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/tools/stats/wiggle_to_simple.xml

https://bitbucket.org/cistrome/cistrome-harvard/
XML | 84 lines | 69 code | 15 blank | 0 comment | 0 complexity | 5343ca502ebca770e17c0a5788d7cf69 MD5 | raw file
 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  </tests>
16  <help>
17**Syntax**
18
19This tool converts wiggle data into interval type.
20
21- **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.
22
23  - **BED format** with no declaration line and four columns of data::
24
25      chromA  chromStartA  chromEndA  dataValueA
26      chromB  chromStartB  chromEndB  dataValueB
27
28  - **variableStep** two column data; started by a declaration line and followed with chromosome positions and data values::
29
30      variableStep  chrom=chrN  [span=windowSize]
31      chromStartA  dataValueA
32      chromStartB  dataValueB
33
34  - **fixedStep** single column data; started by a declaration line and followed with data values::
35
36      fixedStep  chrom=chrN  start=position  step=stepInterval  [span=windowSize]
37      dataValue1
38      dataValue2
39
40-----
41
42**Example**
43
44- input wiggle format file::
45
46    #track type=wiggle_0 name="Bed Format" description="BED format"
47    chr19 59302000 59302300 -1.0
48    chr19 59302300 59302600 -0.75
49    chr19 59302600 59302900 -0.50
50    chr19 59302900 59303200 -0.25
51    chr19 59303200 59303500 0.0
52    #track type=wiggle_0 name="variableStep" description="variableStep format"
53    variableStep chrom=chr19 span=150
54    59304701 10.0
55    59304901 12.5
56    59305401 15.0
57    59305601 17.5
58    #track type=wiggle_0 name="fixedStep" description="fixed step" visibility=full
59    fixedStep chrom=chr19 start=59307401 step=300 span=200
60    1000
61    900
62    800
63    700
64    600
65
66- convert the above file to interval file::
67
68    chr19	59302000	59302300	+	-1.0
69    chr19	59302300	59302600	+	-0.75
70    chr19	59302600	59302900	+	-0.5
71    chr19	59302900	59303200	+	-0.25
72    chr19	59303200	59303500	+	0.0
73    chr19	59304701	59304851	+	10.0
74    chr19	59304901	59305051	+	12.5
75    chr19	59305401	59305551	+	15.0
76    chr19	59305601	59305751	+	17.5
77    chr19	59307701	59307901	+	1000.0
78    chr19	59308001	59308201	+	900.0
79    chr19	59308301	59308501	+	800.0
80    chr19	59308601	59308801	+	700.0
81    chr19	59308901	59309101	+	600.0
82
83</help>
84</tool>