# HG changeset patch
# User bgruening
# Date 1455550440 18000
# Node ID 275ed3e83de0d9818127159c02e43fa96af40e1e
# Parent  14cb57237e46d57cd71102b387a249c509c2665f
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920

diff -r 14cb57237e46 -r 275ed3e83de0 computeMatrix.xml
--- a/computeMatrix.xml	Mon Jan 25 20:26:32 2016 -0500
+++ b/computeMatrix.xml	Mon Feb 15 10:34:00 2016 -0500
@@ -8,18 +8,25 @@
     <command>
 <![CDATA[
         #import tempfile
+        #set bw_files=[]
+        #for $counter, $bigwig in enumerate($scoreFileName):
+            ln -s "${bigwig}" "file_${counter}.bw" &&
+            #silent $bw_files.append('file_%s.bw' % $counter)
+        #end for
+
+        #set bed_files=[]
+        #for $counter, $rf in enumerate($regionsFiles):
+            ln -s "${rf.regionsFile}" "group_${counter}.bed" &&
+            #silent $bed_files.append('group_%s.bed' % $counter)
+        #end for
 
         @BINARY@
 
             $mode.mode_select
-            --regionsFileName
-            #for $rf in $regionsFiles:
-                '$rf.regionsFile' 
-            #end for
-            --scoreFileName
-            #for $bw in $scoreFileName:
-                '$bw' 
-            #end for
+            --regionsFileName '#echo "' '".join($bed_files)#'
+
+            --scoreFileName '#echo "' '".join($bw_files)#'
+
             --outFileName '$outFileName'
 
             @THREADS@
@@ -51,8 +58,8 @@
                 --sortRegions '$advancedOpt.sortRegions'
                 --sortUsing '$advancedOpt.sortUsing'
                 --averageTypeBins '$advancedOpt.averageTypeBins'
-                $advancedOpt.skipNAs
                 $advancedOpt.skipZeros
+                $advancedOpt.missingDataAsZero
                 --binSize $advancedOpt.binSize
 
                 #if $advancedOpt.minThreshold is not None and str($advancedOpt.minThreshold) != '':
@@ -77,17 +84,16 @@
 
         <param name="scoreFileName" format="bigwig" type="data"
             label="Score file" multiple="True"
-            help="You can generate a bigWig file from either a
-            bedGraph or WIG file using UCSC tools or from a BAM file using the
+            help="You can generate a bigWig file from a BAM file using the
             bamCoverage tool. (--scoreFileName)"/>
 
         <conditional name="mode" >
             <param name="mode_select" type="select"
                 label="computeMatrix has two main output options"
                 help="In the scale-regions mode, all regions in the BED file are
-                stretched or shrunk to the same length (in bases) that is indicated
+                stretched or shrunken to the same length (in bases) that is indicated
                 by the user. Reference-point refers to a position within the BED
-                regions (e.g start of region). In the reference-point mode only
+                regions (start or end of each region). In the reference-point mode only
                 those genomic positions before (upstream) and/or after (downstream)
                 the reference point will be considered.">
                 <option value="scale-regions" selected="true">scale-regions</option>
@@ -164,19 +170,21 @@
                 </param>
 
                 <param name="missingDataAsZero" type="boolean" truevalue="--missingDataAsZero" falsevalue="" checked="False"
-                    label="Convert missing values to 0?."
-                    help="If set to 'yes', missing values (NAs) are converted to 0.
-                          The default is to ignore such cases, which will be
-                          depicted as black areas once a heatmap is created." />
+                    label="Convert missing values to 0?"
+                    help="If set to 'yes', missing values (NAs) are converted
+                     to 0. If you want to use clustering with plotHeatmap
+                     or plotProfile, set this to 'yes'.
+                          The default is to ignore missing values, which will be
+                          depicted as black areas once a heatmap is created.
+                           (--missingDataAsZero)" />
 
                 <expand macro="skipZeros" />
-                <expand macro="skipNAs" />
 
                 <param name="minThreshold" type="float" optional="True"
                     label="Minimum threshold"
                     help="Any region containing a value that is equal or less than this numeric
                     value will be skipped. This is useful to skip, for example, genes where the
-                    read count is zero for any of the bins. This could be the result of
+                    read count is zero for any of the bins which could be the result of
                     unmappable areas and can bias the overall results. (--minThreshold)"/>
                 <param name="maxThreshold" type="float" optional="True"
                     label="Maximum threshold"
@@ -206,7 +214,6 @@
             <param name="binSize" value="10" />
             <param name="sortUsing" value="sum" />
             <param name="averageTypeBins" value="sum" />
-            <param name="skipNAs" value="False" />
             <param name="beforeRegionStartLength" value="10" />
             <param name="afterRegionStartLength" value="10" />
             <output name="outFileName" file="computeMatrix_result1.gz" ftype="deeptools_compute_matrix_archive" compare="sim_size" />
@@ -233,27 +240,80 @@
     </tests>
   <help>
 <![CDATA[
-**What it does**
+
+What it does
+----------------
 
 This tool prepares an intermediate file (a gzipped table of values)
-that contains scores associated with genomic regions and can be used
-afterwards to plot a heatmap or profile.
+that contains scores associated with genomic regions.
+The regions can either be scaled to the same size (using the ``scale-regions`` mode) or you can choose the start, end, or center of each region as the focus point for the score calculations.
+For more details, check out the explanation `here <file:///Users/frd2007/Documents/MPI/deepTools/docs/_build/html/content/tools/computeMatrix.html#details>`_.
+
+The intermediate file produced by ``computeMatrix`` is meant to be used with ``plotHeatmap`` and ``plotProfile``.
+See the descriptions of ``plotHeatmap`` and ``plotProfile`` for example plots.
+
+.. image:: $PATH_TO_IMAGES/computeMatrix_overview.png
+   :alt: Relationship between computeMatrix, heatmapper and profiler
+   :width: 600
+   :height: 418
+
+=======
+
+Usage hints
+-------------
 
