<tool id="mfassignr_snplot" name="MFAssignR SNplot" version="@TOOL_VERSION@+galaxy1" profile="23.0">
    <description>Noise level assessment using the SNplot function.</description>
    <macros>
        <import>macros.xml</import>
        <import>help.xml</import>
    </macros>
    <edam_topics>
        <edam_topic>topic_3172</edam_topic>    
    </edam_topics>
    <expand macro="creator"/>
    <expand macro="requirements" />
    <command detect_errors="exit_code"><![CDATA[
        Rscript '${run_script}'
    ]]></command>
    <configfiles>
        <configfile name="run_script"><![CDATA[
        cut = $sn_ratio * $kmdn
                    
        SNplot <- MFAssignR::SNplot(
            df = read.delim("$input_file", sep="\t"),
            cut = cut,
            mass = $mass,
            mass_window = $window_x,
            abundance_window = $window_y
        )

        ggplot2::ggsave(filename = "SNplot.png", SNplot)
        ]]></configfile>
    </configfiles>
    <inputs>
        <expand macro="snplot_param"/>
    </inputs>
    <outputs>
        <data name="SNplot" format="png" label="SNplot by ${tool.name} on ${on_string}" from_work_dir="SNplot.png"/>
    </outputs>
    <tests>
        <test>
            <param name="input_file" value="QC1_1_POS_500.tabular"/>
            <param name="kmdn" value="549117.606606315"/>
            <param name="mass" value="300"/>
            <output name="SNplot" ftype="png" file="snplot/plot.png" />
        </test>
    </tests>
    <help><![CDATA[
        @SNPLOT_HELP@

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