<tool id="ip_threshold" name="Threshold image" version="0.0.5-2" profile="20.05">
    <description>with scikit-image</description>
    <edam_operations>
        <edam_operation>operation_3443</edam_operation>
    </edam_operations>
    <xrefs>
        <xref type="bio.tools">scikit-image</xref>
        <xref type="biii">scikit-image</xref>
    </xrefs>
    <requirements> 
        <requirement type="package" version="0.18.1">scikit-image</requirement>
        <requirement type="package" version="2020.10.1">tifffile</requirement>
    </requirements>
    <command detect_errors="aggressive">
    <![CDATA[
    python '$__tool_directory__/auto_threshold.py'
    '$input'
    ./out.tif
    '$th_method'
    '$block_size'
    '$dark_bg'
    ]]>
    </command>
    <inputs>
        <param name="input" type="data" format="tiff,png" label="Input image" />
        <param name="th_method" type="select" label="Thresholding method">
          <option value="otsu" selected="True">Otsu</option>
          <option value="li">Li's Minimum Cross Entropy</option>
          <option value="isodata">Isodata</option>
          <option value="yen">Yen</option>
          <option value="loc_gaussian">Adaptive (Gaussian)</option>
          <option value="loc_median">Adaptive (Median)</option>
          <option value="loc_mean">Adaptive (Mean)</option>
        </param>
        <param name="block_size" type="integer" value="5" label="Odd size of pixel neighborhood for determining the threshold (only valid for adaptive thresholding methods)" />
        <param name="dark_bg" type="boolean" checked="true" truevalue="True" falsevalue="False" label="Dark Background" />
    </inputs>
    <outputs>
       <data format="tiff" name="output" from_work_dir="out.tif" />
    </outputs>
    <tests>
        <test>
            <param name="input" value="sample.tif"/>
            <output name="output" value="out.tif" ftype="tiff" compare="sim_size"/>
            <param name="th_method" value="loc_gaussian"/>
            <param name="block_size" value="3"/>
            <param name="dark_bg" value="True"/>
        </test>
        <test>
            <param name="input" value="sample.tif"/>
            <output name="output" value="out2.tif" ftype="tiff" compare="sim_size"/>
            <param name="th_method" value="otsu"/>
            <param name="block_size" value="5"/>
            <param name="dark_bg" value="True"/>
        </test>
    </tests>
    <help>
        Applies a standard thresholding algorithm to an image.
    </help>
    <citations>
        <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation>
    </citations>
</tool>