Mercurial > repos > bgruening > bedtools_test_bag

changeset 12:c782e0edc4f1 draft default tip

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Uploaded
author bgruening
date Thu, 19 Jun 2014 10:12:00 -0400
parents e526617a6bb9
children
files Bed12ToBed6.xml BedToBam.xml annotateBed.xml bamToBed.xml bamToFastq.xml bedpeToBam.xml closestBed.xml clusterBed.xml complementBed.xml coverageBed.xml expandBed.xml flankbed.xml genomeCoverageBed_bedgraph.xml genomeCoverageBed_histogram.xml getfastaBed.xml groupbyBed.xml intersectBed.xml intersectBed_bam_obsolete.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 subtractBed.xml tagBed.xml unionBedGraphs.xml windowBed.xml
diffstat 38 files changed, 76 insertions(+), 239 deletions(-) [+]
line wrap: on
line diff
--- a/Bed12ToBed6.xml	Wed Jun 18 15:07:04 2014 -0400
+++ b/Bed12ToBed6.xml	Thu Jun 19 10:12:00 2014 -0400
@@ -1,4 +1,4 @@
-<tool id="bedtools_bed12tobed6" name="Convert from BED12 to BED6" version="0.1.0">
+<tool id="bedtools_bed12tobed6" name="Convert from BED12 to BED6" version="@WRAPPER_VERSION@.0">
     <description></description>
     <macros>
         <import>macros.xml</import>
@@ -9,7 +9,6 @@
         bed12ToBed16
         -i '$input'
         &gt; '$output'
-
     </command>
     <inputs>
         <param format="bed" name="input" type="data" label="Convert the following BED12 file to BED6"/>
--- a/BedToBam.xml	Wed Jun 18 15:07:04 2014 -0400
+++ b/BedToBam.xml	Thu Jun 19 10:12:00 2014 -0400
@@ -1,4 +1,4 @@
-<tool id="bedtools_bedtobam" name="Convert from BED to BAM" version="0.1.0">
+<tool id="bedtools_bedtobam" name="Convert from BED to BAM" version="@WRAPPER_VERSION@.0">
     <description></description>
     <macros>
         <import>macros.xml</import>
@@ -12,14 +12,12 @@
         -mapq $mapq
         -i '$input'
         &gt; '$output'
-
     </command>
     <inputs>
         <param format="bed" name="input" type="data" label="Convert the following BED file to BAM"/>
         <param name="bed12" type="boolean" label="Indicate that the input BED file is in BED12 (a.k.a “blocked” BED) format" truevalue="-bed12" falsevalue="" checked="false" help="If Selected, bedToBam will convert blocked BED features (e.g., gene annotaions) into “spliced” BAM alignments by creating an appropriate CIGAR string.."/>
         <param name="mapq" type="integer" label="Set a mapping quality (SAM MAPQ field) value for all BED entries" value="255" />
         <param name="ubam" type="boolean" label="Write uncompressed BAM output." truevalue="-ubam" falsevalue="" checked="false"/>
-
     </inputs>
     <outputs>
         <data format="bam" name="output" metadata_source="input" label="${input.name} (as BAM)"/>
--- a/annotateBed.xml	Wed Jun 18 15:07:04 2014 -0400
+++ b/annotateBed.xml	Thu Jun 19 10:12:00 2014 -0400
@@ -1,4 +1,4 @@
-<tool id="bedtools_annotatebed" name="AnnotateBed" version="0.2.0">
+<tool id="bedtools_annotatebed" name="AnnotateBed" version="@WRAPPER_VERSION@.0">
     <description></description>
     <macros>
         <import>macros.xml</import>
@@ -14,10 +14,10 @@
         #end for
 
