<tool id="picrust_normalize_by_copy_number" name="Normalize" version="@TOOL_VERSION@.1">
    <description>the relative abundance of each OTU by the predicted number of 16S copies</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <expand macro="version_command"/>
    <command detect_errors="aggressive"><![CDATA[
        normalize_by_copy_number.py
            -i '$input_data'
            -o tempbiom
            -c '$gg.precalc'

            @OUTPUT_CONVERSION_COMMANDS@
    ]]></command>
    <inputs>
        <param name="input_data" type="data" format="tabular,biom1,h5" label="Input file" help="biom file"/>
        <expand macro="otu-reference-precalculated"/>
        <expand macro="biom_format_select"/>
    </inputs>
    <outputs>
        <expand macro="biom_output"/>
    </outputs>
    <tests>
        <test> <!-- test with biom input -->
            <param name="input_data" value="closed_picked_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_biom" ftype="biom1">
                <assert_contents>
                    <has_text text="Biological Observation Matrix"/>
                    <has_text text="generated_by"/>
                </assert_contents>
            </output>
        </test>
        <test> <!-- test with QIIME input and classic output -->
            <param name="input_data" value="closed_picked_otus.tab"/>
            <param name="source" value="hist"/>
            <param name="precalc" value="16S_13_5_precalculated_minimal.tab"/>
            <param name="output_type" value="tsv"/>
            <output name="out_biom" file="normalized_otus.classic" ftype="tabular"/>
        </test>
    </tests>
    <help>
<![CDATA[
@PICRUST_OVERVIEW@

**Command Documenation**

This module corrects the abundance of each OTU to better reflect the true organism abundance by normalizing by PICRUSt's prediction of 16S copy number for each OTU.

Please ensure that you have properly created your OTU table to be compatible with PICRUSt by following this guide_.
A sample file can be downloaded here_

Make sure that you specify an appropriate 16S database for this command (usually 16S 13_5).

.. _guide: http://picrust.github.io/picrust/tutorials/quickstart.html#quickstart-guide
.. _here: https://raw.github.com/picrust/picrust/master/tutorials/hmp_mock_16S.tab
]]>
    </help>
    <expand macro="citations"/>
</tool>