--- a/macs21_wrapper.xml	Wed Mar 22 11:36:07 2017 -0400
+++ b/macs21_wrapper.xml	Tue Mar 20 11:25:04 2018 -0400
@@ -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
     $input_chipseq_file1
@@ -96,10 +98,10 @@
     #else
        --output-peaks=$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"
+    <param name="experiment_name" type="text" value="MACS2.1 in Galaxy" size="50"
 	   label="Experiment Name"/>
     <!--choose 'broad' or 'narrow' regions-->
     <conditional name="broad_options">
@@ -277,7 +279,7 @@
     <!-- Peak calling without bigwig output -->
     <test>
       <!-- Inputs -->
-      <param name="experiment_name" value="test_MACS2.1.0" />
+      <param name="experiment_name" value="test_MACS2.1.1" />
       <param name="broad_regions" value="" />
       <param name="format" value="BED" />
       <param name="input_chipseq_file1" value="test_region_IP.bed" dbkey="galGal3"
@@ -303,20 +305,20 @@
       <param name="nomodel_type_selector" value="nomodel" />
       <param name="nomodel_type|extsize" value="243" />
       <!-- Outputs -->
-      <output name="output_extra_files" file="test_MACS2.1.0_html_report.zip"
+      <output name="output_extra_files" file="test_MACS2.1.1_html_report.zip"
 	      compare="sim_size" delta="1500" />
-      <output name="output_summits_bed_file" file="test_MACS2.1.0_summits.bed" />
-      <output name="output_narrowpeaks_file" file="test_MACS2.1.0_peaks_narrowPeak.interval" />
+      <output name="output_summits_bed_file" file="test_MACS2.1.1_summits.bed" />
+      <output name="output_narrowpeaks_file" file="test_MACS2.1.1_peaks_narrowPeak.interval" />
       <output name="output_xls_to_interval_peaks_file"
-	      file="test_MACS2.1.0_peaks.xls.re_match"
+	      file="test_MACS2.1.1_peaks.xls.re_match"
 	      compare="re_match" lines_diff="1" />
-      <output name="output_treat_pileup_file" file="test_MACS2.1.0_treat_pileup.bdg" />
-      <output name="output_lambda_bedgraph_file" file="test_MACS2.1.0_control_lambda.bdg" />
+      <output name="output_treat_pileup_file" file="test_MACS2.1.1_treat_pileup.bdg" />
+      <output name="output_lambda_bedgraph_file" file="test_MACS2.1.1_control_lambda.bdg" />
     </test>
     <!-- Peak calling with bigwig output -->
     <test>
       <!-- Inputs -->
-      <param name="experiment_name" value="test_MACS2.1.0" />
+      <param name="experiment_name" value="test_MACS2.1.1" />
       <param name="broad_regions" value="" />
       <param name="format" value="BED" />
       <param name="input_chipseq_file1" value="test_region_IP.bed" dbkey="galGal3"
@@ -342,23 +344,23 @@
       <param name="nomodel_type_selector" value="nomodel" />
       <param name="nomodel_type|extsize" value="243" />
       <!-- Outputs -->
-      <output name="output_extra_files" file="test_MACS2.1.0_bw_html_report.zip"
+      <output name="output_extra_files" file="test_MACS2.1.1_bw_html_report.zip"
 	      compare="sim_size" delta="2500" />
-      <output name="output_summits_bed_file" file="test_MACS2.1.0_summits.bed" />
-      <output name="output_narrowpeaks_file" file="test_MACS2.1.0_peaks_narrowPeak.interval" />
+      <output name="output_summits_bed_file" file="test_MACS2.1.1_summits.bed" />
+      <output name="output_narrowpeaks_file" file="test_MACS2.1.1_peaks_narrowPeak.interval" />
       <output name="output_xls_to_interval_peaks_file"
-	      file="test_MACS2.1.0_peaks.xls.re_match"
+	      file="test_MACS2.1.1_peaks.xls.re_match"
 	      compare="re_match" lines_diff="1" />
-      <output name="output_treat_pileup_file" file="test_MACS2.1.0_treat_pileup.bdg" />
-      <output name="output_lambda_bedgraph_file" file="test_MACS2.1.0_control_lambda.bdg" />
-      <output name="output_bigwig_file" file="test_MACS2.1.0_treat_pileup.bw"
+      <output name="output_treat_pileup_file" file="test_MACS2.1.1_treat_pileup.bdg" />
+      <output name="output_lambda_bedgraph_file" file="test_MACS2.1.1_control_lambda.bdg" />
+      <output name="output_bigwig_file" file="test_MACS2.1.1_treat_pileup.bw"
 	      compare="sim_size" />
     </test>
   </tests>
   <help>
 **What it does**
 
-MACS (Model-based Analysis of ChIP-seq) 2.1.0 provides algorithms for identifying
+MACS (Model-based Analysis of ChIP-seq) 2.1.1 provides algorithms for identifying
 transcript factor binding sites. The program can be used either for ChIP-Seq data alone,
 or with control sample data to improve specificity.