         #if $names.names_select == 'yes':
-        -names
-        #for $bed in $names.beds:
-            $bed.inputName
-        #end for
+            -names
+            #for $bed in $names.beds:
+                $bed.inputName
+            #end for
         #end if
         $strand
         $counts
--- a/bamToBed.xml	Wed Jun 18 15:07:04 2014 -0400
+++ b/bamToBed.xml	Thu Jun 19 10:12:00 2014 -0400
@@ -1,4 +1,4 @@
-<tool id="bedtools_bamtobed" name="Convert from BAM to BED" version="0.2.0">
+<tool id="bedtools_bamtobed" name="Convert from BAM to BED" version="@WRAPPER_VERSION@.0">
     <description></description>
     <macros>
         <import>macros.xml</import>
@@ -12,7 +12,7 @@
         -i '$input'
         &gt; '$output'
         #if str($tag):
-          -tag      $tag
+          -tag $tag
         #end if
     </command>
     <inputs>
--- a/bamToFastq.xml	Wed Jun 18 15:07:04 2014 -0400
+++ b/bamToFastq.xml	Thu Jun 19 10:12:00 2014 -0400
@@ -1,4 +1,4 @@
-<tool id="bedtools_bamtofastq" name="Convert from BAM to FastQ" version="0.2.0">
+<tool id="bedtools_bamtofastq" name="Convert from BAM to FastQ" version="@WRAPPER_VERSION@.0">
     <description></description>
     <macros>
         <import>macros.xml</import>
--- a/bedpeToBam.xml	Wed Jun 18 15:07:04 2014 -0400
+++ b/bedpeToBam.xml	Thu Jun 19 10:12:00 2014 -0400
@@ -1,4 +1,4 @@
-<tool id="bedtools_bedpetobam" name="Convert from BEDPE to BAM" version="0.1.0">
+<tool id="bedtools_bedpetobam" name="Convert from BEDPE to BAM" version="@WRAPPER_VERSION@.0">
     <description></description>
     <macros>
         <import>macros.xml</import>
@@ -12,14 +12,12 @@
         -i '$input'
         -g $genome
         &gt; '$output'
-
     </command>
     <inputs>
         <param format="bed,gff,vcf" name="input" type="data" label="BED/VCF/GFF file"/>
         <expand macro="genome" />
         <param name="mapq" type="integer" label="Set a mapping quality (SAM MAPQ field) value for all BED entries" value="255" />
         <param name="ubam" type="boolean" label="Write uncompressed BAM output." truevalue="-ubam" falsevalue="" checked="false"/>
-
     </inputs>
     <outputs>
         <data format="bam" name="output" metadata_source="input" label="${input.name} (as BAM)"/>
--- a/closestBed.xml	Wed Jun 18 15:07:04 2014 -0400
+++ b/closestBed.xml	Thu Jun 19 10:12:00 2014 -0400
@@ -1,4 +1,4 @@
-<tool id="bedtools_closestbed" name="ClosestBed" version="0.2.0">
+<tool id="bedtools_closestbed" name="ClosestBed" version="@WRAPPER_VERSION@.0">
     <description></description>
     <macros>
         <import>macros.xml</import>
@@ -35,6 +35,7 @@
 **What it does**
 
 Similar to intersectBed, closestBed searches for overlapping features in A and B. In the event that no feature in B overlaps the current feature in A, closestBed will report the closest (that is, least genomic distance from the start or end of A) feature in B. For example, one might want to find which is the closest gene to a significant GWAS polymorphism. Note that closestBed will report an overlapping feature as the closest—that is, it does not restrict to closest non-overlapping feature.
+
 @REFERENCES@
     </help>
 </tool>
--- a/clusterBed.xml	Wed Jun 18 15:07:04 2014 -0400
+++ b/clusterBed.xml	Thu Jun 19 10:12:00 2014 -0400
@@ -1,4 +1,4 @@
-<tool id="bedtools_clusterbed" name="ClusterBed" version="0.2.0">
+<tool id="bedtools_clusterbed" name="ClusterBed" version="@WRAPPER_VERSION@.0">
     <description></description>
     <macros>
         <import>macros.xml</import>
@@ -14,9 +14,11 @@
     </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." 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" help="Default is 0. That is, overlapping and/or book-ended features are clustered." />
+        <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" 
+            help="Default is 0. That is, overlapping and/or book-ended features are clustered." />
     </inputs>
     <outputs>
         <data format_source="inputA" name="output" metadata_source="inputA" label=""/>
--- a/complementBed.xml	Wed Jun 18 15:07:04 2014 -0400
+++ b/complementBed.xml	Thu Jun 19 10:12:00 2014 -0400
@@ -1,4 +1,4 @@
-<tool id="bedtools_complementbed" name="ComplementBed" version="0.2.0">
+<tool id="bedtools_complementbed" name="ComplementBed" version="@WRAPPER_VERSION@.0">
     <description></description>
     <macros>
         <import>macros.xml</import>
--- a/coverageBed.xml	Wed Jun 18 15:07:04 2014 -0400
+++ b/coverageBed.xml	Thu Jun 19 10:12:00 2014 -0400
@@ -1,4 +1,4 @@
-<tool id="bedtools_coveragebed" name="Compute both the depth and breadth of coverage" version="0.2.0">
+<tool id="bedtools_coveragebed" name="Compute both the depth and breadth of coverage" version="@WRAPPER_VERSION@.0">
     <description>of features in file A across the features in file B (coverageBed)</description>
     <macros>
         <import>macros.xml</import>
--- a/expandBed.xml	Wed Jun 18 15:07:04 2014 -0400
+++ b/expandBed.xml	Thu Jun 19 10:12:00 2014 -0400
@@ -1,4 +1,4 @@
-<tool id="bedtools_expandbed" name="ExpandBed" version="0.2.0">
+<tool id="bedtools_expandbed" name="ExpandBed" version="@WRAPPER_VERSION@.0">
     <description></description>
     <macros>
         <import>macros.xml</import>
--- a/flankbed.xml	Wed Jun 18 15:07:04 2014 -0400
+++ b/flankbed.xml	Thu Jun 19 10:12:00 2014 -0400
@@ -1,4 +1,4 @@
-<tool id="bedtools_flankbed" name="FlankBed" version="0.2.0">
+<tool id="bedtools_flankbed" name="FlankBed" version="@WRAPPER_VERSION@.0">
     <description></description>
     <macros>
         <import>macros.xml</import>
@@ -11,13 +11,15 @@
         $strand
         -g $genome
         -i $inputA
-        &gt; $output
+
         #if $addition.addition_select == 'b':
-        -b $addition.b
+            -b $addition.b
         #else:
-        -l $addition.l
-        -r $addition.r
+            -l $addition.l
+            -r $addition.r
         #end if
+
+        &gt; $output
     </command>
     <inputs>
         <param format="bed,vcf,gff,gff3" name="inputA" type="data" label="BED/VCF/GFF file"/>
@@ -25,8 +27,6 @@
         <param name="pct" type="boolean" checked="false" truevalue="-pct" falsevalue="" label="Define -l and -r as a fraction of the feature’s length" help="E.g. if used on a 1000bp feature, -l 0.50, will add 500 bp “upstream”" />
         <param name="strand" type="boolean" checked="false" truevalue="-s" falsevalue="" label="Define -l and -r based on strand" help="For example. if used, -l 500 for a negative-stranded feature, it will add 500 bp to the end coordinate" />
         <expand macro="addition" />
-
-        
     </inputs>
     <outputs>
         <data format="bed" name="output"  label=""/>
--- a/genomeCoverageBed_bedgraph.xml	Wed Jun 18 15:07:04 2014 -0400
+++ b/genomeCoverageBed_bedgraph.xml	Thu Jun 19 10:12:00 2014 -0400
@@ -1,4 +1,4 @@
-<tool id="bedtools_genomecoveragebed_bedgraph" name="Create a BedGraph of genome coverage" version="0.2.0">
+<tool id="bedtools_genomecoveragebed_bedgraph" name="Create a BedGraph of genome coverage" version="@WRAPPER_VERSION@.0">
     <description>
     </description>
     <macros>
@@ -45,23 +45,6 @@
     <outputs>
         <data format="bedgraph" name="output"  metadata_source="input" label="${input.name} (Genome Coverage BedGraph)" />
     </outputs>
-
-$ cat A.bed
-chr1  10  20
-chr1  20  30
-chr2  0   500
-
-$ cat my.genome
-chr1  1000
-chr2  500
-
-$ bedtools genomecov -i A.bed -g my.genome
-chr1   0  980  1000  0.98
-chr1   1  20   1000  0.02
-chr2   1  500  500   1
-genome 0  980  1500  0.653333
-genome 1  520  1500  0.346667
-
     <help>
 
