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comparison bam2wig.xml @ 12:6189b9d1a458

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author nilesh
date Mon, 08 Jul 2013 22:14:42 -0400
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11:a7dae6653479 12:6189b9d1a458
1 <tool id="bam2wig" name="BAM to Wiggle">
2 <description>
3 converts all types of RNA-seq data from .bam to .wig
4 </description>
5 <requirements>
6 <requirement type="package" version="2.15.1">R</requirement>
7 <requirement type="package" version="0.1.18">samtools</requirement>
8 <requirement type="package" version="2.3.7">rseqc</requirement>
9 </requirements>
10 <command interpreter="python">
11 samtoolshelper.py /home/nilesh/RSeQC-2.3.3/scripts/bam2wig.py -i $input -s $chromsize -o outfile
12
13 #if str($strand_type.strand_specific) == "pair"
14 -d
15 #if str($strand_type.pair_type) == "sd"
16 '1++,1--,2+-,2-+'
17 #else
18 '1+-,1-+,2++,2--'
19 #end if
20 #end if
21
22 #if str($strand_type.strand_specific) == "single"
23 -d
24 #if str($strand_type.single_type) == "s"
25 '++,--'
26 #else
27 '+-,-+'
28 #end if
29 #end if
30
31 #if $wigsum.wigsum_type
32 -t $wigsum.totalwig
33 #end if
34
35 #if $skipmultihits
36 -u
37 #end if
38 </command>
39 <inputs>
40 <param name="input" type="data" label="Input .bam File" format="bam" />
41 <param name="chromsize" type="data" label="Chromosome size file (tab or space separated)" format="txt,tabular" />
42 <param name="skipmultihits" type="boolean" label="Skip Multiple Hit Reads/Only Use Uniquely Mapped Reads" value="false" />
43 <conditional name="wigsum">
44 <param name="wigsum_type" type="boolean" label="Specify wigsum?" value="false">
45 </param>
46 <when value="true">
47 <param name="totalwig" value="0" type="integer" label="specified wigsum" />
48 </when>
49 <when value="false"></when>
50 </conditional>
51 <conditional name="strand_type">
52 <param name="strand_specific" type="select" label="Strand-specific?" value="None">
53 <option value="none">None</option>
54 <option value="pair">Pair-End RNA-seq</option>
55 <option value="single">Single-End RNA-seq</option>
56 </param>
57 <when value="pair">
58 <param name="pair_type" type="select" display="radio" label="Pair-End Read Type (format: mapped --> parent)" value="sd">
59 <option value="sd"> read1 (positive --> positive; negative --> negative), read2 (positive --> negative; negative --> positive)</option>
60 <option value="ds">read1 (positive --> negative; negative --> positive), read2 (positive --> positive; negative --> negative)</option>
61 </param>
62 </when>
63 <when value="single">
64 <param name="single_type" type="select" display="radio" label="Single-End Read Type (format: mapped --> parent)" value="s">
65 <option value="s">positive --> positive; negative --> negative</option>
66 <option value="d">positive --> negative; negative --> positive</option>
67 </param>
68 </when>
69 <when value="none"></when>
70 </conditional>
71 </inputs>
72 <outputs>
73 <data format="wig" name="output" from_work_dir="outfile.wig">
74 <filter>strand_type['strand_specific'] == 'none'</filter>
75 </data>
76 <data format="wig" name="outputfwd" from_work_dir="outfile_Forward.wig">
77 <filter>strand_type['strand_specific'] != 'none'</filter>
78 </data>
79 <data format="wig" name="outputrv" from_work_dir="outfile_Reverse.wig">
80 <filter>strand_type['strand_specific'] != 'none'</filter>
81 </data>
82 </outputs>
83 <help>
84 .. image:: https://code.google.com/p/rseqc/logo?cct=1336721062
85
86 -----
87
88 About RSeQC
89 +++++++++++
90
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.
92
93 The RSeQC package is licensed under the GNU GPL v3 license.
94
95 Inputs
96 ++++++++++++++
97
98 Input BAM file
99 Alignment file in BAM format (SAM is not supported). BAM file will be sorted and indexed using samTools.
100
101 Chromosome size file
102 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.
103
104 Specified wigsum (default=none)
105 Specified wigsum. Wigsum of 100000000 equals to coverage achieved by 1 million 100nt reads. Ignore this option to disable normalization.
106
107 Skip multiple Hit reads
108 skips multiple hit reads or only use uniquely mapped reads
109
110 Strand-specific (default=none)
111 How read(s) were stranded during sequencing. If you are not sure about the strand rule, run infer_experiment.py
112
113 Outputs
114 ++++++++++++++
115
116 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.
118
119
120 </help>
121 </tool>