<tool id="picrust_predict_metagenomes" name="Predict Metagenome" version="@WRAPPER_VERSION@.0">
    <description>create a virtual metagenome of KEGG Ortholog abundances</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <expand macro="version_command"/>
    <command detect_errors="aggressive"><![CDATA[
        predict_metagenomes.py
            -i '$input_data'
            -o tempbiom
            -c '$gg.precalc'
            $normalize_by_otu
            $normalize_by_function
            #if $accuracy_metrics:
                -a $out_summary
            #end if

            @OUTPUT_CONVERSION_COMMANDS@
    ]]></command>
    <inputs>
        <param name="input_data" type="data" format="tabular,biom1" label="Input file"/>
        <expand macro="otu-reference-precalculated"/>
        <expand macro="biom_format_select"/>
        <param argument="normalize_by_function" type="boolean" truevalue="--normalize_by_function" falsevalue="" checked="false" label="Normalize by function?"
               help="Normalizes the predicted functional abundances by dividing each abundance by the sum of functional abundances in the sample. Total sum of abundances for each sample will equal 1"/>
        <param argument="normalize_by_otu" type="boolean" truevalue="--normalize_by_otu" falsevalue="" checked="false" label="Normalize by OTU?"
               help="Normalizes the predicted functional abundances by dividing each abundance by the sum of OTUs in the sample. Note: total sum of abundances for each sample will NOT equal 1"/>
        <param argument="accuracy_metrics" type="boolean" truevalue="T" falsevalue="F" checked="false" label="Calculate accuracy metrics"
               help="requires that per-genome accuracy metrics were calculated during genome prediction (predict_traits tool) (e.g. there are NSTI values in the genome biom file metadata)"/>
    </inputs>
    <outputs>
        <expand macro="biom_output"/>
        <data name="out_summary" format="tabular">
           <filter>accuracy_metrics</filter>
       </data>
    </outputs>
    <tests>
        <test> <!-- test with defaults -->
            <param name="input_data" value="normalized_otus.biom"/>
            <param name="source" value="hist"/>
            <param name="precalc" value="16S_13_5_precalculated_minimal.tab"/>
            <param name="output_type" value="json"/>
            <output name="out_file" ftype="json">
                <assert_contents>
                    <has_text text="Biological Observation Matrix"/>
                    <has_text text="generated_by"/>
                </assert_contents>
            </output>
        </test>
        <test> <!-- test with accuracy metrics and normalizations -->
            <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"/>
            <param name="output_type" value="tsv"/>
            <param name="accuracy_metrics" value="T"/>
            <param name="normalize_by_function" value="--normalize_by_function"/>
            <param name="normalize_by_otu" value="--normalize_by_otu"/>
            <output name="out_file" ftype="tabular">
                <assert_contents>
                    <has_text text="trait2"/>
                    <has_text text="Sample4"/>
                </assert_contents>
            </output>
            <output name="out_summary" ftype="tabular">
                <assert_contents>
                    <has_line_matching expression="#Sample\tMetric\tValue"/>
                    <has_text text="NSTI"/>
                    <has_text text="Sample4"/>
                </assert_contents>
            </output>
        </test>
    </tests>
    <help>
<![CDATA[
@PICRUST_OVERVIEW@

**Command Documentation**

This module produces a 'virtual' metagenome of KEGG Ortholog abundances for each sample in the given OTU table.

**Input file:** This should be a normalized OTU table populated by the output of the PICRUSt Normalize by Copy Number module.

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