--- a/get.otulist.xml	Tue Sep 05 16:55:50 2017 -0400
+++ b/get.otulist.xml	Tue Mar 20 22:16:35 2018 -0400
@@ -7,31 +7,34 @@
     <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 'get.otulist(
-            list=otu.dat,
-            #if $label:
-                label=${ str($label).replace(",","-") },
-            #end if
-            sort=$sort
-        )'
-        | sed 's/ //g'  ## mothur trips over whitespace
-        | mothur
-        | tee mothur.out.log
+echo 'get.otulist(
+    list=otu.dat,
+    #if $label:
+        label=${ str($label).replace(",","-") },
+    #end if
+    sort=$sort
+)'
+| sed 's/ //g'  ## mothur trips over whitespace
+| mothur
+| tee mothur.out.log
     ]]></command>
     <inputs>
         <param name="otu" type="data" format="mothur.list" label="list - OTU List"/>
         <param name="label" type="select" multiple="true" label="label - select OTU distance labels" help="By default, uses all if none are selected.">
             <expand macro="labeloptions"/>
         </param>
-        <param name="sort" type="select" label="sort - select the output format" help="If otu is selected the output will be otu number followed by the list of names in that otu. If name is selected the output will be a sequence name followed by its otu number">
+        <param name="sort" type="select" label="sort - select the output format"
+            help="If otu is selected the output will be otu number followed by the list of names in that otu.
+            If name is selected the output will be a sequence name followed by its otu number">
             <option value="otu" selected="true">otu</option>
             <option value="name">name</option>
         </param>
+        <expand macro="param-savelog"/>
     </inputs>
     <outputs>
         <expand macro="logfile-output"/>
@@ -45,6 +48,7 @@
             <output_collection name="otufiles" count="36">
                 <element name="0.22" md5="9dfa8c449a45d66e7ae6b30b34a821cb" ftype="mothur.list"/>
             </output_collection>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
         <test>
@@ -53,11 +57,11 @@
             <output_collection name="otufiles" count="4">
                 <element name="0.41" md5="b40486b3739a6d5b86459dc17a23c253" ftype="mothur.list"/>
             </output_collection>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
     </tests>
-    <help>
-<![CDATA[
+    <help><![CDATA[
 
 @MOTHUR_OVERVIEW@
 
@@ -69,7 +73,7 @@
 .. _get.otulist: https://www.mothur.org/wiki/Get.otulist
 
 v.1.20.0: Updated to Mothur 1.33
-]]>
-    </help>
+
+    ]]></help>
     <expand macro="citations"/>
 </tool>