--- a/collect.shared.xml	Tue Sep 05 16:33:20 2017 -0400
+++ b/collect.shared.xml	Wed Feb 14 10:12:35 2018 -0500
@@ -7,29 +7,29 @@
     <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.shared(
-            shared=otu.dat,
-            #if $label:
-                label=${ str($label).replace(",","-") },
-            #end if
-            #if $calc:
-                calc=${ str($calc).replace(",","-") },
-            #end if
-            #if $groups:
-                groups=${ str($groups).replace(",","-") },
-            #end if
-            freq=$freq,
-            all=true
-        )'
-        | sed 's/ //g'  ## mothur trips over whitespace
-        | mothur
-        | tee mothur.out.log
-        && rm otu.dat  ## don't want this collected into datacollection
+echo 'collect.shared(
+    shared=otu.dat,
+    #if $label:
+        label=${ str($label).replace(",","-") },
+    #end if
+    #if $calc:
+        calc=${ str($calc).replace(",","-") },
+    #end if
+    #if $groups:
+        groups=${ str($groups).replace(",","-") },
+    #end if
+    freq=$freq,
+    all=true
+)'
+| 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.shared" label="shared - OTU Shared"/>
@@ -56,7 +56,8 @@
             <option value="thetan" selected="true">thetan - Community Structure Similarity the Smith theta similarity coefficient</option>
             <option value="thetayc" selected="true">thetayc - Community Structure Similarity the Yue &amp; Clayton theta similarity coefficient</option>
         </param>
-        <param name="freq" type="float" value="100" label="freq - indicates when to output your data" help="by default it is set to 100. But you can set it to a percentage of the number of sequence. For example freq=0.10, means 10%" min="0.0" max="100.0"/>
+        <param name="freq" type="float" value="100" label="freq - indicates when to output your data"
+            help="by default it is set to 100. But you can set it to a percentage of the number of sequence. For example freq=0.10, means 10%" min="0.0" max="100.0"/>
     </inputs>
     <outputs>
         <expand macro="logfile-output"/>
@@ -83,8 +84,7 @@
             <expand macro="logfile-test"/>
         </test>
     </tests>
-    <help>
-<![CDATA[
+    <help><![CDATA[
 
 @MOTHUR_OVERVIEW@
 
@@ -94,7 +94,7 @@
 
 .. _calculators: https://www.mothur.org/wiki/Calculators
 .. _collect.shared: https://www.mothur.org/wiki/Collect.shared
-]]>
-    </help>
+
+    ]]></help>
     <expand macro="citations"/>
 </tool>