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comparison bam2wig.xml @ 31:cc5eaa9376d8

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Lance's updates
author nilesh
date Wed, 02 Oct 2013 02:20:04 -0400
parents 907d4b021ff6
children 580ee0c4bc4e
comparison
equal deleted inserted replaced
30:b5d2f575ccb6 31:cc5eaa9376d8
1 <tool id="bam2wig" name="BAM to Wiggle"> 1 <tool id="bam2wig" name="BAM to Wiggle" version="1.1">
2 <description> 2 <description>
3 converts all types of RNA-seq data from .bam to .wig 3 converts all types of RNA-seq data from .bam to .wig
4 </description> 4 </description>
5 <requirements> 5 <requirements>
6 <requirement type="package" version="2.15.1">R</requirement> 6 <requirement type="package" version="2.11.0">R</requirement>
7 <requirement type="package" version="0.1.18">samtools</requirement> 7 <requirement type="package" version="1.7.1">numpy</requirement>
8 <requirement type="package" version="2.3.7">rseqc</requirement> 8 <requirement type="package" version="2.3.7">rseqc</requirement>
9 </requirements> 9 </requirements>
10 <command interpreter="python"> 10 <command>
11 samtoolshelper.py /home/nilesh/RSeQC-2.3.3/scripts/bam2wig.py -i $input -s $chromsize -o outfile 11 ln -s "${input}" "local_input.bam" &amp;&amp;
12 ln -s "${input.metadata.bam_index}" "local_input.bam.bai" &amp;&amp;
13 bam2wig.py -i "local_input.bam" -s $chromsize -o outfile
12 14
13 #if str($strand_type.strand_specific) == "pair" 15 #if str($strand_type.strand_specific) == "pair"
14 -d 16 -d
15 #if str($strand_type.pair_type) == "sd" 17 #if str($strand_type.pair_type) == "sd"
16 '1++,1--,2+-,2-+' 18 '1++,1--,2+-,2-+'
71 </inputs> 73 </inputs>
72 <outputs> 74 <outputs>
73 <data format="wig" name="output" from_work_dir="outfile.wig"> 75 <data format="wig" name="output" from_work_dir="outfile.wig">
74 <filter>strand_type['strand_specific'] == 'none'</filter> 76 <filter>strand_type['strand_specific'] == 'none'</filter>
75 </data> 77 </data>
76 <data format="wig" name="outputfwd" from_work_dir="outfile_Forward.wig"> 78 <data format="wig" name="outputfwd" from_work_dir="outfile_Forward.wig" label="${tool.name} on ${on_string} (Forward Reads)">
77 <filter>strand_type['strand_specific'] != 'none'</filter> 79 <filter>strand_type['strand_specific'] != 'none'</filter>
78 </data> 80 </data>
79 <data format="wig" name="outputrv" from_work_dir="outfile_Reverse.wig"> 81 <data format="wig" name="outputrv" from_work_dir="outfile_Reverse.wig" label="${tool.name} on ${on_string} (Reverse Reads)">
80 <filter>strand_type['strand_specific'] != 'none'</filter> 82 <filter>strand_type['strand_specific'] != 'none'</filter>
81 </data> 83 </data>
82 </outputs> 84 </outputs>
85 <stdio>
86 <exit_code range="1:" level="fatal" description="An error occured during execution, see stderr and stdout for more information" />
87 <regex match="[Ee]rror" source="both" description="An error occured during execution, see stderr and stdout for more information" />
88 </stdio>
83 <help> 89 <help>
84 .. image:: https://code.google.com/p/rseqc/logo?cct=1336721062 90 bam2wig.py
91 ++++++++++
85 92
86 ----- 93 Visualization is the most straightforward and effective way to QC your RNA-seq
87 94 data. For example, change of expression or new splicing can be easily checked
88 About RSeQC 95 by visually comparing two RNA-seq tracks using genome browser such as UCSC_,
89 +++++++++++ 96 IGB_ and IGV_. `bam2wig.py` converts all types of RNA-seq data from BAM_
90 97 format into wiggle_ format in one-stop. wiggle_ files can then be easily
91 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. 98 converted into bigwig_. Bigwig is indexed, binary format of wiggle file, and
92 99 it's particular useful to display large, continuous dataset on genome
93 The RSeQC package is licensed under the GNU GPL v3 license. 100 browser.
94 101
95 Inputs 102 Inputs
96 ++++++++++++++ 103 ++++++++++++++
97 104
98 Input BAM file 105 Input BAM file
114 ++++++++++++++ 121 ++++++++++++++
115 122
116 If RNA-seq is not strand specific, one wig file will be generated, if RNA-seq 123 If RNA-seq is not strand specific, one wig file will be generated, if RNA-seq
117 is strand specific, two wig files corresponding to Forward and Reverse will be generated. 124 is strand specific, two wig files corresponding to Forward and Reverse will be generated.
118 125
126 -----
127
128 About RSeQC
129 +++++++++++
130
131
132 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.
133
134 The RSeQC package is licensed under the GNU GPL v3 license.
135
136 .. image:: http://rseqc.sourceforge.net/_static/logo.png
137
138 .. _RSeQC: http://rseqc.sourceforge.net/
139 .. _UCSC: http://genome.ucsc.edu/index.html
140 .. _IGB: http://bioviz.org/igb/
141 .. _IGV: http://www.broadinstitute.org/igv/home
142 .. _BAM: http://genome.ucsc.edu/goldenPath/help/bam.html
143 .. _wiggle: http://genome.ucsc.edu/goldenPath/help/wiggle.html
144 .. _bigwig: http://genome.ucsc.edu/FAQ/FAQformat.html#format6.1
119 145
120 </help> 146 </help>
121 </tool> 147 </tool>