--- a/intersectbed.xml	Sat Mar 10 08:17:36 2012 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,103 +0,0 @@
-<tool id="intersectbed" name="intersectBed">
-  <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>
-