<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="version"/>
    <command detect_errors="exit_code"><![CDATA[
humann2_rename_table
    --input '$input'
    -o '$output_table'
    #if $renaming.type == 'standard'
        --names '$renaming.names'
    #else
        --custom '$renaming.custom'
    #end if
    $simplify 
    ]]></command>
    <inputs>
        <param argument="--input" type="data" format="tsv,tabular" label="Gene/pathway table"/>
        <conditional name="renaming">
            <param name="type" type="select" label="Type of renaming">
                <option value="standard">Standard renaming</option>
                <option value="custom">Custom renaming</option>
            </param>
            <when value="standard">
                <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="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="uniref90">UniRef90</option>-->
                    <option value="kegg-pathway">KEGG Pathway</option>
                    <option value="kegg-orthology">KEGG Orthology</option>
                </param>
            </when>
            <when value="custom">
                <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"/>
            </when>
        </conditional>
        <param argument="--simplify" type="boolean" truevalue="--simplify" falsevalue="" checked="false" label="Remove non-alphanumeric characters from names?"/>
    </inputs>
    <outputs>
        <data format="tsv" name="output_table" label="${tool.name} on ${on_string}: Renamed table" />
    </outputs>
    <tests>
        <test>
            <param name="input" value="regrouped_gene_families_to_infogo1000.tsv"/>
            <conditional name="renaming">
                <param name="type" value="standard"/>
                <param name="names" value="infogo1000" />
            </conditional>
            <param name="simplify" value=""/>
            <output name="output_table">
                <assert_contents>
                    <has_text text="GO:0000015: [CC] phosphopyruvate hydratase complex" />
                    <has_text text="GO:0000287: [MF] magnesium ion binding" />
                </assert_contents>
            </output>
        </test>
        <test>
            <param name="input" value="regrouped_gene_families_to_infogo1000.tsv"/>
            <conditional name="renaming">
                <param name="type" value="custom"/>
                <param name="custom" value="rename_mapping" />
            </conditional>
            <param name="simplify" value=""/>
            <output name="output_table">
                <assert_contents>
                    <has_text text="GO:0000015: GO1" />
                    <has_text text="GO:0000107: NO_NAME" />
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[
@HELP_HEADER@

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>