--- a/metastats.xml	Tue Sep 05 17:08:36 2017 -0400
+++ b/metastats.xml	Tue Mar 20 22:26:03 2018 -0400
@@ -7,31 +7,31 @@
     <expand macro="stdio"/>
     <expand macro="version_command"/>
     <command><![CDATA[
-        @SHELL_OPTIONS@
+@SHELL_OPTIONS@
 
-        ## create symlinks to input datasets
-        ln -s "$otu" otu.dat &&
-        ln -s "$design" design.dat &&
+## 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
+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"/>
@@ -51,6 +51,7 @@
         </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"/>
+        <expand macro="param-savelog"/>
     </inputs>
     <outputs>
         <expand macro="logfile-output"/>
@@ -63,7 +64,7 @@
             <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">
+                <element name="0.23.tardis_dalek" ftype="txt">
                     <assert_contents>
                         <has_text text="group1"/>
                         <has_text text="group2"/>
@@ -73,6 +74,7 @@
                     </assert_contents>
                 </element>
             </output_collection>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
         <test>
@@ -84,7 +86,7 @@
             <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">
+                <element name="0.23.tardis_dalek" ftype="txt">
                     <assert_contents>
                         <has_text text="group1"/>
                         <has_text text="group2"/>
@@ -94,11 +96,11 @@
                     </assert_contents>
                 </element>
             </output_collection>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
     </tests>
-    <help>
-<![CDATA[
+    <help><![CDATA[
 
 @MOTHUR_OVERVIEW@
 
@@ -109,7 +111,7 @@
 .. _metastats: https://www.mothur.org/wiki/Metastats
 
 v.1.21.0: Updated to mothur 1.33
-]]>
-    </help>
+
+    ]]></help>
     <expand macro="citations"/>
 </tool>