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bgruening / galaxytools

:microscope::books: Galaxy Tool wrappers
MIT License
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MitoHiFi defaulting to animal data #1454

Open Hymenium opened 1 month ago

Hymenium commented 1 month ago

tools/mitohifi/mitohifi.xml

I didn't realise from the help that this tool is designed for and defaulting to animal data. When I tried with fungal data then all of the blast matches were filtered out, looking at the mitohifi source then this seems to be due to the animal NUMT criteria.

It might be a good idea to highlight this information and maybe expose the -a parameter to choose animal, plant, or fungi (see https://github.com/marcelauliano/MitoHiFi/blob/1683dbc6c0d0a0d4ea7b0aa5aa1e1701b63cb6aa/src/mitohifi.py#L57).

bgruening commented 1 month ago

@SaimMomin12 can you please look at this?