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Changeset 0:dfc5a344e2c2 (2018-02-15)

Next changeset 1:48d08791d4f2 (2018-03-02)

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

diff -r 000000000000 -r dfc5a344e2c2 alignmentSieve.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/alignmentSieve.xml Thu Feb 15 08:13:20 2018 -0500

[

b'@@ -0,0 +1,216 @@\n+<tool id="deeptools_alignmentsieve" name="alignmentsieve" version="@WRAPPER_VERSION@.0">\n+ <description>Filter BAM/CRAM files according to specified parameters</description>\n+ <macros>\n+ <token name="@BINARY@">alignmentSieve</token>\n+ <import>deepTools_macros.xml</import>\n+ </macros>\n+ <expand macro="requirements" />\n+ <command>\n+<![CDATA[\n+ #import re\n+ #set label = re.sub(\'[^\\.\\s\\w\\-]\', \'_\', str($bamfile.element_identifier))\n+ ln -s \'$bamfile\' one.bam &&\n+ #if $bamfile.ext == \'bam\':\n+ ln -s \'${bamfile.metadata.bam_index}\' one.bam.bai &&\n+ #else:\n+ ln -s \'${bamfile.metadata.cram_index}\' one.bam.crai &&\n+ #end if\n+\n+ @BINARY@\n+ @THREADS@\n+ -b one.bam\n+\n+ --label \'$label\'\n+\n+ #if str($filterRNAstrand) != \'no\':\n+ --filterRNAstrand \'$filterRNAstrand\'\n+ #end if\n+\n+ $ignoreDuplicates\n+\n+ #if $minMappingQuality:\n+ --minMappingQuality \'$minMappingQuality\'\n+ #end if\n+\n+ #if $samFlagInclude:\n+ --samFlagInclude $samFlagInclude\n+ #end if\n+\n+ #if $samFlagExclude:\n+ --samFlagExclude $samFlagExclude\n+ #end if\n+\n+ #if $minFragmentLength:\n+ --minFragmentLength $minFragmentLength\n+ #end if\n+\n+ #if $maxFragmentLength:\n+ --maxFragmentLength $maxFragmentLength\n+ #end if\n+\n+ #if \' \'.join( map(str, $blackListFileName) ) != \'None\':\n+ #set blfiles=[]\n+ #for $f in $blackListFileName:\n+ #silent $blfiles.append("\'%s\'" % $f)\n+ #end for\n+ #if $blfiles != ["\'None\'"]:\n+ --blackListFileName #echo \' \'.join($blfiles)#\n+ #end if\n+ #end if\n+\n+ #if $filterMetrics:\n+ --filterMetrics \'$filterMetricsFile\'\n+ #end if\n+\n+ #if $filteredOutReads:\n+ --filteredOutReads \'$outFileFiltered\'\n+ #end if\n+\n+ #if str($shift) != "":\n+ #set shifts = " ".join(["\'{}\'".format(x) for x in $shift.split(" ")])\n+ --shift $shifts\n+ #elif $ATACshift:\n+ --ATACshift\n+ #end if\n+ #if $BED:\n+ --BED\n+ -o \'$outFile\'\n+ #elif str($shift) != "":\n+ -o foo.bam &&\n+ samtools sort -o \'$outFile\' -T foo.tmp -@ "\\${GALAXY_SLOTS:-4}" foo.bam &&\n+ rm foo.bam\n+ #else:\n+ -o \'$outFile\'\n+ #end if\n+]]>\n+ </command>\n+\n+ <inputs>\n+ <param name="bamfile" format="bam,cram" type="data" label="BAM file" />\n+ <param name="BED" argument="--BED" type="boolean" label="Output in BEDPE format?"\n+ help="Instead of producing BAM files, write output in BEDPE format (as defined by MACS2). Note that only reads/fragments passing filtering criterion are written in BEDPE format." />\n+ <param argument="--shift" type="text" label="Amount to shift fragments" value=""\n+ help="Shift the left and right end of a fragment. A positive\n+ value shift an end to the right (on the + strand) and\n+ a negative value shifts a fragment to the left. Either\n+ 2 or 4 integers can be provided. For example, \'2 -3\'\n+ will shift the left-most fragment end two bases to the\n+ right and the right-most end 3 bases to the left. If 4\n+ integers are provided, then the first and last two\n+ refer to fragments whose read 1 is on the left or\n+ right, respectively. Consequently, it is possible to\n+ take strand into consideration for strand-specific\n+ protocols. Note that only properly paired reads are considered."