 
--- a/genomeCoverageBed_histogram.xml	Wed Jun 18 15:07:04 2014 -0400
+++ b/genomeCoverageBed_histogram.xml	Thu Jun 19 10:12:00 2014 -0400
@@ -1,4 +1,4 @@
-<tool id="bedtools_genomecoveragebed_histogram" name="Create a histogram of genome coverage" version="0.2.0">
+<tool id="bedtools_genomecoveragebed_histogram" name="Create a histogram of genome coverage" version="@WRAPPER_VERSION@.0">
     <description>
     </description>
     <macros>
--- a/getfastaBed.xml	Wed Jun 18 15:07:04 2014 -0400
+++ b/getfastaBed.xml	Thu Jun 19 10:12:00 2014 -0400
@@ -1,4 +1,4 @@
-<tool id="bedtools_getfastabed" name="GetFastaBed" version="0.2.0">
+<tool id="bedtools_getfastabed" name="GetFastaBed" version="@WRAPPER_VERSION@.0">
     <description></description>
     <macros>
         <import>macros.xml</import>
--- a/groupbyBed.xml	Wed Jun 18 15:07:04 2014 -0400
+++ b/groupbyBed.xml	Thu Jun 19 10:12:00 2014 -0400
@@ -1,4 +1,4 @@
-<tool id="bedtools_groupbybed" name="GroupByBed" version="0.2.0">
+<tool id="bedtools_groupbybed" name="GroupByBed" version="@WRAPPER_VERSION@.0">
     <description></description>
     <macros>
         <import>macros.xml</import>
@@ -21,17 +21,12 @@
             <option value="sum" selected="True">Sum - numeric only</option>
             <option value="stdev">Stdev - numeric only</option>
             <option value="sstdev">Sstdev - numeric only</option>
-            <option value="freqasc">Freqasc - print a comma separated list of values observed and the number of times they were observed.
-Reported in ascending order of frequency*
-</option>
-            <option value="freqdesc">Freqdesc - - print a comma separated list of values observed and the number of times they were observed.
-Reported in descending order of frequency*
-</option>
+            <option value="freqasc">Freqasc - print a comma separated list of values observed and the number of times they were observed. Reported in ascending order of frequency*</option>
+            <option value="freqdesc">Freqdesc - - print a comma separated list of values observed and the number of times they were observed. Reported in descending order of frequency*</option>
             <option value="first">First - numeric or text</option>
             <option value="last">Last - numeric or text</option>
             <expand macro="math_options" />
             <expand macro="additional_math_options" />
-            
         </param>
     </inputs>
     <outputs>
--- a/intersectBed.xml	Wed Jun 18 15:07:04 2014 -0400
+++ b/intersectBed.xml	Thu Jun 19 10:12:00 2014 -0400
@@ -1,4 +1,4 @@
-<tool id="bedtools_intersectbed" name="Intersect interval files" version="0.2.0">
+<tool id="bedtools_intersectbed" name="Intersect interval files" version="@WRAPPER_VERSION@.0">
     <description></description>
     <macros>
         <import>macros.xml</import>
--- a/intersectBed_bam_obsolete.xml	Wed Jun 18 15:07:04 2014 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,135 +0,0 @@
-<tool id="bedtools_intersectBed" name="intersectBed">
-  <description>reports overlaps between two feature files.</description>
-	<requirements>
-	<requirement type="package">bedtools</requirement>
-        <requirement type="binary">intersectBed</requirement>
-    </requirements>  
-  <command>intersectBed 
-#if $intype.inselect == "bam"
--abam $intype.inputBam -b $input $intype.bed
-#else
--a $intype.inputBed -b $input
-#end if
-#if $outputopt.showoutputopt == "yes"
-$outputopt.wa $outputopt.wb $outputopt.wo $outputopt.wao $outputopt.u $outputopt.c $outputopt.v 
-#end if
-#if $overlapopt.showoverlapopt == "yes"
-	#if str($overlapopt.f.value) != "None" 
-	-f $overlapopt.f
-	#end if
-$overlapopt.r $overlapopt.s
-#end if
-$split
-> $output
-  </command>
-  <inputs>	
-    	<conditional name="intype">
-		<param name="inselect" type="select" label="Select input file type">
-			<option value="bed" selected="true">BED, GFF</option>
-			<option value="bam">BAM</option>
-		</param>
-		<when value="bed">
-			<param name="inputBed" type="data" format="bed,gff" label="Input A" help="Each feature in A is compared to B in search of overlaps."/>
-		</when>
-		<when value="bam">
-			<param name="inputBam" type="data" format="bam" label="Input A" help="Each BAM alignment in A is compared to B in search of overlaps."/>
-			<param name="bed" type="boolean" truevalue="-bed" falsevalue="" checked="False" label="Write output as BED" help="The default is to write output in BAM when using BAM as input."/>
-		</when>
-	</conditional>
-
-	<param name="input" type="data" format="bed" label="Input B"/>
-
-	<conditional name="outputopt">
-		<param name="showoutputopt" type="select" label="Show output options">
-			<option value="no" selected="true">No</option>
-			<option value="yes">Yes</option>
-		</param>
-		<when value="yes">s
-    <param name="wa" type="boolean" truevalue="-wa" falsevalue="" checked="False" label="Write the original entry in A for each overlap"/>
-    <param name="wb" type="boolean" truevalue="-wb" falsevalue="" checked="False" label="Write the original entry in B for each overlap" help="Useful for knowing what A overlaps."/>
-    <param name="wo" type="boolean" truevalue="-wo" falsevalue="" checked="False" label="Write the original A and B entries plus the number of base pairs of overlap between the two features"/>
-    <param name="wao" type="boolean" truevalue="-wao" falsevalue="" checked="False" label="Write the original A and B entries plus the number of base pairs of overlap between the two features. However, A features without overlap are also reported with a NULL B feature and overlap = 0"/>
