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comparison clipping_profile.xml @ 16:366799f58c6b

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author nilesh
date Thu, 11 Jul 2013 12:23:29 -0400
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15:2f55e1d520cd 16:366799f58c6b
1 <tool id="clipping_profile" name="Clipping Profile">
2 <description>
3 estimates clipping profile of RNA-seq reads from BAM or SAM file
4 </description>
5 <requirements>
6 <requirement type="package" version="2.15.1">R</requirement>
7 <requirement type="package" version="2.3.7">rseqc</requirement>
8 </requirements>
9 <command interpreter="python">
10 clipping_profile.py -i $input -o output
11 </command>
12 <inputs>
13 <param name="input" type="data" label="Input .bam/.sam File" format="bam,sam" />
14 </inputs>
15 <outputs>
16 <data format="xls" name="outputxls" from_work_dir="output.clipping_profile.xls" />
17 <data format="r" name="outputr" from_work_dir="output.clipping_profile.r" />
18 </outputs>
19 <help>
20 .. image:: https://code.google.com/p/rseqc/logo?cct=1336721062
21
22 -----
23
24 About RSeQC
25 +++++++++++
26
27 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.
28
29 The RSeQC package is licensed under the GNU GPL v3 license.
30
31 Inputs
32 ++++++++++++++
33
34 Input BAM/SAM file
35 Alignment file in BAM/SAM format.
36
37
38 Sample Output
39 ++++++++++++++
40
41 .. image:: http://dldcc-web.brc.bcm.edu/lilab/liguow/RSeQC/figure/clipping_good.png
42
43
44 </help>
45 </tool>