Mercurial > repos > bgruening > deeptools_plot_correlation

changeset 33:f1518335ac27 draft

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planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
author bgruening
date Thu, 15 Feb 2018 04:12:20 -0500
parents d97b5324b279
children 3de1d0d2d628
files deepTools_macros.xml plotCorrelation.xml readme.rst test-data/alignmentSieve.bam test-data/alignmentSieve.bed test-data/alignmentSieve.txt test-data/alignmentSieve2.bam test-data/alignmentSieve3.bam test-data/bamPEFragmentSize_histogram_result1.png test-data/bamPEFragmentSize_lengths1.txt test-data/bamPEFragmentSize_result1.txt test-data/bamPEFragmentSize_table1.txt test-data/estimateReadFiltering.txt test-data/heatmapper_result1.png test-data/heatmapper_result2.png test-data/multiBamSummary_result1.npz test-data/multiBamSummary_result2.npz test-data/paired_chr2L.cram test-data/plotCorrelation_result1.tabular test-data/plotCorrelation_result2.png test-data/plotCoverage_result1.png test-data/plotCoverage_result1.tabular test-data/plotEnrichment_output.txt test-data/plotFingerprint_result2.tabular test-data/plotPCA_result1.png test-data/plotPCA_result2.tabular
diffstat 26 files changed, 4380 insertions(+), 44 deletions(-) [+]
line wrap: on
line diff
--- a/deepTools_macros.xml	Mon Feb 05 11:30:46 2018 -0500
+++ b/deepTools_macros.xml	Thu Feb 15 04:12:20 2018 -0500
@@ -1,11 +1,11 @@
 <macros>
 
     <token name="@THREADS@">--numberOfProcessors "\${GALAXY_SLOTS:-4}"</token>
-    <token name="@WRAPPER_VERSION@">2.5.7</token>
+    <token name="@WRAPPER_VERSION@">3.0.0</token>
     <xml name="requirements">
         <requirements>
-            <requirement type="package" version="2.5.7">deeptools</requirement>
-            <yield />
+            <requirement type="package" version="3.0.0">deeptools</requirement>
+            <requirement type="package" version="1.7">samtools</requirement>
         </requirements>
         <expand macro="stdio" />
         <version_command>@BINARY@ --version</version_command>
@@ -100,7 +100,7 @@
     <xml name="includeZeros">
         <param argument="--includeZeros" type="boolean" truevalue="--includeZeros" falsevalue=""
             label="Include zeros"
-            help="If set, then regions with zero counts for *all* BAM files are included. The default behavior is to ignore such regions." />
+            help="If set, then regions with zero counts for *all* BAM/CRAM files are included. The default behavior is to ignore such regions." />
     </xml>
 
     <xml name="zMin_zMax">
@@ -238,7 +238,7 @@
     <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.
+                help="If selected : Single-end reads and singletons are extended to match the given length and Paired-end reads are extended to match the fragment size.
                      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.
@@ -312,7 +312,7 @@
     <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="no">maintain the same ordering as the input files</option>
             <option value="descend" selected="true">descending order</option>
             <option value="ascend">ascending order</option>
         </param>
@@ -321,19 +321,19 @@
     <xml name="minMappingQuality">
         <param argument="--minMappingQuality" type="integer" optional="true" value="1" min="0"
             label="Minimum mapping quality"
-            help= "If set, only reads with a mapping quality score higher than this value are considered."/>
+            help= "If set, only reads with a mapping quality score at least this high 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." />
+            help ="If set, then zero counts that happen for *all* BAM/CRAM files given are ignored. This may result in fewer considered regions." />
     </xml>
 
     <xml name="fragmentLength">
-        <param argument="--fragmentLength" type="integer" value="300" min="1"
+        <param argument="--fragmentLength" type="integer" min="1" optional="true"
             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."/>
+            help ="If paired-end reads are used, the fragment length is computed from the BAM/CRAM file, so this is only needed for single-end data."/>
     </xml>
 
     <xml name="scaleFactor">
@@ -390,13 +390,13 @@
             <option value="Yes">Yes</option>
         </param>
         <when value="No">
-            <param argument="--bamfiles" type="data" format="bam" min="@MIN@"
-                label="Bam file" multiple="true"
+            <param argument="--bamfiles" type="data" format="bam,cram" min="@MIN@"
+                label="BAM/CRAM file" multiple="true"
                 help=""/>
         </when>
         <when value="Yes">
-            <repeat name="multibam_repeats" min="@MIN@" title="BAM Files">
-                <param argument="--bamfiles" type="data" format="bam" label="BAM file" help="" />
+            <repeat name="multibam_repeats" min="@MIN@" title="BAM/CRAM Files">
+                <param argument="--bamfiles" type="data" format="bam,cram" label="BAM/CRAM file" help="" />
             </repeat>
         </when>
         </conditional>
@@ -404,7 +404,7 @@
 
