--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/computeMatrix.xml	Mon Jan 25 20:26:32 2016 -0500
@@ -0,0 +1,264 @@
+<tool id="deeptools_compute_matrix" name="computeMatrix" version="@WRAPPER_VERSION@.0">
+    <description>prepares data for plotting a heatmap or a profile of given regions</description>
+    <macros>
+        <token name="@BINARY@">computeMatrix</token>
+        <import>deepTools_macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command>
+<![CDATA[
+        #import tempfile
+
+        @BINARY@
+
+            $mode.mode_select
+            --regionsFileName
+            #for $rf in $regionsFiles:
+                '$rf.regionsFile' 
+            #end for
+            --scoreFileName
+            #for $bw in $scoreFileName:
+                '$bw' 
+            #end for
+            --outFileName '$outFileName'
+
+            @THREADS@
+
+            #if $output.showOutputSettings == "yes"
+                #if $output.saveMatrix:
+                --outFileNameMatrix '$outFileNameMatrix'
+                #end if
+
+                #if $output.saveSortedRegions:
+                    --outFileSortedRegions '$outFileSortedRegions'
+                #end if
+            #end if
+
+            #if $mode.mode_select == "reference-point":
+                --referencePoint $mode.referencePoint
+                $mode.nanAfterEnd
+                --beforeRegionStartLength $mode.beforeRegionStartLength
+                --afterRegionStartLength $mode.afterRegionStartLength
+            #else
+                --regionBodyLength $mode.regionBodyLength
+                #if $mode.regionStartLength.regionStartLength_select == "yes":
+                    --beforeRegionStartLength $mode.regionStartLength.beforeRegionStartLength
+                    --afterRegionStartLength $mode.regionStartLength.afterRegionStartLength
+                #end if
+            #end if
+
+            #if $advancedOpt.showAdvancedOpt == "yes":
+                --sortRegions '$advancedOpt.sortRegions'
+                --sortUsing '$advancedOpt.sortUsing'
+                --averageTypeBins '$advancedOpt.averageTypeBins'
+                $advancedOpt.skipNAs
+                $advancedOpt.skipZeros
+                --binSize $advancedOpt.binSize
+
+                #if $advancedOpt.minThreshold is not None and str($advancedOpt.minThreshold) != '':
+                    --minThreshold $advancedOpt.minThreshold
+                #end if
+                #if $advancedOpt.maxThreshold is not None and str($advancedOpt.maxThreshold) != '':
+                    --maxThreshold $advancedOpt.maxThreshold
+                #end if
+                #if $advancedOpt.scale is not None and str($advancedOpt.scale) != '':
+                    --scale $advancedOpt.scale
+                #end if
+
+            #end if
+]]>
+    </command>
+    <inputs>
+
+        <repeat name="regionsFiles" title="Select regions" min="1">
+            <param name="regionsFile" format="bed" type="data" label="Regions to plot"
+                help="File, in BED format, containing the regions to plot."/>
+        </repeat>
+
+        <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
+            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
+                by the user. Reference-point refers to a position within the BED
+                regions (e.g start of 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>
+                <option value="reference-point">reference-point</option>
+            </param>
+
+            <when value="scale-regions" >
+                <param argument="--regionBodyLength" type="integer" value="500"
+                    label="Distance in bases to which all regions are going to be fit" help=""/>
+                <conditional name="regionStartLength">
+                    <param name="regionStartLength_select" type="select" label="Set distance up- and downstream of the given regions">
+                        <option value="no" selected="true">no</option>
+                        <option value="yes">yes</option>
+                    </param>
+                    <when value="no" />
+                    <when value="yes">
+                        <param argument="--beforeRegionStartLength" type="integer" value="1000" min="1"
+                            label="Distance upstream of the region start position"
+                            help="If the regions are genes, this would be the
+                            distance upstream of the transcription start site."/>
+                        <param argument="--afterRegionStartLength" type="integer" value="1000" min="1"
+                            label="Distance downstream of the region end position"
+                            help="If the regions are genes, this would be the
+                            distance downstream of the transcription end site."/>
+                    </when>
+                </conditional>
+            </when>
+            <when value="reference-point">
+                <param name="referencePoint" type="select" label="The reference point for the plotting">
+                    <option value="TSS" selected="true">beginning of region (e.g. TSS)</option>
+                    <option	 value="TES">end of region (e.g. TES)</option>
+                    <option value="center">center of region</option>
+                </param>
