaxy0 + version: 0.1.3+galaxy0 + - id: toolshed.g2.bx.psu.edu/repos/iuc/tb_variant_filter/tb_variant_filter/0.3.5+galaxy2 servers: - server: http://apostl.moffitt.org/ state: missing @@ -33927,8 +14807,7 @@ - server: https://hyperbrowser.uio.no/coloc-stats state: missing - server: https://galaxy.mesocentre.uca.fr - state: exact - version: 3.9+galaxy0 + state: missing - server: https://galaxy.pasteur.fr/ state: missing - server: https://galaxytrakr.org/ @@ -33943,8 +14822,6 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr @@ -33955,34 +14832,34 @@ state: missing - server: http://pepsimili.e-nios.com:8080/ state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - server: https://usegalaxy.org.au state: exact - version: 3.9+galaxy0 + version: 0.3.5+galaxy2 - server: https://usegalaxy.be/ state: exact - version: 3.9+galaxy0 + version: 0.3.5+galaxy2 - server: https://usegalaxy.cz/ - state: exact - version: 3.9+galaxy0 + state: inexact + versions: + - 0.3.6+galaxy0 + - 0.4.0+galaxy0 - server: https://usegalaxy.eu state: exact - version: 3.9+galaxy0 + version: 0.3.5+galaxy2 - server: https://usegalaxy.fr/ - state: exact - version: 3.9+galaxy0 - - server: https://usegalaxy.no/ state: inexact versions: - - 3.6.0+galaxy0 + - 0.4.0+galaxy0 + - server: https://usegalaxy.no/ + state: exact + version: 0.3.5+galaxy2 - server: https://usegalaxy.org state: exact - version: 3.9+galaxy0 + version: 0.3.5+galaxy2 - server: https://viralvariant.anses.fr/ state: missing - version: 3.9+galaxy0 - - id: toolshed.g2.bx.psu.edu/repos/iuc/humann_split_stratified_table/humann_split_stratified_table/3.9+galaxy0 + version: 0.3.5+galaxy2 + - id: toolshed.g2.bx.psu.edu/repos/iuc/tb_variant_filter/tb_variant_filter/0.3.6+galaxy0 servers: - server: http://apostl.moffitt.org/ state: missing @@ -33995,8 +14872,7 @@ - server: https://hyperbrowser.uio.no/coloc-stats state: missing - server: https://galaxy.mesocentre.uca.fr - state: exact - version: 3.9+galaxy0 + state: missing - server: https://galaxy.pasteur.fr/ state: missing - server: https://galaxytrakr.org/ @@ -34011,8 +14887,6 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr @@ -34023,34 +14897,38 @@ state: missing - server: http://pepsimili.e-nios.com:8080/ state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - server: https://usegalaxy.org.au state: exact - version: 3.9+galaxy0 + version: 0.3.6+galaxy0 - server: https://usegalaxy.be/ - state: exact - version: 3.9+galaxy0 + state: inexact + versions: + - 0.1.3+galaxy0 + - 0.3.5+galaxy2 + - 0.4.0+galaxy0 - server: https://usegalaxy.cz/ state: exact - version: 3.9+galaxy0 + version: 0.3.6+galaxy0 - server: https://usegalaxy.eu state: exact - version: 3.9+galaxy0 + version: 0.3.6+galaxy0 - server: https://usegalaxy.fr/ - state: exact - version: 3.9+galaxy0 + state: inexact + versions: + - 0.4.0+galaxy0 - server: https://usegalaxy.no/ state: inexact versions: - - 3.6.0+galaxy0 + - 0.1.3+galaxy0 + - 0.3.5+galaxy2 + - 0.3.5+galaxy1 - server: https://usegalaxy.org state: exact - version: 3.9+galaxy0 + version: 0.3.6+galaxy0 - server: https://viralvariant.anses.fr/ state: missing - version: 3.9+galaxy0 - - id: toolshed.g2.bx.psu.edu/repos/iuc/humann_unpack_pathways/humann_unpack_pathways/3.9+galaxy0 + version: 0.3.6+galaxy0 + - id: toolshed.g2.bx.psu.edu/repos/iuc/tbprofiler/tb_profiler_profile/3.0.8+galaxy0 servers: - server: http://apostl.moffitt.org/ state: missing @@ -34063,13 +14941,11 @@ - server: https://hyperbrowser.uio.no/coloc-stats state: missing - server: https://galaxy.mesocentre.uca.fr - state: exact - version: 3.9+galaxy0 + state: missing - server: https://galaxy.pasteur.fr/ state: missing - server: https://galaxytrakr.org/ - state: exact - version: 3.9+galaxy0 + state: missing - server: http://igg.cloud.ba.infn.it/galaxy state: missing - server: https://galaxy.hyphy.org/ @@ -34080,8 +14956,6 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr @@ -34092,34 +14966,36 @@ state: missing - 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id: toolshed.g2.bx.psu.edu/repos/mvdbeek/add_input_name_as_column/addName/0.2.0 servers: - server: http://apostl.moffitt.org/ state: missing @@ -34132,12 +15008,12 @@ - server: https://hyperbrowser.uio.no/coloc-stats state: missing - server: https://galaxy.mesocentre.uca.fr - state: exact - version: 4.1.1+galaxy4 + state: missing - server: https://galaxy.pasteur.fr/ state: missing - server: https://galaxytrakr.org/ - state: missing + state: exact + version: 0.2.0 - server: http://igg.cloud.ba.infn.it/galaxy state: missing - server: https://galaxy.hyphy.org/ @@ -34148,46 +15024,42 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr - state: missing + state: exact + version: 0.2.0 - server: http://galaxy.inf.ethz.ch state: missing - server: https://palfinder.ls.manchester.ac.uk/ state: missing - server: http://pepsimili.e-nios.com:8080/ state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - server: https://usegalaxy.org.au state: exact - version: 4.1.1+galaxy4 + version: 0.2.0 - server: https://usegalaxy.be/ state: exact - version: 4.1.1+galaxy4 + version: 0.2.0 - server: https://usegalaxy.cz/ state: exact - version: 4.1.1+galaxy4 + version: 0.2.0 - server: https://usegalaxy.eu state: exact - version: 4.1.1+galaxy4 + version: 0.2.0 - server: https://usegalaxy.fr/ state: exact - version: 4.1.1+galaxy4 + version: 0.2.0 - server: https://usegalaxy.no/ - state: inexact - versions: - - 4.0.3+galaxy0 + state: exact + version: 0.2.0 - server: https://usegalaxy.org state: exact - version: 4.1.1+galaxy4 + version: 0.2.0 - server: https://viralvariant.anses.fr/ state: missing - version: 4.1.1+galaxy4 - - id: toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.27+galaxy3 + version: 0.2.0 + - id: toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0 servers: - server: http://apostl.moffitt.org/ state: missing @@ -34201,77 +15073,60 @@ state: missing - 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server: http://galaxy.interactomix.com/ - state: missing + state: local - server: https://galaxy-web.ipk-gatersleben.de - state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing + state: local - server: https://neo.engr.uconn.edu/ - state: missing + state: local - server: https://mississippi.sorbonne-universite.fr - state: missing + state: local - server: http://galaxy.inf.ethz.ch - state: missing + state: local - server: https://palfinder.ls.manchester.ac.uk/ - state: missing + state: local - server: http://pepsimili.e-nios.com:8080/ - state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing + state: local - server: https://usegalaxy.org.au - state: exact - version: 4.3.6+galaxy0 + state: missing - server: https://usegalaxy.be/ - state: exact - version: 4.3.6+galaxy0 + state: local - server: https://usegalaxy.cz/ - state: exact - version: 4.3.6+galaxy0 + state: local - server: https://usegalaxy.eu - state: exact - version: 4.3.6+galaxy0 + state: local - server: https://usegalaxy.fr/ - state: exact - version: 4.3.6+galaxy0 + state: local - server: https://usegalaxy.no/ - state: exact - version: 4.3.6+galaxy0 + state: local - server: https://usegalaxy.org - state: exact - version: 4.3.6+galaxy0 + state: local - server: https://viralvariant.anses.fr/ - state: missing - version: 4.3.6+galaxy0 + state: local + version: local symlink: null tags: - - metatranscriptomics + - prokaryote + - one-health - microgalaxy - time_estimation: 3H - title: Metatranscriptomics analysis using microbiome RNA-seq data (short) + time: null + time_estimation: 2H + title: 'Identifying tuberculosis transmission links: from SNPs to transmission clusters' tools: - - Cut1 - Grep1 - - toolshed.g2.bx.psu.edu/repos/bebatut/combine_metaphlan2_humann2/combine_metaphlan2_humann2/0.2.0 - - toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.4 - - toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.5+galaxy2 - - toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/9.5+galaxy2 - 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- toolshed.g2.bx.psu.edu/repos/iuc/metaphlan/metaphlan/4.1.1+galaxy4 - - toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.27+galaxy3 - - toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/5.0+galaxy0 - - toolshed.g2.bx.psu.edu/repos/rnateam/sortmerna/bg_sortmerna/4.3.6+galaxy0 - topic_name: microbiome - topic_name_human: Microbiome + - __MERGE_COLLECTION__ + - toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.1 + - toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.2 + - toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/1.1.1 + - toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/1.1.2 + - toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/1.1.1 + - toolshed.g2.bx.psu.edu/repos/iuc/bcftools_consensus/bcftools_consensus/1.15.1+galaxy3 + - toolshed.g2.bx.psu.edu/repos/iuc/bcftools_consensus/bcftools_consensus/1.9+galaxy2 + - toolshed.g2.bx.psu.edu/repos/iuc/clustering_from_distmat/clustering_from_distmat/1.1.1 + - toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.13+galaxy2 + - toolshed.g2.bx.psu.edu/repos/iuc/snippy/snippy/3.2 + - toolshed.g2.bx.psu.edu/repos/iuc/snippy/snippy/4.6.0+galaxy0 + - toolshed.g2.bx.psu.edu/repos/iuc/snp_dists/snp_dists/0.6.3+galaxy0 + - toolshed.g2.bx.psu.edu/repos/iuc/snp_dists/snp_dists/0.8.2+galaxy0 + - toolshed.g2.bx.psu.edu/repos/iuc/snp_sites/snp_sites/2.5.1+galaxy0 + - toolshed.g2.bx.psu.edu/repos/iuc/tb_variant_filter/tb_variant_filter/0.1.3+galaxy0 + - toolshed.g2.bx.psu.edu/repos/iuc/tb_variant_filter/tb_variant_filter/0.3.5+galaxy2 + - toolshed.g2.bx.psu.edu/repos/iuc/tb_variant_filter/tb_variant_filter/0.3.6+galaxy0 + - toolshed.g2.bx.psu.edu/repos/iuc/tbprofiler/tb_profiler_profile/3.0.8+galaxy0 + - toolshed.g2.bx.psu.edu/repos/mvdbeek/add_input_name_as_column/addName/0.2.0 + - toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0 + - toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.38.1 + - upload1 + topic_name: evolution + topic_name_human: Evolution tours: false translations: slides: [] tutorial: [] video: false - tutorial_name: metatranscriptomics-short + tutorial_name: mtb_transmission type: tutorial - url: https://training.galaxyproject.org//topics/microbiome/tutorials/metatranscriptomics-short/tutorial.html + url: https://training.galaxyproject.org//topics/evolution/tutorials/mtb_transmission/tutorial.html urls: - hands_on: https://training.galaxyproject.org/training-material/api/topics/microbiome/tutorials/metatranscriptomics-short/tutorial.json - slides: https://training.galaxyproject.org/training-material/api/topics/microbiome/tutorials/metatranscriptomics-short/tutorial.json - version: 6 - video: true - video_versions: 2 - video_view: 0 - visit_duration: 599 - visitors: 1036 - workflows: - - creators: - - class: Person - identifier: 0000-0001-9852-1987 - name: "B\xE9r\xE9nice Batut" - - class: Person - identifier: 0000-0003-0984-0973 - name: Pratik Jagtap - - class: Person - identifier: 0000-0001-9818-0537 - name: Subina Mehta - - class: Person - identifier: 0000-0003-3803-468X - name: Saskia Hiltemann - - class: Person - identifier: 0000-0003-2982-388X - name: Paul Zierep - description: Metatranscriptomics analysis using microbiome RNA-seq data (short) - features: - comments: true - parameters: false - report: - markdown: ' - - # Workflow Execution Report - - - ## Workflow Inputs - - ```galaxy - - invocation_inputs() - - ``` - - - ## Workflow Outputs - - ```galaxy - - invocation_outputs() - - ``` - - - ## Workflow - - ```galaxy - - workflow_display() - - ``` - - ' - subworkflows: false - graph_dot: "digraph main {\n node [fontname=\"Atkinson Hyperlegible\", shape=box,\ - \ color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n edge [fontname=\"\ - Atkinson Hyperlegible\"];\n 0[color=lightblue,label=\"\u2139\uFE0F Input Dataset\\\ - nReverse raw reads\"]\n 1[color=lightblue,label=\"\u2139\uFE0F Input Dataset\\\ - nForward raw reads\"]\n 2[label=\"FastQC\"]\n 0 -> 2 [label=\"output\"]\n\ - \ k676cd11f047947c4a23bc6c8ed5a7790[color=lightseagreen,label=\"Output\\nfastqc_reverse_html_file\"\ - ]\n 2 -> k676cd11f047947c4a23bc6c8ed5a7790\n 3[label=\"FastQC\"]\n 1 -> 3\ - \ [label=\"output\"]\n k1fb52b78c90543c7a295d628c996d35a[color=lightseagreen,label=\"\ - Output\\nfastqc_forward_html_file\"]\n 3 -> k1fb52b78c90543c7a295d628c996d35a\n\ - \ 4[label=\"Cutadapt\"]\n 1 -> 4 [label=\"output\"]\n 0 -> 4 [label=\"output\"\ - ]\n k0e7406ed9eca486eb19a4cbbf04b5138[color=lightseagreen,label=\"Output\\\ - ncutadapt_report\"]\n 4 -> k0e7406ed9eca486eb19a4cbbf04b5138\n 5[label=\"\ - MultiQC\"]\n 3 -> 5 [label=\"text_file\"]\n 2 -> 5 [label=\"text_file\"]\n\ - \ kd9f371ddaa6c4540b62b0e34c0b71afa[color=lightseagreen,label=\"Output\\nmultiqc_html_report\"\ - ]\n 5 -> kd9f371ddaa6c4540b62b0e34c0b71afa\n 6[label=\"Filter with SortMeRNA\"\ - ]\n 4 -> 6 [label=\"out1\"]\n 4 -> 6 [label=\"out2\"]\n k3092eb62d7fc4d66bf574c6cf491d0e3[color=lightseagreen,label=\"\ - Output\\nsortmerna_unaligned_reverse\"]\n 6 -> k3092eb62d7fc4d66bf574c6cf491d0e3\n\ - \ kdb3bb8ee8af74528be4bf3ea6d381856[color=lightseagreen,label=\"Output\\nsortmerna_unaligned_forward\"\ - ]\n 6 -> kdb3bb8ee8af74528be4bf3ea6d381856\n 7[label=\"FASTQ interlacer\"\ - ]\n 6 -> 7 [label=\"unaligned_forward\"]\n 6 -> 7 [label=\"unaligned_reverse\"\ - ]\n}" - history: - - hash: 604d1261ba4f89d6650304d72c7b6d8e4166b3a6 - message: 'Update metatranscriptomics tutorials:' - num: 2 - short_hash: 604d1261b - unix: '1750082204' - - hash: 0e0a2f2ccb650b0aab1ffc13838045164bdb5d30 - message: Rename metagenomics topic to microbiome - num: 1 - short_hash: 0e0a2f2cc - unix: '1704901629' - inputs: - - annotation: Metatranscriptomics reverse raw reads - content_id: null - errors: null - id: 0 - input_connections: {} - inputs: - - description: Metatranscriptomics reverse raw reads - name: Reverse raw reads - label: Reverse raw reads - name: Input dataset - outputs: [] - position: - left: 0 - top: 550 - tool_id: null - tool_state: '{"optional": false, "tag": null}' - tool_version: null - type: data_input - uuid: 9871068a-7fcf-4e95-8e77-958e3f536c55 - when: null - workflow_outputs: [] - - annotation: Metatranscriptomics forward raw reads - content_id: null - errors: null - id: 1 - input_connections: {} - inputs: - - description: Metatranscriptomics forward raw reads - name: Forward raw reads - label: Forward raw reads - name: Input dataset - outputs: [] - position: - left: 0 - top: 690 - tool_id: null - tool_state: '{"optional": false, "tag": null}' - tool_version: null - type: data_input - uuid: 4bf6d16f-73df-4104-8282-46b69813c225 - when: null - workflow_outputs: [] - license: MIT - mermaid: "flowchart TD\n 0[\"\u2139\uFE0F Input Dataset\\nReverse raw reads\"\ - ];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"\u2139\uFE0F Input Dataset\\\ - nForward raw reads\"];\n style 1 stroke:#2c3143,stroke-width:4px;\n 2[\"FastQC\"\ - ];\n 0 -->|output| 2;\n 676cd11f-0479-47c4-a23b-c6c8ed5a7790[\"Output\\nfastqc_reverse_html_file\"\ - ];\n 2 --> 676cd11f-0479-47c4-a23b-c6c8ed5a7790;\n style 676cd11f-0479-47c4-a23b-c6c8ed5a7790\ - \ stroke:#2c3143,stroke-width:4px;\n 3[\"FastQC\"];\n 1 -->|output| 3;\n \ - \ 1fb52b78-c905-43c7-a295-d628c996d35a[\"Output\\nfastqc_forward_html_file\"\ - 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- label: sortmerna_unaligned_forward - output_name: unaligned_forward - uuid: db3bb8ee-8af7-4528-be4b-f3ea6d381856 - parent_id: microbiome/metatranscriptomics-short - path: topics/microbiome/tutorials/metatranscriptomics-short/workflows/workflow1_preprocessing.ga - tags: - - microbiome - test_results: null - tests: true - title: 'Metatranscriptomics analysis using microbiome RNA-seq data - Workflow - 1: Preprocessing' - topic_id: microbiome - trs_endpoint: https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/microbiome-metatranscriptomics-short/versions/workflow1-preprocessing - tutorial_id: metatranscriptomics-short - url: https://training.galaxyproject.org/training-material/topics/microbiome/tutorials/metatranscriptomics-short/workflows/workflow1_preprocessing.ga - url_html: https://training.galaxyproject.org/training-material/topics/microbiome/tutorials/metatranscriptomics-short/workflows/workflow1_preprocessing.html - version: 2 - wfid: microbiome-metatranscriptomics-short - wfname: workflow1-preprocessing - workflow: workflow1_preprocessing.ga - workflow_tools: - - toolshed.g2.bx.psu.edu/repos/devteam/fastq_paired_end_interlacer/fastq_paired_end_interlacer/1.2.0.1+galaxy0 - - toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy1 - - toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.27+galaxy3 - - toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/5.0+galaxy0 - - toolshed.g2.bx.psu.edu/repos/rnateam/sortmerna/bg_sortmerna/4.3.6+galaxy0 - workflowhub_id: '1444' - - creators: - - class: Person - identifier: 0000-0001-9852-1987 - name: "B\xE9r\xE9nice Batut" - - class: Person - identifier: 0000-0003-0984-0973 - name: Pratik Jagtap - - class: Person - identifier: 0000-0001-9818-0537 - name: Subina Mehta - - class: Person - identifier: 0000-0003-3803-468X - name: Saskia Hiltemann - - class: Person - identifier: 0000-0003-2982-388X - name: Paul Zierep - description: Metatranscriptomics analysis using microbiome RNA-seq data (short) - features: - comments: true - parameters: false - report: - markdown: ' - - # Workflow Execution Report - - - ## Workflow Inputs - - ```galaxy - - invocation_inputs() - - ``` - - - ## Workflow Outputs - - ```galaxy - - invocation_outputs() - - ``` - - - ## Workflow - - ```galaxy - - workflow_display() - - ``` - - ' + hands_on: https://training.galaxyproject.org/training-material/api/topics/evolution/tutorials/mtb_transmission/tutorial.json + slides: https://training.galaxyproject.org/training-material/api/topics/evolution/tutorials/mtb_transmission/tutorial.json + version: 13 + video: false + video_versions: 0 + video_view: 0 + visit_duration: 465 + visitors: 3741 + workflows: + - creators: [] + description: Starting from the BAM files produced by snippy, generate a table + that summarizes the drug-resistance profile for each sample + features: + comments: false + parameters: false + report: null subworkflows: false graph_dot: "digraph main {\n node [fontname=\"Atkinson Hyperlegible\", shape=box,\ \ color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n edge [fontname=\"\ - 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- hash: 604d1261ba4f89d6650304d72c7b6d8e4166b3a6 - message: 'Update metatranscriptomics tutorials:' + - hash: 103d419430b5164ef56e7de3bd3ef13e798967cd + message: update tag num: 2 - short_hash: 604d1261b - unix: '1750082204' - - hash: 0e0a2f2ccb650b0aab1ffc13838045164bdb5d30 - message: Rename metagenomics topic to microbiome + short_hash: 103d41943 + unix: '1647422971' + - hash: 2e7ba78522415b81e10f3f5a74144f4f419b218d + message: tweak num: 1 - short_hash: 0e0a2f2cc - unix: '1704901629' + short_hash: 2e7ba7852 + unix: '1647422653' inputs: - - annotation: Metatranscriptomics forward preprocessed reads + - annotation: BAMs obtained from single-end mappings with snippy content_id: null errors: null id: 0 input_connections: {} inputs: - - description: Metatranscriptomics forward preprocessed reads - name: Forward reads - label: Forward reads - name: Input dataset + - description: BAMs obtained from single-end mappings with snippy + name: MTB single-end BAMs + label: MTB single-end BAMs + name: Input dataset collection outputs: [] position: - left: 0 - top: 50 + bottom: 586.3333282470703 + height: 89.09999084472656 + left: -233.6999969482422 + right: -13.699996948242188 + top: 497.23333740234375 + width: 220 + x: -233.6999969482422 + y: 497.23333740234375 tool_id: null - tool_state: '{"optional": false, "tag": null}' + tool_state: '{"optional": false, "collection_type": "list"}' tool_version: null - type: data_input - uuid: 4bf6d16f-73df-4104-8282-46b69813c225 - when: null + type: data_collection_input + uuid: 5befe3e8-ccba-4b78-b7f1-dab039ef1011 workflow_outputs: [] - - annotation: Metatranscriptomics reverse preprocessed reads + - annotation: BAMs obtained from paired-end mappings with snippy content_id: null errors: null id: 1 input_connections: {} inputs: - - description: Metatranscriptomics reverse preprocessed reads - name: Reverse reads - label: Reverse reads - name: Input dataset + - description: BAMs obtained from paired-end mappings with snippy + name: MTB paired-end BAMs + label: MTB paired-end BAMs + name: Input dataset collection outputs: [] position: - left: 0 - top: 170 + bottom: 695.3333282470703 + height: 89.09999084472656 + left: -234.6999969482422 + right: -14.699996948242188 + top: 606.2333374023438 + width: 220 + x: -234.6999969482422 + y: 606.2333374023438 tool_id: null - tool_state: '{"optional": false, "tag": null}' + tool_state: '{"optional": false, "collection_type": "list"}' tool_version: null - type: data_input - uuid: 9871068a-7fcf-4e95-8e77-958e3f536c55 - when: null + type: data_collection_input + uuid: d6f269d8-66e8-4baf-9b5c-de9e7313c4a0 workflow_outputs: [] - license: MIT - mermaid: "flowchart TD\n 0[\"\u2139\uFE0F Input Dataset\\nForward reads\"];\n\ - \ style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"\u2139\uFE0F Input Dataset\\\ - nReverse reads\"];\n style 1 stroke:#2c3143,stroke-width:4px;\n 2[\"MetaPhlAn\"\ - ];\n 0 -->|output| 2;\n 1 -->|output| 2;\n b13521db-f5e7-4bf3-b7fa-673d13fc2911[\"\ - Output\\nmetaphlan_predicted_taxons\"];\n 2 --> b13521db-f5e7-4bf3-b7fa-673d13fc2911;\n\ - \ style b13521db-f5e7-4bf3-b7fa-673d13fc2911 stroke:#2c3143,stroke-width:4px;\n\ - \ 3[\"Cut\"];\n 2 -->|output_file| 3;\n 4[\"Krona pie chart\"];\n 2 -->|krona_output_file|\ - \ 4;\n 5[\"Export to GraPhlAn\"];\n 3 -->|out_file1| 5;\n 6[\"Generation,\ - \ personalization and annotation of tree\"];\n 5 -->|annotation| 6;\n 5 -->|tree|\ - \ 6;\n 7[\"GraPhlAn\"];\n 6 -->|output_tree| 7;\n 21fca66f-dce0-496f-994f-dc8e855e0c8f[\"\ - Output\\ngraphlan_output_image\"];\n 7 --> 21fca66f-dce0-496f-994f-dc8e855e0c8f;\n\ - \ style 21fca66f-dce0-496f-994f-dc8e855e0c8f stroke:#2c3143,stroke-width:4px;" - modified: 2026-05-21 00:30:25 +0000 - name: 'Metatranscriptomics analysis using microbiome RNA-seq data - Workflow 2: - Community profile' + license: null + mermaid: "flowchart TD\n 0[\"\u2139\uFE0F Input Collection\\nMTB single-end BAMs\"\ + ];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"\u2139\uFE0F Input Collection\\\ + nMTB paired-end BAMs\"];\n style 1 stroke:#2c3143,stroke-width:4px;\n 2[\"\ + Merge collections\"];\n 0 -->|output| 2;\n 1 -->|output| 2;\n 3[\"Samtools\ + \ view BAM > SAM\"];\n 2 -->|output| 3;\n aa220027-9d10-4328-b2c2-e4d139d5d5bd[\"\ + Output\\nSamtools view on input dataset(s): filtered alignments\"];\n 3 -->\ + \ aa220027-9d10-4328-b2c2-e4d139d5d5bd;\n style aa220027-9d10-4328-b2c2-e4d139d5d5bd\ + \ stroke:#2c3143,stroke-width:4px;\n 4[\"Sed MTB_anc to Chromosome\"];\n 3\ + \ -->|outputsam| 4;\n 5[\"Samtools view SAM > BAM\"];\n 4 -->|output| 5;\n\ + \ 6[\"TB-profiler\"];\n 5 -->|outputsam| 6;\n 7[\"Get drug resistance profile\"\ + ];\n 6 -->|output_txt| 7;\n 8[\"Add Sample Name\"];\n 7 -->|output| 8;\n\ + \ 9[\"Concatenate DR profiles in a single table\"];\n 8 -->|output| 9;\n \ + \ 10[\"Cleanup the table\"];\n 9 -->|out_file1| 10;" + modified: 2026-07-01 00:31:38 +0000 + name: From BAMs to drug resistance prediction with TB-profiler outputs: - - annotation: '' - content_id: toolshed.g2.bx.psu.edu/repos/iuc/metaphlan/metaphlan/4.1.1+galaxy4 + - annotation: Merge single-end and paired-end BAMs in a single collection to be + analyzed alltogether + content_id: __MERGE_COLLECTION__ errors: null id: 2 input_connections: - inputs|in|raw_in|in_f: + inputs_0|input: id: 0 output_name: output - inputs|in|raw_in|in_r: + inputs_1|input: id: 1 output_name: output inputs: [] - label: null - name: MetaPhlAn + label: Merge collections + name: Merge collections outputs: - - name: output_file - type: tabular - - name: bowtie2out - type: tabular - - name: sam_output_file - type: sam - - name: biom_output_file - type: biom1 - - name: krona_output_file - type: tabular + - name: output + type: input position: - left: 340 - top: 50 + bottom: 720.5 + height: 222.26666259765625 + left: 34.80000305175781 + right: 254.8000030517578 + top: 498.23333740234375 + width: 220 + x: 34.80000305175781 + y: 498.23333740234375 post_job_actions: {} - tool_id: toolshed.g2.bx.psu.edu/repos/iuc/metaphlan/metaphlan/4.1.1+galaxy4 - tool_shed_repository: - changeset_revision: eca2e2e20436 - name: metaphlan - owner: iuc - tool_shed: toolshed.g2.bx.psu.edu - tool_state: '{"__input_ext": "input", "analysis": {"analysis_type": {"t": "rel_ab", - "__current_case__": 0, "tax_lev": {"tax_lev": "a", "__current_case__": 0, - "split_levels": false}}, "min_cu_len": "2000", "min_alignment_len": null, - "organism_profiling": "add_viruses", "stat": "tavg_g", "stat_q": "0.2", "perc_nonzero": - "0.33", "ignore_markers": null, "avoid_disqm": true}, "chromInfo": "/shared/ifbstor1/galaxy/mutable-config/tool-data/shared/ucsc/chrom/?.len", - "inputs": {"in": {"selector": "raw", "__current_case__": 0, "raw_in": {"selector": - "paired", "__current_case__": 3, "in_f": {"__class__": "ConnectedValue"}, - "in_r": {"__class__": "ConnectedValue"}}, "read_min_len": "70", "mapping": - {"bt2_ps": "very-sensitive", "min_mapq_val": "5"}}, "db": {"db_selector": - "cached", "__current_case__": 0, "cached_db": "mpa_vJun23_CHOCOPhlAnSGB_202403-16062025"}}, - "out": {"sample_id_key": "SampleID", "sample_id": "Metaphlan_Analysis", "use_group_representative": - false, "legacy_output": false, "CAMI_format_output": false, "unclassified_estimation": - false, "krona_output": true}, "subsample": {"selector": "no", "__current_case__": - 0}, "test": "false", "viral_analysis": {"profile_vsc": "", "__current_case__": - 1}, "__page__": 0, "__rerun_remap_job_id__": null}' - tool_version: 4.1.1+galaxy4 + tool_id: __MERGE_COLLECTION__ + tool_state: '{"advanced": {"conflict": {"duplicate_options": "keep_first", "__current_case__": + 3}}, "inputs": [{"__index__": 0, "input": {"__class__": "ConnectedValue"}}, + {"__index__": 1, "input": {"__class__": "ConnectedValue"}}], "__page__": null, + "__rerun_remap_job_id__": null}' + tool_version: 1.0.0 type: tool - uuid: ec00e8bd-0a82-40ba-b9e3-40279fbc4dbf - when: null + uuid: 2142f124-4731-49fb-8e65-8e050705e001 workflow_outputs: - - label: metaphlan_predicted_taxons - output_name: output_file - uuid: b13521db-f5e7-4bf3-b7fa-673d13fc2911 - - annotation: '' - content_id: toolshed.g2.bx.psu.edu/repos/iuc/graphlan/graphlan/1.1.3 + - label: null + output_name: output + uuid: 180a1bdf-d552-49b7-93e9-4daf609096a6 + - annotation: We want a text (SAM) file to substitute the string "MTB_anc" by + "Chromosome" so it is compatible with TB-profiler + content_id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.13+galaxy2 errors: null - id: 7 + id: 3 input_connections: - input_tree: - id: 6 - output_name: output_tree + input: + id: 2 + output_name: output inputs: [] - label: null - name: GraPhlAn + label: Samtools view BAM > SAM + name: Samtools view outputs: - - name: png_output_image - type: png + - name: outputsam + type: input position: - left: 1340 - top: 50 + bottom: 951.5000152587891 + height: 189.8333282470703 + left: 277.6000061035156 + right: 497.6000061035156 + top: 761.6666870117188 + width: 220 + x: 277.6000061035156 + y: 761.6666870117188 post_job_actions: {} - tool_id: toolshed.g2.bx.psu.edu/repos/iuc/graphlan/graphlan/1.1.3 + tool_id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.13+galaxy2 tool_shed_repository: - changeset_revision: 6e8eb0c0d91f - name: graphlan + changeset_revision: 0dbf49c414ae + name: samtools_view owner: iuc tool_shed: toolshed.g2.bx.psu.edu - tool_state: '{"__input_ext": "phyloxml", "chromInfo": "/shared/ifbstor1/galaxy/mutable-config/tool-data/shared/ucsc/chrom/?.len", - "image_format": {"format": "png", "__current_case__": 0, "dpi": null}, "input_tree": - {"__class__": "ConnectedValue"}, "pad": null, "size": "7", "__page__": 0, - "__rerun_remap_job_id__": null}' - tool_version: 1.1.3 + tool_state: '{"addref_cond": {"addref_select": "no", "__current_case__": 0}, + "input": {"__class__": "ConnectedValue"}, "mode": {"outtype": "all_reads", + "__current_case__": 0, "output_options": {"reads_report_type": "retained", + "__current_case__": 0, "adv_output": {"readtags": [], "collapsecigar": "false"}, + "output_format": {"oformat": "sam", "__current_case__": 1, "with_header": + "true"}}}, "__page__": null, "__rerun_remap_job_id__": null}' + tool_version: 1.13+galaxy2 type: tool - uuid: 95ab0fae-fbec-40d1-a43b-5b0f276760aa - when: null + uuid: 1040a122-5729-41a4-bd45-2406231f8024 workflow_outputs: - - label: graphlan_output_image - output_name: png_output_image - uuid: 21fca66f-dce0-496f-994f-dc8e855e0c8f - parent_id: microbiome/metatranscriptomics-short - path: topics/microbiome/tutorials/metatranscriptomics-short/workflows/workflow2_community_profile.ga - tags: - - microbiome - test_results: null - tests: true - title: 'Metatranscriptomics analysis using microbiome RNA-seq data - Workflow - 2: Community profile' - topic_id: microbiome - trs_endpoint: https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/microbiome-metatranscriptomics-short/versions/workflow2-community-profile - tutorial_id: metatranscriptomics-short - url: https://training.galaxyproject.org/training-material/topics/microbiome/tutorials/metatranscriptomics-short/workflows/workflow2_community_profile.ga - url_html: https://training.galaxyproject.org/training-material/topics/microbiome/tutorials/metatranscriptomics-short/workflows/workflow2_community_profile.html - version: 2 - wfid: microbiome-metatranscriptomics-short - wfname: workflow2-community-profile - workflow: workflow2_community_profile.ga - workflow_tools: - - Cut1 - - toolshed.g2.bx.psu.edu/repos/crs4/taxonomy_krona_chart/taxonomy_krona_chart/2.7.1+galaxy0 - - toolshed.g2.bx.psu.edu/repos/iuc/export2graphlan/export2graphlan/0.20+galaxy0 - - toolshed.g2.bx.psu.edu/repos/iuc/graphlan/graphlan/1.1.3 - - toolshed.g2.bx.psu.edu/repos/iuc/graphlan_annotate/graphlan_annotate/1.1.3 - - toolshed.g2.bx.psu.edu/repos/iuc/metaphlan/metaphlan/4.1.1+galaxy4 - workflowhub_id: '1451' - - creators: - - class: Person - identifier: 0000-0001-9852-1987 - name: "B\xE9r\xE9nice Batut" - - class: Person - identifier: 0000-0003-0984-0973 - name: Pratik Jagtap - - class: Person - identifier: 0000-0001-9818-0537 - name: Subina Mehta - - class: Person - identifier: 0000-0003-3803-468X - name: Saskia Hiltemann - - class: Person - identifier: 0000-0003-2982-388X - name: Paul Zierep - description: Metatranscriptomics analysis using microbiome RNA-seq data (short) - features: - comments: true - parameters: false - report: - markdown: ' - - # Workflow Execution Report - - - ## Workflow Inputs - - ```galaxy - - invocation_inputs() - - ``` - - - ## Workflow Outputs - - ```galaxy - - invocation_outputs() - - ``` - - - ## Workflow - - ```galaxy - - workflow_display() - - ``` - - ' - subworkflows: false - graph_dot: "digraph main {\n node [fontname=\"Atkinson Hyperlegible\", shape=box,\ - \ color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n edge [fontname=\"\ - Atkinson Hyperlegible\"];\n 0[color=lightblue,label=\"\u2139\uFE0F Input Dataset\\\ - nInterleaced reads\"]\n 1[color=lightblue,label=\"\u2139\uFE0F Input Dataset\\\ - nTaxonomic profile\"]\n 2[label=\"HUMAnN\"]\n 0 -> 2 [label=\"output\"]\n\ - \ 1 -> 2 [label=\"output\"]\n k53259a0607834db8828e328e7337f5b3[color=lightseagreen,label=\"\ - Output\\nhumann_gene_families\"]\n 2 -> k53259a0607834db8828e328e7337f5b3\n\ - \ k5aec39b6317a4fd0b90622d5a965e957[color=lightseagreen,label=\"Output\\nhumann_pathabundance\"\ - ]\n 2 -> k5aec39b6317a4fd0b90622d5a965e957\n 3[label=\"Split a HUMAnN table\"\ - ]\n 2 -> 3 [label=\"gene_families_tsv\"]\n 4[label=\"Regroup\"]\n 2 -> 4\ - \ [label=\"gene_families_tsv\"]\n 5[label=\"Renormalize\"]\n 2 -> 5 [label=\"\ - gene_families_tsv\"]\n k4bd1c47e66ac41ffbce951d0d86d2252[color=lightseagreen,label=\"\ - Output\\nrenormalize_gene_families\"]\n 5 -> k4bd1c47e66ac41ffbce951d0d86d2252\n\ - \ 6[label=\"Rename features\"]\n 2 -> 6 [label=\"gene_families_tsv\"]\n 7[label=\"\ - Renormalize\"]\n 2 -> 7 [label=\"pathabundance_tsv\"]\n k1715a5f63ac34ad2a0309307721e2b49[color=lightseagreen,label=\"\ - Output\\nrenormalize_pathabundance\"]\n 7 -> k1715a5f63ac34ad2a0309307721e2b49\n\ - \ 8[label=\"Split a HUMAnN table\"]\n 2 -> 8 [label=\"pathabundance_tsv\"\ - ]\n 9[label=\"Split a HUMAnN table\"]\n 4 -> 9 [label=\"output\"]\n 10[label=\"\ - Rename features\"]\n 4 -> 10 [label=\"output\"]\n 11[label=\"Replace\"]\n\ - \ 5 -> 11 [label=\"output\"]\n 12[label=\"Unpack pathway abundances\"]\n \ - \ 5 -> 12 [label=\"output\"]\n 7 -> 12 [label=\"output\"]\n kb24357e8b6d34893af63ac4cf7494b33[color=lightseagreen,label=\"\ - Output\\nunpack_pathway_abundance\"]\n 12 -> kb24357e8b6d34893af63ac4cf7494b33\n\ - \ 13[label=\"Select\"]\n 10 -> 13 [label=\"output\"]\n k946a04fd18544f088df11a3165651bae[color=lightseagreen,label=\"\ - Output\\ncc_go\"]\n 13 -> k946a04fd18544f088df11a3165651bae\n 14[label=\"\ - Select\"]\n 10 -> 14 [label=\"output\"]\n k4f5f059739eb42ce8dd8d920b52231c3[color=lightseagreen,label=\"\ - Output\\nbp_go\"]\n 14 -> k4f5f059739eb42ce8dd8d920b52231c3\n 15[label=\"\ - Select\"]\n 10 -> 15 [label=\"output\"]\n 16[label=\"Split a HUMAnN table\"\ - ]\n 13 -> 16 [label=\"out_file1\"]\n 17[label=\"Split a HUMAnN table\"]\n\ - \ 14 -> 17 [label=\"out_file1\"]\n 18[label=\"Sort\"]\n 15 -> 18 [label=\"\ - out_file1\"]\n k71abb759b51f4383a79127d8b1325e81[color=lightseagreen,label=\"\ - Output\\nsorted_mf_go\"]\n 18 -> k71abb759b51f4383a79127d8b1325e81\n 19[label=\"\ - Split a HUMAnN table\"]\n 15 -> 19 [label=\"out_file1\"]\n}" - history: - - hash: 604d1261ba4f89d6650304d72c7b6d8e4166b3a6 - message: 'Update metatranscriptomics tutorials:' - num: 2 - short_hash: 604d1261b - unix: '1750082204' - - hash: 0e0a2f2ccb650b0aab1ffc13838045164bdb5d30 - message: Rename metagenomics topic to microbiome - num: 1 - short_hash: 0e0a2f2cc - unix: '1704901629' - inputs: - - annotation: Metatranscriptomics interleaced reads - content_id: null - errors: null - id: 0 - input_connections: {} - inputs: - - description: Metatranscriptomics interleaced reads - name: Interleaced reads - label: Interleaced reads - name: Input dataset - outputs: [] - position: - left: 0.0 - top: 432.13598882837186 - tool_id: null - tool_state: '{"optional": false, "tag": null}' - tool_version: null - type: data_input - uuid: a89e6296-7ab8-4a94-865c-840652bb6fbe - when: null - workflow_outputs: [] - - annotation: Taxonomic profile generated by MetaPhlAn - content_id: null - errors: null - id: 1 - input_connections: {} - inputs: - - description: Taxonomic profile generated by MetaPhlAn - name: Taxonomic profile - label: Taxonomic profile - name: Input dataset - outputs: [] - position: - left: 11.132786128095177 - top: 623.6000061035156 - tool_id: null - tool_state: '{"optional": false, "tag": null}' - tool_version: null - type: data_input - uuid: a40d68df-fdf3-441a-bc58-faf123df908f - when: null - workflow_outputs: [] - license: MIT - mermaid: "flowchart TD\n 0[\"\u2139\uFE0F Input Dataset\\nInterleaced reads\"\ - ];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"\u2139\uFE0F Input Dataset\\\ - nTaxonomic profile\"];\n style 1 stroke:#2c3143,stroke-width:4px;\n 2[\"HUMAnN\"\ - ];\n 0 -->|output| 2;\n 1 -->|output| 2;\n 53259a06-0783-4db8-828e-328e7337f5b3[\"\ - Output\\nhumann_gene_families\"];\n 2 --> 53259a06-0783-4db8-828e-328e7337f5b3;\n\ - \ style 53259a06-0783-4db8-828e-328e7337f5b3 stroke:#2c3143,stroke-width:4px;\n\ - \ 5aec39b6-317a-4fd0-b906-22d5a965e957[\"Output\\nhumann_pathabundance\"];\n\ - \ 2 --> 5aec39b6-317a-4fd0-b906-22d5a965e957;\n style 5aec39b6-317a-4fd0-b906-22d5a965e957\ - \ stroke:#2c3143,stroke-width:4px;\n 3[\"Split a HUMAnN table\"];\n 2 -->|gene_families_tsv|\ - \ 3;\n 4[\"Regroup\"];\n 2 -->|gene_families_tsv| 4;\n 5[\"Renormalize\"\ - ];\n 2 -->|gene_families_tsv| 5;\n 4bd1c47e-66ac-41ff-bce9-51d0d86d2252[\"\ - Output\\nrenormalize_gene_families\"];\n 5 --> 4bd1c47e-66ac-41ff-bce9-51d0d86d2252;\n\ - \ style 4bd1c47e-66ac-41ff-bce9-51d0d86d2252 stroke:#2c3143,stroke-width:4px;\n\ - \ 6[\"Rename features\"];\n 2 -->|gene_families_tsv| 6;\n 7[\"Renormalize\"\ - ];\n 2 -->|pathabundance_tsv| 7;\n 1715a5f6-3ac3-4ad2-a030-9307721e2b49[\"\ - Output\\nrenormalize_pathabundance\"];\n 7 --> 1715a5f6-3ac3-4ad2-a030-9307721e2b49;\n\ - \ style 1715a5f6-3ac3-4ad2-a030-9307721e2b49 stroke:#2c3143,stroke-width:4px;\n\ - \ 8[\"Split a HUMAnN table\"];\n 2 -->|pathabundance_tsv| 8;\n 9[\"Split\ - \ a HUMAnN table\"];\n 4 -->|output| 9;\n 10[\"Rename features\"];\n 4 -->|output|\ - \ 10;\n 11[\"Replace\"];\n 5 -->|output| 11;\n 12[\"Unpack pathway abundances\"\ - ];\n 5 -->|output| 12;\n 7 -->|output| 12;\n b24357e8-b6d3-4893-af63-ac4cf7494b33[\"\ - Output\\nunpack_pathway_abundance\"];\n 12 --> b24357e8-b6d3-4893-af63-ac4cf7494b33;\n\ - \ style b24357e8-b6d3-4893-af63-ac4cf7494b33 stroke:#2c3143,stroke-width:4px;\n\ - \ 13[\"Select\"];\n 10 -->|output| 13;\n 946a04fd-1854-4f08-8df1-1a3165651bae[\"\ - Output\\ncc_go\"];\n 13 --> 946a04fd-1854-4f08-8df1-1a3165651bae;\n style\ - \ 946a04fd-1854-4f08-8df1-1a3165651bae stroke:#2c3143,stroke-width:4px;\n 14[\"\ - Select\"];\n 10 -->|output| 14;\n 4f5f0597-39eb-42ce-8dd8-d920b52231c3[\"\ - Output\\nbp_go\"];\n 14 --> 4f5f0597-39eb-42ce-8dd8-d920b52231c3;\n style\ - \ 4f5f0597-39eb-42ce-8dd8-d920b52231c3 stroke:#2c3143,stroke-width:4px;\n 15[\"\ - Select\"];\n 10 -->|output| 15;\n 16[\"Split a HUMAnN table\"];\n 13 -->|out_file1|\ - \ 16;\n 17[\"Split a HUMAnN table\"];\n 14 -->|out_file1| 17;\n 18[\"Sort\"\ - ];\n 15 -->|out_file1| 18;\n 71abb759-b51f-4383-a791-27d8b1325e81[\"Output\\\ - nsorted_mf_go\"];\n 18 --> 71abb759-b51f-4383-a791-27d8b1325e81;\n style 71abb759-b51f-4383-a791-27d8b1325e81\ - \ stroke:#2c3143,stroke-width:4px;\n 19[\"Split a HUMAnN table\"];\n 15 -->|out_file1|\ - \ 19;" - modified: 2026-05-21 00:30:25 +0000 - name: 'Metatranscriptomics analysis using microbiome RNA-seq data - Workflow 3: - Functional Information' - outputs: - - annotation: '' - content_id: toolshed.g2.bx.psu.edu/repos/iuc/humann/humann/3.9+galaxy0 + - label: 'Samtools view on input dataset(s): filtered alignments' + output_name: outputsam + uuid: aa220027-9d10-4328-b2c2-e4d139d5d5bd + - annotation: Change the string MTB_anc to "Chromosome" so it is compatible with + TB-profiler + content_id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/1.1.1 errors: null - id: 2 + id: 4 input_connections: - in|input: - id: 0 - output_name: output - wf|taxonomic_profile: - id: 1 - output_name: output - inputs: - - description: runtime parameter for tool HUMAnN - name: in - - description: runtime parameter for tool HUMAnN - name: wf - label: null - name: HUMAnN + infile: + id: 3 + output_name: outputsam + inputs: [] + label: Sed (MTB_anc to Chromosome) + name: Text transformation outputs: - - name: gene_families_tsv - type: tabular - - name: pathcoverage_tsv - type: tabular - - name: pathabundance_tsv - type: tabular - - name: log - type: txt + - name: output + type: input position: - left: 462.5176261280958 - top: 380 + bottom: 943.2000122070312 + height: 122.5333251953125 + left: 537.5999755859375 + right: 757.5999755859375 + top: 820.6666870117188 + width: 220 + x: 537.5999755859375 + y: 820.6666870117188 post_job_actions: {} - tool_id: toolshed.g2.bx.psu.edu/repos/iuc/humann/humann/3.9+galaxy0 + tool_id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/1.1.1 tool_shed_repository: - changeset_revision: c2803012bbb3 - name: humann - owner: iuc + changeset_revision: ddf54b12c295 + name: text_processing + owner: bgruening tool_shed: toolshed.g2.bx.psu.edu - tool_state: '{"__input_ext": "input", "chromInfo": "/shared/ifbstor1/galaxy/mutable-config/tool-data/shared/ucsc/chrom/?.len", - "g_p_quant": {"gap_fill": true, "minpath": true, "pathways": "metacyc", "xipe": - false, "annotation_gene_index": "3", "id_mapping": null}, "in": {"selector": - "raw", "__current_case__": 0, "input": {"__class__": "ConnectedValue"}}, "out": - {"output_basename": "humann", "output_format": "tsv", "output_max_decimals": - "10", "remove_column_description_output": false, "remove_stratified_output": - false, "intermediate_temp": null}, "wf": {"selector": "bypass_taxonomic_profiling", - "__current_case__": 1, "taxonomic_profile": {"__class__": "ConnectedValue"}, - "nucleotide_search": {"nucleotide_db": {"selector": "cached", "__current_case__": - 0, "nucleotide_database": "chocophlan-full-3.6.1-30072024"}, "nucleotide_identity_threshold": - "0.0", "nucleotide_subject_coverage_threshold": "50.0", "nucleotide_query_coverage_threshold": - "90.0"}, "translated_search": {"protein_db": {"selector": "cached", "__current_case__": - 0, "protein_database": "uniref-uniref90_diamond-3.6.1-30072024"}, "evalue": - "1.0", "translated_identity_threshold": null, "translated_subject_coverage_threshold": - 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id: 2 - output_name: gene_families_tsv + id: 4 + output_name: output inputs: [] - label: null - name: Renormalize + label: Samtools view SAM > BAM + name: Samtools view outputs: - - name: output - type: tabular + - name: outputsam + type: input position: - left: 712.5176261280958 - top: 380 + bottom: 945.5000152587891 + height: 189.8333282470703 + left: 810.5999755859375 + right: 1030.5999755859375 + top: 755.6666870117188 + width: 220 + x: 810.5999755859375 + y: 755.6666870117188 post_job_actions: {} - tool_id: toolshed.g2.bx.psu.edu/repos/iuc/humann_renorm_table/humann_renorm_table/3.9+galaxy0 + tool_id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.13+galaxy2 tool_shed_repository: - changeset_revision: 2bdd84912a2b - name: humann_renorm_table + changeset_revision: 0dbf49c414ae + name: samtools_view owner: iuc tool_shed: toolshed.g2.bx.psu.edu - tool_state: '{"__input_ext": "input", "chromInfo": "/shared/ifbstor1/galaxy/mutable-config/tool-data/shared/ucsc/chrom/?.len", - "input": {"__class__": "ConnectedValue"}, "mode": "community", "special": - true, "units": "relab", "update_snames": true, "__page__": 0, "__rerun_remap_job_id__": - null}' - tool_version: 3.9+galaxy0 + tool_state: '{"addref_cond": {"addref_select": "no", "__current_case__": 0}, + "input": {"__class__": "ConnectedValue"}, "mode": {"outtype": "all_reads", + "__current_case__": 0, "output_options": {"reads_report_type": "retained", + "__current_case__": 0, "adv_output": {"readtags": [], "collapsecigar": "false"}, + "output_format": {"oformat": "bam", "__current_case__": 2}}}, "__page__": + null, "__rerun_remap_job_id__": null}' + tool_version: 1.13+galaxy2 type: tool - uuid: a09c0f16-d4b5-4aff-9589-1ae8ae4f3ec6 - when: null + uuid: 729169fd-682e-4394-8421-1cde0aa2ac37 workflow_outputs: - - label: renormalize_gene_families - output_name: output - uuid: 4bd1c47e-66ac-41ff-bce9-51d0d86d2252 - - annotation: '' - content_id: toolshed.g2.bx.psu.edu/repos/iuc/humann_renorm_table/humann_renorm_table/3.9+galaxy0 + - label: null + output_name: outputsam + uuid: 67aacaf4-b657-4269-b3eb-5cf22e1e9596 + - annotation: Generate TB-profiler reports with drug resistance determinants + content_id: toolshed.g2.bx.psu.edu/repos/iuc/tbprofiler/tb_profiler_profile/3.0.8+galaxy0 errors: null - id: 7 + id: 6 input_connections: - input: - id: 2 - output_name: pathabundance_tsv + fastq_or_bam|bam_input: + id: 5 + output_name: outputsam inputs: [] - label: null - name: Renormalize + label: TB-profiler + name: TB-Profiler Profile outputs: - - name: output - type: tabular + - name: results_json + type: json + - name: output_vcf + type: vcf + - name: output_txt + type: txt position: - left: 712.5176261280958 - top: 680 + bottom: 724.9333343505859 + height: 254.6999969482422 + left: 1069.800048828125 + right: 1289.800048828125 + top: 470.23333740234375 + width: 220 + x: 1069.800048828125 + y: 470.23333740234375 post_job_actions: {} - tool_id: toolshed.g2.bx.psu.edu/repos/iuc/humann_renorm_table/humann_renorm_table/3.9+galaxy0 + tool_id: toolshed.g2.bx.psu.edu/repos/iuc/tbprofiler/tb_profiler_profile/3.0.8+galaxy0 tool_shed_repository: - changeset_revision: 2bdd84912a2b - name: humann_renorm_table + changeset_revision: 809dfc93d593 + name: tbprofiler owner: iuc tool_shed: toolshed.g2.bx.psu.edu - tool_state: '{"__input_ext": "input", "chromInfo": "/shared/ifbstor1/galaxy/mutable-config/tool-data/shared/ucsc/chrom/?.len", - "input": {"__class__": "ConnectedValue"}, "mode": "community", "special": - true, "units": "relab", "update_snames": true, "__page__": 0, "__rerun_remap_job_id__": - null}' - tool_version: 3.9+galaxy0 + tool_state: '{"advanced": {"options": "no", "__current_case__": 0}, "fastq_or_bam": + {"input_select": "bam", "__current_case__": 3, "bam_input": {"__class__": + "ConnectedValue"}}, "output_format": "txt", "platform": "illumina", "__page__": + null, "__rerun_remap_job_id__": null}' + tool_version: 3.0.8+galaxy0 type: tool - uuid: b73d0744-c6a3-4457-8c38-cb1213f07842 - when: null + uuid: 07d7e2cc-9669-45b5-bc1e-27bda80752c4 workflow_outputs: - - label: renormalize_pathabundance - output_name: output - uuid: 1715a5f6-3ac3-4ad2-a030-9307721e2b49 - - annotation: '' - content_id: toolshed.g2.bx.psu.edu/repos/iuc/humann_unpack_pathways/humann_unpack_pathways/3.9+galaxy0 + - label: null + output_name: output_vcf + uuid: 89e84a41-76ce-46eb-acec-1563e8d20ef6 + - label: null + output_name: output_txt + uuid: c148b074-5e6a-4846-86e7-0193a5ce38b5 + - label: null + output_name: results_json + uuid: b22dcd19-5127-4dc3-b329-8a09ab7f5db3 + - annotation: 'From TB profiler, search with `grep` the part of the text that + describes the DR profile (e.g Drug-Resistance: MDR) ' + content_id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/1.1.1 errors: null - id: 12 + id: 7 input_connections: - input_genes: - id: 5 - output_name: output - input_pathways: - id: 7 - output_name: output + infile: + id: 6 + output_name: output_txt inputs: [] - label: null - name: Unpack pathway abundances + label: Get drug resistance profile + name: Search in textfiles outputs: - name: output - type: tabular + type: input position: - left: 962.5176261280958 - top: 660 + bottom: 594.7666625976562 + height: 122.5333251953125 + left: 1343.800048828125 + right: 1563.800048828125 + top: 472.23333740234375 + width: 220 + x: 1343.800048828125 + y: 472.23333740234375 post_job_actions: {} - tool_id: toolshed.g2.bx.psu.edu/repos/iuc/humann_unpack_pathways/humann_unpack_pathways/3.9+galaxy0 + tool_id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/1.1.1 tool_shed_repository: - changeset_revision: 4e5e73d03f0d - name: humann_unpack_pathways - owner: iuc + changeset_revision: ddf54b12c295 + name: text_processing + owner: bgruening tool_shed: toolshed.g2.bx.psu.edu - tool_state: '{"__input_ext": "input", "chromInfo": "/shared/ifbstor1/galaxy/mutable-config/tool-data/shared/ucsc/chrom/?.len", - "gene_mapping": null, "input_genes": {"__class__": "ConnectedValue"}, "input_pathways": - {"__class__": "ConnectedValue"}, "pathway_mapping": null, "remove_taxonomy": - false, "__page__": 0, "__rerun_remap_job_id__": null}' - tool_version: 3.9+galaxy0 + tool_state: '{"case_sensitive": "-i", "color": "NOCOLOR", "infile": {"__class__": + "ConnectedValue"}, "invert": "", "lines_after": "0", "lines_before": "0", + "regex_type": "-P", "url_paste": "Drug-Resistance:", "__page__": null, "__rerun_remap_job_id__": + null}' + tool_version: 1.1.1 type: tool - uuid: efefeb7c-2501-4585-a17c-fd33bdad8238 - when: null + uuid: 9b418ac9-364d-4877-a858-b33a1e335900 workflow_outputs: - - label: unpack_pathway_abundance + - label: null output_name: output - uuid: b24357e8-b6d3-4893-af63-ac4cf7494b33 - - annotation: '' - content_id: Grep1 + uuid: b876e27d-6013-4265-ae70-cffad0895db9 + - annotation: 'We have generated one file per sample, that contains the DR profile + (e.g Drug-Resistance: MDR) We want to prepend the name of the sample so we + have: (Sample_name Drug-Resistance: MDR) ' + content_id: toolshed.g2.bx.psu.edu/repos/mvdbeek/add_input_name_as_column/addName/0.2.0 errors: null - id: 13 + id: 8 input_connections: input: - id: 10 + id: 7 output_name: output inputs: [] - label: null - name: Select + label: Add Sample Name + name: Add input name as column outputs: - - name: out_file1 - type: input + - name: output + type: tabular position: - left: 1212.5176261280958 - top: 820 + bottom: 596.7666625976562 + height: 122.5333251953125 + left: 1605.800048828125 + right: 1825.800048828125 + top: 474.23333740234375 + width: 220 + x: 1605.800048828125 + y: 474.23333740234375 post_job_actions: {} - tool_id: Grep1 - tool_state: '{"__input_ext": "input", "chromInfo": "/shared/ifbstor1/galaxy/mutable-config/tool-data/shared/ucsc/chrom/?.len", - "input": {"__class__": "ConnectedValue"}, "invert": "", "keep_header": false, - "pattern": "\\[CC\\]", "__page__": 0, "__rerun_remap_job_id__": null}' - tool_version: 1.0.4 + tool_id: toolshed.g2.bx.psu.edu/repos/mvdbeek/add_input_name_as_column/addName/0.2.0 + tool_shed_repository: + changeset_revision: 3284b72eef56 + name: add_input_name_as_column + owner: mvdbeek + tool_shed: toolshed.g2.bx.psu.edu + tool_state: '{"header": {"contains_header": "no", "__current_case__": 1}, "input": + {"__class__": "ConnectedValue"}, "prepend": "true", "__page__": null, "__rerun_remap_job_id__": + null}' + tool_version: 0.2.0 type: tool - uuid: cee2fc03-2b6c-4162-a156-faf23786ca6e - when: null + uuid: d92f5d19-212d-4d8b-a7f7-f249788088ac workflow_outputs: - - label: cc_go - output_name: out_file1 - uuid: 946a04fd-1854-4f08-8df1-1a3165651bae - - annotation: '' - content_id: Grep1 + - label: null + output_name: output + uuid: 1b9d5610-2f91-450a-a1b9-1718d8afde1a + - annotation: 'The output will be: + + Sample_A DR_profile_A + + Sample_B DR_profile_B + + Sample_Z DR_profile_Z' + content_id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.1 errors: null - id: 14 + id: 9 input_connections: - input: - id: 10 + inputs: + id: 8 output_name: output - inputs: [] - label: null - name: Select + inputs: + - description: runtime parameter for tool Concatenate datasets + name: inputs + label: Concatenate DR profiles in a single table + name: Concatenate datasets outputs: - name: out_file1 type: input position: - left: 1212.5176261280958 - top: 990 + bottom: 596.7666625976562 + height: 122.5333251953125 + left: 1871.800048828125 + right: 2091.800048828125 + top: 474.23333740234375 + width: 220 + x: 1871.800048828125 + y: 474.23333740234375 post_job_actions: {} - 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annotation: Remove unnecessary text from the table like ".txt" or "Drug-resistance:" + content_id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/1.1.2 errors: null - id: 18 + id: 10 input_connections: infile: - id: 15 + id: 9 output_name: out_file1 - inputs: [] - label: null - name: Sort + inputs: + - description: runtime parameter for tool Replace Text + name: infile + label: Cleanup the table + name: Replace Text outputs: - name: outfile type: input position: - left: 1462.5176261280958 - top: 1160 + bottom: 599.8666534423828 + height: 122.53334045410156 + left: 2136.300048828125 + right: 2356.300048828125 + top: 477.33331298828125 + width: 220 + x: 2136.300048828125 + y: 477.33331298828125 post_job_actions: {} - tool_id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/9.5+galaxy2 + tool_id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/1.1.2 tool_shed_repository: - changeset_revision: c41d78ae5fee + changeset_revision: ddf54b12c295 name: text_processing owner: bgruening tool_shed: toolshed.g2.bx.psu.edu - 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name: Ray Sajulga - - class: Person - name: Emma Leith - - class: Person - name: Praveen Kumar - - class: Person - identifier: 0000-0003-3803-468X - name: Saskia Hiltemann - - class: Person - identifier: 0000-0003-2982-388X - name: Paul Zierep - description: Metatranscriptomics analysis using microbiome RNA-seq data (short) + - __MERGE_COLLECTION__ + - toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.1 + - toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/1.1.1 + - toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/1.1.2 + - toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/1.1.1 + - toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.13+galaxy2 + - toolshed.g2.bx.psu.edu/repos/iuc/tbprofiler/tb_profiler_profile/3.0.8+galaxy0 + - toolshed.g2.bx.psu.edu/repos/mvdbeek/add_input_name_as_column/addName/0.2.0 + workflowhub_id: '1564' + - creators: [] + description: From Fastqs to VCFs and BAMs features: comments: false parameters: false @@ -35660,38 +15847,31 @@ subworkflows: false graph_dot: "digraph main {\n node [fontname=\"Atkinson Hyperlegible\", shape=box,\ \ color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n edge [fontname=\"\ - 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page: https://training.galaxyproject.org/training-material/hall-of-fame/melbournebioinformatics/ - url: https://training.galaxyproject.org/training-material/api/organisations/melbournebioinformatics.json - - avatar: /training-material/shared/images/Australian-Biocommons-Favicon-RGB.png - id: AustralianBioCommons - members: - - annasyme - - burkemlou - - cat-bro - - igormakunin - - mthang - - PatCapon39 - - supernord - - tflowers15 - - uwwint - name: Australian BioCommons - page: https://training.galaxyproject.org/training-material/hall-of-fame/AustralianBioCommons/ - url: https://training.galaxyproject.org/training-material/api/organisations/AustralianBioCommons.json - - affiliations: - - uni-freiburg - - nfdi4plants - - elixir-europe - bio: Researcher at Erasmus Medical Center - bluesky: shiltemann.bsky.social - contact_for_training: true - elixir_node: nl - email: saskia.hiltemann@gmail.com - fediverse: https://mstdn.science/@shiltemann - fediverse_flavor: mastodon - former_affiliations: - - CINECA-Project - - gallantries - - erasmusmc - id: shiltemann - joined: 2017-09 - linkedin: shiltemann - location: - country: NL - lat: 51.912 - lon: 4.462 - maintainer_contact: gitter - matrix: shiltemann:matrix.org - name: Saskia Hiltemann - orcid: 0000-0003-3803-468X - page: https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/ - url: https://training.galaxyproject.org/training-material/api/contributors/shiltemann.json + - vloux + reviewing: + - abretaud + contributors: + - elixir_node: fr + id: hchiapello + joined: 2025-03 + name: "H\xE9l\xE8ne Chiapello" + page: https://training.galaxyproject.org/training-material/hall-of-fame/hchiapello/ + url: https://training.galaxyproject.org/training-material/api/contributors/hchiapello.json - affiliations: - gallantries - ifb @@ -36443,384 +16690,195 @@ page: https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/ twitter: bebatut url: https://training.galaxyproject.org/training-material/api/contributors/bebatut.json + - id: vloux + joined: 2019-04 + name: Valentin Loux + page: https://training.galaxyproject.org/training-material/hall-of-fame/vloux/ + url: https://training.galaxyproject.org/training-material/api/contributors/vloux.json - affiliations: - - uni-freiburg - - elixir-europe - - deNBI - - mwk - - materialvitaldigital - email: zierep@informatik.uni-freiburg.de - id: paulzierep - joined: 2023-02 - name: Paul Zierep - orcid: 0000-0003-2982-388X - page: https://training.galaxyproject.org/training-material/hall-of-fame/paulzierep/ - url: https://training.galaxyproject.org/training-material/api/contributors/paulzierep.json - - affiliations: - - erasmusmc - - gallantries - - by-covid - elixir-europe - - elixir-converge - contact_for_training: false - elixir_node: nl + bluesky: abretaud.bsky.social + contact_for_training: true + elixir_node: fr + email: anthony.bretaudeau@irisa.fr + fediverse: https://genomic.social/@abretaud + fediverse_flavor: mastodon former_affiliations: - - deNBI - - avans-atgm - - uni-freiburg - id: hexylena + - eurosciencegateway + - gallantries + id: abretaud joined: 2017-09 location: - country: NL - lat: 51.91 - lon: 4.46 - maintainer_contact: gitter - matrix: hexylena:matrix.org - name: Helena Rasche - orcid: 0000-0001-9760-8992 - page: https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/ - url: https://training.galaxyproject.org/training-material/api/contributors/hexylena.json - - elixir_node: de - former_affiliations: - - uni-freiburg - - elixir-europe - id: gallardoalba - joined: 2020-11 - name: "Crist\xF3bal Gallardo" - orcid: 0000-0002-5752-2155 - page: https://training.galaxyproject.org/training-material/hall-of-fame/gallardoalba/ - url: https://training.galaxyproject.org/training-material/api/contributors/gallardoalba.json - - affiliations: - - uni-freiburg - - elixir-europe - - deNBI - - mwk - - biont - contact_for_training: true - elixir_node: de - email: muellert@informatik.uni-freibrug.de - id: teresa-m - joined: 2022-09 - linkedin: teresamueller87 - matrix: teresa-m:matrix.org - name: "Teresa M\xFCller" - orcid: 0000-0003-1252-9684 - page: https://training.galaxyproject.org/training-material/hall-of-fame/teresa-m/ - url: https://training.galaxyproject.org/training-material/api/contributors/teresa-m.json - dir: topics/microbiome/tutorials/taxonomic-profiling + country: FR + lat: 48.11 + lon: -1.64 + matrix: abretaud:matrix.org + name: Anthony Bretaudeau + orcid: 0000-0003-0914-2470 + page: https://training.galaxyproject.org/training-material/hall-of-fame/abretaud/ + url: https://training.galaxyproject.org/training-material/api/contributors/abretaud.json + dir: topics/evolution/tutorials/bacterial-comparative-genomics + draft: true edam_ontology: - - topic_3174 - - topic_3697 - - topic_0637 - - topic_0080 - edam_operation: - - Taxonomic classification - - Aggregation - - Statistical calculation - - Visualisation - - Genome annotation + - topic_0622 + - topic_3301 + - topic_0084 + edam_operation: [] edam_topic: - - Metagenomics - - Microbial ecology - - Taxonomy - - Sequence analysis + - Genomics + - Microbiology + - Phylogeny exact_supported_servers: - - UseGalaxy.org.au + - Galaxy@AuBi + - MISSISSIPPI - UseGalaxy.be + - UseGalaxy.cz - UseGalaxy.eu - UseGalaxy.fr + - UseGalaxy.no - UseGalaxy.org (Main) feedback_mean_note: null feedback_number: 0 hands_on: true - id: microbiome/taxonomic-profiling - inexact_supported_servers: [] + id: evolution/bacterial-comparative-genomics + inexact_supported_servers: + - GalaxyTrakr js_requirements: - mathjax: 4920 + mathjax: null mermaid: false key_points: - - There are 3 different types of taxonomic assignment (genome, gene or k-mer based) - - Kraken or MetaPhlAn can be used in Galaxy for taxonomic assignment - - Visualization of community profiles can be done using Krona or Pavian - - The taxonomic classification tool to use depends on the data + - to do + - to do layout: tutorial_hands_on level: Introductory license: CC-BY-4.0 - mod_date: '2026-05-11' + mod_date: '2025-03-14' objectives: - - Explain what taxonomic assignment is - - Explain how taxonomic assignment works - - Apply Kraken and MetaPhlAn to assign taxonomic labels - - Apply Krona and Pavian to visualize results of assignment and understand the output - - Identify taxonomic classification tool that fits best depending on their data - pageviews: 19544 - pub_date: '2023-05-03' + - to do + - to do + pageviews: 261 + pub_date: '2025-03-14' questions: - - Which species (or genera, families, ...) are present in my sample? - - What are the different approaches and tools to get the community profile of my - sample? - - How can we visualize and compare community profiles? - recordings: - - captioners: - - sophia120199 - date: '2023-05-16' - galaxy_version: '23.01' - length: 1H15M - speakers: - - bebatut - youtube_id: jszMnBKm6ig - - bot-timestamp: 1744833733 - captioners: - - Tarnima-Omara - date: '2025-04-16' - galaxy_version: 24.2.4.dev0 - length: 2H4M - speakers: - - Tarnima-Omara - youtube_id: FdtdsCdqY5U - redirect_from: - - /topics/metagenomics/tutorials/taxonomic-profiling/tutorial - - /short/microbiome/taxonomic-profiling - - /short/T00338 - - /short/T00395 - short_id: T00395 + - to do + - to do + short_id: T00489 short_tools: - - taxonomy_krona_chart - - interactive_tool_phinch - - est_abundance - - kraken_biom - - metaphlan - - __UNZIP_COLLECTION__ - - krakentools_kreport2krona - - interactive_tool_pavian - - kraken2 + - upload1 + - fasttree slides: false slides_recordings: false - subtopic: metagenomics supported_servers: exact: - - name: UseGalaxy.org.au - url: https://usegalaxy.org.au - usegalaxy: true - - name: UseGalaxy.be - url: https://usegalaxy.be/ - usegalaxy: false - - name: UseGalaxy.eu - url: https://usegalaxy.eu - usegalaxy: true - - name: UseGalaxy.fr - url: https://usegalaxy.fr/ - usegalaxy: true - - name: UseGalaxy.org (Main) - url: https://usegalaxy.org - usegalaxy: true - inexact: [] - supported_servers_matrix: - servers: - - name: APOSTL - url: http://apostl.moffitt.org/ - usegalaxy: false - - name: MBAC Metabiome Portal - url: http://mbac.gmu.edu:8080/ - usegalaxy: false - - name: ChemFlow - url: https://vm-chemflow-francegrille.eu/ - usegalaxy: false - - name: CIRM-CFBP - url: https://iris.angers.inra.fr/galaxypub-cfbp - usegalaxy: false - - name: Coloc-stats - url: https://hyperbrowser.uio.no/coloc-stats - usegalaxy: false - name: Galaxy@AuBi url: https://galaxy.mesocentre.uca.fr usegalaxy: false - - name: Galaxy@Pasteur - url: https://galaxy.pasteur.fr/ - usegalaxy: false - - name: GalaxyTrakr - url: https://galaxytrakr.org/ - usegalaxy: false - - name: GASLINI - url: http://igg.cloud.ba.infn.it/galaxy - usegalaxy: false - - name: HyPhy HIV NGS Tools - url: https://galaxy.hyphy.org/ - usegalaxy: false - - name: ImmPort Galaxy - url: https://www.immportgalaxy.org/ - usegalaxy: false - - name: InteractoMIX - url: http://galaxy.interactomix.com/ - usegalaxy: false - - name: IPK Galaxy Blast Suite - url: https://galaxy-web.ipk-gatersleben.de - usegalaxy: false - - name: Lebanese University Galaxy - url: http://galaxy.ul.edu.lb/ - usegalaxy: false - - name: Mandoiu Lab - url: https://neo.engr.uconn.edu/ - usegalaxy: false - name: MISSISSIPPI url: https://mississippi.sorbonne-universite.fr usegalaxy: false - - name: Oqtans - url: http://galaxy.inf.ethz.ch - usegalaxy: false - - name: Palfinder - url: https://palfinder.ls.manchester.ac.uk/ - usegalaxy: false - - name: PepSimili - url: http://pepsimili.e-nios.com:8080/ - usegalaxy: false - - name: PhagePromotor - url: https://galaxy.bio.di.uminho.pt/ - usegalaxy: false - - name: UseGalaxy.org.au - url: https://usegalaxy.org.au - usegalaxy: true - name: UseGalaxy.be url: https://usegalaxy.be/ - usegalaxy: false - - name: UseGalaxy.cz - url: https://usegalaxy.cz/ - usegalaxy: false - - name: UseGalaxy.eu - url: https://usegalaxy.eu - usegalaxy: true - - name: UseGalaxy.fr - url: https://usegalaxy.fr/ - usegalaxy: true - - name: UseGalaxy.no - url: https://usegalaxy.no/ - usegalaxy: false - - name: UseGalaxy.org (Main) - url: https://usegalaxy.org - usegalaxy: true - - name: Viral Variant Visualizer (VVV) - url: https://viralvariant.anses.fr/ - usegalaxy: false - tools: - - id: __UNZIP_COLLECTION__ - servers: - - server: http://apostl.moffitt.org/ - state: missing - - server: http://mbac.gmu.edu:8080/ - state: missing - - server: https://vm-chemflow-francegrille.eu/ - state: missing - - server: https://iris.angers.inra.fr/galaxypub-cfbp - state: missing - - server: https://hyperbrowser.uio.no/coloc-stats - state: missing - - server: https://galaxy.mesocentre.uca.fr - state: local - - server: https://galaxy.pasteur.fr/ - state: missing - - server: https://galaxytrakr.org/ - state: local - - server: http://igg.cloud.ba.infn.it/galaxy - state: local - - server: https://galaxy.hyphy.org/ - state: local - - server: https://www.immportgalaxy.org/ - state: missing - - server: http://galaxy.interactomix.com/ - state: local - - server: https://galaxy-web.ipk-gatersleben.de - state: missing - - server: http://galaxy.ul.edu.lb/ - state: local - - server: https://neo.engr.uconn.edu/ - state: missing - - server: https://mississippi.sorbonne-universite.fr - state: local - - server: http://galaxy.inf.ethz.ch - state: missing - - server: https://palfinder.ls.manchester.ac.uk/ - state: missing - - server: http://pepsimili.e-nios.com:8080/ - state: local - - server: https://galaxy.bio.di.uminho.pt/ - state: local - - server: https://usegalaxy.org.au - state: local - - server: https://usegalaxy.be/ - state: local - - server: https://usegalaxy.cz/ - state: local - - server: https://usegalaxy.eu - state: local - - server: https://usegalaxy.fr/ - state: local - - server: https://usegalaxy.no/ - state: local - - server: https://usegalaxy.org - state: local - - server: https://viralvariant.anses.fr/ - state: local - version: local - - id: interactive_tool_pavian - servers: - - server: http://apostl.moffitt.org/ - state: missing - - server: http://mbac.gmu.edu:8080/ - state: missing - - server: https://vm-chemflow-francegrille.eu/ - state: missing - - server: https://iris.angers.inra.fr/galaxypub-cfbp - state: missing - - server: https://hyperbrowser.uio.no/coloc-stats - state: missing - - server: https://galaxy.mesocentre.uca.fr - state: missing - - server: https://galaxy.pasteur.fr/ - state: missing - - server: https://galaxytrakr.org/ - state: missing - - server: http://igg.cloud.ba.infn.it/galaxy - state: missing - - server: https://galaxy.hyphy.org/ - state: missing - - server: https://www.immportgalaxy.org/ - state: missing - - server: http://galaxy.interactomix.com/ - state: missing - - server: https://galaxy-web.ipk-gatersleben.de - state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - - server: https://neo.engr.uconn.edu/ - state: missing - - server: https://mississippi.sorbonne-universite.fr - state: missing - - server: http://galaxy.inf.ethz.ch - state: missing - - server: https://palfinder.ls.manchester.ac.uk/ - state: missing - - server: http://pepsimili.e-nios.com:8080/ - state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - - server: https://usegalaxy.org.au - state: local - - server: https://usegalaxy.be/ - state: local - - server: https://usegalaxy.cz/ - state: missing - - server: https://usegalaxy.eu - state: local - - server: https://usegalaxy.fr/ - state: local - - server: https://usegalaxy.no/ - state: missing - - server: https://usegalaxy.org - state: local - - server: https://viralvariant.anses.fr/ - state: missing - version: local - - id: interactive_tool_phinch + usegalaxy: false + - name: UseGalaxy.cz + url: https://usegalaxy.cz/ + usegalaxy: false + - name: UseGalaxy.eu + url: https://usegalaxy.eu + usegalaxy: true + - name: UseGalaxy.fr + url: https://usegalaxy.fr/ + usegalaxy: true + - name: UseGalaxy.no + url: https://usegalaxy.no/ + usegalaxy: false + - name: UseGalaxy.org (Main) + url: https://usegalaxy.org + usegalaxy: true + inexact: + - name: GalaxyTrakr + url: https://galaxytrakr.org/ + usegalaxy: false + supported_servers_matrix: + servers: + - name: APOSTL + url: http://apostl.moffitt.org/ + usegalaxy: false + - name: MBAC Metabiome Portal + url: http://mbac.gmu.edu:8080/ + usegalaxy: false + - name: ChemFlow + url: https://vm-chemflow-francegrille.eu/ + usegalaxy: false + - name: CIRM-CFBP + url: https://iris.angers.inra.fr/galaxypub-cfbp + usegalaxy: false + - name: Coloc-stats + url: https://hyperbrowser.uio.no/coloc-stats + usegalaxy: false + - name: Galaxy@AuBi + url: https://galaxy.mesocentre.uca.fr + usegalaxy: false + - name: Galaxy@Pasteur + url: https://galaxy.pasteur.fr/ + usegalaxy: false + - name: GalaxyTrakr + url: https://galaxytrakr.org/ + usegalaxy: false + - name: GASLINI + url: http://igg.cloud.ba.infn.it/galaxy + usegalaxy: false + - name: HyPhy HIV NGS Tools + url: https://galaxy.hyphy.org/ + usegalaxy: false + - name: ImmPort Galaxy + url: https://www.immportgalaxy.org/ + usegalaxy: false + - name: InteractoMIX + url: http://galaxy.interactomix.com/ + usegalaxy: false + - name: IPK Galaxy Blast Suite + url: https://galaxy-web.ipk-gatersleben.de + usegalaxy: false + - name: Mandoiu Lab + url: https://neo.engr.uconn.edu/ + usegalaxy: false + - name: MISSISSIPPI + url: https://mississippi.sorbonne-universite.fr + usegalaxy: false + - name: Oqtans + url: http://galaxy.inf.ethz.ch + usegalaxy: false + - name: Palfinder + url: https://palfinder.ls.manchester.ac.uk/ + usegalaxy: false + - name: PepSimili + url: http://pepsimili.e-nios.com:8080/ + usegalaxy: false + - name: UseGalaxy.org.au + url: https://usegalaxy.org.au + usegalaxy: true + - name: UseGalaxy.be + url: https://usegalaxy.be/ + usegalaxy: false + - name: UseGalaxy.cz + url: https://usegalaxy.cz/ + usegalaxy: false + - name: UseGalaxy.eu + url: https://usegalaxy.eu + usegalaxy: true + - name: UseGalaxy.fr + url: https://usegalaxy.fr/ + usegalaxy: true + - name: UseGalaxy.no + url: https://usegalaxy.no/ + usegalaxy: false + - name: UseGalaxy.org (Main) + url: https://usegalaxy.org + usegalaxy: true + - name: Viral Variant Visualizer (VVV) + url: https://viralvariant.anses.fr/ + usegalaxy: false + tools: + - id: toolshed.g2.bx.psu.edu/repos/iuc/fasttree/fasttree/2.1.10+galaxy1 servers: - server: http://apostl.moffitt.org/ state: missing @@ -36833,78 +16891,14 @@ - server: https://hyperbrowser.uio.no/coloc-stats state: missing - server: https://galaxy.mesocentre.uca.fr - state: missing + state: exact + version: 2.1.10+galaxy1 - server: https://galaxy.pasteur.fr/ state: missing - - server: https://galaxytrakr.org/ - state: missing - - server: http://igg.cloud.ba.infn.it/galaxy - state: missing - - server: https://galaxy.hyphy.org/ - state: missing - - server: https://www.immportgalaxy.org/ - state: missing - - server: http://galaxy.interactomix.com/ - state: missing - - server: https://galaxy-web.ipk-gatersleben.de - state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - - server: https://neo.engr.uconn.edu/ - state: missing - - server: https://mississippi.sorbonne-universite.fr - state: missing - - server: http://galaxy.inf.ethz.ch - state: missing - - server: https://palfinder.ls.manchester.ac.uk/ - state: missing - - server: http://pepsimili.e-nios.com:8080/ - 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microgalaxy + - work-in-progress + time: null + time_estimation: 1H + title: Phylogenetic analysis for bacterial comparative genomics + tools: + - toolshed.g2.bx.psu.edu/repos/iuc/fasttree/fasttree/2.1.10+galaxy1 + - upload1 + topic_name: evolution + topic_name_human: Evolution + tours: false + translations: + slides: [] + tutorial: [] + video: false + tutorial_name: bacterial-comparative-genomics + type: tutorial + url: https://training.galaxyproject.org//topics/evolution/tutorials/bacterial-comparative-genomics/tutorial.html + urls: + hands_on: https://training.galaxyproject.org/training-material/api/topics/evolution/tutorials/bacterial-comparative-genomics/tutorial.json + slides: https://training.galaxyproject.org/training-material/api/topics/evolution/tutorials/bacterial-comparative-genomics/tutorial.json + version: 1 + video: false + video_versions: 0 + video_view: 0 + visit_duration: 736 + visitors: 220 + zenodo_link: https://zenodo.org/records/1 +- admin_install: + install_repository_dependencies: true + install_resolver_dependencies: true + install_tool_dependencies: true + tools: + - name: prokka + owner: crs4 + revisions: bf68eb663bc3 + tool_panel_section_label: Annotation + tool_shed_url: https://toolshed.g2.bx.psu.edu/ + - name: prokka + owner: crs4 + revisions: 111884f0d912 + tool_panel_section_label: Annotation + tool_shed_url: https://toolshed.g2.bx.psu.edu/ + - name: jbrowse + owner: iuc + revisions: a6e57ff585c0 + tool_panel_section_label: Graph/Display Data + tool_shed_url: https://toolshed.g2.bx.psu.edu/ + admin_install_yaml: "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies:\ + \ true\ninstall_resolver_dependencies: true\ntools:\n- name: prokka\n owner:\ + \ crs4\n revisions: bf68eb663bc3\n tool_panel_section_label: Annotation\n tool_shed_url:\ + \ https://toolshed.g2.bx.psu.edu/\n- name: prokka\n owner: crs4\n revisions:\ + \ 111884f0d912\n tool_panel_section_label: Annotation\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n\ + - name: jbrowse\n owner: iuc\n revisions: a6e57ff585c0\n tool_panel_section_label:\ + \ Graph/Display Data\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n" + api: https://training.galaxyproject.org/training-material/api/topics/genome-annotation/tutorials/annotation-with-prokka/tutorial.json + contributions: + authorship: + - annasyme + - tseemann + - slugger70 + funding: + - unimelb + - melbournebioinformatics + - AustralianBioCommons + reviewing: + - bgruening + - hexylena + - shiltemann + - bebatut + - abretaud + - annasyme + - nsoranzo + - slugger70 + - njall + - mblue9 + contributors: + - affiliations: + - AustralianBioCommons + - unimelb + former_affiliations: + - melbournebioinformatics + id: annasyme + joined: 2017-09 + name: Anna Syme + orcid: 0000-0002-9906-0673 + page: https://training.galaxyproject.org/training-material/hall-of-fame/annasyme/ + url: https://training.galaxyproject.org/training-material/api/contributors/annasyme.json + - affiliations: + - elixir-europe + elixir_node: au + id: tseemann + joined: 2018-06 + name: Torsten Seemann + page: https://training.galaxyproject.org/training-material/hall-of-fame/tseemann/ + url: https://training.galaxyproject.org/training-material/api/contributors/tseemann.json + - elixir_node: au + email: simon.gladman@unimelb.edu.au + id: slugger70 + in_memoriam: "Simon\ + \ Gladman, system administrator of UseGalaxy.org.au, passed away on November\ + \ 26, 2022\n\nHe was a fantastic teacher, tutorial author, system administrator, and warm\ + \ and welcoming friend. He contributed heavily to the Galaxy Training Network\ + \ and especially the Galaxy Administration community over the years, we will\ + \ miss him dearly. The GTN and GAT would not be what they are today, without\ + \ him.\n\n\u201CHave I told you about my watch?\u201D" + joined: 2017-09 + name: Simon Gladman + orcid: 0000-0002-6100-4385 + page: https://training.galaxyproject.org/training-material/hall-of-fame/slugger70/ + url: https://training.galaxyproject.org/training-material/api/contributors/slugger70.json + - avatar: /training-material/shared/images/unimelb_Logo_RGB.png + id: unimelb + members: + - annasyme + - cat-bro + - GraceAHall + - supernord + - tflowers15 + - uwwint + - vinisalazar + name: The University of Melbourne + page: https://training.galaxyproject.org/training-material/hall-of-fame/unimelb/ + url: https://training.galaxyproject.org/training-material/api/organisations/unimelb.json + - avatar: /training-material/shared/images/Melbourne-Bioinformatics-logo.png + former_members: + - annasyme + id: melbournebioinformatics + members: + - GraceAHall + - tflowers15 + - vinisalazar + name: Melbourne Bioinformatics + page: https://training.galaxyproject.org/training-material/hall-of-fame/melbournebioinformatics/ + url: https://training.galaxyproject.org/training-material/api/organisations/melbournebioinformatics.json + - avatar: /training-material/shared/images/Australian-Biocommons-Favicon-RGB.png + id: AustralianBioCommons + members: + - annasyme + - burkemlou + - cat-bro + - igormakunin + - mthang + - PatCapon39 + - supernord + - tflowers15 + - uwwint + name: Australian BioCommons + page: https://training.galaxyproject.org/training-material/hall-of-fame/AustralianBioCommons/ + url: https://training.galaxyproject.org/training-material/api/organisations/AustralianBioCommons.json + - affiliations: + - deNBI + - mwk + - uni-freiburg + - elixir-europe + - materialvitaldigital + contact_for_training: true + elixir_node: de + email: bjoern.gruening@gmail.com + fediverse: https://fosstodon.org/@bgruening + fediverse_flavor: mastodon + former_affiliations: + - eurosciencegateway + - eosc-life + - by-covid + - crc992 + - elixir-converge + id: bgruening + joined: 2017-09 + linkedin: bgruening + location: + country: DE + lat: 47.997791 + lon: 7.842609 + matrix: bgruening:matrix.org + name: "Bj\xF6rn Gr\xFCning" + orcid: 0000-0002-3079-6586 + page: https://training.galaxyproject.org/training-material/hall-of-fame/bgruening/ + twitter: bjoerngruening + url: https://training.galaxyproject.org/training-material/api/contributors/bgruening.json + - affiliations: + - elixir-europe + contact_for_training: false + elixir_node: nl + former_affiliations: + - deNBI + - avans-atgm + - uni-freiburg + - erasmusmc + - gallantries + - by-covid + - elixir-converge + id: hexylena + joined: 2017-09 + location: + country: NL + lat: 51.91 + lon: 4.46 + maintainer_contact: gitter + matrix: hexylena:matrix.org + name: Helena Rasche + orcid: 0000-0001-9760-8992 + page: https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/ + url: https://training.galaxyproject.org/training-material/api/contributors/hexylena.json + - affiliations: + - uni-freiburg + - nfdi4plants + - elixir-europe + bio: Researcher at Erasmus Medical Center + bluesky: shiltemann.bsky.social + contact_for_training: true + elixir_node: nl + email: saskia.hiltemann@gmail.com + fediverse: https://mstdn.science/@shiltemann + fediverse_flavor: mastodon + former_affiliations: + - CINECA-Project + - gallantries + - erasmusmc + id: shiltemann + joined: 2017-09 + linkedin: shiltemann + location: + country: NL + lat: 51.912 + lon: 4.462 + maintainer_contact: gitter + matrix: shiltemann:matrix.org + name: Saskia Hiltemann + orcid: 0000-0003-3803-468X + page: https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/ + url: https://training.galaxyproject.org/training-material/api/contributors/shiltemann.json + - affiliations: + - gallantries + - ifb + - elixir-europe + contact_for_training: true + elixir_node: fr + email: berenice.batut@gmail.com + fediverse: https://piaille.fr/@bebatut + fediverse_flavor: mastodon + former_affiliations: + - uni-freiburg + - deNBI + id: bebatut + joined: 2017-09 + linkedin: berenicebatut + location: + country: FR + lat: 45.77 + lon: 3.08 + matrix: bebatut:matrix.org + name: "B\xE9r\xE9nice Batut" + orcid: 0000-0001-9852-1987 + page: https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/ + twitter: bebatut + url: https://training.galaxyproject.org/training-material/api/contributors/bebatut.json + - affiliations: + - elixir-europe + bluesky: abretaud.bsky.social + contact_for_training: true + elixir_node: fr + email: anthony.bretaudeau@irisa.fr + fediverse: https://genomic.social/@abretaud + fediverse_flavor: mastodon + former_affiliations: + - eurosciencegateway + - gallantries + id: abretaud + joined: 2017-09 + location: + country: FR + lat: 48.11 + lon: -1.64 + matrix: abretaud:matrix.org + name: Anthony Bretaudeau + orcid: 0000-0003-0914-2470 + page: https://training.galaxyproject.org/training-material/hall-of-fame/abretaud/ + url: https://training.galaxyproject.org/training-material/api/contributors/abretaud.json + - affiliations: + - AustralianBioCommons + - unimelb + former_affiliations: + - melbournebioinformatics + id: annasyme + joined: 2017-09 + name: Anna Syme + orcid: 0000-0002-9906-0673 + page: https://training.galaxyproject.org/training-material/hall-of-fame/annasyme/ + url: https://training.galaxyproject.org/training-material/api/contributors/annasyme.json + - affiliations: + - biofair + - earlham + - elixir-europe + - elixir-steers + bluesky: nsoranzo.bsky.social + elixir_node: uk + fediverse: https://mstdn.science/@nsoranzo + fediverse_flavor: mastodon + id: nsoranzo + joined: 2017-09 + linkedin: nicola-soranzo-7884125 + location: + country: UK + lat: 52.62188 + lon: 1.21899 + matrix: nsoranzo:matrix.org + name: Nicola Soranzo + orcid: 0000-0003-3627-5340 + page: https://training.galaxyproject.org/training-material/hall-of-fame/nsoranzo/ + twitter: NicolaSoranzo + url: https://training.galaxyproject.org/training-material/api/contributors/nsoranzo.json + - elixir_node: au + email: simon.gladman@unimelb.edu.au + id: slugger70 + in_memoriam: "Simon\ + \ Gladman, system administrator of UseGalaxy.org.au, passed away on November\ + \ 26, 2022\n\nHe was a fantastic teacher, tutorial author, system administrator, and warm\ + \ and welcoming friend. He contributed heavily to the Galaxy Training Network\ + \ and especially the Galaxy Administration community over the years, we will\ + \ miss him dearly. The GTN and GAT would not be what they are today, without\ + \ him.\n\n\u201CHave I told you about my watch?\u201D" + joined: 2017-09 + name: Simon Gladman + orcid: 0000-0002-6100-4385 + page: https://training.galaxyproject.org/training-material/hall-of-fame/slugger70/ + url: https://training.galaxyproject.org/training-material/api/contributors/slugger70.json + - id: njall + joined: 2019-02 + name: Niall Beard + page: https://training.galaxyproject.org/training-material/hall-of-fame/njall/ + url: https://training.galaxyproject.org/training-material/api/contributors/njall.json + - id: mblue9 + joined: 2018-09 + name: Maria Doyle + orcid: 0000-0003-4847-8436 + page: https://training.galaxyproject.org/training-material/hall-of-fame/mblue9/ + url: https://training.galaxyproject.org/training-material/api/contributors/mblue9.json + dir: topics/genome-annotation/tutorials/annotation-with-prokka + edam_ontology: + - topic_0622 + - topic_3301 + - topic_0623 + - topic_0080 + edam_operation: + - Genome annotation + - Gene prediction + - Genome visualisation + - Coding region prediction + edam_topic: + - Genomics + - Microbiology + - Gene and protein families + - Sequence analysis + exact_supported_servers: + - UseGalaxy.be + - UseGalaxy.eu + - UseGalaxy.org (Main) + feedback_mean_note: null + feedback_number: 0 + follow_up_training: + - topic_name: genome-annotation + tutorials: + - apollo + type: internal + hands_on: true + id: genome-annotation/annotation-with-prokka + inexact_supported_servers: + - Galaxy@AuBi + - GalaxyTrakr + - MISSISSIPPI + - UseGalaxy.org.au + - UseGalaxy.cz + - UseGalaxy.fr + - UseGalaxy.no + js_requirements: + mathjax: null + mermaid: false + key_points: + - Prokka is a useful tool to annotate a bacterial genome. + - JBrowse can be used to inspect the annotation of a genome. + layout: tutorial_hands_on + level: Introductory + license: CC-BY-4.0 + mod_date: '2026-01-23' + objectives: + - Load genome into Galaxy + - Annotate genome with Prokka + - View annotations in JBrowse + pageviews: 9269864 + pub_date: '2018-03-06' + questions: + - How can we annotate a bacterial genome? + - How can we visualize annotated genomic features? + recordings: + - captioners: + - abretaud + date: '2021-02-15' + galaxy_version: '21.01' + length: 20M + speakers: + - abretaud + youtube_id: B8pIQZPf21Y + short_id: T00168 + short_tools: + - prokka + - jbrowse + slides: true + slides_recordings: + - captioners: + - abretaud + date: '2021-02-15' + galaxy_version: '21.01' + length: 3M + speakers: + - awspolly + youtube_id: eqHy-Cc7k4Q + subtopic: prokaryote + supported_servers: + exact: + - name: UseGalaxy.be + url: https://usegalaxy.be/ + usegalaxy: false + - name: UseGalaxy.eu + url: https://usegalaxy.eu + usegalaxy: true + - name: UseGalaxy.org (Main) + url: https://usegalaxy.org + usegalaxy: true + inexact: + - name: Galaxy@AuBi + url: https://galaxy.mesocentre.uca.fr + usegalaxy: false + - name: GalaxyTrakr + url: https://galaxytrakr.org/ + usegalaxy: false + - name: MISSISSIPPI + url: https://mississippi.sorbonne-universite.fr + usegalaxy: false + - 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state: missing - - server: https://neo.engr.uconn.edu/ - state: missing - - server: https://mississippi.sorbonne-universite.fr - state: missing + - 1.14.6+galaxy1 - server: http://galaxy.inf.ethz.ch state: missing - server: https://palfinder.ls.manchester.ac.uk/ @@ -37218,104 +17581,39 @@ - server: http://pepsimili.e-nios.com:8080/ state: inexact versions: - - 2.1.1+galaxy1 - - server: https://galaxy.bio.di.uminho.pt/ - state: missing + - 1.14.6+galaxy1 - server: https://usegalaxy.org.au state: exact - version: 2.1.3+galaxy2 + version: 1.14.5 - server: https://usegalaxy.be/ state: exact - version: 2.1.3+galaxy2 + version: 1.14.5 - server: https://usegalaxy.cz/ - state: exact - version: 2.1.3+galaxy2 - - server: https://usegalaxy.eu - state: exact - version: 2.1.3+galaxy2 - - server: https://usegalaxy.fr/ - state: exact - version: 2.1.3+galaxy2 - - server: https://usegalaxy.no/ state: inexact - versions: - - 2.1.1+galaxy0 - - 2.1.1+galaxy1 - - 2.0.8_beta+galaxy0 - - server: https://usegalaxy.org - 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state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - - server: https://neo.engr.uconn.edu/ - state: missing - - server: https://mississippi.sorbonne-universite.fr - state: missing - - server: http://galaxy.inf.ethz.ch - state: missing - - server: https://palfinder.ls.manchester.ac.uk/ - state: missing - - server: http://pepsimili.e-nios.com:8080/ - state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - - server: https://usegalaxy.org.au - state: exact - version: 1.2.0+galaxy1 - - server: https://usegalaxy.be/ - state: exact - version: 1.2.0+galaxy1 - - server: https://usegalaxy.cz/ - state: exact - version: 1.2.0+galaxy1 + versions: + - 1.14.6+galaxy1 + - 1.14.6+galaxy2 - server: https://usegalaxy.eu state: exact - version: 1.2.0+galaxy1 + version: 1.14.5 - server: https://usegalaxy.fr/ - state: exact - version: 1.2.0+galaxy1 + state: inexact + versions: + - 1.14.6+galaxy1 + - 1.14.6+galaxy2 + - '1.13' + - 1.14.5+galaxy0 - server: https://usegalaxy.no/ - state: exact - version: 1.2.0+galaxy1 + state: inexact + versions: + - 1.14.5+galaxy0 - server: https://usegalaxy.org state: exact - version: 1.2.0+galaxy1 + version: 1.14.5 - server: https://viralvariant.anses.fr/ state: missing - version: 1.2.0+galaxy1 - - id: toolshed.g2.bx.psu.edu/repos/iuc/krakentools_kreport2krona/krakentools_kreport2krona/1.2+galaxy2 + version: 1.14.5 + - id: toolshed.g2.bx.psu.edu/repos/crs4/prokka/prokka/1.14.5+galaxy0 servers: - server: http://apostl.moffitt.org/ state: missing @@ -37328,16 +17626,16 @@ - server: https://hyperbrowser.uio.no/coloc-stats state: missing - server: https://galaxy.mesocentre.uca.fr - state: exact - version: 1.2+galaxy2 - - server: https://galaxy.pasteur.fr/ state: inexact versions: - - 1.2+galaxy1 + - 1.14.6+galaxy1 + - server: https://galaxy.pasteur.fr/ + state: missing - server: https://galaxytrakr.org/ state: inexact versions: - - 1.2.1+galaxy0 + - 1.14.6+galaxy1 + - 1.14.6+galaxy2 - server: http://igg.cloud.ba.infn.it/galaxy state: missing - server: https://galaxy.hyphy.org/ @@ -37348,45 +17646,52 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr - state: missing + state: inexact + versions: + - 1.14.6+galaxy1 - server: http://galaxy.inf.ethz.ch state: missing - server: https://palfinder.ls.manchester.ac.uk/ state: missing - server: http://pepsimili.e-nios.com:8080/ - state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing + state: inexact + versions: + - 1.14.6+galaxy1 - server: https://usegalaxy.org.au - state: exact - version: 1.2+galaxy2 + state: inexact + versions: + - 1.14.6+galaxy1 + - 1.14.6+galaxy2 + - 1.14.6+galaxy0 + - 1.14.5 + - 1.12.0 - server: https://usegalaxy.be/ state: exact - version: 1.2+galaxy2 + version: 1.14.5+galaxy0 - server: https://usegalaxy.cz/ - state: exact - version: 1.2+galaxy2 + state: inexact + versions: + - 1.14.6+galaxy1 + - 1.14.6+galaxy2 - server: https://usegalaxy.eu state: exact - version: 1.2+galaxy2 + version: 1.14.5+galaxy0 - server: https://usegalaxy.fr/ state: exact - version: 1.2+galaxy2 + version: 1.14.5+galaxy0 - server: https://usegalaxy.no/ state: exact - version: 1.2+galaxy2 + version: 1.14.5+galaxy0 - server: https://usegalaxy.org state: exact - version: 1.2+galaxy2 + version: 1.14.5+galaxy0 - server: https://viralvariant.anses.fr/ state: missing - version: 1.2+galaxy2 - - id: toolshed.g2.bx.psu.edu/repos/iuc/metaphlan/metaphlan/4.1.1+galaxy4 + version: 1.14.5+galaxy0 + - id: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1 servers: - server: http://apostl.moffitt.org/ state: missing @@ -37400,11 +17705,13 @@ state: missing - server: https://galaxy.mesocentre.uca.fr state: exact - version: 4.1.1+galaxy4 + version: 1.16.11+galaxy1 - server: https://galaxy.pasteur.fr/ - state: missing + state: exact + version: 1.16.11+galaxy1 - server: https://galaxytrakr.org/ - state: missing + state: exact + version: 1.16.11+galaxy1 - server: http://igg.cloud.ba.infn.it/galaxy state: missing - server: https://galaxy.hyphy.org/ @@ -37415,183 +17722,147 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr - state: missing + state: exact + version: 1.16.11+galaxy1 - server: http://galaxy.inf.ethz.ch state: missing - server: https://palfinder.ls.manchester.ac.uk/ state: missing - server: http://pepsimili.e-nios.com:8080/ state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - server: https://usegalaxy.org.au state: exact - version: 4.1.1+galaxy4 + version: 1.16.11+galaxy1 - server: https://usegalaxy.be/ state: exact - version: 4.1.1+galaxy4 + version: 1.16.11+galaxy1 - server: https://usegalaxy.cz/ state: exact - version: 4.1.1+galaxy4 + version: 1.16.11+galaxy1 - server: https://usegalaxy.eu state: exact - version: 4.1.1+galaxy4 + version: 1.16.11+galaxy1 - server: https://usegalaxy.fr/ state: exact - version: 4.1.1+galaxy4 + version: 1.16.11+galaxy1 - server: https://usegalaxy.no/ - state: inexact - versions: - - 4.0.3+galaxy0 + state: exact + version: 1.16.11+galaxy1 - server: https://usegalaxy.org state: exact - version: 4.1.1+galaxy4 + version: 1.16.11+galaxy1 - server: https://viralvariant.anses.fr/ state: missing - version: 4.1.1+galaxy4 + version: 1.16.11+galaxy1 symlink: null tags: - - metagenomics - - taxonomic profiling + - gmod + - prokaryote - microgalaxy + - jbrowse1 time: null - time_estimation: 2H - title: Taxonomic Profiling and Visualization of Metagenomic Data + time_estimation: 1h + title: Genome annotation with Prokka tools: - - __UNZIP_COLLECTION__ - - interactive_tool_pavian - - interactive_tool_phinch - - toolshed.g2.bx.psu.edu/repos/crs4/taxonomy_krona_chart/taxonomy_krona_chart/2.7.1 - - toolshed.g2.bx.psu.edu/repos/crs4/taxonomy_krona_chart/taxonomy_krona_chart/2.7.1+galaxy0 - - toolshed.g2.bx.psu.edu/repos/iuc/bracken/est_abundance/3.1+galaxy0 - - toolshed.g2.bx.psu.edu/repos/iuc/kraken2/kraken2/2.1.3+galaxy1 - - toolshed.g2.bx.psu.edu/repos/iuc/kraken2/kraken2/2.1.3+galaxy2 - - toolshed.g2.bx.psu.edu/repos/iuc/kraken_biom/kraken_biom/1.2.0+galaxy1 - - toolshed.g2.bx.psu.edu/repos/iuc/krakentools_kreport2krona/krakentools_kreport2krona/1.2+galaxy2 - - toolshed.g2.bx.psu.edu/repos/iuc/metaphlan/metaphlan/4.1.1+galaxy4 - topic_name: microbiome - topic_name_human: Microbiome + - toolshed.g2.bx.psu.edu/repos/crs4/prokka/prokka/1.14.5 + - toolshed.g2.bx.psu.edu/repos/crs4/prokka/prokka/1.14.5+galaxy0 + - toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1 + topic_name: genome-annotation + topic_name_human: Genome Annotation tours: false translations: slides: [] tutorial: [] - video: false - tutorial_name: taxonomic-profiling + video: true + tutorial_name: annotation-with-prokka type: tutorial - url: https://training.galaxyproject.org//topics/microbiome/tutorials/taxonomic-profiling/tutorial.html + url: https://training.galaxyproject.org//topics/genome-annotation/tutorials/annotation-with-prokka/tutorial.html urls: - hands_on: https://training.galaxyproject.org/training-material/api/topics/microbiome/tutorials/taxonomic-profiling/tutorial.json - slides: https://training.galaxyproject.org/training-material/api/topics/microbiome/tutorials/taxonomic-profiling/tutorial.json - version: 8 + hands_on: https://training.galaxyproject.org/training-material/api/topics/genome-annotation/tutorials/annotation-with-prokka/tutorial.json + slides: https://training.galaxyproject.org/training-material/api/topics/genome-annotation/tutorials/annotation-with-prokka/tutorial.json + version: 27 video: true - video_versions: 2 + video_versions: 1 video_view: 0 - visit_duration: 335 - visitors: 14694 + visit_duration: 430 + visitors: 3937916 workflows: - creators: - class: Person - identifier: 0000-0001-9852-1987 - name: "B\xE9r\xE9nice Batut" + identifier: 0000-0002-9906-0673 + name: Anna Syme - class: Person - identifier: 0009-0002-2951-4075 - name: Tarnima Omara + identifier: 0000-0001-6046-610X + name: Torsten Seemann - class: Person - identifier: 0000-0002-6606-5953 - name: Tristan Reynolds - description: This workflow performs taxonomic profiling of metagenomic data and - visualizes microbial community composition using Kraken2 and Bracken as well - as MetaPhlAn. + identifier: 0000-0002-6100-4385 + name: Simon Gladman + description: Genome annotation with Prokka features: comments: false parameters: false - report: - markdown: ' - - # Workflow Execution Report - - - ## Workflow Inputs - - ```galaxy - - invocation_inputs() - - ``` - - - ## Workflow Outputs - - ```galaxy - - invocation_outputs() - - ``` - - - ## Workflow - - ```galaxy - - workflow_display() - - ``` - - ' + report: null subworkflows: false graph_dot: "digraph main {\n node [fontname=\"Atkinson Hyperlegible\", shape=box,\ \ color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n edge [fontname=\"\ - Atkinson Hyperlegible\"];\n 0[color=lightblue,label=\"\u2139\uFE0F Input Collection\\\ - nraw-reads\"]\n 1[color=lightblue,label=\"\u2139\uFE0F Input Dataset\\nmetadata\"\ - ]\n 2[label=\"Unzip collection\"]\n 0 -> 2 [label=\"output\"]\n 3[label=\"\ - Kraken2\"]\n 0 -> 3 [label=\"output\"]\n 4[label=\"MetaPhlAn\"]\n 2 -> 4\ - \ [label=\"forward\"]\n 2 -> 4 [label=\"reverse\"]\n k9affde3bb159486ebb38c628ac72e7fc[color=lightseagreen,label=\"\ - Output\\nmetaphlan_output\"]\n 4 -> k9affde3bb159486ebb38c628ac72e7fc\n 5[label=\"\ - Krakentools: Convert kraken report file\"]\n 3 -> 5 [label=\"report_output\"\ - ]\n kb14415d566e24f7989d6ae0bcd837796[color=lightseagreen,label=\"Output\\\ - nkrakentool_report\"]\n 5 -> kb14415d566e24f7989d6ae0bcd837796\n 6[label=\"\ - Kraken-biom\"]\n 3 -> 6 [label=\"report_output\"]\n 1 -> 6 [label=\"output\"\ - ]\n 7[label=\"Pavian\"]\n 3 -> 7 [label=\"report_output\"]\n 8[label=\"Bracken\"\ - ]\n 3 -> 8 [label=\"report_output\"]\n 9[label=\"Krona pie chart\"]\n 4 ->\ - \ 9 [label=\"krona_output_file\"]\n 10[label=\"Krona pie chart\"]\n 5 -> 10\ - \ [label=\"output\"]\n 11[label=\"Phinch Visualisation\"]\n 6 -> 11 [label=\"\ - biomOutput\"]\n}" + Atkinson Hyperlegible\"];\n 0[color=lightblue,label=\"\u2139\uFE0F Input Dataset\\\ + ncontigs.fasta\"]\n 1[label=\"Prokka\"]\n 0 -> 1 [label=\"output\"]\n ka336c364e69e47ebace6a7fe46d285fe[color=lightseagreen,label=\"\ + Output\\ngff_output\"]\n 1 -> ka336c364e69e47ebace6a7fe46d285fe\n 2[label=\"\ + JBrowse\"]\n 1 -> 2 [label=\"out_fna\"]\n 1 -> 2 [label=\"out_gff\"]\n}" history: - - hash: 501a57f0ee0f8d9a12374d3cad9d498a000a3c61 - message: Add orcid ID for creator Tarnima Omara + - hash: 70a555355ed2ebc563a4388cd1da50f7f1a5952f + message: Update topics/genome-annotation/tutorials/annotation-with-prokka/workflows/Galaxy-Workflow-Workflow_constructed_from_history__prokka-workflow_.ga + num: 10 + short_hash: 70a555355 + unix: '1715074163' + - hash: 466b451a082b7d2d5e60777a45289874bbbde721 + message: Add creators and license to workflow + num: 9 + short_hash: 466b451a0 + unix: '1714990318' + - hash: 499e257dee992b4645adf4c79844b8cc89e68c24 + message: update prokka workflow + num: 8 + short_hash: 499e257de + unix: '1714456964' + - hash: 56413bab75ab75be269668d70e3929e01bbaa5fb + message: Add workflow test. + num: 7 + short_hash: 56413bab7 + unix: '1603310943' + - hash: a3829a12322232647926a394b1ecae3af17a858b + message: Update Galaxy-Workflow-Workflow_constructed_from_history__prokka-workflow_.ga num: 6 - short_hash: 501a57f0e - unix: '1765757948' - - hash: 9bfe386d04a4227438b50d6ee837f4b242ca4728 - message: Update workflow and workflow tests + short_hash: a3829a123 + unix: '1580832292' + - hash: bab7ab72c6a4436a3ac3e6745b364696332399b5 + message: prokka@1.14.5 jbrowse@1.16.5+galaxy7 num: 5 - short_hash: 9bfe386d0 - unix: '1765756254' - - hash: dde20503929908deeee6ec1fc448c11e16a75a9f - message: Update topics/microbiome/tutorials/taxonomic-profiling/workflows/main-workflow.ga + short_hash: bab7ab72c + unix: '1580433748' + - hash: c69f09dd0cb211d5621af293fe400892e343f78e + message: Adding tag num: 4 - short_hash: dde205039 - unix: '1743721902' - - hash: 364bb343b77778931b064588e8d3623db0f8d75f - message: Update topics/microbiome/tutorials/taxonomic-profiling/workflows/main-workflow.ga + short_hash: c69f09dd0 + unix: '1579796672' + - hash: 920732bc2295d6120b075934b758290ad56f5759 + message: Updated prokka workflow to newest tool versions num: 3 - short_hash: 364bb343b - unix: '1743721794' - - hash: 2159350d9efc52192ade1a8060fd0645959892bc - message: Update main-workflow.ga + short_hash: 920732bc2 + unix: '1579634888' + - hash: eb4d724e0064c77beb20efa626a0f28fd0500676 + message: Workflow renaming num: 2 - short_hash: 2159350d9 - unix: '1743647309' - - hash: 0e0a2f2ccb650b0aab1ffc13838045164bdb5d30 - message: Rename metagenomics topic to microbiome + short_hash: eb4d724e0 + unix: '1579084895' + - hash: b9a6072964bce056112a36326600e4c80bd133ec + message: move tutorials to new topic num: 1 - short_hash: 0e0a2f2cc - unix: '1704901629' + short_hash: b9a607296 + unix: '1528898987' inputs: - annotation: '' content_id: null @@ -37600,989 +17871,731 @@ input_connections: {} inputs: - description: '' - name: raw-reads - label: raw-reads - name: Input dataset collection - outputs: [] - position: - left: 0 - top: 32 - tool_id: null - tool_state: '{"optional": false, "tag": null, "collection_type": "list:paired", - "fields": null}' - tool_version: null - type: data_collection_input - uuid: 8ceaae85-1ed7-4488-b839-53d36e642378 - when: null - workflow_outputs: [] - - annotation: '' - content_id: null - errors: null - id: 1 - input_connections: {} - inputs: - - description: '' - name: metadata - label: metadata + name: contigs.fasta + label: contigs.fasta name: Input dataset outputs: [] position: - left: 35.48228574271107 - top: 575.2289046420843 + left: 0 + top: 76.845458984375 tool_id: null tool_state: '{"optional": false, "tag": null}' tool_version: null type: data_input - uuid: 715bbeb3-cb9a-49dd-a9c5-1f184f3eb34a + uuid: 79e73b85-8d44-413f-83b7-c0e668ec963c when: null workflow_outputs: [] - license: MIT - mermaid: "flowchart TD\n 0[\"\u2139\uFE0F Input Collection\\nraw-reads\"];\n\ - \ style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"\u2139\uFE0F Input Dataset\\\ - nmetadata\"];\n style 1 stroke:#2c3143,stroke-width:4px;\n 2[\"Unzip collection\"\ - ];\n 0 -->|output| 2;\n 3[\"Kraken2\"];\n 0 -->|output| 3;\n 4[\"MetaPhlAn\"\ - ];\n 2 -->|forward| 4;\n 2 -->|reverse| 4;\n 9affde3b-b159-486e-bb38-c628ac72e7fc[\"\ - Output\\nmetaphlan_output\"];\n 4 --> 9affde3b-b159-486e-bb38-c628ac72e7fc;\n\ - \ style 9affde3b-b159-486e-bb38-c628ac72e7fc stroke:#2c3143,stroke-width:4px;\n\ - \ 5[\"Krakentools: Convert kraken report file\"];\n 3 -->|report_output| 5;\n\ - \ b14415d5-66e2-4f79-89d6-ae0bcd837796[\"Output\\nkrakentool_report\"];\n \ - \ 5 --> b14415d5-66e2-4f79-89d6-ae0bcd837796;\n style b14415d5-66e2-4f79-89d6-ae0bcd837796\ - \ stroke:#2c3143,stroke-width:4px;\n 6[\"Kraken-biom\"];\n 3 -->|report_output|\ - \ 6;\n 1 -->|output| 6;\n 7[\"Pavian\"];\n 3 -->|report_output| 7;\n 8[\"\ - Bracken\"];\n 3 -->|report_output| 8;\n 9[\"Krona pie chart\"];\n 4 -->|krona_output_file|\ - \ 9;\n 10[\"Krona pie chart\"];\n 5 -->|output| 10;\n 11[\"Phinch Visualisation\"\ - ];\n 6 -->|biomOutput| 11;" - modified: 2026-05-21 00:30:25 +0000 - name: Taxonomic Profiling and Visualization of Metagenomic Data + license: GPL-3.0-or-later + mermaid: "flowchart TD\n 0[\"\u2139\uFE0F Input Dataset\\ncontigs.fasta\"];\n\ + \ style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"Prokka\"];\n 0 -->|output|\ + \ 1;\n a336c364-e69e-47eb-ace6-a7fe46d285fe[\"Output\\ngff_output\"];\n 1\ + \ --> a336c364-e69e-47eb-ace6-a7fe46d285fe;\n style a336c364-e69e-47eb-ace6-a7fe46d285fe\ + \ stroke:#2c3143,stroke-width:4px;\n 2[\"JBrowse\"];\n 1 -->|out_fna| 2;\n\ + \ 1 -->|out_gff| 2;" + modified: 2026-07-01 00:31:39 +0000 + name: 'Genome Annotation with Prokka ' outputs: - 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avatar: /training-material/shared/images/ifb.png + github: false + id: ifb + members: + - bebatut + - clsiguret + - yvesvdb + name: "Institut Fran\xE7ais de Bioinformatique" + page: https://training.galaxyproject.org/training-material/hall-of-fame/ifb/ + ror: 045f7pv37 + short_name: IFB + url: https://training.galaxyproject.org/training-material/api/organisations/ifb.json - affiliations: - elixir-europe + contact_for_training: false elixir_node: nl - id: willemdek11 - joined: 2018-09 - name: Willem de Koning - page: https://training.galaxyproject.org/training-material/hall-of-fame/willemdek11/ - url: https://training.galaxyproject.org/training-material/api/contributors/willemdek11.json + former_affiliations: + - deNBI + - avans-atgm + - uni-freiburg + - erasmusmc + - gallantries + - by-covid + - elixir-converge + id: hexylena + joined: 2017-09 + location: + country: NL + lat: 51.91 + lon: 4.46 + maintainer_contact: gitter + matrix: hexylena:matrix.org + name: Helena Rasche + orcid: 0000-0001-9760-8992 + page: https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/ + url: https://training.galaxyproject.org/training-material/api/contributors/hexylena.json + - affiliations: + - gallantries + - ifb + - elixir-europe + contact_for_training: true + elixir_node: fr + email: berenice.batut@gmail.com + fediverse: https://piaille.fr/@bebatut + fediverse_flavor: mastodon + former_affiliations: + - uni-freiburg + - deNBI + id: bebatut + joined: 2017-09 + linkedin: berenicebatut + location: + country: FR + lat: 45.77 + lon: 3.08 + matrix: bebatut:matrix.org + name: "B\xE9r\xE9nice Batut" + orcid: 0000-0001-9852-1987 + page: https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/ + twitter: bebatut + url: https://training.galaxyproject.org/training-material/api/contributors/bebatut.json - affiliations: - uni-freiburg - - nfdi4plants - elixir-europe - bio: Researcher at Erasmus Medical Center - bluesky: shiltemann.bsky.social + - deNBI + - mwk + - biont contact_for_training: true - elixir_node: nl - email: saskia.hiltemann@gmail.com - fediverse: https://mstdn.science/@shiltemann + elixir_node: de + email: muellert@informatik.uni-freibrug.de + id: teresa-m + joined: 2022-09 + linkedin: teresamueller87 + matrix: teresa-m:matrix.org + name: "Teresa M\xFCller" + orcid: 0000-0003-1252-9684 + page: https://training.galaxyproject.org/training-material/hall-of-fame/teresa-m/ + url: https://training.galaxyproject.org/training-material/api/contributors/teresa-m.json + - affiliations: + - uni-freiburg + - elixir-europe + - deNBI + - mwk + - materialvitaldigital + email: zierep@informatik.uni-freiburg.de + id: paulzierep + joined: 2023-02 + name: Paul Zierep + orcid: 0000-0003-2982-388X + page: https://training.galaxyproject.org/training-material/hall-of-fame/paulzierep/ + url: https://training.galaxyproject.org/training-material/api/contributors/paulzierep.json + - affiliations: + - elixir-europe + bluesky: abretaud.bsky.social + contact_for_training: true + elixir_node: fr + email: anthony.bretaudeau@irisa.fr + fediverse: https://genomic.social/@abretaud fediverse_flavor: mastodon former_affiliations: - - CINECA-Project + - eurosciencegateway - gallantries - - erasmusmc - id: shiltemann + id: abretaud joined: 2017-09 - linkedin: shiltemann location: - country: NL - lat: 51.912 - lon: 4.462 - maintainer_contact: gitter - matrix: shiltemann:matrix.org - name: Saskia Hiltemann - orcid: 0000-0003-3803-468X - page: https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/ - url: https://training.galaxyproject.org/training-material/api/contributors/shiltemann.json - dir: topics/microbiome/tutorials/plasmid-metagenomics-nanopore + country: FR + lat: 48.11 + lon: -1.64 + matrix: abretaud:matrix.org + name: Anthony Bretaudeau + orcid: 0000-0003-0914-2470 + page: https://training.galaxyproject.org/training-material/hall-of-fame/abretaud/ + url: https://training.galaxyproject.org/training-material/api/contributors/abretaud.json + - affiliations: + - deNBI + - mwk + - uni-freiburg + - elixir-europe + - materialvitaldigital + contact_for_training: true + elixir_node: de + email: bjoern.gruening@gmail.com + fediverse: https://fosstodon.org/@bgruening + fediverse_flavor: mastodon + former_affiliations: + - eurosciencegateway + - eosc-life + - by-covid + - crc992 + - elixir-converge + id: bgruening + joined: 2017-09 + linkedin: bgruening + location: + country: DE + lat: 47.997791 + lon: 7.842609 + matrix: bgruening:matrix.org + name: "Bj\xF6rn Gr\xFCning" + orcid: 0000-0002-3079-6586 + page: https://training.galaxyproject.org/training-material/hall-of-fame/bgruening/ + twitter: bjoerngruening + url: https://training.galaxyproject.org/training-material/api/contributors/bgruening.json + dir: topics/genome-annotation/tutorials/bacterial-genome-annotation edam_ontology: - 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UseGalaxy.eu + - UseGalaxy.fr feedback_mean_note: null feedback_number: 0 + follow_up_training: + - topic_name: genome-annotation + tutorials: + - apollo + type: internal + - topic_name: visualisation + tutorials: + - circos + - jbrowse + type: internal + - topic_name: galaxy-interface + tutorials: + - history-to-workflow + type: internal hands_on: true - id: microbiome/plasmid-metagenomics-nanopore + id: genome-annotation/bacterial-genome-annotation inexact_supported_servers: - - UseGalaxy.org.au + - Galaxy@AuBi - UseGalaxy.be - UseGalaxy.cz - - UseGalaxy.fr - - UseGalaxy.no - UseGalaxy.org (Main) js_requirements: mathjax: null mermaid: false key_points: - - Minimap2, Miniasm, and Racon can be used for quickly assembling Nanopore data - - Unicycler can be used to optimize settings of assembly tools - - Nanopore sequencing is useful for reconstruction of genomes - - Antimicrobial resistance genes are detectable after fast assembly - - The CARD database is a useful resource describing antibiotic resistance genes + - Bakta is a powerful tool to annotate a bacterial genome + - Annotation can be easily visualized to understand the genomic context and help + making sense of the annotations layout: tutorial_hands_on + level: Introductory license: CC-BY-4.0 - mod_date: '2024-06-14' - objectives: - - Perform Quality control on your reads - - Assemble a genome with Minimap2/Miniasm/Racon - - Determine the structure of the genome(s) - - Scan for antimicrobial resistance genes with Staramr - pageviews: 5713 - pub_date: '2019-06-25' + mod_date: '2024-10-15' + objectives: + - Run a series of tool to annotate a draft bacterial genome for different types + of genomic components + - Evaluate the annotation + - Process the outputs to formate them for visualization needs + - Visualize a draft bacterial genome and its annotations + pageviews: 12131 + pub_date: '2024-02-01' questions: - - How do I assemble a genome with Nanopore data? - - How do I get more information about the structure of the genomes? - - How do I get more information about the antimicrobial resistance genes? + - 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state: missing - - server: https://iris.angers.inra.fr/galaxypub-cfbp - state: missing - - server: https://hyperbrowser.uio.no/coloc-stats - state: missing - - server: https://galaxy.mesocentre.uca.fr - state: missing - - server: https://galaxy.pasteur.fr/ - state: missing - - server: https://galaxytrakr.org/ - state: missing - - server: http://igg.cloud.ba.infn.it/galaxy - state: missing - - server: https://galaxy.hyphy.org/ - state: missing - - server: https://www.immportgalaxy.org/ - state: missing - - server: http://galaxy.interactomix.com/ - state: missing - - server: https://galaxy-web.ipk-gatersleben.de - state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - - server: https://neo.engr.uconn.edu/ - state: missing - - server: https://mississippi.sorbonne-universite.fr - state: missing - - server: http://galaxy.inf.ethz.ch - state: missing - - server: https://palfinder.ls.manchester.ac.uk/ - state: missing - - server: http://pepsimili.e-nios.com:8080/ - state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - - server: https://usegalaxy.org.au - state: inexact - versions: - - 0.1.1 - - 0.1.2 - - server: https://usegalaxy.be/ - state: exact - version: 0.1.0 - - server: https://usegalaxy.cz/ - state: inexact - versions: - - 0.1.2 - - server: https://usegalaxy.eu - state: exact - version: 0.1.0 - - server: https://usegalaxy.fr/ - state: inexact - versions: - - 0.1.2 - - server: https://usegalaxy.no/ - state: inexact - versions: - - 0.1.1 - - 0.1.2 - - server: https://usegalaxy.org - state: inexact - versions: - - 0.1.1 - - 0.1.2 - - server: https://viralvariant.anses.fr/ - state: missing - version: 0.1.0 - - id: toolshed.g2.bx.psu.edu/repos/iuc/gfa_to_fa/gfa_to_fa/0.1.1 + supported_servers_matrix: + servers: + - name: APOSTL + url: http://apostl.moffitt.org/ + usegalaxy: false + - name: MBAC Metabiome Portal + url: http://mbac.gmu.edu:8080/ + usegalaxy: false + - name: ChemFlow + url: https://vm-chemflow-francegrille.eu/ + usegalaxy: false + - name: CIRM-CFBP + url: https://iris.angers.inra.fr/galaxypub-cfbp + usegalaxy: false + - name: Coloc-stats + url: https://hyperbrowser.uio.no/coloc-stats + usegalaxy: false + - name: Galaxy@AuBi + url: https://galaxy.mesocentre.uca.fr + usegalaxy: false + - name: Galaxy@Pasteur + url: https://galaxy.pasteur.fr/ + usegalaxy: false + - name: GalaxyTrakr + url: https://galaxytrakr.org/ + usegalaxy: false + - name: GASLINI + url: http://igg.cloud.ba.infn.it/galaxy + usegalaxy: false + - name: HyPhy HIV NGS Tools + url: https://galaxy.hyphy.org/ + usegalaxy: false + - name: ImmPort Galaxy + url: https://www.immportgalaxy.org/ + usegalaxy: false + - name: InteractoMIX + url: http://galaxy.interactomix.com/ + usegalaxy: false + - name: IPK Galaxy Blast Suite + url: https://galaxy-web.ipk-gatersleben.de + usegalaxy: false + - name: Mandoiu Lab + url: https://neo.engr.uconn.edu/ + usegalaxy: false + - name: MISSISSIPPI + url: https://mississippi.sorbonne-universite.fr + usegalaxy: false + - name: Oqtans + url: http://galaxy.inf.ethz.ch + usegalaxy: false + - name: Palfinder + url: https://palfinder.ls.manchester.ac.uk/ + usegalaxy: false + - name: PepSimili + url: http://pepsimili.e-nios.com:8080/ + usegalaxy: false + - name: UseGalaxy.org.au + url: https://usegalaxy.org.au + usegalaxy: true + - name: UseGalaxy.be + url: https://usegalaxy.be/ + usegalaxy: false + - name: UseGalaxy.cz + url: https://usegalaxy.cz/ + usegalaxy: false + - name: UseGalaxy.eu + url: https://usegalaxy.eu + usegalaxy: true + - name: UseGalaxy.fr + url: https://usegalaxy.fr/ + usegalaxy: true + - name: UseGalaxy.no + url: https://usegalaxy.no/ + usegalaxy: false + - name: UseGalaxy.org (Main) + url: https://usegalaxy.org + usegalaxy: true + - name: Viral Variant Visualizer (VVV) + url: https://viralvariant.anses.fr/ + usegalaxy: false + tools: + - id: Grouping1 servers: - server: http://apostl.moffitt.org/ - state: missing + state: local - server: http://mbac.gmu.edu:8080/ - state: missing + state: local - server: https://vm-chemflow-francegrille.eu/ state: missing - server: https://iris.angers.inra.fr/galaxypub-cfbp state: missing - server: https://hyperbrowser.uio.no/coloc-stats - state: missing + state: local - server: https://galaxy.mesocentre.uca.fr - state: missing + state: local - server: https://galaxy.pasteur.fr/ - state: missing + state: local - server: https://galaxytrakr.org/ - state: missing + state: local - server: http://igg.cloud.ba.infn.it/galaxy - state: missing + state: local - server: https://galaxy.hyphy.org/ - state: missing + state: local - server: https://www.immportgalaxy.org/ state: missing - server: http://galaxy.interactomix.com/ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr - state: missing + state: local - server: http://galaxy.inf.ethz.ch - state: missing + state: local - server: https://palfinder.ls.manchester.ac.uk/ state: missing - server: http://pepsimili.e-nios.com:8080/ - state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing + state: local - server: https://usegalaxy.org.au - state: exact - version: 0.1.1 + state: local - server: https://usegalaxy.be/ - state: exact - version: 0.1.1 + state: local - server: https://usegalaxy.cz/ - state: inexact - versions: - - 0.1.2 + state: local - server: https://usegalaxy.eu - state: exact - version: 0.1.1 + state: local - server: https://usegalaxy.fr/ - state: inexact - versions: - - 0.1.2 + state: local - server: https://usegalaxy.no/ - state: exact - version: 0.1.1 + state: local - server: https://usegalaxy.org - state: exact - version: 0.1.1 + state: local - server: https://viralvariant.anses.fr/ - state: missing - version: 0.1.1 - - id: toolshed.g2.bx.psu.edu/repos/iuc/miniasm/miniasm/0.2+galaxy0 + state: local + version: local + - id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/9.3+galaxy1 servers: - server: http://apostl.moffitt.org/ state: missing @@ -38597,140 +18610,74 @@ - server: https://galaxy.mesocentre.uca.fr state: inexact versions: - - 0.3_r179+galaxy1 + - 9.5+galaxy3 + - 1.1.3 - server: https://galaxy.pasteur.fr/ state: missing - server: https://galaxytrakr.org/ state: inexact versions: - - 0.3_r179+galaxy1 + - 9.5+galaxy3 + - 1.1.3 + - 9.5+galaxy2 - server: http://igg.cloud.ba.infn.it/galaxy state: missing - server: https://galaxy.hyphy.org/ - state: missing - - server: https://www.immportgalaxy.org/ - state: missing - - server: http://galaxy.interactomix.com/ - state: missing - - server: https://galaxy-web.ipk-gatersleben.de - state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - - server: https://neo.engr.uconn.edu/ - state: missing - - server: https://mississippi.sorbonne-universite.fr - state: missing - - server: http://galaxy.inf.ethz.ch - state: missing - - server: https://palfinder.ls.manchester.ac.uk/ - state: missing - - server: http://pepsimili.e-nios.com:8080/ - state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - - server: https://usegalaxy.org.au - state: exact - version: 0.2+galaxy0 - - server: https://usegalaxy.be/ - state: exact - version: 0.2+galaxy0 - - server: https://usegalaxy.cz/ - state: inexact - versions: - - 0.3_r179+galaxy1 - - server: https://usegalaxy.eu - state: exact - version: 0.2+galaxy0 - - server: https://usegalaxy.fr/ - state: inexact - versions: - - 0.3_r179+galaxy1 - - server: https://usegalaxy.no/ - state: inexact - versions: - - 0.3_r179+galaxy1 - - 0.3+galaxy1 - - 0.3_r179+galaxy0 - - 0.3+galaxy0 - - server: https://usegalaxy.org - state: exact - version: 0.2+galaxy0 - - server: https://viralvariant.anses.fr/ - state: missing - version: 0.2+galaxy0 - - id: toolshed.g2.bx.psu.edu/repos/iuc/miniasm/miniasm/0.3+galaxy0 - servers: - - server: http://apostl.moffitt.org/ - state: missing - - server: http://mbac.gmu.edu:8080/ - state: missing - - server: https://vm-chemflow-francegrille.eu/ - state: missing - - server: https://iris.angers.inra.fr/galaxypub-cfbp - state: missing - - server: https://hyperbrowser.uio.no/coloc-stats - state: missing - - server: https://galaxy.mesocentre.uca.fr - state: inexact - versions: - - 0.3_r179+galaxy1 - - server: https://galaxy.pasteur.fr/ - state: missing - - server: https://galaxytrakr.org/ state: inexact versions: - - 0.3_r179+galaxy1 - - server: http://igg.cloud.ba.infn.it/galaxy - state: missing - - server: https://galaxy.hyphy.org/ - state: missing + - 9.5+galaxy3 - server: https://www.immportgalaxy.org/ state: missing - server: http://galaxy.interactomix.com/ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr - state: missing + state: inexact + versions: + - 9.5+galaxy3 - server: http://galaxy.inf.ethz.ch state: missing - server: https://palfinder.ls.manchester.ac.uk/ state: missing - server: http://pepsimili.e-nios.com:8080/ state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - server: https://usegalaxy.org.au state: exact - version: 0.3+galaxy0 + version: 9.3+galaxy1 - server: https://usegalaxy.be/ state: exact - version: 0.3+galaxy0 + version: 9.3+galaxy1 - server: https://usegalaxy.cz/ state: inexact versions: - - 0.3_r179+galaxy1 + - 9.5+galaxy3 + - 1.1.3 + - 9.5+galaxy2 + - 9.5+galaxy0 + - 1.1.0 - server: https://usegalaxy.eu state: exact - version: 0.3+galaxy0 + version: 9.3+galaxy1 - server: https://usegalaxy.fr/ + state: exact + version: 9.3+galaxy1 + - server: https://usegalaxy.no/ state: inexact versions: - - 0.3_r179+galaxy1 - - server: https://usegalaxy.no/ - state: exact - version: 0.3+galaxy0 + - 1.1.3 + - 1.1.2 + - 1.1.1 + - 1.1.0 - server: https://usegalaxy.org state: exact - version: 0.3+galaxy0 + version: 9.3+galaxy1 - server: https://viralvariant.anses.fr/ state: missing - version: 0.3+galaxy0 - - id: toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.17 + version: 9.3+galaxy1 + - id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_tail_tool/9.3+galaxy1 servers: - server: http://apostl.moffitt.org/ state: missing @@ -38745,89 +18692,70 @@ - server: https://galaxy.mesocentre.uca.fr state: inexact versions: - - 2.28+galaxy1 - - 2.28+galaxy2 - - 2.24+galaxy0 - - 2.28+galaxy0 + - 1.1.0 + - 9.5+galaxy3 - server: https://galaxy.pasteur.fr/ state: missing - server: https://galaxytrakr.org/ state: inexact versions: - - 2.28+galaxy2 + - 1.1.0 + - 9.5+galaxy3 + - 9.5+galaxy2 - server: http://igg.cloud.ba.infn.it/galaxy state: missing - server: https://galaxy.hyphy.org/ state: inexact versions: - - 2.28+galaxy2 + - 9.5+galaxy3 - server: https://www.immportgalaxy.org/ state: missing - server: http://galaxy.interactomix.com/ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr state: inexact versions: - - 2.30+galaxy0 + - 9.5+galaxy3 - server: http://galaxy.inf.ethz.ch state: missing - server: https://palfinder.ls.manchester.ac.uk/ state: missing - server: http://pepsimili.e-nios.com:8080/ state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - server: https://usegalaxy.org.au state: exact - version: '2.17' + version: 9.3+galaxy1 - server: https://usegalaxy.be/ state: exact - version: '2.17' + version: 9.3+galaxy1 - server: https://usegalaxy.cz/ state: inexact versions: - - 2.28+galaxy1 - - 2.28+galaxy2 - - 2.28+galaxy0 - - 2.17+galaxy2 - - 2.26+galaxy0 + - 1.1.0 + - 9.5+galaxy3 + - 9.5+galaxy2 + - 9.5+galaxy0 - server: https://usegalaxy.eu state: exact - version: '2.17' + version: 9.3+galaxy1 - server: https://usegalaxy.fr/ - state: inexact - versions: - - 2.28+galaxy1 - - 2.28+galaxy2 - - 2.24+galaxy0 - - 2.28+galaxy0 - - 2.30+galaxy0 - - 2.17+galaxy2 - - 2.22+galaxy0 - - 2.26+galaxy0 - - 2.23+galaxy0 - - '2.12' - - 2.27+galaxy0 + state: exact + version: 9.3+galaxy1 - server: https://usegalaxy.no/ state: inexact versions: - - 2.24+galaxy0 - - 2.17+galaxy0 + - 1.1.0 - server: https://usegalaxy.org state: exact - version: '2.17' + version: 9.3+galaxy1 - server: https://viralvariant.anses.fr/ - state: inexact - versions: - - 2.28+galaxy2 - version: '2.17' - - id: toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.17+galaxy2 + state: missing + version: 9.3+galaxy1 + - id: toolshed.g2.bx.psu.edu/repos/iuc/bakta/bakta/1.9.3+galaxy0 servers: - server: http://apostl.moffitt.org/ state: missing @@ -38842,182 +18770,73 @@ - server: https://galaxy.mesocentre.uca.fr state: inexact versions: - - 2.28+galaxy1 - - 2.28+galaxy2 - - 2.24+galaxy0 - - 2.28+galaxy0 + - 1.8.1+galaxy1 + - 1.9.2+galaxy0 + - 1.8.2+galaxy0 + - 1.9.4+galaxy0 - server: https://galaxy.pasteur.fr/ state: missing - server: https://galaxytrakr.org/ - state: inexact - versions: - - 2.28+galaxy2 + state: missing - server: http://igg.cloud.ba.infn.it/galaxy state: missing - server: https://galaxy.hyphy.org/ - state: inexact - versions: - - 2.28+galaxy2 + state: missing - server: https://www.immportgalaxy.org/ state: missing - server: http://galaxy.interactomix.com/ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr - state: inexact - versions: - - 2.30+galaxy0 + state: missing - server: http://galaxy.inf.ethz.ch state: missing - server: https://palfinder.ls.manchester.ac.uk/ state: missing - server: http://pepsimili.e-nios.com:8080/ state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - server: https://usegalaxy.org.au - state: exact - version: 2.17+galaxy2 + state: inexact + versions: + - 1.9.2+galaxy0 + - 1.8.2+galaxy0 + - 1.9.4+galaxy0 + - 1.9.4+galaxy1 + - 1.5.0+galaxy0 - server: https://usegalaxy.be/ state: inexact versions: - - 2.28+galaxy1 - - 2.28+galaxy2 - - 2.24+galaxy0 - - 2.28+galaxy0 - - 2.30+galaxy0 - - '2.17' - - 2.17+galaxy1 - - 2.26+galaxy0 - - 2.17+galaxy0 - - '2.5' - - '2.3' - - 2.5+gx1 - - '2.12' + - 1.8.2+galaxy0 + - 1.9.4+galaxy1 - server: https://usegalaxy.cz/ - state: exact - version: 2.17+galaxy2 + state: inexact + versions: + - 1.8.2+galaxy0 + - 1.9.4+galaxy0 + - 1.9.4+galaxy1 + - 1.6.1+galaxy0 - server: https://usegalaxy.eu state: exact - version: 2.17+galaxy2 + version: 1.9.3+galaxy0 - server: https://usegalaxy.fr/ state: exact - version: 2.17+galaxy2 + version: 1.9.3+galaxy0 - server: https://usegalaxy.no/ state: inexact versions: - - 2.24+galaxy0 - - 2.17+galaxy0 + - 1.9.2+galaxy0 - server: https://usegalaxy.org - state: exact - version: 2.17+galaxy2 - - server: https://viralvariant.anses.fr/ - state: inexact - versions: - - 2.28+galaxy2 - version: 2.17+galaxy2 - - id: toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.25.0+galaxy1 - servers: - - server: http://apostl.moffitt.org/ - state: missing - - server: http://mbac.gmu.edu:8080/ - state: missing - - server: https://vm-chemflow-francegrille.eu/ - state: missing - - server: https://iris.angers.inra.fr/galaxypub-cfbp - state: missing - - server: https://hyperbrowser.uio.no/coloc-stats - state: missing - - server: https://galaxy.mesocentre.uca.fr - state: inexact - versions: - - 1.46.2+galaxy0 - - 1.28.2+galaxy1 - - 1.42.0+galaxy1 - - 1.46.1+galaxy0 - - 1.44.1+galaxy0 - - 1.41.0+galaxy0 - - 1.36.2+galaxy1 - - 1.42.0+galaxy0 - - 1.43.0+galaxy0 - - server: https://galaxy.pasteur.fr/ - state: inexact - versions: - - 1.43.0+galaxy0 - - server: https://galaxytrakr.org/ - state: inexact - versions: - - 1.28.2+galaxy1 - - server: http://igg.cloud.ba.infn.it/galaxy - state: missing - - server: https://galaxy.hyphy.org/ - state: missing - - server: https://www.immportgalaxy.org/ - state: missing - - server: http://galaxy.interactomix.com/ - state: missing - - server: https://galaxy-web.ipk-gatersleben.de - state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - - server: https://neo.engr.uconn.edu/ - state: missing - - server: https://mississippi.sorbonne-universite.fr - state: inexact - versions: - - 1.46.2+galaxy0 - - server: http://galaxy.inf.ethz.ch - state: missing - - server: https://palfinder.ls.manchester.ac.uk/ - state: missing - - server: http://pepsimili.e-nios.com:8080/ - state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - - server: https://usegalaxy.org.au - state: exact - version: 1.25.0+galaxy1 - - server: https://usegalaxy.be/ - state: exact - version: 1.25.0+galaxy1 - - server: https://usegalaxy.cz/ - state: inexact - versions: - - 1.46.2+galaxy0 - - 1.42.0+galaxy1 - - 1.46.1+galaxy0 - - 1.44.1+galaxy0 - - 1.41.0+galaxy0 - - server: https://usegalaxy.eu - state: exact - version: 1.25.0+galaxy1 - - server: https://usegalaxy.fr/ state: inexact versions: - - 1.46.2+galaxy0 - - 1.28.2+galaxy1 - - 1.42.0+galaxy1 - - 1.46.1+galaxy0 - - 1.44.1+galaxy0 - - 1.41.0+galaxy0 - - 1.36.2+galaxy1 - - 1.42.0+galaxy0 - - 1.43.0+galaxy0 - - server: https://usegalaxy.no/ - state: exact - version: 1.25.0+galaxy1 - - server: https://usegalaxy.org - state: exact - version: 1.25.0+galaxy1 + - 1.9.4+galaxy0 + - 1.9.4+galaxy1 - server: https://viralvariant.anses.fr/ state: missing - version: 1.25.0+galaxy1 - - id: toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.28.2+galaxy1 + version: 1.9.3+galaxy0 + - id: toolshed.g2.bx.psu.edu/repos/iuc/integron_finder/integron_finder/2.0.5+galaxy0 servers: - server: http://apostl.moffitt.org/ state: missing @@ -39031,14 +18850,12 @@ state: missing - server: https://galaxy.mesocentre.uca.fr state: exact - version: 1.28.2+galaxy1 + version: 2.0.5+galaxy0 - server: https://galaxy.pasteur.fr/ - state: inexact - versions: - - 1.43.0+galaxy0 + state: missing - server: https://galaxytrakr.org/ state: exact - version: 1.28.2+galaxy1 + version: 2.0.5+galaxy0 - server: http://igg.cloud.ba.infn.it/galaxy state: missing - server: https://galaxy.hyphy.org/ @@ -39049,52 +18866,40 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr - state: inexact - versions: - - 1.46.2+galaxy0 + state: missing - server: http://galaxy.inf.ethz.ch state: missing - server: https://palfinder.ls.manchester.ac.uk/ state: missing - server: http://pepsimili.e-nios.com:8080/ state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - server: https://usegalaxy.org.au state: exact - version: 1.28.2+galaxy1 + version: 2.0.5+galaxy0 - server: https://usegalaxy.be/ state: exact - version: 1.28.2+galaxy1 + version: 2.0.5+galaxy0 - server: https://usegalaxy.cz/ - state: inexact - versions: - - 1.46.2+galaxy0 - - 1.42.0+galaxy1 - - 1.46.1+galaxy0 - - 1.44.1+galaxy0 - - 1.41.0+galaxy0 + state: exact + version: 2.0.5+galaxy0 - server: https://usegalaxy.eu state: exact - version: 1.28.2+galaxy1 + version: 2.0.5+galaxy0 - server: https://usegalaxy.fr/ state: exact - version: 1.28.2+galaxy1 + version: 2.0.5+galaxy0 - server: https://usegalaxy.no/ - state: exact - version: 1.28.2+galaxy1 + state: missing - server: https://usegalaxy.org state: exact - version: 1.28.2+galaxy1 + version: 2.0.5+galaxy0 - server: https://viralvariant.anses.fr/ - state: missing - version: 1.28.2+galaxy1 - - id: toolshed.g2.bx.psu.edu/repos/iuc/plasflow/PlasFlow/1.0 + state: missing + version: 2.0.5+galaxy0 + - id: toolshed.g2.bx.psu.edu/repos/iuc/isescan/isescan/1.7.2.3+galaxy1 servers: - server: http://apostl.moffitt.org/ state: missing @@ -39108,13 +18913,13 @@ state: missing - server: https://galaxy.mesocentre.uca.fr state: exact - version: '1.0' + version: 1.7.2.3+galaxy1 - server: https://galaxy.pasteur.fr/ state: missing - server: https://galaxytrakr.org/ state: inexact versions: - - 1.1.0+galaxy0 + - 1.7.2.3+galaxy0 - server: http://igg.cloud.ba.infn.it/galaxy state: missing - server: https://galaxy.hyphy.org/ @@ -39125,8 +18930,6 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr @@ -39137,36 +18940,32 @@ state: missing - server: http://pepsimili.e-nios.com:8080/ state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - server: https://usegalaxy.org.au - state: inexact - versions: - - 1.1.0+galaxy0 - - server: https://usegalaxy.be/ state: exact - version: '1.0' - - server: https://usegalaxy.cz/ + version: 1.7.2.3+galaxy1 + - server: https://usegalaxy.be/ state: inexact versions: - - 1.1.0+galaxy0 + - 1.7.2.3+galaxy0 + - 1.7.3+galaxy0 + - server: https://usegalaxy.cz/ + state: exact + version: 1.7.2.3+galaxy1 - server: https://usegalaxy.eu state: exact - version: '1.0' + version: 1.7.2.3+galaxy1 - server: https://usegalaxy.fr/ - state: inexact - versions: - - 1.1.0+galaxy0 - - server: https://usegalaxy.no/ state: exact - version: '1.0' + version: 1.7.2.3+galaxy1 + - server: https://usegalaxy.no/ + state: missing - server: https://usegalaxy.org state: exact - version: '1.0' + version: 1.7.2.3+galaxy1 - server: https://viralvariant.anses.fr/ state: missing - version: '1.0' - - id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.4.7.0 + version: 1.7.2.3+galaxy1 + - id: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1 servers: - server: http://apostl.moffitt.org/ state: missing @@ -39179,16 +18978,14 @@ - server: https://hyperbrowser.uio.no/coloc-stats state: missing - server: https://galaxy.mesocentre.uca.fr - state: inexact - versions: - - 0.5.1+galaxy0 - - 0.5.0+galaxy1 + state: exact + version: 1.16.11+galaxy1 - server: https://galaxy.pasteur.fr/ - state: missing + state: exact + version: 1.16.11+galaxy1 - server: https://galaxytrakr.org/ - state: inexact - versions: - - 0.5.1+galaxy0 + state: exact + version: 1.16.11+galaxy1 - server: http://igg.cloud.ba.infn.it/galaxy state: missing - server: https://galaxy.hyphy.org/ @@ -39199,50 +18996,42 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr - state: inexact - versions: - - 0.5.1+galaxy0 + state: exact + version: 1.16.11+galaxy1 - server: http://galaxy.inf.ethz.ch state: missing - server: https://palfinder.ls.manchester.ac.uk/ state: missing - server: http://pepsimili.e-nios.com:8080/ state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - server: https://usegalaxy.org.au state: exact - version: 0.4.7.0 + version: 1.16.11+galaxy1 - server: https://usegalaxy.be/ state: exact - version: 0.4.7.0 + version: 1.16.11+galaxy1 - server: https://usegalaxy.cz/ - state: inexact - versions: - - 0.5.1+galaxy0 - - 0.5.0+galaxy1 + state: exact + version: 1.16.11+galaxy1 - server: https://usegalaxy.eu state: exact - version: 0.4.7.0 + version: 1.16.11+galaxy1 - server: https://usegalaxy.fr/ state: exact - version: 0.4.7.0 + version: 1.16.11+galaxy1 - server: https://usegalaxy.no/ - state: inexact - versions: - - 0.4.8.0 + state: exact + version: 1.16.11+galaxy1 - server: https://usegalaxy.org state: exact - version: 0.4.7.0 + version: 1.16.11+galaxy1 - server: https://viralvariant.anses.fr/ state: missing - version: 0.4.7.0 - - id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.4.8.0 + version: 1.16.11+galaxy1 + - id: toolshed.g2.bx.psu.edu/repos/iuc/plasmidfinder/plasmidfinder/2.1.6+galaxy1 servers: - server: http://apostl.moffitt.org/ state: missing @@ -39255,16 +19044,13 @@ - server: https://hyperbrowser.uio.no/coloc-stats state: missing - server: https://galaxy.mesocentre.uca.fr - state: inexact - versions: - - 0.5.1+galaxy0 - - 0.5.0+galaxy1 + state: exact + version: 2.1.6+galaxy1 - server: https://galaxy.pasteur.fr/ state: missing - server: https://galaxytrakr.org/ - state: inexact - versions: - - 0.5.1+galaxy0 + state: exact + version: 2.1.6+galaxy1 - server: http://igg.cloud.ba.infn.it/galaxy state: missing - server: https://galaxy.hyphy.org/ @@ -39275,49 +19061,40 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr - state: inexact - versions: - - 0.5.1+galaxy0 + state: missing - server: http://galaxy.inf.ethz.ch state: missing - server: https://palfinder.ls.manchester.ac.uk/ state: missing - server: http://pepsimili.e-nios.com:8080/ state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - server: https://usegalaxy.org.au state: exact - version: 0.4.8.0 + version: 2.1.6+galaxy1 - server: https://usegalaxy.be/ state: exact - version: 0.4.8.0 + version: 2.1.6+galaxy1 - server: https://usegalaxy.cz/ - state: inexact - versions: - - 0.5.1+galaxy0 - - 0.5.0+galaxy1 + state: exact + version: 2.1.6+galaxy1 - server: https://usegalaxy.eu state: exact - version: 0.4.8.0 + version: 2.1.6+galaxy1 - server: https://usegalaxy.fr/ state: exact - version: 0.4.8.0 + version: 2.1.6+galaxy1 - server: https://usegalaxy.no/ - state: exact - version: 0.4.8.0 + state: missing - server: https://usegalaxy.org state: exact - version: 0.4.8.0 + version: 2.1.6+galaxy1 - server: https://viralvariant.anses.fr/ state: missing - version: 0.4.8.0 - - id: toolshed.g2.bx.psu.edu/repos/nml/staramr/staramr_search/0.5.1 + version: 2.1.6+galaxy1 + - id: toolshed.g2.bx.psu.edu/repos/iuc/tbl2gff3/tbl2gff3/1.2 servers: - server: http://apostl.moffitt.org/ state: missing @@ -39330,19 +19107,12 @@ - server: https://hyperbrowser.uio.no/coloc-stats state: missing - server: https://galaxy.mesocentre.uca.fr - state: inexact - versions: - - 0.11.0+galaxy0 - - 0.10.0+galaxy0 - - 0.10.0+galaxy1 - - 0.7.2+galaxy0 + state: exact + version: '1.2' - server: https://galaxy.pasteur.fr/ state: missing - server: https://galaxytrakr.org/ - state: inexact - versions: - - 0.11.0+galaxy0 - - 0.9.1+galaxy0 + state: missing - server: http://igg.cloud.ba.infn.it/galaxy state: missing - server: https://galaxy.hyphy.org/ @@ -39353,8 +19123,6 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr @@ -39365,187 +19133,133 @@ state: missing - server: http://pepsimili.e-nios.com:8080/ state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - server: https://usegalaxy.org.au - state: inexact - versions: - - 0.11.0+galaxy0 - - 0.10.0+galaxy0 - - 0.10.0+galaxy1 - - 0.7.2+galaxy0 - - 0.9.1+galaxy0 - - 0.12.2+galaxy0 - - 0.8.0+galaxy0 - - 0.7.1+galaxy2 - - 0.7.1+galaxy1 - - 0.12.1+galaxy0 + state: exact + version: '1.2' - server: https://usegalaxy.be/ state: exact - version: 0.5.1 + version: '1.2' - server: https://usegalaxy.cz/ - state: inexact - versions: - - 0.11.0+galaxy0 - - 0.10.0+galaxy1 - - 0.9.1+galaxy0 - - 0.12.1+galaxy0 + state: exact + version: '1.2' - server: https://usegalaxy.eu state: exact - version: 0.5.1 + version: '1.2' - server: https://usegalaxy.fr/ - 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- 0.10.0+galaxy0 - - 0.10.0+galaxy1 - - 0.7.2+galaxy0 + state: local - server: https://galaxy.pasteur.fr/ - state: missing + state: local - server: https://galaxytrakr.org/ - state: inexact - versions: - - 0.11.0+galaxy0 - - 0.9.1+galaxy0 + state: local - server: http://igg.cloud.ba.infn.it/galaxy - state: missing + state: local - server: https://galaxy.hyphy.org/ - state: missing + state: local - server: https://www.immportgalaxy.org/ - state: missing + state: local - server: http://galaxy.interactomix.com/ - state: missing + state: local - server: https://galaxy-web.ipk-gatersleben.de - state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing + state: local - server: https://neo.engr.uconn.edu/ - state: missing + state: local - server: https://mississippi.sorbonne-universite.fr - state: missing + state: local - server: http://galaxy.inf.ethz.ch - state: missing + state: local - server: https://palfinder.ls.manchester.ac.uk/ - state: missing + state: local - server: http://pepsimili.e-nios.com:8080/ - state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing + state: local - server: https://usegalaxy.org.au - state: exact - version: 0.7.1+galaxy2 + state: missing - server: https://usegalaxy.be/ - state: inexact - versions: - - 0.11.0+galaxy0 - - 0.10.0+galaxy1 - - 0.5.1 + state: local - server: https://usegalaxy.cz/ - state: inexact - versions: - - 0.11.0+galaxy0 - - 0.10.0+galaxy1 - - 0.9.1+galaxy0 - - 0.12.1+galaxy0 + state: local - server: https://usegalaxy.eu - state: exact - version: 0.7.1+galaxy2 + state: local - server: https://usegalaxy.fr/ - state: inexact - versions: - - 0.10.0+galaxy0 - - 0.10.0+galaxy1 - - 0.9.1+galaxy0 - - 0.12.2+galaxy0 + state: local - server: https://usegalaxy.no/ - state: exact - version: 0.7.1+galaxy2 + state: local - server: https://usegalaxy.org - state: exact - version: 0.7.1+galaxy2 + state: local - server: https://viralvariant.anses.fr/ - state: missing - version: 0.7.1+galaxy2 + state: local + version: local symlink: null tags: - - nanopore - - plasmids - - assembly - - amr + - gmod + - illumina + - bacteria - microgalaxy - time_estimation: 3h - title: Antibiotic resistance detection + - jbrowse1 + time: null + time_estimation: 3H + title: Bacterial Genome Annotation tools: - - toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.3.1.1 - - toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.4.13 - - toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/0.8.1+galaxy0 - - toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/0.8.1+galaxy2 - - toolshed.g2.bx.psu.edu/repos/iuc/gfa_to_fa/gfa_to_fa/0.1.0 - - toolshed.g2.bx.psu.edu/repos/iuc/gfa_to_fa/gfa_to_fa/0.1.1 - - toolshed.g2.bx.psu.edu/repos/iuc/miniasm/miniasm/0.2+galaxy0 - - toolshed.g2.bx.psu.edu/repos/iuc/miniasm/miniasm/0.3+galaxy0 - - toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.17 - - toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.17+galaxy2 - - toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.25.0+galaxy1 - - toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.28.2+galaxy1 - - toolshed.g2.bx.psu.edu/repos/iuc/plasflow/PlasFlow/1.0 - - toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.4.7.0 - - toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.4.8.0 - - toolshed.g2.bx.psu.edu/repos/nml/staramr/staramr_search/0.5.1 - - toolshed.g2.bx.psu.edu/repos/nml/staramr/staramr_search/0.7.1+galaxy2 - topic_name: microbiome - topic_name_human: Microbiome + - Grouping1 + - toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/9.3+galaxy1 + - toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_tail_tool/9.3+galaxy1 + - toolshed.g2.bx.psu.edu/repos/iuc/bakta/bakta/1.9.3+galaxy0 + - toolshed.g2.bx.psu.edu/repos/iuc/integron_finder/integron_finder/2.0.5+galaxy0 + - toolshed.g2.bx.psu.edu/repos/iuc/isescan/isescan/1.7.2.3+galaxy1 + - toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1 + - toolshed.g2.bx.psu.edu/repos/iuc/plasmidfinder/plasmidfinder/2.1.6+galaxy1 + - toolshed.g2.bx.psu.edu/repos/iuc/tbl2gff3/tbl2gff3/1.2 + - upload1 + topic_name: genome-annotation + topic_name_human: Genome Annotation tours: false translations: slides: [] tutorial: [] video: false - tutorial_name: plasmid-metagenomics-nanopore + tutorial_name: bacterial-genome-annotation type: tutorial - url: https://training.galaxyproject.org//topics/microbiome/tutorials/plasmid-metagenomics-nanopore/tutorial.html + url: https://training.galaxyproject.org//topics/genome-annotation/tutorials/bacterial-genome-annotation/tutorial.html urls: - hands_on: https://training.galaxyproject.org/training-material/api/topics/microbiome/tutorials/plasmid-metagenomics-nanopore/tutorial.json - slides: https://training.galaxyproject.org/training-material/api/topics/microbiome/tutorials/plasmid-metagenomics-nanopore/tutorial.json - version: 4 + hands_on: https://training.galaxyproject.org/training-material/api/topics/genome-annotation/tutorials/bacterial-genome-annotation/tutorial.json + slides: https://training.galaxyproject.org/training-material/api/topics/genome-annotation/tutorials/bacterial-genome-annotation/tutorial.json + version: 6 video: true video_versions: 1 video_view: 0 - visit_duration: 407 - visitors: 4171 + visit_duration: 476 + visitors: 8849 workflows: - - creators: [] - description: Antibiotic resistance detection + - creators: + - class: Person + identifier: https://orcid.org/0000-0001-9852-1987 + name: "B\xE9r\xE9nice Batut" + - class: Person + identifier: https://orcid.org/0000-0002-8304-138X + name: Pierre Marin + description: Bacterial Genome Annotation features: comments: false parameters: false @@ -39553,259 +19267,732 @@ subworkflows: false graph_dot: "digraph main {\n node [fontname=\"Atkinson Hyperlegible\", shape=box,\ \ color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n edge [fontname=\"\ - Atkinson Hyperlegible\"];\n 0[color=lightblue,label=\"\u2139\uFE0F Input Collection\\\ - nPlasmids\"]\n 1[label=\"NanoPlot\"]\n 0 -> 1 [label=\"output\"]\n 10[label=\"\ - NanoPlot\"]\n 9 -> 10 [label=\"out_fa\"]\n 11[label=\"Map with minimap2\"\ - ]\n 0 -> 11 [label=\"output\"]\n 9 -> 11 [label=\"out_fa\"]\n 12[label=\"\ - Racon\"]\n 9 -> 12 [label=\"out_fa\"]\n 11 -> 12 [label=\"alignment_output\"\ - ]\n 0 -> 12 [label=\"output\"]\n 2[label=\"Map with minimap2\"]\n 0 -> 2\ - \ [label=\"output\"]\n 0 -> 2 [label=\"output\"]\n 3[label=\"Create assemblies\ - \ with Unicycler\"]\n 0 -> 3 [label=\"output\"]\n 4[label=\"miniasm\"]\n \ - \ 2 -> 4 [label=\"alignment_output\"]\n 0 -> 4 [label=\"output\"]\n 5[label=\"\ - Bandage Image\"]\n 3 -> 5 [label=\"assembly_graph\"]\n 6[label=\"PlasFlow\"\ - ]\n 3 -> 6 [label=\"assembly\"]\n 7[label=\"staramr\"]\n 3 -> 7 [label=\"\ - assembly\"]\n 8[label=\"Bandage Image\"]\n 4 -> 8 [label=\"gfa\"]\n 9[label=\"\ - GFA to FASTA\"]\n 4 -> 9 [label=\"gfa\"]\n}" + Atkinson Hyperlegible\"];\n 0[color=lightblue,label=\"\u2139\uFE0F Input Dataset\\\ + ncontigs\"]\n 1[label=\"ISEScan\"]\n 0 -> 1 [label=\"output\"]\n k2bb672cb453646b08a228590a0ca36c7[color=lightseagreen,label=\"\ + Output\\nisescan_results\"]\n 1 -> k2bb672cb453646b08a228590a0ca36c7\n 2[label=\"\ + PlasmidFinder\"]\n 0 -> 2 [label=\"output\"]\n k614064e64b0f4e38b04ee3f61ba41b46[color=lightseagreen,label=\"\ + Output\\nplasmidfinder_results\"]\n 2 -> k614064e64b0f4e38b04ee3f61ba41b46\n\ + \ 3[label=\"Integron Finder\"]\n 0 -> 3 [label=\"output\"]\n kd26788cf24414f29ac39b6be96f192eb[color=lightseagreen,label=\"\ + Output\\nintegronfinder_summary\"]\n 3 -> kd26788cf24414f29ac39b6be96f192eb\n\ + \ 4[label=\"Bakta\"]\n 0 -> 4 [label=\"output\"]\n kd3a40a8b1bd142b6a91e756379b86d94[color=lightseagreen,label=\"\ + Output\\nbakta_summary\"]\n 4 -> kd3a40a8b1bd142b6a91e756379b86d94\n 5[label=\"\ + Group\"]\n 1 -> 5 [label=\"all_results\"]\n 6[label=\"Group\"]\n 1 -> 6 [label=\"\ + all_results\"]\n 7[label=\"Replace Text\"]\n 2 -> 7 [label=\"result_file\"\ + ]\n 8[label=\"Select last\"]\n 7 -> 8 [label=\"outfile\"]\n 9[label=\"Table\ + \ to GFF3\"]\n 8 -> 9 [label=\"outfile\"]\n 10[label=\"JBrowse\"]\n 0 ->\ + \ 10 [label=\"output\"]\n 4 -> 10 [label=\"annotation_gff3\"]\n 9 -> 10 [label=\"\ + output\"]\n 1 -> 10 [label=\"annotation\"]\n}" history: - - hash: 0e0a2f2ccb650b0aab1ffc13838045164bdb5d30 - message: Rename metagenomics topic to microbiome + - hash: 87968f9a6953ebf322d9fb0fae3a4193b6222288 + message: Update tool versions + num: 2 + short_hash: 87968f9a6 + unix: '1722510143' + - hash: 217f251aaa898a91dbb18b5cec3daebaf582c712 + message: Update worklow and add tests num: 1 - short_hash: 0e0a2f2cc - unix: '1704901629' + short_hash: 217f251aa + unix: '1706526984' inputs: + - annotation: contigs + content_id: null + errors: null + id: 0 + input_connections: {} + inputs: + - description: contigs + name: contigs + label: contigs + name: Input dataset + outputs: [] + position: + left: 0 + top: 424 + tool_id: null + tool_state: '{"optional": false, "tag": ""}' + tool_version: null + type: data_input + uuid: 8cde8af1-c277-4b9f-97f7-54f5997f2c5d + when: null + workflow_outputs: [] + license: AGPL-3.0-or-later + mermaid: "flowchart TD\n 0[\"\u2139\uFE0F Input Dataset\\ncontigs\"];\n style\ + \ 0 stroke:#2c3143,stroke-width:4px;\n 1[\"ISEScan\"];\n 0 -->|output| 1;\n\ + \ 2bb672cb-4536-46b0-8a22-8590a0ca36c7[\"Output\\nisescan_results\"];\n 1\ + \ --> 2bb672cb-4536-46b0-8a22-8590a0ca36c7;\n style 2bb672cb-4536-46b0-8a22-8590a0ca36c7\ + \ stroke:#2c3143,stroke-width:4px;\n 2[\"PlasmidFinder\"];\n 0 -->|output|\ + \ 2;\n 614064e6-4b0f-4e38-b04e-e3f61ba41b46[\"Output\\nplasmidfinder_results\"\ + ];\n 2 --> 614064e6-4b0f-4e38-b04e-e3f61ba41b46;\n style 614064e6-4b0f-4e38-b04e-e3f61ba41b46\ + \ stroke:#2c3143,stroke-width:4px;\n 3[\"Integron Finder\"];\n 0 -->|output|\ + \ 3;\n d26788cf-2441-4f29-ac39-b6be96f192eb[\"Output\\nintegronfinder_summary\"\ + ];\n 3 --> d26788cf-2441-4f29-ac39-b6be96f192eb;\n style d26788cf-2441-4f29-ac39-b6be96f192eb\ + \ stroke:#2c3143,stroke-width:4px;\n 4[\"Bakta\"];\n 0 -->|output| 4;\n d3a40a8b-1bd1-42b6-a91e-756379b86d94[\"\ + Output\\nbakta_summary\"];\n 4 --> d3a40a8b-1bd1-42b6-a91e-756379b86d94;\n\ + \ style d3a40a8b-1bd1-42b6-a91e-756379b86d94 stroke:#2c3143,stroke-width:4px;\n\ + \ 5[\"Group\"];\n 1 -->|all_results| 5;\n 6[\"Group\"];\n 1 -->|all_results|\ + \ 6;\n 7[\"Replace Text\"];\n 2 -->|result_file| 7;\n 8[\"Select last\"];\n\ + \ 7 -->|outfile| 8;\n 9[\"Table to GFF3\"];\n 8 -->|outfile| 9;\n 10[\"\ + JBrowse\"];\n 0 -->|output| 10;\n 4 -->|annotation_gff3| 10;\n 9 -->|output|\ + \ 10;\n 1 -->|annotation| 10;" + modified: 2026-07-01 00:31:39 +0000 + name: Bacterial Genome Annotation + outputs: + - annotation: '' + content_id: toolshed.g2.bx.psu.edu/repos/iuc/isescan/isescan/1.7.2.3+galaxy1 + errors: null + id: 1 + input_connections: + input_file: + id: 0 + output_name: output + inputs: [] + label: null + name: ISEScan + outputs: + - name: summary + type: tabular + - name: all_results + type: tabular + - name: annotation + type: gff + - name: is_fasta + type: fasta + - name: orf_fna + type: fasta + - name: orf_faa + type: fasta + position: + left: 280 + top: 133 + post_job_actions: {} + tool_id: toolshed.g2.bx.psu.edu/repos/iuc/isescan/isescan/1.7.2.3+galaxy1 + tool_shed_repository: + changeset_revision: 19f42b3ea391 + name: isescan + owner: iuc + tool_shed: toolshed.g2.bx.psu.edu + tool_state: '{"__input_ext": "input", "chromInfo": "/shared/ifbstor1/galaxy/mutable-config/tool-data/shared/ucsc/chrom/?.len", + "input_file": {"__class__": "ConnectedValue"}, "log_activate": false, "remove_short_is": + false, "__page__": null, "__rerun_remap_job_id__": null}' + tool_version: 1.7.2.3+galaxy1 + type: tool + uuid: 334b327f-be00-4e75-ae01-c3ba674dbc9b + when: null + workflow_outputs: + - label: isescan_results + output_name: all_results + uuid: 2bb672cb-4536-46b0-8a22-8590a0ca36c7 + - annotation: '' + content_id: toolshed.g2.bx.psu.edu/repos/iuc/plasmidfinder/plasmidfinder/2.1.6+galaxy1 + errors: null + id: 2 + input_connections: + input|input_file: + id: 0 + output_name: output + inputs: [] + label: null + name: PlasmidFinder + outputs: + - name: hit_file + type: fasta + - name: plasmid_file + type: fasta + - name: result_file + type: tabular + - name: raw_file + type: txt + position: + left: 280 + top: 420 + post_job_actions: {} + tool_id: toolshed.g2.bx.psu.edu/repos/iuc/plasmidfinder/plasmidfinder/2.1.6+galaxy1 + tool_shed_repository: + changeset_revision: 7075b7a5441b + name: plasmidfinder + owner: iuc + tool_shed: toolshed.g2.bx.psu.edu + tool_state: '{"input": {"input_file": {"__class__": "ConnectedValue"}, "database_name": + "plasmidfinder_1307168_2019_08_28"}, "options": {"min_cov": "0.6", "threshold": + "0.95"}, "output_files": {"output_selection": ["hit_fasta", "plasmid_fasta", + "result_tsv", "result_txt"]}, "__page__": null, "__rerun_remap_job_id__": + null}' + tool_version: 2.1.6+galaxy1 + type: tool + uuid: 484ea537-4097-4097-b19c-84fef6c7de9a + when: null + workflow_outputs: + - label: plasmidfinder_results + output_name: result_file + uuid: 614064e6-4b0f-4e38-b04e-e3f61ba41b46 + - annotation: '' + content_id: toolshed.g2.bx.psu.edu/repos/iuc/integron_finder/integron_finder/2.0.5+galaxy0 + errors: null + id: 3 + input_connections: + sequence: + id: 0 + output_name: output + inputs: [] + label: null + name: Integron Finder + outputs: + - name: integrons_table + type: tsv + - name: summary + type: tsv + position: + left: 280 + top: 665 + post_job_actions: + ChangeDatatypeActionintegrons_table: + action_arguments: + newtype: tabular + action_type: ChangeDatatypeAction + output_name: integrons_table + tool_id: toolshed.g2.bx.psu.edu/repos/iuc/integron_finder/integron_finder/2.0.5+galaxy0 + tool_shed_repository: + changeset_revision: 4768f7f8e93f + name: integron_finder + owner: iuc + tool_shed: toolshed.g2.bx.psu.edu + tool_state: '{"__input_ext": "input", "chromInfo": "/shared/ifbstor1/galaxy/mutable-config/tool-data/shared/ucsc/chrom/?.len", + "gbk": false, "local_max": true, "no_logfile": true, "pdf": false, "promoter_attI": + true, "sequence": {"__class__": "ConnectedValue"}, "settings": {"attc_settings": + {"dist_thresh": "4000", "calin_threshold": "2", "max_attc_size": "200", "min_attc_size": + "40", "keep_palindromes": false, "covar_matrix": null}, "protein_settings": + {"no_proteins": false, "union_integrases": false, "func_annot": false}}, "topology_file": + null, "type_replicon": null, "__page__": null, "__rerun_remap_job_id__": null}' + tool_version: 2.0.5+galaxy0 + type: tool + uuid: 29a9252c-5c3b-4024-99ff-637d0572320a + when: null + workflow_outputs: + - label: integronfinder_summary + output_name: summary + uuid: d26788cf-2441-4f29-ac39-b6be96f192eb - annotation: '' - content_id: null + content_id: toolshed.g2.bx.psu.edu/repos/iuc/bakta/bakta/1.9.3+galaxy0 errors: null - id: 0 - input_connections: {} + id: 4 + input_connections: + input_option|input_file: + id: 0 + output_name: output inputs: [] - label: Plasmids - name: Input dataset collection - outputs: [] + label: null + name: Bakta + outputs: + - name: annotation_tsv + type: tabular + - name: annotation_gff3 + type: gff3 + - name: annotation_ffn + type: fasta + - name: summary_txt + type: txt + - name: annotation_plot + type: svg position: - left: 173 - top: 696 - tool_id: null - tool_state: '{"collection_type": "list"}' - tool_version: null - type: data_collection_input - uuid: 348dcd93-2d40-4bdd-90f4-b321a1bd901d - workflow_outputs: [] - license: null - mermaid: "flowchart TD\n 0[\"\u2139\uFE0F Input Collection\\nPlasmids\"];\n \ - \ style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"NanoPlot\"];\n 0 -->|output|\ - \ 1;\n 10[\"NanoPlot\"];\n 9 -->|out_fa| 10;\n 11[\"Map with minimap2\"];\n\ - \ 0 -->|output| 11;\n 9 -->|out_fa| 11;\n 12[\"Racon\"];\n 9 -->|out_fa|\ - \ 12;\n 11 -->|alignment_output| 12;\n 0 -->|output| 12;\n 2[\"Map with minimap2\"\ - ];\n 0 -->|output| 2;\n 0 -->|output| 2;\n 3[\"Create assemblies with Unicycler\"\ - ];\n 0 -->|output| 3;\n 4[\"miniasm\"];\n 2 -->|alignment_output| 4;\n 0\ - \ -->|output| 4;\n 5[\"Bandage Image\"];\n 3 -->|assembly_graph| 5;\n 6[\"\ - PlasFlow\"];\n 3 -->|assembly| 6;\n 7[\"staramr\"];\n 3 -->|assembly| 7;\n\ - \ 8[\"Bandage Image\"];\n 4 -->|gfa| 8;\n 9[\"GFA to FASTA\"];\n 4 -->|gfa|\ - \ 9;" - modified: 2026-05-21 00:30:25 +0000 - name: Copy Of GTN Training - Antibiotic Resistance Detection - outputs: [] - parent_id: microbiome/plasmid-metagenomics-nanopore - path: topics/microbiome/tutorials/plasmid-metagenomics-nanopore/workflows/Workflow-plasmid-metagenomics-nanopore.ga + left: 850 + top: 0 + post_job_actions: {} + tool_id: toolshed.g2.bx.psu.edu/repos/iuc/bakta/bakta/1.9.3+galaxy0 + tool_shed_repository: + changeset_revision: 728dacaf08a9 + name: bakta + owner: iuc + tool_shed: toolshed.g2.bx.psu.edu + tool_state: '{"__input_ext": "input", "annotation": {"complete": false, "prodigal": + null, "translation_table": "11", "keep_contig_headers": true, "replicons": + null, "compliant": false, "proteins": null, "meta": false}, "chromInfo": "/shared/ifbstor1/galaxy/mutable-config/tool-data/shared/ucsc/chrom/?.len", + "input_option": {"bakta_db_select": "V5.0_2023-02-20", "amrfinder_db_select": + "amrfinderplus_V3.11_2022-12-19.1", "input_file": {"__class__": "ConnectedValue"}, + "min_contig_length": null}, "organism": {"genus": null, "species": null, "strain": + null, "plasmid": null}, "output_files": {"output_selection": ["file_tsv", + "file_gff3", "file_ffn", "file_plot", "sum_txt"]}, "workflow": {"skip_analysis": + null}, "__page__": null, "__rerun_remap_job_id__": null}' + tool_version: 1.9.3+galaxy0 + type: tool + uuid: 181220e7-9082-48bc-b855-f10baf78fc2a + when: null + workflow_outputs: + - label: bakta_summary + output_name: summary_txt + uuid: d3a40a8b-1bd1-42b6-a91e-756379b86d94 + parent_id: genome-annotation/bacterial-genome-annotation + path: topics/genome-annotation/tutorials/bacterial-genome-annotation/workflows/Bacterial-Genome-Annotation.ga tags: - - microbiome + - genome-annotation test_results: null - tests: false - title: Copy Of GTN Training - Antibiotic Resistance Detection - topic_id: microbiome - trs_endpoint: https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/microbiome-plasmid-metagenomics-nanopore/versions/workflow-plasmid-metagenomics-nanopore - tutorial_id: plasmid-metagenomics-nanopore - url: https://training.galaxyproject.org/training-material/topics/microbiome/tutorials/plasmid-metagenomics-nanopore/workflows/Workflow-plasmid-metagenomics-nanopore.ga - url_html: https://training.galaxyproject.org/training-material/topics/microbiome/tutorials/plasmid-metagenomics-nanopore/workflows/Workflow-plasmid-metagenomics-nanopore.html - version: 1 - wfid: microbiome-plasmid-metagenomics-nanopore - wfname: workflow-plasmid-metagenomics-nanopore - workflow: Workflow-plasmid-metagenomics-nanopore.ga + tests: true + title: Bacterial Genome Annotation + topic_id: genome-annotation + trs_endpoint: https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/genome-annotation-bacterial-genome-annotation/versions/bacterial-genome-annotation + tutorial_id: bacterial-genome-annotation + url: https://training.galaxyproject.org/training-material/topics/genome-annotation/tutorials/bacterial-genome-annotation/workflows/Bacterial-Genome-Annotation.ga + url_html: https://training.galaxyproject.org/training-material/topics/genome-annotation/tutorials/bacterial-genome-annotation/workflows/Bacterial-Genome-Annotation.html + version: 2 + wfid: genome-annotation-bacterial-genome-annotation + wfname: bacterial-genome-annotation + workflow: Bacterial-Genome-Annotation.ga workflow_tools: - - toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.3.1.1 - 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toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1 + - toolshed.g2.bx.psu.edu/repos/iuc/plasmidfinder/plasmidfinder/2.1.6+galaxy1 + - toolshed.g2.bx.psu.edu/repos/iuc/tbl2gff3/tbl2gff3/1.2 + workflowhub_id: '1513' + zenodo_link: https://zenodo.org/record/10572227 +- abbreviations: + OGS: Official Gene Set + admin_install: install_repository_dependencies: true install_resolver_dependencies: true install_tool_dependencies: true tools: - - name: text_processing - owner: bgruening - revisions: d698c222f354 - tool_panel_section_label: Text Manipulation - tool_shed_url: https://toolshed.g2.bx.psu.edu/ - - name: taxonomy_krona_chart - owner: crs4 - revisions: 1334cb4c6b68 - tool_panel_section_label: Metagenomic Analysis - tool_shed_url: https://toolshed.g2.bx.psu.edu/ - - name: fastqc - owner: devteam - revisions: e7b2202befea - tool_panel_section_label: FASTA/FASTQ - tool_shed_url: https://toolshed.g2.bx.psu.edu/ - - name: datamash_reverse - owner: iuc - revisions: 0f1724dd59d2 - tool_panel_section_label: Join, Subtract and Group + - name: apollo_create_account + owner: gga + revisions: e80d29fd2a33 + tool_panel_section_label: Apollo tool_shed_url: https://toolshed.g2.bx.psu.edu/ - - name: fastp - owner: iuc - revisions: dbf9c561ef29 - tool_panel_section_label: FASTA/FASTQ + - name: apollo_create_or_update + owner: gga + revisions: 4abaab60f9e1 + tool_panel_section_label: Apollo tool_shed_url: https://toolshed.g2.bx.psu.edu/ - - name: kraken2 - owner: iuc - revisions: 328c607150ff - tool_panel_section_label: Metagenomic Analysis + - name: apollo_iframe + owner: gga + revisions: f4e3f9480307 + tool_panel_section_label: Apollo tool_shed_url: https://toolshed.g2.bx.psu.edu/ - - name: multiqc - owner: iuc - revisions: 5e33b465d8d5 - tool_panel_section_label: Quality Control + - name: apollo_list_organism + owner: gga + revisions: 2c749ed310da + tool_panel_section_label: Apollo tool_shed_url: https://toolshed.g2.bx.psu.edu/ - - name: porechop + - name: jbrowse owner: iuc - revisions: 93d623d9979c - tool_panel_section_label: Nanopore + revisions: a6e57ff585c0 + tool_panel_section_label: Graph/Display Data tool_shed_url: https://toolshed.g2.bx.psu.edu/ admin_install_yaml: "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies:\ - \ true\ninstall_resolver_dependencies: true\ntools:\n- name: text_processing\n\ - \ owner: bgruening\n revisions: d698c222f354\n tool_panel_section_label: Text\ - \ Manipulation\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: taxonomy_krona_chart\n\ - \ owner: crs4\n revisions: 1334cb4c6b68\n tool_panel_section_label: Metagenomic\ - \ Analysis\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fastqc\n\ - \ owner: devteam\n revisions: e7b2202befea\n tool_panel_section_label: FASTA/FASTQ\n\ - \ tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: datamash_reverse\n\ - \ owner: iuc\n revisions: 0f1724dd59d2\n tool_panel_section_label: Join, Subtract\ - \ and Group\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fastp\n\ - \ owner: iuc\n revisions: dbf9c561ef29\n tool_panel_section_label: FASTA/FASTQ\n\ - \ tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: kraken2\n owner: iuc\n\ - \ revisions: 328c607150ff\n tool_panel_section_label: Metagenomic Analysis\n\ - \ tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: multiqc\n owner: iuc\n\ - \ revisions: 5e33b465d8d5\n tool_panel_section_label: Quality Control\n tool_shed_url:\ - \ https://toolshed.g2.bx.psu.edu/\n- name: porechop\n owner: iuc\n revisions:\ - \ 93d623d9979c\n tool_panel_section_label: Nanopore\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n" - api: https://training.galaxyproject.org/training-material/api/topics/microbiome/tutorials/nanopore-16S-metagenomics/tutorial.json + \ true\ninstall_resolver_dependencies: true\ntools:\n- name: apollo_create_account\n\ + \ owner: gga\n revisions: e80d29fd2a33\n tool_panel_section_label: Apollo\n\ + \ tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: apollo_create_or_update\n\ + \ owner: gga\n revisions: 4abaab60f9e1\n tool_panel_section_label: Apollo\n\ + \ tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: apollo_iframe\n owner:\ + \ gga\n revisions: f4e3f9480307\n tool_panel_section_label: Apollo\n tool_shed_url:\ + \ https://toolshed.g2.bx.psu.edu/\n- name: apollo_list_organism\n owner: gga\n\ + \ revisions: 2c749ed310da\n tool_panel_section_label: Apollo\n tool_shed_url:\ + \ https://toolshed.g2.bx.psu.edu/\n- name: jbrowse\n owner: iuc\n revisions:\ + \ a6e57ff585c0\n tool_panel_section_label: Graph/Display Data\n tool_shed_url:\ + \ https://toolshed.g2.bx.psu.edu/\n" + api: https://training.galaxyproject.org/training-material/api/topics/genome-annotation/tutorials/apollo/tutorial.json + contributions: + authorship: + - abretaud + - hexylena + - nathandunn + - mboudet + funding: + - gallantries + - eurosciencegateway + reviewing: + - abretaud + - bgruening + - shiltemann + - hexylena + - bebatut + - stephanierobin + - simonbray contributors: + - affiliations: + - elixir-europe + bluesky: abretaud.bsky.social + contact_for_training: true + elixir_node: fr + email: anthony.bretaudeau@irisa.fr + fediverse: https://genomic.social/@abretaud + fediverse_flavor: mastodon + former_affiliations: + - eurosciencegateway + - gallantries + id: abretaud + joined: 2017-09 + location: + country: FR + lat: 48.11 + lon: -1.64 + matrix: abretaud:matrix.org + name: Anthony Bretaudeau + orcid: 0000-0003-0914-2470 + page: https://training.galaxyproject.org/training-material/hall-of-fame/abretaud/ + url: https://training.galaxyproject.org/training-material/api/contributors/abretaud.json + - affiliations: + - elixir-europe + contact_for_training: false + elixir_node: nl + former_affiliations: + - deNBI + - avans-atgm + - uni-freiburg + - erasmusmc + - gallantries + - by-covid + - elixir-converge + id: hexylena + joined: 2017-09 + location: + country: NL + lat: 51.91 + lon: 4.46 + maintainer_contact: gitter + matrix: hexylena:matrix.org + name: Helena Rasche + orcid: 0000-0001-9760-8992 + page: https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/ + url: https://training.galaxyproject.org/training-material/api/contributors/hexylena.json + - email: nathandunn@lbl.gov + id: nathandunn + joined: 2019-07 + name: Nathan Dunn + page: https://training.galaxyproject.org/training-material/hall-of-fame/nathandunn/ + twitter: precogincog + url: https://training.galaxyproject.org/training-material/api/contributors/nathandunn.json + - affiliations: + - elixir-europe + elixir_node: fr + email: mateo.boudet@inrae.fr + id: mboudet + joined: 2021-05 + name: Mateo Boudet + orcid: 0000-0002-7028-7620 + page: https://training.galaxyproject.org/training-material/hall-of-fame/mboudet/ + url: https://training.galaxyproject.org/training-material/api/contributors/mboudet.json + - avatar: https://gallantries.github.io/assets/images/gallantries-logo.png + end_date: '2023-09-30' + former_members: + - abretaud + - hexylena + - shiltemann + funder_name: Erasmus+ Programme + funding_database: erasmusplus + funding_id: 2020-1-NL01-KA203-064717 + funding_statement: 'This project (2020-1-NL01-KA203-064717) + is funded with the support of the Erasmus+ programme of the European Union. + Their funding has supported a large number of tutorials within the GTN across + a wide array of topics. + + eu flag with the text: with the support of the erasmus programme of the + european union + + erasmus plus + logo' + github: false + id: gallantries + joined: 2020-09 + members: + - bebatut + - colineroyaux + - fpsom + - yvanlebras + name: 'Gallantries: Bridging Training Communities in Life Science, Environment + and Health' + page: https://training.galaxyproject.org/training-material/hall-of-fame/gallantries/ + short_name: Gallantries + start_date: '2020-09-01' + url: https://training.galaxyproject.org/training-material/api/grants/gallantries.json + - avatar: /training-material/assets/images/eurosciencegateway.png + former_members: + - abretaud + - abdulrahmanazab + - bgruening + - B0r1sD + - dadrasarmin + - elichad + - ElectronicBlueberry + - erxleben + - kysrpex + - leandro-liborio + - lopiola + - martenson + - mira-miracoli + - patrick-austin + - pauldg + - rlibouba + - SaimMomin12 + - sanjaysrikakulam + - sebastian-schaaf + - stain + - torfinnnome + - wm75 + funding_database: cordis + funding_id: '101057388' + funding_statement: "EuroScienceGateway was funded by the European Union programme\ + \ Horizon Europe (HORIZON-INFRA-2021-EOSC-01-04) under grant agreement number\ + \ 101057388 and by UK Research and Innovation (UKRI) under the UK government\u2019\ + s Horizon Europe funding guarantee grant number 10038963." + github: false + id: eurosciencegateway + joined: 2023-10 + members: + - davelopez + name: EuroScienceGateway + page: https://training.galaxyproject.org/training-material/hall-of-fame/eurosciencegateway/ + url: https://training.galaxyproject.org/training-material/api/grants/eurosciencegateway.json + - affiliations: + - elixir-europe + bluesky: abretaud.bsky.social + contact_for_training: true + elixir_node: fr + email: anthony.bretaudeau@irisa.fr + fediverse: https://genomic.social/@abretaud + fediverse_flavor: mastodon + former_affiliations: + - eurosciencegateway + - gallantries + id: abretaud + joined: 2017-09 + location: + country: FR + lat: 48.11 + lon: -1.64 + matrix: abretaud:matrix.org + name: Anthony Bretaudeau + orcid: 0000-0003-0914-2470 + page: https://training.galaxyproject.org/training-material/hall-of-fame/abretaud/ + url: https://training.galaxyproject.org/training-material/api/contributors/abretaud.json + - affiliations: + - deNBI + - mwk + - uni-freiburg + - elixir-europe + - materialvitaldigital + contact_for_training: true + elixir_node: de + email: bjoern.gruening@gmail.com + fediverse: https://fosstodon.org/@bgruening + fediverse_flavor: mastodon + former_affiliations: + - eurosciencegateway + - eosc-life + - by-covid + - crc992 + - elixir-converge + id: bgruening + joined: 2017-09 + linkedin: bgruening + location: + country: DE + lat: 47.997791 + lon: 7.842609 + matrix: bgruening:matrix.org + name: "Bj\xF6rn Gr\xFCning" + orcid: 0000-0002-3079-6586 + page: https://training.galaxyproject.org/training-material/hall-of-fame/bgruening/ + twitter: bjoerngruening + url: https://training.galaxyproject.org/training-material/api/contributors/bgruening.json + - affiliations: + - uni-freiburg + - nfdi4plants + - elixir-europe + bio: Researcher at Erasmus Medical Center + bluesky: shiltemann.bsky.social + contact_for_training: true + elixir_node: nl + email: saskia.hiltemann@gmail.com + fediverse: https://mstdn.science/@shiltemann + fediverse_flavor: mastodon + former_affiliations: + - CINECA-Project + - gallantries + - erasmusmc + id: shiltemann + joined: 2017-09 + linkedin: shiltemann + location: + country: NL + lat: 51.912 + lon: 4.462 + maintainer_contact: gitter + matrix: shiltemann:matrix.org + name: Saskia Hiltemann + orcid: 0000-0003-3803-468X + page: https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/ + url: https://training.galaxyproject.org/training-material/api/contributors/shiltemann.json + - affiliations: + - elixir-europe + contact_for_training: false + elixir_node: nl + former_affiliations: + - deNBI + - avans-atgm + - uni-freiburg + - erasmusmc + - gallantries + - by-covid + - elixir-converge + id: hexylena + joined: 2017-09 + location: + country: NL + lat: 51.91 + lon: 4.46 + maintainer_contact: gitter + matrix: hexylena:matrix.org + name: Helena Rasche + orcid: 0000-0001-9760-8992 + page: https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/ + url: https://training.galaxyproject.org/training-material/api/contributors/hexylena.json + - affiliations: + - gallantries + - ifb + - elixir-europe + contact_for_training: true + elixir_node: fr + email: berenice.batut@gmail.com + fediverse: https://piaille.fr/@bebatut + fediverse_flavor: mastodon + former_affiliations: + - uni-freiburg + - deNBI + id: bebatut + joined: 2017-09 + linkedin: berenicebatut + location: + country: FR + lat: 45.77 + lon: 3.08 + matrix: bebatut:matrix.org + name: "B\xE9r\xE9nice Batut" + orcid: 0000-0001-9852-1987 + page: https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/ + twitter: bebatut + url: https://training.galaxyproject.org/training-material/api/contributors/bebatut.json + - email: stephanie.robin@inrae.fr + id: stephanierobin + joined: 2021-11 + name: "St\xE9phanie Robin" + orcid: 0000-0001-7379-9173 + page: https://training.galaxyproject.org/training-material/hall-of-fame/stephanierobin/ + twitter: robinstphanie1 + url: https://training.galaxyproject.org/training-material/api/contributors/stephanierobin.json - elixir_node: de former_affiliations: - uni-freiburg - elixir-europe - id: gallardoalba - joined: 2020-11 - name: "Crist\xF3bal Gallardo" - orcid: 0000-0002-5752-2155 - page: https://training.galaxyproject.org/training-material/hall-of-fame/gallardoalba/ - url: https://training.galaxyproject.org/training-material/api/contributors/gallardoalba.json - dir: topics/microbiome/tutorials/nanopore-16S-metagenomics + id: simonbray + joined: 2019-05 + name: Simon Bray + page: https://training.galaxyproject.org/training-material/hall-of-fame/simonbray/ + url: https://training.galaxyproject.org/training-material/api/contributors/simonbray.json + dir: topics/genome-annotation/tutorials/apollo edam_ontology: - - topic_3697 - - topic_0637 + - topic_0622 + - topic_3301 + - topic_0623 - topic_0080 - - topic_4038 edam_operation: - - Sequence contamination filtering - - Validation - - Sequence composition calculation - - Taxonomic classification - - Statistical calculation - - Visualisation - - Sequencing quality control + - Genome visualisation edam_topic: - - Microbial ecology - - Taxonomy + - Genomics + - Microbiology + - Gene and protein families - Sequence analysis - - Metabarcoding - exact_supported_servers: - - UseGalaxy.org.au - - UseGalaxy.be - - UseGalaxy.eu - - UseGalaxy.no - - UseGalaxy.org (Main) + exact_supported_servers: [] feedback_mean_note: null feedback_number: 0 hands_on: true - id: microbiome/nanopore-16S-metagenomics + id: genome-annotation/apollo inexact_supported_servers: - - GalaxyTrakr + - UseGalaxy.be - UseGalaxy.cz - - UseGalaxy.fr + - UseGalaxy.eu + - UseGalaxy.no js_requirements: mathjax: null mermaid: false key_points: - - We learned to use MinION Nanopore data for analyzing the health status of the - soil - - We preprocessed Nanopore sequences in order to improve their quality + - Apollo is the Google Docs of the genome annotation world, real-time collaborative + genome annotation. + - Apollo allows a group to view and manually refine predicted genome annotations + - Use Apollo to edit annotations within your group. + - Export manual annotations as GFF3. layout: tutorial_hands_on + level: Intermediate license: CC-BY-4.0 - mod_date: '2024-07-31' + mod_date: '2025-05-15' objectives: - - Use Nanopore data for studying soil metagenomics - - Analyze and preprocess Nanopore reads - - Use Kraken2 to assign a taxonomic labels - pageviews: 13873 - pub_date: '2020-11-24' + - Load a genome into Galaxy + - View annotations in JBrowse + - Learn how to load JBrowse data into Apollo + - Learn how to manually refine genome annotations within Apollo + - Export refined genome annotations + pageviews: 8460925 + pub_date: '2021-06-04' questions: - - How can we analyse the health status of the soil? - - How do plants modify the composition of microbial communities? - redirect_from: - - /topics/metagenomics/tutorials/nanopore-16S-metagenomics/tutorial - - /short/microbiome/nanopore-16S-metagenomics - - /short/T00207 - - /short/T00392 - short_id: T00392 + - How to visualize your genome after automated annotations have been performed? + - How to manually annotate genome after automated annotations have been performed? + - How to evaluate and visualize annotated genomic features? + - How do I collaborate when doing genome annotation? + recordings: + - captioners: + - abretaud + date: '2021-02-15' + galaxy_version: '21.01' + length: 1H + speakers: + - abretaud + youtube_id: ywK1fhM-QFU + requirements: + - topic_name: galaxy-interface + tutorials: + - upload-rules + type: internal + - topic_name: genome-annotation + tutorials: + - annotation-with-prokka + type: internal + short_id: T00169 short_tools: - - taxonomy_krona_chart - - porechop - - datamash_reverse - - multiqc - - Remove beginning1 - - fastqc - - fastp - - tp_replace_in_line - - kraken2 - slides: false - slides_recordings: false - subtopic: metabarcoding + - list_organism + - jbrowse + - create_or_update + - create_account + - iframe + slides: true + slides_recordings: + - captioners: + - abretaud + date: '2021-02-15' + galaxy_version: '21.01' + length: 5M + speakers: + - awspolly + youtube_id: ailUycRVHtE + subtopic: prokaryote supported_servers: - exact: - - name: UseGalaxy.org.au - url: https://usegalaxy.org.au - usegalaxy: true + exact: [] + inexact: - name: UseGalaxy.be url: https://usegalaxy.be/ usegalaxy: false + - name: UseGalaxy.cz + url: https://usegalaxy.cz/ + usegalaxy: false - name: UseGalaxy.eu url: https://usegalaxy.eu usegalaxy: true - name: UseGalaxy.no url: https://usegalaxy.no/ usegalaxy: false - - name: UseGalaxy.org (Main) - url: https://usegalaxy.org - usegalaxy: true - inexact: - - name: GalaxyTrakr - url: https://galaxytrakr.org/ - usegalaxy: false - - name: UseGalaxy.cz - url: https://usegalaxy.cz/ - usegalaxy: false - - name: UseGalaxy.fr - url: https://usegalaxy.fr/ - usegalaxy: true supported_servers_matrix: servers: - name: APOSTL @@ -39847,9 +20034,6 @@ - name: IPK Galaxy Blast Suite url: https://galaxy-web.ipk-gatersleben.de usegalaxy: false - - name: Lebanese University Galaxy - url: http://galaxy.ul.edu.lb/ - usegalaxy: false - 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- metabarcoding - - 16S - - nanopore + - gmod + - prokaryote - microgalaxy - - plants + - jbrowse1 + - biodiversity + - apollo2 time: null - time_estimation: 2H - title: 16S Microbial analysis with Nanopore data + time_estimation: 3h + title: Refining Genome Annotations with Apollo (prokaryotes) tools: - - Remove beginning1 - - toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/1.1.2 - - toolshed.g2.bx.psu.edu/repos/crs4/taxonomy_krona_chart/taxonomy_krona_chart/2.7.1 - - toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1 - - toolshed.g2.bx.psu.edu/repos/iuc/datamash_reverse/datamash_reverse/1.1.0 - - toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.20.1+galaxy0 - - toolshed.g2.bx.psu.edu/repos/iuc/kraken2/kraken2/2.0.8_beta+galaxy0 - - toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.8+galaxy1 - - toolshed.g2.bx.psu.edu/repos/iuc/porechop/porechop/0.2.3 - topic_name: microbiome - topic_name_human: Microbiome + - toolshed.g2.bx.psu.edu/repos/gga/apollo_create_account/create_account/3.1 + - toolshed.g2.bx.psu.edu/repos/gga/apollo_create_or_update/create_or_update/4.2.5 + - toolshed.g2.bx.psu.edu/repos/gga/apollo_iframe/iframe/4.2.5 + - toolshed.g2.bx.psu.edu/repos/gga/apollo_list_organism/list_organism/3.1 + - toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1 + topic_name: genome-annotation + topic_name_human: Genome Annotation tours: false translations: slides: [] tutorial: [] - video: false - tutorial_name: nanopore-16S-metagenomics + video: true + tutorial_name: apollo type: tutorial - url: https://training.galaxyproject.org//topics/microbiome/tutorials/nanopore-16S-metagenomics/tutorial.html + url: https://training.galaxyproject.org//topics/genome-annotation/tutorials/apollo/tutorial.html urls: - hands_on: https://training.galaxyproject.org/training-material/api/topics/microbiome/tutorials/nanopore-16S-metagenomics/tutorial.json - slides: https://training.galaxyproject.org/training-material/api/topics/microbiome/tutorials/nanopore-16S-metagenomics/tutorial.json - version: 5 - video: false - video_versions: 0 + hands_on: https://training.galaxyproject.org/training-material/api/topics/genome-annotation/tutorials/apollo/tutorial.json + slides: https://training.galaxyproject.org/training-material/api/topics/genome-annotation/tutorials/apollo/tutorial.json + version: 22 + video: true + video_versions: 1 video_view: 0 - visit_duration: 326 - visitors: 10045 + visit_duration: 793 + visitors: 3693456 workflows: - creators: [] - description: 16S rRNA analysis with Nanopore reads + description: Refining Genome Annotations with Apollo features: comments: false parameters: false @@ -40631,83 +20430,540 @@ subworkflows: false graph_dot: "digraph main {\n node [fontname=\"Atkinson Hyperlegible\", shape=box,\ \ color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n edge [fontname=\"\ - Atkinson Hyperlegible\"];\n 0[color=lightblue,label=\"\u2139\uFE0F Input Collection\\\ - nInput dataset collection\"]\n 1[label=\"FastQC\"]\n 0 -> 1 [label=\"output\"\ - 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name: jbrowse\n owner: iuc\n revisions: a6e57ff585c0\n tool_panel_section_label:\ + \ Graph/Display Data\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name:\ + \ tbl2gff3\n owner: iuc\n revisions: 4a7f4b0cc0a3\n tool_panel_section_label:\ + \ Annotation\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: staramr\n\ + \ owner: nml\n revisions: 3b22de20bd4b\n tool_panel_section_label: Metagenomic\ \ Analysis\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n" - api: https://training.galaxyproject.org/training-material/api/topics/microbiome/tutorials/metagenomics-binning/tutorial.json + api: https://training.galaxyproject.org/training-material/api/topics/genome-annotation/tutorials/amr-gene-detection/tutorial.json contributions: authorship: - - paulzierep - - npechl - - fpsom - - vinisalazar - editing: - - bebatut - reviewing: - - teresa-m - - deeptivarshney + - bazante1 - bebatut - - npechl + editing: - hexylena + - bazante1 - shiltemann - - paulzierep - - dadrasarmin - - natalie-wa - contributors: - - affiliations: - - uni-freiburg - - elixir-europe - - deNBI - - mwk - - materialvitaldigital - email: zierep@informatik.uni-freiburg.de - id: paulzierep - joined: 2023-02 - name: Paul Zierep - orcid: 0000-0003-2982-388X - page: https://training.galaxyproject.org/training-material/hall-of-fame/paulzierep/ - url: https://training.galaxyproject.org/training-material/api/contributors/paulzierep.json - - affiliations: - - inab-certh - elixir_node: gr - id: npechl - joined: 2023-05 - linkedin: npechl - name: Nikos Pechlivanis - orcid: 0000-0003-2502-612X - page: https://training.galaxyproject.org/training-material/hall-of-fame/npechl/ - twitter: npechl - url: https://training.galaxyproject.org/training-material/api/contributors/npechl.json - - affiliations: - - gallantries + - miaomiaozhou88 + - tflowers15 + funding: + - avans-atgm + - abromics - elixir-europe - elixir_node: gr - email: fpsom@certh.gr - id: fpsom - joined: 2019-03 - linkedin: fpsom - matrix: fpsom:matrix.org - name: Fotis E. Psomopoulos - orcid: 0000-0002-0222-4273 - page: https://training.galaxyproject.org/training-material/hall-of-fame/fpsom/ - twitter: fopsom - url: https://training.galaxyproject.org/training-material/api/contributors/fpsom.json - - affiliations: - unimelb - melbournebioinformatics - id: vinisalazar - joined: 2025-10 - name: Vini Salazar - orcid: 0000-0002-8362-3195 - page: https://training.galaxyproject.org/training-material/hall-of-fame/vinisalazar/ - url: https://training.galaxyproject.org/training-material/api/contributors/vinisalazar.json - - affiliations: - - gallantries - - ifb - - elixir-europe - contact_for_training: true - elixir_node: fr - email: berenice.batut@gmail.com - fediverse: https://piaille.fr/@bebatut - fediverse_flavor: mastodon - former_affiliations: - - uni-freiburg - - deNBI - id: bebatut - joined: 2017-09 - linkedin: berenicebatut - location: - country: FR - lat: 45.77 - lon: 3.08 - matrix: bebatut:matrix.org - name: "B\xE9r\xE9nice Batut" - orcid: 0000-0001-9852-1987 - page: https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/ - twitter: bebatut - url: https://training.galaxyproject.org/training-material/api/contributors/bebatut.json - - affiliations: - - uni-freiburg - - elixir-europe - - deNBI - - mwk - - biont - contact_for_training: true - elixir_node: de - email: muellert@informatik.uni-freibrug.de - id: teresa-m - joined: 2022-09 - linkedin: teresamueller87 - matrix: teresa-m:matrix.org - name: "Teresa M\xFCller" - orcid: 0000-0003-1252-9684 - page: https://training.galaxyproject.org/training-material/hall-of-fame/teresa-m/ - url: https://training.galaxyproject.org/training-material/api/contributors/teresa-m.json + - AustralianBioCommons + reviewing: + - hexylena + - deeptivarshney + - shiltemann + - pimarin + - bebatut + - abretaud + - bgruening + contributors: - affiliations: - - uni-freiburg - - elixir-europe - bluesky: dvarshney.bsky.social - email: varshney@informatik.uni-freiburg.de - id: deeptivarshney - joined: 2022-12 - name: Deepti Varshney - orcid: 0000-0003-0419-6832 - page: https://training.galaxyproject.org/training-material/hall-of-fame/deeptivarshney/ - url: https://training.galaxyproject.org/training-material/api/contributors/deeptivarshney.json + - avans-atgm + id: bazante1 + joined: 2020-12 + name: Bazante Sanders + page: https://training.galaxyproject.org/training-material/hall-of-fame/bazante1/ + url: https://training.galaxyproject.org/training-material/api/contributors/bazante1.json - affiliations: - gallantries - ifb @@ -40973,28 +21065,257 @@ twitter: bebatut url: https://training.galaxyproject.org/training-material/api/contributors/bebatut.json - affiliations: - - inab-certh - elixir_node: gr - id: npechl - joined: 2023-05 - linkedin: npechl - name: Nikos Pechlivanis - orcid: 0000-0003-2502-612X - page: https://training.galaxyproject.org/training-material/hall-of-fame/npechl/ - twitter: npechl - url: https://training.galaxyproject.org/training-material/api/contributors/npechl.json - - affiliations: + - elixir-europe + contact_for_training: false + elixir_node: nl + former_affiliations: + - deNBI + - avans-atgm + - uni-freiburg - erasmusmc - gallantries - by-covid - - elixir-europe - elixir-converge + id: hexylena + joined: 2017-09 + location: + country: NL + lat: 51.91 + lon: 4.46 + maintainer_contact: gitter + matrix: hexylena:matrix.org + name: Helena Rasche + orcid: 0000-0001-9760-8992 + page: https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/ + url: https://training.galaxyproject.org/training-material/api/contributors/hexylena.json + - affiliations: + - avans-atgm + id: bazante1 + joined: 2020-12 + name: Bazante Sanders + page: https://training.galaxyproject.org/training-material/hall-of-fame/bazante1/ + url: https://training.galaxyproject.org/training-material/api/contributors/bazante1.json + - affiliations: + - uni-freiburg + - nfdi4plants + - elixir-europe + bio: Researcher at Erasmus Medical Center + bluesky: shiltemann.bsky.social + contact_for_training: true + elixir_node: nl + email: saskia.hiltemann@gmail.com + fediverse: https://mstdn.science/@shiltemann + fediverse_flavor: mastodon + former_affiliations: + - CINECA-Project + - gallantries + - erasmusmc + id: shiltemann + joined: 2017-09 + linkedin: shiltemann + location: + country: NL + lat: 51.912 + lon: 4.462 + maintainer_contact: gitter + matrix: shiltemann:matrix.org + name: Saskia Hiltemann + orcid: 0000-0003-3803-468X + page: https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/ + url: https://training.galaxyproject.org/training-material/api/contributors/shiltemann.json + - email: m.zhou1@avans.nl + id: miaomiaozhou88 + joined: 2020-12 + name: Miaomiao Zhou + orcid: 0000-0003-4426-1758 + page: https://training.galaxyproject.org/training-material/hall-of-fame/miaomiaozhou88/ + url: https://training.galaxyproject.org/training-material/api/contributors/miaomiaozhou88.json + - affiliations: + - AustralianBioCommons + - unimelb + - melbournebioinformatics + email: treynolds@unimelb.edu.au + id: tflowers15 + joined: 2025-03 + name: Tristan Reynolds + orcid: 0000-0002-6606-5953 + page: https://training.galaxyproject.org/training-material/hall-of-fame/tflowers15/ + url: https://training.galaxyproject.org/training-material/api/contributors/tflowers15.json + - avatar: /training-material/shared/images/logo-avans.png + former_members: + - dirowa + - hexylena + id: avans-atgm + joined: 2020-11 + members: + - bazante1 + name: Avans Hogeschool + page: https://training.galaxyproject.org/training-material/hall-of-fame/avans-atgm/ + ror: 015d5s513 + short_name: Avans + url: https://training.galaxyproject.org/training-material/api/organisations/avans-atgm.json + - avatar: /training-material/assets/images/abromics.png + github: false + id: abromics + joined: 2024-01 + name: ABRomics + page: https://training.galaxyproject.org/training-material/hall-of-fame/abromics/ + url: https://training.galaxyproject.org/training-material/api/organisations/abromics.json + - avatar: /training-material/shared/images/elixir.png + bio: ELIXIR, the European Life Science + Infrastructure for Biological Information, was founded in 2013 as an intergovernmental + organisation with the aim to consolidate life science resources across Europe. + former_members: + - blankclemens + - ElectronicBlueberry + - erxleben + - gallardoalba + - gmauro + - heylf + - joachimwolff + - khanteymoori + - mtekman + - simonbray + - thomaswollmann + - torhou + id: elixir-europe + joined: 2017-09 + members: + - abretaud + - anuprulez + - bebatut + - bedroesb + - bgruening + - bfranicevic + - B0r1sD + - cat-bro + - carolegoble + - claresloggett + - clsiguret + - colineroyaux + - combesf + - Sch-Da + - deeptivarshney + - eancelet + - EngyNasr + - fbacall + - foellmelanie + - fpsom + - frederikcoppens + - hexylena + - hmenager + - hrhotz + - jfaulon + - JasperO98 + - khaled196 + - kinow + - kikkomep + - kostrykin + - kysrpex + - Lain-inrae + - lecorguille + - lldelisle + - lisanna + - kkamieniecka + - poterlowicz-lab + - mjostaszewski + - MarisaJL + - martenson + - MattiHoch + - mbaardwijk + - mboudet + - mcmaniou + - minamehr + - mira-miracoli + - martinwolst + - Nilchia + - neoformit + - nomadscientist + - nsoranzo + - odoppelt + - onorvez + - pauldg + - paulzierep + - pavanvidem + - PhilReedData + - proccaserra + - robertmand + - rlibouba + - SaimMomin12 + - sanjaysrikakulam + - sbenateau + - scorreard + - shiltemann + - simleo + - sitjart + - stain + - teresa-m + - torfinnnome + - tseemann + - TKlingstrom + - unode + - willemdek11 + - wm75 + - yvanlebras + - ThibaudGlinez + - sfragkoul + - gdefazio + - kevinrue + name: ELIXIR Europe + page: https://training.galaxyproject.org/training-material/hall-of-fame/elixir-europe/ + ror: 044rwnt51 + url: https://training.galaxyproject.org/training-material/api/organisations/elixir-europe.json + - avatar: /training-material/shared/images/unimelb_Logo_RGB.png + id: unimelb + members: + - annasyme + - cat-bro + - GraceAHall + - supernord + - tflowers15 + - uwwint + - vinisalazar + name: The University of Melbourne + page: https://training.galaxyproject.org/training-material/hall-of-fame/unimelb/ + url: https://training.galaxyproject.org/training-material/api/organisations/unimelb.json + - avatar: /training-material/shared/images/Melbourne-Bioinformatics-logo.png + former_members: + - annasyme + id: melbournebioinformatics + members: + - GraceAHall + - tflowers15 + - vinisalazar + name: Melbourne Bioinformatics + page: https://training.galaxyproject.org/training-material/hall-of-fame/melbournebioinformatics/ + url: https://training.galaxyproject.org/training-material/api/organisations/melbournebioinformatics.json + - avatar: /training-material/shared/images/Australian-Biocommons-Favicon-RGB.png + id: AustralianBioCommons + members: + - annasyme + - burkemlou + - cat-bro + - igormakunin + - mthang + - PatCapon39 + - supernord + - tflowers15 + - uwwint + name: Australian BioCommons + page: https://training.galaxyproject.org/training-material/hall-of-fame/AustralianBioCommons/ + url: https://training.galaxyproject.org/training-material/api/organisations/AustralianBioCommons.json + - affiliations: + - elixir-europe contact_for_training: false elixir_node: nl former_affiliations: - deNBI - avans-atgm - uni-freiburg + - erasmusmc + - gallantries + - by-covid + - elixir-converge id: hexylena joined: 2017-09 location: @@ -41007,6 +21328,17 @@ orcid: 0000-0001-9760-8992 page: https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/ url: https://training.galaxyproject.org/training-material/api/contributors/hexylena.json + - affiliations: + - uni-freiburg + - elixir-europe + bluesky: dvarshney.bsky.social + email: varshney@informatik.uni-freiburg.de + id: deeptivarshney + joined: 2022-12 + name: Deepti Varshney + orcid: 0000-0003-0419-6832 + page: https://training.galaxyproject.org/training-material/hall-of-fame/deeptivarshney/ + url: https://training.galaxyproject.org/training-material/api/contributors/deeptivarshney.json - affiliations: - uni-freiburg - nfdi4plants @@ -41035,162 +21367,178 @@ orcid: 0000-0003-3803-468X page: https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/ url: https://training.galaxyproject.org/training-material/api/contributors/shiltemann.json + - id: pimarin + name: pimarin + page: https://training.galaxyproject.org/training-material/hall-of-fame/pimarin/ + url: https://training.galaxyproject.org/training-material/api/contributors/pimarin.json - affiliations: + - gallantries + - ifb + - elixir-europe + contact_for_training: true + elixir_node: fr + email: berenice.batut@gmail.com + fediverse: https://piaille.fr/@bebatut + fediverse_flavor: mastodon + former_affiliations: - uni-freiburg + - deNBI + id: bebatut + joined: 2017-09 + linkedin: berenicebatut + location: + country: FR + lat: 45.77 + lon: 3.08 + matrix: bebatut:matrix.org + name: "B\xE9r\xE9nice Batut" + orcid: 0000-0001-9852-1987 + page: https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/ + twitter: bebatut + url: https://training.galaxyproject.org/training-material/api/contributors/bebatut.json + - affiliations: - elixir-europe + bluesky: abretaud.bsky.social + contact_for_training: true + elixir_node: fr + email: anthony.bretaudeau@irisa.fr + fediverse: https://genomic.social/@abretaud + fediverse_flavor: mastodon + former_affiliations: + - eurosciencegateway + - gallantries + id: abretaud + joined: 2017-09 + location: + country: FR + lat: 48.11 + lon: -1.64 + matrix: abretaud:matrix.org + name: Anthony Bretaudeau + orcid: 0000-0003-0914-2470 + page: https://training.galaxyproject.org/training-material/hall-of-fame/abretaud/ + url: https://training.galaxyproject.org/training-material/api/contributors/abretaud.json + - affiliations: - deNBI - mwk - - materialvitaldigital - email: zierep@informatik.uni-freiburg.de - id: paulzierep - joined: 2023-02 - name: Paul Zierep - orcid: 0000-0003-2982-388X - page: https://training.galaxyproject.org/training-material/hall-of-fame/paulzierep/ - url: https://training.galaxyproject.org/training-material/api/contributors/paulzierep.json - - affiliations: - uni-freiburg - bluesky: dadrasarmin.bsky.social + - elixir-europe + - materialvitaldigital contact_for_training: true - email: dadras@informatik.uni-freiburg.de - fediverse: https://mastodon.social/@dadrasarmin + elixir_node: de + email: bjoern.gruening@gmail.com + fediverse: https://fosstodon.org/@bgruening fediverse_flavor: mastodon former_affiliations: - eurosciencegateway - id: dadrasarmin - joined: 2025-01 - linkedin: armindadras + - eosc-life + - by-covid + - crc992 + - elixir-converge + id: bgruening + joined: 2017-09 + linkedin: bgruening location: country: DE lat: 47.997791 lon: 7.842609 - maintainer_contact: matrix - matrix: armin.dadras:matrix.org - name: Armin Dadras - orcid: 0000-0001-7649-2388 - page: https://training.galaxyproject.org/training-material/hall-of-fame/dadrasarmin/ - url: https://training.galaxyproject.org/training-material/api/contributors/dadrasarmin.json - - email: nwhitak5@jh.edu - id: natalie-wa - joined: 2024-08 - name: Natalie Whitaker-Allen - page: https://training.galaxyproject.org/training-material/hall-of-fame/natalie-wa/ - url: https://training.galaxyproject.org/training-material/api/contributors/natalie-wa.json - dir: topics/microbiome/tutorials/metagenomics-binning + matrix: bgruening:matrix.org + name: "Bj\xF6rn Gr\xFCning" + orcid: 0000-0002-3079-6586 + page: https://training.galaxyproject.org/training-material/hall-of-fame/bgruening/ + twitter: bjoerngruening + url: https://training.galaxyproject.org/training-material/api/contributors/bgruening.json + dir: topics/genome-annotation/tutorials/amr-gene-detection edam_ontology: - - topic_3174 - - topic_0196 + - topic_3673 + - topic_3305 + - topic_0622 + - topic_3301 + - topic_0080 + - topic_3324 + - topic_4013 edam_operation: - - Read mapping - - Statistical calculation - - Sequencing quality control - - Sequence assembly validation - - Read binning - - Validation - - Genome comparison - - Sequence composition calculation - - Sequence clustering + - Antimicrobial resistance prediction - Genome annotation - - Sequence assembly + - Genome visualisation + - Read mapping edam_topic: - - Metagenomics - - Sequence assembly + - Whole genome sequencing + - Public health and epidemiology + - Genomics + - Microbiology + - Sequence analysis + - Infectious disease + - Antimicrobial resistance exact_supported_servers: + - Galaxy@AuBi - UseGalaxy.be - UseGalaxy.cz - UseGalaxy.eu - UseGalaxy.fr feedback_mean_note: null feedback_number: 0 + follow_up_training: + - topic_name: visualisation + tutorials: + - jbrowse + type: internal + - topic_name: galaxy-interface + tutorials: + - history-to-workflow + type: internal hands_on: true - id: microbiome/metagenomics-binning + id: genome-annotation/amr-gene-detection inexact_supported_servers: - - GalaxyTrakr - - UseGalaxy.org.au - UseGalaxy.org (Main) js_requirements: mathjax: null mermaid: false key_points: - - Metagenomics binning is a computational approach to grouping together DNA sequences - from a mixed microbial sample into metagenome-assembled genomes (MAGs) - - The metagenomics binning workflow involves several steps, including preprocessing - of raw sequencing data, assembly of sequencing reads into contigs, binning of - contigs into MAGs, quality assessment of MAGs, and annotation of functional genes - and metabolic pathways in MAGs - - The quality and completeness of MAGs can be evaluated using standard metrics, - such as completeness, contamination, and genome size - - Metagenomics binning can be used to gain insights into the composition, diversity, - and functional potential of microbial communities, and can be applied to a range - of research areas, such as human health, environmental microbiology, and biotechnology + - staramr is a powerful tool to predict ARGs and plasmid genes + - Visualization of the ARGs and plasmid genes in their genomic context helps to + make sense of the data layout: tutorial_hands_on - level: Intermediate + level: Introductory license: CC-BY-4.0 - mod_date: '2026-04-09' + mod_date: '2025-12-18' objectives: - - Describe what is metagenomics binning. - - Describe common challenges in metagenomics binning. - - Perform metagenomic binning using MetaBAT 2 software. - - Evaluation of MAG quality and completeness using CheckM software. - pageviews: 8810 - pub_date: '2023-12-05' + - Run a series of tool to assess the presence of antimicrobial resistance genes + (ARG) + - Get information about ARGs + - Visualize the ARGs and plasmid genes in their genomic context + pageviews: 6177 + pub_date: '2024-01-23' questions: - - What is metagenomic binning refers to? - - Which tools may be used for metagenomic binning? - - How to assess the quality of metagenomic binning? + - Which resistance genes are on a bacterial genome? + - Where are the genes located on the genome? recordings: - - bot-timestamp: 1725013820 + - bot-timestamp: 1727199012 captioners: - - npechl - date: '2024-08-30' + - SaimMomin12 + date: '2024-09-24' galaxy_version: 24.1.2.dev0 - length: 25M - speakers: - - npechl - youtube_id: m8ADGsRVqYI - - bot-timestamp: 1774437607 - captioners: - - paulzierep - date: '2026-03-25' - galaxy_version: 25.1.2.dev0 - length: 34M - speakers: - - paulzierep - youtube_id: https://youtu.be/RjsWjuBzCd4 - redirect_from: - - /topics/metagenomics/tutorials/metagenomics-binning/tutorial - - /short/microbiome/metagenomics-binning - - /short/T00377 - - /short/T00387 - requirements: - - topic_name: microbiome - tutorials: - - metagenomics-assembly - type: internal - short_id: T00387 - short_tools: - - concoct - - concoct_cut_up_fasta - - __BUILD_LIST__ - - Fasta_to_Contig2Bin - - concoct_coverage_table - - das_tool - - metabat2_jgi_summarize_bam_contig_depths - - bowtie2 - - samtools_sort - - drep_dereplicate - - maxbin2 - - metabat2 - - concoct_merge_cut_up_clustering - - semibin - - binette - - checkm_lineage_wf - - concoct_extract_fasta_bins + length: 26M + speakers: + - SaimMomin12 + youtube_id: hfiYCIcD0ww + short_id: T00401 + short_tools: + - bowtie2 + - jbrowse + - bakta + - staramr_search + - upload1 + - Grep1 + - tbl2gff3 slides: false slides_recordings: false - subtopic: metagenomics + subtopic: prokaryote supported_servers: exact: + - name: Galaxy@AuBi + url: https://galaxy.mesocentre.uca.fr + usegalaxy: false - name: UseGalaxy.be url: https://usegalaxy.be/ usegalaxy: false @@ -41204,12 +21552,6 @@ url: https://usegalaxy.fr/ usegalaxy: true inexact: - - name: GalaxyTrakr - url: https://galaxytrakr.org/ - usegalaxy: false - - name: UseGalaxy.org.au - url: https://usegalaxy.org.au - usegalaxy: true - name: UseGalaxy.org (Main) url: https://usegalaxy.org usegalaxy: true @@ -41254,9 +21596,6 @@ - name: IPK Galaxy Blast Suite url: https://galaxy-web.ipk-gatersleben.de usegalaxy: false - - name: Lebanese University Galaxy - url: http://galaxy.ul.edu.lb/ - usegalaxy: false - name: Mandoiu Lab url: https://neo.engr.uconn.edu/ usegalaxy: false @@ -41272,9 +21611,6 @@ - name: PepSimili url: http://pepsimili.e-nios.com:8080/ usegalaxy: false - - name: PhagePromotor - url: https://galaxy.bio.di.uminho.pt/ - usegalaxy: false - name: UseGalaxy.org.au url: https://usegalaxy.org.au usegalaxy: true @@ -41300,22 +21636,22 @@ url: https://viralvariant.anses.fr/ usegalaxy: false tools: - - id: __BUILD_LIST__ + - id: Grep1 servers: - server: http://apostl.moffitt.org/ - state: missing + state: local - server: http://mbac.gmu.edu:8080/ - state: missing + state: local - server: https://vm-chemflow-francegrille.eu/ state: missing - server: https://iris.angers.inra.fr/galaxypub-cfbp state: missing - server: https://hyperbrowser.uio.no/coloc-stats - state: missing + state: local - server: https://galaxy.mesocentre.uca.fr state: local - server: https://galaxy.pasteur.fr/ - state: missing + state: local - server: https://galaxytrakr.org/ state: local - server: http://igg.cloud.ba.infn.it/galaxy @@ -41325,23 +21661,19 @@ - server: https://www.immportgalaxy.org/ state: missing - server: http://galaxy.interactomix.com/ - state: local - - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ + - server: https://galaxy-web.ipk-gatersleben.de state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr state: local - server: http://galaxy.inf.ethz.ch - state: missing + state: local - server: https://palfinder.ls.manchester.ac.uk/ state: missing - server: http://pepsimili.e-nios.com:8080/ state: local - - server: https://galaxy.bio.di.uminho.pt/ - state: local - server: https://usegalaxy.org.au state: local - server: https://usegalaxy.be/ @@ -41391,8 +21723,6 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr @@ -41406,8 +21736,6 @@ state: missing - server: http://pepsimili.e-nios.com:8080/ state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - server: https://usegalaxy.org.au state: exact version: 2.5.4+galaxy0 @@ -41426,8 +21754,8 @@ - server: https://usegalaxy.no/ state: inexact versions: - - 2.4.2+galaxy0 - 2.5.3+galaxy1 + - 2.4.2+galaxy0 - 2.4.5+galaxy1 - 2.4.5+galaxy0 - 2.3.4.3+galaxy0 @@ -41438,7 +21766,7 @@ - server: https://viralvariant.anses.fr/ state: missing version: 2.5.4+galaxy0 - - id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_sort/samtools_sort/2.0.7 + - id: toolshed.g2.bx.psu.edu/repos/iuc/bakta/bakta/1.8.2+galaxy0 servers: - server: http://apostl.moffitt.org/ state: missing @@ -41452,12 +21780,11 @@ state: missing - server: https://galaxy.mesocentre.uca.fr state: exact - version: 2.0.7 + version: 1.8.2+galaxy0 - server: https://galaxy.pasteur.fr/ state: missing - server: https://galaxytrakr.org/ - state: exact - version: 2.0.7 + state: missing - server: http://igg.cloud.ba.infn.it/galaxy state: missing - server: https://galaxy.hyphy.org/ @@ -41468,8 +21795,6 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr @@ -41480,36 +21805,34 @@ state: missing - server: http://pepsimili.e-nios.com:8080/ state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - server: https://usegalaxy.org.au state: exact - version: 2.0.7 + version: 1.8.2+galaxy0 - server: https://usegalaxy.be/ state: exact - version: 2.0.7 + version: 1.8.2+galaxy0 - server: https://usegalaxy.cz/ state: exact - version: 2.0.7 + version: 1.8.2+galaxy0 - server: https://usegalaxy.eu state: exact - version: 2.0.7 + version: 1.8.2+galaxy0 - server: https://usegalaxy.fr/ state: exact - version: 2.0.7 + version: 1.8.2+galaxy0 - server: https://usegalaxy.no/ state: inexact versions: - - 2.0.4 - - 2.0.3 - - '2.0' + - 1.9.2+galaxy0 - server: https://usegalaxy.org - state: exact - version: 2.0.7 + state: inexact + versions: + - 1.9.4+galaxy0 + - 1.9.4+galaxy1 - server: https://viralvariant.anses.fr/ state: missing - version: 2.0.7 - - id: toolshed.g2.bx.psu.edu/repos/iuc/binette/binette/1.2.0+galaxy0 + version: 1.8.2+galaxy0 + - id: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1 servers: - server: http://apostl.moffitt.org/ state: missing @@ -41522,12 +21845,14 @@ - server: https://hyperbrowser.uio.no/coloc-stats state: missing - server: https://galaxy.mesocentre.uca.fr - state: missing + state: exact + version: 1.16.11+galaxy1 - server: https://galaxy.pasteur.fr/ - state: missing + state: exact + version: 1.16.11+galaxy1 - server: https://galaxytrakr.org/ state: exact - version: 1.2.0+galaxy0 + version: 1.16.11+galaxy1 - server: http://igg.cloud.ba.infn.it/galaxy state: missing - server: https://galaxy.hyphy.org/ @@ -41538,46 +21863,42 @@ state: missing - 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server: https://usegalaxy.no/ - state: missing + state: exact + version: 1.16.11+galaxy1 - server: https://usegalaxy.org state: exact - version: 1.2.0+galaxy0 + version: 1.16.11+galaxy1 - server: https://viralvariant.anses.fr/ state: missing - version: 1.2.0+galaxy0 - - id: toolshed.g2.bx.psu.edu/repos/iuc/checkm_lineage_wf/checkm_lineage_wf/1.2.0+galaxy0 + version: 1.16.11+galaxy1 + - id: toolshed.g2.bx.psu.edu/repos/iuc/tbl2gff3/tbl2gff3/1.2 servers: - server: http://apostl.moffitt.org/ state: missing @@ -41590,87 +21911,12 @@ - server: https://hyperbrowser.uio.no/coloc-stats state: missing - server: https://galaxy.mesocentre.uca.fr - state: missing - - server: https://galaxy.pasteur.fr/ - state: missing - - server: https://galaxytrakr.org/ - state: inexact - versions: - - 1.2.4+galaxy2 - - server: http://igg.cloud.ba.infn.it/galaxy - state: missing - - server: https://galaxy.hyphy.org/ - state: missing - - server: https://www.immportgalaxy.org/ - state: missing - - server: http://galaxy.interactomix.com/ - state: missing - - server: https://galaxy-web.ipk-gatersleben.de - state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - - server: https://neo.engr.uconn.edu/ - state: missing - - server: https://mississippi.sorbonne-universite.fr - state: missing - - server: http://galaxy.inf.ethz.ch - state: missing - - server: https://palfinder.ls.manchester.ac.uk/ - state: missing - - server: http://pepsimili.e-nios.com:8080/ - state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - - server: https://usegalaxy.org.au - state: inexact - versions: - - 1.2.4+galaxy2 - - 1.2.3+galaxy0 - - 1.2.4+galaxy1 - - 1.2.5+galaxy0 - - server: https://usegalaxy.be/ - state: exact - version: 1.2.0+galaxy0 - - server: https://usegalaxy.cz/ - state: exact - version: 1.2.0+galaxy0 - - server: https://usegalaxy.eu - state: exact - version: 1.2.0+galaxy0 - - server: https://usegalaxy.fr/ state: exact - version: 1.2.0+galaxy0 - - server: https://usegalaxy.no/ - state: missing - - server: https://usegalaxy.org - state: inexact - versions: - - 1.2.4+galaxy2 - - 1.2.3+galaxy0 - - 1.2.4+galaxy1 - - 1.2.5+galaxy0 - - server: https://viralvariant.anses.fr/ - state: missing - version: 1.2.0+galaxy0 - - id: toolshed.g2.bx.psu.edu/repos/iuc/concoct/concoct/1.1.0+galaxy2 - servers: - - server: http://apostl.moffitt.org/ - state: missing - - server: http://mbac.gmu.edu:8080/ - state: missing - - server: https://vm-chemflow-francegrille.eu/ - state: missing - - server: https://iris.angers.inra.fr/galaxypub-cfbp - state: missing - - server: https://hyperbrowser.uio.no/coloc-stats - state: missing - - server: https://galaxy.mesocentre.uca.fr - state: missing + version: '1.2' - server: https://galaxy.pasteur.fr/ state: missing - server: https://galaxytrakr.org/ - state: exact - version: 1.1.0+galaxy2 + state: missing - server: http://igg.cloud.ba.infn.it/galaxy state: missing - server: https://galaxy.hyphy.org/ @@ -41681,8 +21927,6 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr @@ -41693,32 +21937,30 @@ state: missing - server: http://pepsimili.e-nios.com:8080/ state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - server: https://usegalaxy.org.au state: exact - version: 1.1.0+galaxy2 + version: '1.2' - server: https://usegalaxy.be/ state: exact - version: 1.1.0+galaxy2 + version: '1.2' - server: https://usegalaxy.cz/ state: exact - version: 1.1.0+galaxy2 + version: '1.2' - server: https://usegalaxy.eu state: exact - version: 1.1.0+galaxy2 + version: '1.2' - server: https://usegalaxy.fr/ state: exact - version: 1.1.0+galaxy2 + version: '1.2' - server: https://usegalaxy.no/ state: missing - server: https://usegalaxy.org state: exact - version: 1.1.0+galaxy2 + version: '1.2' - server: https://viralvariant.anses.fr/ state: missing - version: 1.1.0+galaxy2 - - id: toolshed.g2.bx.psu.edu/repos/iuc/concoct_coverage_table/concoct_coverage_table/1.1.0+galaxy2 + version: '1.2' + - id: toolshed.g2.bx.psu.edu/repos/nml/staramr/staramr_search/0.10.0+galaxy1 servers: - server: http://apostl.moffitt.org/ state: missing @@ -41731,12 +21973,15 @@ - server: https://hyperbrowser.uio.no/coloc-stats state: missing - server: https://galaxy.mesocentre.uca.fr - state: missing + state: exact + version: 0.10.0+galaxy1 - server: https://galaxy.pasteur.fr/ state: missing - server: https://galaxytrakr.org/ - state: exact - version: 1.1.0+galaxy2 + state: inexact + versions: + - 0.11.0+galaxy0 + - 0.9.1+galaxy0 - server: http://igg.cloud.ba.infn.it/galaxy state: missing - server: https://galaxy.hyphy.org/ @@ -41747,8 +21992,6 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr @@ -41759,366 +22002,1032 @@ state: missing - server: http://pepsimili.e-nios.com:8080/ state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - server: https://usegalaxy.org.au state: exact - version: 1.1.0+galaxy2 + version: 0.10.0+galaxy1 - server: https://usegalaxy.be/ state: exact - version: 1.1.0+galaxy2 + version: 0.10.0+galaxy1 - server: https://usegalaxy.cz/ state: exact - version: 1.1.0+galaxy2 + version: 0.10.0+galaxy1 - server: https://usegalaxy.eu state: exact - version: 1.1.0+galaxy2 + version: 0.10.0+galaxy1 - server: https://usegalaxy.fr/ state: exact - version: 1.1.0+galaxy2 + version: 0.10.0+galaxy1 - server: https://usegalaxy.no/ - state: missing + state: inexact + versions: + - 0.7.2+galaxy0 + - 0.8.0+galaxy0 + - 0.7.1+galaxy2 - server: https://usegalaxy.org state: exact - version: 1.1.0+galaxy2 + version: 0.10.0+galaxy1 - server: https://viralvariant.anses.fr/ state: missing - version: 1.1.0+galaxy2 - - id: toolshed.g2.bx.psu.edu/repos/iuc/concoct_cut_up_fasta/concoct_cut_up_fasta/1.1.0+galaxy2 + version: 0.10.0+galaxy1 + - id: upload1 servers: - server: http://apostl.moffitt.org/ - state: missing + state: local - 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state: missing + state: local - server: https://mississippi.sorbonne-universite.fr - state: missing + state: local - server: http://galaxy.inf.ethz.ch - state: missing + state: local - server: https://palfinder.ls.manchester.ac.uk/ - state: missing + state: local - server: http://pepsimili.e-nios.com:8080/ - state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing + state: local - server: https://usegalaxy.org.au - state: exact - version: 1.1.0+galaxy2 + state: missing - server: https://usegalaxy.be/ - state: exact - version: 1.1.0+galaxy2 + state: local - server: https://usegalaxy.cz/ - state: exact - version: 1.1.0+galaxy2 + state: local - server: https://usegalaxy.eu - state: exact - version: 1.1.0+galaxy2 + state: local - server: https://usegalaxy.fr/ - state: exact - version: 1.1.0+galaxy2 + state: local - server: https://usegalaxy.no/ - state: missing + state: local - server: https://usegalaxy.org - state: exact - version: 1.1.0+galaxy2 + state: local - server: https://viralvariant.anses.fr/ - state: missing - version: 1.1.0+galaxy2 - - id: toolshed.g2.bx.psu.edu/repos/iuc/concoct_extract_fasta_bins/concoct_extract_fasta_bins/1.1.0+galaxy2 + state: local + version: local + symlink: null + tags: + - gmod + - illumina + - amr + - one-health + - jbrowse1 + - microgalaxy + time: null + time_estimation: 2h + title: Identification of AMR genes in an assembled bacterial genome + tools: + - Grep1 + - toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.5.4+galaxy0 + - toolshed.g2.bx.psu.edu/repos/iuc/bakta/bakta/1.8.2+galaxy0 + - toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1 + - toolshed.g2.bx.psu.edu/repos/iuc/tbl2gff3/tbl2gff3/1.2 + - toolshed.g2.bx.psu.edu/repos/nml/staramr/staramr_search/0.10.0+galaxy1 + - upload1 + topic_name: genome-annotation + topic_name_human: Genome Annotation + tours: false + translations: + slides: [] + tutorial: [] + video: false + tutorial_name: amr-gene-detection + type: tutorial + url: https://training.galaxyproject.org//topics/genome-annotation/tutorials/amr-gene-detection/tutorial.html + urls: + hands_on: https://training.galaxyproject.org/training-material/api/topics/genome-annotation/tutorials/amr-gene-detection/tutorial.json + slides: https://training.galaxyproject.org/training-material/api/topics/genome-annotation/tutorials/amr-gene-detection/tutorial.json + version: 10 + video: true + video_versions: 1 + video_view: 0 + visit_duration: 548 + visitors: 4562 + workflows: + - creators: + - class: Person + identifier: https://orcid.org/0000-0003-2255-1631 + name: Bazante Sanders + - class: Person + identifier: https://orcid.org/0000-0001-9852-1987 + name: "B\xE9r\xE9nice Batut" + - class: Person + identifier: 0000-0002-6606-5953 + name: Tristan Reynolds + description: Identification of AMR genes in an assembled bacterial genome + features: + comments: false + parameters: false + report: + markdown: ' + + # Workflow Execution Report + + + ## Workflow Inputs + + ```galaxy + + invocation_inputs() + + ``` + + + ## Workflow Outputs + + ```galaxy + + invocation_outputs() + + ``` + + + ## Workflow + + ```galaxy + + workflow_display() + + ``` + + ' + subworkflows: false + graph_dot: "digraph main {\n node [fontname=\"Atkinson Hyperlegible\", shape=box,\ + \ color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n edge [fontname=\"\ + Atkinson Hyperlegible\"];\n 0[color=lightblue,label=\"\u2139\uFE0F Input Dataset\\\ + ncontigs\"]\n 1[color=lightblue,label=\"\u2139\uFE0F Input Collection\\nInput\ + \ Paired End Reads Collection\"]\n 2[label=\"staramr\"]\n 0 -> 2 [label=\"\ + output\"]\n ka84f1c100c72423ca85c643c39e44dac[color=lightseagreen,label=\"\ + Output\\nstararm_detailed_summary\"]\n 2 -> ka84f1c100c72423ca85c643c39e44dac\n\ + \ 3[label=\"Bakta\"]\n 0 -> 3 [label=\"output\"]\n kb9beba767b6e42aea085819f4b577100[color=lightseagreen,label=\"\ + Output\\nbakta_annotation_summary\"]\n 3 -> kb9beba767b6e42aea085819f4b577100\n\ + \ 4[label=\"Bowtie2\"]\n 1 -> 4 [label=\"output\"]\n 0 -> 4 [label=\"output\"\ + ]\n kb85fac67e102475e95d935e0adecb0c9[color=lightseagreen,label=\"Output\\\ + nmapping_stats\"]\n 4 -> kb85fac67e102475e95d935e0adecb0c9\n 5[label=\"Select\"\ + ]\n 2 -> 5 [label=\"detailed_summary\"]\n 6[label=\"Table to GFF3\"]\n 5\ + \ -> 6 [label=\"out_file1\"]\n 7[label=\"JBrowse\"]\n 0 -> 7 [label=\"output\"\ + ]\n 3 -> 7 [label=\"annotation_gff3\"]\n 6 -> 7 [label=\"output\"]\n 4 ->\ + \ 7 [label=\"output\"]\n kc4e08c514520483ab48a99adc9a5d09f[color=lightseagreen,label=\"\ + Output\\njbrowse_output\"]\n 7 -> kc4e08c514520483ab48a99adc9a5d09f\n}" + history: + - hash: f52ead1fa4d239d06e53378776f7a78ee02dae8c + message: Correct creator names + num: 6 + short_hash: f52ead1fa + unix: '1765497330' + - hash: 8f5019e24f767aedb7863e58784f1f826feef711 + message: Updated workflow and workflow tests + num: 5 + short_hash: 8f5019e24 + unix: '1765326710' + - hash: 597f8ce954083c7cd4e43765b6c4709619637e6a + message: Add Bazante's ORCID + num: 4 + short_hash: 597f8ce95 + unix: '1706018263' + - hash: 03e4290900ade23b2dffb3f61ea2875a64f2c396 + message: Fix workflows + num: 3 + short_hash: 03e429090 + unix: '1706004257' + - hash: c88bcbb6f04ad1847e0747f7fb9256ee0ec858de + message: Add license and creator to workflows + num: 2 + short_hash: c88bcbb6f + unix: '1705678137' + - hash: 6d6129376b624fe20278f8df09b13cae881c5484 + message: Expand the AMR detection tutorial + num: 1 + short_hash: 6d6129376 + unix: '1705334494' + inputs: + - annotation: '' + content_id: null + errors: null + id: 0 + input_connections: {} + inputs: + - description: '' + name: contigs + label: contigs + name: Input dataset + outputs: [] + position: + left: 29.389650909383253 + top: 266.7171950950425 + tool_id: null + tool_state: '{"optional": false, "tag": null}' + tool_version: null + type: data_input + uuid: a18c5e52-124f-4480-80b4-ea5936618bc6 + when: null + workflow_outputs: [] + - annotation: '' + content_id: null + errors: null + id: 1 + input_connections: {} + inputs: + - description: '' + name: Input Paired End Reads Collection + label: Input Paired End Reads Collection + name: Input dataset collection + outputs: [] + position: + left: 0 + top: 818.5059327479345 + tool_id: null + tool_state: '{"optional": false, "format": ["fastq", "fastqsanger", "fastqsanger.gz", + "fastqsolexa.bz2", "fasta"], "tag": null, "collection_type": "list:paired", + "fields": null}' + tool_version: null + type: data_collection_input + uuid: 8a82b6e0-f92f-4f1f-8bdd-fd53a0c1e0ff + when: null + workflow_outputs: [] + license: MIT + mermaid: "flowchart TD\n 0[\"\u2139\uFE0F Input Dataset\\ncontigs\"];\n style\ + \ 0 stroke:#2c3143,stroke-width:4px;\n 1[\"\u2139\uFE0F Input Collection\\\ + nInput Paired End Reads Collection\"];\n style 1 stroke:#2c3143,stroke-width:4px;\n\ + \ 2[\"staramr\"];\n 0 -->|output| 2;\n a84f1c10-0c72-423c-a85c-643c39e44dac[\"\ + Output\\nstararm_detailed_summary\"];\n 2 --> a84f1c10-0c72-423c-a85c-643c39e44dac;\n\ + \ style a84f1c10-0c72-423c-a85c-643c39e44dac stroke:#2c3143,stroke-width:4px;\n\ + \ 3[\"Bakta\"];\n 0 -->|output| 3;\n b9beba76-7b6e-42ae-a085-819f4b577100[\"\ + Output\\nbakta_annotation_summary\"];\n 3 --> b9beba76-7b6e-42ae-a085-819f4b577100;\n\ + \ style b9beba76-7b6e-42ae-a085-819f4b577100 stroke:#2c3143,stroke-width:4px;\n\ + \ 4[\"Bowtie2\"];\n 1 -->|output| 4;\n 0 -->|output| 4;\n b85fac67-e102-475e-95d9-35e0adecb0c9[\"\ + Output\\nmapping_stats\"];\n 4 --> b85fac67-e102-475e-95d9-35e0adecb0c9;\n\ + \ style b85fac67-e102-475e-95d9-35e0adecb0c9 stroke:#2c3143,stroke-width:4px;\n\ + \ 5[\"Select\"];\n 2 -->|detailed_summary| 5;\n 6[\"Table to GFF3\"];\n \ + \ 5 -->|out_file1| 6;\n 7[\"JBrowse\"];\n 0 -->|output| 7;\n 3 -->|annotation_gff3|\ + \ 7;\n 6 -->|output| 7;\n 4 -->|output| 7;\n c4e08c51-4520-483a-b48a-99adc9a5d09f[\"\ + Output\\njbrowse_output\"];\n 7 --> c4e08c51-4520-483a-b48a-99adc9a5d09f;\n\ + \ style c4e08c51-4520-483a-b48a-99adc9a5d09f stroke:#2c3143,stroke-width:4px;" + modified: 2026-07-01 00:31:39 +0000 + name: mrsa AMR gene detection + outputs: + - annotation: '' + content_id: toolshed.g2.bx.psu.edu/repos/nml/staramr/staramr_search/0.10.0+galaxy1 + errors: null + id: 2 + input_connections: + genomes: + id: 0 + output_name: output + inputs: [] + label: null + name: staramr + outputs: + - name: blast_hits + type: input + - name: mlst + type: tabular + - name: summary + type: tabular + - name: detailed_summary + type: tabular + - name: resfinder + type: tabular + - name: plasmidfinder + type: tabular + - name: settings + type: txt + - name: excel + type: xlsx + position: + left: 398.8052573857074 + top: 418.36193849302833 + post_job_actions: {} + tool_id: toolshed.g2.bx.psu.edu/repos/nml/staramr/staramr_search/0.10.0+galaxy1 + tool_shed_repository: + changeset_revision: 3b22de20bd4b + name: staramr + owner: nml + tool_shed: toolshed.g2.bx.psu.edu + tool_state: '{"__input_ext": "input", "advanced": {"pid_threshold": "98.0", + "plength_resfinder": "60.0", "plength_pointfinder": "95.0", "plength_plasmidfinder": + "60.0", "genome_size_lower_bound": "4000000", "genome_size_upper_bound": "6000000", + "minimum_N50_value": "10000", "minimum_contig_length": "300", "unacceptable_number_contigs": + "1000", "report_all_blast": false, "exclude_negatives": false, "exclude_resistance_phenotypes": + false, "mlst_scheme": "auto", "exclude_genes": {"exclude_genes_condition": + "default", "__current_case__": 0}, "complex_mutations": {"complex_mutations_condition": + "default", "__current_case__": 0}, "plasmidfinder_type": "include_all"}, "chromInfo": + "/opt/galaxy/tool-data/shared/ucsc/chrom/?.len", "genomes": {"__class__": + "ConnectedValue"}, "pointfinder_db": {"use_pointfinder": "disabled", "__current_case__": + 0}, "__page__": null, "__rerun_remap_job_id__": null}' + tool_version: 0.10.0+galaxy1 + type: tool + uuid: 2554da56-e9f9-4e65-98b6-25b4a2861df9 + when: null + workflow_outputs: + - label: stararm_detailed_summary + output_name: detailed_summary + uuid: a84f1c10-0c72-423c-a85c-643c39e44dac + - annotation: '' + content_id: toolshed.g2.bx.psu.edu/repos/iuc/bakta/bakta/1.8.2+galaxy0 + errors: null + id: 3 + input_connections: + input_option|input_file: + id: 0 + output_name: output + inputs: + - description: runtime parameter for tool Bakta + name: annotation + - description: runtime parameter for tool Bakta + name: annotation + - description: runtime parameter for tool Bakta + name: annotation + - description: runtime parameter for tool Bakta + name: input_option + label: null + name: Bakta + outputs: + - name: annotation_tsv + type: tabular + - name: annotation_gff3 + type: gff3 + - name: annotation_ffn + type: fasta + - name: annotation_plot + type: svg + position: + left: 693.9379011571834 + top: 0.0 + post_job_actions: {} + tool_id: toolshed.g2.bx.psu.edu/repos/iuc/bakta/bakta/1.8.2+galaxy0 + tool_shed_repository: + changeset_revision: 728dacaf08a9 + name: bakta + owner: iuc + tool_shed: toolshed.g2.bx.psu.edu + tool_state: '{"annotation": {"complete": false, "prodigal": {"__class__": "RuntimeValue"}, + "translation_table": "11", "keep_contig_headers": true, "replicons": {"__class__": + "RuntimeValue"}, "compliant": false, "proteins": {"__class__": "RuntimeValue"}, + "meta": false}, "input_option": {"bakta_db_select": "V5.0_2023-02-20", "amrfinder_db_select": + "amrfinderplus_V3.11_2022-12-19.1", "input_file": {"__class__": "ConnectedValue"}, + "min_contig_length": null}, "organism": {"genus": null, "species": null, "strain": + null, "plasmid": null}, "output_files": {"output_selection": ["file_tsv", + "file_gff3", "file_ffn", "file_plot"]}, "workflow": {"skip_analysis": null}, + "__page__": null, "__rerun_remap_job_id__": null}' + tool_version: 1.8.2+galaxy0 + type: tool + uuid: 0b92601d-5b78-438c-998d-f9f4dc61c52d + when: null + workflow_outputs: + - label: bakta_annotation_summary + output_name: annotation_tsv + uuid: b9beba76-7b6e-42ae-a085-819f4b577100 + - annotation: '' + content_id: toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.5.4+galaxy0 + errors: null + id: 4 + input_connections: + library|input_1: + id: 1 + output_name: output + reference_genome|own_file: + id: 0 + output_name: output + inputs: + - description: runtime parameter for tool Bowtie2 + name: library + - description: runtime parameter for tool Bowtie2 + name: reference_genome + label: null + name: Bowtie2 + outputs: + - name: output + type: bam + - name: mapping_stats + type: txt + position: + left: 401.9067837031812 + top: 879.3889752174059 + post_job_actions: {} + tool_id: toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.5.4+galaxy0 + tool_shed_repository: + changeset_revision: f76cbb84d67f + name: bowtie2 + owner: devteam + tool_shed: toolshed.g2.bx.psu.edu + tool_state: '{"analysis_type": {"analysis_type_selector": "simple", "__current_case__": + 0, "presets": "no_presets"}, "library": {"type": "paired_collection", "__current_case__": + 1, "input_1": {"__class__": "ConnectedValue"}, "unaligned_file": false, "aligned_file": + false, "paired_options": {"paired_options_selector": "no", "__current_case__": + 1}}, "reference_genome": {"source": "history", "__current_case__": 1, "own_file": + {"__class__": "ConnectedValue"}}, "rg": {"rg_selector": "do_not_set", "__current_case__": + 3}, "sam_options": {"sam_options_selector": "no", "__current_case__": 1}, + "save_mapping_stats": true, "__page__": 0, "__rerun_remap_job_id__": null}' + tool_version: 2.5.4+galaxy0 + type: tool + uuid: bff0e1b9-fca3-4c48-a7c0-4eaf2b7ae77f + when: null + workflow_outputs: + - label: mapping_stats + output_name: mapping_stats + uuid: b85fac67-e102-475e-95d9-35e0adecb0c9 + - annotation: '' + content_id: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1 + errors: null + id: 7 + input_connections: + reference_genome|genome: + id: 0 + output_name: output + track_groups_0|data_tracks_0|data_format|annotation: + id: 3 + output_name: annotation_gff3 + track_groups_1|data_tracks_0|data_format|annotation: + id: 6 + output_name: output + track_groups_2|data_tracks_0|data_format|annotation: + id: 4 + output_name: output + inputs: + - description: runtime parameter for tool JBrowse + name: reference_genome + label: null + name: JBrowse + outputs: + - name: output + type: html + position: + left: 1290.2758853942887 + top: 540.5369252019697 + post_job_actions: {} + tool_id: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1 + tool_shed_repository: + changeset_revision: a6e57ff585c0 + name: jbrowse + owner: iuc + tool_shed: toolshed.g2.bx.psu.edu + tool_state: '{"__input_ext": "fasta", "action": {"action_select": "create", + "__current_case__": 0}, "chromInfo": "/opt/galaxy/tool-data/shared/ucsc/chrom/?.len", + "gencode": "1", "jbgen": {"defaultLocation": "", "trackPadding": "20", "shareLink": + true, "aboutDescription": "", "show_tracklist": true, "show_nav": true, "show_overview": + true, "show_menu": true, "hideGenomeOptions": false}, "plugins": {"BlastView": + true, "ComboTrackSelector": false, "GCContent": false}, "reference_genome": + {"genome_type_select": "history", "__current_case__": 1, "genome": {"__class__": + "ConnectedValue"}}, "standalone": "minimal", "track_groups": [{"__index__": + 0, "category": "Bakta", "data_tracks": [{"__index__": 0, "data_format": {"data_format_select": + "gene_calls", "__current_case__": 2, "annotation": {"__class__": "ConnectedValue"}, + "match_part": {"match_part_select": false, "__current_case__": 1}, "index": + false, "track_config": {"track_class": "NeatHTMLFeatures/View/Track/NeatFeatures", + "__current_case__": 3, "html_options": {"topLevelFeatures": null}}, "jbstyle": + {"style_classname": "feature", "style_label": "product,name,id", "style_description": + "note,description", "style_height": "10px", "max_height": "600"}, "jbcolor_scale": + {"color_score": {"color_score_select": "none", "__current_case__": 0, "color": + {"color_select": "automatic", "__current_case__": 0}}}, "jb_custom_config": + {"option": []}, "jbmenu": {"track_menu": []}, "track_visibility": "default_off", + "override_apollo_plugins": "False", "override_apollo_drag": "False"}}]}, {"__index__": + 1, "category": "ARGs and plasmid genes", "data_tracks": [{"__index__": 0, + "data_format": {"data_format_select": "gene_calls", "__current_case__": 2, + "annotation": {"__class__": "ConnectedValue"}, "match_part": {"match_part_select": + false, "__current_case__": 1}, "index": false, "track_config": {"track_class": + "NeatHTMLFeatures/View/Track/NeatFeatures", "__current_case__": 3, "html_options": + {"topLevelFeatures": null}}, "jbstyle": {"style_classname": "feature", "style_label": + "product,name,id", "style_description": "note,description", "style_height": + "10px", "max_height": "600"}, "jbcolor_scale": {"color_score": {"color_score_select": + "none", "__current_case__": 0, "color": {"color_select": "automatic", "__current_case__": + 0}}}, "jb_custom_config": {"option": []}, "jbmenu": {"track_menu": []}, "track_visibility": + "default_off", "override_apollo_plugins": "False", "override_apollo_drag": + "False"}}]}, {"__index__": 2, "category": "Coverage", "data_tracks": [{"__index__": + 0, "data_format": {"data_format_select": "pileup", "__current_case__": 3, + "annotation": {"__class__": "ConnectedValue"}, "auto_snp": false, "chunkSizeLimit": + "5000000", "jb_custom_config": {"option": []}, "track_visibility": "default_off", + "override_apollo_plugins": "False", "override_apollo_drag": "False"}}]}], + "uglyTestingHack": "", "__page__": null, "__rerun_remap_job_id__": null}' + tool_version: 1.16.11+galaxy1 + type: tool + uuid: 9f973678-ce81-458a-a5d0-575d93d61429 + when: null + workflow_outputs: + - label: jbrowse_output + output_name: output + uuid: c4e08c51-4520-483a-b48a-99adc9a5d09f + parent_id: genome-annotation/amr-gene-detection + path: topics/genome-annotation/tutorials/amr-gene-detection/workflows/main-workflow.ga + tags: + - genome-annotation + - microgalaxy + test_results: null + tests: true + title: mrsa AMR gene detection + topic_id: genome-annotation + trs_endpoint: https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/genome-annotation-amr-gene-detection/versions/main-workflow + tutorial_id: amr-gene-detection + url: https://training.galaxyproject.org/training-material/topics/genome-annotation/tutorials/amr-gene-detection/workflows/main-workflow.ga + url_html: https://training.galaxyproject.org/training-material/topics/genome-annotation/tutorials/amr-gene-detection/workflows/main-workflow.html + version: 2 + wfid: genome-annotation-amr-gene-detection + wfname: main-workflow + workflow: main-workflow.ga + workflow_tools: + - Grep1 + - toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.5.4+galaxy0 + - 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hchiapello + - bebatut + - vloux + reviewing: + - abretaud + - shiltemann + contributors: + - elixir_node: fr + id: hchiapello + joined: 2025-03 + name: "H\xE9l\xE8ne Chiapello" + page: https://training.galaxyproject.org/training-material/hall-of-fame/hchiapello/ + url: https://training.galaxyproject.org/training-material/api/contributors/hchiapello.json + - affiliations: + - gallantries + - ifb + - elixir-europe + contact_for_training: true + elixir_node: fr + email: berenice.batut@gmail.com + fediverse: https://piaille.fr/@bebatut + fediverse_flavor: mastodon + former_affiliations: + - uni-freiburg + - deNBI + id: bebatut + joined: 2017-09 + linkedin: berenicebatut + location: + country: FR + lat: 45.77 + lon: 3.08 + matrix: bebatut:matrix.org + name: "B\xE9r\xE9nice Batut" + orcid: 0000-0001-9852-1987 + page: https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/ + twitter: bebatut + url: https://training.galaxyproject.org/training-material/api/contributors/bebatut.json + - 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name: checkm2 + owner: iuc + revisions: 0f5f7fa9c08f + tool_panel_section_label: Metagenomic Analysis + tool_shed_url: https://toolshed.g2.bx.psu.edu/ + - name: drep_dereplicate + owner: iuc + revisions: 76b57044069d + tool_panel_section_label: Metagenomic Analysis + tool_shed_url: https://toolshed.g2.bx.psu.edu/ + admin_install_yaml: "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies:\ + \ true\ninstall_resolver_dependencies: true\ntools:\n- name: checkm2\n owner:\ + \ iuc\n revisions: 0f5f7fa9c08f\n tool_panel_section_label: Metagenomic Analysis\n\ + \ tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: drep_dereplicate\n\ + \ owner: iuc\n revisions: 76b57044069d\n tool_panel_section_label: Metagenomic\ + \ Analysis\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n" + api: https://training.galaxyproject.org/training-material/api/topics/genome-annotation/tutorials/bacterial-genome-quality-control/tutorial.json + contributions: + authorship: + - hchiapello + - bebatut + - vloux + reviewing: + - abretaud + contributors: + - elixir_node: fr + id: hchiapello + joined: 2025-03 + name: "H\xE9l\xE8ne Chiapello" + page: https://training.galaxyproject.org/training-material/hall-of-fame/hchiapello/ + url: https://training.galaxyproject.org/training-material/api/contributors/hchiapello.json + - affiliations: + - gallantries + - ifb + - elixir-europe + contact_for_training: true + elixir_node: fr + email: berenice.batut@gmail.com + fediverse: https://piaille.fr/@bebatut + fediverse_flavor: mastodon + former_affiliations: + - uni-freiburg + - deNBI + id: bebatut + joined: 2017-09 + linkedin: berenicebatut + location: + country: FR + lat: 45.77 + lon: 3.08 + matrix: bebatut:matrix.org + name: "B\xE9r\xE9nice Batut" + orcid: 0000-0001-9852-1987 + page: https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/ + twitter: bebatut + url: https://training.galaxyproject.org/training-material/api/contributors/bebatut.json + - id: vloux + joined: 2019-04 + name: Valentin Loux + page: https://training.galaxyproject.org/training-material/hall-of-fame/vloux/ + url: https://training.galaxyproject.org/training-material/api/contributors/vloux.json + - affiliations: + - elixir-europe + bluesky: abretaud.bsky.social + contact_for_training: true + elixir_node: fr + email: anthony.bretaudeau@irisa.fr + fediverse: https://genomic.social/@abretaud + fediverse_flavor: mastodon + former_affiliations: + - eurosciencegateway + - gallantries + id: abretaud + joined: 2017-09 + location: + country: FR + lat: 48.11 + lon: -1.64 + matrix: abretaud:matrix.org + name: Anthony Bretaudeau + orcid: 0000-0003-0914-2470 + page: https://training.galaxyproject.org/training-material/hall-of-fame/abretaud/ + url: https://training.galaxyproject.org/training-material/api/contributors/abretaud.json + dir: topics/genome-annotation/tutorials/bacterial-genome-quality-control + draft: true + edam_ontology: + - topic_0622 + - topic_3301 + edam_operation: + - Statistical calculation + - Sequencing quality control + - Sequence assembly validation + - Genome comparison + - Validation + - Sequence composition calculation + edam_topic: + - Genomics + - Microbiology + exact_supported_servers: + - UseGalaxy.eu + - UseGalaxy.fr + - UseGalaxy.org (Main) + feedback_mean_note: null + feedback_number: 0 + hands_on: true + id: genome-annotation/bacterial-genome-quality-control + inexact_supported_servers: + - GalaxyTrakr + - UseGalaxy.cz + js_requirements: + mathjax: null + mermaid: false + key_points: + - to do + - to do + layout: tutorial_hands_on + level: Introductory + license: CC-BY-4.0 + mod_date: '2025-03-14' + objectives: + - to do + - to do + pageviews: 263 + pub_date: '2025-03-14' + questions: + - to do + - to do + short_id: T00495 + short_tools: + - upload1 + - drep_dereplicate + - checkm2 + slides: false + slides_recordings: false + supported_servers: + exact: + - name: UseGalaxy.eu + url: https://usegalaxy.eu + usegalaxy: true + - name: UseGalaxy.fr + url: https://usegalaxy.fr/ + usegalaxy: true + - name: UseGalaxy.org (Main) + url: https://usegalaxy.org + usegalaxy: true + inexact: + - name: GalaxyTrakr + url: https://galaxytrakr.org/ + usegalaxy: false + - name: UseGalaxy.cz + url: https://usegalaxy.cz/ + usegalaxy: false + supported_servers_matrix: + servers: + - name: APOSTL + url: http://apostl.moffitt.org/ + usegalaxy: false + - name: MBAC Metabiome Portal + url: http://mbac.gmu.edu:8080/ + usegalaxy: false + - name: ChemFlow + url: https://vm-chemflow-francegrille.eu/ + usegalaxy: false + - name: CIRM-CFBP + url: https://iris.angers.inra.fr/galaxypub-cfbp + usegalaxy: false + - name: Coloc-stats + url: https://hyperbrowser.uio.no/coloc-stats + usegalaxy: false + - name: Galaxy@AuBi + url: https://galaxy.mesocentre.uca.fr + usegalaxy: false + - name: Galaxy@Pasteur + url: https://galaxy.pasteur.fr/ + usegalaxy: false + - name: GalaxyTrakr + url: https://galaxytrakr.org/ + usegalaxy: false + - name: GASLINI + url: http://igg.cloud.ba.infn.it/galaxy + usegalaxy: false + - name: HyPhy HIV NGS Tools + url: https://galaxy.hyphy.org/ + usegalaxy: false + - name: ImmPort Galaxy + url: https://www.immportgalaxy.org/ + usegalaxy: false + - name: InteractoMIX + url: http://galaxy.interactomix.com/ + usegalaxy: false + - name: IPK Galaxy Blast Suite + url: https://galaxy-web.ipk-gatersleben.de + usegalaxy: false + - name: Mandoiu Lab + url: https://neo.engr.uconn.edu/ + usegalaxy: false + - name: MISSISSIPPI + url: https://mississippi.sorbonne-universite.fr + usegalaxy: false + - name: Oqtans + url: http://galaxy.inf.ethz.ch + usegalaxy: false + - name: Palfinder + url: https://palfinder.ls.manchester.ac.uk/ + usegalaxy: false + - name: PepSimili + url: http://pepsimili.e-nios.com:8080/ + usegalaxy: false + - name: UseGalaxy.org.au + url: https://usegalaxy.org.au + usegalaxy: true + - name: UseGalaxy.be + url: https://usegalaxy.be/ + usegalaxy: false + - name: UseGalaxy.cz + url: https://usegalaxy.cz/ + usegalaxy: false + - name: UseGalaxy.eu + url: https://usegalaxy.eu + usegalaxy: true + - name: UseGalaxy.fr + url: https://usegalaxy.fr/ + usegalaxy: true + - name: UseGalaxy.no + url: https://usegalaxy.no/ + usegalaxy: false + - name: UseGalaxy.org (Main) + url: https://usegalaxy.org + usegalaxy: true + - name: Viral Variant Visualizer (VVV) + url: https://viralvariant.anses.fr/ + usegalaxy: false + tools: + - id: toolshed.g2.bx.psu.edu/repos/iuc/checkm2/checkm2/1.0.2+galaxy0 servers: - server: http://apostl.moffitt.org/ state: missing @@ -42397,12 +23520,15 @@ - server: https://hyperbrowser.uio.no/coloc-stats state: missing - server: https://galaxy.mesocentre.uca.fr - state: missing + state: inexact + versions: + - 1.1.0+galaxy0 - server: https://galaxy.pasteur.fr/ state: missing - server: https://galaxytrakr.org/ - state: exact - version: 2.2.7+galaxy6 + state: inexact + versions: + - 1.1.0+galaxy0 - server: http://igg.cloud.ba.infn.it/galaxy state: missing - server: https://galaxy.hyphy.org/ @@ -42413,564 +23539,394 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr state: missing - server: http://galaxy.inf.ethz.ch - state: missing - - server: https://palfinder.ls.manchester.ac.uk/ - state: missing - - server: http://pepsimili.e-nios.com:8080/ - state: inexact - versions: - - 2.2.7+galaxy4 - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - - server: https://usegalaxy.org.au - state: exact - version: 2.2.7+galaxy6 - - server: https://usegalaxy.be/ - state: exact - version: 2.2.7+galaxy6 - - server: https://usegalaxy.cz/ - state: exact - version: 2.2.7+galaxy6 - - server: https://usegalaxy.eu - state: exact - version: 2.2.7+galaxy6 - - server: https://usegalaxy.fr/ - state: exact - version: 2.2.7+galaxy6 - - server: https://usegalaxy.no/ - state: inexact - versions: - - 2.2.7+galaxy2 - - server: https://usegalaxy.org - state: exact - version: 2.2.7+galaxy6 - - server: https://viralvariant.anses.fr/ - state: missing - version: 2.2.7+galaxy6 - symlink: null - tags: - - binning - - metagenomics - - microgalaxy - time: null - time_estimation: 2H - title: Binning of metagenomic sequencing data - tools: - - __BUILD_LIST__ - - toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.5.4+galaxy0 - - toolshed.g2.bx.psu.edu/repos/devteam/samtools_sort/samtools_sort/2.0.7 - - toolshed.g2.bx.psu.edu/repos/iuc/binette/binette/1.2.0+galaxy0 - - toolshed.g2.bx.psu.edu/repos/iuc/checkm_lineage_wf/checkm_lineage_wf/1.2.0+galaxy0 - - toolshed.g2.bx.psu.edu/repos/iuc/concoct/concoct/1.1.0+galaxy2 - - toolshed.g2.bx.psu.edu/repos/iuc/concoct_coverage_table/concoct_coverage_table/1.1.0+galaxy2 - - toolshed.g2.bx.psu.edu/repos/iuc/concoct_cut_up_fasta/concoct_cut_up_fasta/1.1.0+galaxy2 - - toolshed.g2.bx.psu.edu/repos/iuc/concoct_extract_fasta_bins/concoct_extract_fasta_bins/1.1.0+galaxy2 - - toolshed.g2.bx.psu.edu/repos/iuc/concoct_merge_cut_up_clustering/concoct_merge_cut_up_clustering/1.1.0+galaxy2 - - toolshed.g2.bx.psu.edu/repos/iuc/das_tool/das_tool/1.1.7+galaxy1 - - toolshed.g2.bx.psu.edu/repos/iuc/drep_dereplicate/drep_dereplicate/3.6.2+galaxy1 - - toolshed.g2.bx.psu.edu/repos/iuc/fasta_to_contig2bin/Fasta_to_Contig2Bin/1.1.7+galaxy1 - - toolshed.g2.bx.psu.edu/repos/iuc/metabat2/metabat2/2.17+galaxy0 - - toolshed.g2.bx.psu.edu/repos/iuc/metabat2_jgi_summarize_bam_contig_depths/metabat2_jgi_summarize_bam_contig_depths/2.17+galaxy0 - - toolshed.g2.bx.psu.edu/repos/iuc/semibin/semibin/2.1.0+galaxy1 - - toolshed.g2.bx.psu.edu/repos/mbernt/maxbin2/maxbin2/2.2.7+galaxy6 - topic_name: microbiome - topic_name_human: Microbiome - tours: false - translations: - slides: [] - tutorial: [] - video: false - tutorial_name: metagenomics-binning - type: tutorial - url: https://training.galaxyproject.org//topics/microbiome/tutorials/metagenomics-binning/tutorial.html - urls: - hands_on: https://training.galaxyproject.org/training-material/api/topics/microbiome/tutorials/metagenomics-binning/tutorial.json - slides: https://training.galaxyproject.org/training-material/api/topics/microbiome/tutorials/metagenomics-binning/tutorial.json - version: 9 - video: true - video_versions: 2 - video_view: 0 - visit_duration: 320 - visitors: 7203 - workflows: - - creators: - - class: Person - identifier: https://orcid.org/0000-0003-2982-388X - name: Paul Zierep - description: Binning workflows that uses abundance information and performs binning - of metagenomic contigs using 4 different binners as well as bin refinement. - features: - comments: true - parameters: true - report: - markdown: ' - - # Workflow Execution Report - - - ## Workflow Inputs - - ```galaxy - - invocation_inputs() - - ``` - - - ## Workflow Outputs - - ```galaxy - - invocation_outputs() - - ``` - - - ## Workflow - - ```galaxy - - workflow_display() - - ``` - - ' - subworkflows: false - graph_dot: "digraph main {\n node [fontname=\"Atkinson Hyperlegible\", shape=box,\ - \ color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n edge [fontname=\"\ - Atkinson Hyperlegible\"];\n 0[color=lightblue,label=\"\u2139\uFE0F Input Collection\\\ - nTrimmed reads\"]\n 1[color=lightgreen,label=\"\u2139\uFE0F Input Parameter\\\ - nRead length CONCOCT\"]\n 2[color=lightblue,label=\"\u2139\uFE0F Input Collection\\\ - nAssemblies\"]\n 3[color=lightgreen,label=\"\u2139\uFE0F Input Parameter\\\ - nEnvironment for the built-in model SemiBin\"]\n 4[label=\"CONCOCT: Cut up\ - \ contigs\"]\n 2 -> 4 [label=\"output\"]\n 5[label=\"Bowtie2\"]\n 0 -> 5\ - \ [label=\"output\"]\n 2 -> 5 [label=\"output\"]\n 6[label=\"Samtools sort\"\ - ]\n 5 -> 6 [label=\"output\"]\n 7[label=\"CONCOCT: Generate the input coverage\ - \ table\"]\n 4 -> 7 [label=\"output_bed\"]\n 6 -> 7 [label=\"output1\"]\n\ - \ 8[label=\"Calculate contig depths\"]\n 6 -> 8 [label=\"output1\"]\n 9[label=\"\ - SemiBin\"]\n 3 -> 9 [label=\"output\"]\n 6 -> 9 [label=\"output1\"]\n 2 ->\ - \ 9 [label=\"output\"]\n 10[label=\"CONCOCT\"]\n 1 -> 10 [label=\"output\"\ - ]\n 4 -> 10 [label=\"output_fasta\"]\n 7 -> 10 [label=\"output\"]\n 11[label=\"\ - MetaBAT2\"]\n 8 -> 11 [label=\"outputDepth\"]\n 2 -> 11 [label=\"output\"\ - ]\n 12[label=\"MaxBin2\"]\n 8 -> 12 [label=\"outputDepth\"]\n 2 -> 12 [label=\"\ - output\"]\n 13[label=\"Converts genome bins in fasta format\"]\n 9 -> 13 [label=\"\ - output_bins\"]\n 14[label=\"CONCOCT: Merge cut clusters\"]\n 10 -> 14 [label=\"\ - output_clustering\"]\n 15[label=\"Converts genome bins in fasta format\"]\n\ - \ 11 -> 15 [label=\"bins\"]\n 16[label=\"Converts genome bins in fasta format\"\ - ]\n 12 -> 16 [label=\"bins\"]\n 17[label=\"CONCOCT: Extract a fasta file\"\ - ]\n 14 -> 17 [label=\"output\"]\n 2 -> 17 [label=\"output\"]\n 18[label=\"\ - Converts genome bins in fasta format\"]\n 17 -> 18 [label=\"bins\"]\n 19[label=\"\ - Build list\"]\n 18 -> 19 [label=\"contigs2bin\"]\n 15 -> 19 [label=\"contigs2bin\"\ - ]\n 16 -> 19 [label=\"contigs2bin\"]\n 13 -> 19 [label=\"contigs2bin\"]\n\ - \ 20[label=\"Binette\"]\n 19 -> 20 [label=\"output\"]\n 2 -> 20 [label=\"\ - output\"]\n}" - history: - - hash: e2a9e0b193454e35cf49665231c615fd667ecbfd - message: add wf tags - num: 2 - short_hash: e2a9e0b19 - unix: '1763726007' - - hash: 8d7de5c673e409858ef5c9ca5b7d05c2b0cc63bf - message: add combine, add workflow, add wf test, add result question - num: 1 - short_hash: 8d7de5c67 - unix: '1763725573' - inputs: - - annotation: Samples grouped for co-assembly. For individual assembly use same - reads as `Trimmed reads input`. The tool fastq_groupmerge can be used to perform - the grouping. - content_id: null - errors: null - id: 0 - input_connections: {} - inputs: - - description: Samples grouped for co-assembly. For individual assembly use - same reads as `Trimmed reads input`. The tool fastq_groupmerge can be used - to perform the grouping. - name: Trimmed reads - label: Trimmed reads - name: Input dataset collection - outputs: [] - position: - left: 0 - top: 896.6187286877193 - tool_id: null - tool_state: '{"optional": false, "tag": null, "collection_type": "list:paired", - "fields": null}' - tool_version: null - type: data_collection_input - uuid: dd8faa6e-3f29-4fa2-befb-38ef4a7832b5 - when: null - workflow_outputs: [] - - annotation: CONCOCT requires the read length for coverage. Best use fastQC to - estimate the mean value. - content_id: null - errors: null - id: 1 - input_connections: {} - inputs: - - description: CONCOCT requires the read length for coverage. Best use fastQC - to estimate the mean value. - name: Read length (CONCOCT) - label: Read length (CONCOCT) - name: Input parameter - outputs: [] - position: - left: 1097.0837390044621 - top: 41.539782924321685 - tool_id: null - tool_state: '{"default": 100, "validators": [{"min": null, "max": null, "negate": - false, "type": "in_range"}], "parameter_type": "integer", "optional": false}' - tool_version: null - type: parameter_input - uuid: 30109f1d-816b-4f85-a0b3-e54506ae32ae - when: null - workflow_outputs: [] - - annotation: 'This workflow allows using a custom assembly as input. If provided, - select `custom assembly` as Assembler. - - Provide one assembly for each group of trimmed input reads.' - content_id: null - errors: null - id: 2 - input_connections: {} - inputs: - - description: 'This workflow allows using a custom assembly as input. If provided, - select `custom assembly` as Assembler. - - Provide one assembly for each group of trimmed input reads.' - name: Assemblies - label: Assemblies - name: Input dataset collection - outputs: [] - position: - left: 248.96247766826204 - top: 1670.8582741820105 - tool_id: null - tool_state: '{"optional": false, "tag": null, "collection_type": "list", "fields": - null}' - tool_version: null - type: data_collection_input - uuid: e2f5ad16-674f-4687-94a4-a5e55680440a - when: null - workflow_outputs: [] - - annotation: 'Environment for the built-in model (SemiBin), options are: human_gut, - dog_gut, ocean, soil, cat_gut, human_oral, mouse_gut, pig_gut, built_environment, - wastewater, chicken_caecum, global' - content_id: null - errors: null - id: 3 - input_connections: {} - inputs: - - description: 'Environment for the built-in model (SemiBin), options are: human_gut, - dog_gut, ocean, soil, cat_gut, human_oral, mouse_gut, pig_gut, built_environment, - wastewater, chicken_caecum, global' - name: Environment for the built-in model (SemiBin) - label: Environment for the built-in model (SemiBin) - name: Input parameter - outputs: [] - position: - left: 1139.1165875728577 - top: 2094.707949827118 - tool_id: null - tool_state: '{"default": "global", "multiple": false, "validators": [], "restrictions": - ["global", "human_gut", "dog_gut", "ocean", "soil", "cat_gut", "human_oral", - "mouse_gut", "pig_gut", "built_environment", "wastewater", "chicken_caecum"], - "parameter_type": "text", "optional": false}' - tool_version: null - type: parameter_input - uuid: 86fc3246-f756-49ce-b196-ffa358e5ac41 - when: null - workflow_outputs: [] - license: MIT - mermaid: "flowchart TD\n 0[\"\u2139\uFE0F Input Collection\\nTrimmed reads\"\ - ];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"\u2139\uFE0F Input Parameter\\\ - nRead length CONCOCT\"];\n style 1 fill:#ded,stroke:#393,stroke-width:4px;\n\ - \ 2[\"\u2139\uFE0F Input Collection\\nAssemblies\"];\n style 2 stroke:#2c3143,stroke-width:4px;\n\ - \ 3[\"\u2139\uFE0F Input Parameter\\nEnvironment for the built-in model SemiBin\"\ - ];\n style 3 fill:#ded,stroke:#393,stroke-width:4px;\n 4[\"CONCOCT: Cut up\ - \ contigs\"];\n 2 -->|output| 4;\n 5[\"Bowtie2\"];\n 0 -->|output| 5;\n \ - \ 2 -->|output| 5;\n 6[\"Samtools sort\"];\n 5 -->|output| 6;\n 7[\"CONCOCT:\ - \ Generate the input coverage table\"];\n 4 -->|output_bed| 7;\n 6 -->|output1|\ - \ 7;\n 8[\"Calculate contig depths\"];\n 6 -->|output1| 8;\n 9[\"SemiBin\"\ - ];\n 3 -->|output| 9;\n 6 -->|output1| 9;\n 2 -->|output| 9;\n 10[\"CONCOCT\"\ - ];\n 1 -->|output| 10;\n 4 -->|output_fasta| 10;\n 7 -->|output| 10;\n 11[\"\ - MetaBAT2\"];\n 8 -->|outputDepth| 11;\n 2 -->|output| 11;\n 12[\"MaxBin2\"\ - ];\n 8 -->|outputDepth| 12;\n 2 -->|output| 12;\n 13[\"Converts genome bins\ - \ in fasta format\"];\n 9 -->|output_bins| 13;\n 14[\"CONCOCT: Merge cut clusters\"\ - ];\n 10 -->|output_clustering| 14;\n 15[\"Converts genome bins in fasta format\"\ - ];\n 11 -->|bins| 15;\n 16[\"Converts genome bins in fasta format\"];\n 12\ - 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- affiliations: - - uni-freiburg - - elixir-europe - - deNBI - - mwk - elixir_node: de - email: mina.ansari82@gmail.com - id: minamehr - joined: 2024-03 - matrix: mina24:matrix.org - name: Mina Hojat Ansari - orcid: 0000-0002-3602-7884 - page: https://training.galaxyproject.org/training-material/hall-of-fame/minamehr/ - url: https://training.galaxyproject.org/training-material/api/contributors/minamehr.json - - affiliations: - - gallantries - - ifb - - elixir-europe - contact_for_training: true - elixir_node: fr - email: berenice.batut@gmail.com - fediverse: https://piaille.fr/@bebatut - fediverse_flavor: mastodon - former_affiliations: - - uni-freiburg - - deNBI - id: bebatut - joined: 2017-09 - linkedin: berenicebatut - location: - country: FR - lat: 45.77 - lon: 3.08 - matrix: bebatut:matrix.org - name: "B\xE9r\xE9nice Batut" - orcid: 0000-0001-9852-1987 - page: https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/ - twitter: bebatut - url: https://training.galaxyproject.org/training-material/api/contributors/bebatut.json - - affiliations: - - unimelb - - melbournebioinformatics - id: vinisalazar - joined: 2025-10 - name: Vini Salazar - orcid: 0000-0002-8362-3195 - page: https://training.galaxyproject.org/training-material/hall-of-fame/vinisalazar/ - url: https://training.galaxyproject.org/training-material/api/contributors/vinisalazar.json - - affiliations: - - uni-freiburg - - elixir-europe - - deNBI - - mwk - - materialvitaldigital - email: zierep@informatik.uni-freiburg.de - id: paulzierep - joined: 2023-02 - name: Paul Zierep - orcid: 0000-0003-2982-388X - page: https://training.galaxyproject.org/training-material/hall-of-fame/paulzierep/ - url: https://training.galaxyproject.org/training-material/api/contributors/paulzierep.json - - affiliations: - - uni-freiburg - - nfdi4plants - - elixir-europe - bio: Researcher at Erasmus Medical Center - bluesky: shiltemann.bsky.social - contact_for_training: true - elixir_node: nl - email: saskia.hiltemann@gmail.com - fediverse: https://mstdn.science/@shiltemann - fediverse_flavor: mastodon - former_affiliations: - - CINECA-Project - - gallantries - - erasmusmc - id: shiltemann + - email: anton@nekrut.org + id: nekrut joined: 2017-09 - linkedin: shiltemann - location: - country: NL - lat: 51.912 - lon: 4.462 - maintainer_contact: gitter - matrix: shiltemann:matrix.org - name: Saskia Hiltemann - orcid: 0000-0003-3803-468X - page: https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/ - url: https://training.galaxyproject.org/training-material/api/contributors/shiltemann.json - - email: nwhitak5@jh.edu - id: natalie-wa - joined: 2024-08 - name: Natalie Whitaker-Allen - page: https://training.galaxyproject.org/training-material/hall-of-fame/natalie-wa/ - url: https://training.galaxyproject.org/training-material/api/contributors/natalie-wa.json - dir: topics/microbiome/tutorials/host-removal + name: Anton Nekrutenko + page: https://training.galaxyproject.org/training-material/hall-of-fame/nekrut/ + url: https://training.galaxyproject.org/training-material/api/contributors/nekrut.json + dir: topics/genome-annotation/tutorials/gene-centric + edam_ontology: + - topic_0622 + - topic_0623 + - topic_0080 + - topic_0084 + - topic_0797 edam_operation: - - Validation - - Sequencing quality control - - Read mapping - edam_topic: [] + - De-novo assembly + - Sequence alignment analysis + - Multiple sequence alignment + - Database search + - Transcriptome assembly + - Phylogenetic tree generation + - Coding region prediction + edam_topic: + - Genomics + - Gene and protein families + - Sequence analysis + - Phylogeny + - Comparative genomics exact_supported_servers: - - Galaxy@AuBi - - UseGalaxy.org.au - - UseGalaxy.be - - UseGalaxy.cz - UseGalaxy.eu - - UseGalaxy.fr - UseGalaxy.org (Main) feedback_mean_note: null feedback_number: 0 hands_on: true - id: microbiome/host-removal + id: genome-annotation/gene-centric inexact_supported_servers: - - GalaxyTrakr - - MISSISSIPPI - - UseGalaxy.no + - UseGalaxy.cz js_requirements: mathjax: null mermaid: false key_points: - - Identifying and removing contaminant and host reads is a critical preprocessing - step in metagenomic workflows. - - Clean reads improve the accuracy of downstream assembly, binning, and taxonomic - profiling. + - You can locate gene of interest in unannotated genomes and compare its structure + across multiple species layout: tutorial_hands_on - level: Introductory license: CC-BY-4.0 - mod_date: '2026-05-12' + mod_date: '2025-06-03' objectives: - - Identify reads originating from contaminants or host genomes. - - Remove those reads to produce high-quality, clean metagenomic data suitable for - downstream analyses. - pageviews: 431 - pub_date: '2025-12-18' + - Provide a quick method for identifying genes of interest in unannotated or newly + assembled genomes + pageviews: 2869 + priority: 2 + pub_date: '2022-09-08' questions: - - What preprocessing steps are required to obtain cleaned reads for downstream analysis? - - How can we identify and remove contaminant or host-derived reads from raw sequencing - data? - recordings: - - bot-timestamp: 1778066484 - captioners: - - minamehr - date: '2026-05-06' - galaxy_version: 26.0.1.dev1 - length: 23M - speakers: - - minamehr - youtube_id: DNO3ZG-EOBo - short_id: T00568 + - I have several genomes assemblies that are not annotated (or I do not trust annotations) + - I am interested to compare structure of a particular gene across these genome + assemblies + - How do I do that? + requirements: + - topic_name: introduction + tutorials: + - galaxy-intro-101 + type: internal + - topic_name: galaxy-interface + tutorials: + - collections + type: internal + short_id: T00174 short_tools: - - bowtie2 - - __ZIP_COLLECTION__ - - multiqc - slides: false - slides_recordings: false - subtopic: metagenomics - supported_servers: - exact: - - name: Galaxy@AuBi - url: https://galaxy.mesocentre.uca.fr - usegalaxy: false - - name: UseGalaxy.org.au - url: https://usegalaxy.org.au - usegalaxy: true - - name: UseGalaxy.be - url: https://usegalaxy.be/ - usegalaxy: false - - name: UseGalaxy.cz - url: https://usegalaxy.cz/ - usegalaxy: false + - bg_diamond_view + - bg_diamond + - gops_intersect_1 + - cat1 + - Filter1 + - rapidnj + - regexColumn1 + - tab2fasta + - join1 + - collapse_dataset + - orfipy + - Add_a_column1 + - tp_split_on_column + - rbc_mafft + - bg_diamond_makedb + - Cut1 + slides: false + slides_recordings: false + supported_servers: + exact: - name: UseGalaxy.eu url: https://usegalaxy.eu usegalaxy: true - - name: UseGalaxy.fr - url: https://usegalaxy.fr/ - usegalaxy: true - name: UseGalaxy.org (Main) url: https://usegalaxy.org usegalaxy: true inexact: - - name: GalaxyTrakr - url: https://galaxytrakr.org/ - usegalaxy: false - - name: MISSISSIPPI - url: https://mississippi.sorbonne-universite.fr - usegalaxy: false - - name: UseGalaxy.no - url: https://usegalaxy.no/ + - name: UseGalaxy.cz + url: https://usegalaxy.cz/ usegalaxy: false supported_servers_matrix: servers: @@ -43013,9 +23969,6 @@ - name: IPK Galaxy Blast Suite url: https://galaxy-web.ipk-gatersleben.de usegalaxy: false - - name: Lebanese University Galaxy - url: http://galaxy.ul.edu.lb/ - usegalaxy: false - name: Mandoiu Lab url: https://neo.engr.uconn.edu/ usegalaxy: false @@ -43031,9 +23984,6 @@ - name: PepSimili url: http://pepsimili.e-nios.com:8080/ usegalaxy: false - - name: PhagePromotor - url: https://galaxy.bio.di.uminho.pt/ - usegalaxy: false - name: UseGalaxy.org.au url: https://usegalaxy.org.au usegalaxy: true @@ -43059,7 +24009,552 @@ url: https://viralvariant.anses.fr/ usegalaxy: false tools: - - id: __ZIP_COLLECTION__ + - id: Cut1 + servers: + - server: http://apostl.moffitt.org/ + state: local + - server: http://mbac.gmu.edu:8080/ + state: local + - server: https://vm-chemflow-francegrille.eu/ + state: missing + - server: https://iris.angers.inra.fr/galaxypub-cfbp + state: missing + - server: https://hyperbrowser.uio.no/coloc-stats + state: local + - server: https://galaxy.mesocentre.uca.fr + state: local + - server: https://galaxy.pasteur.fr/ + state: local + - server: https://galaxytrakr.org/ + state: local + - server: http://igg.cloud.ba.infn.it/galaxy + state: local + - 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- __ZIP_COLLECTION__ - - toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.5.3+galaxy1 - - toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.27+galaxy3 - topic_name: microbiome - topic_name_human: Microbiome + - Cut1 + - Filter1 + - cat1 + - join1 + - toolshed.g2.bx.psu.edu/repos/bgruening/diamond/bg_diamond/2.0.15+galaxy0 + - toolshed.g2.bx.psu.edu/repos/bgruening/diamond/bg_diamond_makedb/2.0.15+galaxy0 + - toolshed.g2.bx.psu.edu/repos/bgruening/diamond/bg_diamond_view/2.0.15+galaxy0 + - toolshed.g2.bx.psu.edu/repos/bgruening/split_file_on_column/tp_split_on_column/0.4 + - toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/1.6 + - toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.0 + - toolshed.g2.bx.psu.edu/repos/devteam/intersect/gops_intersect_1/1.0.0 + - toolshed.g2.bx.psu.edu/repos/devteam/tabular_to_fasta/tab2fasta/1.1.1 + - toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regexColumn1/1.0.1 + - toolshed.g2.bx.psu.edu/repos/iuc/orfipy/orfipy/0.0.4+galaxy0 + - toolshed.g2.bx.psu.edu/repos/iuc/rapidnj/rapidnj/2.3.2 + - toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0 + - toolshed.g2.bx.psu.edu/repos/rnateam/mafft/rbc_mafft/7.489+galaxy0 + topic_name: genome-annotation + topic_name_human: Genome Annotation tours: false translations: slides: [] tutorial: [] video: false - tutorial_name: host-removal + tutorial_name: gene-centric type: tutorial - url: https://training.galaxyproject.org//topics/microbiome/tutorials/host-removal/tutorial.html + url: https://training.galaxyproject.org//topics/genome-annotation/tutorials/gene-centric/tutorial.html urls: - hands_on: https://training.galaxyproject.org/training-material/api/topics/microbiome/tutorials/host-removal/tutorial.json - slides: https://training.galaxyproject.org/training-material/api/topics/microbiome/tutorials/host-removal/tutorial.json - version: 3 - video: true - video_versions: 1 + hands_on: https://training.galaxyproject.org/training-material/api/topics/genome-annotation/tutorials/gene-centric/tutorial.json + slides: https://training.galaxyproject.org/training-material/api/topics/genome-annotation/tutorials/gene-centric/tutorial.json + version: 10 + video: false + video_versions: 0 video_view: 0 - visit_duration: 370 - visitors: 355 + visit_duration: 597 + visitors: 2094 workflows: - creators: - class: Person - identifier: 0000-0003-2982-388X - name: Paul Zierep - description: '' + identifier: 0000-0002-5987-8032 + name: Anton Nekrutenko + description: Workflows for comparison of genes in annotated genomes features: comments: false - parameters: true - report: - markdown: ' - - # Workflow Execution Report - - - ## Workflow Inputs - - ```galaxy - - invocation_inputs() - - ``` - - - ## Workflow Outputs - - ```galaxy - - invocation_outputs() - - ``` - - - ## Workflow - - ```galaxy - - workflow_display() - - ``` - - ' + parameters: false + report: null subworkflows: false graph_dot: "digraph main {\n node [fontname=\"Atkinson Hyperlegible\", shape=box,\ \ color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n edge [fontname=\"\ - Atkinson Hyperlegible\"];\n 0[color=lightblue,label=\"\u2139\uFE0F Input Collection\\\ - nInput paired fastq \"]\n 1[color=lightgreen,label=\"\u2139\uFE0F Input Parameter\\\ - nReference Genome Build In\"]\n 2[label=\"Bowtie2\"]\n 0 -> 2 [label=\"output\"\ - ]\n 1 -> 2 [label=\"output\"]\n 3[label=\"Zip collections\"]\n 2 -> 3 [label=\"\ - output_unaligned_reads_l\"]\n 2 -> 3 [label=\"output_unaligned_reads_r\"]\n\ - \ 4[label=\"MultiQC\"]\n 2 -> 4 [label=\"mapping_stats\"]\n}" + Atkinson Hyperlegible\"];\n 0[color=lightblue,label=\"\u2139\uFE0F Input Dataset\\\ + nExons\"]\n 1[color=lightblue,label=\"\u2139\uFE0F Input Collection\\nDiamond\ + \ makedb\"]\n 2[color=lightblue,label=\"\u2139\uFE0F Input Collection\\nORFipy\ + \ BED\"]\n 3[label=\"Diamond: Find hits in ORFs\"]\n 0 -> 3 [label=\"output\"\ + ]\n 1 -> 3 [label=\"output\"]\n 4[label=\"Column Regex Find And Replace\"\ + ]\n 2 -> 4 [label=\"output\"]\n 5[label=\"Alignments\"]\n 3 -> 5 [label=\"\ + daa_output\"]\n 6[label=\"Cut\"]\n 4 -> 6 [label=\"out_file1\"]\n 7[label=\"\ + Alignments + BED\"]\n 6 -> 7 [label=\"out_file1\"]\n 5 -> 7 [label=\"blast_tabular\"\ + ]\n 8[label=\"Cut\"]\n 7 -> 8 [label=\"out_file1\"]\n 9[label=\"Collapse\ + \ Collection\"]\n 7 -> 9 [label=\"out_file1\"]\n 10[label=\"Intersect\"]\n\ + \ 6 -> 10 [label=\"out_file1\"]\n 8 -> 10 [label=\"out_file1\"]\n 11[label=\"\ + Filter\"]\n 9 -> 11 [label=\"output\"]\n 12[label=\"Overlapping ORFs\"]\n\ + \ 10 -> 12 [label=\"output\"]\n 13[label=\"Cut\"]\n 11 -> 13 [label=\"out_file1\"\ + ]\n 14[label=\"Compute\"]\n 12 -> 14 [label=\"output\"]\n 15[label=\"Compute\"\ + ]\n 13 -> 15 [label=\"out_file1\"]\n 16[label=\"Split file\"]\n 15 -> 16\ + \ [label=\"out_file1\"]\n 17[label=\"Report\"]\n 15 -> 17 [label=\"out_file1\"\ + ]\n 18[label=\"Tabular-to-FASTA\"]\n 16 -> 18 [label=\"split_output\"]\n \ + \ 19[label=\"Cut\"]\n 17 -> 19 [label=\"out_file1\"]\n 20[label=\"MAFFT\"\ + ]\n 18 -> 20 [label=\"output\"]\n 21[label=\"Filter: Plus strand matches\"\ + ]\n 19 -> 21 [label=\"out_file1\"]\n 22[label=\"Filter: Minus strand matches\"\ + ]\n 19 -> 22 [label=\"out_file1\"]\n 23[label=\"Join neighbors\"]\n 20 ->\ + \ 23 [label=\"outputAlignment\"]\n k54ea37cc63d1422a9f5e124b8d39e6bd[color=lightseagreen,label=\"\ + Output\\nJoin neighbors on input dataset(s): Calculated distances\"]\n 23 ->\ + \ k54ea37cc63d1422a9f5e124b8d39e6bd\n 24[label=\"Compute\"]\n 21 -> 24 [label=\"\ + out_file1\"]\n 25[label=\"Compute\"]\n 22 -> 25 [label=\"out_file1\"]\n 26[label=\"\ + Concatenate datasets\"]\n 24 -> 26 [label=\"out_file1\"]\n 25 -> 26 [label=\"\ + out_file1\"]\n 27[label=\"Compute\"]\n 26 -> 27 [label=\"out_file1\"]\n 28[label=\"\ + Cut\"]\n 27 -> 28 [label=\"out_file1\"]\n 29[label=\"Compute\"]\n 28 -> 29\ + \ [label=\"out_file1\"]\n 30[label=\"Join two Datasets\"]\n 14 -> 30 [label=\"\ + out_file1\"]\n 29 -> 30 [label=\"out_file1\"]\n 31[label=\"Mapping report\"\ + ]\n 30 -> 31 [label=\"out_file1\"]\n}" history: - - hash: 4920ecd42496f439fa65591cc788ef1080fdd8cc - message: 'Add new tutorial: host removal and update contributor info' + - hash: 476d3d57ff2b0ce249879b60aa03500ab62685d6 + message: workflow update num: 1 - short_hash: 4920ecd42 - unix: '1759837405' + short_hash: 476d3d57f + unix: '1662055154' inputs: - - annotation: '' + - annotation: Amino acid sequences of CDS exons from the gene of interest content_id: null errors: null id: 0 input_connections: {} inputs: - - description: '' - name: 'Input paired fastq ' - label: 'Input paired fastq ' + - description: Amino acid sequences of CDS exons from the gene of interest + name: Exons + label: Exons + name: Input dataset + outputs: [] + position: + left: 1.90625 + top: 74.21875 + tool_id: null + tool_state: '{"optional": false, "format": ["fasta"], "tag": ""}' + tool_version: null + type: data_input + uuid: 107c06e7-51a6-41a1-a026-45a9dddf29a9 + workflow_outputs: [] + - annotation: Diamond DB created from ORF predicted from genomes used in the analysis + content_id: null + errors: null + id: 1 + input_connections: {} + inputs: + - description: Diamond DB created from ORF predicted from genomes used in the + analysis + name: Diamond makedb + label: Diamond makedb name: Input dataset collection outputs: [] position: - left: 10 - top: 50 + left: 0.0 + top: 185.71875 tool_id: null - tool_state: '{"optional": false, "tag": null, "collection_type": "list:paired", - "fields": null}' + tool_state: '{"optional": false, "tag": "", "collection_type": "list"}' tool_version: null type: data_collection_input - uuid: 13e4060f-f337-4f44-824f-ee85235fcc8e - when: null + uuid: 0acc2c20-91fb-4470-80ac-2eeb7e2f32ae workflow_outputs: [] - - annotation: '' + - annotation: BED dataset containing information about ORFs predicted in genomes + of interest content_id: null errors: null - id: 1 + id: 2 input_connections: {} inputs: - - description: '' - name: Reference Genome Build In - label: Reference Genome Build In - name: Input parameter + - description: BED dataset containing information about ORFs predicted in genomes + of interest + name: ORFipy BED + label: ORFipy BED + name: Input dataset collection outputs: [] position: - left: 0 - top: 240 + left: 1.90625 + top: 313.203125 tool_id: null - tool_state: '{"multiple": false, "validators": [], "restrictOnConnections": - true, "parameter_type": "text", "optional": false}' + tool_state: '{"optional": false, "format": ["bed"], "tag": "", "collection_type": + "list"}' tool_version: null - type: parameter_input - uuid: 47ad0b2d-0d31-4260-82df-8fed2da6b150 - when: null + type: data_collection_input + uuid: 329b3c07-f0ee-4882-abf7-1215062a0fec workflow_outputs: [] - license: MIT - mermaid: "flowchart TD\n 0[\"\u2139\uFE0F Input Collection\\nInput paired fastq\ - \ \"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"\u2139\uFE0F Input\ - \ Parameter\\nReference Genome Build In\"];\n style 1 fill:#ded,stroke:#393,stroke-width:4px;\n\ - \ 2[\"Bowtie2\"];\n 0 -->|output| 2;\n 1 -->|output| 2;\n 3[\"Zip collections\"\ - ];\n 2 -->|output_unaligned_reads_l| 3;\n 2 -->|output_unaligned_reads_r|\ - \ 3;\n 4[\"MultiQC\"];\n 2 -->|mapping_stats| 4;" - modified: 2026-05-21 00:30:25 +0000 - name: Host contamination removal - outputs: [] - parent_id: microbiome/host-removal - path: topics/microbiome/tutorials/host-removal/workflows/main_workflow.ga + license: null + mermaid: "flowchart TD\n 0[\"\u2139\uFE0F Input Dataset\\nExons\"];\n style\ + \ 0 stroke:#2c3143,stroke-width:4px;\n 1[\"\u2139\uFE0F Input Collection\\\ + nDiamond makedb\"];\n style 1 stroke:#2c3143,stroke-width:4px;\n 2[\"\u2139\ + \uFE0F Input Collection\\nORFipy BED\"];\n style 2 stroke:#2c3143,stroke-width:4px;\n\ + \ 3[\"Diamond: Find hits in ORFs\"];\n 0 -->|output| 3;\n 1 -->|output| 3;\n\ + \ 4[\"Column Regex Find And Replace\"];\n 2 -->|output| 4;\n 5[\"Alignments\"\ + ];\n 3 -->|daa_output| 5;\n 6[\"Cut\"];\n 4 -->|out_file1| 6;\n 7[\"Alignments\ + \ + BED\"];\n 6 -->|out_file1| 7;\n 5 -->|blast_tabular| 7;\n 8[\"Cut\"];\n\ + \ 7 -->|out_file1| 8;\n 9[\"Collapse Collection\"];\n 7 -->|out_file1| 9;\n\ + \ 10[\"Intersect\"];\n 6 -->|out_file1| 10;\n 8 -->|out_file1| 10;\n 11[\"\ + Filter\"];\n 9 -->|output| 11;\n 12[\"Overlapping ORFs\"];\n 10 -->|output|\ + \ 12;\n 13[\"Cut\"];\n 11 -->|out_file1| 13;\n 14[\"Compute\"];\n 12 -->|output|\ + \ 14;\n 15[\"Compute\"];\n 13 -->|out_file1| 15;\n 16[\"Split file\"];\n\ + \ 15 -->|out_file1| 16;\n 17[\"Report\"];\n 15 -->|out_file1| 17;\n 18[\"\ + Tabular-to-FASTA\"];\n 16 -->|split_output| 18;\n 19[\"Cut\"];\n 17 -->|out_file1|\ + \ 19;\n 20[\"MAFFT\"];\n 18 -->|output| 20;\n 21[\"Filter: Plus strand matches\"\ + ];\n 19 -->|out_file1| 21;\n 22[\"Filter: Minus strand matches\"];\n 19 -->|out_file1|\ + \ 22;\n 23[\"Join neighbors\"];\n 20 -->|outputAlignment| 23;\n 54ea37cc-63d1-422a-9f5e-124b8d39e6bd[\"\ + Output\\nJoin neighbors on input dataset(s): Calculated distances\"];\n 23\ + \ --> 54ea37cc-63d1-422a-9f5e-124b8d39e6bd;\n style 54ea37cc-63d1-422a-9f5e-124b8d39e6bd\ + \ stroke:#2c3143,stroke-width:4px;\n 24[\"Compute\"];\n 21 -->|out_file1|\ + \ 24;\n 25[\"Compute\"];\n 22 -->|out_file1| 25;\n 26[\"Concatenate datasets\"\ + ];\n 24 -->|out_file1| 26;\n 25 -->|out_file1| 26;\n 27[\"Compute\"];\n \ + \ 26 -->|out_file1| 27;\n 28[\"Cut\"];\n 27 -->|out_file1| 28;\n 29[\"Compute\"\ + ];\n 28 -->|out_file1| 29;\n 30[\"Join two Datasets\"];\n 14 -->|out_file1|\ + \ 30;\n 29 -->|out_file1| 30;\n 31[\"Mapping report\"];\n 30 -->|out_file1|\ + \ 31;" + modified: 2026-07-01 00:31:39 +0000 + name: Comparative gene analysis + outputs: + - annotation: Compute NJ phylogenetic trees + content_id: toolshed.g2.bx.psu.edu/repos/iuc/rapidnj/rapidnj/2.3.2 + errors: null + id: 23 + input_connections: + alignments: + id: 20 + output_name: outputAlignment + inputs: [] + label: null + name: Join neighbors + outputs: + - name: distances + type: nhx + position: + left: 2200.03125 + top: 0 + post_job_actions: + TagDatasetActiondistances: + action_arguments: + tags: Trees + action_type: TagDatasetAction + output_name: distances + tool_id: toolshed.g2.bx.psu.edu/repos/iuc/rapidnj/rapidnj/2.3.2 + tool_shed_repository: + changeset_revision: 9f4a66e22580 + name: rapidnj + owner: iuc + tool_shed: toolshed.g2.bx.psu.edu + tool_state: '{"__job_resource": {"__job_resource__select": "no", "__current_case__": + 0}, "alignment_type": "p", "alignments": {"__class__": "ConnectedValue"}, + "bootstrap": null, "evolution_model": "kim", "no_negative_length": "false", + "output_format": "t", "__page__": null, "__rerun_remap_job_id__": null}' + tool_version: 