# HG changeset patch
# User bgruening
# Date 1517848955 18000
# Node ID 9ccbe8e8fd7481285d0f7737840a2a04bef34523
# Parent  38e3f226248bbfbbcbe98b61a0a7af169fff89cd
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4abb1e731efdaa32fadb32c9e23883f7c17fb85c

diff -r 38e3f226248b -r 9ccbe8e8fd74 deepTools_macros.xml
--- a/deepTools_macros.xml	Mon May 15 03:58:11 2017 -0400
+++ b/deepTools_macros.xml	Mon Feb 05 11:42:35 2018 -0500
@@ -1,10 +1,10 @@
 <macros>
 
     <token name="@THREADS@">--numberOfProcessors "\${GALAXY_SLOTS:-4}"</token>
-    <token name="@WRAPPER_VERSION@">2.5.1.1</token>
+    <token name="@WRAPPER_VERSION@">2.5.7</token>
     <xml name="requirements">
         <requirements>
-            <requirement type="package" version="2.5.1">deeptools</requirement>
+            <requirement type="package" version="2.5.7">deeptools</requirement>
             <yield />
         </requirements>
         <expand macro="stdio" />
@@ -211,7 +211,7 @@
     </xml>
 
     <xml name="gtf_options">
-        <param argument="--metagene" type="boolean" truevalue="--boolean" falsevalue=""
+        <param argument="--metagene" type="boolean" truevalue="--metagene" falsevalue=""
             label="Use a metagene model"
             help="If set and a BED12 or GTF file or files is used to provide regions, only exons will be used. This is convenient for looking at coverage over mature mRNA transcripts or similar uses where introns should be ignored." />
         <param argument="--transcriptID" optional="True" value="transcript" type="text"
diff -r 38e3f226248b -r 9ccbe8e8fd74 deepTools_macros.xml.orig
--- a/deepTools_macros.xml.orig	Mon May 15 03:58:11 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,639 +0,0 @@
-<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 38e3f226248b -r 9ccbe8e8fd74 test-data/bamCoverage_result4.bg
--- a/test-data/bamCoverage_result4.bg	Mon May 15 03:58:11 2017 -0400
+++ b/test-data/bamCoverage_result4.bg	Mon Feb 05 11:42:35 2018 -0500
@@ -1,472 +1,472 @@
-phiX174	0	10	16302.8
-phiX174	10	20	48908.5
-phiX174	20	70	146725
-phiX174	70	80	195634
-phiX174	80	90	179331
-phiX174	90	100	163028
-phiX174	100	120	114120
-phiX174	120	140	146725
-phiX174	140	150	163028
-phiX174	150	160	130423
-phiX174	160	170	163028
-phiX174	170	180	179331
-phiX174	180	200	211937
-phiX174	200	210	195634
-phiX174	210	220	244542
-phiX174	220	230	277148
-phiX174	230	240	342359
-phiX174	240	250	326057
-phiX174	250	260	293451
-phiX174	260	270	342359
-phiX174	270	280	407571
-phiX174	280	300	423874
-phiX174	300	310	358662
-phiX174	310	320	326057
-phiX174	320	330	374965
-phiX174	330	340	358662
-phiX174	340	350	293451
-phiX174	350	360	260845
-phiX174	360	370	228240
-phiX174	370	380	244542
-phiX174	380	390	309754
-phiX174	390	400	260845
-phiX174	400	410	244542
-phiX174	410	420	228240
-phiX174	420	450	293451
-phiX174	450	460	309754
-phiX174	460	470	342359
-phiX174	470	490	423874
-phiX174	490	510	505388
-phiX174	510	520	472782
-phiX174	520	530	570599
-phiX174	530	540	505388
-phiX174	540	550	537993
-phiX174	550	560	554296
-phiX174	560	570	652113
-phiX174	570	580	635810
-phiX174	580	590	570599
-phiX174	590	600	619508
-phiX174	600	610	554296
-phiX174	610	630	635810
-phiX174	630	640	586902
-phiX174	640	650	521691
-phiX174	650	660	554296
-phiX174	660	670	570599
-phiX174	670	680	603205
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-phiX174	690	700	652113
