<tool id="metaphlan2krona" name="Format MetaPhlAn2" version="0.1.0">

    <description>output for Krona</description>

    <requirements>
        <requirement type="package" version="2.2.5">bowtie2</requirement>
        <requirement type="package" version="2.2.0">metaphlan2</requirement>
    </requirements>

    <stdio>
        <exit_code range="1:" level="fatal"   description="" />
        <regex match="ERROR"
               source="stderr"
               level="fatal"
               description="" />
        <regex match="WARNING"
               source="stderr"
               level="warning"
               description="" />
    </stdio>

    <version_command>
<![CDATA[
metaphlan2krona.py -v
]]>
    </version_command>

    <command>
<![CDATA[        
        metaphlan2krona.py
            -p $input_file
            -k $krona
]]>
    </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}: Krona file" />
    </outputs>

    <tests>
        <test>
            <param name="input_file" value="metaphlan2_profiled_metagenome.txt"/>
            <output name="krona" file="metaphlan2krona_output_file.txt"/>
        </test>      
    </tests>

    <help><![CDATA[

**What it does**

MetaPhlAn is a computational tool for profiling 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 format MetaPhlAn2 output for Krona.

    ]]></help>

    <citations>
        <citation type="doi">10.1038/nmeth.3589</citation>
    </citations>
</tool>