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1 <tool id="intersectbed" name="intersectBed">
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2 <description>intersect two interval sets</description>
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3 <command> intersectBed -a $inputa -b $inputb $output_opt $strandness $r -f $f $split > $output_data
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4 </command>
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5 <inputs>
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6 <param name="inputa" type="data" format="interval,bam,bed,gff,vcf" label="Input A (-a)"/>
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7 <param name="inputb" type="data" format="interval,bam,bed,gff,vcf" label="Input B (-b)"/>
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8 <param name="output_opt" type="select" label="Output style" >
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9 <option value="-wa" selected="true"> -wa: entry in A that overlaps B</option>
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10 <option value="-wb" > -wb: entry in B that overlaps A</option>
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11 <option value="-wo" > -wo: A,B, and num bases overlap </option>
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12 <option value="-wao" > -wao: A,B, and num bases overlap </option>
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13 <option value="-u" > -u: A only </option>
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14 <option value="-c" > -c: A, num B features overlap </option>
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15 <option value="-v" > -v: A without overlap </option>
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16 </param>
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17
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18 <param name="f" size="10" type="float" value="1E-9" label="Minimum overlap required as a fraction of A"/>
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19
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20 <param name="strandness" type="select" label="Strand requirement" >
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21 <option value="" selected="true"> none </option>
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22 <option value="-s" > -s: require overlap on the same strand</option>
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23 <option value="-S" > -S: require overlap on the opposite strand </option>
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24 </param>
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25
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26 <param name="r" label="Require that the fraction overlap be reciprocal for A and B (-r)." type="boolean" truevalue="-r" falsevalue="" checked="False"/>
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27 <param name="split" label="Treat'split' BAM or BED12 entries as distinct BED intervals (-split)." type="boolean" truevalue="-split" falsevalue="" checked="False"/></inputs>
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28 <outputs>
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29 <data format="bed" name="output_data"/>
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30 </outputs>
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31 <help>
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32
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33 **What it does**
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34
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35 This is a wrapper for intersecBed.
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36
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37 Program: intersectBed (v2.13.3)
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38 Author: Aaron Quinlan (aaronquinlan@gmail.com)
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39 Summary: Report overlaps between two feature files.
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40
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41 Usage::
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42
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43 intersectBed [OPTIONS] -a (bed/gff/vcf) -b (bed/gff/vcf)
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44
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45 Options::
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46 -abam The A input file is in BAM format. Output will be BAM as well.
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47
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48 -ubam Write uncompressed BAM output. Default is to write compressed BAM.
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49
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50 -bed When using BAM input (-abam), write output as BED. The default
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51 is to write output in BAM when using -abam.
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52
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53 -wa Write the original entry in A for each overlap.
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54
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55 -wb Write the original entry in B for each overlap.
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56 - Useful for knowing _what_ A overlaps. Restricted by -f and -r.
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57
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58 -wo Write the original A and B entries plus the number of base
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59 pairs of overlap between the two features.
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60 - Overlaps restricted by -f and -r.
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61 Only A features with overlap are reported.
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62
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63 -wao Write the original A and B entries plus the number of base
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64 pairs of overlap between the two features.
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65 - Overlapping features restricted by -f and -r.
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66 However, A features w/o overlap are also reported
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67 with a NULL B feature and overlap = 0.
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68
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69 -u Write the original A entry _once_ if _any_ overlaps found in B.
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70 - In other words, just report the fact >=1 hit was found.
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71 - Overlaps restricted by -f and -r.
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72
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73 -c For each entry in A, report the number of overlaps with B.
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74 - Reports 0 for A entries that have no overlap with B.
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75 - Overlaps restricted by -f and -r.
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76
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77 -v Only report those entries in A that have _no overlaps_ with B.
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78 - Similar to "grep -v" (an homage).
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79
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80 -f Minimum overlap required as a fraction of A.
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81 - Default is 1E-9 (i.e., 1bp).
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82 - FLOAT (e.g. 0.50)
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83
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84 -r Require that the fraction overlap be reciprocal for A and B.
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85 - In other words, if -f is 0.90 and -r is used, this requires
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86 that B overlap 90% of A and A _also_ overlaps 90% of B.
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87
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88 -s Require same strandedness. That is, only report hits in B that
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89 overlap A on the _same_ strand.
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90 - By default, overlaps are reported without respect to strand.
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91
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92 -S Require different strandedness. That is, only report hits in B that
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93 overlap A on the _opposite_ strand.
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94 - By default, overlaps are reported without respect to strand.
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95
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96 -split Treat "split" BAM or BED12 entries as distinct BED intervals.
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97
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98 -sorted Use the "chromsweep" algorithm for sorted (-k1,1 -k2,2n) input
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99 NOTE: this will trust, but not enforce that data is sorted. Caveat emptor.
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100
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101 </help>
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102 </tool>
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103
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