--- a/make.group.xml	Tue Sep 05 16:21:58 2017 -0400
+++ b/make.group.xml	Wed Feb 14 09:13:47 2018 -0500
@@ -7,35 +7,34 @@
     <expand macro="stdio"/>
     <expand macro="version_command"/>
     <command><![CDATA[
-        @SHELL_OPTIONS@
+@SHELL_OPTIONS@
 
-        #set fastas = ''
-        #set groups = ''
-        #set count = 0
+#set fastas = ''
+#set groups = ''
+#set count = 0
 
-        #if $method.how == 'collection':
-            #for $i in $method.fasta_collection:
-                ln -s '$i' fasta_${i.element_identifier}.dat &&
-                #set fastas+='fasta_'+$i.element_identifier+'.dat-'
-                #set groups+=$i.element_identifier+'-'
-            #end for
-        #else
-            #for $i in $method.inputs:
-                ln -s '$i.fasta' fasta_${count}.dat &&
-                #set fastas+='fasta_'+str($count)+'.dat-'
-                #set groups+=str($i.group)+'-'
-                #set count+=1
-            #end for
-        #end if
+#if $method.how == 'collection':
+    #for $i in $method.fasta_collection:
+        ln -s '$i' fasta_${i.element_identifier}.dat &&
+        #set fastas+='fasta_'+$i.element_identifier+'.dat-'
+        #set groups+=$i.element_identifier+'-'
+    #end for
+#else
+    #for $i in $method.inputs:
+        ln -s '$i.fasta' fasta_${count}.dat &&
+        #set fastas+='fasta_'+str($count)+'.dat-'
+        #set groups+=str($i.group)+'-'
+        #set count+=1
+    #end for
+#end if
 
-        echo 'make.group(
-            fasta=${ str($fastas).rstrip('-') },
-            groups=${ str($groups).rstrip('-') }
-        )'
-        | sed 's/ //g'  ## mothur trips over whitespace
-        | mothur
-        | tee mothur.out.log
-
+echo 'make.group(
+    fasta=${ str($fastas).rstrip('-') },
+    groups=${ str($groups).rstrip('-') }
+)'
+| sed 's/ //g'  ## mothur trips over whitespace
+| mothur
+| tee mothur.out.log
     ]]></command>
     <inputs>
         <conditional name="method">
@@ -84,8 +83,7 @@
            <expand macro="logfile-test"/>
         </test>
     </tests>
-    <help>
-<![CDATA[
+    <help><![CDATA[
 
 @MOTHUR_OVERVIEW@
 
@@ -96,7 +94,6 @@
 .. _group: https://www.mothur.org/wiki/Group_file
 .. _make.group: https://www.mothur.org/wiki/Make.group
 
-]]>
-    </help>
+    ]]></help>
     <expand macro="citations"/>
 </tool>