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RTAnnotator

Adds RT information to identifications in mzid.

pot. predecessor tools $ \longrightarrow $ QCCalculator $ \longrightarrow $ pot. successor tools
XTandemAdapter MascotAdapterOnline
IDFilter QCCalculator

RT is no mandatory attribute in a PSM representation of MzIdentML. Some identification engines do omit this information. Though, as the RT will be crucial for further analyses, all (e.g. ) reading MzIdentML will warn you about missing RT. This tool performs the annotation of the identification given the source file to the identification process.

Note
For mzid in-/out- put, due to legacy reason issues you are temporarily asked to use IDFileConverter as a wrapper. The command line parameters of this tool are:
RTAnnotator -- Annotates identification files that are missing the RT field
Version: 2.0.0 May 29 2015, 13:57:09, Revision: GIT-NOTFOUND

Usage:
  RTAnnotator <options>

Options (mandatory options marked with '*'):
  -in_msref <file>*  Mass spectra file as reference input for RT lookup (valid formats: 'mzML')
  -in <file>*        Identifications without RT field (valid formats: 'mzid', 'idXML')
  -out <file>*       Output file (identifications). (valid formats: 'mzid', 'idXML')
                     
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
+RTAnnotatorAnnotates identification files that are missing the RT field
version2.0.0 Version of the tool that generated this parameters file.
++1Instance '1' section for 'RTAnnotator'
in_msref Mass spectra file as reference input for RT lookupinput file*.mzML
in Identifications without RT fieldinput file*.mzid,*.idXML
out Output file (identifications).output file*.mzid,*.idXML
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

OpenMS / TOPP release 2.0.0 Documentation generated on Fri May 29 2015 17:20:34 using doxygen 1.8.9.1