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changeset 4:607c0576c6ab draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 6692e3a4fa1bf6e9a407735afdbb2454ed32b316
author iuc
date Wed, 27 Jan 2016 15:15:59 -0500
parents 2cd7e321d259
children f8b7dc21b4ee
files annotateBed.xml bamToBed.xml bamToFastq.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/annotateBed_result.bed test-data/bedToBam_result.bam test-data/closestBed_result6.bed test-data/spacingBed_result1.bed tool_dependencies.xml unionBedGraphs.xml windowBed.xml
diffstat 41 files changed, 195 insertions(+), 81 deletions(-) [+]
line wrap: on
line diff
--- 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
--- 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@
 ]]>
--- /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>
--- 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>
--- 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>
--- 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[
--- 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>
--- 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>
--- 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>
--- 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>
--- 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>
--- 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)" />
--- 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>
--- 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>
--- 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>
--- 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>
--- 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>
--- 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">
--- 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>
--- 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>
--- 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>
--- 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>
--- 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>
--- 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>
--- 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>
--- 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>
--- 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>
--- 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>
--- 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>
--- 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>
--- 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>
--- /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>
--- 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>
--- 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>
--- 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
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	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
--- /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
--- 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>
--- 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>
--- 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>