     <xml name="multiple_input_bigwigs" tokens="MIN,LABEL,TITLE">
         <conditional name="multibigwig_conditional">
-        <param name="orderMatters" type="select" label="Sample order matters" help="By default, the order of samples given to the program is dependent on their order in your history. If the order of the samples 
+        <param name="orderMatters" type="select" label="Sample order matters" help="By default, the order of samples given to the program is dependent on their order in your history. If the order of the samples
 is vital to you, select Yes below.">
             <option value="No" selected="true">No</option>
             <option value="Yes">Yes</option>
@@ -412,11 +412,11 @@
         <when value="No">
             <param argument="--bigwigfiles" type="data" format="bigwig" multiple="True" min="@MIN@"
                 label="@LABEL@"
-                help="You can generate a bigWig file from a BAM file using the bamCoverage tool."/>
+                help="You can generate a bigWig file from a BAM/CRAM file using the bamCoverage tool."/>
         </when>
         <when value="Yes">
             <repeat name="multibigwig_repeats" min="@MIN@" title="@TITLE@">
-                <param argument="--bigwigfiles" type="data" format="bigwig" label="@LABEL@" help="You can generate a bigWig file from a BAM file using the bamCoverage tool."/>
+                <param argument="--bigwigfiles" type="data" format="bigwig" label="@LABEL@" help="You can generate a bigWig file from a BAM/CRAM file using the bamCoverage tool."/>
             </repeat>
         </when>
         </conditional>
@@ -428,6 +428,12 @@
             help="Title of the plot, to be printed on top of the generated image." />
     </xml>
 
+    <xml name="labelRotation">
+        <param argument="--labelRotation" type="integer" value="0"
+            label="Rotation of the X-axis labels (in degrees)"
+            help="The rotation of things like TSS or TES on the X-axis of profile plots in both plotHeatmap and plotProfile. The default is 0, positive values denome a counter-clockwise rotation." />
+    </xml>
+
 
     <token name="@multiple_input_bams@">
 <![CDATA[
@@ -438,8 +444,12 @@
             #for $counter, $bamfile in enumerate($multibam_conditional.bamfiles):
                 #set identifier = re.sub('[^\.\s\w\-]', '_', str($bamfile.element_identifier))
                 ln -s "${bamfile}" "./${counter}.bam" &&
-                ln -s "${bamfile.metadata.bam_index}" "./${counter}.bam.bai" &&
-                #silent $files.append('%s.bam' % $counter)
+                #if $bamfile.ext == 'bam':
+                    ln -s '${bamfile.metadata.bam_index}' './${counter}.bam.bai' &&
+                #else:
+                    ln -s '${bamfile.metadata.cram_index}' './${counter}.bam.crai' &&
+                #end if
+                #silent $files.append("'%s.bam'" % $counter)
                 #silent $labels.append("'%s'" % identifier)
             #end for
         #else:
@@ -447,7 +457,12 @@
                 #set identifier = re.sub('[^\.\s\w\-]', '_', str($f.bamfiles.element_identifier))
                 ln -s "${f.bamfiles}" "./${counter}.bam" &&
                 ln -s "${f.bamfiles.metadata.bam_index}" "./${counter}.bam.bai" &&
-                #silent $files.append('%s.bam' % $counter)
+                #if $f.bamfiles.ext == 'bam':
+                    ln -s '${f.bamfiles.metadata.bam_index}' './${counter}.bam.bai' &&
+                #else:
+                    ln -s '${f.bamfiles.metadata.cram_index}' './${counter}.bam.crai' &&
+                #end if
+                #silent $files.append("'%s.bam'" % $counter)
                 #silent $labels.append("'%s'" % $identifier)
             #end for
         #end if
@@ -463,14 +478,14 @@
             #for $counter, $bigwig in enumerate($multibigwig_conditional.bigwigfiles):
                 #set identifier = re.sub('[^\.\s\w\-]', '_', str($bigwig.element_identifier))
                 ln -f -s "${bigwig}" "${identifier}_${counter}.bw" &&
-                #silent $files.append('%s_%s.bw' % ($identifier, $counter))
+                #silent $files.append("'%s_%s.bw'" % ($identifier, $counter))
                 #silent $labels.append("'%s'" % $identifier)
             #end for
         #else:
             #for $counter, $f in enumerate($multibigwig_conditional.multibigwig_repeats):
                 #set identifier = re.sub('[^\.\s\w\-]', '_', str($f.bigwigfiles.element_identifier))
                 ln -f -s "${f.bigwigfiles}" "${identifier}_${counter}.bw" &&
-                #silent $files.append('%s_%s.bw' % ($identifier, $counter))
+                #silent $files.append("'%s_%s.bw'" % ($identifier, $counter))
                 #silent $labels.append("'%s'" % $identifier)
             #end for
         #end if
@@ -494,7 +509,7 @@
                 --blackListFileName #echo ' '.join($blfiles)#
             #end if
         #end if
-]]> 
+]]>
     </token>
 
