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comparison junction_annotation.xml @ 21:93c0e1cc65c6

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author nilesh
date Thu, 11 Jul 2013 12:24:45 -0400
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20:adc934fb9a76 21:93c0e1cc65c6
1 <tool id="junction_annotation" name="Junction Annotation">
2 <description>compares detected splice junctions to reference gene model</description>
3 <requirements>
4 <requirement type="package" version="2.15.1">R</requirement>
5 <requirement type="package" version="2.3.7">rseqc</requirement>
6 </requirements>
7 <command interpreter="python"> junction_annotation.py -i $input -o output -r $refgene
8
9 #if $intron.hasIntron
10 -m $intron.min_Intron
11 #end if
12
13 </command>
14 <inputs>
15 <param name="input" type="data" format="bam,sam" label="input bam/sam file" />
16 <param name="refgene" type="data" format="bed" label="reference gene model" />
17 <conditional name="intron">
18 <param name="hasIntron" type="boolean" label="Specify minimum intron length" value="false"/>
19 <when value="true">
20 <param name="min_Intron" type="integer" value="50" label="Minimum intron length (bp, default=50)" />
21 </when>
22 </conditional>
23 </inputs>
24 <outputs>
25 <data format="xls" name="outputxls" from_work_dir="output.junction.xls"/>
26 <data format="r" name="outputr" from_work_dir="output.junction_plot.r" />
27 <data format="pdf" name="outputpdf" from_work_dir="output.splice_events.pdf"/>
28 <data format="pdf" name="outputjpdf" from_work_dir="output.splice_junction.pdf" />
29 </outputs>
30 <help>
31 .. image:: https://code.google.com/p/rseqc/logo?cct=1336721062
32
33 -----
34
35 About RSeQC
36 +++++++++++
37
38 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.
39
40 The RSeQC package is licensed under the GNU GPL v3 license.
41
42 Inputs
43 ++++++++++++++
44
45 Input BAM/SAM file
46 Alignment file in BAM/SAM format.
47
48 Reference gene model
49 Gene model in BED format.
50
51 Minimum intron length (default=50)
52 Minimum intron length (bp).
53
54
55 Output
56 ++++++++++++++
57
58 1. output.junc.anno.junction.xls:
59 - chrom ID
60 - start position of junction (coordinate is 0 based)
61 - end position of junction (coordinate is 1 based)
62 - number of splice events supporting this junction
63 - 'annotated', 'complete_novel' or 'partial_novel'.
64 2. output.anno.junction_plot.r: R script to generate pie chart
65 3. output.splice_junction.pdf: plot of splice junctions
66 4. output.splice_events.pdf: plot of splice events
67 .. image:: http://dldcc-web.brc.bcm.edu/lilab/liguow/RSeQC/figure/junction.png
68
69
70
71
72 </help>
73 </tool>