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comparison read_duplication.xml @ 31:cc5eaa9376d8

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Lance's updates
author nilesh
date Wed, 02 Oct 2013 02:20:04 -0400
parents 80f857718ca0
children 580ee0c4bc4e
comparison
equal deleted inserted replaced
30:b5d2f575ccb6 31:cc5eaa9376d8
1 <tool id="read_duplication" name="Read Duplication"> 1 <tool id="read_duplication" name="Read Duplication" version="1.1">
2 <description>determines reads duplication rate with sequence-based and mapping-based strategies</description> 2 <description>determines reads duplication rate with sequence-based and mapping-based strategies</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="2.15.1">R</requirement> 4 <requirement type="package" version="2.11.0">R</requirement>
5 <requirement type="package" version="1.7.1">numpy</requirement>
5 <requirement type="package" version="2.3.7">rseqc</requirement> 6 <requirement type="package" version="2.3.7">rseqc</requirement>
6 </requirements> 7 </requirements>
7 <command interpreter="python"> read_duplication.py -i $input -o output -u $upLimit 8 <command> read_duplication.py -i $input -o output -u $upLimit
8 </command> 9 </command>
9 <inputs> 10 <inputs>
10 <param name="input" type="data" format="bam,sam" label="input bam/sam file" /> 11 <param name="input" type="data" format="bam,sam" label="input bam/sam file" />
11 <param name="upLimit" type="integer" label="Upper Limit of Plotted Duplicated Times (default=500)" value="500" /> 12 <param name="upLimit" type="integer" label="Upper Limit of Plotted Duplicated Times (default=500)" value="500" />
12 </inputs> 13 </inputs>
13 <outputs> 14 <outputs>
14 <data format="xls" name="outputxls" from_work_dir="output.dup.pos.DupRate.xls"/> 15 <data format="xls" name="outputxls" from_work_dir="output.dup.pos.DupRate.xls" label="${tool.name} on ${on_string} (Position XLS)"/>
15 <data format="xls" name="outputseqxls" from_work_dir="output.dup.seq.DupRate.xls"/> 16 <data format="xls" name="outputseqxls" from_work_dir="output.dup.seq.DupRate.xls" label="${tool.name} on ${on_string} (Sequence XLS)"/>
16 <data format="r" name="outputr" from_work_dir="output.DupRate_plot.r" /> 17 <data format="r" name="outputr" from_work_dir="output.DupRate_plot.r" label="${tool.name} on ${on_string} (R Script)" />
17 <data format="pdf" name="outputpdf" from_work_dir="output.DupRate_plot.pdf" /> 18 <data format="pdf" name="outputpdf" from_work_dir="output.DupRate_plot.pdf" label="${tool.name} on ${on_string} (PDF)" />
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 read_duplication.py
26 +++++++++++++++++++
21 27
22 ----- 28 Two strategies were used to determine reads duplication rate:
23 29
24 About RSeQC 30 * Sequence based: reads with exactly the same sequence content are regarded as duplicated reads.
25 +++++++++++ 31 * Mapping based: reads mapped to the same genomic location are regarded as duplicated reads. For splice reads, reads mapped to the same starting position and splice the same way are regarded as duplicated reads.
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 32
31 Inputs 33 Inputs
32 ++++++++++++++ 34 ++++++++++++++
33 35
34 Input BAM/SAM file 36 Input BAM/SAM file
43 1. output.dup.pos.DupRate.xls: Read duplication rate determined from mapping position of read. First column is "occurrence" or duplication times, second column is number of uniquely mapped reads. 45 1. output.dup.pos.DupRate.xls: Read duplication rate determined from mapping position of read. First column is "occurrence" or duplication times, second column is number of uniquely mapped reads.
44 2. output.dup.seq.DupRate.xls: Read duplication rate determined from sequence of read. First column is "occurrence" or duplication times, second column is number of uniquely mapped reads. 46 2. output.dup.seq.DupRate.xls: Read duplication rate determined from sequence of read. First column is "occurrence" or duplication times, second column is number of uniquely mapped reads.
45 3. output.DupRate_plot.r: R script to generate pdf file 47 3. output.DupRate_plot.r: R script to generate pdf file
46 4. output.DupRate_plot.pdf: graphical output generated from R script 48 4. output.DupRate_plot.pdf: graphical output generated from R script
47 49
48 .. image:: http://dldcc-web.brc.bcm.edu/lilab/liguow/RSeQC/figure/duplicate.png 50 .. image:: http://rseqc.sourceforge.net/_images/duplicate.png
51 :height: 600 px
52 :width: 600 px
53 :scale: 80 %
54
55 -----
56
57 About RSeQC
58 +++++++++++
59
60 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.
61
62 The RSeQC package is licensed under the GNU GPL v3 license.
63
64 .. image:: http://rseqc.sourceforge.net/_static/logo.png
65
66 .. _RSeQC: http://rseqc.sourceforge.net/
67
49 68
50 </help> 69 </help>
51 </tool> 70 </tool>