Add colabfold

[astrovsky01]

Adds colabfold tool. Testing output requires data caches, so the tests here just check for command line content
FOR CONTRIBUTOR:

• - I have read the CONTRIBUTING.md document and this tool is appropriate for the tools-iuc repo.
• - License permits unrestricted use (educational + commercial)
• - This PR adds a new tool or tool collection
• - This PR updates an existing tool or tool collection
• - This PR does something else (explain below)

[bernt-matthias]

Just stumbled over https://academic.oup.com/bioinformatics/article/39/1/btac749/6839971 .. wondering if the collabfold output could be used for this as is.

[astrovsky01]

@bernt-matthias That's using a different part of colabfold than we use here, specifically Search instead of Batch. Part of why I made it a suite is that there will be different future versions of the tool depending on where it's being run, and that is one of them. If that is made into a tool, the output should be useable, though, from what I understand

[astrovsky01]

Also, the shed error that's happening here is not occurring locally, and I'm unsure how to fix.
The other error is the lack of datatype, which should have been taken care of in the above datatype PR...

[astrovsky01]

Current failure is on the msa step is due to a new param I added to standardize naming. Easily fixed, but requires minor testing first

[astrovsky01]

@bernt-matthias The fail for the msa step is the same error as it was before where it doesn't see that new datatype, but I can't even tell what's going wrong with the alphafold step, it looks like it's just shutting down immediately?

[bernt-matthias]

Do you know how much memory is used in the msa step test?

[astrovsky01]

It was only allocated 2.7GB on test, but we're not sure how much of that is actually used

[astrovsky01]

@bernt-matthias @bgruening the most I have found that gives a hint is Tool colabfold_alphafold created job None (16.176 ms) in the test log

[astrovsky01]

Woo passing! Before any merge, though, I wanted to ask for clarification about the expect_failure. Does that still test the command line against the assert_command I have, or is it just expecting a non-zero error code? I can't tell based on other tools in iuc that have been published

[astrovsky01]

@bernt-matthias @bgruening intentionally breaking the command assertion failed, which means the test is doing what I thought it was, and the tool is ready

[bernt-matthias]

intentionally breaking the command assertion failed

Thanks for testing this. Can you test for the exit code?

[astrovsky01]

Thanks for testing this. Can you test for the exit code?

It's failing with exit code 1, which is what the test is specifying, but the test itself is still failing despite that

[astrovsky01]

The linter will not allow both expect_num_outputs and expect_fail, so this is what I can do with the test

[bernt-matthias]

Gave it one last round. Sorry.

[bernt-matthias]

Thanks for the efforts

[bernt-matthias]

Anything left from your side @bgruening?

[gxydevbot]

Attention: deployment failure!

https://github.com/galaxyproject/tools-iuc/actions/runs/8412373924

[gxydevbot]

Attention: deployment failure!

https://github.com/galaxyproject/tools-iuc/actions/runs/8412373924

[bernt-matthias]

We have this one again:

Unexpected HTTP status code: 500: {"err_msg": "Metadata may have been defined for some items in revision '66cd8f416122'.  Correct the following problems if necessary and reset metadata.<br/><b>colabfold_alphafold.xml<\/b> - parameter 'num_models': the attribute 'value' must be set for non optional parameters<br/>"}

we had this on matrix recently, but forgot the conclusion...

[bernt-matthias]

Should actually be allowed galaxyproject/galaxy#16966 ..

[bernt-matthias]

Quick fix is to set value="".

[astrovsky01]

I set it to optional here #5908