--- a/macs21_wrapper.xml	Wed Mar 22 11:24:52 2017 -0400
+++ b/macs21_wrapper.xml	Fri Mar 09 09:21:56 2018 -0500
@@ -1,15 +1,17 @@
-<tool id="macs2_1_peakcalling" name="MACS2.1.0" version="2.1.0-6">
+<tool id="macs2_1_peakcalling" name="MACS2.1.1" version="2.1.1.0">
   <description>Model-based Analysis of ChIP-Seq: peak calling</description>
   <requirements>
     <requirement type="package" version="2.7">python</requirement>
-    <requirement type="package" version="1.9">numpy</requirement>
-    <requirement type="package" version="2.1.0.20140616">macs2</requirement>
-    <requirement type="package" version="3.1.2">R</requirement>
-    <requirement type="package" version="2.0">ucsc_tools_for_macs21</requirement>
+    <requirement type="package" version="2.1.1">macs2</requirement>
+    <requirement type="package" version="3.4">R</requirement>
+    <requirement type="package" version="357">ucsc-fetchchromsizes</requirement>
+    <requirement type="package" version="357">ucsc-bedclip</requirement>
+    <requirement type="package" version="357">ucsc-bedsort</requirement>
+    <requirement type="package" version="357">ucsc-bedgraphtobigwig</requirement>
   </requirements>
   <version_command>macs2 --version</version_command>
-  <command interpreter="python">
-    macs21_wrapper.py callpeak
+  <command><![CDATA[
+    python $__tool_directory__/macs21_wrapper.py callpeak
     ##
     ## ChIP-seq input
     $input_chipseq_file1
@@ -96,7 +98,7 @@
     #else
        --output-peaks=$output_peaks_file
     #end if
-  </command>
+  ]]></command>
   <inputs>
     <!--experiment name used as base for output file names -->
     <param name="experiment_name" type="text" value="MACS2.1.0 in Galaxy" size="50"