--- a/collect.single.xml	Tue Sep 05 16:33:02 2017 -0400
+++ b/collect.single.xml	Wed Feb 14 09:17:21 2018 -0500
@@ -7,32 +7,32 @@
     <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 'collect.single(
-            #if $otu.is_of_type("mothur.rabund"):
-                rabund=otu.dat,
-            #elif $otu.is_of_type("mothur.sabund"):
-                sabund=otu.dat,
-            #elif $otu.is_of_type("mothur.shared"):
-                shared=otu.dat,
-            #elif $otu.is_of_type("mothur.list"):
-                list=otu.dat,
-            #end if
-            #if $label:
-                label=${ str($label).replace(",","-") },
-            #end if
-            calc=${ str($calc).replace(",","-") },
-            abund=$abund,
-            freq=$freq
-        )'
-        | sed 's/ //g'  ## mothur trips over whitespace
-        | mothur
-        | tee mothur.out.log
-        && rm otu.dat  ## don't want this collected into datacollection
+echo 'collect.single(
+    #if $otu.is_of_type("mothur.rabund"):
+        rabund=otu.dat,
+    #elif $otu.is_of_type("mothur.sabund"):
+        sabund=otu.dat,
+    #elif $otu.is_of_type("mothur.shared"):
+        shared=otu.dat,
+    #elif $otu.is_of_type("mothur.list"):
+        list=otu.dat,
+    #end if
+    #if $label:
+        label=${ str($label).replace(",","-") },
+    #end if
+    calc=${ str($calc).replace(",","-") },
+    abund=$abund,
+    freq=$freq
+)'
+| sed 's/ //g'  ## mothur trips over whitespace
+| mothur
+| tee mothur.out.log
+&& rm otu.dat  ## don't want this collected into datacollection
     ]]></command>
     <inputs>
         <param name="otu" type="data" format="mothur.list,mothur.rabund,mothur.sabund,mothur.shared" label="list,rabund,sabund,shared - OTU List"/>
@@ -67,7 +67,8 @@
             <option value="nseqs">nseqs - Utility the number of sequences in a sample</option>
         </param>
         <param name="abund" type="integer" value="10" min="0" label="abund - ACE Estimator threshold for abundant versus rare OTUs (default 10)"/>
-        <param name="freq" type="float" value="100" min="0" label="freq - frequency for output (default is every 100 sequences)" help="Use a decimal between 0 and 1 to set the frequency as a percentage of the number of sequences"/>
+        <param name="freq" type="float" value="100" min="0" label="freq - frequency for output (default is every 100 sequences)"
+            help="Use a decimal between 0 and 1 to set the frequency as a percentage of the number of sequences"/>
     </inputs>
     <outputs>
         <expand macro="logfile-output"/>
@@ -93,8 +94,7 @@
             <expand macro="logfile-test"/>
         </test>
     </tests>
-    <help>
-<![CDATA[
+    <help><![CDATA[
 
 @MOTHUR_OVERVIEW@
 
@@ -105,7 +105,7 @@
 
 .. _calculators: https://www.mothur.org/wiki/Calculators
 .. _collect.single: https://www.mothur.org/wiki/Collect.single
-]]>
-    </help>
+
+    ]]></help>
     <expand macro="citations"/>
 </tool>