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comparison read_GC.xml @ 31:cc5eaa9376d8

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Lance's updates
author nilesh
date Wed, 02 Oct 2013 02:20:04 -0400
parents 7cac660d1c0a
children 580ee0c4bc4e
comparison
equal deleted inserted replaced
30:b5d2f575ccb6 31:cc5eaa9376d8
1 <tool id="read_GC" name="Read GC"> 1 <tool id="read_GC" name="Read GC" version="1.1">
2 <description>determines GC% and read count</description> 2 <description>determines GC% and read count</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_GC.py -i $input -o output 8 <command> read_GC.py -i $input -o output
8 </command> 9 </command>
9 <inputs> 10 <inputs>
10 <param name="input" type="data" format="bam,sam" label="input bam/sam file" /> 11 <param name="input" type="data" format="bam,sam" label="input bam/sam file" />
11 </inputs> 12 </inputs>
12 <outputs> 13 <outputs>
13 <data format="xls" name="outputxls" from_work_dir="output.dup.pos.DupRate.xls"/> 14 <data format="xls" name="outputxls" from_work_dir="output.GC.xls" label="${tool.name} on ${on_string} (XLS)"/>
14 <data format="xls" name="outputseqxls" from_work_dir="output.dup.seq.DupRate.xls"/> 15 <data format="r" name="outputr" from_work_dir="output.GC_plot.r" label="${tool.name} on ${on_string} (R Script)" />
15 <data format="r" name="outputr" from_work_dir="output.DupRate_plot.r" /> 16 <data format="pdf" name="outputpdf" from_work_dir="output.GC_plot.pdf" label="${tool.name} on ${on_string} (PDF)" />
16 <data format="pdf" name="outputpdf" from_work_dir="output.DupRate_plot.pdf" />
17 </outputs> 17 </outputs>
18 <stdio>
19 <exit_code range="1:" level="fatal" description="An error occured during execution, see stderr and stdout for more information" />
20 <regex match="[Ee]rror" source="both" description="An error occured during execution, see stderr and stdout for more information" />
21 </stdio>
18 <help> 22 <help>
19 .. image:: https://code.google.com/p/rseqc/logo?cct=1336721062 23 read_GC.py
24 ++++++++++
20 25
21 -----
22
23 About RSeQC
24 +++++++++++
25
26 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.
27
28 The RSeQC package is licensed under the GNU GPL v3 license.
29 26
30 Inputs 27 Inputs
31 ++++++++++++++ 28 ++++++++++++++
32 29
33 Input BAM/SAM file 30 Input BAM/SAM file
38 35
39 1. output.GC.xls: Two column, plain text file, first column is GC%, second column is read count 36 1. output.GC.xls: Two column, plain text file, first column is GC%, second column is read count
40 2. output.GC_plot.r: R script to generate pdf file. 37 2. output.GC_plot.r: R script to generate pdf file.
41 3. output.GC_plot.pdf: graphical output generated from R script. 38 3. output.GC_plot.pdf: graphical output generated from R script.
42 39
43 .. image:: http://dldcc-web.brc.bcm.edu/lilab/liguow/RSeQC/figure/read_gc.png 40 .. image:: http://rseqc.sourceforge.net/_images/read_gc.png
41 :height: 600 px
42 :width: 600 px
43 :scale: 80 %
44
45 -----
46
47 About RSeQC
48 +++++++++++
49
50 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.
51
52 The RSeQC package is licensed under the GNU GPL v3 license.
53
54 .. image:: http://rseqc.sourceforge.net/_static/logo.png
55
56 .. _RSeQC: http://rseqc.sourceforge.net/
57
44 58
45 </help> 59 </help>
46 </tool> 60 </tool>