annotate humann2_regroup_table.xml @ 0:3d6f37e7e3a8 draft

planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 7aadbbdef6da644837f62ea428cb859eeff34f04-dirty

<tool id="humann2_regroup_table" name="Regroup" version="0.6.1">
    <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
            -i $input_table
            -o $output_table
            --function $function

            #if $built_in.built_in_test == "true":
                --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="(-i)"/>

        <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='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">
                <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 families 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="${tool.name} on ${on_string}: Regrouped table" />
    </outputs>

    <tests>
        <test>
            <param name="input_table" value="expected_gene_family_abundance.tsv"/>
            <param name="function" value="sum"/>
            <param name="built_in_test" value="true"/>
            <param name="groups" value="uniref50_ec"/>
            <output name="output_table" file="regrouped_gene_families_to_ec.tsv"/>
        </test>
         <test>
            <param name="input_table" value="expected_gene_family_abundance.tsv"/>
            <param name="function" value="mean"/>
            <param name="built_in_test" value="true"/>
            <param name="groups" value="uniref50_ko"/>
            <output name="output_table" file="regrouped_gene_families_to_ko.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>