--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/beta_diversity_through_plots.xml	Tue Feb 02 05:50:37 2016 -0500
@@ -0,0 +1,132 @@
+<tool id="qiime_beta_diversity_through_plots" name="Compute beta diversity distance 
+    matrices" version="1.9.1">
+
+    <description>and generate PCoA plots</description>
+
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+
+    <expand macro="requirements" />
+
+    <version_command><![CDATA[
+        beta_diversity_through_plots.py --version
+    ]]>
+    </version_command>
+
+    <stdio>
+        <regex match="VisibleDeprecationWarning"
+               source="both"
+               level="warning"
+               description="VisibleDeprecationWarning on numpy for `rank`" />
+    </stdio>
+
+    <command>
+<![CDATA[  
+        beta_diversity_through_plots.py 
+            -i $otu_table_fp
+            -m $mapping_fp
+            -o beta_diversity_through_plots
+
+            #if $tree_fp
+                -t $tree_fp
+            #end if
+
+            #if $parameter_fp
+                -p $parameter_fp
+            #end if
+
+            $parallel
+            -O "\${GALAXY_SLOTS:-4}"
+
+            #if $seqs_per_sample
+                -e $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 name="otu_table_fp" type="data" format="tabular,txt,tsv,biom" 
+            label="OTU table" help="(-i/--otu_table_fp)" 
+            multiple="True"/>
+
+        <param name="mapping_fp" type="data" format="tabular,txt,tsv" 
+            label="Mapping file" help="(-m/--mapping_fp)" 
+            multiple="True"/>
+
+        <param name="tree_fp" type="data" format="txt" 
+            label="Tree file (Optional)" help="(-t/--tree_fp)" 
+            optional="True"/>
+
+        <param name="parameter_fp" type="data" format="txt" 
+            label="Parameter file (Optional)" help="It specifies changes to the default 
+            behavior, e.g. beta diversity metrics (-p/--parameter_fp)" 
+            optional="true"/>
+
+        <param name="color_by_all_fields" type="text" label="Colored mapping 
+            fields" optional="True" help="Can be included only fields with 
+            greater than one value and fewer values than the number of samples
+            (--color_by_all_fields)" />
+
+        <param name="parallel" type="boolean" label="Run in parallel where 
+            available?" truevalue="--parallel" falsevalue="" checked="False" 
+            help="(-a, --parallel)" />
+
+        <param name="seqs_per_sample" type="integer" label="Depth of coverage for 
+            even sampling (Optional)" help="(-e/--seqs_per_sample)" optional="True"/>
+
+        <param name="suppress_emperor_plots" type="boolean" label="Generate 
+            emperor plots?" truevalue="" falsevalue="--suppress_emperor_plots" checked="True" 
+            help="(--suppress_emperor_plots)" />
+
+    </inputs>
+
+    <outputs>
+        <data format="txt" name="beta_diversity_matrix">
+            <discover_datasets pattern="(?P&lt;designation&gt;.+)_dm\.txt" ext="txt" 
+                directory="beta_diversity_through_plots" visible="true" />
+        </data>
+
+        <data format="txt" name="beta_diversity_pc">
+            <discover_datasets pattern="(?P&lt;designation&gt;.+)_pc\.txt" ext="txt" 
+                directory="beta_diversity_through_plots" visible="true" />
+        </data>
+
+        <data format="html" name="beta_diversity_pcoa" 
+            label="${tool.name} on ${on_string}: PCoA"/>
+    </outputs>
+
+    <tests>
+        <test>
+        </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>