-
-    <param name="u" type="boolean" truevalue="-u" falsevalue="" checked="False" label="Write original A entry once if any overlaps found in B" help="Frequently a feature in &quot;A&quot; will overlap with multiple features in &quot;B&quot;. By default, intersectBed will report each overlap as a separate output line. However, one may want to simply know that there is at least one overlap (or none). When one uses this option, &quot;A&quot; features that overlap with one or more &quot;B&quot; features are reported once. Those that overlap with no &quot;B&quot; features are not reported at all."/>
-
-    <param name="c" type="boolean" truevalue="-c" falsevalue="" checked="False" label="For each entry in A, report the number of hits in B while restricting to the minimum overlap fraction. Reports 0 for A entries that have no overlap with B" help="Reports a column after each &quot;A&quot; feature indicating the number (0 or more) of overlapping features found in &quot;B&quot;."/>
-
-    <param name="v" type="boolean" truevalue="-v" falsevalue="" checked="False" label="Only report those entries in A that have no overlap in B"/>
-		</when>
-		<when value="no"/>
-	</conditional>
-
-	<conditional name="overlapopt">
-		<param name="showoverlapopt" type="select" label="Show options for overlap definition">
-			<option value="no" selected="true">No</option>
-			<option value="yes">Yes</option>
-		</param>
-		<when value="yes">
-    <param name="f" type="float" min="0" max="1" value="" optional="true" label="Minimum overlap required as a fraction of A" help="By default, intersectBed will report an overlap between A and B so long as there is at least one base pair is overlapping. Yet sometimes you may want to restrict reported overlaps between A and B to cases where the feature in B overlaps at least X% (e.g. 50%) of the A feature. This option does exactly this. Default is 1E-9 (i.e. 1bp)."/>
-    <param name="r" type="boolean" truevalue="-r" falsevalue="" checked="False" label="Require that the fraction of overlap be reciprocal for A and B" help="In other words, if the minimum overlap fraction is 0.90 and this option is used, it requires that B overlap at least 90% of A and that A also overlaps at least 90% of B."/>
-   <param name="s" type="boolean" truevalue="-s" falsevalue="" checked="False" label="Force &quot;strandedness&quot;" help="That is, only report hits in B that overlap A on the same strand. By default, overlaps are reported without respect to strand."/>
-		</when>
-		<when value="no"/>
-	</conditional>
-	<param name="split" type="boolean" truevalue="-split" falsevalue="" checked="false" label="Treat &quot;split&quot; BAM (i.e., having an &quot;N&quot; CIGAR operation) or BED12 entries as distinct BED intervals"/>
-
-
-
-
-
-
-
-
-
-
-
-
-
-  </inputs>
-  <outputs>
-    	<data name="output" format="bed">
-	<change_format>
-		<when input="intype.bed" value="" format="bam"/>
-	</change_format>
-	</data>
-  </outputs>
-  
-  <help>
-
-**What it does**
-
-By far, the most common question asked of two sets of genomic features is whether or not any of the
-features in the two sets &quot;overlap&quot; with one another. This is known as feature intersection. intersectBed
-allows one to screen for overlaps between two sets of genomic features. Moreover, it allows one to have
-fine control as to how the intersections are reported. intersectBed works with both BED/GFF
-and BAM files as input.
-
-By default, if an overlap is found, intersectBed reports the shared interval between the two
-overlapping features.
-
-
-**Default behavior when using BAM input**
-
-When comparing alignments in BAM format to features in BED format, intersectBed
-will, by default, write the output in BAM format. That is, each alignment in the BAM file that meets
-the user's criteria will be written in BAM format. This serves as a mechanism to
-create subsets of BAM alignments are of biological interest, etc. Note that only the mate in the BAM
-alignment is compared to the BED file. Thus, if only one end of a paired-end sequence overlaps with a
-feature in B, then that end will be written to the BAM output. By contrast, the other mate for the
-pair will not be written. One should use pairToBed if one wants each BAM alignment
-for a pair to be written to BAM output.
-
-
-**Output BED format when using BAM input**
-
-When comparing alignments in BAM format to features in BED format, intersectBed
-will optionally write the output in BED format. That is, each alignment in the BAM file is converted
-to a 6 column BED feature and if overlaps are found (or not) based on the user's criteria, the BAM
-alignment will be reported in BED format. The BED &quot;name&quot; field is comprised of the RNAME field in
-the BAM alignment. If mate information is available, the mate (e.g., &quot;/1&quot; or &quot;/2&quot;) field will be
-appended to the name. The &quot;score&quot; field is the mapping quality score from the BAM alignment.
-
-
-  </help>
-
-</tool>
--- a/jaccardBed.xml	Wed Jun 18 15:07:04 2014 -0400
+++ b/jaccardBed.xml	Thu Jun 19 10:12:00 2014 -0400
@@ -1,4 +1,4 @@
-<tool id="bedtools_jaccard" name="JaccardBed" version="0.2.0">
+<tool id="bedtools_jaccard" name="JaccardBed" version="@WRAPPER_VERSION@.0">
     <description></description>
     <macros>
         <import>macros.xml</import>
@@ -35,6 +35,7 @@
 
