<tool id="CalcFeatures" name="CalcFeatures" version="1.0">
    <description>A wrapper around the feature calculation function of PREDICT.</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="CalcFeatures_tool.py" />
    </targets>
    <description>
       CalcFeatures.py image metadata segmentation parameters
       output = Radiomics features
    </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="image" name="image" datatype="ITKImageFile" prefix="--im" cardinality="1" repeat_prefix="false" required="true" />
        <input id="metadata" name="metadata" datatype="DicomImageFile" prefix="--md" cardinality="as:image" repeat_prefix="false" required="false" />
        <input id="semantics" name="semantics" datatype="CSVFile" prefix="--sem" cardinality="1-*" repeat_prefix="false" required="false" />
        <input id="segmentation" name="segmentation" datatype="ITKImageFile" prefix="--seg" cardinality="as:image" repeat_prefix="false" required="true" />
        <input id="parameters" name="parameters" datatype="ParameterFile" prefix="--para" cardinality="1-*" repeat_prefix="false" required="true" />
     </inputs>
    <outputs>
      <output id="features" name="Output feature files" datatype="HDF5" cardinality="as:parameters" nospace="False" order="0" prefix="--out" required="false"/>
    </outputs>
  </interface>
  <requirements />
  <tests />
  <help> usage: CalcFeatures.py [-h] -im IMAGE.ITKIM [-md METADATA.dcm] [-sem SEMANTICS.csv] -seg SEGMENTATION.ITKIM -para PARAMETERS.ini -out OUTPUT.hdf5

        Compute Radiomics features.

        optional arguments:
        -h, --help show this help message and exit
        -im IMAGE.ITKIM ITK image file containing an image
        -seg SEGMENTATION.ITKIM ITK image file containing a matching segmentations
        -sem SEMANTICS.csv CSV file containing the semantic features for this sample.
        -para PARAMETERS.ini parameters used in feature extraction
        -out OUTPUT.hdf5f Path to save computed features to
  </help>
  <cite>
  </cite>
  <references />
</tool>
