<tool id="window_coverage" name="Calculate window coverage" version="0.1.0">
    <description> Determines spanning and total read coverage for overlapping windows spanning peaks of interest. </description>
    <requirements>
        <requirement type="package" version="1.3">samtools</requirement>
        <requirement type="package" version="2.27.0.0">bedtools</requirement>
    </requirements>
    <stdio>
        <exit_code range="1:" />
    </stdio>
    <command><![CDATA[
        #set input_list = '","'.join( [str( $input.name ) for $input in $input1 ] )
        $__tool_directory__/./window_coverage.bash "$input1" "$input_list" "$input2" "$input3" "$output1" "$output2"
    ]]></command>
    <inputs>
        <param type="data" name="input1" format="bam" multiple="true" label="Filtered Bam Files"/>
        <param type="data" name="input2" format="bed" label="qPCR Window Bed File"/>
        <param type="float" name="input3" value="0.9" label="Coverage Cutoff"/>
    </inputs>
    <outputs>
        <data name="output1" format="bed" label="Coverage Bed File"/>
        <data name="output2" format="bed" label="Spanning Fragment Coverage Bed File" />
    </outputs>
    <tests>
        <test>
            <param name="input1" value="Ch1-1.pe.q10.sort.bam.rmdup.filter.bam,Ch13-1.pe.q10.sort.rmdup.filter.bam"/>
            <param name="input2" value="qPCR_windows.bed" />
            <param name="input3" value="0.9" />
            <output name="output1" file="combined.o.coverage"/>
            <output name="output2" file="combined.f9.coverage"/>
        </test>
    </tests>
    <help><![CDATA[
        This tools takes a series of bam files and a bed file of overlapping windows spanning peaks of interest and determines the read coverage and spanning fragment coverage for each window.  
    ]]></help>
    <citations>
        <citation type="doi">doi:10.1038/nmeth.4663</citation>
    </citations>
</tool>