-Genomic regions can really be anything - genes, parts of genes, ChIP-seq
-peaks, favorite genome regions... as long as you provide a proper file
-in BED or INTERVAL format. If you would like to compare different groups of regions
-(i.e. genes from chromosome 2 and 3), you can supply more than 1 BED file, one for each group.
+The supplied genomic regions can really be anything - genes, parts of genes, ChIP-seq peaks, favorite genome regions... as long as you provide a proper file
+in BED or INTERVAL format. If you would like to compare different groups of regions (e.g., genes from chromosome 2 and 3), you can supply more than 1 regions file, one for each group by selecting "Insert Select regions".
+
+.. image:: $PATH_TO_IMAGES/computeMatrix_selectRegions.png
+   :width: 600
+   :height: 150
+
+You can select as many score (bigWig) files as you like. Simply use the Shift and/or Command key while clicking on the files of interest.
 
-computeMatrix can also be used to filter and sort
-regions according to their score by making use of its advanced output options.
+.. image:: $PATH_TO_IMAGES/computeMatrix_selectScores.png
+   :width: 600
+   :height: 136
+
+The multitude of parameters can seem daunting at first - here are the options that we tend to tune most often:
+
+* ``bin Size`` -- The default value works well most of the time, but if you want to have a more finely grained image, decrease the default value (but not smaller than your bigWig file(s)' bin size). If you want to reduce the computation time, increase it.
+* ``Skip zeros`` -- useful to avoid completely blank lines in the heatmap.
+* ``Convert missing values to 0?`` -- If you want to identify clusters of similar regions in an unsupervised fashion using ``plotHeatmap`` and/or ``plotProfile``, you should definitely set this to 'yes'.
 
 
-.. image:: $PATH_TO_IMAGES/flowChart_computeMatrixetc.png
-   :alt: Relationship between computeMatrix, heatmapper and profiler
+Output files
+---------------
+
+The default output is a **gzipped table of values** that is used by both ``plotHeatmap`` and ``plotProfile``.
+
+The optional output files include a) the **regions after sorting and filtering (if selected)** as they were used to calculate the values for the plotting, and b) the uncompressed table that **underlies the heatmap**.
+
+**TIP:** ``computeMatrix`` can also be used to filter and sort regions according to their score by making use of the "advanced output settings".
+
+.. image:: $PATH_TO_IMAGES/computeMatrix_advancedOutput.png
+   :width: 600
+   :height: 189
 
+.. image:: $PATH_TO_IMAGES/computeMatrix_output.png
+   :width: 600
+   :height: 297
 
-You can find more details on the computeMatrix doc page: https://deeptools.readthedocs.org/en/master/content/tools/computeMatrix.html
+Note that these advanced output options are available for ``plotHeatmap`` and ``plotProfile``, too.
+
+See the following table for the optional output options:
 
++-----------------------------------+--------------------+-----------------+-----------------+
+|  **optional output type**         |  **computeMatrix** | **plotHeatmap** | **plotProfile** |
++-----------------------------------+--------------------+-----------------+-----------------+
+| values underlying the heatmap     |  yes               | yes             | no              |
++-----------------------------------+--------------------+-----------------+-----------------+
+| values underlying the profile     | no                 | no              | yes             |
++-----------------------------------+--------------------+-----------------+-----------------+
+| sorted and/or filtered regions    | yes                | yes             | yes             |
++-----------------------------------+--------------------+-----------------+-----------------+
+
+**More examples** can be found in our `Gallery <http://deeptools.readthedocs.org/en/latest/content/example_gallery.html#normalized-chip-seq-signals-and-peak-regions>`_.
 
 -----
 
diff -r 14cb57237e46 -r 275ed3e83de0 deepTools_macros.xml
--- a/deepTools_macros.xml	Mon Jan 25 20:26:32 2016 -0500
+++ b/deepTools_macros.xml	Mon Feb 15 10:34:00 2016 -0500
@@ -72,12 +72,12 @@
     </xml>
 
     <token name="@THREADS@">--numberOfProcessors "\${GALAXY_SLOTS:-4}"</token>
-    <token name="@WRAPPER_VERSION@">2.0.1</token>
+    <token name="@WRAPPER_VERSION@">2.1.0</token>
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="2.7.10">python</requirement>
             <requirement type="binary">@BINARY@</requirement>
-            <requirement type="package" version="2.0.1">deepTools</requirement>
+            <requirement type="package" version="2.1.0">deepTools</requirement>
             <yield />
         </requirements>
         <expand macro="stdio" />
@@ -104,6 +104,7 @@
                     <param name="clustering_options" type="select" label="Clustering algorithm">
                         <option value="none">No clustering</option>
                         <option value="kmeans">Kmeans clustering</option>
+                        <option value="hclust">Hierarchical clustering</option>
                     </param>
                     <when value="kmeans">
                         <param name="k_kmeans" type="integer" value="0" label="Number of clusters to compute"
@@ -112,6 +113,15 @@
                             If more specific clustering methods are required it is advisable to save the underlying matrix and
                             run the clustering using other software."/>
                     </when>
+                    <when value="hclust">
+                        <param name="n_hclust" type="integer" value="0" label="number of clusters to compute."
+                            help="WARNING: This option causes the tool to run for a very long time! When this option is
+                            set, the matrix is split into clusters using the hierarchical clustering algorithm, using ward linkage.
+                            This only works for data that is not grouped, otherwise only the first group will be clustered.
+                            Note that you must have used the '--missingDataAsZero' option within computeMatrix!
+                            If more specific clustering methods are required it is advisable to save the underlying matrix and
+                            run the clustering using other software."/>
+                    </when>
                     <when value="none" />
                 </conditional>
             </when>
@@ -126,6 +136,11 @@
                     --kmeans $advancedOpt.used_multiple_regions.clustering.k_kmeans
                 #end if
             #end if
+            #if $advancedOpt.used_multiple_regions.clustering.clustering_options == 'hclust':
+                #if int($advancedOpt.used_multiple_regions.clustering.n_hclust) > 0:
+                    --hclust $advancedOpt.used_multiple_regions.clustering.n_hclust
+                #end if
+            #end if
         #end if
     </token>
 
