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