2.3.2 + type: tool + uuid: a9f1ebbf-4a88-4ddb-aec7-6a1c3a3921db + workflow_outputs: + - label: 'Join neighbors on input dataset(s): Calculated distances' + output_name: distances + uuid: 54ea37cc-63d1-422a-9f5e-124b8d39e6bd + - annotation: '' + content_id: Cut1 + errors: null + id: 31 + input_connections: + input: + id: 30 + output_name: out_file1 + inputs: [] + label: Mapping report + name: Cut + outputs: + - name: out_file1 + type: tabular + position: + left: 3450.75 + top: 1309.90625 + post_job_actions: + RenameDatasetActionout_file1: + action_arguments: + newname: Mapping report + action_type: RenameDatasetAction + output_name: out_file1 + TagDatasetActionout_file1: + action_arguments: + tags: PlottingData + action_type: TagDatasetAction + output_name: out_file1 + tool_id: Cut1 + tool_state: '{"columnList": "c1,c2,c3,c4,c5,c6,c7,c11,c12,c13,c14,c15", "delimiter": + "T", "input": {"__class__": "ConnectedValue"}, "__page__": null, "__rerun_remap_job_id__": + null}' + tool_version: 1.0.2 + type: tool + uuid: 341c7257-c027-421b-afc1-a8dc11d2f6cd + workflow_outputs: + - label: null + output_name: out_file1 + uuid: bb199f1a-1402-4f00-9a02-e5743a8662b6 + parent_id: genome-annotation/gene-centric + path: topics/genome-annotation/tutorials/gene-centric/workflows/Comparative-gene-analysis.ga tags: - - name:FAIRyMAGs + - vgp + - genome-annotation test_results: null - tests: true - title: Host contamination removal - topic_id: microbiome - trs_endpoint: https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/microbiome-host-removal/versions/main-workflow - tutorial_id: host-removal - url: https://training.galaxyproject.org/training-material/topics/microbiome/tutorials/host-removal/workflows/main_workflow.ga - url_html: https://training.galaxyproject.org/training-material/topics/microbiome/tutorials/host-removal/workflows/main_workflow.html + tests: false + title: Comparative gene analysis + topic_id: genome-annotation + trs_endpoint: https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/genome-annotation-gene-centric/versions/comparative-gene-analysis + tutorial_id: gene-centric + url: https://training.galaxyproject.org/training-material/topics/genome-annotation/tutorials/gene-centric/workflows/Comparative-gene-analysis.ga + url_html: https://training.galaxyproject.org/training-material/topics/genome-annotation/tutorials/gene-centric/workflows/Comparative-gene-analysis.html version: 1 - wfid: microbiome-host-removal - wfname: main-workflow - workflow: main_workflow.ga + wfid: genome-annotation-gene-centric + wfname: comparative-gene-analysis + workflow: Comparative-gene-analysis.ga workflow_tools: - - __ZIP_COLLECTION__ - - toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.5.3+galaxy1 - - toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.27+galaxy3 - workflowhub_id: '2042' - zenodo_link: https://zenodo.org/records/17829290 + - Cut1 + - Filter1 + - cat1 + - join1 + - toolshed.g2.bx.psu.edu/repos/bgruening/diamond/bg_diamond/2.0.15+galaxy0 + - toolshed.g2.bx.psu.edu/repos/bgruening/diamond/bg_diamond_view/2.0.15+galaxy0 + - toolshed.g2.bx.psu.edu/repos/bgruening/split_file_on_column/tp_split_on_column/0.4 + - toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/1.6 + - toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.0 + - toolshed.g2.bx.psu.edu/repos/devteam/intersect/gops_intersect_1/1.0.0 + - toolshed.g2.bx.psu.edu/repos/devteam/tabular_to_fasta/tab2fasta/1.1.1 + - toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regexColumn1/1.0.1 + - toolshed.g2.bx.psu.edu/repos/iuc/rapidnj/rapidnj/2.3.2 + - toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0 + - toolshed.g2.bx.psu.edu/repos/rnateam/mafft/rbc_mafft/7.489+galaxy0 + workflowhub_id: '1518' + zenodo_link: https://zenodo.org/record/7034885 - admin_install: install_repository_dependencies: true install_resolver_dependencies: true install_tool_dependencies: true tools: - - name: combine_metaphlan2_humann2 - owner: bebatut - revisions: 662a334004b4 - tool_panel_section_label: Metagenomic Analysis + - name: deeptools_bam_coverage + owner: bgruening + revisions: bb1e4f63e0e6 + tool_panel_section_label: deepTools + tool_shed_url: https://toolshed.g2.bx.psu.edu/ + - name: find_subsequences + owner: bgruening + revisions: d882a0a75759 + tool_panel_section_label: Annotation tool_shed_url: https://toolshed.g2.bx.psu.edu/ - name: text_processing owner: bgruening - revisions: c41d78ae5fee + revisions: d698c222f354 tool_panel_section_label: Text Manipulation tool_shed_url: https://toolshed.g2.bx.psu.edu/ - 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\ owner: lparsons\n revisions: c0b2c2e39c9c\n tool_panel_section_label: FASTA/FASTQ\n\ - \ tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: sortmerna\n owner:\ - \ rnateam\n revisions: 10b84b577117\n tool_panel_section_label: Annotation\n\ - \ tool_shed_url: https://toolshed.g2.bx.psu.edu/\n" - api: https://training.galaxyproject.org/training-material/api/topics/microbiome/tutorials/metatranscriptomics/tutorial.json - contributions: - authorship: - - pratikdjagtap - - subinamehta - - jraysajulga - - bebatut - - emmaleith - - pravs3683 - - shiltemann - editing: - - paulzierep - - EngyNasr - - ogerdfx - reviewing: - - shiltemann - - bebatut - - hexylena - - paulzierep - - bgruening + revisions: 49370cb85f0f + tool_panel_section_label: FASTA/FASTQ + tool_shed_url: https://toolshed.g2.bx.psu.edu/ + admin_install_yaml: "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies:\ + \ true\ninstall_resolver_dependencies: true\ntools:\n- name: deeptools_bam_coverage\n\ + \ owner: bgruening\n revisions: bb1e4f63e0e6\n tool_panel_section_label: deepTools\n\ + \ tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: find_subsequences\n\ + \ owner: bgruening\n revisions: d882a0a75759\n tool_panel_section_label: Annotation\n\ + \ tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n \ + \ owner: bgruening\n revisions: d698c222f354\n tool_panel_section_label: Text\ + \ Manipulation\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n\ + \ owner: bgruening\n revisions: d698c222f354\n tool_panel_section_label: Text\ + \ Manipulation\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bowtie_wrappers\n\ + \ owner: devteam\n revisions: b46e7d48076a\n tool_panel_section_label: Mapping\n\ + \ tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: column_maker\n owner:\ + \ devteam\n revisions: be25c075ed54\n tool_panel_section_label: Text Manipulation\n\ + \ tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: gff_to_prot\n owner:\ + \ iuc\n revisions: 07d7991bf205\n tool_panel_section_label: Annotation\n tool_shed_url:\ + \ https://toolshed.g2.bx.psu.edu/\n- name: transit_gumbel\n owner: iuc\n revisions:\ + \ f50807720df1\n tool_panel_section_label: Annotation\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n\ + - name: cutadapt\n owner: lparsons\n revisions: 49370cb85f0f\n tool_panel_section_label:\ + \ FASTA/FASTQ\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n" + api: https://training.galaxyproject.org/training-material/api/topics/genome-annotation/tutorials/tnseq/tutorial.json contributors: - - email: pjagtap@umn.edu - id: pratikdjagtap - joined: 2017-09 - name: Pratik Jagtap - orcid: 0000-0003-0984-0973 - page: https://training.galaxyproject.org/training-material/hall-of-fame/pratikdjagtap/ - url: https://training.galaxyproject.org/training-material/api/contributors/pratikdjagtap.json - - email: subinamehta@gmail.com - id: subinamehta - joined: 2018-06 - linkedin: subinamehta - matrix: subinamehta:matrix.org - name: Subina Mehta - orcid: 0000-0001-9818-0537 - page: https://training.galaxyproject.org/training-material/hall-of-fame/subinamehta/ - twitter: Subina_Mehta - url: https://training.galaxyproject.org/training-material/api/contributors/subinamehta.json - - email: rsajulga@umn.edu - id: jraysajulga - joined: 2018-11 - name: Ray Sajulga - page: https://training.galaxyproject.org/training-material/hall-of-fame/jraysajulga/ - url: https://training.galaxyproject.org/training-material/api/contributors/jraysajulga.json - - affiliations: - - gallantries - - ifb - - elixir-europe - contact_for_training: true - elixir_node: fr - email: berenice.batut@gmail.com - fediverse: https://piaille.fr/@bebatut - fediverse_flavor: mastodon - former_affiliations: - - uni-freiburg - - deNBI - id: bebatut - joined: 2017-09 - linkedin: berenicebatut - location: - country: FR - lat: 45.77 - lon: 3.08 - matrix: bebatut:matrix.org - name: "B\xE9r\xE9nice Batut" - orcid: 0000-0001-9852-1987 - page: https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/ - twitter: bebatut - url: https://training.galaxyproject.org/training-material/api/contributors/bebatut.json - - email: leith023@umn.edu - id: emmaleith - joined: 2019-07 - name: Emma Leith - page: https://training.galaxyproject.org/training-material/hall-of-fame/emmaleith/ - url: https://training.galaxyproject.org/training-material/api/contributors/emmaleith.json - - email: kumar207@umn.edu - id: pravs3683 - joined: 2019-04 - name: Praveen Kumar - page: https://training.galaxyproject.org/training-material/hall-of-fame/pravs3683/ - url: https://training.galaxyproject.org/training-material/api/contributors/pravs3683.json - - affiliations: - - uni-freiburg - - nfdi4plants - - elixir-europe - bio: Researcher at Erasmus Medical Center - bluesky: shiltemann.bsky.social - contact_for_training: true - elixir_node: nl - email: saskia.hiltemann@gmail.com - fediverse: https://mstdn.science/@shiltemann - fediverse_flavor: mastodon - former_affiliations: - - CINECA-Project - - gallantries - - erasmusmc - id: shiltemann - joined: 2017-09 - linkedin: shiltemann - location: - country: NL - lat: 51.912 - lon: 4.462 - maintainer_contact: gitter - matrix: shiltemann:matrix.org - name: Saskia Hiltemann - orcid: 0000-0003-3803-468X - page: https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/ - url: https://training.galaxyproject.org/training-material/api/contributors/shiltemann.json - - affiliations: - - uni-freiburg - - elixir-europe - - deNBI - - mwk - - materialvitaldigital - email: zierep@informatik.uni-freiburg.de - id: paulzierep - joined: 2023-02 - name: Paul Zierep - orcid: 0000-0003-2982-388X - page: https://training.galaxyproject.org/training-material/hall-of-fame/paulzierep/ - url: https://training.galaxyproject.org/training-material/api/contributors/paulzierep.json - - affiliations: - - uni-freiburg - - elixir-europe - elixir_node: de - email: engynasr94@gmail.com - id: EngyNasr - joined: 2021-05 - matrix: EngyNasr:matrix.org - name: Engy Nasr - orcid: 0000-0001-9047-4215 - page: https://training.galaxyproject.org/training-material/hall-of-fame/EngyNasr/ - url: https://training.galaxyproject.org/training-material/api/contributors/EngyNasr.json - - elixir_node: fr - id: ogerdfx - joined: 2025-06 - name: Christine Oger - page: https://training.galaxyproject.org/training-material/hall-of-fame/ogerdfx/ - url: https://training.galaxyproject.org/training-material/api/contributors/ogerdfx.json - - affiliations: - - uni-freiburg - - nfdi4plants - - elixir-europe - bio: Researcher at Erasmus Medical Center - bluesky: shiltemann.bsky.social - contact_for_training: true - elixir_node: nl - email: saskia.hiltemann@gmail.com - fediverse: https://mstdn.science/@shiltemann - fediverse_flavor: mastodon - former_affiliations: - - CINECA-Project - - gallantries - - erasmusmc - id: shiltemann + - email: delphine.lariviere@galaxy.org + id: delphine-l joined: 2017-09 - linkedin: shiltemann - location: - country: NL - lat: 51.912 - lon: 4.462 - maintainer_contact: gitter - matrix: shiltemann:matrix.org - name: Saskia Hiltemann - orcid: 0000-0003-3803-468X - page: https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/ - url: https://training.galaxyproject.org/training-material/api/contributors/shiltemann.json + name: Delphine Lariviere + orcid: 0000-0001-6421-3484 + page: https://training.galaxyproject.org/training-material/hall-of-fame/delphine-l/ + url: https://training.galaxyproject.org/training-material/api/contributors/delphine-l.json - affiliations: - gallantries - ifb @@ -43772,211 +25491,89 @@ page: https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/ twitter: bebatut url: https://training.galaxyproject.org/training-material/api/contributors/bebatut.json - - affiliations: - - erasmusmc - - gallantries - - by-covid - - elixir-europe - - elixir-converge - contact_for_training: false - elixir_node: nl - former_affiliations: - - deNBI - - avans-atgm - - uni-freiburg - id: hexylena - joined: 2017-09 - location: - country: NL - lat: 51.91 - lon: 4.46 - maintainer_contact: gitter - matrix: hexylena:matrix.org - name: Helena Rasche - orcid: 0000-0001-9760-8992 - page: https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/ - url: https://training.galaxyproject.org/training-material/api/contributors/hexylena.json - - affiliations: - - uni-freiburg - - elixir-europe - - deNBI - - mwk - - materialvitaldigital - email: zierep@informatik.uni-freiburg.de - id: paulzierep - joined: 2023-02 - name: Paul Zierep - orcid: 0000-0003-2982-388X - page: https://training.galaxyproject.org/training-material/hall-of-fame/paulzierep/ - url: https://training.galaxyproject.org/training-material/api/contributors/paulzierep.json - - affiliations: - - deNBI - - mwk - - uni-freiburg - - elixir-europe - - materialvitaldigital - contact_for_training: true - elixir_node: de - email: bjoern.gruening@gmail.com - fediverse: https://fosstodon.org/@bgruening - fediverse_flavor: mastodon - former_affiliations: - - eurosciencegateway - - eosc-life - - by-covid - - crc992 - - elixir-converge - id: bgruening - joined: 2017-09 - linkedin: bgruening - location: - country: DE - lat: 47.997791 - lon: 7.842609 - matrix: bgruening:matrix.org - name: "Bj\xF6rn Gr\xFCning" - orcid: 0000-0002-3079-6586 - page: https://training.galaxyproject.org/training-material/hall-of-fame/bgruening/ - twitter: bjoerngruening - url: https://training.galaxyproject.org/training-material/api/contributors/bgruening.json - dir: topics/microbiome/tutorials/metatranscriptomics + dir: topics/genome-annotation/tutorials/tnseq edam_ontology: - - topic_3941 - - topic_3697 - - topic_0637 - - topic_1775 + - topic_0622 + - topic_3301 - topic_0080 + - topic_0798 edam_operation: - - Sequence alignment analysis - - Phylogenetic tree visualisation - - Statistical calculation + - Sequence trimming + - Transposon prediction - Primer removal - - Phylogenetic inference - - Visualisation - - Species frequency estimation - - Sequence composition calculation - - Sequence comparison - - Phylogenetic tree editing - - Phylogenetic analysis - - Taxonomic classification - - Conversion - - Validation - - Sequence similarity search - - Aggregation - Read pre-processing - - Sequence trimming - - Sequencing quality control edam_topic: - - Metatranscriptomics - - Microbial ecology - - Taxonomy - - Function analysis + - Genomics + - Microbiology - Sequence analysis + - Mobile genetic elements exact_supported_servers: + - UseGalaxy.org.au - UseGalaxy.be - - UseGalaxy.cz - - UseGalaxy.fr - - UseGalaxy.org (Main) + - UseGalaxy.no feedback_mean_note: null feedback_number: 0 hands_on: true - id: microbiome/metatranscriptomics + id: genome-annotation/tnseq inexact_supported_servers: + - UseGalaxy.cz - UseGalaxy.eu js_requirements: mathjax: null mermaid: false key_points: - - Metatranscriptomics data have the same QC profile that RNA-seq data - - A lot of metatranscriptomics sequences are identified as rRNA sequences - - With shotgun data, we can extract information about the studied community structure - and also the functions realised by the community - - Metatranscriptomics data analyses are complex and must be careful done, specially - when they are done without combination to metagenomics data analyses + - TnSeq is a useful analysis to detect essential genes and conditional essential + genes + - The saturation of the library must be sufficient so that every gene must have + been impacted at least once + - Be sure you have removed every transposon sequence before starting your analysis + - Verify the results manually do separate domain essential and essential genes layout: tutorial_hands_on - level: Introductory license: CC-BY-4.0 - mod_date: '2025-06-16' + mod_date: '2024-03-18' objectives: - - Choose the best approach to analyze metatranscriptomics data - - Understand the functional microbiome characterization using metatranscriptomic - results - - Understand where metatranscriptomics fits in 'multi-omic' analysis of microbiomes - - Visualise a community structure - pageviews: 9046054 - pub_date: '2019-11-21' + - Understand the read structure of TnSeq analyses + - Predict Essential genes with Transit + - Compare gene essentiality in control sample and an different experimental condition + pageviews: 9252504 + priority: 4 + pub_date: '2019-07-02' questions: - - How to analyze metatranscriptomics data? - - What information can be extracted of metatranscriptomics data? - - How to assign taxa and function to the identified sequences? - recordings: - - captioners: - - paulzierep - date: '2023-05-17' - galaxy_version: '23.01' - length: 1H5M - speakers: - - paulzierep - youtube_id: HNYop3vLpoM - - captioners: - - EngyNasr - - shiltemann - date: '2021-02-15' - galaxy_version: '21.01' - length: 1H30M - speakers: - - pratikdjagtap - - timothygriffin - - subinamehta - - shiltemann - youtube_id: EMaos5u1_a8 - redirect_from: - - /topics/metagenomics/tutorials/metatranscriptomics/tutorial - - /short/microbiome/metatranscriptomics - - /short/T00203 - - /short/T00388 - short_id: T00388 + - What is Transposon insertion Sequencing? + - 'How to get TA sites Coverage ? ' + - How to predict essential genes ? + short_id: T00179 short_tools: - - graphlan_annotate - - tp_find_and_replace - - graphlan - - multiqc - - bg_sortmerna - - tp_sort_header_tool - - export2graphlan + - gff_to_prot - cutadapt - - fastq_paired_end_interlacer - - Grouping1 - - fastqc - - combine_metaphlan_humann + - bowtie_wrapper + - tp_easyjoin_tool + - deeptools_bam_coverage + - Filter1 + - __EXTRACT_DATASET__ + - bg_find_subsequences + - Add_a_column1 + - transit_gumbel + - tp_sort_header_tool - Cut1 - - humann_renorm_table - - humann - - Grep1 - - taxonomy_krona_chart - - metaphlan - - humann_rename_table - - humann_regroup_table - - humann_unpack_pathways - - humann_split_stratified_table slides: true slides_recordings: false - subtopic: metatranscriptomics + subtopic: prokaryote supported_servers: exact: + - name: UseGalaxy.org.au + url: https://usegalaxy.org.au + usegalaxy: true - name: UseGalaxy.be url: https://usegalaxy.be/ usegalaxy: false + - name: UseGalaxy.no + url: https://usegalaxy.no/ + usegalaxy: false + inexact: - 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server: http://pepsimili.e-nios.com:8080/ state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - server: https://usegalaxy.org.au state: exact - version: 9.5+galaxy2 + version: 3.3.2.0.0 - server: https://usegalaxy.be/ state: exact - version: 9.5+galaxy2 + version: 3.3.2.0.0 - server: https://usegalaxy.cz/ - state: exact - version: 9.5+galaxy2 + state: inexact + versions: + - 3.5.4+galaxy0 + - 3.5.2+galaxy0 - server: https://usegalaxy.eu state: exact - version: 9.5+galaxy2 + version: 3.3.2.0.0 - server: https://usegalaxy.fr/ state: exact - version: 9.5+galaxy2 + version: 3.3.2.0.0 - server: https://usegalaxy.no/ - state: inexact - versions: - - 1.1.1 - - 1.1.0 + state: exact + version: 3.3.2.0.0 - server: https://usegalaxy.org state: exact - version: 9.5+galaxy2 + version: 3.3.2.0.0 - server: https://viralvariant.anses.fr/ state: missing - version: 9.5+galaxy2 - - id: toolshed.g2.bx.psu.edu/repos/crs4/taxonomy_krona_chart/taxonomy_krona_chart/2.7.1+galaxy0 + version: 3.3.2.0.0 + - id: toolshed.g2.bx.psu.edu/repos/bgruening/find_subsequences/bg_find_subsequences/0.2 servers: - server: http://apostl.moffitt.org/ state: missing @@ -44475,14 +25907,11 @@ - server: https://hyperbrowser.uio.no/coloc-stats state: missing - server: https://galaxy.mesocentre.uca.fr - state: exact - version: 2.7.1+galaxy0 + state: missing - server: https://galaxy.pasteur.fr/ - state: exact - version: 2.7.1+galaxy0 + state: missing - server: https://galaxytrakr.org/ - state: exact - version: 2.7.1+galaxy0 + state: missing - server: http://igg.cloud.ba.infn.it/galaxy state: missing - server: https://galaxy.hyphy.org/ @@ -44493,8 +25922,6 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr @@ -44504,36 +25931,31 @@ - server: https://palfinder.ls.manchester.ac.uk/ state: missing - server: http://pepsimili.e-nios.com:8080/ - state: exact - version: 2.7.1+galaxy0 - - server: https://galaxy.bio.di.uminho.pt/ state: missing - server: https://usegalaxy.org.au state: exact - version: 2.7.1+galaxy0 + version: '0.2' - server: https://usegalaxy.be/ state: exact - version: 2.7.1+galaxy0 + version: '0.2' - server: https://usegalaxy.cz/ state: exact - version: 2.7.1+galaxy0 + version: '0.2' - server: https://usegalaxy.eu state: exact - version: 2.7.1+galaxy0 + version: '0.2' - server: https://usegalaxy.fr/ - state: exact - version: 2.7.1+galaxy0 + state: missing - server: https://usegalaxy.no/ - state: inexact - versions: - - 2.7.1 + state: exact + version: '0.2' - server: https://usegalaxy.org state: exact - version: 2.7.1+galaxy0 + version: '0.2' - server: https://viralvariant.anses.fr/ state: missing - version: 2.7.1+galaxy0 - - id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_paired_end_interlacer/fastq_paired_end_interlacer/1.2.0.1+galaxy0 + version: '0.2' + - id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.2 servers: - server: http://apostl.moffitt.org/ state: missing @@ -44547,62 +25969,61 @@ state: missing - server: https://galaxy.mesocentre.uca.fr state: exact - version: 1.2.0.1+galaxy0 + version: 1.1.2 - server: https://galaxy.pasteur.fr/ - state: exact - version: 1.2.0.1+galaxy0 + state: missing - server: https://galaxytrakr.org/ state: exact - version: 1.2.0.1+galaxy0 + version: 1.1.2 - server: http://igg.cloud.ba.infn.it/galaxy state: missing - server: https://galaxy.hyphy.org/ - state: missing + state: inexact + versions: + - 9.5+galaxy3 - server: https://www.immportgalaxy.org/ state: missing - server: http://galaxy.interactomix.com/ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr - state: missing + state: inexact + versions: + - 9.5+galaxy3 - server: http://galaxy.inf.ethz.ch state: missing - server: https://palfinder.ls.manchester.ac.uk/ state: missing - 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server: http://apostl.moffitt.org/ state: missing @@ -44615,79 +26036,62 @@ - server: https://hyperbrowser.uio.no/coloc-stats state: missing - server: https://galaxy.mesocentre.uca.fr - state: inexact - versions: - - '0.72' - - 0.73+galaxy0 - - 0.72+galaxy1 + state: exact + version: 1.1.1 - server: https://galaxy.pasteur.fr/ - state: inexact - versions: - - 0.74+galaxy0 + state: missing - server: https://galaxytrakr.org/ state: exact - version: 0.74+galaxy1 + version: 1.1.1 - server: http://igg.cloud.ba.infn.it/galaxy state: missing - server: https://galaxy.hyphy.org/ - state: missing + state: inexact + versions: + - 9.5+galaxy3 - server: https://www.immportgalaxy.org/ state: missing - server: http://galaxy.interactomix.com/ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr - state: exact - version: 0.74+galaxy1 + state: inexact + versions: + - 9.5+galaxy3 - server: http://galaxy.inf.ethz.ch state: missing - server: https://palfinder.ls.manchester.ac.uk/ - state: inexact - versions: - - '0.72' - - 0.72+galaxy1 - - '0.71' - - '0.65' + state: missing - server: http://pepsimili.e-nios.com:8080/ - state: inexact - versions: - - 0.74+galaxy0 - - server: https://galaxy.bio.di.uminho.pt/ - state: inexact - versions: - - 0.74+galaxy0 + state: missing - server: https://usegalaxy.org.au state: exact - version: 0.74+galaxy1 + version: 1.1.1 - server: https://usegalaxy.be/ state: exact - version: 0.74+galaxy1 + version: 1.1.1 - server: https://usegalaxy.cz/ state: exact - version: 0.74+galaxy1 + version: 1.1.1 - server: https://usegalaxy.eu state: exact - version: 0.74+galaxy1 + version: 1.1.1 - server: https://usegalaxy.fr/ state: exact - version: 0.74+galaxy1 + version: 1.1.1 - server: https://usegalaxy.no/ - state: inexact - versions: - - 0.73+galaxy0 - - 0.72+galaxy1 + state: exact + version: 1.1.1 - server: https://usegalaxy.org state: exact - version: 0.74+galaxy1 + version: 1.1.1 - server: https://viralvariant.anses.fr/ state: missing - version: 0.74+galaxy1 - - id: toolshed.g2.bx.psu.edu/repos/iuc/export2graphlan/export2graphlan/0.20+galaxy0 + version: 1.1.1 + - id: toolshed.g2.bx.psu.edu/repos/devteam/bowtie_wrappers/bowtie_wrapper/1.2.0 servers: - server: http://apostl.moffitt.org/ state: missing @@ -44700,8 +26104,7 @@ - server: https://hyperbrowser.uio.no/coloc-stats state: missing - server: https://galaxy.mesocentre.uca.fr - state: exact - version: 0.20+galaxy0 + state: missing - server: https://galaxy.pasteur.fr/ state: missing - server: https://galaxytrakr.org/ @@ -44716,45 +26119,40 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr - state: missing + state: exact + version: 1.2.0 - server: http://galaxy.inf.ethz.ch state: missing - server: https://palfinder.ls.manchester.ac.uk/ state: missing - server: http://pepsimili.e-nios.com:8080/ state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - server: https://usegalaxy.org.au state: exact - version: 0.20+galaxy0 + version: 1.2.0 - server: https://usegalaxy.be/ state: exact - version: 0.20+galaxy0 + version: 1.2.0 - server: https://usegalaxy.cz/ state: exact - version: 0.20+galaxy0 + version: 1.2.0 - server: https://usegalaxy.eu state: exact - version: 0.20+galaxy0 + version: 1.2.0 - server: https://usegalaxy.fr/ - state: exact - version: 0.20+galaxy0 + state: missing - server: https://usegalaxy.no/ state: exact - version: 0.20+galaxy0 + version: 1.2.0 - server: https://usegalaxy.org - state: exact - version: 0.20+galaxy0 + state: missing - server: https://viralvariant.anses.fr/ state: missing - version: 0.20+galaxy0 - - id: toolshed.g2.bx.psu.edu/repos/iuc/graphlan/graphlan/1.1.3 + version: 1.2.0 + - id: toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/1.3.0 servers: - server: http://apostl.moffitt.org/ state: missing @@ -44768,12 +26166,15 @@ state: missing - server: https://galaxy.mesocentre.uca.fr state: exact - version: 1.1.3 + version: 1.3.0 - server: https://galaxy.pasteur.fr/ state: missing - server: https://galaxytrakr.org/ - state: exact - version: 1.1.3 + state: inexact + versions: + - '1.6' + - 2.1+galaxy0 + - '2.1' - server: http://igg.cloud.ba.infn.it/galaxy state: missing - server: https://galaxy.hyphy.org/ @@ -44784,45 +26185,49 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr - state: missing + state: inexact + versions: + - '2.0' + - 2.1+galaxy0 - server: http://galaxy.inf.ethz.ch state: missing - server: https://palfinder.ls.manchester.ac.uk/ state: missing - server: http://pepsimili.e-nios.com:8080/ state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - server: https://usegalaxy.org.au state: exact - version: 1.1.3 + version: 1.3.0 - server: https://usegalaxy.be/ state: exact - version: 1.1.3 + version: 1.3.0 - server: https://usegalaxy.cz/ - state: exact - version: 1.1.3 + state: inexact + versions: + - '2.0' + - '1.4' + - '1.6' + - 2.1+galaxy0 + - 1.1.0 - server: https://usegalaxy.eu state: exact - version: 1.1.3 + version: 1.3.0 - server: https://usegalaxy.fr/ state: exact - version: 1.1.3 + version: 1.3.0 - server: https://usegalaxy.no/ state: exact - version: 1.1.3 + version: 1.3.0 - server: https://usegalaxy.org state: exact - version: 1.1.3 + version: 1.3.0 - server: https://viralvariant.anses.fr/ state: missing - version: 1.1.3 - - id: toolshed.g2.bx.psu.edu/repos/iuc/graphlan_annotate/graphlan_annotate/1.1.3 + version: 1.3.0 + - id: toolshed.g2.bx.psu.edu/repos/iuc/gff_to_prot/gff_to_prot/3.0.2+galaxy0 servers: - server: http://apostl.moffitt.org/ state: missing @@ -44835,13 +26240,11 @@ - server: https://hyperbrowser.uio.no/coloc-stats state: missing - server: https://galaxy.mesocentre.uca.fr - state: exact - version: 1.1.3 + state: missing - server: https://galaxy.pasteur.fr/ state: missing - server: https://galaxytrakr.org/ - state: exact - version: 1.1.3 + state: missing - server: http://igg.cloud.ba.infn.it/galaxy state: missing - server: https://galaxy.hyphy.org/ @@ -44852,8 +26255,6 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr @@ -44864,33 +26265,30 @@ state: missing - server: http://pepsimili.e-nios.com:8080/ state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - server: https://usegalaxy.org.au state: exact - version: 1.1.3 + version: 3.0.2+galaxy0 - server: https://usegalaxy.be/ state: exact - version: 1.1.3 + version: 3.0.2+galaxy0 - server: https://usegalaxy.cz/ state: exact - version: 1.1.3 + version: 3.0.2+galaxy0 - server: https://usegalaxy.eu state: exact - version: 1.1.3 + version: 3.0.2+galaxy0 - server: https://usegalaxy.fr/ - state: exact - version: 1.1.3 + state: missing - server: https://usegalaxy.no/ state: exact - version: 1.1.3 + version: 3.0.2+galaxy0 - server: https://usegalaxy.org state: exact - version: 1.1.3 + version: 3.0.2+galaxy0 - server: https://viralvariant.anses.fr/ state: missing - version: 1.1.3 - - id: toolshed.g2.bx.psu.edu/repos/iuc/humann/humann/3.9+galaxy0 + version: 3.0.2+galaxy0 + - id: toolshed.g2.bx.psu.edu/repos/iuc/transit_gumbel/transit_gumbel/3.0.2+galaxy0 servers: - server: http://apostl.moffitt.org/ state: missing @@ -44903,13 +26301,11 @@ - server: https://hyperbrowser.uio.no/coloc-stats state: missing - server: https://galaxy.mesocentre.uca.fr - state: exact - version: 3.9+galaxy0 + state: missing - server: https://galaxy.pasteur.fr/ state: missing - server: https://galaxytrakr.org/ - state: exact - version: 3.9+galaxy0 + state: missing - server: http://igg.cloud.ba.infn.it/galaxy state: missing - server: https://galaxy.hyphy.org/ @@ -44920,8 +26316,6 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr @@ -44932,35 +26326,32 @@ state: missing - server: http://pepsimili.e-nios.com:8080/ state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - server: https://usegalaxy.org.au state: exact - version: 3.9+galaxy0 + version: 3.0.2+galaxy0 - server: https://usegalaxy.be/ state: exact - version: 3.9+galaxy0 + version: 3.0.2+galaxy0 - server: https://usegalaxy.cz/ - state: exact - version: 3.9+galaxy0 + state: inexact + versions: + - 3.2.3+galaxy0 + - 3.0.2+galaxy1 - server: https://usegalaxy.eu state: exact - version: 3.9+galaxy0 + version: 3.0.2+galaxy0 - server: https://usegalaxy.fr/ - state: exact - version: 3.9+galaxy0 + state: missing - server: https://usegalaxy.no/ - state: inexact - versions: - - 3.0.0+galaxy1 - - 3.6.0+galaxy0 + state: exact + version: 3.0.2+galaxy0 - server: https://usegalaxy.org state: exact - version: 3.9+galaxy0 + version: 3.0.2+galaxy0 - server: https://viralvariant.anses.fr/ state: missing - version: 3.9+galaxy0 - - id: toolshed.g2.bx.psu.edu/repos/iuc/humann_regroup_table/humann_regroup_table/3.9+galaxy0 + version: 3.0.2+galaxy0 + - id: toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/1.16.5 servers: - server: http://apostl.moffitt.org/ state: missing @@ -44973,13 +26364,21 @@ - server: https://hyperbrowser.uio.no/coloc-stats state: missing - server: https://galaxy.mesocentre.uca.fr - state: exact - version: 3.9+galaxy0 + state: inexact + versions: + - 4.8+galaxy1 + - 5.1+galaxy0 + - 5.0+galaxy0 + - 4.0+galaxy0 + - 4.9+galaxy1 - server: https://galaxy.pasteur.fr/ - state: missing + state: inexact + versions: + - 4.9+galaxy1 - server: https://galaxytrakr.org/ - state: exact - version: 3.9+galaxy0 + state: inexact + versions: + - 1.16.9 - server: http://igg.cloud.ba.infn.it/galaxy state: missing - server: https://galaxy.hyphy.org/ @@ -44990,53 +26389,2246 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr - state: missing + state: inexact + versions: + - 4.8+galaxy1 + - 5.2+galaxy2 - server: http://galaxy.inf.ethz.ch state: missing - server: https://palfinder.ls.manchester.ac.uk/ state: missing - server: http://pepsimili.e-nios.com:8080/ state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - server: https://usegalaxy.org.au state: exact - version: 3.9+galaxy0 + version: 1.16.5 - server: https://usegalaxy.be/ state: exact - version: 3.9+galaxy0 + version: 1.16.5 - server: https://usegalaxy.cz/ - state: exact - version: 3.9+galaxy0 + state: inexact + versions: + - 5.1+galaxy0 + - 5.0+galaxy0 + - 4.9+galaxy1 + - 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name: snippy + owner: iuc + revisions: c9a8ef2aa380 + tool_panel_section_label: Variant Calling + tool_shed_url: https://toolshed.g2.bx.psu.edu/ + admin_install_yaml: "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies:\ + \ true\ninstall_resolver_dependencies: true\ntools:\n- name: jbrowse\n owner:\ + \ iuc\n revisions: 836d1aa3e89a\n tool_panel_section_label: Graph/Display Data\n\ + \ tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: snippy\n owner: iuc\n\ + \ revisions: c9a8ef2aa380\n tool_panel_section_label: Variant Calling\n tool_shed_url:\ + \ https://toolshed.g2.bx.psu.edu/\n" + api: https://training.galaxyproject.org/training-material/api/topics/variant-analysis/tutorials/microbial-variants/tutorial.json + contributions: + authorship: + - annasyme + - slugger70 + - tseemann + funding: + - unimelb + - melbournebioinformatics + - AustralianBioCommons + reviewing: + - jennaj + - hexylena + - bgruening + - shiltemann + - bebatut + - abretaud + - nsoranzo + - slugger70 + - pvanheus + - njall + - mblue9 + contributors: + - affiliations: + - AustralianBioCommons + - unimelb + former_affiliations: + - melbournebioinformatics + id: annasyme + joined: 2017-09 + name: Anna Syme + orcid: 0000-0002-9906-0673 + page: https://training.galaxyproject.org/training-material/hall-of-fame/annasyme/ + url: https://training.galaxyproject.org/training-material/api/contributors/annasyme.json + - elixir_node: au + email: simon.gladman@unimelb.edu.au + id: slugger70 + in_memoriam: "Simon\ + \ Gladman, system administrator of UseGalaxy.org.au, passed away on November\ + \ 26, 2022\n\nHe was a fantastic teacher, tutorial author, system administrator, and warm\ + \ and welcoming friend. He contributed heavily to the Galaxy Training Network\ + \ and especially the Galaxy Administration community over the years, we will\ + \ miss him dearly. The GTN and GAT would not be what they are today, without\ + \ him.\n\n\u201CHave I told you about my watch?\u201D" + joined: 2017-09 + name: Simon Gladman + orcid: 0000-0002-6100-4385 + page: https://training.galaxyproject.org/training-material/hall-of-fame/slugger70/ + url: https://training.galaxyproject.org/training-material/api/contributors/slugger70.json + - affiliations: + - elixir-europe + elixir_node: au + id: tseemann + joined: 2018-06 + name: Torsten Seemann + page: https://training.galaxyproject.org/training-material/hall-of-fame/tseemann/ + url: https://training.galaxyproject.org/training-material/api/contributors/tseemann.json + - avatar: /training-material/shared/images/unimelb_Logo_RGB.png + id: unimelb + members: + - annasyme + - cat-bro + - GraceAHall + - supernord + - tflowers15 + - uwwint + - vinisalazar + name: The University of Melbourne + page: https://training.galaxyproject.org/training-material/hall-of-fame/unimelb/ + url: https://training.galaxyproject.org/training-material/api/organisations/unimelb.json + - avatar: /training-material/shared/images/Melbourne-Bioinformatics-logo.png + former_members: + - annasyme + id: melbournebioinformatics + members: + - GraceAHall + - tflowers15 + - vinisalazar + name: Melbourne Bioinformatics + page: https://training.galaxyproject.org/training-material/hall-of-fame/melbournebioinformatics/ + url: https://training.galaxyproject.org/training-material/api/organisations/melbournebioinformatics.json + - avatar: /training-material/shared/images/Australian-Biocommons-Favicon-RGB.png + id: AustralianBioCommons + members: + - annasyme + - burkemlou + - cat-bro + - igormakunin + - mthang + - PatCapon39 + - supernord + - tflowers15 + - uwwint + name: Australian BioCommons + page: https://training.galaxyproject.org/training-material/hall-of-fame/AustralianBioCommons/ + url: https://training.galaxyproject.org/training-material/api/organisations/AustralianBioCommons.json + - contact_for_training: true + email: jen@galaxyproject.org + id: jennaj + joined: 2018-06 + linkedin: jennifer.hillman.jackson + location: + country: US + lat: 36.969918 + lon: -122.0226576 + maintainer_contact: https://help.galaxyproject.org/ + matrix: jennaj:matrix.org + name: Jennifer Hillman-Jackson + orcid: 0000-0003-4012-8116 + page: https://training.galaxyproject.org/training-material/hall-of-fame/jennaj/ + twitter: jennaj_io + url: https://training.galaxyproject.org/training-material/api/contributors/jennaj.json + - affiliations: + - elixir-europe + contact_for_training: false + elixir_node: nl + former_affiliations: + - deNBI + - avans-atgm + - uni-freiburg + - erasmusmc + - gallantries + - by-covid + - elixir-converge + id: hexylena + joined: 2017-09 + location: + country: NL + lat: 51.91 + lon: 4.46 + maintainer_contact: gitter + matrix: hexylena:matrix.org + name: Helena Rasche + orcid: 0000-0001-9760-8992 + page: https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/ + url: https://training.galaxyproject.org/training-material/api/contributors/hexylena.json + - affiliations: + - deNBI + - mwk + - uni-freiburg + - elixir-europe + - materialvitaldigital + contact_for_training: true + elixir_node: de + email: bjoern.gruening@gmail.com + fediverse: https://fosstodon.org/@bgruening + fediverse_flavor: mastodon + former_affiliations: + - eurosciencegateway + - eosc-life + - by-covid + - crc992 + - elixir-converge + id: bgruening + joined: 2017-09 + linkedin: bgruening + location: + country: DE + lat: 47.997791 + lon: 7.842609 + matrix: bgruening:matrix.org + name: "Bj\xF6rn Gr\xFCning" + orcid: 0000-0002-3079-6586 + page: https://training.galaxyproject.org/training-material/hall-of-fame/bgruening/ + twitter: bjoerngruening + url: https://training.galaxyproject.org/training-material/api/contributors/bgruening.json + - affiliations: + - uni-freiburg + - nfdi4plants + - elixir-europe + bio: Researcher at Erasmus Medical Center + bluesky: shiltemann.bsky.social + contact_for_training: true + elixir_node: nl + email: saskia.hiltemann@gmail.com + fediverse: https://mstdn.science/@shiltemann + fediverse_flavor: mastodon + former_affiliations: + - CINECA-Project + - gallantries + - erasmusmc + id: shiltemann + joined: 2017-09 + linkedin: shiltemann + location: + country: NL + lat: 51.912 + lon: 4.462 + maintainer_contact: gitter + matrix: shiltemann:matrix.org + name: Saskia Hiltemann + orcid: 0000-0003-3803-468X + page: https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/ + url: https://training.galaxyproject.org/training-material/api/contributors/shiltemann.json + - affiliations: + - gallantries + - ifb + - elixir-europe + contact_for_training: true + elixir_node: fr + email: berenice.batut@gmail.com + fediverse: https://piaille.fr/@bebatut + fediverse_flavor: mastodon + former_affiliations: + - uni-freiburg + - deNBI + id: bebatut + joined: 2017-09 + linkedin: berenicebatut + location: + country: FR + lat: 45.77 + lon: 3.08 + matrix: bebatut:matrix.org + name: "B\xE9r\xE9nice Batut" + orcid: 0000-0001-9852-1987 + page: https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/ + twitter: bebatut + url: https://training.galaxyproject.org/training-material/api/contributors/bebatut.json + - affiliations: + - elixir-europe + bluesky: abretaud.bsky.social + contact_for_training: true + elixir_node: fr + email: anthony.bretaudeau@irisa.fr + fediverse: https://genomic.social/@abretaud + fediverse_flavor: mastodon + former_affiliations: + - eurosciencegateway + - gallantries + id: abretaud + joined: 2017-09 + location: + country: FR + lat: 48.11 + lon: -1.64 + matrix: abretaud:matrix.org + name: Anthony Bretaudeau + orcid: 0000-0003-0914-2470 + page: https://training.galaxyproject.org/training-material/hall-of-fame/abretaud/ + url: https://training.galaxyproject.org/training-material/api/contributors/abretaud.json + - affiliations: + - biofair + - earlham + - elixir-europe + - elixir-steers + bluesky: nsoranzo.bsky.social + elixir_node: uk + fediverse: https://mstdn.science/@nsoranzo + fediverse_flavor: mastodon + id: nsoranzo + joined: 2017-09 + linkedin: nicola-soranzo-7884125 + location: + country: UK + lat: 52.62188 + lon: 1.21899 + matrix: nsoranzo:matrix.org + name: Nicola Soranzo + orcid: 0000-0003-3627-5340 + page: https://training.galaxyproject.org/training-material/hall-of-fame/nsoranzo/ + twitter: NicolaSoranzo + url: https://training.galaxyproject.org/training-material/api/contributors/nsoranzo.json + - elixir_node: au + email: simon.gladman@unimelb.edu.au + id: slugger70 + in_memoriam: "Simon\ + \ Gladman, system administrator of UseGalaxy.org.au, passed away on November\ + \ 26, 2022\n\nHe was a fantastic teacher, tutorial author, system administrator, and warm\ + \ and welcoming friend. He contributed heavily to the Galaxy Training Network\ + \ and especially the Galaxy Administration community over the years, we will\ + \ miss him dearly. The GTN and GAT would not be what they are today, without\ + \ him.\n\n\u201CHave I told you about my watch?\u201D" + joined: 2017-09 + name: Simon Gladman + orcid: 0000-0002-6100-4385 + page: https://training.galaxyproject.org/training-material/hall-of-fame/slugger70/ + url: https://training.galaxyproject.org/training-material/api/contributors/slugger70.json + - bio: Research at the South African National Bioinformatics Institute + id: pvanheus + joined: 2017-09 + name: Peter van Heusden + orcid: 0000-0001-6553-5274 + page: https://training.galaxyproject.org/training-material/hall-of-fame/pvanheus/ + twitter: pvanheus + url: https://training.galaxyproject.org/training-material/api/contributors/pvanheus.json + - id: njall + joined: 2019-02 + name: Niall Beard + page: https://training.galaxyproject.org/training-material/hall-of-fame/njall/ + url: https://training.galaxyproject.org/training-material/api/contributors/njall.json + - id: mblue9 + joined: 2018-09 + name: Maria Doyle + orcid: 0000-0003-4847-8436 + page: https://training.galaxyproject.org/training-material/hall-of-fame/mblue9/ + url: https://training.galaxyproject.org/training-material/api/contributors/mblue9.json + dir: topics/variant-analysis/tutorials/microbial-variants + edam_ontology: + - topic_0622 + - topic_0196 + - topic_2885 + - topic_3301 + - topic_0080 + - topic_0199 + edam_operation: + - Variant calling + - Phylogenetic tree visualisation + - Genome visualisation + - Phylogenetic tree generation + edam_topic: + - Genomics + - Sequence assembly + - DNA polymorphism + - Microbiology + - Sequence analysis + - Genetic variation + exact_supported_servers: + - UseGalaxy.be + - UseGalaxy.eu + - UseGalaxy.org (Main) + feedback_mean_note: null + feedback_number: 0 + hands_on: true + id: variant-analysis/microbial-variants + inexact_supported_servers: + - GalaxyTrakr + - UseGalaxy.org.au + - UseGalaxy.cz + - UseGalaxy.fr + - UseGalaxy.no + js_requirements: + mathjax: null + mermaid: false + key_points: + - We used a tool called Snippy to call variants between our reads and our reference + genome. + - As our reference genome had annotations, we could see what effect the changes + have on the features as annotated in the reference and therefore make inferences + on the possible changes to the phenotype. + - We used the JBrowse genome browser to visualise what these changes look like. + layout: tutorial_hands_on + license: CC-BY-4.0 + mod_date: '2026-01-23' + objectives: + - Find variants between a reference genome and a set of reads + - Visualise the SNP in context of the reads aligned to the genome + - Determine the effect of those variants on genomic features + - Understand if the SNP is potentially affecting the phenotype + pageviews: 25775 + pub_date: '2018-02-26' + questions: + - How do we detect differences between a set of reads from a microorganism and a + reference genome + short_id: T00313 + short_tools: + - snippy + - jbrowse + slides: false + slides_recordings: false + 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toolshed.g2.bx.psu.edu/repos/iuc/snippy/snippy/3.2 servers: - server: http://apostl.moffitt.org/ state: missing @@ -45552,15 +28721,13 @@ - server: https://hyperbrowser.uio.no/coloc-stats state: missing - server: https://galaxy.mesocentre.uca.fr - state: exact - version: 4.3.6+galaxy0 + state: missing - server: https://galaxy.pasteur.fr/ - state: exact - version: 4.3.6+galaxy0 + state: missing - server: https://galaxytrakr.org/ state: inexact versions: - - 2.1b.6 + - 4.6.0+galaxy0 - server: http://igg.cloud.ba.infn.it/galaxy state: missing - server: https://galaxy.hyphy.org/ @@ -45571,8 +28738,6 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr @@ -45583,1187 +28748,556 @@ state: missing - server: http://pepsimili.e-nios.com:8080/ state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - server: https://usegalaxy.org.au - state: exact - version: 4.3.6+galaxy0 + state: inexact + versions: + - 4.6.0+galaxy0 + - 4.5.0+galaxy1 + - 4.5.0 - server: https://usegalaxy.be/ state: exact - version: 4.3.6+galaxy0 + version: '3.2' - server: https://usegalaxy.cz/ - state: exact - version: 4.3.6+galaxy0 + state: inexact + versions: + - 4.6.0+galaxy0 - server: https://usegalaxy.eu state: exact - version: 4.3.6+galaxy0 + version: '3.2' - server: https://usegalaxy.fr/ - state: exact - version: 4.3.6+galaxy0 - - server: https://usegalaxy.no/ - state: exact - version: 4.3.6+galaxy0 - - server: https://usegalaxy.org - state: exact - version: 4.3.6+galaxy0 - - server: https://viralvariant.anses.fr/ - state: missing - version: 4.3.6+galaxy0 - symlink: null - tags: - - metatranscriptomics - - microgalaxy - time: null - time_estimation: 5H - title: Metatranscriptomics analysis using microbiome RNA-seq data - tools: - - Cut1 - - Grep1 - - Grouping1 - - toolshed.g2.bx.psu.edu/repos/bebatut/combine_metaphlan2_humann2/combine_metaphlan_humann/0.3.0 - - toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.5+galaxy2 - - toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/9.5+galaxy2 - - toolshed.g2.bx.psu.edu/repos/crs4/taxonomy_krona_chart/taxonomy_krona_chart/2.7.1+galaxy0 - - toolshed.g2.bx.psu.edu/repos/devteam/fastq_paired_end_interlacer/fastq_paired_end_interlacer/1.2.0.1+galaxy0 - - toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy1 - - toolshed.g2.bx.psu.edu/repos/iuc/export2graphlan/export2graphlan/0.20+galaxy0 - - toolshed.g2.bx.psu.edu/repos/iuc/graphlan/graphlan/1.1.3 - - toolshed.g2.bx.psu.edu/repos/iuc/graphlan_annotate/graphlan_annotate/1.1.3 - - toolshed.g2.bx.psu.edu/repos/iuc/humann/humann/3.9+galaxy0 - - toolshed.g2.bx.psu.edu/repos/iuc/humann_regroup_table/humann_regroup_table/3.9+galaxy0 - - toolshed.g2.bx.psu.edu/repos/iuc/humann_rename_table/humann_rename_table/3.9+galaxy0 - - toolshed.g2.bx.psu.edu/repos/iuc/humann_renorm_table/humann_renorm_table/3.9+galaxy0 - - toolshed.g2.bx.psu.edu/repos/iuc/humann_split_stratified_table/humann_split_stratified_table/3.9+galaxy0 - - toolshed.g2.bx.psu.edu/repos/iuc/humann_unpack_pathways/humann_unpack_pathways/3.9+galaxy0 - - toolshed.g2.bx.psu.edu/repos/iuc/metaphlan/metaphlan/4.1.1+galaxy4 - - toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.27+galaxy3 - - toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/5.0+galaxy0 - - toolshed.g2.bx.psu.edu/repos/rnateam/sortmerna/bg_sortmerna/4.3.6+galaxy0 - topic_name: microbiome - topic_name_human: Microbiome - tours: false - translations: - slides: [] - tutorial: [] - video: false - tutorial_name: metatranscriptomics - type: tutorial - url: https://training.galaxyproject.org//topics/microbiome/tutorials/metatranscriptomics/tutorial.html - urls: - hands_on: https://training.galaxyproject.org/training-material/api/topics/microbiome/tutorials/metatranscriptomics/tutorial.json - slides: https://training.galaxyproject.org/training-material/api/topics/microbiome/tutorials/metatranscriptomics/tutorial.json - version: 6 - video: true - video_versions: 2 - video_view: 0 - visit_duration: 409 - visitors: 3818338 - workflows: - - creators: - - class: Person - identifier: 0000-0001-9852-1987 - name: "B\xE9r\xE9nice Batut" - - class: Person - identifier: 0000-0003-0984-0973 - name: Pratik Jagtap - - class: Person - identifier: 0000-0001-9818-0537 - name: Subina Mehta - - class: Person - identifier: 0000-0003-3803-468X - name: Saskia Hiltemann - - class: Person - identifier: 0000-0003-2982-388X - name: Paul Zierep - description: Metatranscriptomics analysis using microbiome RNA-seq data - features: - comments: true - parameters: false - report: - markdown: ' - - # Workflow Execution Report - - - ## Workflow Inputs - - ```galaxy - - invocation_inputs() - - ``` - - - ## Workflow Outputs - - ```galaxy - - invocation_outputs() - - ``` - - - ## Workflow - - ```galaxy - - workflow_display() - - ``` - - ' - subworkflows: false - graph_dot: "digraph main {\n node [fontname=\"Atkinson Hyperlegible\", shape=box,\ - \ color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n edge [fontname=\"\ - Atkinson Hyperlegible\"];\n 0[color=lightblue,label=\"\u2139\uFE0F Input Dataset\\\ - nReverse raw reads\"]\n 1[color=lightblue,label=\"\u2139\uFE0F Input Dataset\\\ - nForward raw reads\"]\n 2[label=\"FastQC\"]\n 0 -> 2 [label=\"output\"]\n\ - \ k676cd11f047947c4a23bc6c8ed5a7790[color=lightseagreen,label=\"Output\\nfastqc_reverse_html_file\"\ - ]\n 2 -> k676cd11f047947c4a23bc6c8ed5a7790\n 3[label=\"FastQC\"]\n 1 -> 3\ - \ [label=\"output\"]\n k1fb52b78c90543c7a295d628c996d35a[color=lightseagreen,label=\"\ - Output\\nfastqc_forward_html_file\"]\n 3 -> k1fb52b78c90543c7a295d628c996d35a\n\ - \ 4[label=\"Cutadapt\"]\n 1 -> 4 [label=\"output\"]\n 0 -> 4 [label=\"output\"\ - ]\n k0e7406ed9eca486eb19a4cbbf04b5138[color=lightseagreen,label=\"Output\\\ - ncutadapt_report\"]\n 4 -> k0e7406ed9eca486eb19a4cbbf04b5138\n 5[label=\"\ - MultiQC\"]\n 2 -> 5 [label=\"text_file\"]\n 3 -> 5 [label=\"text_file\"]\n\ - \ kd9f371ddaa6c4540b62b0e34c0b71afa[color=lightseagreen,label=\"Output\\nmultiqc_html_report\"\ - ]\n 5 -> kd9f371ddaa6c4540b62b0e34c0b71afa\n 6[label=\"Filter with SortMeRNA\"\ - ]\n 4 -> 6 [label=\"out1\"]\n 4 -> 6 [label=\"out2\"]\n k3092eb62d7fc4d66bf574c6cf491d0e3[color=lightseagreen,label=\"\ - Output\\nsortmerna_unaligned_reverse\"]\n 6 -> k3092eb62d7fc4d66bf574c6cf491d0e3\n\ - \ kdb3bb8ee8af74528be4bf3ea6d381856[color=lightseagreen,label=\"Output\\nsortmerna_unaligned_forward\"\ - ]\n 6 -> kdb3bb8ee8af74528be4bf3ea6d381856\n 7[label=\"FASTQ interlacer\"\ - ]\n 6 -> 7 [label=\"unaligned_forward\"]\n 6 -> 7 [label=\"unaligned_reverse\"\ - ]\n 8[label=\"MetaPhlAn\"]\n 6 -> 8 [label=\"unaligned_forward\"]\n 6 ->\ - \ 8 [label=\"unaligned_reverse\"]\n kb13521dbf5e74bf3b7fa673d13fc2911[color=lightseagreen,label=\"\ - Output\\nmetaphlan_predicted_taxons\"]\n 8 -> kb13521dbf5e74bf3b7fa673d13fc2911\n\ - \ 9[label=\"Cut\"]\n 8 -> 9 [label=\"output_file\"]\n 10[label=\"Krona pie\ - \ chart\"]\n 8 -> 10 [label=\"krona_output_file\"]\n 11[label=\"HUMAnN\"]\n\ - \ 7 -> 11 [label=\"outfile_pairs\"]\n 8 -> 11 [label=\"output_file\"]\n k5aec39b6317a4fd0b90622d5a965e957[color=lightseagreen,label=\"\ - Output\\nhumann_pathabundance\"]\n 11 -> k5aec39b6317a4fd0b90622d5a965e957\n\ - \ k53259a0607834db8828e328e7337f5b3[color=lightseagreen,label=\"Output\\nhumann_gene_families\"\ - ]\n 11 -> k53259a0607834db8828e328e7337f5b3\n 12[label=\"Export to GraPhlAn\"\ - ]\n 9 -> 12 [label=\"out_file1\"]\n 13[label=\"Split a HUMAnN table\"]\n \ - \ 11 -> 13 [label=\"gene_families_tsv\"]\n 14[label=\"Regroup\"]\n 11 -> 14\ - \ [label=\"gene_families_tsv\"]\n 15[label=\"Renormalize\"]\n 11 -> 15 [label=\"\ - gene_families_tsv\"]\n 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-->|output| 27;\n 28[\"Combine MetaPhlAn and HUMAnN outputs\"\ - ];\n 22 -->|outfile| 28;\n 8 -->|output_file| 28;\n 4730e437-6259-44d8-8374-60d6a737b720[\"\ - Output\\ncombined_metaphlan_humann\"];\n 28 --> 4730e437-6259-44d8-8374-60d6a737b720;\n\ - \ style 4730e437-6259-44d8-8374-60d6a737b720 stroke:#2c3143,stroke-width:4px;\n\ - \ 29[\"Split a HUMAnN table\"];\n 25 -->|out_file1| 29;\n 30[\"Split a HUMAnN\ - \ table\"];\n 26 -->|out_file1| 30;\n 31[\"Sort\"];\n 27 -->|out_file1| 31;\n\ - \ 71abb759-b51f-4383-a791-27d8b1325e81[\"Output\\nsorted_mf_go\"];\n 31 -->\ - \ 71abb759-b51f-4383-a791-27d8b1325e81;\n style 71abb759-b51f-4383-a791-27d8b1325e81\ - \ stroke:#2c3143,stroke-width:4px;\n 32[\"Split a HUMAnN table\"];\n 27 -->|out_file1|\ - \ 32;\n 33[\"Group\"];\n 28 -->|gene_families_output_file| 33;\n 34[\"Group\"\ - ];\n 28 -->|gene_families_output_file| 34;" - modified: 2026-05-21 00:30:25 +0000 - name: Metatranscriptomics analysis using microbiome RNA-seq data - outputs: - - 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name: mothur_summary_seqs\n\ + \ owner: iuc\n revisions: e4a4cb8b6bbf\n tool_panel_section_label: Mothur\n\ + \ tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: mothur_unique_seqs\n\ + \ owner: iuc\n revisions: 1f72d9a3d09f\n tool_panel_section_label: Mothur\n\ + \ tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: krona_text\n owner:\ + \ saskia-hiltemann\n revisions: b14f1444e464\n tool_panel_section_label: Graph/Display\ + \ Data\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n" + api: https://training.galaxyproject.org/training-material/api/topics/microbiome/tutorials/general-tutorial/tutorial.json + contributors: - affiliations: - uni-freiburg - nfdi4plants @@ -46792,17 +29326,6 @@ orcid: 0000-0003-3803-468X page: https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/ url: https://training.galaxyproject.org/training-material/api/contributors/shiltemann.json - - affiliations: - - uni-freiburg - - elixir-europe - bluesky: dvarshney.bsky.social - email: varshney@informatik.uni-freiburg.de - id: deeptivarshney - joined: 2022-12 - name: Deepti Varshney - orcid: 0000-0003-0419-6832 - page: https://training.galaxyproject.org/training-material/hall-of-fame/deeptivarshney/ - url: https://training.galaxyproject.org/training-material/api/contributors/deeptivarshney.json - affiliations: - gallantries - ifb @@ -46828,183 +29351,103 @@ page: https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/ twitter: bebatut url: https://training.galaxyproject.org/training-material/api/contributors/bebatut.json - - affiliations: - - erasmusmc - - gallantries - - by-covid - - elixir-europe - - elixir-converge - contact_for_training: false - elixir_node: nl - former_affiliations: - - deNBI - - avans-atgm - - uni-freiburg - id: hexylena - joined: 2017-09 - location: - country: NL - lat: 51.91 - lon: 4.46 - maintainer_contact: gitter - matrix: hexylena:matrix.org - name: Helena Rasche - orcid: 0000-0001-9760-8992 - page: https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/ - url: https://training.galaxyproject.org/training-material/api/contributors/hexylena.json - - id: abueg - joined: 2022-01 - name: Linelle Abueg - orcid: 0000-0002-6879-3954 - page: https://training.galaxyproject.org/training-material/hall-of-fame/abueg/ - twitter: llabueg - url: https://training.galaxyproject.org/training-material/api/contributors/abueg.json - - elixir_node: de - id: bernt-matthias - joined: 2017-09 - name: Matthias Bernt - page: https://training.galaxyproject.org/training-material/hall-of-fame/bernt-matthias/ - url: https://training.galaxyproject.org/training-material/api/contributors/bernt-matthias.json - - affiliations: - - uni-freiburg - - elixir-europe - - deNBI - - mwk - - materialvitaldigital - email: zierep@informatik.uni-freiburg.de - id: paulzierep - joined: 2023-02 - name: Paul Zierep - orcid: 0000-0003-2982-388X - page: https://training.galaxyproject.org/training-material/hall-of-fame/paulzierep/ - url: https://training.galaxyproject.org/training-material/api/contributors/paulzierep.json - - affiliations: - - uni-freiburg - id: santamccloud - joined: 2025-07 - name: Santino Faack - orcid: 0009-0004-0382-2023 - page: https://training.galaxyproject.org/training-material/hall-of-fame/santamccloud/ - url: https://training.galaxyproject.org/training-material/api/contributors/santamccloud.json - dir: topics/microbiome/tutorials/dada-16S + dir: topics/microbiome/tutorials/general-tutorial edam_ontology: + - topic_3174 - topic_3697 - topic_0637 - topic_0080 - topic_4038 edam_operation: - - Analysis - - Deposition + - Sequencing quality control + - Phylogenetic analysis - Visualisation - - Variant calling + - Sequence read processing + - Taxonomic classification + - Sequence clustering - DNA barcoding edam_topic: + - Metagenomics - Microbial ecology - Taxonomy - Sequence analysis - Metabarcoding - exact_supported_servers: - - UseGalaxy.org.au - - UseGalaxy.eu - - UseGalaxy.fr - - UseGalaxy.org (Main) + exact_supported_servers: [] feedback_mean_note: null feedback_number: 0 hands_on: true - id: microbiome/dada-16S - inexact_supported_servers: [] + id: microbiome/general-tutorial + inexact_supported_servers: + - UseGalaxy.org.au + - UseGalaxy.fr + - UseGalaxy.no js_requirements: - mathjax: 14601 + mathjax: null mermaid: false key_points: - - DADA2 allows for the generation of precise ASV tables, providing higher resolution - and more accurate representation of microbial communities compared to traditional - OTU-based methods. - - Key steps such as quality filtering, error rate learning, and chimera removal - are essential in the DADA2 pipeline to ensure the reliability and accuracy of - the resulting ASV data. - - Tools like phyloseq can be effectively used to explore and visualize ASV tables, - facilitating deeper ecological and evolutionary insights into microbial diversity - and community structure. + - With amplicon data, we can extract information about the studied community structure + - With shotgun data, we can extract information about the studied community structure + and also the functions realised by the community + - The tools used to analyze amplicon and shotgun data are different, except for + the visualisation + - Metagenomics data analyses are complex and time-consuming layout: tutorial_hands_on license: CC-BY-4.0 - mod_date: '2026-04-13' + mod_date: '2024-08-09' objectives: - - Identify the key steps in the DADA2 workflow for generating an ASV table from - 16S rRNA gene sequencing data - - Explain the importance of quality filtering, error rate learning, and chimera - removal in ensuring accurate microbial community analysis - - Execute the DADA2 pipeline to process raw 16S sequencing data and produce a high-resolution - ASV table - - Compare the advantages of ASV-based methods over traditional OTU-based approaches - in terms of accuracy and resolution - - Assess the effectiveness of using phyloseq for exploring and visualizing ASV data - to gain ecological and evolutionary insights - pageviews: 13212 - pub_date: '2024-06-05' + - Choosing the best approach to analyze metagenomics data + - Selection of tools to analyze amplicon data or shotgun data + - Visualisation of a community structure + pageviews: 15412 + pub_date: '2017-06-22' questions: - - What are the primary steps involved in generating an ASV table using DADA2 from - 16S rRNA gene sequencing data? - - How does DADA2 improve the accuracy of microbial community analysis compared to - traditional OTU-based methods? - - What is the importance of quality filtering in the DADA2 workflow, and how does - it impact downstream analyses? - - How does the error rate learning process contribute to the identification of true - biological sequences in DADA2? - - What role does chimera removal play in the DADA2 pipeline, and why is it crucial - for obtaining reliable ASV data? - - How can phyloseq be used to explore and visualize the ASV table generated by DADA2, - and what types of ecological insights can it provide? - recordings: - - bot-timestamp: 1726830881 - captioners: - - bernt-matthias - date: '2024-09-20' - galaxy_version: 24.1.2.dev0 - length: 1H36M - speakers: - - bernt-matthias - youtube_id: ISocxcJZEjw - short_id: T00441 + - How to analyze metagenomics data? + - What information can be extracted of metagenomics data? + - What is the difference between amplicon and shotgun data? + - What are the difference in the analyses of amplicon and shotgun data? + redirect_from: + - /topics/metagenomics/tutorials/general-tutorial/tutorial + - /short/microbiome/general-tutorial + - /short/T00201 + - /short/T00385 + short_id: T00385 short_tools: - - dada2_plotQualityProfile - - dada2_mergePairs - - cat1 - - tp_replace_in_column - - tp_replace_in_line - - __UNZIP_COLLECTION__ - - tp_head_tool - - phyloseq_from_dada2 - - Grouping1 - - dada2_makeSequenceTable - 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url: https://usegalaxy.fr/ usegalaxy: true - - name: UseGalaxy.org (Main) - url: https://usegalaxy.org - usegalaxy: true - inexact: [] + - name: UseGalaxy.no + url: https://usegalaxy.no/ + usegalaxy: false supported_servers_matrix: servers: - name: APOSTL @@ -47046,9 +29489,6 @@ - name: IPK Galaxy Blast Suite url: https://galaxy-web.ipk-gatersleben.de usegalaxy: false - - name: Lebanese University Galaxy - url: http://galaxy.ul.edu.lb/ - usegalaxy: false - name: Mandoiu Lab url: https://neo.engr.uconn.edu/ usegalaxy: false @@ -47064,9 +29504,6 @@ - name: PepSimili url: http://pepsimili.e-nios.com:8080/ usegalaxy: false - - name: PhagePromotor - url: https://galaxy.bio.di.uminho.pt/ - usegalaxy: false - name: UseGalaxy.org.au url: https://usegalaxy.org.au usegalaxy: true @@ -47092,66 +29529,81 @@ url: https://viralvariant.anses.fr/ usegalaxy: false tools: - - id: Grouping1 + - id: toolshed.g2.bx.psu.edu/repos/crs4/taxonomy_krona_chart/taxonomy_krona_chart/2.6.1 servers: - server: 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https://viralvariant.anses.fr/ - state: local - version: local - - id: __UNZIP_COLLECTION__ + state: missing + version: 0.9.9.0 + - id: toolshed.g2.bx.psu.edu/repos/iuc/humann2_regroup_table/humann2_regroup_table/0.9.9.0 servers: - server: http://apostl.moffitt.org/ state: missing @@ -47223,112 +29683,124 @@ - server: https://hyperbrowser.uio.no/coloc-stats state: missing - server: https://galaxy.mesocentre.uca.fr - state: local + state: missing - server: https://galaxy.pasteur.fr/ state: missing - server: https://galaxytrakr.org/ - state: local + state: missing - server: http://igg.cloud.ba.infn.it/galaxy - state: local + state: missing - server: https://galaxy.hyphy.org/ - state: local + state: missing - server: https://www.immportgalaxy.org/ state: missing - server: http://galaxy.interactomix.com/ - state: local + state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: local - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr - state: local + state: missing - server: http://galaxy.inf.ethz.ch state: missing - server: https://palfinder.ls.manchester.ac.uk/ state: missing - server: http://pepsimili.e-nios.com:8080/ - state: local - - server: https://galaxy.bio.di.uminho.pt/ - state: local + state: missing - server: https://usegalaxy.org.au - state: local + state: inexact + versions: + - 0.11.1.0 + - 0.11.1.1 - server: https://usegalaxy.be/ - state: local + state: exact + version: 0.9.9.0 - server: https://usegalaxy.cz/ - state: local + state: missing - server: https://usegalaxy.eu - state: local + state: missing - server: https://usegalaxy.fr/ - state: local + state: inexact + versions: + - 0.11.1.0 + - 0.11.1.1 - server: https://usegalaxy.no/ - state: local + state: inexact + versions: + - 0.11.1.0 + - 0.11.1.1 - server: https://usegalaxy.org - state: local + state: missing - server: https://viralvariant.anses.fr/ - state: local - version: local - - id: cat1 + state: missing + version: 0.9.9.0 + - id: toolshed.g2.bx.psu.edu/repos/iuc/humann2_renorm_table/humann2_renorm_table/0.9.9.0 servers: - server: http://apostl.moffitt.org/ - state: local + state: missing - server: http://mbac.gmu.edu:8080/ - state: local + state: missing - server: https://vm-chemflow-francegrille.eu/ state: missing - server: https://iris.angers.inra.fr/galaxypub-cfbp state: missing - server: https://hyperbrowser.uio.no/coloc-stats - state: local + state: missing - server: https://galaxy.mesocentre.uca.fr - state: local + state: missing - server: https://galaxy.pasteur.fr/ - state: local + state: missing - server: https://galaxytrakr.org/ - state: local + state: missing - server: http://igg.cloud.ba.infn.it/galaxy - state: local + state: missing - server: https://galaxy.hyphy.org/ - state: local + state: missing - server: https://www.immportgalaxy.org/ state: missing - server: http://galaxy.interactomix.com/ state: missing - server: 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versions: + - 0.11.1.1 + - 0.11.1.0 - server: https://usegalaxy.org - state: local + state: missing - server: https://viralvariant.anses.fr/ - state: local - version: local - - id: interactive_tool_phyloseq + state: missing + version: 0.9.9.0 + - id: toolshed.g2.bx.psu.edu/repos/iuc/metaphlan2/metaphlan2/2.6.0.0 servers: - server: http://apostl.moffitt.org/ state: missing @@ -47341,7 +29813,9 @@ - server: https://hyperbrowser.uio.no/coloc-stats state: missing - server: https://galaxy.mesocentre.uca.fr - state: missing + state: inexact + versions: + - 2.6.0.1 - server: https://galaxy.pasteur.fr/ state: missing - server: https://galaxytrakr.org/ @@ -47356,8 +29830,6 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr @@ -47368,26 +29840,92 @@ state: missing - server: http://pepsimili.e-nios.com:8080/ 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state: missing + - server: https://galaxy.mesocentre.uca.fr + state: exact + version: 2.6.0.0 + - server: https://galaxy.pasteur.fr/ + state: missing + - server: https://galaxytrakr.org/ state: missing + - server: http://igg.cloud.ba.infn.it/galaxy + state: missing + - server: https://galaxy.hyphy.org/ + state: missing + - server: https://www.immportgalaxy.org/ + state: missing + - server: http://galaxy.interactomix.com/ + state: missing + - server: https://galaxy-web.ipk-gatersleben.de + state: missing + - server: https://neo.engr.uconn.edu/ + state: missing + - server: https://mississippi.sorbonne-universite.fr + state: missing + - server: http://galaxy.inf.ethz.ch + state: missing + - server: https://palfinder.ls.manchester.ac.uk/ + state: missing + - server: http://pepsimili.e-nios.com:8080/ + state: missing + - server: https://usegalaxy.org.au + state: exact + version: 2.6.0.0 + - server: https://usegalaxy.be/ + state: exact + version: 2.6.0.0 + - server: https://usegalaxy.cz/ + state: exact + version: 2.6.0.0 - server: https://usegalaxy.eu - state: local + state: exact + version: 2.6.0.0 - server: https://usegalaxy.fr/ - state: local + state: exact + version: 2.6.0.0 - server: https://usegalaxy.no/ - state: missing + state: exact + version: 2.6.0.0 - server: https://usegalaxy.org - state: local + state: missing - server: https://viralvariant.anses.fr/ state: missing - version: local - - id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_head_tool/9.5+galaxy2 + version: 2.6.0.0 + - id: toolshed.g2.bx.psu.edu/repos/iuc/mothur_align_seqs/mothur_align_seqs/1.36.1.0 servers: - server: http://apostl.moffitt.org/ state: missing @@ -47402,67 +29940,60 @@ - server: https://galaxy.mesocentre.uca.fr state: inexact versions: - - 9.5+galaxy3 - - 1.1.0 + - 1.39.5.0 - server: https://galaxy.pasteur.fr/ state: missing - server: https://galaxytrakr.org/ - state: exact - version: 9.5+galaxy2 + state: missing - server: http://igg.cloud.ba.infn.it/galaxy state: missing - server: https://galaxy.hyphy.org/ - state: inexact - versions: - - 9.5+galaxy3 + state: missing - server: https://www.immportgalaxy.org/ state: missing - server: http://galaxy.interactomix.com/ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr - state: inexact - versions: - - 9.5+galaxy3 + state: missing - server: http://galaxy.inf.ethz.ch state: missing - server: https://palfinder.ls.manchester.ac.uk/ state: missing - server: http://pepsimili.e-nios.com:8080/ state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - server: https://usegalaxy.org.au - state: exact - version: 9.5+galaxy2 + state: inexact + versions: + - 1.39.5.0 - server: https://usegalaxy.be/ state: exact - version: 9.5+galaxy2 + version: 1.36.1.0 - server: https://usegalaxy.cz/ - state: exact - version: 9.5+galaxy2 + state: inexact + versions: + - 1.39.5.0 - server: https://usegalaxy.eu state: exact - version: 9.5+galaxy2 + version: 1.36.1.0 - server: https://usegalaxy.fr/ - state: exact - version: 9.5+galaxy2 + state: inexact + versions: + - 1.39.5.0 - server: https://usegalaxy.no/ state: inexact versions: - - 1.1.0 + - 1.39.5.0 - server: https://usegalaxy.org state: exact - version: 9.5+galaxy2 + version: 1.36.1.0 - server: https://viralvariant.anses.fr/ state: missing - version: 9.5+galaxy2 - - id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/9.3+galaxy1 + version: 1.36.1.0 + - id: toolshed.g2.bx.psu.edu/repos/iuc/mothur_classify_otu/mothur_classify_otu/1.36.1.0 servers: - server: http://apostl.moffitt.org/ state: missing @@ -47477,78 +30008,60 @@ - server: https://galaxy.mesocentre.uca.fr state: inexact versions: - - 1.1.3 - - 9.5+galaxy3 + - 1.39.5.0 - server: https://galaxy.pasteur.fr/ state: missing - server: https://galaxytrakr.org/ - state: inexact - versions: - - 1.1.3 - - 9.5+galaxy3 - - 9.5+galaxy2 + state: missing - server: http://igg.cloud.ba.infn.it/galaxy state: missing - server: https://galaxy.hyphy.org/ - state: inexact - versions: - - 9.5+galaxy3 + state: missing - server: https://www.immportgalaxy.org/ state: missing - server: http://galaxy.interactomix.com/ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr - state: inexact - versions: - - 9.5+galaxy3 + state: missing - server: http://galaxy.inf.ethz.ch state: missing - server: https://palfinder.ls.manchester.ac.uk/ state: missing - server: http://pepsimili.e-nios.com:8080/ state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - server: https://usegalaxy.org.au - state: exact - version: 9.3+galaxy1 + state: inexact + versions: + - 1.39.5.0 - server: https://usegalaxy.be/ state: exact - version: 9.3+galaxy1 + version: 1.36.1.0 - server: https://usegalaxy.cz/ state: inexact versions: - - 1.1.3 - - 9.5+galaxy3 - - 9.5+galaxy2 - - 9.5+galaxy0 - - 1.1.0 + - 1.39.5.0 - server: https://usegalaxy.eu state: exact - version: 9.3+galaxy1 + version: 1.36.1.0 - server: https://usegalaxy.fr/ - state: exact - version: 9.3+galaxy1 + state: inexact + versions: + - 1.39.5.0 - server: https://usegalaxy.no/ state: inexact versions: - - 1.1.3 - - 1.1.2 - - 1.1.1 - - 1.1.0 + - 1.39.5.0 - server: https://usegalaxy.org state: exact - version: 9.3+galaxy1 + version: 1.36.1.0 - server: https://viralvariant.anses.fr/ state: missing - version: 9.3+galaxy1 - - id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/9.5+galaxy2 + version: 1.36.1.0 + - id: toolshed.g2.bx.psu.edu/repos/iuc/mothur_classify_seqs/mothur_classify_seqs/1.36.1.0 servers: - server: http://apostl.moffitt.org/ state: missing @@ -47563,69 +30076,60 @@ - server: https://galaxy.mesocentre.uca.fr state: inexact versions: - - 9.5+galaxy3 - - 1.1.2 + - 1.39.5.0 - server: https://galaxy.pasteur.fr/ state: missing - server: https://galaxytrakr.org/ - state: exact - version: 9.5+galaxy2 + state: missing - server: http://igg.cloud.ba.infn.it/galaxy state: missing - server: https://galaxy.hyphy.org/ - state: inexact - versions: - - 9.5+galaxy3 + state: missing - server: https://www.immportgalaxy.org/ state: missing - server: http://galaxy.interactomix.com/ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr - state: inexact - versions: - - 9.5+galaxy3 + state: missing - server: http://galaxy.inf.ethz.ch state: missing - server: https://palfinder.ls.manchester.ac.uk/ state: missing - server: http://pepsimili.e-nios.com:8080/ state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - server: https://usegalaxy.org.au - state: exact - version: 9.5+galaxy2 + state: inexact + versions: + - 1.39.5.0 - server: https://usegalaxy.be/ state: exact - version: 9.5+galaxy2 + version: 1.36.1.0 - server: https://usegalaxy.cz/ - state: exact - version: 9.5+galaxy2 + state: inexact + versions: + - 1.39.5.0 - server: https://usegalaxy.eu state: exact - version: 9.5+galaxy2 + version: 1.36.1.0 - server: https://usegalaxy.fr/ - state: exact - version: 9.5+galaxy2 + state: inexact + versions: + - 1.39.5.0 - server: https://usegalaxy.no/ state: inexact versions: - - 1.1.2 - - 1.1.1 - - 1.1.0 + - 1.39.5.0 - server: https://usegalaxy.org state: exact - version: 9.5+galaxy2 + version: 1.36.1.0 - server: https://viralvariant.anses.fr/ state: missing - version: 9.5+galaxy2 - - id: toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.1 + version: 1.36.1.0 + - id: toolshed.g2.bx.psu.edu/repos/iuc/mothur_cluster_split/mothur_cluster_split/1.36.1.0 servers: - server: http://apostl.moffitt.org/ state: missing @@ -47640,17 +30144,11 @@ - server: https://galaxy.mesocentre.uca.fr state: inexact versions: - - '1.5' - - '1.4' - - 1.3.0 - - '2.0' - - '1.6' - - 1.2.0 + - 1.39.5.0 - server: https://galaxy.pasteur.fr/ state: missing - server: https://galaxytrakr.org/ - state: exact - version: '2.1' + state: missing - server: http://igg.cloud.ba.infn.it/galaxy state: missing - server: https://galaxy.hyphy.org/ @@ -47661,58 +30159,45 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr - state: inexact - versions: - - '2.0' - - 2.1+galaxy0 + state: missing - server: http://galaxy.inf.ethz.ch state: missing - server: https://palfinder.ls.manchester.ac.uk/ state: missing - server: http://pepsimili.e-nios.com:8080/ state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - server: https://usegalaxy.org.au - state: exact - version: '2.1' + state: inexact + versions: + - 1.39.5.0 - server: https://usegalaxy.be/ state: exact - version: '2.1' + version: 1.36.1.0 - server: https://usegalaxy.cz/ state: inexact versions: - - '1.4' - - '2.0' - - '1.6' - - 1.1.0 + - 1.39.5.0 - server: https://usegalaxy.eu state: exact - version: '2.1' + version: 1.36.1.0 - server: https://usegalaxy.fr/ - state: exact - version: '2.1' + state: inexact + versions: + - 1.39.5.0 - server: https://usegalaxy.no/ state: inexact versions: - - '1.5' - - '1.4' - - 1.3.0 - - '2.0' - - '1.6' - - 1.3.1 + - 1.39.5.0 - server: https://usegalaxy.org state: exact - version: '2.1' + version: 1.36.1.0 - server: https://viralvariant.anses.fr/ state: missing - version: '2.1' - - id: toolshed.g2.bx.psu.edu/repos/iuc/collection_element_identifiers/collection_element_identifiers/0.0.2 + version: 1.36.1.0 + - id: toolshed.g2.bx.psu.edu/repos/iuc/mothur_count_seqs/mothur_count_seqs/1.36.1.0 servers: - server: http://apostl.moffitt.org/ state: missing @@ -47725,13 +30210,13 @@ - server: https://hyperbrowser.uio.no/coloc-stats state: missing - server: https://galaxy.mesocentre.uca.fr - state: exact - version: 0.0.2 + state: inexact + versions: + - 1.39.5.0 - server: https://galaxy.pasteur.fr/ state: missing - server: https://galaxytrakr.org/ - state: exact - version: 0.0.2 + state: missing - server: http://igg.cloud.ba.infn.it/galaxy state: missing - server: https://galaxy.hyphy.org/ @@ -47742,46 +30227,45 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr - state: exact - version: 0.0.2 + state: missing - server: http://galaxy.inf.ethz.ch state: missing - server: https://palfinder.ls.manchester.ac.uk/ state: missing - server: http://pepsimili.e-nios.com:8080/ state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - server: https://usegalaxy.org.au - state: exact - version: 0.0.2 + state: inexact + versions: + - 1.39.5.0 - server: https://usegalaxy.be/ state: exact - version: 0.0.2 + version: 1.36.1.0 - server: https://usegalaxy.cz/ - state: exact - version: 0.0.2 + state: inexact + versions: + - 1.39.5.0 - server: https://usegalaxy.eu state: exact - version: 0.0.2 + version: 1.36.1.0 - server: https://usegalaxy.fr/ - state: exact - version: 0.0.2 + state: inexact + versions: + - 1.39.5.0 - server: https://usegalaxy.no/ - state: exact - version: 0.0.2 + state: inexact + versions: + - 1.39.5.0 - server: https://usegalaxy.org state: exact - version: 0.0.2 + version: 1.36.1.0 - server: https://viralvariant.anses.fr/ state: missing - version: 0.0.2 - - id: 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exact - version: 1.34.0+galaxy0 + state: inexact + versions: + - 1.39.5.0 - server: https://usegalaxy.be/ state: exact - version: 1.34.0+galaxy0 + version: 1.36.1.0 - server: https://usegalaxy.cz/ - state: exact - version: 1.34.0+galaxy0 + state: inexact + versions: + - 1.39.5.0 - server: https://usegalaxy.eu state: exact - version: 1.34.0+galaxy0 + version: 1.36.1.0 - server: https://usegalaxy.fr/ - state: exact - version: 1.34.0+galaxy0 + state: inexact + versions: + - 1.39.5.0 - server: https://usegalaxy.no/ state: inexact versions: - - 1.20+galaxy0 - - 1.18+galaxy0 - - 1.14+galaxy0 - - 1.16+galaxy0 + - 1.39.5.0 - server: https://usegalaxy.org state: exact - version: 1.34.0+galaxy0 + version: 1.36.1.0 - server: https://viralvariant.anses.fr/ state: missing - version: 1.34.0+galaxy0 - - id: toolshed.g2.bx.psu.edu/repos/iuc/dada2_mergepairs/dada2_mergePairs/1.34.0+galaxy0 + version: 1.36.1.0 + - id: toolshed.g2.bx.psu.edu/repos/iuc/mothur_pre_cluster/mothur_pre_cluster/1.36.1.0 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+30760,9 @@ - server: https://galaxy.mesocentre.uca.fr state: inexact versions: - - 1.34.0+galaxy1 - - 1.20+galaxy1 - - 1.28+galaxy0 - - 1.30.0+galaxy0 - - 1.20+galaxy0 + - 1.39.5.0 - server: https://galaxy.pasteur.fr/ - state: inexact - versions: - - 1.30.0+galaxy0 + state: missing - server: https://galaxytrakr.org/ state: missing - server: http://igg.cloud.ba.infn.it/galaxy @@ -48363,8 +30775,6 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr @@ -48375,37 +30785,35 @@ state: missing - server: http://pepsimili.e-nios.com:8080/ state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - server: https://usegalaxy.org.au - state: exact - version: 1.34.0+galaxy0 + state: inexact + versions: + - 1.39.5.0 - server: https://usegalaxy.be/ state: exact - version: 1.34.0+galaxy0 + 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1.34.0+galaxy0 + state: inexact + versions: + - 1.39.5.0 - server: https://usegalaxy.eu state: exact - version: 1.34.0+galaxy0 + version: 1.36.1.0 - server: https://usegalaxy.fr/ - state: exact - version: 1.34.0+galaxy0 + state: inexact + versions: + - 1.39.5.0 - server: https://usegalaxy.no/ state: inexact versions: - - 1.20+galaxy0 - - 1.18+galaxy0 - - 1.14+galaxy0 - - 1.16+galaxy0 + - 1.39.5.0 - server: https://usegalaxy.org state: exact - version: 1.34.0+galaxy0 + version: 1.36.1.0 - server: https://viralvariant.anses.fr/ state: missing - version: 1.34.0+galaxy0 - - id: toolshed.g2.bx.psu.edu/repos/iuc/phyloseq_from_dada2/phyloseq_from_dada2/1.50.0+galaxy3 + version: 1.36.1.0 + - id: toolshed.g2.bx.psu.edu/repos/saskia-hiltemann/krona_text/krona-text/1 servers: - server: http://apostl.moffitt.org/ state: missing @@ -48496,8 +30894,7 @@ - server: https://hyperbrowser.uio.no/coloc-stats state: missing - server: https://galaxy.mesocentre.uca.fr - state: exact - version: 1.50.0+galaxy3 + state: missing - server: https://galaxy.pasteur.fr/ state: missing - server: https://galaxytrakr.org/ @@ -48512,8 +30909,6 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr @@ -48524,62 +30919,57 @@ state: missing - server: http://pepsimili.e-nios.com:8080/ state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - server: https://usegalaxy.org.au state: exact - version: 1.50.0+galaxy3 + version: '1' - server: https://usegalaxy.be/ state: exact - version: 1.50.0+galaxy3 + version: '1' - server: https://usegalaxy.cz/ state: exact - version: 1.50.0+galaxy3 + version: '1' - server: https://usegalaxy.eu state: exact - version: 1.50.0+galaxy3 + version: '1' - server: https://usegalaxy.fr/ state: exact - version: 1.50.0+galaxy3 + version: '1' - server: https://usegalaxy.no/ - state: 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general-tutorial type: tutorial - url: https://training.galaxyproject.org//topics/microbiome/tutorials/dada-16S/tutorial.html + url: https://training.galaxyproject.org//topics/microbiome/tutorials/general-tutorial/tutorial.html urls: - hands_on: https://training.galaxyproject.org/training-material/api/topics/microbiome/tutorials/dada-16S/tutorial.json - slides: https://training.galaxyproject.org/training-material/api/topics/microbiome/tutorials/dada-16S/tutorial.json - version: 12 - video: true - video_versions: 1 + hands_on: https://training.galaxyproject.org/training-material/api/topics/microbiome/tutorials/general-tutorial/tutorial.json + slides: https://training.galaxyproject.org/training-material/api/topics/microbiome/tutorials/general-tutorial/tutorial.json + version: 4 + video: false + video_versions: 0 video_view: 0 - visit_duration: 328 - visitors: 9282 + visit_duration: 344 + visitors: 11493 workflows: - - creators: - - class: Organization - isNew: true - name: '' - - class: 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tool_panel_section_label: Quality\ + \ Control\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: multiqc\n\ + \ owner: iuc\n revisions: abfd8a6544d7\n tool_panel_section_label: Quality\ + \ Control\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: nanoplot\n\ + \ owner: iuc\n revisions: edbb6c5028f5\n tool_panel_section_label: Nanopore\n\ + \ tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: nanoplot\n owner:\ + \ iuc\n revisions: a02b8b3f5a0c\n tool_panel_section_label: Nanopore\n tool_shed_url:\ + \ https://toolshed.g2.bx.psu.edu/\n- name: newick_utils\n owner: iuc\n revisions:\ + \ b4163d2f64ab\n tool_panel_section_label: Graph/Display Data\n tool_shed_url:\ + \ https://toolshed.g2.bx.psu.edu/\n- name: porechop\n owner: iuc\n revisions:\ + \ 5f76b20953e5\n tool_panel_section_label: Nanopore\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n\ + - name: porechop\n owner: iuc\n revisions: 543cbeef3949\n tool_panel_section_label:\ + \ Nanopore\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: samtools_coverage\n\ + \ owner: iuc\n revisions: c4ff13d2aab3\n tool_panel_section_label: SAM/BAM\n\ + \ tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: samtools_depth\n owner:\ + \ iuc\n revisions: 971dc85e9441\n tool_panel_section_label: SAM/BAM\n tool_shed_url:\ + \ https://toolshed.g2.bx.psu.edu/\n- name: samtools_fastx\n owner: iuc\n revisions:\ + \ 66e23b11feae\n tool_panel_section_label: SAM/BAM\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n\ + - name: snpsift\n owner: iuc\n revisions: 5fab4f81391d\n tool_panel_section_label:\ + \ Variant Calling\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: snpsift\n\ + \ owner: iuc\n revisions: 5fab4f81391d\n tool_panel_section_label: Variant\ + \ Calling\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: table_compute\n\ + \ owner: iuc\n revisions: 3bf5661c0280\n tool_panel_section_label: Text Manipulation\n\ + \ tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: collapse_collections\n\ + \ owner: nml\n revisions: 90981f86000f\n tool_panel_section_label: Collection\ + \ Operations\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n" + api: https://training.galaxyproject.org/training-material/api/topics/microbiome/tutorials/pathogen-detection-from-nanopore-foodborne-data/tutorial.json contributions: authorship: - - plushz - bebatut - - vinisalazar + - EngyNasr - paulzierep + editing: + - hrhotz + - wm75 funding: - gallantries + - eosc-life reviewing: - - bebatut - shiltemann - - plushz - - hexylena - - bgruening + - deeptivarshney - paulzierep - - natalie-wa + - bebatut + - bgruening + - gallardoalba + - EngyNasr + - wm75 + - hexylena contributors: - - affiliations: - - uni-freiburg - id: plushz - joined: 2022-03 - name: Polina Polunina - orcid: 0000-0002-0507-4602 - page: https://training.galaxyproject.org/training-material/hall-of-fame/plushz/ - url: https://training.galaxyproject.org/training-material/api/contributors/plushz.json - affiliations: - gallantries - ifb @@ -49146,14 +31773,17 @@ twitter: bebatut url: https://training.galaxyproject.org/training-material/api/contributors/bebatut.json - affiliations: - - unimelb - - melbournebioinformatics - id: vinisalazar - joined: 2025-10 - name: Vini Salazar - orcid: 0000-0002-8362-3195 - page: https://training.galaxyproject.org/training-material/hall-of-fame/vinisalazar/ - url: https://training.galaxyproject.org/training-material/api/contributors/vinisalazar.json + - uni-freiburg + - elixir-europe + elixir_node: de + email: engynasr94@gmail.com + id: EngyNasr + joined: 2021-05 + matrix: EngyNasr:matrix.org + name: Engy Nasr + orcid: 0000-0001-9047-4215 + page: https://training.galaxyproject.org/training-material/hall-of-fame/EngyNasr/ + url: https://training.galaxyproject.org/training-material/api/contributors/EngyNasr.json - affiliations: - uni-freiburg - elixir-europe @@ -49167,10 +31797,49 @@ orcid: 0000-0003-2982-388X page: https://training.galaxyproject.org/training-material/hall-of-fame/paulzierep/ url: https://training.galaxyproject.org/training-material/api/contributors/paulzierep.json + - affiliations: + - elixir-europe + bluesky: hrhotz.bsky.social + contact_for_training: true + elixir_node: ch + email: hrhotz@googlemail.com + fediverse: https://genomic.social/@hrhotz + fediverse_flavor: mastodon + id: hrhotz + joined: 2017-09 + linkedin: hans-rudolf-hotz-542b31 + location: + country: CH + lat: 47.575694 + lon: 7.578796 + matrix: hrhotz:matrix.org + name: Hans-Rudolf Hotz + orcid: 0000-0002-2799-424X + page: https://training.galaxyproject.org/training-material/hall-of-fame/hrhotz/ + url: https://training.galaxyproject.org/training-material/api/contributors/hrhotz.json + - affiliations: + - by-covid + - uni-freiburg + - elixir-europe + - deNBI + - mwk + elixir_node: de + fediverse: https://fediscience.org/@zerodivision + fediverse_flavor: mastodon + former_affiliations: + - eurosciencegateway + id: wm75 + joined: 2017-09 + matrix: wm75:matrix.org + name: Wolfgang Maier + orcid: 0000-0002-9464-6640 + page: https://training.galaxyproject.org/training-material/hall-of-fame/wm75/ + url: https://training.galaxyproject.org/training-material/api/contributors/wm75.json - avatar: https://gallantries.github.io/assets/images/gallantries-logo.png end_date: '2023-09-30' former_members: - abretaud + - hexylena - shiltemann funder_name: Erasmus+ Programme funding_database: erasmusplus @@ -49194,7 +31863,6 @@ - bebatut - colineroyaux - fpsom - - hexylena - yvanlebras name: 'Gallantries: Bridging Training Communities in Life Science, Environment and Health' @@ -49202,31 +31870,19 @@ short_name: Gallantries start_date: '2020-09-01' url: https://training.galaxyproject.org/training-material/api/grants/gallantries.json - - affiliations: - - gallantries - - ifb - - elixir-europe - contact_for_training: true - elixir_node: fr - email: berenice.batut@gmail.com - fediverse: https://piaille.fr/@bebatut - fediverse_flavor: mastodon - former_affiliations: - - uni-freiburg - - deNBI - id: bebatut - joined: 2017-09 - linkedin: berenicebatut - location: - country: FR - lat: 45.77 - lon: 3.08 - matrix: bebatut:matrix.org - name: "B\xE9r\xE9nice Batut" - orcid: 0000-0001-9852-1987 - page: https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/ - twitter: bebatut - url: https://training.galaxyproject.org/training-material/api/contributors/bebatut.json + - avatar: https://www.eosc-life.eu/wp-content/themes/eosc-life-v2/assets/images/eosclogo.png + former_members: + - bgruening + funding_database: cordis + funding_id: '824087' + funding_statement: "EOSC-Life has received funding from the European Union\u2019\ + s Horizon 2020 programme under grant agreement number 824087" + github: false + id: eosc-life + joined: 2023-04 + name: EOSC-Life + page: https://training.galaxyproject.org/training-material/hall-of-fame/eosc-life/ + url: https://training.galaxyproject.org/training-material/api/grants/eosc-life.json - affiliations: - uni-freiburg - nfdi4plants @@ -49257,36 +31913,53 @@ url: https://training.galaxyproject.org/training-material/api/contributors/shiltemann.json - affiliations: - uni-freiburg - id: plushz - joined: 2022-03 - name: Polina Polunina - orcid: 0000-0002-0507-4602 - page: https://training.galaxyproject.org/training-material/hall-of-fame/plushz/ - url: https://training.galaxyproject.org/training-material/api/contributors/plushz.json + - elixir-europe + bluesky: dvarshney.bsky.social + email: varshney@informatik.uni-freiburg.de + id: deeptivarshney + joined: 2022-12 + name: Deepti Varshney + orcid: 0000-0003-0419-6832 + page: https://training.galaxyproject.org/training-material/hall-of-fame/deeptivarshney/ + url: https://training.galaxyproject.org/training-material/api/contributors/deeptivarshney.json + - affiliations: + - uni-freiburg + - elixir-europe + - deNBI + - mwk + - materialvitaldigital + email: zierep@informatik.uni-freiburg.de + id: paulzierep + joined: 2023-02 + name: Paul Zierep + orcid: 0000-0003-2982-388X + page: https://training.galaxyproject.org/training-material/hall-of-fame/paulzierep/ + url: https://training.galaxyproject.org/training-material/api/contributors/paulzierep.json - affiliations: - - erasmusmc - gallantries - - by-covid + - ifb - elixir-europe - - elixir-converge - contact_for_training: false - elixir_node: nl + contact_for_training: true + elixir_node: fr + email: berenice.batut@gmail.com + fediverse: https://piaille.fr/@bebatut + fediverse_flavor: mastodon former_affiliations: - - deNBI - - avans-atgm - uni-freiburg - id: hexylena + - deNBI + id: bebatut joined: 2017-09 + linkedin: berenicebatut location: - country: NL - lat: 51.91 - lon: 4.46 - maintainer_contact: gitter - matrix: hexylena:matrix.org - name: Helena Rasche - orcid: 0000-0001-9760-8992 - page: https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/ - url: https://training.galaxyproject.org/training-material/api/contributors/hexylena.json + country: FR + lat: 45.77 + lon: 3.08 + matrix: bebatut:matrix.org + name: "B\xE9r\xE9nice Batut" + orcid: 0000-0001-9852-1987 + page: https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/ + twitter: bebatut + url: https://training.galaxyproject.org/training-material/api/contributors/bebatut.json - affiliations: - deNBI - mwk @@ -49317,150 +31990,253 @@ page: https://training.galaxyproject.org/training-material/hall-of-fame/bgruening/ twitter: bjoerngruening url: https://training.galaxyproject.org/training-material/api/contributors/bgruening.json + - elixir_node: de + former_affiliations: + - uni-freiburg + - elixir-europe + id: gallardoalba + joined: 2020-11 + name: "Crist\xF3bal Gallardo" + orcid: 0000-0002-5752-2155 + page: https://training.galaxyproject.org/training-material/hall-of-fame/gallardoalba/ + url: https://training.galaxyproject.org/training-material/api/contributors/gallardoalba.json + - affiliations: + - uni-freiburg + - elixir-europe + elixir_node: de + email: engynasr94@gmail.com + id: EngyNasr + joined: 2021-05 + matrix: EngyNasr:matrix.org + name: Engy Nasr + orcid: 0000-0001-9047-4215 + page: https://training.galaxyproject.org/training-material/hall-of-fame/EngyNasr/ + url: https://training.galaxyproject.org/training-material/api/contributors/EngyNasr.json - affiliations: + - by-covid - uni-freiburg - elixir-europe - deNBI - mwk - - materialvitaldigital - email: zierep@informatik.uni-freiburg.de - id: paulzierep - joined: 2023-02 - name: Paul Zierep - orcid: 0000-0003-2982-388X - page: https://training.galaxyproject.org/training-material/hall-of-fame/paulzierep/ - url: https://training.galaxyproject.org/training-material/api/contributors/paulzierep.json - - email: nwhitak5@jh.edu - id: natalie-wa - joined: 2024-08 - name: Natalie Whitaker-Allen - page: https://training.galaxyproject.org/training-material/hall-of-fame/natalie-wa/ - url: https://training.galaxyproject.org/training-material/api/contributors/natalie-wa.json - dir: topics/microbiome/tutorials/metagenomics-assembly + elixir_node: de + fediverse: https://fediscience.org/@zerodivision + fediverse_flavor: mastodon + former_affiliations: + - eurosciencegateway + id: wm75 + joined: 2017-09 + matrix: wm75:matrix.org + name: Wolfgang Maier + orcid: 0000-0002-9464-6640 + page: https://training.galaxyproject.org/training-material/hall-of-fame/wm75/ + url: https://training.galaxyproject.org/training-material/api/contributors/wm75.json + - affiliations: + - elixir-europe + contact_for_training: false + elixir_node: nl + former_affiliations: + - deNBI + - avans-atgm + - uni-freiburg + - erasmusmc + - gallantries + - by-covid + - elixir-converge + id: hexylena + joined: 2017-09 + location: + country: NL + lat: 51.91 + lon: 4.46 + maintainer_contact: gitter + matrix: hexylena:matrix.org + name: Helena Rasche + orcid: 0000-0001-9760-8992 + page: https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/ + url: https://training.galaxyproject.org/training-material/api/contributors/hexylena.json + dir: topics/microbiome/tutorials/pathogen-detection-from-nanopore-foodborne-data edam_ontology: - topic_3174 + - topic_3305 + - topic_0637 - topic_0196 + - topic_0634 + - topic_0080 edam_operation: - - Sequence alignment analysis - - Statistical calculation - - Primer removal - - Genome assembly + - Variant calling + - Phylogenetic tree reconstruction + - Mapping assembly + - Multiple sequence alignment + - Base-calling - Visualisation - - Local alignment - Sequence composition calculation - - Formatting - - Variant calling - - Sequence file editing + - Aggregation + - Phylogenetic tree generation + - Phylogenetic tree analysis + - De-novo assembly + - Pairwise sequence alignment + - Mapping + - Scatter plot plotting + - Sequence assembly + - Box-Whisker plot plotting - Sequence assembly visualisation - - Read mapping - - Sequence assembly validation - - Data handling - - Read pre-processing - - Sequence contamination filtering - - Sequence trimming - Sequencing quality control + - Statistical calculation + - Genome assembly + - Multilocus sequence typing + - Sequence contamination filtering + - Antimicrobial resistance prediction + - Data handling + - Sequence alignment analysis + - Cross-assembly + - Taxonomic classification + - Validation edam_topic: - Metagenomics + - Public health and epidemiology + - Taxonomy - Sequence assembly - exact_supported_servers: [] + - Pathology + - Sequence analysis + exact_supported_servers: + - UseGalaxy.eu feedback_mean_note: null feedback_number: 0 hands_on: true - id: microbiome/metagenomics-assembly + id: microbiome/pathogen-detection-from-nanopore-foodborne-data inexact_supported_servers: + - UseGalaxy.org.au + - UseGalaxy.be - UseGalaxy.cz - - UseGalaxy.eu - - UseGalaxy.fr - - UseGalaxy.org (Main) js_requirements: - mathjax: 27693 + mathjax: null mermaid: false - key_points: - - Assembly groups reads into contigs and scaffolds. - - de Brujin Graphs use k-mers to assembly reads. - - MetaSPAdes and MEGAHIT are short-read assemblers. - - MetaQUAST is a tool to assess metagenomic assembly quality. layout: tutorial_hands_on level: Introductory license: CC-BY-4.0 - mod_date: '2026-05-11' + mod_date: '2025-11-18' objectives: - - Describe what an assembly is. - - Explain the difference between co-assembly and individual assembly. - - Explain the difference between reads, contigs and scaffolds. - - Explain how tools based on de Bruijn graph work. - - Evaluate the quality of the Assembly with QUAST, Bowtie2, and CoverM-Contig. - - Construct and apply simple assembly pipelines on short read data. - pageviews: 7491 - pub_date: '2022-12-05' + - Check quality reports generated by FastQC and NanoPlot for metagenomics Nanopore + data + - Preprocess the sequencing data to remove adapters, poor quality base content and + host/contaminating reads + - Perform taxonomy profiling indicating and visualizing up to species level in the + samples + - Identify pathogens based on the found virulence factor gene products via assembly, + identify strains and indicate all antimicrobial resistance genes in samples + - Identify pathogens via SNP calling and build the consensus gemone of the samples + - Relate all samples' pathogenic genes for tracking pathogens via phylogenetic trees + and heatmaps + pageviews: 8528 + pub_date: '2023-01-26' questions: - - Why metagenomic data should be assembled? - - What is the difference between co-assembly and individual assembly? - - What is the difference between reads, contigs and scaffolds? - - How tools based on De Bruijn graph work? - - How to assess the quality of metagenomic data assembly? + - What are the preprocessing steps to prepare ONT sequencing data for further analysis? + - How to identify pathogens using sequencing data? + - How to track the found pathogens through all your samples datasets? recordings: - captioners: - - bebatut - - sophia120199 - date: '2023-05-02' + - EngyNasr + date: '2023-05-01' galaxy_version: '23.01' - length: 1H - speakers: - - bebatut - youtube_id: 1ZYGy85Im7w - - captioners: - - gdefazio - - natalie-wa - date: '2026-03-26' - galaxy_version: 25.1.2.dev0 - length: 1H15M + length: 1H45M speakers: - - gdefazio - youtube_id: KzqLR4btsic + - EngyNasr + youtube_id: gQHb_jkj-Z0 + - bot-timestamp: 1723837296 + captioners: + - EngyNasr + date: '2024-08-16' + galaxy_version: '24.1.2.dev0 ' + length: 1H55M + speakers: + - EngyNasr + youtube_id: rGP-BKYwUbc redirect_from: - - /topics/metagenomics/tutorials/metagenomics-assembly/tutorial - - /short/microbiome/metagenomics-assembly - - /short/T00202 - - /short/T00386 - short_id: T00386 + - /topics/metagenomics/tutorials/pathogen-detection-from-nanopore-foodborne-data/tutorial + - /short/microbiome/pathogen-detection-from-nanopore-foodborne-data + - /short/T00208 + - /short/T00393 + short_id: T00393 short_tools: - - metaspades - - collection_column_join + - __FILTER_EMPTY_DATASETS__ + - abricate + - bcftools_consensus + - __FILTER_FAILED_DATASETS__ - bandage_image - - filter_tabular - - coverm_contig - - megahit_contig2fastg - - bamtools + - collection_column_join + - clair3 + - Remove beginning1 + - ggplot2_heatmap + - Count1 + - collapse_dataset + - collection_element_identifiers + - regex1 + - tp_head_tool + - fasta2tab + - fasta_merge_files_and_filter_unique_sequences + - bamtools_split_mapped + - porechop + - bedtools_getfastabed + - samtools_depth + - medaka_consensus_pipeline + - minimap2 + - taxonomy_krona_chart + - krakentools_kreport2krona + - samtools_fastx + - flye + - mlst + - kraken2 + - bcftools_norm + - split_file_to_collection + - clustalw + - Cut1 + - snpSift_extractFields + - Grouping1 + - samtools_coverage + - tp_replace_in_column + - param_value_from_file + - tp_multijoin_tool + - newick_display + - fastp + - barchart_gnuplot + - Add_a_column1 + - tp_find_and_replace + - krakentools_extract_kraken_reads + - Paste1 + - nanoplot + - tp_sorted_uniq + - snpSift_filter + - tp_cut_tool + - Grep1 + - tab2fasta + - __BUILD_LIST__ + - regexColumn1 + - table_compute + - compose_text_param + - add_line_to_file - fastqc - - bandage_info - - megahit - - bowtie2 - - tp_cat - - quast - - ngsutils_bam_filter - - seqtk_subseq - - random_lines1 - - cutadapt - - bg_uniq + - fasttree + - tp_split_on_column + - multiqc + - CONVERTER_gz_to_uncompressed slides: false slides_recordings: false subtopic: metagenomics supported_servers: - exact: [] - inexact: - - name: UseGalaxy.cz - url: https://usegalaxy.cz/ - usegalaxy: false + exact: - name: UseGalaxy.eu url: https://usegalaxy.eu usegalaxy: true - - name: UseGalaxy.fr - url: https://usegalaxy.fr/ - usegalaxy: true - - name: UseGalaxy.org (Main) - url: https://usegalaxy.org + inexact: + - name: UseGalaxy.org.au + url: https://usegalaxy.org.au usegalaxy: true + - name: UseGalaxy.be + url: https://usegalaxy.be/ + usegalaxy: false + - name: UseGalaxy.cz + url: https://usegalaxy.cz/ + usegalaxy: false supported_servers_matrix: servers: - name: APOSTL @@ -49502,9 +32278,6 @@ - name: IPK Galaxy Blast Suite url: https://galaxy-web.ipk-gatersleben.de usegalaxy: false - - name: Lebanese University Galaxy - url: http://galaxy.ul.edu.lb/ - usegalaxy: false - name: Mandoiu Lab url: https://neo.engr.uconn.edu/ usegalaxy: false @@ -49520,9 +32293,6 @@ - name: PepSimili url: http://pepsimili.e-nios.com:8080/ usegalaxy: false - - name: PhagePromotor - url: https://galaxy.bio.di.uminho.pt/ - usegalaxy: false - name: UseGalaxy.org.au url: https://usegalaxy.org.au usegalaxy: true @@ -49548,66 +32318,3073 @@ url: https://viralvariant.anses.fr/ usegalaxy: false tools: - - id: random_lines1 + - id: CONVERTER_gz_to_uncompressed + servers: + - server: http://apostl.moffitt.org/ + state: missing + - server: http://mbac.gmu.edu:8080/ + state: missing + - server: 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https://usegalaxy.fr/ + state: exact + version: 0.23.4+galaxy0 + - server: https://usegalaxy.no/ + state: inexact + versions: + - 0.20.1+galaxy0 + - 0.23.2+galaxy0 + - 0.19.5+galaxy1 + - server: https://usegalaxy.org + state: exact + version: 0.23.4+galaxy0 + - server: https://viralvariant.anses.fr/ + state: inexact + versions: + - 0.23.2+galaxy0 + - 1.0.1+galaxy2 + version: 0.23.4+galaxy0 + - id: toolshed.g2.bx.psu.edu/repos/iuc/fasttree/fasttree/2.1.10+galaxy1 + servers: + - server: http://apostl.moffitt.org/ + state: missing + - server: http://mbac.gmu.edu:8080/ + state: missing + - server: https://vm-chemflow-francegrille.eu/ + state: missing + - server: https://iris.angers.inra.fr/galaxypub-cfbp + state: missing + - server: https://hyperbrowser.uio.no/coloc-stats + state: missing + - server: https://galaxy.mesocentre.uca.fr + state: exact + version: 2.1.10+galaxy1 + - server: https://galaxy.pasteur.fr/ + state: missing + - server: https://galaxytrakr.org/ + state: inexact + 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+ version: 2.1.10+galaxy1 - server: https://usegalaxy.fr/ state: exact - version: 0.1.1 + version: 2.1.10+galaxy1 - server: https://usegalaxy.no/ state: exact - version: 0.1.1 + version: 2.1.10+galaxy1 - server: https://usegalaxy.org state: exact - version: 0.1.1 + version: 2.1.10+galaxy1 - server: https://viralvariant.anses.fr/ state: missing - version: 0.1.1 - - id: toolshed.g2.bx.psu.edu/repos/bgruening/unique/bg_uniq/0.3 + version: 2.1.10+galaxy1 + - id: toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_heatmap/ggplot2_heatmap/3.4.0+galaxy0 servers: - server: http://apostl.moffitt.org/ state: missing @@ -49692,12 +35545,15 @@ - server: https://hyperbrowser.uio.no/coloc-stats state: missing - server: https://galaxy.mesocentre.uca.fr - state: exact - version: '0.3' + state: inexact + versions: + - 3.3.5+galaxy0 - server: https://galaxy.pasteur.fr/ state: missing - server: https://galaxytrakr.org/ - state: missing + state: inexact + versions: + - 3.5.1+galaxy1 - server: http://igg.cloud.ba.infn.it/galaxy state: missing - server: https://galaxy.hyphy.org/ @@ -49708,8 +35564,6 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr @@ -49720,30 +35574,33 @@ state: missing - server: http://pepsimili.e-nios.com:8080/ state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - server: https://usegalaxy.org.au - state: missing + state: exact + version: 3.4.0+galaxy0 - server: https://usegalaxy.be/ - state: missing + state: exact + version: 3.4.0+galaxy0 - server: https://usegalaxy.cz/ state: exact - version: '0.3' + version: 3.4.0+galaxy0 - server: https://usegalaxy.eu state: exact - version: '0.3' + version: 3.4.0+galaxy0 - server: https://usegalaxy.fr/ state: exact - version: '0.3' + version: 3.4.0+galaxy0 - server: https://usegalaxy.no/ - state: missing + state: inexact + versions: + - 3.3.5+galaxy0 + - 2.2.1 - server: https://usegalaxy.org state: exact - version: '0.3' + version: 3.4.0+galaxy0 - server: https://viralvariant.anses.fr/ state: missing - version: '0.3' - - id: toolshed.g2.bx.psu.edu/repos/devteam/bamtools/bamtools/2.5.1+galaxy0 + version: 3.4.0+galaxy0 + - id: toolshed.g2.bx.psu.edu/repos/iuc/kraken2/kraken2/2.1.1+galaxy1 servers: - server: http://apostl.moffitt.org/ state: missing @@ -49757,12 +35614,15 @@ state: missing - server: https://galaxy.mesocentre.uca.fr state: exact - version: 2.5.1+galaxy0 + version: 2.1.1+galaxy1 - server: https://galaxy.pasteur.fr/ state: missing - server: https://galaxytrakr.org/ - state: exact - version: 2.5.1+galaxy0 + state: inexact + versions: + - 2.1.3+galaxy2 + - 2.17.1+galaxy0 + - 2.0.8_beta+galaxy0 - server: http://igg.cloud.ba.infn.it/galaxy state: missing - server: https://galaxy.hyphy.org/ @@ -49773,54 +35633,175 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr - state: inexact - versions: - - 2.5.3+galaxy0 + state: missing - server: http://galaxy.inf.ethz.ch state: missing - server: https://palfinder.ls.manchester.ac.uk/ state: missing - server: http://pepsimili.e-nios.com:8080/ + state: exact + version: 2.1.1+galaxy1 + - server: https://usegalaxy.org.au + state: exact + version: 2.1.1+galaxy1 + - server: https://usegalaxy.be/ + state: exact + version: 2.1.1+galaxy1 + - server: https://usegalaxy.cz/ + state: exact + version: 2.1.1+galaxy1 + - server: https://usegalaxy.eu + state: exact + version: 2.1.1+galaxy1 + - server: https://usegalaxy.fr/ + state: exact + version: 2.1.1+galaxy1 + - server: https://usegalaxy.no/ + state: exact + version: 2.1.1+galaxy1 + - server: https://usegalaxy.org + state: exact + version: 2.1.1+galaxy1 + - server: https://viralvariant.anses.fr/ + state: missing + version: 2.1.1+galaxy1 + - id: toolshed.g2.bx.psu.edu/repos/iuc/krakentools_extract_kraken_reads/krakentools_extract_kraken_reads/1.2+galaxy1 + servers: + - server: http://apostl.moffitt.org/ state: missing - - server: https://galaxy.bio.di.uminho.pt/ + - server: http://mbac.gmu.edu:8080/ state: missing - - server: https://usegalaxy.org.au + - server: https://vm-chemflow-francegrille.eu/ + state: missing + - server: https://iris.angers.inra.fr/galaxypub-cfbp + state: missing + - server: https://hyperbrowser.uio.no/coloc-stats + state: missing + - server: https://galaxy.mesocentre.uca.fr state: inexact versions: - - 2.5.3+galaxy0 - - 2.5.2+galaxy2 - - 2.5.2+galaxy3 + - 1.2+galaxy2 + - 1.2.1+galaxy0 + - server: https://galaxy.pasteur.fr/ + state: exact + version: 1.2+galaxy1 + - server: https://galaxytrakr.org/ + state: inexact + versions: + - 1.2.1+galaxy0 + - server: http://igg.cloud.ba.infn.it/galaxy + state: missing + - server: https://galaxy.hyphy.org/ + state: missing + - server: https://www.immportgalaxy.org/ + state: missing + - server: http://galaxy.interactomix.com/ + state: missing + - server: https://galaxy-web.ipk-gatersleben.de + state: missing + - server: https://neo.engr.uconn.edu/ + state: missing + - server: https://mississippi.sorbonne-universite.fr + state: missing + - server: http://galaxy.inf.ethz.ch + state: missing + - server: https://palfinder.ls.manchester.ac.uk/ + state: missing + - server: http://pepsimili.e-nios.com:8080/ + state: missing + - server: https://usegalaxy.org.au + state: exact + version: 1.2+galaxy1 - server: https://usegalaxy.be/ state: exact - version: 2.5.1+galaxy0 + version: 1.2+galaxy1 - server: https://usegalaxy.cz/ + state: exact + version: 1.2+galaxy1 + - server: https://usegalaxy.eu + state: exact + version: 1.2+galaxy1 + - server: https://usegalaxy.fr/ + state: exact + version: 1.2+galaxy1 + - server: https://usegalaxy.no/ + state: missing + - server: https://usegalaxy.org + state: exact + 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https://www.immportgalaxy.org/ + state: missing + - server: http://galaxy.interactomix.com/ + state: missing + - server: https://galaxy-web.ipk-gatersleben.de + state: missing + - server: https://neo.engr.uconn.edu/ + state: missing + - server: https://mississippi.sorbonne-universite.fr + state: missing + - server: http://galaxy.inf.ethz.ch + state: missing + - server: https://palfinder.ls.manchester.ac.uk/ + state: missing + - server: http://pepsimili.e-nios.com:8080/ + state: missing + - server: https://usegalaxy.org.au + state: exact + version: 1.2+galaxy1 + - server: https://usegalaxy.be/ + state: exact + version: 1.2+galaxy1 + - server: https://usegalaxy.cz/ + state: exact + version: 1.2+galaxy1 - server: https://usegalaxy.eu state: exact - version: 2.5.1+galaxy0 + version: 1.2+galaxy1 - server: https://usegalaxy.fr/ state: exact - version: 2.5.1+galaxy0 + version: 1.2+galaxy1 - server: https://usegalaxy.no/ state: exact - version: 2.5.1+galaxy0 + version: 1.2+galaxy1 - server: https://usegalaxy.org state: exact - version: 2.5.1+galaxy0 + version: 1.2+galaxy1 - server: https://viralvariant.anses.fr/ state: missing - version: 2.5.1+galaxy0 - - id: toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.4.5+galaxy1 + version: 1.2+galaxy1 + - id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_consensus_pipeline/medaka_consensus_pipeline/1.7.2+galaxy0 servers: - server: http://apostl.moffitt.org/ state: missing @@ -49833,15 +35814,14 @@ - server: https://hyperbrowser.uio.no/coloc-stats state: missing - server: https://galaxy.mesocentre.uca.fr - state: exact - version: 2.4.5+galaxy1 + state: missing - server: https://galaxy.pasteur.fr/ state: missing - server: https://galaxytrakr.org/ state: inexact versions: - - 2.4.5+galaxy0 - - 2.3.4.3+galaxy0 + - 1.7.2+galaxy1 + - 2.1.1+galaxy0 - server: http://igg.cloud.ba.infn.it/galaxy state: missing - server: https://galaxy.hyphy.org/ @@ -49852,59 +35832,45 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr - state: inexact - versions: - - 2.5.3+galaxy1 - - 2.5.5+galaxy0 + state: missing - server: http://galaxy.inf.ethz.ch state: missing - server: https://palfinder.ls.manchester.ac.uk/ state: missing - server: http://pepsimili.e-nios.com:8080/ state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - server: https://usegalaxy.org.au state: exact - version: 2.4.5+galaxy1 + version: 1.7.2+galaxy0 - server: https://usegalaxy.be/ state: exact - version: 2.4.5+galaxy1 + version: 1.7.2+galaxy0 - server: https://usegalaxy.cz/ - state: inexact - versions: - - 2.5.4+galaxy0 - - 2.5.3+galaxy1 - - 2.5.5+galaxy0 - - 2.5.0+galaxy0 - - 2.2.6.2 - - '0.2' - - 2.3.2.2 - - '0.4' - - '0.3' - - '0.6' - - 2.2.6 + state: exact + version: 1.7.2+galaxy0 - server: https://usegalaxy.eu state: exact - version: 2.4.5+galaxy1 + version: 1.7.2+galaxy0 - server: https://usegalaxy.fr/ state: exact - version: 2.4.5+galaxy1 + version: 1.7.2+galaxy0 - server: https://usegalaxy.no/ - state: exact - version: 2.4.5+galaxy1 + state: inexact + versions: + - 1.4.4+galaxy0 + - 1.0.3+galaxy2 + - 1.3.2+galaxy0 + - 1.4.4+galaxy1 - server: https://usegalaxy.org state: exact - version: 2.4.5+galaxy1 + version: 1.7.2+galaxy0 - server: https://viralvariant.anses.fr/ state: missing - version: 2.4.5+galaxy1 - - id: toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.5.3+galaxy1 + version: 1.7.2+galaxy0 + - id: toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.24+galaxy0 servers: - server: http://apostl.moffitt.org/ state: missing @@ -49918,64 +35884,73 @@ state: missing - server: https://galaxy.mesocentre.uca.fr state: exact - version: 2.5.3+galaxy1 + version: 2.24+galaxy0 - server: https://galaxy.pasteur.fr/ state: missing - server: https://galaxytrakr.org/ state: inexact versions: - - 2.4.5+galaxy0 - - 2.3.4.3+galaxy0 + - 2.28+galaxy2 + - 2.31+galaxy1 - server: http://igg.cloud.ba.infn.it/galaxy state: missing - server: https://galaxy.hyphy.org/ - state: missing + state: inexact + versions: + - 2.28+galaxy2 - server: https://www.immportgalaxy.org/ state: missing - server: http://galaxy.interactomix.com/ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr - state: exact - version: 2.5.3+galaxy1 + state: inexact + versions: + - 2.30+galaxy0 - server: http://galaxy.inf.ethz.ch state: missing - server: https://palfinder.ls.manchester.ac.uk/ state: missing - server: http://pepsimili.e-nios.com:8080/ state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - server: https://usegalaxy.org.au state: exact - version: 2.5.3+galaxy1 + version: 2.24+galaxy0 - server: https://usegalaxy.be/ state: exact - version: 2.5.3+galaxy1 + version: 2.24+galaxy0 - server: https://usegalaxy.cz/ - state: exact - version: 2.5.3+galaxy1 + state: inexact + versions: + - 2.28+galaxy1 + - 2.28+galaxy2 + - 2.28+galaxy0 + - 2.31+galaxy1 + - 2.30+galaxy0 + - 2.17+galaxy2 + - 2.26+galaxy0 + - 2.31+galaxy0 - server: https://usegalaxy.eu state: exact - version: 2.5.3+galaxy1 + version: 2.24+galaxy0 - server: https://usegalaxy.fr/ state: exact - version: 2.5.3+galaxy1 + version: 2.24+galaxy0 - server: https://usegalaxy.no/ state: exact - version: 2.5.3+galaxy1 + version: 2.24+galaxy0 - server: https://usegalaxy.org state: exact - version: 2.5.3+galaxy1 + version: 2.24+galaxy0 - server: https://viralvariant.anses.fr/ - state: missing - version: 2.5.3+galaxy1 - - id: toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.73+galaxy0 + state: inexact + versions: + - 2.28+galaxy2 + version: 2.24+galaxy0 + - id: toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.28+galaxy0 servers: - server: http://apostl.moffitt.org/ state: missing @@ -49989,85 +35964,67 @@ state: missing - server: https://galaxy.mesocentre.uca.fr state: exact - version: 0.73+galaxy0 + version: 2.28+galaxy0 - server: https://galaxy.pasteur.fr/ - state: inexact - versions: - - 0.74+galaxy0 + state: missing - server: https://galaxytrakr.org/ state: inexact versions: - - 0.74+galaxy1 + - 2.28+galaxy2 + - 2.31+galaxy1 - server: http://igg.cloud.ba.infn.it/galaxy state: missing - server: https://galaxy.hyphy.org/ - state: missing + state: inexact + versions: + - 2.28+galaxy2 - server: https://www.immportgalaxy.org/ state: missing - server: http://galaxy.interactomix.com/ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr state: inexact versions: - - 0.74+galaxy1 + - 2.30+galaxy0 - server: http://galaxy.inf.ethz.ch state: missing - server: https://palfinder.ls.manchester.ac.uk/ - state: inexact - versions: - - '0.72' - - 0.72+galaxy1 - - '0.71' - - '0.65' + state: missing - server: http://pepsimili.e-nios.com:8080/ - state: inexact - versions: - - 0.74+galaxy0 - - server: https://galaxy.bio.di.uminho.pt/ - state: inexact - versions: - - 0.74+galaxy0 + state: missing - server: https://usegalaxy.org.au state: exact - version: 0.73+galaxy0 + version: 2.28+galaxy0 - server: https://usegalaxy.be/ state: exact - version: 0.73+galaxy0 + version: 2.28+galaxy0 - server: https://usegalaxy.cz/ - state: inexact - versions: - - 0.74+galaxy0 - - 0.74+galaxy1 - - '0.65' - - '0.69' - - '0.68' - - '0.52' - - '0.67' - - '0.63' - - '0.64' - - '0.62' + state: exact + version: 2.28+galaxy0 - server: https://usegalaxy.eu state: exact - version: 0.73+galaxy0 + version: 2.28+galaxy0 - server: https://usegalaxy.fr/ state: exact - version: 0.73+galaxy0 + version: 2.28+galaxy0 - server: https://usegalaxy.no/ - state: exact - version: 0.73+galaxy0 + state: inexact + versions: + - 2.24+galaxy0 + - 2.17+galaxy0 - server: https://usegalaxy.org state: exact - version: 0.73+galaxy0 + version: 2.28+galaxy0 - server: https://viralvariant.anses.fr/ - state: missing - version: 0.73+galaxy0 - - id: toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/0.8.1+galaxy4 + state: inexact + versions: + - 2.28+galaxy2 + version: 2.28+galaxy0 + - id: toolshed.g2.bx.psu.edu/repos/iuc/mlst/mlst/2.22.0 servers: - server: http://apostl.moffitt.org/ state: missing @@ -50080,14 +36037,12 @@ - server: https://hyperbrowser.uio.no/coloc-stats state: missing - server: https://galaxy.mesocentre.uca.fr - state: exact - version: 0.8.1+galaxy4 + state: missing - server: https://galaxy.pasteur.fr/ - state: inexact - versions: - - 0.8.1+galaxy3 - - server: https://galaxytrakr.org/ state: missing + - server: https://galaxytrakr.org/ + state: exact + version: 2.22.0 - server: http://igg.cloud.ba.infn.it/galaxy state: missing - server: https://galaxy.hyphy.org/ @@ -50098,52 +36053,41 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr - state: inexact - versions: - - 2022.09+galaxy4 - - 0.8.1+galaxy3 + state: missing - server: http://galaxy.inf.ethz.ch state: missing - server: https://palfinder.ls.manchester.ac.uk/ state: missing - server: http://pepsimili.e-nios.com:8080/ state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - server: https://usegalaxy.org.au state: exact - version: 0.8.1+galaxy4 + version: 2.22.0 - server: https://usegalaxy.be/ state: exact - version: 0.8.1+galaxy4 + version: 2.22.0 - server: https://usegalaxy.cz/ - state: inexact - versions: - - 2022.09+galaxy4 + state: exact + version: 2.22.0 - server: https://usegalaxy.eu state: exact - version: 0.8.1+galaxy4 + version: 2.22.0 - server: https://usegalaxy.fr/ state: exact - version: 0.8.1+galaxy4 + version: 2.22.0 - server: https://usegalaxy.no/ - state: inexact - versions: - - 2022.09+galaxy4 - - 0.8.1+galaxy3 - - 0.8.1+galaxy2 + state: exact + version: 2.22.0 - server: https://usegalaxy.org state: exact - version: 0.8.1+galaxy4 + version: 2.22.0 - server: https://viralvariant.anses.fr/ state: missing - version: 0.8.1+galaxy4 - - id: toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_info/0.8.1+galaxy2 + version: 2.22.0 + - id: toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy0 servers: - server: http://apostl.moffitt.org/ state: missing @@ -50157,13 +36101,17 @@ state: missing - server: https://galaxy.mesocentre.uca.fr state: exact - version: 0.8.1+galaxy2 + version: 1.11+galaxy0 - server: https://galaxy.pasteur.fr/ + state: missing + - server: https://galaxytrakr.org/ state: inexact versions: - - 0.8.1+galaxy1 - - server: https://galaxytrakr.org/ - state: missing + - 1.27+galaxy4 + - 1.11+galaxy1 + - '1.7' + - 1.35+galaxy1 + - 1.33+galaxy3 - server: http://igg.cloud.ba.infn.it/galaxy state: missing - server: https://galaxy.hyphy.org/ @@ -50174,47 +36122,58 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr - state: exact - version: 0.8.1+galaxy2 + state: inexact + versions: + - 1.34+galaxy0 - server: http://galaxy.inf.ethz.ch state: missing - server: https://palfinder.ls.manchester.ac.uk/ state: missing - server: http://pepsimili.e-nios.com:8080/ state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - server: https://usegalaxy.org.au state: exact - version: 0.8.1+galaxy2 + version: 1.11+galaxy0 - server: https://usegalaxy.be/ state: exact - version: 0.8.1+galaxy2 + version: 1.11+galaxy0 - server: https://usegalaxy.cz/ - state: inexact - versions: - - 2022.09+galaxy2 + state: exact + version: 1.11+galaxy0 - server: https://usegalaxy.eu state: exact - version: 0.8.1+galaxy2 + version: 1.11+galaxy0 - server: https://usegalaxy.fr/ - state: exact - version: 0.8.1+galaxy2 + state: inexact + versions: + - 1.27+galaxy3 + - 1.27+galaxy4 + - 1.11+galaxy1 + - 1.24.1+galaxy0 + - 1.33+galaxy0 + - '1.7' + - 1.35+galaxy1 + - 1.34+galaxy0 + - 1.8+galaxy0 + - 1.27+galaxy0 + - 1.9+galaxy1 + - 1.8+galaxy1 + - 1.27+galaxy1 + - '1.9' + - 1.35+galaxy0 - server: https://usegalaxy.no/ state: exact - version: 0.8.1+galaxy2 + version: 1.11+galaxy0 - server: https://usegalaxy.org state: exact - version: 0.8.1+galaxy2 + version: 1.11+galaxy0 - server: https://viralvariant.anses.fr/ state: missing - version: 0.8.1+galaxy2 - - id: toolshed.g2.bx.psu.edu/repos/iuc/collection_column_join/collection_column_join/0.0.3 + version: 1.11+galaxy0 + - id: toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1 servers: - server: http://apostl.moffitt.org/ state: missing @@ -50227,12 +36186,13 @@ - server: https://hyperbrowser.uio.no/coloc-stats state: missing - server: https://galaxy.mesocentre.uca.fr - state: missing + state: exact + version: 1.11+galaxy1 - server: https://galaxy.pasteur.fr/ state: missing - server: https://galaxytrakr.org/ state: exact - version: 0.0.3 + version: 1.11+galaxy1 - server: http://igg.cloud.ba.infn.it/galaxy state: missing - server: https://galaxy.hyphy.org/ @@ -50243,46 +36203,51 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr - state: exact - version: 0.0.3 + state: inexact + versions: + - 1.34+galaxy0 - server: http://galaxy.inf.ethz.ch state: missing - server: https://palfinder.ls.manchester.ac.uk/ state: missing - server: http://pepsimili.e-nios.com:8080/ state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - server: https://usegalaxy.org.au state: exact - version: 0.0.3 + version: 1.11+galaxy1 - server: https://usegalaxy.be/ state: exact - version: 0.0.3 + version: 1.11+galaxy1 - server: https://usegalaxy.cz/ state: exact - version: 0.0.3 + version: 1.11+galaxy1 - server: https://usegalaxy.eu state: exact - version: 0.0.3 + version: 1.11+galaxy1 - server: https://usegalaxy.fr/ state: exact - version: 0.0.3 + version: 1.11+galaxy1 - server: https://usegalaxy.no/ - state: exact - version: 0.0.3 + state: inexact + versions: + - 1.11+galaxy0 + - '1.7' + - 1.7.1 + - 1.8+galaxy0 + - 1.9+galaxy1 + - 1.8+galaxy1 + - '1.9' + - 1.8+galaxy2 - server: https://usegalaxy.org state: exact - version: 0.0.3 + version: 1.11+galaxy1 - server: https://viralvariant.anses.fr/ state: missing - version: 0.0.3 - - id: toolshed.g2.bx.psu.edu/repos/iuc/coverm_contig/coverm_contig/0.7.0+galaxy0 + version: 1.11+galaxy1 + - id: toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.28.2+galaxy1 servers: - server: http://apostl.moffitt.org/ state: missing @@ -50295,12 +36260,15 @@ - server: https://hyperbrowser.uio.no/coloc-stats state: missing - server: https://galaxy.mesocentre.uca.fr - state: missing + state: exact + version: 1.28.2+galaxy1 - server: https://galaxy.pasteur.fr/ - state: missing + state: inexact + versions: + - 1.43.0+galaxy0 - server: https://galaxytrakr.org/ state: exact - version: 0.7.0+galaxy0 + version: 1.28.2+galaxy1 - server: http://igg.cloud.ba.infn.it/galaxy state: missing - server: https://galaxy.hyphy.org/ @@ -50311,44 +36279,50 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr - state: missing + state: inexact + versions: + - 1.46.2+galaxy0 - server: http://galaxy.inf.ethz.ch state: missing - server: https://palfinder.ls.manchester.ac.uk/ state: missing - server: http://pepsimili.e-nios.com:8080/ state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - server: https://usegalaxy.org.au state: exact - version: 0.7.0+galaxy0 + version: 1.28.2+galaxy1 - server: https://usegalaxy.be/ state: exact - version: 0.7.0+galaxy0 + version: 1.28.2+galaxy1 - server: https://usegalaxy.cz/ - state: exact - version: 0.7.0+galaxy0 + state: inexact + versions: + - 1.42.0+galaxy1 + - 1.44.1+galaxy0 + - 1.46.2+galaxy0 + - 1.46.1+galaxy0 + - 1.41.0+galaxy0 + - 1.47.0+galaxy0 + - 1.47.1+galaxy0 - server: https://usegalaxy.eu state: exact - version: 0.7.0+galaxy0 + version: 1.28.2+galaxy1 - server: https://usegalaxy.fr/ state: exact - version: 0.7.0+galaxy0 + version: 1.28.2+galaxy1 - server: https://usegalaxy.no/ - state: missing + state: exact + version: 1.28.2+galaxy1 - server: https://usegalaxy.org state: exact - version: 0.7.0+galaxy0 + version: 1.28.2+galaxy1 - server: https://viralvariant.anses.fr/ state: missing - version: 0.7.0+galaxy0 - - id: toolshed.g2.bx.psu.edu/repos/iuc/filter_tabular/filter_tabular/2.0.0 + version: 1.28.2+galaxy1 + - id: toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.42.0+galaxy1 servers: - server: http://apostl.moffitt.org/ state: missing @@ -50361,13 +36335,16 @@ - server: https://hyperbrowser.uio.no/coloc-stats state: missing - server: https://galaxy.mesocentre.uca.fr - state: missing + state: exact + version: 1.42.0+galaxy1 - server: https://galaxy.pasteur.fr/ state: inexact versions: - - 3.3.0 + - 1.43.0+galaxy0 - server: https://galaxytrakr.org/ - state: missing + state: inexact + versions: + - 1.28.2+galaxy1 - server: http://igg.cloud.ba.infn.it/galaxy state: missing - server: https://galaxy.hyphy.org/ @@ -50378,50 +36355,46 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr state: inexact versions: - - 3.1.2 - - 3.3.1 + - 1.46.2+galaxy0 - server: http://galaxy.inf.ethz.ch state: missing - server: https://palfinder.ls.manchester.ac.uk/ state: missing - server: http://pepsimili.e-nios.com:8080/ state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - server: https://usegalaxy.org.au state: exact - version: 2.0.0 + version: 1.42.0+galaxy1 - server: https://usegalaxy.be/ state: exact - version: 2.0.0 + version: 1.42.0+galaxy1 - server: https://usegalaxy.cz/ - state: inexact - versions: - - 3.3.0 + state: exact + version: 1.42.0+galaxy1 - server: https://usegalaxy.eu state: exact - version: 2.0.0 + version: 1.42.0+galaxy1 - server: https://usegalaxy.fr/ + state: exact + version: 1.42.0+galaxy1 + - server: https://usegalaxy.no/ state: inexact versions: - - 3.3.1 - - server: https://usegalaxy.no/ - state: exact - version: 2.0.0 + - 1.28.2+galaxy1 + - 1.36.2+galaxy1 + - 1.25.0+galaxy1 - server: https://usegalaxy.org state: exact - version: 2.0.0 + version: 1.42.0+galaxy1 - server: https://viralvariant.anses.fr/ state: missing - version: 2.0.0 - - id: toolshed.g2.bx.psu.edu/repos/iuc/megahit/megahit/1.2.9+galaxy0 + version: 1.42.0+galaxy1 + - id: toolshed.g2.bx.psu.edu/repos/iuc/newick_utils/newick_display/1.6+galaxy1 servers: - server: http://apostl.moffitt.org/ state: missing @@ -50434,19 +36407,12 @@ - server: https://hyperbrowser.uio.no/coloc-stats state: missing - server: https://galaxy.mesocentre.uca.fr - state: inexact - versions: - - 1.2.9+galaxy2 - - 1.2.9+galaxy1 - - 1.1.3.5 + state: missing - server: https://galaxy.pasteur.fr/ - state: inexact - versions: - - 1.2.9+galaxy1 + state: missing - server: https://galaxytrakr.org/ - state: inexact - versions: - - 1.2.9+galaxy2 + state: exact + version: 1.6+galaxy1 - server: http://igg.cloud.ba.infn.it/galaxy state: missing - server: https://galaxy.hyphy.org/ @@ -50457,50 +36423,41 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr - state: inexact - versions: - - 1.2.9+galaxy2 - - 1.2.9+galaxy1 + state: missing - server: http://galaxy.inf.ethz.ch state: missing - server: https://palfinder.ls.manchester.ac.uk/ state: missing - server: http://pepsimili.e-nios.com:8080/ - state: inexact - versions: - - 1.2.9+galaxy1 - - server: https://galaxy.bio.di.uminho.pt/ state: missing - server: https://usegalaxy.org.au state: exact - version: 1.2.9+galaxy0 + version: 1.6+galaxy1 - server: https://usegalaxy.be/ state: exact - version: 1.2.9+galaxy0 + version: 1.6+galaxy1 - server: https://usegalaxy.cz/ state: exact - version: 1.2.9+galaxy0 + version: 1.6+galaxy1 - server: https://usegalaxy.eu state: exact - version: 1.2.9+galaxy0 + version: 1.6+galaxy1 - server: https://usegalaxy.fr/ state: exact - version: 1.2.9+galaxy0 + version: 1.6+galaxy1 - server: https://usegalaxy.no/ state: exact - version: 1.2.9+galaxy0 + version: 1.6+galaxy1 - server: https://usegalaxy.org state: exact - version: 1.2.9+galaxy0 + version: 1.6+galaxy1 - server: https://viralvariant.anses.fr/ state: missing - version: 1.2.9+galaxy0 - - id: toolshed.g2.bx.psu.edu/repos/iuc/megahit/megahit/1.2.9+galaxy2 + version: 1.6+galaxy1 + - id: toolshed.g2.bx.psu.edu/repos/iuc/porechop/porechop/0.2.4 servers: - server: http://apostl.moffitt.org/ state: missing @@ -50513,15 +36470,16 @@ - server: https://hyperbrowser.uio.no/coloc-stats state: missing - server: https://galaxy.mesocentre.uca.fr - state: exact - version: 1.2.9+galaxy2 + state: missing - server: https://galaxy.pasteur.fr/ state: inexact versions: - - 1.2.9+galaxy1 + - 0.2.4+galaxy0 - server: https://galaxytrakr.org/ - state: exact - version: 1.2.9+galaxy2 + state: inexact + versions: + - 0.2.4+galaxy0 + - 0.2.4+galaxy1 - server: http://igg.cloud.ba.infn.it/galaxy state: missing - server: https://galaxy.hyphy.org/ @@ -50532,51 +36490,47 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr - state: exact - version: 1.2.9+galaxy2 + state: missing - server: http://galaxy.inf.ethz.ch state: missing - server: https://palfinder.ls.manchester.ac.uk/ state: missing - server: http://pepsimili.e-nios.com:8080/ - state: inexact - versions: - - 1.2.9+galaxy1 - - server: https://galaxy.bio.di.uminho.pt/ state: missing - server: https://usegalaxy.org.au state: exact - version: 1.2.9+galaxy2 + version: 0.2.4 - server: https://usegalaxy.be/ - state: exact - version: 1.2.9+galaxy2 + state: inexact + versions: + - 0.2.4+galaxy0 + - 0.2.4+galaxy1 + - 0.2.3 - server: https://usegalaxy.cz/ - state: exact - version: 1.2.9+galaxy2 + state: inexact + versions: + - 0.2.4+galaxy0 + - 0.2.4+galaxy1 - server: https://usegalaxy.eu state: exact - version: 1.2.9+galaxy2 + version: 0.2.4 - server: https://usegalaxy.fr/ - state: exact - version: 1.2.9+galaxy2 - - server: https://usegalaxy.no/ state: inexact versions: - - 1.1.3.5 - - 1.2.9+galaxy0 - - 1.1.3.4 + - 0.2.4+galaxy1 + - server: https://usegalaxy.no/ + state: exact + version: 0.2.4 - server: https://usegalaxy.org state: exact - version: 1.2.9+galaxy2 + version: 0.2.4 - server: https://viralvariant.anses.fr/ state: missing - version: 1.2.9+galaxy2 - - id: toolshed.g2.bx.psu.edu/repos/iuc/megahit_contig2fastg/megahit_contig2fastg/1.1.3+galaxy1 + version: 0.2.4 + - id: toolshed.g2.bx.psu.edu/repos/iuc/porechop/porechop/0.2.4+galaxy0 servers: - server: http://apostl.moffitt.org/ state: missing @@ -50591,9 +36545,11 @@ - server: https://galaxy.mesocentre.uca.fr state: missing - server: https://galaxy.pasteur.fr/ - state: missing + state: exact + version: 0.2.4+galaxy0 - server: https://galaxytrakr.org/ - state: missing + state: exact + version: 0.2.4+galaxy0 - server: http://igg.cloud.ba.infn.it/galaxy state: missing - server: https://galaxy.hyphy.org/ @@ -50604,46 +36560,42 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr - state: exact - version: 1.1.3+galaxy1 + state: missing - server: http://galaxy.inf.ethz.ch state: missing - server: https://palfinder.ls.manchester.ac.uk/ state: missing - server: http://pepsimili.e-nios.com:8080/ state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - server: https://usegalaxy.org.au state: exact - version: 1.1.3+galaxy1 + version: 0.2.4+galaxy0 - server: https://usegalaxy.be/ state: exact - version: 1.1.3+galaxy1 + version: 0.2.4+galaxy0 - server: https://usegalaxy.cz/ state: exact - version: 1.1.3+galaxy1 + version: 0.2.4+galaxy0 - server: https://usegalaxy.eu state: exact - version: 1.1.3+galaxy1 + version: 0.2.4+galaxy0 - server: https://usegalaxy.fr/ - state: exact - version: 1.1.3+galaxy1 + state: inexact + versions: + - 0.2.4+galaxy1 - server: https://usegalaxy.no/ state: exact - version: 1.1.3+galaxy1 + version: 0.2.4+galaxy0 - server: https://usegalaxy.org state: exact - version: 1.1.3+galaxy1 + version: 0.2.4+galaxy0 - server: https://viralvariant.anses.fr/ state: missing - version: 1.1.3+galaxy1 - - id: toolshed.g2.bx.psu.edu/repos/iuc/megahit_contig2fastg/megahit_contig2fastg/1.1.3+galaxy10 + version: 0.2.4+galaxy0 + - id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_coverage/samtools_coverage/1.15.1+galaxy2 servers: - server: http://apostl.moffitt.org/ state: missing @@ -50660,7 +36612,10 @@ - server: https://galaxy.pasteur.fr/ state: missing - server: https://galaxytrakr.org/ - state: missing + state: inexact + versions: + - 1.21+galaxy3 + - 1.22+galaxy3 - server: http://igg.cloud.ba.infn.it/galaxy state: missing - server: https://galaxy.hyphy.org/ @@ -50671,54 +36626,40 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr - state: inexact - versions: - - 1.1.3+galaxy1 + state: missing - server: http://galaxy.inf.ethz.ch state: missing - server: https://palfinder.ls.manchester.ac.uk/ state: missing - server: http://pepsimili.e-nios.com:8080/ state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - server: https://usegalaxy.org.au - state: inexact - versions: - - 1.1.3+galaxy1 + state: exact + version: 1.15.1+galaxy2 - server: https://usegalaxy.be/ - state: inexact - versions: - - 1.1.3+galaxy1 + state: exact + version: 1.15.1+galaxy2 - server: https://usegalaxy.cz/ - state: inexact - versions: - - 1.1.3+galaxy1 + state: exact + version: 1.15.1+galaxy2 - server: https://usegalaxy.eu - state: inexact - versions: - - 1.1.3+galaxy1 + state: exact + version: 1.15.1+galaxy2 - server: https://usegalaxy.fr/ - state: inexact - versions: - - 1.1.3+galaxy1 + state: exact + version: 1.15.1+galaxy2 - server: https://usegalaxy.no/ - state: inexact - versions: - - 1.1.3+galaxy1 + state: missing - server: https://usegalaxy.org - state: inexact - versions: - - 1.1.3+galaxy1 + state: exact + version: 1.15.1+galaxy2 - server: https://viralvariant.anses.fr/ state: missing - version: 1.1.3+galaxy10 - - id: toolshed.g2.bx.psu.edu/repos/iuc/ngsutils_bam_filter/ngsutils_bam_filter/0.5.9 + version: 1.15.1+galaxy2 + - id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_depth/samtools_depth/1.15.1+galaxy2 servers: - server: http://apostl.moffitt.org/ state: missing @@ -50731,11 +36672,15 @@ - server: https://hyperbrowser.uio.no/coloc-stats state: missing - server: https://galaxy.mesocentre.uca.fr - state: missing + state: exact + version: 1.15.1+galaxy2 - server: https://galaxy.pasteur.fr/ state: missing - server: https://galaxytrakr.org/ - state: missing + state: inexact + versions: + - 1.22+galaxy1 + - 1.21+galaxy0 - server: http://igg.cloud.ba.infn.it/galaxy state: missing - server: https://galaxy.hyphy.org/ @@ -50746,8 +36691,6 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr @@ -50758,33 +36701,36 @@ state: missing - server: http://pepsimili.e-nios.com:8080/ state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - server: https://usegalaxy.org.au state: exact - version: 0.5.9 + version: 1.15.1+galaxy2 - server: https://usegalaxy.be/ state: exact - version: 0.5.9 + version: 1.15.1+galaxy2 - server: https://usegalaxy.cz/ state: exact - version: 0.5.9 + version: 1.15.1+galaxy2 - server: https://usegalaxy.eu state: exact - version: 0.5.9 + version: 1.15.1+galaxy2 - server: https://usegalaxy.fr/ state: exact - version: 0.5.9 + version: 1.15.1+galaxy2 - server: https://usegalaxy.no/ - state: exact - version: 0.5.9 + state: inexact + versions: + - '1.9' + - 1.15.1+galaxy0 + - '1.13' - server: https://usegalaxy.org state: exact - version: 0.5.9 + version: 1.15.1+galaxy2 - server: https://viralvariant.anses.fr/ - state: missing - version: 0.5.9 - - id: toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.2.0+galaxy1 + state: inexact + versions: + - 1.21+galaxy0 + version: 1.15.1+galaxy2 + - id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_fastx/samtools_fastx/1.15.1+galaxy2 servers: - server: http://apostl.moffitt.org/ state: missing @@ -50796,14 +36742,22 @@ state: missing - server: https://hyperbrowser.uio.no/coloc-stats state: missing - - server: https://galaxy.mesocentre.uca.fr - state: exact - version: 5.2.0+galaxy1 - - server: https://galaxy.pasteur.fr/ - state: missing + - server: https://galaxy.mesocentre.uca.fr + state: inexact + versions: + - 1.21+galaxy0 + - 1.9+galaxy1 + - 1.20+galaxy2 + - 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version: 1.15.1+galaxy2 - server: https://usegalaxy.be/ state: exact - version: 5.2.0+galaxy1 + version: 1.15.1+galaxy2 - server: https://usegalaxy.cz/ state: exact - version: 5.2.0+galaxy1 + version: 1.15.1+galaxy2 - server: https://usegalaxy.eu state: exact - version: 5.2.0+galaxy1 + version: 1.15.1+galaxy2 - server: https://usegalaxy.fr/ state: exact - version: 5.2.0+galaxy1 + version: 1.15.1+galaxy2 - server: https://usegalaxy.no/ - state: exact - version: 5.2.0+galaxy1 + state: inexact + versions: + - 1.9+galaxy1 + - 1.15.1+galaxy0 + - '1.13' - server: https://usegalaxy.org state: exact - version: 5.2.0+galaxy1 + version: 1.15.1+galaxy2 - server: https://viralvariant.anses.fr/ state: missing - version: 5.2.0+galaxy1 - - id: toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.3.0+galaxy0 + version: 1.15.1+galaxy2 + - id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_extractFields/4.3+t.galaxy0 servers: - server: http://apostl.moffitt.org/ state: missing @@ -50866,19 +36820,12 @@ - server: https://hyperbrowser.uio.no/coloc-stats state: missing - server: https://galaxy.mesocentre.uca.fr - state: inexact - versions: - - 5.3.0+galaxy1 - - 5.2.0+galaxy1 - - 5.0.2+galaxy0 + state: missing - server: https://galaxy.pasteur.fr/ state: missing - server: https://galaxytrakr.org/ - state: inexact - versions: - - 5.3.0+galaxy1 - - 5.2.0+galaxy1 - - '4.5' + state: exact + version: 4.3+t.galaxy0 - server: http://igg.cloud.ba.infn.it/galaxy state: missing - server: https://galaxy.hyphy.org/ @@ -50889,55 +36836,43 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr state: inexact versions: - - 5.3.0+galaxy1 - - 5.2.0+galaxy1 + - 5.4.0c+galaxy0 - server: http://galaxy.inf.ethz.ch state: missing - server: https://palfinder.ls.manchester.ac.uk/ state: missing - server: 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toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_subseq/1.3.1 + version: 4.3+t.galaxy0 + - id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_filter/4.3+t.galaxy1 servers: - server: http://apostl.moffitt.org/ state: missing @@ -50950,13 +36885,12 @@ - server: https://hyperbrowser.uio.no/coloc-stats state: missing - server: https://galaxy.mesocentre.uca.fr - state: exact - version: 1.3.1 + state: missing - server: https://galaxy.pasteur.fr/ state: missing - server: https://galaxytrakr.org/ state: exact - version: 1.3.1 + version: 4.3+t.galaxy1 - server: http://igg.cloud.ba.infn.it/galaxy state: missing - server: https://galaxy.hyphy.org/ @@ -50967,47 +36901,43 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr state: inexact versions: - - 1.5+galaxy0 + - 5.4.0c+galaxy0 - server: 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toolshed.g2.bx.psu.edu/repos/iuc/table_compute/table_compute/1.2.4+galaxy0 + - toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0 topic_name: microbiome topic_name_human: Microbiome tours: false @@ -51204,1408 +37158,5118 @@ slides: [] tutorial: [] video: false - tutorial_name: metagenomics-assembly + tutorial_name: pathogen-detection-from-nanopore-foodborne-data type: tutorial - url: https://training.galaxyproject.org//topics/microbiome/tutorials/metagenomics-assembly/tutorial.html + url: https://training.galaxyproject.org//topics/microbiome/tutorials/pathogen-detection-from-nanopore-foodborne-data/tutorial.html urls: - hands_on: https://training.galaxyproject.org/training-material/api/topics/microbiome/tutorials/metagenomics-assembly/tutorial.json - slides: https://training.galaxyproject.org/training-material/api/topics/microbiome/tutorials/metagenomics-assembly/tutorial.json - version: 11 + hands_on: https://training.galaxyproject.org/training-material/api/topics/microbiome/tutorials/pathogen-detection-from-nanopore-foodborne-data/tutorial.json + slides: https://training.galaxyproject.org/training-material/api/topics/microbiome/tutorials/pathogen-detection-from-nanopore-foodborne-data/tutorial.json + version: 12 video: true video_versions: 2 video_view: 0 - visit_duration: 609 - visitors: 5414 + visit_duration: 518 + visitors: 5895 workflows: - creators: - class: Person - identifier: 0000-0002-0507-4602 - name: Polina Polunina + identifier: 0000-0001-9047-4215 + name: Engy Nasr + url: https://orcid.org/0000-0001-9047-4215 + - class: Person + identifier: 0000-0001-9852-1987 + name: "B\xE9r\xE9nice Batut" + url: https://orcid.org/0000-0001-9852-1987 + - class: Person + identifier: 0000-0003-2982-388X + name: Paul Zierep + description: Microbiome - Variant calling and Consensus Building + features: + comments: true + parameters: true + report: + markdown: "# Allele based Pathogen Identification Workflow Report\nBelow are\ + \ the results for the Allele based Pathogenic Identification Workflow\n\n\ + This workflow was run on:\n\n```galaxy\ngenerate_time()\n```\n\nWith Galaxy\ + \ version:\n\n```galaxy\ngenerate_galaxy_version()\n```\n\n## Workflow Inputs\n\ + The Perprocessing workflow main output (Collection of all samples reads\ + \ after quality retaining and hosts filtering), and a FASTA file of the\ + \ reference genome of the main Pathogen identified in the Gene based Pathogen\ + \ Identification workflow, or per-known to the user.