<tool id="metaphlan2_merge_metaphlan_tables" name="Merge" version="@WRAPPER_VERSION@.0">

    <description>MetaPhlAn2 files</description>

    <macros>
        <import>metaphlan2_macros.xml</import>
    </macros>

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

    <version_command>merge_metaphlan_tables.py -v</version_command>

    <command>
<![CDATA[
        merge_metaphlan_tables.py
            #for $element in $input_files
                '$element'
            #end for
            > '$output'
]]>
    </command>

    <inputs>
        <param name="input_files" type="data" format="tabular,txt" multiple="True" label="MetaPhlAn2 output file to join" />
    </inputs>

    <outputs>
        <data format="tabular" name="output" label="${tool.name} on ${on_string}: Merged MetaPhlAn2 files" />
    </outputs>

    <tests>
        <test>
            <param name="input_files" value="community_profile.tabular,community_profile.tabular"/>
            <output name="output">
                <assert_contents>
                    <has_text text="#SampleID" />
                    <has_text text="k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides_thetaiotaomicron|t__Bacteroides_thetaiotaomicron_unclassified" />
                </assert_contents>
            </output>
        </test>
    </tests>

    <help><![CDATA[

**What it does**

MetaPhlAn is a computational tool to profile the structure and the composition of microbial communities (Bacteria, Archaea, Eukaryotes and Viruses) from metagenomic shotgun sequencing data with species level resolution. For more information, check the `user manual <https://bitbucket.org/biobakery/metaphlan2/>`_.

This tool performs a table join on one or more metaphlan output files

    ]]></help>

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

Add wrapper to merge metaphlan2 outputs
Add wrapper to merge metaphlan2 outputs
