GNPS_Workflows [FBMN] Validator for quant table to make sure it is formatted correctly

[x] Create negative control failure cases (e.g. missing columns, incorrect delimeter)
[x] MZMine2 - Implement delimiter is correct
[x] MZMine2 - Implement missing columns

Sep 18 '19 14:09 mwang87

Would be a great starter issue for Kevin.

Oct 23 '19 04:10 mwang87

Should this be a general validator or for the MZmine output?

We should also consider the Ion Identity Networking columns in the quant table

Oct 23 '19 07:10 robinschmid

Should this be a general validator or for the MZmine output?

We should also consider the Ion Identity Networking columns in the quant table

This can be done with IIN as a separate issue. For now we will only evaluate the standard expected output from MZMine2.

Oct 24 '19 19:10 mwang87

@kevinnguyen1413 Any updates on this issue?

Oct 28 '19 22:10 mwang87

@kevinnguyen1413 Any updates on this issue?

@mwang87 I have some questions regarding the problem, so can I meet you tomorrow morning and discuss them?

Oct 29 '19 02:10 kevinnguyen1413

The code that should be updated is here:

https://github.com/CCMS-UCSD/GNPS_Workflows/blob/master/feature-based-molecular-networking/tools/feature-based-molecular-networking/scripts/mzmine2_formatter.py

The specific aims are outlined in the main issue text.

If you have questions about the mzmine2 output format, we have a readme here:

https://github.com/CCMS-UCSD/GNPS_Workflows/blob/master/feature-based-molecular-networking/README.md

Do you have any questions regarding the task?

Oct 29 '19 16:10 mwang87

@kevinnguyen1413 Any updates on this issue?

Nov 13 '19 01:11 mwang87

I have updated the testing:

https://github.com/CCMS-UCSD/GNPS_Workflows/blob/master/README.md#testing

Nov 15 '19 20:11 mwang87

@ntbeileh

Dec 10 '19 21:12 cmaceves

The basic functionality is there, needs to be hooked up into workflow code. @mwang87 will tackle

Jan 28 '20 18:01 mwang87