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comparison geneBody_coverage.xml @ 38:a447651be8ee

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Reupload 2.3.7 fix (tarball upload issues)
author lparsons
date Wed, 23 Jul 2014 10:14:01 -0400
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37:ddbe13d2855d 38:a447651be8ee
1 <tool id="rseqc_geneBody_coverage" name="Gene Body Converage (BAM)" version="1.1">
2 <description>
3 Read coverage over gene body.
4 </description>
5 <requirements>
6 <requirement type="package" version="3.0.1">R</requirement>
7 <requirement type="package" version="1.7.1">numpy</requirement>
8 <requirement type="package" version="2.3.7">rseqc</requirement>
9 </requirements>
10 <command>
11 geneBody_coverage.py -i $input -r $refgene -o output
12 </command>
13 <stdio>
14 <exit_code range="1:" level="fatal" description="An error occured during execution, see stderr and stdout for more information" />
15 <regex match="[Ee]rror" source="both" description="An error occured during execution, see stderr and stdout for more information" />
16 </stdio>
17 <inputs>
18 <param name="input" type="data" label="Input .bam file" format="bam" />
19 <param name="refgene" type="data" label="Reference Genome" format="bed" />
20 </inputs>
21 <outputs>
22 <data name="outputpdf" format="pdf" from_work_dir="output.geneBodyCoverage.pdf" label="${tool.name} on ${on_string} (PDF)" />
23 <data name="outputr" format="txt" from_work_dir="output.geneBodyCoverage_plot.r" label="${tool.name} on ${on_string} (R Script)" />
24 <data name="outputtxt" format="txt" from_work_dir="output.geneBodyCoverage.txt" label="${tool.name} on ${on_string} (Text)" />
25 </outputs>
26 <help>
27 geneBody_coverage.py
28 ++++++++++++++++++++
29
30 Read coverage over gene body. This module is used to check if reads coverage is uniform and
31 if there is any 5\'/3\' bias. This module scales all transcripts to 100 nt and calculates the
32 number of reads covering each nucleotide position. Finally, it generates a plot illustrating
33 the coverage profile along the gene body. NOTE: this module requires lots of memory for large
34 BAM files, because it load the entire BAM file into memory. We add another script
35 "geneBody_coverage2.py" into v2.3.1 which takes bigwig (instead of BAM) as input.
36 It only use 200M RAM, but users need to convert BAM into WIG, and then WIG into BigWig.
37
38 Inputs
39 ++++++++++++++
40
41 Input BAM/SAM file
42 Alignment file in BAM/SAM format.
43
44 Reference gene model
45 Gene Model in BED format.
46
47
48 Outputs
49 ++++++++++++++
50
51 Read coverage over gene body. This module is used to check if reads coverage is uniform and if there is any 5’/3’ bias. This module scales all transcripts to 100 nt and calculates the number of reads covering each nucleotide position. Finally, it generates a plot illustrating the coverage profile along the gene body. NOTE: this module requires lots of memory for large BAM files, because it load the entire BAM file into memory. We add another script "geneBody_coverage2.py" into v2.3.1 which takes bigwig (instead of BAM) as input. It only use 200M RAM, but users need to convert BAM into WIG, and then WIG into BigWig.
52
53 Example output:
54 .. image:: http://rseqc.sourceforge.net/_images/geneBody_coverage.png
55 :height: 600 px
56 :width: 600 px
57 :scale: 80 %
58
59
60 -----
61
62 About RSeQC
63 +++++++++++
64
65 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.
66
67 The RSeQC package is licensed under the GNU GPL v3 license.
68
69 .. image:: http://rseqc.sourceforge.net/_static/logo.png
70
71 .. _RSeQC: http://rseqc.sourceforge.net/
72
73
74
75 </help>
76 </tool>