Galaxy |

Changeset 17:3f84770b69cd (2018-02-15)

Previous changeset 16:f177dde2ae22 (2018-02-05) Next changeset 18:cef5cec10544 (2018-03-02)

Commit message:
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty

modified:
correctGCBias.xml
deepTools_macros.xml
readme.rst
test-data/bamPEFragmentSize_histogram_result1.png
test-data/bamPEFragmentSize_result1.txt
test-data/heatmapper_result1.png
test-data/heatmapper_result2.png
test-data/multiBamSummary_result1.npz
test-data/multiBamSummary_result2.npz
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

added:
test-data/alignmentSieve.bam
test-data/alignmentSieve.bed
test-data/alignmentSieve.txt
test-data/alignmentSieve2.bam
test-data/alignmentSieve3.bam
test-data/bamPEFragmentSize_lengths1.txt
test-data/bamPEFragmentSize_table1.txt
test-data/estimateReadFiltering.txt
test-data/paired_chr2L.cram

diff -r f177dde2ae22 -r 3f84770b69cd correctGCBias.xml
--- a/correctGCBias.xml Mon Feb 05 11:43:07 2018 -0500
+++ b/correctGCBias.xml Thu Feb 15 07:44:32 2018 -0500

[

@@ -1,5 +1,5 @@
<tool id="deeptools_correct_gc_bias" name="correctGCBias" version="@WRAPPER_VERSION@.0">
-    <description>uses the output from computeGCBias to generate GC-corrected BAM files</description>
+    <description>uses the output from computeGCBias to generate GC-corrected BAM/CRAM files</description>
     <macros>
         <token name="@BINARY@">correctGCBias</token>
         <import>deepTools_macros.xml</import>
@@ -8,7 +8,11 @@
     <command>
<![CDATA[
         ln -s "$bamInput" "local_bamInput.bam" &&
-        ln -s "$bamInput.metadata.bam_index" local_bamInput.bam.bai &&
+        #if $bamInput.ext == 'bam':
+            ln -s '${bamInput.metadata.bam_index}' local_bamInput.bam.bai &&
+        #else:
+            ln -s '${bamInput.metadata.cram_index}' local_bamInput.bam.crai &&
+        #end if

         @BINARY@
             @THREADS@
@@ -31,8 +35,8 @@
     </command>
     <inputs>
         <param argument="--GCbiasFrequenciesFile" type="data" format="tabular" label="Output of computeGCBias" help="" />
-        <param argument="--bamInput" format="bam" type="data"
-            label="BAM file" help="This should be same file that was used for computeGCbias." />
+        <param argument="--bamInput" format="bam,cram" type="data"
+            label="BAM/CRAM file" help="This should be same file that was used for computeGCbias." />
         <expand macro="reference_genome_source" />
         <expand macro="effectiveGenomeSize" />
         <expand macro="region_limit_operation" />
@@ -48,7 +52,7 @@
             <param name="input1" value="sequence.2bit" />
             <param name="effectiveGenomeSize_opt" value="specific" />
             <param name="effectiveGenomeSize" value="10050" />
-            <output name="outFileName" file="correctGCBias_result1.bam" ftype="bam" lines_diff="100" />
+            <output name="outFileName" file="correctGCBias_result1.bam" ftype="bam" lines_diff="200" />
         </test>
     </tests>
     <help>

diff -r f177dde2ae22 -r 3f84770b69cd deepTools_macros.xml
--- a/deepTools_macros.xml Mon Feb 05 11:43:07 2018 -0500
+++ b/deepTools_macros.xml Thu Feb 15 07:44:32 2018 -0500

