Unclear explanation and options for Funannotate --augustus_species parameter

[Hymenium]

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]

@rlibouba can you please look at this one?

[rlibouba]

I'll take a look

[rlibouba]

Hello, I apologise for my late reply. I took a closer look at the --augustus_species parma meter. This parameter can be used by specifying a species for which pre-trained data is available. If the species is not specified, the --augustus_species parameter will default to the species indicated in the --species parameter. If you have augustus and/or genemark predictions (in gff/gtf format), you can use them to funannotate predict. To do this, use the --augustus_gff and --genemark_gtf parameters. I hope I've answered the question correctly. If it's not clear, don't hesitate to contact me.

[Hymenium]

Thank you. So it is used to select parameters that come preloaded in augustus.