# HG changeset patch
# User iuc
# Date 1407536279 14400
# Node ID 7511823bdea14975b155cf4c4be6dd2049ef1530
# Parent  4fb5ea02b4418816e94866f856d497ea5d783ca0
Uploaded

diff -r 4fb5ea02b441 -r 7511823bdea1 Bed12ToBed6.xml
--- a/Bed12ToBed6.xml	Tue Jul 15 14:42:23 2014 -0400
+++ b/Bed12ToBed6.xml	Fri Aug 08 18:17:59 2014 -0400
@@ -24,4 +24,5 @@
 
 @REFERENCES@
     </help>
+    <expand macro="citations" />
 </tool>
diff -r 4fb5ea02b441 -r 7511823bdea1 BedToBam.xml
--- a/BedToBam.xml	Tue Jul 15 14:42:23 2014 -0400
+++ b/BedToBam.xml	Fri Aug 08 18:17:59 2014 -0400
@@ -30,4 +30,5 @@
 
 @REFERENCES@
     </help>
+    <expand macro="citations" />
 </tool>
diff -r 4fb5ea02b441 -r 7511823bdea1 annotateBed.xml
--- a/annotateBed.xml	Tue Jul 15 14:42:23 2014 -0400
+++ b/annotateBed.xml	Fri Aug 08 18:17:59 2014 -0400
@@ -62,4 +62,5 @@
 @REFERENCES@
 
     </help>
+    <expand macro="citations" />
 </tool>
diff -r 4fb5ea02b441 -r 7511823bdea1 bamToBed.xml
--- a/bamToBed.xml	Tue Jul 15 14:42:23 2014 -0400
+++ b/bamToBed.xml	Fri Aug 08 18:17:59 2014 -0400
@@ -51,4 +51,5 @@
 @REFERENCES@
 
     </help>
+    <expand macro="citations" />
 </tool>
diff -r 4fb5ea02b441 -r 7511823bdea1 bamToFastq.xml
--- a/bamToFastq.xml	Tue Jul 15 14:42:23 2014 -0400
+++ b/bamToFastq.xml	Fri Aug 08 18:17:59 2014 -0400
@@ -29,4 +29,5 @@
 @REFERENCES@
 
     </help>
+    <expand macro="citations" />
 </tool>
diff -r 4fb5ea02b441 -r 7511823bdea1 bedpeToBam.xml
--- a/bedpeToBam.xml	Tue Jul 15 14:42:23 2014 -0400
+++ b/bedpeToBam.xml	Fri Aug 08 18:17:59 2014 -0400
@@ -34,4 +34,5 @@
 
 @REFERENCES@
     </help>
+    <expand macro="citations" />
 </tool>
diff -r 4fb5ea02b441 -r 7511823bdea1 closestBed.xml
--- a/closestBed.xml	Tue Jul 15 14:42:23 2014 -0400
+++ b/closestBed.xml	Fri Aug 08 18:17:59 2014 -0400
@@ -38,4 +38,5 @@
 
 @REFERENCES@
     </help>
+    <expand macro="citations" />
 </tool>
diff -r 4fb5ea02b441 -r 7511823bdea1 clusterBed.xml
--- a/clusterBed.xml	Tue Jul 15 14:42:23 2014 -0400
+++ b/clusterBed.xml	Fri Aug 08 18:17:59 2014 -0400
@@ -37,4 +37,5 @@
 
 @REFERENCES@
     </help>
+    <expand macro="citations" />
 </tool>
diff -r 4fb5ea02b441 -r 7511823bdea1 complementBed.xml
--- a/complementBed.xml	Tue Jul 15 14:42:23 2014 -0400
+++ b/complementBed.xml	Fri Aug 08 18:17:59 2014 -0400
@@ -28,4 +28,5 @@
 
 @REFERENCES@
     </help>
+    <expand macro="citations" />
 </tool>
diff -r 4fb5ea02b441 -r 7511823bdea1 coverageBed.xml
--- a/coverageBed.xml	Tue Jul 15 14:42:23 2014 -0400
+++ b/coverageBed.xml	Fri Aug 08 18:17:59 2014 -0400
@@ -1,4 +1,4 @@
-<tool id="bedtools_coveragebed" name="Compute both the depth and breadth of coverage" version="@WRAPPER_VERSION@.0">
+<tool id="bedtools_coveragebed" name="Compute both the depth and breadth of coverage" version="@WRAPPER_VERSION@.1">
     <description>of features in file A across the features in file B (coverageBed)</description>
     <macros>
         <import>macros.xml</import>
@@ -14,6 +14,7 @@
         #end if
         -b '$inputB'
         $d
+        $hist
         $split
         $strandedness
         | sort -k1,1 -k2,2n
@@ -32,6 +33,8 @@
             help="That is, only features in A are only counted towards coverage in B if they are the same strand. (-s)"/>
         <param name="d" type="boolean" checked="false" truevalue="-d" falsevalue="" label="Report the depth at each position in each B feature"
             help="Positions reported are one based.  Each position and depth follow the complete B feature. (-d)" />
+        <param name="hist" type="boolean" checked="false" truevalue="-hist" falsevalue="" label="Report a histogram of coverage for each feature in B as well as a summary histogram for all features in B"
+            help="Additonal columns after each feature in B: 1) depth 2) # bases at depth 3) size of B 4) % of B at depth. (-hist)" />
     </inputs>
 
