--- a/clipping_profile.xml	Tue May 03 16:36:57 2016 -0400
+++ b/clipping_profile.xml	Tue Mar 14 10:23:21 2017 -0400
@@ -1,4 +1,4 @@
-<tool id="rseqc_clipping_profile" name="Clipping Profile" version="2.4galaxy1">
+<tool id="rseqc_clipping_profile" name="Clipping Profile" version="@WRAPPER_VERSION@">
     <description>
      estimates clipping profile of RNA-seq reads from BAM or SAM file
     </description>
@@ -7,37 +7,42 @@
         <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[clipping_profile.py --version]]></version_command>
 
     <command><![CDATA[
-        clipping_profile.py -i $input -o output
+        clipping_profile.py -i '${input}' -o output -q ${mapq} -s "${layout}"
         ]]>
     </command>
 
     <inputs>
-        <param name="input" type="data" label="Input .bam File" format="bam" help="(--input-file)"/>
+        <expand macro="bam_param" />
+        <expand macro="mapq_param" />
+        <expand macro="layout_param" />
+        <expand macro="rscript_output_param" />
     </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" />
+        <expand macro="pdf_output_data" filename="output.clipping_profile.pdf" />
+        <expand macro="xls_output_data" filename="output.clipping_profile.xls" />
+        <expand macro="rscript_output_data" filename="output.clipping_profile.r" />
     </outputs>
 
     <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"/>
+            <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam" />
+            <output name="outputpdf" file="output.clipping_profile.pdf" compare="sim_size" />
+            <output name="outputxls" file="output.clipping_profile.xls" />
+        </test>
+        <test>
+            <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam" />
+            <param name="rscript_output" value="true" />
+            <output name="outputpdf" file="output.clipping_profile.pdf" compare="sim_size" />
+            <output name="outputxls" file="output.clipping_profile.xls" />
+            <output name="outputr" file="output.clipping_profile.r" />
         </test>
     </tests>
 
@@ -53,29 +58,25 @@
 ++++++++++++++
 
 Input BAM/SAM file
-	Alignment file in BAM/SAM format.
+    Alignment file in BAM/SAM format.
 
+Minimum mapping quality
+    Minimum mapping quality for an alignment to be considered as "uniquely
+    mapped". default=30
+
+Sequencing layout
+    Denotes whether the sequecing was single-end (SE) or paired-end (PE).
 
 Sample Output
 ++++++++++++++
 
-.. image:: http://rseqc.sourceforge.net/_images/clipping_good.png
+.. image:: $PATH_TO_IMAGES/clipping_good.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>