 By default, bedtools jaccard reports the length of the intersection, the length of the union (minus the intersection), the final Jaccard statistic reflecting the similarity of the two sets, as well as the number of intersections.
 Whereas the bedtools intersect tool enumerates each an every intersection between two sets of genomic intervals, one often needs a single statistic reflecting the similarity of the two sets based on the intersections between them. The Jaccard statistic is used in set theory to represent the ratio of the intersection of two sets to the union of the two sets. Similarly, Favorov et al [1] reported the use of the Jaccard statistic for genome intervals: specifically, it measures the ratio of the number of intersecting base pairs between two sets to the number of base pairs in the union of the two sets. The bedtools jaccard tool implements this statistic, yet modifies the statistic such that the length of the intersection is subtracted from the length of the union. As a result, the final statistic ranges from 0.0 to 1.0, where 0.0 represents no overlap and 1.0 represent complete overlap.
+
 .. image:: $PATH_TO_IMAGES/jaccard-glyph.png
 
 .. class:: warningmark
--- a/linksBed.xml	Wed Jun 18 15:07:04 2014 -0400
+++ b/linksBed.xml	Thu Jun 19 10:12:00 2014 -0400
@@ -1,4 +1,4 @@
-<tool id="bedtools_links" name="LinksBed" version="0.1.0">
+<tool id="bedtools_links" name="LinksBed" version="@WRAPPER_VERSION@.0">
     <description></description>
     <macros>
         <import>macros.xml</import>
--- a/macros.xml	Wed Jun 18 15:07:04 2014 -0400
+++ b/macros.xml	Thu Jun 19 10:12:00 2014 -0400
@@ -1,4 +1,11 @@
 <macros>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="2.19.1">bedtools</requirement>
+        </requirements>
+        <version_command>bedtools --version</version_command>
+    </xml>
+    <token name="@WRAPPER_VERSION@">2.19</token>
     <xml name="stdio">
         <stdio>
             <!-- Anything other than zero is an error -->
@@ -29,14 +36,9 @@
         </conditional>
     </xml>
     <xml name="split">
-        <param name="split" type="boolean" checked="true" truevalue="-split" falsevalue="" label="Treat split/spliced BAM or BED12 entries as distinct BED intervals when computing coverage." help="If set, the coverage will be calculated based the spliced intervals only. For BAM files, this inspects the CIGAR N operation to infer the blocks for computing coverage. For BED12 files, this inspects the BlockCount, BlockStarts, and BlockEnds fields (i.e., columns 10,11,12). If this option is not set, coverage will be calculated based on the interval's START/END coordinates, and would include introns in the case of RNAseq data." />
-
-    </xml>
-    <xml name="requirements">
-        <requirements>
-            <requirement type="package" version="2.19.1">bedtools</requirement>
-        </requirements>
-        <version_command>bedtools --version</version_command>
+        <param name="split" type="boolean" checked="true" truevalue="-split" falsevalue="" 
+            label="Treat split/spliced BAM or BED12 entries as distinct BED intervals when computing coverage." 
+            help="If set, the coverage will be calculated based the spliced intervals only. For BAM files, this inspects the CIGAR N operation to infer the blocks for computing coverage. For BED12 files, this inspects the BlockCount, BlockStarts, and BlockEnds fields (i.e., columns 10,11,12). If this option is not set, coverage will be calculated based on the interval's START/END coordinates, and would include introns in the case of RNAseq data." />
     </xml>
     <xml name="genome">
         <param format="bed,vcf,gff,gff3" name="genome" type="data" label="Genome file" />
@@ -51,8 +53,8 @@
                 <param name="b" label="Give Value" type="integer" value="0"  />
             </when>
             <when value="lr">
-                <param name="l" label="The number of base pairs to subtract from the start coordinate" type="integer" value="0"  />
-                <param name="r" label="The number of base pairs to add to the end coordinate" type="integer" value="0"  />
+                <param name="l" label="The number of base pairs to subtract from the start coordinate" type="integer" value="0" />
+                <param name="r" label="The number of base pairs to add to the end coordinate" type="integer" value="0" />
             </when>
         </conditional>
     </xml>
@@ -71,9 +73,6 @@
             <option value="distinct">distinct (i.e., print a comma separated list) - numeric or text</option>
             <option value="concat">concat (i.e., print a comma separated list) - numeric or text</option>
     </xml>
-
-
-
     <token name="@REFERENCES@">
 ------
 
