--- a/bamCompare.xml	Wed Dec 23 07:33:54 2015 -0500
+++ b/bamCompare.xml	Wed Dec 23 14:44:06 2015 -0500
@@ -1,5 +1,5 @@
 <tool id="deeptools_bam_compare" name="bamCompare" version="@WRAPPER_VERSION@.0">
-    <description>normalizes and compares two BAM files to obtain the ratio, log2ratio or difference</description>
+    <description>normalizes and compares two BAM files to obtain the ratio, log2ratio or difference between them</description>
     <macros>
         <token name="@BINARY@">bamCompare</token>
         <import>deepTools_macros.xml</import>
@@ -75,9 +75,9 @@
             help="The BAM file must be sorted."/>
 
         <param argument="--binSize" type="integer" value="50" min="1"
-            label="Bin size in bp"
-            help="The genome will be divided in bins (also called tiles) of the specified length. For each bin the overlaping number of fragments (or reads) will be reported.
-                If only half a fragment overlaps, this fraction will be reported."/>
+            label="Bin size in bases"
+            help="The genome will be divided into bins of the specified size. For each bin, the overlaping number of fragments (or reads) will be reported.
+                If only half a fragment overlaps then this fraction will be reported."/>
 
         <conditional name="scaling">
             <param name="method" type="select"
@@ -88,7 +88,7 @@
             </param>
             <when value="SES">
                 <param argument="--sampleLength" type="integer" value="1000" min="10"
-                    label="Length in base pairs used to sample the genome and compute the size or scaling factors to compare the two  BAM files "
+                    label="Length in bases used to sample the genome and compute the size or scaling factors."
                     help="The default is fine. Only change it if you know what you are doing." />
                 <param argument="--numberOfSamples" type="integer" value="100000" min="0"
                     label="Number of samplings taken from the genome to compute the scaling factors"
@@ -157,9 +157,9 @@
                 <param argument="--ignoreForNormalization" type="text" value="" size="50"
                     label="regions that should be excluded for calculating the scaling factor"
                     help="Sometimes it makes sense to exclude certain regions when calculating the scaling factor.
-                        For example, if you know some regions that you suspect to be present more often in your sample's genome than in
-                        the reference genome that will therefore accumulate reads (CNV). Another typical example is the single X chromosome
-                        in male samples that should be scaled separately from the diploid autosomes. For example chrX,chrY,chr3. or chr10:12220-128932" />
+                        For example, if you know of copy number variations between samples then you may want to exclude these.
+                        Another typical example is the difference in chromosome X copies between males and females in many species.
+                        Example inputs are chrX,chrY,chr3 or chr10:12220-128932" />
             </when>
         </conditional>
     </inputs>
@@ -200,18 +200,18 @@
 
 This tool compares two BAM files based on the number of mapped reads. To
 compare the BAM files, the genome is partitioned into bins of equal size, then
-the number of reads found in each BAM file is counted for such bins and
-finally a summarizing value is reported. This value can be the ratio of the
+the number of reads found in each BAM file is counted per bin and
+finally a summary value reported. This value can be the ratio of the
 number of reads per bin, the log2 of the ratio or the difference. This tool
-can normalize the number of reads on each BAM file using the SES method
-proposed by Diaz et al. (2012). "Normalization, bias correction, and peak
+can normalize the number of reads in each BAM file using the SES method
+proposed in Diaz et al. (2012). "Normalization, bias correction, and peak
 calling for ChIP-seq". Statistical applications in genetics and molecular
 biology, 11(3). Normalization based on read counts is also available. The
 output is either a bedgraph or a bigwig file containing the bin location and
 the resulting comparison values. By default, if reads are mated, the fragment
-length reported in the BAM file is used. In the case of paired-end mapping
+length reported in the BAM file is used. 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
+concordant and discordant pairs are present. This means that *each end* will be
 extended to match the fragment length.