--- a/cooccurrence.xml	Tue Sep 05 17:12:25 2017 -0400
+++ b/cooccurrence.xml	Tue Mar 20 22:13:29 2018 -0400
@@ -7,26 +7,26 @@
     <expand macro="stdio"/>
     <expand macro="version_command"/>
     <command><![CDATA[
-        @SHELL_OPTIONS@
+@SHELL_OPTIONS@
 
-        ## create symlinks to input datasets
-        ln -s "$otu" otu.dat &&
+## create symlinks to input datasets
+ln -s '$otu' otu.dat &&
 
-        echo 'cooccurrence(
-            shared=otu.dat,
-            metric=$metric,
-            matrixmodel=$matrixmodel,
-            iters=$iters
-            #if $label:
-                ,label=${ str($label).replace(",","-") }
-            #end if
-            #if $groups:
-                ,groups=${ str($groups).replace(",","-") }
-            #end if
-        )'
-        | sed 's/ //g'  ## mothur trips over whitespace
-        | mothur
-        | tee mothur.out.log
+echo 'cooccurrence(
+    shared=otu.dat,
+    metric=$metric,
+    matrixmodel=$matrixmodel,
+    iters=$iters
+    #if $label:
+        ,label=${ str($label).replace(",","-") }
+    #end if
+    #if $groups:
+        ,groups=${ str($groups).replace(",","-") }
+    #end if
+)'
+| 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 file"/>
@@ -56,6 +56,7 @@
         <param name="label" type="select" optional="true" label="label - Select OTU Labels to include" multiple="true" help="By default all are included if no selection is made.">
             <expand macro="labeloptions"/>
         </param>
+        <expand macro="param-savelog"/>
     </inputs>
     <outputs>
         <expand macro="logfile-output"/>
@@ -72,6 +73,7 @@
                     <has_text text="0.05"/>
                 </assert_contents>
             </output>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
         <test><!-- test with label and group select -->
@@ -87,11 +89,11 @@
                     <has_text text="0.05"/>
                 </assert_contents>
             </output>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
     </tests>
-    <help>
-<![CDATA[
+    <help><![CDATA[
 
 @MOTHUR_OVERVIEW@
 
@@ -162,7 +164,7 @@
 .. _cooccurrence: https://www.mothur.org/wiki/Cooccurrence
 
 v1.26.0: Updated to Mothur 1.33
-]]>
-    </help>
+
+    ]]></help>
     <expand macro="citations"/>
 </tool>