--- a/read_duplication.xml	Tue Apr 21 10:27:06 2015 -0400
+++ b/read_duplication.xml	Thu Jul 16 17:43:43 2015 -0400
@@ -1,35 +1,54 @@
-<tool id="rseqc_read_duplication" name="Read Duplication" version="2.4">
+<tool id="rseqc_read_duplication" name="Read Duplication" version="2.4galaxy1">
     <description>determines reads duplication rate with sequence-based and mapping-based strategies</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[read_duplication.py --version]]></version_command>
+
+    <command><![CDATA[
         read_duplication.py -i $input -o output -u $upLimit
+        ]]>
     </command>
-    <stdio>
-        <exit_code range="1:" level="fatal" description="An error occured during execution, see stderr and stdout for more information" />
-        <regex match="[Ee]rror" source="both" description="An error occured during execution, see stderr and stdout for more information" />
-    </stdio>
+
     <inputs>
-        <param name="input" type="data" format="bam,sam" label="input bam/sam file" />
-        <param name="upLimit" type="integer" label="Upper Limit of Plotted Duplicated Times (default=500)" value="500" />
+        <param name="input" type="data" format="bam,sam" label="input bam/sam file" help="(--input-file)"/>
+        <param name="upLimit" type="integer" label="Upper Limit of Plotted Duplicated Times (default=500)" value="500" help="(--up-limit)"/>
     </inputs>
+
     <outputs>
-        <data format="xls" name="outputxls" from_work_dir="output.dup.pos.DupRate.xls" label="${tool.name} on ${on_string} (Position XLS)"/>
-        <data format="xls" name="outputseqxls" from_work_dir="output.dup.seq.DupRate.xls" label="${tool.name} on ${on_string} (Sequence XLS)"/>
+        <data format="xls" name="outputxls" from_work_dir="output.pos.DupRate.xls" label="${tool.name} on ${on_string} (Position XLS)"/>
+        <data format="xls" name="outputseqxls" from_work_dir="output.seq.DupRate.xls" label="${tool.name} on ${on_string} (Sequence XLS)"/>
         <data format="txt" name="outputr" from_work_dir="output.DupRate_plot.r" label="${tool.name} on ${on_string} (R Script)" />
         <data format="pdf" name="outputpdf" from_work_dir="output.DupRate_plot.pdf" label="${tool.name} on ${on_string} (PDF)" />
     </outputs>
-    <help>
+
+    <tests>
+        <test>
+            <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/>
+            <output name="outputxls" file="output.pos.DupRate.xls"/>
+            <output name="outputseqxls" file="output.seq.DupRate.xls"/>
+            <output name="outputr" file="output.DupRate_plot.r"/>
+        </test>
+    </tests>
+
+    <help><![CDATA[
 read_duplication.py
 +++++++++++++++++++
 
-Two strategies were used to determine reads duplication rate: 
+Two strategies were used to determine reads duplication rate:
 
-* Sequence based: reads with exactly the same sequence content are regarded as duplicated reads. 
-* Mapping based: reads mapped to the same genomic location are regarded as duplicated reads. For splice reads, reads mapped to the same starting position and splice the same way are regarded as duplicated reads. 
+* Sequence based: reads with exactly the same sequence content are regarded as duplicated reads.
+* Mapping based: reads mapped to the same genomic location are regarded as duplicated reads. For splice reads, reads mapped to the same starting position and splice the same way are regarded as duplicated reads.
 
 Inputs
 ++++++++++++++
@@ -51,11 +70,11 @@
 .. image:: http://rseqc.sourceforge.net/_images/duplicate.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 +84,9 @@
 .. image:: http://rseqc.sourceforge.net/_static/logo.png
 
 .. _RSeQC: http://rseqc.sourceforge.net/
-
+]]>
+    </help>
 
-    </help>
+    <expand macro="citations" />
+
 </tool>