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changeset 17:a2d4c30ba2f9 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
author iuc
date Sun, 21 Jun 2015 22:49:46 -0400
parents e30113df8cf6
children 5efc48568d8d
files annotateBed.xml bamToBed.xml bedToBam.xml bedpeToBam.xml closestBed.xml clusterBed.xml complementBed.xml expandBed.xml fisherBed.xml flankBed.xml genomeCoverageBed.xml getfastaBed.xml groupbyBed.xml intersectBed.xml jaccardBed.xml linksBed.xml macros.xml makeWindowsBed.xml mapBed.xml maskFastaBed.xml mergeBed.xml multiCov.xml multiIntersectBed.xml nucBed.xml overlapBed.xml randomBed.xml reldist.xml shuffleBed.xml slopBed.xml sortBed.xml spacingBed.xml subtractBed.xml tagBed.xml test-data/bedToBam_result.bam test-data/closestBed_result6.bed test-data/spacingBed_result1.bed tool_dependencies.xml unionBedGraphs.xml windowBed.xml
diffstat 39 files changed, 122 insertions(+), 66 deletions(-) [+]
line wrap: on
line diff
--- a/annotateBed.xml	Mon May 25 22:48:52 2015 -0400
+++ b/annotateBed.xml	Sun Jun 21 22:49:46 2015 -0400
@@ -1,5 +1,5 @@
 <tool id="bedtools_annotatebed" name="AnnotateBed" version="@WRAPPER_VERSION@.0">
-    <description></description>
+    <description>annotate coverage of features from multiple files</description>
     <macros>
         <import>macros.xml</import>
     </macros>
--- a/bamToBed.xml	Mon May 25 22:48:52 2015 -0400
+++ b/bamToBed.xml	Sun Jun 21 22:49:46 2015 -0400
@@ -1,5 +1,5 @@
-<tool id="bedtools_bamtobed" name="Convert from BAM to BED" version="@WRAPPER_VERSION@.0">
-    <description></description>
+<tool id="bedtools_bamtobed" name="BAM to BED" version="@WRAPPER_VERSION@.0">
+    <description>converter</description>
     <macros>
         <import>macros.xml</import>
     </macros>
--- a/bedToBam.xml	Mon May 25 22:48:52 2015 -0400
+++ b/bedToBam.xml	Sun Jun 21 22:49:46 2015 -0400
@@ -1,5 +1,5 @@
-<tool id="bedtools_bedtobam" name="Convert from BED to BAM" version="@WRAPPER_VERSION@.0">
-    <description></description>
+<tool id="bedtools_bedtobam" name="BED to BAM" version="@WRAPPER_VERSION@.0">
+    <description>converter</description>
     <macros>
         <import>macros.xml</import>
     </macros>
@@ -31,7 +31,7 @@
         <test>
             <param name="input" value="bedToBam1.bed" ftype="bed" />
             <param name="genome" value="mm9_chr1.len" ftype="tabular" />
-            <output name="output" file="bedToBam_result.bam" lines_diff="2" ftype="bam" />
+            <output name="output" file="bedToBam_result.bam" lines_diff="4" ftype="bam" />
         </test>
     </tests>
     <help>
--- a/bedpeToBam.xml	Mon May 25 22:48:52 2015 -0400
+++ b/bedpeToBam.xml	Sun Jun 21 22:49:46 2015 -0400
@@ -1,5 +1,5 @@
-<tool id="bedtools_bedpetobam" name="Convert from BEDPE to BAM" version="@WRAPPER_VERSION@.0">
-    <description></description>
+<tool id="bedtools_bedpetobam" name="BEDPE to BAM" version="@WRAPPER_VERSION@.0">
+    <description>converter</description>
     <macros>
         <import>macros.xml</import>
     </macros>
--- a/closestBed.xml	Mon May 25 22:48:52 2015 -0400
+++ b/closestBed.xml	Sun Jun 21 22:49:46 2015 -0400
@@ -1,5 +1,5 @@
 <tool id="bedtools_closestbed" name="ClosestBed" version="@WRAPPER_VERSION@.0">
-    <description></description>
+    <description>find the closest, potentially non-overlapping interval</description>
     <macros>
         <import>macros.xml</import>
     </macros>
@@ -20,6 +20,9 @@
         $io
         -mdb $mdb
         -t $ties
+        #if $k:
+            -k $k
+        #end if
         -a $inputA
         -b $inputBs
         > $output
@@ -53,34 +56,19 @@
                 <option value="b">Report distance with respect to B. When B is on the - strand, "upstream" means A has a higher (start,stop). (-b)</option>
             </param>
             <when value="ref">
-                <param name="iu" type="boolean" checked="false" truevalue="-iu" falsevalue=""
