# HG changeset patch
# User nilesh
# Date 1373559809 14400
# Node ID 366799f58c6b0c2dd8fa6e0d23fbd29ca97164ff
# Parent  2f55e1d520cd49f61fb29470d60993ea553208a7
Uploaded

diff -r 2f55e1d520cd -r 366799f58c6b clipping_profile.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/clipping_profile.xml	Thu Jul 11 12:23:29 2013 -0400
@@ -0,0 +1,45 @@
+<tool id="clipping_profile" name="Clipping Profile">
+	<description>
+	 estimates clipping profile of RNA-seq reads from BAM or SAM file
+	</description>
+	<requirements>
+		<requirement type="package" version="2.15.1">R</requirement>
+		<requirement type="package" version="2.3.7">rseqc</requirement>
+	</requirements>
+	<command interpreter="python">
+		clipping_profile.py -i $input -o output
+	</command>
+	<inputs>
+		<param name="input" type="data" label="Input .bam/.sam File" format="bam,sam" />
+	</inputs>
+	<outputs>
+		<data format="xls" name="outputxls" from_work_dir="output.clipping_profile.xls" />
+		<data format="r" name="outputr" from_work_dir="output.clipping_profile.r" />
+	</outputs>
+	<help>
+.. image:: https://code.google.com/p/rseqc/logo?cct=1336721062
+
+-----
+
+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.
+
+Inputs
+++++++++++++++
+
+Input BAM/SAM file
+	Alignment file in BAM/SAM format.
+
+
+Sample Output
+++++++++++++++
+
+.. image:: http://dldcc-web.brc.bcm.edu/lilab/liguow/RSeQC/figure/clipping_good.png
+
+
+	</help>
+</tool>
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