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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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