-                    label="Ignore features in B that are upstream of features in A" 
-                    help="This option requires -D and follows its orientation rules for determining what is 'upstream'. (-iu)" />
-
-                <param name="id" type="boolean" checked="false" truevalue="-id" falsevalue=""
-                    label="Ignore features in B that are downstream of features in A" 
-                    help="This option requires -D and follows its orientation rules for determining what is 'downstream'. (-id)" />
+                <expand macro="closest_D_option" />
             </when>
             <when value="a">
-                <param name="iu" type="boolean" checked="false" truevalue="-iu" falsevalue=""
-                    label="Ignore features in B that are upstream of features in A" 
-                    help="This option requires -D and follows its orientation rules for determining what is 'upstream'. (-iu)" />
-
-                <param name="id" type="boolean" checked="false" truevalue="-id" falsevalue=""
-                    label="Ignore features in B that are downstream of features in A" 
-                    help="This option requires -D and follows its orientation rules for determining what is 'downstream'. (-id)" />
+                <expand macro="closest_D_option" />
             </when>
             <when value="b">
-                <param name="iu" type="boolean" checked="false" truevalue="-iu" falsevalue=""
-                    label="Ignore features in B that are upstream of features in A" 
-                    help="This option requires -D and follows its orientation rules for determining what is 'upstream'. (-iu)" />
-
-                <param name="id" type="boolean" checked="false" truevalue="-id" falsevalue=""
-                    label="Ignore features in B that are downstream of features in A" 
-                    help="This option requires -D and follows its orientation rules for determining what is 'downstream'. (-id)" />
+                <expand macro="closest_D_option" />
             </when>
         </conditional>
 
+        <param name="k" type="integer" value="1" optional="True" min="1"
+            label="Report the k closest hits" help="(-k)"/>
+
         <param name="io" type="boolean" checked="false" truevalue="-io" falsevalue=""
             label="Ignore features in B that overlap A" 
             help="That is, we want close, yet not touching features only. (-io)" />
@@ -126,6 +114,12 @@
             <param name="addition2_select" value="a" />
             <output name="output" file="closestBed_result5.bed" ftype="bed" />
         </test>
+        <test>
+            <param name="inputA" value="closestBedA.bed" ftype="bed" />
+            <param name="inputB" value="a.bed" ftype="bed" />
+            <param name="k" value="3" />
+            <output name="output" file="closestBed_result6.bed" ftype="bed" />
+        </test>
     </tests>
     <help>
 <![CDATA[
--- a/clusterBed.xml	Mon May 25 22:48:52 2015 -0400
+++ b/clusterBed.xml	Sun Jun 21 22:49:46 2015 -0400
@@ -1,5 +1,5 @@
 <tool id="bedtools_clusterbed" name="ClusterBed" version="@WRAPPER_VERSION@.0">
-    <description></description>
+    <description>cluster overlapping/nearby intervals</description>
     <macros>
         <import>macros.xml</import>
     </macros>
--- a/complementBed.xml	Mon May 25 22:48:52 2015 -0400
+++ b/complementBed.xml	Sun Jun 21 22:49:46 2015 -0400
@@ -1,5 +1,5 @@
 <tool id="bedtools_complementbed" name="ComplementBed" version="@WRAPPER_VERSION@.0">
-    <description></description>
+    <description>Extract intervals not represented by an interval file</description>
     <macros>
         <import>macros.xml</import>
     </macros>
--- a/expandBed.xml	Mon May 25 22:48:52 2015 -0400
+++ b/expandBed.xml	Sun Jun 21 22:49:46 2015 -0400
@@ -1,5 +1,5 @@
 <tool id="bedtools_expandbed" name="ExpandBed" version="@WRAPPER_VERSION@.0">
