--- a/phylo.diversity.xml	Tue Sep 05 17:10:13 2017 -0400
+++ b/phylo.diversity.xml	Tue Mar 20 22:24:23 2018 -0400
@@ -7,41 +7,41 @@
     <expand macro="stdio"/>
     <expand macro="version_command"/>
     <command><![CDATA[
-        @SHELL_OPTIONS@
+@SHELL_OPTIONS@
 
-        ## create symlinks to input datasets
-        ln -s "$tree" tree.dat &&
-        ln -s "$name" name.dat &&
-        ln -s "$count" count.dat &&
-        #if $grouping.use == "yes":
-            ln -s "$grouping.group" grouping.group.dat &&
-        #end if
+## create symlinks to input datasets
+ln -s '$tree' tree.dat &&
+ln -s '$name' name.dat &&
+ln -s '$count' count.dat &&
+#if $grouping.use == "yes":
+    ln -s '$grouping.group' grouping.group.dat &&
+#end if
 
-        echo 'phylo.diversity(
-            tree=tree.dat,
-            #if $grouping.use == "yes":
-                group=grouping.group.dat,
-                #if $grouping.groups:
-                    groups=${ str($grouping.groups).replace(",","-") },
-                #end if
-            #end if
-            #if $name:
-                name=name.dat,
-            #end if
-            iters=$iters,
-            freq=$freq,
-            scale=$scale,
-            collect=$collect,
-            rarefy=$rarefy,
-            summary=$summary,
-            #if $count:
-                count=count.dat,
-            #end if
-            processors='\${GALAXY_SLOTS:-8}'
-        )'
-        | sed 's/ //g'  ## mothur trips over whitespace
-        | mothur
-        | tee mothur.out.log
+echo 'phylo.diversity(
+    tree=tree.dat,
+    #if $grouping.use == "yes":
+        group=grouping.group.dat,
+        #if $grouping.groups:
+            groups=${ str($grouping.groups).replace(",","-") },
+        #end if
+    #end if
+    #if $name:
+        name=name.dat,
+    #end if
+    iters=$iters,
+    freq=$freq,
+    scale=$scale,
+    collect=$collect,
+    rarefy=$rarefy,
+    summary=$summary,
+    #if $count:
+        count=count.dat,
+    #end if
+    processors='\${GALAXY_SLOTS:-8}'
+)'
+| sed 's/ //g'  ## mothur trips over whitespace
+| mothur
+| tee mothur.out.log
     ]]></command>
     <inputs>
         <param name="tree" type="data" format="mothur.tre" label="tree - Phylogenetic Tree"/>
@@ -69,6 +69,7 @@
         <param name="summary" type="boolean" truevalue="true" falsevalue="false" checked="true" label="summary - Generate a summary file"/>
         <param name="collect" type="boolean" truevalue="true" falsevalue="false" checked="false" label="collect - Create a collectors curve"/>
         <param name="count" type="data" format="mothur.count_table" optional="true" label="count - a count_table" help="generated by count.seqs"/>
+        <expand macro="param-savelog"/>
     </inputs>
     <outputs>
         <expand macro="logfile-output"/>
@@ -87,6 +88,7 @@
             <param name="tree" value="treetest.tre" ftype="mothur.tre"/>
             <param name="use" value="no"/>
             <output name="summary_out" md5="a9feb4031094b555baf62e0165dd3637" ftype="tabular"/>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
         <test><!-- test with tree file and group file and all outputs -->
@@ -111,11 +113,11 @@
                     <has_text text="green"/>
                 </assert_contents>
             </output>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
     </tests>
-    <help>
-<![CDATA[
+    <help><![CDATA[
 
 @MOTHUR_OVERVIEW@
 
@@ -128,7 +130,6 @@
 
 v.1.21.0: Updated to Mothur 1.33, added count parameter
 
-]]>
-    </help>
+    ]]></help>
     <expand macro="citations"/>
 </tool>