# HG changeset patch
# User iuc
# Date 1453925759 18000
# Node ID 607c0576c6ab19ddee9753ba97e86a8725f89741
# Parent  2cd7e321d259e430118a4a40b81b78a983a2ac71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 6692e3a4fa1bf6e9a407735afdbb2454ed32b316

diff -r 2cd7e321d259 -r 607c0576c6ab annotateBed.xml
--- a/annotateBed.xml	Wed May 27 12:54:35 2015 -0400
+++ b/annotateBed.xml	Wed Jan 27 15:15:59 2016 -0500
@@ -1,5 +1,5 @@
-<tool id="bedtools_annotatebed" name="AnnotateBed" version="@WRAPPER_VERSION@.0">
-    <description></description>
+<tool id="bedtools_annotatebed" name="AnnotateBed" version="@WRAPPER_VERSION@.1">
+    <description>annotate coverage of features from multiple files</description>
     <macros>
         <import>macros.xml</import>
     </macros>
@@ -7,6 +7,7 @@
     <expand macro="stdio" />
     <command>
 <![CDATA[
+
         bedtools annotate
         -i "${inputA}"
         #if $names.names_select == 'yes':
@@ -22,6 +23,8 @@
         #else:
             #set files = '" "'.join( [ str( $file ) for $file in $names.beds ] )
             -files "${files}"
+            #set names = '" "'.join( [ str( $name.display_name ) for $name in $names.beds ] )
+            -names "${names}"
         #end if
         $strand
         $counts
diff -r 2cd7e321d259 -r 607c0576c6ab bamToBed.xml
--- a/bamToBed.xml	Wed May 27 12:54:35 2015 -0400
+++ b/bamToBed.xml	Wed Jan 27 15:15:59 2016 -0500
@@ -1,12 +1,21 @@
-<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>
-    <expand macro="requirements" />
+    <expand macro="requirements">
+        <requirement type="package" version="1.2">samtools</requirement>
+    </expand>
     <expand macro="stdio" />
     <command>
 <![CDATA[
+
+        #if $input.extension == 'bam' and $option == "-bedpe":
+            samtools sort -n "${input}" ./input &&
+        #else
+            ln -s "${input}" ./input.bam &&
+        #end if
+
         bedtools bamtobed
         $option
         $ed_score
@@ -14,20 +23,20 @@
         #if $tag and str($tag).strip():
           -tag "${tag}"
         #end if
-        -i "${input}"
+        -i ./input.bam
         > "${output}"
 ]]>
     </command>
     <inputs>
         <param format="bam" name="input" type="data" label="Convert the following BAM file to BED"/>
         <param name="option" type="select" label="What type of BED output would you like">
-            <option value="">Create a 6-column BED file.</option>
-            <option value="-bed12">Create a full, 12-column "blocked" BED file.</option>
-            <option value="-bedpe">Create a paired-end, BEDPE format.</option>
+            <option value="">Create a 6-column BED file</option>
+            <option value="-bed12">Create a full, 12-column "blocked" BED file</option>
+            <option value="-bedpe">Create a paired-end, BEDPE format</option>
         </param>
         <expand macro="split" />
         <param name="ed_score" type="boolean" truevalue="-ed" falsevalue="" checked="false"
-            label="Use alignment's edit-distance for BED score" />
+            label="Use alignment's edit-distance for BED score" help="(-ed)" />
         <param name="tag" type="text" optional="true" label="Use other NUMERIC BAM alignment tag as the BED score"
             help="(-tag)"/>
     </inputs>
@@ -56,16 +65,16 @@
 
 .. class:: infomark
 
-The "Report spliced BAM alignment..." option breaks BAM alignments with the "N" (splice) operator into distinct BED entries.  For example, using this option on a CIGAR such as 50M1000N50M would, by default, produce a single BED record that spans 1100bp.  However, using this option, it would create two separate BED records that are each 50bp in size and are separated by 1000bp (the size of the N operation).  This is important for RNA-seq and structural variation experiments.
