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view alignment_size_distribution.xml @ 3:21b5a9170b90 draft

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planemo upload for repository https://github.com/bardin-lab/smallRNA_tools commit c8e0a703fcdff580ba0a0c5806a37c088c03ab7b
author mvdbeek
date Mon, 20 Aug 2018 14:27:49 -0400
parents c8c7b6113241
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<tool id="alignment_size_distribution" name="Create size distribution for alignment files" version="0.1.0">
    <requirements>
        <requirement type="package" version="6.7">click</requirement>
        <requirement type="package" version="0.23">pandas</requirement>
        <requirement type="package" version="0.15">pysam</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
python '$__tool_directory__/size_distributions.py' '$alignment_file' --minimum_size $minimum_size --maximum_size $maximum_size $wide --output '$distribution'
    ]]></command>
    <inputs>
        <param name="alignment_file" type="data" format="bam,unsorted.bam"/>
        <param argument="--minimum_size" type="integer" value="18" min="1" label="Minimum read length to consider"/>
        <param argument="--maximum_size" type="integer" value="30" min="1" label="Maximum read length to consider"/>
        <param argument="--wide" type="boolean" checked="false" truevalue="--wide" falsevalue="--long" label="Output wide instead of long tabular format"/>
    </inputs>
    <outputs>
        <data name="distribution" format="tabular"/>
    </outputs>
    <tests>
        <test>
            <param name="alignment_file" value="test_data.bam" ftype="bam"/>
            <output name="distribution" value="distribution.tab" ftype="tabular"/>
        </test>
    </tests>
    <help><![CDATA[
Generates a table with reference sequence, sense and antisense counts.
    ]]></help>
</tool>