--- a/consensus.seqs.xml	Tue Sep 05 16:06:06 2017 -0400
+++ b/consensus.seqs.xml	Wed Feb 14 09:43:32 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 "$fasta" fasta.dat &&
-        ln -s "$name" name.dat &&
-        ln -s "$count" count.dat &&
-        #if $perotu.use == "yes":
-            ln -s "$perotu.otu" perotu.otu.dat &&
-        #end if
+## create symlinks to input datasets
+ln -s '$fasta' fasta.dat &&
+ln -s '$name' name.dat &&
+ln -s '$count' count.dat &&
+#if $perotu.use == "yes":
+    ln -s '$perotu.otu' perotu.otu.dat &&
+#end if
 
-        echo 'consensus.seqs(
-            fasta=fasta.dat
-            #if $name:
-                ,name=name.dat
-            #end if
-            #if $cutoff:
-                ,cutoff=$cutoff
-            #end if
-            #if $perotu.use == "yes":
-                ,list=perotu.otu.dat
-                #if $perotu.label:
-                    ,label=${ str($perotu.label).replace(",","-") }
-                #end if
-            #end if
-            #if $count:
-                ,count=count.dat
-            #end if
-        )'
-        | sed 's/ //g'  ## mothur trips over whitespace
-        | mothur
-        | tee mothur.out.log
+echo 'consensus.seqs(
+    fasta=fasta.dat
+    #if $name:
+        ,name=name.dat
+    #end if
+    #if $cutoff:
+        ,cutoff=$cutoff
+    #end if
+    #if $perotu.use == "yes":
+        ,list=perotu.otu.dat
+        #if $perotu.label:
+            ,label=${ str($perotu.label).replace(",","-") }
+        #end if
+    #end if
+    #if $count:
+        ,count=count.dat
+    #end if
+)'
+| sed 's/ //g'  ## mothur trips over whitespace
+| mothur
+| tee mothur.out.log
     ]]></command>
     <inputs>
         <param name="fasta" type="data" format="mothur.align" label="fasta - Sequences to Bin" help="Sequences must be aligned"/>
@@ -55,7 +55,8 @@
             </when>
             <when value="no"/>
         </conditional>
-        <param name="cutoff" type="integer" value="" optional="True" min="1" max="100" label="Cutoff - set a percentage of sequences that support the base" help="For example: cutoff=95 would return the base that was supported by at least 95% of sequences. Must be between 1 and 100. Optional"/>
+        <param name="cutoff" type="integer" value="" optional="True" min="1" max="100" label="Cutoff - set a percentage of sequences that support the base"
+            help="For example: cutoff=95 would return the base that was supported by at least 95% of sequences. Must be between 1 and 100. Optional"/>
         <param name="count" type="data" format="mothur.count_table" optional="true" label="Count - a count table" help="this file can be generated by count.seqs"/>
     </inputs>
     <outputs>
@@ -104,8 +105,7 @@
             <expand macro="logfile-test"/>
         </test>
     </tests>
-    <help>
-<![CDATA[
+    <help><![CDATA[
 
 @MOTHUR_OVERVIEW@
 
@@ -114,7 +114,7 @@
 The consensus.seqs_ command can be used in 2 ways: create a consensus sequence from a fastafile, or with a listfile create a consensus sequence for each otu. Sequences must be aligned.
 
 .. _consensus.seqs: https://www.mothur.org/wiki/Consensus.seqs
-]]>
-    </help>
+
+    ]]></help>
     <expand macro="citations"/>
 </tool>