diff bamCoverage.xml @ 8:9e8925f84444 draft

planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4f515024772311c950d277246db548453d24abd7

--- a/bamCoverage.xml	Wed Dec 23 07:29:21 2015 -0500
+++ b/bamCoverage.xml	Wed Dec 23 14:38:45 2015 -0500
@@ -55,8 +55,8 @@
             help="The BAM file must be sorted."/>
 
         <param name="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, this fraction will be reported. "/>
 
         <conditional name="scaling">
             <param name="type" type="select" label="Scaling/Normalization method" >
@@ -94,16 +94,16 @@
                     label="Regions that should be excluded for normalization"
                     help="A list of chromosome names separated by spaces
                         containing those chromosomes that should be excluded
-                        for computing the normalization. This is useful when
+                        during normalization. This is useful when
                         considering samples with unequal coverage across
-                        chromosomes like male samples. Example: chrX chrM" />
+                        chromosomes, like male and female samples. Example: chrX chrM" />
 
                 <expand macro="skipNAs" />
                 <expand macro="read_processing_options" />
 
                 <param argument="--MNase" type="boolean" truevalue="--MNase" falsevalue=""
                     label="Determine nucleosome positions from MNase-seq data"
-                    help="Only 3 nucleotides at the center of each fragment are counted. The fragment ends are defined by the two mate reads. *NOTE*: Requires paired-end data." />
+                    help="Only the 3 nucleotides at the center of each fragment are counted. The fragment ends are defined by the two mate reads. *NOTE*: Requires paired-end data." />
 
             </when>
         </conditional>
@@ -163,7 +163,7 @@
 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
+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.