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: 3.6.0-pre-nightly-2026-03-06 Mar  7 2026, 01:46:19, Revision: c92c980
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

This section lists all parameters supported by the tool. Parameters are organized into hierarchical subsections that group related settings together. Subsections may contain further subsections or individual parameters.

Each parameter entry contains the following information:

• Name The identifier used in configuration files and on the command line.
• Default value The value used if the parameter is not explicitly specified.
• Description A short explanation describing the purpose and behavior of the parameter.
• Tags Additional metadata associated with the parameter.
• Restrictions Allowed value ranges for numeric parameters or valid options for string parameters.

Parameter tags provide additional information about how a parameter is used. Some tags indicate whether a parameter is required or intended for advanced configuration, while others may be used internally by OpenMS or workflow tools.

Parameters highlighted as required must be specified for the tool to run successfully. Parameters marked as advanced allow fine-tuning of algorithm behavior and are typically not needed for standard workflows.

+CVInspectorVisualize and validate PSI mapping and CV files.

version3.6.0-pre-nightly-2026-03-06 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