<tool id="ip_binary_to_labelimage" name="Convert binary image to label map" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> 
    <description></description>
    <macros>
        <token name="@TOOL_VERSION@">0.5</token>
        <token name="@VERSION_SUFFIX@">0</token>
    </macros>
    <edam_operations>
        <edam_operation>operation_3443</edam_operation>
    </edam_operations>
    <xrefs>
        <xref type="bio.tools">galaxy_image_analysis</xref>
    </xrefs>
    <requirements>
        <requirement type="package" version="0.14.2">scikit-image</requirement> 
        <requirement type="package" version="0.15.1">tifffile</requirement>
        <requirement type="package" version="1.15.4">numpy</requirement>
        <requirement type="package" version="5.3.0">pillow</requirement>
        <requirement type="package" version="1.2.1">scipy</requirement>
    </requirements>
    <command detect_errors="aggressive">
        <![CDATA[
        #if str($mode.mode_selector) == 'cca':
            python '$__tool_directory__/binary2label.py' '$input' '$output'
        #elif str($mode.mode_selector) == 'watershed':
            python '$__tool_directory__/2d_split_binaryimage_by_watershed.py' '$input' '$output' $min_distance
        #end if
        ]]>
    </command>
    <inputs>
        <param name="input" type="data" format="tiff,png,jpg,bmp" label="Binary image"/>
        <conditional name="mode">
            <param name="mode_selector" type="select" label="Mode">
                <option value="cca">Connected component analysis</option>
                <option value="watershed">Watershed transform</option>
            </param>
            <when value="cca">
            </when>
            <when value="watershed">
                <param name="min_distance" type="integer" min="0" value="5" label="Minimum distance between two objects" />
            </when>
        </conditional>
    </inputs>
    <outputs>
        <data format="tiff" name="output"/>
    </outputs>
    <tests>
        <test>
            <param name="input" value="galaxyIcon_noText.tif" />
            <conditional name="mode">
                <param name="mode_selector" value="cca" />
            </conditional>
            <output name="output" value="label.tif" ftype="tiff" compare="sim_size"/>
        </test>
        <test>
            <param name="input" value="in.tif"/>
            <conditional name="mode">
                <param name="mode_selector" value="watershed" />
                <param name="min_distance" value="10" />
            </conditional>
            <output name="output" value="out.tif" ftype="tiff" compare="sim_size"/>
        </test>
    </tests>
    <help>
    This tool assigns each object a unique label.

    Individual objects are determined using connected component analysis, or distance transform and watershed.
    </help>
    <citations>
        <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation>
    </citations>
</tool>