<tool id="humann2_regroup_table" name="Regroup HUMAnN2 table features" 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_regroup_table --version
]]>
    </version_command>

    <command><![CDATA[
        humann2_regroup_table
            -i $input_table
            -o $output_table
            --function $function

            #if $built_in.test:
                --groups $built_in.groups
            #else:
                --custom $built_in.file
                $built_in.reversed
            #end if  
    ]]></command>

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

        <param name="function" type="select" label="How to combine grouped features?" help="(--function)">
            <option value="sum" selected="true">Sum</option>
            <option value="mean">Mean</option>
        </param>

        <conditional name="built_in">
            <param name='test' type='boolean' checked="false" truevalue='true' 
                falsevalue='false' label="Use built-in grouping options?" 
                help=""/>
            <when value="true">
                <param name="groups" type="select" label="Grouping options" help="(--groups)">
                    <option value="uniref50_ec" selected="true">Collapses UniRef50 gene families into top level enzyme commission (EC) categories (associations inferred from UniProt)</option>
                    <option value="uniref50_go">Collapses UniRef50 gene families into a subset of non-redundant, high-level Gene Ontology (GO) categories (associations inferred from UniProt and a HUMAnN2-specific parsing of the GO hierarchy)</option>
                    <option value="uniref50_ko">Collapses UniRef50 gene fammilies into KEGG Orthogroups (KOs) (associations inferred from UniProt)</option>
                    <option value="uniref50_rxn">Collapses UniRef50 gene families into metacyc reactions (use of reaction abundances to compute the abundance and coverage of broader metabolic pathways)</option>
                </param>
            </when>
            <when value="false">
                <param name="file" type="data" format="tsv" label="Custom groups file" help="(--custom)"/>
                <param name='reversed' type='boolean' checked="false" truevalue='--reversed' 
                    falsevalue='' label="Is the groups file reversed?" 
                    help="Mapping from features to groups. (--reversed)"/>
            </when>
        </conditional>
    </inputs>

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

    <tests>
        <test>
            <param name="input_table" value="humann2_fasta_pathabundance.tsv"/>
            <param name="function" value="sum"/>
            <param name="test" value="true"/>
            <param name="groups" value="uniref50_ec"/>
            <output name="output_table" file="humann2_fasta_pathabundance_cpm_renormalized.tsv"/>
        </test>
    </tests>

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

        Regroup HUMAnN2 table features is a tool for egrouping table features. Given a table of feature values and a mapping of groups to component features, produce a new table with group values in place of feature values.

        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>