From 6ada8f03bb701a160ed757e35e2ac5c23666682f Mon Sep 17 00:00:00 2001 From: scorreard <54953390+scorreard@users.noreply.github.com> Date: Wed, 1 Jul 2026 14:07:39 +0000 Subject: [PATCH] proteomics community resources update --- communities/proteomics/lab/README.md | 1 + communities/proteomics/lab/conclusion.html | 53 + communities/proteomics/lab/intro.html | 41 + .../1_data_import_and_preparation.yml | 74 + .../proteomics/lab/sections/2_tools.yml | 3 + .../proteomics/lab/sections/3_workflows.yml | 11 + .../proteomics/lab/sections/4_tutorials.yml | 3 + .../lab/sections/5_support_and_help.yml | 55 + .../proteomics/lab/sections/6_community.yml | 67 + .../proteomics/metadata/tool_status.tsv | 4 +- .../tools_filtered_by_ts_categories.json | 3125 ++++++++--------- 11 files changed, 1828 insertions(+), 1609 deletions(-) create mode 100644 communities/proteomics/lab/README.md create mode 100644 communities/proteomics/lab/conclusion.html create mode 100644 communities/proteomics/lab/intro.html create mode 100644 communities/proteomics/lab/sections/1_data_import_and_preparation.yml create mode 100644 communities/proteomics/lab/sections/2_tools.yml create mode 100644 communities/proteomics/lab/sections/3_workflows.yml create mode 100644 communities/proteomics/lab/sections/4_tutorials.yml create mode 100644 communities/proteomics/lab/sections/5_support_and_help.yml create mode 100644 communities/proteomics/lab/sections/6_community.yml diff --git a/communities/proteomics/lab/README.md b/communities/proteomics/lab/README.md new file mode 100644 index 000000000..4d0d576e9 --- /dev/null +++ b/communities/proteomics/lab/README.md @@ -0,0 +1 @@ +# Community subdomain/Lab diff --git a/communities/proteomics/lab/conclusion.html b/communities/proteomics/lab/conclusion.html new file mode 100644 index 000000000..0e3b2b5aa --- /dev/null +++ b/communities/proteomics/lab/conclusion.html @@ -0,0 +1,53 @@ +{% load markdown %} + + + +{% if feedback_email %} +
+

What do you think of the {{ lab_name }}?

+ +
+{% endif %} + +
+

Cite Us

+
+ +
+ If you find the {{ lab_name }} Lab and the effort of the {{ lab_name }} community useful for your research, please cite us using this webpage. + +
+ +
+ {{ conclusion_extra_md|safe }} +
diff --git a/communities/proteomics/lab/intro.html b/communities/proteomics/lab/intro.html new file mode 100644 index 000000000..73e923ac9 --- /dev/null +++ b/communities/proteomics/lab/intro.html @@ -0,0 +1,41 @@ +
+

+ Welcome to the Galaxy {{ site_name }} {{ lab_name }} by the {{ lab_name }} community! +

+ +

+#Here include an intro to your page, see the ex mple below from the microgalaxy community +# Whether you're working with microbiome samples or bacterial isolates, long or short reads, shotgun or 16S sequencing, genomics, transcriptomics, proteomics, metabolomics, or integrative multi-omics analysis—this is the place for you! Learn more about the Microbiology Lab and the effort of the microGalaxy community in our preprint.

+

+ + How does this page relate to Galaxy {{ site_name }}? + +

+ + {{ intro_extra_md }} + + +
diff --git a/communities/proteomics/lab/sections/1_data_import_and_preparation.yml b/communities/proteomics/lab/sections/1_data_import_and_preparation.yml new file mode 100644 index 000000000..bc60ce4e3 --- /dev/null +++ b/communities/proteomics/lab/sections/1_data_import_and_preparation.yml @@ -0,0 +1,74 @@ +id: data +title: Getting started +tabs: + - id: data-import + title: Data import + heading_md: > + Common tools that allow for data import. + content: + - title_md: Import data to Galaxy + description_md: > + Standard upload of data to Galaxy, from your computer or from the web. + button_link: "{{ galaxy_base_url }}/tool_runner?tool_id=upload1" + button_tip: Upload Data + - title_md: Download data from NCBI GenBank/RefSeq + description_md: > + Download sequences from GenBank/RefSeq by accession through the NCBI ENTREZ API + button_link: "{{ galaxy_base_url }}/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fncbi_acc_download%2Fncbi_acc_download" + button_tip: Download Data from NCBI + - title_md: Download raw reads from NCBI SRA + description_md: > + Faster Download and Extract Reads in FASTQ format from NCBI SRA + button_link: "{{ galaxy_base_url }}/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fsra_tools%2Ffasterq_dump" + button_tip: Download raw reads from NCBI SRA + - title_md: Download run data from EBI SRA + description_md: > + ENA data can be searched and retrieved interactively and programmatically and visualized using this ENA Browser tool + button_link: "https://www.ebi.ac.uk/ena/browser/search" + button_tip: Download run data from EBI SRA + - title_md: Download run data from UCSC + description_md: > + Use this tool to retrieve and export data from the Genome Browser annotation track database + button_link: "https://genome.ucsc.edu/cgi-bin/hgTables" + button_tip: Download run data from UCSC + +# - id: highlight-tools +# title: Highlight tools +# heading_md: > +# Flagship tools for +# content: +# - title_md: Bakta - Rapid and standardized annotation of bacterial genomes, MAGs and plasmids +# description_md: > +# A tool for the rapid & standardized annotation of bacterial genomes and plasmids from both isolates and Metagenomic Assembled Genomes (MAGs). +# inputs: +# - datatypes: +# - fasta +# button_link: "{{ galaxy_base_url }}/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/bakta/bakta" + +# - id: interactive-tools +# title: Interactive tools +# heading_md: > +# Interactive tools for +# content: +# - title_md: Pavian - Interactive analysis of metagenomics data +# description_md: > +# An interactive browser application for analyzing and visualization metagenomics classification results from classifiers such as Kraken, KrakenUniq, Kraken 2, Centrifuge and MetaPhlAn. Pavian also provides an alignment viewer for validation of matches to a particular genome. +# inputs: +# - datatypes: +# - Kraken report +# - MetaPhlAn report +# button_link: "{{ galaxy_base_url }}/root?tool_id=interactive_tool_pavian" + +# - id: learning-pathways +# title: Learning pathways +# heading_md: > +# Connected tutorials to train you to perform microbial data analysis. +# content: +# - title_md: Introduction to Galaxy and Sequence analysis +# description_md: > +# New to Galaxy and/or the field of genomics? In this learning pathway, you will learn how to use Galaxy for analysis, and will be guided through the most common first steps of any genome analysis; quality control and a mapping or assembly of your genomic sequences. +# button_link: https://training.galaxyproject.org/training-material/learning-pathways/intro-to-galaxy-and-genomics.html +# button_icon: tutorial +# button_tip: Open Learning Pathway +# heading_md: > +# Connected tutorials to train you to perform microbial data analysis. diff --git a/communities/proteomics/lab/sections/2_tools.yml b/communities/proteomics/lab/sections/2_tools.yml new file mode 100644 index 000000000..d168fbf10 --- /dev/null +++ b/communities/proteomics/lab/sections/2_tools.yml @@ -0,0 +1,3 @@ +id: tools +title: Community curated tools +tabs: [] diff --git a/communities/proteomics/lab/sections/3_workflows.yml b/communities/proteomics/lab/sections/3_workflows.yml new file mode 100644 index 000000000..0432691c7 --- /dev/null +++ b/communities/proteomics/lab/sections/3_workflows.yml @@ -0,0 +1,11 @@ +id: workflows +title: Community curated workflows +tabs: + - id: iwc + content: [] + - id: other_workflowhub + content: [] + - id: gtn + content: [] + - id: public + content: [] diff --git a/communities/proteomics/lab/sections/4_tutorials.yml b/communities/proteomics/lab/sections/4_tutorials.yml new file mode 100644 index 000000000..ca1c62aca --- /dev/null +++ b/communities/proteomics/lab/sections/4_tutorials.yml @@ -0,0 +1,3 @@ +id: tutorials +title: Community curated tutorials +tabs: [] diff --git a/communities/proteomics/lab/sections/5_support_and_help.yml b/communities/proteomics/lab/sections/5_support_and_help.yml new file mode 100644 index 000000000..fa2285d3a --- /dev/null +++ b/communities/proteomics/lab/sections/5_support_and_help.yml @@ -0,0 +1,55 @@ +id: support +title: Support & Help +tabs: + - id: help + title: Help + heading_md: > + You can request help through different channels. If you think your problem might help other users as well, + please post it in the Galaxy Help Forum. Please report tool bugs through our + [support channel]({{ support_url }}) + and for specific questions feel free to reach out via the matrix chat. + content: + - title_md: Troubleshooting + description_md: > + Find specific advice for + {gtn modal}[troubleshooting Galaxy errors](https://training.galaxyproject.org/training-material/faqs/galaxy/analysis_troubleshooting.html) + on the GTN. + - title_md: Galaxy Support + description_md: > + Any user of Galaxy {{ site_name }} can request support online! + button_md: Request support + button_link: "{{ support_url }}" + button_icon: help + button_tip: Request support +# - title_md: microGalaxy chat room +# description_md: > +# Chat with members of the microGalaxy community on Matrix +# button_link: "{{ microgalaxy_matrix }}" +# button_md: Matrix channel +# button_icon: social +# button_tip: Join the chat + + - id: faq + title: FAQ + content: + - title_md: How can I increase my storage quota? + description_md: > + Please submit a quota request if your Galaxy account reaches its data storage limit. Requests are usually provisioned quickly if you provide a reasonable use case for your request. + button_md: Request + button_link: "{{ quota_request_url }}" + button_tip: Request quota + button_icon: help + - title_md: Can I upload sensitive data? + description_md: > + No, please do not upload personal or sensitive, such as human health or clinical data. Please see our + [Privacy Policy]({{ data_policy_url }}) + page for definitions of sensitive and health-related information. + + Please also make sure you have read our + [Terms of Service]({{ terms_url }}), + which covers hosting and analysis of research data. + - title_md: Is my data private? + description_md: > + Please read our + [Privacy Policy]({{ data_policy_url }}) + for information on your personal data and any data that you upload. diff --git a/communities/proteomics/lab/sections/6_community.yml b/communities/proteomics/lab/sections/6_community.yml new file mode 100644 index 000000000..53430883d --- /dev/null +++ b/communities/proteomics/lab/sections/6_community.yml @@ -0,0 +1,67 @@ +id: community +title: Community +tabs: + - id: participate + title: Participate + content: + - title_md: Join our community! + description_md: > + This Galaxy space is the result of hard, collaborative work by many contributors. +# It is maintained by the microGalaxy Community of Practice. +# This group unites scientists like yourself with software developers and bioinformaticians to create, share, and test resources to make microvial data analysis easier. +# Check out our site and join our community via [microGalaxy mailing list](https://lists.galaxyproject.org/lists/microgalaxy@lists.galaxyproject.org)! +# - title_md: Chat with others! +# description_md: > +# Use our matrix channel to chat with others from microGalaxy community +# button_link: "{{ microgalaxy_matrix }}" +# button_md: +# button_tip: Visit microGalaxy +# button_icon: social + + - id: governance + title: How is the Galaxy Community organised? + heading_md: > + Learn about the + {gtn modal}[governance structure of Galaxy communities](https://training.galaxyproject.org/training-material/topics/community/faqs/governance_structure.html) on the GTN. + content: [] + + - id: links + title: Galaxy Community support links + content: + - title_md: "For general Galaxy support" + description_md: "General Galaxy support" + button_link: "{{ general_support }}" + button_tip: Galaxy Support + button_icon: help + - title_md: "General Help Forum" + description_md: "Access general Galaxy help" + button_link: "{{ galaxy_help_url }}" + button_tip: Help forum + button_icon: help + - title_md: "Galaxy Training Network Slack Workspace" + description_md: "Join the GTN Slack community" + button_link: "{{ gtn_slack_url }}" + button_tip: Slack channel - Join the GTN Slack community. + button_icon: social + - title_md: "Galaxy Training Network Community Chat Room" + description_md: "Connect on the GTN Matrix chat" + button_link: "{{ gtn_matrix_channel }}" + button_tip: Matrix channel - Connect on the GTN Matrix chat. + button_icon: social +# - title_md: "microGalaxy User Community Chat Room" +# description_md: "Join the microGalaxy Matrix chat" +# button_link: "{{ microgalaxy_matrix }}" +# button_tip: Matrix channel - Join the microGalaxy Matrix chat. +# button_icon: social + - title_md: "General Galaxy Project Chat Room" + description_md: "Join the Galaxy project chat" + button_link: "{{ galaxy_matrix_channel }}" + button_tip: Matrix channel - Join the Galaxy project chat. + button_icon: social + - title_md: "European Galaxy Server Chat Room" + description_md: "Join the usegalaxy.eu chat" + button_link: "{{ european_server_matrix_channel }}" + button_tip: Matrix channel - Join the usegalaxy.eu chat. + button_icon: social + exclude_from: + - usegalaxy.org.au diff --git a/communities/proteomics/metadata/tool_status.tsv b/communities/proteomics/metadata/tool_status.tsv index 0b8b1f8a9..a9f23665c 100644 --- a/communities/proteomics/metadata/tool_status.tsv +++ b/communities/proteomics/metadata/tool_status.tsv @@ -5,6 +5,7 @@ bed_to_protein_map galaxyp Converts a BED file to a tabular list of exon locatio bioconductor-msnbase recetox MSnbase provides infrastructure for manipulation, processing and visualisation of mass spectrometry and proteomics data, ranging from raw to quantitative and annotated data. False False bioconductor_mzr recetox Galaxy wrapper for the Bioconductor mzR package, enabling conversion between common mass spectrometry data formats (mzML, mzXML, netCDF) within Galaxy workflows. bioconductor_scp recetox scp is a package for the single cell proteomics data processing. False False +biosigner workflow4metabolomics [W4M][Metabolomics][LC-MS][GC-MS][NMR] Discovery of significant signatures from omics data. bumbershoot galaxyp calisp galaxyp Calgary approach to isotopes in proteomics False False cardinal galaxyp Statistical and computational tools for analyzing mass spectrometry imaging datasets @@ -65,6 +66,7 @@ percolator galaxyp Percolator False False pmd_fdr galaxyp Calculate Precursor Mass Discrepancy (PMD) for MS/MS False 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. +protein_mosaic_q galaxyp Calculate the Mosaic Q descriptor and visualise amino acid clustering in protein structures proteinortho iuc Proteinortho is a tool to detect orthologous proteins/genes within different species. False False proteomics_improviser bgruening Visualisation of PepXML files proteomics_moff galaxyp moFF (a modest Feature Finder) extracts MS1 intensities from RAW and mzML spectrum files. False False @@ -87,10 +89,10 @@ pyteomics galaxyp Tools using the pyteomics library False False quantp galaxyp Correlation between protein and transcript abundance False False quantwiz_iq galaxyp Isobaric Quantitation using QuantWiz-IQ False False rawtools galaxyp Raw Tools False False -reactome_pathwaymatcher galaxyp Reactome Pathway Matcher False False scop3p iuc Fetch post-translational modifications (PTMs) from Scop3P database sipros ufz Labeled protein identification sixgill galaxyp Six-frame Genome-Inferred Libraries for LC-MS/MS False False +sopa iuc sopa – Spatial-omics pipeline and analysis spectrast2spectrast_irt galaxyp Filter from spectraST files to swath input files False False spectrast2tsv galaxyp Filter from spectraST files to swath input files False False swissmodel_modelling_api iuc Fully automated protein structure homology-modelling diff --git a/communities/proteomics/resources/tools_filtered_by_ts_categories.json b/communities/proteomics/resources/tools_filtered_by_ts_categories.json index 5c2cff69f..147d7f9d9 100644 --- a/communities/proteomics/resources/tools_filtered_by_ts_categories.json +++ b/communities/proteomics/resources/tools_filtered_by_ts_categories.json @@ -32,22 +32,20 @@ "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": 4, "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 CorGAT": 0, - "Number of tools on CropGalaxy": 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 Genomic Hyperbrowser": 0, "Number of tools on HyPhy HIV NGS Tools": 0, "Number of tools on ImmPort Galaxy": 0, "Number of tools on InteractoMIX": 0, @@ -55,12 +53,13 @@ "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 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.