b'@@ -1,11 +1,11 @@\n <macros>\n \n <token name="@THREADS@">--numberOfProcessors "\\${GALAXY_SLOTS:-4}"</token>\n- <token name="@WRAPPER_VERSION@">2.5.7</token>\n+ <token name="@WRAPPER_VERSION@">3.0.0</token>\n <xml name="requirements">\n <requirements>\n- <requirement type="package" version="2.5.7">deeptools</requirement>\n- <yield />\n+ <requirement type="package" version="3.0.0">deeptools</requirement>\n+ <requirement type="package" version="1.7">samtools</requirement>\n </requirements>\n <expand macro="stdio" />\n <version_command>@BINARY@ --version</version_command>\n@@ -100,7 +100,7 @@\n <xml name="includeZeros">\n <param argument="--includeZeros" type="boolean" truevalue="--includeZeros" falsevalue=""\n label="Include zeros"\n- help="If set, then regions with zero counts for *all* BAM files are included. The default behavior is to ignore such regions." />\n+ help="If set, then regions with zero counts for *all* BAM/CRAM files are included. The default behavior is to ignore such regions." />\n </xml>\n \n <xml name="zMin_zMax">\n@@ -238,7 +238,7 @@\n <xml name="extendReads">\n <conditional name="doExtendCustom">\n <param name="doExtend" type="select" label="Extend reads to the given average fragment size."\n- 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.\n+ 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.\n By default *each* read mate is extended.\n This can be modified using the SAM flags (see --samFlagInclude and --samFlagExclude options) to keep only the first or the second mate.\n Unmated reads, mate reads that map to different chromosomes or too far apart are extended to the given value.\n@@ -312,7 +312,7 @@\n <xml name="sortRegions">\n <param argument="--sortRegions" type="select" label="Sort regions"\n help="Whether the heatmap should present the regions sorted. The default is to sort in descending order based on the mean value per region.">\n- <option value="no">no ordering</option>\n+ <option value="no">maintain the same ordering as the input files</option>\n <option value="descend" selected="true">descending order</option>\n <option value="ascend">ascending order</option>\n </param>\n@@ -321,19 +321,19 @@\n <xml name="minMappingQuality">\n <param argument="--minMappingQuality" type="integer" optional="true" value="1" min="0"\n label="Minimum mapping quality"\n- help= "If set, only reads with a mapping quality score higher than this value are considered."/>\n+ help= "If set, only reads with a mapping quality score at least this high are considered."/>\n </xml>\n \n <xml name="skipZeros">\n <param argument="--skipZeros" type="boolean" truevalue="--skipZeros" falsevalue=""\n label ="Skip zeros"\n- help ="If set, then zero counts that happen for *all* BAM files given are ignored. This may result in fewer considered regions." />\n+ help ="If set, then zero counts that happen for *all* BAM/CRAM files given are ignored. This may result in fewer considered regions." />\n </xml>\n \n <xml name="fragmentLength">\n- <param argument="--fragmentLength" type="integer" value="300" min="1"\n+ <param argument="--fragmentLength" type="integer" min="1" optional="true"\n label="Fragment length used for the sequencing"\n- 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."