biocore / biocore/gemelli

Qiime2 Version - not able to do multiple states

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#68 3 comments 0 reactions 0 assignees View on GitHub
enhancement
Dominant language
Python
Stars
92
Forks
20
PR merge metrics
No merged PRs in 30d

Description

Working on doing CTF using the qiime2 CLI, but got an error I don't quite understand.
```
!qiime gemelli ctf \
--i-table ../data/Microbiome/pool_filtered/RPCA/gemelli_filtered.qza \
--m-sample-metadata-file ../data/Microbiome/14577_fixed.txt \
--m-feature-metadata-file ../../shotgun_scripts/woltka_v2_taxonomy.qza \
--p-state-column timepoint_number \
--p-state-column timepoint_group \
--p-individual-id-column marmoset_id \
--output-dir ../data/Microbiome/pool_filtered/ctf-results
```
Error: (1/1?) Option '--p-state-column' was specified multiple times in the command.

But...
```
--p-state-column TEXT Metadata column containing state (e.g.,Time,
BodySite) across which samples are paired. At least
one is required but up to four are allowed by other
state inputs. [required]
```
So how do I specify more than one state?
`--p-state-column timepoint_number,timepoint_group \`
also did not work.

@gibsramen dug into this a bit, but sounds like it might not actually allow multiple states

Contributor guide

No contributing guide indexed for this repository

Research direction

Reproduce the qiime gemelli ctf invocation with two --p-state-column values and with the comma-separated form, then inspect the CTF CLI parameter definition and its tests; no files or tests are named in the report. Done means the supported way to provide multiple state columns is established and the command behaves consistently with the help text or documents the limitation.

Written by the indexing model from the issue text.

Assessment

Tech stack
python
Domain
bioinformatics
Issue type
Bug
Difficulty
4/5
Estimated time
3-5 days
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
35/100

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