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comparison read_NVC.xml @ 32:580ee0c4bc4e

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Fixes from Bjorn Gruning: create symlinks under $TMP and clean them up afterwards, replace R dependency with the Tool Shed R3 package, add --install-scripts, prepend tool-ids with rseqc
author lparsons
date Mon, 07 Oct 2013 15:01:13 -0400
parents cc5eaa9376d8
children
comparison
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31:cc5eaa9376d8 32:580ee0c4bc4e
1 <tool id="read_NVC" name="Read NVC" version="1.1"> 1 <tool id="rseqc_read_NVC" name="Read NVC" version="1.1">
2 <description>to check the nucleotide composition bias</description> 2 <description>to check the nucleotide composition bias</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="2.11.0">R</requirement> 4 <requirement type="package" version="3.0.1">R</requirement>
5 <requirement type="package" version="1.7.1">numpy</requirement> 5 <requirement type="package" version="1.7.1">numpy</requirement>
6 <requirement type="package" version="2.3.7">rseqc</requirement> 6 <requirement type="package" version="2.3.7">rseqc</requirement>
7 </requirements> 7 </requirements>
8 <command> read_NVC.py -i $input -o output 8 <command>
9 9 read_NVC.py -i $input -o output $nx
10 #if $nx 10 </command>
11 -x
12 #end if
13 </command>
14 <inputs>
15 <param name="input" type="data" format="bam,sam" label="input bam/sam file" />
16 <param name="nx" type="boolean" label="Include N,X in NVC plot" value="false" />
17 </inputs>
18 <outputs>
19 <data format="xls" name="outputxls" from_work_dir="output.NVC.xls" label="${tool.name} on ${on_string} (XLS)" />
20 <data format="r" name="outputr" from_work_dir="output.NVC_plot.r" label="${tool.name} on ${on_string} (R Script)" />
21 <data format="pdf" name="outputpdf" from_work_dir="output.NVC_plot.pdf" label="${tool.name} on ${on_string} (PDF)" />
22 </outputs>
23 <stdio> 11 <stdio>
24 <exit_code range="1:" level="fatal" description="An error occured during execution, see stderr and stdout for more information" /> 12 <exit_code range="1:" level="fatal" description="An error occured during execution, see stderr and stdout for more information" />
25 <regex match="[Ee]rror" source="both" description="An error occured during execution, see stderr and stdout for more information" /> 13 <regex match="[Ee]rror" source="both" description="An error occured during execution, see stderr and stdout for more information" />
26 </stdio> 14 </stdio>
27 <help> 15 <inputs>
16 <param name="input" type="data" format="bam,sam" label="input bam/sam file" />
17 <param name="nx" type="boolean" value="false" truevalue="-x" falsevalue="" label="Include N,X in NVC plot"/>
18 </inputs>
19 <outputs>
20 <data format="xls" name="outputxls" from_work_dir="output.NVC.xls" label="${tool.name} on ${on_string} (XLS)" />
21 <data format="txt" name="outputr" from_work_dir="output.NVC_plot.r" label="${tool.name} on ${on_string} (R Script)" />
22 <data format="pdf" name="outputpdf" from_work_dir="output.NVC_plot.pdf" label="${tool.name} on ${on_string} (PDF)" />
23 </outputs>
24 <help>
28 read_NVC.py 25 read_NVC.py
29 +++++++++++ 26 +++++++++++
30 27
31 This module is used to check the nucleotide composition bias. Due to random priming, certain 28 This module is used to check the nucleotide composition bias. Due to random priming, certain
32 patterns are over represented at the beginning (5'end) of reads. This bias could be easily 29 patterns are over represented at the beginning (5'end) of reads. This bias could be easily
39 36
40 Inputs 37 Inputs
41 ++++++++++++++ 38 ++++++++++++++
42 39
43 Input BAM/SAM file 40 Input BAM/SAM file
44 Alignment file in BAM/SAM format. 41 Alignment file in BAM/SAM format.
45 42
46 Include N,X in NVC plot 43 Include N,X in NVC plot
47 Plots N and X alongside A, T, C, and G in plot. 44 Plots N and X alongside A, T, C, and G in plot.
48 45
49 Output 46 Output
50 ++++++++++++++ 47 ++++++++++++++
51 48
52 This module is used to check the nucleotide composition bias. Due to random priming, certain patterns are over represented at the beginning (5'end) of reads. This bias could be easily examined by NVC (Nucleotide versus cycle) plot. NVC plot is generated by overlaying all reads together, then calculating nucleotide composition for each position of read (or each sequencing cycle). In ideal condition (genome is random and RNA-seq reads is randomly sampled from genome), we expect A%=C%=G%=T%=25% at each position of reads. 49 This module is used to check the nucleotide composition bias. Due to random priming, certain patterns are over represented at the beginning (5'end) of reads. This bias could be easily examined by NVC (Nucleotide versus cycle) plot. NVC plot is generated by overlaying all reads together, then calculating nucleotide composition for each position of read (or each sequencing cycle). In ideal condition (genome is random and RNA-seq reads is randomly sampled from genome), we expect A%=C%=G%=T%=25% at each position of reads.
74 .. image:: http://rseqc.sourceforge.net/_static/logo.png 71 .. image:: http://rseqc.sourceforge.net/_static/logo.png
75 72
76 .. _RSeQC: http://rseqc.sourceforge.net/ 73 .. _RSeQC: http://rseqc.sourceforge.net/
77 74
78 75
79 </help> 76 </help>
80 </tool> 77 </tool>