<tool id="ip_coordinates_of_roi" name="Coordinates of ROI" version="0.0.3">
    <description></description>
    <requirements>
        <requirement type="package" version="0.14.2">scikit-image</requirement>
        <requirement type="package" version="0.23.4">pandas</requirement>
    </requirements>
    <command detect_errors="aggressive">
        <![CDATA[
            python '$__tool_directory__/coordinates_of_roi.py'
            '$im'
            '$pixel_table'
            $offset_x $offset_y
            $white_obj
            --threshold $threshold
        ]]>
    </command>
    <inputs>
        <param name="im" type="data" format="png" label="Source file" />
        <param name="white_obj" type="boolean" truevalue="--white_obj" falsevalue="" checked="false"
            label="Set to Yes if object is white and background black, otherwise set to No" />
        <param name="threshold" type="float" value="0.5" label="Threshold value" />
        <param name="offset_x" type="integer" value="0" label="Added offset in x direction (=width direction)" />
        <param name="offset_y" type="integer" value="0" label="Added offset in y direction (=height direction)" />
    </inputs>
    <outputs>
       <data format="tabular" name="pixel_table" />
    </outputs>
    <tests>
        <test>
            <param name="im" value="test.png"/>
            <param name="white_obj" value="true"/>
            <output name="pixel_table" value="table.tsv" ftype="tabular"/>
        </test>
        <test>
            <param name="im" value="test.png"/>
            <param name="white_obj" value="true"/>
            <param name="offset_x" value="1"/>
            <param name="offset_y" value="2"/>
            <output name="pixel_table" value="table2.tsv" ftype="tabular"/>
        </test>
    </tests>
    <help>
    **What it does**

    This tool creates a table containing the pixelcoordinates of the Region of Interest (ROI).
    </help>
    <citations>
        <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation>
    </citations>
</tool>