Mercurial > repos > nilesh > rseqc

annotate junction_annotation.xml @ 48:2e6190c29c54 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Upload tar.gz again - toolshed removed all files (grrr...)
author lparsons
date Tue, 21 Apr 2015 10:27:06 -0400
parents eb339c5849bb
children 6b33e31bda10
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
45
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
1 <tool id="rseqc_junction_annotation" name="Junction Annotation" version="2.4">
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
2 <description>compares detected splice junctions to reference gene model</description>
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
3 <requirements>
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
4 <requirement type="package" version="3.0.3">R</requirement>
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
5 <requirement type="package" version="1.7.1">numpy</requirement>
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
6 <requirement type="package" version="2.4">rseqc</requirement>
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
7 </requirements>
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
8 <command>
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
9 junction_annotation.py
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
10 -i $input -o output -r $refgene
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
11 #if $intron.hasIntron
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
12 -m $intron.min_Intron
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
13 #end if
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
14 </command>
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
15 <stdio>
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
16 <exit_code range="1:" level="fatal" description="An error occured during execution, see stderr and stdout for more information" />
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
17 <regex match="[Ee]rror" source="both" description="An error occured during execution, see stderr and stdout for more information" />
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
18 </stdio>
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
19 <inputs>
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
20 <param name="input" type="data" format="bam,sam" label="input bam/sam file" />
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
21 <param name="refgene" type="data" format="bed" label="reference gene model" />
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
22 <conditional name="intron">
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
23 <param name="hasIntron" type="boolean" label="Specify minimum intron length" value="false"/>
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
24 <when value="true">
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
25 <param name="min_Intron" type="integer" value="50" label="Minimum intron length (bp, default=50)" />
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
26 </when>
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
27 </conditional>
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
28 </inputs>
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
29 <outputs>
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
30 <data format="xls" name="outputxls" from_work_dir="output.junction.xls" label="${tool.name} on ${on_string} (XLS)"/>
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
31 <data format="txt" name="outputr" from_work_dir="output.junction_plot.r" label="${tool.name} on ${on_string} (R Script)" />
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
32 <data format="pdf" name="outputpdf" from_work_dir="output.splice_events.pdf" label="${tool.name} on ${on_string} (Splice Events PDF)"/>
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
33 <data format="pdf" name="outputjpdf" from_work_dir="output.splice_junction.pdf" label="${tool.name} on ${on_string} (Splice Junction PDF)" />
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
34 </outputs>
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
35 <help>
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
36 junction_annotation.py
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
37 ++++++++++++++++++++++
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
38
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
39 For a given alignment file (-i) in BAM or SAM format and a reference gene model (-r) in BED
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
40 format, this program will compare detected splice junctions to reference gene model. splicing
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
41 annotation is performed in two levels: splice event level and splice junction level.
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
42
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
43 * splice event: An RNA read, especially long read, can be spliced 2 or more times, each time is called a splicing event; In this sense, 100 spliced reads can produce >= 100 splicing events.
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
44 * splice junction: multiple splicing events spanning the same intron can be consolidated into one splicing junction.
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
45
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
46 All detected junctions can be grouped to 3 exclusive categories:
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
47
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
48 1. Annotated: The junction is part of the gene model. Both splice sites, 5' splice site
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
49 (5'SS) and 3'splice site (3'SS) can be annotated by reference gene model.
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
50 2. complete_novel: Complete new junction. Neither of the two splice sites cannot be annotated by gene model
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
51 3. partial_novel: One of the splice site (5'SS or 3'SS) is new, while the other splice site is annotated (known)
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
52
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
53 Inputs
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
54 ++++++++++++++
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
55
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
56 Input BAM/SAM file
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
57 Alignment file in BAM/SAM format.
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 Reference gene model
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
60 Gene model in BED format.
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 Minimum intron length (default=50)
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
63 Minimum intron length (bp).
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
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
66 Output
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
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
69 1. output.junc.anno.junction.xls:
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
70 - chrom ID
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
71 - start position of junction (coordinate is 0 based)
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
72 - end position of junction (coordinate is 1 based)
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
73 - number of splice events supporting this junction
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
74 - 'annotated', 'complete_novel' or 'partial_novel'.
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
75 2. output.anno.junction_plot.r: R script to generate pie chart
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
76 3. output.splice_junction.pdf: plot of splice junctions
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
77 4. output.splice_events.pdf: plot of splice events
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/junction.png
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
80 :height: 400 px
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
81 :width: 850 px
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
82 :scale: 80 %
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
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
86 About RSeQC
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/
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
96
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
97
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
98
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
99
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
100 </help>
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
101 </tool>