--- a/get.sabund.xml	Tue Sep 05 17:03:32 2017 -0400
+++ b/get.sabund.xml	Tue Mar 20 22:27:36 2018 -0400
@@ -7,35 +7,37 @@
     <expand macro="stdio"/>
     <expand macro="version_command"/>
     <command><![CDATA[
-        @SHELL_OPTIONS@
+@SHELL_OPTIONS@
 
-        ## create symlinks to input datasets
-        ln -s "$otu" otu.dat &&
-        ln -s "$count" count.dat &&
+## create symlinks to input datasets
+ln -s '$otu' otu.dat &&
+ln -s '$count' count.dat &&
 
-        echo 'get.sabund(
-            #if $label:
-               label=${ str($label).replace(",","-") },
-            #end if
-            #if $count:
-                count=count.dat,
-            #end if
-            #if $otu.is_of_type("mothur.list"):
-                list=otu.dat
-            #elif $otu.is_of_type("mothur.rabund"):
-                rabund=otu.dat
-            #end if
-        )'
-        | sed 's/ //g'  ## mothur trips over whitespace
-        | mothur
-        | tee mothur.out.log
+echo 'get.sabund(
+    #if $label:
+       label=${ str($label).replace(",","-") },
+    #end if
+    #if $count:
+        count=count.dat,
+    #end if
+    #if $otu.is_of_type("mothur.list"):
+        list=otu.dat
+    #elif $otu.is_of_type("mothur.rabund"):
+        rabund=otu.dat
+    #end if
+)'
+| sed 's/ //g'  ## mothur trips over whitespace
+| mothur
+| tee mothur.out.log
     ]]></command>
     <inputs>
         <param name="otu" type="data" format="mothur.list,mothur.rabund" label="list,rabund - List or Rabund"/>
         <param name="label" type="select" optional="true" multiple="true" label="label - select OTU distance labels" help="(all used if none are selected)">
             <expand macro="labeloptions"/>
         </param>
-        <param name="count" type="data" format="mothur.count_table" optional="true" help="If your list file contains only the unique sequence names because you ran cluster with a count file, be sure to include the count file."/>
+        <param name="count" type="data" format="mothur.count_table" optional="true"
+            help="If your list file contains only the unique sequence names because you ran cluster with a count file, be sure to include the count file."/>
+        <expand macro="param-savelog"/>
     </inputs>
     <outputs>
         <expand macro="logfile-output"/>
@@ -45,17 +47,18 @@
         <test><!-- test rabund input -->
             <param name="otu" value="amazon.an.rabund" ftype="mothur.rabund"/>
             <output name="sabund" file="amazon.an.sabund2" ftype="mothur.sabund"/>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
         <test><!-- test otu list input -->
             <param name="otu" value="amazon.an.list" ftype="mothur.list"/>
             <param name="label" value="0.03,0.05"/>
             <output name="sabund" file="amazon.an.sabund3" ftype="mothur.sabund"/>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
     </tests>
-    <help>
-        <![CDATA[
+    <help><![CDATA[
 
 @MOTHUR_OVERVIEW@
 
@@ -69,7 +72,6 @@
 .. _rabund: https://www.mothur.org/wiki/Rabund_file
 .. _get.sabund: https://www.mothur.org/wiki/Get.sabund
 
-]]>
-    </help>
+    ]]></help>
     <expand macro="citations"/>
 </tool>