# HG changeset patch
# User iuc
# Date 1476713615 14400
# Node ID 7308cc546a3699adb7b9586473505c44c598cb3d
# Parent  c78cf6fe3018f142f2198394a8642be1ebf90a98
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 19967671ddd4e750f53d71274e5c12325a402811

diff -r c78cf6fe3018 -r 7308cc546a36 annotateBed.xml
--- a/annotateBed.xml	Mon Oct 03 07:36:08 2016 -0400
+++ b/annotateBed.xml	Mon Oct 17 10:13:35 2016 -0400
@@ -1,4 +1,4 @@
-<tool id="bedtools_annotatebed" name="AnnotateBed" version="@WRAPPER_VERSION@.1">
+<tool id="bedtools_annotatebed" name="AnnotateBed" version="@WRAPPER_VERSION@.0">
     <description>annotate coverage of features from multiple files</description>
     <macros>
         <import>macros.xml</import>
@@ -52,10 +52,10 @@
         </conditional>
         <expand macro="strand2" />
         <param name="counts" type="boolean" checked="false" truevalue="-counts" falsevalue=""
-            label="Report the count of features followed by the % coverage for each annotation file" 
+            label="Report the count of features followed by the % coverage for each annotation file"
             help="Default is to report solely the fraction of -i covered by each file." />
         <param name="both" type="boolean" checked="false" truevalue="-both" falsevalue=""
-            label="Report the count of features followed by the % coverage for each annotation file" 
+            label="Report the count of features followed by the % coverage for each annotation file"
             help="Default is to report solely the fraction of the input file covered by each file." />
     </inputs>
     <outputs>
diff -r c78cf6fe3018 -r 7308cc546a36 closestBed.xml
--- a/closestBed.xml	Mon Oct 03 07:36:08 2016 -0400
+++ b/closestBed.xml	Mon Oct 17 10:13:35 2016 -0400
@@ -25,7 +25,7 @@
         #end if
         -a '$inputA'
         -b '$inputBs'
-        > $output
+        > '$output'
 ]]>
     </command>
     <inputs>
diff -r c78cf6fe3018 -r 7308cc546a36 clusterBed.xml
--- a/clusterBed.xml	Mon Oct 03 07:36:08 2016 -0400
+++ b/clusterBed.xml	Mon Oct 17 10:13:35 2016 -0400
@@ -10,16 +10,16 @@
         bedtools cluster
         $strand
         -d $distance
-        -i $inputA
-        > $output
+        -i '$inputA'
+        > '$output'
 ]]>
     </command>
     <inputs>
         <param format="bed,vcf,gff,gff3" name="inputA" type="data" label="BED/VCF/GFF file"/>
-        <param name="strand" type="boolean" checked="false" truevalue="-s" falsevalue="" label="Force strandedness." 
+        <param name="strand" type="boolean" checked="false" truevalue="-s" falsevalue="" label="Force strandedness."
             help="That is, only cluster features that are the same strand. By default, this is disabled." />
-        <param name="distance" type="integer" value="0" 
-            label="Maximum distance between features allowed for features to be clustered" 
+        <param name="distance" type="integer" value="0"
+            label="Maximum distance between features allowed for features to be clustered"
             help="Default is 0. That is, overlapping and/or book-ended features are clustered." />
     </inputs>
     <outputs>
diff -r c78cf6fe3018 -r 7308cc546a36 coverageBed.xml
--- a/coverageBed.xml	Mon Oct 03 07:36:08 2016 -0400
+++ b/coverageBed.xml	Mon Oct 17 10:13:35 2016 -0400
@@ -1,4 +1,4 @@
-<tool id="bedtools_coveragebed" name="Compute both the depth and breadth of coverage" version="@WRAPPER_VERSION@.1">
+<tool id="bedtools_coveragebed" name="Compute both the depth and breadth of coverage" version="@WRAPPER_VERSION@.0">
     <description>of features in file B on the features in file A (bedtools coverage)</description>
     <macros>
         <import>macros.xml</import>
@@ -24,7 +24,7 @@
         <param format="bam,bed,gff,gff3,vcf" name="inputA" type="data" label="File A (on which coverage is calculated)" help="BAM/BED/GFF/VCF format" />
         <param format="bam,bed,gff,gff3,vcf" name="inputB" type="data" multiple="true" label="File(s) B (for which coverage is calculated)" help="BAM/BED/GFF/VCF format" />
         <expand macro="split" />
-        <param name="strandedness" type="boolean" label="Force strandedness" truevalue="-s" falsevalue="" checked="false" 
+        <param name="strandedness" type="boolean" label="Force strandedness" truevalue="-s" falsevalue="" checked="false"
             help="Only report hits in B that overlap A on the same strand. By default, overlaps are reported without respect to strand (-s)"/>
         <param name="d" type="boolean" checked="false" truevalue="-d" falsevalue=""
             label="Report the depth at each position in each A feature"
@@ -47,10 +47,10 @@
 <![CDATA[
 **What it does**
 
-`bedtools coverage`_ computes both the *depth* and *breadth* of coverage of features in 
-file B on the features in file A. For example, ``bedtools coverage`` can compute the coverage of sequence alignments 
-(file B) across 1 kilobase (arbitrary) windows (file A) tiling a genome of interest. 