@@ -293,6 +308,12 @@
     </xml>
 
     <xml name="multiple_input_bams">
+        <param argument="--bamfiles" type="data" format="bam" min="1"
+            label="Bam file" multiple="true"
+            help="The BAM file must be sorted."/>
+    </xml>
+
+    <xml name="multiple_input_bams_min2">
         <param argument="--bamfiles" type="data" format="bam" min="2"
             label="Bam file" multiple="true"
             help="The BAM file must be sorted."/>
@@ -310,6 +331,7 @@
             help="Title of the plot, to be printed on top of the generated image." />
     </xml>
 
+
     <token name="@multiple_input_bams@">
 <![CDATA[
         #set files=[]
diff -r 14cb57237e46 -r 275ed3e83de0 deepTools_macros.xml.orig
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/deepTools_macros.xml.orig	Mon Feb 15 10:34:00 2016 -0500
@@ -0,0 +1,639 @@
+<macros>
+
+    <xml name="advancedOpt_scaffold">
+        <conditional name="advancedOpt">
+            <param name="showAdvancedOpt" type="select" label="Show advanced options" >
+                <option value="no" selected="true">no</option>
+                <option value="yes">yes</option>
+            </param>
+            <when value="no" />
+            <when value="yes">
+                <yield/>
+            </when>
+        </conditional>
+    </xml>
+
+    <token name="@ADVANCED_OPTS_READ_PROCESSING@">
+        #if $advancedOpt.doExtendCustom.doExtend == 'custom':
+            --extendReads $advancedOpt.doExtendCustom.extendReadsValue
+        #else if $advancedOpt.doExtendCustom.doExtend == 'yes':
+            --extendReads
+        #end if
+        $advancedOpt.ignoreDuplicates
+        $advancedOpt.centerReads
+        #if $advancedOpt.minMappingQuality:
+            --minMappingQuality '$advancedOpt.minMappingQuality'
+        #end if
+        #if $advancedOpt.samFlagInclude:
+            --samFlagInclude $advancedOpt.samFlagInclude
+        #end if
+        #if $advancedOpt.samFlagExclude:
+            --samFlagExclude $advancedOpt.samFlagExclude
+        #end if
+    </token>
+
+    <xml name="heatmap_options">
+        <expand macro="zMin_zMax" />
+        <expand macro="colorMap" />
+        <expand macro="plotTitle" />
+        <expand macro="plotNumbers" />
+    </xml>
+
+    <token name="@HEATMAP_OPTIONS@">
+        #if str($plotting_type.zMin) != "":
+            --zMin $plotting_type.zMin
+        #end if
+        #if str($plotting_type.zMax) != "":
+            --zMax $plotting_type.zMax
+        #end if
+        --colorMap '$plotting_type.colorMap'
+        $plotting_type.plotNumbers
+        --plotTitle '$plotting_type.plotTitle'
+    </token>
+
+
+    <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 are included. The default behavior is to ignore such regions." />
+    </xml>
+
+    <xml name="zMin_zMax">
+        <param argument="--zMin" type="float" value="" optional="true" label="Minimum value for the heatmap intensities"
+            help="If not specified the value is set automatically."/>
+        <param argument="--zMax" type="float" value="" optional="true" label="Maximum value for the heatmap intensities"
+            help="If not specified the value is set automatically."/>
+    </xml>
+
+    <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 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>
+<<<<<<< HEAD
+    <token name="@WRAPPER_VERSION@">2.0.1.0</token>
+=======
+    <token name="@WRAPPER_VERSION@">2.1.0</token>
+>>>>>>> d56067f86089e75354a2fad266002db3730766d9
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="2.7.10">python</requirement>
+            <requirement type="binary">@BINARY@</requirement>
+<<<<<<< HEAD
+            <requirement type="package" version="2.0.1">deepTools</requirement>
+=======
+            <requirement type="package" version="2.1.0">deepTools</requirement>
+>>>>>>> d56067f86089e75354a2fad266002db3730766d9
+            <yield />
+        </requirements>
+        <expand macro="stdio" />
+        <version_command>@BINARY@ --version</version_command>
+    </xml>
+
+    <xml name="smoothLength">
+        <param argument="--smoothLength" type="integer" value="" optional="True" min="1"
+            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>
+
+
+    <xml name="kmeans_clustering">
+        <conditional name="used_multiple_regions">
+            <param name="used_multiple_regions_options" type="select"
+                label="Did you compute the matrix with more than one groups of regions?"
+                help="Would you like to cluster the regions according to the similarity of the signal distribution? This is only possible if you used computeMatrix on only one group of regions.">
+                <option value="yes">Yes, I used multiple groups of regions</option>
+                <option value="no">No, I used only one group</option>
+            </param>
+            <when value="no">
+                <conditional name="clustering">
+                    <param name="clustering_options" type="select" label="Clustering algorithm">
+                        <option value="none">No clustering</option>
+                        <option value="kmeans">Kmeans clustering</option>
+                        <option value="hclust">Hierarchical clustering</option>
+                    </param>
+                    <when value="kmeans">
+                        <param name="k_kmeans" type="integer" value="0" label="Number of clusters to compute"
+                            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."/>
+                    </when>
+                    <when value="hclust">
+                        <param name="n_hclust" type="integer" value="0" label="number of clusters to compute."
+                            help="WARNING: This option causes the tool to run for a very long time! When this option is
+                            set, the matrix is split into clusters using the hierarchical clustering algorithm, using ward linkage.
