<tool id="ip_points_to_label" name="Convert point coordinates to label map" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05">
    <description></description>
    <macros>
        <import>creators.xml</import>
        <import>tests.xml</import>
        <token name="@TOOL_VERSION@">0.4</token>
        <token name="@VERSION_SUFFIX@">0</token>
    </macros>
    <creator>
        <expand macro="creators/bmcv" />
    </creator>
    <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="0.21">scikit-image</requirement> 
        <requirement type="package" version="1.26.4">numpy</requirement>
        <requirement type="package" version="1.2.4">pandas</requirement>
        <requirement type="package" version="2024.6.18">tifffile</requirement>
        <requirement type="package" version="0.3.1">giatools</requirement> 
    </requirements>
    <command detect_errors="aggressive"><![CDATA[

        python '$__tool_directory__/points2label.py'
        '$input'
        '$output'
        $shapex
        $shapey
        $has_header
        $swap_xy
        $binary

    ]]></command>
    <inputs> 
        <param name="input" type="data" format="tabular" label="Tabular list of points"/> 
        <param name="shapex" type="integer" value="500" min="1" label="Width of output image" />
        <param name="shapey" type="integer" value="500" min="1" label="Height of output image" />
        <param name="has_header" type="boolean" checked="true" truevalue="--has_header True" falsevalue="" optional="true" label="Tabular list of points has header" help="Turning this off will ignore the first row and assume that the X and Y coordinates correspond to the first and second column, respectively." /> 
        <param name="swap_xy" type="boolean" checked="false" falsevalue="" truevalue="--swap_xy True" optional="true" label="Swap X and Y coordinates" help="Swap the X and Y coordinates, regardless of whether the tabular list has a header or not." />
        <param name="binary" type="boolean" checked="false" truevalue="--binary True" falsevalue="" optional="true" label="Produce binary image" help="Use the same label for all points (65535)." /> 
    </inputs>
    <outputs>
        <data name="output" format="tiff" />
    </outputs>
    <tests>
        <!-- Binary / TSV without header -->
        <test>
            <param name="input" value="input1.tsv" />
            <param name="shapex" value="30" />
            <param name="shapey" value="20" />
            <param name="has_header" value="false" />
            <param name="swap_xy" value="true" />
            <param name="binary" value="true" />
            <expand macro="tests/binary_image_diff" name="output" value="output1_binary.tif" ftype="tiff" />
        </test>
        <!-- Binary / TSV with header -->
        <test>
            <param name="input" value="input2.tsv" />
            <param name="shapex" value="205" />
            <param name="shapey" value="84" />
            <param name="has_header" value="true" />
            <param name="swap_xy" value="false" />
            <param name="binary" value="true" />
            <expand macro="tests/binary_image_diff" name="output" value="output2_binary.tif" ftype="tiff" />
        </test>
        <!-- Labeled / TSV with header -->
        <test>
            <param name="input" value="input2.tsv" />
            <param name="shapex" value="205" />
            <param name="shapey" value="84" />
            <param name="has_header" value="true" />
            <param name="swap_xy" value="false" />
            <param name="binary" value="false" />
            <expand macro="tests/label_image_diff" name="output" value="output2.tif" ftype="tiff" />
        </test>
        <!-- Binary / TSV with header / TSV with labels -->
        <test>
            <param name="input" value="input3.tsv" />
            <param name="shapex" value="200" />
            <param name="shapey" value="100" />
            <param name="has_header" value="true" />
            <param name="swap_xy" value="false" />
            <param name="binary" value="true" />
            <expand macro="tests/binary_image_diff" name="output" value="output3_binary.tif" ftype="tiff" />
        </test>
        <!-- Labeled / TSV with header / TSV with labels -->
        <test>
            <param name="input" value="input3.tsv" />
            <param name="shapex" value="200" />
            <param name="shapey" value="100" />
            <param name="has_header" value="true" />
            <param name="swap_xy" value="false" />
            <param name="binary" value="false" />
            <expand macro="tests/label_image_diff" name="output" value="output3.tif" ftype="tiff" />
        </test>
    </tests>
    <help>

        **Converts a tabular list of points to a label map by rasterizing the point coordinates.**

        The created image is a single-channel image with 16 bits per pixel (unsigned integer). The points are
        rasterized with unique labels, or the value 65535 (white) for binary image output. Pixels not corresponding to
        any points in the tabular file are assigned the value 0 (black).

        The tabular list of points can either be header-less. In this case, the first and second columns are expected
        to be the X and Y coordinates, respectively. Otherwise, if a header is present, it is searched for the
        following column names:

        - ``pos_x`` or ``POS_X``: This column corresponds to the X coordinates.
        - ``pos_y`` or ``POS_Y``: This column corresponds to the Y coordinates.
        - If a ``radius`` or ``RADIUS`` column is present, then the points will be rasterized as circles of the
          corresponding radii.
        - If a ``label`` or ``LABEL`` column is present, then the corresponding labels will be used for rasterization
          (unless "Produce binary image" is activated). Different points are allowed to use the same label.

    </help>
    <citations>
        <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation> 
    </citations>
</tool>