+The "Report spliced BAM alignment..." option breaks BAM alignments with the "N" (splice) operator into distinct BED entries.
+For example, using this option on a CIGAR such as 50M1000N50M would, by default, produce a single BED record that spans 1100bp.
+However, using this option, it would create two separate BED records that are each 50bp in size and are separated by 1000bp (the size of the N operation).
+This is important for RNA-seq and structural variation experiments.
 
 
 .. class:: warningmark
 
-If using a custom BAM alignment TAG as  the BED score, note that this must be a numeric tag (e.g., type "i" as in NM:i:0).
+If using a custom BAM alignment TAG as the BED score, note that this must be a numeric tag (e.g., type "i" as in NM:i:0).
 
-.. class:: warningmark
-
-If creating a BEDPE output (see output formatting options), the BAM file should be sorted by query name.
 
 @REFERENCES@
 ]]>
diff -r 2cd7e321d259 -r 607c0576c6ab bamToFastq.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bamToFastq.xml	Wed Jan 27 15:15:59 2016 -0500
@@ -0,0 +1,39 @@
+<tool id="bedtools_bamtofastq" name="Convert from BAM to FastQ" version="@WRAPPER_VERSION@.0">
+    <description></description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <expand macro="stdio" />
+    <command>
+        bedtools bamtofastq
+        $tags
+        -i '$input'
+        -fq '$output'
+        #if $fq2:
+           -fq2 '$output2'
+        #end if
+    </command>
+    <inputs>
+        <param format="bam" name="input" type="data" label="Convert the following BAM file to FASTQ"/>
+        <param name="tags" type="boolean" truevalue="-tags" falsevalue="" selected="False" label="Create FASTQ based on the mate info in the BAM R2 and Q2 tags."/>
+        <param name="fq2" type="boolean" truevalue="-fq2" falsevalue="" selected="False" label="FASTQ for second end.
+            Used if BAM contains paired-end data. BAM should be sorted by query name if creating paired FASTQ with this option."/>
+    </inputs>
+    <outputs>
+        <data format="fastq" name="output" metadata_source="input" label="${input.name} (as FASTQ)"/>
+        <data format="fastq2" name="output2" metadata_source="input" label="${input.name} (as FASTQ)">
+            <filter>fq2 is True</filter>
+        </data>
+    </outputs>
+<help>
+
+**What it does**
+
+bedtools bamtofastq is a conversion utility for extracting FASTQ records from sequence alignments in BAM format.
+
+@REFERENCES@
+
+    </help>
+    <expand macro="citations" />
+</tool>
diff -r 2cd7e321d259 -r 607c0576c6ab bedToBam.xml
--- a/bedToBam.xml	Wed May 27 12:54:35 2015 -0400
+++ b/bedToBam.xml	Wed Jan 27 15:15:59 2016 -0500
@@ -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 2cd7e321d259 -r 607c0576c6ab bedpeToBam.xml
--- a/bedpeToBam.xml	Wed May 27 12:54:35 2015 -0400
+++ b/bedpeToBam.xml	Wed Jan 27 15:15:59 2016 -0500
@@ -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 2cd7e321d259 -r 607c0576c6ab closestBed.xml
--- a/closestBed.xml	Wed May 27 12:54:35 2015 -0400
+++ b/closestBed.xml	Wed Jan 27 15:15:59 2016 -0500
@@ -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
@@ -52,35 +55,21 @@
                 <option value="a">Report distance with respect to A. When A is on the - strand, "upstream" means B has a higher (start,stop). (-a)</option>
                 <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="" />