-    <description></description>
+    <description>replicate lines based on lists of values in columns</description>
     <macros>
         <import>macros.xml</import>
     </macros>
--- a/fisherBed.xml	Mon May 25 22:48:52 2015 -0400
+++ b/fisherBed.xml	Sun Jun 21 22:49:46 2015 -0400
@@ -1,5 +1,5 @@
 <tool id="bedtools_fisher" name="FisherBed" version="@WRAPPER_VERSION@.0">
-    <description></description>
+    <description>calculate Fisher statistic between two feature files</description>
     <macros>
         <import>macros.xml</import>
     </macros>
--- a/flankBed.xml	Mon May 25 22:48:52 2015 -0400
+++ b/flankBed.xml	Sun Jun 21 22:49:46 2015 -0400
@@ -1,5 +1,5 @@
 <tool id="bedtools_flankbed" name="FlankBed" version="@WRAPPER_VERSION@.0">
-    <description></description>
+    <description>create new intervals from the flanks of existing intervals</description>
     <macros>
         <import>macros.xml</import>
     </macros>
--- a/genomeCoverageBed.xml	Mon May 25 22:48:52 2015 -0400
+++ b/genomeCoverageBed.xml	Sun Jun 21 22:49:46 2015 -0400
@@ -1,5 +1,5 @@
 <tool id="bedtools_genomecoveragebed" name="Genome Coverage" version="@WRAPPER_VERSION@.0">
-    <description>in bedGraph or histogram format</description>
+    <description>compute the coverage over an entire genome</description>
     <macros>
         <import>macros.xml</import>
     </macros>
--- a/getfastaBed.xml	Mon May 25 22:48:52 2015 -0400
+++ b/getfastaBed.xml	Sun Jun 21 22:49:46 2015 -0400
@@ -1,5 +1,5 @@
 <tool id="bedtools_getfastabed" name="GetFastaBed" version="@WRAPPER_VERSION@.0">
-    <description></description>
+    <description>use intervals to extract sequences from a FASTA file</description>
     <macros>
         <import>macros.xml</import>
     </macros>
--- a/groupbyBed.xml	Mon May 25 22:48:52 2015 -0400
+++ b/groupbyBed.xml	Sun Jun 21 22:49:46 2015 -0400
@@ -1,5 +1,5 @@
 <tool id="bedtools_groupbybed" name="GroupByBed" version="@WRAPPER_VERSION@.0">
-    <description></description>
+    <description>group by common cols and summarize other cols</description>
     <macros>
         <import>macros.xml</import>
     </macros>
--- a/intersectBed.xml	Mon May 25 22:48:52 2015 -0400
+++ b/intersectBed.xml	Sun Jun 21 22:49:46 2015 -0400
@@ -1,5 +1,5 @@
-<tool id="bedtools_intersectbed" name="Intersect interval files" version="@WRAPPER_VERSION@.0">
-    <description></description>
+<tool id="bedtools_intersectbed" name="Intersect intervals" version="@WRAPPER_VERSION@.0">
+    <description>find overlapping intervals in various ways</description>
     <macros>
         <import>macros.xml</import>
     </macros>
--- a/jaccardBed.xml	Mon May 25 22:48:52 2015 -0400
+++ b/jaccardBed.xml	Sun Jun 21 22:49:46 2015 -0400
@@ -1,5 +1,5 @@
 <tool id="bedtools_jaccard" name="JaccardBed" version="@WRAPPER_VERSION@.0">
-    <description></description>
+    <description>calculate the distribution of relative distances between two files</description>
     <macros>
         <import>macros.xml</import>
     </macros>
--- a/linksBed.xml	Mon May 25 22:48:52 2015 -0400
+++ b/linksBed.xml	Sun Jun 21 22:49:46 2015 -0400
@@ -1,5 +1,5 @@
 <tool id="bedtools_links" name="LinksBed" version="@WRAPPER_VERSION@.0">
-    <description></description>
+    <description>create a HTML page of links to UCSC locations</description>
     <macros>
         <import>macros.xml</import>
     </macros>
--- a/macros.xml	Mon May 25 22:48:52 2015 -0400
+++ b/macros.xml	Sun Jun 21 22:49:46 2015 -0400
@@ -1,11 +1,11 @@
 <macros>
     <xml name="requirements">
         <requirements>
-            <requirement type="package" version="2.22">bedtools</requirement>
+            <requirement type="package" version="2.24">bedtools</requirement>
             <yield/>
         </requirements>
     </xml>
-    <token name="@WRAPPER_VERSION@">2.22</token>
+    <token name="@WRAPPER_VERSION@">2.24</token>
