--- a/bamCoverage.xml	Mon Mar 17 16:23:58 2014 -0400
+++ b/bamCoverage.xml	Wed Apr 02 09:15:44 2014 -0400
@@ -1,4 +1,4 @@
-<tool id="deeptools_bamCoverage" name="bamCoverage" version="1.0.5">
+<tool id="deeptools_bamCoverage" name="bamCoverage" version="@WRAPPER_VERSION@.0">
     <description> generates a coverage bigWig file from a given BAM file.  Multiple options are available to count reads and normalize coverage. (bam2bigwig)</description>
     <expand macro="requirements" />
     <expand macro="stdio" />
@@ -133,11 +133,15 @@
 
 **What it does**
 
-Given a BAM file, this tool generates a bigWig or bedGraph file with genome-wide coverage of fragment or read coverages. 
-The way the method works is by first calculating all the number of reads (either extended to match the fragment length or not) 
-that overlap each bin (a region of fixed length, i.e. 25 bp) in the genome. Bins with zero counts are skipped, i.e. not added to the output file. 
-The resulting read counts can be normalized using either a given scaling factor, the RPKM formula or to get a 1x depth of coverage (RPGC).
-
+Given a BAM file, this tool generates a bigWig or bedGraph file of fragment or
+read coverages. The way the method works is by first calculating all the
+number of reads (either extended to match the fragment length or not) that
+overlap each bin in the genome. The resulting read counts can be normalized
+using either a given scaling factor, the RPKM formula or to get a 1x depth of
+coverage (RPGC). In the case of paired-end mapping each read mate is treated
+independently to avoid a bias when a mixture of concordant and discordant
+pairs is present. This means that *each end* will be extended to match the
+fragment length.
 
 .. image:: $PATH_TO_IMAGES/norm_IGVsnapshot_indFiles.png