Update msdial_formatter.py

[chrispook]

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]

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]

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]

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.

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]

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

[chrispook]

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]

Thanks @chrispook will take a look soon.

[lfnothias]

Addressed with #869