     <outputs>
@@ -41,10 +44,14 @@
 
 **What it does**
 
-coverageBed_ computes both the depth and breadth of coverage of features in file A across the features in file B. For example, coverageBed can compute the coverage of sequence alignments (file A) across 1 kilobase (arbitrary) windows (file B) tiling a genome of interest. One advantage that coverageBed offers is that it not only counts the number of features that overlap an interval in file B, it also computes the fraction of bases in B interval that were overlapped by one or more features.
+coverageBed_ computes both the depth and breadth of coverage of features in 
+file A across the features in file B. For example, coverageBed can compute the coverage of sequence alignments 
+(file A) across 1 kilobase (arbitrary) windows (file B) tiling a genome of interest. 
+One advantage that coverageBed offers is that it not only counts the number of features that 
+overlap an interval in file B, it also computes the fraction of bases in B interval that were overlapped by one or more features.
 Thus, coverageBed also computes the breadth of coverage for each interval in B.
 
-.. coverageBed: http://bedtools.readthedocs.org/en/latest/content/tools/coverage.html
+.. _coverageBed: http://bedtools.readthedocs.org/en/latest/content/tools/coverage.html
 
 .. class:: infomark
 
@@ -53,4 +60,5 @@
 @REFERENCES@
 
     </help>
+    <expand macro="citations" />
 </tool>
diff -r 4fb5ea02b441 -r 7511823bdea1 expandBed.xml
--- a/expandBed.xml	Tue Jul 15 14:42:23 2014 -0400
+++ b/expandBed.xml	Fri Aug 08 18:17:59 2014 -0400
@@ -26,4 +26,5 @@
 
 @REFERENCES@
     </help>
+    <expand macro="citations" />
 </tool>
diff -r 4fb5ea02b441 -r 7511823bdea1 flankbed.xml
--- a/flankbed.xml	Tue Jul 15 14:42:23 2014 -0400
+++ b/flankbed.xml	Fri Aug 08 18:17:59 2014 -0400
@@ -45,4 +45,5 @@
 
 @REFERENCES@
     </help>
+    <expand macro="citations" />
 </tool>
diff -r 4fb5ea02b441 -r 7511823bdea1 genomeCoverageBed_bedgraph.xml
--- a/genomeCoverageBed_bedgraph.xml	Tue Jul 15 14:42:23 2014 -0400
+++ b/genomeCoverageBed_bedgraph.xml	Fri Aug 08 18:17:59 2014 -0400
@@ -102,4 +102,5 @@
 
 @REFERENCES@
     </help>
+    <expand macro="citations" />
 </tool>
diff -r 4fb5ea02b441 -r 7511823bdea1 genomeCoverageBed_histogram.xml
--- a/genomeCoverageBed_histogram.xml	Tue Jul 15 14:42:23 2014 -0400
+++ b/genomeCoverageBed_histogram.xml	Fri Aug 08 18:17:59 2014 -0400
@@ -64,4 +64,5 @@
 
 @REFERENCES@
     </help>
+    <expand macro="citations" />
 </tool>
diff -r 4fb5ea02b441 -r 7511823bdea1 getfastaBed.xml
--- a/getfastaBed.xml	Tue Jul 15 14:42:23 2014 -0400
+++ b/getfastaBed.xml	Fri Aug 08 18:17:59 2014 -0400
@@ -41,4 +41,5 @@
 
 @REFERENCES@
     </help>
+    <expand macro="citations" />
 </tool>
diff -r 4fb5ea02b441 -r 7511823bdea1 groupbyBed.xml
--- a/groupbyBed.xml	Tue Jul 15 14:42:23 2014 -0400
+++ b/groupbyBed.xml	Fri Aug 08 18:17:59 2014 -0400
@@ -40,4 +40,5 @@
 