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, @@ -81,8 +80,91 @@ "Suite runs (last 5 years) on main servers": 6, "Suite users on main servers": 1, "Suite users (last 5 years) on main servers": 1, + "To keep": null, + "Deprecated": null + }, + { + "Suite ID": "biosigner", + "Tool IDs": [ + "biosigner" + ], + "Tool output formats": [ + "tabular", + "pdf", + "txt" + ], + "Description": "[W4M][Metabolomics][LC-MS][GC-MS][NMR] Discovery of significant signatures from omics data.", + "Suite first commit date": "2026-06-30", + "Homepage": "http://workflow4metabolomics.org", + "Suite version": "3.0.0+galaxy@VERSION_SUFFIX@", + "Suite conda package": "r-batch", + "Latest suite conda package version": "1.1_4", + "Suite version status": "To update", + "ToolShed categories": [ + "Metabolomics", + "Transcriptomics", + "Proteomics", + "Statistics" + ], + "EDAM operations": [], + "EDAM reduced operations": [], + "EDAM topics": [], + "EDAM reduced topics": [], + "Suite owner": "workflow4metabolomics", + "Suite source": "https://github.com/workflow4metabolomics/tools-metabolomics/tools/biosigner", + "Suite parsed folder": "https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/biosigner", + "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)": 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 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, + "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": 1, + "Number of tools on UseGalaxy.no": 1, + "Number of tools on Viral Variant Visualizer (VVV)": 0, + "Suite users (last 5 years) (usegalaxy.eu)": 9, + "Suite users (usegalaxy.eu)": 12, + "Suite runs (last 5 years) (usegalaxy.eu)": 82, + "Suite runs (usegalaxy.eu)": 281, + "Suite users (last 5 years) (usegalaxy.org)": 17, + "Suite users (usegalaxy.org)": 17, + "Suite runs (last 5 years) (usegalaxy.org)": 46, + "Suite runs (usegalaxy.org)": 46, + "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)": 127, + "Suite users (usegalaxy.fr)": 133, + "Suite runs (last 5 years) (usegalaxy.fr)": 4081, + "Suite runs (usegalaxy.fr)": 4264, + "Suite runs on main servers": 4591, + "Suite runs (last 5 years) on main servers": 4209, + "Suite users on main servers": 162, + "Suite users (last 5 years) on main servers": 153, "To keep": null, "Deprecated": null }, @@ -272,55 +354,6 @@ "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 CorGAT": 0, - "Number of tools on CropGalaxy": 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 Genomic Hyperbrowser": 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 Palfinder": 0, - "Number of tools on PepSimili": 0, - "Number of tools on PhagePromotor": 0, - "Number of tools on UseGalaxy.be": 27, - "Number of tools on UseGalaxy.cz": 135, - "Number of tools on UseGalaxy.no": 134, - "Suite users (last 5 years) (usegalaxy.eu)": 583, - "Suite users (usegalaxy.eu)": 698, - "Suite runs (last 5 years) (usegalaxy.eu)": 30109, - "Suite runs (usegalaxy.eu)": 114383, - "Suite users (last 5 years) (usegalaxy.org)": 10, - "Suite users (usegalaxy.org)": 10, - "Suite runs (last 5 years) (usegalaxy.org)": 417, - "Suite runs (usegalaxy.org)": 417, - "Suite users (last 5 years) (usegalaxy.org.au)": 33, - "Suite users (usegalaxy.org.au)": 34, - "Suite runs (last 5 years) (usegalaxy.org.au)": 1321, - "Suite runs (usegalaxy.org.au)": 1325, - "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": 116125, - "Suite runs (last 5 years) on main servers": 31847, - "Suite users on main servers": 742, - "Suite users (last 5 years) on main servers": 626, "Related Workflows": [ "https://usegalaxy.eu/published/workflow?id=41d096891bada138", "https://usegalaxy.eu/published/workflow?id=68edbb8eec38ad00", @@ -328,6 +361,7 @@ "https://usegalaxy.eu/published/workflow?id=86d50bbaaa3936dc", "https://usegalaxy.eu/published/workflow?id=a2cdadcd549c9c3c", "https://usegalaxy.eu/published/workflow?id=afb138fc03ca61a8", + "https://usegalaxy.eu/published/workflow?id=d30e15a9dea36e31", "https://usegalaxy.eu/published/workflow?id=d55df785d4c71876", "https://usegalaxy.eu/published/workflow?id=da10c475c83c5469", "https://usegalaxy.eu/published/workflow?id=e9e41c23261d4ac5", @@ -344,6 +378,7 @@ "https://usegalaxy.org.au/published/workflow?id=c2f449e69d06ccf5", "https://usegalaxy.org.au/published/workflow?id=da79aa2dfd6b34bc", "https://usegalaxy.org/published/workflow?id=0775ff66d1bc04b5", + "https://usegalaxy.org/published/workflow?id=82fb12e53c5b0139", "https://usegalaxy.org/published/workflow?id=9865fee6c68fc201", "https://usegalaxy.org/published/workflow?id=f9048d9678e21f36", "https://workflowhub.eu/workflows/1394?version=1", @@ -356,7 +391,7 @@ "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=2" + "https://workflowhub.eu/workflows/613?version=3" ], "Related Tutorials": [ "proteomics/DIA_Analysis_OSW", @@ -367,6 +402,52 @@ "proteomics/protein-id-sg-ps", "proteomics/protein-quant-sil" ], + "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 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, + "Number of tools on Oqtans": 0, + "Number of tools on Palfinder": 0, + "Number of tools on PhagePromotor": 0, + "Number of tools on UseGalaxy.be": 27, + "Number of tools on UseGalaxy.cz": 135, + "Number of tools on UseGalaxy.no": 134, + "Number of tools on Viral Variant Visualizer (VVV)": 0, + "Suite users (last 5 years) (usegalaxy.eu)": 583, + "Suite users (usegalaxy.eu)": 698, + "Suite runs (last 5 years) (usegalaxy.eu)": 30109, + "Suite runs (usegalaxy.eu)": 114383, + "Suite users (last 5 years) (usegalaxy.org)": 10, + "Suite users (usegalaxy.org)": 10, + "Suite runs (last 5 years) (usegalaxy.org)": 417, + "Suite runs (usegalaxy.org)": 417, + "Suite users (last 5 years) (usegalaxy.org.au)": 33, + "Suite users (usegalaxy.org.au)": 34, + "Suite runs (last 5 years) (usegalaxy.org.au)": 1321, + "Suite runs (usegalaxy.org.au)": 1325, + "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": 116125, + "Suite runs (last 5 years) on main servers": 31847, + "Suite users on main servers": 742, + "Suite users (last 5 years) on main servers": 626, "To keep": null, "Deprecated": null }, @@ -401,22 +482,20 @@ "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, - "Number of tools on CorGAT": 0, - "Number of tools on CropGalaxy": 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 Genomic Hyperbrowser": 0, "Number of tools on HyPhy HIV NGS Tools": 0, "Number of tools on ImmPort Galaxy": 0, "Number of tools on InteractoMIX": 0, @@ -424,12 +503,13 @@ "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 PepSimili": 0, "Number of tools on PhagePromotor": 0, "Number of tools on UseGalaxy.be": 0, "Number of tools on UseGalaxy.cz": 1, "Number of tools on UseGalaxy.no": 1, + "Number of tools on Viral Variant Visualizer (VVV)": 0, "Suite users (last 5 years) (usegalaxy.eu)": 18, "Suite users (usegalaxy.eu)": 26, "Suite runs (last 5 years) (usegalaxy.eu)": 37, @@ -450,8 +530,6 @@ "Suite runs (last 5 years) on main servers": 37, "Suite users on main servers": 26, "Suite users (last 5 years) on main servers": 18, - "Related Workflows": [], - "Related Tutorials": [], "To keep": null, "Deprecated": null }, @@ -484,22 +562,20 @@ "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, - "Number of tools on CorGAT": 0, - "Number of tools on CropGalaxy": 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 Genomic Hyperbrowser": 0, "Number of tools on HyPhy HIV NGS Tools": 0, "Number of tools on ImmPort Galaxy": 0, "Number of tools on InteractoMIX": 0, @@ -507,12 +583,13 @@ "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 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.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, @@ -533,8 +610,6 @@ "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": null, "Deprecated": null }, @@ -579,22 +654,20 @@ "bio.tool name": "PSORTb", "bio.tool description": "It is a high-precision localization prediction method for bacterial proteins. It has remained the most precise bacterial protein subcellular localization (SCL) predictor. \u00a0PSORTb version improved recall, higher proteome-scale prediction coverage, and new refined localization subcategories. It is the first SCL predictor specifically geared for all prokaryotes, including archaea and bacteria with atypical membrane/cell wall topologies.", "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, - "Number of tools on CorGAT": 0, - "Number of tools on CropGalaxy": 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 Genomic Hyperbrowser": 0, "Number of tools on HyPhy HIV NGS Tools": 0, "Number of tools on ImmPort Galaxy": 0, "Number of tools on InteractoMIX": 0, @@ -602,12 +675,13 @@ "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 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.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, @@ -628,8 +702,6 @@ "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": null, "Deprecated": null }, @@ -663,22 +735,20 @@ "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, - 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"Related Workflows": [], - "Related Tutorials": [], "To keep": null, "Deprecated": null }, @@ -728,7 +797,7 @@ "Description": "Search for transcription associated proteins (TAPs)", "Suite first commit date": "2024-02-14", "Homepage": "https://plantcode.cup.uni-freiburg.de/tapscan/", - "Suite version": "4.76+galaxy0", + "Suite version": "4.76", "Suite conda package": "hmmer", "Latest suite conda package version": "3.4", "Suite version status": "To update", @@ -746,22 +815,25 @@ "bio.tool name": null, "bio.tool description": null, "biii ID": null, + "Related Workflows": [ + "https://usegalaxy.eu/published/workflow?id=21fc597d983f1194", + "https://workflowhub.eu/workflows/1650?version=1" + ], + "Related Tutorials": [ + "sequence-analysis/tapscan-streptophyte-algae" + ], "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, - 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"Related Workflows": [ - "https://usegalaxy.eu/published/workflow?id=21fc597d983f1194", - "https://workflowhub.eu/workflows/1650?version=1" - ], - "Related Tutorials": [ - "sequence-analysis/tapscan-streptophyte-algae" - ], "To keep": null, "Deprecated": null }, @@ -838,22 +904,29 @@ "bio.tool name": null, "bio.tool description": null, "biii ID": null, + "Related Workflows": [ + "https://usegalaxy.eu/published/workflow?id=cde27d06b74ad2fd", + "https://usegalaxy.eu/published/workflow?id=d22dac11eba8c5a3", + "https://usegalaxy.org.au/published/workflow?id=1727d16fa4dec19c", + "https://workflowhub.eu/workflows/1417?version=1", + "https://workflowhub.eu/workflows/1426?version=1" + ], + "Related Tutorials": [ + "proteomics/maxquant-msstats-dda-lfq", + "proteomics/secretome-prediction" + ], "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, - "Number of tools on CorGAT": 0, - "Number of tools on CropGalaxy": 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 Genomic Hyperbrowser": 0, "Number of tools on HyPhy HIV NGS Tools": 0, "Number of tools on ImmPort Galaxy": 0, "Number of tools on InteractoMIX": 0, @@ -861,12 +934,13 @@ "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 PepSimili": 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.no": 1, + "Number of tools on Viral Variant Visualizer (VVV)": 0, "Suite users (last 5 years) (usegalaxy.eu)": 387, "Suite users (usegalaxy.eu)": 494, "Suite runs (last 5 years) (usegalaxy.eu)": 2533, @@ -887,17 +961,6 @@ "Suite runs (last 5 years) on main servers": 6260, "Suite users on main servers": 1674, "Suite users (last 5 years) on main servers": 1016, - "Related Workflows": [ - "https://usegalaxy.eu/published/workflow?id=cde27d06b74ad2fd", - "https://usegalaxy.eu/published/workflow?id=d22dac11eba8c5a3", - "https://usegalaxy.org.au/published/workflow?id=1727d16fa4dec19c", - "https://workflowhub.eu/workflows/1417?version=1", - "https://workflowhub.eu/workflows/1426?version=1" - ], - "Related Tutorials": [ - "proteomics/maxquant-msstats-dda-lfq", - "proteomics/secretome-prediction" - ], "To keep": null, "Deprecated": null }, @@ -912,9 +975,9 @@ "Description": "This software suite provides structural predictions for protein sequences made by Bio2Byte group.About Bio2Byte: We investigate how the dynamics, conformational states, and available experimental data of proteins relate to their amino acid sequence.Underlying physical and chemical principles are computationally unraveled through data integration, analysis, and machine learning, so connecting themto biological events and improving our understanding of the way proteins work.", "Suite first commit date": "2022-08-09", "Homepage": "https://bio2byte.be", - "Suite version": "3.0.5+galaxy0", + "Suite version": "3.0.5", "Suite conda package": "b2btools", - "Latest suite conda package version": "3.0.7", + "Latest suite conda package version": "3.0.8", "Suite version status": "To update", "ToolShed categories": [ "Computational chemistry", @@ -936,27 +999,25 @@ "EDAM reduced topics": [], "Suite owner": "iuc", "Suite source": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/b2btools", - "Suite parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/b2btools", + "Suite parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/b2btools", "bio.tool ID": "b2btools", "bio.tool name": "b2bTools", "bio.tool description": "The bio2byte tools server (b2btools) offers the following single protein sequence based predictions:- Backbone and sidechain dynamics (DynaMine)- Helix, sheet, coil and polyproline-II propensity- Early folding propensity (EFoldMine)- Disorder (DisoMine)- Beta-sheet aggregation (Agmata)In addition, multiple sequence alignments (MSAs) can be uploaded to scan the 'biophysical limits' of a protein family as defined in the MSA", "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, - 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"Suite parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/syndiva", + "Suite parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/syndiva", "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, - "Number of tools on CorGAT": 0, - "Number of tools on CropGalaxy": 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 Genomic Hyperbrowser": 0, "Number of tools on HyPhy HIV NGS Tools": 0, "Number of tools on ImmPort Galaxy": 0, "Number of tools on InteractoMIX": 0, @@ -1841,12 +1991,13 @@ "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, - 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], "To keep": null, "Deprecated": null }, @@ -2375,7 +2514,7 @@ "fasta" ], "Description": "Protein Database Downloader", - "Suite first commit date": "2015-01-24", + "Suite first commit date": "2015-01-23", "Homepage": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dbbuilder", "Suite version": "0.3.4", "Suite conda package": "wget", @@ -2395,55 +2534,6 @@ "bio.tool name": null, "bio.tool description": null, "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 CorGAT": 0, - "Number of tools on CropGalaxy": 0, - "Number of tools on Galaxy@AuBi": 0, - "Number of tools on Galaxy@Pasteur": 0, - "Number of tools on GalaxyTrakr": 0, - 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"Suite first commit date": "2015-01-24", + "Suite first commit date": "2015-01-23", "Homepage": null, "Suite version": null, "Suite conda package": null, @@ -2532,22 +2668,20 @@ "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, - "Number of tools on CorGAT": 0, - "Number of tools on CropGalaxy": 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 Genomic Hyperbrowser": 0, "Number of tools on HyPhy HIV NGS Tools": 0, "Number of tools on ImmPort Galaxy": 0, "Number of tools on InteractoMIX": 0, @@ -2555,12 +2689,13 @@ "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 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.