OpenMS
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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.
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/release/3.3.0/html/TOPP_IDExtractor.html Version: 3.3.0 Dec 21 2024, 15:25:20, Revision: 35c5e65 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: