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comparison bam2wig.xml @ 0:e73f30d518f9

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author nilesh
date Mon, 08 Jul 2013 22:02:58 -0400
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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 </requirements>
8 <requirements>
9 <requirement type="package" version="0.1.18">samtools</requirement>
10 </requirements>
11 <requirements>
12 <requirement type="package" version="2.3.7">rseqc</requirement>
13 </requirements>
14 <command interpreter="python">
15 samtoolshelper.py /home/nilesh/RSeQC-2.3.3/scripts/bam2wig.py -i $input -s $chromsize -o outfile
16
17 #if str($strand_type.strand_specific) == "pair"
18 -d
19 #if str($strand_type.pair_type) == "sd"
20 '1++,1--,2+-,2-+'
21 #else
22 '1+-,1-+,2++,2--'
23 #end if
24 #end if
25
26 #if str($strand_type.strand_specific) == "single"
27 -d
28 #if str($strand_type.single_type) == "s"
29 '++,--'
30 #else
31 '+-,-+'
32 #end if
33 #end if
34
35 #if $wigsum.wigsum_type
36 -t $wigsum.totalwig
37 #end if
38
39 #if $skipmultihits
40 -u
41 #end if
42 </command>
43 <inputs>
44 <param name="input" type="data" label="Input .bam File" format="bam" />
45 <param name="chromsize" type="data" label="Chromosome size file (tab or space separated)" format="txt,tabular" />
46 <param name="skipmultihits" type="boolean" label="Skip Multiple Hit Reads/Only Use Uniquely Mapped Reads" value="false" />
47 <conditional name="wigsum">
48 <param name="wigsum_type" type="boolean" label="Specify wigsum?" value="false">
49 </param>
50 <when value="true">
51 <param name="totalwig" value="0" type="integer" label="specified wigsum" />
52 </when>
53 <when value="false"></when>
54 </conditional>
55 <conditional name="strand_type">
56 <param name="strand_specific" type="select" label="Strand-specific?" value="None">
57 <option value="none">None</option>
58 <option value="pair">Pair-End RNA-seq</option>
59 <option value="single">Single-End RNA-seq</option>
60 </param>
61 <when value="pair">
62 <param name="pair_type" type="select" display="radio" label="Pair-End Read Type (format: mapped --> parent)" value="sd">
63 <option value="sd"> read1 (positive --> positive; negative --> negative), read2 (positive --> negative; negative --> positive)</option>
64 <option value="ds">read1 (positive --> negative; negative --> positive), read2 (positive --> positive; negative --> negative)</option>
65 </param>
66 </when>
67 <when value="single">
68 <param name="single_type" type="select" display="radio" label="Single-End Read Type (format: mapped --> parent)" value="s">
69 <option value="s">positive --> positive; negative --> negative</option>
70 <option value="d">positive --> negative; negative --> positive</option>
71 </param>
72 </when>
73 <when value="none"></when>
74 </conditional>
75 </inputs>
76 <outputs>
77 <data format="wig" name="output" from_work_dir="outfile.wig">
78 <filter>strand_type['strand_specific'] == 'none'</filter>
79 </data>
80 <data format="wig" name="outputfwd" from_work_dir="outfile_Forward.wig">
81 <filter>strand_type['strand_specific'] != 'none'</filter>
82 </data>
83 <data format="wig" name="outputrv" from_work_dir="outfile_Reverse.wig">
84 <filter>strand_type['strand_specific'] != 'none'</filter>
85 </data>
86 </outputs>
87 <help>
88 .. image:: https://code.google.com/p/rseqc/logo?cct=1336721062
89
90 -----
91
92 About RSeQC
93 +++++++++++
94
95 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.
96
97 The RSeQC package is licensed under the GNU GPL v3 license.
98
99 Inputs
100 ++++++++++++++
101
102 Input BAM file
103 Alignment file in BAM format (SAM is not supported). BAM file will be sorted and indexed using samTools.
104
105 Chromosome size file
106 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.
107
108 Specified wigsum (default=none)
109 Specified wigsum. Wigsum of 100000000 equals to coverage achieved by 1 million 100nt reads. Ignore this option to disable normalization.
110
111 Skip multiple Hit reads
112 skips multiple hit reads or only use uniquely mapped reads
113
114 Strand-specific (default=none)
115 How read(s) were stranded during sequencing. If you are not sure about the strand rule, run infer_experiment.py
116
117 Outputs
118 ++++++++++++++
119
120 If RNA-seq is not strand specific, one wig file will be generated, if RNA-seq
121 is strand specific, two wig files corresponding to Forward and Reverse will be generated.
122
123
124 </help>
125 </tool>