> I get an error from Galaxy indicating that it is trying to find a file
> name $genbank_filename.gff, I.e. the ${genbank_filename} is not expanded.
> Is there any way to deal with this situation?

Not currently. This is a nice idea and should be done, but it's not obvious to 
implement. I'll try to take a look in the near future.

> Of course the other option
> is to create a tiny wrapper around bp_genbank2gff that takes an output
> filename argument and does the renaming...

Yes, the whole point of from_work_dir is to alleviate the need to write 
wrappers to deal with hard-coded outputs files.

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