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Added additional arguments with associated descriptions.
| ## Required Arguments | ||
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| ### `--prediction` | ||
| ### `-bed, --bed, -bw, --bw, --bigwig` |
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We do not have flags as listed here. The flags are usually --signal for a bw prediction track and different flags for bed files ("--bed", "--peaks", "--regions", "--roi", "-roi", and "--windows", "-w" for 1024 bp wide windowed BED file inputs. Please re-write, Thank you!
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Hmmm, are you sure this is the case? I am currently running benchmark successfully with the --bw option, and the current version of parser.py accepts the listed arguments (as indicated in this screenshot).
| ### `-bed, --bed, -bw, --bw, --bigwig` | ||
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| The input bigwig file of transcription factor binding predictions. This file can also be any bigwig signal track that you want to compare against a gold standard. | ||
| The input file of transcription factor binding predictions (in either BED or bigWig format). This file can also be any BED/bigWig signal track that you want to compare against a gold standard. |
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How do you get a BED file at the end of prediction? You should only be getting a bw file. The input flag should --bw here
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I might totally be wrong, but this is what I was pointing out in the previous screenshot! Please let me know if I am wrong and I am happy to change what I have written.
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This seems to be from one of the Tariean's update here: e08be57#diff-2b28b3ee9d11c4502b4d3fa82584cd292b165b7ee3f43cfb7873d31005bbba87L673, in parser.py file and around line 670 in the updated version.
We might want to also update the *.md file to mention the mutually exclusive nature between bed input and bw input.
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Added additional arguments with associated descriptions.