             <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 +115,12 @@
             <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 2cd7e321d259 -r 607c0576c6ab clusterBed.xml
--- a/clusterBed.xml	Wed May 27 12:54:35 2015 -0400
+++ b/clusterBed.xml	Wed Jan 27 15:15:59 2016 -0500
@@ -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 2cd7e321d259 -r 607c0576c6ab complementBed.xml
--- a/complementBed.xml	Wed May 27 12:54:35 2015 -0400
+++ b/complementBed.xml	Wed Jan 27 15:15:59 2016 -0500
@@ -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 2cd7e321d259 -r 607c0576c6ab expandBed.xml
--- a/expandBed.xml	Wed May 27 12:54:35 2015 -0400
+++ b/expandBed.xml	Wed Jan 27 15:15:59 2016 -0500
@@ -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 2cd7e321d259 -r 607c0576c6ab fisherBed.xml
--- a/fisherBed.xml	Wed May 27 12:54:35 2015 -0400
+++ b/fisherBed.xml	Wed Jan 27 15:15:59 2016 -0500
@@ -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 2cd7e321d259 -r 607c0576c6ab flankBed.xml
--- a/flankBed.xml	Wed May 27 12:54:35 2015 -0400
+++ b/flankBed.xml	Wed Jan 27 15:15:59 2016 -0500
@@ -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>
@@ -27,10 +27,10 @@
         <expand macro="genome" />
         <param name="pct" type="boolean" checked="false" truevalue="-pct" falsevalue=""
             label="Define -l and -r as a fraction of the feature’s length"
-            help="E.g. if used on a 1000bp feature, -l 0.50, will add 500 bp “upstream”" />
+            help="E.g. if used on a 1000bp feature, -l 0.50, will add 500 bp “upstream”. (-pct)" />
         <param name="strand" type="boolean" checked="false" truevalue="-s" falsevalue=""
             label="Define -l and -r based on strand"
-            help="For example. if used, -l 500 for a negative-stranded feature, it will add 500 bp to the end coordinate" />
+            help="For example. if used, -l 500 for a negative-stranded feature, it will add 500 bp to the end coordinate. (-s)" />
         <expand macro="addition" />
     </inputs>
     <outputs>
diff -r 2cd7e321d259 -r 607c0576c6ab genomeCoverageBed.xml
--- a/genomeCoverageBed.xml	Wed May 27 12:54:35 2015 -0400
+++ b/genomeCoverageBed.xml	Wed Jan 27 15:15:59 2016 -0500
@@ -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>
@@ -74,7 +74,7 @@
             label="Report the depth at each genome position with 1-based coordinates" help="(-d)" />
         <param name="dz" type="boolean" checked="False" truevalue="-dz" falsevalue=""
             label="Report the depth at each genome position with 0-based coordinatess" help="(-dz)" />
-        <param name="five" type="boolean" checked="False" truevalue="-d" falsevalue=""
+        <param name="five" type="boolean" checked="False" truevalue="-5" falsevalue=""
             label="Calculate coverage of 5’ positions" help="Instead of entire interval. (-5)" />
         <param name="three" type="boolean" checked="False" truevalue="-3" falsevalue=""
             label="Calculate coverage of 3’ positions" help="Instead of entire interval. (-3)" />
diff -r 2cd7e321d259 -r 607c0576c6ab getfastaBed.xml
--- a/getfastaBed.xml	Wed May 27 12:54:35 2015 -0400
+++ b/getfastaBed.xml	Wed Jan 27 15:15:59 2016 -0500
@@ -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 2cd7e321d259 -r 607c0576c6ab groupbyBed.xml
--- a/groupbyBed.xml	Wed May 27 12:54:35 2015 -0400
+++ b/groupbyBed.xml	Wed Jan 27 15:15:59 2016 -0500
