<tool id="humann2_join_tables" name="Join" version="@WRAPPER_VERSION@.0">
    <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="demo_pathabundance.tsv"/>
            <param name="input_tables_1|input_table" value="demo_pathcoverage.tsv"/>
            <output name="joined_table">
                <assert_contents>
                    <has_text text="PWY490-3: nitrate reduction VI (assimilatory)|unclassified" />
                    <has_text text="PWY-1269: CMP-3-deoxy-D-manno-octulosonate biosynthesis I" />
                    <has_text text="VALSYN-PWY: L-valine biosynthesis" />
                    <has_text text="UNINTEGRATED|g__Bacteroides.s__Bacteroides_vulgatus" />
                </assert_contents>
            </output>
        </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>