+                <param name="nanAfterEnd" type="boolean" truevalue="--nanAfterEnd" falsevalue=""
+                    label="Discard any values after the region end"
+                    help="This is useful to visualize the region end when not using the
+                    scale-regions mode and when the reference-point is set to the TSS. (--nanAfterEnd)"/>
+                <param name="beforeRegionStartLength" type="integer" value="1000" min="1"
+                    label="Distance upstream of the start site of the regions defined in the region file"
+                    help="If the regions are genes, this would be the distance upstream of the transcription start site. (--beforeRegionStartLength)"/>
+                <param name="afterRegionStartLength" type="integer" value="1000" min="1"
+                    label="Distance downstream of the end site of the given regions"
+                    help="If the regions are genes, this would be the distance downstream of the transcription end site. (--afterRegionStartLength)"/>
+            </when>
+        </conditional>
+
+        <expand macro="input_graphic_output_settings">
+            <expand macro="input_save_matrix_values" />
+        </expand>
+
+        <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">
+                <param name="binSize" type="integer" value="50" min="1"
+                    label="Length, in bases, of non-overlapping bins used for averaging the score over the regions length"
+                    help="(--binSize)"/>
+
+                <expand macro="sortRegions" />
+                <expand macro="sortUsing" />
+
+                <param name="averageTypeBins" type="select"
+                    label="Define the type of statistic that should be displayed."
+                    help="The value is computed for each bin. (--averageTypeBins)">
+                    <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="std">std</option>
+                </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." />
+
+                <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
+                    unmappable areas and can bias the overall results. (--minThreshold)"/>
+                <param name="maxThreshold" type="float" optional="True"
+                    label="Maximum threshold"
+                    help="Any region containing a value that is equal or higher that this
+                    numeric value will be skipped. The max threshold is useful to skip those
+                    few regions with very high read counts (e.g. major satellites) that may
+                    bias the average values. (--maxThreshold)"/>
+                <param name="scale" type="float" optional="True" label="Scaling factor"
+                    help="If set, all values are multiplied by this number. (--scale)"/>
+            </when>
+        </conditional>
+    </inputs>
+    <outputs>
+        <data format="deeptools_compute_matrix_archive" name="outFileName" label="${tool.name} on ${on_string}: Matrix" />
+        <expand macro="output_graphic_outputs" />
+        <expand macro="output_save_matrix_values" />
+    </outputs>
+    <!--
+    computeMatrix -S test.bw -R test2.bed -a 100 -b 100 -bs 1
+    -->
+    <tests>
+        <test>
+            <param name="regionsFile" value="computeMatrix1.bed" ftype="bed" />
+            <param name="scoreFileName" value="bamCoverage_result4.bw" ftype="bigwig" />
+            <param name="showAdvancedOpt" value="yes" />
+            <param name="mode_select" value="reference-point" />
+            <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" />
+        </test>
+        <test>
+            <param name="regionsFile" value="computeMatrix2.bed" ftype="bed" />
+            <param name="scoreFileName" value="computeMatrix2.bw" ftype="bigwig" />
+            <param name="showAdvancedOpt" value="yes" />
+            <param name="mode_select" value="reference-point" />
+            <param name="binSize" value="10" />
+            <param name="beforeRegionStartLength" value="10" />
+            <param name="afterRegionStartLength" value="10" />
+            <output name="outFileName" file="computeMatrix_result2.gz" ftype="deeptools_compute_matrix_archive" compare="sim_size" />
+        </test>
+        <test>
+            <param name="regionsFile" value="computeMatrix2.bed" ftype="bed" />
+            <param name="scoreFileName" value="computeMatrix2.bw" ftype="bigwig" />
+            <param name="showAdvancedOpt" value="yes" />
+            <param name="mode_select" value="scale-regions" />
+            <param name="endLabel" value="END" />
+            <param name="regionStartLength" value="yes" />
+            <output name="outFileName" file="computeMatrix_result3.gz" ftype="deeptools_compute_matrix_archive" compare="sim_size" />
+        </test>
+    </tests>
+  <help>
+<![CDATA[
+**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.
+
+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.
+
+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/flowChart_computeMatrixetc.png
+   :alt: Relationship between computeMatrix, heatmapper and profiler
+
+
+You can find more details on the computeMatrix doc page: https://deeptools.readthedocs.org/en/master/content/tools/computeMatrix.html
+
+
+-----
+
+@REFERENCES@
+]]>
+    </help>
+    <expand macro="citations" />
+</tool>