-One advantage that ``bedtools coverage`` offers is that it not only *counts* the number of features that 
+`bedtools coverage`_ computes both the *depth* and *breadth* of coverage of features in
+file B on the features in file A. For example, ``bedtools coverage`` can compute the coverage of sequence alignments
+(file B) across 1 kilobase (arbitrary) windows (file A) tiling a genome of interest.
+One advantage that ``bedtools coverage`` offers is that it not only *counts* the number of features that
 overlap an interval in file A, it also computes the fraction of bases in the interval in A that were overlapped by one or more features.
 Thus, ``bedtools coverage`` also computes the *breadth* of coverage for each interval in A.
 
diff -r c78cf6fe3018 -r 7308cc546a36 fisherBed.xml
--- a/fisherBed.xml	Mon Oct 03 07:36:08 2016 -0400
+++ b/fisherBed.xml	Mon Oct 17 10:13:35 2016 -0400
@@ -10,13 +10,13 @@
         bedtools fisher
         $strand
         $split
-        -a $inputA
-        -b $inputB
+        -a '$inputA'
+        -b '$inputB'
         -f $overlap
         -g $genome
         $reciprocal
         $m
-        > $output
+        > '$output'
 ]]>
     </command>
     <inputs>
diff -r c78cf6fe3018 -r 7308cc546a36 flankBed.xml
--- a/flankBed.xml	Mon Oct 03 07:36:08 2016 -0400
+++ b/flankBed.xml	Mon Oct 17 10:13:35 2016 -0400
@@ -11,7 +11,7 @@
         $pct
         $strand
         -g $genome
-        -i $input
+        -i '$input'
 
         #if $addition.addition_select == 'b':
             -b $addition.b
@@ -19,7 +19,7 @@
             -l $addition.l
             -r $addition.r
         #end if
-        > $output
+        > '$output'
 ]]>
     </command>
     <inputs>
diff -r c78cf6fe3018 -r 7308cc546a36 genomeCoverageBed.xml
--- a/genomeCoverageBed.xml	Mon Oct 03 07:36:08 2016 -0400
+++ b/genomeCoverageBed.xml	Mon Oct 17 10:13:35 2016 -0400
@@ -1,4 +1,4 @@
-<tool id="bedtools_genomecoveragebed" name="Genome Coverage" version="@WRAPPER_VERSION@.1">
+<tool id="bedtools_genomecoveragebed" name="Genome Coverage" version="@WRAPPER_VERSION@.0">
     <description>compute the coverage over an entire genome</description>
     <macros>
         <import>macros.xml</import>
@@ -158,7 +158,7 @@
     * 5. The fraction of bases on chromosome (or entire genome) with depth equal to column 2.