+                            This only works for data that is not grouped, otherwise only the first group will be clustered.
+                            Note that you must have used the '--missingDataAsZero' option within computeMatrix!
+                            If more specific clustering methods are required it is advisable to save the underlying matrix and
+                            run the clustering using other software."/>
+                    </when>
+                    <when value="none" />
+                </conditional>
+            </when>
+            <when value="yes" />
+        </conditional>
+    </xml>
+
+    <token name="@KMEANS_CLUSTERING@">
+        #if $advancedOpt.used_multiple_regions.used_multiple_regions_options == 'no':
+            #if $advancedOpt.used_multiple_regions.clustering.clustering_options == 'kmeans':
+                #if int($advancedOpt.used_multiple_regions.clustering.k_kmeans) > 0:
+                    --kmeans $advancedOpt.used_multiple_regions.clustering.k_kmeans
+                #end if
+            #end if
+            #if $advancedOpt.used_multiple_regions.clustering.clustering_options == 'hclust':
+                #if int($advancedOpt.used_multiple_regions.clustering.n_hclust) > 0:
+                    --hclust $advancedOpt.used_multiple_regions.clustering.n_hclust
+                #end if
+            #end if
+        #end if
+    </token>
+
+    <xml name="samFlags">
+        <param argument="--samFlagInclude" type="integer" optional="True" value=""
+            label="Include reads based on the SAM flag"
+            help= "For example, to get only reads that are the first mate use a flag of 64. This is useful to count properly paired reads only once, otherwise the second mate will be also considered for the coverage."/>
+        <param argument="--samFlagExclude" type="integer" optional="True" value=""
+            label="Exclude reads based on the SAM flag"
+            help= "For example, to get only reads that map to the forward strand, use --samFlagExclude 16, where 16 is the SAM flag for reads that map to the reverse strand."/>
+    </xml>
+
+    <xml name="read_processing_options">
+        <expand macro="extendReads" />
+        <expand macro="ignoreDuplicates" />
+        <expand macro="centerReads" />
+        <expand macro="minMappingQuality" />
+        <expand macro="samFlags" />
+    </xml>
+
+    <xml name="plotNumbers">
+        <param argument="--plotNumbers" type="boolean" truevalue="--plotNumbers" falsevalue=""
+            label="Plot the correlation value"
+            help="If set, then the correlation number is plotted on top of the heatmap."/>
+    </xml>
+
+    <xml name="extendReads">
+        <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 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>
+            </param>
+            <when value="no" />
+            <when value="yes" />
+            <when value="custom">
+                <param name="extendReadsValue" type="integer" value="300" min="1"
+                    label="Extend reads to the given average fragment size"
+                    help="Extend all reads to this length" />
+            </when>
+        </conditional>
+    </xml>
+
+    <xml name="corMethod">
+        <param argument="--corMethod" type="select" label="Correlation method">
+            <option value="spearman" selected="True">Spearman</option>
+            <option value="pearson">Pearson</option>
+        </param>
+    </xml>
+
+    <xml name="distanceBetweenBins">
+        <param argument="--distanceBetweenBins" type="integer" value="0" min="0"
+            label="Distance between bins"
+            help="By default, multiBamSummary considers consecutive bins of
+                the specified 'Bin size'. However, to reduce the
+                computation time, a larger distance between bins can
+                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 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">
+        <param argument="--ignoreDuplicates" type="boolean" truevalue="--ignoreDuplicates" falsevalue=""
+            label="Ignore duplicates"
+            help="If set, reads that have the same orientation and start position will be considered only once. If reads are paired, the mate position also has to coincide to ignore a read." />
+    </xml>
+
+    <xml name="sortUsing">
+        <param argument="--sortUsing" type="select" label="Method used for sorting"
+            help="For each row the method is computed.">
+            <option value="mean" selected="true">mean</option>
+            <option value="median">median</option>
+            <option value="min">min</option>
+            <option value="max">max</option>
+            <option value="sum">sum</option>
+            <option value="region_length">region length</option>
+        </param>
+    </xml>
+
+    <xml name="sortRegions">
+        <param argument="--sortRegions" type="select" label="Sort regions"
+            help="Whether the heatmap should present the regions sorted. The default is to sort in descending order based on the mean value per region.">
+            <option value="no">no ordering</option>
+            <option value="descend" selected="true">descending order</option>
+            <option value="ascend">ascending order</option>
+        </param>
+    </xml>
+
+    <xml name="minMappingQuality">
+        <param argument="--minMappingQuality" type="integer" optional="true" value="1" min="1"
+            label="Minimum mapping quality"
+            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 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, so this is only needed for single-end data."/>
+    </xml>
+
+    <xml name="scaleFactor">
+        <param argument="--scaleFactor" type="float" value="1" label="Scaling factor"
+            help="When used in combination with --normalizeTo1x or
