| OpenMS 2.5.0

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/documentation/UTILS_SequenceCoverageCalculator.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:

      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 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
+SequenceCoverageCalculator Prints information about idXML files.
version 2.5.0-GIT-NOTFOUND-GIT-NOTFOUND Version of the tool that generated this parameters file.
++1 Instance '1' section for 'SequenceCoverageCalculator'
in_database input file containing the database in FASTA format input file*.fasta
in_peptides input file containing the identified peptides input 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)
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