<tool id="humann2_reduce_table" name="Reduce 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_reduce_table --version
]]>
    </version_command>

    <command><![CDATA[
        humann2_reduce_table
            -i $input_table
            -o $output_table
            --function $function
            --sort-by $sort 
    ]]></command>

    <inputs>
        <param name="input_table" type="data" format="tsv" label="Gene/pathway 
            table" help=""/>

        <param name="function" type="select" label="Function to apply" help="(--function)">
            <option value="max" selected="true">Max</option>
            <option value="sum">Sum</option>
            <option value="mean">Mean</option>
            <option value="min">Min</option>
        </param>

        <param name="sort" type="select" label="How to sort the output" help="(--sort-by)">
            <option value="name" selected="true">Name</option>
            <option value="value">value</option>
            <option value="level">level</option>
        </param>
    </inputs>

    <outputs>
        <data format="tsv" name="output_table" label="Reduced table for 
            ${on_string} (HUMAnN2)" />
    </outputs>

    <tests>
        <test>
            <param name="input_table" value="humann2_sam_pathcoverage.tsv"/>
            <param name="function" value="max"/>
            <param name="sort" value="name"/>
            <output name="output_table" file="humann2_sam_reduced_pathcoverage.tsv"/>
        </test>
    </tests>

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

        Reduce HUMAnN2 table is a tool to reduce the table given a function (max, sum, mean or min).

        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>