\n\n## Workflow Output:\ + \ \n\n### All variants found per sample against the reference genome\n\n\ + ```galaxy\nhistory_dataset_display(output=\"extracted_fields_from_the_vcf_output\"\ + )\n```\n\n### Number of variants per sample\n\n```galaxy\nhistory_dataset_display(output=\"\ + number_of_variants_per_sample\")\n```\n\n### Mapping mean depth per sample\n\ + \n```galaxy\nhistory_dataset_display(output=\"mapping_mean_depth_per_sample\"\ + )\n```\n\n### Mapping coverage per sample\n\n```galaxy\nhistory_dataset_display(output=\"\ + mapping_coverage_percentage_per_sample\")\n```\n" + subworkflows: false + graph_dot: "digraph main {\n node [fontname=\"Atkinson Hyperlegible\", shape=box,\ + \ color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n edge [fontname=\"\ + Atkinson Hyperlegible\"];\n 0[color=lightblue,label=\"\u2139\uFE0F Input Collection\\\ + ncollection_of_preprocessed_samples\"]\n 1[color=lightgreen,label=\"\u2139\uFE0F\ + \ Input Parameter\\nsamples_profile\"]\n 2[color=lightblue,label=\"\u2139\uFE0F\ + \ Input Dataset\\nreference_genome_of_tested_strain\"]\n 3[label=\"Convert\ + \ compressed file to uncompressed.\"]\n 2 -> 3 [label=\"output\"]\n k9d6bde4a718040979ffd6992111a617c[color=lightseagreen,label=\"\ + Output\\ndecompressed_rg_file\"]\n 3 -> k9d6bde4a718040979ffd6992111a617c\n\ + \ 4[label=\"Map with 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[label=\"output1\"]\n k22553aa1f5db4d3787c41164dbb3d2d5[color=lightseagreen,label=\"\ + Output\\nnormalized_vcf_output\"]\n 8 -> k22553aa1f5db4d3787c41164dbb3d2d5\n\ + \ 9[label=\"Advanced Cut\"]\n 6 -> 9 [label=\"output\"]\n 10[label=\"Remove\ + \ beginning\"]\n 7 -> 10 [label=\"output\"]\n 11[label=\"SnpSift Filter\"\ + ]\n 8 -> 11 [label=\"output_file\"]\n k3e7981ec2205457193eb10c0dd14b288[color=lightseagreen,label=\"\ + Output\\nquality_filtered_vcf_output\"]\n 11 -> k3e7981ec2205457193eb10c0dd14b288\n\ + \ 12[label=\"Table Compute\"]\n 9 -> 12 [label=\"output\"]\n 13[label=\"\ + Cut\"]\n 10 -> 13 [label=\"out_file1\"]\n 14[label=\"SnpSift Extract Fields\"\ + ]\n 11 -> 14 [label=\"output\"]\n k1b0f4f2c471745beb580fe10cba78c35[color=lightseagreen,label=\"\ + Output\\nextracted_fields_from_the_vcf_output\"]\n 14 -> k1b0f4f2c471745beb580fe10cba78c35\n\ + \ 15[label=\"bcftools consensus\"]\n 11 -> 15 [label=\"output\"]\n 3 -> 15\ + \ [label=\"output1\"]\n 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24[label=\"\ + Collapse Collection\"]\n 23 -> 24 [label=\"outfile\"]\n 25[label=\"Column\ + \ Regex Find And Replace\"]\n 24 -> 25 [label=\"output\"]\n k2852c4ee24ea4df7b59e54eb6e2f470b[color=lightseagreen,label=\"\ + Output\\nnumber_of_variants_per_sample\"]\n 25 -> k2852c4ee24ea4df7b59e54eb6e2f470b\n\ + }" + history: + - hash: fea16c6949ebaafe1f872bfe3a5f05958a15e7f9 + message: updating to include all previous comments + num: 1 + short_hash: fea16c694 + unix: '1718833675' + inputs: + - annotation: Output collection from the Nanopore Preprocessing workflow + content_id: null + errors: null + id: 0 + input_connections: {} + inputs: + - description: Output collection from the Nanopore Preprocessing workflow + name: collection_of_preprocessed_samples + label: collection_of_preprocessed_samples + name: Input dataset collection + outputs: [] + position: + left: 6 + top: 205 + tool_id: null + tool_state: '{"optional": false, "tag": null, "collection_type": "list"}' + tool_version: null + type: data_collection_input + uuid: 7aaa03a4-2647-411b-863d-90f28ed01f32 + when: null + workflow_outputs: [] + - annotation: 'based on the lab preparation of the samples during sequencing, + there should be a sample profile better than the other, to be chosen as an + optional input to Minimap2. e.g. PacBio/Oxford Nanpore + + + For more details check: https://github.com/lh3/minimap2?tab=readme-ov-file#use-cases' + content_id: null + errors: null + id: 1 + input_connections: {} + inputs: + - description: 'based on the lab preparation of the samples during sequencing, + there should be a sample profile better than the other, to be chosen as + an optional input to Minimap2. e.g. PacBio/Oxford Nanpore + + + For more details check: https://github.com/lh3/minimap2?tab=readme-ov-file#use-cases' + name: samples_profile + label: samples_profile + name: Input parameter + outputs: [] + position: + left: 260 + top: 35 + tool_id: null + tool_state: '{"restrictOnConnections": true, "parameter_type": "text", "optional": + true}' + tool_version: null + type: parameter_input + uuid: d28b9bed-c674-406c-b58b-165bcc8eec17 + when: null + workflow_outputs: [] + - annotation: Can be built in the tool later + content_id: null + errors: null + id: 2 + input_connections: {} + inputs: + - description: Can be built in the tool later + name: reference_genome_of_tested_strain + label: reference_genome_of_tested_strain + name: Input dataset + outputs: [] + position: + left: 0 + top: 374 + tool_id: null + tool_state: '{"optional": false, "tag": ""}' + tool_version: null + type: data_input + uuid: 773b7592-d66c-4a85-92ba-06c0ab0f843f + when: null + workflow_outputs: [] + license: MIT + mermaid: "flowchart TD\n 0[\"\u2139\uFE0F Input Collection\\ncollection_of_preprocessed_samples\"\ + ];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"\u2139\uFE0F Input Parameter\\\ + nsamples_profile\"];\n style 1 fill:#ded,stroke:#393,stroke-width:4px;\n 2[\"\ + \u2139\uFE0F Input 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987f9145-83ab-44f1-801a-b0d527ecbce8[\"Output\\nclair3_full_alignment_vcf\"\ + ];\n 5 --> 987f9145-83ab-44f1-801a-b0d527ecbce8;\n style 987f9145-83ab-44f1-801a-b0d527ecbce8\ + \ stroke:#2c3143,stroke-width:4px;\n fab82215-f59a-43b1-92d7-37629a1fdb65[\"\ + Output\\nclair3_merged_output\"];\n 5 --> fab82215-f59a-43b1-92d7-37629a1fdb65;\n\ + \ style fab82215-f59a-43b1-92d7-37629a1fdb65 stroke:#2c3143,stroke-width:4px;\n\ + \ 6[\"Samtools depth\"];\n 4 -->|alignment_output| 6;\n 7[\"Samtools coverage\"\ + ];\n 4 -->|alignment_output| 7;\n 8[\"bcftools norm\"];\n 5 -->|merge_output|\ + \ 8;\n 3 -->|output1| 8;\n 22553aa1-f5db-4d37-87c4-1164dbb3d2d5[\"Output\\\ + nnormalized_vcf_output\"];\n 8 --> 22553aa1-f5db-4d37-87c4-1164dbb3d2d5;\n\ + \ style 22553aa1-f5db-4d37-87c4-1164dbb3d2d5 stroke:#2c3143,stroke-width:4px;\n\ + \ 9[\"Advanced Cut\"];\n 6 -->|output| 9;\n 10[\"Remove beginning\"];\n \ + \ 7 -->|output| 10;\n 11[\"SnpSift Filter\"];\n 8 -->|output_file| 11;\n \ + \ 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toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_head_tool/9.3+galaxy1 + - toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regexColumn1/1.0.3 + - toolshed.g2.bx.psu.edu/repos/iuc/bcftools_consensus/bcftools_consensus/1.9+galaxy1 + - toolshed.g2.bx.psu.edu/repos/iuc/bcftools_norm/bcftools_norm/1.9+galaxy1 + - toolshed.g2.bx.psu.edu/repos/iuc/clair3/clair3/0.1.12+galaxy0 + - toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.24+galaxy0 + - toolshed.g2.bx.psu.edu/repos/iuc/samtools_coverage/samtools_coverage/1.15.1+galaxy2 + - toolshed.g2.bx.psu.edu/repos/iuc/samtools_depth/samtools_depth/1.15.1+galaxy2 + - toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_extractFields/4.3+t.galaxy0 + - toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_filter/4.3+t.galaxy1 + - toolshed.g2.bx.psu.edu/repos/iuc/table_compute/table_compute/1.2.4+galaxy0 + - toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0 + workflowhub_id: '1479' + - creators: + - class: Person + identifier: 0000-0001-9047-4215 + name: Engy Nasr + url: https://orcid.org/0000-0001-9047-4215 + - class: Person + identifier: 0000-0001-9852-1987 + name: "B\xE9r\xE9nice Batut" + url: https://orcid.org/0000-0001-9852-1987 + - class: Person + identifier: 0000-0003-2982-388X + name: Paul Zierep + description: Nanopore datasets analysis - Phylogenetic Identification - antibiotic + resistance genes detection and contigs building + features: + comments: true + parameters: false + report: + markdown: '# Gene based Pathogen Identification Workflow Report + + + Below are the results for the Gene based Pathogen Identification Workflow + + + This workflow was run on: + + + ```galaxy + + generate_time() + + ``` + + + With Galaxy version: + + + ```galaxy + + generate_galaxy_version() + + ``` + + + ## Workflow Inputs + + The Perprocessing workflow main output (Collection of all samples reads + after quality retaining and hosts filtering) + + + ## Workflow Output + + + ### Identified contigs per sample + + + ```galaxy + + history_dataset_display(output="contigs") + + ``` + + + ### Identified pathogenic genes per sample + + + ```galaxy + + history_dataset_display(output="vfs") + + ``` + + + ### Identified Antimicrobial Resistance genes per sample + + + ```galaxy + + history_dataset_display(output="amrs") + + ``` + + ' + subworkflows: false + graph_dot: "digraph main {\n node [fontname=\"Atkinson Hyperlegible\", shape=box,\ + \ color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n edge [fontname=\"\ + Atkinson Hyperlegible\"];\n 0[color=lightblue,label=\"\u2139\uFE0F Input Collection\\\ + ncollection_of_preprocessed_samples\"]\n 1[label=\"Extract element identifiers\"\ + ]\n 0 -> 1 [label=\"output\"]\n kd82a93c623a94f85879cecd759a31087[color=lightseagreen,label=\"\ + Output\\nextracted_samples_IDs\"]\n 1 -> kd82a93c623a94f85879cecd759a31087\n\ + \ 2[label=\"Build list\"]\n 0 -> 2 [label=\"output\"]\n kf5b5b2568ddf4da88111b1f6d3025a0d[color=lightseagreen,label=\"\ + 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[label=\"list_output_txt\"]\n\ + \ k3608e170c46242a28003f3f65baa3834[color=lightseagreen,label=\"Output\\nparsed_extracted_samples_IDs_to_text\"\ + ]\n 5 -> k3608e170c46242a28003f3f65baa3834\n 6[label=\"medaka consensus pipeline\"\ + ]\n 4 -> 6 [label=\"consensus\"]\n 0 -> 6 [label=\"output\"]\n k9e5ad6ecb4084132ba07dec9fa626923[color=lightseagreen,label=\"\ + Output\\nmedaka_gaps_in_draft_bed_file\"]\n 6 -> k9e5ad6ecb4084132ba07dec9fa626923\n\ + \ kfcbd3e3f2e934798b696dad7db9f2efd[color=lightseagreen,label=\"Output\\nmedaka_log_file\"\ + ]\n 6 -> kfcbd3e3f2e934798b696dad7db9f2efd\n k60656aacad2a4c9b9a68b9fb18ae5595[color=lightseagreen,label=\"\ + Output\\nmedaka_propability_h5_file\"]\n 6 -> k60656aacad2a4c9b9a68b9fb18ae5595\n\ + \ kc790d4348e784df0a0d48f9da0692158[color=lightseagreen,label=\"Output\\nmedaka_calls_of_draft_bam_file\"\ + ]\n 6 -> kc790d4348e784df0a0d48f9da0692158\n kdf361e19b6d1405b96ccb48c1ab7c604[color=lightseagreen,label=\"\ + Output\\nsample_all_contigs\"]\n 6 -> kdf361e19b6d1405b96ccb48c1ab7c604\n \ + \ 7[label=\"Bandage Image\"]\n 4 -> 7 [label=\"assembly_gfa\"]\n k9612a8511f944d54b0015d082bcc9055[color=lightseagreen,label=\"\ + Output\\nbandage_assembly_graph_image\"]\n 7 -> k9612a8511f944d54b0015d082bcc9055\n\ + \ 8[label=\"Compose text parameter value\"]\n 5 -> 8 [label=\"text_param\"\ + ]\n 9[label=\"FASTA-to-Tabular\"]\n 6 -> 9 [label=\"out_consensus\"]\n kde06c3625b0a4c29956efbf02539789a[color=lightseagreen,label=\"\ + Output\\nsample_specific_contigs_tabular_file_preparation\"]\n 9 -> kde06c3625b0a4c29956efbf02539789a\n\ + \ 10[label=\"ABRicate\"]\n 6 -> 10 [label=\"out_consensus\"]\n k8f227fc72d924c6faf64e841c1315b4f[color=lightseagreen,label=\"\ + Output\\nabricate_with_vfdb_to_identify_genes_with_VFs\"]\n 10 -> k8f227fc72d924c6faf64e841c1315b4f\n\ + \ 11[label=\"ABRicate\"]\n 6 -> 11 [label=\"out_consensus\"]\n kfa021d98d8854834ac62f30d5792260e[color=lightseagreen,label=\"\ + Output\\nabricate_report_using_ncbi_database_to_indentify_amr\"]\n 11 -> kfa021d98d8854834ac62f30d5792260e\n\ + \ 12[label=\"Replace\"]\n 8 -> 12 [label=\"out1\"]\n 9 -> 12 [label=\"output\"\ + ]\n k174cb2c3ed28453c8afb85150e0b51ad[color=lightseagreen,label=\"Output\\\ + nsample_specific_contigs_tabular_file\"]\n 12 -> k174cb2c3ed28453c8afb85150e0b51ad\n\ + \ 13[label=\"Replace\"]\n 8 -> 13 [label=\"out1\"]\n 10 -> 13 [label=\"report\"\ + ]\n k19e56e006eef4a4e9cc6d93dbf9420ad[color=lightseagreen,label=\"Output\\\ + nvfs\"]\n 13 -> k19e56e006eef4a4e9cc6d93dbf9420ad\n 14[label=\"Replace\"]\n\ + \ 8 -> 14 [label=\"out1\"]\n 11 -> 14 [label=\"report\"]\n ka8eb74a5362b4f0fa944672e27981a41[color=lightseagreen,label=\"\ + Output\\namrs\"]\n 14 -> ka8eb74a5362b4f0fa944672e27981a41\n 15[label=\"Tabular-to-FASTA\"\ + ]\n 12 -> 15 [label=\"outfile\"]\n ka5bb1cbe1bde49a1ad866d57b1319fbe[color=lightseagreen,label=\"\ + Output\\ncontigs\"]\n 15 -> ka5bb1cbe1bde49a1ad866d57b1319fbe\n}" + history: + - hash: cdd93376adc6ce80742881c25d6810bcce85fc05 + message: adding tags to some of the workflow outputs, updating the training + with the latest PathoGFAIR workflows updates + num: 2 + short_hash: cdd93376a + unix: '1717675229' + - hash: c63ce23c7a7a631f1256b8e733defce3ca4e009b + message: updating workflows file names + num: 1 + short_hash: c63ce23c7 + unix: '1716726587' + inputs: + - annotation: Output collection from the Nanopore Preprocessing workflow + content_id: null + errors: null + id: 0 + input_connections: {} + inputs: + - description: Output collection from the Nanopore Preprocessing workflow + name: collection_of_preprocessed_samples + label: collection_of_preprocessed_samples + name: Input dataset collection + outputs: [] + position: + left: 0 + top: 316.35 + tool_id: null + tool_state: '{"optional": false, "tag": null, "collection_type": "list"}' + tool_version: null + type: data_collection_input + uuid: fb7f7c4b-70a7-4d6d-8b20-a3bfdc4380ff + when: null + workflow_outputs: [] + license: MIT + mermaid: "flowchart TD\n 0[\"\u2139\uFE0F Input Collection\\ncollection_of_preprocessed_samples\"\ + ];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"Extract element identifiers\"\ + ];\n 0 -->|output| 1;\n d82a93c6-23a9-4f85-879c-ecd759a31087[\"Output\\nextracted_samples_IDs\"\ + ];\n 1 --> d82a93c6-23a9-4f85-879c-ecd759a31087;\n style d82a93c6-23a9-4f85-879c-ecd759a31087\ + \ stroke:#2c3143,stroke-width:4px;\n 2[\"Build list\"];\n 0 -->|output| 2;\n\ + \ f5b5b256-8ddf-4da8-8111-b1f6d3025a0d[\"Output\\nlist_of_lists_of_preprocessed_samples\"\ + ];\n 2 --> f5b5b256-8ddf-4da8-8111-b1f6d3025a0d;\n style f5b5b256-8ddf-4da8-8111-b1f6d3025a0d\ + \ stroke:#2c3143,stroke-width:4px;\n 3[\"Split file\"];\n 1 -->|output| 3;\n\ + \ eb5317bd-4bad-4cad-9219-3ac379221d6e[\"Output\\nsplitted_extracted_samples_IDs\"\ + ];\n 3 --> eb5317bd-4bad-4cad-9219-3ac379221d6e;\n style eb5317bd-4bad-4cad-9219-3ac379221d6e\ + \ stroke:#2c3143,stroke-width:4px;\n 4[\"Flye\"];\n 2 -->|output| 4;\n ff0d8c7b-2ac7-4c6d-a110-f71418dad938[\"\ + Output\\nflye_consensus_fasta\"];\n 4 --> ff0d8c7b-2ac7-4c6d-a110-f71418dad938;\n\ + \ style ff0d8c7b-2ac7-4c6d-a110-f71418dad938 stroke:#2c3143,stroke-width:4px;\n\ + \ 2385436f-fbe8-4d77-a40b-27a097d02941[\"Output\\nflye_assembly_graph\"];\n\ + \ 4 --> 2385436f-fbe8-4d77-a40b-27a097d02941;\n style 2385436f-fbe8-4d77-a40b-27a097d02941\ + \ stroke:#2c3143,stroke-width:4px;\n 0e42ce51-c46b-45d8-baa4-45c0e98ac712[\"\ + Output\\nflye_assembly_gfa\"];\n 4 --> 0e42ce51-c46b-45d8-baa4-45c0e98ac712;\n\ + \ style 0e42ce51-c46b-45d8-baa4-45c0e98ac712 stroke:#2c3143,stroke-width:4px;\n\ + \ 3f297aed-7cee-4999-bbf4-69d84de6b64f[\"Output\\nflye_assembly_info_tabular\"\ + ];\n 4 --> 3f297aed-7cee-4999-bbf4-69d84de6b64f;\n style 3f297aed-7cee-4999-bbf4-69d84de6b64f\ + \ stroke:#2c3143,stroke-width:4px;\n 5[\"Parse parameter value\"];\n 3 -->|list_output_txt|\ + \ 5;\n 3608e170-c462-42a2-8003-f3f65baa3834[\"Output\\nparsed_extracted_samples_IDs_to_text\"\ + ];\n 5 --> 3608e170-c462-42a2-8003-f3f65baa3834;\n style 3608e170-c462-42a2-8003-f3f65baa3834\ + \ stroke:#2c3143,stroke-width:4px;\n 6[\"medaka consensus pipeline\"];\n 4\ + \ -->|consensus| 6;\n 0 -->|output| 6;\n 9e5ad6ec-b408-4132-ba07-dec9fa626923[\"\ + Output\\nmedaka_gaps_in_draft_bed_file\"];\n 6 --> 9e5ad6ec-b408-4132-ba07-dec9fa626923;\n\ + \ style 9e5ad6ec-b408-4132-ba07-dec9fa626923 stroke:#2c3143,stroke-width:4px;\n\ + \ fcbd3e3f-2e93-4798-b696-dad7db9f2efd[\"Output\\nmedaka_log_file\"];\n 6\ + \ --> fcbd3e3f-2e93-4798-b696-dad7db9f2efd;\n style fcbd3e3f-2e93-4798-b696-dad7db9f2efd\ + \ stroke:#2c3143,stroke-width:4px;\n 60656aac-ad2a-4c9b-9a68-b9fb18ae5595[\"\ + Output\\nmedaka_propability_h5_file\"];\n 6 --> 60656aac-ad2a-4c9b-9a68-b9fb18ae5595;\n\ + \ style 60656aac-ad2a-4c9b-9a68-b9fb18ae5595 stroke:#2c3143,stroke-width:4px;\n\ + \ c790d434-8e78-4df0-a0d4-8f9da0692158[\"Output\\nmedaka_calls_of_draft_bam_file\"\ + ];\n 6 --> c790d434-8e78-4df0-a0d4-8f9da0692158;\n style c790d434-8e78-4df0-a0d4-8f9da0692158\ + \ stroke:#2c3143,stroke-width:4px;\n df361e19-b6d1-405b-96cc-b48c1ab7c604[\"\ + Output\\nsample_all_contigs\"];\n 6 --> df361e19-b6d1-405b-96cc-b48c1ab7c604;\n\ + \ style df361e19-b6d1-405b-96cc-b48c1ab7c604 stroke:#2c3143,stroke-width:4px;\n\ + \ 7[\"Bandage Image\"];\n 4 -->|assembly_gfa| 7;\n 9612a851-1f94-4d54-b001-5d082bcc9055[\"\ + Output\\nbandage_assembly_graph_image\"];\n 7 --> 9612a851-1f94-4d54-b001-5d082bcc9055;\n\ + \ style 9612a851-1f94-4d54-b001-5d082bcc9055 stroke:#2c3143,stroke-width:4px;\n\ + \ 8[\"Compose text parameter value\"];\n 5 -->|text_param| 8;\n 9[\"FASTA-to-Tabular\"\ + ];\n 6 -->|out_consensus| 9;\n de06c362-5b0a-4c29-956e-fbf02539789a[\"Output\\\ + nsample_specific_contigs_tabular_file_preparation\"];\n 9 --> de06c362-5b0a-4c29-956e-fbf02539789a;\n\ + \ style de06c362-5b0a-4c29-956e-fbf02539789a stroke:#2c3143,stroke-width:4px;\n\ + \ 10[\"ABRicate\"];\n 6 -->|out_consensus| 10;\n 8f227fc7-2d92-4c6f-af64-e841c1315b4f[\"\ + Output\\nabricate_with_vfdb_to_identify_genes_with_VFs\"];\n 10 --> 8f227fc7-2d92-4c6f-af64-e841c1315b4f;\n\ + \ style 8f227fc7-2d92-4c6f-af64-e841c1315b4f stroke:#2c3143,stroke-width:4px;\n\ + \ 11[\"ABRicate\"];\n 6 -->|out_consensus| 11;\n fa021d98-d885-4834-ac62-f30d5792260e[\"\ + Output\\nabricate_report_using_ncbi_database_to_indentify_amr\"];\n 11 -->\ + \ fa021d98-d885-4834-ac62-f30d5792260e;\n style fa021d98-d885-4834-ac62-f30d5792260e\ + \ stroke:#2c3143,stroke-width:4px;\n 12[\"Replace\"];\n 8 -->|out1| 12;\n\ + \ 9 -->|output| 12;\n 174cb2c3-ed28-453c-8afb-85150e0b51ad[\"Output\\nsample_specific_contigs_tabular_file\"\ + ];\n 12 --> 174cb2c3-ed28-453c-8afb-85150e0b51ad;\n style 174cb2c3-ed28-453c-8afb-85150e0b51ad\ + \ stroke:#2c3143,stroke-width:4px;\n 13[\"Replace\"];\n 8 -->|out1| 13;\n\ + \ 10 -->|report| 13;\n 19e56e00-6eef-4a4e-9cc6-d93dbf9420ad[\"Output\\nvfs\"\ + ];\n 13 --> 19e56e00-6eef-4a4e-9cc6-d93dbf9420ad;\n style 19e56e00-6eef-4a4e-9cc6-d93dbf9420ad\ + \ stroke:#2c3143,stroke-width:4px;\n 14[\"Replace\"];\n 8 -->|out1| 14;\n\ + \ 11 -->|report| 14;\n a8eb74a5-362b-4f0f-a944-672e27981a41[\"Output\\namrs\"\ + ];\n 14 --> a8eb74a5-362b-4f0f-a944-672e27981a41;\n style a8eb74a5-362b-4f0f-a944-672e27981a41\ + \ stroke:#2c3143,stroke-width:4px;\n 15[\"Tabular-to-FASTA\"];\n 12 -->|outfile|\ + \ 15;\n a5bb1cbe-1bde-49a1-ad86-6d57b1319fbe[\"Output\\ncontigs\"];\n 15 -->\ + \ a5bb1cbe-1bde-49a1-ad86-6d57b1319fbe;\n style a5bb1cbe-1bde-49a1-ad86-6d57b1319fbe\ + \ stroke:#2c3143,stroke-width:4px;" + modified: 2026-07-01 00:31:39 +0000 + name: Gene-based Pathogen Identification + outputs: + - annotation: '' + content_id: toolshed.g2.bx.psu.edu/repos/iuc/collection_element_identifiers/collection_element_identifiers/0.0.2 + errors: null + id: 1 + input_connections: + input_collection: + id: 0 + output_name: output + inputs: [] + label: null + name: Extract element identifiers + outputs: + - name: output + type: txt + position: + left: 322.37152236646415 + top: 59.69265140673434 + post_job_actions: + RenameDatasetActionoutput: + action_arguments: + newname: extracted_samples_IDs + action_type: RenameDatasetAction + output_name: output + tool_id: toolshed.g2.bx.psu.edu/repos/iuc/collection_element_identifiers/collection_element_identifiers/0.0.2 + tool_shed_repository: + changeset_revision: d3c07d270a50 + name: collection_element_identifiers + owner: iuc + tool_shed: toolshed.g2.bx.psu.edu + tool_state: '{"input_collection": {"__class__": "ConnectedValue"}, "__page__": + null, "__rerun_remap_job_id__": null}' + tool_version: 0.0.2 + type: tool + uuid: 80a87744-c9fa-498c-9412-b59346fb7904 + when: null + workflow_outputs: + - label: extracted_samples_IDs + output_name: output + uuid: d82a93c6-23a9-4f85-879c-ecd759a31087 + - annotation: '' + content_id: __BUILD_LIST__ + errors: null + id: 2 + input_connections: + datasets_0|input: + id: 0 + output_name: output + inputs: [] + label: null + name: Build list + outputs: + - name: output + type: input + position: + left: 330 + top: 597.5999771118164 + post_job_actions: + RenameDatasetActionoutput: + action_arguments: + newname: list_of_lists_of_preprocessed_samples + action_type: RenameDatasetAction + output_name: output + tool_id: __BUILD_LIST__ + tool_state: '{"datasets": [{"__index__": 0, "input": {"__class__": "ConnectedValue"}, + "id_cond": {"id_select": "idx", "__current_case__": 0}}], "__page__": null, + "__rerun_remap_job_id__": null}' + tool_version: 1.2.0 + type: tool + uuid: 38bc82a3-b563-44cf-b0db-9e3311fe99bb + when: null + workflow_outputs: + - label: list_of_lists_of_preprocessed_samples + output_name: output + uuid: f5b5b256-8ddf-4da8-8111-b1f6d3025a0d + - annotation: '' + content_id: toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.0 + errors: null + id: 3 + input_connections: + split_parms|input: + id: 1 + output_name: output + inputs: + - description: runtime parameter for tool Split file + name: split_parms + label: null + name: Split file + outputs: + - name: list_output_txt + type: input + position: + left: 608.6215223664642 + top: 47.19265140673434 + post_job_actions: + RenameDatasetActionlist_output_txt: + action_arguments: + newname: splitted_extracted_samples_IDs + action_type: RenameDatasetAction + output_name: list_output_txt + tool_id: toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.0 + tool_shed_repository: + changeset_revision: 6cbe2f30c2d7 + name: split_file_to_collection + owner: bgruening + tool_shed: toolshed.g2.bx.psu.edu + tool_state: '{"split_parms": {"select_ftype": "txt", "__current_case__": 5, + "input": {"__class__": "ConnectedValue"}, "select_mode": {"mode": "chunk", + "__current_case__": 0, "chunksize": "1"}, "newfilenames": "split_file", "select_allocate": + {"allocate": "byrow", "__current_case__": 2}}, "__page__": null, "__rerun_remap_job_id__": + null}' + tool_version: 0.5.0 + type: tool + uuid: f1e00cb8-a264-4acb-aff6-8c8b5aa0b48b + when: null + workflow_outputs: + - label: splitted_extracted_samples_IDs + output_name: list_output_txt + uuid: eb5317bd-4bad-4cad-9219-3ac379221d6e + - annotation: '' + content_id: toolshed.g2.bx.psu.edu/repos/bgruening/flye/flye/2.9.1+galaxy0 + errors: null + id: 4 + input_connections: + inputs: + id: 2 + output_name: output + inputs: [] + label: null + name: Flye + outputs: + - name: consensus + type: fasta + - name: assembly_graph + type: graph_dot + - name: assembly_gfa + type: txt + - name: assembly_info + type: tabular + position: + left: 576.4000244140625 + top: 602.433349609375 + post_job_actions: + RenameDatasetActionassembly_gfa: + action_arguments: + newname: flye_assembly_gfa + action_type: RenameDatasetAction + output_name: assembly_gfa + RenameDatasetActionassembly_graph: + action_arguments: + newname: flye_assembly_graph + action_type: RenameDatasetAction + output_name: assembly_graph + RenameDatasetActionassembly_info: + action_arguments: + newname: flye_assembly_info_tabular + action_type: RenameDatasetAction + output_name: assembly_info + RenameDatasetActionconsensus: + action_arguments: + newname: flye_consensus_fasta + action_type: RenameDatasetAction + output_name: consensus + tool_id: toolshed.g2.bx.psu.edu/repos/bgruening/flye/flye/2.9.1+galaxy0 + tool_shed_repository: + changeset_revision: cb8dfd28c16f + name: flye + owner: bgruening + tool_shed: toolshed.g2.bx.psu.edu + tool_state: '{"asm": {"asm_select": "false", "__current_case__": 1}, "generate_log": + false, "inputs": {"__class__": "ConnectedValue"}, "iterations": "1", "keep_haplotypes": + false, "meta": true, "min_overlap": null, "mode_conditional": {"mode": "--nano-hq", + "__current_case__": 2}, "no_alt_contigs": false, "scaffold": false, "__page__": + null, "__rerun_remap_job_id__": 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'{"input": {"__class__": "ConnectedValue"}, "seq_col": "2", "title_col": + "1", "__page__": null, "__rerun_remap_job_id__": null}' + tool_version: 1.1.1 + type: tool + uuid: 52af9a9c-0c9c-4605-a2a6-caefde8efa89 + when: null + workflow_outputs: + - label: contigs + output_name: output + uuid: a5bb1cbe-1bde-49a1-ad86-6d57b1319fbe + parent_id: microbiome/pathogen-detection-from-nanopore-foodborne-data + path: topics/microbiome/tutorials/pathogen-detection-from-nanopore-foodborne-data/workflows/gene_based_pathogen_identification.ga + tags: + - name:Collection + - name:PathoGFAIR + - name:IWC + - name:microGalaxy + test_results: null + tests: true + title: Gene-based Pathogen Identification + topic_id: microbiome + trs_endpoint: https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/microbiome-pathogen-detection-from-nanopore-foodborne-data/versions/gene-based-pathogen-identification + tutorial_id: pathogen-detection-from-nanopore-foodborne-data + url: https://training.galaxyproject.org/training-material/topics/microbiome/tutorials/pathogen-detection-from-nanopore-foodborne-data/workflows/gene_based_pathogen_identification.ga + url_html: https://training.galaxyproject.org/training-material/topics/microbiome/tutorials/pathogen-detection-from-nanopore-foodborne-data/workflows/gene_based_pathogen_identification.html + version: 2 + wfid: microbiome-pathogen-detection-from-nanopore-foodborne-data + wfname: gene-based-pathogen-identification + workflow: gene_based_pathogen_identification.ga + workflow_tools: + - __BUILD_LIST__ + - param_value_from_file + - toolshed.g2.bx.psu.edu/repos/bgruening/flye/flye/2.9.1+galaxy0 + - toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.0 + - toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.4 + - toolshed.g2.bx.psu.edu/repos/devteam/fasta_to_tabular/fasta2tab/1.1.1 + - toolshed.g2.bx.psu.edu/repos/devteam/tabular_to_fasta/tab2fasta/1.1.1 + - toolshed.g2.bx.psu.edu/repos/iuc/abricate/abricate/1.0.1 + - toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/2022.09+galaxy4 + - toolshed.g2.bx.psu.edu/repos/iuc/collection_element_identifiers/collection_element_identifiers/0.0.2 + - toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1 + - toolshed.g2.bx.psu.edu/repos/iuc/medaka_consensus_pipeline/medaka_consensus_pipeline/1.7.2+galaxy0 + workflowhub_id: '1495' + - creators: + - class: Person + identifier: 0000-0001-9852-1987 + name: "B\xE9r\xE9nice Batut" + url: https://orcid.org/0000-0001-9852-1987 + - class: Person + identifier: 0000-0001-9047-4215 + name: Engy Nasr + url: https://orcid.org/0000-0001-9047-4215 + - class: Person + identifier: 0000-0003-2982-388X + name: Paul Zierep + description: Microbiome - QC and Contamination Filtering + features: + comments: true + parameters: true + report: + markdown: '# Nanopore - Preprocessing Workflow Report + + Below are the results of the Preprocessing Workflow + + + This workflow was run on: + + + ```galaxy + + generate_time() + + ``` + + + With Galaxy version: + + + ```galaxy + + generate_galaxy_version() + + ``` + + + ## Workflow Inputs + + A collection of all sample reads (all in the same sequence file format, + e.g.: Fastq, Fastq.gz, Fastqsanger, etc.) + + + ## Workflow Outputs + + + ### Multi QC Report of all samples before reads quality retaining + + + ```galaxy + + history_dataset_as_image(output="multiQC_html_report_before_preprocessing") + + ``` + + ### Multi QC Report of all samples after reads quality retaining + + + ```galaxy + + history_dataset_as_image(output="multiQC_html_report_after_preprocessing") + + ``` + + + ### Percentages of removed host sequences in every sample + + + ```galaxy + + history_dataset_display(output="removed_hosts_percentage_tabular") + + ``` + + ' + subworkflows: false + graph_dot: "digraph main {\n node [fontname=\"Atkinson Hyperlegible\", shape=box,\ + \ color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n edge [fontname=\"\ + Atkinson Hyperlegible\"];\n 0[color=lightgreen,label=\"\u2139\uFE0F Input Parameter\\\ + nsamples_profile\"]\n 1[color=lightblue,label=\"\u2139\uFE0F Input Collection\\\ + ncollection_of_all_samples\"]\n 2[label=\"Porechop\"]\n 1 -> 2 [label=\"output\"\ + ]\n k34ea26db11cb41ee85c375af8a53a2c0[color=lightseagreen,label=\"Output\\\ + nporechop_output_trimmed_reads\"]\n 2 -> k34ea26db11cb41ee85c375af8a53a2c0\n\ + \ 3[label=\"NanoPlot\"]\n 1 -> 3 [label=\"output\"]\n k304110f960d04ba28b3bfae0e2a49554[color=lightseagreen,label=\"\ + Output\\nnanoplot_on_reads_before_preprocessing_nanostats_post_filtering\"]\n\ + \ 3 -> k304110f960d04ba28b3bfae0e2a49554\n kf2bd0a1fcd604a36a7d08025cc19ea2e[color=lightseagreen,label=\"\ + Output\\nnanoplot_qc_on_reads_before_preprocessing_html_report\"]\n 3 -> kf2bd0a1fcd604a36a7d08025cc19ea2e\n\ + \ k15ecf5b1e0eb405aac3a359feb66d4cd[color=lightseagreen,label=\"Output\\nnanoplot_qc_on_reads_before_preprocessing_nanostats\"\ + ]\n 3 -> k15ecf5b1e0eb405aac3a359feb66d4cd\n 4[label=\"FastQC\"]\n 1 -> 4\ + \ [label=\"output\"]\n ke61fef5d1bc84c8ebe6af74e210e9920[color=lightseagreen,label=\"\ + Output\\nfastqc_quality_check_before_preprocessing_text_file\"]\n 4 -> ke61fef5d1bc84c8ebe6af74e210e9920\n\ + \ kd0a6462405d04068835ba025fc011760[color=lightseagreen,label=\"Output\\nfastqc_quality_check_before_preprocessing_html_file\"\ + ]\n 4 -> kd0a6462405d04068835ba025fc011760\n 5[label=\"fastp\"]\n 2 -> 5\ + \ [label=\"outfile\"]\n k2a9a8b4d458b40e79a21fb7108d5bbe4[color=lightseagreen,label=\"\ + Output\\nnanopore_sequenced_reads_processed_with_fastp_after_host_removal_html_report\"\ + ]\n 5 -> k2a9a8b4d458b40e79a21fb7108d5bbe4\n ka221948350b74aed98dd333ad2e12eb8[color=lightseagreen,label=\"\ + Output\\nnanopore_sequenced_reads_processed_with_fastp_after_host_removal\"\ + ]\n 5 -> ka221948350b74aed98dd333ad2e12eb8\n 6[label=\"MultiQC\"]\n 4 ->\ + \ 6 [label=\"text_file\"]\n kebffe782a56c431f8af4c0cb8d7a02fc[color=lightseagreen,label=\"\ + Output\\nmultiQC_stats_before_preprocessing\"]\n 6 -> kebffe782a56c431f8af4c0cb8d7a02fc\n\ + \ k0f92196d047d4918819dc0ff7cd3ae85[color=lightseagreen,label=\"Output\\nmultiQC_html_report_before_preprocessing\"\ + ]\n 6 -> k0f92196d047d4918819dc0ff7cd3ae85\n 7[label=\"Map with minimap2\"\ + ]\n 0 -> 7 [label=\"output\"]\n 5 -> 7 [label=\"out1\"]\n k9d7bb3b709a1401fa132bb35a53375ea[color=lightseagreen,label=\"\ + Output\\nbam_map_to_host\"]\n 7 -> k9d7bb3b709a1401fa132bb35a53375ea\n 8[label=\"\ + NanoPlot\"]\n 5 -> 8 [label=\"out1\"]\n kb58992904c574662ad22860654652ade[color=lightseagreen,label=\"\ + Output\\nnanoplot_qc_on_reads_after_preprocessing_html_report\"]\n 8 -> kb58992904c574662ad22860654652ade\n\ + \ k949bfdf53d794dadbdd8c3a25e6af4cf[color=lightseagreen,label=\"Output\\nnanoplot_on_reads_after_preprocessing_nanostats_post_filtering\"\ + ]\n 8 -> k949bfdf53d794dadbdd8c3a25e6af4cf\n k42db7f93919e4bbb81a106411a9da410[color=lightseagreen,label=\"\ + Output\\nnanoplot_qc_on_reads_after_preprocessing_nanostats\"]\n 8 -> k42db7f93919e4bbb81a106411a9da410\n\ + \ 9[label=\"FastQC\"]\n 5 -> 9 [label=\"out1\"]\n k084f982f20f1457e801291ebbb85633d[color=lightseagreen,label=\"\ + Output\\nfastqc_quality_check_after_preprocessing_html_file\"]\n 9 -> k084f982f20f1457e801291ebbb85633d\n\ + \ k09306471afa041069cc7259b93dfc862[color=lightseagreen,label=\"Output\\nfastqc_quality_check_after_preprocessing_text_file\"\ + ]\n 9 -> k09306471afa041069cc7259b93dfc862\n 10[label=\"Split BAM by reads\ + \ mapping status\"]\n 7 -> 10 [label=\"alignment_output\"]\n k3b1e626f6bc1484cbe01366534361b73[color=lightseagreen,label=\"\ + Output\\nhost_sequences_bam\"]\n 10 -> k3b1e626f6bc1484cbe01366534361b73\n\ + \ k14a53fe2f29643aa86b7243278c1050c[color=lightseagreen,label=\"Output\\nnon_host_sequences_bam\"\ + ]\n 10 -> k14a53fe2f29643aa86b7243278c1050c\n 11[label=\"Select\"]\n 9 ->\ + \ 11 [label=\"text_file\"]\n ka809853b119f44d2986b8d2006439fbe[color=lightseagreen,label=\"\ + Output\\ntotal_sequences_before_hosts_sequences_removal\"]\n 11 -> ka809853b119f44d2986b8d2006439fbe\n\ + \ 12[label=\"Samtools fastx\"]\n 10 -> 12 [label=\"mapped\"]\n k10d4eaec81d8444e80757b77a1fb6870[color=lightseagreen,label=\"\ + Output\\nhost_sequences_fastq\"]\n 12 -> k10d4eaec81d8444e80757b77a1fb6870\n\ + \ 13[label=\"Samtools fastx\"]\n 10 -> 13 [label=\"unmapped\"]\n k0c2dd74dac4f45cf839c50386a7ece28[color=lightseagreen,label=\"\ + Output\\nnon_host_sequences_fastq\"]\n 13 -> k0c2dd74dac4f45cf839c50386a7ece28\n\ + \ 14[label=\"Collapse Collection\"]\n 11 -> 14 [label=\"out_file1\"]\n 15[label=\"\ + Filter failed datasets\"]\n 12 -> 15 [label=\"output\"]\n 16[label=\"Kraken2\"\ + ]\n 13 -> 16 [label=\"output\"]\n k203d303e8f3a4242971fb345842ebdb8[color=lightseagreen,label=\"\ + Output\\nkraken2_with_kalamri_database_output\"]\n 16 -> k203d303e8f3a4242971fb345842ebdb8\n\ + \ k843afd4d23a846e7b9458b67dd7ae341[color=lightseagreen,label=\"Output\\nkraken2_with_kalamri_database_report\"\ + ]\n 16 -> k843afd4d23a846e7b9458b67dd7ae341\n 17[label=\"Cut\"]\n 14 -> 17\ + \ [label=\"output\"]\n kd07be9f1d250400891ee59a68521eb56[color=lightseagreen,label=\"\ + Output\\nquality_retained_all_reads\"]\n 17 -> kd07be9f1d250400891ee59a68521eb56\n\ + \ 18[label=\"FastQC\"]\n 15 -> 18 [label=\"output\"]\n kb72ff57b092143bfa8176cd444c8f3cb[color=lightseagreen,label=\"\ + Output\\nhosts_qc_html\"]\n 18 -> kb72ff57b092143bfa8176cd444c8f3cb\n kb0ee6e310eb1437d8c04fc3640b9a0b7[color=lightseagreen,label=\"\ + Output\\nhosts_qc_text_file\"]\n 18 -> kb0ee6e310eb1437d8c04fc3640b9a0b7\n\ + \ 19[label=\"Krakentools: Extract Kraken Reads By ID\"]\n 5 -> 19 [label=\"\ + out1\"]\n 16 -> 19 [label=\"report_output\"]\n 16 -> 19 [label=\"output\"\ + ]\n k57e3b7258e1340b29acc31fd56ebc80a[color=lightseagreen,label=\"Output\\\ + ncollection_of_preprocessed_samples\"]\n 19 -> k57e3b7258e1340b29acc31fd56ebc80a\n\ + \ 20[label=\"Select\"]\n 18 -> 20 [label=\"text_file\"]\n k3ba35c7132f0474198d4ea8522e27500[color=lightseagreen,label=\"\ + Output\\ntotal_sequences_after_hosts_sequences_removal\"]\n 20 -> k3ba35c7132f0474198d4ea8522e27500\n\ + \ 21[label=\"Collapse Collection\"]\n 20 -> 21 [label=\"out_file1\"]\n 22[label=\"\ + Cut\"]\n 21 -> 22 [label=\"output\"]\n kcef36c6845494fd6b7c871fb21df012f[color=lightseagreen,label=\"\ + Output\\nquality_retained_hosts_reads\"]\n 22 -> kcef36c6845494fd6b7c871fb21df012f\n\ + \ 23[label=\"Column join\"]\n 17 -> 23 [label=\"out_file1\"]\n 22 -> 23 [label=\"\ + out_file1\"]\n 24[label=\"Compute\"]\n 23 -> 24 [label=\"tabular_output\"\ + ]\n 25[label=\"Column Regex Find And Replace\"]\n 24 -> 25 [label=\"out_file1\"\ + ]\n k470892eedab948d7ad9745dbd52afaa7[color=lightseagreen,label=\"Output\\\ + nremoved_hosts_percentage_tabular\"]\n 25 -> k470892eedab948d7ad9745dbd52afaa7\n\ + \ 26[label=\"MultiQC\"]\n 9 -> 26 [label=\"text_file\"]\n 25 -> 26 [label=\"\ + out_file1\"]\n k0b1b5a7336ee42a2a2201ced6ec7378b[color=lightseagreen,label=\"\ + Output\\nmultiQC_html_report_after_preprocessing\"]\n 26 -> k0b1b5a7336ee42a2a2201ced6ec7378b\n\ + \ k13cbf6c769544458aa66a5b020c63822[color=lightseagreen,label=\"Output\\nmultiQC_stats_after_preprocessing\"\ + ]\n 26 -> k13cbf6c769544458aa66a5b020c63822\n}" + history: + - hash: 43b59f45eec3262ec9b66a55ef2707a9c442ba5a + message: renaming the preprocessing.ga workflow name + num: 7 + short_hash: 43b59f45e + unix: '1751535523' + - hash: 20b1c5a11c7ea68a1cefd70cbe72b3783d7887ad + message: GTN-Foodborne tutorial, updating 2/5 workflows, which contains filter + failed datasets tool with the new tool + num: 6 + short_hash: 20b1c5a11 + unix: '1751535250' + - hash: cdd93376adc6ce80742881c25d6810bcce85fc05 + message: adding tags to some of the workflow outputs, updating the training + with the latest PathoGFAIR workflows updates + num: 5 + short_hash: cdd93376a + unix: '1717675229' + - hash: e230001f416aa3035d90535521418fa798ab643e + message: updating preprocessing workflow and allele based workflow with a single + user input parameter and adjusting the md file accodingly + num: 4 + short_hash: e230001f4 + unix: '1716982398' + - hash: 211b69394d6ef4d129eaa18cd76b93c8dece8cf3 + message: adding workflow reports to the workflows of the training to match the + latest version of the IWC PR + num: 3 + short_hash: 211b69394 + unix: '1716716727' + - hash: d320748c5c8ea425a77aa03ac78a5956eb75b005 + message: Foodborne training update 2024 + num: 2 + short_hash: d320748c5 + unix: '1716229068' + - hash: 0e0a2f2ccb650b0aab1ffc13838045164bdb5d30 + message: Rename metagenomics topic to microbiome + num: 1 + short_hash: 0e0a2f2cc + unix: '1704901629' + inputs: + - annotation: 'based on the lab preparation of the samples during sequencing, + there should be a sample profile better than the other, to be chosen as an + optional input to Minimap2. e.g. PacBio/Oxford Nanpore + + + For more details check: https://github.com/lh3/minimap2?tab=readme-ov-file#use-cases' + content_id: null + errors: null + id: 0 + input_connections: {} + inputs: + - description: 'based on the lab preparation of the samples during sequencing, + there should be a sample profile better than the other, to be chosen as + an optional input to Minimap2. e.g. PacBio/Oxford Nanpore + + + For more details check: https://github.com/lh3/minimap2?tab=readme-ov-file#use-cases' + name: samples_profile + label: samples_profile + name: Input parameter + outputs: [] + position: + left: 655 + top: 19.602400000005026 + tool_id: null + tool_state: '{"validators": [], "restrictOnConnections": true, "parameter_type": + "text", "optional": true}' + tool_version: null + type: parameter_input + uuid: 1435b9fc-84c0-4a1a-af49-007da98f4d5f + when: null + workflow_outputs: [] + - annotation: Nanopore reads of each sample are all in a single fastq or fastq.gz + file + content_id: null + errors: null + id: 1 + input_connections: {} + inputs: + - description: Nanopore reads of each sample are all in a single fastq or fastq.gz + file + name: collection_of_all_samples + label: collection_of_all_samples + name: Input dataset collection + outputs: [] + position: + left: 20 + top: 981.4 + tool_id: null + tool_state: '{"optional": false, "tag": null, "collection_type": "list", "fields": + null}' + tool_version: null + type: data_collection_input + uuid: 6a0dea4c-3d2c-4ab9-bb87-82cff75ac6d0 + when: null + workflow_outputs: [] + license: MIT + mermaid: "flowchart TD\n 0[\"\u2139\uFE0F Input Parameter\\nsamples_profile\"\ + ];\n style 0 fill:#ded,stroke:#393,stroke-width:4px;\n 1[\"\u2139\uFE0F Input\ + \ Collection\\ncollection_of_all_samples\"];\n style 1 stroke:#2c3143,stroke-width:4px;\n\ + \ 2[\"Porechop\"];\n 1 -->|output| 2;\n 34ea26db-11cb-41ee-85c3-75af8a53a2c0[\"\ + Output\\nporechop_output_trimmed_reads\"];\n 2 --> 34ea26db-11cb-41ee-85c3-75af8a53a2c0;\n\ + \ style 34ea26db-11cb-41ee-85c3-75af8a53a2c0 stroke:#2c3143,stroke-width:4px;\n\ + \ 3[\"NanoPlot\"];\n 1 -->|output| 3;\n 304110f9-60d0-4ba2-8b3b-fae0e2a49554[\"\ + Output\\nnanoplot_on_reads_before_preprocessing_nanostats_post_filtering\"];\n\ + \ 3 --> 304110f9-60d0-4ba2-8b3b-fae0e2a49554;\n style 304110f9-60d0-4ba2-8b3b-fae0e2a49554\ + \ stroke:#2c3143,stroke-width:4px;\n f2bd0a1f-cd60-4a36-a7d0-8025cc19ea2e[\"\ + Output\\nnanoplot_qc_on_reads_before_preprocessing_html_report\"];\n 3 -->\ + \ f2bd0a1f-cd60-4a36-a7d0-8025cc19ea2e;\n style f2bd0a1f-cd60-4a36-a7d0-8025cc19ea2e\ + \ stroke:#2c3143,stroke-width:4px;\n 15ecf5b1-e0eb-405a-ac3a-359feb66d4cd[\"\ + Output\\nnanoplot_qc_on_reads_before_preprocessing_nanostats\"];\n 3 --> 15ecf5b1-e0eb-405a-ac3a-359feb66d4cd;\n\ + \ style 15ecf5b1-e0eb-405a-ac3a-359feb66d4cd stroke:#2c3143,stroke-width:4px;\n\ + \ 4[\"FastQC\"];\n 1 -->|output| 4;\n e61fef5d-1bc8-4c8e-be6a-f74e210e9920[\"\ + Output\\nfastqc_quality_check_before_preprocessing_text_file\"];\n 4 --> e61fef5d-1bc8-4c8e-be6a-f74e210e9920;\n\ + \ style e61fef5d-1bc8-4c8e-be6a-f74e210e9920 stroke:#2c3143,stroke-width:4px;\n\ + \ d0a64624-05d0-4068-835b-a025fc011760[\"Output\\nfastqc_quality_check_before_preprocessing_html_file\"\ + ];\n 4 --> d0a64624-05d0-4068-835b-a025fc011760;\n style d0a64624-05d0-4068-835b-a025fc011760\ + \ stroke:#2c3143,stroke-width:4px;\n 5[\"fastp\"];\n 2 -->|outfile| 5;\n \ + \ 2a9a8b4d-458b-40e7-9a21-fb7108d5bbe4[\"Output\\nnanopore_sequenced_reads_processed_with_fastp_after_host_removal_html_report\"\ + ];\n 5 --> 2a9a8b4d-458b-40e7-9a21-fb7108d5bbe4;\n style 2a9a8b4d-458b-40e7-9a21-fb7108d5bbe4\ + \ stroke:#2c3143,stroke-width:4px;\n a2219483-50b7-4aed-98dd-333ad2e12eb8[\"\ + Output\\nnanopore_sequenced_reads_processed_with_fastp_after_host_removal\"\ + ];\n 5 --> a2219483-50b7-4aed-98dd-333ad2e12eb8;\n style a2219483-50b7-4aed-98dd-333ad2e12eb8\ + \ stroke:#2c3143,stroke-width:4px;\n 6[\"MultiQC\"];\n 4 -->|text_file| 6;\n\ + \ ebffe782-a56c-431f-8af4-c0cb8d7a02fc[\"Output\\nmultiQC_stats_before_preprocessing\"\ + ];\n 6 --> ebffe782-a56c-431f-8af4-c0cb8d7a02fc;\n style ebffe782-a56c-431f-8af4-c0cb8d7a02fc\ + \ stroke:#2c3143,stroke-width:4px;\n 0f92196d-047d-4918-819d-c0ff7cd3ae85[\"\ + Output\\nmultiQC_html_report_before_preprocessing\"];\n 6 --> 0f92196d-047d-4918-819d-c0ff7cd3ae85;\n\ + \ style 0f92196d-047d-4918-819d-c0ff7cd3ae85 stroke:#2c3143,stroke-width:4px;\n\ + \ 7[\"Map with minimap2\"];\n 0 -->|output| 7;\n 5 -->|out1| 7;\n 9d7bb3b7-09a1-401f-a132-bb35a53375ea[\"\ + Output\\nbam_map_to_host\"];\n 7 --> 9d7bb3b7-09a1-401f-a132-bb35a53375ea;\n\ + \ style 9d7bb3b7-09a1-401f-a132-bb35a53375ea stroke:#2c3143,stroke-width:4px;\n\ + \ 8[\"NanoPlot\"];\n 5 -->|out1| 8;\n b5899290-4c57-4662-ad22-860654652ade[\"\ + Output\\nnanoplot_qc_on_reads_after_preprocessing_html_report\"];\n 8 --> b5899290-4c57-4662-ad22-860654652ade;\n\ + \ style b5899290-4c57-4662-ad22-860654652ade stroke:#2c3143,stroke-width:4px;\n\ + \ 949bfdf5-3d79-4dad-bdd8-c3a25e6af4cf[\"Output\\nnanoplot_on_reads_after_preprocessing_nanostats_post_filtering\"\ + ];\n 8 --> 949bfdf5-3d79-4dad-bdd8-c3a25e6af4cf;\n style 949bfdf5-3d79-4dad-bdd8-c3a25e6af4cf\ + \ stroke:#2c3143,stroke-width:4px;\n 42db7f93-919e-4bbb-81a1-06411a9da410[\"\ + Output\\nnanoplot_qc_on_reads_after_preprocessing_nanostats\"];\n 8 --> 42db7f93-919e-4bbb-81a1-06411a9da410;\n\ + \ style 42db7f93-919e-4bbb-81a1-06411a9da410 stroke:#2c3143,stroke-width:4px;\n\ + \ 9[\"FastQC\"];\n 5 -->|out1| 9;\n 084f982f-20f1-457e-8012-91ebbb85633d[\"\ + Output\\nfastqc_quality_check_after_preprocessing_html_file\"];\n 9 --> 084f982f-20f1-457e-8012-91ebbb85633d;\n\ + \ style 084f982f-20f1-457e-8012-91ebbb85633d stroke:#2c3143,stroke-width:4px;\n\ + \ 09306471-afa0-4106-9cc7-259b93dfc862[\"Output\\nfastqc_quality_check_after_preprocessing_text_file\"\ + ];\n 9 --> 09306471-afa0-4106-9cc7-259b93dfc862;\n style 09306471-afa0-4106-9cc7-259b93dfc862\ + \ stroke:#2c3143,stroke-width:4px;\n 10[\"Split BAM by reads mapping status\"\ + ];\n 7 -->|alignment_output| 10;\n 3b1e626f-6bc1-484c-be01-366534361b73[\"\ + Output\\nhost_sequences_bam\"];\n 10 --> 3b1e626f-6bc1-484c-be01-366534361b73;\n\ + \ style 3b1e626f-6bc1-484c-be01-366534361b73 stroke:#2c3143,stroke-width:4px;\n\ + \ 14a53fe2-f296-43aa-86b7-243278c1050c[\"Output\\nnon_host_sequences_bam\"\ + ];\n 10 --> 14a53fe2-f296-43aa-86b7-243278c1050c;\n style 14a53fe2-f296-43aa-86b7-243278c1050c\ + \ stroke:#2c3143,stroke-width:4px;\n 11[\"Select\"];\n 9 -->|text_file| 11;\n\ + \ a809853b-119f-44d2-986b-8d2006439fbe[\"Output\\ntotal_sequences_before_hosts_sequences_removal\"\ + ];\n 11 --> 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https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/microbiome-pathogen-detection-from-nanopore-foodborne-data/versions/nanopore-preprocessing + tutorial_id: pathogen-detection-from-nanopore-foodborne-data + url: https://training.galaxyproject.org/training-material/topics/microbiome/tutorials/pathogen-detection-from-nanopore-foodborne-data/workflows/nanopore_preprocessing.ga + url_html: https://training.galaxyproject.org/training-material/topics/microbiome/tutorials/pathogen-detection-from-nanopore-foodborne-data/workflows/nanopore_preprocessing.html + version: 4 + wfid: microbiome-pathogen-detection-from-nanopore-foodborne-data + wfname: nanopore-preprocessing + workflow: nanopore_preprocessing.ga + workflow_tools: + - Cut1 + - Grep1 + - __FILTER_FAILED_DATASETS__ + - toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.0 + - toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy0 + - toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regexColumn1/1.0.3 + - toolshed.g2.bx.psu.edu/repos/iuc/bamtools_split_mapped/bamtools_split_mapped/2.5.2+galaxy2 + - toolshed.g2.bx.psu.edu/repos/iuc/collection_column_join/collection_column_join/0.0.3 + - toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.4+galaxy0 + - toolshed.g2.bx.psu.edu/repos/iuc/kraken2/kraken2/2.1.1+galaxy1 + - toolshed.g2.bx.psu.edu/repos/iuc/krakentools_extract_kraken_reads/krakentools_extract_kraken_reads/1.2+galaxy1 + - toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.28+galaxy0 + - toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1 + - toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.42.0+galaxy1 + - toolshed.g2.bx.psu.edu/repos/iuc/porechop/porechop/0.2.4+galaxy0 + - toolshed.g2.bx.psu.edu/repos/iuc/samtools_fastx/samtools_fastx/1.15.1+galaxy2 + - toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0 + workflowhub_id: '1492' + - creators: + - class: Person + identifier: 0000-0001-9047-4215 + name: Engy Nasr + url: https://orcid.org/0000-0001-9047-4215 - class: Person identifier: 0000-0001-9852-1987 name: "B\xE9r\xE9nice Batut" - description: Assembly of metagenomic sequencing data + url: https://orcid.org/0000-0001-9852-1987 + - class: Person + identifier: 0000-0003-2982-388X + name: Paul Zierep + description: Pathogens of all samples report generation and visualization features: - comments: false + comments: true parameters: false report: - markdown: ' - - # Workflow Execution Report - - - ## Workflow Inputs - - ```galaxy - - invocation_inputs() - - ``` - - - ## Workflow Outputs - - ```galaxy - - invocation_outputs() - - ``` - - - ## Workflow - - ```galaxy - - workflow_display() - - ``` - - ' + markdown: "# Pathogen Detection - PathoGFAIR Samples Aggregation and Visualisation\ + \ workflow Report\nBelow are the results for the PathoGFAIR Samples Aggregation\ + \ and Visualisation Workflow\n\nThis workflow was run on:\n\n```galaxy\n\ + generate_time()\n```\n\nWith Galaxy version:\n\n```galaxy\ngenerate_galaxy_version()\n\ + ```\n\n## Workflow Inputs\nTabular files and a FASTA file from the Gene\ + \ based Pathogenic Identification workflow, four other tabular files from\ + \ Nanopore Preprocessing and Nanopore - Allele bases Pathogen Identification\ + \ workflow, and an optional Metadata tabular file with more sample information:\n\ + \nFrom Gene based Pathogenic Identification workflow: \n- contigs, FASTA\ + \ file\n- vfs, Tabular file\n- vfs_of_genes_identified_by_vfdb, Tabular\ + \ file\n- amrs, Tabular file\n- amr_identified_by_ncbi, Tabular file\n\n\ + From Nanopore - Allele bases Pathogen Identification workflow: \n- number_of_variants_per_sample,\ + \ Tabular file\n- mapping_mean_depth_per_sample, Tabular file\n- mapping_coverage_percentage_per_sample,\ + \ Tabular file\n\nFrom Nanopore Preprocessing: \n- removed_hosts_percentage_tabular,\ + \ Tabular file\n\n## Some of the Workflow Outputs\n\n1- All Samples VFs\ + \ Heatmap\n\n```galaxy\nhistory_dataset_as_image(output=\"heatmap_png\"\ + )\n```\n\n2- All samples phylogenetic tree VFs based\n\n```galaxy\nhistory_dataset_as_image(output=\"\ + all_samples_phylogenetic_tree_based_vfs\")\n```\n\n3- All samples Phylogenetic\ + \ tree AMR based \n\n```galaxy\nhistory_dataset_as_image(output=\"all_samples_phylogenetic_tree_based_amrs\"\ + )\n```\n\n4- Barplot for the Number of reads before host sequences removal\ + \ and Number of found host reads per sample, performed in the Nanopore -\ + \ Preprocessing workflow\n\n```galaxy\nhistory_dataset_as_image(output=\"\ + number_of_reads_before_host_removal_and_number_of_host_reads_found_per_sample_fig\"\ + )\n```\n\n5- Barplot for the total number of removed host sequences per\ + \ sample\n\n```galaxy\nhistory_dataset_as_image(output=\"removed_host_percentage_fig\"\ + )\n```\n \n6- Barplot for the Mapping mean depth per sample\n\n```galaxy\n\ + history_dataset_as_image(output=\"mapping_mean_depth_per_sample_fig\")\n\ + ```\n\n6- Barplot for the Mapping coverage percentage per sample\n\n```galaxy\n\ + history_dataset_as_image(output=\"mapping_coverage_percentage_per_sample_fig\"\ + )\n```\n\n7- Barplot for the total number of variants and SNPs identified\ + \ per sample\n\n```galaxy\nhistory_dataset_as_image(output=\"number_of_Variants_and_SNPs_indentified_fig\"\ + )\n```\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n" subworkflows: false graph_dot: "digraph main {\n node [fontname=\"Atkinson Hyperlegible\", shape=box,\ \ color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n edge [fontname=\"\ Atkinson Hyperlegible\"];\n 0[color=lightblue,label=\"\u2139\uFE0F Input Collection\\\ - nQC controlled reads\"]\n 1[label=\"metaSPAdes\"]\n 0 -> 1 [label=\"output\"\ - ]\n kba8ef041cea5479a8aab38b3d6f0af60[color=lightseagreen,label=\"Output\\\ - nout_ag\"]\n 1 -> kba8ef041cea5479a8aab38b3d6f0af60\n 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kaacdfe45eb0c4f6ea479eeb170774757[color=lightseagreen,label=\"\ + Output\\nfasttree_nhx\"]\n 60 -> kaacdfe45eb0c4f6ea479eeb170774757\n 61[label=\"\ + Cut\"]\n 58 -> 61 [label=\"output\"]\n 62[label=\"Group\"]\n 59 -> 62 [label=\"\ + out_file1\"]\n 63[label=\"Newick Display\"]\n 60 -> 63 [label=\"output\"]\n\ + \ k0c22178cdc85413780e2f3040b92bd20[color=lightseagreen,label=\"Output\\nnewick_genes_tree_graphs_collection\"\ + ]\n 63 -> k0c22178cdc85413780e2f3040b92bd20\n 64[label=\"Group\"]\n 61 ->\ + \ 64 [label=\"out_file1\"]\n 65[label=\"Tabular-to-FASTA\"]\n 62 -> 65 [label=\"\ + out_file1\"]\n 66[label=\"Tabular-to-FASTA\"]\n 64 -> 66 [label=\"out_file1\"\ + ]\n 67[label=\"FASTA Merge Files and Filter Unique Sequences\"]\n 65 -> 67\ + \ [label=\"output\"]\n 68[label=\"FASTA Merge Files and Filter Unique Sequences\"\ + ]\n 66 -> 68 [label=\"output\"]\n 69[label=\"ClustalW\"]\n 67 -> 69 [label=\"\ + output\"]\n 70[label=\"ClustalW\"]\n 68 -> 70 [label=\"output\"]\n 71[label=\"\ + FASTTREE\"]\n 69 -> 71 [label=\"output\"]\n 72[label=\"FASTTREE\"]\n 70 ->\ + \ 72 [label=\"output\"]\n 73[label=\"Newick Display\"]\n 71 -> 73 [label=\"\ + output\"]\n k1f9cb2cf219f48de8058d6d45f3b3158[color=lightseagreen,label=\"\ + Output\\nall_samples_phylogenetic_tree_based_amrs\"]\n 73 -> k1f9cb2cf219f48de8058d6d45f3b3158\n\ + \ 74[label=\"Newick Display\"]\n 72 -> 74 [label=\"output\"]\n k6bb4b32b7cca4e048120be9f64ccba39[color=lightseagreen,label=\"\ + Output\\nall_samples_phylogenetic_tree_based_vfs\"]\n 74 -> k6bb4b32b7cca4e048120be9f64ccba39\n\ + }" history: - - hash: 65e24d135887a0fad9a1cc667b98a66040949936 - message: Update metagenomics assembly tutorial + - hash: 20b1c5a11c7ea68a1cefd70cbe72b3783d7887ad + message: GTN-Foodborne tutorial, updating 2/5 workflows, which contains filter + failed datasets tool with the new tool + num: 4 + short_hash: 20b1c5a11 + unix: '1751535250' + - hash: cdd93376adc6ce80742881c25d6810bcce85fc05 + message: adding tags to some of the workflow outputs, updating the training + with the latest PathoGFAIR workflows updates + num: 3 + short_hash: cdd93376a + unix: '1717675229' + - hash: 211b69394d6ef4d129eaa18cd76b93c8dece8cf3 + message: adding workflow reports to the workflows of the training to match the + latest version of the IWC PR num: 2 - short_hash: 65e24d135 - unix: '1749722054' - - hash: 0e0a2f2ccb650b0aab1ffc13838045164bdb5d30 - message: Rename metagenomics topic to microbiome + short_hash: 211b69394 + unix: '1716716727' + - hash: d320748c5c8ea425a77aa03ac78a5956eb75b005 + message: Foodborne training update 2024 num: 1 - short_hash: 0e0a2f2cc - unix: '1704901629' + short_hash: d320748c5 + unix: '1716229068' inputs: - - annotation: Metagenomics reads that have been controlled for quality + - annotation: output_of_abricate_with_amrfinderncbi content_id: null errors: null id: 0 input_connections: {} inputs: - - description: Metagenomics reads that have been controlled for quality - name: QC controlled reads - label: QC controlled reads + - description: output_of_abricate_with_amrfinderncbi + name: amr_identified_by_ncbi + label: amr_identified_by_ncbi name: Input dataset collection outputs: [] position: - left: 0 - top: 434.0193226947046 + left: 19.98333740234375 + top: 1006.3443929882739 tool_id: null - tool_state: '{"optional": false, "tag": null, "collection_type": "list:paired"}' + tool_state: '{"optional": false, "tag": null, "collection_type": "list", "fields": + null}' tool_version: null type: data_collection_input - uuid: 768bd692-5d23-4394-b236-03d68f086b6f + uuid: a7f1c4a9-5d07-49df-82cd-1bbcf3fd628f + when: null + workflow_outputs: [] + - annotation: output_of_abricate_with_vfdb + content_id: null + errors: null + id: 1 + input_connections: {} + inputs: + - description: output_of_abricate_with_vfdb + name: vfs_of_genes_identified_by_vfdb + label: vfs_of_genes_identified_by_vfdb + name: Input dataset collection + outputs: [] + position: + left: 34.98484848484827 + top: 1508.441282170953 + tool_id: null + tool_state: '{"optional": false, "tag": null, "collection_type": "list", "fields": + null}' + tool_version: null + type: data_collection_input + uuid: 2908a402-5edf-4bcc-a970-1db21c474d09 + when: null + workflow_outputs: [] + - annotation: samples_metadata + content_id: null + errors: null + id: 2 + input_connections: {} + inputs: + - description: samples_metadata + name: metadata + label: metadata + name: Input dataset + outputs: [] + position: + left: 1858.3512218637072 + top: 209.99121532505262 + tool_id: null + tool_state: '{"optional": true, "tag": null}' + tool_version: null + type: data_input + uuid: f4765d9d-b134-4462-bae6-9695c95ae596 + when: null + workflow_outputs: [] + - annotation: removed_hosts_percentage_tabular + content_id: null + errors: null + id: 3 + input_connections: {} + inputs: + - description: removed_hosts_percentage_tabular + name: removed_hosts_percentage_tabular + label: removed_hosts_percentage_tabular + name: Input dataset + outputs: [] + position: + left: 1853.666381138832 + top: 289.6725384559728 + tool_id: null + tool_state: '{"optional": false, "tag": null}' + tool_version: null + type: data_input + uuid: e7dccd07-76a8-48a2-8931-67567fb31598 + when: null + workflow_outputs: [] + - annotation: mapping_mean_depth_per_sample + content_id: null + errors: null + id: 4 + input_connections: {} + inputs: + - description: mapping_mean_depth_per_sample + name: mapping_mean_depth_per_sample + label: mapping_mean_depth_per_sample + name: Input dataset + outputs: [] + position: + left: 1854.0957915122806 + top: 419.61832235919906 + tool_id: null + tool_state: '{"optional": false, "tag": null}' + tool_version: null + type: data_input + uuid: c18104cc-35d8-43ed-85e6-15e4f7af0b4d + when: null + workflow_outputs: [] + - annotation: amrs + content_id: null + errors: null + id: 5 + input_connections: {} + inputs: + - description: amrs + name: amrs + label: amrs + name: Input dataset collection + outputs: [] + position: + left: 50.9848484848481 + top: 1934.2745890557185 + tool_id: null + tool_state: '{"optional": false, "tag": null, "collection_type": "list", "fields": + null}' + tool_version: null + type: data_collection_input + uuid: 297bede6-bef8-44f1-bcbb-134464821c44 + when: null + workflow_outputs: [] + - annotation: mapping_coverage_percentage_per_sample + content_id: null + errors: null + id: 6 + input_connections: {} + inputs: + - description: mapping_coverage_percentage_per_sample + name: mapping_coverage_percentage_per_sample + label: mapping_coverage_percentage_per_sample + name: Input dataset + outputs: [] + position: + left: 1856.926239945225 + top: 545.6990912189043 + tool_id: null + tool_state: '{"optional": false, "tag": null}' + tool_version: null + type: data_input + uuid: bbf94808-86af-468d-bbdd-6872ddbf6c30 + when: null + workflow_outputs: [] + - annotation: number_of_variants_per_sample + content_id: null + errors: null + id: 7 + input_connections: {} + inputs: + - description: number_of_variants_per_sample + name: number_of_variants_per_sample + label: number_of_variants_per_sample + name: Input dataset + outputs: [] + position: + left: 1858.9173115502963 + top: 671.3113831546217 + tool_id: null + tool_state: '{"optional": false, "tag": null}' + tool_version: null + type: data_input + uuid: 833bedfd-e345-4c8a-8d19-1623faaaf602 + when: null + workflow_outputs: [] + - annotation: Contigs + content_id: null + errors: null + id: 8 + input_connections: {} + inputs: + - description: Contigs + name: contigs + label: contigs + name: Input dataset collection + outputs: [] + position: + left: 600.9833984375 + top: 2266.2999877929688 + tool_id: null + tool_state: '{"optional": false, "tag": "", "collection_type": "list", "fields": + null}' + tool_version: null + type: data_collection_input + uuid: ce948faa-f897-47e3-ac8c-0227afdd8203 + when: null + workflow_outputs: [] + - annotation: VFs + content_id: null + errors: null + id: 9 + input_connections: {} + inputs: + - description: VFs + name: vfs + label: vfs + name: Input dataset collection + outputs: [] + position: + left: 46.984848484848044 + top: 2487.3079752861872 + tool_id: null + tool_state: '{"optional": false, "tag": "", "collection_type": "list", "fields": + null}' + tool_version: null + type: data_collection_input + uuid: 8ff72508-664e-4af1-b0e6-ca2643626295 when: null workflow_outputs: [] license: MIT - mermaid: "flowchart TD\n 0[\"\u2139\uFE0F Input Collection\\nQC controlled reads\"\ - ];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"metaSPAdes\"];\n 0 -->|output|\ - \ 1;\n ba8ef041-cea5-479a-8aab-38b3d6f0af60[\"Output\\nout_ag\"];\n 1 -->\ - \ ba8ef041-cea5-479a-8aab-38b3d6f0af60;\n style ba8ef041-cea5-479a-8aab-38b3d6f0af60\ - \ stroke:#2c3143,stroke-width:4px;\n c3b9a234-94d2-4579-8eba-895e7e49e129[\"\ - Output\\nout_ags\"];\n 1 --> c3b9a234-94d2-4579-8eba-895e7e49e129;\n style\ - \ c3b9a234-94d2-4579-8eba-895e7e49e129 stroke:#2c3143,stroke-width:4px;\n 2[\"\ - MEGAHIT\"];\n 0 -->|output| 2;\n 759ce084-a80b-4a04-b74e-6e387357e25a[\"Output\\\ - noutput\"];\n 2 --> 759ce084-a80b-4a04-b74e-6e387357e25a;\n style 759ce084-a80b-4a04-b74e-6e387357e25a\ - \ stroke:#2c3143,stroke-width:4px;\n 3[\"Bowtie2\"];\n 0 -->|output| 3;\n\ - \ 2 -->|output| 3;\n 95b806c7-53ee-4a78-8e24-a5794c9c220a[\"Output\\nmapping_stats\"\ - ];\n 3 --> 95b806c7-53ee-4a78-8e24-a5794c9c220a;\n style 95b806c7-53ee-4a78-8e24-a5794c9c220a\ - \ stroke:#2c3143,stroke-width:4px;\n 4[\"CoverM contig\"];\n 0 -->|output|\ - \ 4;\n 2 -->|output| 4;\n 51a8a5a9-b3bb-43b9-80e5-7ec7b84a6cd5[\"Output\\\ - noutput\"];\n 4 --> 51a8a5a9-b3bb-43b9-80e5-7ec7b84a6cd5;\n style 51a8a5a9-b3bb-43b9-80e5-7ec7b84a6cd5\ - \ stroke:#2c3143,stroke-width:4px;\n 5[\"Quast\"];\n 2 -->|output| 5;\n 0\ - \ -->|output| 5;\n 5553b6a6-863d-4846-944f-7ed609a3734a[\"Output\\nreport_html_meta\"\ - ];\n 5 --> 5553b6a6-863d-4846-944f-7ed609a3734a;\n style 5553b6a6-863d-4846-944f-7ed609a3734a\ - \ stroke:#2c3143,stroke-width:4px;\n 6[\"megahit contig2fastg\"];\n 2 -->|output|\ - \ 6;\n 7[\"Bandage Image\"];\n 6 -->|fastg| 7;\n 63861d0b-e0a6-4604-bd09-1b0f7ee9d54b[\"\ - Output\\noutfile\"];\n 7 --> 63861d0b-e0a6-4604-bd09-1b0f7ee9d54b;\n style\ - \ 63861d0b-e0a6-4604-bd09-1b0f7ee9d54b stroke:#2c3143,stroke-width:4px;\n 8[\"\ - Bandage Info\"];\n 6 -->|fastg| 8;\n 9[\"Column join\"];\n 8 -->|outfile|\ - \ 9;\n c882d313-5084-40d4-8c97-9552fb7b35ad[\"Output\\ntabular_output\"];\n\ - \ 9 --> c882d313-5084-40d4-8c97-9552fb7b35ad;\n style c882d313-5084-40d4-8c97-9552fb7b35ad\ + mermaid: "flowchart TD\n 0[\"\u2139\uFE0F Input Collection\\namr_identified_by_ncbi\"\ + ];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"\u2139\uFE0F Input Collection\\\ + nvfs_of_genes_identified_by_vfdb\"];\n style 1 stroke:#2c3143,stroke-width:4px;\n\ + \ 2[\"\u2139\uFE0F Input Dataset\\nmetadata\"];\n style 2 stroke:#2c3143,stroke-width:4px;\n\ + \ 3[\"\u2139\uFE0F Input Dataset\\nremoved_hosts_percentage_tabular\"];\n \ + \ style 3 stroke:#2c3143,stroke-width:4px;\n 4[\"\u2139\uFE0F Input Dataset\\\ + nmapping_mean_depth_per_sample\"];\n style 4 stroke:#2c3143,stroke-width:4px;\n\ + \ 5[\"\u2139\uFE0F Input Collection\\namrs\"];\n style 5 stroke:#2c3143,stroke-width:4px;\n\ + \ 6[\"\u2139\uFE0F Input Dataset\\nmapping_coverage_percentage_per_sample\"\ + ];\n style 6 stroke:#2c3143,stroke-width:4px;\n 7[\"\u2139\uFE0F Input Dataset\\\ + nnumber_of_variants_per_sample\"];\n style 7 stroke:#2c3143,stroke-width:4px;\n\ + \ 8[\"\u2139\uFE0F Input Collection\\ncontigs\"];\n style 8 stroke:#2c3143,stroke-width:4px;\n\ + \ 9[\"\u2139\uFE0F Input Collection\\nvfs\"];\n style 9 stroke:#2c3143,stroke-width:4px;\n\ + \ 10[\"Filter failed datasets\"];\n 0 -->|output| 10;\n 11[\"Filter failed\ + \ datasets\"];\n 1 -->|output| 11;\n 12[\"Bar chart\"];\n 3 -->|output| 12;\n\ + \ 0961166e-38b6-44e3-93db-100d821b0070[\"Output\\nnumber_of_reads_before_host_removal_and_number_of_host_reads_found_per_sample_fig\"\ + ];\n 12 --> 0961166e-38b6-44e3-93db-100d821b0070;\n style 0961166e-38b6-44e3-93db-100d821b0070\ + \ stroke:#2c3143,stroke-width:4px;\n 13[\"Bar chart\"];\n 3 -->|output| 13;\n\ + \ 548975e5-4619-49fc-9e95-4d7f4d761dfd[\"Output\\nremoved_host_percentage_fig\"\ + ];\n 13 --> 548975e5-4619-49fc-9e95-4d7f4d761dfd;\n style 548975e5-4619-49fc-9e95-4d7f4d761dfd\ + \ stroke:#2c3143,stroke-width:4px;\n 14[\"Bar chart\"];\n 4 -->|output| 14;\n\ + \ a71ebb67-1154-4f25-a62d-e8fa2b839e2e[\"Output\\nmapping_mean_depth_per_sample_fig\"\ + ];\n 14 --> a71ebb67-1154-4f25-a62d-e8fa2b839e2e;\n style a71ebb67-1154-4f25-a62d-e8fa2b839e2e\ + \ stroke:#2c3143,stroke-width:4px;\n 15[\"Filter failed datasets\"];\n 5 -->|output|\ + \ 15;\n 16[\"Bar chart\"];\n 6 -->|output| 16;\n 2567360e-d39f-4316-84f5-77aaf8e8198c[\"\ + Output\\nmapping_coverage_percentage_per_sample_fig\"];\n 16 --> 2567360e-d39f-4316-84f5-77aaf8e8198c;\n\ + \ style 2567360e-d39f-4316-84f5-77aaf8e8198c stroke:#2c3143,stroke-width:4px;\n\ + \ 17[\"Bar chart\"];\n 7 -->|output| 17;\n 68c76f06-d2ea-4280-9e6f-a7b4f1568389[\"\ + Output\\nnumber_of_Variants_and_SNPs_indentified_fig\"];\n 17 --> 68c76f06-d2ea-4280-9e6f-a7b4f1568389;\n\ + \ style 68c76f06-d2ea-4280-9e6f-a7b4f1568389 stroke:#2c3143,stroke-width:4px;\n\ + \ 18[\"Filter failed datasets\"];\n 8 -->|output| 18;\n 19[\"Filter failed\ + \ datasets\"];\n 9 -->|output| 19;\n 20[\"Remove beginning\"];\n 10 -->|output|\ + \ 20;\n 21[\"Remove beginning\"];\n 11 -->|output| 21;\n 22[\"Remove beginning\"\ + ];\n 15 -->|output| 22;\n 23[\"Collapse Collection\"];\n 18 -->|output| 23;\n\ + \ 86910e39-57bf-4a76-ac4c-739340fd2387[\"Output\\nall_samples_contigs_in_one_fasta_file\"\ + ];\n 23 --> 86910e39-57bf-4a76-ac4c-739340fd2387;\n style 86910e39-57bf-4a76-ac4c-739340fd2387\ + \ stroke:#2c3143,stroke-width:4px;\n 24[\"Collapse Collection\"];\n 19 -->|output|\ + \ 24;\n 02b996c6-a912-4e4e-b3ec-49601faaa452[\"Output\\nall_vfs_in_one_tabular\"\ + ];\n 24 --> 02b996c6-a912-4e4e-b3ec-49601faaa452;\n style 02b996c6-a912-4e4e-b3ec-49601faaa452\ + \ stroke:#2c3143,stroke-width:4px;\n 25[\"Remove beginning\"];\n 19 -->|output|\ + \ 25;\n 26[\"Count\"];\n 20 -->|out_file1| 26;\n 27[\"Count\"];\n 21 -->|out_file1|\ + \ 27;\n 28[\"Group\"];\n 21 -->|out_file1| 28;\n 29[\"Unique\"];\n 22 -->|out_file1|\ + \ 29;\n 30[\"Split by group\"];\n 24 -->|output| 30;\n 59f8cb09-424b-47b1-b94b-a612c2610cab[\"\ + Output\\nsplit_by_group_collection\"];\n 30 --> 59f8cb09-424b-47b1-b94b-a612c2610cab;\n\ + \ style 59f8cb09-424b-47b1-b94b-a612c2610cab stroke:#2c3143,stroke-width:4px;\n\ + \ 31[\"Unique\"];\n 25 -->|out_file1| 31;\n 32[\"Cut\"];\n 26 -->|out_file1|\ + \ 32;\n 33[\"Cut\"];\n 27 -->|out_file1| 33;\n 34[\"Filter empty datasets\"\ + ];\n 28 -->|out_file1| 34;\n 35[\"Cut\"];\n 29 -->|outfile| 35;\n 36[\"\ + Cut\"];\n 30 -->|split_output| 36;\n eeb25a51-ea21-4a19-a196-55d5bd919b10[\"\ + Output\\nadjusted_abricate_vfs_tabular_part1\"];\n 36 --> eeb25a51-ea21-4a19-a196-55d5bd919b10;\n\ + \ style eeb25a51-ea21-4a19-a196-55d5bd919b10 stroke:#2c3143,stroke-width:4px;\n\ + \ 37[\"Cut\"];\n 31 -->|outfile| 37;\n 38[\"Collapse Collection\"];\n 32\ + \ -->|out_file1| 38;\n 39[\"Collapse Collection\"];\n 33 -->|out_file1| 39;\n\ + \ 40[\"Column join\"];\n 34 -->|output| 40;\n 41[\"bedtools getfasta\"];\n\ + \ 23 -->|output| 41;\n 35 -->|out_file1| 41;\n 42[\"Remove beginning\"];\n\ + \ 36 -->|out_file1| 42;\n aaaa4446-0817-4e5c-aa1b-9ec384f2a363[\"Output\\\ + nadjusted_abricate_vfs_tabular_part2\"];\n 42 --> aaaa4446-0817-4e5c-aa1b-9ec384f2a363;\n\ + \ style aaaa4446-0817-4e5c-aa1b-9ec384f2a363 stroke:#2c3143,stroke-width:4px;\n\ + \ 43[\"bedtools getfasta\"];\n 23 -->|output| 43;\n 37 -->|out_file1| 43;\n\ + \ 44[\"Column Regex Find And Replace\"];\n 38 -->|output| 44;\n 4809c36b-31ef-4664-8e4e-47f0f72152de[\"\ + Output\\namrs_count\"];\n 44 --> 4809c36b-31ef-4664-8e4e-47f0f72152de;\n style\ + \ 4809c36b-31ef-4664-8e4e-47f0f72152de stroke:#2c3143,stroke-width:4px;\n 45[\"\ + Column Regex Find And Replace\"];\n 39 -->|output| 45;\n 87efc81d-4d84-4af3-831f-dfe033c59f78[\"\ + Output\\nvfs_count\"];\n 45 --> 87efc81d-4d84-4af3-831f-dfe033c59f78;\n style\ + \ 87efc81d-4d84-4af3-831f-dfe033c59f78 stroke:#2c3143,stroke-width:4px;\n 46[\"\ + Column Regex Find And Replace\"];\n 40 -->|tabular_output| 46;\n f5c221e3-00ef-4834-9a5f-a94c97fd6764[\"\ + Output\\nheatmap_table\"];\n 46 --> f5c221e3-00ef-4834-9a5f-a94c97fd6764;\n\ + \ style f5c221e3-00ef-4834-9a5f-a94c97fd6764 stroke:#2c3143,stroke-width:4px;\n\ + \ 47[\"Regex Find And Replace\"];\n 41 -->|output| 47;\n 48[\"bedtools getfasta\"\ + ];\n 23 -->|output| 48;\n 42 -->|out_file1| 48;\n 82ce2107-89a3-438c-95bb-dc871b5258b7[\"\ + Output\\nfiltered_sequences_with_vfs_fasta\"];\n 48 --> 82ce2107-89a3-438c-95bb-dc871b5258b7;\n\ + \ style 82ce2107-89a3-438c-95bb-dc871b5258b7 stroke:#2c3143,stroke-width:4px;\n\ + \ 49[\"Regex Find And Replace\"];\n 43 -->|output| 49;\n 50[\"Multi-Join\"\ + ];\n 45 -->|out_file1| 50;\n 44 -->|out_file1| 50;\n 51[\"Heatmap w ggplot\"\ + ];\n 46 -->|out_file1| 51;\n 97816bc2-fd0c-4077-a721-8dd1470879d1[\"Output\\\ + nheatmap_png\"];\n 51 --> 97816bc2-fd0c-4077-a721-8dd1470879d1;\n style 97816bc2-fd0c-4077-a721-8dd1470879d1\ + \ stroke:#2c3143,stroke-width:4px;\n c0417c91-a513-4c6a-9a62-3aac2f1f8e85[\"\ + Output\\nheatmap_pdf\"];\n 51 --> c0417c91-a513-4c6a-9a62-3aac2f1f8e85;\n \ + \ style c0417c91-a513-4c6a-9a62-3aac2f1f8e85 stroke:#2c3143,stroke-width:4px;\n\ + \ 52[\"Filter empty datasets\"];\n 47 -->|out_file1| 52;\n 53[\"ClustalW\"\ + ];\n 48 -->|output| 53;\n 6af20322-24da-4036-80de-37bed2d25848[\"Output\\\ + nclustalw_on_input_clustal\"];\n 53 --> 6af20322-24da-4036-80de-37bed2d25848;\n\ + \ style 6af20322-24da-4036-80de-37bed2d25848 stroke:#2c3143,stroke-width:4px;\n\ + \ 9b7bd78c-f112-480b-a7df-c10711af254c[\"Output\\nclustalw_on_input_dnd\"];\n\ + \ 53 --> 9b7bd78c-f112-480b-a7df-c10711af254c;\n style 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workflowhub_id: '1487' + - creators: + - class: Person + identifier: 0000-0001-9047-4215 + name: Engy Nasr + url: https://orcid.org/0000-0001-9047-4215 + - class: Person + identifier: 0000-0001-9852-1987 + name: "B\xE9r\xE9nice Batut" + url: https://orcid.org/0000-0001-9852-1987 + - class: Person + identifier: 0000-0003-2982-388X + name: Paul Zierep + description: Microbiome - Taxonomy Profiling + features: + comments: true + parameters: true + report: + markdown: '# Taxonomy Profiling and Visualisation with Krona Workflow Report + + + In this workflow you can identify your microbial community, but identifying + all possible Taxon found in your samples, from the kingdom level down to + the species level. In the application of the pathogen detection, this workflow + gives an overview of the possible bacterial found in samples and what might + be a possible suspect for pathogenicity. + + + The workflow uses Kraken2 tool and allow the user to choose any Kraken2 + database or other added ones depending on the user application or the input + samples. All Kraken2 tool databases are available in Galaxy. More description + about these databases can be found [here](https://benlangmead.github.io/aws-indexes/k2). + Other databases can be also added to the tool, just contact us anytime for + that. We recommend using StandardPF database. + + + Visualization is done using Krona Pie Chart, and you can replace it with + any other tool. e.g. Phinch interactive tool, which is also available in + Galaxy + + + ## Workflow Inputs: + + + The per-processing workflow main output (Collection of all samples reads + after quality retaining and hosts filtering) + + + ## Workflow Outputs are: + + + ### Taxonomy Tabular Report + + + The report shows the abundance of every taxon from the kingdom level down + to the species level + + + ```galaxy + + history_dataset_display(output="converted_kraken_report") + + ``` + + + ### Taxonomy Profiling Visualization with Krona + + An interactive Pie chart showing the different identified taxons along with + their percentages, which is one of the ways to visualize the previous taxonomy + tabular + + + ```galaxy + + history_dataset_as_image(output="krona_pie_chart") + + ``` + + ' + subworkflows: false + graph_dot: "digraph main {\n node [fontname=\"Atkinson 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pie chart\"]\n 3 -> 4 [label=\"output\"]\n kdcc857c6f5794c7484ecbb6ce3794a56[color=lightseagreen,label=\"\ + Output\\nkrona_pie_chart\"]\n 4 -> kdcc857c6f5794c7484ecbb6ce3794a56\n}" + history: + - hash: cdd93376adc6ce80742881c25d6810bcce85fc05 + message: adding tags to some of the workflow outputs, updating the training + with the latest PathoGFAIR workflows updates + num: 2 + short_hash: cdd93376a + unix: '1717675229' + - hash: c63ce23c7a7a631f1256b8e733defce3ca4e009b + message: updating workflows file names + num: 1 + short_hash: c63ce23c7 + unix: '1716726587' + inputs: + - annotation: Output collection from the Nanopore Preprocessing workflow + content_id: null errors: null - id: 14 - input_connections: - input: - id: 12 - output_name: output - inputs: [] - label: null - name: Unique - outputs: - - name: outfile - type: input + id: 0 + input_connections: {} + inputs: + - description: Output collection from the Nanopore Preprocessing workflow + name: 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revisions: a6f820992693\n tool_panel_section_label: Metagenomic\ + \ Analysis\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: krakentools_kreport2krona\n\ + \ owner: iuc\n revisions: 02bbace216f2\n tool_panel_section_label: Metagenomic\ + \ Analysis\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: metaphlan\n\ + \ owner: iuc\n revisions: eca2e2e20436\n tool_panel_section_label: Metagenomic\ + \ Analysis\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n" + answer_histories: + - history: https://usegalaxy.eu/u/tarnima/h/taxonomic-profiling-and-visualization-of-metagenomic-data-answer-key-history + label: GTA2025 + api: https://training.galaxyproject.org/training-material/api/topics/microbiome/tutorials/taxonomic-profiling/tutorial.json contributions: authorship: - - plushz - - chensy96 + - sophia120199 - bebatut - - teresa-m + - paulzierep + editing: + - Tarnima-Omara + - tflowers15 funding: - gallantries + - unimelb + - melbournebioinformatics + - AustralianBioCommons reviewing: - - hexylena - shiltemann - - teresa-m - - chensy96 - - nuwang - bebatut + - paulzierep + - hexylena - gallardoalba + - teresa-m contributors: - - affiliations: - - uni-freiburg - id: plushz - joined: 2022-03 - name: Polina Polunina - orcid: 0000-0002-0507-4602 - page: https://training.galaxyproject.org/training-material/hall-of-fame/plushz/ - url: https://training.galaxyproject.org/training-material/api/contributors/plushz.json - - id: chensy96 - joined: 2022-05 - name: Siyu Chen - page: https://training.galaxyproject.org/training-material/hall-of-fame/chensy96/ - url: https://training.galaxyproject.org/training-material/api/contributors/chensy96.json + - id: sophia120199 + joined: 2023-04 + name: Sophia Hampe + page: https://training.galaxyproject.org/training-material/hall-of-fame/sophia120199/ + url: https://training.galaxyproject.org/training-material/api/contributors/sophia120199.json - affiliations: - gallantries - ifb @@ -52636,22 +42300,36 @@ - elixir-europe - deNBI - mwk - - biont - contact_for_training: true - elixir_node: de - email: muellert@informatik.uni-freibrug.de - id: teresa-m - joined: 2022-09 - linkedin: teresamueller87 - matrix: teresa-m:matrix.org - name: "Teresa M\xFCller" - orcid: 0000-0003-1252-9684 - page: https://training.galaxyproject.org/training-material/hall-of-fame/teresa-m/ - url: https://training.galaxyproject.org/training-material/api/contributors/teresa-m.json + - materialvitaldigital + email: zierep@informatik.uni-freiburg.de + id: paulzierep + joined: 2023-02 + name: Paul Zierep + orcid: 0000-0003-2982-388X + page: https://training.galaxyproject.org/training-material/hall-of-fame/paulzierep/ + url: https://training.galaxyproject.org/training-material/api/contributors/paulzierep.json + - email: otarnima@gmail.com + id: Tarnima-Omara + joined: 2025-04 + name: Tarnima Omara + page: https://training.galaxyproject.org/training-material/hall-of-fame/Tarnima-Omara/ + url: https://training.galaxyproject.org/training-material/api/contributors/Tarnima-Omara.json + - affiliations: + - AustralianBioCommons + - unimelb + - melbournebioinformatics + email: treynolds@unimelb.edu.au + id: tflowers15 + joined: 2025-03 + name: Tristan Reynolds + orcid: 0000-0002-6606-5953 + page: https://training.galaxyproject.org/training-material/hall-of-fame/tflowers15/ + url: https://training.galaxyproject.org/training-material/api/contributors/tflowers15.json - avatar: https://gallantries.github.io/assets/images/gallantries-logo.png end_date: '2023-09-30' former_members: - abretaud + - hexylena - shiltemann funder_name: Erasmus+ Programme funding_database: erasmusplus @@ -52675,7 +42353,6 @@ - bebatut - colineroyaux - fpsom - - hexylena - yvanlebras name: 'Gallantries: Bridging Training Communities in Life Science, Environment and Health' @@ -52683,30 +42360,45 @@ short_name: Gallantries start_date: '2020-09-01' url: https://training.galaxyproject.org/training-material/api/grants/gallantries.json - - affiliations: - - erasmusmc - - gallantries - - by-covid - - elixir-europe - - elixir-converge - contact_for_training: false - elixir_node: nl - former_affiliations: - - deNBI - - avans-atgm - - uni-freiburg - id: hexylena - joined: 2017-09 - location: - country: NL - lat: 51.91 - lon: 4.46 - maintainer_contact: gitter - matrix: hexylena:matrix.org - name: Helena Rasche - orcid: 0000-0001-9760-8992 - page: https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/ - url: https://training.galaxyproject.org/training-material/api/contributors/hexylena.json + - avatar: /training-material/shared/images/unimelb_Logo_RGB.png + id: unimelb + members: + - annasyme + - cat-bro + - GraceAHall + - supernord + - tflowers15 + - uwwint + - vinisalazar + name: The University of Melbourne + page: https://training.galaxyproject.org/training-material/hall-of-fame/unimelb/ + url: https://training.galaxyproject.org/training-material/api/organisations/unimelb.json + - avatar: /training-material/shared/images/Melbourne-Bioinformatics-logo.png + former_members: + - annasyme + id: melbournebioinformatics + members: + - GraceAHall + - tflowers15 + - vinisalazar + name: Melbourne Bioinformatics + page: https://training.galaxyproject.org/training-material/hall-of-fame/melbournebioinformatics/ + url: https://training.galaxyproject.org/training-material/api/organisations/melbournebioinformatics.json + - avatar: /training-material/shared/images/Australian-Biocommons-Favicon-RGB.png + id: AustralianBioCommons + members: + - annasyme + - burkemlou + - cat-bro + - igormakunin + - mthang + - PatCapon39 + - supernord + - tflowers15 + - uwwint + name: Australian BioCommons + page: https://training.galaxyproject.org/training-material/hall-of-fame/AustralianBioCommons/ + url: https://training.galaxyproject.org/training-material/api/organisations/AustralianBioCommons.json - affiliations: - uni-freiburg - nfdi4plants @@ -52735,33 +42427,6 @@ orcid: 0000-0003-3803-468X page: https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/ url: https://training.galaxyproject.org/training-material/api/contributors/shiltemann.json - - affiliations: - - uni-freiburg - - elixir-europe - - deNBI - - mwk - - biont - contact_for_training: true - elixir_node: de - email: muellert@informatik.uni-freibrug.de - id: teresa-m - joined: 2022-09 - linkedin: teresamueller87 - matrix: teresa-m:matrix.org - name: "Teresa M\xFCller" - orcid: 0000-0003-1252-9684 - page: https://training.galaxyproject.org/training-material/hall-of-fame/teresa-m/ - url: https://training.galaxyproject.org/training-material/api/contributors/teresa-m.json - - id: chensy96 - joined: 2022-05 - name: Siyu Chen - page: https://training.galaxyproject.org/training-material/hall-of-fame/chensy96/ - url: https://training.galaxyproject.org/training-material/api/contributors/chensy96.json - - id: nuwang - joined: 2019-06 - name: Nuwan Goonasekera - page: https://training.galaxyproject.org/training-material/hall-of-fame/nuwang/ - url: https://training.galaxyproject.org/training-material/api/contributors/nuwang.json - affiliations: - gallantries - ifb @@ -52787,6 +42452,43 @@ page: https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/ twitter: bebatut url: https://training.galaxyproject.org/training-material/api/contributors/bebatut.json + - affiliations: + - uni-freiburg + - elixir-europe + - deNBI + - mwk + - materialvitaldigital + email: zierep@informatik.uni-freiburg.de + id: paulzierep + joined: 2023-02 + name: Paul Zierep + orcid: 0000-0003-2982-388X + page: https://training.galaxyproject.org/training-material/hall-of-fame/paulzierep/ + url: https://training.galaxyproject.org/training-material/api/contributors/paulzierep.json + - affiliations: + - elixir-europe + contact_for_training: false + elixir_node: nl + former_affiliations: + - deNBI + - avans-atgm + - uni-freiburg + - erasmusmc + - gallantries + - by-covid + - elixir-converge + id: hexylena + joined: 2017-09 + location: + country: NL + lat: 51.91 + lon: 4.46 + maintainer_contact: gitter + matrix: hexylena:matrix.org + name: Helena Rasche + orcid: 0000-0001-9760-8992 + page: https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/ + url: https://training.galaxyproject.org/training-material/api/contributors/hexylena.json - elixir_node: de former_affiliations: - uni-freiburg @@ -52797,20 +42499,35 @@ orcid: 0000-0002-5752-2155 page: https://training.galaxyproject.org/training-material/hall-of-fame/gallardoalba/ url: https://training.galaxyproject.org/training-material/api/contributors/gallardoalba.json - dir: topics/microbiome/tutorials/beer-data-analysis + - affiliations: + - uni-freiburg + - elixir-europe + - deNBI + - mwk + - biont + contact_for_training: true + elixir_node: de + email: muellert@informatik.uni-freibrug.de + id: teresa-m + joined: 2022-09 + linkedin: teresamueller87 + matrix: teresa-m:matrix.org + name: "Teresa M\xFCller" + orcid: 0000-0003-1252-9684 + page: https://training.galaxyproject.org/training-material/hall-of-fame/teresa-m/ + url: https://training.galaxyproject.org/training-material/api/contributors/teresa-m.json + dir: topics/microbiome/tutorials/taxonomic-profiling edam_ontology: - topic_3174 - topic_3697 - topic_0637 - topic_0080 edam_operation: - - Sequence contamination filtering - - Sequence composition calculation - - Aggregation - Statistical calculation - Taxonomic classification - Visualisation - - Sequencing quality control + - Genome annotation + - Aggregation edam_topic: - Metagenomics - Microbial ecology @@ -52820,63 +42537,71 @@ - UseGalaxy.org.au - UseGalaxy.be - UseGalaxy.eu + - UseGalaxy.fr - UseGalaxy.org (Main) feedback_mean_note: null feedback_number: 0 hands_on: true - id: microbiome/beer-data-analysis - inexact_supported_servers: - - GalaxyTrakr - - UseGalaxy.cz - - UseGalaxy.fr - - UseGalaxy.no + id: microbiome/taxonomic-profiling + inexact_supported_servers: [] js_requirements: - mathjax: 12074 + mathjax: 4920 mermaid: false key_points: - - Data obtained by sequencing needs to be checked for quality and cleaned before - further processing - - Yeast species but also contamination can be identified and visualized directly - from the sequences using several bioinformatics tools - - With its graphical interface, Galaxy makes it easy to use the needed bioinformatics - tools - - Beer microbiome is not just made of yeast and can be quite complex + - There are 3 different types of taxonomic assignment (genome, gene or k-mer based) + - Kraken or MetaPhlAn can be used in Galaxy for taxonomic assignment + - Visualization of community profiles can be done using Krona or Pavian + - The taxonomic classification tool to use depends on the data layout: tutorial_hands_on level: Introductory license: CC-BY-4.0 - mod_date: '2024-11-29' + mod_date: '2026-05-11' objectives: - - Inspect metagenomics data - - Run metagenomics tools - - Identify yeast species contained in a sequenced beer sample using DNA - - Visualize the microbiome community of a beer sample - pageviews: 5021 - pub_date: '2022-09-29' + - Explain what taxonomic assignment is + - Explain how taxonomic assignment works + - Apply Kraken and MetaPhlAn to assign taxonomic labels + - Apply Krona and Pavian to visualize results of assignment and understand the output + - Identify taxonomic classification tool that fits best depending on their data + pageviews: 20295 + pub_date: '2023-05-03' questions: - - How can yeast strains in a beer sample be identified? - - How can we process metagenomic data sequenced using Nanopore? + - Which species (or genera, families, ...) are present in my sample? + - What are the different approaches and tools to get the community profile of my + sample? + - How can we visualize and compare community profiles? recordings: - captioners: - sophia120199 - date: '2023-05-10' + date: '2023-05-16' galaxy_version: '23.01' - length: 1H5M + length: 1H15M speakers: - bebatut - youtube_id: PJeS06yiJUM + youtube_id: jszMnBKm6ig + - bot-timestamp: 1744833733 + captioners: + - Tarnima-Omara + date: '2025-04-16' + galaxy_version: 24.2.4.dev0 + length: 2H4M + speakers: + - Tarnima-Omara + youtube_id: FdtdsCdqY5U redirect_from: - - /topics/metagenomics/tutorials/beer-data-analysis/tutorial - - /short/microbiome/beer-data-analysis - - /short/T00200 - - /short/T00384 - short_id: T00384 + - /topics/metagenomics/tutorials/taxonomic-profiling/tutorial + - /short/microbiome/taxonomic-profiling + - /short/T00338 + - /short/T00395 + short_id: T00395 short_tools: + - metaphlan + - __UNZIP_COLLECTION__ + - interactive_tool_pavian + - interactive_tool_phinch - taxonomy_krona_chart - - porechop - - fastqc - - Filter1 - - fastp - krakentools_kreport2krona + - est_abundance + - kraken_biom - kraken2 slides: false slides_recordings: false @@ -52892,22 +42617,13 @@ - name: UseGalaxy.eu url: https://usegalaxy.eu usegalaxy: true - - name: UseGalaxy.org (Main) - url: https://usegalaxy.org - usegalaxy: true - inexact: - - name: GalaxyTrakr - url: https://galaxytrakr.org/ - usegalaxy: false - - name: UseGalaxy.cz - url: https://usegalaxy.cz/ - usegalaxy: false - name: UseGalaxy.fr url: https://usegalaxy.fr/ usegalaxy: true - - name: UseGalaxy.no - url: https://usegalaxy.no/ - usegalaxy: false + - name: UseGalaxy.org (Main) + url: https://usegalaxy.org + usegalaxy: true + inexact: [] supported_servers_matrix: servers: - name: APOSTL @@ -52949,9 +42665,6 @@ - name: IPK Galaxy Blast Suite url: https://galaxy-web.ipk-gatersleben.de usegalaxy: false - - name: Lebanese University Galaxy - url: http://galaxy.ul.edu.lb/ - usegalaxy: false - name: Mandoiu Lab url: https://neo.engr.uconn.edu/ usegalaxy: false @@ -52967,9 +42680,6 @@ - name: PepSimili url: http://pepsimili.e-nios.com:8080/ usegalaxy: false - - name: PhagePromotor - url: https://galaxy.bio.di.uminho.pt/ - usegalaxy: false - name: UseGalaxy.org.au url: https://usegalaxy.org.au usegalaxy: true @@ -52995,66 +42705,314 @@ url: https://viralvariant.anses.fr/ usegalaxy: false tools: - - id: Filter1 + - id: __UNZIP_COLLECTION__ servers: - server: http://apostl.moffitt.org/ - state: local + state: missing - server: http://mbac.gmu.edu:8080/ - state: local + state: missing - server: https://vm-chemflow-francegrille.eu/ state: missing - server: https://iris.angers.inra.fr/galaxypub-cfbp state: missing - server: https://hyperbrowser.uio.no/coloc-stats + state: missing + - server: https://galaxy.mesocentre.uca.fr + state: local + - server: https://galaxy.pasteur.fr/ + state: missing + - server: https://galaxytrakr.org/ + state: local + - server: http://igg.cloud.ba.infn.it/galaxy + state: local + - server: https://galaxy.hyphy.org/ + state: local + - server: https://www.immportgalaxy.org/ + state: missing + - server: http://galaxy.interactomix.com/ + state: local + - server: https://galaxy-web.ipk-gatersleben.de + state: missing + - server: https://neo.engr.uconn.edu/ + state: missing + - server: https://mississippi.sorbonne-universite.fr + state: local + - server: http://galaxy.inf.ethz.ch + state: missing + - server: https://palfinder.ls.manchester.ac.uk/ + state: missing + - server: http://pepsimili.e-nios.com:8080/ + state: local + - server: https://usegalaxy.org.au + state: local + - server: https://usegalaxy.be/ + state: local + - server: https://usegalaxy.cz/ + state: local + - server: https://usegalaxy.eu state: local + - server: https://usegalaxy.fr/ + state: local + - server: https://usegalaxy.no/ + state: local + - server: https://usegalaxy.org + state: local + - server: https://viralvariant.anses.fr/ + state: local + version: local + - id: interactive_tool_pavian + servers: + - server: http://apostl.moffitt.org/ + state: missing + - server: http://mbac.gmu.edu:8080/ + state: missing + - server: https://vm-chemflow-francegrille.eu/ + state: missing + - server: https://iris.angers.inra.fr/galaxypub-cfbp + state: missing + - server: https://hyperbrowser.uio.no/coloc-stats + state: missing - server: https://galaxy.mesocentre.uca.fr + state: missing + - server: https://galaxy.pasteur.fr/ + state: missing + - server: https://galaxytrakr.org/ + state: missing + - server: http://igg.cloud.ba.infn.it/galaxy + state: missing + - server: https://galaxy.hyphy.org/ + state: missing + - server: https://www.immportgalaxy.org/ + state: missing + - server: http://galaxy.interactomix.com/ + state: missing + - server: https://galaxy-web.ipk-gatersleben.de + state: missing + - server: https://neo.engr.uconn.edu/ + state: missing + - server: https://mississippi.sorbonne-universite.fr + state: missing + - server: http://galaxy.inf.ethz.ch + state: missing + - server: https://palfinder.ls.manchester.ac.uk/ + state: missing + - server: http://pepsimili.e-nios.com:8080/ + state: missing + - server: https://usegalaxy.org.au + state: local + - server: https://usegalaxy.be/ + state: local + - server: https://usegalaxy.cz/ + state: missing + - server: https://usegalaxy.eu + state: local + - server: https://usegalaxy.fr/ + state: local + - server: https://usegalaxy.no/ + state: missing + - server: https://usegalaxy.org state: local + - server: https://viralvariant.anses.fr/ + state: missing + version: local + - id: interactive_tool_phinch + servers: + - server: http://apostl.moffitt.org/ + state: missing + - server: http://mbac.gmu.edu:8080/ + state: missing + - server: https://vm-chemflow-francegrille.eu/ + state: missing + - server: https://iris.angers.inra.fr/galaxypub-cfbp + state: missing + - server: https://hyperbrowser.uio.no/coloc-stats + state: missing + - server: https://galaxy.mesocentre.uca.fr + state: missing - server: https://galaxy.pasteur.fr/ + state: missing + - server: https://galaxytrakr.org/ + state: missing + - server: http://igg.cloud.ba.infn.it/galaxy + state: missing + - server: https://galaxy.hyphy.org/ + state: missing + - server: https://www.immportgalaxy.org/ + state: missing + - server: http://galaxy.interactomix.com/ + state: missing + - server: https://galaxy-web.ipk-gatersleben.de + state: missing + - server: https://neo.engr.uconn.edu/ + state: missing + - server: https://mississippi.sorbonne-universite.fr + state: missing + - server: http://galaxy.inf.ethz.ch + state: missing + - server: https://palfinder.ls.manchester.ac.uk/ + state: missing + - server: http://pepsimili.e-nios.com:8080/ + state: missing + - server: https://usegalaxy.org.au + state: local + - server: https://usegalaxy.be/ + state: local + - server: https://usegalaxy.cz/ + state: missing + - server: https://usegalaxy.eu + state: local + - server: https://usegalaxy.fr/ + state: local + - server: https://usegalaxy.no/ + state: missing + - server: https://usegalaxy.org state: local + - server: https://viralvariant.anses.fr/ + state: missing + version: local + - id: toolshed.g2.bx.psu.edu/repos/crs4/taxonomy_krona_chart/taxonomy_krona_chart/2.7.1 + servers: + - server: http://apostl.moffitt.org/ + state: missing + - server: http://mbac.gmu.edu:8080/ + state: missing + - server: https://vm-chemflow-francegrille.eu/ + state: missing + - server: https://iris.angers.inra.fr/galaxypub-cfbp + state: missing + - server: https://hyperbrowser.uio.no/coloc-stats + state: missing + - server: https://galaxy.mesocentre.uca.fr + state: inexact + versions: + - 2.6.1 + - 2.7.1+galaxy0 + - 2.6.1.1 + - server: https://galaxy.pasteur.fr/ + state: inexact + versions: + - 2.7.1+galaxy0 + - server: https://galaxytrakr.org/ + state: inexact + versions: + - 2.7.1+galaxy0 + - server: http://igg.cloud.ba.infn.it/galaxy + state: missing + - server: https://galaxy.hyphy.org/ + state: missing + - server: https://www.immportgalaxy.org/ + state: missing + - server: http://galaxy.interactomix.com/ + state: missing + - server: https://galaxy-web.ipk-gatersleben.de + state: missing + - server: https://neo.engr.uconn.edu/ + state: missing + - server: https://mississippi.sorbonne-universite.fr + state: missing + - server: http://galaxy.inf.ethz.ch + state: missing + - server: https://palfinder.ls.manchester.ac.uk/ + state: missing + - server: http://pepsimili.e-nios.com:8080/ + state: inexact + versions: + - 2.7.1+galaxy0 + - server: https://usegalaxy.org.au + state: exact + version: 2.7.1 + - server: https://usegalaxy.be/ + state: exact + version: 2.7.1 + - server: https://usegalaxy.cz/ + state: inexact + versions: + - 2.6.1 + - 2.7.1+galaxy0 + - 2.6.1.1 + - server: https://usegalaxy.eu + state: exact + version: 2.7.1 + - server: https://usegalaxy.fr/ + state: exact + version: 2.7.1 + - server: https://usegalaxy.no/ + state: exact + version: 2.7.1 + - server: https://usegalaxy.org + state: exact + version: 2.7.1 + - server: https://viralvariant.anses.fr/ + state: missing + version: 2.7.1 + - id: toolshed.g2.bx.psu.edu/repos/crs4/taxonomy_krona_chart/taxonomy_krona_chart/2.7.1+galaxy0 + servers: + - server: http://apostl.moffitt.org/ + state: missing + - server: http://mbac.gmu.edu:8080/ + state: missing + - server: https://vm-chemflow-francegrille.eu/ + state: missing + - server: https://iris.angers.inra.fr/galaxypub-cfbp + state: missing + - server: https://hyperbrowser.uio.no/coloc-stats + state: missing + - server: https://galaxy.mesocentre.uca.fr + state: exact + version: 2.7.1+galaxy0 + - server: https://galaxy.pasteur.fr/ + state: exact + version: 2.7.1+galaxy0 - server: https://galaxytrakr.org/ - state: local + state: exact + version: 2.7.1+galaxy0 - server: http://igg.cloud.ba.infn.it/galaxy - state: local + state: missing - server: https://galaxy.hyphy.org/ - state: local + state: missing - server: https://www.immportgalaxy.org/ state: missing - server: http://galaxy.interactomix.com/ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: local - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr - state: local + state: missing - server: http://galaxy.inf.ethz.ch - state: local + state: missing - server: https://palfinder.ls.manchester.ac.uk/ state: missing - server: http://pepsimili.e-nios.com:8080/ - state: local - - server: https://galaxy.bio.di.uminho.pt/ - state: local + state: exact + version: 2.7.1+galaxy0 - server: https://usegalaxy.org.au - state: local + state: exact + version: 2.7.1+galaxy0 - server: https://usegalaxy.be/ - state: local + state: exact + version: 2.7.1+galaxy0 - server: https://usegalaxy.cz/ - state: local + state: exact + version: 2.7.1+galaxy0 - server: https://usegalaxy.eu - state: local + state: exact + version: 2.7.1+galaxy0 - server: https://usegalaxy.fr/ - state: local + state: exact + version: 2.7.1+galaxy0 - server: https://usegalaxy.no/ - state: local + state: inexact + versions: + - 2.7.1 - server: https://usegalaxy.org - state: local + state: exact + version: 2.7.1+galaxy0 - server: https://viralvariant.anses.fr/ - state: local - version: local - - id: toolshed.g2.bx.psu.edu/repos/crs4/taxonomy_krona_chart/taxonomy_krona_chart/2.7.1+galaxy0 + state: missing + version: 2.7.1+galaxy0 + - id: toolshed.g2.bx.psu.edu/repos/iuc/bracken/est_abundance/3.1+galaxy0 servers: - server: http://apostl.moffitt.org/ state: missing @@ -53068,13 +43026,12 @@ state: missing - server: https://galaxy.mesocentre.uca.fr state: exact - version: 2.7.1+galaxy0 + version: 3.1+galaxy0 - server: https://galaxy.pasteur.fr/ - state: exact - version: 2.7.1+galaxy0 + state: missing - server: https://galaxytrakr.org/ state: exact - version: 2.7.1+galaxy0 + version: 3.1+galaxy0 - server: http://igg.cloud.ba.infn.it/galaxy state: missing - server: https://galaxy.hyphy.org/ @@ -53085,8 +43042,6 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr @@ -53096,36 +43051,34 @@ - server: https://palfinder.ls.manchester.ac.uk/ state: missing - server: http://pepsimili.e-nios.com:8080/ - state: exact - version: 2.7.1+galaxy0 - - server: https://galaxy.bio.di.uminho.pt/ state: missing - server: https://usegalaxy.org.au state: exact - version: 2.7.1+galaxy0 + version: 3.1+galaxy0 - server: https://usegalaxy.be/ state: exact - version: 2.7.1+galaxy0 + version: 3.1+galaxy0 - server: https://usegalaxy.cz/ state: exact - version: 2.7.1+galaxy0 + version: 3.1+galaxy0 - server: https://usegalaxy.eu state: exact - version: 2.7.1+galaxy0 + version: 3.1+galaxy0 - server: https://usegalaxy.fr/ state: exact - version: 2.7.1+galaxy0 + version: 3.1+galaxy0 - server: https://usegalaxy.no/ state: inexact versions: - - 2.7.1 + - 2.6.1+galaxy0 + - 2.7+galaxy0 - server: https://usegalaxy.org state: exact - version: 2.7.1+galaxy0 + version: 3.1+galaxy0 - server: https://viralvariant.anses.fr/ state: missing - version: 2.7.1+galaxy0 - - id: toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.73+galaxy0 + version: 3.1+galaxy0 + - id: toolshed.g2.bx.psu.edu/repos/iuc/kraken2/kraken2/2.1.3+galaxy1 servers: - server: http://apostl.moffitt.org/ state: missing @@ -53139,15 +43092,15 @@ state: missing - server: https://galaxy.mesocentre.uca.fr state: exact - version: 0.73+galaxy0 + version: 2.1.3+galaxy1 - server: https://galaxy.pasteur.fr/ - state: inexact - versions: - - 0.74+galaxy0 + state: missing - server: https://galaxytrakr.org/ state: inexact versions: - - 0.74+galaxy1 + - 2.1.3+galaxy2 + - 2.17.1+galaxy0 + - 2.0.8_beta+galaxy0 - server: http://igg.cloud.ba.infn.it/galaxy state: missing - server: https://galaxy.hyphy.org/ @@ -53158,66 +43111,46 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr - state: inexact - versions: - - 0.74+galaxy1 + state: missing - server: http://galaxy.inf.ethz.ch state: missing - server: https://palfinder.ls.manchester.ac.uk/ - state: inexact - versions: - - '0.72' - - 0.72+galaxy1 - - '0.71' - - '0.65' + state: missing - server: http://pepsimili.e-nios.com:8080/ state: inexact versions: - - 0.74+galaxy0 - - server: https://galaxy.bio.di.uminho.pt/ - state: inexact - versions: - - 0.74+galaxy0 + - 2.1.1+galaxy1 - server: https://usegalaxy.org.au state: exact - version: 0.73+galaxy0 + version: 2.1.3+galaxy1 - server: https://usegalaxy.be/ state: exact - version: 0.73+galaxy0 + version: 2.1.3+galaxy1 - server: https://usegalaxy.cz/ - state: inexact - versions: - - 0.74+galaxy0 - - 0.74+galaxy1 - - '0.65' - - '0.69' - - '0.68' - - '0.52' - - '0.67' - - '0.63' - - '0.64' - - '0.62' + state: exact + version: 2.1.3+galaxy1 - server: https://usegalaxy.eu state: exact - version: 0.73+galaxy0 + version: 2.1.3+galaxy1 - server: https://usegalaxy.fr/ state: exact - version: 0.73+galaxy0 + version: 2.1.3+galaxy1 - server: https://usegalaxy.no/ - state: exact - version: 0.73+galaxy0 + state: inexact + versions: + - 2.1.1+galaxy0 + - 2.1.1+galaxy1 + - 2.0.8_beta+galaxy0 - server: https://usegalaxy.org state: exact - version: 0.73+galaxy0 + version: 2.1.3+galaxy1 - server: https://viralvariant.anses.fr/ state: missing - version: 0.73+galaxy0 - - id: toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.2+galaxy0 + version: 2.1.3+galaxy1 + - id: toolshed.g2.bx.psu.edu/repos/iuc/kraken2/kraken2/2.1.3+galaxy2 servers: - server: http://apostl.moffitt.org/ state: missing @@ -53231,15 +43164,12 @@ state: missing - server: https://galaxy.mesocentre.uca.fr state: exact - version: 0.23.2+galaxy0 + version: 2.1.3+galaxy2 - server: https://galaxy.pasteur.fr/ - state: exact - version: 0.23.2+galaxy0 + state: missing - server: https://galaxytrakr.org/ - state: inexact - versions: - - 1.0.1+galaxy3 - - 1.0.1+galaxy0 + state: exact + version: 2.1.3+galaxy2 - server: http://igg.cloud.ba.infn.it/galaxy state: missing - server: https://galaxy.hyphy.org/ @@ -53250,48 +43180,46 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr - state: inexact - versions: - - 1.3.3+galaxy0 + state: missing - server: http://galaxy.inf.ethz.ch state: missing - server: https://palfinder.ls.manchester.ac.uk/ state: missing - server: http://pepsimili.e-nios.com:8080/ - state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing + state: inexact + versions: + - 2.1.1+galaxy1 - server: https://usegalaxy.org.au state: exact - version: 0.23.2+galaxy0 + version: 2.1.3+galaxy2 - server: https://usegalaxy.be/ state: exact - version: 0.23.2+galaxy0 + version: 2.1.3+galaxy2 - server: https://usegalaxy.cz/ state: exact - version: 0.23.2+galaxy0 + version: 2.1.3+galaxy2 - server: https://usegalaxy.eu state: exact - version: 0.23.2+galaxy0 + version: 2.1.3+galaxy2 - server: https://usegalaxy.fr/ state: exact - version: 0.23.2+galaxy0 + version: 2.1.3+galaxy2 - server: https://usegalaxy.no/ - state: exact - version: 0.23.2+galaxy0 + state: inexact + versions: + - 2.1.1+galaxy0 + - 2.1.1+galaxy1 + - 2.0.8_beta+galaxy0 - server: https://usegalaxy.org state: exact - version: 0.23.2+galaxy0 + version: 2.1.3+galaxy2 - server: https://viralvariant.anses.fr/ - state: exact - version: 0.23.2+galaxy0 - version: 0.23.2+galaxy0 - - id: toolshed.g2.bx.psu.edu/repos/iuc/kraken2/kraken2/2.1.1+galaxy1 + state: missing + version: 2.1.3+galaxy2 + - id: toolshed.g2.bx.psu.edu/repos/iuc/kraken_biom/kraken_biom/1.2.0+galaxy1 servers: - server: http://apostl.moffitt.org/ state: missing @@ -53305,15 +43233,11 @@ state: missing - server: https://galaxy.mesocentre.uca.fr state: exact - version: 2.1.1+galaxy1 + version: 1.2.0+galaxy1 - server: https://galaxy.pasteur.fr/ state: missing - server: https://galaxytrakr.org/ - state: inexact - versions: - - 2.1.3+galaxy2 - - 2.17.1+galaxy0 - - 2.0.8_beta+galaxy0 + state: missing - server: http://igg.cloud.ba.infn.it/galaxy state: missing - server: https://galaxy.hyphy.org/ @@ -53324,8 +43248,6 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr @@ -53335,35 +43257,32 @@ - server: https://palfinder.ls.manchester.ac.uk/ state: missing - server: http://pepsimili.e-nios.com:8080/ - state: exact - version: 2.1.1+galaxy1 - - server: https://galaxy.bio.di.uminho.pt/ state: missing - server: https://usegalaxy.org.au state: exact - version: 2.1.1+galaxy1 + version: 1.2.0+galaxy1 - server: https://usegalaxy.be/ state: exact - version: 2.1.1+galaxy1 + version: 1.2.0+galaxy1 - server: https://usegalaxy.cz/ state: exact - version: 2.1.1+galaxy1 + version: 1.2.0+galaxy1 - server: https://usegalaxy.eu state: exact - version: 2.1.1+galaxy1 + version: 1.2.0+galaxy1 - server: https://usegalaxy.fr/ state: exact - version: 2.1.1+galaxy1 + version: 1.2.0+galaxy1 - server: https://usegalaxy.no/ state: exact - version: 2.1.1+galaxy1 + version: 1.2.0+galaxy1 - server: https://usegalaxy.org state: exact - version: 2.1.1+galaxy1 + version: 1.2.0+galaxy1 - server: https://viralvariant.anses.fr/ state: missing - version: 2.1.1+galaxy1 - - id: toolshed.g2.bx.psu.edu/repos/iuc/krakentools_kreport2krona/krakentools_kreport2krona/1.2+galaxy0 + version: 1.2.0+galaxy1 + - id: toolshed.g2.bx.psu.edu/repos/iuc/krakentools_kreport2krona/krakentools_kreport2krona/1.2+galaxy2 servers: - server: http://apostl.moffitt.org/ state: missing @@ -53377,7 +43296,7 @@ state: missing - server: https://galaxy.mesocentre.uca.fr state: exact - version: 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4.1.1+galaxy4 + - server: https://usegalaxy.no/ state: inexact versions: - - 0.2.4+galaxy1 - - server: https://usegalaxy.no/ - state: exact - version: 0.2.4+galaxy0 + - 4.0.3+galaxy0 - server: https://usegalaxy.org state: exact - version: 0.2.4+galaxy0 + version: 4.1.1+galaxy4 - server: https://viralvariant.anses.fr/ state: missing - version: 0.2.4+galaxy0 + version: 4.1.1+galaxy4 symlink: null tags: - - nanopore - - beer - - citizen science - metagenomics + - taxonomic profiling - microgalaxy time: null - time_estimation: 1H - title: Identification of the micro-organisms in a beer using Nanopore sequencing + time_estimation: 2H + title: Taxonomic Profiling and Visualization of Metagenomic Data tools: - - Filter1 + - __UNZIP_COLLECTION__ + - interactive_tool_pavian + - interactive_tool_phinch + - toolshed.g2.bx.psu.edu/repos/crs4/taxonomy_krona_chart/taxonomy_krona_chart/2.7.1 - toolshed.g2.bx.psu.edu/repos/crs4/taxonomy_krona_chart/taxonomy_krona_chart/2.7.1+galaxy0 - - toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.73+galaxy0 - - toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.2+galaxy0 - - toolshed.g2.bx.psu.edu/repos/iuc/kraken2/kraken2/2.1.1+galaxy1 - - toolshed.g2.bx.psu.edu/repos/iuc/krakentools_kreport2krona/krakentools_kreport2krona/1.2+galaxy0 - - toolshed.g2.bx.psu.edu/repos/iuc/porechop/porechop/0.2.4+galaxy0 + - toolshed.g2.bx.psu.edu/repos/iuc/bracken/est_abundance/3.1+galaxy0 + - toolshed.g2.bx.psu.edu/repos/iuc/kraken2/kraken2/2.1.3+galaxy1 + - toolshed.g2.bx.psu.edu/repos/iuc/kraken2/kraken2/2.1.3+galaxy2 + - toolshed.g2.bx.psu.edu/repos/iuc/kraken_biom/kraken_biom/1.2.0+galaxy1 + - toolshed.g2.bx.psu.edu/repos/iuc/krakentools_kreport2krona/krakentools_kreport2krona/1.2+galaxy2 + - toolshed.g2.bx.psu.edu/repos/iuc/metaphlan/metaphlan/4.1.1+galaxy4 topic_name: microbiome topic_name_human: Microbiome tours: false @@ -53536,48 +43440,112 @@ slides: [] tutorial: [] video: false - tutorial_name: beer-data-analysis + tutorial_name: taxonomic-profiling type: tutorial - url: https://training.galaxyproject.org//topics/microbiome/tutorials/beer-data-analysis/tutorial.html + url: https://training.galaxyproject.org//topics/microbiome/tutorials/taxonomic-profiling/tutorial.html urls: - hands_on: https://training.galaxyproject.org/training-material/api/topics/microbiome/tutorials/beer-data-analysis/tutorial.json - slides: https://training.galaxyproject.org/training-material/api/topics/microbiome/tutorials/beer-data-analysis/tutorial.json - version: 5 + hands_on: https://training.galaxyproject.org/training-material/api/topics/microbiome/tutorials/taxonomic-profiling/tutorial.json + slides: https://training.galaxyproject.org/training-material/api/topics/microbiome/tutorials/taxonomic-profiling/tutorial.json + version: 8 video: true - video_versions: 1 + video_versions: 2 video_view: 0 - visit_duration: 503 - visitors: 3449 + visit_duration: 339 + visitors: 15278 workflows: - creators: - class: Person identifier: 0000-0001-9852-1987 name: "B\xE9r\xE9nice Batut" - class: Person - identifier: 0000-0003-1252-9684 - name: "Teresa M\xFCller" + identifier: 0009-0002-2951-4075 + name: Tarnima Omara - class: Person - identifier: 0000-0002-0507-4602 - name: Polina Polunina - description: Identification of the micro-organisms in a beer using Nanopore sequencing + identifier: 0000-0002-6606-5953 + name: Tristan Reynolds + description: This workflow performs taxonomic profiling of metagenomic data and + visualizes microbial community composition using Kraken2 and Bracken as well + as MetaPhlAn. features: comments: false parameters: false - report: null + report: + markdown: ' + + # Workflow Execution Report + + + ## Workflow Inputs + + ```galaxy + + invocation_inputs() + + ``` + + + ## Workflow Outputs + + ```galaxy + + invocation_outputs() + + ``` + + + ## Workflow + + ```galaxy + + workflow_display() + + ``` + + ' subworkflows: false graph_dot: "digraph main {\n node [fontname=\"Atkinson Hyperlegible\", shape=box,\ \ color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n edge [fontname=\"\ - Atkinson Hyperlegible\"];\n 0[color=lightblue,label=\"\u2139\uFE0F Input Dataset\\\ - ninput\"]\n 1[label=\"FastQC\"]\n 0 -> 1 [label=\"output\"]\n 2[label=\"\ - Porechop\"]\n 0 -> 2 [label=\"output\"]\n 3[label=\"fastp\"]\n 2 -> 3 [label=\"\ - outfile\"]\n 4[label=\"Kraken2\"]\n 3 -> 4 [label=\"out1\"]\n kb15e3092c41c4769b6944de6a0e59901[color=lightseagreen,label=\"\ - Output\\nkraken_report\"]\n 4 -> kb15e3092c41c4769b6944de6a0e59901\n 5[label=\"\ - Filter\"]\n 4 -> 5 [label=\"report_output\"]\n 6[label=\"Filter\"]\n 4 ->\ - \ 6 [label=\"report_output\"]\n 7[label=\"Krakentools: Convert kraken report\ - \ file\"]\n 4 -> 7 [label=\"report_output\"]\n kb3445cd493b04134ae78a62e0857c1c9[color=lightseagreen,label=\"\ - Output\\nkrakentool_report\"]\n 7 -> kb3445cd493b04134ae78a62e0857c1c9\n 8[label=\"\ - Krona pie chart\"]\n 7 -> 8 [label=\"output\"]\n}" + Atkinson Hyperlegible\"];\n 0[color=lightblue,label=\"\u2139\uFE0F Input Collection\\\ + nraw-reads\"]\n 1[color=lightblue,label=\"\u2139\uFE0F Input Dataset\\nmetadata\"\ + ]\n 2[label=\"Unzip collection\"]\n 0 -> 2 [label=\"output\"]\n 3[label=\"\ + Kraken2\"]\n 0 -> 3 [label=\"output\"]\n 4[label=\"MetaPhlAn\"]\n 2 -> 4\ + \ [label=\"forward\"]\n 2 -> 4 [label=\"reverse\"]\n k9affde3bb159486ebb38c628ac72e7fc[color=lightseagreen,label=\"\ + Output\\nmetaphlan_output\"]\n 4 -> k9affde3bb159486ebb38c628ac72e7fc\n 5[label=\"\ + Krakentools: Convert kraken report file\"]\n 3 -> 5 [label=\"report_output\"\ + ]\n kb14415d566e24f7989d6ae0bcd837796[color=lightseagreen,label=\"Output\\\ + nkrakentool_report\"]\n 5 -> kb14415d566e24f7989d6ae0bcd837796\n 6[label=\"\ + Kraken-biom\"]\n 3 -> 6 [label=\"report_output\"]\n 1 -> 6 [label=\"output\"\ + ]\n 7[label=\"Pavian\"]\n 3 -> 7 [label=\"report_output\"]\n 8[label=\"Bracken\"\ + ]\n 3 -> 8 [label=\"report_output\"]\n 9[label=\"Krona pie chart\"]\n 4 ->\ + \ 9 [label=\"krona_output_file\"]\n 10[label=\"Krona pie chart\"]\n 5 -> 10\ + \ [label=\"output\"]\n 11[label=\"Phinch Visualisation\"]\n 6 -> 11 [label=\"\ + biomOutput\"]\n}" history: + - hash: 501a57f0ee0f8d9a12374d3cad9d498a000a3c61 + message: Add orcid ID for creator Tarnima Omara + num: 6 + short_hash: 501a57f0e + unix: '1765757948' + - hash: 9bfe386d04a4227438b50d6ee837f4b242ca4728 + message: Update workflow and workflow tests + num: 5 + short_hash: 9bfe386d0 + unix: '1765756254' + - hash: dde20503929908deeee6ec1fc448c11e16a75a9f + message: Update topics/microbiome/tutorials/taxonomic-profiling/workflows/main-workflow.ga + num: 4 + short_hash: dde205039 + unix: '1743721902' + - hash: 364bb343b77778931b064588e8d3623db0f8d75f + message: Update topics/microbiome/tutorials/taxonomic-profiling/workflows/main-workflow.ga + num: 3 + short_hash: 364bb343b + unix: '1743721794' + - hash: 2159350d9efc52192ade1a8060fd0645959892bc + message: Update main-workflow.ga + num: 2 + short_hash: 2159350d9 + unix: '1743647309' - hash: 0e0a2f2ccb650b0aab1ffc13838045164bdb5d30 message: Rename metagenomics topic to microbiome num: 1 @@ -53591,85 +43559,128 @@ input_connections: {} inputs: - description: '' - name: input - label: input - name: input + name: raw-reads + label: raw-reads + name: Input dataset collection outputs: [] position: left: 0 - top: 301 + top: 32 tool_id: null - tool_state: '{"optional": false, "tag": null, "name": "input"}' + tool_state: '{"optional": false, "tag": null, "collection_type": "list:paired", + "fields": null}' + tool_version: null + type: data_collection_input + uuid: 8ceaae85-1ed7-4488-b839-53d36e642378 + when: null + workflow_outputs: [] + - annotation: '' + content_id: null + errors: null + id: 1 + input_connections: {} + inputs: + - description: '' + name: metadata + label: metadata + name: Input dataset + outputs: [] + position: + left: 35.48228574271107 + top: 575.2289046420843 + tool_id: null + tool_state: '{"optional": false, "tag": null}' tool_version: null type: data_input - uuid: 31e2b384-0c1d-42fc-9379-8fb62462bffb + uuid: 715bbeb3-cb9a-49dd-a9c5-1f184f3eb34a when: null workflow_outputs: [] license: MIT - mermaid: "flowchart TD\n 0[\"\u2139\uFE0F Input Dataset\\ninput\"];\n style\ - \ 0 stroke:#2c3143,stroke-width:4px;\n 1[\"FastQC\"];\n 0 -->|output| 1;\n\ - \ 2[\"Porechop\"];\n 0 -->|output| 2;\n 3[\"fastp\"];\n 2 -->|outfile| 3;\n\ - \ 4[\"Kraken2\"];\n 3 -->|out1| 4;\n b15e3092-c41c-4769-b694-4de6a0e59901[\"\ - Output\\nkraken_report\"];\n 4 --> b15e3092-c41c-4769-b694-4de6a0e59901;\n\ - \ style b15e3092-c41c-4769-b694-4de6a0e59901 stroke:#2c3143,stroke-width:4px;\n\ - \ 5[\"Filter\"];\n 4 -->|report_output| 5;\n 6[\"Filter\"];\n 4 -->|report_output|\ - \ 6;\n 7[\"Krakentools: Convert kraken report file\"];\n 4 -->|report_output|\ - \ 7;\n b3445cd4-93b0-4134-ae78-a62e0857c1c9[\"Output\\nkrakentool_report\"\ - ];\n 7 --> b3445cd4-93b0-4134-ae78-a62e0857c1c9;\n style b3445cd4-93b0-4134-ae78-a62e0857c1c9\ - \ stroke:#2c3143,stroke-width:4px;\n 8[\"Krona pie chart\"];\n 7 -->|output|\ - \ 8;" - modified: 2026-05-21 00:30:25 +0000 - name: Identification of the micro-organisms in a beer using Nanopore sequencing + mermaid: "flowchart TD\n 0[\"\u2139\uFE0F Input Collection\\nraw-reads\"];\n\ + \ style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"\u2139\uFE0F Input Dataset\\\ + nmetadata\"];\n style 1 stroke:#2c3143,stroke-width:4px;\n 2[\"Unzip collection\"\ + ];\n 0 -->|output| 2;\n 3[\"Kraken2\"];\n 0 -->|output| 3;\n 4[\"MetaPhlAn\"\ + ];\n 2 -->|forward| 4;\n 2 -->|reverse| 4;\n 9affde3b-b159-486e-bb38-c628ac72e7fc[\"\ + Output\\nmetaphlan_output\"];\n 4 --> 9affde3b-b159-486e-bb38-c628ac72e7fc;\n\ + \ style 9affde3b-b159-486e-bb38-c628ac72e7fc stroke:#2c3143,stroke-width:4px;\n\ + \ 5[\"Krakentools: Convert kraken report file\"];\n 3 -->|report_output| 5;\n\ + \ b14415d5-66e2-4f79-89d6-ae0bcd837796[\"Output\\nkrakentool_report\"];\n \ + \ 5 --> b14415d5-66e2-4f79-89d6-ae0bcd837796;\n style b14415d5-66e2-4f79-89d6-ae0bcd837796\ + \ stroke:#2c3143,stroke-width:4px;\n 6[\"Kraken-biom\"];\n 3 -->|report_output|\ + \ 6;\n 1 -->|output| 6;\n 7[\"Pavian\"];\n 3 -->|report_output| 7;\n 8[\"\ + Bracken\"];\n 3 -->|report_output| 8;\n 9[\"Krona pie chart\"];\n 4 -->|krona_output_file|\ + \ 9;\n 10[\"Krona pie chart\"];\n 5 -->|output| 10;\n 11[\"Phinch Visualisation\"\ + ];\n 6 -->|biomOutput| 11;" + modified: 2026-07-01 00:31:39 +0000 + name: Taxonomic Profiling and Visualization of Metagenomic Data outputs: - annotation: '' - content_id: toolshed.g2.bx.psu.edu/repos/iuc/kraken2/kraken2/2.1.1+galaxy1 + content_id: toolshed.g2.bx.psu.edu/repos/iuc/metaphlan/metaphlan/4.1.1+galaxy4 errors: null id: 4 input_connections: - single_paired|input_sequences: - id: 3 - output_name: out1 - inputs: [] + inputs|in|raw_in|in_f: + id: 2 + output_name: forward + inputs|in|raw_in|in_r: + id: 2 + output_name: reverse + inputs: + - description: runtime parameter for tool MetaPhlAn + name: analysis label: null - name: Kraken2 + name: MetaPhlAn outputs: - - name: report_output + - name: output_file type: tabular - - name: output + - name: bowtie2out + type: tabular + - name: sam_output_file + type: sam + - name: biom_output_file + type: biom1 + - name: krona_output_file type: tabular position: - left: 840 - top: 349 + left: 559.9960780215968 + top: 0 post_job_actions: {} - tool_id: toolshed.g2.bx.psu.edu/repos/iuc/kraken2/kraken2/2.1.1+galaxy1 - tool_shed_repository: - changeset_revision: e674066930b2 - name: kraken2 - owner: iuc - tool_shed: toolshed.g2.bx.psu.edu - tool_state: '{"__input_ext": "fastqsanger", "chromInfo": "/opt/galaxy/tool-data/shared/ucsc/chrom/?.len", - "confidence": "0.0", "kraken2_database": "2022-09-04T165121Z_standard_prebuilt_pluspf_2022-06-07", - "min_base_quality": "0", "minimum_hit_groups": "2", "quick": false, "report": - {"create_report": true, "use_mpa_style": false, "report_zero_counts": false, - "report_minimizer_data": false}, "single_paired": {"single_paired_selector": - "no", "__current_case__": 2, "input_sequences": {"__class__": "ConnectedValue"}}, - "split_reads": false, "use_names": true, "__page__": null, "__rerun_remap_job_id__": - null}' - tool_version: 2.1.1+galaxy1 + tool_id: toolshed.g2.bx.psu.edu/repos/iuc/metaphlan/metaphlan/4.1.1+galaxy4 + tool_shed_repository: + changeset_revision: eca2e2e20436 + name: metaphlan + owner: iuc + tool_shed: toolshed.g2.bx.psu.edu + tool_state: '{"analysis": {"analysis_type": {"t": "rel_ab", "__current_case__": + 0, "tax_lev": {"tax_lev": "a", "__current_case__": 0, "split_levels": false}}, + "min_cu_len": "2000", "min_alignment_len": null, "organism_profiling": ["add_viruses"], + "stat": "tavg_g", "stat_q": "0.2", "perc_nonzero": "0.33", "ignore_markers": + {"__class__": "RuntimeValue"}, "avoid_disqm": true}, "inputs": {"in": {"selector": + "raw", "__current_case__": 0, "raw_in": {"selector": "paired", "__current_case__": + 3, "in_f": {"__class__": "ConnectedValue"}, "in_r": 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tool_panel_section_label: FASTA/FASTQ\n\ + \ tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: sortmerna\n owner:\ + \ rnateam\n revisions: 10b84b577117\n tool_panel_section_label: Annotation\n\ + \ tool_shed_url: https://toolshed.g2.bx.psu.edu/\n" + api: https://training.galaxyproject.org/training-material/api/topics/microbiome/tutorials/metatranscriptomics/tutorial.json contributions: authorship: + - pratikdjagtap + - subinamehta + - jraysajulga - bebatut - - EngyNasr - - paulzierep + - emmaleith + - pravs3683 + - shiltemann editing: - - hrhotz - - wm75 - funding: - - gallantries - - eosc-life + - paulzierep + - EngyNasr + - ogerdfx reviewing: - shiltemann - - deeptivarshney - - paulzierep - bebatut - - bgruening - - gallardoalba - - EngyNasr - - wm75 - hexylena + - paulzierep + - bgruening contributors: + - email: pjagtap@umn.edu + id: pratikdjagtap + joined: 2017-09 + name: Pratik Jagtap + orcid: 0000-0003-0984-0973 + page: https://training.galaxyproject.org/training-material/hall-of-fame/pratikdjagtap/ + url: https://training.galaxyproject.org/training-material/api/contributors/pratikdjagtap.json + - email: subinamehta@gmail.com + id: subinamehta + joined: 2018-06 + linkedin: subinamehta + matrix: subinamehta:matrix.org + name: Subina Mehta + orcid: 0000-0001-9818-0537 + page: https://training.galaxyproject.org/training-material/hall-of-fame/subinamehta/ + twitter: Subina_Mehta + url: https://training.galaxyproject.org/training-material/api/contributors/subinamehta.json + - email: rsajulga@umn.edu + id: jraysajulga + joined: 2018-11 + name: Ray Sajulga + page: https://training.galaxyproject.org/training-material/hall-of-fame/jraysajulga/ + url: https://training.galaxyproject.org/training-material/api/contributors/jraysajulga.json - affiliations: - gallantries - ifb @@ -54166,18 +43945,46 @@ page: https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/ twitter: bebatut url: https://training.galaxyproject.org/training-material/api/contributors/bebatut.json + - email: leith023@umn.edu + id: emmaleith + joined: 2019-07 + name: Emma Leith + page: https://training.galaxyproject.org/training-material/hall-of-fame/emmaleith/ + url: https://training.galaxyproject.org/training-material/api/contributors/emmaleith.json + - email: kumar207@umn.edu + id: pravs3683 + joined: 2019-04 + name: Praveen Kumar + page: https://training.galaxyproject.org/training-material/hall-of-fame/pravs3683/ + url: https://training.galaxyproject.org/training-material/api/contributors/pravs3683.json - affiliations: - uni-freiburg + - nfdi4plants - elixir-europe - elixir_node: de - email: engynasr94@gmail.com - id: EngyNasr - joined: 2021-05 - matrix: EngyNasr:matrix.org - name: Engy Nasr - orcid: 0000-0001-9047-4215 - page: https://training.galaxyproject.org/training-material/hall-of-fame/EngyNasr/ - url: https://training.galaxyproject.org/training-material/api/contributors/EngyNasr.json + bio: Researcher at Erasmus Medical Center + bluesky: shiltemann.bsky.social + contact_for_training: true + elixir_node: nl + email: saskia.hiltemann@gmail.com + fediverse: https://mstdn.science/@shiltemann + fediverse_flavor: mastodon + former_affiliations: + - CINECA-Project + - gallantries + - erasmusmc + id: shiltemann + joined: 2017-09 + linkedin: shiltemann + location: + country: NL + lat: 51.912 + lon: 4.462 + maintainer_contact: gitter + matrix: shiltemann:matrix.org + name: Saskia Hiltemann + orcid: 0000-0003-3803-468X + page: https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/ + url: https://training.galaxyproject.org/training-material/api/contributors/shiltemann.json - affiliations: - uni-freiburg - elixir-europe @@ -54192,91 +43999,23 @@ page: https://training.galaxyproject.org/training-material/hall-of-fame/paulzierep/ url: https://training.galaxyproject.org/training-material/api/contributors/paulzierep.json - affiliations: - - elixir-europe - bluesky: hrhotz.bsky.social - contact_for_training: true - elixir_node: ch - email: hrhotz@googlemail.com - fediverse: https://genomic.social/@hrhotz - fediverse_flavor: mastodon - id: hrhotz - joined: 2017-09 - linkedin: hans-rudolf-hotz-542b31 - location: - country: CH - lat: 47.575694 - lon: 7.578796 - matrix: hrhotz:matrix.org - name: Hans-Rudolf Hotz - orcid: 0000-0002-2799-424X - page: https://training.galaxyproject.org/training-material/hall-of-fame/hrhotz/ - url: https://training.galaxyproject.org/training-material/api/contributors/hrhotz.json - - affiliations: - - by-covid - uni-freiburg - elixir-europe - - deNBI - - mwk elixir_node: de - fediverse: https://fediscience.org/@zerodivision - fediverse_flavor: mastodon - former_affiliations: - - eurosciencegateway - id: wm75 - joined: 2017-09 - matrix: wm75:matrix.org - name: Wolfgang Maier - orcid: 0000-0002-9464-6640 - page: https://training.galaxyproject.org/training-material/hall-of-fame/wm75/ - url: 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https://training.galaxyproject.org/training-material/hall-of-fame/EngyNasr/ + url: https://training.galaxyproject.org/training-material/api/contributors/EngyNasr.json + - elixir_node: fr + id: ogerdfx + joined: 2025-06 + name: Christine Oger + page: https://training.galaxyproject.org/training-material/hall-of-fame/ogerdfx/ + url: https://training.galaxyproject.org/training-material/api/contributors/ogerdfx.json - affiliations: - uni-freiburg - nfdi4plants @@ -54305,30 +44044,6 @@ orcid: 0000-0003-3803-468X page: https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/ url: https://training.galaxyproject.org/training-material/api/contributors/shiltemann.json - - affiliations: - - uni-freiburg - - elixir-europe - bluesky: dvarshney.bsky.social - email: varshney@informatik.uni-freiburg.de - id: deeptivarshney - joined: 2022-12 - name: Deepti Varshney - orcid: 0000-0003-0419-6832 - page: https://training.galaxyproject.org/training-material/hall-of-fame/deeptivarshney/ - url: https://training.galaxyproject.org/training-material/api/contributors/deeptivarshney.json - - affiliations: - - uni-freiburg - - elixir-europe - - deNBI - - mwk - - materialvitaldigital - email: zierep@informatik.uni-freiburg.de - id: paulzierep - joined: 2023-02 - name: Paul Zierep - orcid: 0000-0003-2982-388X - page: https://training.galaxyproject.org/training-material/hall-of-fame/paulzierep/ - url: https://training.galaxyproject.org/training-material/api/contributors/paulzierep.json - affiliations: - gallantries - ifb @@ -54354,6 +44069,43 @@ page: https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/ twitter: bebatut url: https://training.galaxyproject.org/training-material/api/contributors/bebatut.json + - affiliations: + - elixir-europe + contact_for_training: false + elixir_node: nl + former_affiliations: + - deNBI + - avans-atgm + - uni-freiburg + - erasmusmc + - gallantries + - by-covid + - elixir-converge + id: hexylena + joined: 2017-09 + location: + country: NL + lat: 51.91 + lon: 4.46 + maintainer_contact: gitter + matrix: hexylena:matrix.org + name: Helena Rasche + orcid: 0000-0001-9760-8992 + page: https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/ + url: https://training.galaxyproject.org/training-material/api/contributors/hexylena.json + - affiliations: + - uni-freiburg + - elixir-europe + - deNBI + - mwk + - materialvitaldigital + email: zierep@informatik.uni-freiburg.de + id: paulzierep + joined: 2023-02 + name: Paul Zierep + orcid: 0000-0003-2982-388X + page: https://training.galaxyproject.org/training-material/hall-of-fame/paulzierep/ + url: https://training.galaxyproject.org/training-material/api/contributors/paulzierep.json - affiliations: - deNBI - mwk @@ -54384,255 +44136,147 @@ page: https://training.galaxyproject.org/training-material/hall-of-fame/bgruening/ twitter: bjoerngruening url: https://training.galaxyproject.org/training-material/api/contributors/bgruening.json - - 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matrix: wm75:matrix.org - name: Wolfgang Maier - orcid: 0000-0002-9464-6640 - page: https://training.galaxyproject.org/training-material/hall-of-fame/wm75/ - url: https://training.galaxyproject.org/training-material/api/contributors/wm75.json - - affiliations: - - erasmusmc - - gallantries - - by-covid - - elixir-europe - - elixir-converge - contact_for_training: false - elixir_node: nl - former_affiliations: - - deNBI - - avans-atgm - - uni-freiburg - id: hexylena - joined: 2017-09 - location: - country: NL - lat: 51.91 - lon: 4.46 - maintainer_contact: gitter - matrix: hexylena:matrix.org - name: Helena Rasche - orcid: 0000-0001-9760-8992 - page: https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/ - url: https://training.galaxyproject.org/training-material/api/contributors/hexylena.json - dir: topics/microbiome/tutorials/pathogen-detection-from-nanopore-foodborne-data + dir: topics/microbiome/tutorials/metatranscriptomics edam_ontology: - - topic_3174 - - topic_3305 + - topic_3941 + - topic_3697 - topic_0637 - - topic_0196 - - topic_0634 + - topic_1775 - topic_0080 edam_operation: - - Sequence alignment analysis - - Statistical calculation - - Genome assembly + - Phylogenetic tree visualisation + - Primer removal - Visualisation - - Antimicrobial resistance prediction - - Mapping - - Phylogenetic tree generation (maximum likelihood and Bayesian methods) - - Box-Whisker plot plotting - Sequence composition calculation - - Phylogenetic tree generation (from molecular sequences) - - Base-calling - - Phylogenetic tree analysis - - Variant calling - - Sequence assembly - - Phylogenetic tree reconstruction - - Phylogenetic tree generation - - Scatter plot plotting - - De-novo assembly - - Taxonomic classification - - Sequence assembly visualisation - - Pairwise sequence alignment - - Multilocus sequence typing - - Data handling - - Validation - - Multiple sequence alignment - Aggregation - - Cross-assembly - - Mapping assembly - - Sequence contamination filtering + - Phylogenetic tree editing + - Phylogenetic inference + - Statistical calculation - Sequencing quality control + - Phylogenetic analysis + - Conversion + - Sequence trimming + - Taxonomic classification + - Species frequency estimation + - Sequence alignment analysis + - Sequence comparison + - Validation + - Read pre-processing + - Sequence similarity search edam_topic: - - Metagenomics - - Public health and epidemiology + - Metatranscriptomics + - Microbial ecology - Taxonomy - - Sequence assembly - - Pathology + - Function analysis - Sequence analysis exact_supported_servers: - - UseGalaxy.eu + - UseGalaxy.be + - UseGalaxy.cz + - UseGalaxy.fr + - UseGalaxy.org (Main) feedback_mean_note: null feedback_number: 0 hands_on: true - id: microbiome/pathogen-detection-from-nanopore-foodborne-data + id: microbiome/metatranscriptomics inexact_supported_servers: - - UseGalaxy.org.au - - UseGalaxy.be - - UseGalaxy.cz + - UseGalaxy.eu js_requirements: mathjax: null mermaid: false + key_points: + - Metatranscriptomics data have the same QC profile that RNA-seq data + - A lot of metatranscriptomics sequences are identified as rRNA sequences + - With shotgun data, we can extract information about the studied community structure + and also the functions realised by the community + - Metatranscriptomics data analyses are complex and must be careful done, specially + when they are done without combination to metagenomics data analyses layout: tutorial_hands_on level: Introductory license: CC-BY-4.0 - mod_date: '2025-11-18' + mod_date: '2025-06-16' objectives: - - Check quality reports generated by FastQC and NanoPlot for metagenomics Nanopore - data - - Preprocess the sequencing data to remove adapters, poor quality base content and - host/contaminating reads - - Perform taxonomy profiling indicating and visualizing up to species level in the - samples - - Identify pathogens based on the found virulence factor gene products via assembly, - identify strains and indicate all antimicrobial resistance genes in samples - - Identify pathogens via SNP calling and build the consensus gemone of the samples - - Relate all samples' pathogenic genes for tracking pathogens via phylogenetic trees - and heatmaps - pageviews: 8267 - pub_date: '2023-01-26' + - Choose the best approach to analyze metatranscriptomics data + - Understand the functional microbiome characterization using metatranscriptomic + results + - Understand where metatranscriptomics fits in 'multi-omic' analysis of microbiomes + - Visualise a community structure + pageviews: 9247565 + pub_date: '2019-11-21' questions: - - What are the preprocessing steps to prepare ONT sequencing data for further analysis? - - How to identify pathogens using sequencing data? - - How to track the found pathogens through all your samples datasets? + - How to analyze metatranscriptomics data? + - What information can be extracted of metatranscriptomics data? + - How to assign taxa and function to the identified sequences? recordings: - captioners: - - EngyNasr - date: '2023-05-01' + - paulzierep + date: '2023-05-17' galaxy_version: '23.01' - length: 1H45M + length: 1H5M speakers: + - paulzierep + youtube_id: HNYop3vLpoM + - captioners: - EngyNasr - youtube_id: gQHb_jkj-Z0 - - bot-timestamp: 1723837296 - captioners: - - EngyNasr - date: '2024-08-16' - galaxy_version: '24.1.2.dev0 ' - length: 1H55M + - shiltemann + date: '2021-02-15' + galaxy_version: '21.01' + length: 1H30M speakers: - - EngyNasr - youtube_id: rGP-BKYwUbc + - pratikdjagtap + - timothygriffin + - subinamehta + - shiltemann + youtube_id: EMaos5u1_a8 redirect_from: - - /topics/metagenomics/tutorials/pathogen-detection-from-nanopore-foodborne-data/tutorial - - /short/microbiome/pathogen-detection-from-nanopore-foodborne-data - - /short/T00208 - - /short/T00393 - short_id: T00393 + - /topics/metagenomics/tutorials/metatranscriptomics/tutorial + - /short/microbiome/metatranscriptomics + - /short/T00203 + - /short/T00388 + short_id: T00388 short_tools: - - ggplot2_heatmap - - Count1 - - Paste1 - - tp_find_and_replace - - abricate - - multiqc - - fastp - - table_compute - - collapse_dataset - - barchart_gnuplot - - tp_replace_in_column - - compose_text_param - - minimap2 - - regexColumn1 - - mlst - - __FILTER_FAILED_DATASETS__ - - CONVERTER_gz_to_uncompressed - - __BUILD_LIST__ - - clair3 - - tp_split_on_column - - krakentools_extract_kraken_reads - - bamtools_split_mapped - - samtools_fastx - - tab2fasta - - krakentools_kreport2krona - - tp_head_tool - - bedtools_getfastabed - - fasta_merge_files_and_filter_unique_sequences - - medaka_consensus_pipeline + - metaphlan + - cutadapt + - fastq_paired_end_interlacer + - humann_rename_table + - combine_metaphlan_humann + - graphlan + - bg_sortmerna + - humann_regroup_table + - tp_sort_header_tool + - taxonomy_krona_chart + - humann - Grouping1 - - split_file_to_collection - - bcftools_consensus - - tp_cut_tool - - __FILTER_EMPTY_DATASETS__ - - samtools_coverage - - snpSift_filter - - Remove beginning1 + - tp_find_and_replace + - humann_renorm_table + - humann_split_stratified_table + - Grep1 + - export2graphlan + - humann_unpack_pathways - fastqc - - flye - - fasta2tab - - newick_display - - regex1 + - graphlan_annotate + - multiqc - Cut1 - - snpSift_extractFields - - bcftools_norm - - Grep1 - - tp_multijoin_tool - - param_value_from_file - - taxonomy_krona_chart - - bandage_image - - collection_element_identifiers - - fasttree - - nanoplot - - tp_sorted_uniq - - porechop - - Add_a_column1 - - add_line_to_file - - clustalw - - samtools_depth - - collection_column_join - - kraken2 - slides: false + slides: true slides_recordings: false - subtopic: metagenomics + subtopic: metatranscriptomics supported_servers: exact: - - name: UseGalaxy.eu - url: https://usegalaxy.eu - usegalaxy: true - inexact: - - name: UseGalaxy.org.au - url: https://usegalaxy.org.au - usegalaxy: true - name: UseGalaxy.be url: https://usegalaxy.be/ 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state: exact + version: 4.3.6+galaxy0 - server: https://usegalaxy.org - state: local + state: exact + version: 4.3.6+galaxy0 - server: https://viralvariant.anses.fr/ - state: local - version: local - - id: __BUILD_LIST__ + state: missing + version: 4.3.6+galaxy0 + symlink: null + tags: + - metatranscriptomics + - microgalaxy + time: null + time_estimation: 5H + title: Metatranscriptomics analysis using microbiome RNA-seq data + tools: + - Cut1 + - Grep1 + - Grouping1 + - toolshed.g2.bx.psu.edu/repos/bebatut/combine_metaphlan2_humann2/combine_metaphlan_humann/0.3.0 + - toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.5+galaxy2 + - toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/9.5+galaxy2 + - toolshed.g2.bx.psu.edu/repos/crs4/taxonomy_krona_chart/taxonomy_krona_chart/2.7.1+galaxy0 + - toolshed.g2.bx.psu.edu/repos/devteam/fastq_paired_end_interlacer/fastq_paired_end_interlacer/1.2.0.1+galaxy0 + - toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy1 + - toolshed.g2.bx.psu.edu/repos/iuc/export2graphlan/export2graphlan/0.20+galaxy0 + - toolshed.g2.bx.psu.edu/repos/iuc/graphlan/graphlan/1.1.3 + - toolshed.g2.bx.psu.edu/repos/iuc/graphlan_annotate/graphlan_annotate/1.1.3 + - toolshed.g2.bx.psu.edu/repos/iuc/humann/humann/3.9+galaxy0 + - toolshed.g2.bx.psu.edu/repos/iuc/humann_regroup_table/humann_regroup_table/3.9+galaxy0 + - toolshed.g2.bx.psu.edu/repos/iuc/humann_rename_table/humann_rename_table/3.9+galaxy0 + - toolshed.g2.bx.psu.edu/repos/iuc/humann_renorm_table/humann_renorm_table/3.9+galaxy0 + - toolshed.g2.bx.psu.edu/repos/iuc/humann_split_stratified_table/humann_split_stratified_table/3.9+galaxy0 + - toolshed.g2.bx.psu.edu/repos/iuc/humann_unpack_pathways/humann_unpack_pathways/3.9+galaxy0 + - toolshed.g2.bx.psu.edu/repos/iuc/metaphlan/metaphlan/4.1.1+galaxy4 + - toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.27+galaxy3 + - toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/5.0+galaxy0 + - toolshed.g2.bx.psu.edu/repos/rnateam/sortmerna/bg_sortmerna/4.3.6+galaxy0 + topic_name: microbiome + topic_name_human: Microbiome + tours: false + translations: + slides: [] + tutorial: [] + video: false + tutorial_name: metatranscriptomics + type: tutorial + url: https://training.galaxyproject.org//topics/microbiome/tutorials/metatranscriptomics/tutorial.html + urls: + hands_on: https://training.galaxyproject.org/training-material/api/topics/microbiome/tutorials/metatranscriptomics/tutorial.json + slides: https://training.galaxyproject.org/training-material/api/topics/microbiome/tutorials/metatranscriptomics/tutorial.json + version: 6 + video: true + video_versions: 2 + video_view: 0 + visit_duration: 413 + visitors: 3926230 + workflows: + - creators: + - class: Person + identifier: 0000-0001-9852-1987 + name: "B\xE9r\xE9nice Batut" + - class: Person + identifier: 0000-0003-0984-0973 + name: Pratik Jagtap + - class: Person + identifier: 0000-0001-9818-0537 + name: Subina Mehta + - class: Person + identifier: 0000-0003-3803-468X + name: Saskia Hiltemann + - class: Person + identifier: 0000-0003-2982-388X + name: Paul Zierep + description: Metatranscriptomics analysis using microbiome RNA-seq data + features: + comments: true + parameters: false + report: + markdown: ' + + # Workflow Execution Report + + + ## Workflow Inputs + + ```galaxy + + invocation_inputs() + + ``` + + + ## Workflow Outputs + + ```galaxy + + invocation_outputs() + + ``` + + + ## Workflow + + ```galaxy + + workflow_display() + + ``` + + ' + subworkflows: false + graph_dot: "digraph main {\n node [fontname=\"Atkinson Hyperlegible\", shape=box,\ + \ color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n edge [fontname=\"\ + Atkinson Hyperlegible\"];\n 0[color=lightblue,label=\"\u2139\uFE0F Input Dataset\\\ + nReverse raw reads\"]\n 1[color=lightblue,label=\"\u2139\uFE0F Input Dataset\\\ + nForward raw reads\"]\n 2[label=\"FastQC\"]\n 0 -> 2 [label=\"output\"]\n\ + \ k676cd11f047947c4a23bc6c8ed5a7790[color=lightseagreen,label=\"Output\\nfastqc_reverse_html_file\"\ + ]\n 2 -> k676cd11f047947c4a23bc6c8ed5a7790\n 3[label=\"FastQC\"]\n 1 -> 3\ + \ [label=\"output\"]\n k1fb52b78c90543c7a295d628c996d35a[color=lightseagreen,label=\"\ + Output\\nfastqc_forward_html_file\"]\n 3 -> k1fb52b78c90543c7a295d628c996d35a\n\ + \ 4[label=\"Cutadapt\"]\n 1 -> 4 [label=\"output\"]\n 0 -> 4 [label=\"output\"\ + ]\n k0e7406ed9eca486eb19a4cbbf04b5138[color=lightseagreen,label=\"Output\\\ + ncutadapt_report\"]\n 4 -> k0e7406ed9eca486eb19a4cbbf04b5138\n 5[label=\"\ + MultiQC\"]\n 2 -> 5 [label=\"text_file\"]\n 3 -> 5 [label=\"text_file\"]\n\ + \ kd9f371ddaa6c4540b62b0e34c0b71afa[color=lightseagreen,label=\"Output\\nmultiqc_html_report\"\ + ]\n 5 -> kd9f371ddaa6c4540b62b0e34c0b71afa\n 6[label=\"Filter with SortMeRNA\"\ + ]\n 4 -> 6 [label=\"out1\"]\n 4 -> 6 [label=\"out2\"]\n k3092eb62d7fc4d66bf574c6cf491d0e3[color=lightseagreen,label=\"\ + Output\\nsortmerna_unaligned_reverse\"]\n 6 -> k3092eb62d7fc4d66bf574c6cf491d0e3\n\ + \ kdb3bb8ee8af74528be4bf3ea6d381856[color=lightseagreen,label=\"Output\\nsortmerna_unaligned_forward\"\ + ]\n 6 -> kdb3bb8ee8af74528be4bf3ea6d381856\n 7[label=\"FASTQ interlacer\"\ + ]\n 6 -> 7 [label=\"unaligned_forward\"]\n 6 -> 7 [label=\"unaligned_reverse\"\ + ]\n 8[label=\"MetaPhlAn\"]\n 6 -> 8 [label=\"unaligned_forward\"]\n 6 ->\ + \ 8 [label=\"unaligned_reverse\"]\n kb13521dbf5e74bf3b7fa673d13fc2911[color=lightseagreen,label=\"\ + Output\\nmetaphlan_predicted_taxons\"]\n 8 -> kb13521dbf5e74bf3b7fa673d13fc2911\n\ + \ 9[label=\"Cut\"]\n 8 -> 9 [label=\"output_file\"]\n 10[label=\"Krona pie\ + \ chart\"]\n 8 -> 10 [label=\"krona_output_file\"]\n 11[label=\"HUMAnN\"]\n\ + \ 7 -> 11 [label=\"outfile_pairs\"]\n 8 -> 11 [label=\"output_file\"]\n k5aec39b6317a4fd0b90622d5a965e957[color=lightseagreen,label=\"\ + Output\\nhumann_pathabundance\"]\n 11 -> k5aec39b6317a4fd0b90622d5a965e957\n\ + \ k53259a0607834db8828e328e7337f5b3[color=lightseagreen,label=\"Output\\nhumann_gene_families\"\ + ]\n 11 -> k53259a0607834db8828e328e7337f5b3\n 12[label=\"Export to GraPhlAn\"\ + ]\n 9 -> 12 [label=\"out_file1\"]\n 13[label=\"Split a HUMAnN table\"]\n \ + \ 11 -> 13 [label=\"gene_families_tsv\"]\n 14[label=\"Regroup\"]\n 11 -> 14\ + \ [label=\"gene_families_tsv\"]\n 15[label=\"Renormalize\"]\n 11 -> 15 [label=\"\ + gene_families_tsv\"]\n k4bd1c47e66ac41ffbce951d0d86d2252[color=lightseagreen,label=\"\ + Output\\nrenormalize_gene_families\"]\n 15 -> k4bd1c47e66ac41ffbce951d0d86d2252\n\ + \ 16[label=\"Rename features\"]\n 11 -> 16 [label=\"gene_families_tsv\"]\n\ + \ 17[label=\"Renormalize\"]\n 11 -> 17 [label=\"pathabundance_tsv\"]\n k1715a5f63ac34ad2a0309307721e2b49[color=lightseagreen,label=\"\ + Output\\nrenormalize_pathabundance\"]\n 17 -> k1715a5f63ac34ad2a0309307721e2b49\n\ + \ 18[label=\"Split a HUMAnN table\"]\n 11 -> 18 [label=\"pathabundance_tsv\"\ + ]\n 19[label=\"Generation, personalization and annotation of tree\"]\n 12\ + \ -> 19 [label=\"annotation\"]\n 12 -> 19 [label=\"tree\"]\n 20[label=\"Split\ + \ a HUMAnN table\"]\n 14 -> 20 [label=\"output\"]\n 21[label=\"Rename features\"\ + ]\n 14 -> 21 [label=\"output\"]\n 22[label=\"Replace\"]\n 15 -> 22 [label=\"\ + output\"]\n 23[label=\"Unpack pathway abundances\"]\n 15 -> 23 [label=\"output\"\ + ]\n 17 -> 23 [label=\"output\"]\n kb24357e8b6d34893af63ac4cf7494b33[color=lightseagreen,label=\"\ + Output\\nunpack_pathway_abundance\"]\n 23 -> kb24357e8b6d34893af63ac4cf7494b33\n\ + \ 24[label=\"GraPhlAn\"]\n 19 -> 24 [label=\"output_tree\"]\n k21fca66fdce0496f994fdc8e855e0c8f[color=lightseagreen,label=\"\ + Output\\ngraphlan_output_image\"]\n 24 -> k21fca66fdce0496f994fdc8e855e0c8f\n\ + \ 25[label=\"Select\"]\n 21 -> 25 [label=\"output\"]\n k946a04fd18544f088df11a3165651bae[color=lightseagreen,label=\"\ + Output\\ncc_go\"]\n 25 -> k946a04fd18544f088df11a3165651bae\n 26[label=\"\ + Select\"]\n 21 -> 26 [label=\"output\"]\n k4f5f059739eb42ce8dd8d920b52231c3[color=lightseagreen,label=\"\ + Output\\nbp_go\"]\n 26 -> k4f5f059739eb42ce8dd8d920b52231c3\n 27[label=\"\ + Select\"]\n 21 -> 27 [label=\"output\"]\n 28[label=\"Combine MetaPhlAn and\ + \ HUMAnN outputs\"]\n 22 -> 28 [label=\"outfile\"]\n 8 -> 28 [label=\"output_file\"\ + ]\n k4730e437625944d8837460d6a737b720[color=lightseagreen,label=\"Output\\\ + ncombined_metaphlan_humann\"]\n 28 -> k4730e437625944d8837460d6a737b720\n \ + \ 29[label=\"Split a HUMAnN table\"]\n 25 -> 29 [label=\"out_file1\"]\n 30[label=\"\ + Split a HUMAnN table\"]\n 26 -> 30 [label=\"out_file1\"]\n 31[label=\"Sort\"\ + ]\n 27 -> 31 [label=\"out_file1\"]\n k71abb759b51f4383a79127d8b1325e81[color=lightseagreen,label=\"\ + Output\\nsorted_mf_go\"]\n 31 -> k71abb759b51f4383a79127d8b1325e81\n 32[label=\"\ + Split a HUMAnN table\"]\n 27 -> 32 [label=\"out_file1\"]\n 33[label=\"Group\"\ + ]\n 28 -> 33 [label=\"gene_families_output_file\"]\n 34[label=\"Group\"]\n\ + \ 28 -> 34 [label=\"gene_families_output_file\"]\n}" + history: + - hash: 604d1261ba4f89d6650304d72c7b6d8e4166b3a6 + message: 'Update metatranscriptomics tutorials:' + num: 2 + short_hash: 604d1261b + unix: '1750082204' + - hash: 0e0a2f2ccb650b0aab1ffc13838045164bdb5d30 + message: Rename metagenomics topic to microbiome + num: 1 + short_hash: 0e0a2f2cc + unix: '1704901629' + inputs: + - annotation: Metatranscriptomics reverse raw reads + content_id: null + errors: null + id: 0 + input_connections: {} + inputs: + - description: Metatranscriptomics reverse raw reads + name: Reverse raw reads + label: Reverse raw reads + name: Input dataset + outputs: [] + position: + left: 0 + top: 350 + tool_id: null + tool_state: '{"optional": false, "tag": null}' + tool_version: null + type: data_input + uuid: 9871068a-7fcf-4e95-8e77-958e3f536c55 + when: null + workflow_outputs: [] + - annotation: Metatranscriptomics forward raw reads + content_id: null + errors: null + id: 1 + input_connections: {} + inputs: + - description: Metatranscriptomics forward raw reads + name: Forward raw reads + label: Forward raw reads + name: Input dataset + outputs: [] + position: + left: 0 + top: 680 + tool_id: null + tool_state: '{"optional": false, "tag": null}' + tool_version: null + type: data_input + uuid: 4bf6d16f-73df-4104-8282-46b69813c225 + when: null + workflow_outputs: [] + license: MIT + mermaid: "flowchart TD\n 0[\"\u2139\uFE0F Input Dataset\\nReverse raw reads\"\ + ];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"\u2139\uFE0F Input Dataset\\\ + nForward raw reads\"];\n style 1 stroke:#2c3143,stroke-width:4px;\n 2[\"FastQC\"\ + ];\n 0 -->|output| 2;\n 676cd11f-0479-47c4-a23b-c6c8ed5a7790[\"Output\\nfastqc_reverse_html_file\"\ + ];\n 2 --> 676cd11f-0479-47c4-a23b-c6c8ed5a7790;\n style 676cd11f-0479-47c4-a23b-c6c8ed5a7790\ + \ stroke:#2c3143,stroke-width:4px;\n 3[\"FastQC\"];\n 1 -->|output| 3;\n \ + \ 1fb52b78-c905-43c7-a295-d628c996d35a[\"Output\\nfastqc_forward_html_file\"\ + ];\n 3 --> 1fb52b78-c905-43c7-a295-d628c996d35a;\n style 1fb52b78-c905-43c7-a295-d628c996d35a\ + \ stroke:#2c3143,stroke-width:4px;\n 4[\"Cutadapt\"];\n 1 -->|output| 4;\n\ + \ 0 -->|output| 4;\n 0e7406ed-9eca-486e-b19a-4cbbf04b5138[\"Output\\ncutadapt_report\"\ + ];\n 4 --> 0e7406ed-9eca-486e-b19a-4cbbf04b5138;\n style 0e7406ed-9eca-486e-b19a-4cbbf04b5138\ + \ stroke:#2c3143,stroke-width:4px;\n 5[\"MultiQC\"];\n 2 -->|text_file| 5;\n\ + \ 3 -->|text_file| 5;\n d9f371dd-aa6c-4540-b62b-0e34c0b71afa[\"Output\\nmultiqc_html_report\"\ + ];\n 5 --> d9f371dd-aa6c-4540-b62b-0e34c0b71afa;\n style d9f371dd-aa6c-4540-b62b-0e34c0b71afa\ + \ stroke:#2c3143,stroke-width:4px;\n 6[\"Filter with SortMeRNA\"];\n 4 -->|out1|\ + \ 6;\n 4 -->|out2| 6;\n 3092eb62-d7fc-4d66-bf57-4c6cf491d0e3[\"Output\\nsortmerna_unaligned_reverse\"\ + ];\n 6 --> 3092eb62-d7fc-4d66-bf57-4c6cf491d0e3;\n style 3092eb62-d7fc-4d66-bf57-4c6cf491d0e3\ + \ stroke:#2c3143,stroke-width:4px;\n db3bb8ee-8af7-4528-be4b-f3ea6d381856[\"\ + Output\\nsortmerna_unaligned_forward\"];\n 6 --> db3bb8ee-8af7-4528-be4b-f3ea6d381856;\n\ + \ style db3bb8ee-8af7-4528-be4b-f3ea6d381856 stroke:#2c3143,stroke-width:4px;\n\ + \ 7[\"FASTQ interlacer\"];\n 6 -->|unaligned_forward| 7;\n 6 -->|unaligned_reverse|\ + \ 7;\n 8[\"MetaPhlAn\"];\n 6 -->|unaligned_forward| 8;\n 6 -->|unaligned_reverse|\ + \ 8;\n b13521db-f5e7-4bf3-b7fa-673d13fc2911[\"Output\\nmetaphlan_predicted_taxons\"\ + ];\n 8 --> b13521db-f5e7-4bf3-b7fa-673d13fc2911;\n style b13521db-f5e7-4bf3-b7fa-673d13fc2911\ + \ stroke:#2c3143,stroke-width:4px;\n 9[\"Cut\"];\n 8 -->|output_file| 9;\n\ + \ 10[\"Krona pie chart\"];\n 8 -->|krona_output_file| 10;\n 11[\"HUMAnN\"\ + ];\n 7 -->|outfile_pairs| 11;\n 8 -->|output_file| 11;\n 5aec39b6-317a-4fd0-b906-22d5a965e957[\"\ + Output\\nhumann_pathabundance\"];\n 11 --> 5aec39b6-317a-4fd0-b906-22d5a965e957;\n\ + \ style 5aec39b6-317a-4fd0-b906-22d5a965e957 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stroke:#2c3143,stroke-width:4px;\n\ + \ 18[\"Split a HUMAnN table\"];\n 11 -->|pathabundance_tsv| 18;\n 19[\"Generation,\ + \ personalization and annotation of tree\"];\n 12 -->|annotation| 19;\n 12\ + \ -->|tree| 19;\n 20[\"Split a HUMAnN table\"];\n 14 -->|output| 20;\n 21[\"\ + Rename features\"];\n 14 -->|output| 21;\n 22[\"Replace\"];\n 15 -->|output|\ + \ 22;\n 23[\"Unpack pathway abundances\"];\n 15 -->|output| 23;\n 17 -->|output|\ + \ 23;\n b24357e8-b6d3-4893-af63-ac4cf7494b33[\"Output\\nunpack_pathway_abundance\"\ + ];\n 23 --> b24357e8-b6d3-4893-af63-ac4cf7494b33;\n style b24357e8-b6d3-4893-af63-ac4cf7494b33\ + \ stroke:#2c3143,stroke-width:4px;\n 24[\"GraPhlAn\"];\n 19 -->|output_tree|\ + \ 24;\n 21fca66f-dce0-496f-994f-dc8e855e0c8f[\"Output\\ngraphlan_output_image\"\ + ];\n 24 --> 21fca66f-dce0-496f-994f-dc8e855e0c8f;\n style 21fca66f-dce0-496f-994f-dc8e855e0c8f\ + \ stroke:#2c3143,stroke-width:4px;\n 25[\"Select\"];\n 21 -->|output| 25;\n\ + \ 946a04fd-1854-4f08-8df1-1a3165651bae[\"Output\\ncc_go\"];\n 25 --> 946a04fd-1854-4f08-8df1-1a3165651bae;\n\ + \ style 946a04fd-1854-4f08-8df1-1a3165651bae stroke:#2c3143,stroke-width:4px;\n\ + \ 26[\"Select\"];\n 21 -->|output| 26;\n 4f5f0597-39eb-42ce-8dd8-d920b52231c3[\"\ + Output\\nbp_go\"];\n 26 --> 4f5f0597-39eb-42ce-8dd8-d920b52231c3;\n style\ + \ 4f5f0597-39eb-42ce-8dd8-d920b52231c3 stroke:#2c3143,stroke-width:4px;\n 27[\"\ + Select\"];\n 21 -->|output| 27;\n 28[\"Combine MetaPhlAn and HUMAnN outputs\"\ + ];\n 22 -->|outfile| 28;\n 8 -->|output_file| 28;\n 4730e437-6259-44d8-8374-60d6a737b720[\"\ + Output\\ncombined_metaphlan_humann\"];\n 28 --> 4730e437-6259-44d8-8374-60d6a737b720;\n\ + \ style 4730e437-6259-44d8-8374-60d6a737b720 stroke:#2c3143,stroke-width:4px;\n\ + \ 29[\"Split a HUMAnN table\"];\n 25 -->|out_file1| 29;\n 30[\"Split a HUMAnN\ + \ table\"];\n 26 -->|out_file1| 30;\n 31[\"Sort\"];\n 27 -->|out_file1| 31;\n\ + \ 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input_connections: + sequencing_type|forward_reads: + id: 4 + output_name: out1 + sequencing_type|reverse_reads: + id: 4 + output_name: out2 + inputs: + - description: runtime parameter for tool Filter with SortMeRNA + name: sequencing_type + - description: runtime parameter for tool Filter with SortMeRNA + name: sequencing_type + label: null + name: Filter with SortMeRNA + outputs: + - name: aligned_forward + type: input + - name: aligned_reverse + type: input + - name: unaligned_forward + type: input + - name: unaligned_reverse + type: input + position: + left: 650 + top: 680 + post_job_actions: {} + tool_id: toolshed.g2.bx.psu.edu/repos/rnateam/sortmerna/bg_sortmerna/4.3.6+galaxy0 + tool_shed_repository: + changeset_revision: 10b84b577117 + name: sortmerna + owner: rnateam + tool_shed: toolshed.g2.bx.psu.edu + tool_state: '{"N": false, "__input_ext": "input", "aligned_fastx": {"aligned_fastx_selector": + "--fastx", "__current_case__": 0, "other": true}, "chromInfo": 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id: 6 + output_name: unaligned_forward + inputs|in|raw_in|in_r: + id: 6 + output_name: unaligned_reverse + inputs: [] + label: null + name: MetaPhlAn + outputs: + - name: output_file + type: tabular + - name: bowtie2out + type: tabular + - name: sam_output_file + type: sam + - name: biom_output_file + type: biom1 + - name: krona_output_file + type: tabular + position: + left: 1270 + top: 720 + post_job_actions: {} + tool_id: toolshed.g2.bx.psu.edu/repos/iuc/metaphlan/metaphlan/4.1.1+galaxy4 + tool_shed_repository: + changeset_revision: eca2e2e20436 + name: metaphlan + owner: iuc + tool_shed: toolshed.g2.bx.psu.edu + tool_state: '{"__input_ext": "input", "analysis": {"analysis_type": {"t": "rel_ab", + "__current_case__": 0, "tax_lev": {"tax_lev": "a", "__current_case__": 0, + "split_levels": false}}, "min_cu_len": "2000", "min_alignment_len": null, + "organism_profiling": "add_viruses", "stat": "tavg_g", "stat_q": "0.2", "perc_nonzero": + "0.33", "ignore_markers": null, "avoid_disqm": 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unicycler\n owner: iuc\n revisions: 9e3e80cc4ad4\n tool_panel_section_label:\ + \ Assembly\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: staramr\n\ + \ owner: nml\n revisions: da787fc8b740\n tool_panel_section_label: Metagenomic\ + \ Analysis\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: staramr\n\ + \ owner: nml\n revisions: 2fd4d4c9c5c2\n tool_panel_section_label: Metagenomic\ + \ Analysis\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n" + api: https://training.galaxyproject.org/training-material/api/topics/microbiome/tutorials/plasmid-metagenomics-nanopore/tutorial.json + contributors: + - affiliations: + - elixir-europe + elixir_node: nl + id: willemdek11 + joined: 2018-09 + name: Willem de Koning + page: https://training.galaxyproject.org/training-material/hall-of-fame/willemdek11/ + url: https://training.galaxyproject.org/training-material/api/contributors/willemdek11.json + - affiliations: + - uni-freiburg + - nfdi4plants + - elixir-europe + bio: Researcher at Erasmus Medical Center + bluesky: shiltemann.bsky.social + contact_for_training: true + elixir_node: nl + email: saskia.hiltemann@gmail.com + fediverse: https://mstdn.science/@shiltemann + fediverse_flavor: mastodon + former_affiliations: + - CINECA-Project + - gallantries + - erasmusmc + id: shiltemann + joined: 2017-09 + linkedin: shiltemann + location: + country: NL + lat: 51.912 + lon: 4.462 + maintainer_contact: gitter + matrix: shiltemann:matrix.org + name: Saskia Hiltemann + orcid: 0000-0003-3803-468X + page: https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/ + url: https://training.galaxyproject.org/training-material/api/contributors/shiltemann.json + dir: topics/microbiome/tutorials/plasmid-metagenomics-nanopore + edam_ontology: + - topic_3837 + - topic_3305 + - topic_3174 + - topic_3301 + - topic_3324 + - topic_0080 + - topic_4013 + edam_operation: + - Mapping assembly + - Sequence assembly visualisation + - Genome assembly + - Antimicrobial resistance prediction + - Aggregation + - De-novo assembly + - Pairwise sequence alignment + - Scatter plot plotting + - Sequence analysis + - Box-Whisker plot plotting + edam_topic: + - Metagenomic sequencing + - Public health and epidemiology + - Metagenomics + - Microbiology + - Infectious disease + - Sequence analysis + - Antimicrobial resistance + exact_supported_servers: + - UseGalaxy.eu + feedback_mean_note: null + feedback_number: 0 + hands_on: true + id: microbiome/plasmid-metagenomics-nanopore + inexact_supported_servers: + - UseGalaxy.org.au + - UseGalaxy.be + - UseGalaxy.cz + - UseGalaxy.fr + - UseGalaxy.no + - UseGalaxy.org (Main) + js_requirements: + mathjax: null + mermaid: false + key_points: + - Minimap2, Miniasm, and Racon can be used for quickly assembling Nanopore data + - Unicycler can be used to optimize settings of assembly tools + - Nanopore sequencing is useful for reconstruction of genomes + - Antimicrobial resistance genes are detectable after fast assembly + - The CARD database is a useful resource describing antibiotic resistance genes + layout: tutorial_hands_on + license: CC-BY-4.0 + mod_date: '2024-06-14' + objectives: + - Perform Quality control on your reads + - Assemble a genome with Minimap2/Miniasm/Racon + - Determine the structure of the genome(s) + - Scan for antimicrobial resistance genes with Staramr + pageviews: 5886 + pub_date: '2019-06-25' + questions: + - How do I assemble a genome with Nanopore data? + - How do I get more information about the structure of the genomes? + - How do I get more information about the antimicrobial resistance genes? + recordings: + - captioners: + - bebatut + date: '2021-02-15' + galaxy_version: '21.01' + length: 45M + speakers: + - willemdek11 + youtube_id: ECIl8ZU1Wko + redirect_from: + - /topics/metagenomics/tutorials/plasmid-metagenomics-nanopore/tutorial + - /short/microbiome/plasmid-metagenomics-nanopore + - /short/T00209 + - /short/T00394 + short_id: T00394 + short_tools: + - PlasFlow + - bandage_image + - minimap2 + - staramr_search + - unicycler + - racon + - gfa_to_fa + - miniasm + - nanoplot + slides: false + slides_recordings: false + subtopic: metabarcoding + supported_servers: + exact: + - name: UseGalaxy.eu + url: https://usegalaxy.eu + usegalaxy: true + inexact: + - name: UseGalaxy.org.au + url: https://usegalaxy.org.au + usegalaxy: true + - name: UseGalaxy.be + url: https://usegalaxy.be/ + usegalaxy: false + - name: UseGalaxy.cz + url: https://usegalaxy.cz/ + usegalaxy: false + - name: UseGalaxy.fr + url: https://usegalaxy.fr/ + usegalaxy: true + - name: UseGalaxy.no + url: https://usegalaxy.no/ + usegalaxy: false + - name: UseGalaxy.org (Main) + url: https://usegalaxy.org + usegalaxy: true + supported_servers_matrix: + servers: + - name: APOSTL + url: http://apostl.moffitt.org/ + usegalaxy: false + - name: MBAC Metabiome Portal + url: http://mbac.gmu.edu:8080/ + usegalaxy: false + - name: ChemFlow + url: https://vm-chemflow-francegrille.eu/ + usegalaxy: false + - name: CIRM-CFBP + url: https://iris.angers.inra.fr/galaxypub-cfbp + usegalaxy: false + - name: Coloc-stats + url: https://hyperbrowser.uio.no/coloc-stats + usegalaxy: false + - name: Galaxy@AuBi + url: https://galaxy.mesocentre.uca.fr + usegalaxy: false + - name: Galaxy@Pasteur + url: https://galaxy.pasteur.fr/ + usegalaxy: false + - name: GalaxyTrakr + url: https://galaxytrakr.org/ + usegalaxy: false + - name: GASLINI + url: http://igg.cloud.ba.infn.it/galaxy + usegalaxy: false + - name: HyPhy HIV NGS Tools + url: https://galaxy.hyphy.org/ + usegalaxy: false + - name: ImmPort Galaxy + url: https://www.immportgalaxy.org/ + usegalaxy: false + - name: InteractoMIX + url: http://galaxy.interactomix.com/ + usegalaxy: false + - name: IPK Galaxy Blast Suite + url: https://galaxy-web.ipk-gatersleben.de + usegalaxy: false + - name: Mandoiu Lab + url: https://neo.engr.uconn.edu/ + usegalaxy: false + - name: MISSISSIPPI + url: https://mississippi.sorbonne-universite.fr + usegalaxy: false + - name: Oqtans + url: http://galaxy.inf.ethz.ch + usegalaxy: false + - name: Palfinder + url: https://palfinder.ls.manchester.ac.uk/ + usegalaxy: false + - name: PepSimili + url: http://pepsimili.e-nios.com:8080/ + usegalaxy: false + - name: UseGalaxy.org.au + url: https://usegalaxy.org.au + usegalaxy: true + - name: UseGalaxy.be + url: https://usegalaxy.be/ + usegalaxy: false + - name: UseGalaxy.cz + url: https://usegalaxy.cz/ + usegalaxy: false + - name: UseGalaxy.eu + url: https://usegalaxy.eu + usegalaxy: true + - name: UseGalaxy.fr + url: https://usegalaxy.fr/ + usegalaxy: true + - name: UseGalaxy.no + url: https://usegalaxy.no/ + usegalaxy: false + - name: UseGalaxy.org (Main) + url: https://usegalaxy.org + usegalaxy: true + - name: Viral Variant Visualizer (VVV) + url: https://viralvariant.anses.fr/ + usegalaxy: false + tools: + - id: toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.3.1.1 servers: - server: http://apostl.moffitt.org/ state: missing @@ 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- state: local - - server: https://usegalaxy.org - state: local - - server: https://viralvariant.anses.fr/ - state: local - version: local - - id: barchart_gnuplot - servers: - - server: http://apostl.moffitt.org/ - state: local - - server: http://mbac.gmu.edu:8080/ - state: local - - server: https://vm-chemflow-francegrille.eu/ - state: missing - - server: https://iris.angers.inra.fr/galaxypub-cfbp - state: missing - - server: https://hyperbrowser.uio.no/coloc-stats state: missing - - server: https://galaxy.mesocentre.uca.fr - state: local - server: https://galaxy.pasteur.fr/ state: missing - server: https://galaxytrakr.org/ - state: missing + state: inexact + versions: + - 1.5.0+galaxy1 - server: http://igg.cloud.ba.infn.it/galaxy state: missing - server: https://galaxy.hyphy.org/ @@ -55338,8 +47247,6 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: local - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr @@ -55350,26 +47257,36 @@ state: missing - server: http://pepsimili.e-nios.com:8080/ state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - server: https://usegalaxy.org.au - state: local + state: exact + version: 1.4.13 - server: https://usegalaxy.be/ - state: local + state: inexact + versions: + - 1.5.0+galaxy1 + - 1.3.1.1 + - 1.3.1 - server: https://usegalaxy.cz/ - state: local + state: exact + version: 1.4.13 - server: https://usegalaxy.eu - state: local + state: exact + version: 1.4.13 - server: https://usegalaxy.fr/ - state: missing + state: inexact + versions: + - 1.5.0+galaxy1 + - 1.5.0+galaxy0 - server: https://usegalaxy.no/ - state: local + state: exact + version: 1.4.13 - server: https://usegalaxy.org - state: missing + state: exact + version: 1.4.13 - server: https://viralvariant.anses.fr/ state: missing - version: local - - id: param_value_from_file + version: 1.4.13 + - id: 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- state: missing - - server: https://hyperbrowser.uio.no/coloc-stats - state: missing - - server: https://galaxy.mesocentre.uca.fr - state: exact - version: 0.1.0 - - server: https://galaxy.pasteur.fr/ - state: missing - - server: https://galaxytrakr.org/ - state: exact - version: 0.1.0 - server: http://igg.cloud.ba.infn.it/galaxy state: missing - server: https://galaxy.hyphy.org/ @@ -55458,44 +47320,52 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr - state: missing + state: inexact + versions: + - 2022.09+galaxy4 + - 0.8.1+galaxy3 - server: http://galaxy.inf.ethz.ch state: missing - server: https://palfinder.ls.manchester.ac.uk/ state: missing - server: http://pepsimili.e-nios.com:8080/ state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - server: 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servers: - server: http://apostl.moffitt.org/ state: missing @@ -55508,16 +47378,17 @@ - server: https://hyperbrowser.uio.no/coloc-stats state: missing - server: https://galaxy.mesocentre.uca.fr - state: exact - version: 2.9+galaxy0 - - server: https://galaxy.pasteur.fr/ state: inexact versions: - - 2.9.4+galaxy0 - - server: https://galaxytrakr.org/ + - 0.8.1+galaxy0+galaxy0 + - 2022.09+galaxy4 + - 0.8.1+galaxy4 + - server: https://galaxy.pasteur.fr/ state: inexact versions: - - 2.9.5+galaxy1 + - 0.8.1+galaxy3 + - server: https://galaxytrakr.org/ + state: missing - server: http://igg.cloud.ba.infn.it/galaxy state: missing - server: https://galaxy.hyphy.org/ @@ -55528,45 +47399,45 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr - state: missing + state: inexact + versions: + - 2022.09+galaxy4 + - 0.8.1+galaxy3 - server: http://galaxy.inf.ethz.ch state: missing - server: https://palfinder.ls.manchester.ac.uk/ state: missing - server: http://pepsimili.e-nios.com:8080/ state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - server: https://usegalaxy.org.au state: exact - version: 2.9+galaxy0 + version: 0.8.1+galaxy2 - server: https://usegalaxy.be/ state: exact - version: 2.9+galaxy0 + version: 0.8.1+galaxy2 - server: https://usegalaxy.cz/ - state: exact - version: 2.9+galaxy0 + state: inexact + versions: + - 2022.09+galaxy4 - server: https://usegalaxy.eu state: exact - version: 2.9+galaxy0 + version: 0.8.1+galaxy2 - server: https://usegalaxy.fr/ state: exact - version: 2.9+galaxy0 + version: 0.8.1+galaxy2 - server: https://usegalaxy.no/ state: exact - version: 2.9+galaxy0 + version: 0.8.1+galaxy2 - server: https://usegalaxy.org state: exact - version: 2.9+galaxy0 + version: 0.8.1+galaxy2 - server: https://viralvariant.anses.fr/ state: missing - version: 2.9+galaxy0 - - id: toolshed.g2.bx.psu.edu/repos/bgruening/flye/flye/2.9.1+galaxy0 + version: 0.8.1+galaxy2 + - id: toolshed.g2.bx.psu.edu/repos/iuc/gfa_to_fa/gfa_to_fa/0.1.0 servers: - server: http://apostl.moffitt.org/ state: missing @@ -55579,16 +47450,11 @@ - server: https://hyperbrowser.uio.no/coloc-stats state: missing - server: https://galaxy.mesocentre.uca.fr - state: exact - version: 2.9.1+galaxy0 + state: missing - server: https://galaxy.pasteur.fr/ - state: inexact - versions: - - 2.9.4+galaxy0 + state: missing - server: https://galaxytrakr.org/ - state: inexact - versions: - - 2.9.5+galaxy1 + state: missing - server: http://igg.cloud.ba.infn.it/galaxy state: missing - server: https://galaxy.hyphy.org/ @@ -55599,8 +47465,6 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr @@ -55611,39 +47475,39 @@ state: missing - server: http://pepsimili.e-nios.com:8080/ state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - server: https://usegalaxy.org.au - state: exact - version: 2.9.1+galaxy0 + state: inexact + versions: + - 0.1.1 + - 0.1.2 - server: https://usegalaxy.be/ state: exact - version: 2.9.1+galaxy0 + version: 0.1.0 - server: https://usegalaxy.cz/ - state: exact - version: 2.9.1+galaxy0 + state: inexact + versions: + - 0.1.2 - server: https://usegalaxy.eu state: exact - version: 2.9.1+galaxy0 + version: 0.1.0 - server: https://usegalaxy.fr/ - state: exact - version: 2.9.1+galaxy0 + state: inexact + versions: + - 0.1.2 - server: https://usegalaxy.no/ state: inexact versions: - - 2.9+galaxy0 - - 2.9.6+galaxy0 - - 2.9.3+galaxy0 - - 2.8.3+galaxy0 - - '2.6' - - 2.6+galaxy0 + - 0.1.1 + - 0.1.2 - server: https://usegalaxy.org - state: exact - version: 2.9.1+galaxy0 + state: inexact + versions: + - 0.1.1 + - 0.1.2 - server: https://viralvariant.anses.fr/ state: missing - version: 2.9.1+galaxy0 - - id: toolshed.g2.bx.psu.edu/repos/bgruening/split_file_on_column/tp_split_on_column/0.6 + version: 0.1.0 + - id: toolshed.g2.bx.psu.edu/repos/iuc/gfa_to_fa/gfa_to_fa/0.1.1 servers: - server: http://apostl.moffitt.org/ state: missing @@ -55671,8 +47535,6 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr @@ -55683,33 +47545,33 @@ state: missing - server: http://pepsimili.e-nios.com:8080/ state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - server: https://usegalaxy.org.au state: exact - version: '0.6' + version: 0.1.1 - server: https://usegalaxy.be/ state: exact - version: '0.6' + version: 0.1.1 - server: https://usegalaxy.cz/ - state: exact - version: '0.6' + state: inexact + versions: + - 0.1.2 - server: https://usegalaxy.eu state: exact - version: '0.6' + version: 0.1.1 - server: https://usegalaxy.fr/ - state: exact - version: '0.6' + state: inexact + versions: + - 0.1.2 - server: https://usegalaxy.no/ state: exact - version: '0.6' + version: 0.1.1 - server: https://usegalaxy.org state: exact - version: '0.6' + version: 0.1.1 - server: https://viralvariant.anses.fr/ state: missing - version: '0.6' - - id: toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.0 + version: 0.1.1 + - id: toolshed.g2.bx.psu.edu/repos/iuc/miniasm/miniasm/0.2+galaxy0 servers: - server: http://apostl.moffitt.org/ state: missing @@ -55722,13 +47584,15 @@ - server: https://hyperbrowser.uio.no/coloc-stats state: missing - server: https://galaxy.mesocentre.uca.fr - state: missing + state: inexact + versions: + - 0.3_r179+galaxy1 - server: https://galaxy.pasteur.fr/ state: missing - server: https://galaxytrakr.org/ state: inexact versions: - - 0.5.2 + - 0.3_r179+galaxy1 - server: http://igg.cloud.ba.infn.it/galaxy state: missing - server: https://galaxy.hyphy.org/ @@ -55739,47 +47603,47 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr - state: inexact - versions: - - 0.5.2 + state: missing - server: http://galaxy.inf.ethz.ch state: missing - server: https://palfinder.ls.manchester.ac.uk/ state: missing - server: http://pepsimili.e-nios.com:8080/ state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - server: https://usegalaxy.org.au state: exact - version: 0.5.0 + version: 0.2+galaxy0 - server: https://usegalaxy.be/ state: exact - version: 0.5.0 + version: 0.2+galaxy0 - server: https://usegalaxy.cz/ - state: exact - version: 0.5.0 + state: inexact + versions: + - 0.3_r179+galaxy1 - server: https://usegalaxy.eu state: exact - version: 0.5.0 + version: 0.2+galaxy0 - server: https://usegalaxy.fr/ - state: exact - version: 0.5.0 + state: inexact + versions: + - 0.3_r179+galaxy1 - server: https://usegalaxy.no/ - state: exact - version: 0.5.0 + state: inexact + versions: + - 0.3_r179+galaxy1 + - 0.3+galaxy1 + - 0.3+galaxy0 + - 0.3_r179+galaxy0 - server: https://usegalaxy.org state: exact - version: 0.5.0 + version: 0.2+galaxy0 - server: https://viralvariant.anses.fr/ state: missing - version: 0.5.0 - - id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/9.3+galaxy1 + version: 0.2+galaxy0 + - id: toolshed.g2.bx.psu.edu/repos/iuc/miniasm/miniasm/0.3+galaxy0 servers: - server: http://apostl.moffitt.org/ state: missing @@ -55794,74 +47658,60 @@ - server: https://galaxy.mesocentre.uca.fr state: inexact versions: - - 9.5+galaxy3 - - 1.1.0 + - 0.3_r179+galaxy1 - server: https://galaxy.pasteur.fr/ state: missing - server: https://galaxytrakr.org/ state: inexact versions: - - 9.5+galaxy3 - - 1.1.0 - - 9.5+galaxy2 + - 0.3_r179+galaxy1 - server: http://igg.cloud.ba.infn.it/galaxy state: missing - server: https://galaxy.hyphy.org/ - state: inexact - versions: - - 9.5+galaxy3 + state: missing - server: https://www.immportgalaxy.org/ state: missing - server: http://galaxy.interactomix.com/ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr - state: inexact - versions: - - 9.5+galaxy3 + state: missing - server: http://galaxy.inf.ethz.ch state: missing - server: https://palfinder.ls.manchester.ac.uk/ state: missing - server: http://pepsimili.e-nios.com:8080/ state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - server: https://usegalaxy.org.au state: exact - version: 9.3+galaxy1 + version: 0.3+galaxy0 - server: https://usegalaxy.be/ state: exact - version: 9.3+galaxy1 + version: 0.3+galaxy0 - server: https://usegalaxy.cz/ state: inexact versions: - - 9.5+galaxy3 - - 1.1.0 - - 9.5+galaxy2 - - 9.5+galaxy0 + - 0.3_r179+galaxy1 - server: https://usegalaxy.eu state: exact - version: 9.3+galaxy1 + version: 0.3+galaxy0 - server: https://usegalaxy.fr/ - state: exact - version: 9.3+galaxy1 - - server: https://usegalaxy.no/ state: inexact versions: - - 1.1.0 + - 0.3_r179+galaxy1 + - server: https://usegalaxy.no/ + state: exact + version: 0.3+galaxy0 - server: https://usegalaxy.org state: exact - version: 9.3+galaxy1 + version: 0.3+galaxy0 - server: https://viralvariant.anses.fr/ state: missing - version: 9.3+galaxy1 - - id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.4 + version: 0.3+galaxy0 + - id: toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.17 servers: - server: http://apostl.moffitt.org/ state: missing @@ -55874,72 +47724,93 @@ - server: https://hyperbrowser.uio.no/coloc-stats state: missing - server: https://galaxy.mesocentre.uca.fr - state: exact - version: 1.1.4 + state: inexact + versions: + - 2.28+galaxy1 + - 2.24+galaxy0 + - 2.28+galaxy2 + - 2.28+galaxy0 - server: https://galaxy.pasteur.fr/ state: missing - server: https://galaxytrakr.org/ state: inexact versions: - - 9.5+galaxy3 - - 1.1.3 - - 9.5+galaxy2 + - 2.28+galaxy2 + - 2.31+galaxy1 - server: http://igg.cloud.ba.infn.it/galaxy state: missing - server: https://galaxy.hyphy.org/ state: inexact versions: - - 9.5+galaxy3 + - 2.28+galaxy2 - server: https://www.immportgalaxy.org/ state: missing - server: http://galaxy.interactomix.com/ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr state: inexact versions: - - 9.5+galaxy3 + - 2.30+galaxy0 - server: http://galaxy.inf.ethz.ch state: missing - server: https://palfinder.ls.manchester.ac.uk/ state: missing - server: http://pepsimili.e-nios.com:8080/ state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - server: https://usegalaxy.org.au state: exact - version: 1.1.4 + version: '2.17' - server: https://usegalaxy.be/ state: exact - version: 1.1.4 + version: '2.17' - server: https://usegalaxy.cz/ - state: exact - version: 1.1.4 + state: inexact + versions: + - 2.28+galaxy1 + - 2.28+galaxy2 + - 2.28+galaxy0 + - 2.31+galaxy1 + - 2.30+galaxy0 + - 2.17+galaxy2 + - 2.26+galaxy0 + - 2.31+galaxy0 - server: https://usegalaxy.eu state: exact - version: 1.1.4 + version: '2.17' - server: https://usegalaxy.fr/ - state: exact - version: 1.1.4 + state: inexact + versions: + - 2.28+galaxy1 + - 2.24+galaxy0 + - 2.28+galaxy2 + - 2.28+galaxy0 + - 2.31+galaxy1 + - 2.30+galaxy0 + - 2.17+galaxy2 + - 2.26+galaxy0 + - 2.22+galaxy0 + - 2.23+galaxy0 + - 2.31+galaxy0 + - '2.12' + - 2.27+galaxy0 - server: https://usegalaxy.no/ state: inexact versions: - - 1.1.3 - - 1.1.1 - - 1.1.0 + - 2.24+galaxy0 + - 2.17+galaxy0 - server: https://usegalaxy.org state: exact - version: 1.1.4 + version: '2.17' - server: https://viralvariant.anses.fr/ - state: missing - version: 1.1.4 - - id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_head_tool/9.3+galaxy1 + state: inexact + versions: + - 2.28+galaxy2 + version: '2.17' + - id: toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.17+galaxy2 servers: - server: http://apostl.moffitt.org/ state: missing @@ -55954,74 +47825,85 @@ - server: https://galaxy.mesocentre.uca.fr state: inexact versions: - - 9.5+galaxy3 - - 1.1.0 + - 2.28+galaxy1 + - 2.24+galaxy0 + - 2.28+galaxy2 + - 2.28+galaxy0 - server: https://galaxy.pasteur.fr/ state: missing - server: https://galaxytrakr.org/ state: inexact versions: - - 9.5+galaxy3 - - 1.1.0 - - 9.5+galaxy2 + - 2.28+galaxy2 + - 2.31+galaxy1 - server: http://igg.cloud.ba.infn.it/galaxy state: missing - server: https://galaxy.hyphy.org/ state: inexact versions: - - 9.5+galaxy3 + - 2.28+galaxy2 - server: https://www.immportgalaxy.org/ state: missing - server: http://galaxy.interactomix.com/ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr state: inexact versions: - - 9.5+galaxy3 + - 2.30+galaxy0 - server: http://galaxy.inf.ethz.ch state: missing - server: https://palfinder.ls.manchester.ac.uk/ state: missing - server: http://pepsimili.e-nios.com:8080/ state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - server: https://usegalaxy.org.au state: exact - version: 9.3+galaxy1 + version: 2.17+galaxy2 - server: https://usegalaxy.be/ - state: exact - version: 9.3+galaxy1 - - server: https://usegalaxy.cz/ state: inexact versions: - - 9.5+galaxy3 - - 1.1.0 - - 9.5+galaxy2 - - 9.5+galaxy0 + - 2.28+galaxy1 + - 2.24+galaxy0 + - 2.28+galaxy2 + - 2.28+galaxy0 + - 2.31+galaxy1 + - 2.30+galaxy0 + - 2.17+galaxy0 + - '2.17' + - 2.26+galaxy0 + - 2.17+galaxy1 + - '2.5' + - '2.3' + - 2.31+galaxy0 + - 2.5+gx1 + - '2.12' + - server: https://usegalaxy.cz/ + state: exact + version: 2.17+galaxy2 - server: https://usegalaxy.eu state: exact - version: 9.3+galaxy1 + version: 2.17+galaxy2 - server: https://usegalaxy.fr/ state: exact - version: 9.3+galaxy1 + version: 2.17+galaxy2 - server: https://usegalaxy.no/ state: inexact versions: - - 1.1.0 + - 2.24+galaxy0 + - 2.17+galaxy0 - server: https://usegalaxy.org state: exact - version: 9.3+galaxy1 + version: 2.17+galaxy2 - server: https://viralvariant.anses.fr/ - state: missing - version: 9.3+galaxy1 - - id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_multijoin_tool/9.3+galaxy1 + state: inexact + versions: + - 2.28+galaxy2 + version: 2.17+galaxy2 + - id: toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.25.0+galaxy1 servers: - server: http://apostl.moffitt.org/ state: missing @@ -56036,76 +47918,88 @@ - server: https://galaxy.mesocentre.uca.fr state: inexact versions: - - 9.5+galaxy3 - - 1.1.1 + - 1.28.2+galaxy1 + - 1.42.0+galaxy1 + - 1.44.1+galaxy0 + - 1.36.2+galaxy1 + - 1.42.0+galaxy0 + - 1.46.2+galaxy0 + - 1.43.0+galaxy0 + - 1.46.1+galaxy0 + - 1.41.0+galaxy0 - server: https://galaxy.pasteur.fr/ - state: missing + state: inexact + versions: + - 1.43.0+galaxy0 - server: https://galaxytrakr.org/ state: inexact versions: - - 9.5+galaxy3 - - 1.1.1 - - 9.5+galaxy2 + - 1.28.2+galaxy1 - server: http://igg.cloud.ba.infn.it/galaxy state: missing - server: https://galaxy.hyphy.org/ - state: inexact - versions: - - 9.5+galaxy3 + state: missing - server: https://www.immportgalaxy.org/ state: missing - server: http://galaxy.interactomix.com/ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr state: inexact versions: - - 9.5+galaxy3 + - 1.46.2+galaxy0 - server: http://galaxy.inf.ethz.ch state: missing - server: https://palfinder.ls.manchester.ac.uk/ state: missing - server: http://pepsimili.e-nios.com:8080/ state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - server: https://usegalaxy.org.au state: exact - version: 9.3+galaxy1 + version: 1.25.0+galaxy1 - server: https://usegalaxy.be/ state: exact - version: 9.3+galaxy1 + version: 1.25.0+galaxy1 - server: https://usegalaxy.cz/ state: inexact versions: - - 9.5+galaxy3 - - 1.1.1 - - 9.5+galaxy2 - - 9.5+galaxy0 - - 1.1.0 + - 1.42.0+galaxy1 + - 1.44.1+galaxy0 + - 1.46.2+galaxy0 + - 1.46.1+galaxy0 + - 1.41.0+galaxy0 + - 1.47.0+galaxy0 + - 1.47.1+galaxy0 - server: https://usegalaxy.eu state: exact - version: 9.3+galaxy1 + version: 1.25.0+galaxy1 - server: https://usegalaxy.fr/ - state: exact - version: 9.3+galaxy1 - - server: https://usegalaxy.no/ state: inexact versions: - - 1.1.1 - - 1.1.0 + - 1.28.2+galaxy1 + - 1.42.0+galaxy1 + - 1.44.1+galaxy0 + - 1.36.2+galaxy1 + - 1.42.0+galaxy0 + - 1.46.2+galaxy0 + - 1.43.0+galaxy0 + - 1.46.1+galaxy0 + - 1.41.0+galaxy0 + - 1.47.0+galaxy0 + - 1.47.1+galaxy0 + - server: https://usegalaxy.no/ + state: exact + version: 1.25.0+galaxy1 - server: https://usegalaxy.org state: exact - version: 9.3+galaxy1 + version: 1.25.0+galaxy1 - server: https://viralvariant.anses.fr/ state: missing - version: 9.3+galaxy1 - - id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/9.3+galaxy1 + version: 1.25.0+galaxy1 + - id: toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.28.2+galaxy1 servers: - server: http://apostl.moffitt.org/ state: missing @@ -56118,80 +48012,69 @@ - server: https://hyperbrowser.uio.no/coloc-stats state: missing - server: https://galaxy.mesocentre.uca.fr - state: inexact - versions: - - 1.1.3 - - 9.5+galaxy3 + state: exact + version: 1.28.2+galaxy1 - server: https://galaxy.pasteur.fr/ - state: missing - - 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0.10.0+galaxy1 + - 0.10.0+galaxy0 + - 0.9.1+galaxy0 + - 0.12.3+galaxy0 + - 0.12.2+galaxy0 - server: https://usegalaxy.no/ state: exact - version: 1.1.1 + version: 0.7.1+galaxy2 - server: https://usegalaxy.org state: exact - version: 1.1.1 + version: 0.7.1+galaxy2 - server: https://viralvariant.anses.fr/ state: missing - version: 1.1.1 - - id: toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.73+galaxy0 + version: 0.7.1+galaxy2 + symlink: null + tags: + - nanopore + - plasmids + - assembly + - amr + - microgalaxy + time_estimation: 3h + title: Antibiotic resistance detection + tools: + - toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.3.1.1 + - toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.4.13 + - toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/0.8.1+galaxy0 + - toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/0.8.1+galaxy2 + - toolshed.g2.bx.psu.edu/repos/iuc/gfa_to_fa/gfa_to_fa/0.1.0 + - toolshed.g2.bx.psu.edu/repos/iuc/gfa_to_fa/gfa_to_fa/0.1.1 + - toolshed.g2.bx.psu.edu/repos/iuc/miniasm/miniasm/0.2+galaxy0 + - toolshed.g2.bx.psu.edu/repos/iuc/miniasm/miniasm/0.3+galaxy0 + - toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.17 + - toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.17+galaxy2 + - toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.25.0+galaxy1 + - toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.28.2+galaxy1 + - toolshed.g2.bx.psu.edu/repos/iuc/plasflow/PlasFlow/1.0 + - toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.4.7.0 + - toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.4.8.0 + - toolshed.g2.bx.psu.edu/repos/nml/staramr/staramr_search/0.5.1 + - toolshed.g2.bx.psu.edu/repos/nml/staramr/staramr_search/0.7.1+galaxy2 + topic_name: microbiome + topic_name_human: Microbiome + tours: false + translations: + slides: [] + tutorial: [] + video: false + tutorial_name: plasmid-metagenomics-nanopore + type: tutorial + url: https://training.galaxyproject.org//topics/microbiome/tutorials/plasmid-metagenomics-nanopore/tutorial.html + urls: + hands_on: https://training.galaxyproject.org/training-material/api/topics/microbiome/tutorials/plasmid-metagenomics-nanopore/tutorial.json + slides: https://training.galaxyproject.org/training-material/api/topics/microbiome/tutorials/plasmid-metagenomics-nanopore/tutorial.json + version: 4 + video: true + video_versions: 1 + video_view: 0 + visit_duration: 414 + visitors: 4331 + workflows: + - creators: [] + description: Antibiotic resistance detection + features: + comments: false + parameters: false + report: null + subworkflows: false + graph_dot: "digraph main {\n node [fontname=\"Atkinson Hyperlegible\", shape=box,\ + \ color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n edge [fontname=\"\ + Atkinson Hyperlegible\"];\n 0[color=lightblue,label=\"\u2139\uFE0F Input Collection\\\ + nPlasmids\"]\n 1[label=\"NanoPlot\"]\n 0 -> 1 [label=\"output\"]\n 10[label=\"\ + NanoPlot\"]\n 9 -> 10 [label=\"out_fa\"]\n 11[label=\"Map with minimap2\"\ + ]\n 0 -> 11 [label=\"output\"]\n 9 -> 11 [label=\"out_fa\"]\n 12[label=\"\ + Racon\"]\n 9 -> 12 [label=\"out_fa\"]\n 11 -> 12 [label=\"alignment_output\"\ + ]\n 0 -> 12 [label=\"output\"]\n 2[label=\"Map with minimap2\"]\n 0 -> 2\ + \ [label=\"output\"]\n 0 -> 2 [label=\"output\"]\n 3[label=\"Create assemblies\ + \ with Unicycler\"]\n 0 -> 3 [label=\"output\"]\n 4[label=\"miniasm\"]\n \ + \ 2 -> 4 [label=\"alignment_output\"]\n 0 -> 4 [label=\"output\"]\n 5[label=\"\ + Bandage Image\"]\n 3 -> 5 [label=\"assembly_graph\"]\n 6[label=\"PlasFlow\"\ + ]\n 3 -> 6 [label=\"assembly\"]\n 7[label=\"staramr\"]\n 3 -> 7 [label=\"\ + assembly\"]\n 8[label=\"Bandage Image\"]\n 4 -> 8 [label=\"gfa\"]\n 9[label=\"\ + GFA to FASTA\"]\n 4 -> 9 [label=\"gfa\"]\n}" + history: + - hash: 0e0a2f2ccb650b0aab1ffc13838045164bdb5d30 + message: Rename metagenomics topic to microbiome + num: 1 + short_hash: 0e0a2f2cc + unix: '1704901629' + inputs: + - annotation: '' + content_id: null + errors: null + id: 0 + input_connections: {} + inputs: [] + label: Plasmids + name: Input dataset collection + outputs: [] + position: + left: 173 + top: 696 + tool_id: null + tool_state: '{"collection_type": "list"}' + tool_version: null + type: data_collection_input + uuid: 348dcd93-2d40-4bdd-90f4-b321a1bd901d + workflow_outputs: [] + license: null + mermaid: "flowchart TD\n 0[\"\u2139\uFE0F Input Collection\\nPlasmids\"];\n \ + \ style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"NanoPlot\"];\n 0 -->|output|\ + \ 1;\n 10[\"NanoPlot\"];\n 9 -->|out_fa| 10;\n 11[\"Map with minimap2\"];\n\ + \ 0 -->|output| 11;\n 9 -->|out_fa| 11;\n 12[\"Racon\"];\n 9 -->|out_fa|\ + \ 12;\n 11 -->|alignment_output| 12;\n 0 -->|output| 12;\n 2[\"Map with minimap2\"\ + ];\n 0 -->|output| 2;\n 0 -->|output| 2;\n 3[\"Create assemblies with Unicycler\"\ + ];\n 0 -->|output| 3;\n 4[\"miniasm\"];\n 2 -->|alignment_output| 4;\n 0\ + \ -->|output| 4;\n 5[\"Bandage Image\"];\n 3 -->|assembly_graph| 5;\n 6[\"\ + PlasFlow\"];\n 3 -->|assembly| 6;\n 7[\"staramr\"];\n 3 -->|assembly| 7;\n\ + \ 8[\"Bandage Image\"];\n 4 -->|gfa| 8;\n 9[\"GFA to FASTA\"];\n 4 -->|gfa|\ + \ 9;" + modified: 2026-07-01 00:31:39 +0000 + name: Copy Of GTN Training - Antibiotic Resistance Detection + outputs: [] + parent_id: microbiome/plasmid-metagenomics-nanopore + path: topics/microbiome/tutorials/plasmid-metagenomics-nanopore/workflows/Workflow-plasmid-metagenomics-nanopore.ga + tags: + - microbiome + test_results: null + tests: false + title: Copy Of GTN Training - Antibiotic Resistance Detection + topic_id: microbiome + trs_endpoint: https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/microbiome-plasmid-metagenomics-nanopore/versions/workflow-plasmid-metagenomics-nanopore + tutorial_id: plasmid-metagenomics-nanopore + url: 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tool_panel_section_label: Metagenomic\ + \ Analysis\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fastqc\n\ + \ owner: devteam\n revisions: e7b2202befea\n tool_panel_section_label: FASTA/FASTQ\n\ + \ tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: datamash_reverse\n\ + \ owner: iuc\n revisions: 0f1724dd59d2\n tool_panel_section_label: Join, Subtract\ + \ and Group\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fastp\n\ + \ owner: iuc\n revisions: dbf9c561ef29\n tool_panel_section_label: FASTA/FASTQ\n\ + \ tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: kraken2\n owner: iuc\n\ + \ revisions: 328c607150ff\n tool_panel_section_label: Metagenomic Analysis\n\ + \ tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: multiqc\n owner: iuc\n\ + \ revisions: 5e33b465d8d5\n tool_panel_section_label: Quality Control\n tool_shed_url:\ + \ https://toolshed.g2.bx.psu.edu/\n- name: porechop\n owner: iuc\n revisions:\ + \ 93d623d9979c\n tool_panel_section_label: Nanopore\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n" + api: https://training.galaxyproject.org/training-material/api/topics/microbiome/tutorials/nanopore-16S-metagenomics/tutorial.json + contributors: + - elixir_node: de + former_affiliations: + - uni-freiburg + - elixir-europe + id: gallardoalba + joined: 2020-11 + name: "Crist\xF3bal Gallardo" + orcid: 0000-0002-5752-2155 + page: https://training.galaxyproject.org/training-material/hall-of-fame/gallardoalba/ + url: https://training.galaxyproject.org/training-material/api/contributors/gallardoalba.json + dir: topics/microbiome/tutorials/nanopore-16S-metagenomics + edam_ontology: + - topic_3697 + - topic_0637 + - topic_0080 + - topic_4038 + edam_operation: + - Sequencing quality control + - Statistical calculation + - Taxonomic classification + - Sequence contamination filtering + - Visualisation + - Validation + - Sequence composition calculation + edam_topic: + - Microbial ecology + - Taxonomy + - Sequence analysis + - Metabarcoding + exact_supported_servers: + - UseGalaxy.org.au + - UseGalaxy.be + - UseGalaxy.eu + - UseGalaxy.no + - UseGalaxy.org (Main) + feedback_mean_note: null + feedback_number: 0 + hands_on: true + id: microbiome/nanopore-16S-metagenomics + inexact_supported_servers: + - GalaxyTrakr + - UseGalaxy.cz + - UseGalaxy.fr + js_requirements: + mathjax: null + mermaid: false + key_points: + - We learned to use MinION Nanopore data for analyzing the health status of the + soil + - We preprocessed Nanopore sequences in order to improve their quality + layout: tutorial_hands_on + license: CC-BY-4.0 + mod_date: '2024-07-31' + objectives: + - Use Nanopore data for studying soil metagenomics + - Analyze and preprocess Nanopore reads + - Use Kraken2 to assign a taxonomic labels + pageviews: 14282 + pub_date: '2020-11-24' + questions: + - How can we analyse the health status of the soil? + - How do plants modify the composition of microbial communities? + redirect_from: + 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1.0.1+galaxy0 - server: http://igg.cloud.ba.infn.it/galaxy state: missing - server: https://galaxy.hyphy.org/ @@ -56967,46 +49240,46 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr - state: exact - version: 1.0.3 + state: inexact + versions: + - 1.3.3+galaxy0 - server: http://galaxy.inf.ethz.ch state: missing - server: https://palfinder.ls.manchester.ac.uk/ state: missing - server: http://pepsimili.e-nios.com:8080/ state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - server: https://usegalaxy.org.au state: exact - version: 1.0.3 + version: 0.20.1+galaxy0 - server: https://usegalaxy.be/ state: exact - version: 1.0.3 + version: 0.20.1+galaxy0 - server: https://usegalaxy.cz/ state: exact - version: 1.0.3 + version: 0.20.1+galaxy0 - server: https://usegalaxy.eu state: exact - version: 1.0.3 + version: 0.20.1+galaxy0 - server: https://usegalaxy.fr/ state: exact - version: 1.0.3 + version: 0.20.1+galaxy0 - server: https://usegalaxy.no/ state: exact - version: 1.0.3 + version: 0.20.1+galaxy0 - server: https://usegalaxy.org state: exact - version: 1.0.3 + version: 0.20.1+galaxy0 - server: https://viralvariant.anses.fr/ - state: missing - version: 1.0.3 - - id: toolshed.g2.bx.psu.edu/repos/iuc/abricate/abricate/1.0.1 + state: inexact + versions: + - 0.23.2+galaxy0 + - 1.0.1+galaxy2 + version: 0.20.1+galaxy0 + - id: toolshed.g2.bx.psu.edu/repos/iuc/kraken2/kraken2/2.0.8_beta+galaxy0 servers: - server: http://apostl.moffitt.org/ state: missing @@ -57019,13 +49292,17 @@ - server: https://hyperbrowser.uio.no/coloc-stats state: missing - server: https://galaxy.mesocentre.uca.fr - state: exact - version: 1.0.1 + state: inexact + versions: + - 2.1.3+galaxy1 + - 2.1.1+galaxy0 + - 2.1.1+galaxy1 + - 2.1.3+galaxy2 - server: https://galaxy.pasteur.fr/ state: missing - server: https://galaxytrakr.org/ state: exact - version: 1.0.1 + version: 2.0.8_beta+galaxy0 - server: http://igg.cloud.ba.infn.it/galaxy state: missing - server: https://galaxy.hyphy.org/ @@ -57036,8 +49313,6 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr @@ -57047,34 +49322,42 @@ - server: https://palfinder.ls.manchester.ac.uk/ state: missing - server: http://pepsimili.e-nios.com:8080/ - state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing + state: inexact + versions: + - 2.1.1+galaxy1 - server: https://usegalaxy.org.au state: exact - version: 1.0.1 + version: 2.0.8_beta+galaxy0 - server: https://usegalaxy.be/ state: exact - version: 1.0.1 + version: 2.0.8_beta+galaxy0 - server: https://usegalaxy.cz/ - state: exact - version: 1.0.1 + state: inexact + versions: + - 2.1.3+galaxy1 + - 2.1.1+galaxy1 + - 2.1.3+galaxy2 + - 2.17.1+galaxy0 - server: https://usegalaxy.eu state: exact - version: 1.0.1 + version: 2.0.8_beta+galaxy0 - server: https://usegalaxy.fr/ - state: exact - version: 1.0.1 + state: inexact + versions: + - 2.1.3+galaxy1 + - 2.1.1+galaxy1 + - 2.1.3+galaxy2 + - 2.17.1+galaxy0 - server: https://usegalaxy.no/ state: exact - version: 1.0.1 + version: 2.0.8_beta+galaxy0 - server: https://usegalaxy.org state: exact - version: 1.0.1 + version: 2.0.8_beta+galaxy0 - server: https://viralvariant.anses.fr/ state: missing - version: 1.0.1 - - id: toolshed.g2.bx.psu.edu/repos/iuc/bamtools_split_mapped/bamtools_split_mapped/2.5.2+galaxy2 + version: 2.0.8_beta+galaxy0 + - id: toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.8+galaxy1 servers: - server: http://apostl.moffitt.org/ state: missing @@ -57087,11 +49370,26 @@ - server: https://hyperbrowser.uio.no/coloc-stats state: missing - server: https://galaxy.mesocentre.uca.fr - state: missing + state: inexact + versions: + - 1.27+galaxy3 + - 1.27+galaxy4 + - 1.11+galaxy1 + - 1.24.1+galaxy0 + - 1.33+galaxy0 + - '1.6' + - 1.11+galaxy0 + - '1.7' - server: https://galaxy.pasteur.fr/ state: missing - server: https://galaxytrakr.org/ - state: missing + state: inexact + versions: + - 1.27+galaxy4 + - 1.11+galaxy1 + - '1.7' + - 1.35+galaxy1 + - 1.33+galaxy3 - server: http://igg.cloud.ba.infn.it/galaxy state: missing - server: https://galaxy.hyphy.org/ @@ -57102,44 +49400,43 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr - state: missing + state: inexact + versions: + - 1.34+galaxy0 - server: http://galaxy.inf.ethz.ch state: missing - server: https://palfinder.ls.manchester.ac.uk/ state: missing - server: http://pepsimili.e-nios.com:8080/ state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - server: https://usegalaxy.org.au state: exact - version: 2.5.2+galaxy2 + version: 1.8+galaxy1 - server: https://usegalaxy.be/ state: exact - version: 2.5.2+galaxy2 + version: 1.8+galaxy1 - server: https://usegalaxy.cz/ state: exact - version: 2.5.2+galaxy2 + version: 1.8+galaxy1 - server: https://usegalaxy.eu state: exact - version: 2.5.2+galaxy2 + version: 1.8+galaxy1 - server: https://usegalaxy.fr/ state: exact - version: 2.5.2+galaxy2 + version: 1.8+galaxy1 - server: https://usegalaxy.no/ - state: missing + state: exact + version: 1.8+galaxy1 - server: https://usegalaxy.org state: exact - version: 2.5.2+galaxy2 + version: 1.8+galaxy1 - server: https://viralvariant.anses.fr/ state: missing - version: 2.5.2+galaxy2 - - id: toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/0.8.1+galaxy2 + version: 1.8+galaxy1 + - id: toolshed.g2.bx.psu.edu/repos/iuc/porechop/porechop/0.2.3 servers: - server: http://apostl.moffitt.org/ state: missing @@ -57152,17 +49449,16 @@ - server: https://hyperbrowser.uio.no/coloc-stats state: missing - server: https://galaxy.mesocentre.uca.fr - state: inexact - versions: - - 0.8.1+galaxy4 - - 0.8.1+galaxy0+galaxy0 - - 2022.09+galaxy4 + state: missing - server: https://galaxy.pasteur.fr/ state: inexact versions: - - 0.8.1+galaxy3 + - 0.2.4+galaxy0 - server: https://galaxytrakr.org/ - state: missing + state: inexact + versions: + - 0.2.4+galaxy0 + - 0.2.4+galaxy1 - server: http://igg.cloud.ba.infn.it/galaxy state: missing - server: https://galaxy.hyphy.org/ @@ -57173,119 +49469,688 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr - state: inexact - versions: - - 2022.09+galaxy4 - - 0.8.1+galaxy3 + state: missing - server: http://galaxy.inf.ethz.ch state: missing - server: https://palfinder.ls.manchester.ac.uk/ state: missing - server: http://pepsimili.e-nios.com:8080/ state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - server: https://usegalaxy.org.au state: exact - version: 0.8.1+galaxy2 + version: 0.2.3 - server: https://usegalaxy.be/ state: exact - version: 0.8.1+galaxy2 + version: 0.2.3 - server: https://usegalaxy.cz/ state: inexact versions: - - 2022.09+galaxy4 + - 0.2.4+galaxy0 + - 0.2.4+galaxy1 - server: https://usegalaxy.eu state: exact - version: 0.8.1+galaxy2 + version: 0.2.3 - server: https://usegalaxy.fr/ - state: exact - version: 0.8.1+galaxy2 + state: inexact + versions: + - 0.2.4+galaxy1 - server: https://usegalaxy.no/ state: exact - version: 0.8.1+galaxy2 + version: 0.2.3 - server: https://usegalaxy.org state: exact - version: 0.8.1+galaxy2 + version: 0.2.3 - server: https://viralvariant.anses.fr/ state: missing - version: 0.8.1+galaxy2 - - id: toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/2022.09+galaxy4 + version: 0.2.3 + symlink: null + tags: + - metabarcoding + - 16S + - nanopore + - microgalaxy + - plants + time: null + time_estimation: 2H + title: 16S Microbial analysis with Nanopore data + tools: + - Remove beginning1 + - toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/1.1.2 + - toolshed.g2.bx.psu.edu/repos/crs4/taxonomy_krona_chart/taxonomy_krona_chart/2.7.1 + - toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1 + - toolshed.g2.bx.psu.edu/repos/iuc/datamash_reverse/datamash_reverse/1.1.0 + - toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.20.1+galaxy0 + - toolshed.g2.bx.psu.edu/repos/iuc/kraken2/kraken2/2.0.8_beta+galaxy0 + - toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.8+galaxy1 + - toolshed.g2.bx.psu.edu/repos/iuc/porechop/porechop/0.2.3 + topic_name: microbiome + topic_name_human: Microbiome + tours: false + translations: + slides: [] + tutorial: [] + video: false + tutorial_name: nanopore-16S-metagenomics + type: tutorial + url: https://training.galaxyproject.org//topics/microbiome/tutorials/nanopore-16S-metagenomics/tutorial.html + urls: + hands_on: https://training.galaxyproject.org/training-material/api/topics/microbiome/tutorials/nanopore-16S-metagenomics/tutorial.json + slides: https://training.galaxyproject.org/training-material/api/topics/microbiome/tutorials/nanopore-16S-metagenomics/tutorial.json + version: 5 + video: false + video_versions: 0 + video_view: 0 + visit_duration: 327 + visitors: 10366 + workflows: + - creators: [] + description: 16S rRNA analysis with Nanopore reads + features: + comments: false + parameters: false + report: null + subworkflows: false + graph_dot: "digraph main {\n node [fontname=\"Atkinson Hyperlegible\", shape=box,\ + \ color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n edge [fontname=\"\ + Atkinson Hyperlegible\"];\n 0[color=lightblue,label=\"\u2139\uFE0F Input Collection\\\ + nInput dataset collection\"]\n 1[label=\"FastQC\"]\n 0 -> 1 [label=\"output\"\ + ]\n 2[label=\"Porechop\"]\n 0 -> 2 [label=\"output\"]\n 3[label=\"MultiQC\"\ + ]\n 1 -> 3 [label=\"text_file\"]\n 4[label=\"fastp\"]\n 2 -> 4 [label=\"\ + outfile\"]\n 5[label=\"FastQC\"]\n 4 -> 5 [label=\"out1\"]\n 6[label=\"Kraken2\"\ + ]\n 4 -> 6 [label=\"out1\"]\n 7[label=\"MultiQC\"]\n 5 -> 7 [label=\"text_file\"\ + ]\n 8[label=\"Reverse\"]\n 6 -> 8 [label=\"report_output\"]\n 9[label=\"\ + Replace Text\"]\n 8 -> 9 [label=\"out_file\"]\n 10[label=\"Remove beginning\"\ + ]\n 9 -> 10 [label=\"outfile\"]\n 11[label=\"Krona pie chart\"]\n 10 -> 11\ + \ [label=\"out_file1\"]\n}" + history: + - hash: 0e0a2f2ccb650b0aab1ffc13838045164bdb5d30 + message: Rename metagenomics topic to microbiome + num: 1 + short_hash: 0e0a2f2cc + unix: '1704901629' + inputs: + - annotation: '' + content_id: null + errors: null + id: 0 + input_connections: {} + inputs: + - description: '' + name: Input Dataset Collection + label: null + name: Input dataset collection + outputs: [] + position: + left: 10 + top: 10 + tool_id: null + tool_state: '{"optional": false, "collection_type": "list"}' + tool_version: null + type: data_collection_input + uuid: 18fc8b44-c752-41a0-a17c-e03797a5fab1 + workflow_outputs: [] + license: null + mermaid: "flowchart TD\n 0[\"\u2139\uFE0F Input Collection\\nInput dataset collection\"\ + ];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"FastQC\"];\n 0 -->|output|\ + \ 1;\n 2[\"Porechop\"];\n 0 -->|output| 2;\n 3[\"MultiQC\"];\n 1 -->|text_file|\ + \ 3;\n 4[\"fastp\"];\n 2 -->|outfile| 4;\n 5[\"FastQC\"];\n 4 -->|out1|\ + \ 5;\n 6[\"Kraken2\"];\n 4 -->|out1| 6;\n 7[\"MultiQC\"];\n 5 -->|text_file|\ + \ 7;\n 8[\"Reverse\"];\n 6 -->|report_output| 8;\n 9[\"Replace Text\"];\n\ + \ 8 -->|out_file| 9;\n 10[\"Remove beginning\"];\n 9 -->|outfile| 10;\n \ + \ 11[\"Krona pie chart\"];\n 10 -->|out_file1| 11;" + modified: 2026-07-01 00:31:39 +0000 + name: 'Training: 16S rRNA Analysis with Nanopore Sequencing Reads' + outputs: [] + parent_id: microbiome/nanopore-16S-metagenomics + path: topics/microbiome/tutorials/nanopore-16S-metagenomics/workflows/main_workflow.ga + tags: + - microbiome + test_results: null + tests: false + title: 'Training: 16S rRNA Analysis with Nanopore Sequencing Reads' + topic_id: microbiome + trs_endpoint: https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/microbiome-nanopore-16S-metagenomics/versions/main-workflow + tutorial_id: nanopore-16S-metagenomics + url: https://training.galaxyproject.org/training-material/topics/microbiome/tutorials/nanopore-16S-metagenomics/workflows/main_workflow.ga + url_html: https://training.galaxyproject.org/training-material/topics/microbiome/tutorials/nanopore-16S-metagenomics/workflows/main_workflow.html + version: 1 + wfid: microbiome-nanopore-16S-metagenomics + wfname: main-workflow + workflow: main_workflow.ga + workflow_tools: + - Remove beginning1 + - toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/1.1.2 + - toolshed.g2.bx.psu.edu/repos/crs4/taxonomy_krona_chart/taxonomy_krona_chart/2.7.1 + - toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1 + - toolshed.g2.bx.psu.edu/repos/iuc/datamash_reverse/datamash_reverse/1.1.0 + - toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.20.1+galaxy0 + - toolshed.g2.bx.psu.edu/repos/iuc/kraken2/kraken2/2.0.8_beta+galaxy0 + - toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.8+galaxy1 + - toolshed.g2.bx.psu.edu/repos/iuc/porechop/porechop/0.2.3 + workflowhub_id: '1473' + zenodo_link: https://zenodo.org/record/4274812 +- admin_install: + install_repository_dependencies: true + install_resolver_dependencies: true + install_tool_dependencies: true + tools: + - name: taxonomy_krona_chart + owner: crs4 + revisions: e9005d1f3cfd + tool_panel_section_label: Metagenomic Analysis + tool_shed_url: https://toolshed.g2.bx.psu.edu/ + - name: fastqc + owner: devteam + revisions: 3d0c7bdf12f5 + tool_panel_section_label: FASTA/FASTQ + tool_shed_url: https://toolshed.g2.bx.psu.edu/ + - name: fastp + owner: iuc + revisions: 65b93b623c77 + tool_panel_section_label: FASTA/FASTQ + tool_shed_url: https://toolshed.g2.bx.psu.edu/ + - name: kraken2 + owner: iuc + revisions: 20e2f64aa1fe + tool_panel_section_label: Metagenomic Analysis + tool_shed_url: https://toolshed.g2.bx.psu.edu/ + - name: krakentools_kreport2krona + owner: iuc + revisions: 88d274322340 + tool_panel_section_label: Metagenomic Analysis + tool_shed_url: https://toolshed.g2.bx.psu.edu/ + - name: porechop + owner: iuc + revisions: 543cbeef3949 + tool_panel_section_label: Nanopore + tool_shed_url: https://toolshed.g2.bx.psu.edu/ + admin_install_yaml: "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies:\ + \ true\ninstall_resolver_dependencies: true\ntools:\n- name: taxonomy_krona_chart\n\ + \ owner: crs4\n revisions: e9005d1f3cfd\n tool_panel_section_label: Metagenomic\ + \ Analysis\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fastqc\n\ + \ owner: devteam\n revisions: 3d0c7bdf12f5\n tool_panel_section_label: FASTA/FASTQ\n\ + \ tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fastp\n owner: iuc\n\ + \ revisions: 65b93b623c77\n tool_panel_section_label: FASTA/FASTQ\n tool_shed_url:\ + \ https://toolshed.g2.bx.psu.edu/\n- name: kraken2\n owner: iuc\n revisions:\ + \ 20e2f64aa1fe\n tool_panel_section_label: Metagenomic Analysis\n tool_shed_url:\ + \ https://toolshed.g2.bx.psu.edu/\n- name: krakentools_kreport2krona\n owner:\ + \ iuc\n revisions: 88d274322340\n tool_panel_section_label: Metagenomic Analysis\n\ + \ tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: porechop\n owner:\ + \ iuc\n revisions: 543cbeef3949\n tool_panel_section_label: Nanopore\n tool_shed_url:\ + \ https://toolshed.g2.bx.psu.edu/\n" + api: https://training.galaxyproject.org/training-material/api/topics/microbiome/tutorials/beer-data-analysis/tutorial.json + contributions: + authorship: + - plushz + - chensy96 + - bebatut + - teresa-m + funding: + - gallantries + reviewing: + - hexylena + - shiltemann + - teresa-m + - chensy96 + - nuwang + - bebatut + - gallardoalba + contributors: + - affiliations: + - uni-freiburg + id: plushz + joined: 2022-03 + name: Polina Polunina + orcid: 0000-0002-0507-4602 + page: https://training.galaxyproject.org/training-material/hall-of-fame/plushz/ + url: https://training.galaxyproject.org/training-material/api/contributors/plushz.json + - id: chensy96 + joined: 2022-05 + name: Siyu Chen + page: https://training.galaxyproject.org/training-material/hall-of-fame/chensy96/ + url: https://training.galaxyproject.org/training-material/api/contributors/chensy96.json + - affiliations: + - gallantries + - ifb + - elixir-europe + contact_for_training: true + elixir_node: fr + email: berenice.batut@gmail.com + fediverse: https://piaille.fr/@bebatut + fediverse_flavor: mastodon + former_affiliations: + - uni-freiburg + - deNBI + id: bebatut + joined: 2017-09 + linkedin: berenicebatut + location: + country: FR + lat: 45.77 + lon: 3.08 + matrix: bebatut:matrix.org + name: "B\xE9r\xE9nice Batut" + orcid: 0000-0001-9852-1987 + page: https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/ + twitter: bebatut + url: https://training.galaxyproject.org/training-material/api/contributors/bebatut.json + - affiliations: + - uni-freiburg + - elixir-europe + - deNBI + - mwk + - biont + contact_for_training: true + elixir_node: de + email: muellert@informatik.uni-freibrug.de + id: teresa-m + joined: 2022-09 + linkedin: teresamueller87 + matrix: teresa-m:matrix.org + name: "Teresa M\xFCller" + orcid: 0000-0003-1252-9684 + page: https://training.galaxyproject.org/training-material/hall-of-fame/teresa-m/ + url: https://training.galaxyproject.org/training-material/api/contributors/teresa-m.json + - avatar: https://gallantries.github.io/assets/images/gallantries-logo.png + end_date: '2023-09-30' + former_members: + - abretaud + - hexylena + - shiltemann + funder_name: Erasmus+ Programme + funding_database: erasmusplus + funding_id: 2020-1-NL01-KA203-064717 + funding_statement: 'This project (2020-1-NL01-KA203-064717) + is funded with the support of the Erasmus+ programme of the European Union. + Their funding has supported a large number of tutorials within the GTN across + a wide array of topics. + + eu flag with the text: with the support of the erasmus programme of the + european union + + erasmus plus + logo' + github: false + id: gallantries + joined: 2020-09 + members: + - bebatut + - colineroyaux + - fpsom + - yvanlebras + name: 'Gallantries: Bridging Training Communities in Life Science, Environment + and Health' + page: https://training.galaxyproject.org/training-material/hall-of-fame/gallantries/ + short_name: Gallantries + start_date: '2020-09-01' + url: https://training.galaxyproject.org/training-material/api/grants/gallantries.json + - affiliations: + - elixir-europe + contact_for_training: false + elixir_node: nl + former_affiliations: + - deNBI + - avans-atgm + - uni-freiburg + - erasmusmc + - gallantries + - by-covid + - elixir-converge + id: hexylena + joined: 2017-09 + location: + country: NL + lat: 51.91 + lon: 4.46 + maintainer_contact: gitter + matrix: hexylena:matrix.org + name: Helena Rasche + orcid: 0000-0001-9760-8992 + page: https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/ + url: https://training.galaxyproject.org/training-material/api/contributors/hexylena.json + - affiliations: + - uni-freiburg + - nfdi4plants + - elixir-europe + bio: Researcher at Erasmus Medical Center + bluesky: shiltemann.bsky.social + contact_for_training: true + elixir_node: nl + email: saskia.hiltemann@gmail.com + fediverse: https://mstdn.science/@shiltemann + fediverse_flavor: mastodon + former_affiliations: + - CINECA-Project + - gallantries + - erasmusmc + id: shiltemann + joined: 2017-09 + linkedin: shiltemann + location: + country: NL + lat: 51.912 + lon: 4.462 + maintainer_contact: gitter + matrix: shiltemann:matrix.org + name: Saskia Hiltemann + orcid: 0000-0003-3803-468X + page: https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/ + url: https://training.galaxyproject.org/training-material/api/contributors/shiltemann.json + - affiliations: + - uni-freiburg + - elixir-europe + - deNBI + - mwk + - biont + contact_for_training: true + elixir_node: de + email: muellert@informatik.uni-freibrug.de + id: teresa-m + joined: 2022-09 + linkedin: teresamueller87 + matrix: teresa-m:matrix.org + name: "Teresa M\xFCller" + orcid: 0000-0003-1252-9684 + page: https://training.galaxyproject.org/training-material/hall-of-fame/teresa-m/ + url: https://training.galaxyproject.org/training-material/api/contributors/teresa-m.json + - id: chensy96 + joined: 2022-05 + name: Siyu Chen + page: https://training.galaxyproject.org/training-material/hall-of-fame/chensy96/ + url: https://training.galaxyproject.org/training-material/api/contributors/chensy96.json + - id: nuwang + joined: 2019-06 + name: Nuwan Goonasekera + page: https://training.galaxyproject.org/training-material/hall-of-fame/nuwang/ + url: https://training.galaxyproject.org/training-material/api/contributors/nuwang.json + - affiliations: + - gallantries + - ifb + - elixir-europe + contact_for_training: true + elixir_node: fr + email: berenice.batut@gmail.com + fediverse: https://piaille.fr/@bebatut + fediverse_flavor: mastodon + former_affiliations: + - uni-freiburg + - deNBI + id: bebatut + joined: 2017-09 + linkedin: berenicebatut + location: + country: FR + lat: 45.77 + lon: 3.08 + matrix: bebatut:matrix.org + name: "B\xE9r\xE9nice Batut" + orcid: 0000-0001-9852-1987 + page: https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/ + twitter: bebatut + url: https://training.galaxyproject.org/training-material/api/contributors/bebatut.json + - elixir_node: de + former_affiliations: + - uni-freiburg + - elixir-europe + id: gallardoalba + joined: 2020-11 + name: "Crist\xF3bal Gallardo" + orcid: 0000-0002-5752-2155 + page: https://training.galaxyproject.org/training-material/hall-of-fame/gallardoalba/ + url: https://training.galaxyproject.org/training-material/api/contributors/gallardoalba.json + dir: topics/microbiome/tutorials/beer-data-analysis + edam_ontology: + - topic_3174 + - topic_3697 + - topic_0637 + - topic_0080 + edam_operation: + - Sequencing quality control + - Statistical calculation + - Taxonomic classification + - Sequence contamination filtering + - Visualisation + - Sequence composition calculation + - Aggregation + edam_topic: + - Metagenomics + - Microbial ecology + - Taxonomy + - Sequence analysis + exact_supported_servers: + - UseGalaxy.org.au + - UseGalaxy.be + - UseGalaxy.eu + - UseGalaxy.org (Main) + feedback_mean_note: null + feedback_number: 0 + hands_on: true + id: microbiome/beer-data-analysis + inexact_supported_servers: + - GalaxyTrakr + - UseGalaxy.cz + - UseGalaxy.fr + - UseGalaxy.no + js_requirements: + mathjax: 12074 + mermaid: false + key_points: + - Data obtained by sequencing needs to be checked for quality and cleaned before + further processing + - Yeast species but also contamination can be identified and visualized directly + from the sequences using several bioinformatics tools + - With its graphical interface, Galaxy makes it easy to use the needed bioinformatics + tools + - Beer microbiome is not just made of yeast and can be quite complex + layout: tutorial_hands_on + level: Introductory + license: CC-BY-4.0 + mod_date: '2024-11-29' + objectives: + - Inspect metagenomics data + - Run metagenomics tools + - Identify yeast species contained in a sequenced beer sample using DNA + - Visualize the microbiome community of a beer sample + pageviews: 5095 + pub_date: '2022-09-29' + questions: + - How can yeast strains in a beer sample be identified? + - How can we process metagenomic data sequenced using Nanopore? + recordings: + - captioners: + - sophia120199 + date: '2023-05-10' + galaxy_version: '23.01' + length: 1H5M + speakers: + - bebatut + youtube_id: PJeS06yiJUM + redirect_from: + - /topics/metagenomics/tutorials/beer-data-analysis/tutorial + - /short/microbiome/beer-data-analysis + - /short/T00200 + - /short/T00384 + short_id: T00384 + short_tools: + - Filter1 + - taxonomy_krona_chart + - fastp + - fastqc + - krakentools_kreport2krona + - porechop + - kraken2 + slides: false + slides_recordings: false + subtopic: metagenomics + supported_servers: + exact: + - name: UseGalaxy.org.au + url: https://usegalaxy.org.au + usegalaxy: true + - name: UseGalaxy.be + url: https://usegalaxy.be/ + usegalaxy: false + - name: UseGalaxy.eu + url: https://usegalaxy.eu + usegalaxy: true + - name: UseGalaxy.org (Main) + url: https://usegalaxy.org + usegalaxy: true + inexact: + - name: GalaxyTrakr + url: https://galaxytrakr.org/ + usegalaxy: false + - name: UseGalaxy.cz + url: https://usegalaxy.cz/ + usegalaxy: false + - name: UseGalaxy.fr + url: https://usegalaxy.fr/ + usegalaxy: true + - name: UseGalaxy.no + url: https://usegalaxy.no/ + usegalaxy: false + supported_servers_matrix: + servers: + - name: APOSTL + url: http://apostl.moffitt.org/ + usegalaxy: false + - name: MBAC Metabiome Portal + url: http://mbac.gmu.edu:8080/ + usegalaxy: false + - name: ChemFlow + url: https://vm-chemflow-francegrille.eu/ + usegalaxy: false + - name: CIRM-CFBP + url: https://iris.angers.inra.fr/galaxypub-cfbp + usegalaxy: false + - name: Coloc-stats + url: https://hyperbrowser.uio.no/coloc-stats + usegalaxy: false + - name: Galaxy@AuBi + url: https://galaxy.mesocentre.uca.fr + usegalaxy: false + - name: Galaxy@Pasteur + url: https://galaxy.pasteur.fr/ + usegalaxy: false + - name: GalaxyTrakr + url: https://galaxytrakr.org/ + usegalaxy: false + - name: GASLINI + url: http://igg.cloud.ba.infn.it/galaxy + usegalaxy: false + - name: HyPhy HIV NGS Tools + url: https://galaxy.hyphy.org/ + usegalaxy: false + - name: ImmPort Galaxy + url: https://www.immportgalaxy.org/ + usegalaxy: false + - name: InteractoMIX + url: http://galaxy.interactomix.com/ + usegalaxy: false + - name: IPK Galaxy Blast Suite + url: https://galaxy-web.ipk-gatersleben.de + usegalaxy: false + - name: Mandoiu Lab + url: https://neo.engr.uconn.edu/ + usegalaxy: false + - name: MISSISSIPPI + url: https://mississippi.sorbonne-universite.fr + usegalaxy: false + - name: Oqtans + url: http://galaxy.inf.ethz.ch + usegalaxy: false + - name: Palfinder + url: https://palfinder.ls.manchester.ac.uk/ + usegalaxy: false + - name: PepSimili + url: http://pepsimili.e-nios.com:8080/ + usegalaxy: false + - name: UseGalaxy.org.au + url: https://usegalaxy.org.au + usegalaxy: true + - name: UseGalaxy.be + url: https://usegalaxy.be/ + usegalaxy: false + - name: UseGalaxy.cz + url: https://usegalaxy.cz/ + usegalaxy: false + - name: UseGalaxy.eu + url: https://usegalaxy.eu + usegalaxy: true + - name: UseGalaxy.fr + url: https://usegalaxy.fr/ + usegalaxy: true + - name: UseGalaxy.no + url: https://usegalaxy.no/ + usegalaxy: false + - name: UseGalaxy.org (Main) + url: https://usegalaxy.org + usegalaxy: true + - name: Viral Variant Visualizer (VVV) + url: https://viralvariant.anses.fr/ + usegalaxy: false + tools: + - id: Filter1 servers: - server: http://apostl.moffitt.org/ - state: missing + state: local - server: http://mbac.gmu.edu:8080/ - state: missing + state: local - server: https://vm-chemflow-francegrille.eu/ state: missing - server: https://iris.angers.inra.fr/galaxypub-cfbp state: missing - server: https://hyperbrowser.uio.no/coloc-stats - state: missing + state: local - server: https://galaxy.mesocentre.uca.fr - state: exact - version: 2022.09+galaxy4 + state: local - server: https://galaxy.pasteur.fr/ - state: inexact - versions: - - 0.8.1+galaxy3 + state: local - server: https://galaxytrakr.org/ - state: missing + state: local - server: http://igg.cloud.ba.infn.it/galaxy - state: missing + state: local - server: https://galaxy.hyphy.org/ - state: missing + state: local - server: https://www.immportgalaxy.org/ state: missing - server: http://galaxy.interactomix.com/ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr - state: exact - version: 2022.09+galaxy4 + state: local - server: http://galaxy.inf.ethz.ch - state: missing + state: local - server: https://palfinder.ls.manchester.ac.uk/ state: missing - server: http://pepsimili.e-nios.com:8080/ - state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing + state: local - server: https://usegalaxy.org.au - state: exact - version: 2022.09+galaxy4 + state: local - server: https://usegalaxy.be/ - state: exact - version: 2022.09+galaxy4 + state: local - server: https://usegalaxy.cz/ - state: exact - version: 2022.09+galaxy4 + state: local - server: https://usegalaxy.eu - state: exact - version: 2022.09+galaxy4 + state: local - server: https://usegalaxy.fr/ - state: exact - version: 2022.09+galaxy4 + state: local - server: https://usegalaxy.no/ - state: exact - version: 2022.09+galaxy4 + state: local - server: https://usegalaxy.org - state: exact - version: 2022.09+galaxy4 + state: local - server: https://viralvariant.anses.fr/ - state: missing - version: 2022.09+galaxy4 - - id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_consensus/bcftools_consensus/1.15.1+galaxy3 + state: local + version: local + - id: toolshed.g2.bx.psu.edu/repos/crs4/taxonomy_krona_chart/taxonomy_krona_chart/2.7.1+galaxy0 servers: - server: http://apostl.moffitt.org/ state: missing @@ -57298,189 +50163,14 @@ - server: https://hyperbrowser.uio.no/coloc-stats state: missing - server: https://galaxy.mesocentre.uca.fr - state: missing - - server: https://galaxy.pasteur.fr/ - 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missing - - server: https://galaxy.mesocentre.uca.fr - state: missing + version: 2.7.1+galaxy0 - server: https://galaxy.pasteur.fr/ - state: inexact - versions: - - 1.15.1+galaxy3 - - server: https://galaxytrakr.org/ - state: inexact - versions: - - 1.22+galaxy0 - - 1.15.1+galaxy4 - - server: http://igg.cloud.ba.infn.it/galaxy - state: missing - - server: https://galaxy.hyphy.org/ - state: missing - - server: https://www.immportgalaxy.org/ - state: missing - - server: http://galaxy.interactomix.com/ - state: missing - - server: https://galaxy-web.ipk-gatersleben.de - state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - - server: https://neo.engr.uconn.edu/ - state: missing - - server: https://mississippi.sorbonne-universite.fr - state: inexact - versions: - - 1.15.1+galaxy3 - - 1.22+galaxy0 - - 1.10+galaxy1 - - server: http://galaxy.inf.ethz.ch - state: missing - - server: https://palfinder.ls.manchester.ac.uk/ - state: missing - - server: http://pepsimili.e-nios.com:8080/ - state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - - server: https://usegalaxy.org.au - state: inexact - versions: - - 1.15.1+galaxy3 - - 1.22+galaxy0 - - 1.15.1+galaxy4 - - 1.10+galaxy1 - - '1.9' - - 1.15.1+galaxy0 - - 1.15.1+galaxy2 - - '1.10' - - 1.4.0 - - server: https://usegalaxy.be/ - state: exact - version: 1.9+galaxy1 - - server: https://usegalaxy.cz/ - state: inexact - versions: - - 1.15.1+galaxy3 - - 1.22+galaxy0 - - 1.15.1+galaxy4 - - server: https://usegalaxy.eu - state: exact - version: 1.9+galaxy1 - - server: https://usegalaxy.fr/ - state: exact - version: 1.9+galaxy1 - - server: https://usegalaxy.no/ state: exact - version: 1.9+galaxy1 - - server: https://usegalaxy.org - state: inexact - versions: - - 1.15.1+galaxy3 - - 1.22+galaxy0 - - 1.15.1+galaxy4 - - 1.10+galaxy1 - - 1.15.1+galaxy2 - - '1.10' - - 1.4.0 - - 1.9+galaxy2 - - server: https://viralvariant.anses.fr/ - state: inexact - versions: - - 1.15.1+galaxy4 - version: 1.9+galaxy1 - - id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_norm/bcftools_norm/1.9+galaxy1 - servers: - - server: http://apostl.moffitt.org/ - state: missing - - server: http://mbac.gmu.edu:8080/ - state: missing - - server: https://vm-chemflow-francegrille.eu/ - state: missing - - server: https://iris.angers.inra.fr/galaxypub-cfbp - state: missing - - server: https://hyperbrowser.uio.no/coloc-stats - state: missing - - server: https://galaxy.mesocentre.uca.fr - state: missing - - server: https://galaxy.pasteur.fr/ - state: inexact - versions: - - 1.15.1+galaxy4 + version: 2.7.1+galaxy0 - server: https://galaxytrakr.org/ - state: inexact - versions: - - 1.15.1+galaxy4 - - 1.22+galaxy0 + state: exact + version: 2.7.1+galaxy0 - server: http://igg.cloud.ba.infn.it/galaxy state: missing - server: https://galaxy.hyphy.org/ @@ -57491,8 +50181,6 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr @@ -57502,124 +50190,34 @@ - server: https://palfinder.ls.manchester.ac.uk/ state: missing - server: http://pepsimili.e-nios.com:8080/ - state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - - server: https://usegalaxy.org.au - state: inexact - versions: - - 1.15.1+galaxy4 - - 1.22+galaxy0 - - '1.9' - - 1.15.1+galaxy3 - - 1.15.1+galaxy2 - - '1.10' - - 1.15.1+galaxy0 - - 1.4.0.0 - - server: https://usegalaxy.be/ - state: exact - version: 1.9+galaxy1 - - server: https://usegalaxy.cz/ - state: inexact - versions: - - 1.15.1+galaxy4 - - 1.22+galaxy0 - - 1.15.1+galaxy3 - - server: https://usegalaxy.eu - state: exact - version: 1.9+galaxy1 - - server: https://usegalaxy.fr/ - state: exact - version: 1.9+galaxy1 - - server: https://usegalaxy.no/ - state: exact - version: 1.9+galaxy1 - - server: https://usegalaxy.org state: exact - version: 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+ versions: + - 0.2.4+galaxy1 - server: https://usegalaxy.no/ state: exact - version: 2.1.10+galaxy1 + version: 0.2.4+galaxy0 - server: https://usegalaxy.org state: exact - version: 2.1.10+galaxy1 + version: 0.2.4+galaxy0 - server: https://viralvariant.anses.fr/ state: missing - version: 2.1.10+galaxy1 - - id: toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_heatmap/ggplot2_heatmap/3.4.0+galaxy0 + version: 0.2.4+galaxy0 + symlink: null + tags: + - nanopore + - beer + - citizen science + - metagenomics + - microgalaxy + time: null + time_estimation: 1H + title: Identification of the micro-organisms in a beer using Nanopore sequencing + tools: + - Filter1 + - toolshed.g2.bx.psu.edu/repos/crs4/taxonomy_krona_chart/taxonomy_krona_chart/2.7.1+galaxy0 + - toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.73+galaxy0 + - toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.2+galaxy0 + - toolshed.g2.bx.psu.edu/repos/iuc/kraken2/kraken2/2.1.1+galaxy1 + - 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M\xFCller" + - class: Person + identifier: 0000-0002-0507-4602 + name: Polina Polunina + description: Identification of the micro-organisms in a beer using Nanopore sequencing + features: + comments: false + parameters: false + report: null + subworkflows: false + graph_dot: "digraph main {\n node [fontname=\"Atkinson Hyperlegible\", shape=box,\ + \ color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n edge [fontname=\"\ + Atkinson Hyperlegible\"];\n 0[color=lightblue,label=\"\u2139\uFE0F Input Dataset\\\ + ninput\"]\n 1[label=\"FastQC\"]\n 0 -> 1 [label=\"output\"]\n 2[label=\"\ + Porechop\"]\n 0 -> 2 [label=\"output\"]\n 3[label=\"fastp\"]\n 2 -> 3 [label=\"\ + outfile\"]\n 4[label=\"Kraken2\"]\n 3 -> 4 [label=\"out1\"]\n kd2edd0b426f6436c81fae3bf8ea001f5[color=lightseagreen,label=\"\ + Output\\nkraken_report\"]\n 4 -> kd2edd0b426f6436c81fae3bf8ea001f5\n 5[label=\"\ + Filter\"]\n 4 -> 5 [label=\"report_output\"]\n 6[label=\"Filter\"]\n 4 ->\ + \ 6 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style\ + \ 0 stroke:#2c3143,stroke-width:4px;\n 1[\"FastQC\"];\n 0 -->|output| 1;\n\ + \ 2[\"Porechop\"];\n 0 -->|output| 2;\n 3[\"fastp\"];\n 2 -->|outfile| 3;\n\ + \ 4[\"Kraken2\"];\n 3 -->|out1| 4;\n d2edd0b4-26f6-436c-81fa-e3bf8ea001f5[\"\ + Output\\nkraken_report\"];\n 4 --> d2edd0b4-26f6-436c-81fa-e3bf8ea001f5;\n\ + \ style d2edd0b4-26f6-436c-81fa-e3bf8ea001f5 stroke:#2c3143,stroke-width:4px;\n\ + \ 5[\"Filter\"];\n 4 -->|report_output| 5;\n 6[\"Filter\"];\n 4 -->|report_output|\ + \ 6;\n 7[\"Krakentools: Convert kraken report file\"];\n 4 -->|report_output|\ + \ 7;\n 1c8dd881-070f-4425-a05f-b1e212c6d2e7[\"Output\\nkrakentool_report\"\ + ];\n 7 --> 1c8dd881-070f-4425-a05f-b1e212c6d2e7;\n style 1c8dd881-070f-4425-a05f-b1e212c6d2e7\ + \ stroke:#2c3143,stroke-width:4px;\n 8[\"Krona pie chart\"];\n 7 -->|output|\ + \ 8;" + modified: 2026-07-01 00:31:39 +0000 + name: Identification of the micro-organisms in a beer using Nanopore sequencing + outputs: + - annotation: '' + content_id: 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url: https://training.galaxyproject.org/training-material/api/contributors/subinamehta.json + - email: rsajulga@umn.edu + id: jraysajulga + joined: 2018-11 + name: Ray Sajulga + page: https://training.galaxyproject.org/training-material/hall-of-fame/jraysajulga/ + url: https://training.galaxyproject.org/training-material/api/contributors/jraysajulga.json + - affiliations: + - gallantries + - ifb + - elixir-europe + contact_for_training: true + elixir_node: fr + email: berenice.batut@gmail.com + fediverse: https://piaille.fr/@bebatut + fediverse_flavor: mastodon + former_affiliations: + - uni-freiburg + - deNBI + id: bebatut + joined: 2017-09 + linkedin: berenicebatut + location: + country: FR + lat: 45.77 + lon: 3.08 + matrix: bebatut:matrix.org + name: "B\xE9r\xE9nice Batut" + orcid: 0000-0001-9852-1987 + page: https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/ + twitter: bebatut + url: 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joined: 2017-09 + linkedin: shiltemann + location: + country: NL + lat: 51.912 + lon: 4.462 + maintainer_contact: gitter + matrix: shiltemann:matrix.org + name: Saskia Hiltemann + orcid: 0000-0003-3803-468X + page: https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/ + url: https://training.galaxyproject.org/training-material/api/contributors/shiltemann.json + - affiliations: + - uni-freiburg + - elixir-europe + - deNBI + - mwk + - materialvitaldigital + email: zierep@informatik.uni-freiburg.de + id: paulzierep + joined: 2023-02 + name: Paul Zierep + orcid: 0000-0003-2982-388X + page: https://training.galaxyproject.org/training-material/hall-of-fame/paulzierep/ + url: https://training.galaxyproject.org/training-material/api/contributors/paulzierep.json + - affiliations: + - uni-freiburg + - elixir-europe + elixir_node: de + email: engynasr94@gmail.com + id: EngyNasr + joined: 2021-05 + matrix: EngyNasr:matrix.org + name: Engy Nasr + orcid: 0000-0001-9047-4215 + page: https://training.galaxyproject.org/training-material/hall-of-fame/EngyNasr/ + url: https://training.galaxyproject.org/training-material/api/contributors/EngyNasr.json + - elixir_node: fr + id: ogerdfx + joined: 2025-06 + name: Christine Oger + page: https://training.galaxyproject.org/training-material/hall-of-fame/ogerdfx/ + url: https://training.galaxyproject.org/training-material/api/contributors/ogerdfx.json + - affiliations: + - gallantries + - ifb + - elixir-europe + contact_for_training: true + elixir_node: fr + email: berenice.batut@gmail.com + fediverse: https://piaille.fr/@bebatut + fediverse_flavor: mastodon + former_affiliations: + - uni-freiburg + - deNBI + id: bebatut + joined: 2017-09 + linkedin: berenicebatut + location: + country: FR + lat: 45.77 + lon: 3.08 + matrix: bebatut:matrix.org + name: "B\xE9r\xE9nice Batut" + orcid: 0000-0001-9852-1987 + page: https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/ + twitter: bebatut + url: https://training.galaxyproject.org/training-material/api/contributors/bebatut.json + - affiliations: + - elixir-europe + contact_for_training: false + elixir_node: nl + former_affiliations: + - deNBI + - avans-atgm + - uni-freiburg + - erasmusmc + - gallantries + - by-covid + - elixir-converge + id: hexylena + joined: 2017-09 + location: + country: NL + lat: 51.91 + lon: 4.46 + maintainer_contact: gitter + matrix: hexylena:matrix.org + name: Helena Rasche + orcid: 0000-0001-9760-8992 + page: https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/ + url: https://training.galaxyproject.org/training-material/api/contributors/hexylena.json + - affiliations: + - uni-freiburg + - nfdi4plants + - elixir-europe + bio: Researcher at Erasmus Medical Center + bluesky: shiltemann.bsky.social + contact_for_training: true + elixir_node: nl + email: saskia.hiltemann@gmail.com + fediverse: https://mstdn.science/@shiltemann + fediverse_flavor: mastodon + former_affiliations: + - CINECA-Project + - gallantries + - erasmusmc + id: shiltemann + joined: 2017-09 + linkedin: shiltemann + location: + country: NL + lat: 51.912 + lon: 4.462 + maintainer_contact: gitter + matrix: shiltemann:matrix.org + name: Saskia Hiltemann + orcid: 0000-0003-3803-468X + page: https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/ + url: https://training.galaxyproject.org/training-material/api/contributors/shiltemann.json + - affiliations: + - uni-freiburg + - elixir-europe + - deNBI + - mwk + - materialvitaldigital + email: zierep@informatik.uni-freiburg.de + id: paulzierep + joined: 2023-02 + name: Paul Zierep + orcid: 0000-0003-2982-388X + page: https://training.galaxyproject.org/training-material/hall-of-fame/paulzierep/ + url: https://training.galaxyproject.org/training-material/api/contributors/paulzierep.json + - affiliations: + - deNBI + - mwk + - uni-freiburg + - elixir-europe + - materialvitaldigital + contact_for_training: true + elixir_node: de + email: bjoern.gruening@gmail.com + fediverse: https://fosstodon.org/@bgruening + fediverse_flavor: mastodon + former_affiliations: + - eurosciencegateway + - eosc-life + - by-covid + - crc992 + - elixir-converge + id: bgruening + joined: 2017-09 + linkedin: bgruening + location: + country: DE + lat: 47.997791 + lon: 7.842609 + matrix: bgruening:matrix.org + name: "Bj\xF6rn Gr\xFCning" + orcid: 0000-0002-3079-6586 + page: https://training.galaxyproject.org/training-material/hall-of-fame/bgruening/ + twitter: bjoerngruening + url: https://training.galaxyproject.org/training-material/api/contributors/bgruening.json + dir: topics/microbiome/tutorials/metatranscriptomics-short + edam_ontology: + - topic_3941 + - topic_3697 + - topic_0637 + - topic_1775 + - topic_0080 + edam_operation: + - Phylogenetic tree visualisation + - Primer removal + - Visualisation + - Sequence composition calculation + - Phylogenetic tree editing + - Phylogenetic inference + - Statistical calculation + - Sequencing quality control + - Phylogenetic analysis + - Conversion + - Sequence trimming + - Taxonomic classification + - Species frequency estimation + - Sequence alignment analysis + - Sequence comparison + - Validation + - Read pre-processing + - Sequence similarity search + edam_topic: + - Metatranscriptomics + - Microbial ecology + - Taxonomy + - Function analysis + - Sequence analysis + exact_supported_servers: + - UseGalaxy.org.au + - UseGalaxy.be + - UseGalaxy.org (Main) + feedback_mean_note: null + feedback_number: 0 + hands_on: true + id: microbiome/metatranscriptomics-short + inexact_supported_servers: + - UseGalaxy.cz + - UseGalaxy.no + js_requirements: + mathjax: null + mermaid: false + key_points: + - Metatranscriptomics data have the same QC profile that RNA-seq data + - A lot of metatranscriptomics sequences are identified as rRNA sequences + - With shotgun data, we can extract information about the studied community structure + and also the functions realised by the community + - Metatranscriptomics data analyses are complex and must be careful done, specially + when they are done without combination to metagenomics data analyses + layout: tutorial_hands_on + level: Introductory + license: CC-BY-4.0 + mod_date: '2025-06-16' + objectives: + - Choose the best approach to analyze metatranscriptomics data + - Understand the functional microbiome characterization using metatranscriptomic + results + - Understand where metatranscriptomics fits in 'multi-omic' analysis of microbiomes + - Visualise a community structure + pageviews: 1386 + pub_date: '2020-02-13' + questions: + - How to analyze metatranscriptomics data?" + - What information can be extracted of metatranscriptomics data? + - How to assign taxa and function to the identified sequences? + recordings: + - captioners: + - paulzierep + date: '2023-05-17' + galaxy_version: '23.01' + length: 1H5M + speakers: + - paulzierep + youtube_id: HNYop3vLpoM + - captioners: + - EngyNasr + - shiltemann + date: '2021-02-15' + galaxy_version: '21.01' + length: 1H30M + speakers: + - pratikdjagtap + - timothygriffin + - subinamehta + - shiltemann + youtube_id: EMaos5u1_a8 + redirect_from: + - /topics/metagenomics/tutorials/metatranscriptomics-short/tutorial + - /short/microbiome/metatranscriptomics-short + - /short/T00204 + - /short/T00389 + short_id: T00389 + short_tools: + - metaphlan + - cutadapt + - fastq_paired_end_interlacer + - humann_rename_table + - graphlan + - bg_sortmerna + - humann_regroup_table + - tp_sort_header_tool + - combine_metaphlan2_humann2 + - taxonomy_krona_chart + - humann + - tp_find_and_replace + - humann_renorm_table + - humann_split_stratified_table + - Grep1 + - export2graphlan + - humann_unpack_pathways + - fastqc + - graphlan_annotate + - multiqc + - Cut1 + slides: false + slides_recordings: false + subtopic: metatranscriptomics + supported_servers: + exact: + - name: UseGalaxy.org.au + url: https://usegalaxy.org.au + usegalaxy: true + - name: UseGalaxy.be + url: https://usegalaxy.be/ + usegalaxy: false + - name: UseGalaxy.org (Main) + url: https://usegalaxy.org + usegalaxy: true + inexact: + - name: UseGalaxy.cz + url: https://usegalaxy.cz/ + usegalaxy: false + - name: UseGalaxy.no + url: https://usegalaxy.no/ + usegalaxy: false + supported_servers_matrix: + servers: + - name: APOSTL + url: http://apostl.moffitt.org/ + usegalaxy: false + - name: MBAC Metabiome Portal + url: http://mbac.gmu.edu:8080/ + usegalaxy: false + - name: ChemFlow + url: https://vm-chemflow-francegrille.eu/ + usegalaxy: false + - name: CIRM-CFBP + url: https://iris.angers.inra.fr/galaxypub-cfbp + usegalaxy: false + - name: Coloc-stats + url: https://hyperbrowser.uio.no/coloc-stats + usegalaxy: false + - name: Galaxy@AuBi + url: https://galaxy.mesocentre.uca.fr + usegalaxy: false + - name: Galaxy@Pasteur + url: https://galaxy.pasteur.fr/ + usegalaxy: false + - name: GalaxyTrakr + url: https://galaxytrakr.org/ + usegalaxy: false + - name: GASLINI + url: http://igg.cloud.ba.infn.it/galaxy + usegalaxy: false + - name: HyPhy HIV NGS Tools + url: https://galaxy.hyphy.org/ + usegalaxy: false + - name: ImmPort Galaxy + url: https://www.immportgalaxy.org/ + usegalaxy: false + - name: InteractoMIX + url: http://galaxy.interactomix.com/ + usegalaxy: false + - name: IPK Galaxy Blast Suite + url: https://galaxy-web.ipk-gatersleben.de + usegalaxy: false + - name: Mandoiu Lab + url: https://neo.engr.uconn.edu/ + usegalaxy: false + - name: MISSISSIPPI + url: https://mississippi.sorbonne-universite.fr + usegalaxy: false + - name: Oqtans + url: http://galaxy.inf.ethz.ch + usegalaxy: false + - name: Palfinder + url: https://palfinder.ls.manchester.ac.uk/ + usegalaxy: false + - name: PepSimili + url: http://pepsimili.e-nios.com:8080/ + usegalaxy: false + - name: UseGalaxy.org.au + url: https://usegalaxy.org.au + usegalaxy: true + - name: UseGalaxy.be + url: https://usegalaxy.be/ + usegalaxy: false + - name: UseGalaxy.cz + url: https://usegalaxy.cz/ + usegalaxy: false + - name: UseGalaxy.eu + url: https://usegalaxy.eu + usegalaxy: true + - name: UseGalaxy.fr + url: https://usegalaxy.fr/ + usegalaxy: true + - name: UseGalaxy.no + url: https://usegalaxy.no/ + usegalaxy: false + - name: UseGalaxy.org (Main) + url: https://usegalaxy.org + usegalaxy: true + - name: Viral Variant Visualizer (VVV) + url: https://viralvariant.anses.fr/ + usegalaxy: false + tools: + - id: Cut1 servers: - server: http://apostl.moffitt.org/ - state: missing + state: local - server: http://mbac.gmu.edu:8080/ - state: missing + state: local - server: https://vm-chemflow-francegrille.eu/ state: missing - server: https://iris.angers.inra.fr/galaxypub-cfbp state: missing - server: https://hyperbrowser.uio.no/coloc-stats - state: missing + state: local - server: https://galaxy.mesocentre.uca.fr - state: inexact - versions: - - 3.3.5+galaxy0 + state: local - server: https://galaxy.pasteur.fr/ - state: missing + state: local - server: https://galaxytrakr.org/ - state: 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state: local - server: https://usegalaxy.cz/ - state: exact - version: 3.4.0+galaxy0 + state: local - server: https://usegalaxy.eu - state: exact - version: 3.4.0+galaxy0 + state: local - server: https://usegalaxy.fr/ - state: exact - version: 3.4.0+galaxy0 + state: local - server: https://usegalaxy.no/ - state: inexact - versions: - - 3.3.5+galaxy0 - - 2.2.1 + state: local - server: https://usegalaxy.org - state: exact - version: 3.4.0+galaxy0 + state: local - server: https://viralvariant.anses.fr/ - state: missing - version: 3.4.0+galaxy0 - - id: toolshed.g2.bx.psu.edu/repos/iuc/kraken2/kraken2/2.1.1+galaxy1 + state: local + version: local + - id: Grep1 servers: - server: http://apostl.moffitt.org/ - state: missing + state: local - server: http://mbac.gmu.edu:8080/ - state: missing + state: local - server: https://vm-chemflow-francegrille.eu/ state: missing - server: https://iris.angers.inra.fr/galaxypub-cfbp state: missing - server: https://hyperbrowser.uio.no/coloc-stats - state: missing + state: local - server: https://galaxy.mesocentre.uca.fr - state: exact - version: 2.1.1+galaxy1 + state: local - server: https://galaxy.pasteur.fr/ - state: missing + state: local - server: https://galaxytrakr.org/ - state: inexact - versions: - - 2.1.3+galaxy2 - - 2.17.1+galaxy0 - - 2.0.8_beta+galaxy0 + state: local - server: http://igg.cloud.ba.infn.it/galaxy - state: missing + state: local - server: https://galaxy.hyphy.org/ - state: missing + state: local - server: https://www.immportgalaxy.org/ state: missing - server: http://galaxy.interactomix.com/ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr - state: missing + state: local - server: http://galaxy.inf.ethz.ch - state: missing + state: local - server: https://palfinder.ls.manchester.ac.uk/ state: missing - server: http://pepsimili.e-nios.com:8080/ - state: exact - version: 2.1.1+galaxy1 - - server: https://galaxy.bio.di.uminho.pt/ - state: missing + state: local - server: https://usegalaxy.org.au - state: exact - version: 2.1.1+galaxy1 + state: local - server: https://usegalaxy.be/ - state: exact - version: 2.1.1+galaxy1 + state: local - server: https://usegalaxy.cz/ - state: exact - version: 2.1.1+galaxy1 + state: local - server: https://usegalaxy.eu - state: exact - version: 2.1.1+galaxy1 + state: local - server: https://usegalaxy.fr/ - state: exact - version: 2.1.1+galaxy1 + state: local - server: https://usegalaxy.no/ - state: exact - version: 2.1.1+galaxy1 + state: local - server: https://usegalaxy.org - state: exact - version: 2.1.1+galaxy1 + state: local - server: https://viralvariant.anses.fr/ - state: missing - version: 2.1.1+galaxy1 - - id: toolshed.g2.bx.psu.edu/repos/iuc/krakentools_extract_kraken_reads/krakentools_extract_kraken_reads/1.2+galaxy1 + state: local + version: local + - id: toolshed.g2.bx.psu.edu/repos/bebatut/combine_metaphlan2_humann2/combine_metaphlan2_humann2/0.2.0 servers: - server: http://apostl.moffitt.org/ state: missing @@ -58283,17 +51545,11 @@ - server: https://hyperbrowser.uio.no/coloc-stats state: missing - server: https://galaxy.mesocentre.uca.fr - state: inexact - versions: - - 1.2+galaxy2 - - 1.2.1+galaxy0 + state: missing - server: https://galaxy.pasteur.fr/ - state: exact - version: 1.2+galaxy1 + state: missing - server: https://galaxytrakr.org/ - state: inexact - versions: - - 1.2.1+galaxy0 + state: missing - server: http://igg.cloud.ba.infn.it/galaxy state: missing - server: https://galaxy.hyphy.org/ @@ -58304,8 +51560,6 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr @@ -58316,32 +51570,30 @@ state: missing - server: 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missing + state: inexact + versions: + - 9.5+galaxy3 - server: http://galaxy.inf.ethz.ch state: missing - server: https://palfinder.ls.manchester.ac.uk/ state: missing - server: http://pepsimili.e-nios.com:8080/ state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - server: https://usegalaxy.org.au state: exact - version: 1.2+galaxy1 + version: 1.1.4 - server: https://usegalaxy.be/ state: exact - version: 1.2+galaxy1 + version: 1.1.4 - server: https://usegalaxy.cz/ state: exact - version: 1.2+galaxy1 + version: 1.1.4 - server: https://usegalaxy.eu state: exact - version: 1.2+galaxy1 + version: 1.1.4 - server: https://usegalaxy.fr/ state: exact - version: 1.2+galaxy1 + version: 1.1.4 - server: https://usegalaxy.no/ - state: exact - version: 1.2+galaxy1 + state: inexact + versions: + - 1.1.3 + - 1.1.1 + - 1.1.0 - server: https://usegalaxy.org state: exact - version: 1.2+galaxy1 + version: 1.1.4 - server: https://viralvariant.anses.fr/ state: missing - version: 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https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr - state: missing + state: inexact + versions: + - 9.5+galaxy3 - server: http://galaxy.inf.ethz.ch state: missing - server: https://palfinder.ls.manchester.ac.uk/ state: missing - server: http://pepsimili.e-nios.com:8080/ state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - server: https://usegalaxy.org.au state: exact - version: 1.7.2+galaxy0 + version: 9.5+galaxy2 - server: https://usegalaxy.be/ state: exact - version: 1.7.2+galaxy0 + version: 9.5+galaxy2 - server: https://usegalaxy.cz/ state: exact - version: 1.7.2+galaxy0 + version: 9.5+galaxy2 - server: https://usegalaxy.eu state: exact - version: 1.7.2+galaxy0 + version: 9.5+galaxy2 - server: https://usegalaxy.fr/ state: exact - version: 1.7.2+galaxy0 + version: 9.5+galaxy2 - server: 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http://pepsimili.e-nios.com:8080/ - state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing + state: exact + version: 2.7.1+galaxy0 - server: https://usegalaxy.org.au state: exact - version: 2.28+galaxy0 + version: 2.7.1+galaxy0 - server: https://usegalaxy.be/ state: exact - version: 2.28+galaxy0 + version: 2.7.1+galaxy0 - server: https://usegalaxy.cz/ state: exact - version: 2.28+galaxy0 + version: 2.7.1+galaxy0 - server: https://usegalaxy.eu state: exact - version: 2.28+galaxy0 + version: 2.7.1+galaxy0 - server: https://usegalaxy.fr/ state: exact - version: 2.28+galaxy0 + version: 2.7.1+galaxy0 - server: https://usegalaxy.no/ state: inexact versions: - - 2.24+galaxy0 - - 2.17+galaxy0 + - 2.7.1 - server: https://usegalaxy.org state: exact - version: 2.28+galaxy0 + version: 2.7.1+galaxy0 - server: https://viralvariant.anses.fr/ - state: inexact - versions: - - 2.28+galaxy2 - version: 2.28+galaxy0 - - id: toolshed.g2.bx.psu.edu/repos/iuc/mlst/mlst/2.22.0 + state: missing + version: 2.7.1+galaxy0 + - id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_paired_end_interlacer/fastq_paired_end_interlacer/1.2.0.1+galaxy0 servers: - server: http://apostl.moffitt.org/ state: missing @@ -58654,12 +51893,14 @@ - server: https://hyperbrowser.uio.no/coloc-stats state: missing - server: https://galaxy.mesocentre.uca.fr - state: missing + state: exact + version: 1.2.0.1+galaxy0 - server: https://galaxy.pasteur.fr/ - state: missing + state: exact + version: 1.2.0.1+galaxy0 - server: https://galaxytrakr.org/ state: exact - version: 2.22.0 + version: 1.2.0.1+galaxy0 - server: http://igg.cloud.ba.infn.it/galaxy state: missing - server: https://galaxy.hyphy.org/ @@ -58670,8 +51911,6 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr @@ -58682,33 +51921,31 @@ state: missing - server: http://pepsimili.e-nios.com:8080/ state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - server: https://usegalaxy.org.au state: exact - version: 2.22.0 + version: 1.2.0.1+galaxy0 - server: https://usegalaxy.be/ state: exact - version: 2.22.0 + version: 1.2.0.1+galaxy0 - server: https://usegalaxy.cz/ state: exact - version: 2.22.0 + version: 1.2.0.1+galaxy0 - server: https://usegalaxy.eu state: exact - version: 2.22.0 + version: 1.2.0.1+galaxy0 - server: https://usegalaxy.fr/ state: exact - version: 2.22.0 + version: 1.2.0.1+galaxy0 - server: https://usegalaxy.no/ state: exact - version: 2.22.0 + version: 1.2.0.1+galaxy0 - server: https://usegalaxy.org state: exact - version: 2.22.0 + version: 1.2.0.1+galaxy0 - server: https://viralvariant.anses.fr/ state: missing - version: 2.22.0 - - id: toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy0 + version: 1.2.0.1+galaxy0 + - id: toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy1 servers: - server: http://apostl.moffitt.org/ state: missing @@ -58721,17 +51958,18 @@ - server: https://hyperbrowser.uio.no/coloc-stats state: missing - server: https://galaxy.mesocentre.uca.fr - state: exact - version: 1.11+galaxy0 + state: inexact + versions: + - '0.72' + - 0.72+galaxy1 + - 0.73+galaxy0 - server: https://galaxy.pasteur.fr/ - state: missing - - server: https://galaxytrakr.org/ state: inexact versions: - - 1.27+galaxy4 - - 1.11+galaxy1 - - '1.7' - - 1.33+galaxy3 + - 0.74+galaxy0 + - server: https://galaxytrakr.org/ + state: exact + version: 0.74+galaxy1 - server: http://igg.cloud.ba.infn.it/galaxy state: missing - server: https://galaxy.hyphy.org/ @@ -58742,62 +51980,51 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr - state: inexact - versions: - - 1.34+galaxy0 + state: exact + version: 0.74+galaxy1 - server: http://galaxy.inf.ethz.ch state: missing - server: https://palfinder.ls.manchester.ac.uk/ - state: missing + state: inexact + versions: + - '0.72' + - 0.72+galaxy1 + - '0.65' + - '0.71' - server: http://pepsimili.e-nios.com:8080/ - state: missing - - server: https://galaxy.bio.di.uminho.pt/ state: inexact versions: - - 1.11+galaxy1 + - 0.74+galaxy0 - server: https://usegalaxy.org.au state: exact - version: 1.11+galaxy0 + version: 0.74+galaxy1 - server: https://usegalaxy.be/ state: exact - version: 1.11+galaxy0 + version: 0.74+galaxy1 - server: https://usegalaxy.cz/ state: exact - version: 1.11+galaxy0 + version: 0.74+galaxy1 - server: https://usegalaxy.eu state: exact - version: 1.11+galaxy0 + version: 0.74+galaxy1 - server: https://usegalaxy.fr/ + state: exact + version: 0.74+galaxy1 + - server: https://usegalaxy.no/ state: inexact versions: - - 1.33+galaxy0 - - 1.27+galaxy4 - - 1.24.1+galaxy0 - - 1.11+galaxy1 - - 1.27+galaxy3 - - '1.7' - - 1.34+galaxy0 - - '1.9' - - 1.9+galaxy1 - - 1.8+galaxy1 - - 1.8+galaxy0 - - 1.27+galaxy0 - - 1.27+galaxy1 - - server: https://usegalaxy.no/ - state: exact - version: 1.11+galaxy0 + - 0.72+galaxy1 + - 0.73+galaxy0 - server: https://usegalaxy.org state: exact - version: 1.11+galaxy0 + version: 0.74+galaxy1 - server: https://viralvariant.anses.fr/ state: missing - version: 1.11+galaxy0 - - id: toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1 + version: 0.74+galaxy1 + - id: toolshed.g2.bx.psu.edu/repos/iuc/export2graphlan/export2graphlan/0.20+galaxy0 servers: - server: http://apostl.moffitt.org/ state: missing @@ -58811,12 +52038,11 @@ state: missing - server: https://galaxy.mesocentre.uca.fr state: exact - version: 1.11+galaxy1 + version: 0.20+galaxy0 - server: https://galaxy.pasteur.fr/ state: missing - server: https://galaxytrakr.org/ - state: exact - version: 1.11+galaxy1 + state: missing - server: http://igg.cloud.ba.infn.it/galaxy state: missing - server: https://galaxy.hyphy.org/ @@ -58827,56 +52053,41 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr - state: inexact - versions: - - 1.34+galaxy0 + state: missing - server: http://galaxy.inf.ethz.ch state: missing - server: https://palfinder.ls.manchester.ac.uk/ state: missing - server: http://pepsimili.e-nios.com:8080/ state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: exact - version: 1.11+galaxy1 - server: https://usegalaxy.org.au state: exact - version: 1.11+galaxy1 + version: 0.20+galaxy0 - server: https://usegalaxy.be/ state: exact - version: 1.11+galaxy1 + version: 0.20+galaxy0 - server: https://usegalaxy.cz/ state: exact - version: 1.11+galaxy1 + version: 0.20+galaxy0 - server: https://usegalaxy.eu state: exact - version: 1.11+galaxy1 + version: 0.20+galaxy0 - server: https://usegalaxy.fr/ state: exact - version: 1.11+galaxy1 + version: 0.20+galaxy0 - server: https://usegalaxy.no/ - state: inexact - versions: - - 1.11+galaxy0 - - '1.7' - - 1.7.1 - - '1.9' - - 1.9+galaxy1 - - 1.8+galaxy1 - - 1.8+galaxy0 - - 1.8+galaxy2 + state: exact + version: 0.20+galaxy0 - server: https://usegalaxy.org state: exact - version: 1.11+galaxy1 + version: 0.20+galaxy0 - server: https://viralvariant.anses.fr/ state: missing - version: 1.11+galaxy1 - - id: toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.28.2+galaxy1 + version: 0.20+galaxy0 + - id: toolshed.g2.bx.psu.edu/repos/iuc/graphlan/graphlan/1.1.3 servers: - server: http://apostl.moffitt.org/ state: missing @@ -58890,14 +52101,12 @@ state: missing - server: https://galaxy.mesocentre.uca.fr state: exact - version: 1.28.2+galaxy1 + version: 1.1.3 - server: https://galaxy.pasteur.fr/ - state: inexact - versions: - - 1.43.0+galaxy0 + state: missing - server: https://galaxytrakr.org/ state: exact - version: 1.28.2+galaxy1 + version: 1.1.3 - server: http://igg.cloud.ba.infn.it/galaxy state: missing - server: https://galaxy.hyphy.org/ @@ -58908,52 +52117,41 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr - state: inexact - versions: - - 1.46.2+galaxy0 + state: missing - server: http://galaxy.inf.ethz.ch state: missing - server: https://palfinder.ls.manchester.ac.uk/ state: missing - server: http://pepsimili.e-nios.com:8080/ state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - server: https://usegalaxy.org.au state: exact - version: 1.28.2+galaxy1 + version: 1.1.3 - server: https://usegalaxy.be/ state: exact - version: 1.28.2+galaxy1 + version: 1.1.3 - server: https://usegalaxy.cz/ - state: inexact - versions: - - 1.46.2+galaxy0 - - 1.42.0+galaxy1 - - 1.46.1+galaxy0 - - 1.44.1+galaxy0 - - 1.41.0+galaxy0 + state: exact + version: 1.1.3 - server: https://usegalaxy.eu state: exact - version: 1.28.2+galaxy1 + version: 1.1.3 - server: https://usegalaxy.fr/ state: exact - version: 1.28.2+galaxy1 + version: 1.1.3 - server: https://usegalaxy.no/ state: exact - version: 1.28.2+galaxy1 + version: 1.1.3 - server: https://usegalaxy.org state: exact - version: 1.28.2+galaxy1 + version: 1.1.3 - server: https://viralvariant.anses.fr/ state: missing - version: 1.28.2+galaxy1 - - id: toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.42.0+galaxy1 + version: 1.1.3 + - id: toolshed.g2.bx.psu.edu/repos/iuc/graphlan_annotate/graphlan_annotate/1.1.3 servers: - server: http://apostl.moffitt.org/ state: missing @@ -58967,15 +52165,12 @@ state: missing - server: https://galaxy.mesocentre.uca.fr state: exact - version: 1.42.0+galaxy1 + version: 1.1.3 - server: https://galaxy.pasteur.fr/ - state: inexact - versions: - - 1.43.0+galaxy0 + state: missing - server: https://galaxytrakr.org/ - state: inexact - versions: - - 1.28.2+galaxy1 + state: exact + version: 1.1.3 - server: http://igg.cloud.ba.infn.it/galaxy state: missing - server: https://galaxy.hyphy.org/ @@ -58986,50 +52181,41 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr - state: inexact - versions: - - 1.46.2+galaxy0 + state: missing - server: http://galaxy.inf.ethz.ch state: missing - server: https://palfinder.ls.manchester.ac.uk/ state: missing - server: http://pepsimili.e-nios.com:8080/ state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - server: https://usegalaxy.org.au state: exact - version: 1.42.0+galaxy1 + version: 1.1.3 - server: https://usegalaxy.be/ state: exact - version: 1.42.0+galaxy1 + version: 1.1.3 - server: https://usegalaxy.cz/ state: exact - version: 1.42.0+galaxy1 + version: 1.1.3 - server: https://usegalaxy.eu state: exact - version: 1.42.0+galaxy1 + version: 1.1.3 - server: https://usegalaxy.fr/ state: exact - version: 1.42.0+galaxy1 + version: 1.1.3 - server: https://usegalaxy.no/ - state: inexact - versions: - - 1.28.2+galaxy1 - - 1.36.2+galaxy1 - - 1.25.0+galaxy1 + state: exact + version: 1.1.3 - server: https://usegalaxy.org state: exact - version: 1.42.0+galaxy1 + version: 1.1.3 - server: https://viralvariant.anses.fr/ state: missing - version: 1.42.0+galaxy1 - - id: toolshed.g2.bx.psu.edu/repos/iuc/newick_utils/newick_display/1.6+galaxy1 + version: 1.1.3 + - id: toolshed.g2.bx.psu.edu/repos/iuc/humann/humann/3.9+galaxy0 servers: - server: http://apostl.moffitt.org/ state: missing @@ -59042,12 +52228,13 @@ - server: https://hyperbrowser.uio.no/coloc-stats state: missing - server: https://galaxy.mesocentre.uca.fr - state: missing + state: exact + version: 3.9+galaxy0 - server: https://galaxy.pasteur.fr/ state: missing - server: https://galaxytrakr.org/ state: exact - version: 1.6+galaxy1 + version: 3.9+galaxy0 - server: http://igg.cloud.ba.infn.it/galaxy state: missing - server: https://galaxy.hyphy.org/ @@ -59058,8 +52245,6 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr @@ -59070,33 +52255,33 @@ state: missing - server: http://pepsimili.e-nios.com:8080/ state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - server: https://usegalaxy.org.au state: exact - version: 1.6+galaxy1 + version: 3.9+galaxy0 - server: https://usegalaxy.be/ state: exact - version: 1.6+galaxy1 + version: 3.9+galaxy0 - server: https://usegalaxy.cz/ state: exact - version: 1.6+galaxy1 + version: 3.9+galaxy0 - server: https://usegalaxy.eu state: exact - version: 1.6+galaxy1 + version: 3.9+galaxy0 - server: https://usegalaxy.fr/ state: exact - version: 1.6+galaxy1 + version: 3.9+galaxy0 - server: https://usegalaxy.no/ - state: exact - version: 1.6+galaxy1 + state: inexact + versions: + - 3.0.0+galaxy1 + - 3.6.0+galaxy0 - server: https://usegalaxy.org state: exact - version: 1.6+galaxy1 + version: 3.9+galaxy0 - server: https://viralvariant.anses.fr/ state: missing - version: 1.6+galaxy1 - - id: toolshed.g2.bx.psu.edu/repos/iuc/porechop/porechop/0.2.4 + version: 3.9+galaxy0 + - id: toolshed.g2.bx.psu.edu/repos/iuc/humann_regroup_table/humann_regroup_table/3.9+galaxy0 servers: - server: http://apostl.moffitt.org/ state: missing @@ -59109,16 +52294,13 @@ - server: https://hyperbrowser.uio.no/coloc-stats state: missing - server: https://galaxy.mesocentre.uca.fr - state: missing + state: exact + version: 3.9+galaxy0 - server: https://galaxy.pasteur.fr/ - state: inexact - versions: - - 0.2.4+galaxy0 + state: missing - server: https://galaxytrakr.org/ - state: inexact - versions: - - 0.2.4+galaxy0 - - 0.2.4+galaxy1 + state: exact + version: 3.9+galaxy0 - server: http://igg.cloud.ba.infn.it/galaxy state: missing - server: https://galaxy.hyphy.org/ @@ -59129,8 +52311,6 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr @@ -59141,39 +52321,39 @@ state: missing - server: http://pepsimili.e-nios.com:8080/ state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - server: https://usegalaxy.org.au state: exact - version: 0.2.4 + version: 3.9+galaxy0 - server: https://usegalaxy.be/ - state: inexact - versions: - - 0.2.4+galaxy0 - - 0.2.4+galaxy1 - - 0.2.3 + state: exact + version: 3.9+galaxy0 - server: https://usegalaxy.cz/ + state: exact + version: 3.9+galaxy0 + - server: https://usegalaxy.eu state: inexact versions: - - 0.2.4+galaxy0 - - 0.2.4+galaxy1 - - server: https://usegalaxy.eu - state: exact - version: 0.2.4 + - 3.0.0+galaxy1 + - 3.6.0+galaxy0 + - 3.8+galaxy0 + - 3.7+galaxy0 + - 3.0.0+galaxy0 + - 3.6.1+galaxy0 - server: https://usegalaxy.fr/ + state: exact + version: 3.9+galaxy0 + - server: https://usegalaxy.no/ state: inexact versions: - - 0.2.4+galaxy1 - - server: https://usegalaxy.no/ - state: exact - version: 0.2.4 + - 3.0.0+galaxy1 + - 3.6.0+galaxy0 - server: https://usegalaxy.org state: exact - version: 0.2.4 + version: 3.9+galaxy0 - server: https://viralvariant.anses.fr/ state: missing - version: 0.2.4 - - id: toolshed.g2.bx.psu.edu/repos/iuc/porechop/porechop/0.2.4+galaxy0 + version: 3.9+galaxy0 + - id: toolshed.g2.bx.psu.edu/repos/iuc/humann_rename_table/humann_rename_table/3.9+galaxy0 servers: - server: http://apostl.moffitt.org/ state: missing @@ -59186,13 +52366,13 @@ - server: https://hyperbrowser.uio.no/coloc-stats state: missing - server: https://galaxy.mesocentre.uca.fr - state: missing - - server: https://galaxy.pasteur.fr/ state: exact - version: 0.2.4+galaxy0 + version: 3.9+galaxy0 + - server: https://galaxy.pasteur.fr/ + state: missing - server: https://galaxytrakr.org/ state: exact - version: 0.2.4+galaxy0 + version: 3.9+galaxy0 - server: http://igg.cloud.ba.infn.it/galaxy state: missing - server: https://galaxy.hyphy.org/ @@ -59203,8 +52383,6 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr @@ -59215,34 +52393,32 @@ state: missing - server: http://pepsimili.e-nios.com:8080/ state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - server: https://usegalaxy.org.au state: exact - version: 0.2.4+galaxy0 + version: 3.9+galaxy0 - server: https://usegalaxy.be/ state: exact - version: 0.2.4+galaxy0 + version: 3.9+galaxy0 - server: https://usegalaxy.cz/ state: exact - version: 0.2.4+galaxy0 + version: 3.9+galaxy0 - server: https://usegalaxy.eu state: exact - version: 0.2.4+galaxy0 + version: 3.9+galaxy0 - server: https://usegalaxy.fr/ + state: exact + version: 3.9+galaxy0 + - server: https://usegalaxy.no/ state: inexact versions: - - 0.2.4+galaxy1 - - server: https://usegalaxy.no/ - state: exact - version: 0.2.4+galaxy0 + - 3.6.0+galaxy0 - server: https://usegalaxy.org state: exact - version: 0.2.4+galaxy0 + version: 3.9+galaxy0 - server: https://viralvariant.anses.fr/ state: missing - version: 0.2.4+galaxy0 - - id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_coverage/samtools_coverage/1.15.1+galaxy2 + version: 3.9+galaxy0 + - id: toolshed.g2.bx.psu.edu/repos/iuc/humann_renorm_table/humann_renorm_table/3.9+galaxy0 servers: - server: http://apostl.moffitt.org/ state: missing @@ -59255,14 +52431,12 @@ - server: https://hyperbrowser.uio.no/coloc-stats state: missing - server: https://galaxy.mesocentre.uca.fr - state: missing + state: exact + version: 3.9+galaxy0 - server: https://galaxy.pasteur.fr/ state: missing - server: https://galaxytrakr.org/ - state: inexact - versions: - - 1.21+galaxy3 - - 1.22+galaxy3 + state: missing - server: http://igg.cloud.ba.infn.it/galaxy state: missing - server: https://galaxy.hyphy.org/ @@ -59273,8 +52447,6 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr @@ -59285,32 +52457,32 @@ state: missing - server: http://pepsimili.e-nios.com:8080/ state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - server: https://usegalaxy.org.au state: exact - version: 1.15.1+galaxy2 + version: 3.9+galaxy0 - server: https://usegalaxy.be/ state: exact - version: 1.15.1+galaxy2 + version: 3.9+galaxy0 - server: https://usegalaxy.cz/ state: exact - version: 1.15.1+galaxy2 + version: 3.9+galaxy0 - server: https://usegalaxy.eu state: exact - version: 1.15.1+galaxy2 + version: 3.9+galaxy0 - server: https://usegalaxy.fr/ state: exact - version: 1.15.1+galaxy2 + version: 3.9+galaxy0 - server: https://usegalaxy.no/ - state: missing + state: inexact + versions: + - 3.6.0+galaxy0 - server: https://usegalaxy.org state: exact - version: 1.15.1+galaxy2 + version: 3.9+galaxy0 - server: https://viralvariant.anses.fr/ state: missing - version: 1.15.1+galaxy2 - - id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_depth/samtools_depth/1.15.1+galaxy2 + version: 3.9+galaxy0 + - id: toolshed.g2.bx.psu.edu/repos/iuc/humann_split_stratified_table/humann_split_stratified_table/3.9+galaxy0 servers: - server: http://apostl.moffitt.org/ state: missing @@ -59324,14 +52496,11 @@ state: missing - server: https://galaxy.mesocentre.uca.fr state: exact - version: 1.15.1+galaxy2 + version: 3.9+galaxy0 - server: https://galaxy.pasteur.fr/ state: missing - server: https://galaxytrakr.org/ - state: inexact - versions: - - 1.22+galaxy1 - - 1.21+galaxy0 + state: missing - server: http://igg.cloud.ba.infn.it/galaxy state: missing - server: https://galaxy.hyphy.org/ @@ -59342,8 +52511,6 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr @@ -59354,38 +52521,32 @@ state: missing - server: http://pepsimili.e-nios.com:8080/ state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - server: https://usegalaxy.org.au state: exact - version: 1.15.1+galaxy2 + version: 3.9+galaxy0 - server: https://usegalaxy.be/ state: exact - version: 1.15.1+galaxy2 + version: 3.9+galaxy0 - server: https://usegalaxy.cz/ state: exact - version: 1.15.1+galaxy2 + version: 3.9+galaxy0 - server: https://usegalaxy.eu state: exact - version: 1.15.1+galaxy2 + version: 3.9+galaxy0 - server: https://usegalaxy.fr/ state: exact - version: 1.15.1+galaxy2 + version: 3.9+galaxy0 - server: https://usegalaxy.no/ state: inexact versions: - - '1.9' - - 1.15.1+galaxy0 - - '1.13' + - 3.6.0+galaxy0 - server: https://usegalaxy.org state: exact - version: 1.15.1+galaxy2 + version: 3.9+galaxy0 - server: https://viralvariant.anses.fr/ - state: inexact - versions: - - 1.21+galaxy0 - version: 1.15.1+galaxy2 - - id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_fastx/samtools_fastx/1.15.1+galaxy2 + state: missing + version: 3.9+galaxy0 + - id: toolshed.g2.bx.psu.edu/repos/iuc/humann_unpack_pathways/humann_unpack_pathways/3.9+galaxy0 servers: - server: http://apostl.moffitt.org/ state: missing @@ -59398,21 +52559,13 @@ - server: https://hyperbrowser.uio.no/coloc-stats state: missing - server: https://galaxy.mesocentre.uca.fr - state: inexact - versions: - - 1.22+galaxy1 - - 1.20+galaxy2 - - 1.9+galaxy1 - - 1.21+galaxy0 + state: exact + version: 3.9+galaxy0 - server: https://galaxy.pasteur.fr/ - state: inexact - versions: - - 1.21+galaxy0 + state: missing - server: https://galaxytrakr.org/ - state: inexact - versions: - - 1.22+galaxy1 - - 1.21+galaxy0 + state: exact + version: 3.9+galaxy0 - server: http://igg.cloud.ba.infn.it/galaxy state: missing - server: https://galaxy.hyphy.org/ @@ -59423,50 +52576,42 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr - state: inexact - versions: - - 1.22+galaxy2 + state: missing - server: http://galaxy.inf.ethz.ch state: missing - server: https://palfinder.ls.manchester.ac.uk/ state: missing - server: http://pepsimili.e-nios.com:8080/ state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - server: https://usegalaxy.org.au state: exact - version: 1.15.1+galaxy2 + version: 3.9+galaxy0 - server: https://usegalaxy.be/ state: exact - version: 1.15.1+galaxy2 + version: 3.9+galaxy0 - server: https://usegalaxy.cz/ state: exact - version: 1.15.1+galaxy2 + version: 3.9+galaxy0 - server: https://usegalaxy.eu state: exact - version: 1.15.1+galaxy2 + version: 3.9+galaxy0 - server: https://usegalaxy.fr/ state: exact - version: 1.15.1+galaxy2 + version: 3.9+galaxy0 - server: https://usegalaxy.no/ state: inexact versions: - - 1.9+galaxy1 - - 1.15.1+galaxy0 - - '1.13' + - 3.6.0+galaxy0 - server: https://usegalaxy.org state: exact - version: 1.15.1+galaxy2 + version: 3.9+galaxy0 - server: https://viralvariant.anses.fr/ state: missing - version: 1.15.1+galaxy2 - - id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_extractFields/4.3+t.galaxy0 + version: 3.9+galaxy0 + - id: toolshed.g2.bx.psu.edu/repos/iuc/metaphlan/metaphlan/4.1.1+galaxy4 servers: - server: http://apostl.moffitt.org/ state: missing @@ -59479,12 +52624,12 @@ - server: https://hyperbrowser.uio.no/coloc-stats state: missing - server: https://galaxy.mesocentre.uca.fr - state: missing + state: exact + version: 4.1.1+galaxy4 - server: https://galaxy.pasteur.fr/ state: missing - server: https://galaxytrakr.org/ - state: exact - version: 4.3+t.galaxy0 + state: missing - server: http://igg.cloud.ba.infn.it/galaxy state: missing - server: https://galaxy.hyphy.org/ @@ -59495,47 +52640,42 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr - state: inexact - versions: - - 5.4.0c+galaxy0 + state: missing - server: http://galaxy.inf.ethz.ch state: missing - server: https://palfinder.ls.manchester.ac.uk/ state: missing - server: http://pepsimili.e-nios.com:8080/ state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - server: https://usegalaxy.org.au state: exact - version: 4.3+t.galaxy0 + version: 4.1.1+galaxy4 - server: https://usegalaxy.be/ state: exact - version: 4.3+t.galaxy0 + version: 4.1.1+galaxy4 - server: https://usegalaxy.cz/ state: exact - version: 4.3+t.galaxy0 + version: 4.1.1+galaxy4 - server: https://usegalaxy.eu state: exact - version: 4.3+t.galaxy0 + version: 4.1.1+galaxy4 - server: https://usegalaxy.fr/ state: exact - version: 4.3+t.galaxy0 + version: 4.1.1+galaxy4 - server: https://usegalaxy.no/ - state: exact - version: 4.3+t.galaxy0 + state: inexact + versions: + - 4.0.3+galaxy0 - server: https://usegalaxy.org state: exact - version: 4.3+t.galaxy0 + version: 4.1.1+galaxy4 - server: https://viralvariant.anses.fr/ state: missing - version: 4.3+t.galaxy0 - - id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_filter/4.3+t.galaxy1 + version: 4.1.1+galaxy4 + - id: toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.27+galaxy3 servers: - server: http://apostl.moffitt.org/ state: missing @@ -59548,12 +52688,18 @@ - server: https://hyperbrowser.uio.no/coloc-stats state: missing - server: https://galaxy.mesocentre.uca.fr - state: missing + state: exact + version: 1.27+galaxy3 - server: https://galaxy.pasteur.fr/ state: missing - server: https://galaxytrakr.org/ - state: exact - version: 4.3+t.galaxy1 + state: inexact + versions: + - 1.27+galaxy4 + - 1.11+galaxy1 + - '1.7' + - 1.35+galaxy1 + - 1.33+galaxy3 - server: http://igg.cloud.ba.infn.it/galaxy state: missing - server: https://galaxy.hyphy.org/ @@ -59564,47 +52710,51 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr state: inexact versions: - - 5.4.0c+galaxy0 + - 1.34+galaxy0 - server: http://galaxy.inf.ethz.ch state: missing - server: https://palfinder.ls.manchester.ac.uk/ state: missing - server: http://pepsimili.e-nios.com:8080/ state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - server: https://usegalaxy.org.au state: exact - version: 4.3+t.galaxy1 + version: 1.27+galaxy3 - server: https://usegalaxy.be/ state: exact - version: 4.3+t.galaxy1 + version: 1.27+galaxy3 - server: https://usegalaxy.cz/ state: exact - version: 4.3+t.galaxy1 + version: 1.27+galaxy3 - server: https://usegalaxy.eu state: exact - version: 4.3+t.galaxy1 + version: 1.27+galaxy3 - server: https://usegalaxy.fr/ state: exact - version: 4.3+t.galaxy1 + version: 1.27+galaxy3 - server: https://usegalaxy.no/ - state: exact - version: 4.3+t.galaxy1 + state: inexact + versions: + - 1.11+galaxy0 + - '1.7' + - 1.7.1 + - 1.8+galaxy0 + - 1.9+galaxy1 + - 1.8+galaxy1 + - '1.9' + - 1.8+galaxy2 - server: https://usegalaxy.org state: exact - version: 4.3+t.galaxy1 + version: 1.27+galaxy3 - server: https://viralvariant.anses.fr/ state: missing - version: 4.3+t.galaxy1 - - id: toolshed.g2.bx.psu.edu/repos/iuc/table_compute/table_compute/1.2.4+galaxy0 + version: 1.27+galaxy3 + - id: toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/5.0+galaxy0 servers: - server: http://apostl.moffitt.org/ state: missing @@ -59618,12 +52768,15 @@ state: missing - server: https://galaxy.mesocentre.uca.fr state: exact - version: 1.2.4+galaxy0 + version: 5.0+galaxy0 - server: https://galaxy.pasteur.fr/ - state: missing + state: inexact + versions: + - 4.9+galaxy1 - server: https://galaxytrakr.org/ - state: exact - version: 1.2.4+galaxy0 + state: inexact + versions: + - 1.16.9 - server: http://igg.cloud.ba.infn.it/galaxy state: missing - server: https://galaxy.hyphy.org/ @@ -59634,45 +52787,45 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr - state: missing + state: inexact + versions: + - 4.8+galaxy1 + - 5.2+galaxy2 - server: http://galaxy.inf.ethz.ch state: missing - server: https://palfinder.ls.manchester.ac.uk/ state: missing - server: http://pepsimili.e-nios.com:8080/ state: missing - - server: 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servers: - server: http://apostl.moffitt.org/ state: missing @@ -59686,146 +52839,87 @@ state: missing - server: https://galaxy.mesocentre.uca.fr state: exact - version: 5.1.0 + version: 4.3.6+galaxy0 - server: https://galaxy.pasteur.fr/ state: exact - version: 5.1.0 + version: 4.3.6+galaxy0 - server: https://galaxytrakr.org/ - state: exact - version: 5.1.0 + state: inexact + versions: + - 2.1b.6 - server: http://igg.cloud.ba.infn.it/galaxy state: missing - server: https://galaxy.hyphy.org/ - state: exact - version: 5.1.0 + state: missing - server: https://www.immportgalaxy.org/ state: missing - server: http://galaxy.interactomix.com/ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr - state: exact - version: 5.1.0 + state: missing - server: http://galaxy.inf.ethz.ch state: missing - server: 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[] tutorial: [] video: false - tutorial_name: pathogen-detection-from-nanopore-foodborne-data + tutorial_name: metatranscriptomics-short type: tutorial - url: https://training.galaxyproject.org//topics/microbiome/tutorials/pathogen-detection-from-nanopore-foodborne-data/tutorial.html + url: https://training.galaxyproject.org//topics/microbiome/tutorials/metatranscriptomics-short/tutorial.html urls: - hands_on: https://training.galaxyproject.org/training-material/api/topics/microbiome/tutorials/pathogen-detection-from-nanopore-foodborne-data/tutorial.json - slides: https://training.galaxyproject.org/training-material/api/topics/microbiome/tutorials/pathogen-detection-from-nanopore-foodborne-data/tutorial.json - version: 12 + hands_on: https://training.galaxyproject.org/training-material/api/topics/microbiome/tutorials/metatranscriptomics-short/tutorial.json + slides: https://training.galaxyproject.org/training-material/api/topics/microbiome/tutorials/metatranscriptomics-short/tutorial.json + version: 6 video: true video_versions: 2 video_view: 0 - visit_duration: 514 - visitors: 5672 + visit_duration: 592 + visitors: 1094 workflows: - creators: - - class: Person - identifier: 0000-0001-9047-4215 - name: Engy Nasr - url: https://orcid.org/0000-0001-9047-4215 - class: Person identifier: 0000-0001-9852-1987 name: "B\xE9r\xE9nice Batut" - url: https://orcid.org/0000-0001-9852-1987 + - class: Person + identifier: 0000-0003-0984-0973 + name: Pratik Jagtap + - class: Person + identifier: 0000-0001-9818-0537 + name: Subina Mehta + - class: Person + identifier: 0000-0003-3803-468X + name: Saskia Hiltemann - class: Person identifier: 0000-0003-2982-388X name: Paul Zierep - description: Microbiome - Variant calling and Consensus Building + description: Metatranscriptomics analysis using microbiome RNA-seq data (short) features: comments: true - parameters: true + parameters: false report: - markdown: "# Allele based Pathogen Identification Workflow Report\nBelow are\ - \ the results for the Allele based Pathogenic Identification Workflow\n\n\ - This workflow was run on:\n\n```galaxy\ngenerate_time()\n```\n\nWith Galaxy\ - \ version:\n\n```galaxy\ngenerate_galaxy_version()\n```\n\n## Workflow Inputs\n\ - The Perprocessing workflow main output (Collection of all samples reads\ - \ after quality retaining and hosts filtering), and a FASTA file of the\ - \ reference genome of the main Pathogen identified in the Gene based Pathogen\ - \ Identification workflow, or per-known to the user.