--- 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>