@@ -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 2cd7e321d259 -r 607c0576c6ab intersectBed.xml
--- a/intersectBed.xml	Wed May 27 12:54:35 2015 -0400
+++ b/intersectBed.xml	Wed Jan 27 15:15:59 2016 -0500
@@ -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>
@@ -28,6 +28,7 @@
             $once
             $header
             $modes
+            $count
             > "${output}"
 ]]>
     </command>
diff -r 2cd7e321d259 -r 607c0576c6ab jaccardBed.xml
--- a/jaccardBed.xml	Wed May 27 12:54:35 2015 -0400
+++ b/jaccardBed.xml	Wed Jan 27 15:15:59 2016 -0500
@@ -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 2cd7e321d259 -r 607c0576c6ab linksBed.xml
--- a/linksBed.xml	Wed May 27 12:54:35 2015 -0400
+++ b/linksBed.xml	Wed Jan 27 15:15:59 2016 -0500
@@ -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 2cd7e321d259 -r 607c0576c6ab macros.xml
--- a/macros.xml	Wed May 27 12:54:35 2015 -0400
+++ b/macros.xml	Wed Jan 27 15:15:59 2016 -0500
@@ -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 2cd7e321d259 -r 607c0576c6ab makeWindowsBed.xml
--- a/makeWindowsBed.xml	Wed May 27 12:54:35 2015 -0400
+++ b/makeWindowsBed.xml	Wed Jan 27 15:15:59 2016 -0500
@@ -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 2cd7e321d259 -r 607c0576c6ab mapBed.xml
--- a/mapBed.xml	Wed May 27 12:54:35 2015 -0400
+++ b/mapBed.xml	Wed Jan 27 15:15:59 2016 -0500
@@ -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>
@@ -41,6 +41,7 @@
             <when value="-g">
                 <expand macro="genome" />
             </when>
+            <when value="" />
         </conditional>
     </inputs>
     <outputs>
diff -r 2cd7e321d259 -r 607c0576c6ab maskFastaBed.xml
--- a/maskFastaBed.xml	Wed May 27 12:54:35 2015 -0400
+++ b/maskFastaBed.xml	Wed Jan 27 15:15:59 2016 -0500
@@ -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 2cd7e321d259 -r 607c0576c6ab mergeBed.xml
--- a/mergeBed.xml	Wed May 27 12:54:35 2015 -0400
+++ b/mergeBed.xml	Wed Jan 27 15:15:59 2016 -0500
@@ -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 2cd7e321d259 -r 607c0576c6ab multiCov.xml
--- a/multiCov.xml	Wed May 27 12:54:35 2015 -0400
+++ b/multiCov.xml	Wed Jan 27 15:15:59 2016 -0500
@@ -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 2cd7e321d259 -r 607c0576c6ab multiIntersectBed.xml
--- a/multiIntersectBed.xml	Wed May 27 12:54:35 2015 -0400
+++ b/multiIntersectBed.xml	Wed Jan 27 15:15:59 2016 -0500
@@ -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 2cd7e321d259 -r 607c0576c6ab nucBed.xml
--- a/nucBed.xml	Wed May 27 12:54:35 2015 -0400
+++ b/nucBed.xml	Wed Jan 27 15:15:59 2016 -0500
@@ -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 2cd7e321d259 -r 607c0576c6ab overlapBed.xml
--- a/overlapBed.xml	Wed May 27 12:54:35 2015 -0400
+++ b/overlapBed.xml	Wed Jan 27 15:15:59 2016 -0500
@@ -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 2cd7e321d259 -r 607c0576c6ab randomBed.xml
--- a/randomBed.xml	Wed May 27 12:54:35 2015 -0400
+++ b/randomBed.xml	Wed Jan 27 15:15:59 2016 -0500
@@ -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 2cd7e321d259 -r 607c0576c6ab reldist.xml
--- a/reldist.xml	Wed May 27 12:54:35 2015 -0400
+++ b/reldist.xml	Wed Jan 27 15:15:59 2016 -0500
@@ -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 2cd7e321d259 -r 607c0576c6ab shuffleBed.xml
--- a/shuffleBed.xml	Wed May 27 12:54:35 2015 -0400