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/datatypes_conf.xml	Mon Jan 25 20:26:32 2016 -0500
@@ -0,0 +1,7 @@
+<?xml version="1.0"?>
+<datatypes>
+    <registration>
+        <datatype extension="deeptools_compute_matrix_archive" type="galaxy.datatypes.binary:CompressedArchive" subclass="True" display_in_upload="True"/>
+        <datatype extension="deeptools_coverage_matrix" type="galaxy.datatypes.binary:CompressedArchive" subclass="True" display_in_upload="True"/>
+    </registration>
+</datatypes>

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/deepTools_macros.xml	Mon Jan 25 20:26:32 2016 -0500
@@ -0,0 +1,615 @@
+<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>
+    <token name="@WRAPPER_VERSION@">2.0.1</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>
+            <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>
+                    </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="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
+        #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>

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/readme.rst	Mon Jan 25 20:26:32 2016 -0500
@@ -0,0 +1,74 @@
+========================
+Galaxy deeptools wrapper
+========================
+
+deepTools are user-friendly tools for the normalization and visualization of 
+deep-sequencing data.
+They address the challenge of visualizing the large amounts of data that are now
+routinely generated from sequencing centers in a meaningful way. 
+To do so, deepTools contain useful routines to process the mapped reads data 
+through removal of duplicates and different filtering options to create coverage
+files in standard bedGraph and bigWig file formats. deepTools allow the creation
+of normalized coverage files or the comparison between two files 
+(for example, treatment and control). Finally, using such normalized and 
+standardized files, multiple visualizations can be created to identify 
+enrichments with functional annotations of the genome. 
+For a gallery of images that can be produced and a description 
+of the tools see our poster_.
+
+.. _poster: http://f1000.com/posters/browse/summary/1094053
+
+deeptools is developed under here:
+
+    https://github.com/fidelram/deepTools
+
+For support, questions, or feature requests contact: deeptools@googlegroups.com
+
+
+============
+Installation
+============
+
+Requirements: python-2.7
+
+Galaxy should be able to automatically install all other dependencies, such as numpy or scipy.
+
+For the best performance we recommend to install blas/lapack/atlas in your environment before
+installing deepTools from the Tool Shed.
+
+
+========
+Citation
+========
+
+deeptools are currently under review. In the meantime please refere to https://github.com/fidelram/deepTools.
+
+
+=======
+History
+=======
+
+ * v1.0:        Initial public release
+ * v1.5.8.2:    Include new citation tag, update version to 1.5.8.2 and change wrapper version
+
+
+Licence (MIT)
+=============
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+THE SOFTWARE.

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/repository_dependencies.xml	Mon Jan 25 20:26:32 2016 -0500
@@ -0,0 +1,4 @@
+<?xml version="1.0"?>
+<repositories>
+    <repository changeset_revision="74b09c8e5f6e" name="data_manager_twobit_builder" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" />
+</repositories>

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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/bamCompare_result1.bg	Mon Jan 25 20:26:32 2016 -0500
@@ -0,0 +1,1 @@
+chrM	0	16569	1.0

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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/bamCoverage_result3.bg	Mon Jan 25 20:26:32 2016 -0500
@@ -0,0 +1,8 @@
+chrM	0	10	18498299.57
+chrM	10	200	9768764.94
+chrM	200	210	10184457.07
+chrM	210	220	9976611.00
+chrM	220	230	7690304.31
+chrM	230	240	6027535.81
+chrM	240	250	3325537.00
+chrM	250	260	623538.19

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/bamCoverage_result4.bg	Mon Jan 25 20:26:32 2016 -0500
@@ -0,0 +1,472 @@
+phiX174	0	10	16038.46
+phiX174	10	20	48115.38
+phiX174	20	70	144346.15
+phiX174	70	80	192461.54
+phiX174	80	90	176423.08
+phiX174	90	100	160384.62
+phiX174	100	120	112269.23
+phiX174	120	140	144346.15
+phiX174	140	150	160384.62
+phiX174	150	160	128307.69
+phiX174	160	170	160384.62
+phiX174	170	180	176423.08
+phiX174	180	200	208500.00
+phiX174	200	210	192461.54
+phiX174	210	220	240576.92
+phiX174	220	230	272653.85
+phiX174	230	240	336807.69
+phiX174	240	250	320769.23
+phiX174	250	260	288692.31
+phiX174	260	270	336807.69
+phiX174	270	280	400961.54
+phiX174	280	300	417000.00
+phiX174	300	310	352846.15
+phiX174	310	320	320769.23
+phiX174	320	330	368884.62
+phiX174	330	340	352846.15
+phiX174	340	350	288692.31
+phiX174	350	360	256615.38
+phiX174	360	370	224538.46
+phiX174	370	380	240576.92
+phiX174	380	390	304730.77
+phiX174	390	400	256615.38
+phiX174	400	410	240576.92
+phiX174	410	420	224538.46
+phiX174	420	450	288692.31
+phiX174	450	460	304730.77
+phiX174	460	470	336807.69
+phiX174	470	490	417000.00
+phiX174	490	510	497192.31
+phiX174	510	520	465115.38
+phiX174	520	530	561346.15
+phiX174	530	540	497192.31
+phiX174	540	550	529269.23
+phiX174	550	560	545307.69
+phiX174	560	570	641538.46
+phiX174	570	580	625500.00
+phiX174	580	590	561346.15
+phiX174	590	600	609461.54
+phiX174	600	610	545307.69
+phiX174	610	630	625500.00
+phiX174	630	640	577384.62
+phiX174	640	650	513230.77
+phiX174	650	660	545307.69
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+phiX174	670	680	593423.08
+phiX174	680	690	657576.92
+phiX174	690	700	641538.46
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+phiX174	740	760	593423.08
+phiX174	760	770	497192.31
+phiX174	770	780	513230.77
+phiX174	780	790	529269.23
+phiX174	790	800	545307.69
+phiX174	800	810	449076.92
+phiX174	810	820	433038.46
+phiX174	820	830	368884.62
+phiX174	830	840	320769.23
+phiX174	840	850	352846.15
+phiX174	850	860	304730.77
+phiX174	860	870	336807.69
+phiX174	870	880	256615.38
+phiX174	880	890	352846.15
+phiX174	890	900	384923.08
+phiX174	900	910	465115.38
+phiX174	910	920	545307.69
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/bamPEFragmentSize_result1.txt	Mon Jan 25 20:26:32 2016 -0500
@@ -0,0 +1,20 @@
+Sample size: 3
+
+
+Fragment lengths:
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+1st Qu.: 241.5
+Mean: 244.666666667
+Median: 242.0
+3rd Qu.: 246.5
+Max.: 251
+Std: 4.49691252108
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+1st Qu.: 251.0
+Mean: 251.0
+Median: 251.0
+3rd Qu.: 251.0
+Max.: 251
+Std: 0.0

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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/computeMatrix1.bed	Mon Jan 25 20:26:32 2016 -0500
@@ -0,0 +1,8 @@
+phiX174	1000	1500	CG11023	0	+
+phiX174	150	1750	cda5	0	-
+phiX174	150	177	cda8	0	-
+phiX174	75	1500	cda9	0	+
+phiX174	101	175	C11023	0	+
+phiX174	125	150	ca5	0	-
+phiX174	450	1750	ca8	0	+
+phiX174	80	1500	cda9	0	+

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/computeMatrix2.bed	Mon Jan 25 20:26:32 2016 -0500
@@ -0,0 +1,6 @@
+ch1	100	150	CG11023	0	+
+ch2	150	175	cda5	0	-
+ch3	100	125	cda8	0	+
+ch1	75	125	C11023	0	+
+ch2	125	150	ca5	0	-
+ch3	75	100	ca8	0	+

Binary file test-data/computeMatrix2.bw has changed

Binary file test-data/computeMatrix_result1.gz has changed

Binary file test-data/computeMatrix_result2.gz has changed

Binary file test-data/computeMatrix_result3.gz has changed

Binary file test-data/correctGCBias_result1.bam has changed

Binary file test-data/heatmapper_result1.png has changed

Binary file test-data/heatmapper_result2.png has changed

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/multiBamSummary_regions.bed	Mon Jan 25 20:26:32 2016 -0500
@@ -0,0 +1,3 @@
+chrM	1	10
+chrM	5	15
+chrM	10	20