/>\n+ help ="If paired-end reads are'..b'ed="true">hg19 (2451960000)</option>\n- <option value="2150570000">mm9 (2150570000)</option>\n+ <option value="130428560">dm3 (130428560)</option>\n+ <option value="125464728">dm6 (125464728)</option>\n+ <option value="2685511504" selected="true">hg19/GRCh37 (2685511504)</option>\n+ <option value="2701495761">GRCh38/hg38 (2701495761)</option>\n+ <option value="2304947926">GRCm37/mm9 (2304947926)</option>\n+ <option value="2308125349">GRCm38/mm10 (2308125349)</option>\n <option value="specific">user specified</option>\n </param>\n <when value="specific">\n <param argument="--effectiveGenomeSize" type="integer" value="" label="Effective genome size"\n- help="e.g. ce10: 93260000, dm3: 121400000, hg19: 2451960000, mm9: 2150570000"/>\n+ help="e.g. ce10: 93260000, dm3: 130428560, hg19: 2685511504, mm9: 2304947926"/>\n </when>\n- <when value="2150570000" />\n- <when value="2451960000" />\n- <when value="121400000" />\n <when value="93260000" />\n+ <when value="130428560" />\n+ <when value="125464728" />\n+ <when value="2685511504" />\n+ <when value="2701495761" />\n+ <when value="2304947926" />\n+ <when value="2308125349" />\n </conditional>\n </xml>\n \n@@ -596,6 +617,7 @@\n <when value="yes">\n <yield />\n <param name="saveSortedRegions" type="boolean"\n+ argument="--outFileSortedRegions"\n label="Save the regions after skipping zeros or min/max threshold values"\n help="The order of the regions in the file follows the sorting order selected. This is useful,\n for example, to generate other heatmaps keeping the sorting of the first heatmap."/>\n@@ -605,11 +627,12 @@\n \n \n <xml name="input_image_file_format">\n- <param argument="--outFileFormat" type="select" label="Image file format">\n+ <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.">\n <option value="png" selected="true">png</option>\n <option value="pdf">pdf</option>\n <option value="svg">svg</option>\n <option value="eps">eps</option>\n+ <option value="plotly">plotly</option>\n </param>\n </xml>\n \n@@ -624,6 +647,7 @@\n <when input="output.outFileFormat" value="pdf" format="pdf" />\n <when input="output.outFileFormat" value="svg" format="svg" />\n <when input="output.outFileFormat" value="eps" format="eps" />\n+ <when input="output.outFileFormat" value="plotly" format="html" />\n </change_format>\n </data>\n </xml>\n@@ -634,6 +658,7 @@\n <when input="outFileFormat" value="pdf" format="pdf" />\n <when input="outFileFormat" value="svg" format="svg" />\n <when input="outFileFormat" value="eps" format="eps" />\n+ <when input="outFileFormat" value="plotly" format="html" />\n </change_format>\n </data>\n </xml>\n@@ -662,8 +687,7 @@\n \n <xml name="colorMap">\n <param name="colorMap" type="select" label="Color map to use for the heatmap"\n- help=" Available color map names can be found here: http://matplotlib.org/examples/color/colormaps_reference.html"\n- multiple="true">\n+ help=" Available color map names can be found here: http://matplotlib.org/examples/color/colormaps_reference.html">\n <option value="RdYlBu" selected="true">RdYlBu</option>\n <option value="Accent">Accent</option>\n <option value="Spectral">Spectral</option>\n'