 @REFERENCES@
     </help>
+    <expand macro="citations" />
 </tool>
diff -r 4fb5ea02b441 -r 7511823bdea1 intersectBed.xml
--- a/intersectBed.xml	Tue Jul 15 14:42:23 2014 -0400
+++ b/intersectBed.xml	Fri Aug 08 18:17:59 2014 -0400
@@ -82,4 +82,5 @@
 @REFERENCES@
 
     </help>
+    <expand macro="citations" />
 </tool>
diff -r 4fb5ea02b441 -r 7511823bdea1 jaccardBed.xml
--- a/jaccardBed.xml	Tue Jul 15 14:42:23 2014 -0400
+++ b/jaccardBed.xml	Fri Aug 08 18:17:59 2014 -0400
@@ -44,4 +44,5 @@
 
 @REFERENCES@
     </help>
+    <expand macro="citations" />
 </tool>
diff -r 4fb5ea02b441 -r 7511823bdea1 linksBed.xml
--- a/linksBed.xml	Tue Jul 15 14:42:23 2014 -0400
+++ b/linksBed.xml	Fri Aug 08 18:17:59 2014 -0400
@@ -30,4 +30,5 @@
 
 @REFERENCES@
     </help>
+    <expand macro="citations" />
 </tool>
diff -r 4fb5ea02b441 -r 7511823bdea1 macros.xml
--- a/macros.xml	Tue Jul 15 14:42:23 2014 -0400
+++ b/macros.xml	Fri Aug 08 18:17:59 2014 -0400
@@ -76,12 +76,15 @@
     <token name="@REFERENCES@">
 ------
 
-This tool is part of the `bedtools package`__ from the `Quinlan laboratory`__.
-If you use this tool, please cite `Quinlan AR, and Hall I.M. BEDTools: A flexible framework for comparing genomic features. Bioinformatics, 2010, 26, 6.`__
+This tool is part of the `bedtools package`_ from the `Quinlan laboratory`_.
+
+.. _bedtools package: https://github.com/arq5x/bedtools2
+.. _Quinlan laboratory: http://cphg.virginia.edu/quinlan/
 
-.. __: https://github.com/arq5x/bedtools2
-.. __: http://cphg.virginia.edu/quinlan/
-.. __: http://bioinformatics.oxfordjournals.org/content/26/6/841.short
-.. __: http://bedtools.readthedocs.org/en/latest/content/bedtools-suite.html
     </token>
+    <xml name="citations">
+        <citations>
+            <citation type="doi">10.1093/bioinformatics/btq033</citation>
+        </citations>
+    </xml>
 </macros>
diff -r 4fb5ea02b441 -r 7511823bdea1 makewindowsBed.xml
--- a/makewindowsBed.xml	Tue Jul 15 14:42:23 2014 -0400
+++ b/makewindowsBed.xml	Fri Aug 08 18:17:59 2014 -0400
@@ -75,4 +75,5 @@
 
 @REFERENCES@
     </help>
+    <expand macro="citations" />
 </tool>
diff -r 4fb5ea02b441 -r 7511823bdea1 mapBed.xml
--- a/mapBed.xml	Tue Jul 15 14:42:23 2014 -0400
+++ b/mapBed.xml	Fri Aug 08 18:17:59 2014 -0400
@@ -66,4 +66,5 @@
 @REFERENCES@
 
     </help>
+    <expand macro="citations" />
 </tool>
diff -r 4fb5ea02b441 -r 7511823bdea1 maskFastaBed.xml
--- a/maskFastaBed.xml	Tue Jul 15 14:42:23 2014 -0400
+++ b/maskFastaBed.xml	Fri Aug 08 18:17:59 2014 -0400
@@ -33,4 +33,5 @@
 
 @REFERENCES@
     </help>
+    <expand macro="citations" />
 </tool>
diff -r 4fb5ea02b441 -r 7511823bdea1 mergeBed.xml
--- a/mergeBed.xml	Tue Jul 15 14:42:23 2014 -0400
+++ b/mergeBed.xml	Fri Aug 08 18:17:59 2014 -0400
@@ -200,4 +200,5 @@
 
 @REFERENCES@
     </help>
+    <expand macro="citations" />
 </tool>
diff -r 4fb5ea02b441 -r 7511823bdea1 multiCov.xml
--- a/multiCov.xml	Tue Jul 15 14:42:23 2014 -0400
+++ b/multiCov.xml	Fri Aug 08 18:17:59 2014 -0400
@@ -54,4 +54,5 @@
 @REFERENCES@
 
     </help>
+    <expand macro="citations" />
 </tool>
diff -r 4fb5ea02b441 -r 7511823bdea1 multiIntersectBed.xml
--- a/multiIntersectBed.xml	Tue Jul 15 14:42:23 2014 -0400
+++ b/multiIntersectBed.xml	Fri Aug 08 18:17:59 2014 -0400
@@ -192,4 +192,5 @@
 @REFERENCES@
 
