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MapAlignmentEvaluation

Evaluates alignment results against a ground truth.

pot. predecessor tools $ \longrightarrow $ MapAlignmentEvaluationAlgorithm $ \longrightarrow $ 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: 2.0.0 May 29 2015, 13:57:09, Revision: GIT-NOTFOUND

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:

Legend:
required parameter
advanced parameter
+MapAlignmentEvaluationEvaluates alignment results against a ground truth.
version2.0.0 Version of the tool that generated this parameters file.
++1Instance '1' section for 'MapAlignmentEvaluation'
in input file: toolinput file*.consensusXML
gt input file: ground truthinput file*.consensusXML
type Caap Evaluation typeprecision,recall,F1
rt_dev0.1 Maximum allowed deviation of the retention time
mz_dev0.1 Maximum allowed deviation of m/z
int_dev100 Maximum allowed deviation of Intensity
use_chargefalse Use charge criterion when assesing if two features are identical.true,false
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