--- a/macs2_filterdup.xml	Mon Feb 06 02:30:37 2017 -0500
+++ b/macs2_filterdup.xml	Sat Apr 08 08:28:57 2017 -0400
@@ -6,29 +6,26 @@
     <expand macro="requirements" />
     <expand macro="stdio" />
     <expand macro="version_command" />
-    <command>
+    <command><![CDATA[
         macs2 filterdup
-            -i "${ infile }"
-            -o temp_outfile
-
+            -i '${ infile }'
+            -o '${ outfile }'
         --format '${ infile.extension.upper() }'
         @effective_genome_size@
         @tag_size@
-        --pvalue "${ pvalue }"
+        --pvalue '${ pvalue }'
         #if str( $keep_dup_options.keep_dup_options_selector ) == "user":
-            --keep-dup "${ keep_dup_options.user_keepdup }"
+            --keep-dup '${ keep_dup_options.user_keepdup }'
         #else
-            --keep-dup "${ keep_dup_options.keep_dup_options_selector }"
+            --keep-dup '${ keep_dup_options.keep_dup_options_selector }'
         #end if
-	;
-	mv temp_outfile "${ outfile }"
+    ]]>
     </command>
     <inputs>
         <param name="infile" type="data" format="sam,bam,bed" label="Sequencing alignment file" />
         <expand macro="conditional_effective_genome_size" />
         <expand macro="tag_size" />
-        <param name="pvalue" type="text" value="1e-5" label="Pvalue cutoff for binomial distribution test" help="default: 1e-5 (--pvalue)" />
-
+        <param name="pvalue" type="text" value="1e-5" label="Pvalue cutoff for binomial distribution test" help="Default=1e-5 (--pvalue)" />
         <expand macro="keep_duplicates" />
 
     </inputs>
@@ -46,12 +43,15 @@
         </test>
     </tests>
     <help>
+<![CDATA[
 **What it does**
 
-Remove duplicate reads at the same position, then convert acceptable format to BED format.
-filterdup tool from macs2
+This is **filterdup** utility from the MACS2_ Package. It removes duplicate reads and converts results to BED format.
+
+.. _MACS2: https://github.com/taoliu/MACS
 
 @citation@
+]]>
   </help>
   <expand macro="citations" />
 </tool>