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