ENH: Adds action to create spectral metadata to be used with q2-vizard

[VinzentRisch]

closes #30

• Adds action that creates Metadata from XCMSExperiment
• Metadata can be used to create TIC, BPC or retention time adjustment plots with lineplot of q2-vizard.
• It can also be used with the action boxplot to plot the total ion intensities as box plots.
• The action takes the file "ms_backend_data.txt" and adds the sample data info to it from the "ms_experiment_sample_data.txt".
• The data is filtered by MS level.

test data
xcms_experiment_rt.qza.zip

qiime ms create-spectral-metadata --i-xcms-experiment xcms_experiment_rt.qza --o-spectral-metadata spectral_metadata.qza

qiime vizard lineplot --m-metadata-file spectral_metadata.qza --p-x-measure rtime --p-y-measure totIonCurrent --p-group-by sampleid_ --p-title 'TIC' --o-visualization TIC.qzv

Set y to "basePeakIntensity" for BPC or to "rtime_adjusted-rtime" for rt adjustment plot

qiime vizard boxplot --p-distribution-measure totIonCurrent --m-metadata-file spectral_metadata.qza --p-group-by sampleid_ --o-visualization boxplot_tic.qzv

[VinzentRisch]

Hey @misialq
I now decided to make it an action that creates metadata that can be used by q2-vizard because it can be used by two different q2-vizard actions.
Or do you think it would be cleaner as two pipelines?

[misialq]

Hey @VinzentRisch, personally, I like it as you have it here - we will need to construct a nice tutorial later (I'm thinking something a bit like the MOSHPIT one) so we just need to make sure to put this there so that the users are aware this is possible :)

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 99.70%. Comparing base (ef26195) to head (7ab6c34).

Additional details and impacted files

@@            Coverage Diff             @@
##             main      #31      +/-   ##
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+ Coverage   99.67%   99.70%   +0.02%     
==========================================
  Files           8        9       +1     
  Lines         311      340      +29     
  Branches       40       43       +3     
==========================================
+ Hits          310      339      +29     
  Misses          1        1              

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[VinzentRisch]

@misialq

[misialq]

LGTM! Approved, conditional on addition of the missing test 😆

[VinzentRisch]

Thank You!

[VinzentRisch]

Hey Michal
I added the test and also the possibility to extract ms2 scans for visualisation.

[misialq]

LGTM!