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biocore / q2-qemistree

Hierarchical orderings for mass spectrometry data. Canonically pronounced "chemis-tree".
BSD 2-Clause "Simplified" License
31 stars 16 forks source link

convert itol functionality into qiime2 command #103

Closed qiyunzhu closed 4 years ago

qiyunzhu commented 4 years ago

Hi @anupriyatripathi I have created the first PR to address issue #100 . It works. It generates a feature table which can be drag & drop into iTOL interface and render as a multi-value bar chart.

However, I refrained from adding the remaining functionality: tip label and clade color, into this module, because I am not sure how to handle it right. As you know, QIIME 2's output file is always .qza. However a .qza file cannot be parsed by iTOL (except for feature table). One still need to unzip it before use. Let alone the trouble of creating two more Artifact types.

I think I may not fully understand the philosophy of QIIME 2 plugin design. I would like to know your opinion of how to proceed. Thank you!

anupriyatripathi commented 4 years ago

@qiyunzhu thanks for starting the PR. I think we might be able to use the semantic type FeatureData[Molecules] for the two other files. Let's chat in person this week to brainstorm how to best engineer this! Adding @ElDeveloper to this discussion.

qiyunzhu commented 4 years ago

@anupriyatripathi To add unit test I will need some feature table and metadata. Do you happen to have them? (needs to be small to fit into data/ directory).

anupriyatripathi commented 4 years ago

@qiyunzhu yes, I'm sending you a small feature table and metadata for unit testing. Thanks!