<tool id="mesmer" name="Mesmer" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="19.01">
    <description>Mesmer for whole-cell segmentation of multiplexed tissue imaging data</description>

    <macros>
        <import>macros.xml</import>
    </macros>

    <expand macro="requirements"/>
    <expand macro="version_cmd"/>

    <command detect_errors="exit_code"><![CDATA[
    ln -s '$nuclear_image' 'input.tif' && 
    @CMD_BEGIN@ 
    --output-directory ./
    --output-name 'mask.tif'
    --nuclear-image 'input.tif'
    --nuclear-channel $nuclear_channel
    --compartment $compartment
    --image-mpp $image_mpp
    $squeeze

    #if $membrane_select.membrane_segment == "True":
        --membrane-image '$membrane_select.membrane_image'
        --membrane-channel '$membrane_select.membrane_channel'
    #end if
    ]]></command>

    <inputs>
        <param name="nuclear_image" type="data" format="tiff, ome.tiff" label="Image containing the nuclear marker(s)"/>
        <param name="nuclear_channel" type="integer" value="0" label="The numerical index of the channel(s) from nuclear-image"/>
        <param name="compartment" type="select"  label="Compartment for segmentation prediction: ">
            <option selected="true" value="whole-cell">Whole cell</option>
            <option value="nuclear">Nuclear</option>
        </param>
        <param name="image_mpp" type="float" value="0.5" label="Resolution of the image in microns-per-pixel"/>
        <param name="squeeze" type="boolean" truevalue="--squeeze" falsevalue="" checked="false" label="Whether to np.squeeze the outputs before saving"/>
        <conditional name="membrane_select">
            <param name="membrane_segment" type="select" label="Segment with Cell Membrane">
                <option selected="True" value="False">No</option>
                <option value="True">Yes</option>
            </param>
            <when value="True">
                <param name="membrane_image" type="data" format="tiff, ome.tiff" label="The path to an image containing the membrane marker(s)"/>
                <param name="membrane_channel" type="integer" value="0"  label="The numerical index of the channel(s) from membrane-image"/>
            </when>
            <when value="False" />
        </conditional>
    </inputs>
    <outputs>
        <data format="tiff" name="mask" from_work_dir="mask.tif" label="${tool.name} on ${on_string}: Mask"/>
    </outputs>
    <tests>
        <test>
            <param name="nuclear_image" value="test.tiff" />
            <param name="compartment" value="nuclear" />
            <param name="membrane_select.membrane_segment" value="False" />
            <param name="image_mmp" value="0.65" />
            <param name="squeeze" value="--squeeze" />
            <output name="mask" ftype="tiff">
                <assert_contents>
                    <has_size value="360000" delta="1000" />
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[
------
Mesmer
------

**Mesmer** is a DeepCell application that uses a pre-trained model for predicting nuclear and whole cell segmentation from multiplex tissue data.

**Inputs**
1. a multiple tissue image that includes a nuclear marker and optionally cytoplasm/membrane markers
        
**Outputs**
1. the nuclear or whole cell segmentation mask 
    ]]></help>
    <expand macro="citations" />
</tool>