--- a/bam2wig.xml	Thu Jul 11 12:33:27 2013 -0400
+++ b/bam2wig.xml	Wed Oct 02 02:20:04 2013 -0400
@@ -1,14 +1,16 @@
-<tool id="bam2wig" name="BAM to Wiggle">
+<tool id="bam2wig" name="BAM to Wiggle" version="1.1">
 	<description> 
 		converts all types of RNA-seq data from .bam to .wig 
 	</description>
 	<requirements>
-		<requirement type="package" version="2.15.1">R</requirement>
-		<requirement type="package" version="0.1.18">samtools</requirement>
+		<requirement type="package" version="2.11.0">R</requirement>
+		<requirement type="package" version="1.7.1">numpy</requirement>
 		<requirement type="package" version="2.3.7">rseqc</requirement>
 	</requirements>
-	<command interpreter="python"> 
-		samtoolshelper.py /home/nilesh/RSeQC-2.3.3/scripts/bam2wig.py -i $input -s $chromsize -o outfile
+	<command> 
+        ln -s "${input}" "local_input.bam" &amp;&amp;
+        ln -s "${input.metadata.bam_index}" "local_input.bam.bai" &amp;&amp;
+		bam2wig.py -i "local_input.bam" -s $chromsize -o outfile
 
 		#if str($strand_type.strand_specific) == "pair"
 			-d
@@ -73,24 +75,29 @@
 		<data format="wig" name="output" from_work_dir="outfile.wig">
 			<filter>strand_type['strand_specific'] == 'none'</filter>
 		</data>
-		<data format="wig" name="outputfwd" from_work_dir="outfile_Forward.wig">
+		<data format="wig" name="outputfwd" from_work_dir="outfile_Forward.wig" label="${tool.name} on ${on_string} (Forward Reads)">
 			<filter>strand_type['strand_specific'] != 'none'</filter>
 		</data>
-		<data format="wig" name="outputrv" from_work_dir="outfile_Reverse.wig">
+		<data format="wig" name="outputrv" from_work_dir="outfile_Reverse.wig" label="${tool.name} on ${on_string} (Reverse Reads)">
 			<filter>strand_type['strand_specific'] != 'none'</filter>
 		</data>
 	</outputs>
+    <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>
 	<help>
-.. image:: https://code.google.com/p/rseqc/logo?cct=1336721062
-
------
+bam2wig.py
+++++++++++
 
-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.
+Visualization is the most straightforward and effective way to QC your RNA-seq
+data. For example, change of expression or new splicing can be easily checked
+by visually comparing two RNA-seq tracks using genome browser such as UCSC_,
+IGB_ and IGV_.  `bam2wig.py` converts all types of RNA-seq data from BAM_
+format into wiggle_ format in one-stop.  wiggle_ files can then be easily
+converted into bigwig_.  Bigwig is indexed, binary format of wiggle file, and
+it's particular useful to display large, continuous dataset on genome
+browser.
 
 Inputs
 ++++++++++++++
@@ -116,6 +123,25 @@
 If RNA-seq is not strand specific, one wig file will be generated, if RNA-seq
 is strand specific, two wig files corresponding to Forward and Reverse will be generated.
 
+-----
+
+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/
+.. _UCSC: http://genome.ucsc.edu/index.html
+.. _IGB: http://bioviz.org/igb/
+.. _IGV: http://www.broadinstitute.org/igv/home
+.. _BAM: http://genome.ucsc.edu/goldenPath/help/bam.html
+.. _wiggle: http://genome.ucsc.edu/goldenPath/help/wiggle.html
+.. _bigwig: http://genome.ucsc.edu/FAQ/FAQformat.html#format6.1
 
 	</help>
-</tool>
\ No newline at end of file
+</tool>