Binary file test-data/multiBamSummary_result1.npz has changed

Binary file test-data/multiBamSummary_result2.npz has changed

Binary file test-data/multiBigwigSummary_result1.npz has changed

Binary file test-data/multiBigwigSummary_result1.png has changed

Binary file test-data/paired_chr2L.bam has changed

Binary file test-data/phiX.2bit has changed

Binary file test-data/phiX.bam has changed

Binary file test-data/phiX.bam.bai has changed

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/phiX.fasta	Mon Jan 25 20:26:32 2016 -0500
@@ -0,0 +1,79 @@
+>phiX174
+GAGTTTTATCGCTTCCATGACGCAGAAGTTAACACTTTCGGATATTTCTGATGAGTCGAAAAATTATCTT
+GATAAAGCAGGAATTACTACTGCTTGTTTACGAATTAAATCGAAGTGGACTGCTGGCGGAAAATGAGAAA
+ATTCGACCTATCCTTGCGCAGCTCGAGAAGCTCTTACTTTGCGACCTTTCGCCATCAACTAACGATTCTG
+TCAAAAACTGACGCGTTGGATGAGGAGAAGTGGCTTAATATGCTTGGCACGTTCGTCAAGGACTGGTTTA
+GATATGAGTCACATTTTGTTCATGGTAGAGATTCTCTTGTTGACATTTTAAAAGAGCGTGGATTACTATC
+TGAGTCCGATGCTGTTCAACCACTAATAGGTAAGAAATCATGAGTCAAGTTACTGAACAATCCGTACGTT
+TCCAGACCGCTTTGGCCTCTATTAAGCTCATTCAGGCTTCTGCCGTTTTGGATTTAACCGAAGATGATTT
+CGATTTTCTGACGAGTAACAAAGTTTGGATTGCTACTGACCGCTCTCGTGCTCGTCGCTGCGTTGAGGCT
+TGCGTTTATGGTACGCTGGACTTTGTGGGATACCCTCGCTTTCCTGCTCCTGTTGAGTTTATTGCTGCCG
+TCATTGCTTATTATGTTCATCCCGTCAACATTCAAACGGCCTGTCTCATCATGGAAGGCGCTGAATTTAC
+GGAAAACATTATTAATGGCGTCGAGCGTCCGGTTAAAGCCGCTGAATTGTTCGCGTTTACCTTGCGTGTA
+CGCGCAGGAAACACTGACGTTCTTACTGACGCAGAAGAAAACGTGCGTCAAAAATTACGTGCAGAAGGAG
+TGATGTAATGTCTAAAGGTAAAAAACGTTCTGGCGCTCGCCCTGGTCGTCCGCAGCCGTTGCGAGGTACT
+AAAGGCAAGCGTAAAGGCGCTCGTCTTTGGTATGTAGGTGGTCAACAATTTTAATTGCAGGGGCTTCGGC
+CCCTTACTTGAGGATAAATTATGTCTAATATTCAAACTGGCGCCGAGCGTATGCCGCATGACCTTTCCCA
+TCTTGGCTTCCTTGCTGGTCAGATTGGTCGTCTTATTACCATTTCAACTACTCCGGTTATCGCTGGCGAC
+TCCTTCGAGATGGACGCCGTTGGCGCTCTCCGTCTTTCTCCATTGCGTCGTGGCCTTGCTATTGACTCTA
+CTGTAGACATTTTTACTTTTTATGTCCCTCATCGTCACGTTTATGGTGAACAGTGGATTAAGTTCATGAA
+GGATGGTGTTAATGCCACTCCTCTCCCGACTGTTAACACTACTGGTTATATTGACCATGCCGCTTTTCTT
+GGCACGATTAACCCTGATACCAATAAAATCCCTAAGCATTTGTTTCAGGGTTATTTGAATATCTATAACA
+ACTATTTTAAAGCGCCGTGGATGCCTGACCGTACCGAGGCTAACCCTAATGAGCTTAATCAAGATGATGC
+TCGTTATGGTTTCCGTTGCTGCCATCTCAAAAACATTTGGACTGCTCCGCTTCCTCCTGAGACTGAGCTT
+TCTCGCCAAATGACGACTTCTACCACATCTATTGACATTATGGGTCTGCAAGCTGCTTATGCTAATTTGC
+ATACTGACCAAGAACGTGATTACTTCATGCAGCGTTACCGTGATGTTATTTCTTCATTTGGAGGTAAAAC
+CTCTTATGACGCTGACAACCGTCCTTTACTTGTCATGCGCTCTAATCTCTGGGCATCTGGCTATGATGTT
+GATGGAACTGACCAAACGTCGTTAGGCCAGTTTTCTGGTCGTGTTCAACAGACCTATAAACATTCTGTGC
+CGCGTTTCTTTGTTCCTGAGCATGGCACTATGTTTACTCTTGCGCTTGTTCGTTTTCCGCCTACTGCGAC
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+

Binary file test-data/plotCorrelation_result1.png has changed

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/plotCorrelation_result1.tabular	Mon Jan 25 20:26:32 2016 -0500
@@ -0,0 +1,3 @@
+	'bowtie2-test1.bam'	'bowtie2-test1.bam'
+'bowtie2-test1.bam'	1.0000	1.0000
+'bowtie2-test1.bam'	1.0000	1.0000

Binary file test-data/plotCorrelation_result2.png has changed

Binary file test-data/plotCoverage_result1.png has changed

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/plotCoverage_result1.tabular	Mon Jan 25 20:26:32 2016 -0500
@@ -0,0 +1,16570 @@
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