 
 **Example Output**:
-    
+
     chr2L       0           1379895     23011544    0.0599653
     chr2L       1           837250      23011544    0.0363839
     chr2L       2           904442      23011544    0.0393038
diff -r c78cf6fe3018 -r 7308cc546a36 getfastaBed.xml
--- a/getfastaBed.xml	Mon Oct 03 07:36:08 2016 -0400
+++ b/getfastaBed.xml	Mon Oct 17 10:13:35 2016 -0400
@@ -24,7 +24,6 @@
     </command>
     <inputs>
         <param format="bed,vcf,gff,gff3" name="input" type="data" label="BED/VCF/GFF file" />
-        
         <conditional name="fasta_source">
             <param name="fasta_source_selector" type="select" label="Choose the source for the fasta file">
                 <option value="history" selected="True">History</option>
@@ -36,7 +35,7 @@
             <when value="preloaded">
                <param name="fasta_id" type="select">
                   <options from_data_table="all_fasta" />
-               </param> 
+               </param>
             </when>
         </conditional>
         <param name="name" type="boolean" checked="false" truevalue="-name" falsevalue=""
diff -r c78cf6fe3018 -r 7308cc546a36 groupbyBed.xml
--- a/groupbyBed.xml	Mon Oct 03 07:36:08 2016 -0400
+++ b/groupbyBed.xml	Mon Oct 17 10:13:35 2016 -0400
@@ -8,17 +8,17 @@
     <command>
 <![CDATA[
         bedtools groupby
+        -i "${inputA}"
+        -g '$group'
         -c "${cols}"
-        -g $group
         -o $operation
-        -i "${inputA}"
         > "${output}"
 ]]>
     </command>
     <inputs>
         <param format="bed" name="inputA" type="data" label="BED file"/>
         <expand macro="choose_columns" />
-        <param name="group" type="text" value="1,2,3" 
+        <param name="group" type="text" value="1,2,3"
             label="Specifies which column(s) (1-based) should be used to group the input"
             help="Columns may be comma-separated with each column must be explicitly listed. Or, ranges (e.g. 1-4) are also allowed. (-g)">
             <sanitizer invalid_char="">
diff -r c78cf6fe3018 -r 7308cc546a36 jaccardBed.xml
--- a/jaccardBed.xml	Mon Oct 03 07:36:08 2016 -0400
+++ b/jaccardBed.xml	Mon Oct 17 10:13:35 2016 -0400
@@ -12,9 +12,9 @@
             $split
             $reciprocal
             -f $overlap
-            -a $inputA
-            -b $inputB
-            > $output
+            -a '$inputA'
+            -b '$inputB'
+            > '$output'
 ]]>
     </command>
     <inputs>
@@ -22,7 +22,7 @@
         <param format="bed,vcf,gff,gff3" name="inputB" type="data" label="BED/VCF/GFF file"/>
         <expand macro="overlap" />
         <expand macro="reciprocal" />
-        <param name="strand" type="boolean" checked="false" truevalue="-s" falsevalue="" 
+        <param name="strand" type="boolean" checked="false" truevalue="-s" falsevalue=""
             label="Force strandedness"
             help="That is, only report hits in B that overlap A on the same strand. By default, overlaps are reported without respect to strand. (-s)" />
         <expand macro="strand2" />
diff -r c78cf6fe3018 -r 7308cc546a36 macros.xml
--- a/macros.xml	Mon Oct 03 07:36:08 2016 -0400
+++ b/macros.xml	Mon Oct 17 10:13:35 2016 -0400
@@ -1,11 +1,11 @@
 <macros>
     <xml name="requirements">
         <requirements>
-            <requirement type="package" version="2.24">bedtools</requirement>
+            <requirement type="package" version="2.26.0gx">bedtools</requirement>
             <yield/>
         </requirements>
     </xml>
-    <token name="@WRAPPER_VERSION@">2.24</token>
+    <token name="@WRAPPER_VERSION@">2.26.0</token>
     <xml name="stdio">
         <stdio>
             <!-- Anything other than zero is an error -->
@@ -55,19 +55,19 @@
     </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" 
+            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" 
+            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" 
