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:

stty: 'standard input': Inappropriate ioctl for device

IDSplitter -- Splits protein/peptide identifications off of annotated data files
Full documentation: http://www.openms.de/doxygen/nightly/html/TOPP_IDSplitter.html
Version: 3.4.0-pre-nightly-2024-12-16 Dec 17 2024, 02:41:12, Revision: 96ad74c
To cite OpenMS:
 + Pfeuffer, J., Bielow, C., Wein, S. et al.. OpenMS 3 enables reproducible analysis of large-scale mass spectrometry 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

version3.4.0-pre-nightly-2024-12-16 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