<tool id="humann2_rename_table" name="Rename 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_rename_table --version
]]>
    </version_command>

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

            --names $built_in.names
            $built_in.simplify 
            -c $built_in.file
    ]]></command>

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

        <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="file" type="data" format="tsv" label="Custom mapping file of feature IDs to full names" help="(--custom)"/>
    </inputs>

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

    <tests>
    </tests>

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

        Rename HUMAnN2 table features is a tool for renaming table features given built-in or custom mapping.

        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>
Add tool to rename humann2 table
Add tool to rename humann2 table