+            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" 
+            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">
diff -r c78cf6fe3018 -r 7308cc546a36 makeWindowsBed.xml
--- a/makeWindowsBed.xml	Mon Oct 03 07:36:08 2016 -0400
+++ b/makeWindowsBed.xml	Mon Oct 17 10:13:35 2016 -0400
@@ -9,9 +9,9 @@
 <![CDATA[
         bedtools makewindows
         #if $type.type_select == 'genome':
-            -g $type.genome
+            -g '$type.genome'
         #else:
-            -b $type.input
+            -b '$type.input'
         #end if
         #if $action.action_select == 'windowsize':
             -w $action.windowsize
@@ -23,7 +23,7 @@
             -s $action.step_size
         #end if
         $sourcename
-        > $output
+        > '$output'
 ]]>
     </command>
     <inputs>
diff -r c78cf6fe3018 -r 7308cc546a36 mapBed.xml
--- a/mapBed.xml	Mon Oct 03 07:36:08 2016 -0400
+++ b/mapBed.xml	Mon Oct 17 10:13:35 2016 -0400
@@ -1,4 +1,4 @@
-<tool id="bedtools_map" name="MapBed" version="@WRAPPER_VERSION@.1">
+<tool id="bedtools_map" name="MapBed" version="@WRAPPER_VERSION@.0">
     <description>apply a function to a column for each overlapping interval</description>
     <macros>
         <import>macros.xml</import>
@@ -26,7 +26,7 @@
         <param format="bam,bed,vcf,gff,gff3" name="inputA" type="data" label="File A (BAM/BED/VCF/GFF)" />
         <param format="bam,bed,gff,vcf,gff3" name="inputB" type="data" label="File B (BAM/BED/VCF/GFF)" />
         <expand macro="overlap" />
-        <param name="reciprocal" type="boolean" checked="false" truevalue="-r" falsevalue="" 
+        <param name="reciprocal" type="boolean" checked="false" truevalue="-r" falsevalue=""
             label="Require reciprocal overlap"
             help="If set, the overlap between the BAM alignment and the BED interval must affect the above fraction of both the alignment and the BED interval. (-r)" />
         <expand macro="strand2" />
diff -r c78cf6fe3018 -r 7308cc546a36 mergeBed.xml
--- a/mergeBed.xml	Mon Oct 03 07:36:08 2016 -0400
+++ b/mergeBed.xml	Mon Oct 17 10:13:35 2016 -0400
@@ -1,4 +1,4 @@
-<tool id="bedtools_mergebed" name="MergeBED" version="@WRAPPER_VERSION@.1">
+<tool id="bedtools_mergebed" name="MergeBED" version="@WRAPPER_VERSION@.0">
     <description>combine overlapping/nearby intervals into a single interval</description>
     <macros>
         <import>macros.xml</import>
@@ -120,12 +120,12 @@
 
 
 ==========================================================================
-*-d* Controlling how close two features must be in order to merge 
+*-d* Controlling how close two features must be in order to merge
 ==========================================================================
-By default, only overlapping or book-ended features are combined into a new 
-feature. However, one can force ``merge`` to combine more distant features 
-with the ``-d`` option. For example, were one to set ``-d`` to 1000, any 
-features that overlap or are within 1000 base pairs of one another will be 
+By default, only overlapping or book-ended features are combined into a new
+feature. However, one can force ``merge`` to combine more distant features
+with the ``-d`` option. For example, were one to set ``-d`` to 1000, any
+features that overlap or are within 1000 base pairs of one another will be
 combined.
 
 ::
@@ -133,7 +133,7 @@
   $ cat A.bed
   chr1  100  200
   chr1  501  1000
-  
+
   $ bedtools merge -i A.bed
   chr1  100  200
   chr1  501  1000
diff -r c78cf6fe3018 -r 7308cc546a36 multiCov.xml
--- a/multiCov.xml	Mon Oct 03 07:36:08 2016 -0400
+++ b/multiCov.xml	Mon Oct 17 10:13:35 2016 -0400
@@ -13,10 +13,10 @@
         #end for
 
         bedtools multicov
-            -bed $input
+            -bed '$input'
             -bams
             #for $i, $bam in enumerate( $bams ):
-                ${i}.bam
+                '${i}.bam'
             #end for
