Nailing down terminology

[mortonjt]

This is the most immediate struggle

Right now, --i-microbes and --i-metabolites may be a bit too restrictive, since it indicates that it is limited to only microbes and metabolites.

We will want to make this more generalizable. I've thought about renaming to input_abundances and output_abundances, but that is quite confusing given that the q2cli will look like --i-input-abundances, --i-output-abundances (the output abundances looks like a contradiction).

I'm going to just push with --i-microbes and --i-metabolites for now. But feedback on appropriate names would be great! Maybe --i-explanatory vs --i-response or something like that??

[nbokulich]

Maybe --i-explanatory vs --i-response or something like that??

+1

[aaksenov1]

How about --i-ome_explained vs --i-ome_input