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.
Version: 2.4.0-HEAD-2019-03-12 Mar 12 2019, 13:43:07, Revision: a8ff34a
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', 'con
                              sensusXML', 'idXML', 'mzid')
  -out <file>*                Output file (mzTab) (valid formats: 'mzTab')
  -first_run_inference_only   (idXML/mzid only): Does the first IdentificationRun in the fileonly represent 
                              inference results? Read peptide information onlyfrom second to last runs.
                              
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.

version2.4.0-HEAD-2019-03-12 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 (idXML/mzid only): Does the first IdentificationRun in the fileonly represent inference results? Read peptide information onlyfrom second to last runs.true,false

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 Overwrite tool specific checks.true,false

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