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planemo upload commit 103cb51ec368438642504c3f98b76c363db478bb

<tool id="filter_bam" name="Filter bam files" version="0.1.0">
    <description> Filters bam files for reads in regions 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_name = str( $input1.name )
        $__tool_directory__/./filter_bam.bash "$input1" "$input2" "$input3" "$output1" "$output2" "$output3" "$input_name"		
    ]]></command>
    <inputs>
        <param type="data" name="input1" format="bam" label="Bam File"/>
        <param type="data" name="input2" format="bed" label="Peak Bed File"/>
        <param type="data" name="input3" format="tabular" label="chrom.sizes"/> 
    </inputs>
    <outputs>
        <data name="output1" format="bed" label="Extended Peak File"/>
        <data name="output2" format="bam" label="Filtered Bam File"/>
        <data name="output3" format="tabular" label="Read Counts" />
    </outputs>
    <tests>
        <test>
            <param name="input1" value="test.bam"/>
            <param name="input2" value="test.bed"/>
            <param name="input3" value="mm9.chrom.sizes.txt"/>
            <output name="output1" file="ext_peak"/>
            <output name="output2" file="test.filter.bam"/>
            <output name="output3" file="test.readcounts.txt"/>
        </test>
    </tests>
    <help><![CDATA[
        This tools takes a bam file and filters to reads mapping to regions specified by input bed file.  Outputs include filtered bam file and count of total numbers of reads in original bam file.
    ]]></help>
    <citations>
        <citation type="doi">doi:10.1038/nmeth.4663</citation>
    </citations>
</tool>