<tool id="metaphlan2_extract_markers" name="Format MetaPhlAn2" version="@WRAPPER_VERSION@.0">

    <description>output for Krona</description>

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

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

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

    <command>
<![CDATA[
        extract_markers.py
            --mpa_pkl MPA_PKL
            --ifn_markers IFN_MARKERS
            --clade CLADE
            --ofn_markers OFN_MARKERS
]]>
    </command>

    <inputs>
        <param name="input_file" type="data" format="tabular,txt" label="Input file (MetaPhlAN2 output)" help="(--profile)"/>
    </inputs>

    <outputs>
        <data format="tabular" name="krona" label="${tool.name} on ${on_string}: Formatted file for Krona" />
    </outputs>

    <tests>
        <test>
            <param name="input_file" value="community_profile.tabular"/>
            <output name="krona" file="formatted_to_krona.tabular"/>
        </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 formats MetaPhlAn2 output to be ready for Krona.

    ]]></help>

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