OpenMS  2.5.0
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:


SemanticValidator -- SemanticValidator for semantically validating certain XML files.

Full documentation: http://www.openms.de/documentation/UTILS_SemanticValidator.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:

  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 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
+SemanticValidatorSemanticValidator for semantically validating certain XML files.
version2.5.0-GIT-NOTFOUND-GIT-NOTFOUND 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 Overwrite tool specific checks.true,false
testfalse Enables the test mode (needed for internal use only)true,false