Mercurial > repos > xuebing > bed_intersect
comparison bed_intersect.xml @ 0:4aa3726515c4 default tip
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author | xuebing |
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date | Sat, 31 Mar 2012 13:51:11 -0400 |
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1 <tool id="bed_intersect" name="bed_intersect"> | |
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 |