| OpenMS 2.5.0

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/documentation/TOPP_MzTabExporter.html

    Version: 2.5.0-GIT-NOTFOUND-GIT-NOTFOUND Sep 10 2020, 12:20:39, Revision: GIT-NOTFOUND

    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
+MzTabExporter Exports various XML formats to an mzTab file.
version 2.5.0-GIT-NOTFOUND-GIT-NOTFOUND Version of the tool that generated this parameters file.
++1 Instance '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_only false 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
opt_columns[subfeatures] Add optional columns which are not part of the mzTab standard.subfeatures
log Name of log file (created only when specified)
debug 0 Sets the debug level
threads 1 Sets the number of threads allowed to be used by the TOPP tool
no_progress false Disables progress logging to command line true,false
force false Overwrite tool specific checks.true,false
test false Enables the test mode (needed for internal use only)true,false