--- a/rm_spurious_events.xml	Sat Dec 19 06:16:22 2015 -0500
+++ b/rm_spurious_events.xml	Tue Jan 26 04:38:27 2016 -0500
@@ -5,7 +5,11 @@
   </macros>
   <expand macro="requirements" />
   <expand macro="stdio" />
-  <version_command>python rm_spurious_events.py --version</version_command>
+  <requirements>
+    <requirement type="package" version="5.18">perl</requirement>
+    <requirement type="package" version="8.22">gnu_coreutils</requirement>
+  </requirements>
+  <version_command>python $__tool_directory__/rm_spurious_events.py --version</version_command>
   <command interpreter="python"><![CDATA[rm_spurious_events.py
 #if $positional_1 and $positional_1 is not None:
 $positional_1
@@ -14,7 +18,7 @@
 #if $threshold and $threshold is not None:
 --threshold $threshold
 #end if
-> $default]]></command>
+--outfile $default]]></command>
   <inputs>
     <param area="false" label="bed6 file containing alignments." name="positional_1" type="data" format="bed"/>
     <param help="(--threshold)" label="Threshold for spurious event removal." name="threshold" optional="true" type="float" value="0.1"/>