<tool id="ip_split_image" name="Split image along axes" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05">
    <description>with NumPy</description>
    <macros>
        <import>creators.xml</import>
        <import>tests.xml</import>
        <token name="@TOOL_VERSION@">2.3.5</token>
        <token name="@VERSION_SUFFIX@">1</token>
    </macros>
    <creator>
        <expand macro="creators/bmcv"/>
        <expand macro="creators/kostrykin"/>
    </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="@TOOL_VERSION@">numpy</requirement>
        <requirement type="package" version="0.7.3">giatools</requirement>
    </requirements>
    <required_files>
        <include type="glob" path="*.py"/>
    </required_files>
    <command detect_errors="aggressive"><![CDATA[

        mkdir output &&
        python '$__tool_directory__/split.py'

        '$input'
        '$axis'
        output

        $offset
        $step
        $squeeze

        #if str($count) != ""
            --count $count
        #end if

    ]]></command>
    <inputs>
        <param name="input" type="data" format="tiff,png" label="Image to split"/>
        <param name="axis" type="select" label="Axis to split along">
            <option value="T">T-axis (split the frames of a temporal image sequence)</option>
            <option value="Z">Z-axis (split the slices of a 3-D image or image sequence)</option>
            <option value="C" selected="true">C-axis (split the channels of an image or image sequence)</option>
            <option value="S">S-axis (split the samples of an image or image sequence)</option>
            <option value="Q">Q-axis (other or unknown axis)</option>
            <option value="">Split dataset that contains multiple images (e.g., multi-series TIFF)</option>
        </param>
        <param name="squeeze" type="boolean" checked="false" truevalue="--squeeze" falsevalue="" label="Squeeze result images"
               help="Only non-singleton axes (axes with more than one element) will be retained in the result images. This does not apply for the X and Y axes which always are retained."/>
        <param name="offset" type="integer" value="0" min="0" label="Offset"
               help="Number of slices to skip at the beginning."/>
        <param name="step" type="integer" value="1" min="1" label="Step"
               help="Number of slices between extracted images (each slice is extracted for a value of 1, each second slice is extracted for a value of two, and so on)."/>
        <param name="count" type="integer" optional="true" min="1" label="Count"
               help="Maximum number of slices to extract."/>
    </inputs>
    <outputs>
        <collection type="list" name="output" label="Split ${on_string} along ${axis} axis">
            <discover_datasets directory="output" pattern="__name__" format="tiff"/>
        </collection>
    </outputs>
    <tests>

        <!-- PNG tests -->
        <test>
            <param name="input" value="rgb1.png" />
            <param name="axis" value="C" />
            <param name="squeeze" value="false" />
            <output_collection name="output" type="list" count="3">
                <expand macro="tests/intensity_image_diff/element" name="1.tiff" value="rgb1_r.tiff" ftype="tiff"/>
                <expand macro="tests/intensity_image_diff/element" name="2.tiff" value="rgb1_g.tiff" ftype="tiff"/>
                <expand macro="tests/intensity_image_diff/element" name="3.tiff" value="rgb1_b.tiff" ftype="tiff"/>
            </output_collection>
            <assert_stdout>
                <has_line line="Input image axes: YXC"/>
                <has_line line="Input image shape: (32, 32, 3)"/>
                <has_line line="Writing 3 out of 3 image(s)"/>
                <has_line line="Output axes: YXC"/>
                <has_line line="Output shape: (32, 32, 1)"/>
            </assert_stdout>
        </test>
        <test>
            <param name="input" value="rgb1.png" />
            <param name="axis" value="" />
            <param name="squeeze" value="false" />
            <output_collection name="output" type="list" count="1">
                <expand macro="tests/intensity_image_diff/element" name="1.tiff" value="rgb1.tiff" ftype="tiff"/>
            </output_collection>
            <assert_stdout>
                <has_line line="Found 1 image(s) in file"/>
                <has_line line="Writing 1 out of 1 image(s)"/>
                <has_line line="Output axes: YXC"/>
                <has_line line="Output shape: (32, 32, 3)"/>
            </assert_stdout>
        </test>

