Mercurial > repos > nilesh > rseqc

annotate read_NVC.xml @ 49:6b33e31bda10 draft

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