Evaluates alignment results against a ground truth.
| pot. predecessor tools |  MapAlignmentEvaluationAlgorithm   | pot. successor tools | 
| FeatureLinkerUnlabeled or FeatureLinkerUnlabeledQT | none (text output) | 
This tool implements the evaluation measures published in
 "Critical assessment of alignment procedures for LC-MS proteomics and metabolomics measurements",
 Eva Lange, Ralf Tautenhahn, Steffen Neumann, Clemens Groepl. BMC Bioinformatics 2008, 9:375.
 doi:10.1186/1471-2105-9-375.
 Input is a ground truth file as described on the CAAP web page
 Output is a recall- or a precision-value.
 The command line parameters of this tool are: 
MapAlignmentEvaluation -- Evaluates alignment results against a ground truth.
Version: 1.11.1 Nov 14 2013, 11:18:15, Revision: 11976
Usage:
  MapAlignmentEvaluation <options>
Options (mandatory options marked with '*'):
  -in <file>*        Input file: tool (valid formats: 'consensusXML')
  -gt <file>*        Input file: ground truth (valid formats: 'consensusXML')
  -type <name>*      Caap Evaluation type (valid: 'precision', 'recall', 'F1')
  -rt_dev <double>   Maximum allowed deviation of the retention time (default: '0.1')
  -mz_dev <double>   Maximum allowed deviation of m/z (default: '0.1')
  -int_dev <double>  Maximum allowed deviation of Intensity (default: '100')
  -use_charge        Use charge criterion when assesing if two features are identical.
                     
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:
| OpenMS / TOPP release 1.11.1 | Documentation generated on Thu Nov 14 2013 11:19:24 using doxygen 1.8.5 |