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Usage

Folder structure

nmrML

nmrml2isa only requires that you put all you nmrML and zipped raw files in the same folder, and parsing should work fine. Note that reference to RAW files is extracted from the mzML files, so if you plan to create an ISA archive after mzml2isa creates ISA files, don't forget to include those as well.

Example structure:

/
└ home/
  └ metabolomics/
    └ nmrML study/     # the name of the folder doesn't matter
      ├ Sample1.nmrML  # the name of the file must correspond to the sample name
      ├ Sample2.zip    # the raw files should be zipped and called exactly like the nmrML
      ├ Sample2.nmrML
      ├ Sample2.zip
      └ ...

CLI

nmrml2isa -i /path/to/nmrml/folder -o /path/to/out_folder -s STUDYID

Python module

from nmrml2isa.parsing import full_parse
full_parse("/path/to/nmrml/folder", "/path/to/out_folder", "STUDYID")
# this will do the same thing as the command line.

See the :doc:`Examples <examples>` and the :doc:`API reference <api/index>` for more hindsights.

Editing with ISAcreator

The ISA-Tab structure can be further populated with the ISAcreator software.

See brief tutorial for more details.