comparison points2label.xml @ 5:dc91192a7150 draft default tip

planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit edac062b00490276ef00d094e0594abdb3a3f23c

4:64c155acb864

<tool id="ip_points_to_label" name="Convert 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@">0.4.1</token>
        <token name="@VERSION_SUFFIX@">1</token>
    </macros>
    <creator>
        <expand macro="creators/bmcv" />
    </creator>
    <edam_operations>

    </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,geojson" label="List of points in tabular or geojson format"/>
        <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. Ignored, if GeoJSON is used for input." />
        <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>

            <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="output4.tiff" ftype="tiff" />
        </test>
        <!-- Labeled / ROI / Rectangles -->
        <test>
            <param name="input" value="rois.geojson" />
            <param name="shapex" value="300" />
            <param name="shapey" value="300" />
            <param name="has_header" value="false" />
            <param name="swap_xy" value="false" />
            <param name="binary" value="false" />
            <expand macro="tests/label_image_diff" name="output" value="output5.tiff" ftype="tiff" />
        </test>
        <test>
            <param name="input" value="rois-noname.geojson" />
            <param name="shapex" value="300" />
            <param name="shapey" value="300" />
            <param name="has_header" value="false" />
            <param name="swap_xy" value="false" />
            <param name="binary" value="false" />
            <expand macro="tests/label_image_diff" name="output" value="output5.tiff" ftype="tiff" />
        </test>
        <test>
            <param name="input" value="rois.geojson" />
            <param name="shapex" value="300" />
            <param name="shapey" value="300" />
            <param name="has_header" value="false" />
            <param name="swap_xy" value="true" />
            <param name="binary" value="false" />
            <expand macro="tests/label_image_diff" name="output" value="output6.tiff" ftype="tiff" />
        </test>
        <test expect_failure="true">
            <!-- The test should fail because the GeoJSON is not rectangular -->
            <param name="input" value="rois-illegal1.geojson" />
            <param name="shapex" value="300" />
            <param name="shapey" value="300" />
            <param name="has_header" value="false" />
            <param name="swap_xy" value="false" />
            <param name="binary" value="false" />
        </test>
        <test expect_failure="true">
            <!-- The test should fail because the GeoJSON is not of `Polygon` type -->
            <param name="input" value="rois-illegal2.geojson" />
            <param name="shapex" value="300" />
            <param name="shapey" value="300" />
            <param name="has_header" value="false" />
            <param name="swap_xy" value="false" />
            <param name="binary" value="false" />
        </test>
    </tests>
    <help>

        **Converts a list of points to a label map by rasterizing the 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).

        **Using a tabular input file:** 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 ``width`` or ``WIDTH`` and ``height`` or ``HEIGHT`` columns are present, then the points will be rasterized
          as rectangles of the corresponding size.
        - 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. If used, the
          label must be numeric and integer.

        **Using a GeoJSON input file:** Only rectangular specifications of `Polygon` type geometry is supported.

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

5:dc91192a7150

<tool id="ip_points_to_label" name="Convert coordinates to label map" version="@TOOL_VERSION@" profile="20.05">
    <description></description>
    <macros>
        <import>creators.xml</import>
        <import>tests.xml</import>
        <token name="@TOOL_VERSION@">0.5.0</token>
    </macros>
    <creator>
        <expand macro="creators/bmcv" />
    </creator>
    <edam_operations>

    </edam_operations>
    <xrefs>
        <xref type="bio.tools">galaxy_image_analysis</xref>
    </xrefs>
    <requirements>
        <requirement type="package" version="0.25.2">scikit-image</requirement>
        <requirement type="package" version="2.3.4">numpy</requirement>
        <requirement type="package" version="2.3.3">pandas</requirement>
        <requirement type="package" version="2025.10.16">tifffile</requirement>
        <requirement type="package" version="0.3.1">giatools</requirement>
    </requirements>
    <command detect_errors="aggressive"><![CDATA[

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

    ]]></command>
    <inputs>
        <param name="input" type="data" format="tabular,geojson" label="Shapes to be rasterized"/>
        <param name="shapex" type="integer" value="500" min="1" label="Width of the output image" />
        <param name="shapey" type="integer" value="500" min="1" label="Height of the output image" />
        <param name="has_header" type="boolean" checked="true" truevalue="--has_header True" falsevalue="" optional="true" label="Tabular list of shapes has header" help="Only used if the input is a tabular file (ignored for GeoJSON). Turning this off will interpret the tabular file as a list of points, where 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 before rasterization. The width and height of the output image is not affected." />
        <param name="binary" type="boolean" checked="false" truevalue="--binary True" falsevalue="" optional="true" label="Produce binary image" help="Use the same label for all shapes (65535)." />
    </inputs>
    <outputs>
        <data name="output" format="tiff" />
    </outputs>
    <tests>