+                --normalizeUsingRPKM, the computed scaling factor will
+                be multiplied by the given scale factor." />
+    </xml>
+
+    <xml name="scaleFactors">
+        <param name="scaleFactor1" type="float" value="1" label="Scale factor for treatment" help="(--scaleFactors)"/>
+        <param name="scaleFactor2" type="float" value="1" label="Scale factor for input" help="(--scaleFactors)"/>
+    </xml>
+
+    <xml name="stdio">
+        <stdio>
+            <exit_code range="1:" />
+            <exit_code range=":-1" />
+            <regex match="Error:" />
+            <regex match="Exception:" />
+            <regex match="EXception:" />
+            <regex match="Traceback" />
+        </stdio>
+    </xml>
+
+    <xml name="pseudocount">
+        <param argument="--pseudocount" type="float" value="1" label="Pseudocount" help="Small number to avoid dividing by zero."/>
+    </xml>
+
+    <token name="@REFERENCES@">
+
+.. class:: infomark
+
+For more information on the tools, please visit our `help site`_.
+
+If you would like to give us feedback or you run into any trouble, please send an email to deeptools@googlegroups.com
+
+This tool is developed by the `Bioinformatics and Deep-Sequencing Unit`_ at the `Max Planck Institute for Immunobiology and Epigenetics`_.
+
+.. _Bioinformatics and Deep-Sequencing Unit: http://www.ie-freiburg.mpg.de/bioinformaticsfac
+.. _Max Planck Institute for Immunobiology and Epigenetics: http://www3.ie-freiburg.mpg.de
+.. _help site: https://deeptools.readthedocs.org/
+
+    </token>
+    <xml name="citations">
+        <citations>
+            <citation type="doi">10.1093/nar/gku365</citation>
+            <yield />
+        </citations>
+    </xml>
+
+    <xml name="multiple_input_bams">
+        <param argument="--bamfiles" type="data" format="bam" min="2"
+            label="Bam file" multiple="true"
+            help="The BAM file must be sorted."/>
+    </xml>
+
+    <xml name="multiple_input_bigwigs">
+        <param argument="--bigwigfiles" type="data" format="bigwig" multiple="True" min="2"
+            label="Bigwig file"
+            help="A Bigwig file."/>
+    </xml>
+
+    <xml name="plotTitle">
+        <param argument="--plotTitle" type="text" value="" size="30" optional="True"
+            label="Title of the plot"
+            help="Title of the plot, to be printed on top of the generated image." />
+    </xml>
+
+
+    <token name="@multiple_input_bams@">
+<![CDATA[
+        #set files=[]
+        #set labels=[]
+        #for $counter, $bamfile in enumerate($bamfiles):
+            ln -s "${bamfile}" "./${counter}.bam" &&
+            ln -s "${bamfile.metadata.bam_index}" "./${counter}.bam.bai" &&
+            #silent $files.append('%s.bam' % $counter)
+            #silent $labels.append('%s' % ($bamfile.display_name))
+        #end for
+]]>
+    </token>
+
+    <token name="@multiple_input_bigwigs@">
+<![CDATA[
+        #set files=[]
+        #set labels=[]
+        #for $counter, $bigwig in enumerate($bigwigfiles):
+            ln -s "${bigwig}" "${counter}.bw" &&
+            #silent $files.append('%s.bw' % $counter)
+            #silent $labels.append('%s' % ($bigwig.display_name))
+        #end for
+]]>
+    </token>
+
+    <xml name="reference_genome_source">
+        <conditional name="source">
+            <param name="ref_source" type="select" label="Reference genome">
+                <option value="cached">locally cached</option>
+                <option value="history">in your history</option>
+            </param>
+            <when value="cached">
+                <param name="input1_2bit" type="select" label="Using reference genome" help="If your genome of interest is not listed, contact the Galaxy team">
+                    <options from_data_table="lastz_seqs">
+                        <filter type="sort_by" column="1" />
+                        <validator type="no_options" message="No indexes are available." />
+                    </options>
+                </param>
+            </when>
+            <when value="history">
+                <param name="input1" type="data" format="twobit" label="Select a reference dataset in 2bit format" />
+            </when>
+        </conditional>
+    </xml>
+
+    <token name="@reference_genome_source@">
+    #if $source.ref_source=="history":
+        --genome $source.input1
+    #else:
+        --genome "$source.input1_2bit.fields.path"
+    #end if
+    </token>
+
+    <xml name="effectiveGenomeSize">
+        <conditional name="effectiveGenomeSize">
+            <param name="effectiveGenomeSize_opt" type="select" label="Effective genome size"
+                help="The effective genome size is the portion of the genome that is mappable. Large fractions of the genome are stretches of NNNN that should be discarded.
+                    Also, if repetitive regions were not included in the mapping of reads, the effective genome size needs to be adjusted accordingly.
+                    See Table 2 of http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0030377 or http://www.nature.com/nbt/journal/v27/n1/fig_tab/nbt.1518_T1.html for several effective genome sizes.">
+                <option value="93260000">ce10 (93260000)</option>
+                <option value="121400000">dm3 (121400000)</option>
+                <option value="2451960000" selected="true">hg19 (2451960000)</option>
+                <option value="2150570000">mm9 (2150570000)</option>
+                <option value="specific">user specified</option>
+            </param>
+            <when value="specific">
+                <param argument="--effectiveGenomeSize" type="integer" value="" label="Effective genome size" help="e.g. ce10: 93260000, dm3: 121400000, hg19: 2451960000, mm9: 2150570000"/>
+            </when>
+            <when value="2150570000" />
+            <when value="2451960000" />
+            <when value="121400000" />
+            <when value="93260000" />