--- a/makewindowsBed.xml	Wed Jun 18 15:07:04 2014 -0400
+++ b/makewindowsBed.xml	Thu Jun 19 10:12:00 2014 -0400
@@ -1,4 +1,4 @@
-<tool id="bedtools_makewindowsbed" name="MakeWindowsBed" version="0.2.0">
+<tool id="bedtools_makewindowsbed" name="MakeWindowsBed" version="@WRAPPER_VERSION@.0">
     <description></description>
     <macros>
         <import>macros.xml</import>
--- a/mapBed.xml	Wed Jun 18 15:07:04 2014 -0400
+++ b/mapBed.xml	Thu Jun 19 10:12:00 2014 -0400
@@ -1,4 +1,4 @@
-<tool id="bedtools_map" name="MapBed" version="0.2.0">
+<tool id="bedtools_map" name="MapBed" version="@WRAPPER_VERSION@.0">
     <description></description>
     <macros>
         <import>macros.xml</import>
--- a/maskFastaBed.xml	Wed Jun 18 15:07:04 2014 -0400
+++ b/maskFastaBed.xml	Thu Jun 19 10:12:00 2014 -0400
@@ -1,4 +1,4 @@
-<tool id="bedtools_maskfastabed" name="MaskFastaBed" version="0.2.0">
+<tool id="bedtools_maskfastabed" name="MaskFastaBed" version="@WRAPPER_VERSION@.0">
     <description></description>
     <macros>
         <import>macros.xml</import>
--- a/mergeBed.xml	Wed Jun 18 15:07:04 2014 -0400
+++ b/mergeBed.xml	Thu Jun 19 10:12:00 2014 -0400
@@ -1,4 +1,4 @@
-<tool id="bedtools_mergebed" name="Merge BED files" version="0.1.0">
+<tool id="bedtools_mergebed" name="Merge BED files" version="@WRAPPER_VERSION@.0">
     <description>(mergeBed)</description>
     <macros>
         <import>macros.xml</import>
--- a/multiCov.xml	Wed Jun 18 15:07:04 2014 -0400
+++ b/multiCov.xml	Thu Jun 19 10:12:00 2014 -0400
@@ -1,4 +1,4 @@
-<tool id="bedtools_multicovtbed" name="MultiCovBed" version="0.2.0">
+<tool id="bedtools_multicovtbed" name="MultiCovBed" version="@WRAPPER_VERSION@.0">
     <description></description>
     <macros>
         <import>macros.xml</import>
--- a/multiIntersectBed.xml	Wed Jun 18 15:07:04 2014 -0400
+++ b/multiIntersectBed.xml	Thu Jun 19 10:12:00 2014 -0400
@@ -1,4 +1,4 @@
-<tool id="bedtools_multiintersectbed" name="Intersect multiple sorted BED files" version="0.2.0">
+<tool id="bedtools_multiintersectbed" name="Intersect multiple sorted BED files" version="@WRAPPER_VERSION@.0">
     <description></description>
     <macros>
         <import>macros.xml</import>
--- a/nucBed.xml	Wed Jun 18 15:07:04 2014 -0400
+++ b/nucBed.xml	Thu Jun 19 10:12:00 2014 -0400
@@ -1,4 +1,4 @@
-<tool id="bedtools_nucbed" name="NucBed" version="0.2.0">
+<tool id="bedtools_nucbed" name="NucBed" version="@WRAPPER_VERSION@.0">
     <description></description>
     <macros>
         <import>macros.xml</import>
--- a/overlapBed.xml	Wed Jun 18 15:07:04 2014 -0400
+++ b/overlapBed.xml	Thu Jun 19 10:12:00 2014 -0400
@@ -1,4 +1,4 @@
-<tool id="bedtools_overlapbed" name="OverlapBed" version="0.2.0">
+<tool id="bedtools_overlapbed" name="OverlapBed" version="@WRAPPER_VERSION@.0">
     <description></description>
     <macros>
         <import>macros.xml</import>
--- a/randomBed.xml	Wed Jun 18 15:07:04 2014 -0400
+++ b/randomBed.xml	Thu Jun 19 10:12:00 2014 -0400
@@ -1,4 +1,4 @@
-<tool id="bedtools_randombed" name="RandomBed" version="0.2.0">
+<tool id="bedtools_randombed" name="RandomBed" version="@WRAPPER_VERSION@.0">
     <description></description>
     <macros>
         <import>macros.xml</import>
@@ -22,7 +22,6 @@
     </inputs>
     <outputs>
         <data format="bed" name="output" />
-        
     </outputs>
     <help>
 
