annotate points2binaryimage.xml @ 5:5411384e5e1d draft default tip

planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2binaryimage/ commit 6fc9ab8db9ef72ac7ded30d7373768feeae9390d

<tool id="ip_points_to_binaryimage" name="Convert point coordinates to binary image" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05">
    <description></description>
    <macros>
        <import>creators.xml</import>
        <import>tests.xml</import>
        <token name="@TOOL_VERSION@">0.3</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>
    </requirements>
    <command detect_errors="aggressive"><![CDATA[

        python '$__tool_directory__/points2binaryimage.py'
        '$input'
        '$output'
        $shapex
        $shapey
        $has_header
        $swap_xy

    ]]></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="false" truevalue="--has_header True" falsevalue="" optional="true" label="Tabular list of points has header" /> 
        <param name="swap_xy" type="boolean" checked="false" falsevalue="" truevalue="--swap_xy True" optional="true" label="Swap X and Y coordinates" />
    </inputs>
    <outputs>
        <data name="output" format="tiff" />
    </outputs>
    <tests>
        <!-- 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" />
            <expand macro="tests/binary_image_diff" name="output" value="output1.tif" ftype="tiff" />
        </test>
        <!-- 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" />
            <expand macro="tests/binary_image_diff" name="output" value="output2.tif" ftype="tiff" />
        </test>
    </tests>
    <help>

        **Converts a tabular list of points to a binary image 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 value 65535 (white).
        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.

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