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 |