# HG changeset patch
# User bgruening
# Date 1450899846 18000
# Node ID 3748f04eb047001a1e267d4c4b7c8957f380e899
# Parent  c07969d63d7b7170ba304a38a198617be8f0eaec
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4f515024772311c950d277246db548453d24abd7

diff -r c07969d63d7b -r 3748f04eb047 bamCompare.xml
--- 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.
 
 
diff -r c07969d63d7b -r 3748f04eb047 deepTools_macros.xml
--- a/deepTools_macros.xml	Wed Dec 23 07:33:54 2015 -0500
+++ b/deepTools_macros.xml	Wed Dec 23 14:44:06 2015 -0500
@@ -55,7 +55,7 @@
     <xml name="includeZeros">
         <param argument="--includeZeros" type="boolean" truevalue="--includeZeros" falsevalue=""
             label="Include zeros"
-            help="If set, then regions with zero counts for *all* BAM files given are included. The default behavior is to ignore those cases." />
+            help="If set, then regions with zero counts for *all* BAM files are included. The default behavior is to ignore such regions." />
     </xml>
 
     <xml name="zMin_zMax">
@@ -68,7 +68,7 @@
     <xml name="region_limit_operation">
         <param argument="--region" type="text" value=""
             label="Region of the genome to limit the operation to"
-            help="This is useful when testing parameters to reduce the computing time. The format is chr:start:end, for example &quot;chr10&quot; or &quot;chr10:456700:891000&quot;." />
+            help="This is useful when testing parameters to reduce the time required. The format is chr:start:end, for example &quot;chr10&quot; or &quot;chr10:456700:891000&quot;." />
     </xml>
 
     <token name="@THREADS@">--numberOfProcessors "\${GALAXY_SLOTS:-4}"</token>
@@ -86,8 +86,8 @@
 
     <xml name="smoothLength">
         <param argument="--smoothLength" type="integer" value="" optional="True" min="1"
-            label="Smooth values using the following length (in bp)"
-            help ="The smooth length defines a window, larger than the bin size, to average the number of reads. For example, if the bin size is set to 20 bp and the smooth length is set to 60 bp, then, for each bin size the average of it and its left and right neighbors is considered. Any value smaller than the bin size will be ignored and no smoothing will be applied."/>
+            label="Smooth values using the following length (in bases)"
+            help ="The smooth length defines a window, larger than the bin size, over which the number of reads is to be averaged. For example, if the bin size is set to 20 and the smooth length is 60, then, for each bin, its value is set to the average of it and its left and right neighbors. Any value smaller than the bin size will be ignored and no smoothing will be applied."/>
     </xml>
 
 
@@ -107,11 +107,10 @@
                     </param>
                     <when value="kmeans">
                         <param name="k_kmeans" type="integer" value="0" label="Number of clusters to compute"
-                            help="When this option is set, then the matrix is split into clusters using the kmeans algorithm.
-                            Only works for data that is not grouped, otherwise only the first group will be clustered.
+                            help="When this option is set, the matrix is split into clusters using the k-means algorithm.
+                            This only works for data that is not grouped, otherwise only the first group will be clustered.
                             If more specific clustering methods are required it is advisable to save the underlying matrix and
-                            run the clustering using other software. The plotting of the clustering may fail (Error: Segmentation fault)
-                            if a cluster has very few members compared to the total number or regions. (default: 0 [do not cluster])."/>
+                            run the clustering using other software."/>
                     </when>
                     <when value="none" />
                 </conditional>
@@ -157,11 +156,11 @@
         <conditional name="doExtendCustom">
             <param name="doExtend" type="select" label="Extend reads to the given average fragment size."
                 help="(1) Single-end reads and singletons are extended to match this length. (2) Paired-end reads are extended to match the fragment size, regardless of what is set here.
-                        By default *each* read mate is extended.
-                        This can be modified using the SAM flags (see --samFlagInclude and --samFlagExclude options) to keep only the first or the second mate.
-                        Unmated reads, mate reads that map on different chromosomes or too far apart are extended to the given value.
-                        Reads are only extended if --extendReads is set to a value greater than the read length. *NOTE*: For spliced-read data, this option is not
-                        recommended as it will extend reads over skipped regions, e.g. introns in RNA-seq data.">
+                     By default *each* read mate is extended.
+                     This can be modified using the SAM flags (see --samFlagInclude and --samFlagExclude options) to keep only the first or the second mate.
+                     Unmated reads, mate reads that map to different chromosomes or too far apart are extended to the given value.
+                     Reads are only extended if --extendReads is set to a value greater than the read length. *NOTE*: For spliced-read data, this option is not
+                     recommended as it will extend reads over skipped regions, e.g. introns in RNA-seq data.">
                 <option value="no" selected="True">No extension. The default value and most typically appropriate.</option>
                 <option value="yes">Paired-end extension. Suitable only for paired-end datasets.</option>
                 <option value="custom">A custom length, which will be applied to ALL reads.</option>
@@ -189,14 +188,14 @@
             help="By default, bamCorrelate considers consecutive bins of
                 the specified 'Bin size'. However, to reduce the
                 computation time, a larger distance between bins can
-                by given. Larger distances result in less bins being
+                be given. Larger distances result in fewer bins being
                 considered."/>
     </xml>
 
