<tool id="humann2_associate" name="Associate" version="@WRAPPER_VERSION@.1">
    <description>HUMAnN2 functions with metadata</description>
    <macros>
        <import>humann2_macros.xml</import>
    </macros>
    <expand macro="stdio"/>
    <expand macro="requirements"/>
    <expand macro="version"/>
    <command detect_errors="exit_code"><![CDATA[
humann2_associate
    --input '$input'
    --focal-metadatum '$focal_metadatum'
    --last-metadatum '$last_metadatum'
    --focal-type '$focal_type'
    --fdr '$fdr'
    --output '$associated_table'
    ]]></command>
    <inputs>
        <param argument="--input" type="data" format="tsv,tabular" label="HUMAnN2 table with metadata rows at the top"/>
        <param name="focal_metadatum" argument="--focal-metadatum" type="text" value="" label="Metadatum to test vs. community feature totals"/>
        <param name="last_metadatum" argument="--last-metadatum" type="text" value="" label="End of metadata rows"/>
        <param name="focal_type" argument="--focal-type" type="select" label="Metadatum type">
            <option value="continuous">Continuous</option>
            <option value="categorical">Categorical</option>
        </param>
        <param argument="--fdr" type="float" value="0.2" label="FDR threshold"/>
    </inputs>
    <outputs>
        <data format="tabular" name="associated_table" label="${tool.name} on ${on_string}" />
    </outputs>
    <tests>
        <test>
            <param name="input" value="hmp_pathabund.txt"/>
            <param name="focal_metadatum" value="STSite"/>
            <param name="last_metadatum" value="STSite"/>
            <param name="focal_type" value="categorical"/>
            <param name="fdr" value="0.2"/>
            <output name="associated_table" md5="d37e750915a6895145540d15074a9c15"/>
        </test>
    </tests>
    <help><![CDATA[
@HELP_HEADER@

When associating metadata with HUMAnN2 features, it is often beneficial to associate with community totals and avoid testing each individual feature stratification (to improve statistical power). This is the approach used by the HUMAnN2 utility script humann2_associate, which can compare feature totals across samples with 1) a single continuous metadatum (via the Spearman Correlation) or 2) a single categorical metadatum (via the Kruskal-Wallis H-test). Notably, this is a naive approach to association, but it is useful for tutorial purposes.
    ]]></help>
    <expand macro="citations"/>
</tool>