Mafft Changes

[elischberg]

Fixes:

• Fix datatype selection matrix choice
• Autodetection matrix definition
• Update version number

Fixes need to be done:

• according alignment strategies with help section
• insert arguments
• tests correction

[bgruening]

You need to rebase this PR, please.

[elischberg]

Tried for the groupsize param to get a max limit through a validator with the sequence metadata, but I think it then ignored every inserted integer of the groupsize param. Solved it right now with a condition in the command part of mafft.xml.

[bgruening]

This should work https://github.com/galaxyproject/tools-iuc/blob/ef564483fa8dc267c599af8745aab4e03b0c57e0/tools/ampvis2/venn.xml#L32

[elischberg]

In venn.xml it is a fix maximum. Unfortunately not appliable in the groupsize case with a variable maximum. We solved it with a warning for users, when they use a too large number. But thanks!

[elischberg]

There are difficulties with the groupsize parameter. I don't know, how to change the empty value of $cond_flavour.guidetree.partetree_selection.groupsize into the calculated $sequence_count. Do you have an idea?

[bgruening]

Do you test this locally with planemo test --biocontainers ...?

[elischberg]

I tested it with planemo test but not with the --biocontainer argument. What does change by adding it?

[bgruening]

--biocontainers is what is running on CI. So you should get the same errors locally what you get here. Containers are just more isolated and produce more similar results.

[elischberg]

Ok, thank you for the explanation. I tried it with --biocontainers locally and everything was fine. Here it says that Test 4 is a failure. How can this be?

[bgruening]

Unlikely. Have you commited everything?

What does git status . and git diff . show in your maff directory?

[elischberg]

I commited and pushed everything and all tests passed locally.

[elischberg]

git status: clean worktree and git diff:nothing. Its only Test 4 which is online a failure with the error of a different output.

[bgruening]

So the results for test 4 are still different. If you run this already in Containers, then the only explanation I have is that this test is not deterministic and generates a different output based on some other wired stuff.

But the changes look vastly different :(

[bgruening]

GreeeennnnnnnnnnnN!

[elischberg]

Very good. (:

[bgruening]

ping @wm75

[wm75]

@elischberg cool! What about test 4, which you previously changed to check only for a few lines of output. Is it by chance possible to make this one stricter again now that --threadit is set to 0?

[elischberg]

@elischberg cool! What about test 4, which you previously changed to check only for a few lines of output. Is it by chance possible to make this one stricter again now that --threadit is set to 0?

Going to try (:

[wm75]

The mafft_auto_result.aln test file was also used by the mafft_add test, which is now failing.

[bgruening]

failing ...