<tool id="quantification" name="MCQUANT" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="19.01">
    <description>a module for single-cell data extraction</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <expand macro="version_cmd"/>

    <command detect_errors="aggressive"><![CDATA[
    ln -s '$image' 'input.ome.tiff' &&
    ln -s '$primary_mask' 'primary_mask.tiff' &&
    #if $supp_mask
        ln -s '$supp_mask' 'supp_mask.tiff' &&
    #end if

    mkdir './tool_out' &&

    @CMD_BEGIN@

    --masks 'primary_mask.tiff'
    #if $supp_mask
        'supp_mask.tiff'
    #end if

    --image 'input.ome.tiff'
    --output './tool_out'

    #if str($mask_props).strip()
        --mask_props '$mask_props'
    #end if
    #if str($intensity_props).strip()
        --intensity_props '$intensity_props'
    #end if

    --channel_names '$channel_names' &&

    #if $supp_mask
    mv tool_out/*supp_mask.csv supp_mask.csv &&
    #end if

    mv tool_out/*primary_mask.csv primary_mask.csv
    ]]></command>

    <inputs>
        <param name="image" type="data" format="tiff" label="Registered TIFF"/>
        <param name="primary_mask" type="data" format="tiff" label="Primary Mask"/>
        <param name="supp_mask" type="data" optional="true" format="tiff" label="Additional Mask"/>
        <param name="channel_names" type="data" format="csv" label="Marker Channels"/>
        <param name="mask_props" type="text" label="Mask Metrics" help="Space separated list of additional metrics to be calculated for every mask."/>
        <param name="intensity_props" type="text" label="Intensity Metrics" help="Space separated list of additional metrics to be calculated for every marker separately."/>
    </inputs>

    <outputs>
        <data format="csv" name="cellmask" from_work_dir="primary_mask.csv" label="Primary Mask Quantification"/>
        <data format="csv" name="suppmask" from_work_dir="supp_mask.csv" label="Supplemental Mask Quantification">
            <filter>supp_mask</filter>
        </data>
     </outputs>
     <tests>
        <test>
            <param name="image" value="test.tiff" />
            <param name="primary_mask" value="mask.tiff" />
            <param name="supp_mask" value="supp_mask.tiff" />
            <param name="channel_names" value="channels.csv" />
            <output name="cellmask" ftype="csv">
                <assert_contents>
                    <has_n_lines n="264" delta="1" />
                </assert_contents>
            </output>
            <output name="suppmask" ftype="csv">
                <assert_contents>
                    <has_n_lines n="264" delta="1" />
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[
    
--------
MCQUANT
--------
**MCQUANT** module for single cell quantification given a segmentation mask and multi-channel image. The CSV structure is aligned with histoCAT output.

**Inputs**
1. A fully stitched and registered image in .ome.tif format. Nextflow will use images in the registration/ and dearray/ subfolders as appropriate.
2. One or more segmentation masks in .tif format. Nextflow will use files in the segmentation/ subfolder within the project.
3. A .csv file containing a marker_name column specifying names of individual channels. Nextflow will look for this file in the project directory.

**Outputs**
A cell-by-feature table mapping Cell IDs to marker expression and morphological features (including x,y coordinates).

    ]]></help>
    <expand macro="citations" />
</tool>