workflow4metabolomics / isa-extractor Goto Github PK

Hi,

It would be nice to have a tool "isa2zip" that can import into galaxy zip files from NMR studies (like MTBLS1 zip files https://www.ebi.ac.uk/metabolights/MTBLS1/files)

I know that isa2nmrml do exists but nmrML processing tools are not yet available in W4M for example.

Many thanks
Yann and @mtremblayfr

Hi @pkrog ,

maybe not an isa2mzML issue, but just in case.

As you know I'm trying to reproduce MTBLS719 study in W4M. I'm able to get the isa-tab and that all.
Now, I am trying d to get the mzML files with isa2mzML tool, but I get an empty dataset....Maybe it's linked to "incorrect" files in the Metabolights repository or to the structure of that repo.
In fact, mzML files are in a DERIVED_FILES sub-folder see picture

I'm only interested by the a_MTBLS719_LC-MS_positive_reverse-phase_metabolite_profiling.txt related files, is there an option to download only these files?

Many thanks fro your time

mzData dataset are already handled by Galaxy.

Explore the possibility of moving this tool into tools-metabolomics

• Make a bioconda package for the script.
• Move XML and test-data into tools-metabolomics.

For a multi-assay file, the extractor collects too many files. It would be great
if in the tool you can select an assay (just like in the ISA to W4M converter)
and, for maximum flexibility, the column with file names (e.g. Raw Spectral Data File or Derived Spectral Data File) and output that as a collection. Difficulty will be the File type.
Yours, Steffen

When extracting files from ISA dataset subfolder, create symbolic links instead of copying.

• Use planemo lint on all tools.
• Write a test for isa2mzdata.
• Write a test for isa2mzml.
• Write a test for isa2mzxml.
• Write a test for isa2netcdf.
• Write a test for isa2nmrml.
• Publish onto test toolshed.
• Install and test on test instance.
• Publish onto main toolshed.
• Install and test on main instance.