diff -r f177dde2ae22 -r 3f84770b69cd readme.rst
--- a/readme.rst Mon Feb 05 11:43:07 2018 -0500
+++ b/readme.rst Thu Feb 15 07:44:32 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.

=======

diff -r f177dde2ae22 -r 3f84770b69cd test-data/alignmentSieve.bam

Binary file test-data/alignmentSieve.bam has changed

diff -r f177dde2ae22 -r 3f84770b69cd test-data/alignmentSieve.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/alignmentSieve.bed Thu Feb 15 07:44:32 2018 -0500

b'@@ -0,0 +1,4261 @@\n+chr2L\t5093\t5232\n+chr2L\t5101\t5236\n+chr2L\t5105\t5252\n+chr2L\t5108\t5267\n+chr2L\t5105\t5250\n+chr2L\t5108\t5244\n+chr2L\t5108\t5279\n+chr2L\t5105\t5251\n+chr2L\t5105\t5252\n+chr2L\t5105\t5224\n+chr2L\t5108\t5244\n+chr2L\t5108\t5252\n+chr2L\t5108\t5244\n+chr2L\t5108\t5251\n+chr2L\t5105\t5212\n+chr2L\t5105\t5266\n+chr2L\t5108\t5265\n+chr2L\t5106\t5287\n+chr2L\t5106\t5243\n+chr2L\t5106\t5204\n+chr2L\t5109\t5249\n+chr2L\t5109\t5213\n+chr2L\t5106\t5245\n+chr2L\t5118\t5266\n+chr2L\t5116\t5224\n+chr2L\t5117\t5293\n+chr2L\t5117\t5291\n+chr2L\t5120\t5265\n+chr2L\t5117\t5243\n+chr2L\t5122\t5249\n+chr2L\t5119\t5268\n+chr2L\t5119\t5245\n+chr2L\t5123\t5423\n+chr2L\t5120\t5293\n+chr2L\t5120\t5250\n+chr2L\t5123\t5293\n+chr2L\t5129\t5197\n+chr2L\t5129\t5323\n+chr2L\t5130\t5265\n+chr2L\t5127\t5280\n+chr2L\t5127\t5285\n+chr2L\t5133\t5274\n+chr2L\t5138\t5293\n+chr2L\t5141\t5279\n+chr2L\t5138\t5266\n+chr2L\t5141\t5279\n+chr2L\t5152\t5322\n+chr2L\t5149\t5323\n+chr2L\t5149\t5250\n+chr2L\t5149\t5306\n+chr2L\t5152\t5292\n+chr2L\t5152\t5322\n+chr2L\t5149\t5330\n+chr2L\t5151\t5252\n+chr2L\t5154\t5326\n+chr2L\t5154\t5251\n+chr2L\t5153\t5324\n+chr2L\t5154\t5341\n+chr2L\t5157\t5304\n+chr2L\t5157\t5292\n+chr2L\t5159\t5292\n+chr2L\t5156\t5323\n+chr2L\t5160\t5292\n+chr2L\t5157\t5323\n+chr2L\t5160\t5326\n+chr2L\t5160\t5292\n+chr2L\t5161\t5326\n+chr2L\t5167\t5280\n+chr2L\t5168\t5249\n+chr2L\t5168\t5325\n+chr2L\t5165\t5306\n+chr2L\t5166\t5323\n+chr2L\t5166\t5306\n+chr2L\t5171\t5323\n+chr2L\t5181\t5322\n+chr2L\t5179\t5356\n+chr2L\t5179\t5294\n+chr2L\t5179\t5323\n+chr2L\t5182\t5312\n+chr2L\t5185\t5323\n+chr2L\t5197\t5326\n+chr2L\t5206\t5322\n+chr2L\t5207\t5340\n+chr2L\t5207\t5355\n+chr2L\t5211\t5325\n+chr2L\t5212\t5350\n+chr2L\t5212\t5296\n+chr2L\t5209\t5381\n+chr2L\t5219\t5369\n+chr2L\t5216\t5323\n+chr2L\t5219\t5356\n+chr2L\t5216\t5382\n+chr2L\t5219\t5381\n+chr2L\t5219\t5369\n+chr2L\t5224\t5326\n+chr2L\t5221\t5356\n+chr2L\t5224\t5380\n+chr2L\t5224\t5356\n