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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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BUSCO --miniprot parameter seems incorrectly handled #6147

Open Hymenium opened 1 month ago

Hymenium commented 1 month ago

I don't think --miniprot should be a binary parameter or described as output: https://github.com/galaxyproject/tools-iuc/blob/b21f516390fcbbe3c098266ff0d72e64924aab00/tools/busco/busco.xml#L114

From the documentation for BUSCO (https://busco.ezlab.org/busco_userguide.html), there are three modes for gene 'prediction': miniprot, metauk, or augustus.

"--miniprot Use Miniprot gene predictor (default for eukaryota in genome mode)."

The tool uses v5.5.0 and from v5.0.0 until 5.7.0, metauk is the default for eukaryotes (now miniprot).

There is no miniprot output from the tool unless no other predictor parameter is issued (maybe --augustus takes priority but I couldn't find any documentation on this).

This is partially linked to this issue, involving a gff output that only captures data for metauk: https://github.com/galaxyproject/tools-iuc/issues/6132#issue-2394383996

rlibouba commented 1 month ago

Hello, thank you for your comment. I've opened a PR (https://github.com/galaxyproject/tools-iuc/issues/6147) to correct it. Hava a good day!