mqrun.mqparams.data_to_xml

mqrun.mqparams.data_to_xml(user_data, file_paths, fasta_paths, output_dir, tmp_dir=None, logger=None)[source]

Convert parameter set to MaxQuant xml.

Parameters:
  • user_data (dict) – The parameters for MaxQuant as described the module doc of mqparams.
  • file_paths (dict) – Mapping from names in parameter set to actual file paths.
  • fasta_paths (dict # TODO merge with file_paths) – Mapping from names to file paths.
  • output_dir (pathlib.Path) – Write the output files to this directory.
  • tmp_dir (pathlib.Path, optional) – Base dir for temporary data, needs lots of space. Use system default if not specified.
  • logger (logging.Logger, optional) – Logger for the conversion process. Use logging.getLogger('mqparams') if not specified
Returns:

params_xml – Configuration file for use with MaxQuantCmd.exe
Return type:

xml.lxml.ElementTree.ElementTree