--- a/geneBody_coverage.xml	Tue Apr 21 10:27:06 2015 -0400
+++ b/geneBody_coverage.xml	Thu Jul 16 17:43:43 2015 -0400
@@ -1,40 +1,49 @@
-<tool id="rseqc_geneBody_coverage" name="Gene Body Converage (BAM)" version="2.4">
+<tool id="rseqc_geneBody_coverage" name="Gene Body Converage (BAM)" version="2.4galaxy1">
     <description>
         Read coverage over gene body.
     </description>
+
+    <macros>
+        <import>rseqc_macros.xml</import>
+    </macros>
+
     <requirements>
-        <requirement type="package" version="3.0.3">R</requirement>
-        <requirement type="package" version="1.7.1">numpy</requirement>
-        <requirement type="package" version="2.4">rseqc</requirement>
+        <expand macro="requirement_package_r" />
+        <expand macro="requirement_package_numpy" />
+        <expand macro="requirement_package_rseqc" />
     </requirements>
-    <command>
+
+    <expand macro="stdio" />
+
+    <version_command><![CDATA[geneBody_coverage.py --version]]></version_command>
+
+    <command><![CDATA[
         #set $safename = ''.join(c in '_0123456789abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ' and c or '_' for c in $input.display_name)
         #set $fname = "d1_" + str($safename) + ".bam"
-        ln -s '${input}' '${fname}' &amp;&amp;
-        ln -s '${input.metadata.bam_index}' '${fname}.bai' &amp;&amp;
-        echo '${fname}' > input_list.txt &amp;&amp;
+        ln -s '${input}' '${fname}' &&
+        ln -s '${input.metadata.bam_index}' '${fname}.bai' &&
+        echo '${fname}' > input_list.txt &&
         #for $i, $additional_input in enumerate($additionalinputs):
             #set $index = $i+2
             #set $safename = ''.join(c in '_0123456789abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ' and c or '_' for c in $additional_input.file.display_name)
             #set $fname = 'd' + str($index) + '_' + str($safename) + ".bam"
-            ln -s '$additional_input.file' '${fname}' &amp;&amp;
-            ln -s '$additional_input.file.metadata.bam_index' '${fname}.bai' &amp;&amp;
-            echo '${fname}' >> input_list.txt &amp;&amp;
+            ln -s '$additional_input.file' '${fname}' &&
+            ln -s '$additional_input.file.metadata.bam_index' '${fname}.bai' &&
+            echo '${fname}' >> input_list.txt &&
         #end for
         geneBody_coverage.py -i input_list.txt -r $refgene --minimum_length $minimum_length -o output
+        ]]>
     </command>
-    <stdio>
-        <exit_code range="1:" level="fatal" description="An error occured during execution, see stderr and stdout for more information" />
-        <regex match="[Ee]rror" source="both" description="An error occured during execution, see stderr and stdout for more information" />
-    </stdio>
+
     <inputs>
-        <param name="input" type="data" label="Additional input .bam files" format="bam" />
-        <repeat name="additionalinputs" title="Input .bam file">
-            <param name="file" type="data" label="Input .bam file" format="bam" />
+        <param name="input" type="data" label="Input .bam File" format="bam" help="(--input-file)"/>
+        <repeat name="additionalinputs" title="Additional input .bam files">
+            <param name="file" type="data" label="Additional input .bam file" format="bam" />
         </repeat>
-        <param name="refgene" type="data" label="Reference Genome" format="bed" />
-        <param name="minimum_length" type="integer" value="100" label="Minimum mRNA length" help="Minimum mRNA length (bp). mRNA that are shorter than this value will be skipped (default is 100)." />
+        <param name="refgene" type="data" format="bed" label="reference gene model" help="(--refgene)"/>
+        <param name="minimum_length" type="integer" value="100" label="Minimum mRNA length in bp (default: 100)" help="mRNA that are shorter than this value will be skipped (--minimum_length)." />
     </inputs>
+
     <outputs>
         <data name="outputcurvespdf" format="pdf" from_work_dir="output.geneBodyCoverage.curves.pdf" label="${tool.name} on ${on_string} (Curves PDF)" />
         <data name="outputheatmappdf" format="pdf" from_work_dir="output.geneBodyCoverage.heatMap.pdf" label="${tool.name} on ${on_string} (HeatMap PDF)">
@@ -43,7 +52,29 @@
         <data name="outputr" format="txt" from_work_dir="output.geneBodyCoverage.r" label="${tool.name} on ${on_string} (R Script)" />
         <data name="outputtxt" format="txt" from_work_dir="output.geneBodyCoverage.txt" label="${tool.name} on ${on_string} (Text)" />
     </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="outputcurvespdf" file="output.geneBodyCoverage.curves.pdf"/>
+            <output name="outputr" file="output.geneBodyCoverage.r"/>
+            <output name="outputtxt" file="output.geneBodyCoverage.txt"/>
+        </test>
+        <test>
+            <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/>
+            <param name="file_0" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/>
+            <param name="file_1" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/>
+            <param name="refgene" value="hg19_RefSeq_chr1_1-100000.bed"/>
+            <output name="outputcurvespdf" file="output2.geneBodyCoverage.curves.pdf"/>
+            <output name="outputcurvespdf" file="output2.geneBodyCoverage.heatMap.pdf"/>
+            <output name="outputr" file="output2.geneBodycoverage.r"/>
+            <output name="outputtxt" file="output2.geneBodyCoverage.txt"/>
+        </test>
+
+    </tests>
+
+    <help><![CDATA[
 geneBody_coverage.py
 ++++++++++++++++++++
 
@@ -52,7 +83,12 @@
 If 3 or more BAM files were provided. This program generates a lineGraph and a heatmap. If fewer than 3 BAM files were provided, only lineGraph is generated. See below for examples.
 
 When heatmap is generated, samples are ranked by the "skewness" of the coverage: Sample with best (worst) coverage will be displayed at the top (bottom) of the heatmap.
-Coverage skewness was measured by `Pearson’s skewness coefficients &lt;http://en.wikipedia.org/wiki/Skewness#Pearson.27s_skewness_coefficients>`_
+Coverage skewness was measured by `Pearson’s skewness coefficients <http://en.wikipedia.org/wiki/Skewness#Pearson.27s_skewness_coefficients>`_
+
+    .. image:: http://rseqc.sourceforge.net/_images/geneBody_workflow.png
+        :width: 800 px
+        :scale: 80 %
+
 
 Inputs
 ++++++++++++++
@@ -100,8 +136,9 @@
 .. image:: http://rseqc.sourceforge.net/_static/logo.png
 
 .. _RSeQC: http://rseqc.sourceforge.net/
-
-
+]]>
+    </help>
 
-	</help>
+    <expand macro="citations" />
+
 </tool>