<tool id="TrainClassifier" name="TrainClassifier" version="1.0">
    <description>A wrapper around PREDICT's Radiomics patient classification.</description>
    <authors>
      <author name="Martijn Starmans" email="m.starmans@erasmusmc.nl" url="http://www.bigr.nl/people/MartijnStarmans" />
    </authors>
  <command version="1.0" url="" >
    <targets>
      <target os="*" arch="*" interpreter="python" paths='bin/' bin="TrainClassifier.py" />
    </targets>
    <description>
       SVMGS.py images patientinfo seg parameters
       output = Radiomics classification
    </description>
    <authors>
      <author  name="Martijn Starmans" email="m.starmans@erasmusmc.nl" url="http://www.bigr.nl/people/MartijnStarmans" />
      <author  name="Sebastian van der Voort" email="s.vandervoort@erasmusmc.nl" url="http://www.bigr.nl/people/SebastianvanderVoort" />
    </authors>
  </command>
  <repository />
  <interface>
    <inputs>
        <input id="features_train" name="Input feature files of first modality" datatype="HDF5" prefix="--feat_train" cardinality="1" repeat_prefix="false" required="true" />
        <input id="features_test" name="Input feature files of first modality" datatype="HDF5" prefix="--feat_test" cardinality="1" repeat_prefix="false" required="false" />
        <input id="patientclass_train" name="patientclass" datatype="PatientInfoFile" prefix="--pc_train" cardinality="1" repeat_prefix="false" required="true" />
        <input id="patientclass_test" name="patientclass" datatype="PatientInfoFile" prefix="--pc_test" cardinality="1" repeat_prefix="false" required="false" />
        <input id="config" name="config" datatype="ParameterFile" prefix="--conf" cardinality="1-*" repeat_prefix="false" required="true" />
        <input id="fixedsplits" name="File containing fixed splits for cross validation" datatype="XlsxFile" prefix="--fs" cardinality="1" repeat_prefix="false" required="false" />
     </inputs>
    <outputs>
      <output id="classification" name="Radiomics classification" datatype="HDF5" cardinality="as:config" nospace="False" order="0" prefix="--class" required="true"/>
      <output id="performance" name="Radiomics classification performance" datatype="JsonFile" cardinality="as:config" nospace="False" order="0" prefix="--perf" required="true"/>
    </outputs>
  </interface>
  <requirements />
  <tests />
  <help> usage: TrainClassifier.py [-h] -feat_m1/m2/m3 FEATURES.hdf5 -pc PATIENTCLASS.txt-conf CONFIGURATION.ini -parameters PARAMETERS.ini -class CLASSIFICATION.hdf5 -perf PERFORMANCE.json
    Perform a grid search over several features types to train multiple Support Vector Machine (SVM) classifiers.

    -feat_m1, ..m2, ..m3 FEATURES.HDF5 File containing the features for an object. Support up to three feature files for a single object.
    -pc PATIENTCLASS.txt File containing the labels for an object.
    -conf CONFIGURATION.ini File specifiying the configurations for the SVM optimization.
    -parameters PARAMETERS.ini File specifying the grid search parameters containing the feature groups to use.
    -class CLASSIFICATION.hdf5 File to write the SVM output to.
    -perf PERFORMANCE.json File containing the performance statistics of the fitted SVM.
  </help>
  <cite>
  </cite>
  <references />
</tool>