     <xml name="multiple_bed">
@@ -515,7 +530,7 @@
             --BED #echo ' '.join($files)#
             --regionLabels #echo ' '.join($labels)#
         #end if
-]]> 
+]]>
     </token>
 
     <xml name="reference_genome_source">
@@ -551,21 +566,27 @@
             <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.">
+                    We provide a table of useful sizes here: http://deeptools.readthedocs.io/en/latest/content/feature/effectiveGenomeSize.html">
                 <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="130428560">dm3 (130428560)</option>
+                <option value="125464728">dm6 (125464728)</option>
+                <option value="2685511504" selected="true">hg19/GRCh37 (2685511504)</option>
+                <option value="2701495761">GRCh38/hg38 (2701495761)</option>
+                <option value="2304947926">GRCm37/mm9 (2304947926)</option>
+                <option value="2308125349">GRCm38/mm10 (2308125349)</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"/>
+                       help="e.g. ce10: 93260000, dm3: 130428560, hg19: 2685511504, mm9: 2304947926"/>
             </when>
-            <when value="2150570000" />
-            <when value="2451960000" />
-            <when value="121400000" />
             <when value="93260000" />
+            <when value="130428560" />
+            <when value="125464728" />
+            <when value="2685511504" />
+            <when value="2701495761" />
+            <when value="2304947926" />
+            <when value="2308125349" />
         </conditional>
     </xml>
 
@@ -596,6 +617,7 @@
             <when value="yes">
                 <yield />
                 <param name="saveSortedRegions" type="boolean"
+                       argument="--outFileSortedRegions"
                        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."/>
@@ -605,11 +627,12 @@
 
 
     <xml name="input_image_file_format">
-        <param argument="--outFileFormat" type="select" label="Image file format">
+        <param argument="--outFileFormat" type="select" label="Image file format" help="Note that the plotly output can be very large and not all options are supported.">
             <option value="png" selected="true">png</option>
             <option value="pdf">pdf</option>
             <option value="svg">svg</option>
             <option value="eps">eps</option>
+            <option value="plotly">plotly</option>
         </param>
     </xml>
 
@@ -624,6 +647,7 @@
                 <when input="output.outFileFormat" value="pdf" format="pdf" />
                 <when input="output.outFileFormat" value="svg" format="svg" />
                 <when input="output.outFileFormat" value="eps" format="eps" />
+                <when input="output.outFileFormat" value="plotly" format="html" />
             </change_format>
         </data>
     </xml>
@@ -634,6 +658,7 @@
                 <when input="outFileFormat" value="pdf" format="pdf" />
                 <when input="outFileFormat" value="svg" format="svg" />
                 <when input="outFileFormat" value="eps" format="eps" />
+                <when input="outFileFormat" value="plotly" format="html" />
             </change_format>
         </data>
     </xml>
@@ -662,8 +687,7 @@
 