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, @@ -2581,8 +2716,6 @@ "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": false, "Deprecated": false }, @@ -2617,22 +2750,20 @@ "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": 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, - 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"Related Workflows": [], - "Related Tutorials": [], "To keep": false, "Deprecated": false }, @@ -2700,22 +2830,20 @@ "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, - "Number of tools on CorGAT": 0, - "Number of tools on CropGalaxy": 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 Genomic Hyperbrowser": 0, "Number of tools on HyPhy HIV NGS Tools": 0, "Number of tools on ImmPort Galaxy": 0, "Number of tools on InteractoMIX": 0, @@ -2723,12 +2851,13 @@ "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 PepSimili": 0, "Number of tools on PhagePromotor": 0, "Number of tools on UseGalaxy.be": 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)": 2, "Suite users (usegalaxy.eu)": 2, "Suite runs (last 5 years) (usegalaxy.eu)": 40, @@ -2749,8 +2878,6 @@ "Suite runs (last 5 years) on main servers": 40, "Suite users on main servers": 2, "Suite users (last 5 years) on main servers": 2, - "Related Workflows": [], - "Related Tutorials": [], "To keep": false, "Deprecated": false }, @@ -2766,7 +2893,7 @@ "Description": "DiaNN (DIA-based Neural Networks) is a software for DIA/SWATH data processing.", "Suite first commit date": "2023-06-26", "Homepage": "https://github.com/vdemichev/DiaNN", - "Suite version": "1.8.1", + "Suite version": "@TOOL_VERSION@+galaxy@VERSION_SUFFIX@", "Suite conda package": null, "Latest suite conda package version": null, "Suite version status": "To update", @@ -2784,22 +2911,20 @@ "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": 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, - "Number of tools on CorGAT": 0, - "Number of tools on CropGalaxy": 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 Genomic Hyperbrowser": 0, "Number of tools on HyPhy HIV NGS Tools": 0, "Number of tools on ImmPort Galaxy": 0, "Number of tools on InteractoMIX": 0, @@ -2807,12 +2932,13 @@ "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 PepSimili": 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.no": 0, + "Number of tools on Viral Variant Visualizer (VVV)": 0, "Suite users (last 5 years) (usegalaxy.eu)": 31, "Suite users (usegalaxy.eu)": 31, "Suite runs (last 5 years) (usegalaxy.eu)": 181, @@ -2833,8 +2959,6 @@ "Suite runs (last 5 years) on main servers": 514, "Suite users on main servers": 60, "Suite users (last 5 years) on main servers": 60, - "Related Workflows": [], - "Related Tutorials": [], "To keep": false, "Deprecated": false }, @@ -2868,22 +2992,24 @@ "bio.tool name": null, "bio.tool description": null, "biii ID": null, + "Related Workflows": [ + "https://workflowhub.eu/workflows/1421?version=1" + ], + "Related Tutorials": [ + "proteomics/DIA_lib_OSW" + ], "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, - "Number of tools on CorGAT": 0, - "Number of tools on CropGalaxy": 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 Genomic Hyperbrowser": 0, "Number of tools on HyPhy HIV NGS Tools": 0, "Number of tools on ImmPort Galaxy": 0, "Number of tools on InteractoMIX": 0, @@ -2891,12 +3017,13 @@ "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 PepSimili": 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.no": 1, + "Number of tools on Viral Variant Visualizer (VVV)": 0, "Suite users (last 5 years) (usegalaxy.eu)": 47, "Suite users (usegalaxy.eu)": 49, "Suite runs (last 5 years) (usegalaxy.eu)": 175, @@ -2917,12 +3044,6 @@ "Suite runs (last 5 years) on main servers": 566, "Suite users on main servers": 55, "Suite users (last 5 years) on main servers": 53, - "Related Workflows": [ - "https://workflowhub.eu/workflows/1421?version=1" - ], - "Related Tutorials": [ - "proteomics/DIA_lib_OSW" - ], "To keep": false, "Deprecated": false }, @@ -2937,7 +3058,7 @@ "Description": "Diffacto comparative protein abundance estimation", "Suite first commit date": "2021-06-20", "Homepage": "https://github.com/statisticalbiotechnology/diffacto", - "Suite version": "1.0.6", + "Suite version": "@TOOL_VERSION@+galaxy@VERSION_SUFFIX@", "Suite conda package": "diffacto", "Latest suite conda package version": "1.0.7", "Suite version status": "To update", @@ -2955,22 +3076,20 @@ "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, - 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"Related Workflows": [], - "Related Tutorials": [], "To keep": false, "Deprecated": false }, @@ -3034,22 +3152,20 @@ "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, - "Number of tools on CorGAT": 0, - "Number of tools on CropGalaxy": 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 Genomic Hyperbrowser": 0, "Number of tools on HyPhy HIV NGS Tools": 0, "Number of tools on ImmPort Galaxy": 0, "Number of tools on InteractoMIX": 0, @@ -3057,12 +3173,13 @@ "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 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.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, @@ -3083,8 +3200,6 @@ "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": false, "Deprecated": false }, @@ -3113,22 +3228,20 @@ "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, - 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"Related Workflows": [], - "Related Tutorials": [], "To keep": false, "Deprecated": false }, @@ -3220,22 +3332,50 @@ "bio.tool name": "eggNOG-mapper v2", "bio.tool description": "EggNOG-mapper is a tool for fast functional annotation of novel sequences. It uses precomputed orthologous groups and phylogenies from the eggNOG database (http://eggnog5.embl.de) to transfer functional information from fine-grained orthologs only.", "biii ID": null, + "Related Workflows": [ + "https://usegalaxy.cz/published/workflow?id=932f4901960a595a", + "https://usegalaxy.eu/published/workflow?id=2d2862b48918b22f", + "https://usegalaxy.eu/published/workflow?id=2ee0eb74e839b476", + "https://usegalaxy.eu/published/workflow?id=6b79f4974f73593a", + "https://usegalaxy.eu/published/workflow?id=7be08f99f83c927e", + "https://usegalaxy.eu/published/workflow?id=87231a6a7938cb95", + "https://usegalaxy.eu/published/workflow?id=9b9e1e28f3683f92", + "https://usegalaxy.eu/published/workflow?id=a448400f69594135", + "https://usegalaxy.eu/published/workflow?id=c5e6047b3b256b06", + "https://usegalaxy.eu/published/workflow?id=cb81e7e2c0afd90a", + "https://usegalaxy.eu/published/workflow?id=cc59ae1a9878942c", + "https://usegalaxy.eu/published/workflow?id=e5becc6d66b2568c", + "https://usegalaxy.org.au/published/workflow?id=35f39173f0ac9179", + "https://usegalaxy.org.au/published/workflow?id=4e161a8f5098cc49", + "https://usegalaxy.org.au/published/workflow?id=876163677f1cccc4", + "https://usegalaxy.org.au/published/workflow?id=a07809974079a317", + "https://usegalaxy.org/published/workflow?id=80565301ada0d3eb", + "https://usegalaxy.org/published/workflow?id=84233173d92fa506", + "https://usegalaxy.org/published/workflow?id=92613e1e0b13aa0a", + "https://usegalaxy.org/published/workflow?id=d3c400275889ce4b", + "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/2024?version=4", + "https://workflowhub.eu/workflows/754?version=1", + "https://workflowhub.eu/workflows/755?version=1" + ], + "Related Tutorials": [ + "genome-annotation/funannotate", + "genome-annotation/functional" + ], "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, - "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 CorGAT": 0, - "Number of tools on CropGalaxy": 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 Genomic Hyperbrowser": 0, "Number of tools on HyPhy HIV NGS Tools": 0, "Number of tools on ImmPort Galaxy": 0, "Number of tools on InteractoMIX": 0, @@ -3243,12 +3383,13 @@ "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 PepSimili": 3, "Number of tools on PhagePromotor": 0, "Number of tools on UseGalaxy.be": 3, "Number of tools on UseGalaxy.cz": 3, "Number of tools on UseGalaxy.no": 3, + "Number of tools on Viral Variant Visualizer (VVV)": 0, "Suite users (last 5 years) (usegalaxy.eu)": 1977, "Suite users (usegalaxy.eu)": 2018, "Suite runs (last 5 years) (usegalaxy.eu)": 64994, @@ -3269,35 +3410,6 @@ "Suite runs (last 5 years) on main servers": 166838, "Suite users on main servers": 3221, "Suite users (last 5 years) on main servers": 3180, - "Related Workflows": [ - "https://usegalaxy.cz/published/workflow?id=932f4901960a595a", - "https://usegalaxy.eu/published/workflow?id=2d2862b48918b22f", - "https://usegalaxy.eu/published/workflow?id=2ee0eb74e839b476", - "https://usegalaxy.eu/published/workflow?id=87231a6a7938cb95", - "https://usegalaxy.eu/published/workflow?id=9b9e1e28f3683f92", - "https://usegalaxy.eu/published/workflow?id=a448400f69594135", - "https://usegalaxy.eu/published/workflow?id=c5e6047b3b256b06", - "https://usegalaxy.eu/published/workflow?id=cc59ae1a9878942c", - "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=4e161a8f5098cc49", - "https://usegalaxy.org.au/published/workflow?id=876163677f1cccc4", - "https://usegalaxy.org/published/workflow?id=80565301ada0d3eb", - "https://usegalaxy.org/published/workflow?id=92613e1e0b13aa0a", - "https://usegalaxy.org/published/workflow?id=d3c400275889ce4b", - "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/2024?version=3", - "https://workflowhub.eu/workflows/754?version=1", - "https://workflowhub.eu/workflows/755?version=1" - ], - "Related Tutorials": [ - "genome-annotation/funannotate", - "genome-annotation/functional" - ], "To keep": false, "Deprecated": false }, @@ -3342,22 +3454,32 @@ "bio.tool name": null, "bio.tool description": null, "biii ID": null, + "Related Workflows": [ + "https://usegalaxy.eu/published/workflow?id=14f9c2099db30570", + "https://usegalaxy.eu/published/workflow?id=3676aafc35dc2fe7", + "https://usegalaxy.eu/published/workflow?id=5d4e4b9f07a1ec20", + "https://usegalaxy.eu/published/workflow?id=5dec0e5a2d75cdc1", + "https://usegalaxy.eu/published/workflow?id=6d494e2f634eba70", + "https://usegalaxy.eu/published/workflow?id=87c21b682af78ec9", + "https://usegalaxy.eu/published/workflow?id=9ac15b644c805a2b", + "https://usegalaxy.eu/published/workflow?id=f1309010689eb98a", + "https://workflowhub.eu/workflows/1471?version=1" + ], + "Related Tutorials": [ + "proteomics/encyclopedia" + ], "Number of tools on UseGalaxy.org (Main)": 2, "Number of tools on UseGalaxy.org.au": 4, "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, - "Number of tools on CorGAT": 0, - "Number of tools on CropGalaxy": 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 Genomic Hyperbrowser": 0, "Number of tools on HyPhy HIV NGS Tools": 0, "Number of tools on ImmPort Galaxy": 0, "Number of tools on InteractoMIX": 0, @@ -3365,12 +3487,13 @@ "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 PepSimili": 0, "Number of tools on PhagePromotor": 0, "Number of tools on UseGalaxy.be": 2, "Number of tools on UseGalaxy.cz": 7, "Number of tools on UseGalaxy.no": 0, + "Number of tools on Viral Variant Visualizer (VVV)": 0, "Suite users (last 5 years) (usegalaxy.eu)": 34, "Suite users (usegalaxy.eu)": 34, "Suite runs (last 5 years) (usegalaxy.eu)": 893, @@ -3391,20 +3514,6 @@ "Suite runs (last 5 years) on main servers": 993, "Suite users on main servers": 44, "Suite users (last 5 years) on main servers": 44, - "Related Workflows": [ - "https://usegalaxy.eu/published/workflow?id=14f9c2099db30570", - "https://usegalaxy.eu/published/workflow?id=3676aafc35dc2fe7", - "https://usegalaxy.eu/published/workflow?id=5d4e4b9f07a1ec20", - "https://usegalaxy.eu/published/workflow?id=5dec0e5a2d75cdc1", - "https://usegalaxy.eu/published/workflow?id=6d494e2f634eba70", - "https://usegalaxy.eu/published/workflow?id=87c21b682af78ec9", - "https://usegalaxy.eu/published/workflow?id=9ac15b644c805a2b", - "https://usegalaxy.eu/published/workflow?id=f1309010689eb98a", - "https://workflowhub.eu/workflows/1471?version=1" - ], - "Related Tutorials": [ - "proteomics/encyclopedia" - ], "To keep": false, "Deprecated": false }, @@ -3442,22 +3551,20 @@ "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": 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, - "Number of tools on CorGAT": 0, - "Number of tools on CropGalaxy": 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 Genomic Hyperbrowser": 0, "Number of tools on HyPhy HIV NGS Tools": 0, "Number of tools on ImmPort Galaxy": 0, "Number of tools on InteractoMIX": 0, @@ -3465,12 +3572,13 @@ "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 PepSimili": 0, "Number of tools on PhagePromotor": 0, "Number of tools on UseGalaxy.be": 0, "Number of tools on UseGalaxy.cz": 2, "Number of tools on UseGalaxy.no": 0, + "Number of tools on Viral Variant Visualizer (VVV)": 0, "Suite users (last 5 years) (usegalaxy.eu)": 7, "Suite users (usegalaxy.eu)": 7, "Suite runs (last 5 years) (usegalaxy.eu)": 31, @@ -3491,8 +3599,6 @@ "Suite runs (last 5 years) on main servers": 31, "Suite users on main servers": 7, "Suite users (last 5 years) on main servers": 7, - "Related Workflows": [], - "Related Tutorials": [], "To keep": false, "Deprecated": false }, @@ -3505,12 +3611,12 @@ "tabular" ], "Description": "TRIC integrates information from all available runs via a graph-based alignment strategy", - "Suite first commit date": "2015-02-06", + "Suite first commit date": "2015-02-07", "Homepage": null, - "Suite version": "0.11.0", + "Suite version": "@TOOL_VERSION@+galaxy@GALAXY_VERSION@", "Suite conda package": "msproteomicstools", "Latest suite conda package version": "0.11.0", - "Suite version status": "Up-to-date", + "Suite version status": "To update", "ToolShed categories": [ "Proteomics" ], @@ -3525,22 +3631,20 @@ "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, - "Number of tools on CorGAT": 0, - "Number of tools on CropGalaxy": 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 Genomic Hyperbrowser": 0, "Number of tools on HyPhy HIV NGS Tools": 0, "Number of tools on ImmPort Galaxy": 