     <xml name="centerReads">
         <param argument="--centerReads" type="boolean" truevalue="--centerReads" falsevalue=""
             label="Center regions with respect to the fragment length"
-            help="For paired-end data, the read is centered at the fragment length defined by the two ends of the fragment. For single-end data, the given fragment length is used. This option is useful to get a sharper signal around enriched regions. "/>
+            help="For paired-end data the fragment is defined by the bounds of the reads. For single-end data the bounds are defined by the read and the user-definable fragment/extension length. This option is useful to get a sharper signal around enriched regions."/>
     </xml>
 
     <xml name="ignoreDuplicates">
@@ -229,19 +228,19 @@
     <xml name="minMappingQuality">
         <param argument="--minMappingQuality" type="integer" optional="true" value="1" min="1"
             label="Minimum mapping quality"
-            help= "If set, only reads that have a mapping quality score higher than the given value are considered. *Note* Bowtie's Mapping quality is related to uniqueness: the higher the score, the more unique is a read. A mapping quality defined by Bowtie of 10 or less indicates that there is at least a 1 in 10 chance that the read truly originated elsewhere."/>
+            help= "If set, only reads with a mapping quality score higher than this value are considered."/>
     </xml>
 
     <xml name="skipZeros">
         <param argument="--skipZeros" type="boolean" truevalue="--skipZeros" falsevalue=""
             label ="Skip zeros"
-            help ="If set, then zero counts that happen for *all* BAM files given are ignored. This might have the effect that fewer regions are considered than indicated in the option where the number of samples is defined." />
+            help ="If set, then zero counts that happen for *all* BAM files given are ignored. This may result in fewer considered regions." />
     </xml>
 
     <xml name="fragmentLength">
         <param argument="--fragmentLength" type="integer" value="300" min="1"
             label="Fragment length used for the sequencing"
-            help ="If paired-end reads are used, the fragment length is computed from the BAM file."/>
+            help ="If paired-end reads are used, the fragment length is computed from the BAM file, so this is only needed for single-end data."/>
     </xml>
 
     <xml name="scaleFactor">
@@ -302,7 +301,7 @@
     <xml name="multiple_input_bigwigs">
         <param argument="--bigwigfiles" type="data" format="bigwig" multiple="True" min="2"
             label="Bigwig file"
-            help="The Bigwig file must be sorted."/>
+            help="A Bigwig file."/>
     </xml>
 
     <xml name="plotTitle">
@@ -394,8 +393,8 @@
                  should be skipped. The default is to treat those
                  regions as having a value of zero. The decision to
                  skip non-covered regions depends on the interpretation
-                 of the data. Non-covered regions may represent for
-                 example repetitive regions that want to be skipped.
+                 of the data. Non-covered regions may represent, for
+                 example, repetitive regions that should be ignored.
                  (default: False)" />
     </xml>