--- a/read_duplication.xml	Tue May 03 16:36:57 2016 -0400
+++ b/read_duplication.xml	Tue Mar 14 10:23:21 2017 -0400
@@ -1,43 +1,43 @@
-<tool id="rseqc_read_duplication" name="Read Duplication" version="2.4galaxy1">
+<tool id="rseqc_read_duplication" name="Read Duplication" version="@WRAPPER_VERSION@">
     <description>determines reads duplication rate with sequence-based and mapping-based strategies</description>
 
     <macros>
         <import>rseqc_macros.xml</import>
     </macros>
 
-    <requirements>
-        <expand macro="requirement_package_r" />
-        <expand macro="requirement_package_numpy" />
-        <expand macro="requirement_package_rseqc" />
-    </requirements>
+    <expand macro="requirements" />
 
     <expand macro="stdio" />
 
     <version_command><![CDATA[read_duplication.py --version]]></version_command>
 
     <command><![CDATA[
-        read_duplication.py -i $input -o output -u $upLimit
+        read_duplication.py -i '${input}' -o output -u ${upLimit} -q ${mapq}
         ]]>
     </command>
 
     <inputs>
-        <param name="input" type="data" format="bam,sam" label="input bam/sam file" help="(--input-file)"/>
+        <expand macro="bam_sam_param" />
         <param name="upLimit" type="integer" label="Upper Limit of Plotted Duplicated Times (default=500)" value="500" help="(--up-limit)"/>
+        <expand macro="mapq_param" />
+        <expand macro="rscript_output_param" />
     </inputs>
 
     <outputs>
-        <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 ${on_string} (PDF)" />
+        <expand macro="pdf_output_data" filename="output.DupRate_plot.pdf" />
+        <data format="xls" name="outputxls" from_work_dir="output.pos.DupRate.xls" label="${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)"/>
+        <expand macro="rscript_output_data" filename="output.DupRate_plot.r" />
     </outputs>
 
     <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"/>
+            <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam" />
+            <param name="rscript_output" value="true" />
+            <output name="outputxls" file="output.pos.DupRate.xls" />
+            <output name="outputseqxls" file="output.seq.DupRate.xls" />
+            <output name="outputr" file="output.DupRate_plot.r" />
+            <output name="outputpdf" file="output.DupRate_plot.pdf" compare="sim_size" />
         </test>
     </tests>
 
@@ -67,23 +67,13 @@
 3. output.DupRate_plot.r: R script to generate pdf file
 4. output.DupRate_plot.pdf: graphical output generated from R script
 
-.. image:: http://rseqc.sourceforge.net/_images/duplicate.png
+.. image:: $PATH_TO_IMAGES/duplicate.png
    :height: 600 px
    :width: 600 px
    :scale: 80 %
 
------
-
-About RSeQC
-+++++++++++
+@ABOUT@
 
-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.
-
-The RSeQC package is licensed under the GNU GPL v3 license.
-
-.. image:: http://rseqc.sourceforge.net/_static/logo.png
-
-.. _RSeQC: http://rseqc.sourceforge.net/
 ]]>
     </help>