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comparison mytools/intersectbed.xml @ 0:39217fa39ff2

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author xuebing
date Tue, 13 Mar 2012 23:34:52 -0400
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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