OpenMS
SequenceCoverageCalculator

Prints information about 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:

SequenceCoverageCalculator -- Prints information about idXML files.
Full documentation: http://www.openms.de/doxygen/nightly/html/TOPP_SequenceCoverageCalculator.html
Version: 3.2.0-pre-nightly-2024-07-21 Jul 22 2024, 02:13:52, Revision: b650df0
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:
  SequenceCoverageCalculator <options>

Options (mandatory options marked with '*'):
  -in_database <file>*  Input file containing the database in FASTA format (valid formats: 'fasta')
  -in_peptides <file>*  Input file containing the identified peptides (valid formats: 'idXML')
  -out <file>           Optional text output file. If left out, the output is written to the command line. 
                        (valid formats: 'txt')
                        
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
+SequenceCoverageCalculatorPrints information about idXML files.
version3.2.0-pre-nightly-2024-07-21 Version of the tool that generated this parameters file.
++1Instance '1' section for 'SequenceCoverageCalculator'
in_database input file containing the database in FASTA formatinput file*.fasta
in_peptides input file containing the identified peptidesinput file*.idXML
out Optional text output file. If left out, the output is written to the command line.output file*.txt
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