--- a/read_distribution.xml	Tue Apr 21 10:27:06 2015 -0400
+++ b/read_distribution.xml	Thu Jul 16 17:43:43 2015 -0400
@@ -1,24 +1,42 @@
-<tool id="rseqc_read_distribution" name="Read Distribution" version="2.4">
+<tool id="rseqc_read_distribution" name="Read Distribution" version="2.4galaxy1">
     <description>calculates how mapped reads were distributed over genome feature</description>
+
+    <macros>
+        <import>rseqc_macros.xml</import>
+    </macros>
+
     <requirements>
-        <requirement type="package" version="1.7.1">numpy</requirement>
-        <requirement type="package" version="2.4">rseqc</requirement>
+        <expand macro="requirement_package_numpy" />
+        <expand macro="requirement_package_rseqc" />
     </requirements>
-    <command>
+
+    <expand macro="stdio" />
+
+    <version_command><![CDATA[read_distribution.py --version]]></version_command>
+
+    <command><![CDATA[
         read_distribution.py -i $input -r $refgene > $output
+        ]]>
     </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="refgene" type="data" format="bed" label="reference gene model" />
+        <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)"/>
     </inputs>
+
     <outputs>
         <data format="txt" name="output" />
     </outputs>
-    <help>
+
+    <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="output" file="output.read_distribution.txt"/>
+        </test>
+    </tests>
+
+    <help><![CDATA[
 read_distribution.py
 ++++++++++++++++++++
 
@@ -39,7 +57,7 @@
 
 * hit to intergenic regions that beyond region starting from TSS upstream 10Kb to TES downstream 10Kb.
 * hit to regions covered by both 5'UTR and 3' UTR. This is possible when two head-to-tail transcripts are overlapped in UTR regions.
-* hit to regions covered by both TSS upstream 10Kb and TES downstream 10Kb. 
+* hit to regions covered by both TSS upstream 10Kb and TES downstream 10Kb.
 
 
 Inputs
@@ -57,23 +75,23 @@
 Output:
 
 ===============     ============        ===========         ===========
-Group               Total_bases         Tag_count           Tags/Kb    
+Group               Total_bases         Tag_count           Tags/Kb
 ===============     ============        ===========         ===========
-CDS_Exons           33302033            20002271            600.63     
-5'UTR_Exons         21717577            4408991             203.01     
-3'UTR_Exons         15347845            3643326             237.38     
-Introns             1132597354          6325392             5.58       
-TSS_up_1kb          17957047            215331              11.99      
-TSS_up_5kb          81621382            392296              4.81       
-TSS_up_10kb         149730983           769231              5.14       
-TES_down_1kb        18298543            266161              14.55      
-TES_down_5kb        78900674            729997              9.25       
-TES_down_10kb       140361190           896882              6.39       
+CDS_Exons           33302033            20002271            600.63
+5'UTR_Exons         21717577            4408991             203.01
+3'UTR_Exons         15347845            3643326             237.38
+Introns             1132597354          6325392             5.58
+TSS_up_1kb          17957047            215331              11.99
+TSS_up_5kb          81621382            392296              4.81
+TSS_up_10kb         149730983           769231              5.14
+TES_down_1kb        18298543            266161              14.55
+TES_down_5kb        78900674            729997              9.25
+TES_down_10kb       140361190           896882              6.39
 ===============     ============        ===========         ===========
 
 -----
 
-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.
@@ -83,8 +101,9 @@
 .. image:: http://rseqc.sourceforge.net/_static/logo.png
 
 .. _RSeQC: http://rseqc.sourceforge.net/
-
-
+]]>
+    </help>
 
-    </help>
+    <expand macro="citations" />
+
 </tool>