| 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
+SemanticValidator SemanticValidator for semantically validating certain XML files.
version 2.5.0-GIT-NOTFOUND-GIT-NOTFOUND Version of the tool that generated this parameters file.
++1 Instance '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)
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