             $strand
             -f $overlap
@@ -26,7 +26,7 @@
             $duplicate
             $failed
             $proper
-            > $output
+            > '$output'
 ]]>
     </command>
     <inputs>
@@ -43,7 +43,7 @@
             label="Include duplicate reads"
             help="Default counts non-duplicates only. (-D)" />
         <param name="failed" type="boolean" checked="false" truevalue="-F" falsevalue=""
-            label="Include failed-QC reads" 
+            label="Include failed-QC reads"
             help="Default counts pass-QC reads only (-F)"/>
         <param name="proper" type="boolean" checked="false" truevalue="-p" falsevalue=""
             label="Only count proper pairs"
diff -r c78cf6fe3018 -r 7308cc546a36 multiIntersectBed.xml
--- a/multiIntersectBed.xml	Mon Oct 03 07:36:08 2016 -0400
+++ b/multiIntersectBed.xml	Mon Oct 17 10:13:35 2016 -0400
@@ -50,7 +50,7 @@
             </when>
         </conditional>
         <expand macro="genome" />
-        <param name="cluster" type="boolean" checked="false" truevalue="-cluster" falsevalue="" 
+        <param name="cluster" type="boolean" checked="false" truevalue="-cluster" falsevalue=""
             label="Invoke Ryan Layers's clustering algorithm"
             help="(-cluster)" />
         <param name="zero" type="boolean" checked="true"
@@ -119,11 +119,11 @@
     chr1  10  20
     chr1  22  27
     chr1  24  30
-    
+
     # b.bed
     chr1  12  32
     chr1  14  30
-    
+
     # c.bed
     chr1  8   15
     chr1  10  14
diff -r c78cf6fe3018 -r 7308cc546a36 nucBed.xml
--- a/nucBed.xml	Mon Oct 03 07:36:08 2016 -0400
+++ b/nucBed.xml	Mon Oct 17 10:13:35 2016 -0400
@@ -12,9 +12,9 @@
         $seq
         $pattern
         $case
-        -fi $fasta
-        -bed $input
-        > $output
+        -fi '$fasta'
+        -bed '$input'
+        > '$output'
 ]]>
     </command>
     <inputs>
diff -r c78cf6fe3018 -r 7308cc546a36 overlapBed.xml
--- a/overlapBed.xml	Mon Oct 03 07:36:08 2016 -0400
+++ b/overlapBed.xml	Mon Oct 17 10:13:35 2016 -0400
@@ -8,9 +8,9 @@
     <command>
 <![CDATA[
         bedtools overlap
-        -i $input
+        -i '$input'
         -cols $cols
-        > $output
+        > '$output'
 ]]>
     </command>
     <inputs>
diff -r c78cf6fe3018 -r 7308cc546a36 shuffleBed.xml
--- a/shuffleBed.xml	Mon Oct 03 07:36:08 2016 -0400
+++ b/shuffleBed.xml	Mon Oct 17 10:13:35 2016 -0400
@@ -8,8 +8,8 @@
     <command>
 <![CDATA[
         bedtools shuffle
-        -g $genome
-        -i $inputA
+        -g '$genome'
+        -i '$inputA'
         $bedpe
         #if str($seed.seed_choose) == "True":
             -seed $seed.seed
@@ -25,7 +25,7 @@
         $no_overlap
         $allow_beyond
         -maxTries $maxtries
-        > $output
+        > '$output'
 ]]>
     </command>
     <inputs>
diff -r c78cf6fe3018 -r 7308cc546a36 slopBed.xml
--- a/slopBed.xml	Mon Oct 03 07:36:08 2016 -0400
+++ b/slopBed.xml	Mon Oct 17 10:13:35 2016 -0400
@@ -10,8 +10,8 @@
         bedtools slop
         $pct
         $strand
-        -g $genome
-        -i $inputA
+        -g '$genome'
+        -i '$inputA'
         #if $addition.addition_select == 'b':
             -b $addition.b
         #else:
@@ -19,7 +19,7 @@
             -r $addition.r
         #end if
         $header
-        > $output
+        > '$output'
 ]]>
     </command>
     <inputs>
diff -r c78cf6fe3018 -r 7308cc546a36 sortBed.xml
--- a/sortBed.xml	Mon Oct 03 07:36:08 2016 -0400
+++ b/sortBed.xml	Mon Oct 17 10:13:35 2016 -0400
@@ -7,14 +7,14 @@
     <expand macro="stdio" />
     <command>
 <![CDATA[
-        sortBed 
-            -i $input 
-            $option 
-            > $output
+        sortBed
+            -i '$input'
+            $option
+            > '$output'
 ]]>
     </command>
     <inputs>
-        <param format="bed" name="input" type="data" label="Sort the following BED file"/>
