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changeset 1:7511823bdea1 draft

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Uploaded
author iuc
date Fri, 08 Aug 2014 18:17:59 -0400
parents 4fb5ea02b441
children effb7b4e45ed
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 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 37 files changed, 55 insertions(+), 9 deletions(-) [+]
line wrap: on
line diff
--- 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>
--- 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>
--- 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>
--- 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>
--- 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>
--- 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>
--- 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>
--- 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>
--- 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>
--- 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>
--- 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>
--- 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>
--- 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>
--- 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>
--- 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>
--- 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>
--- 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>
--- 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>
--- 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>
--- 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>
--- 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>
--- 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>
--- 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>
--- 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>
--- 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>
--- 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>
--- 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>
--- 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>
--- 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>
--- 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>
--- 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>
--- 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>
--- 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>
--- 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>
--- 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>
--- 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>
--- 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>