<tool id="humann2_unpack_pathways" name="Unpack pathway abundances to show genes included" version="@WRAPPER_VERSION@.0">
    <description></description>
    <macros>
        <import>humann2_macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <expand macro="version"/>
    <command detect_errors="exit_code"><![CDATA[
humann2_unpack_pathways
    --input-genes '$input_genes'
    --input-pathways '$input_pathways'
    #if $gene_mapping
        --gene-mapping '$gene_mapping'
    #end if
    #if $pathway_mapping
        --pathway-mapping '$pathway_mapping'
    #end if               
    $remove_taxonomy
    --output '$output'
    ]]></command>
    <inputs>
        <param name="input_genes" argument="--input-genes" type="data" format="tsv,tabular" label="Gene family or EC abundance file"/>
        <param name="input_pathways" argument="--input-pathways" type="data" format="tsv,tabular" label="Pathway abundance file"/>
        <param name="gene_mapping" argument="--gene-mapping" type="data" format="tsv,tabular" optional="true" label="Gene family to reaction mapping file"/>
        <param name="pathway_mapping" argument="--pathway-mapping" type="data" format="tsv,tabular" optional="true" label="Reaction to pathway mapping file"/>
        <param name="remove_taxonomy" argument="--remove-taxonomy" type="boolean" truevalue="--remove-taxonomy" falsevalue="" checked="false" label="Remove the taxonomy from the output file?"/>
    </inputs>
    <outputs>
        <data format="tsv" name="output" label="${tool.name} on ${on_string}" />
    </outputs>
    <tests>
        <test>
            <param name="input_genes" value="demo_genefamilies.tsv"/>
            <param name="input_pathways" value="demo_pathabundance.tsv"/>
            <param name="remove_taxonomy" value=""/>
            <output name="output" md5="993534d3e8fea242066352a0e4d67c8a"/>
        </test>
        <test>
            <param name="input_genes" value="demo_genefamilies.tsv"/>
            <param name="input_pathways" value="demo_pathabundance.tsv"/>
            <param name="remove_taxonomy" value="--remove-taxonomy"/>
            <output name="output" md5="b145ce760ce656b9e3ddb00d3ff4cf46"/>
        </test>
    </tests>
    <help><![CDATA[
@HELP_HEADER@

This utility will unpack the pathways to show the genes for each. It adds another level of stratification to the pathway abundance table by including the gene families (or EC) abundances.
    ]]></help>
    <expand macro="citations"/>
</tool>