     <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://matplotlib.org/examples/color/colormaps_reference.html"
-               multiple="true">
+               help=" Available color map names can be found here: http://matplotlib.org/examples/color/colormaps_reference.html">
             <option value="RdYlBu" selected="true">RdYlBu</option>
             <option value="Accent">Accent</option>
             <option value="Spectral">Spectral</option>
--- a/plotCorrelation.xml	Mon Feb 05 11:30:46 2018 -0500
+++ b/plotCorrelation.xml	Thu Feb 15 04:12:20 2018 -0500
@@ -18,6 +18,10 @@
                 --plotHeight $plotting_type.plotHeight
             #else:
                 --plotTitle '$plotting_type.plotTitle'
+                #if str($plotting_type.maxRange) != '':
+                    --maxRange '$plotting_type.maxRange'
+                #end if
+                $plotting_type.log1p
             #end if
             $skipZeros
             --plotFileFormat "$outFileFormat"
@@ -43,6 +47,12 @@
             </when>
             <when value="scatterplot">
                 <expand macro="plotTitle" />
+                <param argument="--maxRange" type="integer" value="" optional="true"
+                    label="Maximum Range"
+                    help="Maximum (integer) value for the X and Y axes. The default scales these such that the full range of dots is displayed. If you specify --log1p, please ensure that this value is within the range it will produce." />
+                <param argument="--log1p" type="boolean" truevalue="--log1p" falsevalue=""
+                    label="Log transform"
+                    help="Plot the natural log of the scatter plot after adding 1. Note that this is ONLY for plotting, the correlation is unaffected." />
             </when>
         </conditional>
 
@@ -78,7 +88,7 @@
             <param name="outFileFormat" value="png" />
             <param name="outFileCorMatrix" value="True" />
             <output name="matrix" file="plotCorrelation_result1.tabular" ftype="tabular" />
-            <output name="outFileName" file="plotCorrelation_result1.png" ftype="png" compare="sim_size" delta="300" />
+            <output name="outFileName" file="plotCorrelation_result1.png" ftype="png" compare="sim_size" delta="400" />
         </test>
         <test>
             <param name="corData" value="multiBamSummary_result1.npz" ftype="deeptools_coverage_matrix" />
--- a/readme.rst	Mon Feb 05 11:30:46 2018 -0500
+++ b/readme.rst	Thu Feb 15 04:12:20 2018 -0500
@@ -20,7 +20,7 @@
 
 deeptools is developed under here:
 
-    https://github.com/fidelram/deepTools
+    https://github.com/deeptools/deepTools
 
 For support, questions, or feature requests contact: deeptools@googlegroups.com
 
@@ -41,7 +41,7 @@
 Citation
 ========
 
-deeptools are currently under review. In the meantime please refere to https://github.com/fidelram/deepTools.
+deeptools are currently under review. In the meantime please refere to https://github.com/deeptools/deepTools.
 
