<?xml version="1.0"?>
<macros>
    <xml name="requirements">
        <requirements>
            <container type="docker">quay.io/goeckslab/deepcell:@TOOL_VERSION@</container>
        </requirements>
    </xml>
    <xml name="stdio">
        <stdio>
            <regex match="MemoryError"
               source="both"
               level="fatal_oom"
               description="Out of Memory" />
            <regex match="std::bad_alloc"
               source="both"
               level="fatal_oom"
               description="Out of Memory" />
            <regex match="java.lang.OutOfMemoryError"
               source="both"
               level="fatal_oom"
               description="Out of Memory" />
            <regex match="Out of memory"
               source="both"
               level="fatal_oom"
               description="Out of Memory" />
        </stdio>
    </xml>

    <xml name="watershed_adv_options">
        <param name="maxima_smooth" type="integer" value="0"  label="Maxima Smooth"/>
        <param name="interior_threshold" type="float" value="0.2"  label="Interior Threshold"/>
        <param name="interior_smooth" type="integer" value="2"  label="Interior Smooth"/>
        <param name="small_objects_threshold" type="integer" value="15"  label="Small Objects Threshold"/>
        <param name="fill_holes_threshold" type="integer" value="15"  label="Fill Holes Threshold"/>
        <param name="radius" type="integer" value="1"  label="Radius"/>
    </xml>

    <xml name="nuclear_options_macro">
        <section name="nuclear_options" title="Nuclear Options" expanded="true">   
            <param name="pixel_expansion" type="integer" optional="true"  label="Number of pixels to expand nucleus"/>
            <param name="maxima_threshold" type="float" value="0.1"  label="Maxima Threshold"/>
            <section name="adv_options" title="Advanced Nuclear Options" expanded="false">
                <expand macro="watershed_adv_options"/>
            </section>
        </section>
    </xml>

    <xml name="wc_options_macro">
        <section name="wc_options" title="Whole Cell Options" expanded="true"> 
            <param name="wc_channels" type="text" value="1"  label="The numerical indices of the channel(s) for the membrane markers" help="No quotes, separated by comma. e.g. 0, 1."/>
            <param name="maxima_threshold" type="float" value="0.075"  label="Maxima Threshold"/>
            <section name="adv_options" title="Advanced Whole Cell Options" expanded="false">
                <expand macro="watershed_adv_options"/>
            </section>
        </section>
    </xml>

    <xml name="citations">
        <citations>
            <citation type="doi">10.1038/s41587-021-01094-0</citation>
        </citations>
    </xml>

    <token name="@TOOL_VERSION@">0.12.3</token>
    <token name="@VERSION_SUFFIX@">3</token>
</macros>