+chr2L\t5224\t5325\n+chr2L\t5224\t5375\n+chr2L\t5225\t5380\n+chr2L\t5225\t5325\n+chr2L\t5225\t5377\n+chr2L\t5225\t5381\n+chr2L\t5225\t5440\n+chr2L\t5225\t5375\n+chr2L\t5225\t5325\n+chr2L\t5225\t5355\n+chr2L\t5225\t5355\n+chr2L\t5227\t5380\n+chr2L\t5226\t5500\n+chr2L\t5230\t5326\n+chr2L\t5231\t5423\n+chr2L\t5228\t5400\n+chr2L\t5236\t5383\n+chr2L\t5256\t5401\n+chr2L\t5253\t5455\n+chr2L\t5257\t5467\n+chr2L\t5257\t5402\n+chr2L\t5261\t5423\n+chr2L\t5258\t5355\n+chr2L\t5261\t5428\n+chr2L\t5264\t5401\n+chr2L\t5264\t5401\n+chr2L\t5261\t5467\n+chr2L\t5261\t5403\n+chr2L\t5265\t5426\n+chr2L\t5265\t5377\n+chr2L\t5262\t5370\n+chr2L\t5262\t5392\n+chr2L\t5265\t5423\n+chr2L\t5265\t5375\n+chr2L\t5265\t5401\n+chr2L\t5265\t5401\n+chr2L\t5262\t5427\n+chr2L\t5274\t5465\n+chr2L\t5276\t5381\n+chr2L\t5279\t5402\n+chr2L\t5281\t5423\n+chr2L\t5281\t5431\n+chr2L\t5288\t5411\n+chr2L\t5289\t5382\n+chr2L\t5288\t5421\n+chr2L\t5288\t5421\n+chr2L\t5291\t5420\n+chr2L\t5288\t5424\n+chr2L\t5289\t5467\n+chr2L\t5302\t5462\n+chr2L\t5303\t5401\n+chr2L\t5300\t5425\n+chr2L\t5303\t5464\n+chr2L\t5300\t5464\n+chr2L\t5300\t5464\n+chr2L\t5306\t5401\n+chr2L\t5303\t5428\n+chr2L\t5303\t5414\n+chr2L\t5303\t5465\n+chr2L\t5304\t5407\n+chr2L\t5311\t5423\n+chr2L\t5310\t5467\n+chr2L\t5313\t5463\n+chr2L\t5313\t5423\n+chr2L\t5310\t5465\n+chr2L\t5313\t5423\n+chr2L\t5313\t5462\n+chr2L\t5317\t5500\n+chr2L\t5328\t5467\n+chr2L\t5331\t5485\n+chr2L\t5334\t5467\n+chr2L\t5334\t5466\n+chr2L\t5334\t5467\n+chr2L\t5331\t5480\n+chr2L\t5332\t5467\n+chr2L\t5335\t5480\n+chr2L\t5332\t5485\n+chr2L\t5332\t5484\n+chr2L\t5332\t5517\n+chr2L\t5335\t5465\n+chr2L\t5335\t5464\n+chr2L\t5335\t5464\n+chr2L\t5332\t5469\n+chr2L\t5335\t5467\n+chr2L\t5333\t5472\n+chr2L\t5337\t5480\n+chr2L\t5334\t5488\n+chr2L\t5337\t5467\n+chr2L\t5334\t5503\n+chr2L\t5337\t5527\n+chr2L\t5337\t5497\n+chr2L\t5334\t5498\n+chr2L\t5334\t5497\n+chr2L\t5337\t5463\n+chr2L\t5337\t5516\n+chr2L\t5334\t5483\n+chr2L\t5337\t5517\n+chr2L\t5337\t5453\n+chr2L\t5337\t5466\n+chr2L\t5337\t5440\n+chr2L\t5334\t5454\n+chr2L\t5339\t5503\n+chr2L\t5343\t5451\n+chr2L\t5340\t5518\n+chr2L\t5350\t5466\n+chr2L\t5352\t5464\n+chr2L\t5349\t5467\n+chr2L\t5352\t5496\n+chr2L\t5352\t5453\n+chr2L\t5361\t5527\n+chr2L\t5365\t5500\n+chr2L\t5362\t5527\n+chr2L\t5365\t5517\n+chr2L\t5362\t5464\n+chr2L\t5362\t5497\n+chr2L\t5368\t5517\n+chr2L\t5368\t5496\n+chr2L\t5378\t5500\n+chr2L\t5378\t5499\n+chr2L\t5375\t5527\n+chr2L\t5385\t5517\n+chr2L\t5385\t5497\n+chr2L\t5387\t5527\n+chr2L\t