/>\n+ <param argument="--ATACshift" type="boolean" label="Shift fragment ends as appropriate for ATAC-seq" />\n+ <param argument="filterRNAstrand" type'..b'aram name="bamfile" value="paired_chr2L.bam" ftype="bam" />\n+ <param name="minMappingQuality" value="10" />\n+ <param name="filterMetrics" value="True" />\n+ <output name="outFile" file="alignmentSieve.bam" ftype="bam" />\n+ <output name="filterMetricsFile" file="alignmentSieve.txt" ftype="tabular" />\n+ </test>\n+ <test>\n+ <param name="bamfile" value="paired_chr2L.bam" ftype="bam" />\n+ <param name="minMappingQuality" value="10" />\n+ <param name="BED" value="yes" />\n+ <param name="shift" value="1 -2 3 -4" />\n+ <output name="outFile" file="alignmentSieve.bed" ftype="bed" />\n+ </test>\n+ <test>\n+ <param name="bamfile" value="paired_chr2L.bam" ftype="bam" />\n+ <param name="minMappingQuality" value="10" />\n+ <param name="shift" value="1 -2 3 -4" />\n+ <output name="outFile" file="alignmentSieve2.bam" ftype="bam" />\n+ </test>\n+ <test>\n+ <param name="bamfile" value="paired_chr2L.cram" ftype="cram" />\n+ <param name="minMappingQuality" value="10" />\n+ <param name="shift" value="1 -2 3 -4" />\n+ <output name="outFile" file="alignmentSieve3.bam" ftype="bam" />\n+ </test>\n+ </tests>\n+\n+ <help>\n+<![CDATA[\n+\n+What it does\n+-------------\n+\n+This tool is very much the counterpart of estimateReadFiltering, in that it can filter alignments based on a variety of desired criterion. While much of this can be done with samtools, this tool can additionally filter by fragment strand and length (e.g., for RNA-seq and ATAC-seq experiments, respectively). Finally, this program can produce BEDPE files, which can be used as input into MACS2 for peak calling, where the fragment ends have been optionally shifted.\n+\n+Output\n+--------\n+\n+The primary output is a BAM file with all alignments passing the desired criteria. Note that all unmapped reads are removed. Additionally, an optional text file can be produced with the following entries:\n+\n+ * Number of reads passing the filtering criteria\n+ * Total number of initial reads\n+\n+Instead of producing a filtered BAM file, a BEDPE file appropriate for use with MACS2 can be used, optionally with fragment ends shifted. This is useful in cases like ATAC-seq.\n+\n+The ``--shift`` option can take either 2 or 4 integers. If two integers are given, then the first value shifts the left-most end of a fragment and the second the right-most end. Positive values shift to the right and negative values to the left. See below for how setting ``--shift`` to \'-5 3\' would shift a single fragment::\n+\n+ ----> read 1\n+ read 2 <----\n+\n+ ------------------------ fragment\n+\n+ -------------------------------- shifted fragment\n+\n+The same results will be produced if read 1 and read 2 are swapped. If, instead, the protocol is strand-specific, then the first set of integers in a pair would be applied to fragments where read 1 precedes read 2, and the second set to cases where read 2 precedes read 1. In this case, the first value in each pair is applied to the end of read 1 and the second to the end of read 2. For example, suppose "-5 3 -1 4" were given as the option to ``--shift``. The ``-5 3`` set would produce the following::\n+\n+ ----> read 1\n+ read 2 <----\n+\n+ ------------------------ fragment\n+\n+ -------------------------------- shifted fragment\n+\n+and the ``-1 4`` set would produce the following::\n+\n+ ----> read 2\n+ read 1 <----\n+\n+ ------------------------ fragment\n+\n+ --------------------- shifted fragment\n+\n+As can be seen, such fragments are considered to be on the ``-`` strand, so negative values then shift to the left on its frame of reference (thus, to the right relative to the ``+`` strand).\n+\n+-----\n+\n+@REFERENCES@\n+]]>\n+ </help>\n+ <expand macro="citations" />\n+</tool>\n'

