--- a/heatmap.bin.xml	Tue Sep 05 16:37:11 2017 -0400
+++ b/heatmap.bin.xml	Wed Feb 14 09:28:56 2018 -0500
@@ -7,37 +7,37 @@
     <expand macro="stdio"/>
     <expand macro="version_command"/>
     <command><![CDATA[
-        @SHELL_OPTIONS@
+@SHELL_OPTIONS@
 
-        ## create symlinks to input datasets
-        ln -s "$input.otu" input_otu.dat &&
+## create symlinks to input datasets
+ln -s '$input.otu' input_otu.dat &&
 
-        echo 'heatmap.bin(
-            #if $input.otu.is_of_type("mothur.rabund"):
-                rabund=input_otu.dat,
-            #elif $input.otu.is_of_type("mothur.sabund"):
-                sabund=input_otu.dat,
-            #elif $input.otu.is_of_type("mothur.list"):
-                list=input_otu.dat,
-            #elif $input.otu.is_of_type("mothur.relabund"):
-                relabund=input_otu.dat,
-            #elif $input.otu.is_of_type("mothur.shared"):
-                shared=input_otu.dat,
-            #end if
-            #if $input.has_groups == 'yes' and $input.groups:
-                groups=${ str($input.groups).replace(",","-") },
-            #end if
-            #if $input.label:
-                label=${ str($input.label).replace(",","-") },
-            #end if
-            scale=$scale,
-            sorted=$sorted,
-            numotu=$numotu,
-            fontsize=$fontsize
-        )'
-        | sed 's/ //g'  ## mothur trips over whitespace
-        | mothur
-        | tee mothur.out.log
+echo 'heatmap.bin(
+    #if $input.otu.is_of_type("mothur.rabund"):
+        rabund=input_otu.dat,
+    #elif $input.otu.is_of_type("mothur.sabund"):
+        sabund=input_otu.dat,
+    #elif $input.otu.is_of_type("mothur.list"):
+        list=input_otu.dat,
+    #elif $input.otu.is_of_type("mothur.relabund"):
+        relabund=input_otu.dat,
+    #elif $input.otu.is_of_type("mothur.shared"):
+        shared=input_otu.dat,
+    #end if
+    #if $input.has_groups == 'yes' and $input.groups:
+        groups=${ str($input.groups).replace(",","-") },
+    #end if
+    #if $input.label:
+        label=${ str($input.label).replace(",","-") },
+    #end if
+    scale=$scale,
+    sorted=$sorted,
+    numotu=$numotu,
+    fontsize=$fontsize
+)'
+| sed 's/ //g'  ## mothur trips over whitespace
+| mothur
+| tee mothur.out.log
     ]]></command>
     <inputs>
         <conditional name="input">
@@ -116,8 +116,7 @@
             <expand macro="logfile-test"/>
         </test>
     </tests>
-    <help>
-<![CDATA[
+    <help><![CDATA[
 
 @MOTHUR_OVERVIEW@
 
@@ -131,7 +130,7 @@
 .. _heatmap.bin: https://www.mothur.org/wiki/Heatmap.bin
 
 v.1.21.0: Updated to Mothur 1.33
-]]>
-    </help>
+
+    ]]></help>
     <expand macro="citations"/>
 </tool>