<macros>
    <token name="@TOOL_VERSION@">1.3.0</token>
    <token name="@VERSION_SUFFIX@">2</token>
    <token name="@PROFILE@">23.0</token>
    <xml name="requirements">
        <requirements>
            <container type="docker">quay.io/bgruening/vpt:1.3.0-1</container>
            <yield/>
        </requirements>
    </xml>
    <xml name="creator">
        <creator>
            <organization name="European Galaxy Team" url="https://galaxyproject.org/eu/" />
            <person givenName="Amirhossein" familyName="Naghsh Nilchi" email="nilchia@informatik.uni-freiburg.de" />
            <person givenName="Pavan" familyName="Videm" email="videmp@informatik.uni-freiburg.de" />
            <person givenName="Björn" familyName="Grüning" email="gruening@informatik.uni-freiburg.de" />
        </creator>
    </xml>
    <token name="@CMD@"><![CDATA[
        mkdir -p 'input/images' 'output/' &&
        #for $image in $input_images:
            ln -s '$image' 'input/images/${image.element_identifier}.${image.ext}' &&
        #end for
        ln -s '$input_micron_to_mosaic' 'input/micron_to_mosaic_pixel_transform.csv' &&
        ]]></token>
    <token name="@COMMON_ARGS@"><![CDATA[
        --processes \${GALAXY_SLOTS:-10}
        --verbose
        --log-file 'output/log'
    ]]>
    </token>
    <xml name="common_input">
        <param argument="--input_images" type="data" format="tiff" multiple="true" label="MEROSCOPE tiff images"/>
        <param argument="--input_micron_to_mosaic" type="data" format="csv" label="Micron to mosaic mapping file"/>
    </xml>
    <xml name="normalization_param" token_label="Normalization">
        <param name="normalization" type="select" label="@LABEL@">
            <option value="default">default (min-max range normalization)</option>
            <option value="CLAHE">CLAHE (Contrast Limited Adaptive Histogram Equalization)</option>
        </param>
    </xml>
    <xml name="channel_options_basic">
            <yield/>
            <option value="Cellbound1">Cellbound1</option>
            <option value="Cellbound2">Cellbound2</option>
            <option value="Cellbound3">Cellbound3</option>
        </xml>
    <xml name="channel_options_none">
        <expand macro="channel_options_basic">
            <option value="None" selected="true">None</option>
            <option value="DAPI">DAPI</option>
            <option value="PolyT">PolyT</option>
            <yield/>
        </expand>
</xml>
    <xml name="advanced_output">
        <section name="advanced_output" title="Advanced output options">
            <param name="log" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Output log?"/>
        </section>
    </xml>
    <xml name="common_output">
        <data name="vpt_log" format="txt" from_work_dir="output/log" label="${tool.name} on ${on_string}: VPT log">
            <filter>advanced_output['log']</filter>
        </data>
    </xml>
    <xml name="task_input_data">
        <conditional name="normalize_conditional">
            <param name="normalize_select" type="select" label="Perform Normalization?">
                <option value="Yes" selected="true">Yes</option>
                <option value="No">No</option>
            </param>
            <when value="Yes">
                <conditional name="normalize_type_conditional" label="Select normalization method">
                    <expand macro="normalization_param"/>
                    <when value="default"/>
                    <when value="CLAHE">
                        <param name="clip_limit" type="float" min="0" max="1" value="0.01" label="Clip limit" help="higher values give more contrast"/>
                        <param name="filter_size" type="integer" min="1" value="100" label="Tile grid size"/>
                    </when>
                </conditional>
            </when>
            <when value="No"/>
        </conditional>
        <conditional name="blur_conditional">
            <param name="blur_select" type="select" label="Perform Blur?">
                <option value="Yes">Yes</option>
                <option value="No" selected="true">No</option>
            </param>
            <when value="Yes">
                <param name="blur_options" type="select" label="Blur options">
                    <option value="average">average</option>
                    <option value="median">median</option>
                    <option value="gaussian">gaussian</option>
                </param>
                <param name="kernel_size" type="integer" min="0" value="5" label="Kernel size in pixel"/>
            </when>
            <when value="No"/>
        </conditional>
        <conditional name="downsample_conditional">
            <param name="downsample_select" type="select" label="Perform downsample?">
                <option value="Yes">Yes</option>
                <option value="No" selected="true">No</option>
            </param>
            <when value="Yes">
                <param name="scale" type="float" min="0" value="2.0" label="Downsample" help="Reduces the size of the images during segmentation to decrease processing time" />
            </when>
            <when value="No"/>
        </conditional>
    </xml>
    <xml name="channel_map_conditional_childs">
        <when value="None"/>
        <when value="DAPI">
            <expand macro="task_input_data"/>
        </when>
        <when value="PolyT">
            <expand macro="task_input_data"/>
        </when>
        <when value="Cellbound1">
            <expand macro="task_input_data"/>
        </when>
        <when value="Cellbound2">
            <expand macro="task_input_data"/>
        </when>
        <when value="Cellbound3">
            <expand macro="task_input_data"/>
        </when>
    </xml>
    <xml name="sanitize_digits">
        <sanitizer invalid_char="">
            <valid initial="string.digits">
                <add value=","/>
                <add value="."/>
            </valid>
       </sanitizer>
    </xml>
    <xml name="citations">
        <citations>
            <citation type="bibtex">@Manual{github,
                title = {Vizgen Post-processing Tool},
                author = {Vizgen},
                organization = {Vizgen},
                year = {2022},
                url = {https://github.com/Vizgen/vizgen-postprocessing}}
            </citation>
        </citations>
    </xml>
</macros>