--- a/clipping_profile.xml	Tue Apr 21 10:27:06 2015 -0400
+++ b/clipping_profile.xml	Thu Jul 16 17:43:43 2015 -0400
@@ -1,27 +1,47 @@
-<tool id="rseqc_clipping_profile" name="Clipping Profile" version="2.4">
+<tool id="rseqc_clipping_profile" name="Clipping Profile" version="2.4galaxy1">
     <description>
      estimates clipping profile of RNA-seq reads from BAM or SAM file
     </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[clipping_profile.py --version]]></version_command>
+
+    <command><![CDATA[
         clipping_profile.py -i $input -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 .bam/.sam File" format="bam,sam" />
+        <param name="input" type="data" label="Input .bam File" format="bam" help="(--input-file)"/>
     </inputs>
+
     <outputs>
+        <data format="pdf" name="outputpdf" from_work_dir="output.clipping_profile.pdf" />
         <data format="xls" name="outputxls" from_work_dir="output.clipping_profile.xls" />
         <data format="txt" name="outputr" from_work_dir="output.clipping_profile.r" />
     </outputs>
-    <help>
+
+    <tests>
+        <test>
+            <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/>
+            <output name="outputpdf" file="output.clipping_profile.pdf"/>
+            <output name="outputxls" file="output.clipping_profile.xls"/>
+            <output name="outputr" file="output.clipping_profile.r"/>
+        </test>
+    </tests>
+
+    <help><![CDATA[
 clipping_profile.py
 +++++++++++++++++++
 
@@ -46,7 +66,7 @@
 
 -----
 
-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.
@@ -56,6 +76,9 @@
 .. image:: http://rseqc.sourceforge.net/_static/logo.png
 
 .. _RSeQC: http://rseqc.sourceforge.net/
-
+]]>
     </help>
+
+    <expand macro="citations" />
+
 </tool>