--- a/geneBody_coverage2.xml	Tue Apr 21 10:27:06 2015 -0400
+++ b/geneBody_coverage2.xml	Thu Jul 16 17:43:43 2015 -0400
@@ -1,29 +1,51 @@
-<tool id="rseqc_geneBody_coverage2" name="Gene Body Converage (Bigwig)" version="2.4">
+<tool id="rseqc_geneBody_coverage2" name="Gene Body Converage (Bigwig)" version="2.4galaxy1">
     <description>
         Read coverage over gene body
     </description>
+
+    <macros>
+        <import>rseqc_macros.xml</import>
+    </macros>
+
     <requirements>
-        <requirement type="package" version="3.0.3">R</requirement>
-        <requirement type="package" version="1.7.1">numpy</requirement>
-        <requirement type="package" version="2.4">rseqc</requirement>
+        <expand macro="requirement_package_r" />
+        <expand macro="requirement_package_numpy" />
+        <expand macro="requirement_package_rseqc" />
     </requirements>
-    <command>
+
+    <expand macro="stdio" />
+
+    <version_command><![CDATA[geneBody_coverage2.py --version]]></version_command>
+
+    <command><![CDATA[
         geneBody_coverage2.py -i $input -r $refgene -o output
+        ]]>
     </command>
-    <stdio>
-        <exit_code range="1:" level="fatal" description="An error occured during execution, see stderr and stdout for more information" />
-        <regex match="[Ee]rror" source="both" description="An error occured during execution, see stderr and stdout for more information" />
-    </stdio>
+
     <inputs>
         <param name="input" type="data" label="Input bigwig file" format="bigwig" />
         <param name="refgene" type="data" label="Reference Genome" format="bed" />
     </inputs>
+
     <outputs>
         <data name="outputpdf" format="pdf" from_work_dir="output.geneBodyCoverage.pdf" label="${tool.name} on ${on_string} (PDF)" />
         <data name="outputr" format="txt" from_work_dir="output.geneBodyCoverage_plot.r" label="${tool.name} on ${on_string} (R Script)" />
         <data name="outputtxt" format="txt" from_work_dir="output.geneBodyCoverage.txt" label="${tool.name} on ${on_string} (Text)" />
     </outputs>
-    <help>
+
+    <!-- Unable to succefully run this script, it seems deprecated and should probably be dropped
+    <tests>
+        <test>
+            <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bigwig"/>
+            <param name="refgene" value="hg19_RefSeq_chr1_1-100000.bed"/>
+            <output name="outputcurvespdf" file="output.geneBodyCoverage.curves.pdf"/>
+            <output name="outputr" file="output.geneBodyCoverage.r"/>
+            <output name="outputtxt" file="output.geneBodyCoverage.txt"/>
+        </test>
+    </tests>
+    -->
+
+    <help><![CDATA[
 geneBody_coverage2.py
 +++++++++++++++++++++
 
@@ -50,11 +72,11 @@
     .. image:: http://dldcc-web.brc.bcm.edu/lilab/liguow/RSeQC/figure/geneBody_coverage.png
         :height: 600 px
         :width: 600 px
-        :scale: 80 %    
+        :scale: 80 %
 
 -----
 
-About RSeQC 
+About RSeQC
 +++++++++++
 
 The RSeQC_ package provides a number of useful modules that can comprehensively evaluate high throughput sequence data especially RNA-seq data. "Basic modules" quickly inspect sequence quality, nucleotide composition bias, PCR bias and GC bias, while "RNA-seq specific modules" investigate sequencing saturation status of both splicing junction detection and expression estimation, mapped reads clipping profile, mapped reads distribution, coverage uniformity over gene body, reproducibility, strand specificity and splice junction annotation.
@@ -65,7 +87,9 @@
 
 .. _RSeQC: http://rseqc.sourceforge.net/
 
-
+]]>
+    </help>
 
-    </help>
+    <expand macro="citations" />
+
 </tool>