Tool to extract metadata table from sample .mzml and .json metadata files

[hechth]

For RAMClustR & WaveICA, we need a metadata table with the structure shown below:

sample_name	class	sampleType	injectionOrder	batch
VT_160120_002	sample	sample	1	1
VT_160120_004	sample	sample	2	1
VT_160120_006	sample	sample	3	1
VT_160120_008	sample	sample	4	1
VT_160120_010	sample	sample	5	1

Sample type might be blank or QC.

This information should be extracted from the filename tag contained in the .mzml file and the metadata contained in the .json file.

[martenson]

For testing purposes we have a sample metadata file corresponding to the GC seminal plasma dataset here: https://umsa.cerit-sc.cz/library/list#folders/F1c84aa7fc4490e6d/datasets/fdeac135082b95d1

[maximskorik]

The batch information is also required for two-step-hybrid apLCMS: https://github.com/RECETOX/galaxytools/issues/174.

[hechth]

This tool basically does what we need: https://github.com/ISA-tools/mzml2isa

[bgruening]

A start for a Galaxy integration is here: https://github.com/ISA-tools/mzml2isa-galaxy

ping @tomnl

[xtrojak]

A start for a Galaxy integration is here: https://github.com/ISA-tools/mzml2isa-galaxy

The tool doesn't work for Python 3. https://github.com/ISA-tools/mzml2isa-galaxy/issues/10

[Tomnl]

Hi,

I have updated the mzml2isa tool to work for Python 3

Let me know if you have questions regarding what information you need to extract from the mzML file

[hechth]

Thank you very much :)

[hechth]

@Tomnl I tested the tool and I'm getting the following error:

usage: mzml2isa -i IN_PATH -o OUT_PATH -s STUDY_ID [options]
mzml2isa: error: argument -s: expected one argument

I used the mzml collection as input data - any ideas?

[Tomnl]

Sorry about this. Will have a proper check later. But I think think this might be that the ‘Name study’ was left blank.

If that is the case I will make some changes so there is either a default value or the param is required. Hopefully a quick fix

[hechth]

I retried with the Name study filled in and still got an error.

/mnt/volume/shared/ces-nya/nfs4/home/umsa/dependencies/_conda/envs/mulled-v1-f42eb8a5f4269b14eb9d6f99b2664d2dc7cfd3eb428e3164bd1d58b0f6910a8d/lib/python3.9/site-packages/mzml2isa/parsing.py:151: UserWarning: No files were found in temp.
  warnings.warn("No files were found in {}.".format(in_path), UserWarning)