+        <param format="bed,gff,gff3,vcf" name="input" type="data" label="Sort the following BED file"/>
         <param name="option" type="select" label="Sort by">
             <!-- sort -k 1,1 -k2,2 -n a.bed -->
             <option value="">chromosome, then by start position (asc)</option>
@@ -27,7 +27,7 @@
         </param>
     </inputs>
     <outputs>
-        <data format="bed" name="output" metadata_source="input" label="${input.name} (as BED)"/>
+        <data format_source="input" name="output" metadata_source="input" label="SortBed on ${input.name}"/>
     </outputs>
     <tests>
         <test>
diff -r c78cf6fe3018 -r 7308cc546a36 spacingBed.xml
--- a/spacingBed.xml	Mon Oct 03 07:36:08 2016 -0400
+++ b/spacingBed.xml	Mon Oct 17 10:13:35 2016 -0400
@@ -8,8 +8,8 @@
     <command>
 <![CDATA[
         bedtools spacing
-        -i $input
-        > $output
+        -i '$input'
+        > '$output'
 ]]>
     </command>
     <inputs>
diff -r c78cf6fe3018 -r 7308cc546a36 subtractBed.xml
--- a/subtractBed.xml	Mon Oct 03 07:36:08 2016 -0400
+++ b/subtractBed.xml	Mon Oct 17 10:13:35 2016 -0400
@@ -9,11 +9,11 @@
 <![CDATA[
         bedtools subtract
         $strand
-        -a $inputA
-        -b $inputB
+        -a '$inputA'
+        -b '$inputB'
         -f $overlap
         $removeIfOverlap
-        > $output
+        > '$output'
 ]]>
     </command>
     <inputs>
diff -r c78cf6fe3018 -r 7308cc546a36 test-data/annotateBed_result.bed
--- a/test-data/annotateBed_result.bed	Mon Oct 03 07:36:08 2016 -0400
+++ b/test-data/annotateBed_result.bed	Mon Oct 17 10:13:35 2016 -0400
@@ -1,4 +1,4 @@
-#					annotateBed2.bed	annotateBed3.bed	annotateBed4.bed	
+#						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 c78cf6fe3018 -r 7308cc546a36 test-data/makeWindowBed_result3.bed
--- a/test-data/makeWindowBed_result3.bed	Mon Oct 03 07:36:08 2016 -0400
+++ b/test-data/makeWindowBed_result3.bed	Mon Oct 17 10:13:35 2016 -0400
@@ -1,100 +1,100 @@
-chr1	0	1971955
-chr1	1971955	3943910
-chr1	3943910	5915865
-chr1	5915865	7887820
-chr1	7887820	9859775
-chr1	9859775	11831730
-chr1	11831730	13803685
-chr1	13803685	15775640
-chr1	15775640	17747595
-chr1	17747595	19719550
-chr1	19719550	21691505
-chr1	21691505	23663460
-chr1	23663460	25635415
-chr1	25635415	27607370
-chr1	27607370	29579325
-chr1	29579325	31551280
-chr1	31551280	33523235
-chr1	33523235	35495190
-chr1	35495190	37467145
-chr1	37467145	39439100
-chr1	39439100	41411055
-chr1	41411055	43383010
-chr1	43383010	45354965
-chr1	45354965	47326920
-chr1	47326920	49298875
-chr1	49298875	51270830
-chr1	51270830	53242785
-chr1	53242785	55214740
-chr1	55214740	57186695
-chr1	57186695	59158650
-chr1	59158650	61130605
-chr1	61130605	63102560
-chr1	63102560	65074515
-chr1	65074515	67046470
-chr1	67046470	69018425
-chr1	69018425	70990380
-chr1	70990380	72962335
-chr1	72962335	74934290
-chr1	74934290	76906245
-chr1	76906245	78878200
-chr1	78878200	80850155
-chr1	80850155	82822110
-chr1	82822110	84794065
-chr1	84794065	86766020
-chr1	86766020	88737975
-chr1	88737975	90709930
-chr1	90709930	92681885
-chr1	92681885	94653840
-chr1	94653840	96625795
-chr1	96625795	98597750
-chr1	98597750	100569705
-chr1	100569705	102541660
-chr1	102541660	104513615
-chr1	104513615	106485570
-chr1	106485570	108457525
-chr1	108457525	110429480
-chr1	110429480	112401435
-chr1	112401435	114373390
-chr1	114373390	116345345
-chr1	116345345	118317300
-chr1	118317300	120289255
-chr1	120289255	122261210
-chr1	122261210	124233165
-chr1	124233165	126205120
-chr1	126205120	128177075
-chr1	128177075	130149030
-chr1	130149030	132120985
-chr1	132120985	134092940
-chr1	134092940	136064895
-chr1	136064895	138036850
-chr1	138036850	140008805
-chr1	140008805	141980760
-chr1	141980760	143952715
-chr1	143952715	145924670
-chr1	145924670	147896625
-chr1	147896625	149868580
-chr1	149868580	151840535
-chr1	151840535	153812490
-chr1	153812490	155784445
-chr1	155784445	157756400
-chr1	157756400	159728355
