OpenMS
IDExtractor

Extracts 'n' peptides randomly or best 'n' from idXML files.

Input and output format are 'idXML'. The tools allows you to extract subsets of peptides from idXML files.

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:

IDExtractor -- Extracts 'n' peptides randomly or best 'n' from idXML files.
Full documentation: http://www.openms.de/doxygen/nightly/html/TOPP_IDExtractor.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:
  IDExtractor <options>

Options (mandatory options marked with '*'):
  -in <file>*                        Input file (valid formats: 'idXML')
  -out <file>*                       Output file (valid formats: 'idXML')
  -number_of_peptides <int>          Number of randomly chosen peptides (default: '10') (min: '1')
  -number_of_rand_invokations <int>  Number of rand invocations before random draw (basically a seed) (defaul
                                     t: '0') (min: '0')
  -best_hits                         If this flag is set the best n peptides are chosen.
                                     
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
+IDExtractorExtracts 'n' peptides randomly or best 'n' from idXML files.
version3.2.0-pre-nightly-2024-07-19 Version of the tool that generated this parameters file.
++1Instance '1' section for 'IDExtractor'
in input fileinput file*.idXML
out output fileoutput file*.idXML
number_of_peptides10 Number of randomly chosen peptides1:∞
number_of_rand_invokations0 Number of rand invocations before random draw (basically a seed)0:∞
best_hitsfalse If this flag is set the best n peptides are chosen.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
forcefalse Overrides tool-specific checkstrue, false
testfalse Enables the test mode (needed for internal use only)true, false