--- a/inner_distance.xml	Tue May 03 16:36:57 2016 -0400
+++ b/inner_distance.xml	Tue Mar 14 10:23:21 2017 -0400
@@ -1,55 +1,53 @@
-<tool id="rseqc_inner_distance" name="Inner Distance" version="2.4galaxy1">
+<tool id="rseqc_inner_distance" name="Inner Distance" version="@WRAPPER_VERSION@">
     <description>calculate the inner distance (or insert size) between two paired RNA reads</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[inner_distance.py --version]]></version_command>
 
     <command><![CDATA[
-        inner_distance.py -i $input -o output -r $refgene
-            --sample-size $sample_size
-            --lower-bound $lowerBound
-            --upper-bound $upperBound
-            --step $step
-            --mapq $mapq
+        inner_distance.py -i '${input}' -o output -r '${refgene}'
+            --sample-size ${sample_size}
+            --lower-bound ${lowerBound}
+            --upper-bound ${upperBound}
+            --step ${step}
+            --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="sample_size" type="integer" label="Number of read-pairs used to estimate inner distance (default = 1000000)" value="1000000" help="(--sample-size)"/>
+        <expand macro="bam_sam_param" />
+        <expand macro="refgene_param" />
+        <expand macro="sample_size_param" />
         <param name="lowerBound" type="integer" value="-250" label="Lower bound (bp, default=-250)" help="Used for plotting histogram (--lower-bound)"/>
         <param name="upperBound" type="integer" value="250" label="Upper bound (bp, default=250)" help="Used for plotting histogram (--upper-bound)"/>
         <param name="step" type="integer" value="5" label="Step size of histogram (bp, default=5)" help="(--step)"/>
-        <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="mapq_param" />
+        <expand macro="rscript_output_param" />
     </inputs>
 
     <outputs>
-        <data format="txt" name="outputtxt" from_work_dir="output.inner_distance.txt" label="${tool.name} on ${on_string} (Text)"/>
-        <data format="txt" name="outputfreqtxt" from_work_dir="output.inner_distance_freq.txt" label="${tool.name} on ${on_string} (Freq Text)" />
-        <data format="pdf" name="outputpdf" from_work_dir="output.inner_distance_plot.pdf" label="${tool.name} on ${on_string} (PDF)" />
-        <data format="txt" name="outputr" from_work_dir="output.inner_distance_plot.r" label="${tool.name} on ${on_string} (R Script)" />
+        <expand macro="pdf_output_data" filename="output.inner_distance_plot.pdf" />
+        <data format="txt" name="outputtxt" from_work_dir="output.inner_distance.txt" label="${tool.name} on ${on_string} (text)"/>
+        <data format="txt" name="outputfreqtxt" from_work_dir="output.inner_distance_freq.txt" label="${tool.name} on ${on_string} (frequency text)" />
+        <expand macro="rscript_output_data" filename="output.inner_distance_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="outputtxt" file="output.inner_distance.txt"/>
-            <output name="outputfreqtxt" file="output.inner_distance_freq.txt"/>
-            <output name="outputpdf" file="output.inner_distance_plot.pdf"/>
-            <output name="outputr" file="output.inner_distance_plot.r"/>
+            <param name="rscript_output" value="true" />
+            <output name="outputtxt" file="output.inner_distance.txt" />
+            <output name="outputfreqtxt" file="output.inner_distance_freq.txt" />
+            <output name="outputpdf" file="output.inner_distance_plot.pdf" compare="sim_size"/>
+            <output name="outputr" file="output.inner_distance_plot.r" />
         </test>
     </tests>
 
@@ -100,24 +98,12 @@
 3. output.inner_distance_plot.r: R script to generate histogram
 4. output.inner_distance_plot.pdf: histogram plot
 
-.. image:: http://rseqc.sourceforge.net/_images/inner_distance.png
+.. image:: $PATH_TO_IMAGES/inner_distance.png
    :height: 600 px
    :width: 600 px
    :scale: 80 %
 
-
------
-
-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.
-
-The RSeQC package is licensed under the GNU GPL v3 license.
-
-.. image:: http://rseqc.sourceforge.net/_static/logo.png
-
-.. _RSeQC: http://rseqc.sourceforge.net/
+@ABOUT@
 
 ]]>
     </help>