-chr1	159728355	161700310
-chr1	161700310	163672265
-chr1	163672265	165644220
-chr1	165644220	167616175
-chr1	167616175	169588130
-chr1	169588130	171560085
-chr1	171560085	173532040
-chr1	173532040	175503995
-chr1	175503995	177475950
-chr1	177475950	179447905
-chr1	179447905	181419860
-chr1	181419860	183391815
-chr1	183391815	185363770
-chr1	185363770	187335725
-chr1	187335725	189307680
-chr1	189307680	191279635
-chr1	191279635	193251590
-chr1	193251590	195223545
-chr1	195223545	197195432
+chr1	0	1971954
+chr1	1971954	3943908
+chr1	3943908	5915862
+chr1	5915862	7887816
+chr1	7887816	9859770
+chr1	9859770	11831724
+chr1	11831724	13803678
+chr1	13803678	15775632
+chr1	15775632	17747586
+chr1	17747586	19719540
+chr1	19719540	21691494
+chr1	21691494	23663448
+chr1	23663448	25635402
+chr1	25635402	27607356
+chr1	27607356	29579310
+chr1	29579310	31551264
+chr1	31551264	33523218
+chr1	33523218	35495172
+chr1	35495172	37467126
+chr1	37467126	39439080
+chr1	39439080	41411034
+chr1	41411034	43382988
+chr1	43382988	45354942
+chr1	45354942	47326896
+chr1	47326896	49298850
+chr1	49298850	51270804
+chr1	51270804	53242758
+chr1	53242758	55214712
+chr1	55214712	57186666
+chr1	57186666	59158620
+chr1	59158620	61130574
+chr1	61130574	63102528
+chr1	63102528	65074482
+chr1	65074482	67046436
+chr1	67046436	69018390
+chr1	69018390	70990344
+chr1	70990344	72962298
+chr1	72962298	74934252
+chr1	74934252	76906206
+chr1	76906206	78878160
+chr1	78878160	80850114
+chr1	80850114	82822068
+chr1	82822068	84794022
+chr1	84794022	86765976
+chr1	86765976	88737930
+chr1	88737930	90709884
+chr1	90709884	92681838
+chr1	92681838	94653792
+chr1	94653792	96625746
+chr1	96625746	98597700
+chr1	98597700	100569654
+chr1	100569654	102541608
+chr1	102541608	104513562
+chr1	104513562	106485516
+chr1	106485516	108457470
+chr1	108457470	110429424
+chr1	110429424	112401378
+chr1	112401378	114373332
+chr1	114373332	116345286
+chr1	116345286	118317240
+chr1	118317240	120289194
+chr1	120289194	122261148
+chr1	122261148	124233102
+chr1	124233102	126205056
+chr1	126205056	128177010
+chr1	128177010	130148964
+chr1	130148964	132120918
+chr1	132120918	134092872
+chr1	134092872	136064826
+chr1	136064826	138036780
+chr1	138036780	140008734
+chr1	140008734	141980688
+chr1	141980688	143952642
+chr1	143952642	145924596
+chr1	145924596	147896550
+chr1	147896550	149868504
+chr1	149868504	151840458
+chr1	151840458	153812412
+chr1	153812412	155784366
+chr1	155784366	157756320
+chr1	157756320	159728274
+chr1	159728274	161700228
+chr1	161700228	163672182
+chr1	163672182	165644136
+chr1	165644136	167616090
+chr1	167616090	169588044
+chr1	169588044	171559998
+chr1	171559998	173531952
+chr1	173531952	175503906
+chr1	175503906	177475860
+chr1	177475860	179447814
+chr1	179447814	181419768
+chr1	181419768	183391722
+chr1	183391722	185363676
+chr1	185363676	187335630
+chr1	187335630	189307584
+chr1	189307584	191279538
+chr1	191279538	193251492
+chr1	193251492	195223446
+chr1	195223446	197195432
diff -r c78cf6fe3018 -r 7308cc546a36 test-data/makeWindowBed_result4.bed
--- a/test-data/makeWindowBed_result4.bed	Mon Oct 03 07:36:08 2016 -0400
+++ b/test-data/makeWindowBed_result4.bed	Mon Oct 17 10:13:35 2016 -0400
@@ -1,45 +1,45 @@
-chr5	60000	60667
-chr5	60667	61334
-chr5	61334	62001
-chr5	62001	62668
-chr5	62668	63335
-chr5	63335	64002
-chr5	64002	64669
-chr5	64669	65336
-chr5	65336	66003
-chr5	66003	66670
-chr5	66670	67337
-chr5	67337	68004
-chr5	68004	68671
-chr5	68671	69338
-chr5	69338	70000
-chr5	73000	74134
-chr5	74134	75268
-chr5	75268	76402
-chr5	76402	77536
-chr5	77536	78670
-chr5	78670	79804
-chr5	79804	80938
-chr5	80938	82072
-chr5	82072	83206
-chr5	83206	84340
-chr5	84340	85474
-chr5	85474	86608
-chr5	86608	87742
-chr5	87742	88876
-chr5	88876	90000
-chr5	100000	100067
-chr5	100067	100134
-chr5	100134	100201
-chr5	100201	100268
-chr5	100268	100335
-chr5	100335	100402
-chr5	100402	100469
-chr5	100469	100536
-chr5	100536	100603
