annotate humann2_join_tables.xml @ 0:3d6f37e7e3a8 draft

planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 7aadbbdef6da644837f62ea428cb859eeff34f04-dirty

<tool id="humann2_join_tables" name="Join" version="0.6.1">
    <description>HUMAnN2 generated tables</description>

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

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

    <version_command>
<![CDATA[
    humann2_join_tables --version
]]>
    </version_command>

    <command><![CDATA[
        `mkdir tmp_dir`

        && 

        #for $table in $input_tables
            `cp $table.input_table tmp_dir`
        #end for

        && 
        humann2_join_tables
            -i "tmp_dir"
            -o $joined_table           
    ]]></command>

    <inputs>
        <repeat name="input_tables" title="Gene/pathway tables to join">
            <param name="input_table" type="data" format="tsv,tabular" multiple="true" label="Gene/pathway table" help=""/>
        </repeat>
    </inputs>

    <outputs>
        <data format="tsv" name="joined_table" label="${tool.name} on ${on_string}: Joined table" />
    </outputs>

    <tests>
        <test>
            <param name="input_tables_0|input_table" value="expected_pathway_coverage.tsv"/>
            <param name="input_tables_1|input_table" value="expected_pathway_abundance.tsv"/>
            <output name="joined_table" file="joined_pathway_coverage_abundance.tsv"/>
        </test>
    </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>`_.

Join HUMAnN2 tables is a tool to join gene or pathway tables of multiple samples into a single table.
    ]]></help>

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