/tools/filters/wiggle_to_simple.xml

 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
23This 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>