-chr5	100603	100670
-chr5	100670	100737
-chr5	100737	100804
-chr5	100804	100871
-chr5	100871	100938
-chr5	100938	101000
+chr5	60000	60666
+chr5	60666	61332
+chr5	61332	61998
+chr5	61998	62664
+chr5	62664	63330
+chr5	63330	63996
+chr5	63996	64662
+chr5	64662	65328
+chr5	65328	65994
+chr5	65994	66660
+chr5	66660	67326
+chr5	67326	67992
+chr5	67992	68658
+chr5	68658	69324
+chr5	69324	70000
+chr5	73000	74133
+chr5	74133	75266
+chr5	75266	76399
+chr5	76399	77532
+chr5	77532	78665
+chr5	78665	79798
+chr5	79798	80931
+chr5	80931	82064
+chr5	82064	83197
+chr5	83197	84330
+chr5	84330	85463
+chr5	85463	86596
+chr5	86596	87729
+chr5	87729	88862
+chr5	88862	90000
+chr5	100000	100066
+chr5	100066	100132
+chr5	100132	100198
+chr5	100198	100264
+chr5	100264	100330
+chr5	100330	100396
+chr5	100396	100462
+chr5	100462	100528
+chr5	100528	100594
+chr5	100594	100660
+chr5	100660	100726
+chr5	100726	100792
+chr5	100792	100858
+chr5	100858	100924
+chr5	100924	101000
diff -r c78cf6fe3018 -r 7308cc546a36 tool_dependencies.xml
--- a/tool_dependencies.xml	Mon Oct 03 07:36:08 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,9 +0,0 @@
-<?xml version="1.0"?>
-<tool_dependency>
-    <package name="bedtools" version="2.24">
-        <repository changeset_revision="3416a1d4a582" 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 c78cf6fe3018 -r 7308cc546a36 unionBedGraphs.xml
--- a/unionBedGraphs.xml	Mon Oct 03 07:36:08 2016 -0400
+++ b/unionBedGraphs.xml	Mon Oct 17 10:13:35 2016 -0400
@@ -132,7 +132,7 @@
 **Examples using the Zero Coverage checkbox**
 
 Output example (*without* checking "Report regions with zero coverage")::
-    
+
     chr1     900    1000     0    60     0
     chr1    1000    1500    10    60     0
     chr1    1500    1600     0    60     0
@@ -145,7 +145,7 @@
 
 
 Output example (*with* checking "Report regions with zero coverage"). The lines marked with (*) are not covered in any input file, but are still reported (The asterisk marking does not appear in the file).::
-    
+
     chr1       0          900     0     0     0 (*)
     chr1     900         1000     0    60     0
     chr1    1000         1500    10    60     0
@@ -157,7 +157,7 @@
     chr1    2050         2070    20     0    80
     chr1    2070         2090    20     0     0
     chr1    2090         2100    20     0    20
-    chr1    2100    247249719     0     0     0 (*) 
+    chr1    2100    247249719     0     0     0 (*)
 
 
 ------
@@ -167,7 +167,7 @@
 The default value is '0', but you can use any other value.
 
 Output example with **filler = N/A**::
-    
+
     chr1     900    1000    N/A     60    N/A
     chr1    1000    1500     10     60    N/A
     chr1    1500    1600    N/A     60    N/A
@@ -204,14 +204,14 @@
 The input BedGraph files can contain any kind of value in the fourth column, not necessarily a numeric value.
 
 Input Example::
-        
-    File-1                           File-2 
+
+    File-1                           File-2
     chr1   200   300   Sample1       chr1   100   240   0.75
     chr1   400   450   Sample1       chr1   250   700   0.43
     chr1   530   600   Sample2
 
 Output Example::
-    
+
     chr1   100    200    0         0.75
     chr1   200    240    Sample1   0.75
     chr1   240    250    Sample1   0
diff -r c78cf6fe3018 -r 7308cc546a36 windowBed.xml
--- a/windowBed.xml	Mon Oct 03 07:36:08 2016 -0400
+++ b/windowBed.xml	Mon Oct 17 10:13:35 2016 -0400
@@ -9,11 +9,11 @@
 <![CDATA[
         bedtools window
         #if $inputA.ext == "bam":
-            -abam $inputA
+            -abam '$inputA'
         #else:
-            -a $inputA
+            -a '$inputA'
         #end if
-        -b $inputB
+        -b '$inputB'
         $bed
         $strandB
         #if $addition.addition_select == 'window':
@@ -26,7 +26,7 @@
         $number
         $nooverlaps
         $header
-        > $output
+        > '$output'
 ]]>
     </command>
     <inputs>