<tool id="ip_crop_image" name="Crop image" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05"> 
    <description>with giatools</description>
    <macros>
        <import>creators.xml</import>
        <import>tests.xml</import>
        <token name="@TOOL_VERSION@">0.4.1</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">giatools</xref>
    </xrefs>
    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">giatools</requirement>
    </requirements> 
    <command detect_errors="aggressive"><![CDATA[

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

        '$image'
        '$labelmap'
        '$skip_labels'
        '${image.ext}'

        ./output

    ]]></command>
    <inputs>
        <param name="image" type="data" format="png,tiff" label="Image file" help="The image to be cropped."/>
        <param name="labelmap" type="data" format="png,tiff" label="Label map" help="Each label identifies an individual region of interest, for which a cropped image is produced."/>
        <param name="skip_labels" type="text" label="Skip labels" value="0" optional="true" help="Comma-separated list of labels for which no cropped image shall be produced.">
            <validator type="regex">^\d+(,\d+)*$|^$</validator>
        </param>
    </inputs>
    <outputs>
        <collection type="list" name="output" label="Crop ${on_string}" format_source="image">
            <discover_datasets directory="output" pattern="__name_and_ext__"/>
        </collection>
    </outputs>
    <tests>
        <!-- Test 2D TIFF -->
        <test>
            <param name="image" value="yx_float32.tiff" ftype="tiff"/>
            <param name="labelmap" value="yx_uint8.tiff"/>
            <output_collection name="output" type="list" count="2">
                <expand macro="tests/intensity_image_diff/element" name="1" value="yx_float32_uint8_1.tiff" ftype="tiff"/>
                <expand macro="tests/intensity_image_diff/element" name="2" value="yx_float32_uint8_2.tiff" ftype="tiff"/>
            </output_collection>
        </test>
        <!-- Test with `skip_labels` -->
        <test>
            <param name="image" value="yx_float32.tiff" ftype="tiff"/>
            <param name="labelmap" value="yx_uint8.tiff"/>
            <param name="skip_labels" value="0,1"/>
            <output_collection name="output" type="list" count="1">
                <expand macro="tests/intensity_image_diff/element" name="2" value="yx_float32_uint8_2.tiff" ftype="tiff"/>
            </output_collection>
        </test>
        <!-- Test with empty `skip_labels` -->
        <test>
            <param name="image" value="yx_float32.tiff" ftype="tiff"/>
            <param name="labelmap" value="yx_uint8.tiff"/>
            <param name="skip_labels" value=""/>
            <output_collection name="output" type="list" count="3">
                <expand macro="tests/intensity_image_diff/element" name="0" value="yx_float32_uint8_0.tiff" ftype="tiff"/>
                <expand macro="tests/intensity_image_diff/element" name="1" value="yx_float32_uint8_1.tiff" ftype="tiff"/>
                <expand macro="tests/intensity_image_diff/element" name="2" value="yx_float32_uint8_2.tiff" ftype="tiff"/>
            </output_collection>
        </test>
        <!-- Test 3D TIFF (multi-frame) -->
        <test>
            <param name="image" value="zyx_uint16.tiff" ftype="tiff"/>
            <param name="labelmap" value="yxz_uint8.tiff"/>
            <output_collection name="output" type="list" count="1">
                <expand macro="tests/intensity_image_diff/element" name="1" value="zyx_uint16_uint8_1.tiff" ftype="tiff"/>
            </output_collection>
        </test>
        <!-- Test PNG -->
        <test>
            <param name="image" value="yxc_uint8.png" ftype="png"/>
            <param name="labelmap" value="yxc_uint8_mask.png"/>
            <output_collection name="output" type="list" count="1">
                <expand macro="tests/intensity_image_diff/element" name="2" value="yxc_uint8_uint8_2.png" ftype="png"/>
            </output_collection>
        </test>
    </tests>
    <help>

        **Crops an image using one or more regions of interest.**

        The image is cropped using a label map that identifies individual regions of interest. The image and the label map must be of equal size.

        This operation preserves the file type of the image, the brightness, and the range of values.

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