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-phiX174	730	740	521691
-phiX174	740	760	603205
-phiX174	760	770	505388
-phiX174	770	780	521691
-phiX174	780	790	537993
-phiX174	790	800	554296
-phiX174	800	810	456479
-phiX174	810	820	440176
-phiX174	820	830	374965
-phiX174	830	840	326057
-phiX174	840	850	358662
-phiX174	850	860	309754
-phiX174	860	870	342359
-phiX174	870	880	260845
-phiX174	880	890	358662
-phiX174	890	900	391268
-phiX174	900	910	472782
-phiX174	910	920	554296
-phiX174	920	930	570599
-phiX174	930	940	554296
-phiX174	940	950	586902
-phiX174	950	960	603205
-phiX174	960	970	521691
-phiX174	970	980	489085
-phiX174	980	990	440176
-phiX174	990	1000	423874
-phiX174	1000	1010	456479
-phiX174	1010	1030	586902
-phiX174	1030	1040	766233
-phiX174	1040	1050	798839
-phiX174	1050	1060	831444
-phiX174	1060	1070	880353
-phiX174	1070	1080	847747
-phiX174	1080	1090	880353
-phiX174	1090	1100	782536
-phiX174	1100	1110	749930
-phiX174	1110	1120	668416
-phiX174	1120	1130	652113
-phiX174	1130	1140	635810
-phiX174	1140	1150	684719
-phiX174	1150	1160	635810
-phiX174	1160	1170	603205
-phiX174	1170	1180	619508
-phiX174	1180	1190	586902
-phiX174	1190	1200	521691
-phiX174	1200	1210	489085
-phiX174	1210	1220	570599
-phiX174	1220	1230	489085
-phiX174	1230	1240	456479
-phiX174	1240	1250	358662
-phiX174	1250	1260	342359
-phiX174	1260	1270	407571
-phiX174	1270	1280	358662
-phiX174	1280	1290	374965
-phiX174	1290	1300	326057
-phiX174	1300	1310	391268
-phiX174	1310	1320	521691
-phiX174	1320	1330	505388
-phiX174	1330	1340	521691
-phiX174	1340	1350	489085
-phiX174	1350	1370	505388
-phiX174	1370	1390	472782
-phiX174	1390	1400	358662
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-phiX174	1410	1430	489085
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-phiX174	1470	1480	619508
-phiX174	1480	1490	603205
-phiX174	1490	1500	554296
-phiX174	1500	1510	668416
-phiX174	1510	1520	635810
-phiX174	1520	1540	798839
-phiX174	1540	1550	733627
-phiX174	1550	1570	766233
-phiX174	1570	1580	782536
-phiX174	1580	1590	684719
-phiX174	1590	1600	635810
-phiX174	1600	1610	570599
-phiX174	1610	1620	537993
-phiX174	1620	1630	505388
-phiX174	1630	1640	472782
-phiX174	1640	1650	489085
-phiX174	1650	1660	505388
-phiX174	1660	1670	537993
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-phiX174	1690	1700	537993
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-phiX174	1730	1740	586902
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-phiX174	1770	1780	374965
-phiX174	1780	1790	358662
-phiX174	1790	1810	342359
-phiX174	1810	1820	326057
-phiX174	1820	1830	472782
-phiX174	1830	1860	717325
-phiX174	1860	1870	815142
-phiX174	1870	1880	749930
-phiX174	1880	1890	684719
-phiX174	1890	1900	717325
-phiX174	1900	1910	619508
-phiX174	1910	1920	407571
-phiX174	1920	1930	472782
-phiX174	1930	1940	554296
-phiX174	1940	1950	456479
-phiX174	1950	1960	489085
-phiX174	1960	1970	537993
-phiX174	1970	1980	684719
-phiX174	1980	1990	652113
-phiX174	1990	2000	668416
-phiX174	2000	2010	684719
-phiX174	2010	2020	652113
-phiX174	2020	2030	668416
-phiX174	2030	2050	684719
-phiX174	2050	2060	489085
-phiX174	2060	2070	521691
-phiX174	2070	2080	489085
-phiX174	2080	2100	521691
-phiX174	2100	2110	537993
-phiX174	2110	2120	521691
-phiX174	2120	2130	537993
-phiX174	2130	2140	554296
-phiX174	2140	2150	521691
-phiX174	2150	2160	554296
-phiX174	2160	2170	423874
-phiX174	2170	2180	358662
-phiX174	2180	2190	440176
-phiX174	2190	2200	456479
-phiX174	2200	2210	440176
-phiX174	2210	2220	489085
-phiX174	2220	2230	554296
-phiX174	2230	2240	603205
-phiX174	2240	2250	635810
-phiX174	2250	2260	733627
-phiX174	2260	2270	635810
-phiX174	2270	2290	603205
-phiX174	2290	2300	619508
-phiX174	2300	2310	749930
-phiX174	2310	2320	782536
-phiX174	2320	2330	880353
-phiX174	2330	2340	864050
-phiX174	2340	2350	912959
-phiX174	2350	2360	815142
-phiX174	2360	2370	929261
-phiX174	2370	2380	815142
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-phiX174	2400	2410	423874
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-phiX174	2460	2470	684719
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-phiX174	2480	2490	766233
-phiX174	2490	2500	782536
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-phiX174	2510	2520	652113
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-phiX174	2740	2750	831444
-phiX174	2750	2760	880353
-phiX174	2760	2770	864050
-phiX174	2770	2780	896656
-phiX174	2780	2790	978170
-phiX174	2790	2800	831444
-phiX174	2800	2810	847747
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-phiX174	3080	3100	586902
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-phiX174	3160	3180	782536
-phiX174	3180	3190	717325
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-phiX174	3210	3220	749930
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-phiX174	3230	3240	717325
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-phiX174	3480	3490	733627
-phiX174	3490	3500	847747
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-phiX174	3510	3520	912959
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-phiX174	3530	3540	766233
-phiX174	3540	3550	798839
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-phiX174	3560	3570	701022
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-phiX174	4150	4160	342359
-phiX174	4160	4170	391268
-phiX174	4170	4180	277148
-phiX174	4180	4190	342359
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+phiX174	4970	4980	240577
+phiX174	4980	4990	208500
+phiX174	4990	5020	288692
+phiX174	5020	5030	352846
+phiX174	5030	5040	336808
+phiX174	5040	5050	368885
+phiX174	5050	5060	304731
+phiX174	5060	5070	288692
+phiX174	5070	5080	240577
+phiX174	5080	5090	304731
+phiX174	5090	5100	272654
+phiX174	5100	5110	224538
+phiX174	5110	5120	256615
+phiX174	5120	5130	320769
+phiX174	5130	5140	417000
+phiX174	5140	5160	497192
+phiX174	5160	5170	481154
+phiX174	5170	5180	577385
+phiX174	5180	5190	561346
+phiX174	5190	5200	529269
+phiX174	5200	5210	465115
+phiX174	5210	5220	449077
+phiX174	5220	5230	400962
+phiX174	5230	5240	449077
+phiX174	5240	5250	368885
+phiX174	5250	5260	272654
+phiX174	5260	5270	304731
+phiX174	5270	5280	336808
+phiX174	5280	5290	272654
+phiX174	5290	5300	192462
+phiX174	5300	5310	144346
+phiX174	5310	5340	96230.8
+phiX174	5340	5350	64153.8
+phiX174	5350	5386	32076.9
diff -r 38e3f226248b -r 9ccbe8e8fd74 test-data/bamCoverage_result5.bw
Binary file test-data/bamCoverage_result5.bw has changed
diff -r 38e3f226248b -r 9ccbe8e8fd74 test-data/bamPEFragmentSize_result1.txt
--- a/test-data/bamPEFragmentSize_result1.txt	Mon May 15 03:58:11 2017 -0400
+++ b/test-data/bamPEFragmentSize_result1.txt	Mon Feb 05 11:42:35 2018 -0500
@@ -6,11 +6,11 @@
 Fragment lengths:
 Min.: 241.0
 1st Qu.: 241.5
-Mean: 244.666666667
+Mean: 244.66666666666666
 Median: 242.0
 3rd Qu.: 246.5
 Max.: 251.0
