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MzTabExporter

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

pot. predecessor tools $ \longrightarrow $ MzTabExporter $ \longrightarrow $ potential successor tools
ProteinQuantifier 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: 2.0.0 Mar 30 2016, 12:52:33, Revision: GIT-NOTFOUND

Usage:
  MzTabExporter <options>

Options (mandatory options marked with '*'):
  -in_feature <file>    FeatureXMLs used to generate the mzTab file. (valid formats: 'featureXML')
  -in_consensus <file>  ConsensusXMLs used to generate the mzTab file. (valid formats: 'consensusXML')
  -in_id <file>         Identifications used to generate the mzTab file. (valid formats: 'idXML')
  -out <file>*          Output file (mzTab) (valid formats: 'csv')
                        
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.
version2.0.0 Version of the tool that generated this parameters file.
++1Instance '1' section for 'MzTabExporter'
in_feature FeatureXMLs used to generate the mzTab file.input file*.featureXML
in_consensus ConsensusXMLs used to generate the mzTab file.input file*.consensusXML
in_id Identifications used to generate the mzTab file.input file*.idXML
out Output file (mzTab)output file*.csv
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

OpenMS / TOPP release 2.0.0 Documentation generated on Wed Mar 30 2016 16:18:43 using doxygen 1.8.5