     <xml name="stdio">
         <stdio>
             <!-- Anything other than zero is an error -->
@@ -53,6 +53,23 @@
         <param format="tabular" name="genome" type="data" label="Genome file" />
         <!--TODO: make use of: ${chromInfo} -->
     </xml>
+    <xml name="closest_D_option">
+        <param name="iu" type="boolean" checked="false" truevalue="-iu" falsevalue=""
+            label="Ignore features in B that are upstream of features in A" 
+            help="This option requires -D and follows its orientation rules for determining what is 'upstream'. (-iu)" />
+
+        <param name="id" type="boolean" checked="false" truevalue="-id" falsevalue=""
+            label="Ignore features in B that are downstream of features in A" 
+            help="This option requires -D and follows its orientation rules for determining what is 'downstream'. (-id)" />
+
+        <param name="fu" type="boolean" checked="false" truevalue="-fu" falsevalue=""
+            label="Choose first from features in B that are upstream of features in A" 
+            help="This option requires -D and follows its orientation rules for determining what is 'upstream'. (-fu)" />
+
+        <param name="fd" type="boolean" checked="false" truevalue="-fd" falsevalue=""
+            label="Choose first from features in B that are downstream of features in A" 
+            help="This option requires -D and follows its orientation rules for determining what is 'downstream'. (-fd)" />
+    </xml>
     <xml name="addition">
         <conditional name="addition">
             <param name="addition_select" type="select" label="Choose what you want to do">
--- a/makeWindowsBed.xml	Mon May 25 22:48:52 2015 -0400
+++ b/makeWindowsBed.xml	Sun Jun 21 22:49:46 2015 -0400
@@ -1,5 +1,5 @@
 <tool id="bedtools_makewindowsbed" name="MakeWindowsBed" version="@WRAPPER_VERSION@.0">
-    <description></description>
+    <description>make interval windows across a genome</description>
     <macros>
         <import>macros.xml</import>
     </macros>
--- a/mapBed.xml	Mon May 25 22:48:52 2015 -0400
+++ b/mapBed.xml	Sun Jun 21 22:49:46 2015 -0400
@@ -1,5 +1,5 @@
 <tool id="bedtools_map" name="MapBed" version="@WRAPPER_VERSION@.1">
-    <description></description>
+    <description>apply a function to a column for each overlapping interval</description>
     <macros>
         <import>macros.xml</import>
     </macros>
--- a/maskFastaBed.xml	Mon May 25 22:48:52 2015 -0400
+++ b/maskFastaBed.xml	Sun Jun 21 22:49:46 2015 -0400
@@ -1,5 +1,5 @@
 <tool id="bedtools_maskfastabed" name="MaskFastaBed" version="@WRAPPER_VERSION@.0">
-    <description></description>
+    <description>use intervals to mask sequences from a FASTA file</description>
     <macros>
         <import>macros.xml</import>
     </macros>
--- a/mergeBed.xml	Mon May 25 22:48:52 2015 -0400
+++ b/mergeBed.xml	Sun Jun 21 22:49:46 2015 -0400
@@ -1,5 +1,5 @@
-<tool id="bedtools_mergebed" name="Merge BED files" version="@WRAPPER_VERSION@.1">
-    <description>(mergeBed)</description>
+<tool id="bedtools_mergebed" name="MergeBED" version="@WRAPPER_VERSION@.1">
+    <description>combine overlapping/nearby intervals into a single interval</description>
     <macros>
         <import>macros.xml</import>
     </macros>
--- a/multiCov.xml	Mon May 25 22:48:52 2015 -0400
+++ b/multiCov.xml	Sun Jun 21 22:49:46 2015 -0400
@@ -1,5 +1,5 @@
 <tool id="bedtools_multicovtbed" name="MultiCovBed" version="@WRAPPER_VERSION@.0">
-    <description></description>
+    <description>counts coverage from multiple BAMs at specific intervals</description>
     <macros>
         <import>macros.xml</import>
     </macros>
--- a/multiIntersectBed.xml	Mon May 25 22:48:52 2015 -0400
+++ b/multiIntersectBed.xml	Sun Jun 21 22:49:46 2015 -0400
@@ -1,5 +1,5 @@
-<tool id="bedtools_multiintersectbed" name="Intersect multiple sorted BED files" version="@WRAPPER_VERSION@.0">
