Mercurial > repos > nilesh > rseqc

comparison bam2wig.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
children 6b33e31bda10
comparison
equal deleted inserted replaced
47:10d30c88fe05 48:2e6190c29c54
1 <tool id="rseqc_bam2wig" name="BAM to Wiggle" version="2.4">
2 <description>
3 converts all types of RNA-seq data from .bam to .wig
4 </description>
5 <requirements>
6 <requirement type="package" version="3.0.3">R</requirement>
7 <requirement type="package" version="1.7.1">numpy</requirement>
8 <requirement type="package" version="2.4">rseqc</requirement>
9 </requirements>
10 <command>
11 tmp_input_name=\$(mktemp -u);
12 bai='.bai';
13
14 ln -s "${input}" \$tmp_input_name &amp;&amp;
15 ln -s "${input.metadata.bam_index}" \$tmp_input_name\$bai &amp;&amp;
16 bam2wig.py -i \$tmp_input_name -s $chromsize -o outfile
17
18 #if str($strand_type.strand_specific) == "pair"
19 -d
20 #if str($strand_type.pair_type) == "sd"
21 '1++,1--,2+-,2-+'
22 #else
23 '1+-,1-+,2++,2--'
24 #end if
25 #end if
26
27 #if str($strand_type.strand_specific) == "single"
28 -d
29 #if str($strand_type.single_type) == "s"
30 '++,--'
31 #else
32 '+-,-+'
33 #end if
34 #end if
35
36 #if $wigsum.wigsum_type
37 -t $wigsum.totalwig
38 #end if
39
40 #if $skipmultihits
41 -u
42 #end if
43 ;
44 rm "\$tmp_input_name\$bai";
45 rm \$tmp_input_name
46 </command>
47 <inputs>
48 <param name="input" type="data" label="Input .bam File" format="bam" />
49 <param name="chromsize" type="data" label="Chromosome size file (tab or space separated)" format="txt,tabular" />
50 <param name="skipmultihits" type="boolean" label="Skip Multiple Hit Reads/Only Use Uniquely Mapped Reads" value="false" />
51 <conditional name="wigsum">
52 <param name="wigsum_type" type="boolean" label="Specify wigsum?" value="false">
53 </param>
54 <when value="true">
55 <param name="totalwig" value="0" type="integer" label="specified wigsum" />
56 </when>
57 <when value="false"/>
58 </conditional>
59 <conditional name="strand_type">
60 <param name="strand_specific" type="select" label="Strand-specific?" value="none">
61 <option value="none">none</option>
62 <option value="pair">Pair-End RNA-seq</option>
63 <option value="single">Single-End RNA-seq</option>
64 </param>
65 <when value="pair">
66 <param name="pair_type" type="select" display="radio" label="Pair-End Read Type (format: mapped --> parent)" value="sd">
67 <option value="sd"> read1 (positive --> positive; negative --> negative), read2 (positive --> negative; negative --> positive)</option>
68 <option value="ds">read1 (positive --> negative; negative --> positive), read2 (positive --> positive; negative --> negative)</option>
69 </param>
70 </when>
71 <when value="single">
72 <param name="single_type" type="select" display="radio" label="Single-End Read Type (format: mapped --> parent)" value="s">
73 <option value="s">positive --> positive; negative --> negative</option>
74 <option value="d">positive --> negative; negative --> positive</option>
75 </param>
76 </when>
77 <when value="none"></when>
78 </conditional>
79 </inputs>
80 <outputs>
81 <data format="wig" name="output" from_work_dir="outfile.wig">
82 <filter>strand_type['strand_specific'] == 'none'</filter>
83 </data>
84 <data format="wig" name="outputfwd" from_work_dir="outfile.Forward.wig" label="${tool.name} on ${on_string} (Forward Reads)">
85 <filter>strand_type['strand_specific'] != 'none'</filter>
86 </data>
87 <data format="wig" name="outputrv" from_work_dir="outfile.Reverse.wig" label="${tool.name} on ${on_string} (Reverse Reads)">
88 <filter>strand_type['strand_specific'] != 'none'</filter>
89 </data>
90 </outputs>
91 <stdio>
92 <exit_code range="1:" level="fatal" description="An error occured during execution, see stderr and stdout for more information" />
93 <regex match="[Ee]rror" source="both" description="An error occured during execution, see stderr and stdout for more information" />
94 </stdio>
95 <help>
96 bam2wig.py
97 ++++++++++
98
99 Visualization is the most straightforward and effective way to QC your RNA-seq
100 data. For example, change of expression or new splicing can be easily checked
101 by visually comparing two RNA-seq tracks using genome browser such as UCSC_,
102 IGB_ and IGV_. `bam2wig.py` converts all types of RNA-seq data from BAM_
103 format into wiggle_ format in one-stop. wiggle_ files can then be easily
104 converted into bigwig_. Bigwig is indexed, binary format of wiggle file, and
105 it's particular useful to display large, continuous dataset on genome
106 browser.
107
108 Inputs
109 ++++++++++++++
110
111 Input BAM file
112 Alignment file in BAM format (SAM is not supported). BAM file will be sorted and indexed using samTools.
113
114 Chromosome size file
115 Tab or space separated text file with 2 columns: first column is chromosome name, second column is size of the chromosome. Chromosome names (such as "chr1") should be consistent between this file and BAM file.
116
117 Specified wigsum (default=none)
118 Specified wigsum. Wigsum of 100000000 equals to coverage achieved by 1 million 100nt reads. Ignore this option to disable normalization.
119
120 Skip multiple Hit reads
121 skips multiple hit reads or only use uniquely mapped reads
122
123 Strand-specific (default=none)
124 How read(s) were stranded during sequencing. If you are not sure about the strand rule, run infer_experiment.py
125
126 Outputs
127 ++++++++++++++
128
129 If RNA-seq is not strand specific, one wig file will be generated, if RNA-seq
130 is strand specific, two wig files corresponding to Forward and Reverse will be generated.
131
132 -----
133
134 About RSeQC
135 +++++++++++
136
137
138 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.
139
140 The RSeQC package is licensed under the GNU GPL v3 license.
141
142 .. image:: http://rseqc.sourceforge.net/_static/logo.png
143
144 .. _RSeQC: http://rseqc.sourceforge.net/
145 .. _UCSC: http://genome.ucsc.edu/index.html
146 .. _IGB: http://bioviz.org/igb/
147 .. _IGV: http://www.broadinstitute.org/igv/home
148 .. _BAM: http://genome.ucsc.edu/goldenPath/help/bam.html
149 .. _wiggle: http://genome.ucsc.edu/goldenPath/help/wiggle.html
150 .. _bigwig: http://genome.ucsc.edu/FAQ/FAQformat.html#format6.1
151
152 </help>
153 </tool>