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galaxyproject / tools-iuc

Tool Shed repositories maintained by the Intergalactic Utilities Commission
https://galaxyproject.org/iuc
MIT License
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Fix MaAsLin 2 #5451

Open paulzierep opened 1 year ago

paulzierep commented 1 year ago

When trying MaAsLin 2 I found some issues, that make the wrapper basically unusable. (a) The fixed_effects can be different for every dataset, they are however hard-coded to only allow a choice of the test data: https://github.com/galaxyproject/tools-iuc/blob/bc3831e3648809bd3d46611b2a74bd26a17985e5/tools/maaslin2/maaslin2.xml#L57-L64 (b) The correction method should be a choice not text: https://github.com/galaxyproject/tools-iuc/blob/bc3831e3648809bd3d46611b2a74bd26a17985e5/tools/maaslin2/maaslin2.xml#L89 (c) labels for normalization, transform and analysis_method are cryptic (d) the features output would also be nice to have

paulzierep commented 1 year ago

ping @EngyNasr -> if you find the time, otherwise I or a new bachelor can also look into it when I am back

bgruening commented 3 months ago

@paulzierep still valid?