<?xml version="1.0"?>
<tool name="2D Feature Extraction" id="ip_2d_feature_extraction" version="0.0.8">
  <description>Feature Extraction</description>
  <requirements>
    <requirement type="package" version="0.23.4">pandas</requirement>
    <requirement type="package" version="0.14.0">scikit-image</requirement>
    <requirement type="package" version="1.15.4">numpy</requirement>
    <requirement type="package" version="0.15.1">tifffile</requirement>
  </requirements>
  <command>
  <![CDATA[
    python '$__tool_directory__/2d_feature_extraction.py'
    #if $feature_options['features'] == 'all'
      --all
    #else if $feature_options['features'] == 'select'
      ${' '.join(str( $feature_options['selected_features'] ).split(','))}
    #end if
    #if $use_raw_option['use_raw'] == 'raw_image'
      --raw '$input_raw'
    #end if
    '$input_label' '$output'
    ]]>
  </command>
  <inputs>
        <param name="input_label" type="data" format="tiff" label="Label file" />
        <conditional name="use_raw_option">
          <param label="Use original image to compute additional features" name="use_raw" type="select">
            <option selected="True" value="no_original">No original image</option>
            <option value="raw_image">Use original image</option>
          </param>
          <when value="no_original"> </when>
          <when value="raw_image">
            <param name="input_raw" type="data" format="tiff" label="Original image file" />
          </when>
        </conditional>
        <conditional name="feature_options">
            <param label="Select features to compute" name="features" type="select">
              <option selected="True" value="all">All features</option>
              <option value="select">Select features</option>
            </param>
            <when value="all"> </when>
            <when value="select">
              <param name="selected_features" type="select" label="Available features" multiple="true" display="checkboxes">
                <option value="--label">Add label id of label image</option>
                <option value="--patches">Patches (requires original image)</option>
                <option value="--max_intensity">Max Intensity (requires original image)</option>
                <option value="--mean_intensity">Mean Intensity (requires original image)</option>
                <option value="--min_intensity">Minimum Intensity (requires original image)</option>
                <option value="--moments_hu">Moments Hu</option>
                <option value="--centroid">Centroid</option>
                <option value="--bbox">Bounding Box</option>
                <option value="--area">Area</option>
                <option value="--filled_area">Filled Area</option>
                <option value="--convex_area">Convex Area</option>
                <option value="--perimeter">Perimeter</option>
                <option value="--extent">Extent</option>
                <option value="--eccentricity">Eccentricity</option>
                <option value="--equivalent_diameter">Equivalent Diameter</option>
                <option value="--euler_number">Euler Number</option>
                <option value="--inertia_tensor_eigvals">Inertia Tensor Eigenvalues</option>
                <option value="--major_axis_length">Major Axis Length</option>
                <option value="--minor_axis_length">Minor Axis Length</option>
                <option value="--orientation">Orientation</option>
                <option value="--solidity">Solidity</option>
                <option value="--moments">Moments</option>
                <option value="--convexity">Convexity</option>
              </param>
            </when>
        </conditional>
  </inputs>
  <outputs>
       <data format="tabular" name="output" />
  </outputs>
  <tests>
    <test>
      <param name="input_label" value="input.tiff"/>
      <param name="features" value="select"/>
      <param name="selected_features" value="--area"/>
      <output name="output" ftype="tabular" value="out.csv"/>
    </test>
  </tests>
  <help>
    This tool computes several features of a 2D label image and optionally more features using the original image.
  </help>
  <citations>
      <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation>
  </citations>
</tool>