0, "Number of tools on InteractoMIX": 0, @@ -3548,12 +3652,13 @@ "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 PepSimili": 0, "Number of tools on PhagePromotor": 0, "Number of tools on UseGalaxy.be": 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)": 2, "Suite users (usegalaxy.eu)": 2, "Suite runs (last 5 years) (usegalaxy.eu)": 19, @@ -3574,8 +3679,6 @@ "Suite runs (last 5 years) on main servers": 19, "Suite users on main servers": 2, "Suite users (last 5 years) on main servers": 2, - "Related Workflows": [], - "Related Tutorials": [], "To keep": false, "Deprecated": false }, @@ -3588,7 +3691,7 @@ "fasta" ], "Description": "Filter FASTA on the headers and/or the sequences", - "Suite first commit date": "2015-01-24", + "Suite first commit date": "2015-01-23", "Homepage": null, "Suite version": "2.3", "Suite conda package": "python", @@ -3609,22 +3712,61 @@ "bio.tool name": null, "bio.tool description": null, "biii ID": null, + "Related Workflows": [ + "https://usegalaxy.eu/published/workflow?id=02f240f6cf72080a", + "https://usegalaxy.eu/published/workflow?id=04a4dcac3fd922c5", + "https://usegalaxy.eu/published/workflow?id=1ae9a523ef719a3d", + "https://usegalaxy.eu/published/workflow?id=1b38e0d69e366be1", + "https://usegalaxy.eu/published/workflow?id=21fc597d983f1194", + "https://usegalaxy.eu/published/workflow?id=2d2d0c2231babc50", + "https://usegalaxy.eu/published/workflow?id=4eb9dfe91fc2dc67", + "https://usegalaxy.eu/published/workflow?id=69e603a2da979c93", + "https://usegalaxy.eu/published/workflow?id=7dd7908f4c8d722a", + "https://usegalaxy.eu/published/workflow?id=82a60d94d699efbf", + "https://usegalaxy.eu/published/workflow?id=93d1035a307fe63d", + "https://usegalaxy.eu/published/workflow?id=972db4abc51bb3ab", + "https://usegalaxy.eu/published/workflow?id=afb138fc03ca61a8", + "https://usegalaxy.eu/published/workflow?id=b51559006f86db9e", + "https://usegalaxy.eu/published/workflow?id=b681f7b677b23168", + "https://usegalaxy.eu/published/workflow?id=d2a9d4eb5b3c72a2", + "https://usegalaxy.eu/published/workflow?id=d55df785d4c71876", + "https://usegalaxy.eu/published/workflow?id=df08e520ec3dbcb7", + "https://usegalaxy.fr/published/workflow?id=41264142d3c00016", + "https://usegalaxy.fr/published/workflow?id=8b1678200a1d157a", + "https://usegalaxy.org.au/published/workflow?id=7559224fc32dce3a", + "https://usegalaxy.org.au/published/workflow?id=fba0eb562a710733", + "https://usegalaxy.org/published/workflow?id=386d3b300cf05305", + "https://usegalaxy.org/published/workflow?id=3c7349268d74c576", + "https://usegalaxy.org/published/workflow?id=4884918895db9af0", + "https://usegalaxy.org/published/workflow?id=4b7e73bb7ac93c95", + "https://usegalaxy.org/published/workflow?id=505c826e8c99d7bf", + "https://usegalaxy.org/published/workflow?id=531b96cbf4e33a8e", + "https://usegalaxy.org/published/workflow?id=88bc9aa7090875c1", + "https://usegalaxy.org/published/workflow?id=89d3c800d3be6050", + "https://usegalaxy.org/published/workflow?id=94da3d448bb8a137", + "https://usegalaxy.org/published/workflow?id=ec3cc032a90c44f1", + "https://workflowhub.eu/workflows/1630?version=1", + "https://workflowhub.eu/workflows/1635?version=1", + "https://workflowhub.eu/workflows/1650?version=1", + "https://workflowhub.eu/workflows/1717?version=2" + ], + "Related Tutorials": [ + "sequence-analysis/Manage_AB1_Sanger", + "sequence-analysis/tapscan-streptophyte-algae", + "transcriptomics/mirna-target-finder" + ], "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, - 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"https://usegalaxy.eu/published/workflow?id=d55df785d4c71876", - "https://usegalaxy.eu/published/workflow?id=df08e520ec3dbcb7", - "https://usegalaxy.fr/published/workflow?id=41264142d3c00016", - "https://usegalaxy.fr/published/workflow?id=8b1678200a1d157a", - "https://usegalaxy.org.au/published/workflow?id=7559224fc32dce3a", - "https://usegalaxy.org.au/published/workflow?id=fba0eb562a710733", - "https://usegalaxy.org/published/workflow?id=386d3b300cf05305", - "https://usegalaxy.org/published/workflow?id=3c7349268d74c576", - "https://usegalaxy.org/published/workflow?id=4884918895db9af0", - "https://usegalaxy.org/published/workflow?id=4b7e73bb7ac93c95", - "https://usegalaxy.org/published/workflow?id=505c826e8c99d7bf", - "https://usegalaxy.org/published/workflow?id=88bc9aa7090875c1", - "https://usegalaxy.org/published/workflow?id=89d3c800d3be6050", - "https://usegalaxy.org/published/workflow?id=94da3d448bb8a137", - "https://usegalaxy.org/published/workflow?id=ec3cc032a90c44f1", - "https://workflowhub.eu/workflows/1630?version=1", - 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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, - "Number of tools on CorGAT": 0, - "Number of tools on CropGalaxy": 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 Genomic Hyperbrowser": 0, "Number of tools on HyPhy HIV NGS Tools": 0, "Number of tools on ImmPort Galaxy": 0, "Number of tools on InteractoMIX": 0, @@ -3765,12 +3873,13 @@ "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 PepSimili": 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.no": 1, + "Number of tools on Viral Variant Visualizer (VVV)": 0, "Suite users (last 5 years) (usegalaxy.eu)": 47, "Suite users (usegalaxy.eu)": 59, "Suite runs (last 5 years) (usegalaxy.eu)": 516, @@ -3791,16 +3900,6 @@ "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": false, "Deprecated": false }, @@ -3837,22 +3936,30 @@ "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, - "Number of tools on CorGAT": 0, - "Number of tools on CropGalaxy": 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 Genomic Hyperbrowser": 0, "Number of tools on HyPhy HIV NGS Tools": 0, "Number of tools on ImmPort Galaxy": 0, "Number of tools on InteractoMIX": 0, @@ -3860,12 +3967,13 @@ "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 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.no": 0, + "Number of tools on Viral Variant Visualizer (VVV)": 0, "Suite users (last 5 years) (usegalaxy.eu)": 41, "Suite users (usegalaxy.eu)": 41, "Suite runs (last 5 years) (usegalaxy.eu)": 435, @@ -3886,18 +3994,6 @@ "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": false, "Deprecated": false }, @@ -3914,7 +4010,7 @@ "Description": "Hardkl\u00f6r", "Suite first commit date": "2016-04-26", "Homepage": null, - "Suite version": "2.30.1+galaxy1", + "Suite version": "2.30.1", "Suite conda package": "hardklor", "Latest suite conda package version": "2.3.2", "Suite version status": "To update", @@ -3932,22 +4028,20 @@ "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": 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, - "Number of tools on CorGAT": 0, - "Number of tools on CropGalaxy": 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 Genomic Hyperbrowser": 0, "Number of tools on HyPhy HIV NGS Tools": 0, "Number of tools on ImmPort Galaxy": 0, "Number of tools on InteractoMIX": 0, @@ -3955,12 +4049,13 @@ "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 PepSimili": 0, "Number of tools on PhagePromotor": 0, "Number of tools on UseGalaxy.be": 0, "Number of tools on UseGalaxy.cz": 2, "Number of tools on UseGalaxy.no": 2, + "Number of tools on Viral Variant Visualizer (VVV)": 0, "Suite users (last 5 years) (usegalaxy.eu)": 3, "Suite users (usegalaxy.eu)": 6, "Suite runs (last 5 years) (usegalaxy.eu)": 25, @@ -3981,8 +4076,6 @@ "Suite runs (last 5 years) on main servers": 25, "Suite users on main servers": 6, "Suite users (last 5 years) on main servers": 3, - "Related Workflows": [], - "Related Tutorials": [], "To keep": false, "Deprecated": false }, @@ -3997,7 +4090,7 @@ "Description": "Convert mass spectrometry identification files on linux or MacOSX", "Suite first commit date": "2019-02-22", "Homepage": null, - "Suite version": null, + "Suite version": "@VERSION@.0", "Suite conda package": "proteowizard", "Latest suite conda package version": "3_0_9992", "Suite version status": "To update", @@ -4015,22 +4108,20 @@ "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, - "Number of tools on CorGAT": 0, - "Number of tools on CropGalaxy": 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 Genomic Hyperbrowser": 0, "Number of tools on HyPhy HIV NGS Tools": 0, "Number of tools on ImmPort Galaxy": 0, "Number of tools on InteractoMIX": 0, @@ -4038,12 +4129,13 @@ "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 PepSimili": 0, "Number of tools on PhagePromotor": 0, "Number of tools on UseGalaxy.be": 0, "Number of tools on UseGalaxy.cz": 1, "Number of tools on UseGalaxy.no": 1, + "Number of tools on Viral Variant Visualizer (VVV)": 0, "Suite users (last 5 years) (usegalaxy.eu)": 12, "Suite users (usegalaxy.eu)": 34, "Suite runs (last 5 years) (usegalaxy.eu)": 55, @@ -4064,8 +4156,6 @@ "Suite runs (last 5 years) on main servers": 55, "Suite users on main servers": 34, "Suite users (last 5 years) on main servers": 12, - "Related Workflows": [], - "Related Tutorials": [], "To keep": false, "Deprecated": false }, @@ -4098,22 +4188,20 @@ "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, - "Number of tools on CorGAT": 0, - "Number of tools on CropGalaxy": 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 Genomic Hyperbrowser": 0, "Number of tools on HyPhy HIV NGS Tools": 0, "Number of tools on ImmPort Galaxy": 0, "Number of tools on InteractoMIX": 0, @@ -4121,12 +4209,13 @@ "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 PepSimili": 0, "Number of tools on PhagePromotor": 0, "Number of tools on UseGalaxy.be": 0, "Number of tools on UseGalaxy.cz": 1, "Number of tools on UseGalaxy.no": 1, + "Number of tools on Viral Variant Visualizer (VVV)": 0, "Suite users (last 5 years) (usegalaxy.eu)": 9, "Suite users (usegalaxy.eu)": 19, "Suite runs (last 5 years) (usegalaxy.eu)": 27, @@ -4147,8 +4236,6 @@ "Suite runs (last 5 years) on main servers": 27, "Suite users on main servers": 19, "Suite users (last 5 years) on main servers": 9, - "Related Workflows": [], - "Related Tutorials": [], "To keep": false, "Deprecated": false }, @@ -4184,22 +4271,27 @@ "bio.tool name": null, "bio.tool description": null, "biii ID": null, + "Related Workflows": [ + "https://usegalaxy.eu/published/workflow?id=7ee6976f69131683", + "https://usegalaxy.eu/published/workflow?id=a5ca8b9807ed3f73", + "https://usegalaxy.org.au/published/workflow?id=3678781bf7619a89", + "https://workflowhub.eu/workflows/1587?version=1" + ], + "Related Tutorials": [ + "metabolomics/msi-finding-nglycans" + ], "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, - "Number of tools on CorGAT": 0, - "Number of tools on CropGalaxy": 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 Genomic Hyperbrowser": 0, "Number of tools on HyPhy HIV NGS Tools": 0, "Number of tools on ImmPort Galaxy": 0, "Number of tools on InteractoMIX": 0, @@ -4207,12 +4299,13 @@ "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 PepSimili": 0, "Number of tools on PhagePromotor": 0, "Number of tools on UseGalaxy.be": 2, "Number of tools on UseGalaxy.cz": 2, "Number of tools on UseGalaxy.no": 2, + "Number of tools on Viral Variant Visualizer (VVV)": 0, "Suite users (last 5 years) (usegalaxy.eu)": 31, "Suite users (usegalaxy.eu)": 37, "Suite runs (last 5 years) (usegalaxy.eu)": 985, @@ -4233,15 +4326,6 @@ "Suite runs (last 5 years) on main servers": 2200, "Suite users on main servers": 58, "Suite users (last 5 years) on main servers": 52, - "Related Workflows": [ - "https://usegalaxy.eu/published/workflow?id=7ee6976f69131683", - "https://usegalaxy.eu/published/workflow?id=a5ca8b9807ed3f73", - "https://usegalaxy.org.au/published/workflow?id=3678781bf7619a89", - "https://workflowhub.eu/workflows/1587?version=1" - ], - "Related Tutorials": [ - "metabolomics/msi-finding-nglycans" - ], "To keep": false, "Deprecated": false }, @@ -4254,7 +4338,7 @@ "bed" ], "Description": "Map peptides to a reference genome for display by a genome browser", - "Suite first commit date": "2016-01-13", + "Suite first commit date": "2016-01-12", "Homepage": null, "Suite version": "0.2", "Suite conda package": "biopython", @@ -4274,22 +4358,20 @@ "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, - "Number of tools on CorGAT": 0, - "Number of tools on CropGalaxy": 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 Genomic Hyperbrowser": 0, "Number of tools on HyPhy HIV NGS Tools": 0, "Number of tools on ImmPort Galaxy": 0, "Number of tools on InteractoMIX": 0, @@ -4297,12 +4379,13 @@ "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 PepSimili": 0, "Number of tools on PhagePromotor": 0, "Number of tools on UseGalaxy.be": 0, "Number of tools on UseGalaxy.cz": 1, "Number of tools on UseGalaxy.no": 1, + "Number of tools on Viral Variant Visualizer (VVV)": 0, "Suite users (last 5 years) (usegalaxy.eu)": 5, "Suite users (usegalaxy.eu)": 9, "Suite runs (last 5 years) (usegalaxy.eu)": 10, @@ -4323,8 +4406,6 @@ "Suite runs (last 5 years) on main servers": 10, "Suite users on main servers": 9, "Suite users (last 5 years) on main servers": 5, - "Related Workflows": [], - "Related Tutorials": [], "To keep": false, "Deprecated": false }, @@ -4336,7 +4417,7 @@ ], "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", @@ -4380,22 +4461,57 @@ "bio.tool name": "MaxQuant", "bio.tool description": "Quantitative proteomics software package designed for analyzing large mass-spectrometric data sets. It is specifically aimed at high-resolution MS data.", "biii ID": null, + "Related Workflows": [ + "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" + ], + "Related Tutorials": [ + "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" + ], "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": 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, - "Number of tools on CorGAT": 0, - "Number of tools on CropGalaxy": 0, "Number of tools on Galaxy@AuBi": 0, "Number of tools on Galaxy@Pasteur": 2, "Number of tools on GalaxyTrakr": 0, "Number of tools on GASLINI": 0, - "Number of tools on Genomic Hyperbrowser": 0, "Number of tools on HyPhy HIV NGS Tools": 0, "Number of tools on ImmPort Galaxy": 0, "Number of tools on InteractoMIX": 0, @@ -4403,12 +4519,13 @@ "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 PepSimili": 0, "Number of tools on PhagePromotor": 0, "Number of tools on UseGalaxy.be": 2, "Number of tools on UseGalaxy.cz": 2, "Number of tools on UseGalaxy.no": 2, + "Number of tools on Viral Variant Visualizer (VVV)": 0, "Suite users (last 5 years) (usegalaxy.eu)": 1628, "Suite users (usegalaxy.eu)": 1682, "Suite runs (last 5 years) (usegalaxy.eu)": 7932, @@ -4429,45 +4546,6 @@ "Suite runs (last 5 years) on main servers": 15476, "Suite users on main servers": 2876, "Suite users (last 5 years) on main servers": 2813, - "Related Workflows": [ - "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" - ], - "Related Tutorials": [ - "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" - ], "To keep": false, "Deprecated": false }, @@ -4482,10 +4560,10 @@ "Description": "MetaProteomeAnalyzer", "Suite first commit date": "2017-03-03", "Homepage": "https://github.com/compomics/meta-proteome-analyzer/", - "Suite version": "2.0.0", + "Suite version": "@TOOL_VERSION@+galaxy@WRAPPER_VERSION@", "Suite conda package": "mpa-portable", "Latest suite conda package version": "2.0.0", - "Suite version status": "Up-to-date", + "Suite version status": "To update", "ToolShed categories": [ "Proteomics" ], @@ -4500,22 +4578,20 @@ "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, - "Number of tools on CorGAT": 0, - "Number