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comparison bam2wig.xml @ 1:dc3b3b88fbab

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author nilesh
date Thu, 18 Jul 2013 11:27:43 -0500
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0:0d133c7c387e 1:dc3b3b88fbab
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 <tests>
84 <test>
85 <param name="input" value="Pairend_nonStrandSpecific_36mer_Human_hg19.bam" />
86 <param name="chromsize" value="sample.hg19.chrom.sizes.txt" />
87 <param name="skipmultihits" value="false" />
88 <param name="wigsum.wigsum_type" value="false" />
89 <param name="strand_type.strand_specific" value="none" />
90 <output name="output" file="outfile.wig" />
91 </test>
92 </tests>
93 <help>
94 .. image:: https://code.google.com/p/rseqc/logo?cct=1336721062
95
96 -----
97
98 About RSeQC
99 +++++++++++
100
101 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.
102
103 The RSeQC package is licensed under the GNU GPL v3 license.
104
105 Inputs
106 ++++++++++++++
107
108 Input BAM file
109 Alignment file in BAM format (SAM is not supported). BAM file will be sorted and indexed using samTools.
110
111 Chromosome size file
112 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.
113
114 Specified wigsum (default=none)
115 Specified wigsum. Wigsum of 100000000 equals to coverage achieved by 1 million 100nt reads. Ignore this option to disable normalization.
116
117 Skip multiple Hit reads
118 skips multiple hit reads or only use uniquely mapped reads
119
120 Strand-specific (default=none)
121 How read(s) were stranded during sequencing. If you are not sure about the strand rule, run infer_experiment.py
122
123 Outputs
124 ++++++++++++++
125
126 If RNA-seq is not strand specific, one wig file will be generated, if RNA-seq
127 is strand specific, two wig files corresponding to Forward and Reverse will be generated.
128
129
130 </help>
131 </tool>