<tool id="humann2_join_tables" name="Join HUMAnN2 table" version="0.1.0">
    <description></description>

    <requirements>
        <requirement type="package" version="2.2.4">bowtie2</requirement>
        <requirement type="package" version="2.0">metaphlan2</requirement>
        <requirement type="package" version="0.6.13">diamond</requirement>
        <requirement type="package" version="2.0">humann2</requirement>
    </requirements>

    <stdio>
        <exit_code range="1:" />
    </stdio>

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

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

        #for $file in $input_files
            `cp $file tmp_dir`
        #end for

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

    <inputs>
        <param name="input_files" type="data" format="tsv,biom" multiple="true" 
            label="Gene/pathway tables"
            help=""/>
    </inputs>

    <outputs>
        <data format="tsv,biom" name="joined_table" label="Joined table for 
            ${on_string} (HUMAnN2)" />
    </outputs>

    <tests>
        <test>
            <param name="input_files" value="humann2_sam_pathcoverage.tsv,humann2_fasta_pathcoverage.tsv"/>
            <output name="joined_table" file="humann2_sam_fasta_joined_pathcoverage.tsv"/>
        </test>
    </tests>

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

        Join HUMAnN2 tables is a tool to join gene, pathway, or taxonomy tables of multiple samples in a single table.

        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>`_.
    ]]></help>

    <citations>
    </citations>
</tool>