\n\n## Workflow Output:\ - \ \n\n### All variants found per sample against the reference genome\n\n\ - ```galaxy\nhistory_dataset_display(output=\"extracted_fields_from_the_vcf_output\"\ - )\n```\n\n### Number of variants per sample\n\n```galaxy\nhistory_dataset_display(output=\"\ - number_of_variants_per_sample\")\n```\n\n### Mapping mean depth per sample\n\ - \n```galaxy\nhistory_dataset_display(output=\"mapping_mean_depth_per_sample\"\ - )\n```\n\n### Mapping coverage per sample\n\n```galaxy\nhistory_dataset_display(output=\"\ - mapping_coverage_percentage_per_sample\")\n```\n" + markdown: ' + + # Workflow Execution Report + + + ## Workflow Inputs + + ```galaxy + + invocation_inputs() + + ``` + + + ## Workflow Outputs + + ```galaxy + + invocation_outputs() + + ``` + + + ## Workflow + + ```galaxy + + workflow_display() + + ``` + + ' subworkflows: false graph_dot: "digraph main {\n node [fontname=\"Atkinson Hyperlegible\", shape=box,\ \ color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n edge [fontname=\"\ - Atkinson Hyperlegible\"];\n 0[color=lightblue,label=\"\u2139\uFE0F Input Collection\\\ - ncollection_of_preprocessed_samples\"]\n 1[color=lightgreen,label=\"\u2139\uFE0F\ - \ Input Parameter\\nsamples_profile\"]\n 2[color=lightblue,label=\"\u2139\uFE0F\ - \ Input Dataset\\nreference_genome_of_tested_strain\"]\n 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[label=\"output\"]\n 12 ->\ - \ 22 [label=\"table\"]\n k25b7b87b5ef1487f90cc81351a2f81ce[color=lightseagreen,label=\"\ - Output\\nmapping_mean_depth_per_sample\"]\n 22 -> k25b7b87b5ef1487f90cc81351a2f81ce\n\ - \ 23[label=\"Select first\"]\n 21 -> 23 [label=\"out_file1\"]\n 24[label=\"\ - Collapse Collection\"]\n 23 -> 24 [label=\"outfile\"]\n 25[label=\"Column\ - \ Regex Find And Replace\"]\n 24 -> 25 [label=\"output\"]\n k2852c4ee24ea4df7b59e54eb6e2f470b[color=lightseagreen,label=\"\ - Output\\nnumber_of_variants_per_sample\"]\n 25 -> k2852c4ee24ea4df7b59e54eb6e2f470b\n\ - }" + Atkinson Hyperlegible\"];\n 0[color=lightblue,label=\"\u2139\uFE0F Input Dataset\\\ + nReverse raw reads\"]\n 1[color=lightblue,label=\"\u2139\uFE0F Input Dataset\\\ + nForward raw reads\"]\n 2[label=\"FastQC\"]\n 0 -> 2 [label=\"output\"]\n\ + \ k676cd11f047947c4a23bc6c8ed5a7790[color=lightseagreen,label=\"Output\\nfastqc_reverse_html_file\"\ + ]\n 2 -> k676cd11f047947c4a23bc6c8ed5a7790\n 3[label=\"FastQC\"]\n 1 -> 3\ + \ [label=\"output\"]\n k1fb52b78c90543c7a295d628c996d35a[color=lightseagreen,label=\"\ + Output\\nfastqc_forward_html_file\"]\n 3 -> k1fb52b78c90543c7a295d628c996d35a\n\ + \ 4[label=\"Cutadapt\"]\n 1 -> 4 [label=\"output\"]\n 0 -> 4 [label=\"output\"\ + ]\n k0e7406ed9eca486eb19a4cbbf04b5138[color=lightseagreen,label=\"Output\\\ + ncutadapt_report\"]\n 4 -> k0e7406ed9eca486eb19a4cbbf04b5138\n 5[label=\"\ + MultiQC\"]\n 3 -> 5 [label=\"text_file\"]\n 2 -> 5 [label=\"text_file\"]\n\ + \ kd9f371ddaa6c4540b62b0e34c0b71afa[color=lightseagreen,label=\"Output\\nmultiqc_html_report\"\ + ]\n 5 -> kd9f371ddaa6c4540b62b0e34c0b71afa\n 6[label=\"Filter with SortMeRNA\"\ + ]\n 4 -> 6 [label=\"out1\"]\n 4 -> 6 [label=\"out2\"]\n k3092eb62d7fc4d66bf574c6cf491d0e3[color=lightseagreen,label=\"\ + Output\\nsortmerna_unaligned_reverse\"]\n 6 -> k3092eb62d7fc4d66bf574c6cf491d0e3\n\ + \ kdb3bb8ee8af74528be4bf3ea6d381856[color=lightseagreen,label=\"Output\\nsortmerna_unaligned_forward\"\ + ]\n 6 -> kdb3bb8ee8af74528be4bf3ea6d381856\n 7[label=\"FASTQ interlacer\"\ + ]\n 6 -> 7 [label=\"unaligned_forward\"]\n 6 -> 7 [label=\"unaligned_reverse\"\ + ]\n}" history: - - hash: fea16c6949ebaafe1f872bfe3a5f05958a15e7f9 - message: updating to include all previous comments + - hash: 604d1261ba4f89d6650304d72c7b6d8e4166b3a6 + message: 'Update metatranscriptomics tutorials:' + num: 2 + short_hash: 604d1261b + unix: '1750082204' + - hash: 0e0a2f2ccb650b0aab1ffc13838045164bdb5d30 + message: Rename metagenomics topic to microbiome num: 1 - short_hash: fea16c694 - unix: '1718833675' + short_hash: 0e0a2f2cc + unix: '1704901629' inputs: - - annotation: Output collection from the Nanopore Preprocessing workflow + - annotation: Metatranscriptomics reverse raw reads content_id: null errors: null id: 0 input_connections: {} inputs: - - description: Output collection from the Nanopore Preprocessing workflow - name: collection_of_preprocessed_samples - label: collection_of_preprocessed_samples - name: Input dataset collection + - description: Metatranscriptomics reverse raw reads + name: Reverse raw reads + label: Reverse raw reads + name: Input dataset outputs: [] position: - left: 6 - top: 205 + left: 0 + top: 550 tool_id: null - tool_state: '{"optional": false, "tag": null, "collection_type": "list"}' + tool_state: '{"optional": false, "tag": null}' tool_version: null - type: data_collection_input - uuid: 7aaa03a4-2647-411b-863d-90f28ed01f32 + type: data_input + uuid: 9871068a-7fcf-4e95-8e77-958e3f536c55 when: null workflow_outputs: [] - - annotation: 'based on the lab preparation of the samples during sequencing, - there should be a sample profile better than the other, to be chosen as an - optional input to Minimap2. e.g. PacBio/Oxford Nanpore - - - For more details check: https://github.com/lh3/minimap2?tab=readme-ov-file#use-cases' + - annotation: Metatranscriptomics forward raw reads content_id: null errors: null id: 1 input_connections: {} inputs: - - description: 'based on the lab preparation of the samples during sequencing, - there should be a sample profile better than the other, to be chosen as - an optional input to Minimap2. e.g. PacBio/Oxford Nanpore - - - For more details check: https://github.com/lh3/minimap2?tab=readme-ov-file#use-cases' - name: samples_profile - label: samples_profile - name: Input parameter - outputs: [] - position: - left: 260 - top: 35 - tool_id: null - tool_state: '{"restrictOnConnections": true, "parameter_type": "text", "optional": - true}' - tool_version: null - type: parameter_input - uuid: d28b9bed-c674-406c-b58b-165bcc8eec17 - when: null - workflow_outputs: [] - - annotation: Can be built in the tool later - content_id: null - errors: null - id: 2 - input_connections: {} - inputs: - - description: Can be built in the tool later - name: reference_genome_of_tested_strain - label: reference_genome_of_tested_strain + - description: Metatranscriptomics forward raw reads + name: Forward raw reads + label: Forward raw reads name: Input dataset outputs: [] position: left: 0 - top: 374 + top: 690 tool_id: null - tool_state: '{"optional": false, "tag": ""}' + tool_state: '{"optional": false, "tag": null}' tool_version: null type: data_input - uuid: 773b7592-d66c-4a85-92ba-06c0ab0f843f - when: null - workflow_outputs: [] - license: MIT - mermaid: "flowchart TD\n 0[\"\u2139\uFE0F Input Collection\\ncollection_of_preprocessed_samples\"\ - ];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"\u2139\uFE0F Input Parameter\\\ - nsamples_profile\"];\n style 1 fill:#ded,stroke:#393,stroke-width:4px;\n 2[\"\ - \u2139\uFE0F Input Dataset\\nreference_genome_of_tested_strain\"];\n style\ - \ 2 stroke:#2c3143,stroke-width:4px;\n 3[\"Convert compressed file to uncompressed.\"\ - ];\n 2 -->|output| 3;\n 9d6bde4a-7180-4097-9ffd-6992111a617c[\"Output\\ndecompressed_rg_file\"\ - ];\n 3 --> 9d6bde4a-7180-4097-9ffd-6992111a617c;\n style 9d6bde4a-7180-4097-9ffd-6992111a617c\ - \ stroke:#2c3143,stroke-width:4px;\n 4[\"Map with minimap2\"];\n 1 -->|output|\ - \ 4;\n 0 -->|output| 4;\n 3 -->|output1| 4;\n 31779c23-4f26-418e-9418-2551e883dbe7[\"\ - Output\\nmap_with_minimap2\"];\n 4 --> 31779c23-4f26-418e-9418-2551e883dbe7;\n\ - \ style 31779c23-4f26-418e-9418-2551e883dbe7 stroke:#2c3143,stroke-width:4px;\n\ - \ 5[\"Clair3\"];\n 4 -->|alignment_output| 5;\n 3 -->|output1| 5;\n 1cf1ee6c-4cb7-45e3-9c7b-88a1b678dd53[\"\ - Output\\nclair3_pileup_vcf\"];\n 5 --> 1cf1ee6c-4cb7-45e3-9c7b-88a1b678dd53;\n\ - \ style 1cf1ee6c-4cb7-45e3-9c7b-88a1b678dd53 stroke:#2c3143,stroke-width:4px;\n\ - \ 987f9145-83ab-44f1-801a-b0d527ecbce8[\"Output\\nclair3_full_alignment_vcf\"\ - ];\n 5 --> 987f9145-83ab-44f1-801a-b0d527ecbce8;\n style 987f9145-83ab-44f1-801a-b0d527ecbce8\ - \ stroke:#2c3143,stroke-width:4px;\n fab82215-f59a-43b1-92d7-37629a1fdb65[\"\ - Output\\nclair3_merged_output\"];\n 5 --> fab82215-f59a-43b1-92d7-37629a1fdb65;\n\ - \ style fab82215-f59a-43b1-92d7-37629a1fdb65 stroke:#2c3143,stroke-width:4px;\n\ - \ 6[\"Samtools depth\"];\n 4 -->|alignment_output| 6;\n 7[\"Samtools coverage\"\ - ];\n 4 -->|alignment_output| 7;\n 8[\"bcftools norm\"];\n 5 -->|merge_output|\ - \ 8;\n 3 -->|output1| 8;\n 22553aa1-f5db-4d37-87c4-1164dbb3d2d5[\"Output\\\ - nnormalized_vcf_output\"];\n 8 --> 22553aa1-f5db-4d37-87c4-1164dbb3d2d5;\n\ - \ style 22553aa1-f5db-4d37-87c4-1164dbb3d2d5 stroke:#2c3143,stroke-width:4px;\n\ - \ 9[\"Advanced Cut\"];\n 6 -->|output| 9;\n 10[\"Remove beginning\"];\n \ - \ 7 -->|output| 10;\n 11[\"SnpSift Filter\"];\n 8 -->|output_file| 11;\n \ - \ 3e7981ec-2205-4571-93eb-10c0dd14b288[\"Output\\nquality_filtered_vcf_output\"\ - ];\n 11 --> 3e7981ec-2205-4571-93eb-10c0dd14b288;\n style 3e7981ec-2205-4571-93eb-10c0dd14b288\ - \ stroke:#2c3143,stroke-width:4px;\n 12[\"Table Compute\"];\n 9 -->|output|\ - \ 12;\n 13[\"Cut\"];\n 10 -->|out_file1| 13;\n 14[\"SnpSift Extract Fields\"\ - ];\n 11 -->|output| 14;\n 1b0f4f2c-4717-45be-b580-fe10cba78c35[\"Output\\\ - 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toolshed.g2.bx.psu.edu/repos/rnateam/sortmerna/bg_sortmerna/4.3.6+galaxy0 + workflowhub_id: '1444' - creators: - - class: Person - identifier: 0000-0001-9047-4215 - name: Engy Nasr - url: https://orcid.org/0000-0001-9047-4215 - class: Person identifier: 0000-0001-9852-1987 name: "B\xE9r\xE9nice Batut" - url: https://orcid.org/0000-0001-9852-1987 + - class: Person + identifier: 0000-0003-0984-0973 + name: Pratik Jagtap + - class: Person + identifier: 0000-0001-9818-0537 + name: Subina Mehta + - class: Person + identifier: 0000-0003-3803-468X + name: Saskia Hiltemann - class: Person identifier: 0000-0003-2982-388X - name: Paul Zierep - description: Nanopore datasets analysis - Phylogenetic Identification - antibiotic - resistance genes detection and contigs building - features: - comments: true - parameters: false - report: - markdown: '# Gene based Pathogen Identification Workflow Report - - - Below are the results for the Gene based Pathogen Identification Workflow - - - This workflow was run on: - - - ```galaxy - - generate_time() - - ``` - - - With Galaxy version: - - - ```galaxy - - generate_galaxy_version() + name: Paul Zierep + description: Metatranscriptomics analysis using microbiome RNA-seq data (short) + features: + comments: true + parameters: false + report: + markdown: ' - ``` + # Workflow Execution Report ## Workflow Inputs - The Perprocessing workflow main output (Collection of all samples reads - after quality retaining and hosts filtering) - - - ## Workflow Output - - - ### Identified contigs per sample - - ```galaxy - history_dataset_display(output="contigs") + invocation_inputs() ``` - ### Identified pathogenic genes per sample - + ## Workflow Outputs ```galaxy - history_dataset_display(output="vfs") + invocation_outputs() ``` - ### Identified Antimicrobial Resistance genes per sample - + ## Workflow ```galaxy - history_dataset_display(output="amrs") + workflow_display() ``` @@ -60677,1787 +53422,1114 @@ subworkflows: false graph_dot: "digraph main 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kb13521dbf5e74bf3b7fa673d13fc2911\n\ + \ 3[label=\"Cut\"]\n 2 -> 3 [label=\"output_file\"]\n 4[label=\"Krona pie\ + \ chart\"]\n 2 -> 4 [label=\"krona_output_file\"]\n 5[label=\"Export to GraPhlAn\"\ + ]\n 3 -> 5 [label=\"out_file1\"]\n 6[label=\"Generation, personalization and\ + \ annotation of tree\"]\n 5 -> 6 [label=\"annotation\"]\n 5 -> 6 [label=\"\ + tree\"]\n 7[label=\"GraPhlAn\"]\n 6 -> 7 [label=\"output_tree\"]\n k21fca66fdce0496f994fdc8e855e0c8f[color=lightseagreen,label=\"\ + Output\\ngraphlan_output_image\"]\n 7 -> k21fca66fdce0496f994fdc8e855e0c8f\n\ + }" history: - - hash: cdd93376adc6ce80742881c25d6810bcce85fc05 - message: adding tags to some of the workflow outputs, updating the training - with the latest PathoGFAIR workflows updates + - hash: 604d1261ba4f89d6650304d72c7b6d8e4166b3a6 + message: 'Update metatranscriptomics tutorials:' num: 2 - short_hash: cdd93376a - unix: '1717675229' - - hash: c63ce23c7a7a631f1256b8e733defce3ca4e009b - message: updating workflows file names + short_hash: 604d1261b + unix: '1750082204' + - hash: 0e0a2f2ccb650b0aab1ffc13838045164bdb5d30 + message: Rename metagenomics topic to microbiome num: 1 - short_hash: c63ce23c7 - unix: '1716726587' + short_hash: 0e0a2f2cc + unix: '1704901629' inputs: - - annotation: Output collection from the Nanopore Preprocessing workflow + - annotation: Metatranscriptomics forward preprocessed reads content_id: null errors: null id: 0 input_connections: {} inputs: - - description: Output collection from the Nanopore Preprocessing workflow - name: collection_of_preprocessed_samples - label: collection_of_preprocessed_samples - name: Input dataset collection + - description: Metatranscriptomics forward preprocessed reads + name: Forward reads + label: Forward reads + name: Input dataset outputs: [] position: left: 0 - top: 316.35 + top: 50 tool_id: null - tool_state: '{"optional": false, "tag": null, "collection_type": "list"}' + tool_state: '{"optional": false, "tag": null}' tool_version: null - type: data_collection_input - uuid: fb7f7c4b-70a7-4d6d-8b20-a3bfdc4380ff + type: data_input + uuid: 4bf6d16f-73df-4104-8282-46b69813c225 when: null workflow_outputs: [] - license: MIT - mermaid: "flowchart TD\n 0[\"\u2139\uFE0F Input Collection\\ncollection_of_preprocessed_samples\"\ - ];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"Extract element identifiers\"\ - ];\n 0 -->|output| 1;\n d82a93c6-23a9-4f85-879c-ecd759a31087[\"Output\\nextracted_samples_IDs\"\ - ];\n 1 --> d82a93c6-23a9-4f85-879c-ecd759a31087;\n style d82a93c6-23a9-4f85-879c-ecd759a31087\ - \ stroke:#2c3143,stroke-width:4px;\n 2[\"Build list\"];\n 0 -->|output| 2;\n\ - \ f5b5b256-8ddf-4da8-8111-b1f6d3025a0d[\"Output\\nlist_of_lists_of_preprocessed_samples\"\ - ];\n 2 --> f5b5b256-8ddf-4da8-8111-b1f6d3025a0d;\n style f5b5b256-8ddf-4da8-8111-b1f6d3025a0d\ - \ stroke:#2c3143,stroke-width:4px;\n 3[\"Split file\"];\n 1 -->|output| 3;\n\ - \ 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de06c362-5b0a-4c29-956e-fbf02539789a[\"Output\\\ - nsample_specific_contigs_tabular_file_preparation\"];\n 9 --> de06c362-5b0a-4c29-956e-fbf02539789a;\n\ - \ style de06c362-5b0a-4c29-956e-fbf02539789a stroke:#2c3143,stroke-width:4px;\n\ - \ 10[\"ABRicate\"];\n 6 -->|out_consensus| 10;\n 8f227fc7-2d92-4c6f-af64-e841c1315b4f[\"\ - Output\\nabricate_with_vfdb_to_identify_genes_with_VFs\"];\n 10 --> 8f227fc7-2d92-4c6f-af64-e841c1315b4f;\n\ - \ style 8f227fc7-2d92-4c6f-af64-e841c1315b4f stroke:#2c3143,stroke-width:4px;\n\ - \ 11[\"ABRicate\"];\n 6 -->|out_consensus| 11;\n fa021d98-d885-4834-ac62-f30d5792260e[\"\ - Output\\nabricate_report_using_ncbi_database_to_indentify_amr\"];\n 11 -->\ - \ fa021d98-d885-4834-ac62-f30d5792260e;\n style fa021d98-d885-4834-ac62-f30d5792260e\ - \ stroke:#2c3143,stroke-width:4px;\n 12[\"Replace\"];\n 8 -->|out1| 12;\n\ - \ 9 -->|output| 12;\n 174cb2c3-ed28-453c-8afb-85150e0b51ad[\"Output\\nsample_specific_contigs_tabular_file\"\ - ];\n 12 --> 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content_id: toolshed.g2.bx.psu.edu/repos/iuc/collection_element_identifiers/collection_element_identifiers/0.0.2 + - annotation: Metatranscriptomics reverse preprocessed reads + content_id: null errors: null id: 1 - input_connections: - input_collection: - id: 0 - output_name: output - inputs: [] - label: null - name: Extract element identifiers - outputs: - - name: output - type: txt + input_connections: {} + inputs: + - description: Metatranscriptomics reverse preprocessed reads + name: Reverse reads + label: Reverse reads + name: Input dataset + outputs: [] position: - left: 322.37152236646415 - top: 59.69265140673434 - post_job_actions: - RenameDatasetActionoutput: - action_arguments: - newname: extracted_samples_IDs - action_type: RenameDatasetAction - output_name: output - tool_id: toolshed.g2.bx.psu.edu/repos/iuc/collection_element_identifiers/collection_element_identifiers/0.0.2 - tool_shed_repository: - changeset_revision: d3c07d270a50 - name: collection_element_identifiers - owner: iuc - tool_shed: toolshed.g2.bx.psu.edu - tool_state: '{"input_collection": {"__class__": "ConnectedValue"}, "__page__": - null, "__rerun_remap_job_id__": null}' - tool_version: 0.0.2 - type: tool - uuid: 80a87744-c9fa-498c-9412-b59346fb7904 + left: 0 + top: 170 + tool_id: null + tool_state: '{"optional": false, "tag": null}' + tool_version: null + type: data_input + uuid: 9871068a-7fcf-4e95-8e77-958e3f536c55 when: null - workflow_outputs: - - label: extracted_samples_IDs - output_name: output - uuid: d82a93c6-23a9-4f85-879c-ecd759a31087 + workflow_outputs: [] + license: MIT + mermaid: "flowchart TD\n 0[\"\u2139\uFE0F Input Dataset\\nForward reads\"];\n\ + \ style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"\u2139\uFE0F Input Dataset\\\ + nReverse reads\"];\n style 1 stroke:#2c3143,stroke-width:4px;\n 2[\"MetaPhlAn\"\ + ];\n 0 -->|output| 2;\n 1 -->|output| 2;\n b13521db-f5e7-4bf3-b7fa-673d13fc2911[\"\ + Output\\nmetaphlan_predicted_taxons\"];\n 2 --> 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inputs|in|raw_in|in_f: id: 0 output_name: output - inputs: [] - label: null - name: Build list - outputs: - - name: output - type: input - position: - left: 330 - top: 597.5999771118164 - post_job_actions: - RenameDatasetActionoutput: - action_arguments: - newname: list_of_lists_of_preprocessed_samples - action_type: RenameDatasetAction - output_name: output - tool_id: __BUILD_LIST__ - tool_state: '{"datasets": [{"__index__": 0, "input": {"__class__": "ConnectedValue"}, - "id_cond": {"id_select": "idx", "__current_case__": 0}}], "__page__": null, - "__rerun_remap_job_id__": null}' - tool_version: 1.2.0 - type: tool - uuid: 38bc82a3-b563-44cf-b0db-9e3311fe99bb - when: null - workflow_outputs: - - label: list_of_lists_of_preprocessed_samples - output_name: output - uuid: f5b5b256-8ddf-4da8-8111-b1f6d3025a0d - - annotation: '' - content_id: toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.0 - errors: null - id: 3 - input_connections: - split_parms|input: + inputs|in|raw_in|in_r: id: 1 output_name: output - inputs: - - description: runtime parameter for tool Split file - name: split_parms - label: null - name: Split file - outputs: - - name: list_output_txt - type: input - position: - left: 608.6215223664642 - top: 47.19265140673434 - post_job_actions: - RenameDatasetActionlist_output_txt: - action_arguments: - newname: splitted_extracted_samples_IDs - action_type: RenameDatasetAction - output_name: list_output_txt - tool_id: toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.0 - tool_shed_repository: - changeset_revision: 6cbe2f30c2d7 - name: split_file_to_collection - owner: bgruening - tool_shed: toolshed.g2.bx.psu.edu - tool_state: '{"split_parms": {"select_ftype": "txt", "__current_case__": 5, - "input": {"__class__": "ConnectedValue"}, "select_mode": {"mode": "chunk", - "__current_case__": 0, "chunksize": "1"}, "newfilenames": "split_file", "select_allocate": - 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input_connections: - input_file: - id: 4 - output_name: assembly_gfa + input_tree: + id: 6 + output_name: output_tree inputs: [] label: null - name: Bandage Image + name: GraPhlAn outputs: - - name: outfile - type: jpg + - name: png_output_image + type: png position: - left: 927.4666748046875 - top: 965.5333251953125 - post_job_actions: - RenameDatasetActionoutfile: - action_arguments: - newname: bandage_assembly_graph_image - action_type: RenameDatasetAction - output_name: outfile - TagDatasetActionoutfile: - action_arguments: - tags: bandage_contigs_image - action_type: TagDatasetAction - output_name: outfile - tool_id: toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/2022.09+galaxy4 + left: 1340 + top: 50 + post_job_actions: {} + tool_id: toolshed.g2.bx.psu.edu/repos/iuc/graphlan/graphlan/1.1.3 tool_shed_repository: - changeset_revision: ddddce450736 - name: bandage + changeset_revision: 6e8eb0c0d91f + name: graphlan owner: iuc tool_shed: toolshed.g2.bx.psu.edu - tool_state: 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microbiome/metatranscriptomics-short + path: topics/microbiome/tutorials/metatranscriptomics-short/workflows/workflow2_community_profile.ga + tags: + - microbiome + test_results: null + tests: true + title: 'Metatranscriptomics analysis using microbiome RNA-seq data - Workflow + 2: Community profile' + topic_id: microbiome + trs_endpoint: https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/microbiome-metatranscriptomics-short/versions/workflow2-community-profile + tutorial_id: metatranscriptomics-short + url: https://training.galaxyproject.org/training-material/topics/microbiome/tutorials/metatranscriptomics-short/workflows/workflow2_community_profile.ga + url_html: https://training.galaxyproject.org/training-material/topics/microbiome/tutorials/metatranscriptomics-short/workflows/workflow2_community_profile.html + version: 2 + wfid: microbiome-metatranscriptomics-short + wfname: workflow2-community-profile + workflow: workflow2_community_profile.ga + workflow_tools: + - Cut1 + - toolshed.g2.bx.psu.edu/repos/crs4/taxonomy_krona_chart/taxonomy_krona_chart/2.7.1+galaxy0 + - toolshed.g2.bx.psu.edu/repos/iuc/export2graphlan/export2graphlan/0.20+galaxy0 + - toolshed.g2.bx.psu.edu/repos/iuc/graphlan/graphlan/1.1.3 + - toolshed.g2.bx.psu.edu/repos/iuc/graphlan_annotate/graphlan_annotate/1.1.3 + - toolshed.g2.bx.psu.edu/repos/iuc/metaphlan/metaphlan/4.1.1+galaxy4 + workflowhub_id: '1451' + - creators: + - class: Person + identifier: 0000-0001-9852-1987 + name: "B\xE9r\xE9nice Batut" + - class: Person + identifier: 0000-0003-0984-0973 + name: Pratik Jagtap + - class: Person + identifier: 0000-0001-9818-0537 + name: Subina Mehta + - class: Person + identifier: 0000-0003-3803-468X + name: Saskia Hiltemann + - class: Person + identifier: 0000-0003-2982-388X + name: Paul Zierep + description: Metatranscriptomics analysis using microbiome RNA-seq data (short) + features: + comments: true + parameters: false + report: + markdown: ' + + # Workflow Execution Report + + + ## Workflow Inputs + + ```galaxy + + invocation_inputs() + + ``` + + + ## Workflow Outputs + + ```galaxy + + invocation_outputs() + + ``` + + + ## Workflow + + ```galaxy + + workflow_display() + + ``` + + ' + subworkflows: false + graph_dot: "digraph main {\n node [fontname=\"Atkinson Hyperlegible\", shape=box,\ + \ color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n edge [fontname=\"\ + Atkinson Hyperlegible\"];\n 0[color=lightblue,label=\"\u2139\uFE0F Input Dataset\\\ + nInterleaced reads\"]\n 1[color=lightblue,label=\"\u2139\uFE0F Input Dataset\\\ + nTaxonomic profile\"]\n 2[label=\"HUMAnN\"]\n 0 -> 2 [label=\"output\"]\n\ + \ 1 -> 2 [label=\"output\"]\n k53259a0607834db8828e328e7337f5b3[color=lightseagreen,label=\"\ + Output\\nhumann_gene_families\"]\n 2 -> k53259a0607834db8828e328e7337f5b3\n\ + \ k5aec39b6317a4fd0b90622d5a965e957[color=lightseagreen,label=\"Output\\nhumann_pathabundance\"\ + ]\n 2 -> k5aec39b6317a4fd0b90622d5a965e957\n 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[label=\"output\"]\n 7 -> 12 [label=\"output\"]\n kb24357e8b6d34893af63ac4cf7494b33[color=lightseagreen,label=\"\ + Output\\nunpack_pathway_abundance\"]\n 12 -> kb24357e8b6d34893af63ac4cf7494b33\n\ + \ 13[label=\"Select\"]\n 10 -> 13 [label=\"output\"]\n k946a04fd18544f088df11a3165651bae[color=lightseagreen,label=\"\ + Output\\ncc_go\"]\n 13 -> k946a04fd18544f088df11a3165651bae\n 14[label=\"\ + Select\"]\n 10 -> 14 [label=\"output\"]\n k4f5f059739eb42ce8dd8d920b52231c3[color=lightseagreen,label=\"\ + Output\\nbp_go\"]\n 14 -> k4f5f059739eb42ce8dd8d920b52231c3\n 15[label=\"\ + Select\"]\n 10 -> 15 [label=\"output\"]\n 16[label=\"Split a HUMAnN table\"\ + ]\n 13 -> 16 [label=\"out_file1\"]\n 17[label=\"Split a HUMAnN table\"]\n\ + \ 14 -> 17 [label=\"out_file1\"]\n 18[label=\"Sort\"]\n 15 -> 18 [label=\"\ + out_file1\"]\n k71abb759b51f4383a79127d8b1325e81[color=lightseagreen,label=\"\ + Output\\nsorted_mf_go\"]\n 18 -> k71abb759b51f4383a79127d8b1325e81\n 19[label=\"\ + Split a HUMAnN table\"]\n 15 -> 19 [label=\"out_file1\"]\n}" + history: + - hash: 604d1261ba4f89d6650304d72c7b6d8e4166b3a6 + message: 'Update metatranscriptomics tutorials:' + num: 2 + short_hash: 604d1261b + unix: '1750082204' + - hash: 0e0a2f2ccb650b0aab1ffc13838045164bdb5d30 + message: Rename metagenomics topic to microbiome + num: 1 + short_hash: 0e0a2f2cc + unix: '1704901629' + inputs: + - annotation: Metatranscriptomics interleaced reads + content_id: null + errors: null + id: 0 + input_connections: {} + inputs: + - description: Metatranscriptomics interleaced reads + name: Interleaced reads + label: Interleaced reads + name: Input dataset + outputs: [] + position: + left: 0.0 + top: 432.13598882837186 + tool_id: null + tool_state: '{"optional": false, "tag": null}' + tool_version: null + type: data_input + uuid: a89e6296-7ab8-4a94-865c-840652bb6fbe + when: null + workflow_outputs: [] + - annotation: Taxonomic profile generated by MetaPhlAn + content_id: null + errors: null + id: 1 + input_connections: {} + inputs: + - description: Taxonomic profile generated by MetaPhlAn + name: Taxonomic profile + label: Taxonomic profile + name: Input dataset + outputs: [] + position: + left: 11.132786128095177 + top: 623.6000061035156 + tool_id: null + tool_state: '{"optional": false, "tag": null}' + tool_version: null + type: data_input + uuid: a40d68df-fdf3-441a-bc58-faf123df908f + when: null + workflow_outputs: [] + license: MIT + mermaid: "flowchart TD\n 0[\"\u2139\uFE0F Input Dataset\\nInterleaced reads\"\ + ];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"\u2139\uFE0F Input Dataset\\\ + nTaxonomic profile\"];\n style 1 stroke:#2c3143,stroke-width:4px;\n 2[\"HUMAnN\"\ + ];\n 0 -->|output| 2;\n 1 -->|output| 2;\n 53259a06-0783-4db8-828e-328e7337f5b3[\"\ + Output\\nhumann_gene_families\"];\n 2 --> 53259a06-0783-4db8-828e-328e7337f5b3;\n\ + \ style 53259a06-0783-4db8-828e-328e7337f5b3 stroke:#2c3143,stroke-width:4px;\n\ + \ 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\ a HUMAnN table\"];\n 4 -->|output| 9;\n 10[\"Rename features\"];\n 4 -->|output|\ + \ 10;\n 11[\"Replace\"];\n 5 -->|output| 11;\n 12[\"Unpack pathway abundances\"\ + ];\n 5 -->|output| 12;\n 7 -->|output| 12;\n b24357e8-b6d3-4893-af63-ac4cf7494b33[\"\ + Output\\nunpack_pathway_abundance\"];\n 12 --> b24357e8-b6d3-4893-af63-ac4cf7494b33;\n\ + \ style b24357e8-b6d3-4893-af63-ac4cf7494b33 stroke:#2c3143,stroke-width:4px;\n\ + \ 13[\"Select\"];\n 10 -->|output| 13;\n 946a04fd-1854-4f08-8df1-1a3165651bae[\"\ + Output\\ncc_go\"];\n 13 --> 946a04fd-1854-4f08-8df1-1a3165651bae;\n style\ + \ 946a04fd-1854-4f08-8df1-1a3165651bae stroke:#2c3143,stroke-width:4px;\n 14[\"\ + Select\"];\n 10 -->|output| 14;\n 4f5f0597-39eb-42ce-8dd8-d920b52231c3[\"\ + Output\\nbp_go\"];\n 14 --> 4f5f0597-39eb-42ce-8dd8-d920b52231c3;\n style\ + \ 4f5f0597-39eb-42ce-8dd8-d920b52231c3 stroke:#2c3143,stroke-width:4px;\n 15[\"\ + Select\"];\n 10 -->|output| 15;\n 16[\"Split a HUMAnN table\"];\n 13 -->|out_file1|\ + \ 16;\n 17[\"Split a HUMAnN table\"];\n 14 -->|out_file1| 17;\n 18[\"Sort\"\ + ];\n 15 -->|out_file1| 18;\n 71abb759-b51f-4383-a791-27d8b1325e81[\"Output\\\ + nsorted_mf_go\"];\n 18 --> 71abb759-b51f-4383-a791-27d8b1325e81;\n style 71abb759-b51f-4383-a791-27d8b1325e81\ + \ stroke:#2c3143,stroke-width:4px;\n 19[\"Split a HUMAnN table\"];\n 15 -->|out_file1|\ + \ 19;" + modified: 2026-07-01 00:31:39 +0000 + name: 'Metatranscriptomics analysis using microbiome RNA-seq data - Workflow 3: + Functional Information' + outputs: - annotation: '' - content_id: toolshed.g2.bx.psu.edu/repos/devteam/fasta_to_tabular/fasta2tab/1.1.1 + content_id: toolshed.g2.bx.psu.edu/repos/iuc/humann/humann/3.9+galaxy0 errors: null - id: 9 + id: 2 input_connections: - input: - id: 6 - output_name: out_consensus - inputs: [] + in|input: + id: 0 + output_name: output + wf|taxonomic_profile: + id: 1 + output_name: output + inputs: + - description: runtime parameter for tool HUMAnN + name: in + - description: runtime parameter for tool HUMAnN + name: wf label: null - name: FASTA-to-Tabular + name: HUMAnN outputs: - - name: output + - name: gene_families_tsv + type: tabular + - name: pathcoverage_tsv + type: tabular + - name: pathabundance_tsv type: tabular + - name: log + type: txt position: - left: 1210.4666748046875 - top: 757.7333374023438 - post_job_actions: - RenameDatasetActionoutput: - action_arguments: - newname: sample_specific_contigs_tabular_file_preparation - action_type: RenameDatasetAction - output_name: output - tool_id: toolshed.g2.bx.psu.edu/repos/devteam/fasta_to_tabular/fasta2tab/1.1.1 + left: 462.5176261280958 + top: 380 + post_job_actions: {} + tool_id: toolshed.g2.bx.psu.edu/repos/iuc/humann/humann/3.9+galaxy0 tool_shed_repository: - changeset_revision: e7ed3c310b74 - name: fasta_to_tabular - owner: devteam + changeset_revision: c2803012bbb3 + name: humann + owner: iuc tool_shed: toolshed.g2.bx.psu.edu - tool_state: '{"descr_columns": "1", "input": {"__class__": 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Workflow Outputs - - - ### Multi QC Report of all samples before reads quality retaining - - - ```galaxy - - history_dataset_as_image(output="multiQC_html_report_before_preprocessing") - - ``` - - ### Multi QC Report of all samples after reads quality retaining - - - ```galaxy - - history_dataset_as_image(output="multiQC_html_report_after_preprocessing") - - ``` - - - ### Percentages of removed host sequences in every sample - - - ```galaxy - - history_dataset_display(output="removed_hosts_percentage_tabular") - - ``` - - ' + comments: false + parameters: false + report: null subworkflows: false graph_dot: "digraph main {\n node [fontname=\"Atkinson Hyperlegible\", shape=box,\ \ color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n edge [fontname=\"\ - Atkinson Hyperlegible\"];\n 0[color=lightgreen,label=\"\u2139\uFE0F Input Parameter\\\ - nsamples_profile\"]\n 1[color=lightblue,label=\"\u2139\uFE0F Input Collection\\\ - ncollection_of_all_samples\"]\n 2[label=\"Porechop\"]\n 1 -> 2 [label=\"output\"\ - ]\n k34ea26db11cb41ee85c375af8a53a2c0[color=lightseagreen,label=\"Output\\\ - nporechop_output_trimmed_reads\"]\n 2 -> k34ea26db11cb41ee85c375af8a53a2c0\n\ - \ 3[label=\"NanoPlot\"]\n 1 -> 3 [label=\"output\"]\n k304110f960d04ba28b3bfae0e2a49554[color=lightseagreen,label=\"\ - Output\\nnanoplot_on_reads_before_preprocessing_nanostats_post_filtering\"]\n\ - \ 3 -> k304110f960d04ba28b3bfae0e2a49554\n kf2bd0a1fcd604a36a7d08025cc19ea2e[color=lightseagreen,label=\"\ - Output\\nnanoplot_qc_on_reads_before_preprocessing_html_report\"]\n 3 -> kf2bd0a1fcd604a36a7d08025cc19ea2e\n\ - \ k15ecf5b1e0eb405aac3a359feb66d4cd[color=lightseagreen,label=\"Output\\nnanoplot_qc_on_reads_before_preprocessing_nanostats\"\ - ]\n 3 -> k15ecf5b1e0eb405aac3a359feb66d4cd\n 4[label=\"FastQC\"]\n 1 -> 4\ - \ [label=\"output\"]\n ke61fef5d1bc84c8ebe6af74e210e9920[color=lightseagreen,label=\"\ - Output\\nfastqc_quality_check_before_preprocessing_text_file\"]\n 4 -> ke61fef5d1bc84c8ebe6af74e210e9920\n\ - \ kd0a6462405d04068835ba025fc011760[color=lightseagreen,label=\"Output\\nfastqc_quality_check_before_preprocessing_html_file\"\ - ]\n 4 -> kd0a6462405d04068835ba025fc011760\n 5[label=\"fastp\"]\n 2 -> 5\ - \ [label=\"outfile\"]\n k2a9a8b4d458b40e79a21fb7108d5bbe4[color=lightseagreen,label=\"\ - Output\\nnanopore_sequenced_reads_processed_with_fastp_after_host_removal_html_report\"\ - ]\n 5 -> k2a9a8b4d458b40e79a21fb7108d5bbe4\n ka221948350b74aed98dd333ad2e12eb8[color=lightseagreen,label=\"\ - Output\\nnanopore_sequenced_reads_processed_with_fastp_after_host_removal\"\ - ]\n 5 -> ka221948350b74aed98dd333ad2e12eb8\n 6[label=\"MultiQC\"]\n 4 ->\ - \ 6 [label=\"text_file\"]\n kebffe782a56c431f8af4c0cb8d7a02fc[color=lightseagreen,label=\"\ - Output\\nmultiQC_stats_before_preprocessing\"]\n 6 -> kebffe782a56c431f8af4c0cb8d7a02fc\n\ - \ k0f92196d047d4918819dc0ff7cd3ae85[color=lightseagreen,label=\"Output\\nmultiQC_html_report_before_preprocessing\"\ - ]\n 6 -> k0f92196d047d4918819dc0ff7cd3ae85\n 7[label=\"Map with minimap2\"\ - ]\n 0 -> 7 [label=\"output\"]\n 5 -> 7 [label=\"out1\"]\n k9d7bb3b709a1401fa132bb35a53375ea[color=lightseagreen,label=\"\ - Output\\nbam_map_to_host\"]\n 7 -> k9d7bb3b709a1401fa132bb35a53375ea\n 8[label=\"\ - NanoPlot\"]\n 5 -> 8 [label=\"out1\"]\n kb58992904c574662ad22860654652ade[color=lightseagreen,label=\"\ - Output\\nnanoplot_qc_on_reads_after_preprocessing_html_report\"]\n 8 -> kb58992904c574662ad22860654652ade\n\ - \ k949bfdf53d794dadbdd8c3a25e6af4cf[color=lightseagreen,label=\"Output\\nnanoplot_on_reads_after_preprocessing_nanostats_post_filtering\"\ - ]\n 8 -> k949bfdf53d794dadbdd8c3a25e6af4cf\n k42db7f93919e4bbb81a106411a9da410[color=lightseagreen,label=\"\ - Output\\nnanoplot_qc_on_reads_after_preprocessing_nanostats\"]\n 8 -> k42db7f93919e4bbb81a106411a9da410\n\ - \ 9[label=\"FastQC\"]\n 5 -> 9 [label=\"out1\"]\n k084f982f20f1457e801291ebbb85633d[color=lightseagreen,label=\"\ - Output\\nfastqc_quality_check_after_preprocessing_html_file\"]\n 9 -> k084f982f20f1457e801291ebbb85633d\n\ - \ k09306471afa041069cc7259b93dfc862[color=lightseagreen,label=\"Output\\nfastqc_quality_check_after_preprocessing_text_file\"\ - ]\n 9 -> k09306471afa041069cc7259b93dfc862\n 10[label=\"Split BAM by reads\ - \ mapping status\"]\n 7 -> 10 [label=\"alignment_output\"]\n k3b1e626f6bc1484cbe01366534361b73[color=lightseagreen,label=\"\ - Output\\nhost_sequences_bam\"]\n 10 -> k3b1e626f6bc1484cbe01366534361b73\n\ - \ k14a53fe2f29643aa86b7243278c1050c[color=lightseagreen,label=\"Output\\nnon_host_sequences_bam\"\ - ]\n 10 -> k14a53fe2f29643aa86b7243278c1050c\n 11[label=\"Select\"]\n 9 ->\ - \ 11 [label=\"text_file\"]\n ka809853b119f44d2986b8d2006439fbe[color=lightseagreen,label=\"\ - Output\\ntotal_sequences_before_hosts_sequences_removal\"]\n 11 -> ka809853b119f44d2986b8d2006439fbe\n\ - \ 12[label=\"Samtools fastx\"]\n 10 -> 12 [label=\"mapped\"]\n k10d4eaec81d8444e80757b77a1fb6870[color=lightseagreen,label=\"\ - Output\\nhost_sequences_fastq\"]\n 12 -> k10d4eaec81d8444e80757b77a1fb6870\n\ - \ 13[label=\"Samtools fastx\"]\n 10 -> 13 [label=\"unmapped\"]\n k0c2dd74dac4f45cf839c50386a7ece28[color=lightseagreen,label=\"\ - Output\\nnon_host_sequences_fastq\"]\n 13 -> k0c2dd74dac4f45cf839c50386a7ece28\n\ - \ 14[label=\"Collapse Collection\"]\n 11 -> 14 [label=\"out_file1\"]\n 15[label=\"\ - Filter failed datasets\"]\n 12 -> 15 [label=\"output\"]\n 16[label=\"Kraken2\"\ - ]\n 13 -> 16 [label=\"output\"]\n k203d303e8f3a4242971fb345842ebdb8[color=lightseagreen,label=\"\ - Output\\nkraken2_with_kalamri_database_output\"]\n 16 -> k203d303e8f3a4242971fb345842ebdb8\n\ - \ k843afd4d23a846e7b9458b67dd7ae341[color=lightseagreen,label=\"Output\\nkraken2_with_kalamri_database_report\"\ - ]\n 16 -> k843afd4d23a846e7b9458b67dd7ae341\n 17[label=\"Cut\"]\n 14 -> 17\ - \ [label=\"output\"]\n kd07be9f1d250400891ee59a68521eb56[color=lightseagreen,label=\"\ - Output\\nquality_retained_all_reads\"]\n 17 -> kd07be9f1d250400891ee59a68521eb56\n\ - \ 18[label=\"FastQC\"]\n 15 -> 18 [label=\"output\"]\n kb72ff57b092143bfa8176cd444c8f3cb[color=lightseagreen,label=\"\ - Output\\nhosts_qc_html\"]\n 18 -> kb72ff57b092143bfa8176cd444c8f3cb\n kb0ee6e310eb1437d8c04fc3640b9a0b7[color=lightseagreen,label=\"\ - Output\\nhosts_qc_text_file\"]\n 18 -> kb0ee6e310eb1437d8c04fc3640b9a0b7\n\ - \ 19[label=\"Krakentools: Extract Kraken Reads By ID\"]\n 5 -> 19 [label=\"\ - out1\"]\n 16 -> 19 [label=\"report_output\"]\n 16 -> 19 [label=\"output\"\ - ]\n k57e3b7258e1340b29acc31fd56ebc80a[color=lightseagreen,label=\"Output\\\ - ncollection_of_preprocessed_samples\"]\n 19 -> k57e3b7258e1340b29acc31fd56ebc80a\n\ - \ 20[label=\"Select\"]\n 18 -> 20 [label=\"text_file\"]\n k3ba35c7132f0474198d4ea8522e27500[color=lightseagreen,label=\"\ - Output\\ntotal_sequences_after_hosts_sequences_removal\"]\n 20 -> k3ba35c7132f0474198d4ea8522e27500\n\ - \ 21[label=\"Collapse Collection\"]\n 20 -> 21 [label=\"out_file1\"]\n 22[label=\"\ - Cut\"]\n 21 -> 22 [label=\"output\"]\n kcef36c6845494fd6b7c871fb21df012f[color=lightseagreen,label=\"\ - Output\\nquality_retained_hosts_reads\"]\n 22 -> kcef36c6845494fd6b7c871fb21df012f\n\ - \ 23[label=\"Column join\"]\n 17 -> 23 [label=\"out_file1\"]\n 22 -> 23 [label=\"\ - out_file1\"]\n 24[label=\"Compute\"]\n 23 -> 24 [label=\"tabular_output\"\ - ]\n 25[label=\"Column Regex Find And Replace\"]\n 24 -> 25 [label=\"out_file1\"\ - ]\n k470892eedab948d7ad9745dbd52afaa7[color=lightseagreen,label=\"Output\\\ - nremoved_hosts_percentage_tabular\"]\n 25 -> k470892eedab948d7ad9745dbd52afaa7\n\ - \ 26[label=\"MultiQC\"]\n 9 -> 26 [label=\"text_file\"]\n 25 -> 26 [label=\"\ - out_file1\"]\n k0b1b5a7336ee42a2a2201ced6ec7378b[color=lightseagreen,label=\"\ - Output\\nmultiQC_html_report_after_preprocessing\"]\n 26 -> k0b1b5a7336ee42a2a2201ced6ec7378b\n\ - \ k13cbf6c769544458aa66a5b020c63822[color=lightseagreen,label=\"Output\\nmultiQC_stats_after_preprocessing\"\ - ]\n 26 -> k13cbf6c769544458aa66a5b020c63822\n}" + Atkinson Hyperlegible\"];\n 0[color=lightblue,label=\"\u2139\uFE0F Input Dataset\\\ + nPredicted taxon relative abundances\"]\n 1[color=lightblue,label=\"\u2139\uFE0F\ + \ Input Dataset\\nGene Family abundance\"]\n 2[color=lightblue,label=\"\u2139\ + \uFE0F Input Dataset\\nPathway abundance\"]\n 3[label=\"Cut\"]\n 0 -> 3 [label=\"\ + output\"]\n 4[label=\"Renormalize\"]\n 1 -> 4 [label=\"output\"]\n 5[label=\"\ + Regroup\"]\n 1 -> 5 [label=\"output\"]\n 6[label=\"Renormalize\"]\n 2 ->\ + \ 6 [label=\"output\"]\n 7[label=\"Replace\"]\n 4 -> 7 [label=\"output\"]\n\ + \ 8[label=\"Rename features\"]\n 5 -> 8 [label=\"output\"]\n 9[label=\"Split\ + \ a HUMAnN table\"]\n 5 -> 9 [label=\"output\"]\n k7aba96f3164841268e58ca10cbd2e46d[color=lightseagreen,label=\"\ + Output\\nSplit a HUMAnN table on input dataset(s): Stratified table\"]\n 9\ + \ -> k7aba96f3164841268e58ca10cbd2e46d\n k2c36dc3359814b2cb615a1677002e007[color=lightseagreen,label=\"\ + Output\\nSplit a HUMAnN table on input dataset(s): Unstratified table\"]\n \ + \ 9 -> k2c36dc3359814b2cb615a1677002e007\n 10[label=\"Unpack pathway abundances\"\ + ]\n 4 -> 10 [label=\"output\"]\n 6 -> 10 [label=\"output\"]\n 11[label=\"\ + Combination of taxonomic and metabolic assignations for gene families\"]\n \ + \ 7 -> 11 [label=\"outfile\"]\n 3 -> 11 [label=\"out_file1\"]\n k46161015b2db4241846e27dd803b0fb3[color=lightseagreen,label=\"\ + Output\\nCombine MetaPhlAn2 and HUMAnN2 outputs on input dataset(s): Gene family\ + \ abundances related to genus/species abundances\"]\n 11 -> k46161015b2db4241846e27dd803b0fb3\n\ + \ 12[label=\"Select\"]\n 8 -> 12 [label=\"output\"]\n 13[label=\"Select\"\ + ]\n 8 -> 13 [label=\"output\"]\n 14[label=\"Select\"]\n 8 -> 14 [label=\"\ + output\"]\n}" history: - - hash: 43b59f45eec3262ec9b66a55ef2707a9c442ba5a - message: renaming the preprocessing.ga workflow name - num: 7 - short_hash: 43b59f45e - unix: '1751535523' - - hash: 20b1c5a11c7ea68a1cefd70cbe72b3783d7887ad - message: GTN-Foodborne tutorial, updating 2/5 workflows, which contains filter - failed datasets tool with the new tool - num: 6 - short_hash: 20b1c5a11 - unix: '1751535250' - - hash: cdd93376adc6ce80742881c25d6810bcce85fc05 - message: adding tags to some of the workflow outputs, updating the training - with the latest PathoGFAIR workflows updates - num: 5 - short_hash: cdd93376a - unix: '1717675229' - - hash: e230001f416aa3035d90535521418fa798ab643e - message: updating preprocessing workflow and allele based workflow with a single - user input parameter and adjusting the md file accodingly - num: 4 - short_hash: e230001f4 - unix: '1716982398' - - hash: 211b69394d6ef4d129eaa18cd76b93c8dece8cf3 - message: adding workflow reports to the workflows of the training to match the - latest version of the IWC PR - num: 3 - short_hash: 211b69394 - unix: '1716716727' - - hash: d320748c5c8ea425a77aa03ac78a5956eb75b005 - message: Foodborne training update 2024 + - hash: 48fd28c6edf215be997fb35ff2b4b90da4a56c02 + message: update last tool in tutorial num: 2 - short_hash: d320748c5 - unix: '1716229068' + short_hash: 48fd28c6e + unix: '1751413189' - hash: 0e0a2f2ccb650b0aab1ffc13838045164bdb5d30 message: Rename metagenomics topic to microbiome num: 1 short_hash: 0e0a2f2cc unix: '1704901629' inputs: - - annotation: 'based on the lab preparation of the samples during sequencing, - there should be a sample profile better than the other, to be chosen as an - optional input to Minimap2. e.g. PacBio/Oxford Nanpore - - - For more details check: https://github.com/lh3/minimap2?tab=readme-ov-file#use-cases' + - annotation: '' content_id: null errors: null id: 0 input_connections: {} inputs: - - description: 'based on the lab preparation of the samples during sequencing, - there should be a sample profile better than the other, to be chosen as - an optional input to Minimap2. e.g. PacBio/Oxford Nanpore - - - For more details check: https://github.com/lh3/minimap2?tab=readme-ov-file#use-cases' - name: samples_profile - label: samples_profile - name: Input parameter + - description: '' + name: Predicted taxon relative abundances + label: Predicted taxon relative abundances + name: Input dataset outputs: [] position: - left: 655 - top: 19.602400000005026 + left: 0 + top: 315.16828885381835 tool_id: null - tool_state: '{"validators": [], "restrictOnConnections": true, "parameter_type": - "text", "optional": true}' + tool_state: '{"optional": false, "tag": null}' + tool_version: null + type: data_input + uuid: 37e23d2f-315d-4260-ad1e-82fd98fb9ab4 + when: null + workflow_outputs: [] + - annotation: '' + content_id: null + errors: null + id: 1 + input_connections: {} + inputs: + - description: '' + name: Gene Family abundance + label: Gene Family abundance + name: Input dataset + outputs: [] + position: + left: 364.53758261044254 + top: 523.1616834301867 + tool_id: null + tool_state: '{"optional": false, "tag": null}' tool_version: null - type: parameter_input - uuid: 1435b9fc-84c0-4a1a-af49-007da98f4d5f + type: data_input + uuid: f5151f5e-cf41-42c2-b919-dd255128a91a when: null workflow_outputs: [] - - annotation: Nanopore reads of each sample are all in a single fastq or fastq.gz - file + - annotation: '' content_id: null errors: null - id: 1 + id: 2 input_connections: {} inputs: - - description: Nanopore reads of each sample are all in a single fastq or fastq.gz - file - name: collection_of_all_samples - label: collection_of_all_samples - name: Input dataset collection + - description: '' + name: Pathway abundance + label: Pathway abundance + name: Input dataset outputs: [] position: - left: 20 - top: 981.4 + left: 372.53758261044254 + top: 736.1616834301867 tool_id: null - tool_state: '{"optional": false, "tag": null, "collection_type": "list", "fields": - null}' + tool_state: '{"optional": false, "tag": null}' tool_version: null - type: data_collection_input - uuid: 6a0dea4c-3d2c-4ab9-bb87-82cff75ac6d0 + type: data_input + uuid: dd5c4959-60ba-42f7-830c-cb88817abee3 when: null workflow_outputs: [] license: MIT - mermaid: "flowchart TD\n 0[\"\u2139\uFE0F Input Parameter\\nsamples_profile\"\ - ];\n style 0 fill:#ded,stroke:#393,stroke-width:4px;\n 1[\"\u2139\uFE0F Input\ - \ Collection\\ncollection_of_all_samples\"];\n style 1 stroke:#2c3143,stroke-width:4px;\n\ - \ 2[\"Porechop\"];\n 1 -->|output| 2;\n 34ea26db-11cb-41ee-85c3-75af8a53a2c0[\"\ - Output\\nporechop_output_trimmed_reads\"];\n 2 --> 34ea26db-11cb-41ee-85c3-75af8a53a2c0;\n\ - \ style 34ea26db-11cb-41ee-85c3-75af8a53a2c0 stroke:#2c3143,stroke-width:4px;\n\ - \ 3[\"NanoPlot\"];\n 1 -->|output| 3;\n 304110f9-60d0-4ba2-8b3b-fae0e2a49554[\"\ - Output\\nnanoplot_on_reads_before_preprocessing_nanostats_post_filtering\"];\n\ - \ 3 --> 304110f9-60d0-4ba2-8b3b-fae0e2a49554;\n style 304110f9-60d0-4ba2-8b3b-fae0e2a49554\ - \ stroke:#2c3143,stroke-width:4px;\n f2bd0a1f-cd60-4a36-a7d0-8025cc19ea2e[\"\ - Output\\nnanoplot_qc_on_reads_before_preprocessing_html_report\"];\n 3 -->\ - \ f2bd0a1f-cd60-4a36-a7d0-8025cc19ea2e;\n style f2bd0a1f-cd60-4a36-a7d0-8025cc19ea2e\ - \ stroke:#2c3143,stroke-width:4px;\n 15ecf5b1-e0eb-405a-ac3a-359feb66d4cd[\"\ - Output\\nnanoplot_qc_on_reads_before_preprocessing_nanostats\"];\n 3 --> 15ecf5b1-e0eb-405a-ac3a-359feb66d4cd;\n\ - \ style 15ecf5b1-e0eb-405a-ac3a-359feb66d4cd stroke:#2c3143,stroke-width:4px;\n\ - \ 4[\"FastQC\"];\n 1 -->|output| 4;\n e61fef5d-1bc8-4c8e-be6a-f74e210e9920[\"\ - Output\\nfastqc_quality_check_before_preprocessing_text_file\"];\n 4 --> e61fef5d-1bc8-4c8e-be6a-f74e210e9920;\n\ - \ style e61fef5d-1bc8-4c8e-be6a-f74e210e9920 stroke:#2c3143,stroke-width:4px;\n\ - \ d0a64624-05d0-4068-835b-a025fc011760[\"Output\\nfastqc_quality_check_before_preprocessing_html_file\"\ - ];\n 4 --> d0a64624-05d0-4068-835b-a025fc011760;\n style d0a64624-05d0-4068-835b-a025fc011760\ - \ stroke:#2c3143,stroke-width:4px;\n 5[\"fastp\"];\n 2 -->|outfile| 5;\n \ - \ 2a9a8b4d-458b-40e7-9a21-fb7108d5bbe4[\"Output\\nnanopore_sequenced_reads_processed_with_fastp_after_host_removal_html_report\"\ - ];\n 5 --> 2a9a8b4d-458b-40e7-9a21-fb7108d5bbe4;\n style 2a9a8b4d-458b-40e7-9a21-fb7108d5bbe4\ - \ stroke:#2c3143,stroke-width:4px;\n a2219483-50b7-4aed-98dd-333ad2e12eb8[\"\ - Output\\nnanopore_sequenced_reads_processed_with_fastp_after_host_removal\"\ - ];\n 5 --> a2219483-50b7-4aed-98dd-333ad2e12eb8;\n style a2219483-50b7-4aed-98dd-333ad2e12eb8\ - \ stroke:#2c3143,stroke-width:4px;\n 6[\"MultiQC\"];\n 4 -->|text_file| 6;\n\ - \ ebffe782-a56c-431f-8af4-c0cb8d7a02fc[\"Output\\nmultiQC_stats_before_preprocessing\"\ - ];\n 6 --> ebffe782-a56c-431f-8af4-c0cb8d7a02fc;\n style ebffe782-a56c-431f-8af4-c0cb8d7a02fc\ - \ stroke:#2c3143,stroke-width:4px;\n 0f92196d-047d-4918-819d-c0ff7cd3ae85[\"\ - Output\\nmultiQC_html_report_before_preprocessing\"];\n 6 --> 0f92196d-047d-4918-819d-c0ff7cd3ae85;\n\ - \ style 0f92196d-047d-4918-819d-c0ff7cd3ae85 stroke:#2c3143,stroke-width:4px;\n\ - \ 7[\"Map with minimap2\"];\n 0 -->|output| 7;\n 5 -->|out1| 7;\n 9d7bb3b7-09a1-401f-a132-bb35a53375ea[\"\ - Output\\nbam_map_to_host\"];\n 7 --> 9d7bb3b7-09a1-401f-a132-bb35a53375ea;\n\ - \ style 9d7bb3b7-09a1-401f-a132-bb35a53375ea stroke:#2c3143,stroke-width:4px;\n\ - \ 8[\"NanoPlot\"];\n 5 -->|out1| 8;\n b5899290-4c57-4662-ad22-860654652ade[\"\ - Output\\nnanoplot_qc_on_reads_after_preprocessing_html_report\"];\n 8 --> b5899290-4c57-4662-ad22-860654652ade;\n\ - \ style b5899290-4c57-4662-ad22-860654652ade stroke:#2c3143,stroke-width:4px;\n\ - \ 949bfdf5-3d79-4dad-bdd8-c3a25e6af4cf[\"Output\\nnanoplot_on_reads_after_preprocessing_nanostats_post_filtering\"\ - ];\n 8 --> 949bfdf5-3d79-4dad-bdd8-c3a25e6af4cf;\n style 949bfdf5-3d79-4dad-bdd8-c3a25e6af4cf\ - \ stroke:#2c3143,stroke-width:4px;\n 42db7f93-919e-4bbb-81a1-06411a9da410[\"\ - Output\\nnanoplot_qc_on_reads_after_preprocessing_nanostats\"];\n 8 --> 42db7f93-919e-4bbb-81a1-06411a9da410;\n\ - \ style 42db7f93-919e-4bbb-81a1-06411a9da410 stroke:#2c3143,stroke-width:4px;\n\ - \ 9[\"FastQC\"];\n 5 -->|out1| 9;\n 084f982f-20f1-457e-8012-91ebbb85633d[\"\ - Output\\nfastqc_quality_check_after_preprocessing_html_file\"];\n 9 --> 084f982f-20f1-457e-8012-91ebbb85633d;\n\ - \ style 084f982f-20f1-457e-8012-91ebbb85633d stroke:#2c3143,stroke-width:4px;\n\ - \ 09306471-afa0-4106-9cc7-259b93dfc862[\"Output\\nfastqc_quality_check_after_preprocessing_text_file\"\ - ];\n 9 --> 09306471-afa0-4106-9cc7-259b93dfc862;\n style 09306471-afa0-4106-9cc7-259b93dfc862\ - \ stroke:#2c3143,stroke-width:4px;\n 10[\"Split BAM by reads mapping status\"\ - ];\n 7 -->|alignment_output| 10;\n 3b1e626f-6bc1-484c-be01-366534361b73[\"\ - Output\\nhost_sequences_bam\"];\n 10 --> 3b1e626f-6bc1-484c-be01-366534361b73;\n\ - \ style 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6;\n 7[\"Replace\"];\n 4 -->|output| 7;\n 8[\"Rename features\"];\n 5\ + \ -->|output| 8;\n 9[\"Split a HUMAnN table\"];\n 5 -->|output| 9;\n 7aba96f3-1648-4126-8e58-ca10cbd2e46d[\"\ + Output\\nSplit a HUMAnN table on input dataset(s): Stratified table\"];\n 9\ + \ --> 7aba96f3-1648-4126-8e58-ca10cbd2e46d;\n style 7aba96f3-1648-4126-8e58-ca10cbd2e46d\ + \ stroke:#2c3143,stroke-width:4px;\n 2c36dc33-5981-4b2c-b615-a1677002e007[\"\ + Output\\nSplit a HUMAnN table on input dataset(s): Unstratified table\"];\n\ + \ 9 --> 2c36dc33-5981-4b2c-b615-a1677002e007;\n style 2c36dc33-5981-4b2c-b615-a1677002e007\ + \ stroke:#2c3143,stroke-width:4px;\n 10[\"Unpack pathway abundances\"];\n \ + \ 4 -->|output| 10;\n 6 -->|output| 10;\n 11[\"Combination of taxonomic and\ + \ metabolic assignations for gene families\"];\n 7 -->|outfile| 11;\n 3 -->|out_file1|\ + \ 11;\n 46161015-b2db-4241-846e-27dd803b0fb3[\"Output\\nCombine MetaPhlAn2\ + \ and HUMAnN2 outputs on input dataset(s): Gene family abundances 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toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.27+galaxy3 + topic_name: microbiome + topic_name_human: Microbiome + tours: false + translations: + slides: [] + tutorial: [] + video: false + tutorial_name: host-removal + type: tutorial + url: https://training.galaxyproject.org//topics/microbiome/tutorials/host-removal/tutorial.html + urls: + hands_on: https://training.galaxyproject.org/training-material/api/topics/microbiome/tutorials/host-removal/tutorial.json + slides: https://training.galaxyproject.org/training-material/api/topics/microbiome/tutorials/host-removal/tutorial.json + version: 3 + video: true + video_versions: 1 + video_view: 0 + visit_duration: 575 + visitors: 471 + workflows: + - creators: + - class: Person + identifier: 0000-0003-2982-388X + name: Paul Zierep + description: '' + features: + comments: false + parameters: true + report: + markdown: ' + + # Workflow Execution Report + + + ## Workflow Inputs + + ```galaxy + + invocation_inputs() + + ``` + + + ## Workflow Outputs + + ```galaxy + + invocation_outputs() + + ``` + + + ## Workflow + + ```galaxy + + workflow_display() + + ``` + + ' + subworkflows: false + graph_dot: "digraph main {\n node [fontname=\"Atkinson Hyperlegible\", shape=box,\ + \ color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n edge [fontname=\"\ + Atkinson Hyperlegible\"];\n 0[color=lightblue,label=\"\u2139\uFE0F Input Collection\\\ + nInput paired fastq \"]\n 1[color=lightgreen,label=\"\u2139\uFE0F Input Parameter\\\ + nReference Genome Build In\"]\n 2[label=\"Bowtie2\"]\n 0 -> 2 [label=\"output\"\ + ]\n 1 -> 2 [label=\"output\"]\n 3[label=\"Zip collections\"]\n 2 -> 3 [label=\"\ + output_unaligned_reads_l\"]\n 2 -> 3 [label=\"output_unaligned_reads_r\"]\n\ + \ 4[label=\"MultiQC\"]\n 2 -> 4 [label=\"mapping_stats\"]\n}" + history: + - hash: 4920ecd42496f439fa65591cc788ef1080fdd8cc + message: 'Add new tutorial: host removal and update contributor info' + num: 1 + short_hash: 4920ecd42 + unix: '1759837405' + inputs: - annotation: '' - content_id: toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy0 + content_id: null errors: null - id: 18 - input_connections: - input_file: - id: 15 - output_name: output + id: 0 + input_connections: {} inputs: - - description: runtime parameter for tool FastQC - name: adapters - - description: runtime parameter for tool FastQC - name: contaminants - - description: runtime parameter for tool FastQC - name: limits - label: null - name: FastQC - outputs: - - name: html_file - type: html - - name: text_file - type: txt + - description: '' + name: 'Input paired fastq ' + label: 'Input paired fastq ' + name: Input dataset collection + outputs: [] position: - left: 1766.433349609375 - top: 33.419788701225116 - post_job_actions: - RenameDatasetActionhtml_file: - action_arguments: - newname: hosts_qc_html - action_type: RenameDatasetAction - output_name: html_file - RenameDatasetActiontext_file: - action_arguments: - newname: hosts_qc_text_file - action_type: RenameDatasetAction - output_name: text_file - tool_id: toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy0 - tool_shed_repository: - changeset_revision: 5ec9f6bceaee - name: fastqc - owner: devteam - tool_shed: toolshed.g2.bx.psu.edu - tool_state: '{"adapters": {"__class__": "RuntimeValue"}, "contaminants": {"__class__": - "RuntimeValue"}, "input_file": {"__class__": "ConnectedValue"}, "kmers": "7", - "limits": {"__class__": "RuntimeValue"}, "min_length": null, "nogroup": false, - "__page__": null, "__rerun_remap_job_id__": null}' - tool_version: 0.74+galaxy0 - type: tool - uuid: 7140e440-b547-4cae-baa0-89e29a3f2bda + left: 10 + top: 50 + tool_id: null + tool_state: '{"optional": false, "tag": null, "collection_type": "list:paired", + "fields": null}' + tool_version: null + type: data_collection_input + uuid: 13e4060f-f337-4f44-824f-ee85235fcc8e when: null - workflow_outputs: - - label: hosts_qc_html - output_name: html_file - uuid: b72ff57b-0921-43bf-a817-6cd444c8f3cb - - label: hosts_qc_text_file - output_name: text_file - uuid: b0ee6e31-0eb1-437d-8c04-fc3640b9a0b7 + workflow_outputs: [] - annotation: '' - content_id: toolshed.g2.bx.psu.edu/repos/iuc/krakentools_extract_kraken_reads/krakentools_extract_kraken_reads/1.2+galaxy1 + content_id: null errors: null - id: 19 - input_connections: - library|input_1: - id: 5 - output_name: out1 - report: - id: 16 - output_name: report_output - results: - id: 16 - output_name: output + id: 1 + input_connections: {} inputs: - - description: 'runtime parameter for tool Krakentools: Extract Kraken Reads - By ID' - name: library - label: null - name: 'Krakentools: Extract Kraken Reads By ID' - outputs: - - name: output_1 - type: fasta.gz + - description: '' + name: Reference Genome Build In + label: Reference Genome Build In + name: Input parameter + outputs: [] position: - left: 1897.4166870117188 - top: 442.90312610356887 - post_job_actions: - RenameDatasetActionoutput_1: - action_arguments: - newname: collection_of_preprocessed_samples - action_type: RenameDatasetAction - output_name: output_1 - TagDatasetActionoutput_1: - action_arguments: - tags: collection_of_preprocessed_samples - action_type: TagDatasetAction - output_name: output_1 - tool_id: toolshed.g2.bx.psu.edu/repos/iuc/krakentools_extract_kraken_reads/krakentools_extract_kraken_reads/1.2+galaxy1 - tool_shed_repository: - changeset_revision: f329328da134 - name: krakentools_extract_kraken_reads - owner: iuc - tool_shed: toolshed.g2.bx.psu.edu - tool_state: '{"exclude": true, "fastq_output": true, "include_children": true, - "include_parents": true, "library": {"type": "single", "__current_case__": - 0, "input_1": {"__class__": "ConnectedValue"}}, "max": "100000000", "report": - {"__class__": "ConnectedValue"}, "results": {"__class__": "ConnectedValue"}, - "taxid": "9031 9606 9913", "__page__": null, "__rerun_remap_job_id__": null}' - tool_version: 1.2+galaxy1 - type: tool - uuid: 9d22fc4d-9b85-4f6b-b9df-ac9486de7acd + left: 0 + top: 240 + tool_id: null + tool_state: '{"multiple": false, "validators": [], "restrictOnConnections": + true, "parameter_type": "text", "optional": false}' + tool_version: null + type: parameter_input + uuid: 47ad0b2d-0d31-4260-82df-8fed2da6b150 when: null - workflow_outputs: - - label: collection_of_preprocessed_samples - output_name: output_1 - uuid: 57e3b725-8e13-40b2-9acc-31fd56ebc80a - - annotation: '' - content_id: Grep1 + workflow_outputs: [] + license: MIT + mermaid: "flowchart TD\n 0[\"\u2139\uFE0F Input Collection\\nInput paired fastq\ + \ \"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"\u2139\uFE0F Input\ + \ Parameter\\nReference Genome Build In\"];\n style 1 fill:#ded,stroke:#393,stroke-width:4px;\n\ + \ 2[\"Bowtie2\"];\n 0 -->|output| 2;\n 1 -->|output| 2;\n 3[\"Zip collections\"\ + ];\n 2 -->|output_unaligned_reads_l| 3;\n 2 -->|output_unaligned_reads_r|\ + \ 3;\n 4[\"MultiQC\"];\n 2 -->|mapping_stats| 4;" + modified: 2026-07-01 00:31:39 +0000 + name: Host contamination removal + outputs: [] + parent_id: microbiome/host-removal + path: topics/microbiome/tutorials/host-removal/workflows/main_workflow.ga + tags: + - name:FAIRyMAGs + test_results: null + tests: true + title: Host contamination removal + topic_id: microbiome + trs_endpoint: https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/microbiome-host-removal/versions/main-workflow + tutorial_id: host-removal + url: https://training.galaxyproject.org/training-material/topics/microbiome/tutorials/host-removal/workflows/main_workflow.ga + url_html: https://training.galaxyproject.org/training-material/topics/microbiome/tutorials/host-removal/workflows/main_workflow.html + version: 1 + wfid: microbiome-host-removal + wfname: main-workflow + workflow: main_workflow.ga + workflow_tools: + - __ZIP_COLLECTION__ + - toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.5.3+galaxy1 + - toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.27+galaxy3 + workflowhub_id: '2042' + zenodo_link: https://zenodo.org/records/17829290 +- admin_install: + install_repository_dependencies: true + install_resolver_dependencies: true + install_tool_dependencies: true + tools: + - name: bowtie2 + owner: devteam + revisions: f76cbb84d67f + tool_panel_section_label: Mapping + tool_shed_url: https://toolshed.g2.bx.psu.edu/ + - name: samtools_sort + owner: devteam + revisions: f2f2650aeade + tool_panel_section_label: SAM/BAM + tool_shed_url: https://toolshed.g2.bx.psu.edu/ + - name: binette + owner: iuc + revisions: 37ab2cfedac4 + tool_panel_section_label: Metagenomic Analysis + tool_shed_url: https://toolshed.g2.bx.psu.edu/ + - name: checkm_lineage_wf + owner: iuc + revisions: f0107b9f2dc3 + tool_panel_section_label: Metagenomic Analysis + tool_shed_url: https://toolshed.g2.bx.psu.edu/ + - name: concoct + owner: iuc + revisions: eae7ee167917 + tool_panel_section_label: Metagenomic Analysis + tool_shed_url: https://toolshed.g2.bx.psu.edu/ + - name: concoct_coverage_table + owner: iuc + revisions: fd31cd168efc + tool_panel_section_label: Metagenomic Analysis + tool_shed_url: https://toolshed.g2.bx.psu.edu/ + - name: concoct_cut_up_fasta + owner: iuc + revisions: 4d8bc5dd9e95 + tool_panel_section_label: Metagenomic Analysis + tool_shed_url: https://toolshed.g2.bx.psu.edu/ + - name: concoct_extract_fasta_bins + owner: iuc + revisions: 8b1b09fcd8b7 + tool_panel_section_label: Metagenomic Analysis + tool_shed_url: https://toolshed.g2.bx.psu.edu/ + - name: concoct_merge_cut_up_clustering + owner: iuc + revisions: 20ccec4a2c38 + tool_panel_section_label: Metagenomic Analysis + tool_shed_url: https://toolshed.g2.bx.psu.edu/ + - name: das_tool + owner: iuc + revisions: b048a987dd7d + tool_panel_section_label: Metagenomic Analysis + tool_shed_url: https://toolshed.g2.bx.psu.edu/ + - name: drep_dereplicate + owner: iuc + revisions: f54e7b3da33c + tool_panel_section_label: Metagenomic Analysis + tool_shed_url: https://toolshed.g2.bx.psu.edu/ + - name: fasta_to_contig2bin + owner: iuc + revisions: fb2bed0eb02f + tool_panel_section_label: Metagenomic Analysis + tool_shed_url: https://toolshed.g2.bx.psu.edu/ + - name: metabat2 + owner: iuc + revisions: f375b4f6ef57 + tool_panel_section_label: Metagenomic Analysis + tool_shed_url: https://toolshed.g2.bx.psu.edu/ + - name: metabat2_jgi_summarize_bam_contig_depths + owner: iuc + revisions: 00e3b4ef7e0c + tool_panel_section_label: Metagenomic Analysis + tool_shed_url: https://toolshed.g2.bx.psu.edu/ + - name: semibin + owner: iuc + revisions: afee33334a63 + tool_panel_section_label: Metagenomic Analysis + tool_shed_url: https://toolshed.g2.bx.psu.edu/ + - name: maxbin2 + owner: mbernt + revisions: 0917b2d6010d + tool_panel_section_label: Metagenomic Analysis + tool_shed_url: https://toolshed.g2.bx.psu.edu/ + admin_install_yaml: "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies:\ + \ true\ninstall_resolver_dependencies: true\ntools:\n- name: bowtie2\n owner:\ + \ devteam\n revisions: f76cbb84d67f\n tool_panel_section_label: Mapping\n tool_shed_url:\ + \ https://toolshed.g2.bx.psu.edu/\n- name: samtools_sort\n owner: devteam\n \ + \ revisions: f2f2650aeade\n tool_panel_section_label: SAM/BAM\n tool_shed_url:\ + \ https://toolshed.g2.bx.psu.edu/\n- name: binette\n owner: iuc\n revisions:\ + \ 37ab2cfedac4\n tool_panel_section_label: Metagenomic Analysis\n tool_shed_url:\ + \ https://toolshed.g2.bx.psu.edu/\n- name: checkm_lineage_wf\n owner: iuc\n \ + \ revisions: f0107b9f2dc3\n tool_panel_section_label: Metagenomic Analysis\n\ + \ tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: concoct\n owner: iuc\n\ + \ revisions: eae7ee167917\n tool_panel_section_label: Metagenomic Analysis\n\ + \ tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: concoct_coverage_table\n\ + \ owner: iuc\n revisions: fd31cd168efc\n tool_panel_section_label: Metagenomic\ + \ Analysis\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: concoct_cut_up_fasta\n\ + \ owner: iuc\n revisions: 4d8bc5dd9e95\n tool_panel_section_label: Metagenomic\ + \ Analysis\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: concoct_extract_fasta_bins\n\ + \ owner: iuc\n revisions: 8b1b09fcd8b7\n tool_panel_section_label: Metagenomic\ + \ Analysis\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: concoct_merge_cut_up_clustering\n\ + \ owner: iuc\n revisions: 20ccec4a2c38\n tool_panel_section_label: Metagenomic\ + \ Analysis\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: das_tool\n\ + \ owner: iuc\n revisions: b048a987dd7d\n tool_panel_section_label: Metagenomic\ + \ Analysis\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: drep_dereplicate\n\ + \ owner: iuc\n revisions: f54e7b3da33c\n tool_panel_section_label: Metagenomic\ + \ Analysis\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fasta_to_contig2bin\n\ + \ owner: iuc\n revisions: fb2bed0eb02f\n tool_panel_section_label: Metagenomic\ + \ Analysis\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: metabat2\n\ + \ owner: iuc\n revisions: f375b4f6ef57\n tool_panel_section_label: Metagenomic\ + \ Analysis\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: metabat2_jgi_summarize_bam_contig_depths\n\ + \ owner: iuc\n revisions: 00e3b4ef7e0c\n tool_panel_section_label: Metagenomic\ + \ Analysis\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: semibin\n\ + \ owner: iuc\n revisions: afee33334a63\n tool_panel_section_label: Metagenomic\ + \ Analysis\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: maxbin2\n\ + \ owner: mbernt\n revisions: '0917b2d6010d'\n tool_panel_section_label: Metagenomic\ + \ Analysis\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n" + api: https://training.galaxyproject.org/training-material/api/topics/microbiome/tutorials/metagenomics-binning/tutorial.json + contributions: + authorship: + - paulzierep + - npechl + - fpsom + - vinisalazar + editing: + - bebatut + reviewing: + - teresa-m + - deeptivarshney + - bebatut + - npechl + - hexylena + - shiltemann + - paulzierep + - dadrasarmin + - natalie-wa + contributors: + - affiliations: + - uni-freiburg + - elixir-europe + - deNBI + - mwk + - materialvitaldigital + email: zierep@informatik.uni-freiburg.de + id: paulzierep + joined: 2023-02 + name: Paul Zierep + orcid: 0000-0003-2982-388X + page: https://training.galaxyproject.org/training-material/hall-of-fame/paulzierep/ + url: https://training.galaxyproject.org/training-material/api/contributors/paulzierep.json + - affiliations: + - inab-certh + elixir_node: gr + id: npechl + joined: 2023-05 + linkedin: npechl + name: Nikos Pechlivanis + orcid: 0000-0003-2502-612X + page: https://training.galaxyproject.org/training-material/hall-of-fame/npechl/ + twitter: npechl + url: https://training.galaxyproject.org/training-material/api/contributors/npechl.json + - affiliations: + - gallantries + - elixir-europe + elixir_node: gr + email: fpsom@certh.gr + id: fpsom + joined: 2019-03 + linkedin: fpsom + matrix: fpsom:matrix.org + name: Fotis E. Psomopoulos + orcid: 0000-0002-0222-4273 + page: https://training.galaxyproject.org/training-material/hall-of-fame/fpsom/ + twitter: fopsom + url: https://training.galaxyproject.org/training-material/api/contributors/fpsom.json + - affiliations: + - unimelb + - melbournebioinformatics + id: vinisalazar + joined: 2025-10 + name: Vini Salazar + orcid: 0000-0002-8362-3195 + page: https://training.galaxyproject.org/training-material/hall-of-fame/vinisalazar/ + url: https://training.galaxyproject.org/training-material/api/contributors/vinisalazar.json + - affiliations: + - gallantries + - ifb + - elixir-europe + contact_for_training: true + elixir_node: fr + email: berenice.batut@gmail.com + fediverse: https://piaille.fr/@bebatut + fediverse_flavor: mastodon + former_affiliations: + - uni-freiburg + - deNBI + id: bebatut + joined: 2017-09 + linkedin: berenicebatut + location: + country: FR + lat: 45.77 + lon: 3.08 + matrix: bebatut:matrix.org + name: "B\xE9r\xE9nice Batut" + orcid: 0000-0001-9852-1987 + page: https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/ + twitter: bebatut + url: https://training.galaxyproject.org/training-material/api/contributors/bebatut.json + - affiliations: + - uni-freiburg + - elixir-europe + - deNBI + - mwk + - biont + contact_for_training: true + elixir_node: de + email: muellert@informatik.uni-freibrug.de + id: teresa-m + joined: 2022-09 + linkedin: teresamueller87 + matrix: teresa-m:matrix.org + name: "Teresa M\xFCller" + orcid: 0000-0003-1252-9684 + page: https://training.galaxyproject.org/training-material/hall-of-fame/teresa-m/ + url: https://training.galaxyproject.org/training-material/api/contributors/teresa-m.json + - affiliations: + - uni-freiburg + - elixir-europe + bluesky: dvarshney.bsky.social + email: varshney@informatik.uni-freiburg.de + id: deeptivarshney + joined: 2022-12 + name: Deepti Varshney + orcid: 0000-0003-0419-6832 + page: https://training.galaxyproject.org/training-material/hall-of-fame/deeptivarshney/ + url: https://training.galaxyproject.org/training-material/api/contributors/deeptivarshney.json + - affiliations: + - gallantries + - ifb + - elixir-europe + contact_for_training: true + elixir_node: fr + email: berenice.batut@gmail.com + fediverse: https://piaille.fr/@bebatut + fediverse_flavor: mastodon + former_affiliations: + - uni-freiburg + - deNBI + id: bebatut + joined: 2017-09 + linkedin: berenicebatut + location: + country: FR + lat: 45.77 + lon: 3.08 + matrix: bebatut:matrix.org + name: "B\xE9r\xE9nice Batut" + orcid: 0000-0001-9852-1987 + page: https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/ + twitter: bebatut + url: https://training.galaxyproject.org/training-material/api/contributors/bebatut.json + - affiliations: + - inab-certh + elixir_node: gr + id: npechl + joined: 2023-05 + linkedin: npechl + name: Nikos Pechlivanis + orcid: 0000-0003-2502-612X + page: https://training.galaxyproject.org/training-material/hall-of-fame/npechl/ + twitter: npechl + url: https://training.galaxyproject.org/training-material/api/contributors/npechl.json + - affiliations: + - elixir-europe + contact_for_training: false + elixir_node: nl + former_affiliations: + - deNBI + - avans-atgm + - uni-freiburg + - erasmusmc + - gallantries + - by-covid + - elixir-converge + id: hexylena + joined: 2017-09 + location: + country: NL + lat: 51.91 + lon: 4.46 + maintainer_contact: gitter + matrix: hexylena:matrix.org + name: Helena Rasche + orcid: 0000-0001-9760-8992 + page: https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/ + url: https://training.galaxyproject.org/training-material/api/contributors/hexylena.json + - affiliations: + - uni-freiburg + - nfdi4plants + - elixir-europe + bio: Researcher at Erasmus Medical Center + bluesky: shiltemann.bsky.social + contact_for_training: true + elixir_node: nl + email: saskia.hiltemann@gmail.com + fediverse: https://mstdn.science/@shiltemann + fediverse_flavor: mastodon + former_affiliations: + - CINECA-Project + - gallantries + - erasmusmc + id: shiltemann + joined: 2017-09 + linkedin: shiltemann + location: + country: NL + lat: 51.912 + lon: 4.462 + maintainer_contact: gitter + matrix: shiltemann:matrix.org + name: Saskia Hiltemann + orcid: 0000-0003-3803-468X + page: https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/ + url: https://training.galaxyproject.org/training-material/api/contributors/shiltemann.json + - affiliations: + - uni-freiburg + - elixir-europe + - deNBI + - mwk + - materialvitaldigital + email: zierep@informatik.uni-freiburg.de + id: paulzierep + joined: 2023-02 + name: Paul Zierep + orcid: 0000-0003-2982-388X + page: https://training.galaxyproject.org/training-material/hall-of-fame/paulzierep/ + url: https://training.galaxyproject.org/training-material/api/contributors/paulzierep.json + - 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topic_3174 + - topic_0196 + edam_operation: + - Statistical calculation + - Sequencing quality control + - Read binning + - Sequence assembly validation + - Genome annotation + - Sequence composition calculation + - Sequence assembly + - Sequence clustering + - Genome comparison + - Validation + - Read mapping + edam_topic: + - Metagenomics + - Sequence assembly + exact_supported_servers: + - UseGalaxy.be + - UseGalaxy.cz + - UseGalaxy.eu + - UseGalaxy.fr + feedback_mean_note: null + feedback_number: 0 + hands_on: true + id: microbiome/metagenomics-binning + inexact_supported_servers: + - GalaxyTrakr + - UseGalaxy.org.au + - UseGalaxy.org (Main) + js_requirements: + mathjax: null + mermaid: false + key_points: + - Metagenomics binning is a computational approach to grouping together DNA sequences + from a mixed microbial sample into metagenome-assembled genomes (MAGs) + - The metagenomics binning workflow involves several steps, including preprocessing + of raw sequencing data, assembly of sequencing reads into contigs, binning of + contigs into MAGs, quality assessment of MAGs, and annotation of functional genes + and metabolic pathways in MAGs + - The quality and completeness of MAGs can be evaluated using standard metrics, + such as completeness, contamination, and genome size + - Metagenomics binning can be used to gain insights into the composition, diversity, + and functional potential of microbial communities, and can be applied to a range + of research areas, such as human health, environmental microbiology, and biotechnology + layout: tutorial_hands_on + level: Intermediate + license: CC-BY-4.0 + mod_date: '2026-04-09' + objectives: + - Describe what is metagenomics binning. + - Describe common challenges in metagenomics binning. + - Perform metagenomic binning using MetaBAT 2 software. + - Evaluation of MAG quality and completeness using CheckM software. + pageviews: 9145 + pub_date: '2023-12-05' + questions: + - What is metagenomic binning refers to? + - Which tools may be used for metagenomic binning? + - How to assess the quality of metagenomic binning? + recordings: + - bot-timestamp: 1725013820 + captioners: + - npechl + date: '2024-08-30' + galaxy_version: 24.1.2.dev0 + length: 25M + speakers: + - 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toolshed.g2.bx.psu.edu/repos/iuc/concoct_coverage_table/concoct_coverage_table/1.1.0+galaxy2 + - toolshed.g2.bx.psu.edu/repos/iuc/concoct_cut_up_fasta/concoct_cut_up_fasta/1.1.0+galaxy2 + - toolshed.g2.bx.psu.edu/repos/iuc/concoct_extract_fasta_bins/concoct_extract_fasta_bins/1.1.0+galaxy2 + - toolshed.g2.bx.psu.edu/repos/iuc/concoct_merge_cut_up_clustering/concoct_merge_cut_up_clustering/1.1.0+galaxy2 + - toolshed.g2.bx.psu.edu/repos/iuc/das_tool/das_tool/1.1.7+galaxy1 + - toolshed.g2.bx.psu.edu/repos/iuc/drep_dereplicate/drep_dereplicate/3.6.2+galaxy1 + - toolshed.g2.bx.psu.edu/repos/iuc/fasta_to_contig2bin/Fasta_to_Contig2Bin/1.1.7+galaxy1 + - toolshed.g2.bx.psu.edu/repos/iuc/metabat2/metabat2/2.17+galaxy0 + - toolshed.g2.bx.psu.edu/repos/iuc/metabat2_jgi_summarize_bam_contig_depths/metabat2_jgi_summarize_bam_contig_depths/2.17+galaxy0 + - toolshed.g2.bx.psu.edu/repos/iuc/semibin/semibin/2.1.0+galaxy1 + - toolshed.g2.bx.psu.edu/repos/mbernt/maxbin2/maxbin2/2.2.7+galaxy6 + topic_name: microbiome + topic_name_human: Microbiome + tours: false + translations: + slides: [] + tutorial: [] + video: false + tutorial_name: metagenomics-binning + type: tutorial + url: https://training.galaxyproject.org//topics/microbiome/tutorials/metagenomics-binning/tutorial.html + urls: + hands_on: https://training.galaxyproject.org/training-material/api/topics/microbiome/tutorials/metagenomics-binning/tutorial.json + slides: https://training.galaxyproject.org/training-material/api/topics/microbiome/tutorials/metagenomics-binning/tutorial.json + version: 9 + video: true + video_versions: 2 + video_view: 0 + visit_duration: 327 + visitors: 7493 + workflows: + - creators: + - class: Person + identifier: https://orcid.org/0000-0003-2982-388X + name: Paul Zierep + description: Binning workflows that uses abundance information and performs binning + of metagenomic contigs using 4 different binners as well as bin refinement. + features: + comments: true + parameters: true + report: + markdown: ' + + # Workflow Execution Report + + + ## Workflow Inputs + + ```galaxy + + invocation_inputs() + + ``` + + + ## Workflow Outputs + + ```galaxy + + invocation_outputs() + + ``` + + + ## Workflow + + ```galaxy + + workflow_display() + + ``` + + ' + subworkflows: false + graph_dot: "digraph main {\n node [fontname=\"Atkinson Hyperlegible\", shape=box,\ + \ color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n edge [fontname=\"\ + Atkinson Hyperlegible\"];\n 0[color=lightblue,label=\"\u2139\uFE0F Input Collection\\\ + nTrimmed reads\"]\n 1[color=lightgreen,label=\"\u2139\uFE0F Input Parameter\\\ + nRead length CONCOCT\"]\n 2[color=lightblue,label=\"\u2139\uFE0F Input Collection\\\ + nAssemblies\"]\n 3[color=lightgreen,label=\"\u2139\uFE0F Input Parameter\\\ + nEnvironment for the built-in model SemiBin\"]\n 4[label=\"CONCOCT: Cut up\ + \ contigs\"]\n 2 -> 4 [label=\"output\"]\n 5[label=\"Bowtie2\"]\n 0 -> 5\ + \ [label=\"output\"]\n 2 -> 5 [label=\"output\"]\n 6[label=\"Samtools sort\"\ + ]\n 5 -> 6 [label=\"output\"]\n 7[label=\"CONCOCT: Generate the input coverage\ + \ table\"]\n 4 -> 7 [label=\"output_bed\"]\n 6 -> 7 [label=\"output1\"]\n\ + \ 8[label=\"Calculate contig depths\"]\n 6 -> 8 [label=\"output1\"]\n 9[label=\"\ + SemiBin\"]\n 3 -> 9 [label=\"output\"]\n 6 -> 9 [label=\"output1\"]\n 2 ->\ + \ 9 [label=\"output\"]\n 10[label=\"CONCOCT\"]\n 1 -> 10 [label=\"output\"\ + ]\n 4 -> 10 [label=\"output_fasta\"]\n 7 -> 10 [label=\"output\"]\n 11[label=\"\ + MetaBAT2\"]\n 8 -> 11 [label=\"outputDepth\"]\n 2 -> 11 [label=\"output\"\ + ]\n 12[label=\"MaxBin2\"]\n 8 -> 12 [label=\"outputDepth\"]\n 2 -> 12 [label=\"\ + output\"]\n 13[label=\"Converts genome bins in fasta format\"]\n 9 -> 13 [label=\"\ + output_bins\"]\n 14[label=\"CONCOCT: Merge cut clusters\"]\n 10 -> 14 [label=\"\ + output_clustering\"]\n 15[label=\"Converts genome bins in fasta format\"]\n\ + \ 11 -> 15 [label=\"bins\"]\n 16[label=\"Converts genome bins in fasta format\"\ + ]\n 12 -> 16 [label=\"bins\"]\n 17[label=\"CONCOCT: Extract a fasta file\"\ + ]\n 14 -> 17 [label=\"output\"]\n 2 -> 17 [label=\"output\"]\n 18[label=\"\ + Converts genome bins in fasta format\"]\n 17 -> 18 [label=\"bins\"]\n 19[label=\"\ + Build list\"]\n 18 -> 19 [label=\"contigs2bin\"]\n 15 -> 19 [label=\"contigs2bin\"\ + ]\n 16 -> 19 [label=\"contigs2bin\"]\n 13 -> 19 [label=\"contigs2bin\"]\n\ + \ 20[label=\"Binette\"]\n 19 -> 20 [label=\"output\"]\n 2 -> 20 [label=\"\ + output\"]\n}" + history: + - hash: e2a9e0b193454e35cf49665231c615fd667ecbfd + message: add wf tags + num: 2 + short_hash: e2a9e0b19 + unix: '1763726007' + - hash: 8d7de5c673e409858ef5c9ca5b7d05c2b0cc63bf + message: add combine, add workflow, add wf test, add result question + num: 1 + short_hash: 8d7de5c67 + unix: '1763725573' + inputs: + - annotation: Samples grouped for co-assembly. For individual assembly use same + reads as `Trimmed reads input`. The tool fastq_groupmerge can be used to perform + the grouping. + content_id: null errors: null - id: 20 - input_connections: - input: - id: 18 - output_name: text_file - inputs: [] - label: null - name: Select - outputs: - - name: out_file1 - type: input + id: 0 + input_connections: {} + inputs: + - description: Samples grouped for co-assembly. For individual assembly use + same reads as `Trimmed reads input`. The tool fastq_groupmerge can be used + to perform the grouping. + name: Trimmed reads + label: Trimmed reads + name: Input dataset collection + outputs: [] position: - left: 1985.4666748046875 - top: 32.86977039067824 - post_job_actions: - RenameDatasetActionout_file1: - action_arguments: - newname: total_sequences_after_hosts_sequences_removal - action_type: RenameDatasetAction - output_name: out_file1 - tool_id: Grep1 - tool_state: '{"input": {"__class__": "ConnectedValue"}, "invert": "", "keep_header": - false, "pattern": "Total Sequences", "__page__": null, "__rerun_remap_job_id__": - null}' - tool_version: 1.0.4 - type: tool - uuid: a2a29388-186c-41f3-b9a9-c4a6a9d3ffc3 + left: 0 + top: 896.6187286877193 + tool_id: null + tool_state: '{"optional": false, "tag": null, "collection_type": "list:paired", + "fields": null}' + tool_version: null + type: data_collection_input + uuid: dd8faa6e-3f29-4fa2-befb-38ef4a7832b5 when: null - workflow_outputs: - - label: total_sequences_after_hosts_sequences_removal - output_name: out_file1 - uuid: 3ba35c71-32f0-4741-98d4-ea8522e27500 - - annotation: '' - content_id: Cut1 + workflow_outputs: [] + - annotation: CONCOCT requires the read length for coverage. Best use fastQC to + estimate the mean value. + content_id: null errors: null - id: 22 - input_connections: - input: - id: 21 - output_name: output - inputs: [] - label: null - name: Cut - outputs: - - name: out_file1 - type: tabular + id: 1 + input_connections: {} + inputs: + - description: CONCOCT requires the read length for coverage. Best use fastQC + to estimate the mean value. + name: Read length (CONCOCT) + label: Read length (CONCOCT) + name: Input parameter + outputs: [] position: - left: 2434.11669921875 - top: 40.186451298881366 - post_job_actions: - RenameDatasetActionout_file1: - action_arguments: - newname: quality_retained_hosts_reads - action_type: RenameDatasetAction - output_name: out_file1 - tool_id: Cut1 - tool_state: '{"columnList": "c1,c3", "delimiter": "T", "input": {"__class__": - "ConnectedValue"}, "__page__": null, "__rerun_remap_job_id__": null}' - tool_version: 1.0.2 - type: tool - uuid: 10bee624-ebbf-4173-9444-ae45062bc401 + left: 1097.0837390044621 + top: 41.539782924321685 + tool_id: null + tool_state: '{"default": 100, "validators": [{"min": null, "max": null, "negate": + false, "type": "in_range"}], "parameter_type": "integer", "optional": false}' + tool_version: null + type: parameter_input + uuid: 30109f1d-816b-4f85-a0b3-e54506ae32ae when: null - workflow_outputs: - - label: quality_retained_hosts_reads - output_name: out_file1 - uuid: cef36c68-4549-4fd6-b7c8-71fb21df012f - - annotation: '' - content_id: toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regexColumn1/1.0.3 + workflow_outputs: [] + - annotation: 'This workflow allows using a custom assembly as input. If provided, + select `custom assembly` as Assembler. + + Provide one assembly for each group of trimmed input reads.' + content_id: null errors: null - id: 25 - input_connections: - input: - id: 24 - output_name: out_file1 - inputs: [] - label: null - name: Column Regex Find And Replace - outputs: - - name: out_file1 - type: input + id: 2 + input_connections: {} + inputs: + - description: 'This workflow allows using a custom assembly as input. If provided, + select `custom assembly` as Assembler. + + Provide one assembly for each group of trimmed input reads.' + name: Assemblies + label: Assemblies + name: Input dataset collection + outputs: [] position: - left: 3208.8475559627727 - top: 838.6604815167086 - post_job_actions: - RenameDatasetActionout_file1: - action_arguments: - newname: removed_hosts_percentage_tabular - action_type: RenameDatasetAction - output_name: out_file1 - TagDatasetActionout_file1: - action_arguments: - tags: removed_hosts_percentage_tabular - action_type: TagDatasetAction - output_name: out_file1 - tool_id: toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regexColumn1/1.0.3 - tool_shed_repository: - changeset_revision: 503bcd6ebe4b - name: regex_find_replace - owner: galaxyp - tool_shed: toolshed.g2.bx.psu.edu - tool_state: '{"checks": [{"__index__": 0, "pattern": "#KEY", "replacement": - "key"}], "field": "1", "input": {"__class__": "ConnectedValue"}, "__page__": - null, "__rerun_remap_job_id__": null}' - tool_version: 1.0.3 - type: tool - uuid: 5f41f84c-e27e-4fb7-8128-42ae7f143965 + left: 248.96247766826204 + top: 1670.8582741820105 + tool_id: null + tool_state: '{"optional": false, "tag": null, "collection_type": "list", "fields": + null}' + tool_version: null + type: data_collection_input + uuid: e2f5ad16-674f-4687-94a4-a5e55680440a when: null - workflow_outputs: - - label: removed_hosts_percentage_tabular - output_name: out_file1 - uuid: 470892ee-dab9-48d7-ad97-45dbd52afaa7 - - annotation: 'Quality Control Before and After Preprocessing - - - ' - content_id: toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1 + workflow_outputs: [] + - annotation: 'Environment for the built-in model (SemiBin), options are: human_gut, + dog_gut, ocean, soil, cat_gut, human_oral, mouse_gut, pig_gut, built_environment, + wastewater, chicken_caecum, global' + content_id: null errors: null - id: 26 - input_connections: - results_0|software_cond|output_0|input: - id: 9 - output_name: text_file - results_1|software_cond|input: - id: 25 - output_name: out_file1 - inputs: [] - label: null - name: MultiQC - outputs: - - name: stats - type: input - - name: html_report - type: html + id: 3 + input_connections: {} + inputs: + - description: 'Environment for the built-in model (SemiBin), options are: human_gut, + dog_gut, ocean, soil, cat_gut, human_oral, mouse_gut, pig_gut, built_environment, + wastewater, chicken_caecum, global' + name: Environment for the built-in model (SemiBin) + label: Environment for the built-in model (SemiBin) + name: Input parameter + outputs: [] position: - left: 1241.3867206791317 - top: 975.3576882745778 - post_job_actions: - RenameDatasetActionhtml_report: - action_arguments: - newname: multiQC_html_report_after_preprocessing - action_type: RenameDatasetAction - output_name: html_report - RenameDatasetActionstats: - action_arguments: - newname: multiQC_stats_after_preprocessing - action_type: RenameDatasetAction - output_name: stats - TagDatasetActionhtml_report: - action_arguments: - tags: MultiQC_After_Preprocessing_HTML - action_type: TagDatasetAction - output_name: html_report - tool_id: toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1 - tool_shed_repository: - changeset_revision: abfd8a6544d7 - name: multiqc - owner: iuc - tool_shed: toolshed.g2.bx.psu.edu - tool_state: '{"comment": "", "export": false, "flat": false, "results": [{"__index__": - 0, "software_cond": {"software": "fastqc", "__current_case__": 8, "output": - [{"__index__": 0, "type": "data", "input": {"__class__": "ConnectedValue"}}]}}, - {"__index__": 1, "software_cond": {"software": "custom_content", "__current_case__": - 32, "plot_type": "table", "section_name": "Host Sequences Removal", "title": - "Host Sequences", "description": null, "xlab": null, "ylab": null, "input": - {"__class__": "ConnectedValue"}}}], "saveLog": false, "title": "MultiQC Report - After PreProcessing", "__page__": null, "__rerun_remap_job_id__": null}' - tool_version: 1.11+galaxy1 - type: tool - uuid: df53a320-802c-459a-a4cb-fd41aac4af92 + left: 1139.1165875728577 + top: 2094.707949827118 + tool_id: null + tool_state: '{"default": "global", "multiple": false, "validators": [], "restrictions": + ["global", "human_gut", "dog_gut", "ocean", "soil", "cat_gut", "human_oral", + "mouse_gut", "pig_gut", "built_environment", "wastewater", "chicken_caecum"], + "parameter_type": "text", "optional": false}' + tool_version: null + type: parameter_input + uuid: 86fc3246-f756-49ce-b196-ffa358e5ac41 when: null - workflow_outputs: - - label: multiQC_html_report_after_preprocessing - output_name: html_report - uuid: 0b1b5a73-36ee-42a2-a220-1ced6ec7378b - - label: multiQC_stats_after_preprocessing - output_name: stats - uuid: 13cbf6c7-6954-4458-aa66-a5b020c63822 - parent_id: microbiome/pathogen-detection-from-nanopore-foodborne-data - path: topics/microbiome/tutorials/pathogen-detection-from-nanopore-foodborne-data/workflows/nanopore_preprocessing.ga + workflow_outputs: [] + license: MIT + mermaid: "flowchart TD\n 0[\"\u2139\uFE0F Input Collection\\nTrimmed reads\"\ + ];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"\u2139\uFE0F Input Parameter\\\ + nRead length CONCOCT\"];\n style 1 fill:#ded,stroke:#393,stroke-width:4px;\n\ + \ 2[\"\u2139\uFE0F Input Collection\\nAssemblies\"];\n style 2 stroke:#2c3143,stroke-width:4px;\n\ + \ 3[\"\u2139\uFE0F Input Parameter\\nEnvironment for the built-in model SemiBin\"\ + ];\n style 3 fill:#ded,stroke:#393,stroke-width:4px;\n 4[\"CONCOCT: Cut up\ + \ contigs\"];\n 2 -->|output| 4;\n 5[\"Bowtie2\"];\n 0 -->|output| 5;\n \ + \ 2 -->|output| 5;\n 6[\"Samtools sort\"];\n 5 -->|output| 6;\n 7[\"CONCOCT:\ + \ Generate the input coverage table\"];\n 4 -->|output_bed| 7;\n 6 -->|output1|\ + \ 7;\n 8[\"Calculate contig depths\"];\n 6 -->|output1| 8;\n 9[\"SemiBin\"\ + ];\n 3 -->|output| 9;\n 6 -->|output1| 9;\n 2 -->|output| 9;\n 10[\"CONCOCT\"\ + ];\n 1 -->|output| 10;\n 4 -->|output_fasta| 10;\n 7 -->|output| 10;\n 11[\"\ + MetaBAT2\"];\n 8 -->|outputDepth| 11;\n 2 -->|output| 11;\n 12[\"MaxBin2\"\ + ];\n 8 -->|outputDepth| 12;\n 2 -->|output| 12;\n 13[\"Converts genome bins\ + \ in fasta format\"];\n 9 -->|output_bins| 13;\n 14[\"CONCOCT: Merge cut clusters\"\ + ];\n 10 -->|output_clustering| 14;\n 15[\"Converts genome bins in fasta format\"\ + ];\n 11 -->|bins| 15;\n 16[\"Converts genome bins in fasta format\"];\n 12\ + \ -->|bins| 16;\n 17[\"CONCOCT: Extract a fasta file\"];\n 14 -->|output|\ + \ 17;\n 2 -->|output| 17;\n 18[\"Converts genome bins in fasta format\"];\n\ + \ 17 -->|bins| 18;\n 19[\"Build list\"];\n 18 -->|contigs2bin| 19;\n 15\ + \ -->|contigs2bin| 19;\n 16 -->|contigs2bin| 19;\n 13 -->|contigs2bin| 19;\n\ + \ 20[\"Binette\"];\n 19 -->|output| 20;\n 2 -->|output| 20;" + modified: 2026-07-01 00:31:39 +0000 + name: Metagenomic Binning + outputs: [] + parent_id: microbiome/metagenomics-binning + path: topics/microbiome/tutorials/metagenomics-binning/workflows/Metagenomic-Binning.ga tags: - - name:Collection - - name:microGalaxy - - name:PathoGFAIR - - name:Nanopore - - name:IWC + - microbiome + - microgalaxy + - binning test_results: null tests: true - title: Nanopore Preprocessing + title: Metagenomic Binning topic_id: microbiome - trs_endpoint: https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/microbiome-pathogen-detection-from-nanopore-foodborne-data/versions/nanopore-preprocessing - tutorial_id: pathogen-detection-from-nanopore-foodborne-data - url: https://training.galaxyproject.org/training-material/topics/microbiome/tutorials/pathogen-detection-from-nanopore-foodborne-data/workflows/nanopore_preprocessing.ga - url_html: https://training.galaxyproject.org/training-material/topics/microbiome/tutorials/pathogen-detection-from-nanopore-foodborne-data/workflows/nanopore_preprocessing.html - version: 4 - wfid: microbiome-pathogen-detection-from-nanopore-foodborne-data - wfname: nanopore-preprocessing - workflow: nanopore_preprocessing.ga + trs_endpoint: https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/microbiome-metagenomics-binning/versions/metagenomic-binning + tutorial_id: metagenomics-binning + url: https://training.galaxyproject.org/training-material/topics/microbiome/tutorials/metagenomics-binning/workflows/Metagenomic-Binning.ga + url_html: https://training.galaxyproject.org/training-material/topics/microbiome/tutorials/metagenomics-binning/workflows/Metagenomic-Binning.html + version: 1 + wfid: microbiome-metagenomics-binning + wfname: metagenomic-binning + workflow: Metagenomic-Binning.ga workflow_tools: - 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plushz + - bebatut + - vinisalazar + - paulzierep + funding: + - gallantries + reviewing: + - bebatut + - shiltemann + - plushz + - hexylena + - bgruening + - paulzierep + - natalie-wa + contributors: + - affiliations: + - uni-freiburg + id: plushz + joined: 2022-03 + name: Polina Polunina + orcid: 0000-0002-0507-4602 + page: https://training.galaxyproject.org/training-material/hall-of-fame/plushz/ + url: https://training.galaxyproject.org/training-material/api/contributors/plushz.json + - affiliations: + - gallantries + - ifb + - elixir-europe + contact_for_training: true + elixir_node: fr + email: berenice.batut@gmail.com + fediverse: https://piaille.fr/@bebatut + fediverse_flavor: mastodon + former_affiliations: + - uni-freiburg + - deNBI + id: bebatut + joined: 2017-09 + linkedin: berenicebatut + location: + country: FR + lat: 45.77 + lon: 3.08 + matrix: bebatut:matrix.org + name: "B\xE9r\xE9nice Batut" + orcid: 0000-0001-9852-1987 + page: https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/ + twitter: bebatut + url: https://training.galaxyproject.org/training-material/api/contributors/bebatut.json + - affiliations: + - unimelb + - melbournebioinformatics + id: vinisalazar + joined: 2025-10 + name: Vini Salazar + orcid: 0000-0002-8362-3195 + page: https://training.galaxyproject.org/training-material/hall-of-fame/vinisalazar/ + url: https://training.galaxyproject.org/training-material/api/contributors/vinisalazar.json + - affiliations: + - uni-freiburg + - elixir-europe + - deNBI + - mwk + - materialvitaldigital + email: zierep@informatik.uni-freiburg.de + id: paulzierep + joined: 2023-02 + name: Paul Zierep + orcid: 0000-0003-2982-388X + page: https://training.galaxyproject.org/training-material/hall-of-fame/paulzierep/ + url: https://training.galaxyproject.org/training-material/api/contributors/paulzierep.json + - avatar: https://gallantries.github.io/assets/images/gallantries-logo.png + end_date: '2023-09-30' + former_members: + - abretaud + - hexylena + - shiltemann + funder_name: Erasmus+ Programme + funding_database: erasmusplus + funding_id: 2020-1-NL01-KA203-064717 + funding_statement: 'This project (2020-1-NL01-KA203-064717) + is funded with the support of the Erasmus+ programme of the European Union. + Their funding has supported a large number of tutorials within the GTN across + a wide array of topics. + + eu flag with the text: with the support of the erasmus programme of the + european union + + erasmus plus + logo' + github: false + id: gallantries + joined: 2020-09 + members: + - bebatut + - colineroyaux + - fpsom + - yvanlebras + name: 'Gallantries: Bridging Training Communities in Life Science, Environment + and Health' + page: https://training.galaxyproject.org/training-material/hall-of-fame/gallantries/ + short_name: Gallantries + start_date: '2020-09-01' + url: https://training.galaxyproject.org/training-material/api/grants/gallantries.json + - affiliations: + - gallantries + - ifb + - elixir-europe + contact_for_training: true + elixir_node: fr + email: berenice.batut@gmail.com + fediverse: https://piaille.fr/@bebatut + fediverse_flavor: mastodon + former_affiliations: + - uni-freiburg + - deNBI + id: bebatut + joined: 2017-09 + linkedin: berenicebatut + location: + country: FR + lat: 45.77 + lon: 3.08 + matrix: bebatut:matrix.org + name: "B\xE9r\xE9nice Batut" + orcid: 0000-0001-9852-1987 + page: https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/ + twitter: bebatut + url: https://training.galaxyproject.org/training-material/api/contributors/bebatut.json + - affiliations: + - uni-freiburg + - nfdi4plants + - elixir-europe + bio: Researcher at Erasmus Medical Center + bluesky: shiltemann.bsky.social + contact_for_training: true + elixir_node: nl + email: saskia.hiltemann@gmail.com + fediverse: https://mstdn.science/@shiltemann + fediverse_flavor: mastodon + former_affiliations: + - CINECA-Project + - gallantries + - erasmusmc + id: shiltemann + joined: 2017-09 + linkedin: shiltemann + location: + country: NL + lat: 51.912 + lon: 4.462 + maintainer_contact: gitter + matrix: shiltemann:matrix.org + name: Saskia Hiltemann + orcid: 0000-0003-3803-468X + page: https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/ + url: https://training.galaxyproject.org/training-material/api/contributors/shiltemann.json + - affiliations: + - uni-freiburg + id: plushz + joined: 2022-03 + name: Polina Polunina + orcid: 0000-0002-0507-4602 + page: https://training.galaxyproject.org/training-material/hall-of-fame/plushz/ + url: https://training.galaxyproject.org/training-material/api/contributors/plushz.json + - affiliations: + - elixir-europe + contact_for_training: false + elixir_node: nl + former_affiliations: + - deNBI + - avans-atgm + - uni-freiburg + - erasmusmc + - gallantries + - by-covid + - elixir-converge + id: hexylena + joined: 2017-09 + location: + country: NL + lat: 51.91 + lon: 4.46 + maintainer_contact: gitter + matrix: hexylena:matrix.org + name: Helena Rasche + orcid: 0000-0001-9760-8992 + page: https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/ + url: https://training.galaxyproject.org/training-material/api/contributors/hexylena.json + - affiliations: + - deNBI + - mwk + - uni-freiburg + - elixir-europe + - materialvitaldigital + contact_for_training: true + elixir_node: de + email: bjoern.gruening@gmail.com + fediverse: https://fosstodon.org/@bgruening + fediverse_flavor: mastodon + former_affiliations: + - eurosciencegateway + - eosc-life + - by-covid + - crc992 + - elixir-converge + id: bgruening + joined: 2017-09 + linkedin: bgruening + location: + country: DE + lat: 47.997791 + lon: 7.842609 + matrix: bgruening:matrix.org + name: "Bj\xF6rn Gr\xFCning" + orcid: 0000-0002-3079-6586 + page: https://training.galaxyproject.org/training-material/hall-of-fame/bgruening/ + twitter: bjoerngruening + url: https://training.galaxyproject.org/training-material/api/contributors/bgruening.json + - 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Statistical calculation + - Genome assembly + - Sequence contamination filtering + - Data handling + - Sequence trimming + - Sequence alignment analysis + - Sequence file editing + - Formatting + - Read pre-processing + edam_topic: + - Metagenomics + - Sequence assembly + exact_supported_servers: [] + feedback_mean_note: null + feedback_number: 0 + hands_on: true + id: microbiome/metagenomics-assembly + inexact_supported_servers: + - UseGalaxy.cz + - UseGalaxy.eu + - UseGalaxy.fr + - UseGalaxy.org (Main) + js_requirements: + mathjax: 27693 + mermaid: false + key_points: + - Assembly groups reads into contigs and scaffolds. + - de Brujin Graphs use k-mers to assembly reads. + - MetaSPAdes and MEGAHIT are short-read assemblers. + - MetaQUAST is a tool to assess metagenomic assembly quality. + layout: tutorial_hands_on + level: Introductory + license: CC-BY-4.0 + mod_date: '2026-05-11' + objectives: + - Describe what an assembly is. + - Explain the difference between co-assembly and individual assembly. + - 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server: https://mississippi.sorbonne-universite.fr + state: exact + version: 4.2.0+galaxy0 + - server: http://galaxy.inf.ethz.ch + state: missing + - server: https://palfinder.ls.manchester.ac.uk/ + state: missing + - server: http://pepsimili.e-nios.com:8080/ + state: missing + - server: https://usegalaxy.org.au + state: exact + version: 4.2.0+galaxy0 + - server: https://usegalaxy.be/ + state: exact + version: 4.2.0+galaxy0 + - server: https://usegalaxy.cz/ + state: exact + version: 4.2.0+galaxy0 + - server: https://usegalaxy.eu + state: exact + version: 4.2.0+galaxy0 + - server: https://usegalaxy.fr/ + state: exact + version: 4.2.0+galaxy0 + - server: https://usegalaxy.no/ + state: inexact + versions: + - 3.9.0 + - 3.15.4+galaxy2 + - 3.15.3+galaxy1 + - 3.9.0.1 + - 3.15.4+galaxy0 + - 3.15.3+galaxy2 + - 3.15.4+galaxy1 + - server: https://usegalaxy.org + state: exact + version: 4.2.0+galaxy0 + - server: https://viralvariant.anses.fr/ + state: missing + version: 4.2.0+galaxy0 + symlink: null + tags: + - assembly + - metagenomics + - microgalaxy + time: null + time_estimation: 2H + title: Assembly of metagenomic sequencing data + tools: + - random_lines1 + - toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.1 + - toolshed.g2.bx.psu.edu/repos/bgruening/unique/bg_uniq/0.3 + - toolshed.g2.bx.psu.edu/repos/devteam/bamtools/bamtools/2.5.1+galaxy0 + - toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.4.5+galaxy1 + - toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.5.3+galaxy1 + - toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.73+galaxy0 + - toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/0.8.1+galaxy4 + - toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_info/0.8.1+galaxy2 + - toolshed.g2.bx.psu.edu/repos/iuc/collection_column_join/collection_column_join/0.0.3 + - toolshed.g2.bx.psu.edu/repos/iuc/coverm_contig/coverm_contig/0.7.0+galaxy0 + - toolshed.g2.bx.psu.edu/repos/iuc/filter_tabular/filter_tabular/2.0.0 + - toolshed.g2.bx.psu.edu/repos/iuc/megahit/megahit/1.2.9+galaxy0 + - toolshed.g2.bx.psu.edu/repos/iuc/megahit/megahit/1.2.9+galaxy2 + - toolshed.g2.bx.psu.edu/repos/iuc/megahit_contig2fastg/megahit_contig2fastg/1.1.3+galaxy1 + - toolshed.g2.bx.psu.edu/repos/iuc/megahit_contig2fastg/megahit_contig2fastg/1.1.3+galaxy10 + - toolshed.g2.bx.psu.edu/repos/iuc/ngsutils_bam_filter/ngsutils_bam_filter/0.5.9 + - toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.2.0+galaxy1 + - toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.3.0+galaxy0 + - toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_subseq/1.3.1 + - toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.0+galaxy0 + - toolshed.g2.bx.psu.edu/repos/nml/metaspades/metaspades/4.2.0+galaxy0 + topic_name: microbiome + topic_name_human: Microbiome + tours: false + translations: + slides: [] + tutorial: [] + video: false + tutorial_name: metagenomics-assembly + type: tutorial + url: https://training.galaxyproject.org//topics/microbiome/tutorials/metagenomics-assembly/tutorial.html + urls: + hands_on: https://training.galaxyproject.org/training-material/api/topics/microbiome/tutorials/metagenomics-assembly/tutorial.json + slides: https://training.galaxyproject.org/training-material/api/topics/microbiome/tutorials/metagenomics-assembly/tutorial.json + version: 11 + video: true + video_versions: 2 + video_view: 0 + visit_duration: 623 + visitors: 5645 + workflows: - creators: - class: Person - identifier: 0000-0001-9047-4215 - name: Engy Nasr - url: https://orcid.org/0000-0001-9047-4215 + identifier: 0000-0002-0507-4602 + name: Polina Polunina - class: Person identifier: 0000-0001-9852-1987 name: "B\xE9r\xE9nice Batut" - url: https://orcid.org/0000-0001-9852-1987 - - class: Person - identifier: 0000-0003-2982-388X - name: Paul Zierep - description: Pathogens of all samples report generation and visualization - features: - comments: true - parameters: false - report: - markdown: "# Pathogen Detection - PathoGFAIR Samples Aggregation and Visualisation\ - \ workflow Report\nBelow are the results for the PathoGFAIR Samples Aggregation\ - \ and Visualisation Workflow\n\nThis workflow was run on:\n\n```galaxy\n\ - generate_time()\n```\n\nWith Galaxy version:\n\n```galaxy\ngenerate_galaxy_version()\n\ - ```\n\n## Workflow Inputs\nTabular files and a FASTA file from the Gene\ - \ based Pathogenic Identification workflow, four other tabular files from\ - \ Nanopore Preprocessing and Nanopore - Allele bases Pathogen Identification\ - \ workflow, and an optional Metadata tabular file with more sample information:\n\ - \nFrom Gene based Pathogenic Identification workflow: \n- contigs, FASTA\ - \ file\n- vfs, Tabular file\n- vfs_of_genes_identified_by_vfdb, Tabular\ - \ file\n- amrs, Tabular file\n- amr_identified_by_ncbi, Tabular file\n\n\ - From Nanopore - Allele bases Pathogen Identification workflow: \n- number_of_variants_per_sample,\ - \ Tabular file\n- mapping_mean_depth_per_sample, Tabular file\n- mapping_coverage_percentage_per_sample,\ - \ Tabular file\n\nFrom Nanopore Preprocessing: \n- removed_hosts_percentage_tabular,\ - \ Tabular file\n\n## Some of the Workflow Outputs\n\n1- All Samples VFs\ - \ Heatmap\n\n```galaxy\nhistory_dataset_as_image(output=\"heatmap_png\"\ - )\n```\n\n2- All samples phylogenetic tree VFs based\n\n```galaxy\nhistory_dataset_as_image(output=\"\ - all_samples_phylogenetic_tree_based_vfs\")\n```\n\n3- All samples Phylogenetic\ - \ tree AMR based \n\n```galaxy\nhistory_dataset_as_image(output=\"all_samples_phylogenetic_tree_based_amrs\"\ - )\n```\n\n4- Barplot for the Number of reads before host sequences removal\ - \ and Number of found host reads per sample, performed in the Nanopore -\ - \ Preprocessing workflow\n\n```galaxy\nhistory_dataset_as_image(output=\"\ - number_of_reads_before_host_removal_and_number_of_host_reads_found_per_sample_fig\"\ - )\n```\n\n5- Barplot for the total number of removed host sequences per\ - \ sample\n\n```galaxy\nhistory_dataset_as_image(output=\"removed_host_percentage_fig\"\ - )\n```\n \n6- Barplot for the Mapping mean depth per sample\n\n```galaxy\n\ - history_dataset_as_image(output=\"mapping_mean_depth_per_sample_fig\")\n\ - ```\n\n6- Barplot for the Mapping coverage percentage per sample\n\n```galaxy\n\ - history_dataset_as_image(output=\"mapping_coverage_percentage_per_sample_fig\"\ - )\n```\n\n7- Barplot for the total number of variants and SNPs identified\ - \ per sample\n\n```galaxy\nhistory_dataset_as_image(output=\"number_of_Variants_and_SNPs_indentified_fig\"\ - )\n```\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n" + description: Assembly of metagenomic sequencing data + features: + comments: false + parameters: false + report: + markdown: ' + + # Workflow Execution Report + + + ## Workflow Inputs + + ```galaxy + + invocation_inputs() + + ``` + + + ## Workflow Outputs + + ```galaxy + + invocation_outputs() + + ``` + + + ## Workflow + + ```galaxy + + workflow_display() + + ``` + + ' subworkflows: false graph_dot: "digraph main {\n node [fontname=\"Atkinson Hyperlegible\", shape=box,\ \ color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n edge [fontname=\"\ Atkinson Hyperlegible\"];\n 0[color=lightblue,label=\"\u2139\uFE0F Input Collection\\\ - namr_identified_by_ncbi\"]\n 1[color=lightblue,label=\"\u2139\uFE0F Input Collection\\\ - nvfs_of_genes_identified_by_vfdb\"]\n 2[color=lightblue,label=\"\u2139\uFE0F\ - \ Input Dataset\\nmetadata\"]\n 3[color=lightblue,label=\"\u2139\uFE0F Input\ - \ Dataset\\nremoved_hosts_percentage_tabular\"]\n 4[color=lightblue,label=\"\ - \u2139\uFE0F Input Dataset\\nmapping_mean_depth_per_sample\"]\n 5[color=lightblue,label=\"\ - \u2139\uFE0F Input Collection\\namrs\"]\n 6[color=lightblue,label=\"\u2139\uFE0F\ - \ Input Dataset\\nmapping_coverage_percentage_per_sample\"]\n 7[color=lightblue,label=\"\ - \u2139\uFE0F Input Dataset\\nnumber_of_variants_per_sample\"]\n 8[color=lightblue,label=\"\ - \u2139\uFE0F Input Collection\\ncontigs\"]\n 9[color=lightblue,label=\"\u2139\ - \uFE0F Input Collection\\nvfs\"]\n 10[label=\"Filter failed datasets\"]\n \ - \ 0 -> 10 [label=\"output\"]\n 11[label=\"Filter failed datasets\"]\n 1 ->\ - \ 11 [label=\"output\"]\n 12[label=\"Bar chart\"]\n 3 -> 12 [label=\"output\"\ - ]\n k0961166e38b644e393db100d821b0070[color=lightseagreen,label=\"Output\\\ - nnumber_of_reads_before_host_removal_and_number_of_host_reads_found_per_sample_fig\"\ - ]\n 12 -> k0961166e38b644e393db100d821b0070\n 13[label=\"Bar chart\"]\n 3\ - \ -> 13 [label=\"output\"]\n k548975e5461949fc9e954d7f4d761dfd[color=lightseagreen,label=\"\ - Output\\nremoved_host_percentage_fig\"]\n 13 -> k548975e5461949fc9e954d7f4d761dfd\n\ - \ 14[label=\"Bar chart\"]\n 4 -> 14 [label=\"output\"]\n ka71ebb6711544f25a62de8fa2b839e2e[color=lightseagreen,label=\"\ - Output\\nmapping_mean_depth_per_sample_fig\"]\n 14 -> ka71ebb6711544f25a62de8fa2b839e2e\n\ - \ 15[label=\"Filter failed datasets\"]\n 5 -> 15 [label=\"output\"]\n 16[label=\"\ - Bar chart\"]\n 6 -> 16 [label=\"output\"]\n k2567360ed39f431684f577aaf8e8198c[color=lightseagreen,label=\"\ - Output\\nmapping_coverage_percentage_per_sample_fig\"]\n 16 -> k2567360ed39f431684f577aaf8e8198c\n\ - \ 17[label=\"Bar chart\"]\n 7 -> 17 [label=\"output\"]\n k68c76f06d2ea42809e6fa7b4f1568389[color=lightseagreen,label=\"\ - Output\\nnumber_of_Variants_and_SNPs_indentified_fig\"]\n 17 -> k68c76f06d2ea42809e6fa7b4f1568389\n\ - \ 18[label=\"Filter failed datasets\"]\n 8 -> 18 [label=\"output\"]\n 19[label=\"\ - Filter failed datasets\"]\n 9 -> 19 [label=\"output\"]\n 20[label=\"Remove\ - \ beginning\"]\n 10 -> 20 [label=\"output\"]\n 21[label=\"Remove beginning\"\ - ]\n 11 -> 21 [label=\"output\"]\n 22[label=\"Remove beginning\"]\n 15 ->\ - \ 22 [label=\"output\"]\n 23[label=\"Collapse Collection\"]\n 18 -> 23 [label=\"\ - output\"]\n k86910e3957bf4a76ac4c739340fd2387[color=lightseagreen,label=\"\ - Output\\nall_samples_contigs_in_one_fasta_file\"]\n 23 -> k86910e3957bf4a76ac4c739340fd2387\n\ - \ 24[label=\"Collapse Collection\"]\n 19 -> 24 [label=\"output\"]\n k02b996c6a9124e4eb3ec49601faaa452[color=lightseagreen,label=\"\ - Output\\nall_vfs_in_one_tabular\"]\n 24 -> k02b996c6a9124e4eb3ec49601faaa452\n\ - \ 25[label=\"Remove beginning\"]\n 19 -> 25 [label=\"output\"]\n 26[label=\"\ - Count\"]\n 20 -> 26 [label=\"out_file1\"]\n 27[label=\"Count\"]\n 21 -> 27\ - \ [label=\"out_file1\"]\n 28[label=\"Group\"]\n 21 -> 28 [label=\"out_file1\"\ - ]\n 29[label=\"Unique\"]\n 22 -> 29 [label=\"out_file1\"]\n 30[label=\"Split\ - \ by group\"]\n 24 -> 30 [label=\"output\"]\n k59f8cb09424b47b1b94ba612c2610cab[color=lightseagreen,label=\"\ - Output\\nsplit_by_group_collection\"]\n 30 -> k59f8cb09424b47b1b94ba612c2610cab\n\ - \ 31[label=\"Unique\"]\n 25 -> 31 [label=\"out_file1\"]\n 32[label=\"Cut\"\ - ]\n 26 -> 32 [label=\"out_file1\"]\n 33[label=\"Cut\"]\n 27 -> 33 [label=\"\ - out_file1\"]\n 34[label=\"Filter empty datasets\"]\n 28 -> 34 [label=\"out_file1\"\ - ]\n 35[label=\"Cut\"]\n 29 -> 35 [label=\"outfile\"]\n 36[label=\"Cut\"]\n\ - \ 30 -> 36 [label=\"split_output\"]\n keeb25a51ea214a19a19655d5bd919b10[color=lightseagreen,label=\"\ - Output\\nadjusted_abricate_vfs_tabular_part1\"]\n 36 -> keeb25a51ea214a19a19655d5bd919b10\n\ - \ 37[label=\"Cut\"]\n 31 -> 37 [label=\"outfile\"]\n 38[label=\"Collapse\ - \ Collection\"]\n 32 -> 38 [label=\"out_file1\"]\n 39[label=\"Collapse Collection\"\ - ]\n 33 -> 39 [label=\"out_file1\"]\n 40[label=\"Column join\"]\n 34 -> 40\ - \ [label=\"output\"]\n 41[label=\"bedtools getfasta\"]\n 23 -> 41 [label=\"\ - output\"]\n 35 -> 41 [label=\"out_file1\"]\n 42[label=\"Remove beginning\"\ - ]\n 36 -> 42 [label=\"out_file1\"]\n kaaaa444608174e5caa1b9ec384f2a363[color=lightseagreen,label=\"\ - Output\\nadjusted_abricate_vfs_tabular_part2\"]\n 42 -> kaaaa444608174e5caa1b9ec384f2a363\n\ - \ 43[label=\"bedtools getfasta\"]\n 23 -> 43 [label=\"output\"]\n 37 -> 43\ - \ [label=\"out_file1\"]\n 44[label=\"Column Regex Find And Replace\"]\n 38\ - \ -> 44 [label=\"output\"]\n k4809c36b31ef46648e4e47f0f72152de[color=lightseagreen,label=\"\ - Output\\namrs_count\"]\n 44 -> k4809c36b31ef46648e4e47f0f72152de\n 45[label=\"\ - Column Regex Find And Replace\"]\n 39 -> 45 [label=\"output\"]\n k87efc81d4d844af3831fdfe033c59f78[color=lightseagreen,label=\"\ - Output\\nvfs_count\"]\n 45 -> k87efc81d4d844af3831fdfe033c59f78\n 46[label=\"\ - Column Regex Find And Replace\"]\n 40 -> 46 [label=\"tabular_output\"]\n kf5c221e300ef48349a5fa94c97fd6764[color=lightseagreen,label=\"\ - Output\\nheatmap_table\"]\n 46 -> kf5c221e300ef48349a5fa94c97fd6764\n 47[label=\"\ - Regex Find And Replace\"]\n 41 -> 47 [label=\"output\"]\n 48[label=\"bedtools\ - \ getfasta\"]\n 23 -> 48 [label=\"output\"]\n 42 -> 48 [label=\"out_file1\"\ - ]\n k82ce210789a3438c95bbdc871b5258b7[color=lightseagreen,label=\"Output\\\ - nfiltered_sequences_with_vfs_fasta\"]\n 48 -> k82ce210789a3438c95bbdc871b5258b7\n\ - \ 49[label=\"Regex Find And Replace\"]\n 43 -> 49 [label=\"output\"]\n 50[label=\"\ - Multi-Join\"]\n 45 -> 50 [label=\"out_file1\"]\n 44 -> 50 [label=\"out_file1\"\ - ]\n 51[label=\"Heatmap w ggplot\"]\n 46 -> 51 [label=\"out_file1\"]\n k97816bc2fd0c4077a7218dd1470879d1[color=lightseagreen,label=\"\ - Output\\nheatmap_png\"]\n 51 -> k97816bc2fd0c4077a7218dd1470879d1\n kc0417c91a5134c6a9a623aac2f1f8e85[color=lightseagreen,label=\"\ - Output\\nheatmap_pdf\"]\n 51 -> kc0417c91a5134c6a9a623aac2f1f8e85\n 52[label=\"\ - Filter empty datasets\"]\n 47 -> 52 [label=\"out_file1\"]\n 53[label=\"ClustalW\"\ - ]\n 48 -> 53 [label=\"output\"]\n k6af2032224da403680de37bed2d25848[color=lightseagreen,label=\"\ - Output\\nclustalw_on_input_clustal\"]\n 53 -> k6af2032224da403680de37bed2d25848\n\ - \ k9b7bd78cf112480ba7dfc10711af254c[color=lightseagreen,label=\"Output\\nclustalw_on_input_dnd\"\ - ]\n 53 -> k9b7bd78cf112480ba7dfc10711af254c\n 54[label=\"Filter empty datasets\"\ - ]\n 49 -> 54 [label=\"out_file1\"]\n 55[label=\"Replace Text\"]\n 50 -> 55\ - \ [label=\"outfile\"]\n k91745da00b8d4a7ab927b36107f17ec5[color=lightseagreen,label=\"\ - Output\\nvfs_amrs_count_table\"]\n 55 -> k91745da00b8d4a7ab927b36107f17ec5\n\ - \ 56[label=\"FASTA-to-Tabular\"]\n 52 -> 56 [label=\"output\"]\n 57[label=\"\ - Filter empty datasets\"]\n 53 -> 57 [label=\"output\"]\n k32d00c1d68c440698d5d023aabdfadbe[color=lightseagreen,label=\"\ - Output\\nfiltered_empty_datasets\"]\n 57 -> k32d00c1d68c440698d5d023aabdfadbe\n\ - \ 58[label=\"FASTA-to-Tabular\"]\n 54 -> 58 [label=\"output\"]\n 59[label=\"\ - Cut\"]\n 56 -> 59 [label=\"output\"]\n 60[label=\"FASTTREE\"]\n 57 -> 60\ - \ [label=\"output\"]\n kaacdfe45eb0c4f6ea479eeb170774757[color=lightseagreen,label=\"\ - Output\\nfasttree_nhx\"]\n 60 -> kaacdfe45eb0c4f6ea479eeb170774757\n 61[label=\"\ - Cut\"]\n 58 -> 61 [label=\"output\"]\n 62[label=\"Group\"]\n 59 -> 62 [label=\"\ - out_file1\"]\n 63[label=\"Newick Display\"]\n 60 -> 63 [label=\"output\"]\n\ - \ k0c22178cdc85413780e2f3040b92bd20[color=lightseagreen,label=\"Output\\nnewick_genes_tree_graphs_collection\"\ - ]\n 63 -> k0c22178cdc85413780e2f3040b92bd20\n 64[label=\"Group\"]\n 61 ->\ - \ 64 [label=\"out_file1\"]\n 65[label=\"Tabular-to-FASTA\"]\n 62 -> 65 [label=\"\ - out_file1\"]\n 66[label=\"Tabular-to-FASTA\"]\n 64 -> 66 [label=\"out_file1\"\ - ]\n 67[label=\"FASTA Merge Files and Filter Unique Sequences\"]\n 65 -> 67\ - \ [label=\"output\"]\n 68[label=\"FASTA Merge Files and Filter Unique Sequences\"\ - ]\n 66 -> 68 [label=\"output\"]\n 69[label=\"ClustalW\"]\n 67 -> 69 [label=\"\ - output\"]\n 70[label=\"ClustalW\"]\n 68 -> 70 [label=\"output\"]\n 71[label=\"\ - FASTTREE\"]\n 69 -> 71 [label=\"output\"]\n 72[label=\"FASTTREE\"]\n 70 ->\ - \ 72 [label=\"output\"]\n 73[label=\"Newick Display\"]\n 71 -> 73 [label=\"\ - output\"]\n k1f9cb2cf219f48de8058d6d45f3b3158[color=lightseagreen,label=\"\ - Output\\nall_samples_phylogenetic_tree_based_amrs\"]\n 73 -> k1f9cb2cf219f48de8058d6d45f3b3158\n\ - \ 74[label=\"Newick Display\"]\n 72 -> 74 [label=\"output\"]\n k6bb4b32b7cca4e048120be9f64ccba39[color=lightseagreen,label=\"\ - Output\\nall_samples_phylogenetic_tree_based_vfs\"]\n 74 -> k6bb4b32b7cca4e048120be9f64ccba39\n\ - }" + nQC controlled reads\"]\n 1[label=\"metaSPAdes\"]\n 0 -> 1 [label=\"output\"\ + ]\n kba8ef041cea5479a8aab38b3d6f0af60[color=lightseagreen,label=\"Output\\\ + nout_ag\"]\n 1 -> kba8ef041cea5479a8aab38b3d6f0af60\n kc3b9a23494d245798eba895e7e49e129[color=lightseagreen,label=\"\ + Output\\nout_ags\"]\n 1 -> kc3b9a23494d245798eba895e7e49e129\n 2[label=\"\ + MEGAHIT\"]\n 0 -> 2 [label=\"output\"]\n k759ce084a80b4a04b74e6e387357e25a[color=lightseagreen,label=\"\ + Output\\noutput\"]\n 2 -> k759ce084a80b4a04b74e6e387357e25a\n 3[label=\"Bowtie2\"\ + ]\n 0 -> 3 [label=\"output\"]\n 2 -> 3 [label=\"output\"]\n k95b806c753ee4a788e24a5794c9c220a[color=lightseagreen,label=\"\ + Output\\nmapping_stats\"]\n 3 -> k95b806c753ee4a788e24a5794c9c220a\n 4[label=\"\ + CoverM contig\"]\n 0 -> 4 [label=\"output\"]\n 2 -> 4 [label=\"output\"]\n\ + \ k51a8a5a9b3bb43b980e57ec7b84a6cd5[color=lightseagreen,label=\"Output\\noutput\"\ + ]\n 4 -> k51a8a5a9b3bb43b980e57ec7b84a6cd5\n 5[label=\"Quast\"]\n 2 -> 5\ + \ [label=\"output\"]\n 0 -> 5 [label=\"output\"]\n k5553b6a6863d4846944f7ed609a3734a[color=lightseagreen,label=\"\ + Output\\nreport_html_meta\"]\n 5 -> k5553b6a6863d4846944f7ed609a3734a\n 6[label=\"\ + megahit contig2fastg\"]\n 2 -> 6 [label=\"output\"]\n 7[label=\"Bandage Image\"\ + ]\n 6 -> 7 [label=\"fastg\"]\n k63861d0be0a64604bd091b0f7ee9d54b[color=lightseagreen,label=\"\ + Output\\noutfile\"]\n 7 -> k63861d0be0a64604bd091b0f7ee9d54b\n 8[label=\"\ + Bandage Info\"]\n 6 -> 8 [label=\"fastg\"]\n 9[label=\"Column join\"]\n 8\ + \ -> 9 [label=\"outfile\"]\n kc882d313508440d48c979552fb7b35ad[color=lightseagreen,label=\"\ + Output\\ntabular_output\"]\n 9 -> kc882d313508440d48c979552fb7b35ad\n}" history: - - hash: 20b1c5a11c7ea68a1cefd70cbe72b3783d7887ad - message: GTN-Foodborne tutorial, updating 2/5 workflows, which contains filter - failed datasets tool with the new tool - num: 4 - short_hash: 20b1c5a11 - unix: '1751535250' - - hash: cdd93376adc6ce80742881c25d6810bcce85fc05 - message: adding tags to some of the workflow outputs, updating the training - with the latest PathoGFAIR workflows updates - num: 3 - short_hash: cdd93376a - unix: '1717675229' - - hash: 211b69394d6ef4d129eaa18cd76b93c8dece8cf3 - message: adding workflow reports to the workflows of the training to match the - latest version of the IWC PR + - hash: 65e24d135887a0fad9a1cc667b98a66040949936 + message: Update metagenomics assembly tutorial num: 2 - short_hash: 211b69394 - unix: '1716716727' - - hash: d320748c5c8ea425a77aa03ac78a5956eb75b005 - message: Foodborne training update 2024 + short_hash: 65e24d135 + unix: '1749722054' + - hash: 0e0a2f2ccb650b0aab1ffc13838045164bdb5d30 + message: Rename metagenomics topic to microbiome num: 1 - short_hash: d320748c5 - unix: '1716229068' + short_hash: 0e0a2f2cc + unix: '1704901629' inputs: - - annotation: output_of_abricate_with_amrfinderncbi + - annotation: Metagenomics reads that have been controlled for quality content_id: null errors: null id: 0 - input_connections: {} - inputs: - - description: output_of_abricate_with_amrfinderncbi - name: amr_identified_by_ncbi - label: amr_identified_by_ncbi - name: Input dataset collection - outputs: [] - position: - left: 19.98333740234375 - top: 1006.3443929882739 - tool_id: null - tool_state: '{"optional": false, "tag": null, "collection_type": "list", "fields": - null}' - tool_version: null - type: data_collection_input - uuid: a7f1c4a9-5d07-49df-82cd-1bbcf3fd628f - when: null - workflow_outputs: [] - - annotation: output_of_abricate_with_vfdb - content_id: null - errors: null - id: 1 - input_connections: {} - inputs: - - description: output_of_abricate_with_vfdb - name: vfs_of_genes_identified_by_vfdb - label: vfs_of_genes_identified_by_vfdb - name: Input dataset collection - outputs: [] - position: - left: 34.98484848484827 - top: 1508.441282170953 - tool_id: null - tool_state: '{"optional": false, "tag": null, "collection_type": "list", "fields": - null}' - tool_version: null - type: data_collection_input - uuid: 2908a402-5edf-4bcc-a970-1db21c474d09 - when: null - workflow_outputs: [] - - annotation: samples_metadata - content_id: null - errors: null - id: 2 - input_connections: {} - inputs: - - description: samples_metadata - name: metadata - label: metadata - name: Input dataset - outputs: [] - position: - left: 1858.3512218637072 - top: 209.99121532505262 - tool_id: null - tool_state: '{"optional": true, "tag": null}' - tool_version: null - type: data_input - uuid: f4765d9d-b134-4462-bae6-9695c95ae596 - when: null - workflow_outputs: [] - - annotation: removed_hosts_percentage_tabular - content_id: null - errors: null - id: 3 - input_connections: {} - inputs: - - description: removed_hosts_percentage_tabular - name: removed_hosts_percentage_tabular - label: removed_hosts_percentage_tabular - name: Input dataset - outputs: [] - position: - left: 1853.666381138832 - top: 289.6725384559728 - tool_id: null - tool_state: '{"optional": false, "tag": null}' - tool_version: null - type: data_input - uuid: e7dccd07-76a8-48a2-8931-67567fb31598 - when: null - workflow_outputs: [] - - annotation: mapping_mean_depth_per_sample - content_id: null - errors: null - id: 4 - input_connections: {} - inputs: - - description: mapping_mean_depth_per_sample - name: mapping_mean_depth_per_sample - label: mapping_mean_depth_per_sample - name: Input dataset - outputs: [] - position: - left: 1854.0957915122806 - top: 419.61832235919906 - tool_id: null - tool_state: '{"optional": false, "tag": null}' - tool_version: null - type: data_input - uuid: c18104cc-35d8-43ed-85e6-15e4f7af0b4d - when: null - workflow_outputs: [] - - annotation: amrs - content_id: null - errors: null - id: 5 - input_connections: {} - inputs: - - description: amrs - name: amrs - label: amrs - name: Input dataset collection - outputs: [] - position: - left: 50.9848484848481 - top: 1934.2745890557185 - tool_id: null - tool_state: '{"optional": false, "tag": null, "collection_type": "list", "fields": - null}' - tool_version: null - type: data_collection_input - uuid: 297bede6-bef8-44f1-bcbb-134464821c44 - when: null - workflow_outputs: [] - - annotation: mapping_coverage_percentage_per_sample - content_id: null - errors: null - id: 6 - input_connections: {} - inputs: - - description: mapping_coverage_percentage_per_sample - name: mapping_coverage_percentage_per_sample - label: mapping_coverage_percentage_per_sample - name: Input dataset - outputs: [] - position: - left: 1856.926239945225 - top: 545.6990912189043 - tool_id: null - tool_state: '{"optional": false, "tag": null}' - tool_version: null - type: data_input - uuid: bbf94808-86af-468d-bbdd-6872ddbf6c30 - when: null - workflow_outputs: [] - - annotation: number_of_variants_per_sample - content_id: null - errors: null - id: 7 - input_connections: {} - inputs: - - description: number_of_variants_per_sample - name: number_of_variants_per_sample - label: number_of_variants_per_sample - name: Input dataset - outputs: [] - position: - left: 1858.9173115502963 - top: 671.3113831546217 - tool_id: null - tool_state: '{"optional": false, "tag": null}' - tool_version: null - type: data_input - uuid: 833bedfd-e345-4c8a-8d19-1623faaaf602 - when: null - workflow_outputs: [] - - annotation: Contigs - content_id: null - errors: null - id: 8 - input_connections: {} - inputs: - - description: Contigs - name: contigs - label: contigs - name: Input dataset collection - outputs: [] - position: - left: 600.9833984375 - top: 2266.2999877929688 - tool_id: null - tool_state: '{"optional": false, "tag": "", "collection_type": "list", "fields": - null}' - tool_version: null - type: data_collection_input - uuid: ce948faa-f897-47e3-ac8c-0227afdd8203 - when: null - workflow_outputs: [] - - annotation: VFs - content_id: null - errors: null - id: 9 - input_connections: {} - inputs: - - description: VFs - name: vfs - label: vfs - name: Input dataset collection - outputs: [] - position: - left: 46.984848484848044 - top: 2487.3079752861872 - tool_id: null - tool_state: '{"optional": false, "tag": "", "collection_type": "list", "fields": - null}' - tool_version: null - type: data_collection_input - uuid: 8ff72508-664e-4af1-b0e6-ca2643626295 - when: null - workflow_outputs: [] - license: MIT - mermaid: "flowchart TD\n 0[\"\u2139\uFE0F Input Collection\\namr_identified_by_ncbi\"\ - ];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"\u2139\uFE0F Input Collection\\\ - nvfs_of_genes_identified_by_vfdb\"];\n style 1 stroke:#2c3143,stroke-width:4px;\n\ - \ 2[\"\u2139\uFE0F Input Dataset\\nmetadata\"];\n style 2 stroke:#2c3143,stroke-width:4px;\n\ - \ 3[\"\u2139\uFE0F Input Dataset\\nremoved_hosts_percentage_tabular\"];\n \ - \ style 3 stroke:#2c3143,stroke-width:4px;\n 4[\"\u2139\uFE0F Input Dataset\\\ - nmapping_mean_depth_per_sample\"];\n style 4 stroke:#2c3143,stroke-width:4px;\n\ - 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\ 548975e5-4619-49fc-9e95-4d7f4d761dfd[\"Output\\nremoved_host_percentage_fig\"\ - ];\n 13 --> 548975e5-4619-49fc-9e95-4d7f4d761dfd;\n style 548975e5-4619-49fc-9e95-4d7f4d761dfd\ - \ stroke:#2c3143,stroke-width:4px;\n 14[\"Bar chart\"];\n 4 -->|output| 14;\n\ - \ a71ebb67-1154-4f25-a62d-e8fa2b839e2e[\"Output\\nmapping_mean_depth_per_sample_fig\"\ - ];\n 14 --> a71ebb67-1154-4f25-a62d-e8fa2b839e2e;\n style a71ebb67-1154-4f25-a62d-e8fa2b839e2e\ - \ stroke:#2c3143,stroke-width:4px;\n 15[\"Filter failed datasets\"];\n 5 -->|output|\ - \ 15;\n 16[\"Bar chart\"];\n 6 -->|output| 16;\n 2567360e-d39f-4316-84f5-77aaf8e8198c[\"\ - Output\\nmapping_coverage_percentage_per_sample_fig\"];\n 16 --> 2567360e-d39f-4316-84f5-77aaf8e8198c;\n\ - \ style 2567360e-d39f-4316-84f5-77aaf8e8198c stroke:#2c3143,stroke-width:4px;\n\ - \ 17[\"Bar chart\"];\n 7 -->|output| 17;\n 68c76f06-d2ea-4280-9e6f-a7b4f1568389[\"\ - Output\\nnumber_of_Variants_and_SNPs_indentified_fig\"];\n 17 --> 68c76f06-d2ea-4280-9e6f-a7b4f1568389;\n\ - \ style 68c76f06-d2ea-4280-9e6f-a7b4f1568389 stroke:#2c3143,stroke-width:4px;\n\ - \ 18[\"Filter failed datasets\"];\n 8 -->|output| 18;\n 19[\"Filter failed\ - \ datasets\"];\n 9 -->|output| 19;\n 20[\"Remove beginning\"];\n 10 -->|output|\ - \ 20;\n 21[\"Remove beginning\"];\n 11 -->|output| 21;\n 22[\"Remove beginning\"\ - ];\n 15 -->|output| 22;\n 23[\"Collapse Collection\"];\n 18 -->|output| 23;\n\ - \ 86910e39-57bf-4a76-ac4c-739340fd2387[\"Output\\nall_samples_contigs_in_one_fasta_file\"\ - ];\n 23 --> 86910e39-57bf-4a76-ac4c-739340fd2387;\n style 86910e39-57bf-4a76-ac4c-739340fd2387\ - \ stroke:#2c3143,stroke-width:4px;\n 24[\"Collapse Collection\"];\n 19 -->|output|\ - \ 24;\n 02b996c6-a912-4e4e-b3ec-49601faaa452[\"Output\\nall_vfs_in_one_tabular\"\ - ];\n 24 --> 02b996c6-a912-4e4e-b3ec-49601faaa452;\n style 02b996c6-a912-4e4e-b3ec-49601faaa452\ - \ stroke:#2c3143,stroke-width:4px;\n 25[\"Remove beginning\"];\n 19 -->|output|\ - \ 25;\n 26[\"Count\"];\n 20 -->|out_file1| 26;\n 27[\"Count\"];\n 21 -->|out_file1|\ - \ 27;\n 28[\"Group\"];\n 21 -->|out_file1| 28;\n 29[\"Unique\"];\n 22 -->|out_file1|\ - \ 29;\n 30[\"Split by group\"];\n 24 -->|output| 30;\n 59f8cb09-424b-47b1-b94b-a612c2610cab[\"\ - Output\\nsplit_by_group_collection\"];\n 30 --> 59f8cb09-424b-47b1-b94b-a612c2610cab;\n\ - \ style 59f8cb09-424b-47b1-b94b-a612c2610cab stroke:#2c3143,stroke-width:4px;\n\ - \ 31[\"Unique\"];\n 25 -->|out_file1| 31;\n 32[\"Cut\"];\n 26 -->|out_file1|\ - \ 32;\n 33[\"Cut\"];\n 27 -->|out_file1| 33;\n 34[\"Filter empty datasets\"\ - ];\n 28 -->|out_file1| 34;\n 35[\"Cut\"];\n 