Mercurial > repos > xuebing > sharplabtool
comparison tools/filters/wiggle_to_simple.xml @ 0:9071e359b9a3
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author | xuebing |
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date | Fri, 09 Mar 2012 19:37:19 -0500 |
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-1:000000000000 | 0:9071e359b9a3 |
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1 <tool id="wiggle2simple1" name="Wiggle-to-Interval"> | |
2 <description>converter</description> | |
3 <command interpreter="python">wiggle_to_simple.py $input $out_file1 </command> | |
4 <inputs> | |
5 <param format="wig" name="input" type="data" label="Convert"/> | |
6 </inputs> | |
7 <outputs> | |
8 <data format="interval" name="out_file1" /> | |
9 </outputs> | |
10 <tests> | |
11 <test> | |
12 <param name="input" value="2.wig" /> | |
13 <output name="out_file1" file="2.interval"/> | |
14 </test> | |
15 <test> | |
16 <param name="input" value="3.wig" /> | |
17 <output name="out_file1" file="3_wig.bed"/> | |
18 </test> | |
19 </tests> | |
20 <help> | |
21 **Syntax** | |
22 | |
23 This tool converts wiggle data into interval type. | |
24 | |
25 - **Wiggle format**: The .wig format is line-oriented. Wiggle data is preceded by a UCSC track definition line. Following the track definition line is the track data, which can be entered in three different formats described below. | |
26 | |
27 - **BED format** with no declaration line and four columns of data:: | |
28 | |
29 chromA chromStartA chromEndA dataValueA | |
30 chromB chromStartB chromEndB dataValueB | |
31 | |
32 - **variableStep** two column data; started by a declaration line and followed with chromosome positions and data values:: | |
33 | |
34 variableStep chrom=chrN [span=windowSize] | |
35 chromStartA dataValueA | |
36 chromStartB dataValueB | |
37 | |
38 - **fixedStep** single column data; started by a declaration line and followed with data values:: | |
39 | |
40 fixedStep chrom=chrN start=position step=stepInterval [span=windowSize] | |
41 dataValue1 | |
42 dataValue2 | |
43 | |
44 ----- | |
45 | |
46 **Example** | |
47 | |
48 - input wiggle format file:: | |
49 | |
50 #track type=wiggle_0 name="Bed Format" description="BED format" | |
51 chr19 59302000 59302300 -1.0 | |
52 chr19 59302300 59302600 -0.75 | |
53 chr19 59302600 59302900 -0.50 | |
54 chr19 59302900 59303200 -0.25 | |
55 chr19 59303200 59303500 0.0 | |
56 #track type=wiggle_0 name="variableStep" description="variableStep format" | |
57 variableStep chrom=chr19 span=150 | |
58 59304701 10.0 | |
59 59304901 12.5 | |
60 59305401 15.0 | |
61 59305601 17.5 | |
62 #track type=wiggle_0 name="fixedStep" description="fixed step" visibility=full | |
63 fixedStep chrom=chr19 start=59307401 step=300 span=200 | |
64 1000 | |
65 900 | |
66 800 | |
67 700 | |
68 600 | |
69 | |
70 - convert the above file to interval file:: | |
71 | |
72 chr19 59302000 59302300 + -1.0 | |
73 chr19 59302300 59302600 + -0.75 | |
74 chr19 59302600 59302900 + -0.5 | |
75 chr19 59302900 59303200 + -0.25 | |
76 chr19 59303200 59303500 + 0.0 | |
77 chr19 59304701 59304851 + 10.0 | |
78 chr19 59304901 59305051 + 12.5 | |
79 chr19 59305401 59305551 + 15.0 | |
80 chr19 59305601 59305751 + 17.5 | |
81 chr19 59307701 59307901 + 1000.0 | |
82 chr19 59308001 59308201 + 900.0 | |
83 chr19 59308301 59308501 + 800.0 | |
84 chr19 59308601 59308801 + 700.0 | |
85 chr19 59308901 59309101 + 600.0 | |
86 | |
87 </help> | |
88 </tool> |