<tool id="woundhealing_scratch_assay" name="Wound healing scratch assay" version="@VERSION@+galaxy1" profile="23.1">
    <description>image analysis</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command detect_errors="aggressive">
    <![CDATA[
    mkdir -p ./input &&

    #if $con_input_type.input_type =="yes"
        tar -C ./input -xvf $con_input_type.input_images &&
    #else
        #for $i, $filename in enumerate($con_input_type.input_images):
            ln -s '$filename' './input/${filename.element_identifier}' &&
        #end for
    #end if
    ImageJ --ij2 --headless
    --run '$__tool_directory__/measureWoundClosing.groovy'
    'inputDir="./input",datasetId="$dataset_id",threshold="$threshold",headless="true",saveResults="true",outDirName="./output"'
    ]]>
    </command>
    <inputs>
        <conditional name="con_input_type">
            <param name="input_type" type="select" label="Are the input images packed into a tar archive?">
                <option value="yes">Yes</option>
                <option value="no">No</option>
            </param>
            <when value="no">
                <param name="input_images" type="data" multiple="true" format="@FORMATS@" label="Images" />
            </when>
            <when value="yes">
                <param name="input_images" type="data" format="tar" label="A tarball of images" />
            </when>
        </conditional>
        <param name="dataset_id" type="text" label="Dataset ID" />
        <param name="threshold"  type="text" label="CoV threshold (-1: auto)" value="-1"/>
    </inputs>
    <outputs>
        <data name="tiff_output" format="tiff" from_work_dir="output/*.tiff" label="movie output ${on_string}" />
	<data name="csv_output" format="tabular" from_work_dir="output/*.csv" label="tabular output"/>
    </outputs>
    <tests>
        <test >
            <conditional name="con_input_type">
                <param name="input_type" value="no" />
                <param name="input_images" location="https://github.com/sunyi000/wound-healing-htm-screen/raw/main/assets/data/input/A3ROI2_Slow_0000.tif,https://github.com/sunyi000/wound-healing-htm-screen/raw/main/assets/data/input/A3ROI2_Slow_0002.tif" />
	    </conditional>
	    <param name="dataset_id" value="A3ROI2_Slow" />
	    <output name="tiff_output" location="https://github.com/sunyi000/wound-healing-htm-screen/raw/main/assets/data/A3ROI2_Slow.tif"/>
	    <output name="csv_output" file="A3ROI2_Slow.csv"/>
        </test>
    </tests>
    <help>
        <![CDATA[
            **What it does**
            Automated quantification of wound healing in high-throughput time-lapse transmission microscopy scratch assays.
        ]]>
    </help>
    <expand macro="citations" />
</tool>