mqrun.mqparams.xml_to_data¶
- mqrun.mqparams.xml_to_data(xml_tree, logger=None)[source]¶
Extract parameters and file-paths from MaxQuant configuration file
Parameters: - xml_tree (xml.etree.ElementTree.Element.Tree) – MaxQuant configuration file.
- logger (logging.Logger, optional) – Logger for the conversion process. Use logging.getLogger('mqparams') if not specified.
Returns: - params (dict) – Parameters as described in module doc
- path_data (mqparams.ExtraMQData) – Path information from xml file
- extra_data has the following attributes
- file_paths (dict) – Mapping from names for input files to paths
- fasta_paths (dict # TODO merge with file_paths) – Same for fasta files
- output_dir (pathlib.Path) – Path to the output directory
- tmp_dir (pathlib.Path) – Path to temporary directory