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CCMS-UCSD / GNPS_Workflows

Public Workflows at GNPS
https://gnps.ucsd.edu/
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Update msdial_formatter.py #804

Open chrispook opened 2 years ago

chrispook commented 2 years ago

This doesn't work on recent MS-DIAL exports so I've rewritten it. Tested on output from MS-DIAL v4.70. I can share a test file if you want one.

mwang87 commented 2 years ago

Thanks @chrispook, if you do have an example, that would be awesome. We can add it to our unit tests. I think it might be worth also having v4.7 and <4.7 as options for users.

chrispook commented 2 years ago

Sure, how do I share the file? Shall I upload it to massive?

Very much agree on backwards compatibility. I'm not sure what version your existing script was written for but MS-DIAL v4 was a significant leap forward and was released in 2020. https://www.biorxiv.org/content/10.1101/2020.02.11.944900v1

chrispook commented 2 years ago

A small problem, Ming. I've already converted my data to the format FBMN seems to expect, according to the column headers specified in your script. However, it still seems to want to convert it. My job failed because I selected 'MS-DIAL' format input and it tried to apply the formatting script again. See screenshot. GNPS_FBMN_FAILED

Is there a workflow option for already formatted input? The current options are MZMINE, OpenMS, Optimus, MS-DIAL, Metaboscape, XCMS, Progenesis QI and MZTab-M.

mwang87 commented 2 years ago

The already formatted version is MZmine, so go ahead and select that and give it a go.

chrispook commented 2 years ago

There's an MS-DIAL example file called MS-DIAL_v4.70_export_HILIC_POS_Area_0_20218181223.txt in the root of my massive storage folder.

mwang87 commented 2 years ago

Thanks @chrispook will take a look soon.

lfnothias commented 10 months ago

Addressed with https://github.com/CCMS-UCSD/GNPS_Workflows/pull/869