<tool id="picrust_metagenome_contributions" name="Metagenome Contributions" version="@TOOL_VERSION@.0">
    <description>of OTUs to user-specified functions</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <expand macro="version_command"/>
    <command detect_errors="aggressive"><![CDATA[
        metagenome_contributions.py
            -i '$input_data'
            -o '$contrib_table'
            -c '$gg.precalc'
            -l '$limit_gene'
    ]]></command>
    <inputs>
        <param name="input_data" type="data" format="biom1,h5" label="Input file" help="Biom file, which should be the output of the normalize_by_copy_number command."/>
        <expand macro="otu-reference-precalculated"/>
        <param name="limit_gene" type="text" format="txt" label="Function ids" help="Limit to specified function ids (e.g. K00500). If limiting to multiple ids then separate them by commas with no spaces between them." />
    </inputs>
    <outputs>
        <data name="contrib_table" format="tabular"/>
    </outputs>
    <tests>
        <test>
            <param name="input_data" value="otu_table_for_custom_trait_table.biom"/>
            <param name="source" value="hist"/>
            <param name="precalc" value="custom_trait_table.tab"/>
            <output name="contrib_table" ftype="tabular">
                <assert_contents>
                    <has_text text="GeneCountPerGenome"/>
                    <has_text text="OTUAbundanceInSample"/>
                </assert_contents>
            </output>
        </test>
    </tests>
    <help>
<![CDATA[
@PICRUST_OVERVIEW@

**Command Documenation**

This module outputs the relative contribution of OTUs to the predicted abundances of functions in your samples. The input biom file should be the output of normalize_by_copy_number. One output text file will be generated.

Make sure that you specify an appropriate functional database for this command (usually the ko, cog, or rfam v13_5 database).

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