SemanticValidator

SemanticValidator for XML files which can be semantically validated.

This tool is able to semantically validate an XML file against a CV-mapping file. The CV-mapping file describes the validity of CV-terms for a given tag inside the XML. The CV-mapping file conforms to the CvMapping XML schema (found at /share/OpenMS/SCHEMAS/CvMapping.xsd or http://www.psidev.info/sites/default/files/CvMapping.xsd).

Example files that can be semantically validated using this tool are mzML, TraML, mzIdentML, mzData or any XML file.

The command line parameters of this tool are:

stty: 'standard input': Inappropriate ioctl for device

SemanticValidator -- SemanticValidator for semantically validating certain XML files.
Full documentation: http://www.openms.de/doxygen/nightly/html/TOPP_SemanticValidator.html
Version: 3.4.0-pre-nightly-2024-12-16 Dec 17 2024, 02:41:12, Revision: 96ad74c
To cite OpenMS:
 + Pfeuffer, J., Bielow, C., Wein, S. et al.. OpenMS 3 enables reproducible analysis of large-scale mass spectrometry data. Nat Methods (2024). doi:10.1038/s41592-024-02197-7.

Usage:
  SemanticValidator <options>

Options (mandatory options marked with '*'):
  -in <file>*            Input file (any xml file) (valid formats: 'analysisXML', 'mzML', 'traML', 'mzid', 'mzData', 'xml')
  -mapping_file <file>*  Mapping file which is used to semantically validate the given XML file against this mapping file (see 'share/OpenMS/MAPPING' for templates). (valid formats: 'xml')
  -cv <files>            Controlled Vocabulary files containg the CV terms (if left empty, a set of default files are used) (valid formats: 'obo')
                         
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

+SemanticValidatorSemanticValidator for semantically validating certain XML files.

version3.4.0-pre-nightly-2024-12-16 Version of the tool that generated this parameters file.

++1Instance '1' section for 'SemanticValidator'

in Input file (any xml file)input file*.analysisXML, *.mzML, *.traML, *.mzid, *.mzData, *.xml

mapping_file Mapping file which is used to semantically validate the given XML file against this mapping file (see 'share/OpenMS/MAPPING' for templates).input file*.xml

cv[] Controlled Vocabulary files containg the CV terms (if left empty, a set of default files are used)input file*.obo

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