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comparison read_NVC.xml @ 49:6b33e31bda10 draft

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Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
author lparsons
date Thu, 16 Jul 2015 17:43:43 -0400
parents eb339c5849bb
children 09846d5169fa
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48:2e6190c29c54 49:6b33e31bda10
1 <tool id="rseqc_read_NVC" name="Read NVC" version="2.4"> 1 <tool id="rseqc_read_NVC" name="Read NVC" version="2.4galaxy1">
2 <description>to check the nucleotide composition bias</description> 2 <description>to check the nucleotide composition bias</description>
3
4 <macros>
5 <import>rseqc_macros.xml</import>
6 </macros>
7
3 <requirements> 8 <requirements>
4 <requirement type="package" version="3.0.3">R</requirement> 9 <expand macro="requirement_package_r" />
5 <requirement type="package" version="1.7.1">numpy</requirement> 10 <expand macro="requirement_package_numpy" />
6 <requirement type="package" version="2.4">rseqc</requirement> 11 <expand macro="requirement_package_rseqc" />
7 </requirements> 12 </requirements>
13
14 <expand macro="stdio" />
15
16 <version_command><![CDATA[read_NVC.py --version]]></version_command>
17
8 <command> 18 <command>
9 read_NVC.py -i $input -o output $nx 19 read_NVC.py
20 --input-file $input
21 --out-prefix output
22 $nx
23 --mapq $mapq
10 </command> 24 </command>
11 <stdio> 25
12 <exit_code range="1:" level="fatal" description="An error occured during execution, see stderr and stdout for more information" />
13 <regex match="[Ee]rror" source="both" description="An error occured during execution, see stderr and stdout for more information" />
14 </stdio>
15 <inputs> 26 <inputs>
16 <param name="input" type="data" format="bam,sam" label="input bam/sam file" /> 27 <param name="input" type="data" format="bam,sam" label="input bam/sam file" help="(--input-file)"/>
17 <param name="nx" type="boolean" value="false" truevalue="-x" falsevalue="" label="Include N,X in NVC plot"/> 28 <param name="nx" type="boolean" value="false" truevalue="--nx" falsevalue="" label="Include N,X in NVC plot" help="(--nx)"/>
29 <param name="mapq" type="integer" label="Minimum mapping quality (default=30)" help="Minimum phred scale mapping quality to consider a read 'uniquely mapped' (--mapq)" value="30" />
18 </inputs> 30 </inputs>
31
19 <outputs> 32 <outputs>
20 <data format="xls" name="outputxls" from_work_dir="output.NVC.xls" label="${tool.name} on ${on_string} (XLS)" /> 33 <data format="xls" name="outputxls" from_work_dir="output.NVC.xls" label="${tool.name} on ${on_string} (XLS)" />
21 <data format="txt" name="outputr" from_work_dir="output.NVC_plot.r" label="${tool.name} on ${on_string} (R Script)" /> 34 <data format="txt" name="outputr" from_work_dir="output.NVC_plot.r" label="${tool.name} on ${on_string} (R Script)" />
22 <data format="pdf" name="outputpdf" from_work_dir="output.NVC_plot.pdf" label="${tool.name} on ${on_string} (PDF)" /> 35 <data format="pdf" name="outputpdf" from_work_dir="output.NVC_plot.pdf" label="${tool.name} on ${on_string} (PDF)" />
23 </outputs> 36 </outputs>
24 <help> 37
38 <tests>
39 <test>
40 <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/>
41 <output name="outputxls" file="output.NVC.xls"/>
42 <output name="outputr" file="output.NVC_plot.r"/>
43 </test>
44 </tests>
45
46 <help><![CDATA[
25 read_NVC.py 47 read_NVC.py
26 +++++++++++ 48 +++++++++++
27 49
28 This module is used to check the nucleotide composition bias. Due to random priming, certain 50 This module is used to check the nucleotide composition bias. Due to random priming, certain
29 patterns are over represented at the beginning (5'end) of reads. This bias could be easily 51 patterns are over represented at the beginning (5'end) of reads. This bias could be easily
30 examined by NVC (Nucleotide versus cycle) plot. NVC plot is generated by overlaying all 52 examined by NVC (Nucleotide versus cycle) plot. NVC plot is generated by overlaying all
31 reads together, then calculating nucleotide composition for each position of read 53 reads together, then calculating nucleotide composition for each position of read
32 (or each sequencing cycle). In ideal condition (genome is random and RNA-seq reads is 54 (or each sequencing cycle). In ideal condition (genome is random and RNA-seq reads is
33 randomly sampled from genome), we expect A%=C%=G%=T%=25% at each position of reads. 55 randomly sampled from genome), we expect A%=C%=G%=T%=25% at each position of reads.
34 56
35 NOTE: this program expect a fixed read length 57 NOTE: this program expect a fixed read length
36 58
37 Inputs 59 Inputs
38 ++++++++++++++ 60 ++++++++++++++
55 77
56 78
57 .. image:: http://rseqc.sourceforge.net/_images/NVC_plot.png 79 .. image:: http://rseqc.sourceforge.net/_images/NVC_plot.png
58 :height: 600 px 80 :height: 600 px
59 :width: 600 px 81 :width: 600 px
60 :scale: 80 % 82 :scale: 80 %
61 83
62 ----- 84 -----
63 85
64 About RSeQC 86 About RSeQC
65 +++++++++++ 87 +++++++++++
66 88
67 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. 89 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.
68 90
69 The RSeQC package is licensed under the GNU GPL v3 license. 91 The RSeQC package is licensed under the GNU GPL v3 license.
70 92
71 .. image:: http://rseqc.sourceforge.net/_static/logo.png 93 .. image:: http://rseqc.sourceforge.net/_static/logo.png
72 94
73 .. _RSeQC: http://rseqc.sourceforge.net/ 95 .. _RSeQC: http://rseqc.sourceforge.net/
96 ]]>
97 </help>
74 98
99 <expand macro="citations" />
75 100
76 </help>
77 </tool> 101 </tool>