<?xml version="1.0"?>
<macros>
    <xml name="requirements">
        <requirements>
            <container type="docker">labsyspharm/basic-illumination:@TOOL_VERSION@</container>
        </requirements>
    </xml>

    <xml name="version_cmd">
        <version_command>echo @TOOL_VERSION@</version_command>
    </xml>
    <xml name="citations">
        <citations>
            <citation type="doi">10.1038/ncomms14836</citation>
        </citations>
    </xml>

    <token name="@TOOL_VERSION@">1.1.1</token>
    <token name="@VERSION_SUFFIX@">2</token>
    <token name="@PROFILE@">19.01</token>
    <token name="@CMD_BEGIN@"><![CDATA[
        ## if ImageJ isn't already present, this is the docker-dependency version
        ## as such, ImageJ needs to be registered as a global executable on $PATH

        if ! [ -x "\$(which ImageJ)" ]; then
	    ln -sf "\$(which ImageJ-linux64)" "ImageJ";
            export PATH="\$PATH:\$(pwd)/";
        fi &&

        BASIC_SCRIPT="" &&
        if [ -f "/opt/fiji/imagej_basic_ashlar.py" ]; then
            export BASIC_SCRIPT="/opt/fiji/imagej_basic_ashlar.py";
        else
            export BASIC_SCRIPT="${__tool_directory__}/imagej_basic_ashlar.py";
        fi &&

        ImageJ --ij2 --headless --run \$BASIC_SCRIPT
    ]]></token>
</macros>