<tool id="humann2_rename_table" name="Rename" version="@WRAPPER_VERSION@.0">
    <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
            --input '$input'
            -o '$output_table'
            --names '$names'
            $simplify 
            #if $custom
                --custom '$custom'
            #end if
    ]]></command>

    <inputs>
        <param argument="--input" type="data" format="tsv" label="Gene/pathway table"/>

        <param argument="--names" type="select" label="Table features that can be renamed">
            <option value="metacyc-rxn" selected="true">MetaCyc reactions</option>
            <option value="metacyc-pwy">MetaCyc pathways</option>
            <option value="infogo1000">InfoGO1000</option>
            <option value="uniref90">UniRef90</option>
            <option value="kegg-module">KEGG Module</option>
            <option value="ec">Enzyme commision (EC)</option>
            <option value="go">Gene Ontology (GO)</option>
            <option value="pfam">PFAM</option>
            <option value="eggnog">eggNOG</option>
            <option value="uniref50">UniRef50</option>
            <option value="kegg-pathway">KEGG Pathway</option>
            <option value="kegg-orthology">KEGG Orthology</option>
        </param>
        <param argument='--simplify' type='boolean' checked="false" truevalue='--simplify' falsevalue='' label="Remove non-alphanumeric characters from names?"/>
        <param argument="--custom" 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" optional="true"/>
    </inputs>

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

    <tests>
        <test>
            <param name="input" value="demo_genefamilies.tsv"/>
            <param name="names" value="uniref90" />
            <param name='simplify' value=""/>
            <output name="output_table">
                <assert_contents>
                    <has_text text="UniRef90_R6I0Z3: NO_NAME|g__Bacteroides.s__Bacteroides_vulgatus" />
                    <has_text text="UniRef90_I9RGY5: Tape measure domain-containing protein|g__Bacteroides.s__Bacteroides_dorei" />
                    <has_text text="UniRef90_C3RF26: HRDC domain protein" />
                </assert_contents>
            </output>
        </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>