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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
author shellac
date Mon, 22 Mar 2021 18:12:50 +0000
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<tool id="sam-consensus-v3" name="Sam consensus V3" version="0.2.8" python_template_version="3.5">
    <requirements>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        perl '$__tool_directory__/call_consensus_from_sam_3.pl' '$samfile' 'fastafile' $mapq
    ]]></command>
    <inputs>
        <param name="samfile" type="data" format="sam" label="SAM file"/>
        <param name="fastafile" type="data" format="fasta" label="FASTA file"/>
        <param name="mapq" type="integer" label="MAPQ" value="0"/>
    </inputs>
    <outputs>
        <data name="scv3res" format="txt">
            <discover_datasets pattern="__designation_and_ext__" directory="." visible="true"/>
        </data>
    </outputs>
    <help><![CDATA[
        Sam consensus v3 takes a sam file and a fasta file with a mapq parameter
    ]]></help>
</tool>