Flag/Subparser to specify output path suggestion

[Eremus007]

Reposting here on request:

Hey, my name is Jeremy, and I am currently looking to wrap Hybpiper in a tool for GalaxyProject to make Hybpiper accessible to people without knowledge of a commandline interface.
https://github.com/naturalis/galaxy-pipeline-hybseq/tree/development/tools/hybpiper

My question is, is there a way to pass an argument to Hybpiper of the directory in which they want Hybpiper's output files to go?

If there is not, as a suggestion, I would love to see something like a -o/--hybpiper_output flag/subparser where users can specify this and redirect the output.

I have learned that, at the moment, Hybpiper creates its output directories in the same location as the read files, but this complicates matters for me in Galaxy, as Galaxy does not like things being created in its specialized folders.

Would love to hear about your thoughts on this.