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planemo upload for repository https://github.com/remimarenco/bedclip
author rmarenco
date Sat, 23 Jul 2016 03:20:57 -0400
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<tool id="bedclip" name="bedClip" version="0.1.0">
    <requirements>
        <requirement type="package" version="332">ucsc-fatotwobit</requirement>
        <requirement type="package" version="324">ucsc-twobitinfo</requirement>
        <requirement type="package" version="332">ucsc-bedclip</requirement>
    </requirements>
    <stdio>
        <exit_code range="1:" />
    </stdio>
    <command><![CDATA[
        faToTwoBit "$ref_genome" two_bit_ref_genome;
        twoBitInfo two_bit_ref_genome chrom_sizes;
        bedClip "$bed_file" chrom_sizes "$bed_clipped";
    ]]></command>
    <inputs>
        <param type="data" name="ref_genome" format="fasta" />
        <param type="data" name="bed_file" format="bed" />
    </inputs>
    <outputs>
        <data name="bed_clipped" format="bed" />
    </outputs>
    <tests>
        <test>
            <param name="ref_genome" value="input.fasta"/>
            <param name="bed_file" value="input.bed"/>
            <output name="bed_clipped" file="output.bed"/>
        </test>
    </tests>
    <help><![CDATA[
    ]]></help>
</tool>