--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/metastats.xml	Fri May 19 05:19:54 2017 -0400
@@ -0,0 +1,115 @@
+<tool profile="16.07" id="mothur_metastats" name="Metastats" version="@WRAPPER_VERSION@.0">
+    <description>generate principle components plot data</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <expand macro="stdio"/>
+    <expand macro="version_command"/>
+    <command><![CDATA[
+        @SHELL_OPTIONS@
+
+        ## create symlinks to input datasets
+        ln -s "$otu" otu.dat &&
+        ln -s "$design" design.dat &&
+
+        echo 'metastats(
+            shared=otu.dat,
+            design=design.dat,
+            #if $label:
+                label=${ str($label).replace(",","-") },
+            #end if
+            #if $groups:
+                groups=${ str($groups).replace(",","-") },
+            #end if
+            #if $sets:
+                sets=${ str($sets).replace(",","-") },
+            #end if
+            iters=$iters,
+            threshold=$threshold,
+            processors='\${GALAXY_SLOTS:-8}'
+        )'
+        | sed 's/ //g'  ## mothur trips over whitespace
+        | mothur
+        | tee mothur.out.log
+    ]]></command>
+    <inputs>
+        <param name="otu" type="data" format="mothur.shared" label="shared - OTU Shared"/>
+        <param name="design" type="data" format="mothur.design" label="design - assign groups to new grouping" help="design has 2 columns: group(col 1) and grouping(col 2) (separated by a TAB character) use make.design"/>
+        <param name="label" type="select" label="label - OTU Labels" multiple="true">
+            <expand macro="labeloptions"/>
+        </param>
+        <param name="sets" type="select" label="sets - group sets to analyze" multiple="true">
+            <options>
+                <filter type="data_meta" ref="design" key="groups"/>
+            </options>
+        </param>
+        <param name="groups" type="select" label="groups - Groups to consider" multiple="true">
+            <options>
+                <filter type="data_meta" ref="otu" key="groups"/>
+            </options>
+        </param>
+        <param name="iters" type="integer" value="1000" min="0" label="iters - Number of randomizations (default 1000)"/>
+        <param name="threshold" type="float" value="0.05" min="0" max="1" label="threshold - significance level to reject null hypotheses"/>
+    </inputs>
+    <outputs>
+        <expand macro="logfile-output"/>
+        <collection name="metastats" type="list" label="${tool.name} on ${on_string}: metastats">
+            <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.metastats" format="txt"/>
+        </collection>
+    </outputs>
+    <tests>
+        <test>
+            <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
+            <param name="design" value="toymothur.design2" ftype="mothur.design"/>
+            <output_collection name="metastats" count="36">
+                <element name="0.23.tardis-dalek" ftype="txt">
+                    <assert_contents>
+                        <has_text text="group1"/>
+                        <has_text text="group2"/>
+                        <has_text text="OTU"/>
+                        <has_text text="variance"/>
+                        <has_text text="1000 permutations"/>
+                    </assert_contents>
+                </element>
+            </output_collection>
+            <expand macro="logfile-test"/>
+        </test>
+        <test>
+            <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
+            <param name="design" value="toymothur.design2" ftype="mothur.design"/>
+            <param name="iters" value="42"/>
+            <param name="threshold" value="0.1"/>
+            <param name="label" value="0.03,0.05,0.23"/>
+            <param name="groups" value="forest,pasture"/>
+            <param name="sets" value="tardis,dalek"/>
+            <output_collection name="metastats" count="3">
+                <element name="0.23.tardis-dalek" ftype="txt">
+                    <assert_contents>
+                        <has_text text="group1"/>
+                        <has_text text="group2"/>
+                        <has_text text="OTU"/>
+                        <has_text text="variance"/>
+                        <has_text text="42 permutations"/>
+                    </assert_contents>
+                </element>
+            </output_collection>
+            <expand macro="logfile-test"/>
+        </test>
+    </tests>
+    <help>
+<![CDATA[
+
+@MOTHUR_OVERVIEW@
+
+**Command Documentation**
+
+The metastats_ command generate principle components plot data.
+
+.. _metastats: https://www.mothur.org/wiki/Metastats
+
+v.1.21.0: Updated to mothur 1.33
+]]>
+    </help>
+    <expand macro="citations"/>
+</tool>