<tool id="qiime_beta_diversity_through_plots" name="Compute beta diversity distance matrices" version="@WRAPPER_VERSION@.0">
    <description>and generate PCoA plots</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <stdio>
        <regex match="VisibleDeprecationWarning" source="both" level="warning" description="VisibleDeprecationWarning on numpy for `rank`"/>
    </stdio>
    <version_command>beta_diversity_through_plots.py --version</version_command>
    <command detect_errors="aggressive"><![CDATA[
        beta_diversity_through_plots.py
            --otu_table_fp '$otu_table_fp'
            --mapping_fp '$mapping_fp'
            --output_dir beta_diversity_through_plots
            #if $tree_fp
                --tree_fp '$tree_fp'
            #end if
            #if $parameter_fp
                --parameter_fp '$parameter_fp'
            #end if
            $color_by_all_fields
            $parallel
            -O "\${GALAXY_SLOTS:-4}"
            #if $seqs_per_sample
                --seqs_per_sample '$seqs_per_sample'
            #end if
            $suppress_emperor_plots

        && python $__tool_directory__/beta_diversity_through_plots_html_generation.py
            --data_directory beta_diversity_through_plots
            --html_file '$beta_diversity_pcoa'
            --html_dir '$beta_diversity_pcoa.files_path'
    ]]></command>
    <inputs>
        <param argument="--otu_table_fp" type="data" format="tabular,txt,biom" multiple="True" label="OTU table"/>
        <param argument="--mapping_fp" type="data" format="tabular,txt" multiple="True" label="Mapping file" help=""/>
        <param argument="--tree_fp" type="data" format="txt" optional="True" label="Tree file (Optional)" help=""/>
        <param argument="--parameter_fp" type="data" format="txt" label="Parameter file (Optional)" help="It specifies changes to the default behavior, e.g. beta diversity metrics" optional="true"/>
        <param argument="--color_by_all_fields" type="text" optional="True" label="Colored mapping fields" help="Can be included only fields with greater than one value and fewer values than the number of samples"/>
        <param argument="--parallel" type="boolean" truevalue="--parallel" falsevalue="" checked="False" label="Run in parallel where available?" help=""/>
        <param argument="--seqs_per_sample" type="integer" optional="True" label="Depth of coverage for even sampling (Optional)" help=""/>
        <param argument="--suppress_emperor_plots" type="boolean" truevalue="" falsevalue="--suppress_emperor_plots" checked="True" label="Generate emperor plots?" help=""/>
    </inputs>
    <outputs>
        <collection name="beta_diversity_matrix" type="list" label="${tool.name} on ${on_string}: Distance matrix for each metrics">
            <discover_datasets pattern="(?P&lt;designation&gt;.+)_dm\.txt" ext="txt" directory="beta_diversity_through_plots"/>
        </collection>
        <collection name="beta_diversity_pc" type="list" label="${tool.name} on ${on_string}: Principal coordinates for each metrics">
            <discover_datasets pattern="(?P&lt;designation&gt;.+)_pc\.txt" ext="txt" directory="beta_diversity_through_plots"/>
        </collection>
        <data format="html" name="beta_diversity_pcoa" label="${tool.name} on ${on_string}: Emperor PCoA plots"/>
    </outputs>
    <tests>
        <test>
            <param name="otu_table_fp" value="beta_diversity_through_plots/otu_table.biom"/>
            <param name="mapping_fp" value="beta_diversity_through_plots/map.txt"/>
            <param name="tree_fp" value="beta_diversity_through_plots/rep_set.tre"/>
            <param name="parallel" value="--parallel"/>
            <param name="suppress_emperor_plots" value=""/>
            <output_collection name="beta_diversity_matrix" type="list" count="2">
                <element name="unweighted_unifrac" file="beta_diversity_through_plots/unweighted_unifrac_dm.txt" ftype="txt"/>
                <element name="weighted_unifrac" file="beta_diversity_through_plots/weighted_unifrac_dm.txt" ftype="txt"/>
            </output_collection>
            <output_collection name="beta_diversity_pc" type="list" count="2">
                <element name="unweighted_unifrac" ftype="txt">
                    <assert_contents>
                        <has_text text="PC.355"/>
                        <has_text text="Species"/>
                        <has_text text="Site"/>
                    </assert_contents>
                </element>
                <element name="weighted_unifrac" file="beta_diversity_through_plots/weighted_unifrac_pc.txt" ftype="txt"/>
            </output_collection>
            <output name="beta_diversity_pcoa">
                <assert_contents>
                    <has_text text="unweighted_unifrac" />
                    <has_text text="weighted_unifrac" />
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[
**What it does**

This tool computes beta diversity distance matrices and generates PCoA plots in
several steps

    - Performs beta diversity analysis
    - Performs principal coordinate analysis
    - Generates 3D PCoA Plots

More information about this tool is available on
`QIIME documentation <http://qiime.org/scripts/beta_diversity_through_plots.html>`_.
    ]]></help>
    <citations>
        <expand macro="citations"/>
    </citations>
</tool>