+        </conditional>
+    </xml>
+
+    <xml name="skipNAs">
+        <param argument="--skipNAs" type="boolean" truevalue="--skipNAs" falsevalue="" checked="False"
+            label="Ignore missing data?"
+            help="This parameter determines if non-covered regions
+                 (regions without overlapping reads) in a bam/bigWig file
+                 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 should be ignored.
+                 (default: False)" />
+    </xml>
+
+    <xml name="input_save_matrix_values">
+        <param argument="--saveMatrix" type="boolean" label="Save the matrix of values underlying the heatmap"/>
+    </xml>
+
+    <xml name="input_graphic_output_settings">
+        <conditional name="output" >
+            <param name="showOutputSettings" type="select" label="Show advanced output settings" >
+                <option value="no" selected="true">no</option>
+                <option value="yes">yes</option>
+            </param>
+            <when value="no" />
+            <when value="yes">
+                <yield />
+                <param name="saveSortedRegions" type="boolean" label="Save the regions after skipping zeros or min/max threshold values" help="The order of the regions in the file follows the sorting order selected. This is useful, for example, to generate other heatmaps keeping the sorting of the first heatmap."/>
+            </when>
+        </conditional>
+    </xml>
+
+
+    <xml name="input_image_file_format">
+        <param argument="--outFileFormat" type="select" label="Image file format">
+            <option value="png" selected="true">png</option>
+            <option value="pdf">pdf</option>
+            <option value="svg">svg</option>
+            <option value="eps">eps</option>
+        </param>
+    </xml>
+
+    <xml name="output_image_file_format">
+        <data format="png" name="outFileName" label="${tool.name} image">
+            <change_format>
+                <when input="output.outFileFormat" value="pdf" format="pdf" />
+                <when input="output.outFileFormat" value="svg" format="svg" />
+                <when input="output.outFileFormat" value="eps" format="eps" />
+            </change_format>
+        </data>
+    </xml>
+
+    <xml name="output_image_file_format_not_nested">
+        <data format="png" name="outFileName" label="${tool.name} image">
+            <change_format>
+                <when input="outFileFormat" value="pdf" format="pdf" />
+                <when input="outFileFormat" value="svg" format="svg" />
+                <when input="outFileFormat" value="eps" format="eps" />
+            </change_format>
+        </data>
+    </xml>
+
+    <xml name="output_save_matrix_values">
+        <data format="tabular" name="outFileNameMatrix" label="${tool.name} on ${on_string}: Heatmap values">
+            <filter>
+            ((
+                output['showOutputSettings'] == 'yes' and
+                output['saveMatrix'] is True
+            ))
+            </filter>
+        </data>
+    </xml>
+
+    <xml name="output_graphic_outputs">
+        <data format="bed" name="outFileSortedRegions" label="${tool.name} on ${on_string}: sorted/filtered regions">
+            <filter>
+            ((
+                output['showOutputSettings'] == 'yes' and
+                output['saveSortedRegions'] is True
+            ))
+            </filter>
+        </data>
+    </xml>
+
+    <xml name="colorMap">
+        <param name="colorMap" type="select" label="Color map to use for the heatmap" help=" Available color map names can be found here: http://www.astro.lsa.umich.edu/~msshin/science/code/matplotlib_cm/">
+            <option value="RdYlBu" selected="true">RdYlBu</option>
+            <option value="Accent">Accent</option>
+            <option value="Spectral">Spectral</option>
+            <option value="Set1">Set1</option>
+            <option value="Set2">Set2</option>
+            <option value="Set3">Set3</option>
+            <option value="Dark2">Dark2</option>
+            <option value="Reds">Reds</option>
+            <option value="Oranges">Oranges</option>
+            <option value="Greens">Greens</option>
+            <option value="Blues">Blues</option>
+            <option value="Greys">Greys</option>
+            <option value="Purples">Purples</option>
+            <option value="Paired">Paired</option>
+            <option value="Pastel1">Pastel1</option>
+            <option value="Pastel2">Pastel2</option>
+            <option value="spring">spring</option>
+            <option value="summer">summer</option>
+            <option value="autumn">autumn</option>
+            <option value="winter">winter</option>
+            <option value="hot">hot</option>
+            <option value="coolwarm">coolwarm</option>
+            <option value="cool">cool</option>
+            <option value="seismic">seismic</option>
+            <option value="terrain">terrain</option>
+            <option value="ocean">ocean</option>
+            <option value="rainbow">rainbow</option>
+            <option value="bone">bone</option>
+            <option value="flag">flag</option>
+            <option value="prism">prism</option>
+            <option value="cubehelix">cubehelix</option>
+            <option value="binary">binary</option>
+            <option value="pink">pink</option>
+            <option value="gray">gray</option>
+            <option value="copper">copper</option>
+            <option value="BrBG">BrBG</option>
+            <option value="BuGn">BuGn</option>
+            <option value="BuPu">BuPu</option>
+            <option value="GnBu">GnBu</option>
+            <option value="OrRd">OrRd</option>
+            <option value="PiYG">PiYG</option>
+            <option value="PRGn">PRGn</option>
+            <option value="PuOr">PuOr</option>
+            <option value="PuRd">PuRd</option>
+            <option value="PuBu">PuBu</option>
