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bed_intersect.xml |
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| diff -r 000000000000 -r 4aa3726515c4 bed_intersect.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/bed_intersect.xml Sat Mar 31 13:51:11 2012 -0400 |
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| @@ -0,0 +1,103 @@ +<tool id="bed_intersect" name="bed_intersect"> + <description>intersect two interval sets</description> + <command> intersectBed -a $inputa -b $inputb $output_opt $strandness $r -f $f $split > $output_data + </command> + <inputs> + <param name="inputa" type="data" format="interval,bam,bed,gff,vcf" label="Input A (-a)"/> + <param name="inputb" type="data" format="interval,bam,bed,gff,vcf" label="Input B (-b)"/> + <param name="output_opt" type="select" label="Output style" > + <option value="-wa" selected="true"> -wa: entry in A that overlaps B</option> + <option value="-wb" > -wb: entry in B that overlaps A</option> + <option value="-wo" > -wo: A,B, and num bases overlap </option> + <option value="-wao" > -wao: A,B, and num bases overlap </option> + <option value="-u" > -u: A only </option> + <option value="-c" > -c: A, num B features overlap </option> + <option value="-v" > -v: A without overlap </option> + </param> + + <param name="f" size="10" type="float" value="1E-9" label="Minimum overlap required as a fraction of A"/> + + <param name="strandness" type="select" label="Strand requirement" > + <option value="" selected="true"> none </option> + <option value="-s" > -s: require overlap on the same strand</option> + <option value="-S" > -S: require overlap on the opposite strand </option> + </param> + + <param name="r" label="Require that the fraction overlap be reciprocal for A and B (-r)." type="boolean" truevalue="-r" falsevalue="" checked="False"/> + <param name="split" label="Treat'split' BAM or BED12 entries as distinct BED intervals (-split)." type="boolean" truevalue="-split" falsevalue="" checked="False"/></inputs> + <outputs> + <data format="bed" name="output_data"/> + </outputs> + <help> + +**What it does** + +This is a wrapper for intersecBed. + + Program: intersectBed (v2.13.3) + Author: Aaron Quinlan (aaronquinlan@gmail.com) + Summary: Report overlaps between two feature files. + +Usage:: + + intersectBed [OPTIONS] -a (bed/gff/vcf) -b (bed/gff/vcf) + +Options:: + -abam The A input file is in BAM format. Output will be BAM as well. + + -ubam Write uncompressed BAM output. Default is to write compressed BAM. + + -bed When using BAM input (-abam), write output as BED. The default + is to write output in BAM when using -abam. + + -wa Write the original entry in A for each overlap. + + -wb Write the original entry in B for each overlap. + - Useful for knowing _what_ A overlaps. Restricted by -f and -r. + + -wo Write the original A and B entries plus the number of base + pairs of overlap between the two features. + - Overlaps restricted by -f and -r. + Only A features with overlap are reported. + + -wao Write the original A and B entries plus the number of base + pairs of overlap between the two features. + - Overlapping features restricted by -f and -r. + However, A features w/o overlap are also reported + with a NULL B feature and overlap = 0. + + -u Write the original A entry _once_ if _any_ overlaps found in B. + - In other words, just report the fact >=1 hit was found. + - Overlaps restricted by -f and -r. + + -c For each entry in A, report the number of overlaps with B. + - Reports 0 for A entries that have no overlap with B. + - Overlaps restricted by -f and -r. + + -v Only report those entries in A that have _no overlaps_ with B. + - Similar to "grep -v" (an homage). + + -f Minimum overlap required as a fraction of A. + - Default is 1E-9 (i.e., 1bp). + - FLOAT (e.g. 0.50) + + -r Require that the fraction overlap be reciprocal for A and B. + - In other words, if -f is 0.90 and -r is used, this requires + that B overlap 90% of A and A _also_ overlaps 90% of B. + + -s Require same strandedness. That is, only report hits in B that + overlap A on the _same_ strand. + - By default, overlaps are reported without respect to strand. + + -S Require different strandedness. That is, only report hits in B that + overlap A on the _opposite_ strand. + - By default, overlaps are reported without respect to strand. + + -split Treat "split" BAM or BED12 entries as distinct BED intervals. + + -sorted Use the "chromsweep" algorithm for sorted (-k1,1 -k2,2n) input + NOTE: this will trust, but not enforce that data is sorted. Caveat emptor. + + </help> +</tool> + |