        <!-- TIFF tests -->
        <test>
            <param name="input" value="zcyx.tiff"/>
            <param name="axis" value="Z"/>
            <param name="squeeze" value="false"/>
            <param name="offset" value="9"/>
            <param name="step" value="2"/>
            <param name="count" value="5"/>
            <output_collection name="output" type="list" count="5">
                <expand macro="tests/intensity_image_diff/element" name="10.tiff" value="zcyx_slice10.tiff" ftype="tiff"/>
                <expand macro="tests/intensity_image_diff/element" name="18.tiff" value="zcyx_slice18.tiff" ftype="tiff"/>
            </output_collection>
            <assert_stdout>
                <has_line line="Input image axes: ZCYX"/>
                <has_line line="Input image shape: (25, 2, 50, 50)"/>
                <has_line line="Writing 5 out of 25 image(s)"/>
                <has_line line="Output axes: ZCYX"/>
                <has_line line="Output shape: (1, 2, 50, 50)"/>
            </assert_stdout>
        </test>
        <test>
            <param name="input" value="qyx.tiff" />
            <param name="axis" value="Q" />
            <param name="squeeze" value="false" />
            <output_collection name="output" type="list" count="2">
                <expand macro="tests/intensity_image_diff/element" name="1.tiff" value="qyx_q1.tiff" ftype="tiff"/>
                <expand macro="tests/intensity_image_diff/element" name="2.tiff" value="qyx_q2.tiff" ftype="tiff"/>
            </output_collection>
            <assert_stdout>
                <has_line line="Input image axes: QYX"/>
                <has_line line="Input image shape: (2, 256, 256)"/>
                <has_line line="Writing 2 out of 2 image(s)"/>
                <has_line line="Output axes: QYX"/>
                <has_line line="Output shape: (1, 256, 256)"/>
            </assert_stdout>
        </test>
        <test>
            <param name="input" value="qyx.tiff" />
            <param name="axis" value="" />
            <param name="squeeze" value="false" />
            <output_collection name="output" type="list" count="1">
                <expand macro="tests/intensity_image_diff/element" name="1.tiff" value="qyx.tiff" ftype="tiff"/>
            </output_collection>
            <assert_stdout>
                <has_line line="Found 1 image(s) in file"/>
            </assert_stdout>
        </test>

        <!-- Test splitting multi-series TIFF -->
        <test>
            <param name="input" value="multiseries.ome.tiff" />
            <param name="axis" value="" />
            <param name="squeeze" value="false" />
            <output_collection name="output" type="list" count="6">
                <expand macro="tests/intensity_image_diff/element" name="1.tiff" value="multiseries_series1.tiff" ftype="tiff"/>
                <expand macro="tests/intensity_image_diff/element" name="6.tiff" value="multiseries_series6.tiff" ftype="tiff"/>
            </output_collection>
            <assert_stdout>
                <has_line line="Found 6 image(s) in file"/>
                <has_line line="Writing 6 out of 6 image(s)"/>
                <has_line line="Output 1 axes: CYX"/>
                <has_line line="Output 1 shape: (4, 5, 5)"/>
                <has_line line="Output 2 axes: CYX"/>
                <has_line line="Output 2 shape: (4, 5, 5)"/>
                <has_line line="Output 3 axes: CYX"/>
                <has_line line="Output 3 shape: (4, 5, 5)"/>
                <has_line line="Output 4 axes: CYX"/>
                <has_line line="Output 4 shape: (4, 5, 5)"/>
                <has_line line="Output 5 axes: CYX"/>
                <has_line line="Output 5 shape: (4, 5, 5)"/>
                <has_line line="Output 6 axes: CYX"/>
                <has_line line="Output 6 shape: (4, 5, 5)"/>
            </assert_stdout>
        </test>

        <!-- Test squeezing -->
        <test>
            <param name="input" value="rgb1.png" />
            <param name="axis" value="C" />
            <param name="squeeze" value="true" />
            <output_collection name="output" type="list" count="3">
                <expand macro="tests/intensity_image_diff/element" name="1.tiff" value="rgb1_squeezed_r.tiff" ftype="tiff"/>
                <expand macro="tests/intensity_image_diff/element" name="2.tiff" value="rgb1_squeezed_g.tiff" ftype="tiff"/>
                <expand macro="tests/intensity_image_diff/element" name="3.tiff" value="rgb1_squeezed_b.tiff" ftype="tiff"/>
            </output_collection>
            <assert_stdout>
                <has_line line="Input image axes: YXC"/>
                <has_line line="Input image shape: (32, 32, 3)"/>
                <has_line line="Writing 3 out of 3 image(s)"/>
                <has_line line="Output axes: YX"/>
                <has_line line="Output shape: (32, 32)"/>
            </assert_stdout>
        </test>

        <!-- Test with missing axes -->
        <test>
            <param name="input" value="rgb1.png" />
            <param name="axis" value="Z" />
            <param name="squeeze" value="false" />
            <output_collection name="output" type="list" count="1">
                <expand macro="tests/intensity_image_diff/element" name="1.tiff" value="rgb1_split_z.tiff" ftype="tiff"/>
            </output_collection>
            <assert_stdout>
                <has_line line="Input image axes: YXC"/>
                <has_line line="Input image shape: (32, 32, 3)"/>
                <has_line line="Writing 1 out of 1 image(s)"/>
                <has_line line="Output axes: YXC"/>
                <has_line line="Output shape: (32, 32, 3)"/>
            </assert_stdout>
        </test>

    </tests>
    <help>

        **Splits an image along a specific axis (e.g., channels).**

        This tool splits an image along a specifc axis and yields a collection of images.
        This can be used, for example, to convert a multi-channel image into a collection of single-channel images.

        The pixel data type of the split image is preserved (will be the same as the input image).

    </help>
    <citations>
        <citation type="doi">10.1038/s41586-020-2649-2</citation>
    </citations>
</tool>