<tool id="humann2_renorm_table" name="Renormalize" version="@WRAPPER_VERSION@.0">
    <description>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_renorm_table
    --input '$input'
    -o '$output_table'
    --units '$units'
    --mode '$mode'
    --special '$special'
    $update_snames
    ]]></command>
    <inputs>
        <param argument="--input" type="data" format="tsv,tabular" label="Gene/pathway table"/>
        <param argument="--units" type="select" label="Normalization scheme">
            <option value="cpm" selected="true">Copies per million</option>
            <option value="relab">Relative abundance</option>
        </param>
        <param argument="--mode" type="select" label="Normalization level">
            <option value="community" selected="true">Normalization of all levels by community total</option>
            <option value="levelwise">Normalization of all levels by levelwise total</option>
        </param>
        <param argument="--special" type='boolean' truevalue='y' falsevalue='n' checked="true" label="Include the special features UNMAPPED, UNINTEGRATED, and UNGROUPED?"/>
        <param name="update_snames" argument="--update-snames" type='boolean' truevalue='--update-snames' falsevalue='' checked="true" label="Update '-RPK' in sample names to appropriate suffix?"/>
    </inputs>
    <outputs>
        <data format="tsv" name="output_table" label="${tool.name} on ${on_string}: Normalized table" />
    </outputs>
    <tests>
        <test>
            <param name="input" value="demo_pathabundance.tsv"/>
            <param name="units" value="cpm"/>
            <param name="mode" value="community"/>
            <param name="special" value="n"/>
            <param name="update_snames" value=""/>
            <output name="output_table" file="cpm_community_renormalized_pathway_abundance.tsv"/>
        </test>
        <test>
            <param name="input" value="demo_pathabundance.tsv"/>
            <param name="units" value="relab"/>
            <param name="mode" value="levelwise"/>
            <param name="special" value="y"/>
            <param name="update_snames" value=""/>
            <output name="output_table" file="relab_levelwise_renormalized_pathway_abundance.tsv"/>
        </test>
    </tests>
    <help><![CDATA[
@HELP_HEADER@

Renorm HUMAnN2 table is a tool to renormalize a table, either in copies per million or in relative abundance. Each level of a stratified table will be normalized using the desired scheme.

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