annotate bam2wig.xml @ 23:6a354a3248b6

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