            <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="output4.tiff" ftype="tiff" />
        </test>
        <!-- Labeled / TSV with header / TSV with labels / Circles + Rectangles -->
        <test>
            <param name="input" value="input5.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="output8.tiff" ftype="tiff" />
        </test>
        <test expect_failure="true">
            <!-- The test should fail because simultaneous usage of radius and width/height on a row is forbidden -->
            <param name="input" value="input6.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" />
            <assert_stderr>
                <has_text text="Ambiguous shape type (circle or rectangle)" />
            </assert_stderr>
        </test>
        <!-- Labeled / GeoJSON / mixed name and no-name -->
        <test>
            <param name="input" value="rois.geojson" />
            <param name="shapex" value="300" />
            <param name="shapey" value="300" />
            <param name="has_header" value="false" />
            <param name="swap_xy" value="false" />
            <param name="binary" value="false" />
            <expand macro="tests/label_image_diff" name="output" value="output5.tiff" ftype="tiff" />
        </test>
        <test>
            <param name="input" value="rois.geojson" />
            <param name="shapex" value="300" />
            <param name="shapey" value="300" />
            <param name="has_header" value="false" />
            <param name="swap_xy" value="true" />
            <param name="binary" value="false" />
            <expand macro="tests/label_image_diff" name="output" value="output6.tiff" ftype="tiff" />
        </test>
        <!-- Labeled / GeoJSON / no-name -->
        <test>
            <param name="input" value="rois-noname.geojson" />
            <param name="shapex" value="300" />
            <param name="shapey" value="300" />
            <param name="has_header" value="false" />
            <param name="swap_xy" value="false" />
            <param name="binary" value="false" />
            <expand macro="tests/label_image_diff" name="output" value="output7.tiff" ftype="tiff" />
        </test>
        <test expect_failure="true">
            <!-- The test should fail because the GeoJSON uses the `LineString` primitive type that is not supported yet -->
            <param name="input" value="rois-illegal2.geojson" />
            <param name="shapex" value="300" />
            <param name="shapey" value="300" />
            <param name="has_header" value="false" />
            <param name="swap_xy" value="false" />
            <param name="binary" value="false" />
            <assert_stderr>
                <has_text text='Unsupported geometry type: "LineString"' />
            </assert_stderr>
        </test>
    </tests>
    <help>

        **Converts a list of shapes to a label map via rasterization.**

        The created image is a single-channel image with 16 bits per pixel (unsigned integers). The shapes are
        rasterized with unique labels, explicitly given labels (custom), or the value 65535 (white) for binary image
        output. Pixels not corresponding to any shapes are assigned the value 0 (black).

        **Using a GeoJSON input file (recommended).** Only features (shape specifications) of `Polygon` and `Point`
        type are supported. In conjunction with the `radius` property, a `Point` type feature can also be used to
        represent circles. Custom labels can be encoded in the `name` property (must be numeric and integer), and
        different features are allowed to use the same labels.

        **Using a tabular input file (deprecated).** 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, and each row
        corresponds to a single point. Otherwise, if a header is present, it is searched for the following column
        names:

        - Column ``pos_x`` or ``POS_X`` is mandatory and corresponds to the X coordinates.
        - Column ``pos_y`` or ``POS_Y`` is mandatory and corresponds to the Y coordinates.
        - If a ``radius`` or ``RADIUS`` column is present and the value in a row is positive, then the row will be
          rasterized as a circle of the corresponding size, centered at the given X and Y coordinates.
        - If ``width`` or ``WIDTH`` and ``height`` or ``HEIGHT`` columns are present and the values in a row are
          positive, then the rows will be rasterized as rectangles of the corresponding size, with the upper-left
          corner given by the X and Y coordinates.
        - If a ``label`` or ``LABEL`` column is present, then the corresponding labels will be used for rasterization
          (unless "Produce binary image" is activated). Different rows are allowed to use the same label. If used,
          the label must be numeric and integer.

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