--- a/merge.sfffiles.xml	Tue Sep 05 16:42:24 2017 -0400
+++ b/merge.sfffiles.xml	Wed Feb 14 09:51:56 2018 -0500
@@ -7,21 +7,21 @@
     <expand macro="stdio"/>
     <expand macro="version_command"/>
     <command><![CDATA[
-        @SHELL_OPTIONS@
+@SHELL_OPTIONS@
 
-        ## create symlinks to input datasets
-        #for $i in $input:
-            ln -s "$i" input${input.index($i)}.dat &&
-        #end for
+## create symlinks to input datasets
+#for $i in $input:
+    ln -s '$i' input${input.index($i)}.dat &&
+#end for
 
-        echo 'merge.sfffiles(
-            sff=#for $i in $input#input${input.index($i)}.dat-#end for#,
-            output=$output
-        )'
-        | sed 's/ //g'  ## mothur trips over whitespace
-        | sed 's/-,/,/g'
-        | mothur
-        | tee mothur.out.log
+echo 'merge.sfffiles(
+    sff=#for $i in $input#input${input.index($i)}.dat-#end for#,
+    output=$output
+)'
+| sed 's/ //g'  ## mothur trips over whitespace
+| sed 's/-,/,/g'
+| mothur
+| tee mothur.out.log
     ]]></command>
     <inputs>
         <param name="input" type="data" format="sff" multiple="true" label="input - sff files to merge"/>
@@ -41,8 +41,7 @@
             <expand macro="logfile-test"/>
         </test>
     </tests>
-    <help>
-<![CDATA[
+    <help><![CDATA[
 
 @MOTHUR_OVERVIEW@
 
@@ -54,7 +53,6 @@
 
 .. _merge.sfffiles: https://www.mothur.org/wiki/Merge.sfffiles
 
-]]>
-    </help>
+    ]]></help>
     <expand macro="citations"/>
 </tool>