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planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 79571d981d7d56657699be8aa24a40a36a8d0ab5-dirty
author bebatut
date Thu, 02 Jun 2016 04:23:09 -0400
parents 3d6f37e7e3a8
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<tool id="humann2_download_databases" name="Download" version="0.6.1">
    <description>HUMAnN2 databases</description>

    <macros>
        <import>humann2_macros.xml</import>
    </macros>

    <expand macro="requirements"/>
    <expand macro="stdio"/>

    <version_command>
<![CDATA[
    humann2_databases --version
]]>
    </version_command>

    <command><![CDATA[
        humann2_databases
            --download $database_selector \${HUMANN2_DIR}/databases
            
            > $log
    ]]></command>

    <inputs>
        <param name="database_selector" type="select" label="Database to download" help="">
            <option value="chocophlan full">Nucleotide (ChocoPhlAn)</option>
            <option value="uniref diamond">Protein (UniRef50)</option>
        </param>
    </inputs>

    <outputs>
        <data format="txt" name="log" label="${tool.name}: Log" />
    </outputs>

    <tests>
    </tests>

    <help><![CDATA[
**What it does**

HUMAnN is a pipeline for efficiently and accuretly profiling the presence/absence and abundance of microbial pathways in a community from metagenomic or metatranscriptomic sequencing data. `Read more about the tool <http://huttenhower.sph.harvard.edu/humann2/manual>`_.

Download HUMAnN2 databases is a tool to download needed nucleotide or protein databases. This tool must be run before using HUMAnN2.
    ]]></help>

    <expand macro="citations"/>
</tool>