annotate humann2_regroup_table.xml @ 5:88ff1d78fd30 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann2 commit 55eb503f50c54695ec36c3d4671c2b3e64d05f40"

<tool id="humann2_regroup_table" name="Regroup" version="@WRAPPER_VERSION@.1">
    <description>a HUMAnN2 generated table by features</description>
    <macros>
        <import>humann2_macros.xml</import>
    </macros>
    <expand macro="stdio"/>
    <expand macro="requirements"/>
    <expand macro="version"/>
    <command detect_errors="exit_code"><![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'
        $built_in.reversed
    #end if
    --precision '$precision'
    --ungrouped '$ungrouped'
    --protected '$protected'
    ]]></command>
    <inputs>
        <param argument="--input" type="data" format="tsv,tabular" 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="precision" value="3"/>
            <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="precision" value="3"/>
            <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="precision" value="3"/>
            <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[
@HELP_HEADER@

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>