5390\t5502\n+chr2L\t5387\t5527\n+chr2L\t5390\t5526\n+chr2L\t5394\t5526\n+chr2L\t5391\t5557\n+chr2L\t5395\t5502\n+chr2L\t5395\t5520\n+chr2L\t5392\t5481\n+chr2L\t5392\t5504\n+chr2L\t5395\t5556\n+chr2L\t5394\t5533\n+chr2L\t5395\t5557\n+chr2L\t5398\t5563\n+c'..b'\n+chr2L\t9803\t9973\n+chr2L\t9803\t9959\n+chr2L\t9806\t9946\n+chr2L\t9806\t9949\n+chr2L\t9803\t9891\n+chr2L\t9806\t9958\n+chr2L\t9806\t9958\n+chr2L\t9803\t9942\n+chr2L\t9803\t9949\n+chr2L\t9803\t9956\n+chr2L\t9806\t9948\n+chr2L\t9803\t9942\n+chr2L\t9804\t9954\n+chr2L\t9807\t9958\n+chr2L\t9808\t9953\n+chr2L\t9813\t9912\n+chr2L\t9816\t10018\n+chr2L\t9813\t9950\n+chr2L\t9820\t9978\n+chr2L\t9823\t9949\n+chr2L\t9823\t9975\n+chr2L\t9827\t9949\n+chr2L\t9827\t9955\n+chr2L\t9828\t9936\n+chr2L\t9832\t9954\n+chr2L\t9832\t9971\n+chr2L\t9833\t9942\n+chr2L\t9833\t9953\n+chr2L\t9830\t9942\n+chr2L\t9833\t9973\n+chr2L\t9830\t9950\n+chr2L\t9833\t9942\n+chr2L\t9833\t9932\n+chr2L\t9830\t10006\n+chr2L\t9830\t9974\n+chr2L\t9830\t9946\n+chr2L\t9833\t9971\n+chr2L\t9833\t9932\n+chr2L\t9834\t9960\n+chr2L\t9844\t9953\n+chr2L\t9849\t9973\n+chr2L\t9850\t9974\n+chr2L\t9853\t9972\n+chr2L\t9850\t9955\n+chr2L\t9853\t9997\n+chr2L\t9850\t9972\n+chr2L\t9853\t10029\n+chr2L\t9854\t10017\n+chr2L\t9851\t10003\n+chr2L\t9851\t9938\n+chr2L\t9853\t9959\n+chr2L\t9854\t10005\n+chr2L\t9854\t9973\n+chr2L\t9862\t10010\n+chr2L\t9861\t10031\n+chr2L\t9866\t10039\n+chr2L\t9868\t10017\n+chr2L\t9869\t10018\n+chr2L\t9867\t10011\n+chr2L\t9867\t10022\n+chr2L\t9867\t10025\n+chr2L\t9871\t10024\n+chr2L\t9871\t10075\n+chr2L\t9871\t10004\n+chr2L\t9868\t10025\n+chr2L\t9868\t9959\n+chr2L\t9868\t9957\n+chr2L\t9871\t9975\n+chr2L\t9875\t9961\n+chr2L\t9872\t10030\n+chr2L\t9875\t10009\n+chr2L\t9875\t9961\n+chr2L\t9876\t10017\n+chr2L\t9876\t10024\n+chr2L\t9883\t10018\n+chr2L\t9880\t10025\n+chr2L\t9883\t10004\n+chr2L\t9884\t10046\n+chr2L\t9884\t10030\n+chr2L\t9884\t10144\n+chr2L\t9884\t10018\n+chr2L\t9886\t10017\n+chr2L\t9891\t10018\n+chr2L\t9894\t9972\n+chr2L\t9896\t10054\n+chr2L\t9896\t10050\n+chr2L\t9898\t10077\n+chr2L\t9900\t10050\n+chr2L\t9903\t10055\n+chr2L\t9903\t10049\n+chr2L\t9903\t10056\n+chr2L\t9900\t10064\n+chr2L\t9903\t10067\n+chr2L\t9903\t10067\n+chr2L\t9900\t10076\n+chr2L\t9903\t10062\n+chr2L\t9904\t10018\n+chr2L\t9901\t10030\n+chr2L\t9904\t10063\n+chr2L\t9904\t10073\n+chr2L\t9901\t10019\n+chr2L\t9901\t10018\n+chr2L\t9904\t10046\n+chr2L\t9904\t10055\n+chr2L\t9904\t10072\n+chr2L\t9901\t10051\n+chr2L\t9904\t10029\n+chr2L\t9904\t