MACS2 Callpeak has a few wrapper/option problems

[jennaj]

MACS2 Callpeak

Problem: Wrapper option *--foldenrichment** not recognized?

tool id: toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_callpeak/2.1.0.20140616.0
tool version: 2.1.0.20140616.0
job pid or drm id: 5896379.roundup
job tool version: macs2 2.1.0.20140616

Fatal error: Exit code 2 ()

job stdout:
usage: macs2 [-h] [--version]
{callpeak,diffpeak,bdgpeakcall,bdgbroadcall,bdgcmp,bdgdiff,filterdup,predictd,pileup,randsample,refinepeak}
...
macs2: error: unrecognized arguments: --foldenrichment 4

[lparsons]

This is implemented in the wrapper as a selection between p-value, q-value, and fold enrichment for peak detection. However, looking at the docs for MACS2, p-value and q-value appear to be mutually exclusive options as cutoffs for peak detection, while fold enrichment is implemented as a post-processing step only to filter out peaks.

Thus, I would propose that fold enrichment be moved to a separate parameter in the "Advanced" section and set to the default of 1.0. Also, it should be --fe-cutoff FECUTOFF.

On a related note, I don't see why --call-summits is only available when ``broad-peaks` is not selected.

[jennaj]

@lparsons Agree, what you outline would be a better parameter model on the tool form

[jennaj]

@lparsons Is anyone working on this? Maybe it needs a "triage" to make more visable? I can't do that in this repo.

I did search and couldn't the relevant pull request if already in progress. If you know, and have time and can link it in here, The users tracking this would really appreciate it :) I also want to make sure the update gets on Main (install, test in that env, and so forth).

[lparsons]

@jennaj I don't think anyone is actually working on this at the moment. I'm keeping track of this as well, and will try to help if/when I can. Thanks for staying on top of it.

[bgruening]

@lparsons are you working on this or planning to work on it? I have created a new conda package just in case you want to bump the version as well.
bioconda/bioconda-recipes#1499

[jennaj]

Still an issue users are encountering. Any updates you all can share? Thx!

Error (at http://usegalaxy.org) with tool version:

• https://toolshed.g2.bx.psu.edu/view/iuc/macs2/6d4babad010f
• https://toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_callpeak/2.1.0.20151222.0
• Galaxy Version 2.1.0.20151222.0
• Tool Shed Version 2.1.0.20151222.0

Fatal error: Exit code 2 ()
The tool produced the following additional output:
usage: macs2 [-h] [--version]
{callpeak,bdgpeakcall,bdgbroadcall,bdgcmp,bdgopt,cmbreps,bdgdiff,filterdup,predictd,pileup,randsample,refinepeak}
...
macs2: error: unrecognized arguments: --foldenrichment 5

cc @galaxyproject/guac

[jennaj]

Fixed in version 2.1.1.20160309.0, closing