# HG changeset patch
# User iuc
# Date 1434941386 14400
# Node ID a2d4c30ba2f9c07ba9e55e44d085c2f9082d566e
# Parent  e30113df8cf6d5b6c9c0723a317161ee26bfb040
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 0887009a23d176b21536c9fd8a18c4fecc417d4f

diff -r e30113df8cf6 -r a2d4c30ba2f9 annotateBed.xml
--- 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>
diff -r e30113df8cf6 -r a2d4c30ba2f9 bamToBed.xml
--- 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>
diff -r e30113df8cf6 -r a2d4c30ba2f9 bedToBam.xml
--- 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>
diff -r e30113df8cf6 -r a2d4c30ba2f9 bedpeToBam.xml
--- 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>
diff -r e30113df8cf6 -r a2d4c30ba2f9 closestBed.xml
--- 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[
diff -r e30113df8cf6 -r a2d4c30ba2f9 clusterBed.xml
--- 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>
diff -r e30113df8cf6 -r a2d4c30ba2f9 complementBed.xml
--- 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>
diff -r e30113df8cf6 -r a2d4c30ba2f9 expandBed.xml
--- 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>
diff -r e30113df8cf6 -r a2d4c30ba2f9 fisherBed.xml
--- 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>
diff -r e30113df8cf6 -r a2d4c30ba2f9 flankBed.xml
--- 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>
diff -r e30113df8cf6 -r a2d4c30ba2f9 genomeCoverageBed.xml
--- 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>
diff -r e30113df8cf6 -r a2d4c30ba2f9 getfastaBed.xml
--- 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>
diff -r e30113df8cf6 -r a2d4c30ba2f9 groupbyBed.xml
--- 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>
diff -r e30113df8cf6 -r a2d4c30ba2f9 intersectBed.xml
--- 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>
diff -r e30113df8cf6 -r a2d4c30ba2f9 jaccardBed.xml
--- 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>
diff -r e30113df8cf6 -r a2d4c30ba2f9 linksBed.xml
--- 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>
diff -r e30113df8cf6 -r a2d4c30ba2f9 macros.xml
--- 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">
diff -r e30113df8cf6 -r a2d4c30ba2f9 makeWindowsBed.xml
--- 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>
diff -r e30113df8cf6 -r a2d4c30ba2f9 mapBed.xml
--- 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>
diff -r e30113df8cf6 -r a2d4c30ba2f9 maskFastaBed.xml
--- 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>
diff -r e30113df8cf6 -r a2d4c30ba2f9 mergeBed.xml
--- 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>
diff -r e30113df8cf6 -r a2d4c30ba2f9 multiCov.xml
--- 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>
diff -r e30113df8cf6 -r a2d4c30ba2f9 multiIntersectBed.xml
--- 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>
diff -r e30113df8cf6 -r a2d4c30ba2f9 nucBed.xml
--- 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>
diff -r e30113df8cf6 -r a2d4c30ba2f9 overlapBed.xml
--- 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>
diff -r e30113df8cf6 -r a2d4c30ba2f9 randomBed.xml
--- 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>
diff -r e30113df8cf6 -r a2d4c30ba2f9 reldist.xml
--- 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>
diff -r e30113df8cf6 -r a2d4c30ba2f9 shuffleBed.xml
--- 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>
diff -r e30113df8cf6 -r a2d4c30ba2f9 slopBed.xml
--- 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>
diff -r e30113df8cf6 -r a2d4c30ba2f9 sortBed.xml
--- 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>
diff -r e30113df8cf6 -r a2d4c30ba2f9 spacingBed.xml
--- /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>
diff -r e30113df8cf6 -r a2d4c30ba2f9 subtractBed.xml
--- 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>
diff -r e30113df8cf6 -r a2d4c30ba2f9 tagBed.xml
--- 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>
diff -r e30113df8cf6 -r a2d4c30ba2f9 test-data/bedToBam_result.bam
Binary file test-data/bedToBam_result.bam has changed
diff -r e30113df8cf6 -r a2d4c30ba2f9 test-data/closestBed_result6.bed
--- /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
diff -r e30113df8cf6 -r a2d4c30ba2f9 test-data/spacingBed_result1.bed
--- /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
diff -r e30113df8cf6 -r a2d4c30ba2f9 tool_dependencies.xml
--- 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>
diff -r e30113df8cf6 -r a2d4c30ba2f9 unionBedGraphs.xml
--- 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>
diff -r e30113df8cf6 -r a2d4c30ba2f9 windowBed.xml
--- 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>