29 -->|outfile| 35;\n 36[\"\ - Cut\"];\n 30 -->|split_output| 36;\n eeb25a51-ea21-4a19-a196-55d5bd919b10[\"\ - Output\\nadjusted_abricate_vfs_tabular_part1\"];\n 36 --> eeb25a51-ea21-4a19-a196-55d5bd919b10;\n\ - \ style eeb25a51-ea21-4a19-a196-55d5bd919b10 stroke:#2c3143,stroke-width:4px;\n\ - \ 37[\"Cut\"];\n 31 -->|outfile| 37;\n 38[\"Collapse Collection\"];\n 32\ - \ -->|out_file1| 38;\n 39[\"Collapse Collection\"];\n 33 -->|out_file1| 39;\n\ - \ 40[\"Column join\"];\n 34 -->|output| 40;\n 41[\"bedtools getfasta\"];\n\ - \ 23 -->|output| 41;\n 35 -->|out_file1| 41;\n 42[\"Remove beginning\"];\n\ - \ 36 -->|out_file1| 42;\n aaaa4446-0817-4e5c-aa1b-9ec384f2a363[\"Output\\\ - nadjusted_abricate_vfs_tabular_part2\"];\n 42 --> aaaa4446-0817-4e5c-aa1b-9ec384f2a363;\n\ - \ style aaaa4446-0817-4e5c-aa1b-9ec384f2a363 stroke:#2c3143,stroke-width:4px;\n\ - \ 43[\"bedtools getfasta\"];\n 23 -->|output| 43;\n 37 -->|out_file1| 43;\n\ - \ 44[\"Column Regex Find And Replace\"];\n 38 -->|output| 44;\n 4809c36b-31ef-4664-8e4e-47f0f72152de[\"\ - Output\\namrs_count\"];\n 44 --> 4809c36b-31ef-4664-8e4e-47f0f72152de;\n style\ - \ 4809c36b-31ef-4664-8e4e-47f0f72152de stroke:#2c3143,stroke-width:4px;\n 45[\"\ - Column Regex Find And Replace\"];\n 39 -->|output| 45;\n 87efc81d-4d84-4af3-831f-dfe033c59f78[\"\ - Output\\nvfs_count\"];\n 45 --> 87efc81d-4d84-4af3-831f-dfe033c59f78;\n style\ - \ 87efc81d-4d84-4af3-831f-dfe033c59f78 stroke:#2c3143,stroke-width:4px;\n 46[\"\ - 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bebatut + editing: + - bernt-matthias + - clsiguret + reviewing: + - shiltemann + - deeptivarshney + - bebatut + - hexylena + - abueg + - bernt-matthias + - paulzierep + - santamccloud + contributors: + - affiliations: + - gallantries + - ifb + - elixir-europe + contact_for_training: true + elixir_node: fr + email: berenice.batut@gmail.com + fediverse: https://piaille.fr/@bebatut + fediverse_flavor: mastodon + former_affiliations: + - uni-freiburg + - deNBI + id: bebatut + joined: 2017-09 + linkedin: berenicebatut + location: + country: FR + lat: 45.77 + lon: 3.08 + matrix: bebatut:matrix.org + name: "B\xE9r\xE9nice Batut" + orcid: 0000-0001-9852-1987 + page: https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/ + twitter: bebatut + url: https://training.galaxyproject.org/training-material/api/contributors/bebatut.json + - elixir_node: de + id: bernt-matthias + joined: 2017-09 + name: Matthias Bernt + page: https://training.galaxyproject.org/training-material/hall-of-fame/bernt-matthias/ + url: https://training.galaxyproject.org/training-material/api/contributors/bernt-matthias.json + - affiliations: + - ifb + - elixir-europe + elixir_node: fr + email: clea.siguret@gmail.com + id: clsiguret + joined: 2024-04 + linkedin: "cl\xE9a-siguret-58423b107" + matrix: clsiguret:matrix.org + name: Clea Siguret + orcid: 0009-0005-6140-0379 + page: https://training.galaxyproject.org/training-material/hall-of-fame/clsiguret/ + url: https://training.galaxyproject.org/training-material/api/contributors/clsiguret.json + - affiliations: + - uni-freiburg + - nfdi4plants + - elixir-europe + bio: Researcher at Erasmus Medical Center + bluesky: shiltemann.bsky.social + contact_for_training: true + elixir_node: nl + email: saskia.hiltemann@gmail.com + fediverse: https://mstdn.science/@shiltemann + fediverse_flavor: mastodon + former_affiliations: + - CINECA-Project + - gallantries + - erasmusmc + id: shiltemann + joined: 2017-09 + linkedin: shiltemann + location: + country: NL + lat: 51.912 + lon: 4.462 + maintainer_contact: gitter + matrix: shiltemann:matrix.org + name: Saskia Hiltemann + orcid: 0000-0003-3803-468X + page: https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/ + url: https://training.galaxyproject.org/training-material/api/contributors/shiltemann.json + - affiliations: + - uni-freiburg + - elixir-europe + bluesky: dvarshney.bsky.social + email: varshney@informatik.uni-freiburg.de + id: deeptivarshney + joined: 2022-12 + name: Deepti Varshney + orcid: 0000-0003-0419-6832 + page: https://training.galaxyproject.org/training-material/hall-of-fame/deeptivarshney/ + url: https://training.galaxyproject.org/training-material/api/contributors/deeptivarshney.json + - affiliations: + - gallantries + - ifb + - elixir-europe + contact_for_training: true + elixir_node: fr + email: berenice.batut@gmail.com + fediverse: https://piaille.fr/@bebatut + fediverse_flavor: mastodon + former_affiliations: + - uni-freiburg + - deNBI + id: bebatut + joined: 2017-09 + linkedin: berenicebatut + location: + country: FR + lat: 45.77 + lon: 3.08 + matrix: bebatut:matrix.org + name: "B\xE9r\xE9nice Batut" + orcid: 0000-0001-9852-1987 + page: https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/ + twitter: bebatut + url: https://training.galaxyproject.org/training-material/api/contributors/bebatut.json + - affiliations: + - elixir-europe + contact_for_training: false + elixir_node: nl + former_affiliations: + - deNBI + - avans-atgm + - uni-freiburg + - erasmusmc + - gallantries + - by-covid + - elixir-converge + id: hexylena + joined: 2017-09 + location: + country: NL + lat: 51.91 + lon: 4.46 + maintainer_contact: gitter + matrix: hexylena:matrix.org + name: Helena Rasche + orcid: 0000-0001-9760-8992 + page: https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/ + url: https://training.galaxyproject.org/training-material/api/contributors/hexylena.json + - id: abueg + joined: 2022-01 + name: Linelle Abueg + orcid: 0000-0002-6879-3954 + page: https://training.galaxyproject.org/training-material/hall-of-fame/abueg/ + twitter: llabueg + url: https://training.galaxyproject.org/training-material/api/contributors/abueg.json + - elixir_node: de + id: bernt-matthias + joined: 2017-09 + name: Matthias Bernt + page: https://training.galaxyproject.org/training-material/hall-of-fame/bernt-matthias/ + url: https://training.galaxyproject.org/training-material/api/contributors/bernt-matthias.json + - affiliations: + - uni-freiburg + - elixir-europe + - deNBI + - mwk + - materialvitaldigital + email: zierep@informatik.uni-freiburg.de + id: paulzierep + joined: 2023-02 + name: Paul Zierep + orcid: 0000-0003-2982-388X + page: https://training.galaxyproject.org/training-material/hall-of-fame/paulzierep/ + url: https://training.galaxyproject.org/training-material/api/contributors/paulzierep.json + - affiliations: + - uni-freiburg + id: santamccloud + joined: 2025-07 + name: Santino Faack + orcid: 0009-0004-0382-2023 + page: https://training.galaxyproject.org/training-material/hall-of-fame/santamccloud/ + url: https://training.galaxyproject.org/training-material/api/contributors/santamccloud.json + dir: topics/microbiome/tutorials/dada-16S + edam_ontology: + - topic_3697 + - topic_0637 + - topic_0080 + - topic_4038 + edam_operation: + - Variant calling + - Analysis + - Visualisation + - DNA barcoding + - Deposition + edam_topic: + - Microbial ecology + - Taxonomy + - Sequence analysis + - Metabarcoding + exact_supported_servers: + - UseGalaxy.org.au + - UseGalaxy.eu + - UseGalaxy.fr + - UseGalaxy.org (Main) + feedback_mean_note: null + feedback_number: 0 + hands_on: true + id: microbiome/dada-16S + inexact_supported_servers: [] + js_requirements: + mathjax: 14601 + mermaid: false + key_points: + - DADA2 allows for the generation of precise ASV tables, providing higher resolution + and more accurate representation of microbial communities compared to traditional + OTU-based methods. + - Key steps such as quality filtering, error rate learning, and chimera removal + are essential in the DADA2 pipeline to ensure the reliability and accuracy of + the resulting ASV data. + - Tools like phyloseq can be effectively used to explore and visualize ASV tables, + facilitating deeper ecological and evolutionary insights into microbial diversity + and community structure. + layout: tutorial_hands_on + license: CC-BY-4.0 + mod_date: '2026-04-13' + objectives: + - Identify the key steps in the DADA2 workflow for generating an ASV table from + 16S rRNA gene sequencing data + - Explain the importance of quality filtering, error rate learning, and chimera + removal in ensuring accurate microbial community analysis + - Execute the DADA2 pipeline to process raw 16S sequencing data and produce a high-resolution + ASV table + - Compare the advantages of ASV-based methods over traditional OTU-based approaches + in terms of accuracy and resolution + - Assess the effectiveness of using phyloseq for exploring and visualizing ASV data + to gain ecological and evolutionary insights + pageviews: 14019 + pub_date: '2024-06-05' + questions: + - What are the primary steps involved in generating an ASV table using DADA2 from + 16S rRNA gene sequencing data? + - How does DADA2 improve the accuracy of microbial community analysis compared to + traditional OTU-based methods? + - What is the importance of quality filtering in the DADA2 workflow, and how does + it impact downstream analyses? + - How does the error rate learning process contribute to the identification of true + biological sequences in DADA2? + - What role does chimera removal play in the DADA2 pipeline, and why is it crucial + for obtaining reliable ASV data? + - How can phyloseq be used to explore and visualize the ASV table generated by DADA2, + and what types of ecological insights can it provide? + recordings: + - bot-timestamp: 1726830881 + captioners: + - bernt-matthias + date: '2024-09-20' + galaxy_version: 24.1.2.dev0 + length: 1H36M + speakers: + - bernt-matthias + youtube_id: ISocxcJZEjw + short_id: T00441 + short_tools: + - dada2_removeBimeraDenovo + - __SORTLIST__ + - collection_element_identifiers + - interactive_tool_phyloseq + - tp_head_tool + - __UNZIP_COLLECTION__ + - dada2_filterAndTrim + - dada2_learnErrors + - dada2_plotQualityProfile + - dada2_seqCounts + - phyloseq_from_dada2 + - Grouping1 + - cat1 + - tp_replace_in_column + - Add_a_column1 + - dada2_dada + - tp_replace_in_line + - dada2_assignTaxonomyAddspecies + - dada2_mergePairs + - dada2_makeSequenceTable + slides: false + slides_recordings: false + subtopic: metabarcoding + supported_servers: + exact: + - 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creators: - - class: Person - identifier: 0000-0001-9047-4215 - name: Engy Nasr - url: https://orcid.org/0000-0001-9047-4215 + - class: Organization + isNew: true + name: '' - class: Person identifier: 0000-0001-9852-1987 name: "B\xE9r\xE9nice Batut" - url: https://orcid.org/0000-0001-9852-1987 - - class: Person - identifier: 0000-0003-2982-388X - name: Paul Zierep - description: Microbiome - Taxonomy Profiling + description: Building an amplicon sequence variant (ASV) table from 16S data using + DADA2 features: - comments: true - parameters: true - report: - markdown: '# Taxonomy Profiling and Visualisation with Krona Workflow Report - - - In this workflow you can identify your microbial community, but identifying - all possible Taxon found in your samples, from the kingdom level down to - the species level. In the application of the pathogen detection, this workflow - gives an overview of the possible bacterial found in samples and what might - be a possible suspect for pathogenicity. - - - The workflow uses Kraken2 tool and allow the user to choose any Kraken2 - database or other added ones depending on the user application or the input - samples. All Kraken2 tool databases are available in Galaxy. More description - about these databases can be found [here](https://benlangmead.github.io/aws-indexes/k2). - Other databases can be also added to the tool, just contact us anytime for - that. We recommend using StandardPF database. - - - Visualization is done using Krona Pie Chart, and you can replace it with - any other tool. e.g. Phinch interactive tool, which is also available in - Galaxy - - - ## Workflow Inputs: - - - The per-processing workflow main output (Collection of all samples reads - after quality retaining and hosts filtering) - - - ## Workflow Outputs are: - - - ### Taxonomy Tabular Report - - - The report shows the abundance of every taxon from the kingdom level down - to the species level - - - ```galaxy - - history_dataset_display(output="converted_kraken_report") - - ``` - - - ### Taxonomy Profiling Visualization with Krona - - An interactive Pie chart showing the different identified taxons along with - their percentages, which is one of the ways to visualize the previous taxonomy - tabular - - - ```galaxy - - history_dataset_as_image(output="krona_pie_chart") - - ``` - - ' + comments: false + parameters: false + report: null subworkflows: false graph_dot: "digraph main {\n node [fontname=\"Atkinson Hyperlegible\", shape=box,\ \ color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n edge [fontname=\"\ Atkinson Hyperlegible\"];\n 0[color=lightblue,label=\"\u2139\uFE0F Input Collection\\\ - 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- hash: cdd93376adc6ce80742881c25d6810bcce85fc05 - message: adding tags to some of the workflow outputs, updating the training - with the latest PathoGFAIR workflows updates + - hash: 27323523701df7d1c7d741e06b0990aa3b8c6f5c + message: update workflow + num: 5 + short_hash: '273235237' + unix: '1751450961' + - hash: 1c82739c05804b5ff530590e8c7be9644671e50f + message: Update tools in tutorial to the newest version + num: 4 + short_hash: 1c82739c0 + unix: '1750111586' + - hash: 373ef7183d86901dc5f19d35b76334166f9b88d2 + message: workflow update + num: 3 + short_hash: 373ef7183 + unix: '1744627993' + - hash: 97f8a3d0b5448245415db5a9d9e8ab2182f3cce8 + message: Fix Matthias' comments num: 2 - short_hash: cdd93376a - unix: '1717675229' - - hash: c63ce23c7a7a631f1256b8e733defce3ca4e009b - message: updating workflows file names + short_hash: 97f8a3d0b + unix: '1717577403' + - hash: c1470a165d4a76032ae6f7eec76b94a40b7930bb + message: Finalize tuto, add workflow+test, rename tuto folder num: 1 - short_hash: c63ce23c7 - unix: '1716726587' + short_hash: c1470a165 + unix: '1717074187' inputs: - - annotation: Output collection from the Nanopore Preprocessing workflow + - annotation: raw_reads content_id: null errors: null id: 0 input_connections: {} inputs: - - description: Output collection from the Nanopore Preprocessing workflow - name: collection_of_preprocessed_samples - label: collection_of_preprocessed_samples + - description: raw_reads + name: Raw reads + label: Raw reads name: Input dataset collection outputs: [] position: left: 0 - top: 0 + top: 72 tool_id: null - tool_state: '{"optional": false, "tag": null, "collection_type": "list"}' + tool_state: '{"optional": false, "tag": null, "collection_type": "list:paired"}' tool_version: null type: data_collection_input - uuid: c4a14ff1-1f0c-4cb5-aefe-b56f0a84404e + uuid: 2b66bb2a-4ae5-436a-9428-11ac08ab9e39 when: null workflow_outputs: [] - - annotation: kraken_database_for_user_to_choose + - annotation: header content_id: null errors: null id: 1 input_connections: {} inputs: - - description: kraken_database_for_user_to_choose - name: kraken_database - label: kraken_database - name: Input parameter + - description: header + name: header + label: header + name: Input dataset outputs: [] position: - left: 24.79997558593749 - top: 276.7833526611328 + left: 3019 + top: 196 tool_id: null - tool_state: '{"restrictOnConnections": true, "parameter_type": "text", "optional": - false}' + tool_state: '{"optional": false, "format": ["tabular"], "tag": null}' tool_version: null - type: parameter_input - uuid: cc59191c-1bc9-4007-b88c-8765ff2dfefd + type: data_input + uuid: 582c8937-b1cb-4f01-977f-93d4ccc631b8 when: null workflow_outputs: [] license: MIT - mermaid: "flowchart TD\n 0[\"\u2139\uFE0F Input Collection\\ncollection_of_preprocessed_samples\"\ - ];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"\u2139\uFE0F Input Parameter\\\ - nkraken_database\"];\n style 1 fill:#ded,stroke:#393,stroke-width:4px;\n 2[\"\ - Kraken2\"];\n 1 -->|output| 2;\n 0 -->|output| 2;\n 26f9041f-d8a4-4f64-8a53-404d5c7e2f61[\"\ - Output\\nkraken2_with_pluspf_database_output\"];\n 2 --> 26f9041f-d8a4-4f64-8a53-404d5c7e2f61;\n\ - \ style 26f9041f-d8a4-4f64-8a53-404d5c7e2f61 stroke:#2c3143,stroke-width:4px;\n\ - \ f2ddd05b-66a0-4cea-9da6-ed107eecbe1b[\"Output\\nkraken2_with_pluspf_database_output_report\"\ - ];\n 2 --> f2ddd05b-66a0-4cea-9da6-ed107eecbe1b;\n style f2ddd05b-66a0-4cea-9da6-ed107eecbe1b\ - \ stroke:#2c3143,stroke-width:4px;\n 3[\"Krakentools: Convert kraken report\ - \ file\"];\n 2 -->|report_output| 3;\n c490ab8d-1b1d-4914-aa51-a62a967a4018[\"\ - Output\\nconverted_kraken_report\"];\n 3 --> c490ab8d-1b1d-4914-aa51-a62a967a4018;\n\ - \ style c490ab8d-1b1d-4914-aa51-a62a967a4018 stroke:#2c3143,stroke-width:4px;\n\ - \ 4[\"Krona pie chart\"];\n 3 -->|output| 4;\n dcc857c6-f579-4c74-84ec-bb6ce3794a56[\"\ - Output\\nkrona_pie_chart\"];\n 4 --> dcc857c6-f579-4c74-84ec-bb6ce3794a56;\n\ - \ style dcc857c6-f579-4c74-84ec-bb6ce3794a56 stroke:#2c3143,stroke-width:4px;" - modified: 2026-05-21 00:30:25 +0000 - name: Taxonomy Profiling and Visualization with Krona + mermaid: "flowchart TD\n 0[\"\u2139\uFE0F Input Collection\\nRaw reads\"];\n\ + \ style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"\u2139\uFE0F Input Dataset\\\ + nheader\"];\n style 1 stroke:#2c3143,stroke-width:4px;\n 2[\"Sort collection\"\ + ];\n 0 -->|output| 2;\n 3[\"dada2: filterAndTrim\"];\n 2 -->|output| 3;\n\ + \ 4[\"dada2: plotQualityProfile\"];\n 2 -->|output| 4;\n 5[\"Unzip collection\"\ + ];\n 3 -->|paired_output| 5;\n 6[\"dada2: plotQualityProfile\"];\n 3 -->|paired_output|\ + \ 6;\n 7[\"dada2: learnErrors\"];\n 5 -->|forward| 7;\n 8[\"dada2: learnErrors\"\ + ];\n 5 -->|reverse| 8;\n 9[\"dada2: dada\"];\n 5 -->|forward| 9;\n 7 -->|errors|\ + \ 9;\n 10[\"dada2: dada\"];\n 5 -->|reverse| 10;\n 8 -->|errors| 10;\n 11[\"\ + dada2: mergePairs\"];\n 9 -->|data_collection| 11;\n 10 -->|data_collection|\ + \ 11;\n 5 -->|forward| 11;\n 5 -->|reverse| 11;\n 12[\"Extract element identifiers\"\ + ];\n 11 -->|merged| 12;\n 13[\"dada2: makeSequenceTable\"];\n 11 -->|merged|\ + \ 13;\n 3fd25979-39df-4698-bad1-aabfccbb7bd2[\"Output\\nsequence_table\"];\n\ + \ 13 --> 3fd25979-39df-4698-bad1-aabfccbb7bd2;\n style 3fd25979-39df-4698-bad1-aabfccbb7bd2\ + \ stroke:#2c3143,stroke-width:4px;\n 14[\"Replace Text\"];\n 12 -->|output|\ + \ 14;\n 15[\"dada2: removeBimeraDenovo\"];\n 13 -->|stable| 15;\n 16[\"Select\ + \ first\"];\n 14 -->|outfile| 16;\n 17[\"dada2: sequence counts\"];\n 3 -->|outtab|\ + \ 17;\n 9 -->|data_collection| 17;\n 10 -->|data_collection| 17;\n 11 -->|merged|\ + \ 17;\n 15 -->|stable_sequencetable| 17;\n c758f861-44bc-4208-b1f7-1f5106cb678e[\"\ + Output\\nsequence_counts\"];\n 17 --> c758f861-44bc-4208-b1f7-1f5106cb678e;\n\ + \ style c758f861-44bc-4208-b1f7-1f5106cb678e stroke:#2c3143,stroke-width:4px;\n\ + \ 18[\"dada2: assignTaxonomy and addSpecies\"];\n 15 -->|stable_sequencetable|\ + \ 18;\n 904fe0a2-8329-45ca-8493-fc688fb216c3[\"Output\\ntaxons\"];\n 18 -->\ + \ 904fe0a2-8329-45ca-8493-fc688fb216c3;\n style 904fe0a2-8329-45ca-8493-fc688fb216c3\ + \ stroke:#2c3143,stroke-width:4px;\n 19[\"Compute\"];\n 16 -->|outfile| 19;\n\ + \ 20[\"Replace Text\"];\n 19 -->|out_file1| 20;\n 21[\"Concatenate datasets\"\ + ];\n 1 -->|output| 21;\n 20 -->|outfile| 21;\n 5479d320-3e82-47a9-a92b-6ed5959459cf[\"\ + Output\\nmetada_table\"];\n 21 --> 5479d320-3e82-47a9-a92b-6ed5959459cf;\n\ + \ style 5479d320-3e82-47a9-a92b-6ed5959459cf stroke:#2c3143,stroke-width:4px;\n\ + \ 22[\"Create phyloseq object\"];\n 21 -->|out_file1| 22;\n 15 -->|stable_sequencetable|\ + \ 22;\n 18 -->|output| 22;" + modified: 2026-07-01 00:31:39 +0000 + name: Building an amplicon sequence variant (ASV) table from 16S data using DADA2 outputs: - annotation: '' - content_id: toolshed.g2.bx.psu.edu/repos/iuc/kraken2/kraken2/2.1.1+galaxy1 + content_id: toolshed.g2.bx.psu.edu/repos/iuc/dada2_makesequencetable/dada2_makeSequenceTable/1.34.0+galaxy0 errors: null - id: 2 + id: 13 input_connections: - kraken2_database: - id: 1 - output_name: output - single_paired|input_sequences: - id: 0 - output_name: output - inputs: - - description: runtime parameter for tool Kraken2 - name: single_paired + samples: + id: 11 + output_name: merged + inputs: [] label: null - name: Kraken2 + name: 'dada2: makeSequenceTable' outputs: - - name: report_output - type: tabular - - name: output + - name: stable + type: dada2_sequencetable + - name: plot_output + type: pdf + position: + left: 1970.000125527473 + top: 273.99367961852937 + post_job_actions: {} + tool_id: toolshed.g2.bx.psu.edu/repos/iuc/dada2_makesequencetable/dada2_makeSequenceTable/1.34.0+galaxy0 + tool_shed_repository: + changeset_revision: 75c8945b0da2 + name: dada2_makesequencetable + owner: iuc + tool_shed: toolshed.g2.bx.psu.edu + tool_state: '{"__input_ext": "input", "chromInfo": "/opt/galaxy/tool-data/shared/ucsc/chrom/?.len", + "filter_cond": {"filter_select": "no", "__current_case__": 0}, "orderBy": + "abundance", "plot": true, "samples": {"__class__": "ConnectedValue"}, "__page__": + null, "__rerun_remap_job_id__": null}' + tool_version: 1.34.0+galaxy0 + type: tool + uuid: 609d25ec-eea3-4893-9d8f-1de0bd185664 + when: null + workflow_outputs: + - label: sequence_table + output_name: stable + uuid: 3fd25979-39df-4698-bad1-aabfccbb7bd2 + - annotation: '' + content_id: toolshed.g2.bx.psu.edu/repos/iuc/dada2_seqcounts/dada2_seqCounts/1.34.0+galaxy0 + errors: null + id: 17 + input_connections: + inrep_0|input: + id: 3 + output_name: outtab + inrep_1|input: + id: 9 + output_name: data_collection + inrep_2|input: + id: 10 + output_name: data_collection + inrep_3|input: + id: 11 + output_name: merged + inrep_4|input: + id: 15 + output_name: stable_sequencetable + inputs: [] + label: null + name: 'dada2: sequence counts' + outputs: + - name: counts type: tabular position: - left: 231.99998779296874 - top: 205.00002746582032 - post_job_actions: - RenameDatasetActionoutput: - action_arguments: - newname: kraken2_with_pluspf_database_output - action_type: RenameDatasetAction - output_name: output - RenameDatasetActionreport_output: - action_arguments: - newname: kraken2_with_pluspf_database_output_report - action_type: RenameDatasetAction - output_name: report_output - tool_id: toolshed.g2.bx.psu.edu/repos/iuc/kraken2/kraken2/2.1.1+galaxy1 + left: 2550 + top: 154 + post_job_actions: {} + tool_id: toolshed.g2.bx.psu.edu/repos/iuc/dada2_seqcounts/dada2_seqCounts/1.34.0+galaxy0 tool_shed_repository: - changeset_revision: 20e2f64aa1fe - name: kraken2 + changeset_revision: a7817705348e + name: dada2_seqcounts owner: iuc tool_shed: toolshed.g2.bx.psu.edu - tool_state: '{"confidence": "0.1", "kraken2_database": {"__class__": "ConnectedValue"}, - "min_base_quality": "0", "minimum_hit_groups": "2", "quick": false, "report": - {"create_report": true, "use_mpa_style": false, "report_zero_counts": false, - "report_minimizer_data": false}, "single_paired": {"single_paired_selector": - "no", "__current_case__": 2, "input_sequences": {"__class__": "ConnectedValue"}}, - "split_reads": false, "use_names": false, "__page__": null, "__rerun_remap_job_id__": - null}' - tool_version: 2.1.1+galaxy1 + tool_state: '{"__input_ext": "input", "chromInfo": "/opt/galaxy/tool-data/shared/ucsc/chrom/?.len", + "inrep": [{"__index__": 0, "input": {"__class__": "ConnectedValue"}, "name": + "FiltTrim"}, {"__index__": 1, "input": {"__class__": "ConnectedValue"}, "name": + "Dada Forward"}, {"__index__": 2, "input": {"__class__": "ConnectedValue"}, + "name": "Dada Reverse"}, {"__index__": 3, "input": {"__class__": "ConnectedValue"}, + "name": "SeqTab"}, {"__index__": 4, "input": {"__class__": "ConnectedValue"}, + "name": "Bimera"}], "__page__": null, "__rerun_remap_job_id__": null}' + tool_version: 1.34.0+galaxy0 type: tool - uuid: ddb4e42b-6381-411e-9328-1c7959ecda47 + uuid: e749677d-de5a-4cf8-93de-e709b42b38f7 when: null workflow_outputs: - - label: kraken2_with_pluspf_database_output - output_name: output - uuid: 26f9041f-d8a4-4f64-8a53-404d5c7e2f61 - - label: kraken2_with_pluspf_database_output_report - output_name: report_output - uuid: f2ddd05b-66a0-4cea-9da6-ed107eecbe1b + - label: sequence_counts + output_name: counts + uuid: c758f861-44bc-4208-b1f7-1f5106cb678e - annotation: '' - content_id: toolshed.g2.bx.psu.edu/repos/iuc/krakentools_kreport2krona/krakentools_kreport2krona/1.2+galaxy1 + content_id: toolshed.g2.bx.psu.edu/repos/iuc/dada2_assigntaxonomyaddspecies/dada2_assignTaxonomyAddspecies/1.34.0+galaxy0 errors: null - id: 3 + id: 18 input_connections: - report: - id: 2 - output_name: report_output + seqs: + id: 15 + output_name: stable_sequencetable inputs: [] label: null - name: 'Krakentools: Convert kraken report file' + name: 'dada2: assignTaxonomy and addSpecies' outputs: - name: output type: tabular position: - 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qiime2 + reviewing: + - bebatut + - shiltemann + contributors: + - avatar: https://avatars.githubusercontent.com/u/18176583?s=200&v=4 + id: qiime2 + name: QIIME2 + page: https://training.galaxyproject.org/training-material/hall-of-fame/qiime2/ + short_name: QIIME2 + url: https://training.galaxyproject.org/training-material/api/organisations/qiime2.json + - affiliations: + - gallantries + - ifb + - elixir-europe + contact_for_training: true + elixir_node: fr + email: berenice.batut@gmail.com + fediverse: https://piaille.fr/@bebatut + fediverse_flavor: mastodon + former_affiliations: + - uni-freiburg + - deNBI + id: bebatut + joined: 2017-09 + linkedin: berenicebatut + location: + country: FR + lat: 45.77 + lon: 3.08 + matrix: bebatut:matrix.org + name: "B\xE9r\xE9nice Batut" + orcid: 0000-0001-9852-1987 + page: https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/ + twitter: bebatut + url: https://training.galaxyproject.org/training-material/api/contributors/bebatut.json + - affiliations: + - uni-freiburg + - nfdi4plants + - elixir-europe + bio: Researcher at Erasmus Medical Center + bluesky: shiltemann.bsky.social + contact_for_training: true + elixir_node: nl + email: saskia.hiltemann@gmail.com + fediverse: https://mstdn.science/@shiltemann + fediverse_flavor: mastodon + former_affiliations: + - CINECA-Project + - gallantries + - erasmusmc + id: shiltemann + joined: 2017-09 + linkedin: shiltemann + location: + country: NL + lat: 51.912 + lon: 4.462 + maintainer_contact: gitter + matrix: shiltemann:matrix.org + name: Saskia Hiltemann + orcid: 0000-0003-3803-468X + page: https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/ + url: https://training.galaxyproject.org/training-material/api/contributors/shiltemann.json + dir: topics/microbiome/tutorials/qiime2-moving-pictures + edam_ontology: + - topic_3697 + - topic_0637 + - topic_0080 + - topic_4038 + edam_operation: [] + edam_topic: + - Microbial ecology + - Taxonomy + - Sequence analysis + - Metabarcoding + exact_supported_servers: [] + feedback_mean_note: null + feedback_number: 0 + hands_on: external + hands_on_url: https://amplicon-docs.qiime2.org/en/stable/tutorials/moving-pictures.html + id: microbiome/qiime2-moving-pictures + inexact_supported_servers: + - UseGalaxy.eu + - UseGalaxy.org + - UseGalaxy.org.au + - UseGalaxy.fr + - UseGalaxy.ca + js_requirements: + mathjax: null + mermaid: false + layout: tutorial_hands_on + license: CC-BY-4.0 + mod_date: '2026-02-18' + pageviews: 1215 + pub_date: '2024-03-14' + short_id: T00427 + short_tools: [] + slides: false + slides_recordings: false + subtopic: metabarcoding + supported_servers: + exact: [] + inexact: + - human: Galaxy Europe + id: eu + name: UseGalaxy.eu + url: https://usegalaxy.eu + usegalaxy: true + - human: Galaxy Main + id: us + name: UseGalaxy.org + url: https://usegalaxy.org + usegalaxy: true + - human: Galaxy Australia + id: au + name: UseGalaxy.org.au + url: https://usegalaxy.org.au + usegalaxy: true + - human: Galaxy France + id: fr + name: UseGalaxy.fr + url: https://usegalaxy.fr + usegalaxy: true + - human: Galaxy Canada + id: ca + name: UseGalaxy.ca + url: https://usegalaxy.ca + usegalaxy: true + supported_servers_matrix: + servers: [] + tools: [] + symlink: null + tags: + - metagenomics + - taxonomic profiling + - diversity + - microgalaxy + time_estimation: 10H + title: QIIME 2 Moving Pictures + tools: [] + topic_name: microbiome + topic_name_human: Microbiome + tours: false + translations: + slides: [] + tutorial: [] + video: false + tutorial_name: qiime2-moving-pictures + type: tutorial + url: https://training.galaxyproject.org//topics/microbiome/tutorials/qiime2-moving-pictures/tutorial.html + urls: + hands_on: https://training.galaxyproject.org/training-material/api/topics/microbiome/tutorials/qiime2-moving-pictures/tutorial.json + slides: https://training.galaxyproject.org/training-material/api/topics/microbiome/tutorials/qiime2-moving-pictures/tutorial.json + version: 2 + video: false + video_versions: 0 + video_view: 0 + visit_duration: 453 + visitors: 810 +- admin_install: + install_repository_dependencies: true + install_resolver_dependencies: true + install_tool_dependencies: true + tools: [] + admin_install_yaml: '--- + + install_tool_dependencies: true + + install_repository_dependencies: true + + install_resolver_dependencies: true + + tools: [] + + ' + api: https://training.galaxyproject.org/training-material/api/topics/microbiome/tutorials/qiime2-cancer-microbiome-intervention/tutorial.json + contributions: + authorship: + - qiime2 + reviewing: + - shiltemann + - bebatut + contributors: + - avatar: https://avatars.githubusercontent.com/u/18176583?s=200&v=4 + id: qiime2 + name: QIIME2 + page: https://training.galaxyproject.org/training-material/hall-of-fame/qiime2/ + short_name: QIIME2 + url: https://training.galaxyproject.org/training-material/api/organisations/qiime2.json + - affiliations: + - uni-freiburg + - nfdi4plants + - elixir-europe + bio: Researcher at Erasmus Medical Center + bluesky: shiltemann.bsky.social + contact_for_training: true + elixir_node: nl + email: saskia.hiltemann@gmail.com + fediverse: https://mstdn.science/@shiltemann + fediverse_flavor: mastodon + former_affiliations: + - CINECA-Project + - gallantries + - erasmusmc + id: shiltemann + joined: 2017-09 + linkedin: shiltemann + location: + country: NL + lat: 51.912 + lon: 4.462 + maintainer_contact: gitter + matrix: shiltemann:matrix.org + name: Saskia Hiltemann + orcid: 0000-0003-3803-468X + page: https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/ + url: https://training.galaxyproject.org/training-material/api/contributors/shiltemann.json + - affiliations: + - gallantries + - ifb + - elixir-europe + contact_for_training: true + elixir_node: fr + email: berenice.batut@gmail.com + fediverse: https://piaille.fr/@bebatut + fediverse_flavor: mastodon + former_affiliations: + - uni-freiburg + - deNBI + id: bebatut + joined: 2017-09 + linkedin: berenicebatut + location: + country: FR + lat: 45.77 + lon: 3.08 + matrix: bebatut:matrix.org + name: "B\xE9r\xE9nice Batut" + orcid: 0000-0001-9852-1987 + page: https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/ + twitter: bebatut + url: https://training.galaxyproject.org/training-material/api/contributors/bebatut.json + dir: topics/microbiome/tutorials/qiime2-cancer-microbiome-intervention + edam_ontology: + - topic_3697 + - topic_0637 + - topic_0080 + - topic_4038 + edam_operation: [] + edam_topic: + - Microbial ecology + - Taxonomy + - Sequence analysis + - Metabarcoding + exact_supported_servers: [] + feedback_mean_note: null + feedback_number: 0 + hands_on: external + hands_on_url: https://docs.qiime2.org/jupyterbooks/cancer-microbiome-intervention-tutorial/index.html# + id: microbiome/qiime2-cancer-microbiome-intervention + inexact_supported_servers: + - 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- server: https://galaxy.bio.di.uminho.pt/ - state: local - server: https://usegalaxy.org.au state: local - server: https://usegalaxy.be/ @@ -65618,8 +64154,6 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: local - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr @@ -65630,8 +64164,6 @@ state: missing - server: http://pepsimili.e-nios.com:8080/ state: local - - server: https://galaxy.bio.di.uminho.pt/ - state: local - server: https://usegalaxy.org.au state: local - server: https://usegalaxy.be/ @@ -65677,8 +64209,6 @@ state: local - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr @@ -65689,8 +64219,6 @@ state: missing - server: http://pepsimili.e-nios.com:8080/ state: local - - server: https://galaxy.bio.di.uminho.pt/ - state: local - server: https://usegalaxy.org.au state: local - server: https://usegalaxy.be/ @@ -65736,8 +64264,6 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: local - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr @@ -65748,8 +64274,6 @@ state: missing - server: http://pepsimili.e-nios.com:8080/ state: local - - server: https://galaxy.bio.di.uminho.pt/ - state: local - server: https://usegalaxy.org.au state: local - server: https://usegalaxy.be/ @@ -65795,8 +64319,6 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: local - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr @@ -65807,8 +64329,6 @@ state: missing - server: http://pepsimili.e-nios.com:8080/ state: local - - server: https://galaxy.bio.di.uminho.pt/ - state: local - server: https://usegalaxy.org.au state: local - server: https://usegalaxy.be/ @@ -65854,8 +64374,6 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr @@ -65866,14 +64384,13 @@ state: missing - server: http://pepsimili.e-nios.com:8080/ state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - server: https://usegalaxy.org.au state: missing - server: https://usegalaxy.be/ state: missing - server: https://usegalaxy.cz/ - state: missing + state: exact + version: 2.0+galaxy2 - server: https://usegalaxy.eu state: exact version: 2.0+galaxy2 @@ -65882,7 +64399,8 @@ - server: https://usegalaxy.no/ state: missing - server: https://usegalaxy.org - state: missing + state: exact + version: 2.0+galaxy2 - server: https://viralvariant.anses.fr/ state: missing version: 2.0+galaxy2 @@ -65901,8 +64419,8 @@ - server: https://galaxy.mesocentre.uca.fr state: inexact versions: - - 1.1.3 - 9.5+galaxy3 + - 1.1.3 - server: https://galaxy.pasteur.fr/ state: missing - server: https://galaxytrakr.org/ @@ -65920,8 +64438,6 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr @@ -65934,8 +64450,6 @@ state: missing - server: http://pepsimili.e-nios.com:8080/ state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - server: https://usegalaxy.org.au state: exact version: 9.5+galaxy2 @@ -65998,8 +64512,6 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr @@ -66012,8 +64524,6 @@ state: missing - server: http://pepsimili.e-nios.com:8080/ state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - server: https://usegalaxy.org.au state: exact version: 9.5+galaxy2 @@ -66055,8 +64565,8 @@ - server: https://galaxy.mesocentre.uca.fr state: inexact versions: - - 1.9.2+galaxy0 - 1.8.1+galaxy1 + - 1.9.2+galaxy0 - 1.8.2+galaxy0 - 1.9.4+galaxy0 - server: https://galaxy.pasteur.fr/ @@ -66073,8 +64583,6 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr @@ -66085,8 +64593,6 @@ state: missing - server: http://pepsimili.e-nios.com:8080/ state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - server: https://usegalaxy.org.au state: exact version: 1.9.4+galaxy1 @@ -66141,8 +64647,6 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr @@ -66153,8 +64657,6 @@ state: missing - server: http://pepsimili.e-nios.com:8080/ state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - server: https://usegalaxy.org.au state: exact version: 1.2.4+galaxy2 @@ -66207,8 +64709,6 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr @@ -66220,8 +64720,6 @@ state: missing - server: http://pepsimili.e-nios.com:8080/ state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - server: https://usegalaxy.org.au state: exact version: 0.0.3 @@ -66275,8 +64773,6 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr @@ -66287,8 +64783,6 @@ state: missing - server: http://pepsimili.e-nios.com:8080/ state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - server: https://usegalaxy.org.au state: exact version: 3.6.2+galaxy1 @@ -66307,8 +64801,8 @@ - server: https://usegalaxy.no/ state: inexact versions: - - 2.5.4.0 - 3.3.0+galaxy0 + - 2.5.4.0 - 3.2.2+galaxy0 - server: https://usegalaxy.org state: exact @@ -66346,8 +64840,6 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr @@ -66360,10 +64852,6 @@ state: missing - server: http://pepsimili.e-nios.com:8080/ state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: inexact - versions: - - 1.11+galaxy1 - server: https://usegalaxy.org.au state: exact version: 1.27+galaxy4 @@ -66385,10 +64873,10 @@ - 1.11+galaxy0 - '1.7' - 1.7.1 - - '1.9' + - 1.8+galaxy0 - 1.9+galaxy1 - 1.8+galaxy1 - - 1.8+galaxy0 + - '1.9' - 1.8+galaxy2 - server: https://usegalaxy.org state: exact @@ -66426,8 +64914,6 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr @@ -66439,8 +64925,6 @@ state: missing - server: http://pepsimili.e-nios.com:8080/ state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - server: https://usegalaxy.org.au state: exact version: 3.1.1+galaxy1 @@ -66452,14 +64936,14 @@ versions: - 2.10.4+galaxy1 - 3.1.1+galaxy0 - - 2.10.4 + - 3.0.5+galaxy3 - 2.10.4+galaxy2 - - 2.10.9+galaxy0 - - 2.10.7+galaxy0 + - 3.0.5+galaxy0 - 3.0.3+galaxy0 - - 3.0.5+galaxy3 - 2.10.8+galaxy0 - - 3.0.5+galaxy0 + - 2.10.9+galaxy0 + - 2.10.4 + - 2.10.7+galaxy0 - 2.10.7+galaxy1 - 2.10.7+galaxy2 - server: https://usegalaxy.eu @@ -66510,8 +64994,6 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr @@ -66523,8 +65005,6 @@ state: missing - server: http://pepsimili.e-nios.com:8080/ state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - server: https://usegalaxy.org.au state: exact version: 5.1.0 @@ -66594,356 +65074,9 @@ video: true video_versions: 1 video_view: 0 - visit_duration: 340 - visitors: 1022 + visit_duration: 393 + visitors: 1247 zenodo_link: '' -- admin_install: - install_repository_dependencies: true - install_resolver_dependencies: true - install_tool_dependencies: true - tools: [] - admin_install_yaml: '--- - - install_tool_dependencies: true - - install_repository_dependencies: true - - install_resolver_dependencies: true - - tools: [] - - ' - api: https://training.galaxyproject.org/training-material/api/topics/microbiome/tutorials/qiime2-cancer-microbiome-intervention/tutorial.json - contributions: - 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url: https://training.galaxyproject.org/training-material/api/contributors/shiltemann.json - - affiliations: - - gallantries - - ifb - - elixir-europe - contact_for_training: true - elixir_node: fr - email: berenice.batut@gmail.com - fediverse: https://piaille.fr/@bebatut - fediverse_flavor: mastodon - former_affiliations: - - uni-freiburg - - deNBI - id: bebatut - joined: 2017-09 - linkedin: berenicebatut - location: - country: FR - lat: 45.77 - lon: 3.08 - matrix: bebatut:matrix.org - name: "B\xE9r\xE9nice Batut" - orcid: 0000-0001-9852-1987 - page: https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/ - twitter: bebatut - url: https://training.galaxyproject.org/training-material/api/contributors/bebatut.json - dir: topics/microbiome/tutorials/qiime2-cancer-microbiome-intervention - edam_ontology: - - topic_3697 - - topic_0637 - - topic_0080 - - topic_4038 - edam_operation: [] - edam_topic: - - Microbial ecology - - Taxonomy - - Sequence analysis - - Metabarcoding - exact_supported_servers: [] - feedback_mean_note: null - feedback_number: 0 - hands_on: external - hands_on_url: https://docs.qiime2.org/jupyterbooks/cancer-microbiome-intervention-tutorial/index.html# - id: microbiome/qiime2-cancer-microbiome-intervention - inexact_supported_servers: - - UseGalaxy.eu - - UseGalaxy.org - - UseGalaxy.org.au - - UseGalaxy.fr - js_requirements: - mathjax: null - mermaid: false - layout: tutorial_hands_on - license: CC-BY-4.0 - mod_date: '2024-03-14' - pageviews: 857 - pub_date: '2024-02-12' - short_id: T00412 - short_tools: [] - slides: false - slides_recordings: false - subtopic: metabarcoding - supported_servers: - exact: [] - inexact: - - human: Galaxy Europe - id: eu - name: UseGalaxy.eu - url: https://usegalaxy.eu - usegalaxy: true - - human: Galaxy Main - id: us - name: UseGalaxy.org - url: https://usegalaxy.org - usegalaxy: true - - human: Galaxy Australia - id: au - name: UseGalaxy.org.au - url: https://usegalaxy.org.au - usegalaxy: true - - human: Galaxy France - id: fr - name: UseGalaxy.fr - url: https://usegalaxy.fr - usegalaxy: true - supported_servers_matrix: - servers: [] - tools: [] - symlink: null - tags: - - metabarcoding - - 16S - - taxonomic profiling - - diversity - - microgalaxy - time_estimation: 10H - title: QIIME 2 Cancer Microbiome Intervention - tools: [] - topic_name: microbiome - topic_name_human: Microbiome - tours: false - translations: - slides: [] - tutorial: [] - video: false - tutorial_name: qiime2-cancer-microbiome-intervention - type: tutorial - url: https://training.galaxyproject.org//topics/microbiome/tutorials/qiime2-cancer-microbiome-intervention/tutorial.html - urls: - hands_on: https://training.galaxyproject.org/training-material/api/topics/microbiome/tutorials/qiime2-cancer-microbiome-intervention/tutorial.json - slides: https://training.galaxyproject.org/training-material/api/topics/microbiome/tutorials/qiime2-cancer-microbiome-intervention/tutorial.json - version: 3 - video: false - video_versions: 0 - video_view: 0 - visit_duration: 608 - visitors: 518 -- admin_install: - install_repository_dependencies: true - install_resolver_dependencies: true - install_tool_dependencies: true - tools: [] - admin_install_yaml: '--- - - install_tool_dependencies: true - - install_repository_dependencies: true - - install_resolver_dependencies: true - - tools: [] - - ' - api: https://training.galaxyproject.org/training-material/api/topics/microbiome/tutorials/qiime2-moving-pictures/tutorial.json - contributions: - authorship: - - qiime2 - reviewing: - - bebatut - - shiltemann - contributors: - - avatar: https://avatars.githubusercontent.com/u/18176583?s=200&v=4 - id: qiime2 - name: QIIME2 - page: https://training.galaxyproject.org/training-material/hall-of-fame/qiime2/ - short_name: QIIME2 - url: https://training.galaxyproject.org/training-material/api/organisations/qiime2.json - - affiliations: - - gallantries - - ifb - - elixir-europe - contact_for_training: true - elixir_node: fr - email: berenice.batut@gmail.com - fediverse: https://piaille.fr/@bebatut - fediverse_flavor: mastodon - former_affiliations: - - uni-freiburg - - deNBI - id: bebatut - joined: 2017-09 - linkedin: berenicebatut - location: - country: FR - lat: 45.77 - lon: 3.08 - matrix: bebatut:matrix.org - name: "B\xE9r\xE9nice Batut" - orcid: 0000-0001-9852-1987 - page: https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/ - twitter: bebatut - url: https://training.galaxyproject.org/training-material/api/contributors/bebatut.json - - affiliations: - - uni-freiburg - - nfdi4plants - - elixir-europe - bio: Researcher at Erasmus Medical Center - bluesky: shiltemann.bsky.social - contact_for_training: true - elixir_node: nl - email: saskia.hiltemann@gmail.com - fediverse: https://mstdn.science/@shiltemann - fediverse_flavor: mastodon - former_affiliations: - - CINECA-Project - - gallantries - - erasmusmc - id: shiltemann - joined: 2017-09 - linkedin: shiltemann - location: - country: NL - lat: 51.912 - lon: 4.462 - maintainer_contact: gitter - matrix: shiltemann:matrix.org - name: Saskia Hiltemann - orcid: 0000-0003-3803-468X - page: https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/ - url: https://training.galaxyproject.org/training-material/api/contributors/shiltemann.json - dir: topics/microbiome/tutorials/qiime2-moving-pictures - edam_ontology: - - topic_3697 - - topic_0637 - - topic_0080 - - topic_4038 - edam_operation: [] - edam_topic: - - Microbial ecology - - Taxonomy - - Sequence analysis - - Metabarcoding - exact_supported_servers: [] - feedback_mean_note: null - feedback_number: 0 - hands_on: external - hands_on_url: https://amplicon-docs.qiime2.org/en/stable/tutorials/moving-pictures.html - id: microbiome/qiime2-moving-pictures - inexact_supported_servers: - - UseGalaxy.eu - - UseGalaxy.org - - UseGalaxy.org.au - - UseGalaxy.fr - js_requirements: - mathjax: null - mermaid: false - layout: tutorial_hands_on - license: CC-BY-4.0 - mod_date: '2026-02-18' - pageviews: 1141 - pub_date: '2024-03-14' - short_id: T00427 - short_tools: [] - slides: false - slides_recordings: false - subtopic: metabarcoding - supported_servers: - exact: [] - inexact: - - human: Galaxy Europe - id: eu - name: UseGalaxy.eu - url: https://usegalaxy.eu - usegalaxy: true - - human: Galaxy Main - id: us - name: UseGalaxy.org - url: https://usegalaxy.org - usegalaxy: true - - human: Galaxy Australia - id: au - name: UseGalaxy.org.au - url: https://usegalaxy.org.au - usegalaxy: true - - human: Galaxy France - id: fr - name: UseGalaxy.fr - url: https://usegalaxy.fr - usegalaxy: true - supported_servers_matrix: - servers: [] - tools: [] - symlink: null - tags: - - metagenomics - - taxonomic profiling - - diversity - - microgalaxy - time_estimation: 10H - title: QIIME 2 Moving Pictures - tools: [] - topic_name: microbiome - topic_name_human: Microbiome - tours: false - translations: - slides: [] - tutorial: [] - video: false - tutorial_name: qiime2-moving-pictures - type: tutorial - url: https://training.galaxyproject.org//topics/microbiome/tutorials/qiime2-moving-pictures/tutorial.html - urls: - hands_on: https://training.galaxyproject.org/training-material/api/topics/microbiome/tutorials/qiime2-moving-pictures/tutorial.json - slides: https://training.galaxyproject.org/training-material/api/topics/microbiome/tutorials/qiime2-moving-pictures/tutorial.json - version: 2 - video: false - video_versions: 0 - video_view: 0 - visit_duration: 435 - visitors: 771 - admin_install: install_repository_dependencies: true install_resolver_dependencies: true @@ -67446,17 +65579,17 @@ twitter: NicolaSoranzo url: https://training.galaxyproject.org/training-material/api/contributors/nsoranzo.json - affiliations: - - erasmusmc - - gallantries - - by-covid - elixir-europe - - elixir-converge contact_for_training: false elixir_node: nl former_affiliations: - deNBI - avans-atgm - uni-freiburg + - erasmusmc + - gallantries + - by-covid + - elixir-converge id: hexylena joined: 2017-09 location: @@ -67497,14 +65630,14 @@ - topic_0080 - topic_4038 edam_operation: - - Phylogenetic analysis - - Taxonomic classification + - Phylogenetic tree reconstruction - Sequencing quality control + - Phylogenetic analysis - Visualisation - Phylogenetic tree generation - Sequence read processing - Phylogenetic tree analysis - - Phylogenetic tree reconstruction + - Taxonomic classification - Sequence clustering - DNA barcoding edam_topic: @@ -67543,7 +65676,7 @@ - Analyze of 16S rRNA sequencing data using the mothur toolsuite in Galaxy - Using a mock community to assess the error rate of your sequencing experiment - Visualize sample diversity using Krona and Phinch - pageviews: 20833 + pageviews: 21194 priority: 1000 pub_date: '2017-02-12' questions: @@ -67555,39 +65688,39 @@ - /short/T00390 short_id: T00390 short_tools: + - mothur_sub_sample + - mothur_classify_seqs + - mothur_classify_otu + - mothur_get_groups - mothur_dist_shared + - mothur_cluster + - mothur_summary_single - mothur_filter_seqs - - mothur_count_seqs + - mothur_heatmap_sim + - taxonomy_krona_chart - mothur_tree_shared - - mothur_rarefaction_single - - mothur_dist_seqs - - mothur_summary_single - mothur_chimera_vsearch - - XY_Plot_1 - mothur_pre_cluster - - mothur_cluster - - mothur_cluster_split + - mothur_make_contigs + - mothur_summary_seqs + - XY_Plot_1 - mothur_align_seqs - - mothur_sub_sample - - mothur_screen_seqs - - mothur_taxonomy_to_krona - mothur_make_biom - - mothur_remove_groups - - mothur_classify_otu + - mothur_screen_seqs - mothur_count_groups - - mothur_make_shared - newick_display - - mothur_get_groups - - mothur_summary_seqs + - mothur_remove_seqs + - mothur_unique_seqs + - mothur_count_seqs - mothur_venn - - taxonomy_krona_chart - - mothur_seq_error + - mothur_make_shared + - mothur_rarefaction_single + - mothur_taxonomy_to_krona + - mothur_cluster_split + - mothur_dist_seqs + - mothur_remove_groups - mothur_remove_lineage - - mothur_unique_seqs - - mothur_classify_seqs - - mothur_make_contigs - - mothur_remove_seqs - - mothur_heatmap_sim + - mothur_seq_error slides: false slides_recordings: false subtopic: metabarcoding @@ -67656,9 +65789,6 @@ - name: IPK Galaxy Blast Suite url: https://galaxy-web.ipk-gatersleben.de usegalaxy: false - - name: Lebanese University Galaxy - url: http://galaxy.ul.edu.lb/ - usegalaxy: false - name: Mandoiu Lab url: https://neo.engr.uconn.edu/ usegalaxy: false @@ -67674,9 +65804,6 @@ - name: PepSimili url: http://pepsimili.e-nios.com:8080/ usegalaxy: false - - name: PhagePromotor - url: https://galaxy.bio.di.uminho.pt/ - usegalaxy: false - name: UseGalaxy.org.au url: https://usegalaxy.org.au usegalaxy: true @@ -67735,8 +65862,6 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr @@ -67749,8 +65874,6 @@ state: inexact versions: - 2.7.1+galaxy0 - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - server: https://usegalaxy.org.au state: inexact versions: @@ -67809,8 +65932,6 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr @@ -67821,8 +65942,6 @@ state: missing - server: http://pepsimili.e-nios.com:8080/ state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - server: https://usegalaxy.org.au state: exact version: 1.0.2 @@ -67876,8 +65995,6 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr @@ -67888,8 +66005,6 @@ state: missing - server: http://pepsimili.e-nios.com:8080/ state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - server: https://usegalaxy.org.au state: exact version: 1.39.5.0 @@ -67943,8 +66058,6 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr @@ -67955,8 +66068,6 @@ state: missing - server: http://pepsimili.e-nios.com:8080/ state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - server: https://usegalaxy.org.au state: exact version: 1.39.5.1 @@ -68010,8 +66121,6 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr @@ -68022,8 +66131,6 @@ state: missing - server: http://pepsimili.e-nios.com:8080/ state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - server: https://usegalaxy.org.au state: exact version: 1.39.5.0 @@ -68077,8 +66184,6 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr @@ -68089,8 +66194,6 @@ state: missing - server: http://pepsimili.e-nios.com:8080/ state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - server: https://usegalaxy.org.au state: exact version: 1.39.5.0 @@ -68144,8 +66247,6 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr @@ -68156,8 +66257,6 @@ state: missing - server: http://pepsimili.e-nios.com:8080/ state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - server: https://usegalaxy.org.au state: exact version: 1.39.5.0 @@ -68211,8 +66310,6 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr @@ -68223,8 +66320,6 @@ state: missing - server: http://pepsimili.e-nios.com:8080/ state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - server: https://usegalaxy.org.au state: exact version: 1.39.5.0 @@ -68278,8 +66373,6 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr @@ -68290,8 +66383,6 @@ state: missing - server: http://pepsimili.e-nios.com:8080/ state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - server: https://usegalaxy.org.au state: exact version: 1.39.5.0 @@ -68345,8 +66436,6 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr @@ -68357,8 +66446,6 @@ state: missing - server: http://pepsimili.e-nios.com:8080/ state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - server: https://usegalaxy.org.au state: exact version: 1.39.5.0 @@ -68412,8 +66499,6 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr @@ -68424,8 +66509,6 @@ state: missing - server: http://pepsimili.e-nios.com:8080/ state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - server: https://usegalaxy.org.au state: exact version: 1.39.5.0 @@ -68479,8 +66562,6 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr @@ -68491,8 +66572,6 @@ state: missing - server: http://pepsimili.e-nios.com:8080/ state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - server: https://usegalaxy.org.au state: exact version: 1.39.5.0 @@ -68546,8 +66625,6 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr @@ -68558,8 +66635,6 @@ state: missing - server: http://pepsimili.e-nios.com:8080/ state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - server: https://usegalaxy.org.au state: exact version: 1.39.5.0 @@ -68613,276 +66688,68 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - - server: https://neo.engr.uconn.edu/ - state: missing - - server: https://mississippi.sorbonne-universite.fr - state: missing - - server: http://galaxy.inf.ethz.ch - state: missing - - server: https://palfinder.ls.manchester.ac.uk/ - state: missing - - server: http://pepsimili.e-nios.com:8080/ - 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server: http://pepsimili.e-nios.com:8080/ state: missing - server: https://usegalaxy.org.au state: exact @@ -69016,8 +67067,6 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr @@ -69028,8 +67077,6 @@ state: missing - server: http://pepsimili.e-nios.com:8080/ state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - server: https://usegalaxy.org.au state: exact version: 1.39.5.0 @@ -69083,8 +67130,6 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr @@ -69095,8 +67140,6 @@ state: missing - server: http://pepsimili.e-nios.com:8080/ state: missing - - server: https://galaxy.bio.di.uminho.pt/ - 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- server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr @@ -69436,8 +67461,6 @@ state: missing - server: http://pepsimili.e-nios.com:8080/ state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - server: https://usegalaxy.org.au state: exact version: 1.39.5.0 @@ -69491,8 +67514,6 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr @@ -69503,8 +67524,6 @@ state: missing - server: http://pepsimili.e-nios.com:8080/ state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - server: https://usegalaxy.org.au state: exact version: 1.39.5.0 @@ -69558,8 +67577,6 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr @@ -69570,8 +67587,6 @@ state: missing - server: http://pepsimili.e-nios.com:8080/ state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - server: https://usegalaxy.org.au state: exact version: 1.39.5.0 @@ -69626,8 +67641,6 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr @@ -69638,8 +67651,6 @@ state: missing - server: http://pepsimili.e-nios.com:8080/ state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - server: https://usegalaxy.org.au state: exact version: '1.0' @@ -69693,8 +67704,6 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr @@ -69705,8 +67714,6 @@ state: missing - server: http://pepsimili.e-nios.com:8080/ state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - server: https://usegalaxy.org.au state: exact version: 1.39.5.0 @@ -69760,8 +67767,6 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr @@ -69772,8 +67777,6 @@ state: missing - server: http://pepsimili.e-nios.com:8080/ state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - server: https://usegalaxy.org.au state: exact version: 1.39.5.0 @@ -69827,8 +67830,6 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr @@ -69839,8 +67840,6 @@ state: missing - server: http://pepsimili.e-nios.com:8080/ state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - server: https://usegalaxy.org.au state: exact version: 1.39.5.0 @@ -69895,8 +67894,6 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr @@ -69907,8 +67904,6 @@ state: missing - server: http://pepsimili.e-nios.com:8080/ state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - server: https://usegalaxy.org.au state: inexact versions: @@ -69996,8 +67991,8 @@ video: false video_versions: 0 video_view: 0 - visit_duration: 301 - visitors: 14146 + visit_duration: 300 + visitors: 14424 workflows: - creators: [] description: 16S Microbial Analysis with mothur (extended) @@ -70215,7 +68210,7 @@ \ 6[\"Make.contigs\"];\n 0 -->|output| 6;\n 7[\"Summary.seqs\"];\n 6 -->|fasta|\ \ 7;\n 8[\"Screen.seqs\"];\n 6 -->|fasta| 8;\n 6 -->|group| 8;\n 9[\"Unique.seqs\"\ ];\n 8 -->|fasta_out| 9;" - modified: 2026-05-21 00:30:25 +0000 + modified: 2026-07-01 00:31:39 +0000 name: 'Training: 16S rRNA Sequencing With Mothur: Main Tutorial' outputs: [] parent_id: microbiome/mothur-miseq-sop @@ -70673,17 +68668,17 @@ twitter: bebatut url: https://training.galaxyproject.org/training-material/api/contributors/bebatut.json - affiliations: - - erasmusmc - - gallantries - - by-covid - elixir-europe - - elixir-converge contact_for_training: false elixir_node: nl former_affiliations: - deNBI - avans-atgm - uni-freiburg + - erasmusmc + - gallantries + - by-covid + - elixir-converge id: hexylena joined: 2017-09 location: @@ -70703,14 +68698,14 @@ - topic_0080 - topic_4038 edam_operation: - - Phylogenetic analysis - - Taxonomic classification + - Phylogenetic tree reconstruction - Sequencing quality control + - Phylogenetic analysis - Visualisation - Phylogenetic tree generation - Sequence read processing - Phylogenetic tree analysis - - Phylogenetic tree reconstruction + - Taxonomic classification - Sequence clustering - DNA barcoding edam_topic: @@ -70749,7 +68744,7 @@ - Analyze of 16S rRNA sequencing data using the mothur toolsuite in Galaxy - Using a mock community to assess the error rate of your sequencing experiment - Visualize sample diversity using Krona and Phinch - pageviews: 11212 + pageviews: 11364 priority: 1000 pub_date: '2019-05-13' questions: @@ -70782,33 +68777,33 @@ - /short/T00391 short_id: T00391 short_tools: + - mothur_sub_sample + - mothur_classify_seqs + - mothur_classify_otu + - collapse_dataset - mothur_dist_shared + - mothur_cluster + - mothur_summary_single - mothur_filter_seqs - - mothur_count_seqs + - mothur_heatmap_sim - mothur_tree_shared - - mothur_rarefaction_single - - mothur_dist_seqs - - mothur_summary_single - - collapse_dataset - mothur_chimera_vsearch - - XY_Plot_1 - mothur_pre_cluster - - mothur_cluster - - mothur_cluster_split - - mothur_sub_sample + - mothur_summary_seqs + - XY_Plot_1 - mothur_screen_seqs - - mothur_remove_groups - - mothur_classify_otu - mothur_count_groups - - mothur_make_shared - newick_display - - mothur_summary_seqs + - mothur_remove_seqs + - mothur_unique_seqs + - mothur_count_seqs - mothur_venn + - mothur_make_shared + - mothur_rarefaction_single + - mothur_cluster_split + - mothur_dist_seqs + - mothur_remove_groups - mothur_remove_lineage - - mothur_unique_seqs - - mothur_classify_seqs - - mothur_remove_seqs - - mothur_heatmap_sim slides: false slides_recordings: false subtopic: metabarcoding @@ -70877,9 +68872,6 @@ - name: IPK Galaxy Blast Suite url: https://galaxy-web.ipk-gatersleben.de usegalaxy: false - - name: Lebanese University Galaxy - url: http://galaxy.ul.edu.lb/ - usegalaxy: false - name: Mandoiu Lab url: https://neo.engr.uconn.edu/ usegalaxy: false @@ -70895,9 +68887,6 @@ - name: PepSimili url: http://pepsimili.e-nios.com:8080/ usegalaxy: false - - name: PhagePromotor - url: https://galaxy.bio.di.uminho.pt/ - usegalaxy: false - name: UseGalaxy.org.au url: https://usegalaxy.org.au usegalaxy: true @@ -70952,8 +68941,6 @@ state: missing - 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- server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr @@ -71098,8 +69077,6 @@ state: missing - server: http://pepsimili.e-nios.com:8080/ state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - server: https://usegalaxy.org.au state: exact version: 1.39.5.0 @@ -71153,8 +69130,6 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr @@ -71165,8 +69140,6 @@ state: missing - server: http://pepsimili.e-nios.com:8080/ state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - server: https://usegalaxy.org.au state: exact version: 1.39.5.0 @@ -71220,8 +69193,6 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr @@ -71232,8 +69203,6 @@ state: missing - server: http://pepsimili.e-nios.com:8080/ state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - server: https://usegalaxy.org.au state: exact version: 1.39.5.0 @@ -71287,8 +69256,6 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr @@ -71299,8 +69266,6 @@ state: missing - server: http://pepsimili.e-nios.com:8080/ state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - server: https://usegalaxy.org.au state: exact version: 1.39.5.0 @@ -71354,8 +69319,6 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr @@ -71366,8 +69329,6 @@ state: missing - server: http://pepsimili.e-nios.com:8080/ state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - server: https://usegalaxy.org.au state: exact version: 1.39.5.0 @@ -71421,8 +69382,6 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr @@ -71433,8 +69392,6 @@ state: missing - server: http://pepsimili.e-nios.com:8080/ state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - server: https://usegalaxy.org.au state: exact version: 1.39.5.0 @@ -71488,8 +69445,6 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr @@ -71500,8 +69455,6 @@ state: missing - 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- server: https://galaxy.bio.di.uminho.pt/ - state: missing - server: https://usegalaxy.org.au state: exact version: 1.39.5.0 @@ -71689,8 +69634,6 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr @@ -71701,8 +69644,6 @@ state: missing - server: http://pepsimili.e-nios.com:8080/ state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - server: https://usegalaxy.org.au state: exact version: 1.39.5.0 @@ -71756,8 +69697,6 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr @@ -71768,8 +69707,6 @@ state: missing - server: http://pepsimili.e-nios.com:8080/ state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - server: https://usegalaxy.org.au state: exact version: 1.39.5.0 @@ -71823,8 +69760,6 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr @@ -71835,8 +69770,6 @@ state: missing - server: http://pepsimili.e-nios.com:8080/ state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - server: https://usegalaxy.org.au state: exact version: 1.39.5.0 @@ -71890,8 +69823,6 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr @@ -71902,8 +69833,6 @@ state: missing - server: http://pepsimili.e-nios.com:8080/ state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - server: https://usegalaxy.org.au state: exact version: 1.39.5.0 @@ -71957,8 +69886,6 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr @@ -71969,8 +69896,6 @@ state: missing - server: http://pepsimili.e-nios.com:8080/ state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - server: https://usegalaxy.org.au state: exact version: 1.39.5.0 @@ -72024,8 +69949,6 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr @@ -72036,8 +69959,6 @@ state: missing - server: http://pepsimili.e-nios.com:8080/ state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - server: https://usegalaxy.org.au state: exact version: 1.39.5.0 @@ -72091,8 +70012,6 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr @@ -72103,8 +70022,6 @@ state: missing - server: http://pepsimili.e-nios.com:8080/ state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - server: https://usegalaxy.org.au state: exact version: 1.39.5.0 @@ -72158,8 +70075,6 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr @@ -72170,8 +70085,6 @@ state: missing - server: http://pepsimili.e-nios.com:8080/ state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - server: https://usegalaxy.org.au state: exact version: 1.39.5.1 @@ -72225,8 +70138,6 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr @@ -72237,8 +70148,6 @@ state: missing - server: http://pepsimili.e-nios.com:8080/ state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - server: https://usegalaxy.org.au state: exact version: 1.39.5.0 @@ -72292,8 +70201,6 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr @@ -72304,8 +70211,6 @@ state: missing - server: http://pepsimili.e-nios.com:8080/ state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - server: https://usegalaxy.org.au state: exact version: 1.39.5.0 @@ -72359,8 +70264,6 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr @@ -72371,8 +70274,6 @@ state: missing - server: http://pepsimili.e-nios.com:8080/ state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - server: https://usegalaxy.org.au state: exact version: 1.39.5.2 @@ -72426,8 +70327,6 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr @@ -72438,8 +70337,6 @@ state: missing - server: http://pepsimili.e-nios.com:8080/ state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - server: https://usegalaxy.org.au state: exact version: 1.39.5.0 @@ -72493,8 +70390,6 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr @@ -72505,8 +70400,6 @@ state: missing - server: http://pepsimili.e-nios.com:8080/ state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - server: https://usegalaxy.org.au state: exact version: 1.39.5.0 @@ -72560,8 +70453,6 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr @@ -72572,8 +70463,6 @@ state: missing - server: http://pepsimili.e-nios.com:8080/ state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - server: https://usegalaxy.org.au state: exact version: 1.39.5.0 @@ -72627,8 +70516,6 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr @@ -72639,8 +70526,6 @@ state: missing - server: http://pepsimili.e-nios.com:8080/ state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - server: https://usegalaxy.org.au state: exact version: 1.6+galaxy1 @@ -72700,8 +70585,6 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr @@ -72714,8 +70597,6 @@ state: missing - server: http://pepsimili.e-nios.com:8080/ state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - server: https://usegalaxy.org.au state: exact version: '4.2' @@ -72795,8 +70676,8 @@ video: true video_versions: 2 video_view: 0 - visit_duration: 462 - visitors: 6699 + visit_duration: 465 + visitors: 6785 workflows: - creators: - class: Person @@ -72884,7 +70765,7 @@ \ 3;\n 4[\"Summary.seqs\"];\n 3 -->|fasta_out| 4;\n 5[\"Unique.seqs\"];\n\ \ 3 -->|fasta_out| 5;\n 6[\"Count.seqs\"];\n 3 -->|groups_out| 6;\n 5 -->|out_names|\ \ 6;" - modified: 2026-05-21 00:30:25 +0000 + modified: 2026-07-01 00:31:39 +0000 name: 'Workflow 1: Quality Control [Galaxy Training: 16S Microbial Analysis With Mothur]' outputs: @@ -73256,7 +71137,7 @@ \ 8[\"Chimera.vsearch\"];\n 6 -->|fasta_out| 8;\n 6 -->|count_out| 8;\n \ \ 9[\"Remove.seqs\"];\n 8 -->|out_accnos| 9;\n 8 -->|out_count| 9;\n 6 -->|fasta_out|\ \ 9;\n 10[\"Summary.seqs\"];\n 9 -->|count_out| 10;\n 9 -->|fasta_out| 10;" - modified: 2026-05-21 00:30:25 +0000 + modified: 2026-07-01 00:31:39 +0000 name: 'Workflow 2: Data Cleaning And Chimera Removal [Galaxy Training: 16S Microbial Analysis With Mothur]' outputs: @@ -73860,7 +71741,7 @@ \ 4;\n 3 -->|output| 4;\n 5[\"Remove.lineage\"];\n 1 -->|output| 5;\n 0\ \ -->|output| 5;\n 4 -->|taxonomy_out| 5;\n 6[\"Summary.seqs\"];\n 5 -->|count_out|\ \ 6;\n 5 -->|fasta_out| 6;" - modified: 2026-05-21 00:30:25 +0000 + modified: 2026-07-01 00:31:39 +0000 name: 'Workflow 3: Classification [Galaxy Training: 16S Microbial Analysis With Mothur]' outputs: @@ -74125,7 +72006,7 @@ ];\n 1 -->|output| 2;\n 3[\"Cluster\"];\n 0 -->|output| 3;\n 2 -->|out_dist|\ \ 3;\n 4[\"Make.shared\"];\n 0 -->|output| 4;\n 3 -->|otulist| 4;\n 5[\"\ Rarefaction.single\"];\n 4 -->|shared| 5;" - modified: 2026-05-21 00:30:25 +0000 + modified: 2026-07-01 00:31:39 +0000 name: 'Workflow 4: Mock OTU Clustering [Galaxy Training: 16S Microbial Analysis With Mothur]' outputs: @@ -74440,7 +72321,7 @@ \ -->|otulist| 5;\n 6[\"Classify.otu\"];\n 3 -->|count_out| 6;\n 4 -->|otulist|\ \ 6;\n 3 -->|taxonomy_out| 6;\n 7[\"Count.groups\"];\n 5 -->|shared| 7;\n\ \ 8[\"Sub.sample\"];\n 5 -->|shared| 8;" - modified: 2026-05-21 00:30:25 +0000 + modified: 2026-07-01 00:31:39 +0000 name: 'Workflow 5: OTU Clustering [Galaxy Training: 16S Microbial Analysis With Mothur]' outputs: @@ -74887,7 +72768,7 @@ \ style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"Rarefaction.single\"];\n \ \ 0 -->|output| 1;\n 2[\"Summary.single\"];\n 0 -->|output| 2;\n 3[\"Plotting\ \ tool\"];\n 1 -->|rarefactioncurves| 3;" - modified: 2026-05-21 00:30:25 +0000 + modified: 2026-07-01 00:31:39 +0000 name: 'Workflow 6: Alpha Diversity [Galaxy Training: 16S Microbial Analysis With Mothur]' outputs: @@ -75156,7 +73037,7 @@ \ 4[\"Heatmap.sim\"];\n 2 -->|distfiles| 4;\n 5[\"Tree.shared\"];\n 2 -->|distfiles|\ \ 5;\n 6[\"Venn\"];\n 3 -->|output| 6;\n 7[\"Newick Display\"];\n 5 -->|tre|\ \ 7;" - modified: 2026-05-21 00:30:25 +0000 + modified: 2026-07-01 00:31:39 +0000 name: 'Workflow7: Beta Diversity [Galaxy Training: 16S Microbial Analysis With Mothur]' outputs: @@ -75607,17 +73488,17 @@ page: https://training.galaxyproject.org/training-material/hall-of-fame/AustralianBioCommons/ url: https://training.galaxyproject.org/training-material/api/organisations/AustralianBioCommons.json - affiliations: - - erasmusmc - - gallantries - - by-covid - elixir-europe - - elixir-converge contact_for_training: false elixir_node: nl former_affiliations: - deNBI - avans-atgm - uni-freiburg + - erasmusmc + - gallantries + - by-covid + - elixir-converge id: hexylena joined: 2017-09 location: @@ -75794,22 +73675,22 @@ - topic_3305 - topic_3324 edam_operation: - - Sequence alignment analysis + - Variant calling - Phylogenetic tree visualisation - - Taxonomic classification - - Sequence analysis - - Statistical calculation - - Sequence alignment - Global alignment + - Sequencing quality control + - Statistical calculation - Genome visualisation - - Local alignment + - Sequence contamination filtering - Antimicrobial resistance prediction - - Validation - Sequence composition calculation - - Sequence contamination filtering - - Variant calling - - Sequencing quality control - Phylogenetic tree generation + - Sequence alignment + - Sequence alignment analysis + - Taxonomic classification + - Local alignment + - Validation + - Sequence analysis edam_topic: - Genomics - Microbiology @@ -75842,7 +73723,7 @@ - How should we filter those variants - How can we predict drug resistance from those variants - How do we annotate those variants - pageviews: 12705 + pageviews: 13093 pub_date: '2020-07-25' questions: - How do we detect differences between a set of reads from _M. tuberculosis_ (Mtb) @@ -75868,26 +73749,26 @@ youtube_id: -nJPngFk36c short_id: T00319 short_tools: - - kraken2 - - multiqc - - jbrowse - - qualimap_bamqc - - fastp - - samtools_stats - - 'EMBOSS: seqret84' + - bcftools_consensus + - tbvcfreport + - tb_profiler_profile + - tb_variant_filter - jvarkit_wgscoverageplotter - - mosdepth - snippy - - EMBOSS:%20seqret84 - __FLATTEN__ - - tp_sed_tool - - tb_variant_filter - - bcftools_consensus + - EMBOSS:%20seqret84 - tp_awk_tool - - fastqc - - tb_profiler_profile + - kraken2 + - samtools_stats + - qualimap_bamqc - upload1 - - tbvcfreport + - 'EMBOSS: seqret84' + - fastp + - jbrowse + - mosdepth + - fastqc + - tp_sed_tool + - multiqc slides: false slides_recordings: false subtopic: one-health @@ -75935,9 +73816,6 @@ - name: IPK Galaxy Blast Suite url: https://galaxy-web.ipk-gatersleben.de usegalaxy: false - - name: Lebanese University Galaxy - url: http://galaxy.ul.edu.lb/ - usegalaxy: false - name: Mandoiu Lab url: https://neo.engr.uconn.edu/ usegalaxy: false @@ -75953,9 +73831,6 @@ - name: PepSimili url: http://pepsimili.e-nios.com:8080/ usegalaxy: false - - name: PhagePromotor - url: https://galaxy.bio.di.uminho.pt/ - usegalaxy: false - name: UseGalaxy.org.au url: https://usegalaxy.org.au usegalaxy: true @@ -76009,8 +73884,6 @@ state: local - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: local - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr @@ -76021,8 +73894,6 @@ state: missing - server: http://pepsimili.e-nios.com:8080/ state: local - - server: https://galaxy.bio.di.uminho.pt/ - state: local - server: https://usegalaxy.org.au state: local - server: https://usegalaxy.be/ @@ -76055,9 +73926,9 @@ - server: https://galaxy.mesocentre.uca.fr state: inexact versions: - - 9.5+galaxy3 - - 1.1.2 - 1.1.1 + - 1.1.2 + - 9.5+galaxy3 - server: https://galaxy.pasteur.fr/ state: missing - server: https://galaxytrakr.org/ @@ -76075,8 +73946,6 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr @@ -76089,8 +73958,6 @@ state: missing - server: http://pepsimili.e-nios.com:8080/ state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - server: https://usegalaxy.org.au state: exact version: 9.5+galaxy2 @@ -76109,8 +73976,8 @@ - server: https://usegalaxy.no/ state: inexact versions: - - 1.1.2 - 1.1.1 + - 1.1.2 - 1.1.0 - server: https://usegalaxy.org state: exact @@ -76152,8 +74019,6 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr @@ -76166,8 +74031,6 @@ state: missing - server: http://pepsimili.e-nios.com:8080/ state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - server: https://usegalaxy.org.au state: exact version: 9.5+galaxy2 @@ -76222,8 +74085,6 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr @@ -76235,8 +74096,6 @@ state: missing - server: http://pepsimili.e-nios.com:8080/ state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - server: https://usegalaxy.org.au state: exact version: 5.0.0 @@ -76289,8 +74148,6 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr @@ -76301,8 +74158,6 @@ state: missing - server: http://pepsimili.e-nios.com:8080/ state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - server: https://usegalaxy.org.au state: missing - server: https://usegalaxy.be/ @@ -76336,8 +74191,8 @@ state: inexact versions: - '0.72' - - 0.73+galaxy0 - 0.72+galaxy1 + - 0.73+galaxy0 - server: https://galaxy.pasteur.fr/ state: inexact versions: @@ -76355,8 +74210,6 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr @@ -76369,16 +74222,12 @@ versions: - '0.72' - 0.72+galaxy1 - - '0.71' - '0.65' + - '0.71' - server: http://pepsimili.e-nios.com:8080/ state: inexact versions: - 0.74+galaxy0 - - server: https://galaxy.bio.di.uminho.pt/ - state: inexact - versions: - - 0.74+galaxy0 - server: https://usegalaxy.org.au state: exact version: 0.74+galaxy1 @@ -76397,8 +74246,8 @@ - server: https://usegalaxy.no/ state: inexact versions: - - 0.73+galaxy0 - 0.72+galaxy1 + - 0.73+galaxy0 - server: https://usegalaxy.org state: exact version: 0.74+galaxy1 @@ -76437,8 +74286,6 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr @@ -76452,8 +74299,6 @@ state: missing - server: http://pepsimili.e-nios.com:8080/ state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - server: https://usegalaxy.org.au state: exact version: 2.0.8 @@ -76512,8 +74357,6 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr @@ -76528,8 +74371,6 @@ state: missing - server: http://pepsimili.e-nios.com:8080/ state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - server: https://usegalaxy.org.au state: exact version: 1.15.1+galaxy4 @@ -76590,8 +74431,6 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr @@ -76604,8 +74443,6 @@ state: missing - server: http://pepsimili.e-nios.com:8080/ state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - server: https://usegalaxy.org.au state: exact version: 1.0.1+galaxy3 @@ -76625,16 +74462,16 @@ state: inexact versions: - 0.20.1+galaxy0 - - 0.19.5+galaxy1 - 0.23.2+galaxy0 + - 0.19.5+galaxy1 - server: https://usegalaxy.org state: exact version: 1.0.1+galaxy3 - server: https://viralvariant.anses.fr/ state: inexact versions: - - 1.0.1+galaxy2 - 0.23.2+galaxy0 + - 1.0.1+galaxy2 version: 1.0.1+galaxy3 - id: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1 servers: @@ -76667,8 +74504,6 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr @@ -76680,8 +74515,6 @@ state: missing - server: http://pepsimili.e-nios.com:8080/ state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - server: https://usegalaxy.org.au state: exact version: 1.16.11+galaxy1 @@ -76734,8 +74567,6 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr @@ -76746,8 +74577,6 @@ state: missing - server: http://pepsimili.e-nios.com:8080/ state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - server: https://usegalaxy.org.au state: missing - server: https://usegalaxy.be/ @@ -76783,10 +74612,10 @@ - server: https://galaxy.mesocentre.uca.fr state: inexact versions: - - 2.1.3+galaxy2 - - 2.1.1+galaxy0 - 2.1.3+galaxy1 + - 2.1.1+galaxy0 - 2.1.1+galaxy1 + - 2.1.3+galaxy2 - server: https://galaxy.pasteur.fr/ state: missing - server: https://galaxytrakr.org/ @@ -76802,8 +74631,6 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr @@ -76816,8 +74643,6 @@ state: inexact versions: - 2.1.1+galaxy1 - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - server: https://usegalaxy.org.au state: exact version: 2.17.1+galaxy0 @@ -76874,8 +74699,6 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr @@ -76886,8 +74709,6 @@ state: missing - server: http://pepsimili.e-nios.com:8080/ state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - server: https://usegalaxy.org.au state: exact version: 0.3.12+galaxy0 @@ -76941,8 +74762,6 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr @@ -76955,10 +74774,6 @@ state: missing - server: http://pepsimili.e-nios.com:8080/ state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: inexact - versions: - - 1.11+galaxy1 - server: https://usegalaxy.org.au state: exact version: 1.27+galaxy4 @@ -76980,10 +74795,10 @@ - 1.11+galaxy0 - '1.7' - 1.7.1 - - '1.9' + - 1.8+galaxy0 - 1.9+galaxy1 - 1.8+galaxy1 - - 1.8+galaxy0 + - 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- server: https://galaxy.bio.di.uminho.pt/ - state: missing - server: https://usegalaxy.org.au state: exact version: 6.6.4+galaxy0 @@ -77258,13 +75057,13 @@ - server: https://usegalaxy.no/ state: inexact versions: - - 3.0.6+galaxy0 + - 2.8.4+galaxy1 - 3.0.4+galaxy1 - 3.0.8+galaxy0 - 4.1.1+galaxy0 + - 3.0.6+galaxy0 - 2.8.14+galaxy1 - 3.0.7+galaxy0 - - 2.8.4+galaxy1 - 3.0.7+galaxy1 - server: https://usegalaxy.org state: exact @@ -77300,8 +75099,6 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr @@ -77312,8 +75109,6 @@ state: missing - server: http://pepsimili.e-nios.com:8080/ state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - server: https://usegalaxy.org.au state: exact version: 1.0.1+galaxy0 @@ -77332,9 +75127,9 @@ - server: https://usegalaxy.no/ state: inexact versions: - 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modified: 2026-05-21 00:30:26 +0000 + modified: 2026-07-01 00:31:40 +0000 name: TB variants tutorial main workflow outputs: [] parent_id: variant-analysis/tb-variant-analysis @@ -77955,7 +75746,7 @@ \ 19;\n 6 -->|out_file1| 19;\n 16 -->|outfile| 19;\n c71b135d-35f9-44d0-a20e-f25528e518af[\"\ Output\\nconsensus_genome\"];\n 19 --> c71b135d-35f9-44d0-a20e-f25528e518af;\n\ \ style c71b135d-35f9-44d0-a20e-f25528e518af stroke:#2c3143,stroke-width:4px;" - modified: 2026-05-21 00:30:26 +0000 + modified: 2026-07-01 00:31:40 +0000 name: TB Variant Analysis v1.0 outputs: - annotation: '' @@ -78268,744 +76059,339 @@ action_arguments: tags: consensus_genome action_type: TagDatasetAction - output_name: output_file - tool_id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_consensus/bcftools_consensus/1.15.1+galaxy4 - tool_shed_repository: - changeset_revision: 8aa352093d73 - name: bcftools_consensus - owner: iuc - tool_shed: toolshed.g2.bx.psu.edu - tool_state: '{"absent": "", "chain": false, "input_file": {"__class__": "RuntimeValue"}, - 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name: PepSimili + url: http://pepsimili.e-nios.com:8080/ + usegalaxy: false + - name: UseGalaxy.org.au + url: https://usegalaxy.org.au + usegalaxy: true + - name: UseGalaxy.be + url: https://usegalaxy.be/ + usegalaxy: false + - name: UseGalaxy.cz + url: https://usegalaxy.cz/ + usegalaxy: false + - name: UseGalaxy.eu + url: https://usegalaxy.eu + usegalaxy: true + - name: UseGalaxy.fr + url: https://usegalaxy.fr/ + usegalaxy: true + - name: UseGalaxy.no + url: https://usegalaxy.no/ + usegalaxy: false + - name: UseGalaxy.org (Main) + url: https://usegalaxy.org + usegalaxy: true + - name: Viral Variant Visualizer (VVV) + url: https://viralvariant.anses.fr/ + usegalaxy: false + tools: + - id: toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_db/metaquantome_db/2.0.0-0 servers: - server: http://apostl.moffitt.org/ state: missing @@ -79033,8 +76419,6 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr @@ -79045,182 +76429,40 @@ state: missing - server: http://pepsimili.e-nios.com:8080/ state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - server: https://usegalaxy.org.au state: inexact versions: - - 1.0.3.1 + - 2.0.1+galaxy0 + - 2.0.0-2 + - 2.0.0-1 + - 2.0.2+galaxy0 + - 2.0.4+galaxy0 - server: https://usegalaxy.be/ state: exact - version: 1.0.3.0 + version: 2.0.0-0 - server: https://usegalaxy.cz/ - state: exact - version: 1.0.3.0 - - server: https://usegalaxy.eu - state: exact - version: 1.0.3.0 - - server: https://usegalaxy.fr/ - state: missing - - server: https://usegalaxy.no/ - state: exact - version: 1.0.3.0 - - server: https://usegalaxy.org - state: missing - - server: https://viralvariant.anses.fr/ - state: missing - version: 1.0.3.0 - - id: toolshed.g2.bx.psu.edu/repos/galaxyp/msconvert/msconvert/3.0.19052.0 - servers: - - server: http://apostl.moffitt.org/ - state: missing - - server: http://mbac.gmu.edu:8080/ - state: missing - - server: https://vm-chemflow-francegrille.eu/ - state: missing - - server: https://iris.angers.inra.fr/galaxypub-cfbp - state: missing - - server: https://hyperbrowser.uio.no/coloc-stats - state: missing - - server: https://galaxy.mesocentre.uca.fr - state: missing - - server: https://galaxy.pasteur.fr/ - state: missing - - server: https://galaxytrakr.org/ - state: missing - - server: http://igg.cloud.ba.infn.it/galaxy - state: missing - - server: https://galaxy.hyphy.org/ - state: missing - - server: https://www.immportgalaxy.org/ - state: missing - - server: http://galaxy.interactomix.com/ - state: missing - - server: https://galaxy-web.ipk-gatersleben.de - state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - - server: https://neo.engr.uconn.edu/ - state: missing - - server: https://mississippi.sorbonne-universite.fr - state: missing - - server: http://galaxy.inf.ethz.ch - state: missing - - server: https://palfinder.ls.manchester.ac.uk/ - state: missing - - server: http://pepsimili.e-nios.com:8080/ - state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - - server: https://usegalaxy.org.au - state: inexact - versions: - - 3.0.20287.6 - - 3.0.20287.2 - - server: https://usegalaxy.be/ state: inexact versions: - - 3.0.20287.7 - - 3.0.26121.7 - - server: https://usegalaxy.cz/ - state: exact - version: 3.0.19052.0 + - 2.0.2+galaxy0 + - 2.0.4+galaxy0 - server: https://usegalaxy.eu state: exact - version: 3.0.19052.0 + version: 2.0.0-0 - server: https://usegalaxy.fr/ - state: exact - version: 3.0.19052.0 - - server: https://usegalaxy.no/ - state: inexact - versions: - - 0.3.0 - - 3.0.19052.1 - - server: https://usegalaxy.org - state: inexact - versions: - - 3.0.20287.6 - - 3.0.20287.2 - - 3.0.20287.7 - - 3.0.20287.5 - - 3.0.20287.4 - - 3.0.19052.1 - - 3.0.20287.3 - - server: https://viralvariant.anses.fr/ - state: missing - version: 3.0.19052.0 - - id: toolshed.g2.bx.psu.edu/repos/galaxyp/peptideshaker/peptide_shaker/1.16.36.3 - servers: - - server: http://apostl.moffitt.org/ - state: missing - - server: http://mbac.gmu.edu:8080/ - state: missing - - server: https://vm-chemflow-francegrille.eu/ - state: missing - - server: https://iris.angers.inra.fr/galaxypub-cfbp - state: missing - - server: https://hyperbrowser.uio.no/coloc-stats - state: missing - - server: https://galaxy.mesocentre.uca.fr - state: missing - - server: https://galaxy.pasteur.fr/ - state: missing - - server: https://galaxytrakr.org/ - state: missing - - server: http://igg.cloud.ba.infn.it/galaxy - state: missing - - server: https://galaxy.hyphy.org/ - state: missing - - server: https://www.immportgalaxy.org/ - state: missing - - server: http://galaxy.interactomix.com/ - state: missing - - server: https://galaxy-web.ipk-gatersleben.de - state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - - server: https://neo.engr.uconn.edu/ - state: missing - - server: https://mississippi.sorbonne-universite.fr - state: missing - - server: http://galaxy.inf.ethz.ch - state: missing - - server: https://palfinder.ls.manchester.ac.uk/ - state: missing - - server: http://pepsimili.e-nios.com:8080/ - state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - - server: https://usegalaxy.org.au - state: exact - version: 1.16.36.3 - - server: https://usegalaxy.be/ state: inexact versions: - - 2.0.33+galaxy1 - - 2.0.33+galaxy2 - - 1.11.0 - - 1.16.36.2 - - server: https://usegalaxy.cz/ + - 2.0.2+galaxy0 + - 2.0.4+galaxy0 + - server: https://usegalaxy.no/ state: inexact versions: - - 2.0.33+galaxy1 - - server: https://usegalaxy.eu - state: exact - version: 1.16.36.3 - - server: https://usegalaxy.fr/ - state: exact - version: 1.16.36.3 - - server: https://usegalaxy.no/ - state: exact - version: 1.16.36.3 + - 1.0.0-0 - server: https://usegalaxy.org - state: exact - version: 1.16.36.3 + state: missing - server: https://viralvariant.anses.fr/ state: missing - version: 1.16.36.3 - - id: toolshed.g2.bx.psu.edu/repos/galaxyp/peptideshaker/search_gui/3.3.10.1 + version: 2.0.0-0 + - id: toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_expand/metaquantome_expand/2.0.0-0 servers: - server: http://apostl.moffitt.org/ state: missing @@ -79248,8 +76490,6 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr @@ -79260,116 +76500,40 @@ state: missing - server: http://pepsimili.e-nios.com:8080/ state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - - server: https://usegalaxy.org.au - state: exact - version: 3.3.10.1 - - server: https://usegalaxy.be/ - state: exact - version: 3.3.10.1 - - server: https://usegalaxy.cz/ - state: inexact - versions: - - 4.0.41+galaxy1 - - 4.0.41+galaxy0 - - server: https://usegalaxy.eu - state: exact - version: 3.3.10.1 - - server: https://usegalaxy.fr/ - state: exact - version: 3.3.10.1 - - server: https://usegalaxy.no/ - state: exact - version: 3.3.10.1 - - server: https://usegalaxy.org - state: exact - version: 3.3.10.1 - - server: https://viralvariant.anses.fr/ - state: missing - version: 3.3.10.1 - - id: toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regex1/1.0.0 - servers: - - server: http://apostl.moffitt.org/ - state: missing - - server: http://mbac.gmu.edu:8080/ - state: missing - - server: https://vm-chemflow-francegrille.eu/ - state: missing - - server: https://iris.angers.inra.fr/galaxypub-cfbp - state: missing - - server: https://hyperbrowser.uio.no/coloc-stats - state: missing - - server: https://galaxy.mesocentre.uca.fr - state: missing - - server: https://galaxy.pasteur.fr/ - state: inexact - versions: - - 1.0.3 - - server: https://galaxytrakr.org/ - state: inexact - versions: - - 1.0.3 - - 1.0.1 - - server: http://igg.cloud.ba.infn.it/galaxy - state: missing - - server: https://galaxy.hyphy.org/ - state: missing - - server: https://www.immportgalaxy.org/ - state: missing - - server: http://galaxy.interactomix.com/ - state: missing - - server: https://galaxy-web.ipk-gatersleben.de - state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - - server: https://neo.engr.uconn.edu/ - state: missing - - server: https://mississippi.sorbonne-universite.fr - state: inexact - versions: - - 1.0.3 - - server: http://galaxy.inf.ethz.ch - state: missing - - server: https://palfinder.ls.manchester.ac.uk/ - state: missing - - server: http://pepsimili.e-nios.com:8080/ - state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - server: https://usegalaxy.org.au state: inexact versions: - - 1.0.3 - - 1.0.1 - - 1.0.2 + - 2.0.2+galaxy0 + - 2.0.0-1 + - 2.0.4+galaxy0 + - 2.0.1+galaxy0 + - 2.0.0-2 - server: https://usegalaxy.be/ state: exact - version: 1.0.0 + version: 2.0.0-0 - server: https://usegalaxy.cz/ state: inexact versions: - - 1.0.3 + - 2.0.2+galaxy0 + - 2.0.4+galaxy0 - server: https://usegalaxy.eu state: exact - version: 1.0.0 + version: 2.0.0-0 - server: https://usegalaxy.fr/ state: inexact versions: - - 1.0.3 - - 1.0.1 - - 1.0.2 + - 2.0.2+galaxy0 + - 2.0.4+galaxy0 - server: https://usegalaxy.no/ state: inexact versions: - - 1.0.3 + - 1.0.0-0 - server: https://usegalaxy.org - state: exact - version: 1.0.0 + state: missing - server: https://viralvariant.anses.fr/ state: missing - version: 1.0.0 - - id: toolshed.g2.bx.psu.edu/repos/galaxyp/unipept/unipept/4.0.0 + version: 2.0.0-0 + - id: toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_filter/metaquantome_filter/2.0.0-0 servers: - server: http://apostl.moffitt.org/ state: missing @@ -79382,17 +76546,11 @@ - server: https://hyperbrowser.uio.no/coloc-stats state: missing - server: https://galaxy.mesocentre.uca.fr - state: inexact - versions: - - 6.2.4+galaxy0 - - 4.3.0 - - 4.5.1 + state: missing - server: https://galaxy.pasteur.fr/ state: missing - server: https://galaxytrakr.org/ - state: inexact - versions: - - 4.5.0 + state: missing - server: http://igg.cloud.ba.infn.it/galaxy state: missing - server: https://galaxy.hyphy.org/ @@ -79403,8 +76561,6 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr @@ -79415,52 +76571,40 @@ state: missing - server: http://pepsimili.e-nios.com:8080/ state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - server: https://usegalaxy.org.au state: inexact versions: - - 6.2.4+galaxy0 - - 4.3.0 - - 4.5.1 - - 4.5.0 - - 2.0.1 - - 6.2.4+galaxy1 + - 2.0.0-2 + - 2.0.2+galaxy0 + - 2.0.1+galaxy0 + - 2.0.0-1 + - 2.0.4+galaxy0 - server: https://usegalaxy.be/ state: exact - version: 4.0.0 + version: 2.0.0-0 - server: https://usegalaxy.cz/ state: inexact versions: - - 6.2.4+galaxy0 - - 4.3.0 - - 4.5.1 - - 2.0.1 - - 6.2.4+galaxy1 + - 2.0.2+galaxy0 + - 2.0.4+galaxy0 - server: https://usegalaxy.eu state: exact - version: 4.0.0 + version: 2.0.0-0 - server: https://usegalaxy.fr/ state: inexact versions: - - 6.2.4+galaxy0 - - 4.5.1 - - 6.2.4+galaxy1 - - server: https://usegalaxy.no/ - state: exact - version: 4.0.0 - - server: https://usegalaxy.org - state: inexact - versions: - - 6.2.4+galaxy0 - - 4.3.0 - - 4.5.1 - - 2.0.1 - - 6.2.4+galaxy1 + - 2.0.2+galaxy0 + - 2.0.4+galaxy0 + - server: https://usegalaxy.no/ + state: inexact + versions: + - 1.0.0-0 + - server: https://usegalaxy.org + state: missing - server: https://viralvariant.anses.fr/ state: missing - version: 4.0.0 - - id: toolshed.g2.bx.psu.edu/repos/galaxyp/unipept/unipept/4.3.0 + version: 2.0.0-0 + - id: toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_sample/metaquantome_sample/2.0.0-0 servers: - server: http://apostl.moffitt.org/ state: missing @@ -79473,14 +76617,11 @@ - server: https://hyperbrowser.uio.no/coloc-stats state: missing - server: https://galaxy.mesocentre.uca.fr - state: exact - version: 4.3.0 + state: missing - server: https://galaxy.pasteur.fr/ state: missing - server: https://galaxytrakr.org/ - state: inexact - versions: - - 4.5.0 + state: missing - server: http://igg.cloud.ba.infn.it/galaxy state: missing - server: https://galaxy.hyphy.org/ @@ -79491,8 +76632,6 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr @@ -79503,36 +76642,40 @@ state: missing - server: http://pepsimili.e-nios.com:8080/ state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - server: https://usegalaxy.org.au - state: exact - version: 4.3.0 + state: inexact + versions: + - 2.0.2+galaxy0 + - 2.0.4+galaxy0 + - 2.0.1+galaxy0 + - 2.0.0-1 + - 2.0.0-2 - server: https://usegalaxy.be/ state: exact - version: 4.3.0 + version: 2.0.0-0 - server: https://usegalaxy.cz/ - state: exact - version: 4.3.0 + state: inexact + versions: + - 2.0.2+galaxy0 + - 2.0.4+galaxy0 - server: https://usegalaxy.eu state: exact - version: 4.3.0 + version: 2.0.0-0 - server: https://usegalaxy.fr/ state: inexact versions: - - 6.2.4+galaxy0 - - 4.5.1 - - 6.2.4+galaxy1 + - 2.0.2+galaxy0 + - 2.0.4+galaxy0 - server: https://usegalaxy.no/ - state: exact - version: 4.3.0 + state: inexact + versions: + - 1.0.0-0 - server: https://usegalaxy.org - state: exact - version: 4.3.0 + state: missing - server: https://viralvariant.anses.fr/ state: missing - version: 4.3.0 - - id: toolshed.g2.bx.psu.edu/repos/galaxyp/unipept/unipept/4.5.0 + version: 2.0.0-0 + - id: toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_stat/metaquantome_stat/2.0.0-0 servers: - server: http://apostl.moffitt.org/ state: missing @@ -79545,16 +76688,11 @@ - server: https://hyperbrowser.uio.no/coloc-stats state: missing - server: https://galaxy.mesocentre.uca.fr - state: inexact - versions: - - 6.2.4+galaxy0 - - 4.3.0 - - 4.5.1 + state: missing - server: https://galaxy.pasteur.fr/ state: missing - server: https://galaxytrakr.org/ - state: exact - version: 4.5.0 + state: missing - server: http://igg.cloud.ba.infn.it/galaxy state: missing - server: https://galaxy.hyphy.org/ @@ -79565,8 +76703,6 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr @@ -79577,48 +76713,40 @@ state: missing - server: http://pepsimili.e-nios.com:8080/ state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - server: https://usegalaxy.org.au - state: exact - version: 4.5.0 + state: inexact + versions: + - 2.0.4+galaxy0 + - 2.0.1+galaxy0 + - 2.0.2+galaxy0 + - 2.0.0-1 + - 2.0.0-2 - server: https://usegalaxy.be/ state: exact - version: 4.5.0 + version: 2.0.0-0 - server: https://usegalaxy.cz/ state: inexact versions: - - 6.2.4+galaxy0 - - 4.3.0 - - 4.5.1 - - 2.0.1 - - 6.2.4+galaxy1 + - 2.0.4+galaxy0 + - 2.0.2+galaxy0 - server: https://usegalaxy.eu state: exact - version: 4.5.0 + version: 2.0.0-0 - server: https://usegalaxy.fr/ state: inexact versions: - - 6.2.4+galaxy0 - - 4.5.1 - - 6.2.4+galaxy1 + - 2.0.4+galaxy0 + - 2.0.2+galaxy0 - server: https://usegalaxy.no/ state: inexact versions: - - 4.3.0 - - 4.0.0 + - 1.0.0-0 - server: https://usegalaxy.org - state: inexact - versions: - - 6.2.4+galaxy0 - - 4.3.0 - - 4.5.1 - - 2.0.1 - - 6.2.4+galaxy1 + state: missing - server: https://viralvariant.anses.fr/ state: missing - version: 4.5.0 - - id: toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.0.0 + version: 2.0.0-0 + - id: toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_viz/metaquantome_viz/2.0.0-0 servers: - server: http://apostl.moffitt.org/ state: missing @@ -79633,13 +76761,9 @@ - server: https://galaxy.mesocentre.uca.fr state: missing - server: https://galaxy.pasteur.fr/ - state: inexact - versions: - - 3.3.1 + state: missing - server: https://galaxytrakr.org/ - state: inexact - versions: - - 3.3.0 + state: missing - server: http://igg.cloud.ba.infn.it/galaxy state: missing - server: https://galaxy.hyphy.org/ @@ -79650,8 +76774,6 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr @@ -79662,61 +76784,51 @@ state: missing - server: http://pepsimili.e-nios.com:8080/ state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - server: https://usegalaxy.org.au - state: exact - version: 3.0.0 + state: inexact + versions: + - 2.0.1+galaxy0 + - 2.0.0-1 + - 2.0.2+galaxy0 + - 2.0.0-2 + - 2.0.4+galaxy0 - server: https://usegalaxy.be/ state: exact - version: 3.0.0 + version: 2.0.0-0 - server: https://usegalaxy.cz/ state: inexact versions: - - 3.3.1 - - 3.3.0 + - 2.0.2+galaxy0 + - 2.0.4+galaxy0 - server: https://usegalaxy.eu state: exact - version: 3.0.0 + version: 2.0.0-0 - server: https://usegalaxy.fr/ state: inexact versions: - - 3.3.1 - - 3.3.0 - - 3.3.2 - - 3.1.1 - - 3.2.0 - - 3.0.1 + - 2.0.2+galaxy0 + - 2.0.4+galaxy0 - server: https://usegalaxy.no/ - state: exact - version: 3.0.0 + state: inexact + versions: + - 1.0.0-0 - server: https://usegalaxy.org - state: exact - version: 3.0.0 + state: missing - server: https://viralvariant.anses.fr/ state: missing - version: 3.0.0 + version: 2.0.0-0 symlink: null tags: - microgalaxy time_estimation: 1h - title: 'metaQuantome 1: Data creation' + title: 'metaQuantome 3: Taxonomy' tools: - - Cut1 - - Filter1 - - Grep1 - - Remove beginning1 - - toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/1.1.3 - - toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/1.1.2 - - toolshed.g2.bx.psu.edu/repos/galaxyp/flashlfq/flashlfq/1.0.3.0 - - toolshed.g2.bx.psu.edu/repos/galaxyp/msconvert/msconvert/3.0.19052.0 - - toolshed.g2.bx.psu.edu/repos/galaxyp/peptideshaker/peptide_shaker/1.16.36.3 - - toolshed.g2.bx.psu.edu/repos/galaxyp/peptideshaker/search_gui/3.3.10.1 - - toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regex1/1.0.0 - - toolshed.g2.bx.psu.edu/repos/galaxyp/unipept/unipept/4.0.0 - - toolshed.g2.bx.psu.edu/repos/galaxyp/unipept/unipept/4.3.0 - 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admin_install: install_repository_dependencies: true install_resolver_dependencies: true install_tool_dependencies: true tools: + - name: text_processing + owner: bgruening + revisions: d698c222f354 + tool_panel_section_label: Text Manipulation + tool_shed_url: https://toolshed.g2.bx.psu.edu/ + - name: text_processing + owner: bgruening + revisions: d698c222f354 + tool_panel_section_label: Text Manipulation + tool_shed_url: https://toolshed.g2.bx.psu.edu/ + - name: flashlfq + owner: galaxyp + revisions: 878f6725c4f3 + tool_panel_section_label: Proteomics + tool_shed_url: https://toolshed.g2.bx.psu.edu/ + - name: msconvert + owner: galaxyp + revisions: 9ec469ff191a + tool_panel_section_label: Convert Formats + tool_shed_url: https://toolshed.g2.bx.psu.edu/ - name: peptideshaker owner: galaxyp revisions: 7fdd9119cc4f @@ -80549,9 +77465,24 @@ revisions: 7fdd9119cc4f tool_panel_section_label: Proteomics tool_shed_url: https://toolshed.g2.bx.psu.edu/ + - name: regex_find_replace + owner: galaxyp + revisions: 209b7c5ee9d7 + tool_panel_section_label: Text Manipulation + tool_shed_url: https://toolshed.g2.bx.psu.edu/ - 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\ https://toolshed.g2.bx.psu.edu/\n- name: sqlite_to_tabular\n owner: iuc\n \ - \ revisions: b722161a845a\n tool_panel_section_label: Text Manipulation\n tool_shed_url:\ \ https://toolshed.g2.bx.psu.edu/\n" - api: https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/metaproteomics/tutorial.json + api: https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/metaquantome-data-creation/tutorial.json contributors: + - email: subinamehta@gmail.com + id: subinamehta + joined: 2018-06 + linkedin: subinamehta + matrix: subinamehta:matrix.org + name: Subina Mehta + orcid: 0000-0001-9818-0537 + page: https://training.galaxyproject.org/training-material/hall-of-fame/subinamehta/ + twitter: Subina_Mehta + url: https://training.galaxyproject.org/training-material/api/contributors/subinamehta.json - email: tgriffin@umn.edu github: false id: timothygriffin @@ -80593,64 +77541,50 @@ orcid: 0000-0003-0984-0973 page: https://training.galaxyproject.org/training-material/hall-of-fame/pratikdjagtap/ url: https://training.galaxyproject.org/training-material/api/contributors/pratikdjagtap.json - - email: jj@umn.edu - id: jj-umn - in_memoriam: "James \u2018JJ\u2019 Johnson, was a Galaxy community rock star most known for\ - \ his indispensable contributions to the Galaxy Proteomics community.\n\n\ - JJ\u2019s works will live on in so many Galaxy tools and workflows for years\ - \ to come." - joined: 2017-09 - name: James Johnson - page: https://training.galaxyproject.org/training-material/hall-of-fame/jj-umn/ - url: https://training.galaxyproject.org/training-material/api/contributors/jj-umn.json - - elixir_node: de - email: blankclemens@gmail.com - former_affiliations: - - uni-freiburg - - elixir-europe - id: blankclemens - joined: 2017-09 - name: Clemens Blank - orcid: 0000-0002-1726-2256 - page: https://training.galaxyproject.org/training-material/hall-of-fame/blankclemens/ - url: https://training.galaxyproject.org/training-material/api/contributors/blankclemens.json - - email: subinamehta@gmail.com - id: subinamehta - joined: 2018-06 - linkedin: subinamehta - matrix: subinamehta:matrix.org - name: Subina Mehta - orcid: 0000-0001-9818-0537 - page: https://training.galaxyproject.org/training-material/hall-of-fame/subinamehta/ - twitter: Subina_Mehta - url: https://training.galaxyproject.org/training-material/api/contributors/subinamehta.json - dir: topics/proteomics/tutorials/metaproteomics + - email: leith023@umn.edu + id: emmaleith + joined: 2019-07 + name: Emma Leith + page: https://training.galaxyproject.org/training-material/hall-of-fame/emmaleith/ + url: https://training.galaxyproject.org/training-material/api/contributors/emmaleith.json + - email: crane136@umn.edu + id: mariecrane + joined: 2019-05 + name: Marie Crane + page: https://training.galaxyproject.org/training-material/hall-of-fame/mariecrane/ + url: https://training.galaxyproject.org/training-material/api/contributors/mariecrane.json + dir: topics/proteomics/tutorials/metaquantome-data-creation edam_ontology: - topic_0121 - topic_3922 - topic_3050 - topic_0637 edam_operation: - - Visualisation + - Filtering + - Label-free quantification - Prediction and recognition + - Formatting + - Visualisation edam_topic: - Proteomics - Proteogenomics - Biodiversity - Taxonomy exact_supported_servers: - - UseGalaxy.org.au - UseGalaxy.eu - - UseGalaxy.org (Main) feedback_mean_note: null feedback_number: 0 + follow_up_training: + - topic_name: proteomics + tutorials: + - metaproteomics + type: internal hands_on: true - id: proteomics/metaproteomics + id: proteomics/metaquantome-data-creation inexact_supported_servers: + - UseGalaxy.org.au - UseGalaxy.be - UseGalaxy.cz - - UseGalaxy.fr - UseGalaxy.no js_requirements: mathjax: null @@ -80660,57 +77594,52 @@ - With SearchGUI and PeptideShaker you can gain access to multiple search engines - Learning the basics of SQL queries can pay off layout: tutorial_hands_on + level: Intermediate license: CC-BY-4.0 - mod_date: '2026-05-11' + mod_date: '2024-03-14' objectives: - - A taxonomy and functional analysis of metaproteomic mass spectrometry data. - pageviews: 4879 - pub_date: '2017-06-28' + - A taxonomy, functional and quantitational analysis of metaproteomic mass spectrometry + data. + pageviews: 1579 + pub_date: '2020-10-16' questions: - - How can I match metaproteomic mass spectrometry data to peptide sequences derived - from shotgun metagenomic data? - - How can I perform taxonomy analysis and visualize metaproteomics data? - - How can I perform functional analysis on this metaproteomics data? - recordings: - - captioners: - - emmaleith - date: '2021-02-15' - galaxy_version: '21.01' - length: 1H - speakers: - - pratikdjagtap - youtube_id: 3_yaPp-RCFw - short_id: T00221 + - How do I perform functional and taxonomy analysis on metaproteomics data? + - How can I perform quantitation on metaproteomics data? + - How do I create inputs that can be used in metaquantome to examine differentially + expressed proteins? + short_id: T00222 short_tools: - - sqlite_to_tabular + - peptide_shaker - query_tabular + - tp_replace_in_line + - Remove beginning1 - unipept - - peptide_shaker + - Filter1 + - tp_replace_in_column + - Grep1 + - msconvert + - regex1 + - flashlfq - search_gui + - Cut1 slides: false slides_recordings: false subtopic: multi-omics supported_servers: exact: - - name: UseGalaxy.org.au - url: https://usegalaxy.org.au - usegalaxy: true - name: UseGalaxy.eu url: https://usegalaxy.eu usegalaxy: true - - name: UseGalaxy.org (Main) - url: https://usegalaxy.org - usegalaxy: true inexact: + - name: UseGalaxy.org.au + url: https://usegalaxy.org.au + usegalaxy: true - name: UseGalaxy.be url: https://usegalaxy.be/ usegalaxy: false - name: UseGalaxy.cz url: https://usegalaxy.cz/ usegalaxy: false - - name: UseGalaxy.fr - url: https://usegalaxy.fr/ - usegalaxy: true - name: UseGalaxy.no url: https://usegalaxy.no/ usegalaxy: false @@ -80755,9 +77684,6 @@ - name: IPK Galaxy Blast Suite url: https://galaxy-web.ipk-gatersleben.de usegalaxy: false - - name: Lebanese University Galaxy - url: http://galaxy.ul.edu.lb/ - usegalaxy: false - name: Mandoiu Lab url: https://neo.engr.uconn.edu/ usegalaxy: false @@ -80773,9 +77699,6 @@ - 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server: http://apostl.moffitt.org/ state: missing @@ -80829,7 +78108,66 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ + - server: https://neo.engr.uconn.edu/ + state: missing + - server: https://mississippi.sorbonne-universite.fr + state: missing + - server: http://galaxy.inf.ethz.ch + state: missing + - server: https://palfinder.ls.manchester.ac.uk/ + state: missing + - server: http://pepsimili.e-nios.com:8080/ + state: missing + - server: https://usegalaxy.org.au + state: inexact + versions: + - 1.0.3.1 + - server: https://usegalaxy.be/ + state: exact + version: 1.0.3.0 + - server: https://usegalaxy.cz/ + state: exact + version: 1.0.3.0 + - server: https://usegalaxy.eu + state: exact + version: 1.0.3.0 + - server: https://usegalaxy.fr/ + state: missing + - server: https://usegalaxy.no/ + state: exact + version: 1.0.3.0 + - server: https://usegalaxy.org + state: missing + - server: https://viralvariant.anses.fr/ + state: missing + version: 1.0.3.0 + - 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- server: https://galaxy.bio.di.uminho.pt/ + - server: https://usegalaxy.org.au + state: inexact + versions: + - 3.0.20287.2 + - 3.0.20287.6 + - server: https://usegalaxy.be/ + state: inexact + versions: + - 3.0.20287.7 + - 3.0.26121.7 + - server: https://usegalaxy.cz/ + state: exact + version: 3.0.19052.0 + - server: https://usegalaxy.eu + state: exact + version: 3.0.19052.0 + - server: https://usegalaxy.fr/ + state: exact + version: 3.0.19052.0 + - server: https://usegalaxy.no/ + state: inexact + versions: + - 3.0.19052.1 + - 0.3.0 + - server: https://usegalaxy.org + state: inexact + versions: + - 3.0.20287.2 + - 3.0.20287.6 + - 3.0.20287.7 + - 3.0.26121.7 + - 3.0.20287.5 + - 3.0.19052.1 + - 3.0.20287.4 + - 3.0.20287.3 + - server: https://viralvariant.anses.fr/ + state: missing + version: 3.0.19052.0 + - id: toolshed.g2.bx.psu.edu/repos/galaxyp/peptideshaker/peptide_shaker/1.16.36.3 + servers: + - server: http://apostl.moffitt.org/ + state: missing + - server: http://mbac.gmu.edu:8080/ + state: missing + - server: https://vm-chemflow-francegrille.eu/ + state: missing + - server: https://iris.angers.inra.fr/galaxypub-cfbp + state: missing + - server: https://hyperbrowser.uio.no/coloc-stats + state: missing + - server: https://galaxy.mesocentre.uca.fr + state: missing + - server: https://galaxy.pasteur.fr/ + state: missing + - server: https://galaxytrakr.org/ + state: missing + - server: http://igg.cloud.ba.infn.it/galaxy + state: missing + - server: https://galaxy.hyphy.org/ + state: missing + - server: https://www.immportgalaxy.org/ + state: missing + - server: http://galaxy.interactomix.com/ + state: missing + - server: https://galaxy-web.ipk-gatersleben.de + state: missing + - server: https://neo.engr.uconn.edu/ + state: missing + - server: https://mississippi.sorbonne-universite.fr + state: missing + - server: http://galaxy.inf.ethz.ch + state: missing + - server: https://palfinder.ls.manchester.ac.uk/ + state: missing + - server: http://pepsimili.e-nios.com:8080/ state: missing - server: https://usegalaxy.org.au state: exact @@ -80849,30 +78261,173 @@ - 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4.0.41+galaxy2 + - 4.0.41+galaxy0 + - server: https://usegalaxy.eu + state: exact + version: 3.3.10.1 + - server: https://usegalaxy.fr/ + state: exact + version: 3.3.10.1 + - server: https://usegalaxy.no/ + state: exact + version: 3.3.10.1 + - server: https://usegalaxy.org + state: exact + version: 3.3.10.1 + - server: https://viralvariant.anses.fr/ + state: missing + version: 3.3.10.1 + - id: toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regex1/1.0.0 + servers: + - server: http://apostl.moffitt.org/ + state: missing + - server: http://mbac.gmu.edu:8080/ + state: missing + - server: https://vm-chemflow-francegrille.eu/ + state: missing + - server: https://iris.angers.inra.fr/galaxypub-cfbp + state: missing + - server: https://hyperbrowser.uio.no/coloc-stats + state: missing + - server: https://galaxy.mesocentre.uca.fr + state: missing + - server: https://galaxy.pasteur.fr/ + state: inexact + versions: + - 1.0.3 + - server: https://galaxytrakr.org/ + state: inexact + versions: + - 1.0.3 + - 1.0.1 + - server: http://igg.cloud.ba.infn.it/galaxy + state: missing + - server: https://galaxy.hyphy.org/ + state: missing + - server: https://www.immportgalaxy.org/ + state: missing + - server: http://galaxy.interactomix.com/ + state: missing + - server: https://galaxy-web.ipk-gatersleben.de + state: missing + - server: https://neo.engr.uconn.edu/ + state: missing + - server: https://mississippi.sorbonne-universite.fr + state: inexact + versions: + - 1.0.3 + - server: http://galaxy.inf.ethz.ch + state: missing + - server: https://palfinder.ls.manchester.ac.uk/ + state: missing + - server: http://pepsimili.e-nios.com:8080/ + state: missing + - server: https://usegalaxy.org.au + state: inexact + versions: + - 1.0.3 + - 1.0.1 + - 1.0.2 + - server: https://usegalaxy.be/ + state: exact + version: 1.0.0 - server: https://usegalaxy.cz/ state: inexact versions: - - 2.0.33+galaxy1 + - 1.0.3 - server: https://usegalaxy.eu state: exact - version: 1.16.36.3 + version: 1.0.0 - server: https://usegalaxy.fr/ - state: exact - version: 1.16.36.3 + state: inexact + versions: + - 1.0.3 + - 1.0.1 + - 1.0.2 - server: https://usegalaxy.no/ - state: exact - version: 1.16.36.3 + state: inexact + versions: + - 1.0.3 - server: https://usegalaxy.org state: exact - version: 1.16.36.3 + version: 1.0.0 - server: https://viralvariant.anses.fr/ state: missing - version: 1.16.36.3 - - id: toolshed.g2.bx.psu.edu/repos/galaxyp/peptideshaker/search_gui/3.3.10.1 + version: 1.0.0 + - id: toolshed.g2.bx.psu.edu/repos/galaxyp/unipept/unipept/4.0.0 servers: - server: http://apostl.moffitt.org/ state: missing @@ -80885,11 +78440,17 @@ - server: https://hyperbrowser.uio.no/coloc-stats state: missing - server: https://galaxy.mesocentre.uca.fr - state: missing + state: inexact + versions: + - 4.5.1 + - 6.2.4+galaxy0 + - 4.3.0 - server: https://galaxy.pasteur.fr/ state: missing - server: https://galaxytrakr.org/ - state: missing + state: inexact + versions: + - 4.5.0 - server: http://igg.cloud.ba.infn.it/galaxy state: missing - server: https://galaxy.hyphy.org/ @@ -80900,8 +78461,6 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr @@ -80912,35 +78471,50 @@ state: missing - server: http://pepsimili.e-nios.com:8080/ state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - server: https://usegalaxy.org.au - state: exact - version: 3.3.10.1 + state: inexact + versions: + - 4.5.1 + - 6.2.4+galaxy0 + - 4.3.0 + - 4.5.0 + - 6.2.4+galaxy1 + - 2.0.1 - server: https://usegalaxy.be/ state: exact - version: 3.3.10.1 + version: 4.0.0 - server: https://usegalaxy.cz/ state: inexact versions: - - 4.0.41+galaxy1 - - 4.0.41+galaxy0 + - 4.5.1 + - 6.2.4+galaxy0 + - 4.3.0 + - 6.2.4+galaxy1 + - 2.0.1 - server: https://usegalaxy.eu state: exact - version: 3.3.10.1 + version: 4.0.0 - server: https://usegalaxy.fr/ - state: exact - version: 3.3.10.1 + state: inexact + versions: + - 4.5.1 + - 6.2.4+galaxy0 + - 6.2.4+galaxy1 - server: https://usegalaxy.no/ state: exact - version: 3.3.10.1 + version: 4.0.0 - server: https://usegalaxy.org - state: exact - version: 3.3.10.1 + state: inexact + versions: + - 4.5.1 + - 6.2.4+galaxy0 + - 4.3.0 + - 6.2.4+galaxy1 + - 2.0.1 - server: https://viralvariant.anses.fr/ state: missing - version: 3.3.10.1 - - id: toolshed.g2.bx.psu.edu/repos/galaxyp/unipept/unipept/6.2.4+galaxy1 + version: 4.0.0 + - id: toolshed.g2.bx.psu.edu/repos/galaxyp/unipept/unipept/4.3.0 servers: - server: http://apostl.moffitt.org/ state: missing @@ -80953,11 +78527,8 @@ - server: https://hyperbrowser.uio.no/coloc-stats state: missing - server: https://galaxy.mesocentre.uca.fr - state: inexact - versions: - - 6.2.4+galaxy0 - - 4.3.0 - - 4.5.1 + state: exact + version: 4.3.0 - server: https://galaxy.pasteur.fr/ state: missing - server: https://galaxytrakr.org/ @@ -80974,8 +78545,6 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr @@ -80986,35 +78555,34 @@ state: missing - server: http://pepsimili.e-nios.com:8080/ state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - server: https://usegalaxy.org.au state: exact - version: 6.2.4+galaxy1 + version: 4.3.0 - server: https://usegalaxy.be/ state: exact - version: 6.2.4+galaxy1 + version: 4.3.0 - server: https://usegalaxy.cz/ state: exact - version: 6.2.4+galaxy1 + version: 4.3.0 - server: https://usegalaxy.eu state: exact - version: 6.2.4+galaxy1 + version: 4.3.0 - server: https://usegalaxy.fr/ - state: exact - version: 6.2.4+galaxy1 - - server: https://usegalaxy.no/ state: inexact versions: - - 4.3.0 - - 4.0.0 + - 4.5.1 + - 6.2.4+galaxy0 + - 6.2.4+galaxy1 + - server: https://usegalaxy.no/ + state: exact + version: 4.3.0 - server: https://usegalaxy.org state: exact - version: 6.2.4+galaxy1 + version: 4.3.0 - server: https://viralvariant.anses.fr/ state: missing - version: 6.2.4+galaxy1 - - id: toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.0.0 + version: 4.3.0 + - id: toolshed.g2.bx.psu.edu/repos/galaxyp/unipept/unipept/4.5.0 servers: - server: http://apostl.moffitt.org/ state: missing @@ -81027,15 +78595,16 @@ - server: https://hyperbrowser.uio.no/coloc-stats state: missing - server: https://galaxy.mesocentre.uca.fr - state: missing - - server: https://galaxy.pasteur.fr/ state: inexact versions: - - 3.3.1 + - 4.5.1 + - 6.2.4+galaxy0 + - 4.3.0 + - server: https://galaxy.pasteur.fr/ + state: missing - server: https://galaxytrakr.org/ - state: inexact - versions: - - 3.3.0 + state: exact + version: 4.5.0 - server: http://igg.cloud.ba.infn.it/galaxy state: missing - server: https://galaxy.hyphy.org/ @@ -81046,8 +78615,6 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr @@ -81058,41 +78625,46 @@ state: missing - server: http://pepsimili.e-nios.com:8080/ state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - server: https://usegalaxy.org.au state: exact - version: 3.0.0 + version: 4.5.0 - server: https://usegalaxy.be/ state: exact - version: 3.0.0 + version: 4.5.0 - server: https://usegalaxy.cz/ state: inexact versions: - - 3.3.1 - - 3.3.0 + - 4.5.1 + - 6.2.4+galaxy0 + - 4.3.0 + - 6.2.4+galaxy1 + - 2.0.1 - server: https://usegalaxy.eu state: exact - version: 3.0.0 + version: 4.5.0 - server: https://usegalaxy.fr/ state: inexact versions: - - 3.3.1 - - 3.3.0 - - 3.3.2 - - 3.1.1 - - 3.2.0 - - 3.0.1 + - 4.5.1 + - 6.2.4+galaxy0 + - 6.2.4+galaxy1 - server: https://usegalaxy.no/ - state: exact - version: 3.0.0 + state: inexact + versions: + - 4.3.0 + - 4.0.0 - server: https://usegalaxy.org - state: exact - version: 3.0.0 + state: inexact + versions: + - 4.5.1 + - 6.2.4+galaxy0 + - 4.3.0 + - 6.2.4+galaxy1 + - 2.0.1 - server: https://viralvariant.anses.fr/ state: missing - version: 3.0.0 - - id: toolshed.g2.bx.psu.edu/repos/iuc/sqlite_to_tabular/sqlite_to_tabular/2.0.0 + version: 4.5.0 + - id: toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.0.0 servers: - server: http://apostl.moffitt.org/ state: missing @@ -81109,9 +78681,11 @@ - server: https://galaxy.pasteur.fr/ state: inexact versions: - - 3.2.0 + - 3.3.1 - server: https://galaxytrakr.org/ - state: missing + state: inexact + versions: + - 3.3.0 - server: http://igg.cloud.ba.infn.it/galaxy state: missing - server: https://galaxy.hyphy.org/ @@ -81122,8 +78696,6 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr @@ -81134,45 +78706,59 @@ state: missing - server: http://pepsimili.e-nios.com:8080/ state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - server: https://usegalaxy.org.au state: exact - version: 2.0.0 + version: 3.0.0 - server: https://usegalaxy.be/ state: exact - version: 2.0.0 + version: 3.0.0 - server: https://usegalaxy.cz/ - state: exact - version: 2.0.0 + state: inexact + versions: + - 3.3.1 + - 3.3.0 - server: https://usegalaxy.eu state: exact - version: 2.0.0 + version: 3.0.0 - server: https://usegalaxy.fr/ state: inexact versions: - - 3.2.1 + - 3.3.1 + - 3.3.0 + - 3.3.2 + - 3.1.1 + - 3.2.0 + - 3.0.1 - server: https://usegalaxy.no/ state: exact - version: 2.0.0 + version: 3.0.0 - server: https://usegalaxy.org state: exact - version: 2.0.0 + version: 3.0.0 - server: https://viralvariant.anses.fr/ state: missing - version: 2.0.0 + version: 3.0.0 symlink: null tags: - microgalaxy - time: null - time_estimation: 2h - title: Metaproteomics tutorial + time_estimation: 1h + title: 'metaQuantome 1: Data creation' tools: + - Cut1 + - Filter1 + - Grep1 + - Remove beginning1 + - toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/1.1.3 + - toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/1.1.2 + - toolshed.g2.bx.psu.edu/repos/galaxyp/flashlfq/flashlfq/1.0.3.0 + - toolshed.g2.bx.psu.edu/repos/galaxyp/msconvert/msconvert/3.0.19052.0 - toolshed.g2.bx.psu.edu/repos/galaxyp/peptideshaker/peptide_shaker/1.16.36.3 - toolshed.g2.bx.psu.edu/repos/galaxyp/peptideshaker/search_gui/3.3.10.1 - - toolshed.g2.bx.psu.edu/repos/galaxyp/unipept/unipept/6.2.4+galaxy1 + - toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regex1/1.0.0 + - toolshed.g2.bx.psu.edu/repos/galaxyp/unipept/unipept/4.0.0 + - toolshed.g2.bx.psu.edu/repos/galaxyp/unipept/unipept/4.3.0 + - toolshed.g2.bx.psu.edu/repos/galaxyp/unipept/unipept/4.5.0 - toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.0.0 - - toolshed.g2.bx.psu.edu/repos/iuc/sqlite_to_tabular/sqlite_to_tabular/2.0.0 topic_name: proteomics topic_name_human: Proteomics tours: false @@ -81180,164 +78766,141 @@ slides: [] tutorial: [] video: false - tutorial_name: metaproteomics + tutorial_name: metaquantome-data-creation type: tutorial - url: https://training.galaxyproject.org//topics/proteomics/tutorials/metaproteomics/tutorial.html + url: https://training.galaxyproject.org//topics/proteomics/tutorials/metaquantome-data-creation/tutorial.html urls: - hands_on: https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/metaproteomics/tutorial.json - slides: https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/metaproteomics/tutorial.json - version: 42 - video: true - video_versions: 1 + hands_on: https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/metaquantome-data-creation/tutorial.json + slides: https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/metaquantome-data-creation/tutorial.json + version: 20 + video: false + video_versions: 0 video_view: 0 - visit_duration: 590 - visitors: 3109 + visit_duration: 569 + visitors: 958 workflows: - - creators: - - class: Person - identifier: 0000-0001-9818-0537 - name: Subina P Mehta - description: Metaproteomics 101 tutorial + - creators: [] + description: metaquantome-data-creation features: comments: false parameters: false - report: - markdown: ' - - # Workflow Execution Report - - - ## Workflow Inputs - - ```galaxy - - invocation_inputs() - - ``` - - - ## Workflow Outputs - - ```galaxy - - invocation_outputs() - - ``` - - - ## Workflow - - ```galaxy - - workflow_display() - - ``` - - ' + report: null subworkflows: false graph_dot: "digraph main {\n node [fontname=\"Atkinson Hyperlegible\", shape=box,\ \ color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n edge [fontname=\"\ - Atkinson Hyperlegible\"];\n 0[color=lightblue,label=\"\u2139\uFE0F Input Dataset\\\ - nSixgill generated protein FASTA File\"]\n 1[color=lightblue,label=\"\u2139\ - \uFE0F Input Collection\\nDataset Collection of Bering Strait MGF Files\"]\n\ - \ 2[color=lightblue,label=\"\u2139\uFE0F Input Dataset\\nGene Ontology Terms\ - \ Selected\"]\n 3[label=\"Search GUI\"]\n 0 -> 3 [label=\"output\"]\n 1 ->\ - 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]\n 12[label=\"GO Terms: Cellular Localization\"]\n 8 -> 12 [label=\"sqlitedb\"\ - ]\n}" + Atkinson Hyperlegible\"];\n 0[color=lightblue,label=\"\u2139\uFE0F Input Collection\\\ + nInput dataset collection\"]\n 1[color=lightblue,label=\"\u2139\uFE0F Input\ + \ Dataset\\nExperiment_Design\"]\n 2[color=lightblue,label=\"\u2139\uFE0F Input\ + \ Dataset\\nFASTA_db\"]\n 3[label=\"mzml to mgf\"]\n 0 -> 3 [label=\"output\"\ + ]\n 4[label=\"Search GUI\"]\n 2 -> 4 [label=\"output\"]\n 3 -> 4 [label=\"\ + output\"]\n 5[label=\"Peptide Shaker\"]\n 4 -> 5 [label=\"searchgui_results\"\ + ]\n 6[label=\"Replace Text\"]\n 5 -> 6 [label=\"output_psm\"]\n 7[label=\"\ + Remove beginning\"]\n 5 -> 7 [label=\"output_peptides\"]\n 8[label=\"Unipept_lca\"\ + ]\n 5 -> 8 [label=\"output_peptides\"]\n 9[label=\"FlashLFQ\"]\n 1 -> 9 [label=\"\ + output\"]\n 6 -> 9 [label=\"outfile\"]\n 0 -> 9 [label=\"output\"]\n 10[label=\"\ + Unipept_peptinfo\"]\n 7 -> 10 [label=\"out_file1\"]\n 11[label=\"Replace Text\"\ + ]\n 8 -> 11 [label=\"output_tsv\"]\n 12[label=\"Regex Find And Replace\"]\n\ + \ 9 -> 12 [label=\"quantifiedPeptides\"]\n 13[label=\"selecting EC column\"\ + ]\n 10 -> 13 [label=\"output_ec_tsv\"]\n 14[label=\"filter 5% All_funct\"\ + ]\n 10 -> 14 [label=\"output_go_tsv\"]\n 15[label=\"GO_EC\"]\n 13 -> 15 [label=\"\ + out_file1\"]\n 16[label=\"GO_BP\"]\n 14 -> 16 [label=\"output\"]\n 17[label=\"\ + GO_CC\"]\n 14 -> 17 [label=\"output\"]\n 18[label=\"GO_MF\"]\n 14 -> 18 [label=\"\ + output\"]\n}" history: - 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short_hash: 2e53c11bf - unix: '1502111726' - - hash: f6e08e286c8531ae382c7db6128ba2f419dc7d03 - message: Metaproteomics tutorial (#393) + short_hash: a45af5ea9 + unix: '1602469238' + - hash: c042f2b7195179d8e45abac8d41122ab94538264 + message: planemo workflow-to-tutorial num: 1 - short_hash: f6e08e286 - unix: '1498643437' + short_hash: c042f2b71 + unix: '1600357793' inputs: - - annotation: '' + - annotation: metaquantome-data-creation content_id: null errors: null id: 0 input_connections: {} - inputs: - - description: '' - name: Sixgill generated protein FASTA File - label: Sixgill generated protein FASTA File - name: Input dataset + inputs: [] + label: null + name: Input dataset collection outputs: [] position: - left: 0 - top: 0.59375 + bottom: 134 + height: 81 + left: 347.53125 + right: 547.53125 + top: 53 + width: 200 + x: 347.53125 + y: 53 tool_id: null - tool_state: '{"optional": false, "tag": null}' + tool_state: '{"optional": false, "collection_type": "list"}' tool_version: null - type: data_input - uuid: a3a731aa-022c-4d9b-89d3-475fc855e82e - when: null + type: data_collection_input + uuid: a00a1b36-1600-4833-8cd3-df6ceec33349 workflow_outputs: [] - annotation: '' content_id: null @@ -81346,20 +78909,24 @@ input_connections: {} inputs: - description: '' - name: Dataset Collection of Bering Strait MGF Files - label: Dataset Collection of Bering Strait MGF Files - name: Input dataset collection + name: Experiment_Design + label: Experiment_Design + name: Input dataset outputs: [] position: - left: 2.953125 - top: 159.53125 + bottom: 401.96875 + height: 81 + left: 525.640625 + right: 725.640625 + top: 320.96875 + width: 200 + x: 525.640625 + y: 320.96875 tool_id: null - tool_state: '{"optional": false, "tag": null, "collection_type": "list", "fields": - null, "column_definitions": null}' + tool_state: '{"optional": false}' tool_version: null - type: data_collection_input - uuid: ae22c03f-32ee-47af-9c46-064f32e93ee9 - when: null + type: data_input + uuid: 8dd6e50f-9951-4e8e-af47-783625e46786 workflow_outputs: [] - annotation: '' content_id: null @@ -81368,104 +78935,105 @@ input_connections: {} inputs: - description: '' - name: Gene Ontology Terms (Selected) - label: Gene Ontology Terms (Selected) + name: FASTA_db + label: FASTA_db name: Input dataset outputs: [] position: - left: 1210.40625 - top: 0 + bottom: 629.03125 + height: 61 + left: -408 + right: -208 + top: 568.03125 + width: 200 + x: -408 + y: 568.03125 tool_id: null - tool_state: '{"optional": false, "tag": null}' + tool_state: '{"optional": false}' tool_version: null type: data_input - uuid: 1dfff1a0-d645-4272-b524-39538fcdc95b - when: null + uuid: a9156286-a9e9-402f-b1d9-3e55ddd86ce8 workflow_outputs: [] - license: CC-BY-4.0 - mermaid: "flowchart TD\n 0[\"\u2139\uFE0F Input Dataset\\nSixgill generated protein\ - \ FASTA File\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"\u2139\uFE0F\ - \ Input Collection\\nDataset Collection of Bering Strait MGF Files\"];\n style\ - \ 1 stroke:#2c3143,stroke-width:4px;\n 2[\"\u2139\uFE0F Input Dataset\\nGene\ - \ Ontology Terms Selected\"];\n style 2 stroke:#2c3143,stroke-width:4px;\n\ - \ 3[\"Search GUI\"];\n 0 -->|output| 3;\n 1 -->|output| 3;\n 7516674a-b5aa-45b5-b2e8-38c1889ad2e9[\"\ - Output\\nSearch GUI on input dataset(s)\"];\n 3 --> 7516674a-b5aa-45b5-b2e8-38c1889ad2e9;\n\ - \ style 7516674a-b5aa-45b5-b2e8-38c1889ad2e9 stroke:#2c3143,stroke-width:4px;\n\ - \ 4[\"Peptide Shaker\"];\n 3 -->|searchgui_results| 4;\n ddfe8d62-a7b7-4e30-a84d-91c92fc60bd0[\"\ - Output\\nPeptide Shaker on input dataset(s): mzidentML file\"];\n 4 --> ddfe8d62-a7b7-4e30-a84d-91c92fc60bd0;\n\ - \ style ddfe8d62-a7b7-4e30-a84d-91c92fc60bd0 stroke:#2c3143,stroke-width:4px;\n\ - \ 5[\"Query Tabular Select Peptides\"];\n 4 -->|output_psm| 5;\n 6[\"Unipept\ - \ pept2prot\"];\n 5 -->|output| 6;\n 7[\"Unipept lca\"];\n 5 -->|output|\ - \ 7;\n 8[\"Go Pop2Prot DB\"];\n 2 -->|output| 8;\n 6 -->|output_tsv| 8;\n\ - \ 6 -->|output_tsv| 8;\n 4 -->|output_psm| 8;\n 9[\"Genera | PSMs | Peptides\"\ - ];\n 4 -->|output_psm| 9;\n 7 -->|output_tsv| 9;\n 10[\"GO Terms: Biological\ - 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name: metaquantome_sample owner: galaxyp revisions: 49a957fb353a tool_panel_section_label: Proteomics tool_shed_url: https://toolshed.g2.bx.psu.edu/ + - name: metaquantome_sample + owner: galaxyp + revisions: 06f6826d380c + tool_panel_section_label: Proteomics + tool_shed_url: https://toolshed.g2.bx.psu.edu/ - name: metaquantome_stat owner: galaxyp revisions: 982a442a98dd tool_panel_section_label: Proteomics tool_shed_url: https://toolshed.g2.bx.psu.edu/ + - name: metaquantome_stat + owner: galaxyp + revisions: b9d453dca8d3 + tool_panel_section_label: Proteomics + tool_shed_url: https://toolshed.g2.bx.psu.edu/ - name: metaquantome_viz owner: galaxyp revisions: 02da24eac445 tool_panel_section_label: Proteomics tool_shed_url: https://toolshed.g2.bx.psu.edu/ + - name: metaquantome_viz + owner: galaxyp + revisions: 8bd7734309f6 + tool_panel_section_label: Proteomics + tool_shed_url: https://toolshed.g2.bx.psu.edu/ admin_install_yaml: "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies:\ \ true\ninstall_resolver_dependencies: true\ntools:\n- name: metaquantome_db\n\ \ owner: galaxyp\n revisions: 7c45aa1c9464\n tool_panel_section_label: Proteomics\n\ + \ tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: metaquantome_db\n \ + \ owner: galaxyp\n revisions: e63db1aa82ee\n tool_panel_section_label: Proteomics\n\ \ tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: metaquantome_expand\n\ \ owner: galaxyp\n revisions: eb65ab160a10\n tool_panel_section_label: Proteomics\n\ + \ tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: metaquantome_expand\n\ + \ owner: galaxyp\n revisions: 767c1d761aaf\n tool_panel_section_label: Proteomics\n\ \ tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: metaquantome_filter\n\ \ owner: galaxyp\n revisions: 7d1c20b315ff\n tool_panel_section_label: Proteomics\n\ + \ tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: metaquantome_filter\n\ + \ owner: galaxyp\n revisions: 35cc7ca0bdc7\n tool_panel_section_label: Proteomics\n\ \ tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: metaquantome_sample\n\ \ owner: galaxyp\n revisions: 49a957fb353a\n tool_panel_section_label: Proteomics\n\ + \ tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: metaquantome_sample\n\ + \ owner: galaxyp\n revisions: 06f6826d380c\n tool_panel_section_label: Proteomics\n\ \ tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: metaquantome_stat\n\ \ owner: galaxyp\n revisions: 982a442a98dd\n tool_panel_section_label: Proteomics\n\ + \ tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: metaquantome_stat\n\ + \ owner: galaxyp\n revisions: b9d453dca8d3\n tool_panel_section_label: Proteomics\n\ \ tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: metaquantome_viz\n\ \ owner: galaxyp\n revisions: 02da24eac445\n tool_panel_section_label: Proteomics\n\ + \ tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: metaquantome_viz\n\ + \ owner: galaxyp\n revisions: 8bd7734309f6\n tool_panel_section_label: Proteomics\n\ \ tool_shed_url: https://toolshed.g2.bx.psu.edu/\n" - api: https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/metaquantome-taxonomy/tutorial.json + api: https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/metaquantome-function/tutorial.json contributors: - email: subinamehta@gmail.com id: subinamehta @@ -82061,32 +79712,30 @@ name: Praveen Kumar page: https://training.galaxyproject.org/training-material/hall-of-fame/pravs3683/ url: https://training.galaxyproject.org/training-material/api/contributors/pravs3683.json - dir: topics/proteomics/tutorials/metaquantome-taxonomy + dir: topics/proteomics/tutorials/metaquantome-function edam_ontology: - topic_0121 - topic_3922 - topic_3941 - topic_3697 - topic_3174 - - topic_0637 edam_operation: - - Statistical inference - - Functional clustering - - Visualisation + - Filtering - Differential protein expression analysis - Principal component visualisation - - Heat map generation + - Visualisation + - Indexing + - Functional clustering - Quantification - Query and retrieval - - Filtering - - Indexing + - Statistical inference + - Heat map generation edam_topic: - Proteomics - Proteogenomics - Metatranscriptomics - Microbial ecology - Metagenomics - - Taxonomy exact_supported_servers: - UseGalaxy.be - UseGalaxy.eu @@ -82096,10 +79745,13 @@ - topic_name: proteomics tutorials: - metaproteomics - - metaquantome-function + type: internal + - topic_name: proteomics + tutorials: + - metaquantome-taxonomy type: internal hands_on: true - id: proteomics/metaquantome-taxonomy + id: proteomics/metaquantome-function inexact_supported_servers: - UseGalaxy.org.au - UseGalaxy.cz @@ -82110,32 +79762,33 @@ mermaid: false key_points: - All the inputs should have one column in common i.e. peptides. - - Learning different tools such as Unipept, MEGAN, MetaGOmics etc. for taxonomic - annotation of peptides will benefit. + - Functional annotation can be performed using GO terms and EC numbers + - Having basic knowledge regarding tools that can perform functional annotation + can come in handy layout: tutorial_hands_on level: Intermediate license: CC-BY-4.0 mod_date: '2024-03-15' objectives: - - A taxonomy and quantitational analysis of metaproteomic mass spectrometry data. - pageviews: 626 + - A functional and quantitational analysis of metaproteomic mass spectrometry data. + pageviews: 646 pub_date: '2020-10-29' questions: - - How do I look at differentially expressed taxa? - - Can we get top 5 or 10 taxa present in the sample? + - How do I look at differentially expressed proteins? + - How do I get top 5 or 10 function present in the sample? - How can I visualize my results? requirements: - topic_name: proteomics tutorials: - metaquantome-data-creation type: internal - short_id: T00224 + short_id: T00223 short_tools: - - metaquantome_viz - metaquantome_expand + - metaquantome_viz + - metaquantome_filter - metaquantome_db - metaquantome_sample - - metaquantome_filter - metaquantome_stat slides: false slides_recordings: false @@ -82202,9 +79855,6 @@ - name: IPK Galaxy Blast Suite url: https://galaxy-web.ipk-gatersleben.de usegalaxy: false - - name: Lebanese University Galaxy - 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2.0.1+galaxy0 - - 2.0.0-2 - 2.0.2+galaxy0 - 2.0.0-1 + - 2.0.0-2 - server: https://usegalaxy.be/ state: exact version: 2.0.0-0 - server: https://usegalaxy.cz/ state: inexact versions: + - 2.0.4+galaxy0 - 2.0.2+galaxy0 - server: https://usegalaxy.eu state: exact @@ -82618,7 +80498,7 @@ - server: https://viralvariant.anses.fr/ state: missing version: 2.0.0-0 - - id: toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_viz/metaquantome_viz/2.0.0-0 + - id: toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_stat/metaquantome_stat/2.0.2+galaxy0 servers: - server: http://apostl.moffitt.org/ state: missing @@ -82646,8 +80526,6 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr @@ -82658,16 +80536,76 @@ state: missing - server: http://pepsimili.e-nios.com:8080/ state: missing - - server: https://galaxy.bio.di.uminho.pt/ + - 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server: https://galaxy.pasteur.fr/ + state: missing + - server: https://galaxytrakr.org/ + state: missing + - server: http://igg.cloud.ba.infn.it/galaxy + state: missing + - server: https://galaxy.hyphy.org/ + state: missing + - server: https://www.immportgalaxy.org/ + state: missing + - server: http://galaxy.interactomix.com/ + state: missing + - server: https://galaxy-web.ipk-gatersleben.de + state: missing + - server: https://neo.engr.uconn.edu/ + state: missing + - server: https://mississippi.sorbonne-universite.fr + state: missing + - server: http://galaxy.inf.ethz.ch + state: missing + - server: https://palfinder.ls.manchester.ac.uk/ + state: missing + - server: http://pepsimili.e-nios.com:8080/ state: missing - server: https://usegalaxy.org.au state: inexact versions: - - 2.0.4+galaxy0 - - 2.0.2+galaxy0 + - 2.0.1+galaxy0 - 2.0.0-1 + - 2.0.2+galaxy0 - 2.0.0-2 - - 2.0.1+galaxy0 + - 2.0.4+galaxy0 - server: https://usegalaxy.be/ state: exact version: 2.0.0-0 @@ -82675,14 +80613,15 @@ state: inexact versions: - 2.0.2+galaxy0 + - 2.0.4+galaxy0 - server: https://usegalaxy.eu state: exact version: 2.0.0-0 - server: https://usegalaxy.fr/ state: inexact versions: - - 2.0.4+galaxy0 - 2.0.2+galaxy0 + - 2.0.4+galaxy0 - server: https://usegalaxy.no/ state: inexact versions: @@ -82692,18 +80631,86 @@ - server: https://viralvariant.anses.fr/ state: missing version: 2.0.0-0 + - id: toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_viz/metaquantome_viz/2.0.2+galaxy0 + servers: + - server: http://apostl.moffitt.org/ + state: missing + - server: http://mbac.gmu.edu:8080/ + state: missing + - server: https://vm-chemflow-francegrille.eu/ + state: missing + - server: https://iris.angers.inra.fr/galaxypub-cfbp + state: missing + - server: https://hyperbrowser.uio.no/coloc-stats + state: missing + - server: https://galaxy.mesocentre.uca.fr + state: missing + - server: https://galaxy.pasteur.fr/ + state: missing + - server: https://galaxytrakr.org/ + state: missing + - server: http://igg.cloud.ba.infn.it/galaxy + state: missing + - server: https://galaxy.hyphy.org/ + state: missing + - server: https://www.immportgalaxy.org/ + state: missing + - server: http://galaxy.interactomix.com/ + state: missing + - server: https://galaxy-web.ipk-gatersleben.de + state: missing + - server: https://neo.engr.uconn.edu/ + state: missing + - server: https://mississippi.sorbonne-universite.fr + state: missing + - server: http://galaxy.inf.ethz.ch + state: missing + - server: https://palfinder.ls.manchester.ac.uk/ + state: missing + - server: http://pepsimili.e-nios.com:8080/ + state: missing + - server: https://usegalaxy.org.au + state: exact + version: 2.0.2+galaxy0 + - server: https://usegalaxy.be/ + state: exact + version: 2.0.2+galaxy0 + - server: https://usegalaxy.cz/ + state: exact + version: 2.0.2+galaxy0 + - server: https://usegalaxy.eu + state: exact + version: 2.0.2+galaxy0 + - server: https://usegalaxy.fr/ + state: exact + version: 2.0.2+galaxy0 + - server: https://usegalaxy.no/ + state: inexact + versions: + - 1.0.0-0 + - server: https://usegalaxy.org + state: missing + - server: https://viralvariant.anses.fr/ + state: missing + version: 2.0.2+galaxy0 symlink: null tags: - microgalaxy time_estimation: 1h - title: 'metaQuantome 3: Taxonomy' + title: 'metaQuantome 2: Function' tools: - toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_db/metaquantome_db/2.0.0-0 + - toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_db/metaquantome_db/2.0.2+galaxy0 - toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_expand/metaquantome_expand/2.0.0-0 + - toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_expand/metaquantome_expand/2.0.2+galaxy0 - toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_filter/metaquantome_filter/2.0.0-0 + - toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_filter/metaquantome_filter/2.0.2+galaxy0 - toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_sample/metaquantome_sample/2.0.0-0 + - toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_sample/metaquantome_sample/2.0.2+galaxy0 - toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_stat/metaquantome_stat/2.0.0-0 + - toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_stat/metaquantome_stat/2.0.2+galaxy0 - toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_viz/metaquantome_viz/2.0.0-0 + - toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_viz/metaquantome_viz/2.0.2+galaxy0 topic_name: proteomics topic_name_human: Proteomics tours: false @@ -82711,21 +80718,21 @@ slides: [] tutorial: [] video: false - tutorial_name: metaquantome-taxonomy + tutorial_name: metaquantome-function type: tutorial - url: https://training.galaxyproject.org//topics/proteomics/tutorials/metaquantome-taxonomy/tutorial.html + url: https://training.galaxyproject.org//topics/proteomics/tutorials/metaquantome-function/tutorial.html urls: - hands_on: https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/metaquantome-taxonomy/tutorial.json - slides: https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/metaquantome-taxonomy/tutorial.json + hands_on: https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/metaquantome-function/tutorial.json + slides: https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/metaquantome-function/tutorial.json version: 14 video: false video_versions: 0 video_view: 0 - visit_duration: 879 - visitors: 485 + visit_duration: 908 + visitors: 471 workflows: - creators: [] - description: metaquantome-taxonomy + description: metaquantome-function features: comments: false parameters: false @@ -82733,60 +80740,43 @@ subworkflows: false graph_dot: "digraph main {\n node [fontname=\"Atkinson Hyperlegible\", shape=box,\ \ color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n edge [fontname=\"\ - Atkinson Hyperlegible\"];\n 0[label=\"metaQuantome: create samples file\"]\n\ - \ 1[color=lightblue,label=\"\u2139\uFE0F Input Dataset\\nTaxa\"]\n 2[color=lightblue,label=\"\ - \u2139\uFE0F Input Dataset\\nIntensity\"]\n 3[label=\"metaQuantome: database\"\ - ]\n 4[label=\"metaQuantome: expand\"]\n 3 -> 4 [label=\"outfile\"]\n 2 ->\ - \ 4 [label=\"output\"]\n 1 -> 4 [label=\"output\"]\n 0 -> 4 [label=\"samples_file\"\ - ]\n 5[label=\"metaQuantome: filter\"]\n 4 -> 5 [label=\"outfile\"]\n 0 ->\ - \ 5 [label=\"samples_file\"]\n 6[label=\"metaQuantome: stat\"]\n 5 -> 6 [label=\"\ - 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- hash: 23fe00a8ab231d19aad201787b67446f76d72128 + - hash: 9d12ea3f6c949d0485659fb58ac0eda7c8814a74 + message: Update main_workflow.ga + num: 4 + short_hash: 9d12ea3f6 + unix: '1636475724' + - hash: b44e7f7c70e9638f17ca09238d425e0d8542d2a9 message: Update main_workflow.ga num: 3 - short_hash: 23fe00a8a - unix: '1636494825' - - hash: 6508b46449968fac766df69a5fee4295fa7e362f + short_hash: b44e7f7c7 + unix: '1603726491' + - hash: 619a94b389406eacd755598aa6ce4fab95f867f6 message: Update main_workflow.ga num: 2 - short_hash: 6508b4644 - unix: '1603158930' + short_hash: 619a94b38 + unix: '1603158677' - hash: 426a2746eee3945edd669f81b15b222493c46c82 message: tutorial skeletons generated by planemo num: 1 short_hash: 426a2746e unix: '1602853461' inputs: - - annotation: '' - content_id: null - errors: null - id: 1 - input_connections: {} - inputs: - - description: '' - name: Taxa - label: Taxa - name: Input dataset - outputs: [] - position: - left: 306.6493225097656 - top: 535.6250152587891 - tool_id: null - tool_state: '{"optional": false}' - tool_version: null - type: data_input - uuid: dea4289e-33b0-4215-8768-da6c65f8cd83 - workflow_outputs: - - label: null - output_name: output - uuid: fbf383a9-1774-483c-a1f1-1aa4d0a5659f - annotation: '' content_id: null errors: null @@ -82794,121 +80784,72 @@ input_connections: {} inputs: - description: '' - name: Intensity - label: Intensity - name: Input dataset - outputs: [] - position: - left: 304.6180725097656 - top: 659.6180877685547 - tool_id: null - tool_state: '{"optional": false}' - tool_version: null - type: data_input - uuid: be000472-cc47-456f-8791-b62c1a6308ec - workflow_outputs: - - label: null - output_name: output - uuid: 42e60127-395b-451f-a31c-191f6f82f2e0 - license: null - mermaid: "flowchart TD\n 0[\"metaQuantome: create samples file\"];\n 1[\"\u2139\ - \uFE0F Input Dataset\\nTaxa\"];\n style 1 stroke:#2c3143,stroke-width:4px;\n\ - \ 2[\"\u2139\uFE0F Input Dataset\\nIntensity\"];\n style 2 stroke:#2c3143,stroke-width:4px;\n\ - \ 3[\"metaQuantome: database\"];\n 4[\"metaQuantome: expand\"];\n 3 -->|outfile|\ - \ 4;\n 2 -->|output| 4;\n 1 -->|output| 4;\n 0 -->|samples_file| 4;\n 5[\"\ - metaQuantome: filter\"];\n 4 -->|outfile| 5;\n 0 -->|samples_file| 5;\n 6[\"\ - metaQuantome: stat\"];\n 5 -->|outfile| 6;\n 0 -->|samples_file| 6;\n 7[\"\ - T2-Bar-Plot\"];\n 6 -->|outfile| 7;\n 0 -->|samples_file| 7;\n 8[\"T7-T2_volcano-plot\"\ - ];\n 6 -->|outfile| 8;\n 0 -->|samples_file| 8;\n 9[\"T4-Bar-Plot\"];\n \ - \ 6 -->|outfile| 9;\n 0 -->|samples_file| 9;\n 10[\"T7-Bar-Plot\"];\n 6 -->|outfile|\ - \ 10;\n 0 -->|samples_file| 10;\n 11[\"T4-T2_volcano-plot\"];\n 6 -->|outfile|\ - \ 11;\n 0 -->|samples_file| 11;" - modified: 2026-05-21 00:30:25 +0000 - name: metaquantome-taxonomy-workflow - outputs: - - annotation: '' - content_id: toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_sample/metaquantome_sample/2.0.0-0 - errors: null - id: 0 - input_connections: {} - inputs: [] - label: null - name: 'metaQuantome: create samples file' - outputs: - - name: samples_file - type: tabular - position: - left: 324.2882385253906 - top: 367.9861297607422 - post_job_actions: {} - tool_id: toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_sample/metaquantome_sample/2.0.0-0 - tool_shed_repository: - changeset_revision: 40ca115438d2 - name: metaquantome_sample - owner: galaxyp - tool_shed: toolshed.g2.bx.psu.edu - tool_state: '{"__input_ext": "data", "chromInfo": "/opt/galaxy/tool-data/shared/ucsc/chrom/?.len", - "samps_args": {"samps_src": "build", "__current_case__": 0, "samps": [{"__index__": - 0, "group_name": "T2", "col_names": "T2_A1,T2_B1"}, {"__index__": 1, "group_name": - "T4", "col_names": "T4A_1,T4B_1"}, {"__index__": 2, "group_name": "T7", "col_names": - "T7A_1,T7B_1"}]}, "__page__": null, "__rerun_remap_job_id__": null}' - tool_version: 2.0.2+galaxy0 - type: tool - uuid: 8f8b3a5c-1ada-4b83-988b-46ff7e2e9468 - workflow_outputs: - - label: null - output_name: samples_file - uuid: d0b1aed8-8212-4e20-b1b4-b10bf76a394d - - annotation: '' - content_id: null - errors: null - id: 1 - input_connections: {} - inputs: - - description: '' - name: Taxa - label: Taxa + name: Functional file + label: Functional file name: Input dataset outputs: [] position: - left: 306.6493225097656 - top: 535.6250152587891 + bottom: 856.578125 + height: 81 + left: 397.546875 + right: 597.546875 + top: 775.578125 + width: 200 + x: 397.546875 + y: 775.578125 tool_id: null tool_state: '{"optional": false}' tool_version: null type: data_input - uuid: dea4289e-33b0-4215-8768-da6c65f8cd83 - workflow_outputs: - - label: null - output_name: output - uuid: fbf383a9-1774-483c-a1f1-1aa4d0a5659f + uuid: 7d436bc0-0e63-4445-93d5-5600c9a5c383 + workflow_outputs: [] - annotation: '' content_id: null errors: null - id: 2 + id: 3 input_connections: {} inputs: - description: '' - name: Intensity - label: Intensity + name: Intensity file + label: Intensity file name: Input dataset outputs: [] position: - left: 304.6180725097656 - top: 659.6180877685547 + bottom: 953.578125 + height: 61 + left: 391.5625 + right: 591.5625 + top: 892.578125 + width: 200 + x: 391.5625 + y: 892.578125 tool_id: null tool_state: '{"optional": false}' tool_version: null type: data_input - 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- email: subinamehta@gmail.com - id: subinamehta - joined: 2018-06 - linkedin: subinamehta - matrix: subinamehta:matrix.org - name: Subina Mehta - orcid: 0000-0001-9818-0537 - page: https://training.galaxyproject.org/training-material/hall-of-fame/subinamehta/ - twitter: Subina_Mehta - url: https://training.galaxyproject.org/training-material/api/contributors/subinamehta.json - email: tgriffin@umn.edu github: false id: timothygriffin @@ -83423,66 +81401,62 @@ orcid: 0000-0003-0984-0973 page: https://training.galaxyproject.org/training-material/hall-of-fame/pratikdjagtap/ url: https://training.galaxyproject.org/training-material/api/contributors/pratikdjagtap.json - - email: leith023@umn.edu - id: emmaleith - joined: 2019-07 - name: Emma Leith - page: https://training.galaxyproject.org/training-material/hall-of-fame/emmaleith/ - url: https://training.galaxyproject.org/training-material/api/contributors/emmaleith.json - - email: crane136@umn.edu - id: mariecrane - joined: 2019-05 - name: Marie Crane - 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- Differential protein expression analysis - - Principal component visualisation - - Heat map generation - - Quantification - - Query and retrieval - - Filtering - - Indexing + - Prediction and recognition edam_topic: - Proteomics - Proteogenomics - - Metatranscriptomics - - Microbial ecology - - Metagenomics + - Biodiversity + - Taxonomy exact_supported_servers: - - UseGalaxy.be + - UseGalaxy.org.au - UseGalaxy.eu + - UseGalaxy.org (Main) feedback_mean_note: null feedback_number: 0 - follow_up_training: - - topic_name: proteomics - tutorials: - - metaproteomics - type: internal - - topic_name: proteomics - tutorials: - - metaquantome-taxonomy - type: internal hands_on: true - id: proteomics/metaquantome-function + id: proteomics/metaproteomics inexact_supported_servers: - - UseGalaxy.org.au + - UseGalaxy.be - UseGalaxy.cz - UseGalaxy.fr - UseGalaxy.no @@ -83490,50 +81464,55 @@ mathjax: null mermaid: false key_points: - - All the inputs should have one column in common i.e. peptides. - - Functional annotation can be performed using GO terms and EC numbers - - Having basic knowledge regarding tools that can perform functional annotation - can come in handy + - Use dataset collections + - With SearchGUI and PeptideShaker you can gain access to multiple search engines + - Learning the basics of SQL queries can pay off layout: tutorial_hands_on - level: Intermediate license: CC-BY-4.0 - mod_date: '2024-03-15' + mod_date: '2026-05-11' objectives: - - A functional and quantitational analysis of metaproteomic mass spectrometry data. - pageviews: 626 - pub_date: '2020-10-29' + - A taxonomy and functional analysis of metaproteomic mass spectrometry data. + pageviews: 4985 + pub_date: '2017-06-28' questions: - - How do I look at differentially expressed proteins? - - How do I get top 5 or 10 function present in the sample? - - How can I visualize my results? - requirements: - - topic_name: proteomics - tutorials: - - metaquantome-data-creation - type: internal - short_id: T00223 + - How can I match metaproteomic mass spectrometry data to peptide sequences derived + from shotgun metagenomic data? + - How can I perform taxonomy analysis and visualize metaproteomics data? + - How can I perform functional analysis on this metaproteomics data? + recordings: + - captioners: + - emmaleith + date: '2021-02-15' + galaxy_version: '21.01' + length: 1H + speakers: + - pratikdjagtap + youtube_id: 3_yaPp-RCFw + short_id: T00221 short_tools: - - metaquantome_viz - - metaquantome_expand - - metaquantome_db - - metaquantome_sample - - metaquantome_filter - - metaquantome_stat + - query_tabular + - peptide_shaker + - unipept + - sqlite_to_tabular + - search_gui slides: false slides_recordings: false subtopic: multi-omics supported_servers: exact: - - name: UseGalaxy.be - url: https://usegalaxy.be/ - usegalaxy: false + - name: UseGalaxy.org.au + url: https://usegalaxy.org.au + usegalaxy: true - name: UseGalaxy.eu url: https://usegalaxy.eu usegalaxy: true - inexact: - - name: UseGalaxy.org.au - 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server: https://usegalaxy.org - state: missing + state: exact + version: 3.3.10.1 - server: https://viralvariant.anses.fr/ state: missing - version: 2.0.2+galaxy0 - - id: toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_stat/metaquantome_stat/2.0.0-0 + version: 3.3.10.1 + - id: toolshed.g2.bx.psu.edu/repos/galaxyp/unipept/unipept/6.2.4+galaxy1 servers: - server: http://apostl.moffitt.org/ state: missing @@ -84203,85 +81749,17 @@ - server: https://hyperbrowser.uio.no/coloc-stats state: missing - server: https://galaxy.mesocentre.uca.fr - state: missing - - server: https://galaxy.pasteur.fr/ - state: missing - - server: https://galaxytrakr.org/ - state: missing - - server: http://igg.cloud.ba.infn.it/galaxy - state: missing - - server: https://galaxy.hyphy.org/ - state: missing - - server: https://www.immportgalaxy.org/ - state: missing - - server: http://galaxy.interactomix.com/ - state: missing - - server: https://galaxy-web.ipk-gatersleben.de - state: missing - - server: http://galaxy.ul.edu.lb/ - 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- 2.0.2+galaxy0 - - 2.0.0-1 - - 2.0.0-2 - - 2.0.1+galaxy0 + state: exact + version: 3.0.0 - server: https://usegalaxy.be/ state: exact - version: 2.0.0-0 + version: 3.0.0 - server: https://usegalaxy.cz/ state: inexact versions: - - 2.0.2+galaxy0 + - 3.3.1 + - 3.3.0 - server: https://usegalaxy.eu state: exact - version: 2.0.0-0 + version: 3.0.0 - server: https://usegalaxy.fr/ state: inexact versions: - - 2.0.4+galaxy0 - - 2.0.2+galaxy0 + - 3.3.1 + - 3.3.0 + - 3.3.2 + - 3.1.1 + - 3.2.0 + - 3.0.1 - server: https://usegalaxy.no/ - state: inexact - versions: - - 1.0.0-0 + state: exact + version: 3.0.0 - server: https://usegalaxy.org - state: missing + state: exact + version: 3.0.0 - server: https://viralvariant.anses.fr/ state: missing - version: 2.0.0-0 - - id: toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_viz/metaquantome_viz/2.0.2+galaxy0 + version: 3.0.0 + - id: toolshed.g2.bx.psu.edu/repos/iuc/sqlite_to_tabular/sqlite_to_tabular/2.0.0 servers: - server: http://apostl.moffitt.org/ state: missing @@ -84419,7 +81895,9 @@ - server: https://galaxy.mesocentre.uca.fr state: missing - server: https://galaxy.pasteur.fr/ - state: missing + state: inexact + versions: + - 3.2.0 - server: https://galaxytrakr.org/ state: missing - server: http://igg.cloud.ba.infn.it/galaxy @@ -84432,8 +81910,6 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr @@ -84444,50 +81920,43 @@ state: missing - server: http://pepsimili.e-nios.com:8080/ state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - server: https://usegalaxy.org.au state: exact - version: 2.0.2+galaxy0 + version: 2.0.0 - server: https://usegalaxy.be/ state: exact - version: 2.0.2+galaxy0 + version: 2.0.0 - server: https://usegalaxy.cz/ state: exact - version: 2.0.2+galaxy0 + version: 2.0.0 - server: https://usegalaxy.eu state: exact - version: 2.0.2+galaxy0 + version: 2.0.0 - server: https://usegalaxy.fr/ - state: exact - version: 2.0.2+galaxy0 - - server: https://usegalaxy.no/ state: inexact versions: - - 1.0.0-0 + - 3.2.1 + - server: https://usegalaxy.no/ + state: exact + version: 2.0.0 - server: https://usegalaxy.org - state: missing + state: exact + version: 2.0.0 - server: https://viralvariant.anses.fr/ state: missing - version: 2.0.2+galaxy0 + version: 2.0.0 symlink: null tags: - microgalaxy - time_estimation: 1h - title: 'metaQuantome 2: Function' + time: null + time_estimation: 2h + title: Metaproteomics tutorial tools: - - toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_db/metaquantome_db/2.0.0-0 - - toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_db/metaquantome_db/2.0.2+galaxy0 - - toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_expand/metaquantome_expand/2.0.0-0 - - toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_expand/metaquantome_expand/2.0.2+galaxy0 - - toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_filter/metaquantome_filter/2.0.0-0 - - toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_filter/metaquantome_filter/2.0.2+galaxy0 - - toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_sample/metaquantome_sample/2.0.0-0 - - toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_sample/metaquantome_sample/2.0.2+galaxy0 - - toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_stat/metaquantome_stat/2.0.0-0 - - toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_stat/metaquantome_stat/2.0.2+galaxy0 - - toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_viz/metaquantome_viz/2.0.0-0 - - toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_viz/metaquantome_viz/2.0.2+galaxy0 + - toolshed.g2.bx.psu.edu/repos/galaxyp/peptideshaker/peptide_shaker/1.16.36.3 + - toolshed.g2.bx.psu.edu/repos/galaxyp/peptideshaker/search_gui/3.3.10.1 + - toolshed.g2.bx.psu.edu/repos/galaxyp/unipept/unipept/6.2.4+galaxy1 + - toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.0.0 + - toolshed.g2.bx.psu.edu/repos/iuc/sqlite_to_tabular/sqlite_to_tabular/2.0.0 topic_name: proteomics topic_name_human: Proteomics tours: false @@ -84495,630 +81964,793 @@ slides: [] tutorial: [] video: false - tutorial_name: metaquantome-function + tutorial_name: metaproteomics type: tutorial - url: https://training.galaxyproject.org//topics/proteomics/tutorials/metaquantome-function/tutorial.html + url: https://training.galaxyproject.org//topics/proteomics/tutorials/metaproteomics/tutorial.html urls: - hands_on: https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/metaquantome-function/tutorial.json - slides: https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/metaquantome-function/tutorial.json - version: 14 - video: false - video_versions: 0 + hands_on: https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/metaproteomics/tutorial.json + slides: https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/metaproteomics/tutorial.json + version: 42 + video: true + video_versions: 1 video_view: 0 - visit_duration: 928 - visitors: 452 + visit_duration: 611 + visitors: 3191 workflows: - - creators: [] - description: metaquantome-function + - creators: + - class: Person + identifier: 0000-0001-9818-0537 + name: Subina P Mehta + description: Metaproteomics 101 tutorial features: comments: false parameters: false - report: null + report: + markdown: ' + + # Workflow Execution Report + + + ## Workflow Inputs + + ```galaxy + + invocation_inputs() + + ``` + + + ## Workflow Outputs + + ```galaxy + + invocation_outputs() + + ``` + + + ## Workflow + + ```galaxy + + workflow_display() + + ``` + + ' subworkflows: false graph_dot: "digraph main {\n node [fontname=\"Atkinson Hyperlegible\", shape=box,\ \ color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n edge [fontname=\"\ - Atkinson Hyperlegible\"];\n 0[label=\"metaQuantome: database\"]\n 1[label=\"\ - metaQuantome: create samples file\"]\n 2[color=lightblue,label=\"\u2139\uFE0F\ - \ Input Dataset\\nFunctional file\"]\n 3[color=lightblue,label=\"\u2139\uFE0F\ - \ Input Dataset\\nIntensity file\"]\n 4[label=\"metaQuantome: expand\"]\n \ - \ 0 -> 4 [label=\"outfile\"]\n 3 -> 4 [label=\"output\"]\n 2 -> 4 [label=\"\ - output\"]\n 1 -> 4 [label=\"samples_file\"]\n 5[label=\"metaQuantome: filter\"\ - ]\n 4 -> 5 [label=\"outfile\"]\n 1 -> 5 [label=\"samples_file\"]\n 6[label=\"\ - metaQuantome: stat\"]\n 5 -> 6 [label=\"outfile\"]\n 1 -> 6 [label=\"samples_file\"\ - ]\n 7[label=\"T2-Bar-Plot\"]\n 6 -> 7 [label=\"outfile\"]\n 6 -> 7 [label=\"\ - outfile\"]\n 8[label=\"T4-Bar-Plot\"]\n 6 -> 8 [label=\"outfile\"]\n 1 ->\ - \ 8 [label=\"samples_file\"]\n 9[label=\"T7-Bar-Plot\"]\n 6 -> 9 [label=\"\ - outfile\"]\n 1 -> 9 [label=\"samples_file\"]\n 10[label=\"T7-T2-Volcano-Plot\"\ - ]\n 6 -> 10 [label=\"outfile\"]\n 1 -> 10 [label=\"samples_file\"]\n 11[label=\"\ - T4-T2-Volcano-Plot\"]\n 6 -> 11 [label=\"outfile\"]\n 1 -> 11 [label=\"samples_file\"\ + Atkinson Hyperlegible\"];\n 0[color=lightblue,label=\"\u2139\uFE0F Input Dataset\\\ + nSixgill generated protein FASTA File\"]\n 1[color=lightblue,label=\"\u2139\ + \uFE0F Input Collection\\nDataset Collection of Bering Strait MGF Files\"]\n\ + \ 2[color=lightblue,label=\"\u2139\uFE0F Input Dataset\\nGene Ontology Terms\ + \ Selected\"]\n 3[label=\"Search GUI\"]\n 0 -> 3 [label=\"output\"]\n 1 ->\ + \ 3 [label=\"output\"]\n k7516674ab5aa45b5b2e838c1889ad2e9[color=lightseagreen,label=\"\ + Output\\nSearch GUI on input dataset(s)\"]\n 3 -> k7516674ab5aa45b5b2e838c1889ad2e9\n\ + \ 4[label=\"Peptide Shaker\"]\n 3 -> 4 [label=\"searchgui_results\"]\n kddfe8d62a7b74e30a84d91c92fc60bd0[color=lightseagreen,label=\"\ + Output\\nPeptide Shaker on input dataset(s): mzidentML file\"]\n 4 -> kddfe8d62a7b74e30a84d91c92fc60bd0\n\ + \ 5[label=\"Query Tabular Select Peptides\"]\n 4 -> 5 [label=\"output_psm\"\ + ]\n 6[label=\"Unipept pept2prot\"]\n 5 -> 6 [label=\"output\"]\n 7[label=\"\ + Unipept lca\"]\n 5 -> 7 [label=\"output\"]\n 8[label=\"Go Pop2Prot DB\"]\n\ + \ 2 -> 8 [label=\"output\"]\n 6 -> 8 [label=\"output_tsv\"]\n 6 -> 8 [label=\"\ + output_tsv\"]\n 4 -> 8 [label=\"output_psm\"]\n 9[label=\"Genera | PSMs |\ + \ Peptides\"]\n 4 -> 9 [label=\"output_psm\"]\n 7 -> 9 [label=\"output_tsv\"\ + ]\n 10[label=\"GO Terms: Biological Processes\"]\n 8 -> 10 [label=\"sqlitedb\"\ + ]\n 11[label=\"GO Terms: Molecular Functions\"]\n 8 -> 11 [label=\"sqlitedb\"\ + ]\n 12[label=\"GO Terms: Cellular Localization\"]\n 8 -> 12 [label=\"sqlitedb\"\ ]\n}" history: - 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short_hash: 426a2746e - unix: '1602853461' + short_hash: f6e08e286 + unix: '1498643437' inputs: - annotation: '' content_id: null errors: null - id: 2 + id: 0 input_connections: {} inputs: - description: '' - name: Functional file - label: Functional file + name: Sixgill generated protein FASTA File + label: Sixgill generated protein FASTA File name: Input dataset outputs: [] position: - bottom: 856.578125 - height: 81 - left: 397.546875 - right: 597.546875 - top: 775.578125 - width: 200 - x: 397.546875 - y: 775.578125 + left: 0 + top: 0.59375 tool_id: null - tool_state: '{"optional": false}' + tool_state: '{"optional": false, "tag": null}' tool_version: null type: data_input - uuid: 7d436bc0-0e63-4445-93d5-5600c9a5c383 + uuid: a3a731aa-022c-4d9b-89d3-475fc855e82e + when: null workflow_outputs: [] - annotation: '' content_id: null errors: null - id: 3 + id: 1 input_connections: {} inputs: - description: '' - name: Intensity file - label: Intensity file + name: Dataset Collection of Bering Strait MGF Files + label: Dataset Collection of Bering Strait MGF Files + name: Input dataset collection + outputs: [] + position: + left: 2.953125 + top: 159.53125 + tool_id: null + tool_state: '{"optional": false, "tag": null, "collection_type": "list", "fields": + null, "column_definitions": null}' + tool_version: null + type: data_collection_input + uuid: ae22c03f-32ee-47af-9c46-064f32e93ee9 + when: null + workflow_outputs: [] + - annotation: '' + content_id: null + errors: null + id: 2 + input_connections: {} + inputs: + - description: '' + name: Gene Ontology Terms (Selected) + label: Gene Ontology Terms (Selected) name: Input dataset outputs: [] position: - bottom: 953.578125 - height: 61 - left: 391.5625 - right: 591.5625 - top: 892.578125 - width: 200 - x: 391.5625 - y: 892.578125 + left: 1210.40625 + top: 0 tool_id: null - tool_state: '{"optional": false}' + tool_state: '{"optional": false, "tag": null}' tool_version: null type: data_input - uuid: 1e20e3c4-3b6f-4e0c-a5b6-8f8f3d220441 + uuid: 1dfff1a0-d645-4272-b524-39538fcdc95b + when: null workflow_outputs: [] - license: null - mermaid: "flowchart TD\n 0[\"metaQuantome: database\"];\n 1[\"metaQuantome:\ - \ create samples file\"];\n 2[\"\u2139\uFE0F Input Dataset\\nFunctional file\"\ - ];\n style 2 stroke:#2c3143,stroke-width:4px;\n 3[\"\u2139\uFE0F Input Dataset\\\ - nIntensity file\"];\n style 3 stroke:#2c3143,stroke-width:4px;\n 4[\"metaQuantome:\ - \ expand\"];\n 0 -->|outfile| 4;\n 3 -->|output| 4;\n 2 -->|output| 4;\n\ - \ 1 -->|samples_file| 4;\n 5[\"metaQuantome: filter\"];\n 4 -->|outfile|\ - \ 5;\n 1 -->|samples_file| 5;\n 6[\"metaQuantome: stat\"];\n 5 -->|outfile|\ - \ 6;\n 1 -->|samples_file| 6;\n 7[\"T2-Bar-Plot\"];\n 6 -->|outfile| 7;\n\ - \ 6 -->|outfile| 7;\n 8[\"T4-Bar-Plot\"];\n 6 -->|outfile| 8;\n 1 -->|samples_file|\ - \ 8;\n 9[\"T7-Bar-Plot\"];\n 6 -->|outfile| 9;\n 1 -->|samples_file| 9;\n\ - \ 10[\"T7-T2-Volcano-Plot\"];\n 6 -->|outfile| 10;\n 1 -->|samples_file|\ - \ 10;\n 11[\"T4-T2-Volcano-Plot\"];\n 6 -->|outfile| 11;\n 1 -->|samples_file|\ - \ 11;" - modified: 2026-05-21 00:30:25 +0000 - name: metaquantome-function-worklow + license: CC-BY-4.0 + mermaid: "flowchart TD\n 0[\"\u2139\uFE0F Input Dataset\\nSixgill generated protein\ + \ FASTA File\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"\u2139\uFE0F\ + \ Input Collection\\nDataset Collection of Bering Strait MGF Files\"];\n style\ + \ 1 stroke:#2c3143,stroke-width:4px;\n 2[\"\u2139\uFE0F Input Dataset\\nGene\ + \ Ontology Terms Selected\"];\n style 2 stroke:#2c3143,stroke-width:4px;\n\ + \ 3[\"Search GUI\"];\n 0 -->|output| 3;\n 1 -->|output| 3;\n 7516674a-b5aa-45b5-b2e8-38c1889ad2e9[\"\ + Output\\nSearch GUI on input dataset(s)\"];\n 3 --> 7516674a-b5aa-45b5-b2e8-38c1889ad2e9;\n\ + \ style 7516674a-b5aa-45b5-b2e8-38c1889ad2e9 stroke:#2c3143,stroke-width:4px;\n\ + \ 4[\"Peptide Shaker\"];\n 3 -->|searchgui_results| 4;\n ddfe8d62-a7b7-4e30-a84d-91c92fc60bd0[\"\ + Output\\nPeptide Shaker on input dataset(s): mzidentML file\"];\n 4 --> ddfe8d62-a7b7-4e30-a84d-91c92fc60bd0;\n\ + \ style ddfe8d62-a7b7-4e30-a84d-91c92fc60bd0 stroke:#2c3143,stroke-width:4px;\n\ + \ 5[\"Query Tabular Select Peptides\"];\n 4 -->|output_psm| 5;\n 6[\"Unipept\ + \ pept2prot\"];\n 5 -->|output| 6;\n 7[\"Unipept lca\"];\n 5 -->|output|\ + \ 7;\n 8[\"Go Pop2Prot DB\"];\n 2 -->|output| 8;\n 6 -->|output_tsv| 8;\n\ + \ 6 -->|output_tsv| 8;\n 4 -->|output_psm| 8;\n 9[\"Genera | PSMs | Peptides\"\ + ];\n 4 -->|output_psm| 9;\n 7 -->|output_tsv| 9;\n 10[\"GO Terms: Biological\ + \ Processes\"];\n 8 -->|sqlitedb| 10;\n 11[\"GO Terms: Molecular Functions\"\ + ];\n 8 -->|sqlitedb| 11;\n 12[\"GO Terms: Cellular Localization\"];\n 8 -->|sqlitedb|\ + \ 12;" + modified: 2026-07-01 00:31:40 +0000 + name: Metaproteomics_GTN outputs: - 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Sequencing quality control - Statistical calculation - - Read mapping + - Sequence contamination filtering - Visualisation - Cross-assembly - - Sequence contamination filtering - - Sequencing quality control + - Taxonomic classification + - Read mapping edam_topic: - Whole genome sequencing - Genomics @@ -85464,7 +83096,7 @@ - Improve the quality of sequencing data - Run a series of tool to identify species in bacterial isolate sequencing data - Visualize the species abundance - pageviews: 2730 + pageviews: 2857 pub_date: '2024-07-15' questions: - How to check the quality of MiSeq data? @@ -85482,10 +83114,10 @@ short_id: T00446 short_tools: - upload1 - - est_abundance + - recentrifuge - fastp - falco - - recentrifuge + - est_abundance - kraken2 slides: false slides_recordings: false @@ -85551,9 +83183,6 @@ - name: IPK Galaxy Blast Suite url: https://galaxy-web.ipk-gatersleben.de usegalaxy: false - - name: Lebanese University Galaxy - url: http://galaxy.ul.edu.lb/ - usegalaxy: false - name: Mandoiu Lab url: https://neo.engr.uconn.edu/ usegalaxy: false @@ -85569,9 +83198,6 @@ - name: PepSimili url: http://pepsimili.e-nios.com:8080/ usegalaxy: false - - name: PhagePromotor - url: https://galaxy.bio.di.uminho.pt/ - usegalaxy: false - name: UseGalaxy.org.au url: https://usegalaxy.org.au usegalaxy: true @@ -85627,8 +83253,6 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr @@ -85639,8 +83263,6 @@ state: missing - server: http://pepsimili.e-nios.com:8080/ state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - server: https://usegalaxy.org.au state: exact version: 3.1+galaxy0 @@ -85696,8 +83318,6 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr @@ -85708,8 +83328,6 @@ state: missing - server: http://pepsimili.e-nios.com:8080/ state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - server: https://usegalaxy.org.au state: exact version: 1.2.4+galaxy0 @@ -85765,8 +83383,6 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr @@ -85779,8 +83395,6 @@ state: missing - server: http://pepsimili.e-nios.com:8080/ state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - server: https://usegalaxy.org.au state: exact version: 1.0.1+galaxy3 @@ -85800,16 +83414,16 @@ state: inexact versions: - 0.20.1+galaxy0 - - 0.19.5+galaxy1 - 0.23.2+galaxy0 + - 0.19.5+galaxy1 - server: https://usegalaxy.org state: exact version: 1.0.1+galaxy3 - server: https://viralvariant.anses.fr/ state: inexact versions: - - 1.0.1+galaxy2 - 0.23.2+galaxy0 + - 1.0.1+galaxy2 version: 1.0.1+galaxy3 - id: toolshed.g2.bx.psu.edu/repos/iuc/kraken2/kraken2/2.1.3+galaxy2 servers: @@ -85841,8 +83455,6 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr @@ -85855,8 +83467,6 @@ state: inexact versions: - 2.1.1+galaxy1 - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - server: https://usegalaxy.org.au state: exact version: 2.1.3+galaxy2 @@ -85914,8 +83524,6 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr @@ -85926,8 +83534,6 @@ state: missing - server: http://pepsimili.e-nios.com:8080/ state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - server: https://usegalaxy.org.au state: exact version: 1.16.1+galaxy0 @@ -85979,8 +83585,6 @@ state: local - server: https://galaxy-web.ipk-gatersleben.de state: local - - server: http://galaxy.ul.edu.lb/ - state: local - server: https://neo.engr.uconn.edu/ state: local - server: https://mississippi.sorbonne-universite.fr @@ -85991,8 +83595,6 @@ state: local - server: http://pepsimili.e-nios.com:8080/ state: local - - server: https://galaxy.bio.di.uminho.pt/ - state: local - server: https://usegalaxy.org.au state: missing - server: https://usegalaxy.be/ @@ -86043,8 +83645,8 @@ video: true video_versions: 1 video_view: 0 - visit_duration: 630 - visitors: 2057 + visit_duration: 621 + visitors: 2176 workflows: - creators: - alternateName: bebatut @@ -86198,7 +83800,7 @@ \ stroke:#2c3143,stroke-width:4px;\n b5694f2d-c8cd-4460-bfff-74fd0792ecb3[\"\ Output\\nrecentrifuge_stats_tabular\"];\n 5 --> b5694f2d-c8cd-4460-bfff-74fd0792ecb3;\n\ \ style b5694f2d-c8cd-4460-bfff-74fd0792ecb3 stroke:#2c3143,stroke-width:4px;" - modified: 2026-05-21 00:30:25 +0000 + modified: 2026-07-01 00:31:40 +0000 name: Quality and contamination control in bacterial isolate using Illumina MiSeq Data outputs: @@ -86712,17 +84314,17 @@ - topic_0080 - topic_0199 edam_operation: - - Sequence alignment analysis + - Variant calling - Statistical calculation - - Read mapping - - Generation + - Sequencing quality control - Data handling - - Genome indexing - Sequence composition calculation + - Genome indexing - Sequence alignment + - Sequence alignment analysis + - Generation - Formatting - - Variant calling - - Sequencing quality control + - Read mapping edam_topic: - Genomics - Sequence assembly @@ -86758,22 +84360,22 @@ objectives: - Using Galaxy's main site we will see how to call variants in bacteria, viruses, and organelles. - pageviews: 16898 + pageviews: 17198 pub_date: '2017-02-16' questions: - How does frequency of mitochondrial polymorphisms change from mother to child? short_id: T00314 short_tools: - - bamFilter - - freebayes - bamleftalign + - freebayes - vcffilter2 - picard_MarkDuplicates + - bamFilter - fastqc - - picard_MergeSamFiles - vcf2tsv - - Cut1 + - picard_MergeSamFiles - bwa_mem + - Cut1 slides: false slides_recordings: false subtopic: introduction @@ -86842,9 +84444,6 @@ - name: IPK Galaxy Blast Suite url: https://galaxy-web.ipk-gatersleben.de usegalaxy: false - - name: Lebanese University Galaxy - url: http://galaxy.ul.edu.lb/ - usegalaxy: false - name: Mandoiu Lab url: https://neo.engr.uconn.edu/ usegalaxy: false @@ -86860,9 +84459,6 @@ - name: PepSimili url: http://pepsimili.e-nios.com:8080/ usegalaxy: false - - name: PhagePromotor - url: https://galaxy.bio.di.uminho.pt/ - usegalaxy: false - name: UseGalaxy.org.au url: https://usegalaxy.org.au usegalaxy: true @@ -86916,8 +84512,6 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: local - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr @@ -86928,8 +84522,6 @@ state: missing - server: http://pepsimili.e-nios.com:8080/ state: local - - server: https://galaxy.bio.di.uminho.pt/ - state: local - server: https://usegalaxy.org.au state: local - server: https://usegalaxy.be/ @@ -86980,8 +84572,6 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr @@ -86992,8 +84582,6 @@ state: missing - server: http://pepsimili.e-nios.com:8080/ state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - server: https://usegalaxy.org.au state: exact version: 2.4.1 @@ -87003,10 +84591,10 @@ - server: https://usegalaxy.cz/ state: inexact versions: - - 2.5.3+galaxy0 - - 2.5.2+galaxy3 - 2.5.2+galaxy2 + - 2.5.2+galaxy3 - 2.5.2+galaxy1 + - 2.5.3+galaxy0 - server: https://usegalaxy.eu state: exact version: 2.4.1 @@ -87055,8 +84643,6 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr @@ -87067,8 +84653,6 @@ state: missing - server: http://pepsimili.e-nios.com:8080/ state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - server: https://usegalaxy.org.au state: exact version: 2.5.2+galaxy2 @@ -87087,8 +84671,8 @@ - server: https://usegalaxy.no/ state: inexact versions: - - 2.5.1+galaxy0 - 2.4.1 + - 2.5.1+galaxy0 - server: https://usegalaxy.org state: exact version: 2.5.2+galaxy2 @@ -87128,8 +84712,6 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr @@ -87144,8 +84726,6 @@ state: missing - server: http://pepsimili.e-nios.com:8080/ state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - server: https://usegalaxy.org.au state: exact version: 0.7.17.1 @@ -87203,8 +84783,6 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr @@ -87216,8 +84794,6 @@ state: missing - server: http://pepsimili.e-nios.com:8080/ state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - server: https://usegalaxy.org.au state: exact version: 0.7.19 @@ -87277,8 +84853,6 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr @@ -87294,10 +84868,6 @@ state: inexact versions: - 0.74+galaxy0 - - server: https://galaxy.bio.di.uminho.pt/ - state: inexact - versions: - - 0.74+galaxy0 - server: https://usegalaxy.org.au state: exact version: 0.72+galaxy1 @@ -87314,8 +84884,8 @@ - '0.68' - '0.52' - '0.67' - - '0.63' - '0.64' + - '0.63' - '0.62' - server: https://usegalaxy.eu state: exact @@ -87348,8 +84918,8 @@ state: inexact versions: - '0.72' - - 0.73+galaxy0 - 0.72+galaxy1 + - 0.73+galaxy0 - server: https://galaxy.pasteur.fr/ state: inexact versions: @@ -87367,8 +84937,6 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr @@ -87381,16 +84949,12 @@ versions: - '0.72' - 0.72+galaxy1 - - '0.71' - '0.65' + - '0.71' - server: http://pepsimili.e-nios.com:8080/ state: inexact versions: - 0.74+galaxy0 - - server: https://galaxy.bio.di.uminho.pt/ - state: inexact - versions: - - 0.74+galaxy0 - server: https://usegalaxy.org.au state: exact version: 0.74+galaxy1 @@ -87409,8 +84973,8 @@ - server: https://usegalaxy.no/ state: inexact versions: - - 0.73+galaxy0 - 0.72+galaxy1 + - 0.73+galaxy0 - server: https://usegalaxy.org state: exact version: 0.74+galaxy1 @@ -87449,8 +85013,6 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr @@ -87463,8 +85025,6 @@ state: missing - server: http://pepsimili.e-nios.com:8080/ state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - server: https://usegalaxy.org.au state: exact version: 1.3.1 @@ -87521,8 +85081,6 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr @@ -87535,8 +85093,6 @@ state: missing - server: http://pepsimili.e-nios.com:8080/ state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - server: https://usegalaxy.org.au state: exact version: 1.3.9 @@ -87556,9 +85112,9 @@ state: inexact versions: - 1.3.6 - - 1.1.0.46-0 - 1.3.5 - 1.3.1 + - 1.1.0.46-0 - server: https://usegalaxy.org state: exact version: 1.3.9 @@ -87597,8 +85153,6 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr @@ -87611,8 +85165,6 @@ state: missing - server: http://pepsimili.e-nios.com:8080/ state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - server: https://usegalaxy.org.au state: exact version: 1.3.1 @@ -87669,8 +85221,6 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr @@ -87683,8 +85233,6 @@ state: missing - server: http://pepsimili.e-nios.com:8080/ state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - server: https://usegalaxy.org.au state: exact version: 1.3.9+galaxy0 @@ -87705,8 +85253,8 @@ versions: - 1.3.6+galaxy0 - 1.1.0.46-0 - - 1.3.5+galaxy1 - 1.3.1 + - 1.3.5+galaxy1 - server: https://usegalaxy.org state: exact version: 1.3.9+galaxy0 @@ -87728,8 +85276,8 @@ - server: https://galaxy.mesocentre.uca.fr state: inexact versions: - - 3.1.1.0 - 2.18.2.1 + - 3.1.1.0 - server: https://galaxy.pasteur.fr/ state: missing - server: https://galaxytrakr.org/ @@ -87744,8 +85292,6 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr @@ -87758,8 +85304,6 @@ state: missing - server: http://pepsimili.e-nios.com:8080/ state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - server: https://usegalaxy.org.au state: exact version: 2.18.2.2 @@ -87813,8 +85357,6 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr @@ -87826,8 +85368,6 @@ state: missing - server: http://pepsimili.e-nios.com:8080/ state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - server: https://usegalaxy.org.au state: exact version: 3.1.1.0 @@ -87882,8 +85422,6 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr @@ -87896,8 +85434,6 @@ state: missing - server: http://pepsimili.e-nios.com:8080/ state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - server: https://usegalaxy.org.au state: exact version: 2.18.2.1 @@ -87951,8 +85487,6 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr @@ -87964,8 +85498,6 @@ state: missing - server: http://pepsimili.e-nios.com:8080/ state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - server: https://usegalaxy.org.au state: exact version: 3.1.1.0 @@ -88019,8 +85551,6 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr @@ -88031,8 +85561,6 @@ state: missing - server: http://pepsimili.e-nios.com:8080/ state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - server: https://usegalaxy.org.au state: exact version: 1.0.0_rc1+galaxy0 @@ -88085,8 +85613,6 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr @@ -88097,8 +85623,6 @@ state: missing - server: http://pepsimili.e-nios.com:8080/ state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - server: https://usegalaxy.org.au state: exact version: 1.0.0_rc3+galaxy0 @@ -88153,8 +85677,6 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr @@ -88165,8 +85687,6 @@ state: missing - server: http://pepsimili.e-nios.com:8080/ state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - server: https://usegalaxy.org.au state: inexact versions: @@ -88225,8 +85745,6 @@ state: missing - server: https://galaxy-web.ipk-gatersleben.de state: missing - - server: http://galaxy.ul.edu.lb/ - state: missing - server: https://neo.engr.uconn.edu/ state: missing - server: https://mississippi.sorbonne-universite.fr @@ -88237,8 +85755,6 @@ state: missing - server: http://pepsimili.e-nios.com:8080/ state: missing - - server: https://galaxy.bio.di.uminho.pt/ - state: missing - server: https://usegalaxy.org.au state: exact version: 1.0.0_rc3+galaxy3 @@ -88307,8 +85823,8 @@ video: false video_versions: 0 video_view: 0 - visit_duration: 333 - visitors: 9869 + visit_duration: 343 + visitors: 10064 workflows: - creators: - class: Person @@ -88512,7 +86028,7 @@ Cut\"];\n 16 -->|out_file1| 17;\n 7a28747b-cac3-458c-b785-0cc4d65d7409[\"\ Output\\nout_file1\"];\n 17 --> 7a28747b-cac3-458c-b785-0cc4d65d7409;\n style\ \ 7a28747b-cac3-458c-b785-0cc4d65d7409 stroke:#2c3143,stroke-width:4px;" - modified: 2026-05-21 00:30:26 +0000 + modified: 2026-07-01 00:31:40 +0000 name: Calling variants in non-diploid systems outputs: - annotation: '' diff --git a/communities/microgalaxy/resources/workflows.html b/communities/microgalaxy/resources/workflows.html index db62bf6f4..765db6e38 100644 --- a/communities/microgalaxy/resources/workflows.html +++ b/communities/microgalaxy/resources/workflows.html @@ -92,8 +92,8 @@ 2 2 20.0 - table_pandas_rename_column, multiqc, groot, collection_element_identifiers, tooldistillator_summarize, tooldistillator, Remove a collection level so that outputs can be taken into account by tooldistillator\n__FLATTEN__, __FILTER_FAILED_DATASETS__, tp_text_file_with_recurring_lines, __UNZIP_COLLECTION__, sylph_profile, argnorm, __RELABEL_FROM_FILE__, Removal of the first line because it is not necessary for tooldistillator\nRemove beginning1, Removal of the first argNorm line that causes a multiQC error\nRemove beginning1, fastq_paired_end_interlacer, deeparg_short_reads - Data parsing, Gene functional annotation, Validation, Taxonomic classification, Sequencing quality control, Antimicrobial resistance prediction + tooldistillator_summarize, __RELABEL_FROM_FILE__, groot, collection_element_identifiers, sylph_profile, deeparg_short_reads, fastq_paired_end_interlacer, argnorm, table_pandas_rename_column, multiqc, Removal of the first line because it is not necessary for tooldistillator\nRemove beginning1, tp_text_file_with_recurring_lines, tooldistillator, __UNZIP_COLLECTION__, Removal of the first argNorm line that causes a multiQC error\nRemove beginning1, __FILTER_FAILED_DATASETS__, Remove a collection level so that outputs can be taken into account by tooldistillator\n__FLATTEN__ + Data parsing, Taxonomic classification, Gene functional annotation, Sequencing quality control, Antimicrobial resistance prediction, Validation GPL-3.0-or-later @@ -114,8 +114,8 @@ 2 2 3.0 - coreprofiler_allele_calling, tooldistillator_summarize, tooldistillator - Multilocus sequence typing, Data parsing + tooldistillator, tooldistillator_summarize, coreprofiler_allele_calling + Data parsing, Multilocus sequence typing GPL-3.0-or-later @@ -136,8 +136,8 @@ 3 3 14.0 - pick_value, kraken2, tooldistillator_summarize, tooldistillator, est_abundance, quast, collapse_dataset, checkm2, recentrifuge - Visualisation, Sequence composition calculation, Sequence assembly validation, Statistical calculation, Validation, Cross-assembly, Data parsing, Expression analysis, Taxonomic classification, Sequencing quality control + tooldistillator_summarize, recentrifuge, checkm2, est_abundance, kraken2, pick_value, collapse_dataset, tooldistillator, quast + Statistical calculation, Taxonomic classification, Expression analysis, Sequence assembly validation, Data parsing, Sequencing quality control, Validation, Sequence composition calculation, Visualisation, Cross-assembly GPL-3.0-or-later @@ -158,8 +158,8 @@ 7 7 16.0 - ivar_consensus, samtools_view, multiqc, __FLATTEN__, nextclade, samtools_stats, pangolin, bwa_mem, qualimap_bamqc, ivar_trim, fastp, snpeff_sars_cov_2, tp_cat, tp_sed_tool, ivar_variants - Methylation analysis, Sequence alignment, Genome indexing, SNP detection, Validation, Read mapping, Variant calling, Primer removal, Sequence contamination filtering, Generation, Tree-based sequence alignment, Variant classification, Sequencing quality control + fastp, ivar_variants, nextclade, ivar_trim, samtools_view, ivar_consensus, qualimap_bamqc, multiqc, __FLATTEN__, tp_sed_tool, snpeff_sars_cov_2, samtools_stats, tp_cat, pangolin, bwa_mem + Read mapping, Generation, Variant classification, Variant calling, Tree-based sequence alignment, Sequence alignment, Genome indexing, Sequencing quality control, Sequence contamination filtering, Validation, Methylation analysis, Primer removal, SNP detection MIT @@ -180,8 +180,8 @@ 4 4 11.0 - samtools_view, multiqc, samtools_stats, bwa_mem, lofreq_viterbi, lofreq_indelqual, fastp, picard_MarkDuplicates, lofreq_call, lofreq_filter, snpeff_sars_cov_2 - Formatting, Sequence alignment, Genome indexing, SNP detection, Validation, Read mapping, Sequence contamination filtering, Generation, Sequencing quality control + lofreq_filter, fastp, picard_MarkDuplicates, lofreq_viterbi, samtools_view, lofreq_call, multiqc, snpeff_sars_cov_2, samtools_stats, lofreq_indelqual, bwa_mem + Formatting, Generation, Sequence alignment, Genome indexing, Sequencing quality control, Sequence contamination filtering, Validation, Read mapping, SNP detection MIT @@ -202,8 +202,8 @@ 2 2 23.0 - samtools_view, __FILTER_FAILED_DATASETS__, qualimap_bamqc, tp_sed_tool, snpEff, __FLATTEN__, samtools_stats, bwa_mem, lofreq_viterbi, calculate_numeric_param, collapse_dataset, ivar_variants, ivar_consensus, tp_find_and_replace, map_param_value, ivar_trim, fastp, tp_cat, snpSift_extractFields, pick_value, multiqc, snpEff_build_gb - Sequence alignment, Genome indexing, Validation, Read mapping, Primer removal, Sequence contamination filtering, Generation, Sequencing quality control + ivar_variants, __FLATTEN__, snpSift_extractFields, map_param_value, collapse_dataset, tp_cat, fastp, samtools_view, snpEff, tp_find_and_replace, calculate_numeric_param, samtools_stats, lofreq_viterbi, snpEff_build_gb, ivar_consensus, pick_value, ivar_trim, qualimap_bamqc, multiqc, tp_sed_tool, __FILTER_FAILED_DATASETS__, bwa_mem + Sequencing quality control, Sequence contamination filtering, Generation, Validation, Read mapping, Sequence alignment, Primer removal, Genome indexing AGPL-3.0-or-later @@ -224,8 +224,8 @@ 3 3 68.0 - wc_gnu, samtools_view, __FILTER_FAILED_DATASETS__, tp_text_file_with_recurring_lines, qualimap_bamqc, bwa mem will fail if no reference for any segment got suggested by vapor, i.e. the reference genome is empty. In that case, we need to skip further analysis of the sample.\n__FILTER_FAILED_DATASETS__, __HARMONIZELISTS__, Show beginning1, Filter1, __FLATTEN__, collection_element_identifiers, bwa_mem, __RELABEL_FROM_FILE__, __APPLY_RULES__, __MERGE_COLLECTION__, collapse_dataset, Paste1, bamtools_split_ref, snipit, Grep1, ivar_consensus, param_value_from_file, tp_find_and_replace, __UNZIP_COLLECTION__, tp_easyjoin_tool, fastp, tp_cat, Cut1, rbc_mafft, __FILTER_FROM_FILE__, vapor, This seemingly no-op transformation will remove samples with no remaining segment results (cases where vapor failed for  every segment).\n__APPLY_RULES__, seqtk_subseq, iqtree, __DUPLICATE_FILE_TO_COLLECTION__ - Multiple sequence alignment, Sequence alignment, Genome indexing, Sequence file editing, Phylogenetic analysis, Read mapping, Sequence analysis, Primer removal, Base position variability plotting, Sequence contamination filtering, Data retrieval, Sequence alignment analysis, Data handling, Generation, Sequencing quality control, De-novo assembly + collection_element_identifiers, Paste1, __FLATTEN__, snipit, bwa mem will fail if no reference for any segment got suggested by vapor, i.e. the reference genome is empty. In that case, we need to skip further analysis of the sample.\n__FILTER_FAILED_DATASETS__, collapse_dataset, bamtools_split_ref, tp_cat, Show beginning1, param_value_from_file, fastp, samtools_view, tp_find_and_replace, rbc_mafft, tp_text_file_with_recurring_lines, __APPLY_RULES__, __FILTER_FROM_FILE__, ivar_consensus, __HARMONIZELISTS__, __DUPLICATE_FILE_TO_COLLECTION__, This seemingly no-op transformation will remove samples with no remaining segment results (cases where vapor failed for  every segment).\n__APPLY_RULES__, Grep1, iqtree, vapor, __RELABEL_FROM_FILE__, wc_gnu, seqtk_subseq, tp_easyjoin_tool, qualimap_bamqc, __MERGE_COLLECTION__, __UNZIP_COLLECTION__, __FILTER_FAILED_DATASETS__, Filter1, Cut1, bwa_mem + Data retrieval, Generation, Multiple sequence alignment, Data handling, De-novo assembly, Sequence file editing, Sequence alignment, Base position variability plotting, Genome indexing, Sequencing quality control, Sequence contamination filtering, Sequence alignment analysis, Sequence analysis, Read mapping, Primer removal, Phylogenetic analysis AGPL-3.0-or-later @@ -246,8 +246,8 @@ 4 4 40.0 - compose_text_param, samtools_view, __FILTER_FAILED_DATASETS__, qualimap_bamqc, tp_sed_tool, fasta_compute_length, samtools_merge, __FLATTEN__, collection_element_identifiers, samtools_stats, bwa_mem, __APPLY_RULES__, __ZIP_COLLECTION__, Grep1, ivar_consensus, param_value_from_file, split_file_to_collection, ivar_trim, fastp, tp_cat, Cut1, __SORTLIST__, EMBOSS: maskseq51, multiqc, datamash_ops - Sequence alignment, Genome indexing, Validation, Read mapping, Sequence analysis, Primer removal, Local alignment, Sequence contamination filtering, Global alignment, Sequence alignment analysis, Generation, Sequencing quality control + collection_element_identifiers, __FLATTEN__, EMBOSS: maskseq51, tp_cat, datamash_ops, param_value_from_file, fastp, samtools_view, samtools_merge, samtools_stats, __APPLY_RULES__, __ZIP_COLLECTION__, ivar_consensus, __SORTLIST__, Grep1, fasta_compute_length, ivar_trim, qualimap_bamqc, multiqc, split_file_to_collection, compose_text_param, tp_sed_tool, __FILTER_FAILED_DATASETS__, Cut1, bwa_mem + Generation, Sequence alignment, Genome indexing, Sequencing quality control, Sequence contamination filtering, Sequence alignment analysis, Validation, Global alignment, Sequence analysis, Read mapping, Primer removal, Local alignment MIT @@ -268,7 +268,7 @@ 5 5 23.0 - bcftools_consensus, Paste1, samtools_coverage, regexColumn1, bcftools_norm, CONVERTER_gz_to_uncompressed, snpSift_filter, tp_cut_tool, Cut1, snpSift_extractFields, clair3, collapse_dataset, Remove beginning1, table_compute, tp_head_tool, Count1, samtools_depth, minimap2 + tp_cut_tool, clair3, table_compute, samtools_depth, bcftools_consensus, CONVERTER_gz_to_uncompressed, Paste1, bcftools_norm, Cut1, snpSift_extractFields, samtools_coverage, snpSift_filter, collapse_dataset, minimap2, Count1, tp_head_tool, Remove beginning1, regexColumn1 Pairwise sequence alignment, Variant calling MIT @@ -290,7 +290,7 @@ 2 2 20.0 - , fastq_dl, CONVERTER_uncompressed_to_gz, tp_awk_tool, CONVERTER_gz_to_uncompressed, __MERGE_COLLECTION__ + , tp_awk_tool, CONVERTER_uncompressed_to_gz, CONVERTER_gz_to_uncompressed, __MERGE_COLLECTION__, fastq_dl Apache-2.0 @@ -312,8 +312,8 @@ 2 2 30.0 - , tp_awk_tool, __FILTER_FROM_FILE__, bedtools_maskfastabed, mapseq, collection_element_identifiers, taxonomy_krona_chart, biom_convert, __FILTER_EMPTY_DATASETS__ - k-mer counting, Visualisation, Formatting, Mapping + , bedtools_maskfastabed, mapseq, tp_awk_tool, __FILTER_FROM_FILE__, collection_element_identifiers, taxonomy_krona_chart, biom_convert, __FILTER_EMPTY_DATASETS__ + k-mer counting, Formatting, Visualisation, Mapping Apache-2.0 @@ -334,8 +334,8 @@ 2 2 17.0 - cshl_fasta_formatter, tp_find_and_replace, fastq_to_fasta_python, multiqc, fastqc, __UNZIP_COLLECTION__, prinseq, mgnify_seqprep, fastp, trimmomatic, fastq_filter - Sequence trimming, Sequence composition calculation, Nucleic acid design, Statistical calculation, Validation, Read pre-processing, Sequence contamination filtering, Sequencing quality control + fastp, cshl_fasta_formatter, tp_find_and_replace, multiqc, trimmomatic, fastqc, __UNZIP_COLLECTION__, mgnify_seqprep, fastq_filter, prinseq, fastq_to_fasta_python + Statistical calculation, Sequencing quality control, Sequence contamination filtering, Sequence trimming, Validation, Nucleic acid design, Read pre-processing, Sequence composition calculation Apache-2.0 @@ -356,8 +356,8 @@ 3 3 14.0 - cshl_fasta_formatter, tp_find_and_replace, fastq_to_fasta_python, multiqc, fastqc, prinseq, trimmomatic, fastq_filter - Sequence trimming, Read pre-processing, Sequence composition calculation, Sequence contamination filtering, Statistical calculation, Validation, Sequencing quality control + cshl_fasta_formatter, tp_find_and_replace, multiqc, trimmomatic, fastqc, fastq_filter, prinseq, fastq_to_fasta_python + Sequencing quality control, Statistical calculation, Sequence contamination filtering, Sequence trimming, Validation, Read pre-processing, Sequence composition calculation Apache-2.0 @@ -378,8 +378,8 @@ 2 2 47.0 - , bedtools_getfastabed, tp_awk_tool, cshl_fasta_formatter, __FILTER_FROM_FILE__, infernal_cmsearch, mapseq, collection_element_identifiers, taxonomy_krona_chart, cmsearch_deoverlap, biom_convert, gops_concat_1, __FILTER_EMPTY_DATASETS__, query_tabular - Visualisation, Alignment, Formatting, Mapping, k-mer counting, Comparison, Nucleic acid feature detection + , cshl_fasta_formatter, tp_awk_tool, mapseq, collection_element_identifiers, __FILTER_FROM_FILE__, taxonomy_krona_chart, biom_convert, cmsearch_deoverlap, infernal_cmsearch, bedtools_getfastabed, gops_concat_1, query_tabular, __FILTER_EMPTY_DATASETS__ + k-mer counting, Formatting, Comparison, Mapping, Alignment, Nucleic acid feature detection, Visualisation Apache-2.0 @@ -400,7 +400,7 @@ 2 2 10.0 - Grouping1, collection_column_join, tp_awk_tool, filter_tabular, query_tabular + tp_awk_tool, collection_column_join, Grouping1, filter_tabular, query_tabular MIT @@ -422,8 +422,8 @@ 1 1 24.0 - Grouping1, Grep1, fasta2tab, fasta_merge_files_and_filter_unique_sequences, Filter1, ident_params, Remove beginning1, msconvert, Cut1, query_tabular, dbbuilder, fasta_cli, filter_tabular, tp_cat, search_gui, peptide_shaker, maxquant - Visualisation, Filtering, Formatting, Statistical calculation, Imputation, Standardisation and normalisation, Heat map generation, Protein quantification, Principal component plotting, Clustering + query_tabular, peptide_shaker, Remove beginning1, tp_cat, search_gui, Grouping1, fasta_cli, ident_params, maxquant, msconvert, dbbuilder, Grep1, filter_tabular, Filter1, fasta_merge_files_and_filter_unique_sequences, Cut1, fasta2tab + Statistical calculation, Imputation, Formatting, Heat map generation, Filtering, Standardisation and normalisation, Protein quantification, Clustering, Principal component plotting, Visualisation CC-BY-4.0 @@ -444,8 +444,8 @@ 1 1 6.0 - Grep1, msstatstmt, unipept - Visualisation, Prediction and recognition + msstatstmt, Grep1, unipept + Prediction and recognition, Visualisation CC-BY-4.0 @@ -466,7 +466,7 @@ 1 1 19.0 - Grouping1, fasta_merge_files_and_filter_unique_sequences, Filter1, uniprotxml_downloader, Cut1, pepquery2, tp_cat, dbbuilder, Remove beginning1, collapse_dataset, query_tabular + Filter1, uniprotxml_downloader, Grouping1, Cut1, collapse_dataset, dbbuilder, query_tabular, tp_cat, fasta_merge_files_and_filter_unique_sequences, Remove beginning1, pepquery2 CC-BY-4.0 @@ -489,7 +489,7 @@ 1 3.0 metanovo, fasta_merge_files_and_filter_unique_sequences - Expression analysis, Protein identification, Tag-based peptide identification, de Novo sequencing, Target-Decoy + de Novo sequencing, Target-Decoy, Expression analysis, Tag-based peptide identification, Protein identification CC-BY-4.0 @@ -510,8 +510,8 @@ 1 1 7.0 - maxquant, Quantified-Proteins\nGrouping1, extract proteins\nCut1, extract peptides\nCut1, Quantified-Peptides\nGrouping1, extracting microbial Proteins\nGrep1, extracting microbial Peptides\nGrep1 - Visualisation, Statistical calculation, Imputation, Standardisation and normalisation, Heat map generation, Protein quantification, Principal component plotting, Clustering + extracting microbial Proteins\nGrep1, extract proteins\nCut1, Quantified-Peptides\nGrouping1, extracting microbial Peptides\nGrep1, Quantified-Proteins\nGrouping1, maxquant, extract peptides\nCut1 + Statistical calculation, Imputation, Heat map generation, Standardisation and normalisation, Protein quantification, Clustering, Principal component plotting, Visualisation CC-BY-4.0 @@ -532,8 +532,8 @@ 12 12 5.0 - bandage_info, bandage_image, tooldistillator, tooldistillator_summarize, shovill - Data parsing, Genome assembly, Sequence assembly visualisation + tooldistillator_summarize, shovill, bandage_image, bandage_info, tooldistillator + Data parsing, Sequence assembly visualisation, Genome assembly GPL-3.0-or-later @@ -554,8 +554,8 @@ 11 11 8.0 - kraken2, tooldistillator_summarize, tooldistillator, __UNZIP_COLLECTION__, est_abundance, fastp, recentrifuge, __ZIP_COLLECTION__ - Cross-assembly, Data parsing, Sequence contamination filtering, Expression analysis, Statistical calculation, Taxonomic classification, Sequencing quality control + fastp, tooldistillator_summarize, recentrifuge, __ZIP_COLLECTION__, est_abundance, kraken2, __UNZIP_COLLECTION__, tooldistillator + Sequencing quality control, Sequence contamination filtering, Data parsing, Taxonomic classification, Expression analysis, Statistical calculation, Cross-assembly GPL-3.0-or-later @@ -576,7 +576,7 @@ 2 2 3.0 - Phylogenetic tree for diversity analysis, Taxonomic analysis, Rarefaction + Rarefaction, Taxonomic analysis, Phylogenetic tree for diversity analysis MIT @@ -598,8 +598,8 @@ 1 1 15.0 - medaka_consensus_pipeline, param_value_from_file, compose_text_param, __BUILD_LIST__, tp_find_and_replace, abricate, collection_element_identifiers, bandage_image, split_file_to_collection, flye, fasta2tab, tab2fasta - Antimicrobial resistance prediction, Base-calling, Variant calling, Cross-assembly, Mapping assembly, Sequence assembly, Genome assembly, Sequence assembly visualisation, De-novo assembly + abricate, collection_element_identifiers, bandage_image, flye, tp_find_and_replace, split_file_to_collection, compose_text_param, __BUILD_LIST__, tab2fasta, medaka_consensus_pipeline, param_value_from_file, fasta2tab + Base-calling, Antimicrobial resistance prediction, De-novo assembly, Variant calling, Sequence assembly visualisation, Sequence assembly, Cross-assembly, Mapping assembly, Genome assembly MIT 10.48546/workflowhub.workflow.1062.1 @@ -620,8 +620,8 @@ 1 1 60.0 - Grouping1, regexColumn1, clustalw, __FILTER_FAILED_DATASETS__, fasta2tab, tp_sorted_uniq, fasta_merge_files_and_filter_unique_sequences, collapse_dataset, __FILTER_EMPTY_DATASETS__, bedtools_getfastabed, tp_multijoin_tool, ggplot2_heatmap, Cut1, Remove beginning1, fasttree, tp_split_on_column, collection_column_join, tp_replace_in_column, newick_display, regex1, Count1, tab2fasta - Phylogenetic tree generation (from molecular sequences), Visualisation, Phylogenetic tree generation (maximum likelihood and Bayesian methods), Multiple sequence alignment, Mapping, Phylogenetic tree reconstruction, Phylogenetic tree analysis, Phylogenetic tree generation + tp_split_on_column, ggplot2_heatmap, bedtools_getfastabed, collapse_dataset, regex1, tp_replace_in_column, fasta_merge_files_and_filter_unique_sequences, newick_display, regexColumn1, tp_multijoin_tool, Count1, __FILTER_EMPTY_DATASETS__, fasta2tab, tp_sorted_uniq, Grouping1, fasttree, tab2fasta, Remove beginning1, collection_column_join, clustalw, __FILTER_FAILED_DATASETS__, Cut1 + Phylogenetic tree generation, Visualisation, Multiple sequence alignment, Phylogenetic tree reconstruction, Phylogenetic tree analysis, Mapping MIT 10.48546/workflowhub.workflow.1060.1 @@ -642,8 +642,8 @@ 1 1 3.0 - kraken2, taxonomy_krona_chart, krakentools_kreport2krona - Visualisation, Taxonomic classification, Aggregation + krakentools_kreport2krona, kraken2, taxonomy_krona_chart + Taxonomic classification, Aggregation, Visualisation MIT 10.48546/workflowhub.workflow.1059.1 @@ -664,8 +664,8 @@ 13 13 6.0 - isescan, bakta, integron_finder, tooldistillator_summarize, tooldistillator, plasmidfinder - Scaffolding, Multilocus sequence typing, Structural variation detection, Sequence motif recognition, Genome annotation, Data parsing, Genome assembly, Protein feature detection, Nucleic acid feature detection + tooldistillator_summarize, integron_finder, plasmidfinder, isescan, bakta, tooldistillator + Scaffolding, Genome annotation, Nucleic acid feature detection, Data parsing, Protein feature detection, Structural variation detection, Sequence motif recognition, Multilocus sequence typing, Genome assembly GPL-3.0-or-later @@ -686,7 +686,7 @@ 9 9 5.0 - abricate, amrfinderplus, staramr_search, tooldistillator_summarize, tooldistillator + tooldistillator_summarize, abricate, amrfinderplus, staramr_search, tooldistillator Data parsing, Antimicrobial resistance prediction GPL-3.0-or-later @@ -708,7 +708,7 @@ 3 3 14.0 - dada2_filterAndTrim, dada2_learnErrors, dada2_assignTaxonomyAddspecies, dada2_makeSequenceTable, dada2_seqCounts, __UNZIP_COLLECTION__, dada2_removeBimeraDenovo, __APPLY_RULES__, dada2_mergePairs, dada2_plotQualityProfile, dada2_dada + dada2_dada, dada2_makeSequenceTable, __APPLY_RULES__, dada2_plotQualityProfile, dada2_learnErrors, dada2_assignTaxonomyAddspecies, dada2_seqCounts, dada2_filterAndTrim, __UNZIP_COLLECTION__, dada2_removeBimeraDenovo, dada2_mergePairs DNA barcoding, Variant calling MIT @@ -730,7 +730,7 @@ 1 1 5.0 - jbrowse, iframe, create_or_update, list_organism, create_account + create_or_update, iframe, jbrowse, create_account, list_organism Genome visualisation CC-BY-4.0 @@ -752,8 +752,8 @@ 2 2 15.0 - bcftools_consensus, tp_awk_tool, tb_profiler_profile, kraken2, __FLATTEN__, multiqc, mosdepth, snippy, qualimap_bamqc, tb_variant_filter, tbvcfreport, fastp, tp_sed_tool, EMBOSS: seqret84 - Phylogenetic tree visualisation, Sequence alignment, Validation, Antimicrobial resistance prediction, Phylogenetic tree generation, Variant calling, Sequence analysis, Local alignment, Sequence contamination filtering, Global alignment, Sequence alignment analysis, Taxonomic classification, Sequencing quality control + fastp, tp_awk_tool, qualimap_bamqc, EMBOSS: seqret84, kraken2, mosdepth, __FLATTEN__, tp_sed_tool, snippy, multiqc, bcftools_consensus, tb_variant_filter, tb_profiler_profile, tbvcfreport + Taxonomic classification, Antimicrobial resistance prediction, Variant calling, Sequence alignment, Phylogenetic tree visualisation, Sequencing quality control, Sequence contamination filtering, Sequence alignment analysis, Phylogenetic tree generation, Validation, Global alignment, Sequence analysis, Local alignment AGPL-3.0-or-later @@ -774,8 +774,8 @@ 1 1 5.0 - falco, kraken2, est_abundance, fastp, recentrifuge - Visualisation, Statistical calculation, Read mapping, Cross-assembly, Sequence contamination filtering, Expression analysis, Taxonomic classification, Sequencing quality control + fastp, recentrifuge, est_abundance, kraken2, falco + Statistical calculation, Taxonomic classification, Expression analysis, Sequencing quality control, Sequence contamination filtering, Read mapping, Visualisation, Cross-assembly GPL-3.0-or-later @@ -796,8 +796,8 @@ 2 2 10.0 - interactive_tool_phinch, metaphlan, kraken2, taxonomy_krona_chart, krakentools_kreport2krona, __UNZIP_COLLECTION__, est_abundance, interactive_tool_pavian, kraken_biom - Visualisation, Statistical calculation, Taxonomic classification, Genome annotation, Aggregation + metaphlan, taxonomy_krona_chart, krakentools_kreport2krona, est_abundance, kraken_biom, kraken2, interactive_tool_phinch, __UNZIP_COLLECTION__, interactive_tool_pavian + Statistical calculation, Taxonomic classification, Aggregation, Genome annotation, Visualisation MIT @@ -818,8 +818,8 @@ 2 2 3.0 - kraken2, est_abundance, recentrifuge - Cross-assembly, Statistical calculation, Taxonomic classification, Expression analysis + est_abundance, recentrifuge, kraken2 + Statistical calculation, Taxonomic classification, Expression analysis, Cross-assembly GPL-3.0-or-later @@ -840,8 +840,8 @@ 1 1 17.0 - bowtie2, metabat2, __BUILD_LIST__, concoct_coverage_table, metabat2_jgi_summarize_bam_contig_depths, concoct_extract_fasta_bins, semibin, concoct, samtools_sort, maxbin2, binette, Fasta_to_Contig2Bin, concoct_merge_cut_up_clustering, concoct_cut_up_fasta - Sequence assembly, Read mapping, Genome annotation, Sequence clustering, Read binning + bowtie2, concoct_coverage_table, concoct_merge_cut_up_clustering, concoct_extract_fasta_bins, concoct_cut_up_fasta, samtools_sort, Fasta_to_Contig2Bin, concoct, __BUILD_LIST__, binette, semibin, maxbin2, metabat2, metabat2_jgi_summarize_bam_contig_depths + Sequence assembly, Read mapping, Sequence clustering, Genome annotation, Read binning MIT @@ -862,8 +862,8 @@ 1 1 30.0 - , tp_awk_tool, __FILTER_FROM_FILE__, bedtools_maskfastabed, mapseq, collection_element_identifiers, taxonomy_krona_chart, biom_convert, __FILTER_EMPTY_DATASETS__ - k-mer counting, Visualisation, Formatting, Mapping + , bedtools_maskfastabed, mapseq, tp_awk_tool, __FILTER_FROM_FILE__, collection_element_identifiers, taxonomy_krona_chart, biom_convert, __FILTER_EMPTY_DATASETS__ + k-mer counting, Formatting, Visualisation, Mapping Apache-2.0 @@ -884,8 +884,8 @@ 1 1 9.0 - collection_column_join, ampvis2_load, tp_awk_tool, collapse_dataset, query_tabular - Visualisation, Analysis + tp_awk_tool, collection_column_join, collapse_dataset, ampvis2_load, query_tabular + Analysis, Visualisation MIT @@ -906,8 +906,8 @@ 1 1 17.0 - cshl_fasta_formatter, tp_find_and_replace, fastq_to_fasta_python, multiqc, fastqc, __UNZIP_COLLECTION__, prinseq, mgnify_seqprep, fastp, trimmomatic, fastq_filter - Sequence trimming, Sequence composition calculation, Nucleic acid design, Statistical calculation, Validation, Read pre-processing, Sequence contamination filtering, Sequencing quality control + fastp, cshl_fasta_formatter, tp_find_and_replace, multiqc, trimmomatic, fastqc, __UNZIP_COLLECTION__, mgnify_seqprep, fastq_filter, prinseq, fastq_to_fasta_python + Statistical calculation, Sequencing quality control, Sequence contamination filtering, Sequence trimming, Validation, Nucleic acid design, Read pre-processing, Sequence composition calculation Apache-2.0 @@ -928,7 +928,7 @@ 1 1 20.0 - , fastq_dl, CONVERTER_uncompressed_to_gz, tp_awk_tool, CONVERTER_gz_to_uncompressed, __MERGE_COLLECTION__ + , tp_awk_tool, CONVERTER_uncompressed_to_gz, CONVERTER_gz_to_uncompressed, __MERGE_COLLECTION__, fastq_dl Apache-2.0 @@ -950,7 +950,7 @@ 1 1 10.0 - Grouping1, collection_column_join, tp_awk_tool, filter_tabular, query_tabular + tp_awk_tool, collection_column_join, Grouping1, filter_tabular, query_tabular MIT @@ -972,8 +972,8 @@ 1 1 14.0 - cshl_fasta_formatter, tp_find_and_replace, fastq_to_fasta_python, multiqc, fastqc, prinseq, trimmomatic, fastq_filter - Sequence trimming, Read pre-processing, Sequence composition calculation, Sequence contamination filtering, Statistical calculation, Validation, Sequencing quality control + cshl_fasta_formatter, tp_find_and_replace, multiqc, trimmomatic, fastqc, fastq_filter, prinseq, fastq_to_fasta_python + Sequencing quality control, Statistical calculation, Sequence contamination filtering, Sequence trimming, Validation, Read pre-processing, Sequence composition calculation Apache-2.0 @@ -994,8 +994,8 @@ 1 1 47.0 - , bedtools_getfastabed, tp_awk_tool, cshl_fasta_formatter, __FILTER_FROM_FILE__, infernal_cmsearch, mapseq, collection_element_identifiers, taxonomy_krona_chart, cmsearch_deoverlap, biom_convert, gops_concat_1, __FILTER_EMPTY_DATASETS__, query_tabular - Visualisation, Alignment, Formatting, Mapping, k-mer counting, Comparison, Nucleic acid feature detection + , cshl_fasta_formatter, tp_awk_tool, mapseq, collection_element_identifiers, __FILTER_FROM_FILE__, taxonomy_krona_chart, biom_convert, cmsearch_deoverlap, infernal_cmsearch, bedtools_getfastabed, gops_concat_1, query_tabular, __FILTER_EMPTY_DATASETS__ + k-mer counting, Formatting, Comparison, Mapping, Alignment, Nucleic acid feature detection, Visualisation Apache-2.0 @@ -1016,8 +1016,8 @@ 2 2 12.0 - Grep1, humann_rename_table, tp_find_and_replace, combine_metaphlan2_humann2, Cut1, humann_renorm_table, humann_regroup_table, humann_unpack_pathways, humann_split_stratified_table - Species frequency estimation, Taxonomic classification, Phylogenetic analysis + humann_rename_table, humann_regroup_table, tp_find_and_replace, combine_metaphlan2_humann2, humann_unpack_pathways, humann_split_stratified_table, humann_renorm_table, Grep1, Cut1 + Taxonomic classification, Species frequency estimation, Phylogenetic analysis MIT @@ -1038,8 +1038,8 @@ 2 2 21.0 - dada2_filterAndTrim, dada2_learnErrors, dada2_assignTaxonomyAddspecies, tp_replace_in_column, collection_element_identifiers, phyloseq_from_dada2, dada2_makeSequenceTable, dada2_seqCounts, tp_replace_in_line, __UNZIP_COLLECTION__, dada2_dada, dada2_mergePairs, dada2_removeBimeraDenovo, cat1, Add_a_column1, tp_head_tool, dada2_plotQualityProfile, __SORTLIST__ - Visualisation, DNA barcoding, Deposition, Analysis, Variant calling + dada2_dada, Add_a_column1, dada2_makeSequenceTable, dada2_plotQualityProfile, collection_element_identifiers, __SORTLIST__, dada2_learnErrors, tp_replace_in_line, dada2_seqCounts, dada2_assignTaxonomyAddspecies, cat1, dada2_filterAndTrim, __UNZIP_COLLECTION__, tp_replace_in_column, phyloseq_from_dada2, tp_head_tool, dada2_removeBimeraDenovo, dada2_mergePairs + DNA barcoding, Analysis, Variant calling, Deposition, Visualisation MIT @@ -1060,8 +1060,8 @@ 2 2 33.0 - Grouping1, metaphlan, fastqc, tp_sort_header_tool, humann, humann_unpack_pathways, graphlan, Grep1, humann_rename_table, tp_find_and_replace, combine_metaphlan_humann, Cut1, bg_sortmerna, fastq_paired_end_interlacer, humann_split_stratified_table, multiqc, cutadapt, taxonomy_krona_chart, graphlan_annotate, humann_renorm_table, humann_regroup_table, export2graphlan - Sequence comparison, Phylogenetic tree visualisation, Visualisation, Sequence composition calculation, Statistical calculation, Phylogenetic inference, Validation, Primer removal, Sequence alignment analysis, Sequencing quality control, Phylogenetic analysis, Sequence trimming, Phylogenetic tree editing, Read pre-processing, Species frequency estimation, Taxonomic classification, Sequence similarity search, Conversion, Aggregation + graphlan_annotate, bg_sortmerna, cutadapt, taxonomy_krona_chart, tp_find_and_replace, export2graphlan, humann_split_stratified_table, metaphlan, humann_regroup_table, fastq_paired_end_interlacer, Grouping1, humann_renorm_table, Grep1, graphlan, humann, tp_sort_header_tool, humann_rename_table, multiqc, fastqc, humann_unpack_pathways, combine_metaphlan_humann, Cut1 + Statistical calculation, Phylogenetic inference, Conversion, Sequencing quality control, Sequence alignment analysis, Sequence comparison, Sequence composition calculation, Phylogenetic analysis, Taxonomic classification, Aggregation, Species frequency estimation, Phylogenetic tree visualisation, Sequence similarity search, Phylogenetic tree editing, Sequence trimming, Validation, Read pre-processing, Primer removal, Visualisation MIT @@ -1082,8 +1082,8 @@ 2 2 6.0 - graphlan, metaphlan, taxonomy_krona_chart, graphlan_annotate, Cut1, export2graphlan - Phylogenetic tree visualisation, Visualisation, Phylogenetic inference, Phylogenetic tree editing, Taxonomic classification, Conversion + metaphlan, graphlan_annotate, taxonomy_krona_chart, export2graphlan, Cut1, graphlan + Taxonomic classification, Phylogenetic inference, Conversion, Phylogenetic tree visualisation, Phylogenetic tree editing, Visualisation MIT @@ -1104,8 +1104,8 @@ 2 2 6.0 - multiqc, fastqc, cutadapt, bg_sortmerna, fastq_paired_end_interlacer - Sequence trimming, Sequence composition calculation, Statistical calculation, Validation, Primer removal, Read pre-processing, Sequence similarity search, Sequence alignment analysis, Sequence comparison, Sequencing quality control + fastq_paired_end_interlacer, multiqc, fastqc, bg_sortmerna, cutadapt + Statistical calculation, Sequence similarity search, Primer removal, Sequencing quality control, Sequence trimming, Sequence alignment analysis, Sequence comparison, Validation, Read pre-processing, Sequence composition calculation MIT @@ -1126,8 +1126,8 @@ 2 2 18.0 - Grep1, humann_rename_table, humann, tp_find_and_replace, humann_renorm_table, tp_sort_header_tool, humann_regroup_table, humann_unpack_pathways, humann_split_stratified_table - Species frequency estimation, Taxonomic classification, Phylogenetic analysis + humann_rename_table, humann_regroup_table, tp_find_and_replace, humann_unpack_pathways, humann_split_stratified_table, humann_renorm_table, Grep1, humann, tp_sort_header_tool + Taxonomic classification, Species frequency estimation, Phylogenetic analysis MIT @@ -1148,8 +1148,8 @@ 2 2 9.0 - collection_column_join, bowtie2, megahit_contig2fastg, bandage_info, bandage_image, metaspades, quast, coverm_contig, megahit - Visualisation, Local alignment, Sequence assembly validation, Read mapping, Genome assembly, Sequence assembly visualisation + bowtie2, megahit_contig2fastg, collection_column_join, metaspades, bandage_image, bandage_info, megahit, coverm_contig, quast + Visualisation, Read mapping, Sequence assembly validation, Sequence assembly visualisation, Local alignment, Genome assembly MIT @@ -1170,8 +1170,8 @@ 1 1 8.0 - ncbi_blastn_wrapper, Count1, cshl_fastq_to_fasta, fastp - Sequence contamination filtering, Sequencing quality control + fastp, cshl_fastq_to_fasta, ncbi_blastn_wrapper, Count1 + Sequencing quality control, Sequence contamination filtering CC-BY-4.0 @@ -1192,8 +1192,8 @@ 1 1 6.0 - falco, kraken2, est_abundance, fastp, recentrifuge - Visualisation, Statistical calculation, Read mapping, Cross-assembly, Sequence contamination filtering, Expression analysis, Taxonomic classification, Sequencing quality control + fastp, recentrifuge, est_abundance, kraken2, falco + Statistical calculation, Taxonomic classification, Expression analysis, Sequencing quality control, Sequence contamination filtering, Read mapping, Visualisation, Cross-assembly GPL-3.0-or-later @@ -1214,8 +1214,8 @@ 1 1 14.0 - Grep1, param_value_from_file, compose_text_param, EMBOSS: maskseq51, datamash_ops, Cut1, fasta_compute_length, Add_a_column1 - Local alignment, Sequence alignment, Global alignment, Sequence alignment analysis, Sequence analysis + Add_a_column1, compose_text_param, EMBOSS: maskseq51, Grep1, datamash_ops, fasta_compute_length, Cut1, param_value_from_file + Sequence alignment analysis, Global alignment, Sequence analysis, Sequence alignment, Local alignment MIT @@ -1236,8 +1236,8 @@ 1 1 12.0 - unicycler, racon, staramr_search, miniasm, nanoplot, bandage_image, PlasFlow, gfa_to_fa, minimap2 - Aggregation, Mapping assembly, Antimicrobial resistance prediction, Sequence analysis, Box-Whisker plot plotting, Pairwise sequence alignment, Genome assembly, Sequence assembly visualisation, Scatter plot plotting, De-novo assembly + unicycler, bandage_image, miniasm, staramr_search, PlasFlow, nanoplot, minimap2, racon, gfa_to_fa + Pairwise sequence alignment, Aggregation, Antimicrobial resistance prediction, Box-Whisker plot plotting, De-novo assembly, Scatter plot plotting, Sequence assembly visualisation, Sequence analysis, Mapping assembly, Genome assembly CC-BY-4.0 @@ -1258,8 +1258,8 @@ 1 1 17.0 - mothur_pre_cluster, mothur_make_group, mothur_summary_seqs, mothur_count_seqs, mothur_unique_seqs, mothur_merge_files, mothur_align_seqs, mothur_filter_seqs, mothur_cluster_split, mothur_screen_seqs, mothur_classify_seqs, mothur_make_shared, krona-text, mothur_classify_otu, mothur_make_biom - Visualisation, Sequence clustering, DNA barcoding, Taxonomic classification, Sequence read processing, Sequencing quality control, Phylogenetic analysis + mothur_unique_seqs, mothur_cluster_split, mothur_summary_seqs, mothur_count_seqs, mothur_make_shared, mothur_make_biom, mothur_merge_files, mothur_screen_seqs, mothur_filter_seqs, mothur_make_group, mothur_classify_seqs, mothur_classify_otu, mothur_align_seqs, mothur_pre_cluster, krona-text + Taxonomic classification, DNA barcoding, Sequence read processing, Sequencing quality control, Sequence clustering, Phylogenetic analysis, Visualisation CC-BY-4.0 @@ -1280,8 +1280,8 @@ 1 1 11.0 - multiqc, kraken2, fastqc, taxonomy_krona_chart, porechop, tp_replace_in_line, fastp, Remove beginning1, datamash_reverse - Visualisation, Sequence composition calculation, Sequence contamination filtering, Statistical calculation, Validation, Taxonomic classification, Sequencing quality control + fastp, datamash_reverse, taxonomy_krona_chart, multiqc, kraken2, tp_replace_in_line, fastqc, porechop, Remove beginning1 + Sequencing quality control, Sequence contamination filtering, Taxonomic classification, Statistical calculation, Validation, Sequence composition calculation, Visualisation CC-BY-4.0 @@ -1302,7 +1302,7 @@ 1 1 7.0 - humann2, taxonomy_krona_chart, metaphlan2krona, humann2_renorm_table, humann2_regroup_table, metaphlan2 + metaphlan2krona, metaphlan2, humann2_renorm_table, taxonomy_krona_chart, humann2, humann2_regroup_table Visualisation CC-BY-4.0 @@ -1324,8 +1324,8 @@ 1 1 47.0 - Grouping1, CONVERTER_fasta_to_tabular, tp_sorted_uniq, sort1, Filter1, MQoutputfilter, tp_replace_in_column, histogram_rpy, tp_tail_tool, join1, count_gff_features, tab2fasta, Cut1, cat1, add_column_headers, Add_a_column1, ggplot2_histogram, minimap2 - Visualisation, Pairwise sequence alignment + Add_a_column1, CONVERTER_fasta_to_tabular, tp_sorted_uniq, histogram_rpy, join1, Grouping1, cat1, tp_tail_tool, count_gff_features, ggplot2_histogram, minimap2, add_column_headers, tp_replace_in_column, Filter1, tab2fasta, Cut1, MQoutputfilter, sort1 + Pairwise sequence alignment, Visualisation MIT @@ -1346,8 +1346,8 @@ 1 1 38.0 - mothur_pre_cluster, mothur_make_contigs, mothur_count_seqs, mothur_cluster, mothur_unique_seqs, mothur_venn, mothur_classify_seqs, mothur_make_shared, mothur_make_biom, mothur_summary_seqs, mothur_cluster_split, mothur_chimera_vsearch, mothur_screen_seqs, mothur_remove_lineage, mothur_summary_single, mothur_remove_seqs, XY_Plot_1, mothur_remove_groups, mothur_taxonomy_to_krona, mothur_count_groups, mothur_align_seqs, mothur_filter_seqs, mothur_dist_shared, mothur_tree_shared, mothur_dist_seqs, mothur_classify_otu, mothur_heatmap_sim, mothur_rarefaction_single, mothur_sub_sample, newick_display, taxonomy_krona_chart, mothur_seq_error, mothur_get_groups - Visualisation, Phylogenetic tree reconstruction, Sequence clustering, Phylogenetic tree generation, DNA barcoding, Phylogenetic tree analysis, Taxonomic classification, Sequence read processing, Sequencing quality control, Phylogenetic analysis + mothur_count_seqs, mothur_chimera_vsearch, mothur_get_groups, mothur_screen_seqs, mothur_rarefaction_single, mothur_align_seqs, newick_display, mothur_make_shared, taxonomy_krona_chart, mothur_cluster, mothur_remove_seqs, mothur_summary_single, mothur_sub_sample, mothur_remove_groups, mothur_classify_seqs, mothur_seq_error, mothur_count_groups, mothur_cluster_split, mothur_tree_shared, mothur_summary_seqs, mothur_make_contigs, mothur_dist_shared, mothur_dist_seqs, XY_Plot_1, mothur_filter_seqs, mothur_remove_lineage, mothur_classify_otu, mothur_pre_cluster, mothur_unique_seqs, mothur_venn, mothur_heatmap_sim, mothur_make_biom, mothur_taxonomy_to_krona + Taxonomic classification, DNA barcoding, Sequence read processing, Sequencing quality control, Phylogenetic tree generation, Phylogenetic tree reconstruction, Sequence clustering, Phylogenetic tree analysis, Phylogenetic analysis, Visualisation CC-BY-4.0 @@ -1369,7 +1369,7 @@ 1 1.0 lotus2 - Sequence feature detection, DNA barcoding + DNA barcoding, Sequence feature detection MIT @@ -1390,8 +1390,8 @@ 1 1 8.0 - kraken2, Filter1, fastqc, taxonomy_krona_chart, krakentools_kreport2krona, porechop, fastp - Visualisation, Sequence composition calculation, Sequence contamination filtering, Statistical calculation, Taxonomic classification, Aggregation, Sequencing quality control + fastp, taxonomy_krona_chart, krakentools_kreport2krona, kraken2, fastqc, Filter1, porechop + Sequencing quality control, Sequence contamination filtering, Taxonomic classification, Statistical calculation, Aggregation, Sequence composition calculation, Visualisation MIT @@ -1413,7 +1413,7 @@ 1 6.0 krakentools_alpha_diversity, krakentools_beta_diversity - Visualisation, Aggregation + Aggregation, Visualisation MIT @@ -1434,8 +1434,8 @@ 1 1 3.0 - mothur_summary_seqs, mothur_classify_seqs, mothur_remove_lineage - Visualisation, Sequence clustering, DNA barcoding, Taxonomic classification, Sequence read processing, Sequencing quality control, Phylogenetic analysis + mothur_remove_lineage, mothur_summary_seqs, mothur_classify_seqs + Taxonomic classification, DNA barcoding, Sequence read processing, Sequencing quality control, Sequence clustering, Phylogenetic analysis, Visualisation MIT @@ -1456,8 +1456,8 @@ 1 1 5.0 - mothur_summary_seqs, mothur_count_seqs, mothur_screen_seqs, mothur_unique_seqs - Visualisation, Sequence clustering, DNA barcoding, Taxonomic classification, Sequence read processing, Sequencing quality control, Phylogenetic analysis + mothur_unique_seqs, mothur_summary_seqs, mothur_count_seqs, mothur_screen_seqs + Taxonomic classification, DNA barcoding, Sequence read processing, Sequencing quality control, Sequence clustering, Phylogenetic analysis, Visualisation MIT @@ -1478,8 +1478,8 @@ 1 1 6.0 - mothur_heatmap_sim, newick_display, mothur_dist_shared, mothur_venn, collapse_dataset, mothur_tree_shared - Visualisation, Phylogenetic tree reconstruction, Sequence clustering, Phylogenetic tree generation, DNA barcoding, Phylogenetic tree analysis, Taxonomic classification, Sequence read processing, Sequencing quality control, Phylogenetic analysis + mothur_tree_shared, mothur_venn, mothur_heatmap_sim, mothur_dist_shared, collapse_dataset, newick_display + Taxonomic classification, DNA barcoding, Sequence read processing, Sequencing quality control, Phylogenetic tree generation, Phylogenetic tree reconstruction, Sequence clustering, Phylogenetic tree analysis, Phylogenetic analysis, Visualisation MIT @@ -1501,7 +1501,7 @@ 1 3.0 XY_Plot_1, mothur_rarefaction_single, mothur_summary_single - Visualisation, Sequence clustering, DNA barcoding, Taxonomic classification, Sequence read processing, Sequencing quality control, Phylogenetic analysis + Taxonomic classification, DNA barcoding, Sequence read processing, Sequencing quality control, Sequence clustering, Phylogenetic analysis, Visualisation MIT @@ -1522,8 +1522,8 @@ 1 1 4.0 - mothur_rarefaction_single, mothur_dist_seqs, mothur_make_shared, mothur_cluster - Visualisation, Sequence clustering, DNA barcoding, Taxonomic classification, Sequence read processing, Sequencing quality control, Phylogenetic analysis + mothur_cluster, mothur_dist_seqs, mothur_make_shared, mothur_rarefaction_single + Taxonomic classification, DNA barcoding, Sequence read processing, Sequencing quality control, Sequence clustering, Phylogenetic analysis, Visualisation MIT @@ -1544,8 +1544,8 @@ 1 1 6.0 - mothur_remove_groups, mothur_sub_sample, mothur_count_groups, mothur_cluster_split, mothur_make_shared, mothur_classify_otu - Visualisation, Sequence clustering, DNA barcoding, Taxonomic classification, Sequence read processing, Sequencing quality control, Phylogenetic analysis + mothur_cluster_split, mothur_make_shared, mothur_sub_sample, mothur_remove_groups, mothur_classify_otu, mothur_count_groups + Taxonomic classification, DNA barcoding, Sequence read processing, Sequencing quality control, Sequence clustering, Phylogenetic analysis, Visualisation MIT @@ -1566,8 +1566,8 @@ 1 1 9.0 - mothur_pre_cluster, mothur_summary_seqs, mothur_unique_seqs, mothur_filter_seqs, mothur_chimera_vsearch, mothur_screen_seqs, mothur_remove_seqs - Visualisation, Sequence clustering, DNA barcoding, Taxonomic classification, Sequence read processing, Sequencing quality control, Phylogenetic analysis + mothur_unique_seqs, mothur_summary_seqs, mothur_chimera_vsearch, mothur_remove_seqs, mothur_screen_seqs, mothur_filter_seqs, mothur_pre_cluster + Taxonomic classification, DNA barcoding, Sequence read processing, Sequencing quality control, Sequence clustering, Phylogenetic analysis, Visualisation MIT @@ -1588,8 +1588,8 @@ 1 1 12.0 - unicycler, racon, staramr_search, miniasm, nanoplot, bandage_image, PlasFlow, gfa_to_fa, minimap2 - Aggregation, Mapping assembly, Antimicrobial resistance prediction, Sequence analysis, Box-Whisker plot plotting, Pairwise sequence alignment, Genome assembly, Sequence assembly visualisation, Scatter plot plotting, De-novo assembly + unicycler, bandage_image, miniasm, staramr_search, PlasFlow, nanoplot, minimap2, racon, gfa_to_fa + Pairwise sequence alignment, Aggregation, Antimicrobial resistance prediction, Box-Whisker plot plotting, De-novo assembly, Scatter plot plotting, Sequence assembly visualisation, Sequence analysis, Mapping assembly, Genome assembly Microbiology CC-BY-4.0 @@ -1611,7 +1611,7 @@ 1 2.0 fastp, shovill - Genome assembly, Sequence contamination filtering, Sequencing quality control + Sequencing quality control, Sequence contamination filtering, Genome assembly Apache-2.0 @@ -1632,8 +1632,8 @@ 1 1 7.0 - fasta_merge_files_and_filter_unique_sequences, ncbi_blastn_wrapper, samtools_stats, picard_SamToFastq, shovill, ngsutils_bam_filter, minimap2 - Read pre-processing, Sequence contamination filtering, Formatting, Pairwise sequence alignment, Genome assembly, Sequencing quality control, Variant calling + ncbi_blastn_wrapper, shovill, picard_SamToFastq, ngsutils_bam_filter, minimap2, samtools_stats, fasta_merge_files_and_filter_unique_sequences + Sequencing quality control, Formatting, Sequence contamination filtering, Pairwise sequence alignment, Variant calling, Read pre-processing, Genome assembly Apache-2.0 @@ -1654,8 +1654,8 @@ 1 1 3.0 - kraken2, Kraken2Tax, taxonomy_krona_chart - Visualisation, Taxonomic classification + Kraken2Tax, kraken2, taxonomy_krona_chart + Taxonomic classification, Visualisation Apache-2.0 @@ -1676,8 +1676,8 @@ 1 1 3.0 - kraken2, Kraken2Tax, taxonomy_krona_chart - Visualisation, Taxonomic classification + Kraken2Tax, kraken2, taxonomy_krona_chart + Taxonomic classification, Visualisation Apache-2.0 @@ -1685,6 +1685,50 @@ True False + + + MPXV (Mpox) Phylogenetic Analysis with Squirrel + WorkflowHub + 2196 + https://workflowhub.eu/workflows/2196?version=1 + Tristan Reynolds, Ammar Aziz + amplicon, mpox, ont, virus, mpxv, phylogeny + 2026-06-18 + 2026-06-25 + 1 + 1 + 3.0 + squirrel_phylo, regex1, squirrel_qc + Sequencing quality control, Phylogenetic analysis + Bioinformatics, Biomedical science, Genomics, Virology + MIT + 10.48546/workflowhub.workflow.2196.1 + Melbourne Bioinformatics, Galaxy Australia + True + False + + + + Viral Amplicon Analysis Pipeline for ONT Data + WorkflowHub + 2195 + https://workflowhub.eu/workflows/2195?version=1 + Tristan Reynolds, Ammar Aziz + amplicon, mpox, ont, virus, mpxv, phylogeny + 2026-06-18 + 2026-06-25 + 1 + 1 + 12.0 + artic_minion, multiqc, mosdepth, XY_Plot_1, regex1, __BUILD_LIST__, tp_cat, fastplong, bedtools_makewindowsbed + Sequencing quality control, Sequence alignment, Validation, Mapping + Bioinformatics, Biomedical science, Genomics, Virology + MIT + 10.48546/workflowhub.workflow.2195.1 + Melbourne Bioinformatics, Galaxy Australia + True + False + Taxonomy Assignment with QIIME2 @@ -1698,8 +1742,8 @@ 1 1 19.0 - qiime2__feature_classifier__classify_sklearn, qiime2__feature_table__summarize, qiime2_core__tools__import, qiime2__taxa__barplot, qiime2__feature_classifier__fit_classifier_naive_bayes, qiime2__feature_table__tabulate_seqs, qiime2__feature_classifier__extract_reads, csv_to_tabular, tp_easyjoin_tool, Remove beginning1, biom_convert, qiime_extract_viz, qiime2_core__tools__export, tabular_to_csv - Visualisation, Formatting, Demultiplexing, Taxonomic classification + qiime2__feature_table__tabulate_seqs, biom_convert, csv_to_tabular, tp_easyjoin_tool, qiime2_core__tools__import, qiime2__feature_classifier__classify_sklearn, qiime2__feature_table__summarize, tabular_to_csv, qiime2__taxa__barplot, qiime_extract_viz, qiime2__feature_classifier__fit_classifier_naive_bayes, qiime2_core__tools__export, qiime2__feature_classifier__extract_reads, Remove beginning1 + Taxonomic classification, Formatting, Demultiplexing, Visualisation Taxonomy CC-BY-4.0 10.48546/workflowhub.workflow.2098.1 @@ -1720,8 +1764,8 @@ 2 2 29.0 - collection_column_join, krakentools_beta_diversity, Prepare alpha diversity summary file\nPaste1, Prepare alpha diversity summary file (paste Simpson and Fisher results)\nPaste1, kraken2, Prepare alpha diversity summary file (paste sample identifiers and Simpson results)\nPaste1, taxonomy_krona_chart, collection_element_identifiers, krakentools_kreport2krona, Fisher results contains a header line we want to exclude "Fisher's alpha...loading"\nShow tail1, est_abundance, __RELABEL_FROM_FILE__, add_line_to_file, regex1, krakentools_alpha_diversity, cat_multiple, Extract column name and fraction_total_reads from Bracken report\nCut1, krakentools_combine_kreports - Visualisation, Statistical calculation, Taxonomic classification, Aggregation + __RELABEL_FROM_FILE__, collection_column_join, cat_multiple, Prepare alpha diversity summary file\nPaste1, collection_element_identifiers, krakentools_combine_kreports, krakentools_kreport2krona, krakentools_beta_diversity, est_abundance, taxonomy_krona_chart, kraken2, Prepare alpha diversity summary file (paste sample identifiers and Simpson results)\nPaste1, Prepare alpha diversity summary file (paste Simpson and Fisher results)\nPaste1, add_line_to_file, krakentools_alpha_diversity, regex1, Extract column name and fraction_total_reads from Bracken report\nCut1, Fisher results contains a header line we want to exclude "Fisher's alpha...loading"\nShow tail1 + Statistical calculation, Taxonomic classification, Aggregation, Visualisation Metagenomics, Taxonomy CC-BY-4.0 10.48546/workflowhub.workflow.1199.2 @@ -1742,8 +1786,8 @@ 1 1 17.0 - , humann2, taxonomy_krona_chart, metaphlan2krona, humann2_renorm_table, humann2_regroup_table, Cut1, merge_metaphlan_tables, metaphlan2 - Visualisation, Taxonomic classification + , metaphlan2krona, metaphlan2, taxonomy_krona_chart, humann2_renorm_table, merge_metaphlan_tables, humann2, humann2_regroup_table, Cut1 + Taxonomic classification, Visualisation Metagenomic sequencing, Metagenomics CC-BY-4.0 10.48546/workflowhub.workflow.624.1 @@ -1764,8 +1808,8 @@ 1 1 4.0 - mothur_dist_shared, mothur_tree_shared, mothur_heatmap_sim, newick_display - Visualisation, Phylogenetic tree reconstruction, Sequence clustering, Phylogenetic tree generation, DNA barcoding, Phylogenetic tree analysis, Taxonomic classification, Sequence read processing, Sequencing quality control, Phylogenetic analysis + mothur_tree_shared, mothur_heatmap_sim, newick_display, mothur_dist_shared + Taxonomic classification, DNA barcoding, Sequence read processing, Sequencing quality control, Phylogenetic tree generation, Phylogenetic tree reconstruction, Sequence clustering, Phylogenetic tree analysis, Phylogenetic analysis, Visualisation CC-BY-4.0 @@ -1787,7 +1831,7 @@ 1 3.0 XY_Plot_1, mothur_rarefaction_single, mothur_summary_single - Visualisation, Sequence clustering, DNA barcoding, Taxonomic classification, Sequence read processing, Sequencing quality control, Phylogenetic analysis + Taxonomic classification, DNA barcoding, Sequence read processing, Sequencing quality control, Sequence clustering, Phylogenetic analysis, Visualisation CC-BY-4.0 @@ -1808,8 +1852,8 @@ 1 1 5.0 - mothur_sub_sample, mothur_count_groups, mothur_cluster_split, mothur_make_shared, mothur_classify_otu - Visualisation, Sequence clustering, DNA barcoding, Taxonomic classification, Sequence read processing, Sequencing quality control, Phylogenetic analysis + mothur_cluster_split, mothur_make_shared, mothur_sub_sample, mothur_classify_otu, mothur_count_groups + Taxonomic classification, DNA barcoding, Sequence read processing, Sequencing quality control, Sequence clustering, Phylogenetic analysis, Visualisation CC-BY-4.0 @@ -1830,8 +1874,8 @@ 1 1 2.0 - mothur_classify_seqs, mothur_remove_lineage - Visualisation, Sequence clustering, DNA barcoding, Taxonomic classification, Sequence read processing, Sequencing quality control, Phylogenetic analysis + mothur_remove_lineage, mothur_classify_seqs + Taxonomic classification, DNA barcoding, Sequence read processing, Sequencing quality control, Sequence clustering, Phylogenetic analysis, Visualisation CC-BY-4.0 @@ -1852,8 +1896,8 @@ 1 1 5.0 - mothur_summary_seqs, mothur_count_seqs, mothur_screen_seqs, mothur_unique_seqs - Visualisation, Sequence clustering, DNA barcoding, Taxonomic classification, Sequence read processing, Sequencing quality control, Phylogenetic analysis + mothur_unique_seqs, mothur_summary_seqs, mothur_count_seqs, mothur_screen_seqs + Taxonomic classification, DNA barcoding, Sequence read processing, Sequencing quality control, Sequence clustering, Phylogenetic analysis, Visualisation CC-BY-4.0 @@ -1874,8 +1918,8 @@ 1 1 9.0 - mothur_pre_cluster, mothur_summary_seqs, mothur_unique_seqs, mothur_filter_seqs, mothur_chimera_vsearch, mothur_screen_seqs, mothur_remove_seqs - Visualisation, Sequence clustering, DNA barcoding, Taxonomic classification, Sequence read processing, Sequencing quality control, Phylogenetic analysis + mothur_unique_seqs, mothur_summary_seqs, mothur_chimera_vsearch, mothur_remove_seqs, mothur_screen_seqs, mothur_filter_seqs, mothur_pre_cluster + Taxonomic classification, DNA barcoding, Sequence read processing, Sequencing quality control, Sequence clustering, Phylogenetic analysis, Visualisation CC-BY-4.0 @@ -1896,8 +1940,8 @@ 1 1 15.0 - bcftools_consensus, tp_awk_tool, tb_profiler_profile, kraken2, __FLATTEN__, multiqc, mosdepth, snippy, qualimap_bamqc, tb_variant_filter, tbvcfreport, fastp, tp_sed_tool, EMBOSS: seqret84 - Phylogenetic tree visualisation, Sequence alignment, Validation, Antimicrobial resistance prediction, Phylogenetic tree generation, Variant calling, Sequence analysis, Local alignment, Sequence contamination filtering, Global alignment, Sequence alignment analysis, Taxonomic classification, Sequencing quality control + fastp, tp_awk_tool, qualimap_bamqc, EMBOSS: seqret84, kraken2, mosdepth, __FLATTEN__, tp_sed_tool, snippy, multiqc, bcftools_consensus, tb_variant_filter, tb_profiler_profile, tbvcfreport + Taxonomic classification, Antimicrobial resistance prediction, Variant calling, Sequence alignment, Phylogenetic tree visualisation, Sequencing quality control, Sequence contamination filtering, Sequence alignment analysis, Phylogenetic tree generation, Validation, Global alignment, Sequence analysis, Local alignment Genetic variation, Infectious disease, Microbiology, Public health and epidemiology, Sequence assembly AGPL-3.0-or-later @@ -1918,8 +1962,8 @@ 1 1 14.0 - kma_map, hamronize_summarize, seqsero2, bbtools_bbduk, __UNZIP_COLLECTION__, srst2, shovill, mob_recon, hamronize_tool, sistr_cmd, bbtools_tadpole - Visualisation, Multilocus sequence typing, Sequence alignment, Genome indexing, Read mapping, Sequence contamination filtering, Clustering, Genome alignment, Parsing, Data handling, Genome assembly, RNA-Seq analysis, Sequence trimming, Antimicrobial resistance prediction, Read binning, Sequence analysis + seqsero2, shovill, bbtools_tadpole, hamronize_tool, bbtools_bbduk, sistr_cmd, mob_recon, kma_map, __UNZIP_COLLECTION__, hamronize_summarize, srst2 + Genome alignment, Read binning, Sequence contamination filtering, Clustering, Antimicrobial resistance prediction, Data handling, Sequence alignment, Parsing, Genome indexing, RNA-Seq analysis, Sequence trimming, Sequence analysis, Read mapping, Multilocus sequence typing, Visualisation, Genome assembly GPL-3.0 @@ -1962,8 +2006,8 @@ 1 1 10.0 - hamronize_summarize, tp_find_and_replace, abricate, staramr_search, collapse_dataset, shovill, hamronize_tool - Parsing, Data handling, Genome assembly, Antimicrobial resistance prediction + abricate, shovill, hamronize_tool, tp_find_and_replace, staramr_search, collapse_dataset, hamronize_summarize + Antimicrobial resistance prediction, Data handling, Parsing, Genome assembly GPL-3.0 @@ -2006,8 +2050,8 @@ 2 2 36.0 - , hamronize_summarize, tp_text_file_with_recurring_lines, cat1, hamronize_tool, abricate, addValue, __APPLY_RULES__, __MERGE_COLLECTION__, collapse_dataset, shovill, Grep1, cast, tp_find_and_replace, Cut1, tp_split_on_column, datamash_ops, staramr_search, cat_multi_datasets - Parsing, Data handling, Genome assembly, Antimicrobial resistance prediction + , cat_multi_datasets, shovill, tp_split_on_column, staramr_search, collapse_dataset, datamash_ops, abricate, hamronize_tool, tp_find_and_replace, cat1, tp_text_file_with_recurring_lines, cast, __APPLY_RULES__, addValue, Grep1, hamronize_summarize, __MERGE_COLLECTION__, Cut1 + Antimicrobial resistance prediction, Data handling, Parsing, Genome assembly MIT @@ -2017,21 +2061,43 @@ - Copy of Metaproteomics_GTN shared by user engy.nasr + Training: 16S rRNA Analysis with Nanopore Sequencing Reads https://usegalaxy.eu - 6ca1b4fe047a03d2 - https://usegalaxy.eu/published/workflow?id=6ca1b4fe047a03d2 + 2a093e63ebf6876b + https://usegalaxy.eu/published/workflow?id=2a093e63ebf6876b - proteomics, name:microgalaxy - 2026-04-27 - 2026-04-27 + metagenomics, name:microgalaxy + 2025-12-01 + 2026-06-12 + 3 + 3 + + fastp, datamash_reverse, taxonomy_krona_chart, multiqc, kraken2, tp_replace_in_line, fastqc, porechop, Remove beginning1 + Sequencing quality control, Sequence contamination filtering, Taxonomic classification, Statistical calculation, Validation, Sequence composition calculation, Visualisation + + + + + True + False + + + + Sadowsky_MetaG-DBgen_02102026 + https://usegalaxy.eu + 7be08f99f83c927e + https://usegalaxy.eu/published/workflow?id=7be08f99f83c927e + Subina Mehta + name:microgalaxy + 2026-02-10 + 2026-06-09 1 1 - search_gui, peptide_shaker, sqlite_to_tabular, query_tabular, unipept - Visualisation, Prediction and recognition - + validate_fasta_database, Remove beginning1, regexColumn1, cat_bins, trim_galore, fastqc, eggnog_mapper, collapse_dataset, regex1, query_tabular, tp_cat, tab2fasta, fasta_merge_files_and_filter_unique_sequences, maxbin2, fasta2tab, fraggenescan + Statistical calculation, Taxonomic classification, Genome annotation, Sequencing quality control, Sequence trimming, Sequence assembly, Fold recognition, Information extraction, Homology-based gene prediction, Gene prediction, Read pre-processing, Coding region prediction, Primer removal, Query and retrieval, Sequence composition calculation + CC-BY-4.0 True @@ -2039,19 +2105,19 @@ - Training: 16S rRNA Analysis with Nanopore Sequencing Reads + Copy of Metaproteomics_GTN shared by user engy.nasr https://usegalaxy.eu - 2a093e63ebf6876b - https://usegalaxy.eu/published/workflow?id=2a093e63ebf6876b + 6ca1b4fe047a03d2 + https://usegalaxy.eu/published/workflow?id=6ca1b4fe047a03d2 - metagenomics, name:microgalaxy - 2025-12-01 - 2026-03-16 - 2 - 2 + proteomics, name:microgalaxy + 2026-04-27 + 2026-04-27 + 1 + 1 - multiqc, kraken2, fastqc, taxonomy_krona_chart, porechop, tp_replace_in_line, fastp, Remove beginning1, datamash_reverse - Visualisation, Sequence composition calculation, Sequence contamination filtering, Statistical calculation, Validation, Taxonomic classification, Sequencing quality control + peptide_shaker, unipept, search_gui, sqlite_to_tabular, query_tabular + Prediction and recognition, Visualisation @@ -2072,8 +2138,8 @@ 0 0 - fasplit, tp_awk_tool, tp_grep_tool, fastqc, checkm_lineage_wf, hmmer_hmmscan, coverm_genome, quast, coverm_contig, fraggenescan, maxbin2, cat_bins, tp_cat, trim_galore, interproscan, sort1 - Visualisation, Sequence composition calculation, Formatting, Statistical calculation, Validation, Sequence database search, Format validation, Primer removal, Coding region prediction, Local alignment, Sequence assembly, Database search, Sequence profile generation, Sequencing quality control, Protein feature detection, Sequence trimming, Multiple sequence alignment, Sequence assembly validation, Sequence motif recognition, Sequence generation, Read pre-processing, Data retrieval, Gene prediction, Taxonomic classification, Conversion, Probabilistic sequence generation + coverm_genome, fasplit, tp_awk_tool, tp_grep_tool, sort1, cat_bins, trim_galore, fastqc, checkm_lineage_wf, coverm_contig, hmmer_hmmscan, interproscan, tp_cat, maxbin2, quast, fraggenescan + Statistical calculation, Formatting, Visualisation, Format validation, Conversion, Probabilistic sequence generation, Sequencing quality control, Sequence assembly, Protein feature detection, Gene prediction, Sequence motif recognition, Coding region prediction, Sequence composition calculation, Sequence generation, Database search, Sequence database search, Data retrieval, Taxonomic classification, Multiple sequence alignment, Sequence assembly validation, Sequence trimming, Sequence profile generation, Validation, Read pre-processing, Primer removal, Local alignment @@ -2094,8 +2160,8 @@ 3 3 - metaphlan, kraken2, collection_element_identifiers, taxonomy_krona_chart, metaphlan2krona, krakentools_kreport2krona, taxpasta, est_abundance, sylph_profile, add_line_to_file, datamash_transpose, Remove beginning1, cat1 - Visualisation, Formatting, Statistical calculation, Taxonomic classification, Conversion, Aggregation, Standardisation and normalisation + metaphlan, metaphlan2krona, collection_element_identifiers, sylph_profile, taxonomy_krona_chart, krakentools_kreport2krona, est_abundance, kraken2, cat1, add_line_to_file, taxpasta, datamash_transpose, Remove beginning1 + Statistical calculation, Taxonomic classification, Standardisation and normalisation, Formatting, Aggregation, Conversion, Visualisation MIT @@ -2116,8 +2182,8 @@ 16 16 - multiqc, __FLATTEN__, collection_element_identifiers, __RELABEL_FROM_FILE__, __MERGE_COLLECTION__, regex1, checkm2 - Sequence composition calculation, Sequence assembly validation, Statistical calculation, Validation, Sequencing quality control + __RELABEL_FROM_FILE__, checkm2, collection_element_identifiers, multiqc, __FLATTEN__, __MERGE_COLLECTION__, regex1 + Statistical calculation, Sequencing quality control, Validation, Sequence composition calculation, Sequence assembly validation MIT @@ -2138,8 +2204,8 @@ 193 193 - compose_text_param, ampvis2_heatmap, fastqc, bg_column_arrange_by_header, ampvis2_subset_samples, datamash_transpose, unzip, biom_convert, maaslin2, volcanoplot, __FLATTEN__, calculate_numeric_param, mmuphin, phyloseq_tax_glom, ampvis2_load, param_value_from_file, tp_awk_tool, tp_cut_tool, tp_easyjoin_tool, Remove beginning1, multiqc, ampvis2_ordinate, phyloseq_from_biom, phyloseq_add_rank_names, ampvis2_export_otu, regex1, lotus2, decontam - Visualisation, Sequence feature detection, Sequence composition calculation, Filtering, Formatting, Statistical calculation, Deposition, Validation, Analysis, Standardisation and normalisation, Classification, DNA barcoding, Sequencing quality control + __FLATTEN__, ampvis2_heatmap, datamash_transpose, regex1, ampvis2_load, mmuphin, maaslin2, ampvis2_ordinate, unzip, param_value_from_file, phyloseq_from_biom, tp_awk_tool, phyloseq_add_rank_names, calculate_numeric_param, ampvis2_export_otu, bg_column_arrange_by_header, volcanoplot, tp_cut_tool, biom_convert, Remove beginning1, tp_easyjoin_tool, multiqc, lotus2, compose_text_param, fastqc, ampvis2_subset_samples, decontam, phyloseq_tax_glom + Statistical calculation, Formatting, DNA barcoding, Filtering, Sequence feature detection, Sequencing quality control, Standardisation and normalisation, Analysis, Validation, Deposition, Sequence composition calculation, Visualisation, Classification MIT @@ -2160,8 +2226,8 @@ 18 18 - metaphlan, tp_text_file_with_recurring_lines, est_abundance, datamash_transpose, cat1, tp_sed_tool, sort1, humann, kraken2, collection_element_identifiers, krakentools_kreport2krona, csv_to_tabular, collapse_dataset, humann_unpack_pathways, humann_rename_table, tp_awk_tool, tp_replace_in_line, __UNZIP_COLLECTION__, add_line_to_file, tp_easyjoin_tool, Remove beginning1, krakentools_alpha_diversity, fastq_paired_end_interlacer, collection_column_join, taxonomy_krona_chart, taxpasta, sylph_profile, humann_renorm_table, humann_regroup_table - Visualisation, Formatting, Statistical calculation, Standardisation and normalisation, Species frequency estimation, Taxonomic classification, Conversion, Aggregation, Phylogenetic analysis + collection_element_identifiers, krakentools_kreport2krona, tp_replace_in_line, collapse_dataset, datamash_transpose, krakentools_alpha_diversity, tp_awk_tool, csv_to_tabular, taxonomy_krona_chart, est_abundance, kraken2, cat1, tp_text_file_with_recurring_lines, taxpasta, metaphlan, humann_regroup_table, sylph_profile, fastq_paired_end_interlacer, humann_renorm_table, Remove beginning1, humann, sort1, humann_rename_table, collection_column_join, tp_easyjoin_tool, tp_sed_tool, humann_unpack_pathways, add_line_to_file, __UNZIP_COLLECTION__ + Statistical calculation, Taxonomic classification, Formatting, Aggregation, Species frequency estimation, Conversion, Standardisation and normalisation, Phylogenetic analysis, Visualisation MIT @@ -2182,8 +2248,8 @@ 48 48 - collection_column_join, multiqc, fastqc, __FILTER_FAILED_DATASETS__, featurecounts, umi_tools_dedup, rna_star, umi_tools_extract - Read summarisation, Sequence composition calculation, RNA-Seq quantification, Statistical calculation, Sequence alignment, Validation, Sequencing quality control + umi_tools_dedup, collection_column_join, umi_tools_extract, multiqc, fastqc, featurecounts, __FILTER_FAILED_DATASETS__, rna_star + Sequencing quality control, Statistical calculation, Validation, Read summarisation, Sequence alignment, Sequence composition calculation, RNA-Seq quantification MIT @@ -2204,8 +2270,8 @@ 14 14 - fasplit, tp_awk_tool, tp_grep_tool, fastqc, checkm_lineage_wf, hmmer_hmmscan, coverm_genome, quast, coverm_contig, fraggenescan, maxbin2, tp_cat, cat_bins, kofamscan, trim_galore, interproscan, sort1 - Visualisation, Sequence composition calculation, Formatting, Statistical calculation, Gene functional annotation, Validation, Sequence database search, Format validation, Primer removal, Coding region prediction, Local alignment, Sequence assembly, Database search, Sequence profile generation, Sequencing quality control, Protein feature detection, Sequence trimming, Multiple sequence alignment, Sequence assembly validation, Sequence motif recognition, Sequence generation, Sequence analysis, Read pre-processing, Data retrieval, Gene prediction, Taxonomic classification, Conversion, Probabilistic sequence generation + coverm_genome, fasplit, tp_awk_tool, tp_grep_tool, sort1, cat_bins, trim_galore, fastqc, checkm_lineage_wf, interproscan, coverm_contig, hmmer_hmmscan, kofamscan, tp_cat, maxbin2, quast, fraggenescan + Statistical calculation, Formatting, Gene functional annotation, Visualisation, Format validation, Conversion, Probabilistic sequence generation, Sequencing quality control, Sequence assembly, Protein feature detection, Gene prediction, Sequence motif recognition, Coding region prediction, Sequence composition calculation, Sequence generation, Database search, Sequence database search, Data retrieval, Taxonomic classification, Multiple sequence alignment, Sequence assembly validation, Sequence trimming, Sequence profile generation, Validation, Sequence analysis, Read pre-processing, Primer removal, Local alignment MIT @@ -2226,8 +2292,8 @@ 3 3 - Grouping1, group_humann2_uniref_abundances_to_go, fastqc, humann2_renorm_table, humann2_unpack_pathways, tp_sort_header_tool, humann2_genefamilies_genus_level, humann2, metaphlan2krona, Grep1, format_metaphlan2_output, graphlan, bg_sortmerna, fastq_paired_end_interlacer, multiqc, combine_metaphlan2_humann2, cutadapt, taxonomy_krona_chart, graphlan_annotate, export2graphlan, metaphlan2 - Sequence comparison, Phylogenetic tree visualisation, Visualisation, Sequence composition calculation, Formatting, Statistical calculation, Phylogenetic inference, Validation, Primer removal, Sequence alignment analysis, Sequencing quality control, Sequence trimming, Phylogenetic tree editing, Read pre-processing, Taxonomic classification, Sequence similarity search, Conversion + graphlan_annotate, humann2_renorm_table, combine_metaphlan2_humann2, bg_sortmerna, cutadapt, humann2_genefamilies_genus_level, taxonomy_krona_chart, export2graphlan, metaphlan2, fastq_paired_end_interlacer, group_humann2_uniref_abundances_to_go, Grouping1, Grep1, humann2, graphlan, tp_sort_header_tool, metaphlan2krona, humann2_unpack_pathways, format_metaphlan2_output, multiqc, fastqc + Statistical calculation, Phylogenetic inference, Taxonomic classification, Formatting, Conversion, Phylogenetic tree visualisation, Sequence similarity search, Sequence composition calculation, Phylogenetic tree editing, Sequencing quality control, Sequence trimming, Sequence alignment analysis, Sequence comparison, Validation, Read pre-processing, Primer removal, Visualisation MIT @@ -2248,8 +2314,8 @@ 6 6 - collection_column_join, kallisto_quant, fastqc, __UNZIP_COLLECTION__, trim_galore, bg_sortmerna - Sequence trimming, Sequence composition calculation, Statistical calculation, Gene expression profiling, Primer removal, Read pre-processing, Sequence similarity search, Sequence alignment analysis, Sequence comparison, Sequencing quality control + kallisto_quant, collection_column_join, trim_galore, fastqc, bg_sortmerna, __UNZIP_COLLECTION__ + Statistical calculation, Sequence similarity search, Sequencing quality control, Gene expression profiling, Sequence trimming, Sequence alignment analysis, Sequence comparison, Read pre-processing, Primer removal, Sequence composition calculation MIT @@ -2270,8 +2336,8 @@ 2 2 - tp_split_on_column, regexColumn1, rbc_mafft, bg_diamond_view, Filter1, bg_diamond, join1, tab2fasta, collapse_dataset, Cut1, cat1, rapidnj, Add_a_column1, gops_intersect_1 - Sequence alignment analysis, Multiple sequence alignment, Phylogenetic tree generation + Add_a_column1, tab2fasta, tp_split_on_column, gops_intersect_1, rbc_mafft, join1, bg_diamond, cat1, collapse_dataset, rapidnj, Filter1, bg_diamond_view, Cut1, regexColumn1 + Sequence alignment analysis, Phylogenetic tree generation, Multiple sequence alignment @@ -2292,8 +2358,8 @@ 40 40 - search_gui, peptide_shaker, sqlite_to_tabular, query_tabular, unipept - Visualisation, Prediction and recognition + peptide_shaker, unipept, search_gui, sqlite_to_tabular, query_tabular + Prediction and recognition, Visualisation MIT @@ -2314,7 +2380,7 @@ 5 5 - Grep1, __BUILD_LIST__, map_param_value, __EXTRACT_DATASET__, __FILTER_EMPTY_DATASETS__ + __EXTRACT_DATASET__, map_param_value, Grep1, __BUILD_LIST__, __FILTER_EMPTY_DATASETS__ MIT @@ -2336,8 +2402,8 @@ 1 1 - tp_replace_in_column, flashlfq, Filter1, msconvert, tp_replace_in_line, Cut1, regex1, Remove beginning1, search_gui, peptide_shaker, query_tabular, unipept - Visualisation, Label-free quantification, Prediction and recognition, Filtering, Formatting + peptide_shaker, search_gui, unipept, flashlfq, tp_replace_in_line, Cut1, regex1, msconvert, tp_replace_in_column, query_tabular, Filter1, Remove beginning1 + Formatting, Prediction and recognition, Filtering, Visualisation, Label-free quantification MIT @@ -2358,8 +2424,8 @@ 3 3 - metaquantome_db, metaquantome_sample, metaquantome_stat, metaquantome_filter, metaquantome_viz, metaquantome_expand - Visualisation, Statistical inference, Quantification, Heat map generation, Query and retrieval, Indexing, Differential protein expression analysis, Principal component visualisation, Filtering, Functional clustering + metaquantome_stat, metaquantome_expand, metaquantome_viz, metaquantome_db, metaquantome_filter, metaquantome_sample + Quantification, Differential protein expression analysis, Query and retrieval, Principal component visualisation, Indexing, Heat map generation, Filtering, Functional clustering, Statistical inference, Visualisation MIT @@ -2380,8 +2446,8 @@ 2 2 - bowtie2, kraken2, fastq_to_tabular, filter_tabular, recentrifuge, seq_filter_by_id - Cross-assembly, Taxonomic classification, Read mapping, Expression analysis + bowtie2, recentrifuge, fastq_to_tabular, kraken2, filter_tabular, seq_filter_by_id + Taxonomic classification, Expression analysis, Read mapping, Cross-assembly MIT @@ -2402,8 +2468,8 @@ 4 4 - featurecounts, bowtie2, multiqc - Read summarisation, RNA-Seq quantification, Validation, Read mapping, Sequencing quality control + bowtie2, featurecounts, multiqc + Sequencing quality control, Validation, Read summarisation, Read mapping, RNA-Seq quantification MIT @@ -2424,8 +2490,8 @@ 6 6 - trimmomatic, fastqc, multiqc - Sequence composition calculation, Statistical calculation, Validation, Sequencing quality control + fastqc, multiqc, trimmomatic + Sequencing quality control, Statistical calculation, Validation, Sequence composition calculation MIT @@ -2468,7 +2534,7 @@ 0 0 - mergeCols1, bedtools_complementbed, tp_sort_header_tool, tp_sed_tool, cat1, bedtools_sortbed, fasta_compute_length, Filter1, addValue, join1, collapse_dataset, bedtools_intersectbed, random_lines1, Grep1, tp_cat, Cut1, fasta_filter_by_length, tp_grep_tool, datamash_ops, lastz_wrapper_2 + bedtools_sortbed, collapse_dataset, bedtools_intersectbed, tp_cat, datamash_ops, bedtools_complementbed, cat1, join1, mergeCols1, lastz_wrapper_2, tp_grep_tool, addValue, fasta_filter_by_length, Grep1, fasta_compute_length, tp_sort_header_tool, random_lines1, tp_sed_tool, Filter1, Cut1 Read mapping, Sequence alignment, Mapping @@ -2490,8 +2556,8 @@ 0 0 - tp_split_on_column, regexColumn1, rbc_mafft, bg_diamond_view, Filter1, bg_diamond, join1, tab2fasta, collapse_dataset, Cut1, cat1, rapidnj, Add_a_column1, gops_intersect_1 - Sequence alignment analysis, Multiple sequence alignment, Phylogenetic tree generation + Add_a_column1, tab2fasta, tp_split_on_column, gops_intersect_1, rbc_mafft, join1, bg_diamond, cat1, collapse_dataset, rapidnj, Filter1, bg_diamond_view, Cut1, regexColumn1 + Sequence alignment analysis, Phylogenetic tree generation, Multiple sequence alignment @@ -2512,7 +2578,7 @@ 0 0 - jbrowse, iframe, create_or_update, list_organism, create_account + create_or_update, iframe, jbrowse, create_account, list_organism Genome visualisation @@ -2534,8 +2600,8 @@ 0 0 - jbrowse, bg_column_arrange_by_header, gff2bed1, tp_text_file_with_recurring_lines, circos_gc_skew, trimmomatic, fasta2tab, fasta_compute_length, Add_a_column1, circos_interval_to_tile, tp_sort_header_tool, minimap2, Filter1, bandage_image, nanoplot, join1, PlasFlow, circos, tp_head_tool, deeptools_bam_coverage, Grep1, tp_cut_tool, tp_easyjoin_tool, tp_cat, regex_replace, Cut1, tp_split_on_column, medaka_consensus_pipeline, circos_wiggle_to_scatter, ncbi_blastn_wrapper, staramr_search, prokka, regex1, flye, tbl2gff3, tab2fasta - Genome assembly, Sequence visualisation, Gene prediction, Genome annotation, Sequence analysis, Variant calling, Base-calling, Antimicrobial resistance prediction, Coding region prediction, Cross-assembly, Mapping assembly, Sequence assembly, Box-Whisker plot plotting, Genome visualisation, Pairwise sequence alignment, Sequence assembly visualisation, Scatter plot plotting, De-novo assembly + circos_wiggle_to_scatter, tp_split_on_column, bandage_image, flye, deeptools_bam_coverage, staramr_search, PlasFlow, regex1, jbrowse, tp_cat, tp_head_tool, ncbi_blastn_wrapper, medaka_consensus_pipeline, gff2bed1, circos, tbl2gff3, join1, trimmomatic, tp_text_file_with_recurring_lines, prokka, nanoplot, bg_column_arrange_by_header, fasta2tab, Add_a_column1, tp_cut_tool, minimap2, Grep1, tab2fasta, fasta_compute_length, tp_sort_header_tool, circos_interval_to_tile, tp_easyjoin_tool, regex_replace, circos_gc_skew, Filter1, Cut1 + Base-calling, Pairwise sequence alignment, Sequence visualisation, De-novo assembly, Variant calling, Scatter plot plotting, Genome annotation, Sequence assembly, Gene prediction, Genome visualisation, Mapping assembly, Coding region prediction, Cross-assembly, Antimicrobial resistance prediction, Box-Whisker plot plotting, Sequence assembly visualisation, Sequence analysis, Genome assembly @@ -2556,7 +2622,7 @@ 0 0 - bcftools_consensus, snp_sites, tb_variant_filter, tp_cat, snp_dists + snp_dists, bcftools_consensus, tb_variant_filter, snp_sites, tp_cat @@ -2578,8 +2644,8 @@ 0 0 - trimmomatic, tb_variant_filter, __MERGE_COLLECTION__, snippy - Phylogenetic tree visualisation, Variant calling, Phylogenetic tree generation + snippy, __MERGE_COLLECTION__, tb_variant_filter, trimmomatic + Phylogenetic tree visualisation, Phylogenetic tree generation, Variant calling @@ -2600,7 +2666,7 @@ 0 0 - samtools_view, tb_profiler_profile, tp_grep_tool, tp_replace_in_line, __MERGE_COLLECTION__, tp_cat, addName, tp_sed_tool + addName, samtools_view, tp_grep_tool, tp_sed_tool, tp_replace_in_line, __MERGE_COLLECTION__, tp_cat, tb_profiler_profile Antimicrobial resistance prediction @@ -2622,7 +2688,7 @@ 2 2 - bowtie2, bcftools_norm, tp_awk_tool, snpSift_filter, vcf2tsv, freebayes, bcftools_view + bowtie2, tp_awk_tool, bcftools_view, bcftools_norm, vcf2tsv, snpSift_filter, freebayes Read mapping, Statistical calculation, Variant calling @@ -2644,7 +2710,7 @@ 13 13 - bowtie2, samtools_coverage, bcftools_norm, vcf2tsv, collection_element_identifiers, freebayes, tp_cat, collapse_dataset, samtools_depth + bowtie2, collection_element_identifiers, samtools_depth, bcftools_norm, vcf2tsv, collapse_dataset, samtools_coverage, tp_cat, freebayes Read mapping, Statistical calculation, Variant calling @@ -2666,8 +2732,8 @@ 1 1 - multiqc, __FLATTEN__, collection_element_identifiers, __RELABEL_FROM_FILE__, __MERGE_COLLECTION__, regex1, checkm2 - Sequence composition calculation, Sequence assembly validation, Statistical calculation, Validation, Sequencing quality control + __RELABEL_FROM_FILE__, checkm2, collection_element_identifiers, multiqc, __FLATTEN__, __MERGE_COLLECTION__, regex1 + Statistical calculation, Sequencing quality control, Validation, Sequence composition calculation, Sequence assembly validation MIT @@ -2688,8 +2754,8 @@ 1 1 - multiqc, __FLATTEN__, collection_element_identifiers, __RELABEL_FROM_FILE__, __MERGE_COLLECTION__, regex1, checkm2 - Sequence composition calculation, Sequence assembly validation, Statistical calculation, Validation, Sequencing quality control + __RELABEL_FROM_FILE__, checkm2, collection_element_identifiers, multiqc, __FLATTEN__, __MERGE_COLLECTION__, regex1 + Statistical calculation, Sequencing quality control, Validation, Sequence composition calculation, Sequence assembly validation MIT @@ -2710,7 +2776,7 @@ 1 1 - fastq_dl, CONVERTER_uncompressed_to_gz, tp_awk_tool, CONVERTER_gz_to_uncompressed, __MERGE_COLLECTION__ + tp_awk_tool, CONVERTER_uncompressed_to_gz, CONVERTER_gz_to_uncompressed, __MERGE_COLLECTION__, fastq_dl Apache-2.0 @@ -2732,8 +2798,8 @@ 1 1 - tp_awk_tool, __FILTER_FROM_FILE__, bedtools_maskfastabed, mapseq, collection_element_identifiers, taxonomy_krona_chart, biom_convert, __FILTER_EMPTY_DATASETS__ - k-mer counting, Visualisation, Formatting, Mapping + bedtools_maskfastabed, mapseq, tp_awk_tool, __FILTER_FROM_FILE__, collection_element_identifiers, taxonomy_krona_chart, biom_convert, __FILTER_EMPTY_DATASETS__ + k-mer counting, Formatting, Visualisation, Mapping Apache-2.0 @@ -2754,8 +2820,8 @@ 1 1 - cshl_fasta_formatter, tp_find_and_replace, fastq_to_fasta_python, multiqc, fastqc, __UNZIP_COLLECTION__, prinseq, mgnify_seqprep, fastp, trimmomatic, fastq_filter - Sequence trimming, Sequence composition calculation, Nucleic acid design, Statistical calculation, Validation, Read pre-processing, Sequence contamination filtering, Sequencing quality control + fastp, cshl_fasta_formatter, tp_find_and_replace, multiqc, trimmomatic, fastqc, __UNZIP_COLLECTION__, mgnify_seqprep, fastq_filter, prinseq, fastq_to_fasta_python + Statistical calculation, Sequencing quality control, Sequence contamination filtering, Sequence trimming, Validation, Nucleic acid design, Read pre-processing, Sequence composition calculation Apache-2.0 @@ -2776,8 +2842,8 @@ 1 1 - cshl_fasta_formatter, tp_find_and_replace, fastq_to_fasta_python, multiqc, fastqc, prinseq, trimmomatic, fastq_filter - Sequence trimming, Read pre-processing, Sequence composition calculation, Sequence contamination filtering, Statistical calculation, Validation, Sequencing quality control + cshl_fasta_formatter, tp_find_and_replace, multiqc, trimmomatic, fastqc, fastq_filter, prinseq, fastq_to_fasta_python + Sequencing quality control, Statistical calculation, Sequence contamination filtering, Sequence trimming, Validation, Read pre-processing, Sequence composition calculation Apache-2.0 @@ -2798,7 +2864,7 @@ 1 1 - bcftools_consensus, Paste1, samtools_coverage, regexColumn1, bcftools_norm, CONVERTER_gz_to_uncompressed, snpSift_filter, tp_cut_tool, Cut1, snpSift_extractFields, clair3, collapse_dataset, Remove beginning1, table_compute, tp_head_tool, Count1, samtools_depth, minimap2 + tp_cut_tool, clair3, table_compute, samtools_depth, bcftools_consensus, CONVERTER_gz_to_uncompressed, Paste1, bcftools_norm, Cut1, snpSift_extractFields, samtools_coverage, snpSift_filter, collapse_dataset, minimap2, Count1, tp_head_tool, Remove beginning1, regexColumn1 Pairwise sequence alignment, Variant calling MIT @@ -2820,8 +2886,8 @@ 1 1 - cshl_fasta_formatter, tp_find_and_replace, fastq_to_fasta_python, multiqc, fastqc, prinseq, trimmomatic, fastq_filter - Sequence trimming, Read pre-processing, Sequence composition calculation, Sequence contamination filtering, Statistical calculation, Validation, Sequencing quality control + cshl_fasta_formatter, tp_find_and_replace, multiqc, trimmomatic, fastqc, fastq_filter, prinseq, fastq_to_fasta_python + Sequencing quality control, Statistical calculation, Sequence contamination filtering, Sequence trimming, Validation, Read pre-processing, Sequence composition calculation Apache-2.0 @@ -2842,7 +2908,7 @@ 1 1 - bcftools_consensus, Paste1, samtools_coverage, regexColumn1, bcftools_norm, CONVERTER_gz_to_uncompressed, snpSift_filter, tp_cut_tool, Cut1, snpSift_extractFields, clair3, collapse_dataset, Remove beginning1, table_compute, tp_head_tool, Count1, samtools_depth, minimap2 + tp_cut_tool, clair3, table_compute, samtools_depth, bcftools_consensus, CONVERTER_gz_to_uncompressed, Paste1, bcftools_norm, Cut1, snpSift_extractFields, samtools_coverage, snpSift_filter, collapse_dataset, minimap2, Count1, tp_head_tool, Remove beginning1, regexColumn1 Pairwise sequence alignment, Variant calling MIT @@ -2864,7 +2930,7 @@ 1 1 - fastq_dl, CONVERTER_uncompressed_to_gz, tp_awk_tool, CONVERTER_gz_to_uncompressed, __MERGE_COLLECTION__ + tp_awk_tool, CONVERTER_uncompressed_to_gz, CONVERTER_gz_to_uncompressed, __MERGE_COLLECTION__, fastq_dl Apache-2.0 @@ -2886,8 +2952,8 @@ 1 1 - tp_awk_tool, __FILTER_FROM_FILE__, bedtools_maskfastabed, mapseq, collection_element_identifiers, taxonomy_krona_chart, biom_convert, __FILTER_EMPTY_DATASETS__ - k-mer counting, Visualisation, Formatting, Mapping + bedtools_maskfastabed, mapseq, tp_awk_tool, __FILTER_FROM_FILE__, collection_element_identifiers, taxonomy_krona_chart, biom_convert, __FILTER_EMPTY_DATASETS__ + k-mer counting, Formatting, Visualisation, Mapping Apache-2.0 @@ -2908,8 +2974,8 @@ 1 1 - cshl_fasta_formatter, tp_find_and_replace, fastq_to_fasta_python, multiqc, fastqc, __UNZIP_COLLECTION__, prinseq, mgnify_seqprep, fastp, trimmomatic, fastq_filter - Sequence trimming, Sequence composition calculation, Nucleic acid design, Statistical calculation, Validation, Read pre-processing, Sequence contamination filtering, Sequencing quality control + fastp, cshl_fasta_formatter, tp_find_and_replace, multiqc, trimmomatic, fastqc, __UNZIP_COLLECTION__, mgnify_seqprep, fastq_filter, prinseq, fastq_to_fasta_python + Statistical calculation, Sequencing quality control, Sequence contamination filtering, Sequence trimming, Validation, Nucleic acid design, Read pre-processing, Sequence composition calculation Apache-2.0 @@ -2930,8 +2996,8 @@ 1 1 - cshl_fasta_formatter, tp_find_and_replace, fastq_to_fasta_python, multiqc, fastqc, prinseq, trimmomatic, fastq_filter - Sequence trimming, Read pre-processing, Sequence composition calculation, Sequence contamination filtering, Statistical calculation, Validation, Sequencing quality control + cshl_fasta_formatter, tp_find_and_replace, multiqc, trimmomatic, fastqc, fastq_filter, prinseq, fastq_to_fasta_python + Sequencing quality control, Statistical calculation, Sequence contamination filtering, Sequence trimming, Validation, Read pre-processing, Sequence composition calculation Apache-2.0 @@ -2952,8 +3018,8 @@ 1 1 - collection_column_join, Grep1, samtools_fastx, regexColumn1, multiqc, kraken2, fastqc, bamtools_split_mapped, nanoplot, porechop, __FILTER_FAILED_DATASETS__, krakentools_extract_kraken_reads, fastp, collapse_dataset, Cut1, Add_a_column1, minimap2 - Visualisation, Sequence composition calculation, Statistical calculation, Validation, Sequence contamination filtering, Box-Whisker plot plotting, Sequence alignment analysis, Taxonomic classification, Data handling, Pairwise sequence alignment, Aggregation, Scatter plot plotting, Sequencing quality control + Add_a_column1, fastp, collection_column_join, multiqc, kraken2, samtools_fastx, fastqc, collapse_dataset, nanoplot, minimap2, Grep1, __FILTER_FAILED_DATASETS__, bamtools_split_mapped, porechop, Cut1, regexColumn1, krakentools_extract_kraken_reads + Statistical calculation, Taxonomic classification, Pairwise sequence alignment, Box-Whisker plot plotting, Aggregation, Data handling, Scatter plot plotting, Sequencing quality control, Sequence contamination filtering, Sequence alignment analysis, Validation, Sequence composition calculation, Visualisation MIT @@ -2974,8 +3040,8 @@ 1 1 - multiqc, __FLATTEN__, collection_element_identifiers, __RELABEL_FROM_FILE__, __MERGE_COLLECTION__, regex1, checkm2 - Sequence composition calculation, Sequence assembly validation, Statistical calculation, Validation, Sequencing quality control + __RELABEL_FROM_FILE__, checkm2, collection_element_identifiers, multiqc, __FLATTEN__, __MERGE_COLLECTION__, regex1 + Statistical calculation, Sequencing quality control, Validation, Sequence composition calculation, Sequence assembly validation MIT @@ -2996,7 +3062,7 @@ 1 1 - bcftools_consensus, Paste1, samtools_coverage, regexColumn1, bcftools_norm, CONVERTER_gz_to_uncompressed, snpSift_filter, tp_cut_tool, Cut1, snpSift_extractFields, clair3, collapse_dataset, Remove beginning1, table_compute, tp_head_tool, Count1, samtools_depth, minimap2 + tp_cut_tool, clair3, table_compute, samtools_depth, bcftools_consensus, CONVERTER_gz_to_uncompressed, Paste1, bcftools_norm, Cut1, snpSift_extractFields, samtools_coverage, snpSift_filter, collapse_dataset, minimap2, Count1, tp_head_tool, Remove beginning1, regexColumn1 Pairwise sequence alignment, Variant calling MIT @@ -3018,7 +3084,7 @@ 1 1 - bcftools_consensus, Paste1, samtools_coverage, regexColumn1, bcftools_norm, CONVERTER_gz_to_uncompressed, snpSift_filter, tp_cut_tool, Cut1, snpSift_extractFields, clair3, collapse_dataset, Remove beginning1, table_compute, tp_head_tool, Count1, samtools_depth, minimap2 + tp_cut_tool, clair3, table_compute, samtools_depth, bcftools_consensus, CONVERTER_gz_to_uncompressed, Paste1, bcftools_norm, Cut1, snpSift_extractFields, samtools_coverage, snpSift_filter, collapse_dataset, minimap2, Count1, tp_head_tool, Remove beginning1, regexColumn1 Pairwise sequence alignment, Variant calling MIT