-    <description></description>
+<tool id="bedtools_multiintersectbed" name="Multiple Intersect" version="@WRAPPER_VERSION@.0">
+    <description>identifies common intervals among multiple interval files</description>
     <macros>
         <import>macros.xml</import>
     </macros>
--- a/nucBed.xml	Mon May 25 22:48:52 2015 -0400
+++ b/nucBed.xml	Sun Jun 21 22:49:46 2015 -0400
@@ -1,5 +1,5 @@
 <tool id="bedtools_nucbed" name="NucBed" version="@WRAPPER_VERSION@.0">
-    <description></description>
+    <description>profile the nucleotide content of intervals in a FASTA file</description>
     <macros>
         <import>macros.xml</import>
     </macros>
--- a/overlapBed.xml	Mon May 25 22:48:52 2015 -0400
+++ b/overlapBed.xml	Sun Jun 21 22:49:46 2015 -0400
@@ -1,5 +1,5 @@
 <tool id="bedtools_overlapbed" name="OverlapBed" version="@WRAPPER_VERSION@.0">
-    <description></description>
+    <description>computes the amount of overlap from two intervals</description>
     <macros>
         <import>macros.xml</import>
     </macros>
--- a/randomBed.xml	Mon May 25 22:48:52 2015 -0400
+++ b/randomBed.xml	Sun Jun 21 22:49:46 2015 -0400
@@ -1,5 +1,5 @@
 <tool id="bedtools_randombed" name="RandomBed" version="@WRAPPER_VERSION@.0">
-    <description></description>
+    <description>generate random intervals in a genome</description>
     <macros>
         <import>macros.xml</import>
     </macros>
--- a/reldist.xml	Mon May 25 22:48:52 2015 -0400
+++ b/reldist.xml	Sun Jun 21 22:49:46 2015 -0400
@@ -1,5 +1,5 @@
 <tool id="bedtools_reldistbed" name="ReldistBed" version="@WRAPPER_VERSION@.0">
-    <description></description>
+    <description>calculate the distribution of relative distances</description>
     <macros>
         <import>macros.xml</import>
     </macros>
--- a/shuffleBed.xml	Mon May 25 22:48:52 2015 -0400
+++ b/shuffleBed.xml	Sun Jun 21 22:49:46 2015 -0400
@@ -1,5 +1,5 @@
 <tool id="bedtools_shufflebed" name="ShuffleBed" version="@WRAPPER_VERSION@.0">
-    <description></description>
+    <description>randomly redistrubute intervals in a genome</description>
     <macros>
         <import>macros.xml</import>
     </macros>
--- a/slopBed.xml	Mon May 25 22:48:52 2015 -0400
+++ b/slopBed.xml	Sun Jun 21 22:49:46 2015 -0400
@@ -1,5 +1,5 @@
 <tool id="bedtools_slopbed" name="SlopBed" version="@WRAPPER_VERSION@.0">
-    <description></description>
+    <description>adjust the size of intervals</description>
     <macros>
         <import>macros.xml</import>
     </macros>
--- a/sortBed.xml	Mon May 25 22:48:52 2015 -0400
+++ b/sortBed.xml	Sun Jun 21 22:49:46 2015 -0400
@@ -1,5 +1,5 @@
-<tool id="bedtools_sortbed" name="Sort BED files" version="@WRAPPER_VERSION@.0">
-    <description></description>
+<tool id="bedtools_sortbed" name="SortBED" version="@WRAPPER_VERSION@.0">
+    <description>order the intervals</description>
     <macros>
         <import>macros.xml</import>
     </macros>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/spacingBed.xml	Sun Jun 21 22:49:46 2015 -0400
@@ -0,0 +1,38 @@
+<tool id="bedtools_spacingbed" name="SpacingBed" version="@WRAPPER_VERSION@.0">
+    <description>reports the distances between features</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <expand macro="stdio" />
+    <command>
+<![CDATA[
+        bedtools spacing
+        -i $input
+        > $output
+]]>
+    </command>
+    <inputs>
+        <param format="bed,vcf,gff,gff3,bam" name="input" type="data" label="BED/VCF/GFF/BAM file"/>
+    </inputs>
+    <outputs>
+        <data format_source="input" name="output" metadata_source="input" label="Spaces between intervals of ${input}"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input" value="a.bed" ftype="bed" />
+            <output name="output" file="spacingBed_result1.bed" ftype="bed" />
+        </test>
+    </tests>
+    <help>
+<![CDATA[
+**What it does**
+
+Report the spacing between intervals in a file.
