--- a/read_quality.xml	Thu Jul 11 12:33:27 2013 -0400
+++ b/read_quality.xml	Wed Oct 02 02:20:04 2013 -0400
@@ -1,31 +1,37 @@
-<tool id="read_quality" name="Read Quality">
+<tool id="read_quality" name="Read Quality" version="1.1">
 	<description>determines Phred quality score</description>
 	<requirements>
-		<requirement type="package" version="2.15.1">R</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"> read_quality.py -i $input -o output -r $reduce
+	<command> read_quality.py -i $input -o output -r $reduce
 	</command>
 	<inputs>
 		<param name="input" type="data" format="bam,sam" label="input bam/sam file" />
 		<param name="reduce" type="integer" label="Ignore Phred scores less than this amount (only applies to 'boxplot', default=1000)" value="1000" />
 	</inputs>
 	<outputs>
-		<data format="r" name="outputr" from_work_dir="output.qual.r" />
-		<data format="pdf" name="outputpdf" from_work_dir="output.qual.heatmap.pdf" />
-		<data format="pdf" name="outputpdf" from_work_dir="output.qual.boxplot.pdf" />
+		<data format="r" name="outputr" from_work_dir="output.qual.r" label="${tool.name} on ${on_string} (R Script)" />
+		<data format="pdf" name="outputpdf" from_work_dir="output.qual.heatmap.pdf" label="${tool.name} on ${on_string} (Heatmap PDF)" />
+		<data format="pdf" name="outputpdf" from_work_dir="output.qual.boxplot.pdf" label="${tool.name} on ${on_string} (Boxplot PDF)" />
 	</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
+read_quality.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.
+According to SAM specification, if Q is the character to represent "base calling quality"
+in SAM file, then Phred Quality Score = ord(Q) - 33. Here ord() is python function that
+returns an integer representing the Unicode code point of the character when the argument
+is a unicode object, for example, ord('a') returns 97. Phred quality score is widely used
+to measure "reliability" of base-calling, for example, phred quality score of 20 means
+there is 1/100 chance that the base-calling is wrong, phred quality score of 30 means there 
+is 1/1000 chance that the base-calling is wrong. In general: Phred quality score = -10xlog(10)P,
+here P is probability that base-calling is wrong.
 
 Inputs
 ++++++++++++++
@@ -41,10 +47,31 @@
 
 1. output.qual.r
 2. output.qual.boxplot.pdf
-.. image:: http://dldcc-web.brc.bcm.edu/lilab/liguow/RSeQC/figure/36mer.qual.plot.png
+    .. image:: http://rseqc.sourceforge.net/_images/36mer.qual.plot.png
+        :height: 600 px
+        :width: 600 px
+        :scale: 80 %    
 3. output.qual.heatmap.pdf
-.. image:: http://dldcc-web.brc.bcm.edu/lilab/liguow/RSeQC/figure/36mer.qual.heatmap.png
-use different color to represent nucleotide density ("blue"=low density,"orange"=median density,"red"=high density")
+    .. image:: http://rseqc.sourceforge.net/_images/36mer.qual.heatmap.png
+        :height: 600 px
+        :width: 600 px
+        :scale: 80 %    
+
+Heatmap: use different color to represent nucleotide density ("blue"=low density,"orange"=median density,"red"=high density")
+
+-----
+
+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/
+
 
 	</help>
 </tool>