10017\n+chr2L\t9904\t10068\n+chr2L\t9904\t10050\n+chr2L\t9904\t10072\n+chr2L\t9904\t10049\n+chr2L\t9904\t10067\n+chr2L\t9904\t10049\n+chr2L\t9901\t10047\n+chr2L\t9905\t10050\n+chr2L\t9907\t10049\n+chr2L\t9904\t10047\n+chr2L\t9904\t10030\n+chr2L\t9907\t10067\n+chr2L\t9907\t10036\n+chr2L\t9904\t10026\n+chr2L\t9914\t10068\n+chr2L\t9914\t10017\n+chr2L\t9916\t10048\n+chr2L\t9919\t10068\n+chr2L\t9916\t10064\n+chr2L\t9918\t10019\n+chr2L\t9919\t10068\n+chr2L\t9924\t10069\n+chr2L\t9921\t10056\n+chr2L\t9927\t10019\n+chr2L\t9931\t10067\n+chr2L\t9929\t10090\n+chr2L\t9932\t10072\n+chr2L\t9931\t10089\n+chr2L\t9935\t10100\n+chr2L\t9935\t10072\n+chr2L\t9935\t10067\n+chr2L\t9933\t10089\n+chr2L\t9935\t10088\n+chr2L\t9936\t10045\n+chr2L\t9939\t10094\n+chr2L\t9937\t10030\n+chr2L\t9942\t10135\n+chr2L\t9957\t10049\n+chr2L\t9958\t10095\n+chr2L\t9958\t10106\n+chr2L\t9961\t10088\n+chr2L\t9958\t10086\n+chr2L\t9962\t10089\n+chr2L\t9962\t10100\n+chr2L\t9964\t10108\n+chr2L\t9967\t10088\n+chr2L\t9964\t10073\n+chr2L\t9968\t10134\n+chr2L\t9965\t10068\n+chr2L\t9968\t10107\n+chr2L\t9968\t10067\n+chr2L\t9966\t10089\n+chr2L\t9966\t10074\n+chr2L\t9969\t10089\n+chr2L\t9971\t10089\n+chr2L\t9969\t10103\n+chr2L\t9969\t10142\n+chr2L\t9969\t10094\n+chr2L\t9970\t10106\n+chr2L\t9973\t10132\n+chr2L\t9973\t10121\n+chr2L\t9973\t10116\n+chr2L\t9973\t10095\n+chr2L\t9971\t10280\n+chr2L\t9974\t10113\n+chr2L\t9971\t10088\n+chr2L\t9974\t10116\n+chr2L\t9974\t10088\n+chr2L\t9974\t10117\n+chr2L\t9974\t10134\n+chr2L\t9974\t10104\n+chr2L\t9972\t10141\n+chr2L\t9972\t10073\n+chr2L\t9977\t10101\n+chr2L\t9980\t10118\n+chr2L\t9981\t10125\n+chr2L\t9985\t10135\n+chr2L\t9985\t10134\n+chr2L\t9982\t10133\n+chr2L\t9982\t10237\n+chr2L\t9985\t10113\n+chr2L\t9985\t10134\n+chr2L\t9986\t10362\n+chr2L\t9983\t10146\n+chr2L\t9986\t10132\n+chr2L\t9983\t10141\n+chr2L\t9986\t10149\n+chr2L\t9986\t10141\n+chr2L\t9983\t10142\n+chr2L\t9986\t10100\n+chr2L\t9986\t10134\n+chr2L\t9983\t10136\n+chr2L\t9983\t10108\n+chr2L\t9986\t10141\n+chr2L\t9987\t10121\n+chr2L\t9987\t10134\n+chr2L\t9984\t10141\n+chr2L\t9987\t10089\n+chr2L\t9989\t10171\n+chr2L\t9989\t10099\n+chr2L\t9989\t10141\n+chr2L\t9992\t10134\n+chr2L\t9989\t10158\n+chr2L\t9992\t10150\n+chr2L\t9993\t10147\n+chr2L\t9990\t10108\n+chr2L\t9990\t10142\n+chr2L\t9993\t10170\n+chr2L\t9990\t10135\n+chr2L\t9993\t10091\n+chr2L\t9994\t10135\n+chr2L\t9991\t10145\n+chr2L\t9991\t10101\n+chr2L\t9991\t10145\n+chr2L\t9991\t10133\n+chr2L\t9999\t10134\n+chr2L\t10000\t10173\n'

