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galaxyproject / tools-iuc

Tool Shed repositories maintained by the Intergalactic Utilities Commission
https://galaxyproject.org/iuc
MIT License
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FreeBayes: Can't set workflow variable #1880

Open szeplakib opened 6 years ago

szeplakib commented 6 years ago

Hi,

I have a local Galaxy instance, and have made a workflow for multiple samples. The workflow works as intended, but I can't keep the names of the samples, because I lose them at the FreeBayes step. I could set the workflow variables, to keep filename of the previous step, except for FreeBayes.

I tried to use #{ input_bams } as input_bams is the name of the input file, but it didn't work. I also tried #{ reference_source|batchmode|input_bams} as it's the example for valid input, still, didn't work.

All the other used tool modify the filename according to my intentions, except for this one. It only give that generic : 'FreeBayes on data N, data N, and data N'

I don't know if the workflow variable is broken for this one, or I just don't know the proper syntax.

FreeBayes version: 1.1.0.46-0 under Galaxy version: 18.01

Thanks in advance Bence

jennaj commented 6 years ago

@szeplakib I cannot figure out the correct usage either. Tried a few variations.

Test history: https://usegalaxy.org/u/jen/h/copy-of-workflow-constructed-from-history-test-history-freebayes-renamed-output

Test workflow: https://usegalaxy.org/u/jen/w/copy-of-workflow-constructed-from-history-test-history-freebayes-1

@dannon Could you help us determine if the syntax is wrong or if renaming is not possible with this tool given an individual, non-collection BAM input. The content of the suggested inputs doesn't seem to match the 18.01 PRs in the Release notes. I am testing with 18.05 on main.

So, a few items:

  1. Workout what all the use cases are
  2. Test if Freebayes has one or more that work and if not, ticket the tool to get that addressed
  3. update the "advanced-workflow" hub docs that link from GUI to be current. Renaming: https://galaxyproject.org/learn/advanced-workflow/variables/ is one of them.
  4. convert to tutorial and change GUI link to point to that instead (might get to it at co-fest, if can get this clarified before then).

Reference: https://docs.galaxyproject.org/en/master/releases/18.01_announce.html?highlight=rename%20workflow

Reported 5/18 at https://biostar.usegalaxy.org/p/28043

rahit commented 1 year ago

Any update on this?