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/release/3.1.0/html/TOPP_SequenceCoverageCalculator.html
Version: 3.1.0 Oct 18 2023, 10:27:18, Revision: 17a07f8
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:
  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.

version3.1.0 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