--- a/reldist.xml	Wed Jun 18 15:07:04 2014 -0400
+++ b/reldist.xml	Thu Jun 19 10:12:00 2014 -0400
@@ -1,4 +1,4 @@
-<tool id="bedtools_reldistbed" name="ReldistBed" version="0.2.0">
+<tool id="bedtools_reldistbed" name="ReldistBed" version="@WRAPPER_VERSION@.0">
     <description></description>
     <macros>
         <import>macros.xml</import>
@@ -14,7 +14,6 @@
     <inputs>
         <param format="bed,bam,vcf,gff,gff3" name="inputA" type="data" label="BED/VCF/GFF/BAM file"/>
         <param format="bed,gff,vcf,gff3" name="inputB" type="data" label="BED/VCF/GFF file"/>
-
         <param name="detail" type="boolean" checked="false" truevalue="-detail" falsevalue="" label="Instead of a summary, report the relative distance for each interval in A" help="" />
     </inputs>
     <outputs>
@@ -25,10 +24,9 @@
 **What it does**
 
 Traditional approaches to summarizing the similarity between two sets of genomic intervals are based upon the number or proportion of intersecting intervals. However, such measures are largely blind to spatial correlations between the two sets where, dpesite consistent spacing or proximity, intersections are rare (for example, enhancers and transcription start sites rarely overlap, yet they are much closer to one another than two sets of random intervals). Favorov et al [1] proposed a relative distance metric that describes distribution of relative distances between each interval in one set nd the two closest intervals in another set (see figure above). If there is no spatial correlation between the two sets, one would expect the relative distances to be uniformaly distributed among the relative distances ranging from 0 to 0.5. If, however, the intervals tend to be much closer than expected by chance, the distribution of observed relative distances would be shifted towards low relative distance values (e.g., the figure below).
+
 .. image:: $PATH_TO_IMAGES/reldist-glyph.png
 
-
-.. image:: $PATH_TO_IMAGES/reldist-plot.png
 .. class:: infomark
 
 @REFERENCES@
--- a/shuffleBed.xml	Wed Jun 18 15:07:04 2014 -0400
+++ b/shuffleBed.xml	Thu Jun 19 10:12:00 2014 -0400
@@ -1,4 +1,4 @@
-<tool id="bedtools_shufflebed" name="ShuffleBed" version="0.2.0">
+<tool id="bedtools_shufflebed" name="ShuffleBed" version="@WRAPPER_VERSION@.0">
     <description></description>
     <macros>
         <import>macros.xml</import>
@@ -47,15 +47,14 @@
             </when>
         </conditional>
         
-        <param name="chromfirst" type="boolean" label="Instead of choosing a position randomly among the entire genome (the default), first choose a chrom randomly, and then choose a random start coordinate on that chrom. This leads to features being ~uniformly distributed among the chroms, as opposed to features being distribute as a function of chrom size" selected="False" truevalue="-chromFirst" falsevalue="" />
-
+        <param name="chromfirst" type="boolean" selected="False" truevalue="-chromFirst" falsevalue="" 
+            label="Instead of choosing a position randomly among the entire genome (the default), first choose a chrom randomly, and then choose a random start coordinate on that chrom. This leads to features being ~uniformly distributed among the chroms, as opposed to features being distribute as a function of chrom size" />
         <param name="maxtries" type="integer" value="1000" label="Max. number of attempts to find a home for a shuffled interval in the presence of -incl or -excl" />
-        <param name="nooverlap" type="boolean" label="Don’t allow shuffled intervals to overlap" selected="False" truevalue="-noOverlapping" falsevalue="" />
-        <param name="allowBeyond" type="boolean" label="Allow the original the length of the original records to extebd beyond the length of the chromosome." selected="False" truevalue="-allowBeyondChromEnd" falsevalue="" />
+        <param name="nooverlap" type="boolean" selected="False" truevalue="-noOverlapping" falsevalue="" label="Don’t allow shuffled intervals to overlap" />
+        <param name="allowBeyond" type="boolean" selected="False" truevalue="-allowBeyondChromEnd" falsevalue="" label="Allow the original the length of the original records to extebd beyond the length of the chromosome." />
     </inputs>
     <outputs>
         <data format="bed" name="output" />
-        
     </outputs>
     <help>
 
