<tool id="humann2_regroup_table" name="Regroup" version="@WRAPPER_VERSION@.0">
    <description> a HUMAnN2 generated table by features</description>

    <macros>
        <import>humann2_macros.xml</import>
    </macros>

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

    <version_command>
<![CDATA[
    humann2_regroup_table --version
]]>
    </version_command>

    <command><![CDATA[
        humann2_regroup_table
            --input '$input'
            -o '$output_table'
            --function '$function'

            #if $built_in.built_in_test == "true":
                --groups '$built_in.gene_family_groups.groups'
            #else:
                --custom '$built_in.custom'
                $built_in.reversed
            #end if  

            --ungrouped '$ungrouped'
            --protected '$protected'
    ]]></command>

    <inputs>
        <param argument="--input" type="data" format="tsv" label="Gene/pathway table"/>
        <param argument="--function" type="select" label="How to combine grouped features?">
            <option value="sum" selected="true">Sum</option>
            <option value="mean">Mean</option>
        </param>
        <conditional name="built_in">
            <param name='built_in_test' type='select' label="Use built-in grouping options?" help="">
                <option value="true" selected="true">Yes</option>
                <option value="false">No</option>
            </param>
            <when value="true">
                <conditional name="gene_family_groups">
                    <param name="gene_family_type" type="select" label="Gene family type">
                        <option value="uniref50">UniRef50 gene families</option>
                        <option value="uniref90">UniRef90 gene families</option>
                    </param>
                    <when value="uniref50">
                        <param name="groups" type="select" label="Grouping options" help="(--groups)">
                            <option value="uniref50_go">UniRef50 gene families into GO</option>
                            <option value="uniref50_ko">UniRef90 gene families into KEGG Orthogroups (KOs)</option>
                            <option value="uniref50_eggnog">UniRef50 gene families into eggNOG</option>
                            <option value="uniref50_pfam">UniRef50 gene families into PFAM</option>
                            <option value="uniref50_level4ec">UniRef50 gene families into level4ec</option>
                            <option value="uniref50_infogo1000">UniRef50 gene families into InfoGO1000</option>
                            <option value="uniref50_rxn">UniRef50 gene families into metacyc reactions</option>
                        </param>
                    </when>
                    <when value="uniref90">
                        <param name="groups" type="select" label="Grouping options" help="(--groups)">
                            <option value="uniref90_go">UniRef90 gene families into GO</option>
                            <option value="uniref90_ko">UniRef90 gene families into KEGG Orthogroups (KOs)</option>
                            <option value="uniref90_eggnog">UniRef90 gene families into eggNOG</option>
                            <option value="uniref90_pfam">UniRef90 gene families into PFAM</option>
                            <option value="uniref90_level4ec">UniRef90 gene families into level4ec</option>
                            <option value="uniref90_infogo1000">UniRef90 gene families into InfoGO1000</option>
                            <option value="uniref90_rxn">UniRef90 gene families into metacyc reactions</option>
                        </param>
                    </when>
                </conditional>
            </when>
            <when value="false">
                <param argument="--custom" type="data" format="tsv" label="Custom groups file"/>
                <param argument='--reversed' type='boolean' checked="false" truevalue='--reversed' falsevalue='' label="Is the groups file reversed?" help="Mapping from features to groups"/>
            </when>
        </conditional>
        <param argument="--precision" type="integer" value="3" label="Decimal places to round to after applying function"/>
        <param argument="--ungrouped" type='boolean' checked="true" truevalue='Y' falsevalue='N' label="Include an 'UNGROUPED' group to capture features that did not belong to other groups?"/>
        <param argument="--protected" type='boolean' checked="true" truevalue='Y' falsevalue='N' label="Carry through protected features, such as 'UNMAPPED'?"/>
    </inputs>

    <outputs>
        <data format="tsv" name="output_table" label="${tool.name} on ${on_string}: Regrouped table" />
    </outputs>

    <tests>
        <test>
            <param name="input" value="demo_genefamilies.tsv"/>
            <param name="function" value="sum"/>
            <param name="built_in_test" value="true"/>
            <param name="gene_family_type" value="uniref90"/>
            <param name="groups" value="uniref90_infogo1000"/>
            <param name="ungrouped" value="Y"/>
            <param name="protected" value="Y"/>
            <output name="output_table" file="regrouped_gene_families_to_infogo1000.tsv"/>
        </test>
        <test>
            <param name="input" value="demo_genefamilies.tsv"/>
            <param name="function" value="mean"/>
            <param name="built_in_test" value="true"/>
            <param name="gene_family_type" value="uniref90"/>
            <param name="groups" value="uniref90_ko"/>
            <param name="ungrouped" value="Y"/>
            <param name="protected" value="Y"/>
            <output name="output_table" file="regrouped_gene_families_to_ko.tsv"/>
        </test>
        <test>
            <param name="input" value="demo_genefamilies.tsv"/>
            <param name="function" value="sum"/>
            <param name="built_in_test" value="true"/>
            <param name="gene_family_type" value="uniref90"/>
            <param name="groups" value="uniref90_rxn"/>
            <param name="ungrouped" value="Y"/>
            <param name="protected" value="Y"/>
            <output name="output_table" file="regrouped_gene_families_to_rxn.tsv"/>
        </test>
    </tests>

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

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>`_.

Regroup HUMAnN2 table features is a tool for regrouping table features (abundances or coverage) given a table of feature values and a mapping of groups to component features. It produces a new table with group values in place of feature values.
    ]]></help>

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