--- a/merge_pcr_duplicates.xml	Mon Feb 01 10:05:34 2016 -0500
+++ b/merge_pcr_duplicates.xml	Fri Feb 12 08:37:33 2016 -0500
@@ -1,9 +1,15 @@
 <tool id="merge_pcr_duplicates.py" name="Merge PCR duplicates" version="0.2.0">
   <description>according to random barcode library.</description>
+  <xml name="requirements">
+      <requirements>
+          <requirement type="package" version="4.1.0">gnu_awk</requirement>
+          <requirement type="package" version="8.22">gnu_coreutils</requirement>
+          <requirement type="package" version="1.0.6">datamash</requirement>
+      </requirements>
+  </xml>
   <macros>
     <import>macros.xml</import>
   </macros>
-  <expand macro="requirements" />
   <expand macro="stdio" />
   <version_command>python $__tool_directory__/merge_pcr_duplicates.py --version</version_command>
   <command interpreter="python"><![CDATA[merge_pcr_duplicates.py
@@ -15,7 +21,7 @@
 $positional_2
 #end if
 
-> $default]]></command>
+--outfile $default]]></command>
   <inputs>
     <param area="false" label="bed6 file containing alignments." name="positional_1" type="data" format="bed"/>
     <param area="false" label="fastaq barcode library." name="positional_2" type="data" format="fastq"/>