--- a/junction_annotation.xml	Tue May 03 16:36:57 2016 -0400
+++ b/junction_annotation.xml	Tue Mar 14 10:23:21 2017 -0400
@@ -1,15 +1,11 @@
-<tool id="rseqc_junction_annotation" name="Junction Annotation" version="2.4galaxy1">
+<tool id="rseqc_junction_annotation" name="Junction Annotation" version="@WRAPPER_VERSION@">
     <description>compares detected splice junctions to reference gene model</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" />
 
@@ -17,36 +13,38 @@
 
     <command><![CDATA[
         junction_annotation.py
-            --input-file $input
-            --refgene $refgene
+            --input-file '${input}'
+            --refgene '${refgene}'
             --out-prefix output
-            --min-intron $min_intron
-            --mapq $mapq
+            --min-intron ${min_intron}
+            --mapq ${mapq}
         ]]>
     </command>
 
     <inputs>
-        <param name="input" type="data" format="bam,sam" label="input bam/sam file" help="(--input-file)"/>
-        <param name="refgene" type="data" format="bed" label="reference gene model" help="(--refgene)"/>
-        <param name="min_intron" type="integer" value="50" label="Minimum intron length (bp, default=50)" help="(--min-intron)" />
-        <param name="mapq" type="integer" label="Minimum mapping quality (default=30)" help="Minimum phred scale mapping quality to consider a read 'uniquely mapped' (--mapq)" value="30" />
+        <expand macro="bam_sam_param" />
+        <expand macro="refgene_param" />
+        <expand macro="min_intron_param" />
+        <expand macro="mapq_param" />
+        <expand macro="rscript_output_param" />
     </inputs>
 
     <outputs>
-        <data format="xls" name="outputxls" from_work_dir="output.junction.xls" label="${tool.name} on ${on_string} (XLS)"/>
-        <data format="txt" name="outputr" from_work_dir="output.junction_plot.r" label="${tool.name} on ${on_string} (R Script)" />
-        <data format="pdf" name="outputpdf" from_work_dir="output.splice_events.pdf" label="${tool.name} on ${on_string} (Splice Events PDF)"/>
-        <data format="pdf" name="outputjpdf" from_work_dir="output.splice_junction.pdf" label="${tool.name} on ${on_string} (Splice Junction PDF)" />
+        <data format="pdf" name="outputpdf" from_work_dir="output.splice_events.pdf" label="${tool.name} on ${on_string} (Splice Events pdf)"/>
+        <data format="pdf" name="outputjpdf" from_work_dir="output.splice_junction.pdf" label="${tool.name} on ${on_string} (Splice Junction pdf)" />
+        <expand macro="xls_output_data" filename="output.junction.xls" />
+        <expand macro="rscript_output_data" filename="output.junction_plot.r" />
     </outputs>
 
     <tests>
         <test>
-            <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/>
-            <param name="refgene" value="hg19_RefSeq_chr1_1-100000.bed"/>
-            <output name="outputxls" file="output.junction.xls"/>
-            <output name="outputr" file="output.junction_plot.r"/>
-            <output name="outputpdf" file="output.splice_events.pdf"/>
-            <output name="outputjpdf" file="output.splice_junction.pdf"/>
+            <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam" />
+            <param name="refgene" value="hg19_RefSeq_chr1_1-100000.bed" />
+            <param name="rscript_output" value="true" />
+            <output name="outputxls" file="output.junction.xls" />
+            <output name="outputr" file="output.junction_plot.r" />
+            <output name="outputpdf" file="output.splice_events.pdf" compare="sim_size" />
+            <output name="outputjpdf" file="output.splice_junction.pdf" compare="sim_size" />
         </test>
     </tests>
 
@@ -94,23 +92,13 @@
 3. output.splice_junction.pdf: plot of splice junctions
 4. output.splice_events.pdf: plot of splice events
 
-.. image:: http://rseqc.sourceforge.net/_images/junction.png
+.. image:: $PATH_TO_IMAGES/junction.png
    :height: 400 px
    :width: 850 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>