--- a/tree.shared.xml	Tue Sep 05 16:53:53 2017 -0400
+++ b/tree.shared.xml	Tue Mar 20 22:19:37 2018 -0400
@@ -7,52 +7,52 @@
     <expand macro="stdio"/>
     <expand macro="version_command"/>
     <command><![CDATA[
-        @SHELL_OPTIONS@
+@SHELL_OPTIONS@
 
-        ## create symlinks to input datasets
-        ln -s "$input.dist" input_dist.dat &&
-        #if not $input.source == "shared":
-            ln -s "$input.name" input_name.dat &&
-        #end if
+## create symlinks to input datasets
+ln -s '$input.dist' input_dist.dat &&
+#if not $input.source == "shared":
+    ln -s '$input.name' input_name.dat &&
+#end if
 
-        echo 'tree.shared(
-            #if $input.source == "shared":
-                shared=input_dist.dat,
-                #if $input.groups:
-                    groups=${ str($input.groups).replace(",","-") },
-                #end if
-                #if $input.label:
-                    label=${ str($input.label).replace(",","-") },
-                #end if
-                #if $input.subsampling.use == "yes":
-                    #if $input.subsampling.subsample:
-                        subsample=$input.subsampling.subsample,
-                    #else
-                        subsample=T,
-                    #end if
-                    #if $input.subsampling.iters:
-                        iters="$input.subsampling.iters,
-                    #end if
-                #end if
-            #elif $input.source == "column":
-                column=input_dist.dat,
-                name=input_name.dat,
-            #elif $input.source == "phylip":
-                phylip=input_dist.dat,
-                #if $input.name:
-                    name=input_name.dat,
-                #end if
+echo 'tree.shared(
+    #if $input.source == "shared":
+        shared=input_dist.dat,
+        #if $input.groups:
+            groups=${ str($input.groups).replace(",","-") },
+        #end if
+        #if $input.label:
+            label=${ str($input.label).replace(",","-") },
+        #end if
+        #if $input.subsampling.use == "yes":
+            #if $input.subsampling.subsample:
+                subsample=$input.subsampling.subsample,
             #else
-                count=input_name.dat,
+                subsample=T,
             #end if
-            #if $calc:
-                calc=${ str($calc).replace(",","-") },
+            #if $input.subsampling.iters:
+                iters="$input.subsampling.iters,
             #end if
-            processors='\${GALAXY_SLOTS:-8}'
-        )'
-        | sed 's/ //g'  ## mothur trips over whitespace
-        | mothur
-        | tee mothur.out.log
+        #end if
+    #elif $input.source == "column":
+        column=input_dist.dat,
+        name=input_name.dat,
+    #elif $input.source == "phylip":
+        phylip=input_dist.dat,
+        #if $input.name:
+            name=input_name.dat,
+        #end if
+    #else
+        count=input_name.dat,
+    #end if
+    #if $calc:
+        calc=${ str($calc).replace(",","-") },
+    #end if
+    processors='\${GALAXY_SLOTS:-8}'
+)'
+| sed 's/ //g'  ## mothur trips over whitespace
+| mothur
+| tee mothur.out.log
     ]]></command>
     <inputs>
         <conditional name="input">
@@ -105,6 +105,7 @@
             <option value="jclass" selected="true">jclass - Community Membership Similarity the traditional Jaccard similarity coefficient based on the observed richness</option>
             <option value="thetayc" selected="true">thetayc - Community Structure Similarity the Yue &amp; Clayton theta similarity coefficient</option>
         </param>
+        <expand macro="param-savelog"/>
     </inputs>
     <outputs>
         <expand macro="logfile-output"/>
@@ -121,6 +122,7 @@
             <param name="source" value="phylip"/>
             <param name="dist" value="env.dist"/>
             <output name="tre" md5="c74a88ed448aad2d07059eda0b4161e9" ftype="mothur.tre"/>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
         <test><!-- test with shared and subsampling -->
@@ -131,6 +133,7 @@
             <output_collection name="trefiles" count="108">
                 <element name="jclass.0.32.all" md5="b8adfa6e41397b3815768f987836d102" ftype="mothur.tre"/>
             </output_collection>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
         <test><!-- test with shared and label and group select and all calculators -->
@@ -142,6 +145,7 @@
             <output_collection name="trefiles" count="117">
                 <element name="canberra.0.32" md5="477b061d738d24a7476dd4c90d9666cf" ftype="mothur.tre"/>
             </output_collection>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
         <test><!-- test with column and name file -->
@@ -149,11 +153,11 @@
             <param name="dist" value="amazon.pair.dist"/>
             <param name="name" value="amazon1.names"/>
             <output name="tre" md5="33cc8cb433f123e49b33b998186b74ed" ftype="mothur.tre"/>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
     </tests>
-    <help>
-<![CDATA[
+    <help><![CDATA[
 
 @MOTHUR_OVERVIEW@
 
@@ -163,7 +167,6 @@
 
 .. _tree.shared: https://www.mothur.org/wiki/Tree.shared
 
-]]>
-    </help>
+    ]]></help>
     <expand macro="citations"/>
 </tool>