--- a/unifrac.weighted.xml	Tue Sep 05 17:18:43 2017 -0400
+++ b/unifrac.weighted.xml	Tue Mar 20 22:20:06 2018 -0400
@@ -7,53 +7,54 @@
     <expand macro="stdio"/>
     <expand macro="version_command"/>
     <command><![CDATA[
-        @SHELL_OPTIONS@
+@SHELL_OPTIONS@
 
-        ## create symlinks to input datasets
-        ln -s "$tree" tree.dat &&
-        ln -s "$group" group.dat &&
-        ln -s "$name" name.dat &&
-        ln -s "$count" count.dat &&
+## create symlinks to input datasets
+ln -s '$tree' tree.dat &&
+ln -s '$group' group.dat &&
+ln -s '$name' name.dat &&
+ln -s '$count' count.dat &&
 
-        echo 'unifrac.weighted(
-            tree=tree.dat,
-            #if $group:
-                group=group.dat,
-                #if $groups:
-                    groups=${ str($groups).replace(",","-") },
-                #end if
-            #end if
-            #if $name:
-                name=name.dat,
-            #end if
-            iters=$iters,
-            #if $subsampling.use == "yes":
-                #if $subsampling.subsample:
-                    subsample=$subsampling.subsample,
-                #else
-                    subsample=T,
-                #end if
-                consensus=$subsampling.consensus,
-            #else
-                random=$random,
-            #end if
-            #if $distance:
-                distance=$distance,
-            #end if
-            #if $count:
-                count=count.dat,
-            #end if
-            root=$root,
-            processors='\${GALAXY_SLOTS:-1}'
-        )'
-        | sed 's/ //g'  ## mothur trips over whitespace
-        | mothur
-        | tee mothur.out.log
-        ## rename some datasets
-        #if $subsampling.use == "yes":
-            && mv tree.*.ave.dist tree.ave
-            && mv tree.*.std.dist tree.std
+echo 'unifrac.weighted(
+    tree=tree.dat,
+    #if $group:
+        group=group.dat,
+        #if $groups:
+            groups=${ str($groups).replace(",","-") },
+        #end if
+    #end if
+    #if $name:
+        name=name.dat,
+    #end if
+    iters=$iters,
+    #if $subsampling.use == "yes":
+        #if $subsampling.subsample:
+            subsample=$subsampling.subsample,
+        #else
+            subsample=T,
         #end if
+        consensus=$subsampling.consensus,
+    #else
+        random=$random,
+    #end if
+    #if $distance:
+        distance=$distance,
+    #end if
+    #if $count:
+        count=count.dat,
+    #end if
+    root=$root,
+    processors='\${GALAXY_SLOTS:-1}'
+)'
+| sed 's/ //g'  ## mothur trips over whitespace
+| mothur
+| tee mothur.out.log
+
+## rename some datasets
+#if $subsampling.use == "yes":
+    && mv tree.*.ave.dist tree.ave
+    && mv tree.*.std.dist tree.std
+#end if
     ]]></command>
     <inputs>
         <param name="tree" type="data" format="mothur.tre" label="tree - Tree"/>
@@ -84,6 +85,7 @@
         </param>
         <param name="root" type="boolean" truevalue="true" falsevalue="false" checked="false" label="root - the entire root in your calculations"/>
         <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"/>
@@ -125,6 +127,7 @@
             <param name="groups" value="A,B,C"/>
             <output name="summary" md5="f723493c1b909f5dbe5688d36be9fe73" ftype="tabular"/>
             <output name="dist" md5="3660f333ac1326c8df213d1d3af1f865" ftype="mothur.lower.dist"/>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
         <test><!-- test with random and no subsampling -->
@@ -141,6 +144,7 @@
                 </assert_contents>
             </output>
             <output name="dist" md5="3660f333ac1326c8df213d1d3af1f865" ftype="mothur.lower.dist"/>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
         <test><!-- test with group file and group select -->
@@ -150,6 +154,7 @@
             <param name="distance" value="square"/>
             <output name="summary" md5="c253d4a3225804ad24b6c2e3a1095040" ftype="tabular"/>
             <output name="dist" md5="7df2d4a2e69b9c1259d39fe59165734f" ftype="mothur.square.dist"/>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
         <test><!-- test with subsample and consensus -->
@@ -190,11 +195,11 @@
                     <has_text text="C"/>
                 </assert_contents>
             </output>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
     </tests>
-    <help>
-<![CDATA[
+    <help><![CDATA[
 
 @MOTHUR_OVERVIEW@
 
@@ -204,7 +209,6 @@
 
 .. _unifrac.weighted: https://www.mothur.org/wiki/Unifrac.weighted
 
-]]>
-    </help>
+    ]]></help>
     <expand macro="citations"/>
 </tool>