+            <option value="RdBu">RdBu</option>
+            <option value="RdGy">RdGy</option>
+            <option value="RdPu">RdPu</option>
+            <option value="YlGn">YlGn</option>
+            <option value="PuBuGn">PuBuGn</option>
+            <option value="RdYlGn">RdYlGn</option>
+            <option value="YlGnBu">YlGnBu</option>
+            <option value="YlOrBr">YlOrBr</option>
+            <option value="YlOrRd">YlOrRd</option>
+            <option value="gist_gray">gist_gray</option>
+            <option value="gist_stern">gist_stern</option>
+            <option value="gist_earth">gist_earth</option>
+            <option value="gist_yarg">gist_yarg</option>
+            <option value="gist_ncar">gist_ncar</option>
+            <option value="gist_rainbow">gist_rainbow</option>
+            <option value="gist_heat">gist_heat</option>
+            <option value="gnuplot">gnuplot</option>
+            <option value="gnuplot2">gnuplot2</option>
+            <option value="CMRmap">CMRmap</option>
+            <option value="bwr">bwr</option>
+            <option value="hsv">hsv</option>
+            <option value="brg">brg</option>
+            <option value="jet">jet</option>
+            <option value="afmhot">afmhot</option>
+            <option value="Accent_r">Accent reversed</option>
+            <option value="Spectral_r">Spectral reversed</option>
+            <option value="Set1_r">Set1 reversed</option>
+            <option value="Set2_r">Set2 reversed</option>
+            <option value="Set3_r">Set3 reversed</option>
+            <option value="Dark2_r">Dark2 reversed</option>
+            <option value="Reds_r">Reds reversed</option>
+            <option value="Oranges_r">Oranges reversed</option>
+            <option value="Greens_r">Greens reversed</option>
+            <option value="Blues_r">Blues reversed</option>
+            <option value="Greys_r">Greys reversed</option>
+            <option value="Purples_r">Purples reversed</option>
+            <option value="Paired_r">Paired reversed</option>
+            <option value="Pastel1_r">Pastel1 reversed</option>
+            <option value="Pastel2_r">Pastel2 reversed</option>
+            <option value="spring_r">spring reversed</option>
+            <option value="summer_r">summer reversed</option>
+            <option value="autumn_r">autumn reversed</option>
+            <option value="winter_r">winter reversed</option>
+            <option value="hot_r">hot reversed</option>
+            <option value="coolwarm_r">coolwarm reversed</option>
+            <option value="cool_r">cool reversed</option>
+            <option value="seismic_r">seismic reversed</option>
+            <option value="terrain_r">terrain reversed</option>
+            <option value="ocean_r">ocean reversed</option>
+            <option value="rainbow_r">rainbow reversed</option>
+            <option value="bone_r">bone reversed</option>
+            <option value="flag_r">flag reversed</option>
+            <option value="prism_r">prism reversed</option>
+            <option value="cubehelix_r">cubehelix reversed</option>
+            <option value="binary_r">binary reversed</option>
+            <option value="pink_r">pink reversed</option>
+            <option value="gray_r">gray reversed</option>
+            <option value="copper_r">copper reversed</option>
+            <option value="BrBG_r">BrBG reversed</option>
+            <option value="BuGn_r">BuGn reversed</option>
+            <option value="BuPu_r">BuPu reversed</option>
+            <option value="GnBu_r">GnBu reversed</option>
+            <option value="OrRd_r">OrRd reversed</option>
+            <option value="PiYG_r">PiYG reversed</option>
+            <option value="PRGn_r">PRGn reversed</option>
+            <option value="PuOr_r">PuOr reversed</option>
+            <option value="PuRd_r">PuRd reversed</option>
+            <option value="PuBu_r">PuBu reversed</option>
+            <option value="RdBu_r">RdBu reversed</option>
+            <option value="RdGy_r">RdGy reversed</option>
+            <option value="RdPu_r">RdPu reversed</option>
+            <option value="YlGn_r">YlGn reversed</option>
+            <option value="PuBuGn_r">PuBuGn reversed</option>
+            <option value="RdYlBu_r">RdYlBu reversed</option>
+            <option value="RdYlGn_r">RdYlGn reversed</option>
+            <option value="YlGnBu_r">YlGnBu reversed</option>
+            <option value="YlOrBr_r">YlOrBr reversed</option>
+            <option value="YlOrRd_r">YlOrRd reversed</option>
+            <option value="gist_gray_r">gist_gray reversed</option>
+            <option value="gist_stern_r">gist_stern reversed</option>
+            <option value="gist_earth_r">gist_earth reversed</option>
+            <option value="gist_yarg_r">gist_yarg reversed</option>
+            <option value="gist_ncar_r">gist_ncar reversed</option>
+            <option value="gist_rainbow_r">gist_rainbow reversed</option>
+            <option value="gist_heat_r">gist_heat reversed</option>
+            <option value="gnuplot_r">gnuplot reversed</option>
+            <option value="gnuplot2_r">gnuplot2 reversed</option>
+            <option value="CMRmap_r">CMRmap reversed</option>
+            <option value="bwr_r">bwr reversed</option>
+            <option value="hsv_r">hsv reversed</option>
+            <option value="brg_r">brg reversed</option>
+            <option value="jet_r">jet reversed</option>
+            <option value="afmhot_r">afmhot reversed</option>
+        </param>
+
+    </xml>
+
+</macros>
diff -r 14cb57237e46 -r 275ed3e83de0 readme.rst
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diff -r 14cb57237e46 -r 275ed3e83de0 test-data/bamPEFragmentSize_result1.txt
--- a/test-data/bamPEFragmentSize_result1.txt	Mon Jan 25 20:26:32 2016 -0500
+++ b/test-data/bamPEFragmentSize_result1.txt	Mon Feb 15 10:34:00 2016 -0500
@@ -2,19 +2,19 @@
 
