Clarification for "list" in qiime feature-data merge and qiime feature-data merge-seqs


(Jennifer Fouquier) #1

In the CLI help docs for qiime feature-data merge-seqs (and similar for others I am sure) it says:

--i-data MULTIPLE ARTIFACT PATH List[FeatureData[Sequence]] The collection of feature sequences to be merged. [required]

And I think it’s a bit unclear.

I have done this several times…I’ve provided a list of qzas either spaced or in brackets and comma separated because that’s a list. :slight_smile: And either way I used the --i-data option only once thinking it would know I provided multiple items. I keep forgot to add the option flag multiple times for each item. I think clarification in the CLI would be nice because the word “List” is misleading in a sense.

Just a suggestion, nothing urgent! :sun_with_face:


(Matthew Ryan Dillon) #2

Hey there @Jennifer_Fouquier — I agree, it isn’t super clear. The reason is because QIIME 2 is interface agnostic, so this nomenclature of List[blah] business is meant to be applicable irrespective of how any particular interface chooses to implement it (e.g. a GUI might have some kind of multi-select, or drag-and-drop tiles/cards).

Maybe in the case of q2cli we could append the following at the end of the parameter text: Flag may be specified multiple times., or something along those lines. What do you think?


(Jennifer Fouquier) #3

Ah, I see.

I think what you suggest would improve things. Although could you say Flag must be specified multiple times … since it’s a merge, doesn’t that imply you need more than one input?


(Matthew Ryan Dillon) #4

For this particular example, no, you don’t need more than one input — you can pass just one table to feature-table merge and it will be just fine with that (it is effectively a noop).