Summarize #276

[Clockwork-Rat]

Update to reflect new additions in #276

[Clockwork-Rat]

@Oddant1 Everything should be good here, it's been tested

[Oddant1]

If only I could order the comments lol. Basically let's make it a Collection[FeatureData[Taxonomy]] not a list that way they can name their entries if they want. Most other comments fall out from that,

[gregcaporaso]

@Oddant1, @Clockwork-Rat - I have a note on my to-do list to test this out, but it looks like there are some comments still to be addressed. Can you ping me when those are addressed? I'll do my user-level testing/review then.

[gregcaporaso]

@Clockwork-Rat, @Oddant1 - I'm doing some testing of tabulate-seqs and it's working great. I'm experimenting with variations of the following command with the attached files (tab-seqs-tests.zip).

qiime feature-table tabulate-seqs \
 --i-data rep-seqs.qza \
 --i-taxonomy gg:taxonomy.qza \
 --o-visualization rep-seqs.qzv \
 --i-taxonomy something_else:taxonomy.qza \
--m-metadata-file feature-frequency-detail.csv

A few quick requests:

• add usage example that provides a single taxonomy - let's not name the collection input in this case (e.g., --i-taxonomy taxonomy.qza)
• add usage example that provides two taxonomies, and illustrate how to give them descriptive names in the example (e.g., --i-taxonomy taxonomy_a:taxonomy-1.qza --i-taxonomy taxonomy_b:taxonomy-2.qza). for the purpose of this example, those two inputs could be silva and greengenes taxonomies, or greengenes 13_8 and greengenes2).
• validate merge-method value (though that might be a different PR)? - I accidentally ran the following command, and was confused about why I wasn't see the metadata in the output. it's b/c i accidentally provided --p-merge-method instead of --m-metadata-file

# commands succeeds when receiving --p-merge-method but not --m-metadata-file
qiime feature-table tabulate-seqs --i-data rep-seqs.qza --i-taxonomy gg:taxonomy.qza --p-merge-method feature-frequency-detail.csv --o-visualization rep-seqs.qzv --i-taxonomy something_else:taxonomy.qza
Saved Visualization to: rep-seqs.qzv

# Then, I added --m-metadata-file, and it still succeeded - should definitely have thrown an error here:
qiime feature-table tabulate-seqs --i-data rep-seqs.qza --i-taxonomy gg:taxonomy.qza --p-merge-method feature-frequency-detail.csv --o-visualization rep-seqs.qzv --i-taxonomy something_else:taxonomy.qza --m-metadata-file feature-frequency-detail.csv

I'll poke around a bit more and follow up if I notice anything else (just need to run for a meeting). (EDIT: Done - no additional feedback!)

Great work - this is going to be so handy to have!

[gregcaporaso]

Weirdly, I just noticed the column headers for the Sequence and Sequence length columns are mixed up. Not sure if that was there before or introduced here, but we should fix that in this PR.

[Oddant1]

@gregcaporaso that should all be doable including the validation on --p-merge-method. I probably should have noticed that. We can just add % Choices