| OpenMS 2.5.0

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/documentation/UTILS_IDExtractor.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:

      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 (default: '0' min: '0')

      -best_hits                         If this flag is set the best n peptides are chosen.

    Common UTIL 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
+IDExtractor Extracts 'n' peptides randomly or best 'n' from idXML files.
version 2.5.0-GIT-NOTFOUND-GIT-NOTFOUND Version of the tool that generated this parameters file.
++1 Instance '1' section for 'IDExtractor'
in input file input file*.idXML
out output file output file*.idXML
number_of_peptides 10 Number of randomly chosen peptides 1:∞
number_of_rand_invokations 0 Number of rand invocations before random draw 0:∞
best_hits false If this flag is set the best n peptides are chosen.true,false
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