add flexynesis

[nilchia]

FOR CONTRIBUTOR:

• I have read the CONTRIBUTING.md document and this tool is appropriate for the tools-iuc repo.
• License permits unrestricted use (educational + commercial)
• This PR adds a new tool or tool collection
• This PR updates an existing tool or tool collection
• This PR does something else (explain below)

This PR adds flexynesis to Galaxy

[nilchia]

The problem is that the data_types argument should be the name of the omics file (E.g. gex here).
but when the value is set to "gex" it thinks that it is a file and not a text. So it gives: --data_types {'src': 'hda', 'id': '55d23f6c34fa3eae'} for example.

[nilchia]

I added another omics file and that problem is solved.

[nilchia]

why does it use diff for "job.feature_importance" element?
I did not set compare="diff"

[bgruening]

You specified file so you want to compare the file with something ... and the default comparison method is diff. Remove the file.

[nilchia]

Thanks @bgruening !

[bgruening]

I assume its quite hard for a user to know what this input here is. Any idea?

[nilchia]

The --input_layers and --output_layers should be set to one or more modalities (set in --data_types)
Maybe a better help?
I'll try

[nilchia]

Is it better now?