<tool id="humann2_split_table" name="Split HUMAnN2 table" version="0.1.0">
    <description></description>

    <requirements>
        <requirement type="package" version="2.2.4">bowtie2</requirement>
        <requirement type="package" version="2.0">metaphlan2</requirement>
        <requirement type="package" version="0.6.13">diamond</requirement>
        <requirement type="package" version="2.0">humann2</requirement>
    </requirements>

    <stdio>
        <exit_code range="1:" />
    </stdio>

    <version_command>
<![CDATA[
    humann2_split_table --version
]]>
    </version_command>

    <command><![CDATA[
        humann2_split_table
            -i "input_file"
            -o "output"            
    ]]></command>

    <inputs>
        <param name="input_file" type="data" format="tsv,biom" 
            label="Gene/pathway table to read" help=""/>
    </inputs>

    <outputs>
        <outputs>
            <data format="txt" name="report">
                <discover_datasets pattern="__designation__" ext="tabular" directory="output" visible="true" />
            </data>
        </outputs>
    </outputs>

    <tests>
        <test>
            <param name="input_file" value="humann2_input.fasta"/>
        </test>
    </tests>

    <help><![CDATA[
        **What it does**

        Split HUMAnN2 table is a tool to split a gene/pathway table in table per sample.

        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>`_.
    ]]></help>

    <citations>
    </citations>
</tool>
Add tool to split tables
Add tool to split tables
