MzTabExporter

This application converts several OpenMS XML formats (featureXML, consensusXML, and idXML) to mzTab.

pot. predecessor tools	→ MzTabExporter →	potential successor tools
Any tool producing one of the input formats		External tools (MS Excel, OpenOffice, Notepad)

See the mzTab specification for details on the format.

Experimental classes:

This algorithm and underlying format is work in progress and might change.

Note

Currently mzIdentML (mzid) is not directly supported as an input/output format of this tool. Convert mzid files to/from idXML using IDFileConverter if necessary.

The command line parameters of this tool are:

MzTabExporter -- Exports various XML formats to an mzTab file.
Full documentation: http://www.openms.de/doxygen/release/3.2.0/html/TOPP_MzTabExporter.html
Version: 3.2.0 Sep 18 2024, 16:00:56, Revision: e231942
To cite OpenMS:
 + Pfeuffer, J., Bielow, C., Wein, S. et al.. OpenMS 3 enables reproducible analysis of large-scale mass spec
   trometry data. Nat Methods (2024). doi:10.1038/s41592-024-02197-7.

Usage:
  MzTabExporter <options>

Options (mandatory options marked with '*'):
  -in <file>           Input files used to generate the mzTab file. (valid formats: 'featureXML', 'consensusX
                       ML', 'idXML', 'mzid')
  -out <file>*         Output file (mzTab) (valid formats: 'mzTab')
  -opt_columns <mods>  Add optional columns which are not part of the mzTab standard. (default: '[subfeatures
                       ]') (valid: 'subfeatures')
                       
Common TOPP options:
  -ini <file>          Use the given TOPP INI file
  -threads <n>         Sets the number of threads allowed to be used by the TOPP tool (default: '1')
  -write_ini <file>    Writes the default configuration file
  --help               Shows options
  --helphelp           Shows all options (including advanced)

INI file documentation of this tool:

Legend:

required parameter

advanced parameter

+MzTabExporterExports various XML formats to an mzTab file.

version3.2.0 Version of the tool that generated this parameters file.

++1Instance '1' section for 'MzTabExporter'

in Input files used to generate the mzTab file.input file*.featureXML, *.consensusXML, *.idXML, *.mzid

out Output file (mzTab)output file*.mzTab

first_run_inference_onlyfalse Does the first IdentificationRun in the file only represent (protein) inference results? If so, read peptide information only from second to last runs.true, false

export_all_psmsfalse Export all PSMs instead of only the best per spectrumtrue, false

opt_columns[subfeatures] Add optional columns which are not part of the mzTab standard.subfeatures

log Name of log file (created only when specified)

debug0 Sets the debug level

threads1 Sets the number of threads allowed to be used by the TOPP tool

no_progressfalse Disables progress logging to command linetrue, false

forcefalse Overrides tool-specific checkstrue, false

testfalse Enables the test mode (needed for internal use only)true, false