OpenMS
IDSplitter

Splits protein/peptide identifications off of annotated data files.

This performs the reverse operation as IDMapper.

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:

IDSplitter -- Splits protein/peptide identifications off of annotated data files
Full documentation: http://www.openms.de/doxygen/nightly/html/TOPP_IDSplitter.html
Version: 3.2.0-pre-nightly-2024-07-19 Jul 20 2024, 02:06:43, Revision: f10e72e
To cite OpenMS:
 + Pfeuffer, J., Bielow, C., Wein, S. et al.. OpenMS 3 enables reproducible analysis of large-scale mass spec
   trometry data. Nat Methods (2024). doi:10.1038/s41592-024-02197-7.

Usage:
  IDSplitter <options>

Options (mandatory options marked with '*'):
  -in <file>*        Input file (data annotated with identifications) (valid formats: 'mzML', 'featureXML', 
                     'consensusXML')
  -out <file>        Output file (data without identifications). Either 'out' or 'id_out' are required. They 
                     can be used together. (valid formats: 'mzML', 'featureXML', 'consensusXML')
  -id_out <file>     Output file (identifications). Either 'out' or 'id_out' are required. They can be used 
                     together. (valid formats: 'idXML')
                     
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
+IDSplitterSplits protein/peptide identifications off of annotated data files
version3.2.0-pre-nightly-2024-07-19 Version of the tool that generated this parameters file.
++1Instance '1' section for 'IDSplitter'
in Input file (data annotated with identifications)input file*.mzML, *.featureXML, *.consensusXML
out Output file (data without identifications). Either 'out' or 'id_out' are required. They can be used together.output file*.mzML, *.featureXML, *.consensusXML
id_out Output file (identifications). Either 'out' or 'id_out' are required. They can be used together.output file*.idXML
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