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IDMerger

Merges several idXML files into one idXML file.

potential predecessor tools $ \longrightarrow $ IDMerger $ \longrightarrow $ potential successor tools
MascotAdapter (or other ID engines) ConsensusID
IDFileConverter IDMapper

The peptide hits and protein hits of the input files will be written into the single output file. In general, the number of idXML files that can be merged into one file is not limited.

The combination of search engine and processing date/time should be unique for every identification run over all input files. If this is not the case, the date/time of a conflicting run will be increased in steps of seconds until the combination is unique.

With the pepxml_protxml option, results from corresponding PeptideProphet and ProteinProphet runs can be combined. In this case, exactly two idXML files are expected as input: one containing data from a pepXML file, and the other containing data from a protXML file that was created based on the pepXML (meaningful results can only be obtained for matching files!). pepXML or protXML can be converted to idXML with the IDFileConverter tool.

The command line parameters of this tool are:

IDMerger -- Merges several protein/peptide identification files into one file.
Version: 1.11.1 Nov 14 2013, 11:18:15, Revision: 11976

Usage:
  IDMerger <options>

Options (mandatory options marked with '*'):
  -in <files>*            Two or more input files separated by blanks (valid formats: 'idXML')
  -out <file>*            Output file  (valid formats: 'idXML')
  -annotate_file_origin   Store the original filename in each protein/peptide identification (MetaValue: file
                          _origin).
  -pepxml_protxml         Merge idXML files derived from a pepXML and corresponding protXML file.
                          Exactly two input files are expected in this case.
                          
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
+IDMergerMerges several protein/peptide identification files into one file.
version1.11.1 Version of the tool that generated this parameters file.
++1Instance '1' section for 'IDMerger'
in[] two or more input files separated by blanksinput file*.idXML
out output file output file*.idXML
annotate_file_originfalse Store the original filename in each protein/peptide identification (MetaValue: file_origin).true,false
pepxml_protxmlfalse Merge idXML files derived from a pepXML and corresponding protXML file.
Exactly two input files are expected in this case.
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
testfalse Enables the test mode (needed for internal use only)true,false

OpenMS / TOPP release 1.11.1 Documentation generated on Thu Nov 14 2013 11:19:24 using doxygen 1.8.5