CVInspector

A tool for visualization and validation of PSI mapping and CV files.

This tool is used to validate the correct use of mapping files and CV files.

It can also generate a HTML representation of mapping file and CV.

The command line parameters of this tool are:

CVInspector -- A tool for visualization and validation of PSI mapping and CV files.
Full documentation: http://www.openms.de/documentation/UTILS_CVInspector.html
Version: 2.5.0 Feb 20 2020, 20:13:06, Revision: f649042
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:
  CVInspector <options>

Options (mandatory options marked with '*'):
  -cv_files <files>*    List of ontology files in OBO format. (valid formats: 'obo')
  -cv_names <names>*    List of identifiers (one for each ontology file).
  -mapping_file <file>  Mapping file in CVMapping (XML) format. (valid formats: 'XML')
  -ignore_cv <list>     A list of CV identifiers which should be ignored. (default: '[UO PATO BTO]')
  -html <file>          Writes an HTML version of the mapping file with annotated CV terms (valid formats: 
                        'HTML')
                        
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

+CVInspectorA tool for visualization and validation of PSI mapping and CV files.

version2.5.0 Version of the tool that generated this parameters file.

++1Instance '1' section for 'CVInspector'

cv_files[] List of ontology files in OBO format.input file*.obo

cv_names[] List of identifiers (one for each ontology file).

mapping_file Mapping file in CVMapping (XML) format.input file*.XML

ignore_cv[UO, PATO, BTO] A list of CV identifiers which should be ignored.

html Writes an HTML version of the mapping file with annotated CV termsoutput file*.HTML

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 Overwrite tool specific checks.true,false

testfalse Enables the test mode (needed for internal use only)true,false