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comparison clipping_profile.xml @ 31:cc5eaa9376d8

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Lance's updates
author nilesh
date Wed, 02 Oct 2013 02:20:04 -0400
parents 366799f58c6b
children 580ee0c4bc4e
comparison
equal deleted inserted replaced
30:b5d2f575ccb6 31:cc5eaa9376d8
1 <tool id="clipping_profile" name="Clipping Profile"> 1 <tool id="clipping_profile" name="Clipping Profile" version="1.1">
2 <description> 2 <description>
3 estimates clipping profile of RNA-seq reads from BAM or SAM file 3 estimates clipping profile of RNA-seq reads from BAM or SAM file
4 </description> 4 </description>
5 <requirements> 5 <requirements>
6 <requirement type="package" version="2.15.1">R</requirement> 6 <requirement type="package" version="2.11.0">R</requirement>
7 <requirement type="package" version="1.7.1">numpy</requirement>
7 <requirement type="package" version="2.3.7">rseqc</requirement> 8 <requirement type="package" version="2.3.7">rseqc</requirement>
8 </requirements> 9 </requirements>
9 <command interpreter="python"> 10 <command>
10 clipping_profile.py -i $input -o output 11 clipping_profile.py -i $input -o output
11 </command> 12 </command>
12 <inputs> 13 <inputs>
13 <param name="input" type="data" label="Input .bam/.sam File" format="bam,sam" /> 14 <param name="input" type="data" label="Input .bam/.sam File" format="bam,sam" />
14 </inputs> 15 </inputs>
15 <outputs> 16 <outputs>
16 <data format="xls" name="outputxls" from_work_dir="output.clipping_profile.xls" /> 17 <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 <data format="r" name="outputr" from_work_dir="output.clipping_profile.r" />
18 </outputs> 19 </outputs>
20 <stdio>
21 <exit_code range="1:" level="fatal" description="An error occured during execution, see stderr and stdout for more information" />
22 <regex match="[Ee]rror" source="both" description="An error occured during execution, see stderr and stdout for more information" />
23 </stdio>
19 <help> 24 <help>
20 .. image:: https://code.google.com/p/rseqc/logo?cct=1336721062 25 clipping_profile.py
26 +++++++++++++++++++
21 27
22 ----- 28 This program is used to estimate clipping profile of RNA-seq reads from BAM or SAM file.
23 29 Note that to use this funciton, CIGAR strings within SAM/BAM file should have 'S' operation
24 About RSeQC 30 (This means your reads aligner should support clipped mapping).
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
31 Inputs 32 Inputs
32 ++++++++++++++ 33 ++++++++++++++
33 34
34 Input BAM/SAM file 35 Input BAM/SAM file
36 37
37 38
38 Sample Output 39 Sample Output
39 ++++++++++++++ 40 ++++++++++++++
40 41
41 .. image:: http://dldcc-web.brc.bcm.edu/lilab/liguow/RSeQC/figure/clipping_good.png 42 .. image:: http://rseqc.sourceforge.net/_images/clipping_good.png
43 :height: 600 px
44 :width: 600 px
45 :scale: 80 %
42 46
47 -----
48
49 About RSeQC
50 +++++++++++
51
52 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.
53
54 The RSeQC package is licensed under the GNU GPL v3 license.
55
56 .. image:: http://rseqc.sourceforge.net/_static/logo.png
57
58 .. _RSeQC: http://rseqc.sourceforge.net/
43 59
44 </help> 60 </help>
45 </tool> 61 </tool>