     </help>
+    <expand macro="citations" />
 </tool>
diff -r 4fb5ea02b441 -r 7511823bdea1 nucBed.xml
--- a/nucBed.xml	Tue Jul 15 14:42:23 2014 -0400
+++ b/nucBed.xml	Fri Aug 08 18:17:59 2014 -0400
@@ -35,4 +35,5 @@
 
 @REFERENCES@
     </help>
+    <expand macro="citations" />
 </tool>
diff -r 4fb5ea02b441 -r 7511823bdea1 overlapBed.xml
--- a/overlapBed.xml	Tue Jul 15 14:42:23 2014 -0400
+++ b/overlapBed.xml	Fri Aug 08 18:17:59 2014 -0400
@@ -26,4 +26,5 @@
 
 @REFERENCES@
     </help>
+    <expand macro="citations" />
 </tool>
diff -r 4fb5ea02b441 -r 7511823bdea1 randomBed.xml
--- a/randomBed.xml	Tue Jul 15 14:42:23 2014 -0400
+++ b/randomBed.xml	Fri Aug 08 18:17:59 2014 -0400
@@ -31,4 +31,5 @@
 
 @REFERENCES@
     </help>
+    <expand macro="citations" />
 </tool>
diff -r 4fb5ea02b441 -r 7511823bdea1 reldist.xml
--- a/reldist.xml	Tue Jul 15 14:42:23 2014 -0400
+++ b/reldist.xml	Fri Aug 08 18:17:59 2014 -0400
@@ -32,4 +32,5 @@
 @REFERENCES@
 
     </help>
+    <expand macro="citations" />
 </tool>
diff -r 4fb5ea02b441 -r 7511823bdea1 shuffleBed.xml
--- a/shuffleBed.xml	Tue Jul 15 14:42:23 2014 -0400
+++ b/shuffleBed.xml	Fri Aug 08 18:17:59 2014 -0400
@@ -64,4 +64,5 @@
 .. image:: $PATH_TO_IMAGES/shuffle-glyph.png
 @REFERENCES@
     </help>
+    <expand macro="citations" />
 </tool>
diff -r 4fb5ea02b441 -r 7511823bdea1 slopBed.xml
--- a/slopBed.xml	Tue Jul 15 14:42:23 2014 -0400
+++ b/slopBed.xml	Fri Aug 08 18:17:59 2014 -0400
@@ -45,4 +45,5 @@
 In order to prevent the extension of intervals beyond chromosome boundaries, bedtools slop requires a genome file defining the length of each chromosome or contig.
 @REFERENCES@
     </help>
+    <expand macro="citations" />
 </tool>
diff -r 4fb5ea02b441 -r 7511823bdea1 sortBed.xml
--- a/sortBed.xml	Tue Jul 15 14:42:23 2014 -0400
+++ b/sortBed.xml	Fri Aug 08 18:17:59 2014 -0400
@@ -42,4 +42,5 @@
 @REFERENCES@
 
     </help>
+    <expand macro="citations" />
 </tool>
diff -r 4fb5ea02b441 -r 7511823bdea1 subtractBed.xml
--- a/subtractBed.xml	Tue Jul 15 14:42:23 2014 -0400
+++ b/subtractBed.xml	Fri Aug 08 18:17:59 2014 -0400
@@ -45,4 +45,5 @@
 
 @REFERENCES@
     </help>
+    <expand macro="citations" />
 </tool>
diff -r 4fb5ea02b441 -r 7511823bdea1 tagBed.xml
--- a/tagBed.xml	Tue Jul 15 14:42:23 2014 -0400
+++ b/tagBed.xml	Fri Aug 08 18:17:59 2014 -0400
@@ -47,4 +47,5 @@
 @REFERENCES@
 
     </help>
+    <expand macro="citations" />
 </tool>
diff -r 4fb5ea02b441 -r 7511823bdea1 unionBedGraphs.xml
--- a/unionBedGraphs.xml	Tue Jul 15 14:42:23 2014 -0400
+++ b/unionBedGraphs.xml	Fri Aug 08 18:17:59 2014 -0400
@@ -228,4 +228,5 @@
 @REFERENCES@
  
     </help>
+    <expand macro="citations" />
 </tool>
diff -r 4fb5ea02b441 -r 7511823bdea1 windowBed.xml
--- a/windowBed.xml	Tue Jul 15 14:42:23 2014 -0400
+++ b/windowBed.xml	Fri Aug 08 18:17:59 2014 -0400
@@ -71,4 +71,5 @@
 
 @REFERENCES@
     </help>
+    <expand macro="citations" />
 </tool>