OpenMS
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 -- Visualize and validate PSI mapping and CV files.
Full documentation: http://www.openms.de/doxygen/nightly/html/TOPP_CVInspector.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:
  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 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
+CVInspectorVisualize and validate PSI mapping and CV files.
version3.2.0-pre-nightly-2024-07-21 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 Overrides tool-specific checkstrue, false
testfalse Enables the test mode (needed for internal use only)true, false