annotate humann2_rename_table.xml @ 1:bcd414bb721b draft default tip

planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 79571d981d7d56657699be8aa24a40a36a8d0ab5-dirty

<tool id="humann2_rename_table" name="Rename" version="0.6.1">
    <description>features of a HUMAnN2 generated table</description>

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

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

    <version_command>
<![CDATA[
    humann2_rename_table --version
]]>
    </version_command>

    <command><![CDATA[
        humann2_rename_table
            -i $input_table
            -o $output_table

            --names $names
            $simplify 

            -c $mapping_file
    ]]></command>

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

        <param name="names" type="select" label="Table features that can be renamed" help="(--names)">
            <option value="metacyc-rxn" selected="true">MetaCyc reactions</option>
            <option value="metacyc-pwy">MetaCyc pathways</option>
            <option value="ko">KEGG Orthogroups (KO)</option>
            <option value="ec">Enzyme commision (EC)</option>
            <option value="uniref50">UniRef50 gene families</option>
        </param>

        <param name='simplify' type='boolean' checked="false" truevalue='-s' falsevalue='' label="Remove non-alphanumeric characters from names?" help="(--simplify)"/>

        <param name="mapping_file" type="data" format="tsv" label="Mapping file" help="The mapping file must be tabular format file with two tab-separated columns. The first column must contain the value you want to modify and the second contain the new value (--custom)"/>
       
    </inputs>

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

    <tests>
        <test>
            <param name="input_table" value="expected_pathway_abundance.tsv"/>
            <param name="names" value="metacyc-pwy" />
            <param name='simplify' value=""/>
            <param name="mapping_file" value="pathway_rename_mapping.tsv"/>
            <output name="output_table" file="renamed_metacyc_pathways.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>`_.

Rename HUMAnN2 table features is a tool for renaming table features given a custom mapping. The mapping file must be tabular format file with two tab-separated columns. The first column must contain the value you want to modify and the second contain the new valu
    ]]></help>

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