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:

stty: 'standard input': Inappropriate ioctl for device

SequenceCoverageCalculator -- Annotates coverage information to idXML files.
Full documentation: http://www.openms.de/doxygen/nightly/html/TOPP_SequenceCoverageCalculator.html
Version: 3.4.0-pre-nightly-2024-12-16 Dec 17 2024, 02:41:12, Revision: 96ad74c
To cite OpenMS:
 + Pfeuffer, J., Bielow, C., Wein, S. et al.. OpenMS 3 enables reproducible analysis of large-scale mass spectrometry 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: 'idXML')
                        
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

+SequenceCoverageCalculatorAnnotates coverage information to idXML files.

version3.4.0-pre-nightly-2024-12-16 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*.idXML

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