<tool id="make_window_bed" name="Create bed file of qPCR windows" version="0.1.0">
    <description> Creates bed file of windows spanning peaks of interest.</description>
        <requirements>
            <requirement type="package" version="3.4.2">r-base</requirement>
    </requirements>
    <command><![CDATA[
        Rscript --vanilla $__tool_directory__/make_window_bed.R $input1 $input2 $output
    ]]></command>
    <inputs>
        <param type="data" name="input1" format="bed" label="Peak Bed File"/>
        <param type="integer" name="input2" value="100" label="Window Size"/>
    </inputs>
    <outputs>
	<data name="output" format="bed" label="qPCR Window Bed File"/>
    </outputs>
    <tests>
        <test>
            <param name="input1" value="RAMA_peaks.bed"/>
            <param name="input2" value="100"/>
            <output name="output" file="qPCR_windows.bed"/>
        </test>
    </tests>
    <help><![CDATA[
        Generates bed file containing overlapping windows of specified size spanning peaks in input bed file. 
    ]]></help>
    <citations>
        <citation type="doi">doi:10.1038/nmeth.4663</citation>
    </citations>
</tool>