<macros>
    <token name="@TOOL_VERSION@">2.1.0</token>
    <token name="@VERSION_SUFFIX@">2</token>
    <token name="@PROFILE@">20.01</token>

    <xml name="scimap_requirements">
        <requirements>
            <container type="docker">quay.io/goeckslab/scimap:@TOOL_VERSION@</container>
            <yield />
        </requirements>
    </xml>

    <xml name="macro_stdio">
        <stdio>
            <exit_code range="1:" level="fatal" description="Error occurred. Please check Tool Standard Error" />
        </stdio>
    </xml>
    <xml name="citations">
        <citations>
            <citation type="doi">10.1158/2159-8290.CD-21-1357</citation>
        </citations>
    </xml>
    <xml name="scimap_spatial_options" token_label="spatial_aggregate">
        <section name="options" title="Advanced Options" expanded="false">
            <param argument="x_coordinate" type="text" value="X_centroid" optional="false" label="Column name containing the x-coordinates values" />
            <param argument="y_coordinate" type="text" value="Y_centroid" optional="false" label="Column name containing the y-coordinates values" />
            <yield/>
            <param argument="imageid" type="text" value="imageid" optional="true" label="Column name of the column containing the image id" />
            <param argument="subset" type="text" value="" optional="true" label="Imageid of a single image to be subsetted for analyis" />
            <param argument="label" type="text" value="@LABEL@" optional="true" label="Key for the returned data" help="Stored in adata.obs" />
        </section>
    </xml>
</macros>