of tools on CropGalaxy": 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 GASLINI": 0, - "Number of tools on Genomic Hyperbrowser": 0, "Number of tools on HyPhy HIV NGS Tools": 0, "Number of tools on ImmPort Galaxy": 0, "Number of tools on InteractoMIX": 0, @@ -4523,12 +4599,13 @@ "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 PepSimili": 0, "Number of tools on PhagePromotor": 0, "Number of tools on UseGalaxy.be": 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)": 22, "Suite users (usegalaxy.eu)": 22, "Suite runs (last 5 years) (usegalaxy.eu)": 148, @@ -4549,8 +4626,6 @@ "Suite runs (last 5 years) on main servers": 148, "Suite users on main servers": 22, "Suite users (last 5 years) on main servers": 22, - "Related Workflows": [], - "Related Tutorials": [], "To keep": false, "Deprecated": false }, @@ -4566,10 +4641,10 @@ "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" ], @@ -4608,22 +4683,34 @@ "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, - "Number of tools on CorGAT": 0, - "Number of tools on CropGalaxy": 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 Genomic Hyperbrowser": 0, "Number of tools on HyPhy HIV NGS Tools": 0, "Number of tools on ImmPort Galaxy": 0, "Number of tools on InteractoMIX": 0, @@ -4631,12 +4718,13 @@ "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 PepSimili": 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.no": 0, + "Number of tools on Viral Variant Visualizer (VVV)": 0, "Suite users (last 5 years) (usegalaxy.eu)": 40, "Suite users (usegalaxy.eu)": 40, "Suite runs (last 5 years) (usegalaxy.eu)": 5000, @@ -4657,22 +4745,6 @@ "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", - "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" - ], "To keep": false, "Deprecated": false }, @@ -4694,9 +4766,9 @@ "Description": "quantitative analysis of microbiome taxonomy and function", "Suite first commit date": "2018-11-27", "Homepage": "https://github.com/galaxyproteomics/metaquantome/", - "Suite version": "2.0.2", + "Suite version": "2.0.4", "Suite conda package": "metaquantome", - "Latest suite conda package version": "2.0.2", + "Latest suite conda package version": "2.0.4", "Suite version status": "Up-to-date", "ToolShed categories": [ "Proteomics" @@ -4744,22 +4816,33 @@ "bio.tool name": "metaQuantome", "bio.tool description": "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.", "biii ID": null, + "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", + "https://usegalaxy.org.au/published/workflow?id=f8183bba3a1d150d", + "https://workflowhub.eu/workflows/1453?version=1", + "https://workflowhub.eu/workflows/1459?version=1" + ], + "Related Tutorials": [ + "proteomics/metaquantome-function", + "proteomics/metaquantome-taxonomy" + ], "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, - "Number of tools on CorGAT": 0, - "Number of tools on CropGalaxy": 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 Genomic Hyperbrowser": 0, "Number of tools on HyPhy HIV NGS Tools": 0, "Number of tools on ImmPort Galaxy": 0, "Number of tools on InteractoMIX": 0, @@ -4767,12 +4850,13 @@ "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 PepSimili": 0, "Number of tools on PhagePromotor": 0, "Number of tools on UseGalaxy.be": 6, "Number of tools on UseGalaxy.cz": 6, "Number of tools on UseGalaxy.no": 6, + "Number of tools on Viral Variant Visualizer (VVV)": 0, "Suite users (last 5 years) (usegalaxy.eu)": 80, "Suite users (usegalaxy.eu)": 89, "Suite runs (last 5 years) (usegalaxy.eu)": 2277, @@ -4793,21 +4877,6 @@ "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", - "https://usegalaxy.org.au/published/workflow?id=f8183bba3a1d150d", - "https://workflowhub.eu/workflows/1453?version=1", - "https://workflowhub.eu/workflows/1459?version=1" - ], - "Related Tutorials": [ - "proteomics/metaquantome-function", - "proteomics/metaquantome-taxonomy" - ], "To keep": false, "Deprecated": false }, @@ -4823,10 +4892,10 @@ "Description": "moFF (a modest Feature Finder) extracts MS1 intensities from RAW and mzML spectrum files.", "Suite first commit date": "2017-12-11", "Homepage": "https://github.com/compomics/moFF", - "Suite version": "2.0.3", + "Suite version": "@VERSION@.0", "Suite conda package": "moff", "Latest suite conda package version": "2.0.3", - "Suite version status": "Up-to-date", + "Suite version status": "To update", "ToolShed categories": [ "Proteomics" ], @@ -4841,22 +4910,20 @@ "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": 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, - "Number of tools on CorGAT": 0, - "Number of tools on CropGalaxy": 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 Genomic Hyperbrowser": 0, "Number of tools on HyPhy HIV NGS Tools": 0, "Number of tools on ImmPort Galaxy": 0, "Number of tools on InteractoMIX": 0, @@ -4864,12 +4931,13 @@ "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 PepSimili": 0, "Number of tools on PhagePromotor": 0, "Number of tools on UseGalaxy.be": 0, "Number of tools on UseGalaxy.cz": 1, "Number of tools on UseGalaxy.no": 1, + "Number of tools on Viral Variant Visualizer (VVV)": 0, "Suite users (last 5 years) (usegalaxy.eu)": 14, "Suite users (usegalaxy.eu)": 35, "Suite runs (last 5 years) (usegalaxy.eu)": 280, @@ -4890,8 +4958,6 @@ "Suite runs (last 5 years) on main servers": 452, "Suite users on main servers": 39, "Suite users (last 5 years) on main servers": 18, - "Related Workflows": [], - "Related Tutorials": [], "To keep": false, "Deprecated": false }, @@ -4934,22 +5000,20 @@ "bio.tool name": "Morpheus", "bio.tool description": "A proteomics search algorithm specifically designed for high-resolution tandem mass spectra.", "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, - "Number of tools on CorGAT": 0, - "Number of tools on CropGalaxy": 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 Genomic Hyperbrowser": 0, "Number of tools on HyPhy HIV NGS Tools": 0, "Number of tools on ImmPort Galaxy": 0, "Number of tools on InteractoMIX": 0, @@ -4957,12 +5021,13 @@ "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 PepSimili": 0, "Number of tools on PhagePromotor": 0, "Number of tools on UseGalaxy.be": 0, "Number of tools on UseGalaxy.cz": 1, "Number of tools on UseGalaxy.no": 1, + "Number of tools on Viral Variant Visualizer (VVV)": 0, "Suite users (last 5 years) (usegalaxy.eu)": 10, "Suite users (usegalaxy.eu)": 20, "Suite runs (last 5 years) (usegalaxy.eu)": 77, @@ -4983,8 +5048,6 @@ "Suite runs (last 5 years) on main servers": 1314, "Suite users on main servers": 177, "Suite users (last 5 years) on main servers": 167, - "Related Workflows": [], - "Related Tutorials": [], "To keep": false, "Deprecated": false }, @@ -5022,22 +5085,20 @@ "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": 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, - "Number of tools on CorGAT": 0, - "Number of tools on CropGalaxy": 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 Genomic Hyperbrowser": 0, "Number of tools on HyPhy HIV NGS Tools": 0, "Number of tools on ImmPort Galaxy": 0, "Number of tools on InteractoMIX": 0, @@ -5045,12 +5106,13 @@ "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 PepSimili": 0, "Number of tools on PhagePromotor": 0, "Number of tools on UseGalaxy.be": 0, "Number of tools on UseGalaxy.cz": 2, "Number of tools on UseGalaxy.no": 0, + "Number of tools on Viral Variant Visualizer (VVV)": 0, "Suite users (last 5 years) (usegalaxy.eu)": 4, "Suite users (usegalaxy.eu)": 4, "Suite runs (last 5 years) (usegalaxy.eu)": 15, @@ -5071,8 +5133,6 @@ "Suite runs (last 5 years) on main servers": 15, "Suite users on main servers": 4, "Suite users (last 5 years) on main servers": 4, - "Related Workflows": [], - "Related Tutorials": [], "To keep": false, "Deprecated": false }, @@ -5083,9 +5143,9 @@ ], "Tool output formats": [], "Description": "msconvert Convert and/or filter mass spectrometry files (including vendor formats) using the official Docker container", - "Suite first commit date": "2015-01-24", + "Suite first commit date": "2015-01-23", "Homepage": "http://proteowizard.sourceforge.net/tools.shtml", - "Suite version": "3.0.20287", + "Suite version": "3.0.26121", "Suite conda package": null, "Latest suite conda package version": null, "Suite version status": "To update", @@ -5115,56 +5175,8 @@ "bio.tool name": "msConvert", "bio.tool description": "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). For Windows users, there is also a GUI, msConvertGUI.", "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 CorGAT": 0, - "Number of tools on CropGalaxy": 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 Genomic Hyperbrowser": 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 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, - "Number of tools on UseGalaxy.no": 1, - "Suite users (last 5 years) (usegalaxy.eu)": 550, - "Suite users (usegalaxy.eu)": 604, - "Suite runs (last 5 years) (usegalaxy.eu)": 58574, - "Suite runs (usegalaxy.eu)": 66339, - "Suite users (last 5 years) (usegalaxy.org)": 133, - "Suite users (usegalaxy.org)": 133, - "Suite runs (last 5 years) (usegalaxy.org)": 2254, - "Suite runs (usegalaxy.org)": 2254, - "Suite users (last 5 years) (usegalaxy.org.au)": 76, - "Suite users (usegalaxy.org.au)": 76, - "Suite runs (last 5 years) (usegalaxy.org.au)": 4844, - "Suite runs (usegalaxy.org.au)": 4844, - "Suite users (last 5 years) (usegalaxy.fr)": 108, - "Suite users (usegalaxy.fr)": 113, - "Suite runs (last 5 years) (usegalaxy.fr)": 7765, - "Suite runs (usegalaxy.fr)": 7906, - "Suite runs on main servers": 81343, - "Suite runs (last 5 years) on main servers": 73437, - "Suite users on main servers": 926, - "Suite users (last 5 years) on main servers": 867, "Related Workflows": [ + "https://usegalaxy.cz/published/workflow?id=bc8f2b3ecdad343e", "https://usegalaxy.eu/published/workflow?id=02700454f57eb556", "https://usegalaxy.eu/published/workflow?id=14f9c2099db30570", "https://usegalaxy.eu/published/workflow?id=1809fcaec264eac9", @@ -5203,6 +5215,7 @@ "https://usegalaxy.org.au/published/workflow?id=762791e094457bf2", "https://usegalaxy.org.au/published/workflow?id=8c874ea77827448c", "https://usegalaxy.org.au/published/workflow?id=ba217a34d7e1b5ee", + "https://usegalaxy.org.au/published/workflow?id=f19bb578f2717a31", "https://usegalaxy.org/published/workflow?id=8ecc114eb9097855", "https://usegalaxy.org/published/workflow?id=e97da2da9e0290a7", "https://workflowhub.eu/workflows/1225?version=1", @@ -5225,6 +5238,52 @@ "proteomics/neoantigen-peptide-verification", "proteomics/protein-id-oms" ], + "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 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, + "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.no": 1, + "Number of tools on Viral Variant Visualizer (VVV)": 0, + "Suite users (last 5 years) (usegalaxy.eu)": 550, + "Suite users (usegalaxy.eu)": 604, + "Suite runs (last 5 years) (usegalaxy.eu)": 58574, + "Suite runs (usegalaxy.eu)": 66339, + "Suite users (last 5 years) (usegalaxy.org)": 133, + "Suite users (usegalaxy.org)": 133, + "Suite runs (last 5 years) (usegalaxy.org)": 2254, + "Suite runs (usegalaxy.org)": 2254, + "Suite users (last 5 years) (usegalaxy.org.au)": 76, + "Suite users (usegalaxy.org.au)": 76, + "Suite runs (last 5 years) (usegalaxy.org.au)": 4844, + "Suite runs (usegalaxy.org.au)": 4844, + "Suite users (last 5 years) (usegalaxy.fr)": 108, + "Suite users (usegalaxy.fr)": 113, + "Suite runs (last 5 years) (usegalaxy.fr)": 7765, + "Suite runs (usegalaxy.fr)": 7906, + "Suite runs on main servers": 81343, + "Suite runs (last 5 years) on main servers": 73437, + "Suite users on main servers": 926, + "Suite users (last 5 years) on main servers": 867, "To keep": false, "Deprecated": false }, @@ -5258,22 +5317,20 @@ "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, - "Number of tools on CorGAT": 0, - "Number of tools on CropGalaxy": 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 Genomic Hyperbrowser": 0, "Number of tools on HyPhy HIV NGS Tools": 0, "Number of tools on ImmPort Galaxy": 0, "Number of tools on InteractoMIX": 0, @@ -5281,12 +5338,13 @@ "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 PepSimili": 0, "Number of tools on PhagePromotor": 0, "Number of tools on UseGalaxy.be": 0, "Number of tools on UseGalaxy.cz": 1, "Number of tools on UseGalaxy.no": 1, + "Number of tools on Viral Variant Visualizer (VVV)": 0, "Suite users (last 5 years) (usegalaxy.eu)": 34, "Suite users (usegalaxy.eu)": 54, "Suite runs (last 5 years) (usegalaxy.eu)": 762, @@ -5307,8 +5365,6 @@ "Suite runs (last 5 years) on main servers": 762, "Suite users on main servers": 54, "Suite users (last 5 years) on main servers": 34, - "Related Workflows": [], - "Related Tutorials": [], "To keep": false, "Deprecated": false }, @@ -5341,22 +5397,23 @@ "bio.tool name": null, "bio.tool description": null, "biii ID": null, + "Related Workflows": [ + "https://usegalaxy.eu/published/workflow?id=6b7b86756060659b", + "https://usegalaxy.eu/published/workflow?id=c750484145c9903b" + ], + "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, - "Number of tools on CorGAT": 0, - "Number of tools on CropGalaxy": 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 GASLINI": 0, - "Number of tools on Genomic Hyperbrowser": 0, "Number of tools on HyPhy HIV NGS Tools": 0, "Number of tools on ImmPort Galaxy": 0, "Number of tools on InteractoMIX": 0, @@ -5364,12 +5421,13 @@ "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 PepSimili": 0, "Number of tools on PhagePromotor": 0, "Number of tools on UseGalaxy.be": 0, "Number of tools on UseGalaxy.cz": 1, "Number of tools on UseGalaxy.no": 1, + "Number of tools on Viral Variant Visualizer (VVV)": 0, "Suite users (last 5 years) (usegalaxy.eu)": 7, "Suite users (usegalaxy.eu)": 12, "Suite runs (last 5 years) (usegalaxy.eu)": 21, @@ -5390,11 +5448,6 @@ "Suite runs (last 5 years) on main servers": 21, "Suite users on main servers": 13, "Suite users (last 5 years) on main servers": 7, - "Related Workflows": [ - "https://usegalaxy.eu/published/workflow?id=6b7b86756060659b", - "https://usegalaxy.eu/published/workflow?id=c750484145c9903b" - ], - "Related Tutorials": [], "To keep": false, "Deprecated": false }, @@ -5411,7 +5464,7 @@ "Description": "MSstats tool for analyzing mass spectrometry proteomic datasets", "Suite first commit date": "2020-07-25", "Homepage": "https://github.com/MeenaChoi/MSstats", - "Suite version": "4.0.0", + "Suite version": "@TOOL_VERSION@+galaxy@VERSION_SUFFIX@", "Suite conda package": "bioconductor-msstats", "Latest suite conda package version": "4.18.1", "Suite version status": "To update", @@ -5445,22 +5498,29 @@ "bio.tool name": "MSstatsTMT", "bio.tool description": "Tools for detecting differentially abundant 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, - "Number of tools on CorGAT": 0, - "Number of tools on CropGalaxy": 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 GASLINI": 0, - "Number of tools on Genomic Hyperbrowser": 0, "Number of tools on HyPhy HIV NGS Tools": 0, "Number of tools on ImmPort Galaxy": 0, "Number of tools on InteractoMIX": 0, @@ -5468,12 +5528,13 @@ "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 PepSimili": 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.no": 1, + "Number of tools on Viral Variant Visualizer (VVV)": 0, "Suite users (last 5 years) (usegalaxy.eu)": 800, "Suite users (usegalaxy.eu)": 803, "Suite runs (last 5 years) (usegalaxy.eu)": 2969, @@ -5494,17 +5555,6 @@ "Suite runs (last 5 years) on main servers": 6030, "Suite users on main servers": 1185, "Suite users (last 5 years) on main servers": 1182, - "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" - ], "To keep": false, "Deprecated": false }, @@ -5521,7 +5571,7 @@ "Description": "MSstatsTMT protein significance analysis in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling", "Suite first commit date": "2021-01-20", "Homepage": "http://msstats.org/msstatstmt/", - "Suite version": "2.0.0", + "Suite version": "@TOOL_VERSION@+galaxy@VERSION_SUFFIX@", "Suite conda package": "bioconductor-msstatstmt", "Latest suite conda package version": "2.18.0", "Suite version status": "To update", @@ -5539,22 +5589,34 @@ "bio.tool name": null, "bio.tool description": null, "biii ID": null, + "Related Workflows": [ + "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" + ], + "Related Tutorials": [ + "microbiome/clinical-mp-5-data-interpretation", + "proteomics/clinical-mp-5-data-interpretation", + "proteomics/maxquant-msstats-tmt" + ], "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, - "Number of tools on CorGAT": 0, - "Number of tools on CropGalaxy": 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 Genomic Hyperbrowser": 0, "Number of tools on HyPhy HIV NGS Tools": 0, "Number of tools on ImmPort Galaxy": 0, "Number of tools on InteractoMIX": 0, @@ -5562,12 +5624,13 @@ "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 PepSimili": 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.no": 0, + "Number of tools on Viral Variant Visualizer (VVV)": 0, "Suite users (last 5 years) (usegalaxy.eu)": 113, "Suite users (usegalaxy.eu)": 113, "Suite runs (last 5 years) (usegalaxy.eu)": 844, @@ -5588,22 +5651,6 @@ "Suite runs (last 5 years) on main servers": 1584, "Suite users on main servers": 141, "Suite users (last 5 years) on main servers": 141, - "Related Workflows": [ - "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" - ], - "Related Tutorials": [ - "microbiome/clinical-mp-5-data-interpretation", - "proteomics/clinical-mp-5-data-interpretation", - "proteomics/maxquant-msstats-tmt" - ], "To keep": false, "Deprecated": false }, @@ -5636,22 +5683,20 @@ "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, - "Number of tools on CorGAT": 0, - "Number of tools on CropGalaxy": 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 Genomic Hyperbrowser": 0, "Number of tools on HyPhy HIV NGS Tools": 0, "Number of tools on ImmPort Galaxy": 0, "Number of tools on InteractoMIX": 0, @@ -5659,12 +5704,13 @@ "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 PepSimili": 0, "Number of tools on PhagePromotor": 0, "Number of tools on UseGalaxy.be": 0, "Number of tools on UseGalaxy.cz": 1, "Number of tools on UseGalaxy.no": 1, + "Number of tools on Viral Variant Visualizer (VVV)": 0, "Suite users (last 5 years) (usegalaxy.eu)": 39, "Suite users (usegalaxy.eu)": 43, "Suite runs (last 5 years) (usegalaxy.eu)": 258, @@ -5685,8 +5731,6 @@ "Suite runs (last 5 years) on main servers": 258, "Suite users on main servers": 43, "Suite users (last 5 years) on main servers": 39, - "Related Workflows": [], - "Related Tutorials": [], "To keep": false, "Deprecated": false }, @@ -5701,10 +5745,10 @@ "Description": "Creates a SQLite database for proteomics data", "Suite first commit date": "2015-06-01", "Homepage": "https://github.com/galaxyproteomics/mzToSQLite", - "Suite version": "2.1.1+galaxy0", + "Suite version": "2.1.1", "Suite conda package": "mztosqlite", "Latest suite conda package version": "2.1.1", - "Suite version status": "To update", + "Suite version status": "Up-to-date", "ToolShed categories": [ "Proteomics" ], @@ -5731,22 +5775,37 @@ "bio.tool name": "mzToSQLite", "bio.tool description": "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.", "biii ID": null, + "Related Workflows": [ + "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" + ], + "Related Tutorials": [ + "proteomics/proteogenomics-dbsearch" + ], "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, - "Number of tools on CorGAT": 0, - "Number of tools on CropGalaxy": 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 Genomic Hyperbrowser": 0, "Number of tools on HyPhy HIV NGS Tools": 0, "Number of tools on ImmPort Galaxy": 0, "Number of tools on InteractoMIX": 0, @@ -5754,12 +5813,13 @@ "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 PepSimili": 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.no": 1, + "Number of tools on Viral Variant Visualizer (VVV)": 0, "Suite users (last 5 years) (usegalaxy.eu)": 136, "Suite users (usegalaxy.eu)": 146, "Suite runs (last 5 years) (usegalaxy.eu)": 868, @@ -5780,24 +5840,6 @@ "Suite runs (last 5 years) on main servers": 1287, "Suite users on main servers": 181, "Suite users (last 5 years) on main servers": 171, - 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"https://workflowhub.eu/workflows/613?version=2" + "https://workflowhub.eu/workflows/613?version=3" ], "Related Tutorials": [ "proteomics/DIA_Analysis_OSW", @@ -6099,54 +6094,18 @@ "proteomics/protein-id-sg-ps", "proteomics/protein-quant-sil" ], - "To keep": false, - "Deprecated": false - }, - { - "Suite ID": "reactome_pathwaymatcher", - "Tool IDs": [ - "reactome_pathwaymatcher" - ], - "Tool output formats": [ - "tsv" - ], - "Description": "Reactome Pathway Matcher", - "Suite first commit date": "2018-06-08", - "Homepage": "https://github.com/LuisFranciscoHS/PathwayMatcher", - "Suite version": null, - "Suite conda package": "pathwaymatcher", - "Latest suite conda package version": "1.9.1", - "Suite version status": "To update", - "ToolShed categories": [ - "Proteomics" - ], - "EDAM operations": [], - "EDAM reduced operations": [], - "EDAM topics": [], - "EDAM reduced topics": [], - "Suite owner": "galaxyp", - "Suite source": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher", - 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"Suite first commit date": "2015-01-24", + "Suite first commit date": "2015-01-23", "Homepage": null, "Suite version": null, "Suite conda package": null, @@ -6804,22 +6749,20 @@ "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, - "Number of tools on CorGAT": 0, - "Number of tools on CropGalaxy": 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 Genomic Hyperbrowser": 0, "Number of tools on HyPhy HIV NGS Tools": 0, "Number of tools on ImmPort Galaxy": 0, "Number of tools on InteractoMIX": 0, @@ -6827,12 +6770,13 @@ "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 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.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, @@ -6853,8 +6797,6 @@ "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": false, "Deprecated": false }, @@ -6876,7 +6818,7 @@ "Homepage": null, "Suite version": "3.5", "Suite conda package": "percolator", - "Latest suite conda package version": "3.7.1", + "Latest suite conda package version": "3.9", "Suite version status": "To update", "ToolShed categories": [ "Proteomics" @@ -6892,22 +6834,20 @@ "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": 4, "Number of tools on UseGalaxy.eu": 4, "Number of tools on UseGalaxy.fr": 0, "Number of tools on APOSTL": 0, - 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], - "Related Tutorials": [ - "proteomics/neoantigen-non-reference-database-generation", - "proteomics/proteogenomics-dbcreation" - ], "To keep": false, "Deprecated": false }, @@ -7244,22 +7175,20 @@ "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, - "Number of tools on CorGAT": 0, - "Number of tools on CropGalaxy": 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 Genomic Hyperbrowser": 0, "Number of tools on HyPhy HIV NGS Tools": 0, "Number of tools on ImmPort Galaxy": 0, "Number of tools on InteractoMIX": 0, @@ -7267,12 +7196,13 @@ "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, - 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"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, - "Number of tools on CorGAT": 0, - "Number of tools on CropGalaxy": 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 Genomic Hyperbrowser": 0, "Number of tools on HyPhy HIV NGS Tools": 0, "Number of tools on ImmPort Galaxy": 0, "Number of tools on InteractoMIX": 0, @@ -7434,12 +7457,13 @@ "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 PepSimili": 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.no": 1, + "Number of tools on Viral Variant Visualizer (VVV)": 0, "Suite users (last 5 years) (usegalaxy.eu)": 185, "Suite users (usegalaxy.eu)": 200, "Suite runs (last 5 years) (usegalaxy.eu)": 697, @@ -7460,27 +7484,6 @@ "Suite runs (last 5 years) on main servers": 2283, "Suite users on main servers": 350, "Suite users (last 5 years) on main servers": 335, - "Related Workflows": [ - "https://usegalaxy.eu/published/workflow?id=17916f0229e3c868", - "https://usegalaxy.eu/published/workflow?id=39afbf843b5513bf", - "https://usegalaxy.eu/published/workflow?id=3a8150c81b90a3a7", - "https://usegalaxy.eu/published/workflow?id=67f75ed02a03bf93", - "https://usegalaxy.eu/published/workflow?id=6e6cf59bfeb938bf", - "https://usegalaxy.eu/published/workflow?id=a2f36d4dd48d8ec2", - "https://usegalaxy.eu/published/workflow?id=a7638e7f908fd90d", - "https://usegalaxy.org.au/published/workflow?id=0ebaaecf61dfc921", - "https://usegalaxy.org.au/published/workflow?id=157e7614ae18849b", - "https://usegalaxy.org.au/published/workflow?id=7cd4fcc8e06ce4fd", - "https://usegalaxy.org/published/workflow?id=6a3e47124e32e260", - "https://usegalaxy.org/published/workflow?id=e336bca259abd474", - "https://workflowhub.eu/workflows/1407?version=1", - "https://workflowhub.eu/workflows/1437?version=1", - "https://workflowhub.eu/workflows/1788?version=1" - ], - "Related Tutorials": [ - "proteomics/neoantigen-non-reference-database-generation", - "proteomics/proteogenomics-dbcreation" - ], "To keep": false, "Deprecated": false }, @@ -7495,7 +7498,7 @@ "Description": "The tool JoinQuantPepIonsWithProteins combines results from ProteinInference and PSMBasedQuantification.", "Suite first commit date": "2021-09-16", "Homepage": "https://csbiology.github.io/ProteomIQon/tools/JoinQuantPepIonsWithProteins.html", - "Suite version": "0.0.1", + "Suite version": "@VERSION@", "Suite conda package": "proteomiqon-joinquantpepionswithproteins", "Latest suite conda package version": "0.0.2", "Suite version status": "To update", @@ -7513,22 +7516,20 @@ "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, - "Number of tools on CorGAT": 0, - "Number of tools on CropGalaxy": 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 Genomic Hyperbrowser": 0, "Number of tools on HyPhy HIV NGS Tools": 0, "Number of tools on ImmPort Galaxy": 0, "Number of tools on InteractoMIX": 0, @@ -7536,12 +7537,13 @@ "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 PepSimili": 0, "Number of tools on PhagePromotor": 0, "Number of tools on UseGalaxy.be": 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)": 5, "Suite users (usegalaxy.eu)": 5, "Suite runs (last 5 years) (usegalaxy.eu)": 372, @@ -7562,8 +7564,6 @@ "Suite runs (last 5 years) on main servers": 372, "Suite users on main servers": 5, "Suite users (last 5 years) on main servers": 5, - "Related Workflows": [], - "Related Tutorials": [], "To keep": false, "Deprecated": false }, @@ -7579,7 +7579,7 @@ "Description": "The tool LabeledProteinQuantification estimates protein abundances using quantified peptide ions.", "Suite first commit date": "2021-09-16", "Homepage": "https://csbiology.github.io/ProteomIQon/tools/LabeledProteinQuantification.html", - "Suite version": "0.0.1", + "Suite version": "@VERSION@", "Suite conda package": "proteomiqon-labeledproteinquantification", "Latest suite conda package version": "0.0.3", "Suite version status": "To update", @@ -7597,22 +7597,20 @@ "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, - "Number of tools on CorGAT": 0, - "Number of tools on CropGalaxy": 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 Genomic Hyperbrowser": 0, "Number of tools on HyPhy HIV NGS Tools": 0, "Number of tools on ImmPort Galaxy": 0, "Number of tools on InteractoMIX": 0, @@ -7620,12 +7618,13 @@ "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 PepSimili": 0, "Number of tools on PhagePromotor": 0, "Number of tools on UseGalaxy.be": 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)": 10, "Suite users (usegalaxy.eu)": 10, "Suite runs (last 5 years) (usegalaxy.eu)": 19, @@ -7646,8 +7645,6 @@ "Suite runs (last 5 years) on main servers": 19, "Suite users on main servers": 10, "Suite users (last 5 years) on main servers": 10, - "Related Workflows": [], - "Related Tutorials": [], "To keep": false, "Deprecated": false }, @@ -7663,7 +7660,7 @@ "Description": "The tool LabelFreeProteinQuantification estimates protein abundances using quantified peptide ions.", "Suite first commit date": "2021-10-13", "Homepage": "https://csbiology.github.io/ProteomIQon/tools/LabelfreeProteinQuantification.html", - "Suite version": "0.0.1", + "Suite version": "@VERSION@", "Suite conda package": "proteomiqon-labelfreeproteinquantification", "Latest suite conda package version": "0.0.3", "Suite version status": "To update", @@ -7681,22 +7678,20 @@ "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, - "Number of tools on CorGAT": 0, - "Number of tools on CropGalaxy": 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 Genomic Hyperbrowser": 0, "Number of tools on HyPhy HIV NGS Tools": 0, "Number of tools on ImmPort Galaxy": 0, "Number of tools on InteractoMIX": 0, @@ -7704,12 +7699,13 @@ "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 PepSimili": 0, "Number of tools on PhagePromotor": 0, "Number of tools on UseGalaxy.be": 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)": 7, "Suite users (usegalaxy.eu)": 7, "Suite runs (last 5 years) (usegalaxy.eu)": 11, @@ -7730,8 +7726,6 @@ "Suite runs (last 5 years) on main servers": 11, "Suite users on main servers": 7, "Suite users (last 5 years) on main servers": 7, - "Related Workflows": [], - "Related Tutorials": [], "To keep": false, "Deprecated": false }, @@ -7747,10 +7741,10 @@ "Description": "The tool MzMLToMzLite allows to convert mzML files to mzLite files.", "Suite first commit date": "2021-06-30", "Homepage": "https://csbiology.github.io/ProteomIQon/tools/MzMLToMzLite.html", - "Suite version": "0.0.8", + "Suite version": "@VERSION@", "Suite conda package": "proteomiqon-mzmltomzlite", "Latest suite conda package version": "0.0.8", - "Suite version status": "Up-to-date", + "Suite version status": "To update", "ToolShed categories": [ "Proteomics" ], @@ -7765,22 +7759,20 @@ "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, - "Number of tools on CorGAT": 0, - "Number of tools on CropGalaxy": 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 Genomic Hyperbrowser": 0, "Number of tools on HyPhy HIV NGS Tools": 0, "Number of tools on ImmPort Galaxy": 0, "Number of tools on InteractoMIX": 0, @@ -7788,12 +7780,13 @@ "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 PepSimili": 0, "Number of tools on PhagePromotor": 0, "Number of tools on UseGalaxy.be": 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)": 10, "Suite users (usegalaxy.eu)": 10, "Suite runs (last 5 years) (usegalaxy.eu)": 723, @@ -7814,8 +7807,6 @@ "Suite runs (last 5 years) on main servers": 723, "Suite users on main servers": 10, "Suite users (last 5 years) on main servers": 10, - "Related Workflows": [], - "Related Tutorials": [], "To keep": false, "Deprecated": false }, @@ -7831,10 +7822,10 @@ "Description": "The tool ProteomIQon PeptideDB creates a peptide database in the SQLite format.", "Suite first commit date": "2021-07-04", "Homepage": "https://csbiology.github.io/ProteomIQon/tools/PeptideDB.html", - "Suite version": "0.0.7", + "Suite version": "@VERSION@", "Suite conda package": "proteomiqon-peptidedb", "Latest suite conda package version": "0.0.7", - "Suite version status": "Up-to-date", + "Suite version status": "To update", "ToolShed categories": [ "Proteomics" ], @@ -7849,22 +7840,20 @@ "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, - "Number of tools on CorGAT": 0, - "Number of tools on CropGalaxy": 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 Genomic Hyperbrowser": 0, "Number of tools on HyPhy HIV NGS Tools": 0, "Number of tools on ImmPort Galaxy": 0, "Number of tools on InteractoMIX": 0, @@ -7872,12 +7861,13 @@ "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 PepSimili": 0, "Number of tools on PhagePromotor": 0, "Number of tools on UseGalaxy.be": 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)": 12, "Suite users (usegalaxy.eu)": 12, "Suite runs (last 5 years) (usegalaxy.eu)": 96, @@ -7898,8 +7888,6 @@ "Suite runs (last 5 years) on main servers": 96, "Suite users on main servers": 12, "Suite users (last 5 years) on main servers": 12, - "Related Workflows": [], - "Related Tutorials": [], "To keep": false, "Deprecated": false }, @@ -7915,10 +7903,10 @@ "Description": "Given raw an MS run in the mzLite format, this tool iterates across all MS/MS scans, determines precursor charge states and possible peptide spectrum matches using reimplementations of SEQUEST,Andromeda and XTandem.", "Suite first commit date": "2021-07-15", "Homepage": "https://csbiology.github.io/ProteomIQon/tools/PeptideSpectrumMatching.html", - "Suite version": "0.0.7", + "Suite version": "@VERSION@", "Suite conda package": "proteomiqon-peptidespectrummatching", "Latest suite conda package version": "0.0.7", - "Suite version status": "Up-to-date", + "Suite version status": "To update", "ToolShed categories": [ "Proteomics" ], @@ -7933,22 +7921,20 @@ "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, - "Number of tools on CorGAT": 0, - "Number of tools on CropGalaxy": 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 Genomic Hyperbrowser": 0, "Number of tools on HyPhy HIV NGS Tools": 0, "Number of tools on ImmPort Galaxy": 0, "Number of tools on InteractoMIX": 0, @@ -7956,12 +7942,13 @@ "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 PepSimili": 0, "Number of tools on PhagePromotor": 0, "Number of tools on UseGalaxy.be": 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)": 5, "Suite users (usegalaxy.eu)": 5, "Suite runs (last 5 years) (usegalaxy.eu)": 686, @@ -7982,8 +7969,6 @@ "Suite runs (last 5 years) on main servers": 686, "Suite users on main servers": 5, "Suite users (last 5 years) on main servers": 5, - "Related Workflows": [], - "Related Tutorials": [], "To keep": false, "Deprecated": false }, @@ -7999,10 +7984,10 @@ "Description": "MS-based shotgun proteomics estimates protein abundances using a proxy: peptides. The process of 'Protein Inference' is concerned with the mapping of identified peptides to the proteins they putatively originated from.", "Suite first commit date": "2021-07-09", "Homepage": "https://csbiology.github.io/ProteomIQon/tools/ProteinInference.html", - "Suite version": "0.0.7", + "Suite version": "@VERSION@", "Suite conda package": "proteomiqon-proteininference", "Latest suite conda package version": "0.0.7", - "Suite version status": "Up-to-date", + "Suite version status": "To update", "ToolShed categories": [ "Proteomics" ], @@ -8017,22 +8002,20 @@ "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, - "Number of tools on CorGAT": 0, - "Number of tools on CropGalaxy": 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 Genomic Hyperbrowser": 0, "Number of tools on HyPhy HIV NGS Tools": 0, "Number of tools on ImmPort Galaxy": 0, "Number of tools on InteractoMIX": 0, @@ -8040,12 +8023,13 @@ "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 PepSimili": 0, "Number of tools on PhagePromotor": 0, "Number of tools on UseGalaxy.be": 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)": 6, "Suite users (usegalaxy.eu)": 6, "Suite runs (last 5 years) (usegalaxy.eu)": 89, @@ -8066,8 +8050,6 @@ "Suite runs (last 5 years) on main servers": 89, "Suite users on main servers": 6, "Suite users (last 5 years) on main servers": 6, - "Related Workflows": [], - "Related Tutorials": [], "To keep": false, "Deprecated": false }, @@ -8083,7 +8065,7 @@ "Description": "The PSMBasedQuantification tool was designed to allow label-free quantification as well as quantification of full metabolic labeled samples.", "Suite first commit date": "2021-07-09", "Homepage": "https://csbiology.github.io/ProteomIQon/tools/PSMBasedQuantification.html", - "Suite version": "0.0.8", + "Suite version": "@VERSION@", "Suite conda package": "proteomiqon-psmbasedquantification", "Latest suite conda package version": "0.0.9", "Suite version status": "To update", @@ -8101,22 +8083,20 @@ "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, - "Number of tools on CorGAT": 0, - "Number of tools on CropGalaxy": 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 Genomic Hyperbrowser": 0, "Number of tools on HyPhy HIV NGS Tools": 0, "Number of tools on ImmPort Galaxy": 0, "Number of tools on InteractoMIX": 0, @@ -8124,12 +8104,13 @@ "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 PepSimili": 0, "Number of tools on PhagePromotor": 0, "Number of tools on UseGalaxy.be": 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)": 4, "Suite users (usegalaxy.eu)": 4, "Suite runs (last 5 years) (usegalaxy.eu)": 604, @@ -8150,8 +8131,6 @@ "Suite runs (last 5 years) on main servers": 604, "Suite users on main servers": 4, "Suite users (last 5 years) on main servers": 4, - "Related Workflows": [], - "Related Tutorials": [], "To keep": false, "Deprecated": false }, @@ -8167,10 +8146,10 @@ "Description": "The PSMStatistics tool utilizes semi supervised machine learning techniques to integrate search engine scores as well as the mentioned quality scores into one single consensus score.", "Suite first commit date": "2021-07-09", "Homepage": "https://csbiology.github.io/ProteomIQon/tools/PSMStatistics.html", - "Suite version": "0.0.8", + "Suite version": "@VERSION@", "Suite conda package": "proteomiqon-psmstatistics", "Latest suite conda package version": "0.0.8", - "Suite version status": "Up-to-date", + "Suite version status": "To update", "ToolShed categories": [ "Proteomics" ], @@ -8185,22 +8164,20 @@ "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, - "Number of tools on CorGAT": 0, - "Number of tools on CropGalaxy": 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 Genomic Hyperbrowser": 0, "Number of tools on HyPhy HIV NGS Tools": 0, "Number of tools on ImmPort Galaxy": 0, "Number of tools on InteractoMIX": 0, @@ -8208,12 +8185,13 @@ "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 PepSimili": 0, "Number of tools on PhagePromotor": 0, "Number of tools on UseGalaxy.be": 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)": 6, "Suite users (usegalaxy.eu)": 6, "Suite runs (last 5 years) (usegalaxy.eu)": 694, @@ -8234,8 +8212,6 @@ "Suite runs (last 5 years) on main servers": 694, "Suite users on main servers": 6, "Suite users (last 5 years) on main servers": 6, - "Related Workflows": [], - "Related Tutorials": [], "To keep": false, "Deprecated": false }, @@ -8269,22 +8245,20 @@ "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, - "Number of tools on CorGAT": 0, - "Number of tools on CropGalaxy": 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 Genomic Hyperbrowser": 0, "Number of tools on HyPhy HIV NGS Tools": 0, "Number of tools on ImmPort Galaxy": 0, "Number of tools on InteractoMIX": 0, @@ -8292,12 +8266,13 @@ "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 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.no": 0, + "Number of tools on Viral Variant Visualizer (VVV)": 0, "Suite users (last 5 years) (usegalaxy.eu)": 1, "Suite users (usegalaxy.eu)": 1, "Suite runs (last 5 years) (usegalaxy.eu)": 15, @@ -8318,8 +8293,6 @@ "Suite runs (last 5 years) on main servers": 15, "Suite users on main servers": 1, "Suite users (last 5 years) on main servers": 1, - "Related Workflows": [], - "Related Tutorials": [], "To keep": false, "Deprecated": false }, @@ -8353,22 +8326,20 @@ "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, - "Number of tools on CorGAT": 0, - "Number of tools on CropGalaxy": 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 Genomic Hyperbrowser": 0, "Number of tools on HyPhy HIV NGS Tools": 0, "Number of tools on ImmPort Galaxy": 0, "Number of tools on InteractoMIX": 0, @@ -8376,12 +8347,13 @@ "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 PepSimili": 0, "Number of tools on PhagePromotor": 0, "Number of tools on UseGalaxy.be": 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)": 4, "Suite users (usegalaxy.eu)": 4, "Suite runs (last 5 years) (usegalaxy.eu)": 20, @@ -8402,8 +8374,6 @@ "Suite runs (last 5 years) on main servers": 20, "Suite users on main servers": 4, "Suite users (last 5 years) on main servers": 4, - "Related Workflows": [], - "Related Tutorials": [], "To keep": false, "Deprecated": false }, @@ -8418,7 +8388,7 @@ "Description": "Quality control reports for MaxQuant results", "Suite first commit date": "2025-04-16", "Homepage": "https://github.com/cbielow/PTXQC", - "Suite version": "1.1.2", + "Suite version": "@TOOL_VERSION@+galaxy@VERSION_SUFFIX@", "Suite conda package": "r-ptxqc", "Latest suite conda package version": null, "Suite version status": "To update", @@ -8444,22 +8414,20 @@ "bio.tool name": "PTXQC", "bio.tool description": "PTXQC is a quality control pipeline for proteomics results generated by MaxQuant.", "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, - "Number of tools on CorGAT": 0, - "Number of tools on CropGalaxy": 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 Genomic Hyperbrowser": 0, "Number of tools on HyPhy HIV NGS Tools": 0, "Number of tools on ImmPort Galaxy": 0, "Number of tools on InteractoMIX": 0, @@ -8467,12 +8435,13 @@ "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 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.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, @@ -8493,8 +8462,6 @@ "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": null, "Deprecated": null }, @@ -8514,11 +8481,11 @@ "osw" ], "Description": "Semi-supervised learning and scoring of OpenSWATH results.", - "Suite first commit date": "2015-02-06", + "Suite first commit date": "2015-02-07", "Homepage": "https://github.com/PyProphet/pyprophet", "Suite version": "2.1.4", "Suite conda package": "pyprophet", - "Latest suite conda package version": "3.0.5", + "Latest suite conda package version": "3.0.15", "Suite version status": "To update", "ToolShed categories": [ "Proteomics" @@ -8534,22 +8501,24 @@ "bio.tool name": null, "bio.tool description": null, "biii ID": null, + "Related Workflows": [ + "https://workflowhub.eu/workflows/1463?version=1" + ], + "Related Tutorials": [ + "proteomics/DIA_Analysis_OSW" + ], "Number of tools on UseGalaxy.org (Main)": 0, "Number of tools on UseGalaxy.org.au": 5, "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, - "Number of tools on CorGAT": 0, - "Number of tools on CropGalaxy": 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 Genomic Hyperbrowser": 0, "Number of tools on HyPhy HIV NGS Tools": 0, "Number of tools on ImmPort Galaxy": 0, "Number of tools on InteractoMIX": 0, @@ -8557,12 +8526,13 @@ "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 PepSimili": 0, "Number of tools on PhagePromotor": 0, "Number of tools on UseGalaxy.be": 5, "Number of tools on UseGalaxy.cz": 6, "Number of tools on UseGalaxy.no": 6, + "Number of tools on Viral Variant Visualizer (VVV)": 0, "Suite users (last 5 years) (usegalaxy.eu)": 35, "Suite users (usegalaxy.eu)": 37, "Suite runs (last 5 years) (usegalaxy.eu)": 1794, @@ -8583,12 +8553,6 @@ "Suite runs (last 5 years) on main servers": 2846, "Suite users on main servers": 42, "Suite users (last 5 years) on main servers": 40, - "Related Workflows": [ - "https://workflowhub.eu/workflows/1463?version=1" - ], - "Related Tutorials": [ - "proteomics/DIA_Analysis_OSW" - ], "To keep": null, "Deprecated": null }, @@ -8601,7 +8565,7 @@ "Description": "Tools using the pyteomics library", "Suite first commit date": "2021-01-15", "Homepage": "https://pyteomics.readthedocs.io/en/latest/", - "Suite version": "4.4.1", + "Suite version": "@TOOL_VERSION@", "Suite conda package": "pyteomics", "Latest suite conda package version": "4.7.5", "Suite version status": "To update", @@ -8630,22 +8594,20 @@ "bio.tool name": "Pyteomics", "bio.tool description": "Framework for proteomics data analysis, supporting mzML, MGF, pepXML and more.", "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, - "Number of tools on CorGAT": 0, - "Number of tools on CropGalaxy": 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 Genomic Hyperbrowser": 0, "Number of tools on HyPhy HIV NGS Tools": 0, "Number of tools on ImmPort Galaxy": 0, "Number of tools on InteractoMIX": 0, @@ -8653,12 +8615,13 @@ "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 PepSimili": 0, "Number of tools on PhagePromotor": 0, "Number of tools on UseGalaxy.be": 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)": 5, "Suite users (usegalaxy.eu)": 5, "Suite runs (last 5 years) (usegalaxy.eu)": 93, @@ -8679,8 +8642,6 @@ "Suite runs (last 5 years) on main servers": 93, "Suite users on main servers": 5, "Suite users (last 5 years) on main servers": 5, - "Related Workflows": [], - "Related Tutorials": [], "To keep": false, "Deprecated": false }, @@ -8713,22 +8674,20 @@ "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, - "Number of tools on CorGAT": 0, - "Number of tools on CropGalaxy": 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 Genomic Hyperbrowser": 0, "Number of tools on HyPhy HIV NGS Tools": 0, "Number of tools on ImmPort Galaxy": 0, "Number of tools on InteractoMIX": 0, @@ -8736,12 +8695,13 @@ "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 PepSimili": 0, "Number of tools on PhagePromotor": 0, "Number of tools on UseGalaxy.be": 0, "Number of tools on UseGalaxy.cz": 1, "Number of tools on UseGalaxy.no": 1, + "Number of tools on Viral Variant Visualizer (VVV)": 0, "Suite users (last 5 years) (usegalaxy.eu)": 13, "Suite users (usegalaxy.eu)": 23, "Suite runs (last 5 years) (usegalaxy.eu)": 71, @@ -8762,8 +8722,6 @@ "Suite runs (last 5 years) on main servers": 71, "Suite users on main servers": 23, "Suite users (last 5 years) on main servers": 13, - "Related Workflows": [], - "Related Tutorials": [], "To keep": false, "Deprecated": false }, @@ -8797,22 +8755,20 @@ "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, - "Number of tools on CorGAT": 0, - "Number of tools on CropGalaxy": 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 Genomic Hyperbrowser": 0, "Number of tools on HyPhy HIV NGS Tools": 0, "Number of tools on ImmPort Galaxy": 0, "Number of tools on InteractoMIX": 0, @@ -8820,12 +8776,13 @@ "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 PepSimili": 0, "Number of tools on PhagePromotor": 0, "Number of tools on UseGalaxy.be": 0, "Number of tools on UseGalaxy.cz": 1, "Number of tools on UseGalaxy.no": 1, + "Number of tools on Viral Variant Visualizer (VVV)": 0, "Suite users (last 5 years) (usegalaxy.eu)": 2, "Suite users (usegalaxy.eu)": 4, "Suite runs (last 5 years) (usegalaxy.eu)": 26, @@ -8846,8 +8803,6 @@ "Suite runs (last 5 years) on main servers": 26, "Suite users on main servers": 4, "Suite users (last 5 years) on main servers": 2, - "Related Workflows": [], - "Related Tutorials": [], "To keep": false, "Deprecated": false }, @@ -8860,7 +8815,7 @@ "Description": "Raw Tools", "Suite first commit date": "2019-02-28", "Homepage": "https://github.com/kevinkovalchik/RawTools", - "Suite version": null, + "Suite version": "@RAWTOOLS_VERSION@.