 
 Fragment lengths:
-Min.: 241
+Min.: 241.0
 1st Qu.: 241.5
 Mean: 244.666666667
 Median: 242.0
 3rd Qu.: 246.5
-Max.: 251
+Max.: 251.0
 Std: 4.49691252108
 
 Read lengths:
-Min.: 251
+Min.: 251.0
 1st Qu.: 251.0
 Mean: 251.0
 Median: 251.0
 3rd Qu.: 251.0
-Max.: 251
+Max.: 251.0
 Std: 0.0
diff -r 14cb57237e46 -r 275ed3e83de0 test-data/bigwigCompare_result1.bw
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diff -r 14cb57237e46 -r 275ed3e83de0 test-data/computeMatrix2.bed
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diff -r 14cb57237e46 -r 275ed3e83de0 test-data/correctGCBias_result1.bam
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diff -r 14cb57237e46 -r 275ed3e83de0 test-data/plotCoverage_result1.png
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diff -r 14cb57237e46 -r 275ed3e83de0 test-data/plotCoverage_result1.tabular
--- a/test-data/plotCoverage_result1.tabular	Mon Jan 25 20:26:32 2016 -0500
+++ b/test-data/plotCoverage_result1.tabular	Mon Feb 15 10:34:00 2016 -0500
@@ -1,16570 +1,16570 @@
-'bowtie2-test1.bam'	'bowtie2-test1.bam'
-23	23
-35	35
-35	35
-35	35
-35	35
-35	35
-35	35
-35	35
-35	35
-35	35
-35	35
-35	35
-35	35
-35	35
-35	35
-35	35
-35	35
-35	35
-35	35
-35	35
-35	35
-35	35
-35	35
-35	35
-35	35
-35	35
-35	35
-35	35
-35	35
-35	35
-35	35
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diff -r 14cb57237e46 -r 275ed3e83de0 test-data/sequence.2bit
diff -r 14cb57237e46 -r 275ed3e83de0 test-data/test.bw
diff -r 14cb57237e46 -r 275ed3e83de0 tool-data/deepTools_seqs.loc.sample
diff -r 14cb57237e46 -r 275ed3e83de0 tool_dependencies.xml
--- a/tool_dependencies.xml	Mon Jan 25 20:26:32 2016 -0500
+++ b/tool_dependencies.xml	Mon Feb 15 10:34:00 2016 -0500
@@ -1,9 +1,9 @@
 <?xml version="1.0"?>
 <tool_dependency>
     <package name="python" version="2.7.10">
-        <repository changeset_revision="0339c4a9b87b" name="package_python_2_7_10" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="0339c4a9b87b" name="package_python_2_7_10" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
     </package>
-    <package name="deepTools" version="2.0.1">
-        <repository changeset_revision="1fb61fa32733" name="package_python_2_7_deeptools_2_0_1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
+    <package name="deepTools" version="2.1.0">
+        <repository changeset_revision="2c54c7c38299" name="package_python_2_7_deeptools_2_1_0" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
     </package>
 </tool_dependency>
diff -r 14cb57237e46 -r 275ed3e83de0 tool_dependencies.xml.orig
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml.orig	Mon Feb 15 10:34:00 2016 -0500
@@ -0,0 +1,76 @@
+<?xml version='1.0' encoding='utf-8'?>
+<tool_dependency>
+    <package name="numpy" version="1.9">
+        <repository name="package_python_2_7_numpy_1_9" owner="iuc" prior_installation_required="True" />
+    </package>
+    <package name="pybigwig" version="0.2.4">
+        <repository name="package_python_2_7_10_pybigwig_0_2_4" owner="iuc" prior_installation_required="True"/>
+    </package>
+    <package name="matplotlib" version="1.4">
+        <repository name="package_python_2_7_matplotlib_1_4" owner="iuc" prior_installation_required="True" />
+    </package>
+    <package name="scipy" version="0.14">
+        <repository name="package_python_2_7_scipy_0_14" owner="iuc" prior_installation_required="True" />
+    </package>
+<<<<<<< HEAD
+    <package name="deepTools" version="2.0.1">
+        <repository name="package_python_2_7_deeptools_2_0_1" owner="iuc"/>
+=======
+    <package name="pysam" version="0.8.3">
+        <repository name="package_python_2_7_pysam_0_8_3" owner="iuc" prior_installation_required="True" />
+    </package>
+    <package name="bx-python" version="0.7.2">
+        <repository name="package_python_2_7_bx_python_0_7" owner="iuc" prior_installation_required="True" />
+    </package>
+    <package name="python" version="2.7.10">
+        <repository name="package_python_2_7_10" owner="iuc" prior_installation_required="True" />
+>>>>>>> d56067f86089e75354a2fad266002db3730766d9
+    </package>
+    <package name="deepTools" version="2.1.0">
+        <install version="1.0">
+            <actions>
+                <action type="setup_python_environment">
+                    <repository name="package_python_2_7_10" owner="iuc">
+                        <package name="python" version="2.7.10" />
+                    </repository>
+                    <repository name="package_python_2_7_pysam_0_8_3" owner="iuc">
+                        <package name="pysam" version="0.8.3" />
+                    </repository>
+                    <repository name="package_python_2_7_numpy_1_9" owner="iuc">
+                        <package name="numpy" version="1.9" />
+                    </repository>
+                    <repository name="package_python_2_7_matplotlib_1_4" owner="iuc">
+                        <package name="matplotlib" version="1.4" />
+                    </repository>
+                    <repository name="package_python_2_7_scipy_0_14" owner="iuc">
+                        <package name="scipy" version="0.14" />
+                    </repository>
+                    <repository name="package_python_2_7_bx_python_0_7" owner="iuc">
+                        <package name="bx-python" version="0.7.2" />
+                    </repository>
+                    <repository name="package_python_2_7_10_pybigwig_0_2_4" owner="iuc">
+                        <package name="pybigwig" version="0.2.4" />
+                    </repository>
+                    <package sha256sum="3bf835afde02cd5247198db3e01f690899e1fdb86e1821a83ac940d807baa857">https://pypi.python.org/packages/source/d/deepTools/deepTools-2.1.0.tar.gz</package>
+                </action>
+
+                <action type="set_environment">
+                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
+                    <environment_variable name="PYTHONPATH" action="prepend_to">$INSTALL_DIR</environment_variable>
+                    <environment_variable name="DEEPTOOLS_ROOT_PATH" action="set_to">$INSTALL_DIR</environment_variable>
+                    <environment_variable name="DEEPTOOLS_PYTHONPATH" action="set_to">$INSTALL_DIR</environment_variable>
+                    <environment_variable name="DEEPTOOLS_PATH" action="set_to">$INSTALL_DIR/bin</environment_variable>
+                    <!-- libpng lib path -->
+                    <environment_variable action="set_to" name="LIBPNG_LIB_PATH">$ENV[LIBPNG_LIB_PATH]</environment_variable>
+                    <environment_variable action="prepend_to" name="LD_LIBRARY_PATH">$ENV[LIBPNG_LIB_PATH]</environment_variable>
+                    <!-- disable the config file of deepTools -->
+                    <environment_variable name="DEEP_TOOLS_NO_CONFIG" action="set_to">TRUE</environment_variable>
+                </action>
+             </actions>
+         </install>
+         <readme>
+            Installation of deepTools from Fidel Ramirez.
+            https://github.com/fidelram/deepTools
+         </readme>
+     </package>
+</tool_dependency>