--- a/mantel.xml	Tue Sep 05 17:00:01 2017 -0400
+++ b/mantel.xml	Tue Mar 20 22:18:20 2018 -0400
@@ -7,21 +7,21 @@
     <expand macro="stdio"/>
     <expand macro="version_command"/>
     <command><![CDATA[
-        @SHELL_OPTIONS@
+@SHELL_OPTIONS@
 
-        ## create symlinks to input datasets
-        ln -s "$dist" dist.dat &&
-        ln -s "$dist2" dist2.dat &&
+## create symlinks to input datasets
+ln -s '$dist' dist.dat &&
+ln -s '$dist2' dist2.dat &&
 
-        echo 'mantel(
-            phylip1=dist.dat,
-            phylip2=dist2.dat,
-            method=$method,
-            iters=$iters
-        )'
-        | sed 's/ //g'  ## mothur trips over whitespace
-        | mothur
-        | tee mothur.out.log
+echo 'mantel(
+    phylip1=dist.dat,
+    phylip2=dist2.dat,
+    method=$method,
+    iters=$iters
+)'
+| sed 's/ //g'  ## mothur trips over whitespace
+| mothur
+| tee mothur.out.log
     ]]></command>
     <inputs>
         <param name="dist" type="data" format="mothur.dist,mothur.lower.dist,mothur.square.dist" label="phylip - Distance Matrix"/>
@@ -32,6 +32,7 @@
                 <option value="kendall">kendall</option>
         </param>
         <param name="iters" type="integer" value="1000" label="iters - Number of random configuration to try (default 1000)"/>
+        <expand macro="param-savelog"/>
     </inputs>
     <outputs>
         <expand macro="logfile-output"/>
@@ -46,11 +47,11 @@
                     <has_line_matching expression="^Mantel\tpValue$"/>
                 </assert_contents>
             </output>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
     </tests>
-    <help>
-<![CDATA[
+    <help><![CDATA[
 
 @MOTHUR_OVERVIEW@
 
@@ -61,7 +62,6 @@
 .. _matrices: //www.mothur.org/wiki/Phylip-formatted_distance_matrix
 .. _mantel: https://www.mothur.org/wiki/Mantel
 
-]]>
-    </help>
+    ]]></help>
     <expand macro="citations"/>
 </tool>