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11
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1 <macros>
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2 <xml name="stdio">
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3 <stdio>
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4 <!-- Anything other than zero is an error -->
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5 <exit_code range="1:" />
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6 <exit_code range=":-1" />
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7 <!-- In case the return code has not been set propery check stderr too -->
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8 <regex match="Error:" />
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9 <regex match="Exception:" />
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10 </stdio>
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11 </xml>
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12
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13 <xml name="overlap">
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14 <param name="overlap" type="float" value="0.000000001" label="Minimum overlap required as a fraction of A" />
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15 </xml>
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16 <xml name="strand2">
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17 <param name="strand" type="select" label="Calculation based on strandedness?">
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18 <option value="" selected="True">Overlaps on either strand</option>
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19 <option value="-s">Only overlaps occurring on the **same** strand.</option>
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20 <option value="-S">Only overlaps occurring on the **opposite** strand.</option>
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21 </param>
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22 </xml>
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23 <xml name="seed">
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24 <conditional name="seed">
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25 <param name="choose" type="boolean" label="Choose Seed?" selected="False" truevalue="True" falsevalue="False" />
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26 <when value="True">
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27 <param name="seed" type="integer" value="12345" label="Enter Seed" />
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28 </when>
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29 </conditional>
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30 </xml>
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31 <xml name="split">
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32 <param name="split" type="boolean" checked="true" truevalue="-split" falsevalue="" label="Treat split/spliced BAM or BED12 entries as distinct BED intervals when computing coverage." help="If set, the coverage will be calculated based the spliced intervals only. For BAM files, this inspects the CIGAR N operation to infer the blocks for computing coverage. For BED12 files, this inspects the BlockCount, BlockStarts, and BlockEnds fields (i.e., columns 10,11,12). If this option is not set, coverage will be calculated based on the interval's START/END coordinates, and would include introns in the case of RNAseq data." />
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33
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34 </xml>
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35 <xml name="requirements">
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36 <requirements>
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37 <requirement type="package" version="2.19.1">bedtools</requirement>
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38 </requirements>
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39 <version_command>bedtools --version</version_command>
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40 </xml>
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41 <xml name="genome">
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42 <param format="bed,vcf,gff,gff3" name="genome" type="data" label="Genome file" />
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43 </xml>
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44 <xml name="addition">
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45 <conditional name="addition">
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46 <param name="addition_select" type="select" label="Choose what you want to do">
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47 <option value="b" selected="True">Increase the BED/GFF/VCF entry by the same number base pairs in each direction.</option>
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48 <option value="lr">Increase by Start Coordinate and End Coordinate</option>
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49 </param>
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50 <when value="b">
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51 <param name="b" label="Give Value" type="integer" value="0" />
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52 </when>
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53 <when value="lr">
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54 <param name="l" label="The number of base pairs to subtract from the start coordinate" type="integer" value="0" />
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55 <param name="r" label="The number of base pairs to add to the end coordinate" type="integer" value="0" />
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56 </when>
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57 </conditional>
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58 </xml>
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59 <xml name="math_options">
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60 <option value="min">Min - numeric only</option>
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61 <option value="max">Max - numeric only</option>
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62 <option value="mean">Mean - numeric only</option>
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63 <option value="median">Median - numeric only</option>
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64 <option value="mode">Mode - numeric only</option>
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65 <option value="antimode">Antimode - numeric only</option>
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66 <option value="collapse">collapse (i.e., print a comma separated list) - numeric or text</option>
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67 </xml>
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68 <xml name="additional_math_options">
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69 <option value="count">Count - numeric or text</option>
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70 <option value="count_disctinct">Count Distinct - numeric or text</option>
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71 <option value="distinct">distinct (i.e., print a comma separated list) - numeric or text</option>
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72 <option value="concat">concat (i.e., print a comma separated list) - numeric or text</option>
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73 </xml>
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74
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75
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76
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77 <token name="@REFERENCES@">
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78 ------
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79
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80 This tool is part of the `bedtools package`__ from the `Quinlan laboratory`__.
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81 If you use this tool, please cite `Quinlan AR, and Hall I.M. BEDTools: A flexible framework for comparing genomic features. Bioinformatics, 2010, 26, 6.`__
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82
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83 .. __: https://github.com/arq5x/bedtools2
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84 .. __: http://cphg.virginia.edu/quinlan/
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85 .. __: http://bioinformatics.oxfordjournals.org/content/26/6/841.short
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86 .. __: http://bedtools.readthedocs.org/en/latest/content/bedtools-suite.html
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87 </token>
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88 </macros>
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