OpenMS  3.0.0
MzTabExporter

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

pot. predecessor tools $ \longrightarrow $ MzTabExporter $ \longrightarrow $ 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/nightly/html/TOPP_MzTabExporter.html
Version: 3.0.0-pre-nightly-2022-07-20 Jul 21 2022, 00:07:28, Revision: ea0316e
To cite OpenMS:
  Rost HL, Sachsenberg T, Aiche S, Bielow C et al.. OpenMS: a flexible open-source software platform for mass spectrometry data analysis. Nat Meth. 2016; 13, 9: 741-748. doi:10.1038/nmeth.3959.

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.
version3.0.0-pre-nightly-2022-07-20 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