-Std: 4.49691252108
+Std: 4.496912521077347
 
 Read lengths:
 Min.: 251.0
diff -r 38e3f226248b -r 9ccbe8e8fd74 test-data/heatmapper_result1.png
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diff -r 38e3f226248b -r 9ccbe8e8fd74 test-data/plotCorrelation_result1.png
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diff -r 38e3f226248b -r 9ccbe8e8fd74 test-data/plotCorrelation_result2.png
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diff -r 38e3f226248b -r 9ccbe8e8fd74 test-data/plotCoverage_result1.png
Binary file test-data/plotCoverage_result1.png has changed
diff -r 38e3f226248b -r 9ccbe8e8fd74 test-data/plotEnrichment_output.txt
--- a/test-data/plotEnrichment_output.txt	Mon May 15 03:58:11 2017 -0400
+++ b/test-data/plotEnrichment_output.txt	Mon Feb 05 11:42:35 2018 -0500
@@ -1,5 +1,5 @@
 file	featureType	percent
+bowtie2 test1.bam	up	100.00
 bowtie2 test1.bam	down	100.00
 bowtie2 test1.bam	up	100.00
 bowtie2 test1.bam	down	100.00
-bowtie2 test1.bam	up	100.00
diff -r 38e3f226248b -r 9ccbe8e8fd74 test-data/plotFingerprint_quality_metrics.tabular
--- a/test-data/plotFingerprint_quality_metrics.tabular	Mon May 15 03:58:11 2017 -0400
+++ b/test-data/plotFingerprint_quality_metrics.tabular	Mon Feb 05 11:42:35 2018 -0500
@@ -1,3 +1,3 @@
 Sample	AUC	Synthetic AUC	X-intercept	Synthetic X-intercept	Elbow Point	Synthetic Elbow Point	JS Distance	Synthetic JS Distance	% genome enriched	diff. enrichment	CHANCE divergence
-bowtie2 test1.bam	0.00493632029864	0.481650684758	0.984443061605	1.15310443503e-24	0.984940883634	0.523268829811	NA	0.269004498068	NA	NA	NA
-bowtie2 test1.bam	0.00493632029864	0.481650684758	0.984443061605	1.15310443503e-24	0.984940883634	0.523268829811	0.0	0.269004498068	0	0	0
+bowtie2 test1.bam	0.00493632029863651	0.481650684757865	0.984443061605476	1.1531044350267195e-24	0.9849408836341008	0.5232688298112538	NA	0.26900449806812143	NA	NA	NA
+bowtie2 test1.bam	0.00493632029863651	0.481650684757865	0.984443061605476	1.1531044350267195e-24	0.9849408836341008	0.5232688298112538	0.0	0.26900449806812143	0	0	0
diff -r 38e3f226248b -r 9ccbe8e8fd74 test-data/plotPCA_result1.png
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diff -r 38e3f226248b -r 9ccbe8e8fd74 test-data/plotPCA_result2.png
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diff -r 38e3f226248b -r 9ccbe8e8fd74 test-data/plotPCA_result2.tabular
--- a/test-data/plotPCA_result2.tabular	Mon May 15 03:58:11 2017 -0400
+++ b/test-data/plotPCA_result2.tabular	Mon Feb 05 11:42:35 2018 -0500
@@ -1,3 +1,3 @@
 Component	bowtie2-test1.bam	bowtie2-test1.bam	Eigenvalue
-1	-0.707106781187	-0.707106781187	6.0
-2	-0.707106781187	0.707106781187	1.23259516441e-32
+1	-0.7071067811865476	-0.7071067811865475	6.000000000000001
+2	-0.7071067811865475	0.7071067811865476	1.2325951644078315e-32
diff -r 38e3f226248b -r 9ccbe8e8fd74 test-data/profiler_result1.png
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diff -r 38e3f226248b -r 9ccbe8e8fd74 test-data/profiler_result2.png
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diff -r 38e3f226248b -r 9ccbe8e8fd74 test-data/profiler_result2.tabular
--- a/test-data/profiler_result2.tabular	Mon May 15 03:58:11 2017 -0400
+++ b/test-data/profiler_result2.tabular	Mon Feb 05 11:42:35 2018 -0500
@@ -1,3 +1,3 @@
 bin labels		-0.0Kb	0.0Kb
-bins		1	2
+bins		1.0	2.0
 bamCoverage_result4_bw_0	genes	2477942.875	2610260.125