added squirrel MPXV analysis

[ammaraziz]

First time contributing a galaxy wrapper. Please let me know if there any issues I need to fix.

One possible issue that might cause a block to merging is the lint warning I get:

.. WARNING (HelpInvalidRST): Invalid reStructuredText found in help - [<string>:5: (ERROR/3) Unexpected indentation.
].

Unsure how to solve this issue. Any guidance would be appreciated.

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)

[ammaraziz]

Looking at the errors, in order:

1. Test file size is ~5mb. How do I deal with this issue when the mpxv genomes are large? Testing the alignment
2. Same as above, some of the tests use big files.
3. Tests failed, I think I can identify the issue.
4. Linting fails due to the above mentioned error. Any advice?

Thanks!

[ammaraziz]

Regarding the tests, they are erroring due to differences between what is uploaded and what is run. The outputs contain some date information (I am technically in the future compared to the github runner time zone). If I wait until tomorrow it will probably pass...

Any advice on how to manage such situations?

[bgruening]

Very cool, thanks a lot.

My initial first columns are inline. For the file size, can you just use a subset of the input size? Can you compress it?

[ammaraziz]

My initial first columns are inline. For the file size, can you just use a subset of the input size? Can you compress it?

Unfortunately not but I think I will recreate the background within the input file for testing to replicate the --include-background flag.

Thanks for all your assistance!

[bgruening]

Keep in mind that the Galaxy tests are for testing the Galaxy wrapper, not the functionality of the tool. So small test data even if the result is not super useful is valid. We also can check for tests that we know are failing etc ...

[bgruening]

I see this in the tests: > Incorrect number of outputs - expected 2, found 3 (dataset(s): html,mask,exclude collection(s): )

[ammaraziz]

🥳 all tests pass. Thanks everyone for your help and especially your guidance @bgruening. There's still the issue of how I'm parsing the inputs, which I will fix now.

[ammaraziz]

Ready for (proper) review. All the issues should be fixed now.

[bgruening]

Cool, just the few open comments :)

[bgruening]

ping ...

[pvanheus]

Perhaps use some more capitalization and descriptive text so that this shows up nicely in the tool list? E.g. "MPXV (Mpox virus)" and "Squirrel phylogenetic analysis" ?

[ammaraziz]

That's a really good suggestion. I noticed the name and description fields are concatenated in this manner: {Name} - {Description}. It seems to me the searching happens on both? Or do you recommend the description be as descriptive as possible even if it contains duplicate information?

[ammaraziz]

@pvanheus I've updated the description and name. Let me know if it suits.

[pvanheus]

The typo here (descriptionp) is causing the linting problem that causes tests to fail (i.e. the linting problem seems to refer to the .shed.yml but it is caused by the failure to parse the squirrel-phylo.xml file)