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comparison read_duplication.xml @ 45:eb339c5849bb draft

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Reupload, toolshed removed all files of previous version.
author lparsons
date Fri, 26 Sep 2014 15:04:18 -0400
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children 6b33e31bda10
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44:20e0b2dd7882 45:eb339c5849bb
1 <tool id="rseqc_read_duplication" name="Read Duplication" version="2.4">
2 <description>determines reads duplication rate with sequence-based and mapping-based strategies</description>
3 <requirements>
4 <requirement type="package" version="3.0.3">R</requirement>
5 <requirement type="package" version="1.7.1">numpy</requirement>
6 <requirement type="package" version="2.4">rseqc</requirement>
7 </requirements>
8 <command>
9 read_duplication.py -i $input -o output -u $upLimit
10 </command>
11 <stdio>
12 <exit_code range="1:" level="fatal" description="An error occured during execution, see stderr and stdout for more information" />
13 <regex match="[Ee]rror" source="both" description="An error occured during execution, see stderr and stdout for more information" />
14 </stdio>
15 <inputs>
16 <param name="input" type="data" format="bam,sam" label="input bam/sam file" />
17 <param name="upLimit" type="integer" label="Upper Limit of Plotted Duplicated Times (default=500)" value="500" />
18 </inputs>
19 <outputs>
20 <data format="xls" name="outputxls" from_work_dir="output.dup.pos.DupRate.xls" label="${tool.name} on ${on_string} (Position XLS)"/>
21 <data format="xls" name="outputseqxls" from_work_dir="output.dup.seq.DupRate.xls" label="${tool.name} on ${on_string} (Sequence XLS)"/>
22 <data format="txt" name="outputr" from_work_dir="output.DupRate_plot.r" label="${tool.name} on ${on_string} (R Script)" />
23 <data format="pdf" name="outputpdf" from_work_dir="output.DupRate_plot.pdf" label="${tool.name} on ${on_string} (PDF)" />
24 </outputs>
25 <help>
26 read_duplication.py
27 +++++++++++++++++++
28
29 Two strategies were used to determine reads duplication rate:
30
31 * Sequence based: reads with exactly the same sequence content are regarded as duplicated reads.
32 * 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.
33
34 Inputs
35 ++++++++++++++
36
37 Input BAM/SAM file
38 Alignment file in BAM/SAM format.
39
40 Upper Limit of Plotted Duplicated Times (default=500)
41 Only used for plotting.
42
43 Output
44 ++++++++++++++
45
46 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.
47 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.
48 3. output.DupRate_plot.r: R script to generate pdf file
49 4. output.DupRate_plot.pdf: graphical output generated from R script
50
51 .. image:: http://rseqc.sourceforge.net/_images/duplicate.png
52 :height: 600 px
53 :width: 600 px
54 :scale: 80 %
55
56 -----
57
58 About RSeQC
59 +++++++++++
60
61 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.
62
63 The RSeQC package is licensed under the GNU GPL v3 license.
64
65 .. image:: http://rseqc.sourceforge.net/_static/logo.png
66
67 .. _RSeQC: http://rseqc.sourceforge.net/
68
69
70 </help>
71 </tool>