@TOOL_SUBVERSION@", "Suite conda package": "rawtools", "Latest suite conda package version": "2.0.4", "Suite version status": "To update", @@ -8878,22 +8833,20 @@ "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": 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, - "Number of tools on CorGAT": 0, - "Number of tools on CropGalaxy": 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 Genomic Hyperbrowser": 0, "Number of tools on HyPhy HIV NGS Tools": 0, "Number of tools on ImmPort Galaxy": 0, "Number of tools on InteractoMIX": 0, @@ -8901,12 +8854,13 @@ "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 PepSimili": 0, "Number of tools on PhagePromotor": 0, "Number of tools on UseGalaxy.be": 0, "Number of tools on UseGalaxy.cz": 1, "Number of tools on UseGalaxy.no": 1, + "Number of tools on Viral Variant Visualizer (VVV)": 0, "Suite users (last 5 years) (usegalaxy.eu)": 35, "Suite users (usegalaxy.eu)": 44, "Suite runs (last 5 years) (usegalaxy.eu)": 72, @@ -8927,8 +8881,6 @@ "Suite runs (last 5 years) on main servers": 594, "Suite users on main servers": 60, "Suite users (last 5 years) on main servers": 50, - "Related Workflows": [], - "Related Tutorials": [], "To keep": false, "Deprecated": false }, @@ -8945,7 +8897,7 @@ "fasta" ], "Description": "Six-frame Genome-Inferred Libraries for LC-MS/MS", - "Suite first commit date": "2016-10-11", + "Suite first commit date": "2016-10-10", "Homepage": null, "Suite version": "0.2.4", "Suite conda package": "sixgill", @@ -8966,22 +8918,22 @@ "bio.tool name": null, "bio.tool description": null, "biii ID": null, + "Related Workflows": [ + "https://usegalaxy.eu/published/workflow?id=799b924edd3c401b" + ], + "Related Tutorials": [], "Number of tools on UseGalaxy.org (Main)": 0, "Number of tools on UseGalaxy.org.au": 0, "Number of tools on UseGalaxy.eu": 4, "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 CorGAT": 0, - "Number of tools on CropGalaxy": 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 Genomic Hyperbrowser": 0, "Number of tools on HyPhy HIV NGS Tools": 0, "Number of tools on ImmPort Galaxy": 0, "Number of tools on InteractoMIX": 0, @@ -8989,12 +8941,13 @@ "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 PepSimili": 0, "Number of tools on PhagePromotor": 0, "Number of tools on UseGalaxy.be": 0, "Number of tools on UseGalaxy.cz": 4, "Number of tools on UseGalaxy.no": 4, + "Number of tools on Viral Variant Visualizer (VVV)": 0, "Suite users (last 5 years) (usegalaxy.eu)": 37, "Suite users (usegalaxy.eu)": 41, "Suite runs (last 5 years) (usegalaxy.eu)": 167, @@ -9015,10 +8968,6 @@ "Suite runs (last 5 years) on main servers": 167, "Suite users on main servers": 41, "Suite users (last 5 years) on main servers": 37, - "Related Workflows": [ - "https://usegalaxy.eu/published/workflow?id=799b924edd3c401b" - ], - "Related Tutorials": [], "To keep": false, "Deprecated": false }, @@ -9031,7 +8980,7 @@ "txt" ], "Description": "Filter from spectraST files to swath input files", - "Suite first commit date": "2015-04-13", + "Suite first commit date": "2015-04-14", "Homepage": null, "Suite version": "0.1.0", "Suite conda package": "msproteomicstools", @@ -9051,22 +9000,20 @@ "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, - "Number of tools on CorGAT": 0, - "Number of tools on CropGalaxy": 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 Genomic Hyperbrowser": 0, "Number of tools on HyPhy HIV NGS Tools": 0, "Number of tools on ImmPort Galaxy": 0, "Number of tools on InteractoMIX": 0, @@ -9074,12 +9021,13 @@ "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 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.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, @@ -9100,8 +9048,6 @@ "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": false, "Deprecated": false }, @@ -9134,22 +9080,20 @@ "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, - "Number of tools on CorGAT": 0, - "Number of tools on CropGalaxy": 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 Genomic Hyperbrowser": 0, "Number of tools on HyPhy HIV NGS Tools": 0, "Number of tools on ImmPort Galaxy": 0, "Number of tools on InteractoMIX": 0, @@ -9157,12 +9101,13 @@ "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 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.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, @@ -9183,8 +9128,6 @@ "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": false, "Deprecated": false }, @@ -9218,22 +9161,20 @@ "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, - "Number of tools on CorGAT": 0, - "Number of tools on CropGalaxy": 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 Genomic Hyperbrowser": 0, "Number of tools on HyPhy HIV NGS Tools": 0, "Number of tools on ImmPort Galaxy": 0, "Number of tools on InteractoMIX": 0, @@ -9241,12 +9182,13 @@ "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 PepSimili": 0, "Number of tools on PhagePromotor": 0, "Number of tools on UseGalaxy.be": 0, "Number of tools on UseGalaxy.cz": 1, "Number of tools on UseGalaxy.no": 1, + "Number of tools on Viral Variant Visualizer (VVV)": 0, "Suite users (last 5 years) (usegalaxy.eu)": 14, "Suite users (usegalaxy.eu)": 23, "Suite runs (last 5 years) (usegalaxy.eu)": 37, @@ -9267,8 +9209,6 @@ "Suite runs (last 5 years) on main servers": 37, "Suite users on main servers": 23, "Suite users (last 5 years) on main servers": 14, - "Related Workflows": [], - "Related Tutorials": [], "To keep": false, "Deprecated": false }, @@ -9285,7 +9225,7 @@ "Description": "Unipept retrieves metaproteomics information", "Suite first commit date": "2015-04-03", "Homepage": "https://github.com/galaxyproteomics/tools-galaxyp", - "Suite version": "6.2.4+galaxy1", + "Suite version": "6.2.4", "Suite conda package": "python", "Latest suite conda package version": null, "Suite version status": "To update", @@ -9319,55 +9259,6 @@ "bio.tool name": "Unipept", "bio.tool description": "Metaproteomics data analysis with a focus on interactive data visualizations.", "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, - 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"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": false, "Deprecated": false }, @@ -9649,7 +9582,7 @@ "Description": "Converts coordinates from a tabular file into a formatted text file readable by Zeiss laser-capture microdissection systems", "Suite first commit date": "2024-06-29", "Homepage": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/zeiss_lmd_converter", - "Suite version": "2.0.4", + "Suite version": "@TOOL_VERSION@+galaxy@VERSION_SUFFIX@", "Suite conda package": "shapely", "Latest suite conda package version": null, "Suite version status": "To update", @@ -9667,22 +9600,20 @@ "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, - 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"Related Workflows": [], - "Related Tutorials": [], "To keep": null, "Deprecated": null }, @@ -9768,22 +9698,20 @@ "bio.tool name": "MSnbase", "bio.tool description": "Basic plotting, data manipulation and processing of MS-based Proteomics 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": 3, "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 CorGAT": 0, - "Number of tools on CropGalaxy": 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 Genomic Hyperbrowser": 0, "Number of tools on HyPhy HIV NGS Tools": 0, "Number of tools on ImmPort Galaxy": 0, "Number of tools on InteractoMIX": 0, @@ -9791,12 +9719,13 @@ "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 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.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, @@ -9817,8 +9746,6 @@ "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": false, "Deprecated": false }, @@ -9833,7 +9760,7 @@ "Description": "Galaxy wrapper for the Bioconductor mzR package, enabling conversion between common mass spectrometry data formats (mzML, mzXML, netCDF) within Galaxy workflows.", "Suite first commit date": "2025-06-19", "Homepage": "https://bioconductor.org/packages/mzR", - "Suite version": "2.40.0", + "Suite version": "@TOOL_VERSION@+galaxy@VERSION_SUFFIX@", "Suite conda package": "bioconductor-mzr", "Latest suite conda package version": "2.44.0", "Suite version status": "To update", @@ -9863,22 +9790,20 @@ "bio.tool name": "mzR", "bio.tool description": "Provides a unified API to the common file formats and parsers available for mass spectrometry data. It comes with a wrapper for the ISB random access parser for mass spectrometry mzXML, mzData and mzML files. The package contains the original code written by the ISB, and a subset of the proteowizard library for mzML and mzIdentML. The netCDF reading code has previously been used in XCMS.", "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.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, - "Number of tools on CorGAT": 0, - "Number of tools on CropGalaxy": 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 Genomic Hyperbrowser": 0, "Number of tools on HyPhy HIV NGS Tools": 0, "Number of tools on ImmPort Galaxy": 0, "Number of tools on InteractoMIX": 0, @@ -9886,12 +9811,13 @@ "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 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.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, @@ -9912,8 +9838,6 @@ "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": null, "Deprecated": null }, @@ -9961,22 +9885,22 @@ "bio.tool name": "scp", "bio.tool description": "Utility functions for manipulating, processing, and analyzing mass spectrometry-based single-cell proteomics data. The package is an extension to the 'QFeatures' package and relies on 'SingleCellExpirement' to enable single-cell proteomics analyses. The package offers the user the functionality to process quantitative table (as generated by MaxQuant, Proteome Discoverer, and more) into data tables ready for downstream analysis and data visualization.", "biii ID": null, + "Related Workflows": [], + "Related Tutorials": [ + "proteomics/bioconductor-scp" + ], "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, - "Number of tools on CorGAT": 0, - "Number of tools on CropGalaxy": 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 Genomic Hyperbrowser": 0, "Number of tools on HyPhy HIV NGS Tools": 0, "Number of tools on ImmPort Galaxy": 0, "Number of tools on InteractoMIX": 0, @@ -9984,12 +9908,13 @@ "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 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.no": 0, + "Number of tools on Viral Variant Visualizer (VVV)": 0, "Suite users (last 5 years) (usegalaxy.eu)": 2, "Suite users (usegalaxy.eu)": 2, "Suite runs (last 5 years) (usegalaxy.eu)": 4, @@ -10010,10 +9935,6 @@ "Suite runs (last 5 years) on main servers": 92, "Suite users on main servers": 3, "Suite users (last 5 years) on main servers": 3, - "Related Workflows": [], - "Related Tutorials": [ - "proteomics/bioconductor-scp" - ], "To keep": false, "Deprecated": false }, @@ -10028,10 +9949,10 @@ "Description": "Get frequencies of single amino-acid polymorphisms based on nucleid-acid polymorphism for different populations from UniProt and DbSNP.", "Suite first commit date": "2025-07-18", "Homepage": "https://github.com/RECETOX/galaxytools", - "Suite version": "1.0.0+galaxy0", - "Suite conda package": "pandas", - 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"Number of tools on Genomic Hyperbrowser": 0, "Number of tools on HyPhy HIV NGS Tools": 0, "Number of tools on ImmPort Galaxy": 0, "Number of tools on InteractoMIX": 0, @@ -10069,12 +9988,13 @@ "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 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.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, @@ -10095,8 +10015,6 @@ "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": null, "Deprecated": null }, @@ -10111,7 +10029,7 @@ "Description": "mzML Validator checks if mzML file validates against XML Schema Definition of HUPO Proteomics Standard Initiative.", "Suite first commit date": "2023-01-12", "Homepage": "https://github.com/RECETOX/galaxytools", - "Suite version": "0.1.0+galaxy2", + "Suite version": "0.1.0", "Suite conda package": "lxml", "Latest suite conda package version": null, "Suite version status": "To update", @@ -10130,22 +10048,20 @@ "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, - "Number of tools on CorGAT": 0, - "Number of tools on CropGalaxy": 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 Genomic Hyperbrowser": 0, "Number of tools on HyPhy HIV NGS Tools": 0, "Number of tools on ImmPort Galaxy": 0, "Number of tools on InteractoMIX": 0, @@ -10153,12 +10069,13 @@ "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 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.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, @@ -10179,8 +10096,6 @@ "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": null, "Deprecated": null }, @@ -10228,22 +10143,20 @@ "bio.tool name": "mzspeclib", "bio.tool description": "A python reference implementation of the mzSpecLib spectral library format.", "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.eu": 3, "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 CorGAT": 0, - "Number of tools on CropGalaxy": 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 Genomic Hyperbrowser": 0, "Number of tools on HyPhy HIV NGS Tools": 0, "Number of tools on ImmPort Galaxy": 0, "Number of tools on InteractoMIX": 0, @@ -10251,12 +10164,13 @@ "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 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.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, @@ -10277,8 +10191,6 @@ "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": null, "Deprecated": null }, @@ -10294,10 +10206,10 @@ "Description": "Labeled protein identification", "Suite first commit date": "2025-12-20", "Homepage": "https://github.com/thepanlab/sipros5/", - "Suite version": "5.0.1", + "Suite version": "@TOOL_VERSION@+galaxy@VERSION_SUFFIX@", "Suite conda package": "sipros", "Latest suite conda package version": "5.0.1", - "Suite version status": "Up-to-date", + "Suite version status": "To update", "ToolShed categories": [ "Proteomics" ], @@ -10319,27 +10231,25 @@ ], "Suite owner": "ufz", "Suite source": "https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/sipros", - "Suite parsed folder": "https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/sipros", + "Suite parsed folder": "https://github.com/Helmholtz-UFZ/galaxy-tools/tree/master/tools/sipros", "bio.tool ID": "sipros", "bio.tool name": "Sipros", "bio.tool description": "A database-searching algorithm for peptide and protein identification in shotgun proteomics/metaproteomics.", "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, - 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"Related Workflows": [], - "Related Tutorials": [], "To keep": null, "Deprecated": null }