+
+
+@REFERENCES@
+]]>
+    </help>
+    <expand macro="citations" />
+</tool>
--- a/subtractBed.xml	Mon May 25 22:48:52 2015 -0400
+++ b/subtractBed.xml	Sun Jun 21 22:49:46 2015 -0400
@@ -1,5 +1,5 @@
 <tool id="bedtools_subtractbed" name="SubtractBed" version="@WRAPPER_VERSION@.0">
-    <description></description>
+    <description>remove intervals based on overlaps</description>
     <macros>
         <import>macros.xml</import>
     </macros>
--- a/tagBed.xml	Mon May 25 22:48:52 2015 -0400
+++ b/tagBed.xml	Sun Jun 21 22:49:46 2015 -0400
@@ -1,5 +1,5 @@
 <tool id="bedtools_tagbed" name="TagBed" version="@WRAPPER_VERSION@.0">
-    <description></description>
+    <description>tag BAM alignments based on overlaps with interval files</description>
     <macros>
         <import>macros.xml</import>
     </macros>
Binary file test-data/bedToBam_result.bam has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/closestBed_result6.bed	Sun Jun 21 22:49:46 2015 -0400
@@ -0,0 +1,3 @@
+chr1	100	200	chr1	100	200
+chr1	100	200	chr1	180	250
+chr1	100	200	chr1	250	500
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/spacingBed_result1.bed	Sun Jun 21 22:49:46 2015 -0400
@@ -0,0 +1,4 @@
+chr1	100	200	.
+chr1	180	250	0
+chr1	250	500	0
+chr1	501	1000	1
--- a/tool_dependencies.xml	Mon May 25 22:48:52 2015 -0400
+++ b/tool_dependencies.xml	Sun Jun 21 22:49:46 2015 -0400
@@ -1,6 +1,6 @@
 <?xml version="1.0"?>
 <tool_dependency>
-    <package name="bedtools" version="2.22">
-        <repository changeset_revision="8359d121547e" name="package_bedtools_2_22" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    <package name="bedtools" version="2.23">
+        <repository changeset_revision="c472a4f6a603" name="package_bedtools_2_23" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
 </tool_dependency>
--- a/unionBedGraphs.xml	Mon May 25 22:48:52 2015 -0400
+++ b/unionBedGraphs.xml	Sun Jun 21 22:49:46 2015 -0400
@@ -1,5 +1,5 @@
 <tool id="bedtools_unionbedgraph" name="Merge BedGraph files" version="@WRAPPER_VERSION@.0">
-    <description></description>
+    <description>combines coverage intervals from multiple BEDGRAPH files</description>
     <macros>
         <import>macros.xml</import>
     </macros>
--- a/windowBed.xml	Mon May 25 22:48:52 2015 -0400
+++ b/windowBed.xml	Sun Jun 21 22:49:46 2015 -0400
@@ -1,5 +1,5 @@
 <tool id="bedtools_windowbed" name="WindowBed" version="@WRAPPER_VERSION@.0">
-    <description></description>
+    <description>find overlapping intervals within a window around an interval</description>
     <macros>
         <import>macros.xml</import>
     </macros>