<!-- The tool is broken with current version of HUMAnN. Once it will be fixed (PR merged), we can update this wrapper and add the XML extension to enable it -->
<tool id="humann_genefamilies_genus_level" name="Create a genus level" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
    <description>gene families and pathways from HUMAnN species level gene families</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="edam_ontology"/>
    <expand macro="requirements"/>
    <expand macro="version"/>
    <command detect_errors="exit_code"><![CDATA[
humann_genefamilies_genus_level 
    --input '$input'
    --output '$gene_families'
&&
humann
    --input '$gene_families'
    --output '$pathways'
    ]]></command>
    <inputs>
        <param argument="--input" type="data" format="tsv,tabular" label="Species level gene families" help="Direct output from HUMAnN"/>
    </inputs>
    <outputs>
        <data name="gene_families" format="tabular" label="${tool.name} on ${on_string}: Genus level gene families"/>
        <data name="pathways" format="tabular" label="${tool.name} on ${on_string}: Genus level pathways"/>
    </outputs>
    <tests>
        <test expect_num_outputs="1">
            <param name="input" value="demo_genefamilies.tsv"/>
            <output name="gene_families" ftype="tabular" value="genus-level-gene-families.tsv" compare="sim_size">
                <assert_contents>
                    <has_text text="humann_Abundance"/>
                    <has_text text="PWY-5423: oleoresin monoterpene volatiles biosynthesis|unclassified"/>
                    <has_n_columns n="2"/>
                </assert_contents>
            </output>
            <output name="pathways" ftype="tabular" value="genus-level-pathways.tsv" compare="sim_size">
                <assert_contents>
                    <has_text text="humann_Abundance"/>
                    <has_text text="PWY-5423: oleoresin monoterpene volatiles biosynthesis|unclassified"/>
                    <has_n_columns n="2"/>
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[
@HELP_HEADER@

By default, the gene families and pathways output files from HUMAnN are species level.
This tool generates genus level gene families and pathways
    ]]></help>
    <expand macro="citations"/>
</tool>