<tool id="humann2_join_tables" name="Join" version="@WRAPPER_VERSION@.2">
    <description>HUMAnN2 generated tables</description>
    <macros>
        <import>humann2_macros.xml</import>
    </macros>
    <expand macro="stdio"/>
    <expand macro="requirements"/>
    <expand macro="version"/>
    <command detect_errors="exit_code"><![CDATA[
mkdir tmp_dir
&&
#for $table in $input_table
    #set orig_filename=$table.element_identifier
    #set new_filename='_'.join($orig_filename.split(' '))
    cp '$table' 'tmp_dir/$new_filename' &&
#end for
humann2_join_tables
    -i 'tmp_dir'
    -o '$joined_table'
    ]]></command>
    <inputs>
        <param name="input_table" type="data" format="tsv,tabular" multiple="true" label="Gene/pathway table"/>
    </inputs>
    <outputs>
        <data format="tsv" name="joined_table" label="${tool.name} on ${on_string}: Joined table" />
    </outputs>
    <tests>
        <test>
            <param name="input_table" value="demo_pathabundance.tsv,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[
@HELP_HEADER@

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