<tool id="CF_pyradiomics" name="CF_pyradiomics" version="1.0">
    <description>A wrapper around the pyradiomics feature extractor.</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="CF_pyradiomics_tool.py" />
    </targets>
    <description>
       CF_pyradiomics.py image metadata segmentation semantics parameters output
       output = Radiomics features
    </description>
    <authors>
      <author name="Martijn Starmans" email="m.starmans@erasmusmc.nl" url="http://www.bigr.nl/people/MartijnStarmans" />
    </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="false" />
     </inputs>
    <outputs>
      <output id="features" name="Output feature files" datatype="DataFile" cardinality="as:parameters" nospace="False" order="0" prefix="--out" required="false"/>
    </outputs>
  </interface>
  <requirements />
  <tests />
  <help> usage: CF_pyradiomics.py [-h] -im IMAGE.ITKIM -seg SEGMENTATION.ITKIM [-sem SEMANTICS.csv] [-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>
