<macros>
    <token name="@TOOL_VERSION@">1.1.1</token>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="1.1.1">picrust</requirement>
        </requirements>
    </xml>

    <xml name="version_command">
        <version_command>predict_metagenomes.py --version | cut -d" " -f3 </version_command>
    </xml>

    <xml name="otu-reference-precalculated">
        <!-- selection of "gg" picrust parameter reference data file -->
        <conditional name="gg">
           <param name="source" type="select" label="Select precalculated file from" help="">
               <option value="ref">Cached Reference</option>
               <option value="hist">History</option>
           </param>
           <when value="ref">
               <param name="precalc" type="select" label="Precalculated input marker gene copy number predictions on per-otu basis">
                   <options from_data_table="picrust_precalculated"/>
               </param>
           </when>
           <when value="hist">
               <param name="precalc" type="data" format="tabular" label="Precalculated input marker gene copy number predictions on per-otu basis"
                      help="files may be downloaded from PICRUSt website (see tool help below)" />
           </when>
       </conditional>
    </xml>

    <xml name="biom_format_select">
        <param name="output_type" type="select" label="Format of the output BIOM file">
            <option value="hdf5" selected="true">HDF5</option>
            <option value="json">JSON</option>
            <option value="tsv">Classic (tab-separated text)</option>
        </param>
    </xml>

    <xml name="biom_format_select_no_json">
        <param name="output_type" type="select" label="Format of the output BIOM file">
            <option value="hdf5" selected="true">HDF5</option>
            <option value="tsv">Classic (tab-separated text)</option>
        </param>
    </xml>

    <xml name="biom_output">
        <data name="out_biom" format="tabular" label="${tool.name} on ${on_string}: Normalized OTUs">
            <change_format>
                <when input="output_type" value="json" format="biom1"/>
                <when input="output_type" value="tsv" format="tabular"/>
                <when input="output_type" value="hdf5" format="h5"/>
            </change_format>
        </data>
    </xml>

    <token name="@OUTPUT_CONVERSION_COMMANDS@"><![CDATA[
        #if $output_type == "hdf5":
            && mv tempbiom '$out_biom'
        #elif $output_type == "tsv":
            && biom convert -i tempbiom -o '$out_biom' --to-tsv
        #else:
            && biom convert -i tempbiom -o '$out_biom' --to-json
        #end if
    ]]></token>

    <token name="@PICRUST_OVERVIEW@">
<![CDATA[
**PICRUSt: Phylogenetic Investigation of Communities by Reconstruction of Unobserved States**

The PICRUSt project aims to support prediction of the unobserved character states in a community of
organisms from phylogenetic information about the organisms in that community. The primary application
is to predict gene family abundance (e.g. the metagenome) in environmental DNA samples for which only
marker gene (e.g. 16S rRNA gene) data are available. This is an open source, international, collaborative
bioinformatics project developed in the Huttenhower, Beiko, Langille, Vega Thurber, Knight and Caporaso labs.

For more information please visit:

- PICRUSt Documentation: https://picrust.github.io/picrust/
- PICRUSt GitHub: https://github.com/picrust/picrust/
- PICRUSt Support: https://groups.google.com/d/forum/picrust-users

**Reference Data**

Precalculated files: http://kronos.pharmacology.dal.ca/public_files/picrust/picrust_precalculated_v1.1.1/13_5/

]]>
    </token>

    <xml name="citations">
        <citations>
            <citation type="doi">10.1038/nbt.2676</citation>
            <yield/>
        </citations>
    </xml>

</macros>