diff -r f177dde2ae22 -r 3f84770b69cd test-data/alignmentSieve.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/alignmentSieve.txt Thu Feb 15 07:44:32 2018 -0500

@@ -0,0 +1,3 @@
+#bamFilterReads --filterMetrics
+#File Reads Remaining Total Initial Reads
+paired_chr2L.bam 8440 12644

diff -r f177dde2ae22 -r 3f84770b69cd test-data/alignmentSieve2.bam

Binary file test-data/alignmentSieve2.bam has changed

diff -r f177dde2ae22 -r 3f84770b69cd test-data/alignmentSieve3.bam

Binary file test-data/alignmentSieve3.bam has changed

diff -r f177dde2ae22 -r 3f84770b69cd test-data/bamPEFragmentSize_histogram_result1.png

Binary file test-data/bamPEFragmentSize_histogram_result1.png has changed

diff -r f177dde2ae22 -r 3f84770b69cd test-data/bamPEFragmentSize_lengths1.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/bamPEFragmentSize_lengths1.txt Thu Feb 15 07:44:32 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

diff -r f177dde2ae22 -r 3f84770b69cd test-data/bamPEFragmentSize_result1.txt
--- a/test-data/bamPEFragmentSize_result1.txt Mon Feb 05 11:43:07 2018 -0500
+++ b/test-data/bamPEFragmentSize_result1.txt Thu Feb 15 07:44:32 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
+

diff -r f177dde2ae22 -r 3f84770b69cd test-data/bamPEFragmentSize_table1.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/bamPEFragmentSize_table1.txt Thu Feb 15 07:44:32 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

diff -r f177dde2ae22 -r 3f84770b69cd test-data/estimateReadFiltering.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/estimateReadFiltering.txt Thu Feb 15 07:44:32 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

diff -r f177dde2ae22 -r 3f84770b69cd test-data/heatmapper_result1.png

Binary file test-data/heatmapper_result1.png has changed

diff -r f177dde2ae22 -r 3f84770b69cd test-data/heatmapper_result2.png

Binary file test-data/heatmapper_result2.png has changed

diff -r f177dde2ae22 -r 3f84770b69cd test-data/multiBamSummary_result1.npz

Binary file test-data/multiBamSummary_result1.npz has changed

diff -r f177dde2ae22 -r 3f84770b69cd test-data/multiBamSummary_result2.npz

Binary file test-data/multiBamSummary_result2.npz has changed

diff -r f177dde2ae22 -r 3f84770b69cd test-data/paired_chr2L.cram

Binary file test-data/paired_chr2L.cram has changed

diff -r f177dde2ae22 -r 3f84770b69cd test-data/plotCorrelation_result1.tabular
--- a/test-data/plotCorrelation_result1.tabular Mon Feb 05 11:43:07 2018 -0500
+++ b/test-data/plotCorrelation_result1.tabular Thu Feb 15 07:44:32 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

diff -r f177dde2ae22 -r 3f84770b69cd test-data/plotCorrelation_result2.png

Binary file test-data/plotCorrelation_result2.png has changed

diff -r f177dde2ae22 -r 3f84770b69cd test-data/plotCoverage_result1.png

Binary file test-data/plotCoverage_result1.png has changed

diff -r f177dde2ae22 -r 3f84770b69cd test-data/plotCoverage_result1.tabular
--- a/test-data/plotCoverage_result1.tabular Mon Feb 05 11:43:07 2018 -0500
+++ b/test-data/plotCoverage_result1.tabular Thu Feb 15 07:44:32 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

diff -r f177dde2ae22 -r 3f84770b69cd test-data/plotEnrichment_output.txt
--- a/test-data/plotEnrichment_output.txt Mon Feb 05 11:43:07 2018 -0500
+++ b/test-data/plotEnrichment_output.txt Thu Feb 15 07:44:32 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

diff -r f177dde2ae22 -r 3f84770b69cd test-data/plotFingerprint_result2.tabular
--- a/test-data/plotFingerprint_result2.tabular Mon Feb 05 11:43:07 2018 -0500
+++ b/test-data/plotFingerprint_result2.tabular Thu Feb 15 07:44:32 2018 -0500

@@ -1,3 +1,4 @@
+#plotFingerprint --outRawCounts
'bowtie2 test1.bam' 'bowtie2 test1.bam'
1085 1085
1782 1782

diff -r f177dde2ae22 -r 3f84770b69cd test-data/plotPCA_result1.png

Binary file test-data/plotPCA_result1.png has changed

diff -r f177dde2ae22 -r 3f84770b69cd test-data/plotPCA_result2.tabular
--- a/test-data/plotPCA_result2.tabular Mon Feb 05 11:43:07 2018 -0500
+++ b/test-data/plotPCA_result2.tabular Thu Feb 15 07:44:32 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