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computational-metabolomics / mspurity-galaxy

Galaxy tools for msPurity package: includes precursor ion purity calculations and spectral matching
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[purityA] File naming error in output files #56

Closed Hrodwin closed 2 months ago

Hrodwin commented 3 months ago

Hi, When using purityA with my datasets, I encountered a file naming problem that is as such; in the output .tsv summarizing the features and their purity specifications, the files are named starting from the first file of the collection, and not from the first file containing MS/MS data. Then the recorded data do not correspond to the file cited in the "filename" column of the .tsv. Here is an illustration of this behaviour:

image

I checked manually, and results given as belonging to the file "_Blank5_POS_RA1_16735" indeed belong to "_Pool_TestConst_DDA12-40step_POS_BD1_17615", "_Blank6_POS_RA1_16736" to "_Pool_TestConst_DDA12ev_POS_BD1_17611" and so on...

Best, Quentin

Tomnl commented 2 months ago

Hi @Hrodwin - please could you provide a Galaxy history of this?

I will look into it

Tomnl commented 2 months ago

Ah I think i see where the error is

Tomnl commented 2 months ago

OK - was an error in the Galaxy wrapper script - needed to convert from factor to string. Just testing now

Tomnl commented 2 months ago

@Hrodwin - this should be fixed in v1.28.0+galaxy1 🤞

Hrodwin commented 2 months ago

Problem solved with the update! Thank you 👍

Tomnl commented 2 months ago

Great! Thanks for letting me know. I will close the issue now.