| OpenMS 2.5.0

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-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:

      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
+CVInspector A tool for visualization and validation of PSI mapping and CV files.
version 2.5.0-GIT-NOTFOUND-GIT-NOTFOUND Version of the tool that generated this parameters file.
++1 Instance '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 terms output file*.HTML
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