<tool id="humann_unpack_pathways" name="Unpack pathway abundances" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
    <description>to show the genes for each</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="edam_ontology"/>
    <expand macro="requirements"/>
    <expand macro="version"/>
    <command detect_errors="exit_code"><![CDATA[
humann_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 argument="--input-genes" type="data" format="tsv,tabular" label="Gene family or EC abundance file"/>
        <param argument="--input-pathways" type="data" format="tsv,tabular" label="Pathway abundance file"/>
        <param argument="--gene-mapping" type="data" format="tsv,tabular" optional="true" label="Gene family to reaction mapping file"/>
        <param argument="--pathway-mapping" type="data" format="tsv,tabular" optional="true" label="Reaction to pathway mapping file"/>
        <param argument="--remove-taxonomy" type="boolean" truevalue="--remove-taxonomy" falsevalue="" checked="false" label="Remove the taxonomy from the output file?"/>
    </inputs>
    <outputs>
        <data format="tabular" name="output"/>
    </outputs>
    <tests>
        <test expect_num_outputs="1">
            <param name="input_genes" value="demo_genefamilies.tsv"/>
            <param name="input_pathways" value="demo_pathabundance.tsv"/>
            <param name="remove_taxonomy" value=""/>
            <output name="output" ftype="tabular">
                <assert_contents>
                    <has_text text="humann_Abundance"/>
                    <has_text text="PWY-4203|unclassified|UniRef90_Q6XMI3"/>
                    <has_n_columns n="2"/>
                </assert_contents>
            </output>
        </test>
        <test expect_num_outputs="1">
            <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" ftype="tabular">
                <assert_contents>
                    <has_text text="humann_Abundance"/>
                    <has_text text="PWY-4203|UniRef90_Q6XMI3"/>
                    <has_n_columns n="2"/>
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[
@HELP_HEADER@

This tool unpacks 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>