bgruening
Mafft Changes
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
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.
This should work https://github.com/galaxyproject/tools-iuc/blob/ef564483fa8dc267c599af8745aab4e03b0c57e0/tools/ampvis2/venn.xml#L32
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!
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?
I tested it with planemo test but not with the --biocontainer argument. What does change by adding it?
--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.
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?
Unlikely. Have you commited everything?
What does git status . and git diff . show in your maff directory?
git status: clean worktree and git diff:nothing. Its only Test 4 which is online a failure with the error of a different output.
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 :(
@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 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 (:
The mafft_auto_result.aln test file was also used by the mafft_add test, which is now failing.