Unclear explanation and options for Funannotate --augustus_species parameter

galaxyproject / tools-iuc

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Unclear explanation and options for Funannotate --augustus_species parameter #6137

Open Hymenium opened 4 weeks ago

Hymenium commented 4 weeks ago

The --augustus_species parameter in Funannotate appears to be for reusing Augustus training sets from previous runs of Funannotate. I'm not sure if this data is kept from one run to the next (the command to query this is not exposed), but the options given by the macro do not seem to make sense in this context.

https://github.com/galaxyproject/tools-iuc/blob/8bdd212b8708a9d080e87303dd543fb93bc05c2f/tools/funannotate/funannotate_predict.xml#L216

bgruening commented 4 weeks ago

@rlibouba can you please look at this one?

rlibouba commented 4 weeks ago

I'll take a look