 
 =======
Binary file test-data/alignmentSieve.bam has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/alignmentSieve.bed	Thu Feb 15 04:12:20 2018 -0500
@@ -0,0 +1,4261 @@
+chr2L	5093	5232
+chr2L	5101	5236
+chr2L	5105	5252
+chr2L	5108	5267
+chr2L	5105	5250
+chr2L	5108	5244
+chr2L	5108	5279
+chr2L	5105	5251
+chr2L	5105	5252
+chr2L	5105	5224
+chr2L	5108	5244
+chr2L	5108	5252
+chr2L	5108	5244
+chr2L	5108	5251
+chr2L	5105	5212
+chr2L	5105	5266
+chr2L	5108	5265
+chr2L	5106	5287
+chr2L	5106	5243
+chr2L	5106	5204
+chr2L	5109	5249
+chr2L	5109	5213
+chr2L	5106	5245
+chr2L	5118	5266
+chr2L	5116	5224
+chr2L	5117	5293
+chr2L	5117	5291
+chr2L	5120	5265
+chr2L	5117	5243
+chr2L	5122	5249
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+chr2L	5119	5245
+chr2L	5123	5423
+chr2L	5120	5293
+chr2L	5120	5250
+chr2L	5123	5293
+chr2L	5129	5197
+chr2L	5129	5323
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+chr2L	5127	5280
+chr2L	5127	5285
+chr2L	5133	5274
+chr2L	5138	5293
+chr2L	5141	5279
+chr2L	5138	5266
+chr2L	5141	5279
+chr2L	5152	5322
+chr2L	5149	5323
+chr2L	5149	5250
+chr2L	5149	5306
+chr2L	5152	5292
+chr2L	5152	5322
+chr2L	5149	5330
+chr2L	5151	5252
+chr2L	5154	5326
+chr2L	5154	5251
+chr2L	5153	5324
+chr2L	5154	5341
+chr2L	5157	5304
+chr2L	5157	5292
+chr2L	5159	5292
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+chr2L	5160	5292
+chr2L	5157	5323
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+chr2L	5160	5292
+chr2L	5161	5326
+chr2L	5167	5280
+chr2L	5168	5249
+chr2L	5168	5325
+chr2L	5165	5306
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+chr2L	5166	5306
+chr2L	5171	5323
+chr2L	5181	5322
+chr2L	5179	5356
+chr2L	5179	5294
+chr2L	5179	5323
+chr2L	5182	5312
+chr2L	5185	5323
+chr2L	5197	5326
+chr2L	5206	5322
+chr2L	5207	5340
+chr2L	5207	5355
+chr2L	5211	5325
+chr2L	5212	5350
+chr2L	5212	5296
+chr2L	5209	5381
+chr2L	5219	5369
+chr2L	5216	5323
+chr2L	5219	5356
+chr2L	5216	5382
+chr2L	5219	5381
+chr2L	5219	5369
+chr2L	5224	5326
+chr2L	5221	5356
+chr2L	5224	5380
+chr2L	5224	5356
+chr2L	5224	5325
+chr2L	5224	5375
+chr2L	5225	5380
+chr2L	5225	5325
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+chr2L	5225	5440
+chr2L	5225	5375
+chr2L	5225	5325
+chr2L	5225	5355
+chr2L	5225	5355
+chr2L	5227	5380
+chr2L	5226	5500
+chr2L	5230	5326
+chr2L	5231	5423
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+chr2L	5236	5383
+chr2L	5256	5401
+chr2L	5253	5455
+chr2L	5257	5467
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+chr2L	5261	5428
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+chr2L	5288	5411
+chr2L	5289	5382
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+chr2L	5317	5500
+chr2L	5328	5467
+chr2L	5331	5485
+chr2L	5334	5467
+chr2L	5334	5466
+chr2L	5334	5467
+chr2L	5331	5480
+chr2L	5332	5467
+chr2L	5335	5480
+chr2L	5332	5485
+chr2L	5332	5484
+chr2L	5332	5517
+chr2L	5335	5465
+chr2L	5335	5464
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+chr2L	9999	10134
+chr2L	10000	10173
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/alignmentSieve.txt	Thu Feb 15 04:12:20 2018 -0500
@@ -0,0 +1,3 @@
+#bamFilterReads --filterMetrics
+#File	Reads Remaining	Total Initial Reads
+paired_chr2L.bam	8440	12644
Binary file test-data/alignmentSieve2.bam has changed
Binary file test-data/alignmentSieve3.bam has changed
Binary file test-data/bamPEFragmentSize_histogram_result1.png has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/bamPEFragmentSize_lengths1.txt	Thu Feb 15 04:12:20 2018 -0500
@@ -0,0 +1,5 @@
+#bamPEFragmentSize
+Size	Occurrences	Sample
+241	1	bowtie2 test1.bam
+242	1	bowtie2 test1.bam
+251	1	bowtie2 test1.bam
--- a/test-data/bamPEFragmentSize_result1.txt	Mon Feb 05 11:30:46 2018 -0500
+++ b/test-data/bamPEFragmentSize_result1.txt	Thu Feb 15 04:12:20 2018 -0500
@@ -11,8 +11,21 @@
 3rd Qu.: 246.5
 Max.: 251.0
 Std: 4.496912521077347
+MAD: 1.0
+Len. 10%: 241.20000000000002
+Len. 20%: 241.4
+Len. 30%: 241.6
+Len. 40%: 241.8
+Len. 60%: 243.8
+Len. 70%: 245.6
+Len. 80%: 247.4
+Len. 90%: 249.2
+Len. 99%: 250.82
+
 