+++ b/shuffleBed.xml	Wed Jan 27 15:15:59 2016 -0500
@@ -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 2cd7e321d259 -r 607c0576c6ab slopBed.xml
--- a/slopBed.xml	Wed May 27 12:54:35 2015 -0400
+++ b/slopBed.xml	Wed Jan 27 15:15:59 2016 -0500
@@ -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 2cd7e321d259 -r 607c0576c6ab sortBed.xml
--- a/sortBed.xml	Wed May 27 12:54:35 2015 -0400
+++ b/sortBed.xml	Wed Jan 27 15:15:59 2016 -0500
@@ -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 2cd7e321d259 -r 607c0576c6ab spacingBed.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/spacingBed.xml	Wed Jan 27 15:15:59 2016 -0500
@@ -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 2cd7e321d259 -r 607c0576c6ab subtractBed.xml
--- a/subtractBed.xml	Wed May 27 12:54:35 2015 -0400
+++ b/subtractBed.xml	Wed Jan 27 15:15:59 2016 -0500
@@ -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 2cd7e321d259 -r 607c0576c6ab tagBed.xml
--- a/tagBed.xml	Wed May 27 12:54:35 2015 -0400
+++ b/tagBed.xml	Wed Jan 27 15:15:59 2016 -0500
@@ -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 2cd7e321d259 -r 607c0576c6ab test-data/annotateBed_result.bed
--- a/test-data/annotateBed_result.bed	Wed May 27 12:54:35 2015 -0400
+++ b/test-data/annotateBed_result.bed	Wed Jan 27 15:15:59 2016 -0500
@@ -1,3 +1,4 @@
+#					annotateBed2.bed	annotateBed3.bed	annotateBed4.bed	
 chr1	100	200	nasty	1	-	0.500000	1.000000	0.300000
 chr2	500	1000	ugly	2	+	0.000000	0.600000	1.000000
 chr3	1000	5000	big	3	-	1.000000	0.250000	0.000000
diff -r 2cd7e321d259 -r 607c0576c6ab test-data/bedToBam_result.bam
Binary file test-data/bedToBam_result.bam has changed
diff -r 2cd7e321d259 -r 607c0576c6ab test-data/closestBed_result6.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/closestBed_result6.bed	Wed Jan 27 15:15:59 2016 -0500
@@ -0,0 +1,3 @@
+chr1	100	200	chr1	100	200
+chr1	100	200	chr1	180	250
+chr1	100	200	chr1	250	500
diff -r 2cd7e321d259 -r 607c0576c6ab test-data/spacingBed_result1.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/spacingBed_result1.bed	Wed Jan 27 15:15:59 2016 -0500
@@ -0,0 +1,4 @@
+chr1	100	200	.
+chr1	180	250	0
+chr1	250	500	0
+chr1	501	1000	1
diff -r 2cd7e321d259 -r 607c0576c6ab tool_dependencies.xml
--- a/tool_dependencies.xml	Wed May 27 12:54:35 2015 -0400
+++ b/tool_dependencies.xml	Wed Jan 27 15:15:59 2016 -0500
@@ -1,6 +1,9 @@
 <?xml version="1.0"?>
 <tool_dependency>
-    <package name="bedtools" version="2.22">
-        <repository changeset_revision="960f83563956" name="package_bedtools_2_22" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
+    <package name="bedtools" version="2.24">
+        <repository changeset_revision="39b86c1e267d" name="package_bedtools_2_24" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="samtools" version="1.2">
+        <repository changeset_revision="f6ae3ba3f3c1" name="package_samtools_1_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
     </package>
 </tool_dependency>
diff -r 2cd7e321d259 -r 607c0576c6ab unionBedGraphs.xml
--- a/unionBedGraphs.xml	Wed May 27 12:54:35 2015 -0400
+++ b/unionBedGraphs.xml	Wed Jan 27 15:15:59 2016 -0500
@@ -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 2cd7e321d259 -r 607c0576c6ab windowBed.xml
--- a/windowBed.xml	Wed May 27 12:54:35 2015 -0400
+++ b/windowBed.xml	Wed Jan 27 15:15:59 2016 -0500
@@ -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>