Help with making a plugin for core microbiome

Nicholas_Bokulich · May 19, 2020, 10:17pm

that's exciting news

It is better to output as QZA/QZV so that provenance is stored in these files.

You should check out the developer documentation, there is a great tutorial that's been added here that describes this:
https://dev.qiime2.org/latest/tutorials/

In a nutshell, you would output an html or other file type containing the plots/data you want to display and register your action as a visualizer:
https://dev.qiime2.org/latest/actions/visualizers/

The best way to see how it's done is to look at how other visualizers are registered in existing plugins. Take a look at the adonis action in q2-diversity, it is a relatively simple example to use as a template:

github.com

qiime2/q2-diversity/blob/30c4149400fa44abb409c3eb5e96a45daa3c36f5/q2_diversity/_beta/_visualizer.py#L345


      
              context = {
                  'table': table_html,
                  'sample_size': sample_size,
                  'mismatched_ids': mismatched_ids
              }
              index = os.path.join(
                  TEMPLATES, 'mantel_assets', 'index.html')
              q2templates.render(index, output_dir, context=context)
          
          
          def adonis(output_dir: str,
                     distance_matrix: skbio.DistanceMatrix,
                     metadata: qiime2.Metadata,
                     formula: str,
                     permutations: int = 999,
                     n_jobs: int = 1) -> None:
              # Validate sample metadata is superset et cetera
              metadata_ids = set(metadata.ids)
              dm_ids = distance_matrix.ids
              _validate_metadata_is_superset(metadata_ids, set(dm_ids))
              # filter ids. ids must be in same order as dm

that's right: this output_dir does not get exposed in any of the user interfaces. You need to register one or more outputs as separate arguments that do get exposed to the user (see the examples and documentation above for more details)

Release your plugin in its own github repository (or wherever you like), and document installation and usage instructions on the "library" to share it with the world: https://library.qiime2.org/

Good luck!