 Read lengths:
+Sample size: 3
+
 Min.: 251.0
 1st Qu.: 251.0
 Mean: 251.0
@@ -20,3 +33,14 @@
 3rd Qu.: 251.0
 Max.: 251.0
 Std: 0.0
+MAD: 0.0
+Len. 10%: 251.0
+Len. 20%: 251.0
+Len. 30%: 251.0
+Len. 40%: 251.0
+Len. 60%: 251.0
+Len. 70%: 251.0
+Len. 80%: 251.0
+Len. 90%: 251.0
+Len. 99%: 251.0
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/bamPEFragmentSize_table1.txt	Thu Feb 15 04:12:20 2018 -0500
@@ -0,0 +1,2 @@
+	Frag. Sampled	Frag. Len. Min.	Frag. Len. 1st. Qu.	Frag. Len. Mean	Frag. Len. Median	Frag. Len. 3rd Qu.	Frag. Len. Max	Frag. Len. Std.	Frag. Med. Abs. Dev.	Frag. Len. 10%	Frag. Len. 20%	Frag. Len. 30%	Frag. Len. 40%	Frag. Len. 60%	Frag. Len. 70%	Frag. Len. 80%	Frag. Len. 90%	Frag. Len. 99%	Reads Sampled	Read Len. Min.	Read Len. 1st. Qu.	Read Len. Mean	Read Len. Median	Read Len. 3rd Qu.	Read Len. Max	Read Len. Std.	Read Med. Abs. Dev.	Read Len. 10%	Read Len. 20%	Read Len. 30%	Read Len. 40%	Read Len. 60%	Read Len. 70%	Read Len. 80%	Read Len. 90%	Read Len. 99%
+bowtie2 test1.bam	3	241.0	241.5	244.66666666666666	242.0	246.5	251.0	4.496912521077347	1.0	241.20000000000002	241.4	241.6	241.8	243.8	245.6	247.4	249.2	250.82	3	251.0	251.0	251.0	251.0	251.0	251.0	0.0	0.0	251.0	251.0	251.0	251.0	251.0	251.0	251.0	251.0	251.0
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/estimateReadFiltering.txt	Thu Feb 15 04:12:20 2018 -0500
@@ -0,0 +1,3 @@
+Sample	Total Reads	Mapped Reads	Alignments in blacklisted regions	Estimated mapped reads filtered	Below MAPQ	Missing Flags	Excluded Flags	Internally-determined Duplicates	Marked Duplicates	Singletons	Wrong strand
+paired_chr2L.bam	12644	12589	0	1395.9	4149.0	0.0	0.0	0.0	0.0	55.0	0.0
+paired_chr2L.bam	12644	12589	0	1395.9	4149.0	0.0	0.0	0.0	0.0	55.0	0.0
Binary file test-data/heatmapper_result1.png has changed
Binary file test-data/heatmapper_result2.png has changed
Binary file test-data/multiBamSummary_result1.npz has changed
Binary file test-data/multiBamSummary_result2.npz has changed
Binary file test-data/paired_chr2L.cram has changed
--- a/test-data/plotCorrelation_result1.tabular	Mon Feb 05 11:30:46 2018 -0500
+++ b/test-data/plotCorrelation_result1.tabular	Thu Feb 15 04:12:20 2018 -0500
@@ -1,3 +1,4 @@
+#plotCorrelation --outFileCorMatrix
 	'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
--- a/test-data/plotCoverage_result1.tabular	Mon Feb 05 11:30:46 2018 -0500
+++ b/test-data/plotCoverage_result1.tabular	Thu Feb 15 04:12:20 2018 -0500
@@ -1,3 +1,4 @@
+#plotCoverage --outRawCounts
 #'chr'	'start'	'end'	'bowtie2 test1.bam'	'bowtie2 test1.bam'
 chrM	0	1	23.0	23.0
 chrM	1	2	35.0	35.0
--- a/test-data/plotEnrichment_output.txt	Mon Feb 05 11:30:46 2018 -0500
+++ b/test-data/plotEnrichment_output.txt	Thu Feb 15 04:12:20 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
+file	featureType	percent	featureReadCount	totalReadCount
+bowtie2 test1.bam	up	100.00	47	47
+bowtie2 test1.bam	down	100.00	47	47
+bowtie2 test1.bam	up	100.00	47	47
+bowtie2 test1.bam	down	100.00	47	47
--- a/test-data/plotFingerprint_result2.tabular	Mon Feb 05 11:30:46 2018 -0500
+++ b/test-data/plotFingerprint_result2.tabular	Thu Feb 15 04:12:20 2018 -0500
@@ -1,3 +1,4 @@
+#plotFingerprint --outRawCounts
 'bowtie2 test1.bam'	'bowtie2 test1.bam'
 1085	1085
 1782	1782
Binary file test-data/plotPCA_result1.png has changed
--- a/test-data/plotPCA_result2.tabular	Mon Feb 05 11:30:46 2018 -0500
+++ b/test-data/plotPCA_result2.tabular	Thu Feb 15 04:12:20 2018 -0500
@@ -1,3 +1,4 @@
+#plotPCA --outFileNameData
 Component	bowtie2-test1.bam	bowtie2-test1.bam	Eigenvalue
-1	-0.7071067811865476	-0.7071067811865475	6.000000000000001
+1	-0.7071067811865476	-0.7071067811865475	4.0
 2	-0.7071067811865475	0.7071067811865476	1.2325951644078315e-32