--- a/slopBed.xml	Wed Jun 18 15:07:04 2014 -0400
+++ b/slopBed.xml	Thu Jun 19 10:12:00 2014 -0400
@@ -1,4 +1,4 @@
-<tool id="bedtools_slopbed" name="SlopBed" version="0.2.0">
+<tool id="bedtools_slopbed" name="SlopBed" version="@WRAPPER_VERSION@.0">
     <description></description>
     <macros>
         <import>macros.xml</import>
@@ -20,7 +20,6 @@
         $header
 
         &gt; $output
-        
     </command>
     <inputs>
         <param format="bed,vcf,gff,gff3" name="inputA" type="data" label="BED/VCF/GFF file"/>
@@ -29,7 +28,6 @@
         <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" />
         <expand macro="addition" />
         <param name="header" type="boolean" checked="false" truevalue="-header" falsevalue="" label="Print the header from the input file prior to results." />
-        
     </inputs>
     <outputs>
         <data format="bed" name="output" label=""/>
@@ -39,6 +37,7 @@
 **What it does**
 
 bedtools slop will increase the size of each feature in a feature file by a user-defined number of bases. While something like this could be done with an awk '{OFS="\t" print $1,$2-&lt;slop>,$3+&lt;slop>}', bedtools slop will restrict the resizing to the size of the chromosome (i.e. no start &lt; 0 and no end > chromosome size).
+
 .. image:: $PATH_TO_IMAGES/slop-glyph.png
 
 .. class:: warningmark
--- a/sortBed.xml	Wed Jun 18 15:07:04 2014 -0400
+++ b/sortBed.xml	Thu Jun 19 10:12:00 2014 -0400
@@ -1,4 +1,4 @@
-<tool id="bedtools_sortbed" name="Sort BED files" version="0.2.0">
+<tool id="bedtools_sortbed" name="Sort BED files" version="@WRAPPER_VERSION@.0">
     <description></description>
     <macros>
         <import>macros.xml</import>
--- a/subtractBed.xml	Wed Jun 18 15:07:04 2014 -0400
+++ b/subtractBed.xml	Thu Jun 19 10:12:00 2014 -0400
@@ -1,4 +1,4 @@
-<tool id="bedtools_subtractbed" name="SubtractBed" version="0.2.0">
+<tool id="bedtools_subtractbed" name="SubtractBed" version="@WRAPPER_VERSION@.0">
     <description></description>
     <macros>
         <import>macros.xml</import>
@@ -42,6 +42,7 @@
 bedtools subtract searches for features in B that overlap A. If an overlapping feature is found in B, the overlapping portion is removed from A and the remaining portion of A is reported. If a feature in B overlaps all of a feature in A, the A feature will not be reported.
 
 .. image:: $PATH_TO_IMAGES/subtract-glyph.png
+
 @REFERENCES@
     </help>
 </tool>
--- a/tagBed.xml	Wed Jun 18 15:07:04 2014 -0400
+++ b/tagBed.xml	Thu Jun 19 10:12:00 2014 -0400
@@ -1,4 +1,4 @@
-<tool id="bedtools_tagbed" name="TagBed" version="0.2.0">
+<tool id="bedtools_tagbed" name="TagBed" version="@WRAPPER_VERSION@.0">
     <description></description>
     <macros>
         <import>macros.xml</import>
@@ -35,7 +35,6 @@
             <option value="-labels -intervals">Intervals</option>
         </param>
     </inputs>
-
     <outputs>
         <data format="bed" name="output" label="" />
     </outputs>
--- a/unionBedGraphs.xml	Wed Jun 18 15:07:04 2014 -0400
+++ b/unionBedGraphs.xml	Thu Jun 19 10:12:00 2014 -0400
@@ -1,4 +1,4 @@
-<tool id="bedtools_mergebedgraph" name="Merge BedGraph files" version="0.2.0">
+<tool id="bedtools_mergebedgraph" name="Merge BedGraph files" version="@WRAPPER_VERSION@.0">
     <description></description>
     <macros>
         <import>macros.xml</import>
--- a/windowBed.xml	Wed Jun 18 15:07:04 2014 -0400
+++ b/windowBed.xml	Thu Jun 19 10:12:00 2014 -0400
@@ -1,4 +1,4 @@
-<tool id="bedtools_windowbed" name="WindowBed" version="0.2.0">
+<tool id="bedtools_windowbed" name="WindowBed" version="@WRAPPER_VERSION@.0">
     <description></description>
     <macros>
         <import>macros.xml</import>
@@ -68,6 +68,7 @@
 Similar to bedtools intersect, window searches for overlapping features in A and B. However, window adds a specified number (1000, by default) of base pairs upstream and downstream of each feature in A. In effect, this allows features in B that are “near” features in A to be detected.
 
 .. image:: $PATH_TO_IMAGES/window-glyph.png
+
 @REFERENCES@
     </help>
 </tool>