BUSCO wrapper update to correct issue of empty table

[scorreard]

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)

This PR is to correct the issue raised in #6664

Here is a breakdown of the changes :
When the lineage is set to auto
In that case, BUSCO runs a generic lineage analysis and then go to more specific ones to identify the best lineage for the species

• Extract the names of the specific and generic lineages
• Renames the files with "specific" or "generic" depending on which lineage was used to generate them
• Output the results for both the generic and specific lineages for the output type requested by the user

When the lineage is selected by the user

• Renames the files with "specific"
• Output the results for the specific lineages for the output type requested by the user

I tested it locally and it behaved as expected.

[scorreard]

Set to draft as we may want to add the test (#7209) before solving the issue

[scorreard]

Following feedback from @rlibouba, I'll make an update so that :

• By default, only results from the specific lineage are displayed
• Upon selection from the user, it will also show the results from the generic lineage in their history

[lsterck]

Nice one @scorreard ! :-)
And excellent suggestion @rlibouba , thanks!

[lsterck]

was the test with the bacilli input removed? (or is that file simply renamed?)

[scorreard]

was the test with the bacilli input removed? (or is that file simply renamed?)

Are you talking about the test developped in PR 7209?

[lsterck]

was the test with the bacilli input removed? (or is that file simply renamed?)

Are you talking about the test developped in PR 7209?

ah, yes indeed.
or did we decide not to include it yet?
anyway, not a big point as the 'procedure' is tested with the current dataset as well.

[scorreard]

was the test with the bacilli input removed? (or is that file simply renamed?)

Are you talking about the test developped in PR 7209?

ah, yes indeed. or did we decide not to include it yet? anyway, not a big point as the 'procedure' is tested with the current dataset as well.

I'd like to include it but we did not get replies from bgruening or bernt-matthias. Should I just include your code here? I think it would be great to include it

[bernt-matthias]

I'd like to include it but we did not get replies from bgruening or bernt-matthias

I would say: yes :)

[scorreard]

Ok, it should be in now, wiaiting for the tests to pass and then it's ready for review.

[scorreard]

This PR includes :

• An update to BUSCO outputs to deal with the multiple output with similar names
• A new test to identify empty files in BUSCo ouptuts.

It's ready for reviews

[rlibouba]

Great job, thank you!

[bgruening]

Let's ship this and then work on the 6.0 version :)

Thanks everyone!

[mvdbeek]

Attention: deployment skipped!

https://github.com/galaxyproject/tools-iuc/actions/runs/18247366074

[bernt-matthias]

Send deployed