diff -r 000000000000 -r dfc5a344e2c2 datatypes_conf.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/datatypes_conf.xml Thu Feb 15 08:13:20 2018 -0500

@@ -0,0 +1,7 @@
+<?xml version="1.0"?>
+<datatypes>
+    <registration>
+        <datatype extension="deeptools_compute_matrix_archive" type="galaxy.datatypes.binary:CompressedArchive" subclass="True" display_in_upload="True"/>
+        <datatype extension="deeptools_coverage_matrix" type="galaxy.datatypes.binary:CompressedArchive" subclass="True" display_in_upload="True"/>
+    </registration>
+</datatypes>

diff -r 000000000000 -r dfc5a344e2c2 deepTools_macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/deepTools_macros.xml Thu Feb 15 08:13:20 2018 -0500

b'@@ -0,0 +1,833 @@\n+<macros>\n+\n+ <token name="@THREADS@">--numberOfProcessors "\\${GALAXY_SLOTS:-4}"</token>\n+ <token name="@WRAPPER_VERSION@">3.0.0</token>\n+ <xml name="requirements">\n+ <requirements>\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+ </xml>\n+\n+ <xml name="advancedOpt_scaffold">\n+ <conditional name="advancedOpt">\n+ <param name="showAdvancedOpt" type="select" label="Show advanced options" >\n+ <option value="no" selected="true">no</option>\n+ <option value="yes">yes</option>\n+ </param>\n+ <when value="no" />\n+ <when value="yes">\n+ <yield/>\n+ </when>\n+ </conditional>\n+ </xml>\n+\n+ <token name="@PLOTWIDTHHEIGHT@">\n+ --plotWidth \'$advancedOpt.plotWidth\'\n+ --plotHeight \'$advancedOpt.plotHeight\'\n+ </token>\n+\n+ <xml name="plotWidthHeight" tokens="PLOTWIDTH,PLOTHEIGHT">\n+ <param argument="--plotHeight" type="float" value="@PLOTHEIGHT@" min="1.0"\n+ label="Plot height"\n+ help="Height in cm. The default for the plot height is @PLOTHEIGHT@ centimeters. The minimum value is 1 cm." />\n+\n+ <param argument="--plotWidth" type="float" value="@PLOTWIDTH@" min="1.0"\n+ label="Plot width"\n+ help="Width in cm. The default value is @PLOTWIDTH@ centimeters. The minimum value is 1 cm." />\n+ </xml>\n+\n+ <token name="@ADVANCED_OPTS_READ_PROCESSING@">\n+ #if $advancedOpt.doExtendCustom.doExtend == \'custom\':\n+ --extendReads $advancedOpt.doExtendCustom.extendReadsValue\n+ #else if $advancedOpt.doExtendCustom.doExtend == \'yes\':\n+ --extendReads\n+ #end if\n+ $advancedOpt.ignoreDuplicates\n+ $advancedOpt.centerReads\n+ #if $advancedOpt.minMappingQuality:\n+ --minMappingQuality \'$advancedOpt.minMappingQuality\'\n+ #end if\n+ #if $advancedOpt.samFlagInclude:\n+ --samFlagInclude $advancedOpt.samFlagInclude\n+ #end if\n+ #if $advancedOpt.samFlagExclude:\n+ --samFlagExclude $advancedOpt.samFlagExclude\n+ #end if\n+ #if $advancedOpt.minFragmentLength:\n+ --minFragmentLength $advancedOpt.minFragmentLength\n+ #end if\n+ #if $advancedOpt.maxFragmentLength:\n+ --maxFragmentLength $advancedOpt.maxFragmentLength\n+ #end if\n+ </token>\n+\n+ <token name="@ADVANCED_OPTS_GTF@">\n+ $advancedOpt.metagene\n+ #if $advancedOpt.transcriptID:\n+ --transcriptID $advancedOpt.transcriptID\n+ #end if\n+ #if $advancedOpt.exonID:\n+ --exonID $advancedOpt.exonID\n+ #end if\n+ #if $advancedOpt.transcript_id_designator:\n+ --transcript_id_designator $advancedOpt.transcript_id_designator\n+ #end if\n+ </token>\n+\n+ <xml name="heatmap_options">\n+ <expand macro="zMin_zMax" />\n+ <expand macro="colorMap" />\n+ <expand macro="plotTitle" />\n+ <expand macro="plotNumbers" />\n+ </xml>\n+\n+ <token name="@HEATMAP_OPTIONS@">\n+ #if str($plotting_type.zMin) != "":\n+ --zMin $plotting_type.zMin\n+ #end if\n+ #if str($plotting_type.zMax) != "":\n+ --zMax $plotting_type.zMax\n+ #end if\n+ --colorMap \'$plotting_type.colorMap\'\n+ $plotting_type.plotNumbers\n+ --plotTitle \'$plotting_type.plotTitle\'\n+ </token>\n+\n+\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/CRAM files are included. The default behavior is to ignore such regions." />'..b'k2 reversed</option>\n+ <option value="Reds_r">Reds reversed</option>\n+ <option value="Oranges_r">Oranges reversed</option>\n+ <option value="Greens_r">Greens reversed</option>\n+ <option value="Blues_r">Blues reversed</option>\n+ <option value="Greys_r">Greys reversed</option>\n+ <option value="Purples_r">Purples reversed</option>\n+ <option value="Paired_r">Paired reversed</option>\n+ <option value="Pastel1_r">Pastel1 reversed</option>\n+ <option value="Pastel2_r">Pastel2 reversed</option>\n+ <option value="spring_r">spring reversed</option>\n+ <option value="summer_r">summer reversed</option>\n+ <option value="autumn_r">autumn reversed</option>\n+ <option value="winter_r">winter reversed</option>\n+ <option value="hot_r">hot reversed</option>\n+ <option value="coolwarm_r">coolwarm reversed</option>\n+ <option value="cool_r">cool reversed</option>\n+ <option value="seismic_r">seismic reversed</option>\n+ <option value="terrain_r">terrain reversed</option>\n+ <option value="ocean_r">ocean reversed</option>\n+ <option value="rainbow_r">rainbow reversed</option>\n+ <option value="bone_r">bone reversed</option>\n+ <option value="flag_r">flag reversed</option>\n+ <option value="prism_r">prism reversed</option>\n+ <option value="cubehelix_r">cubehelix reversed</option>\n+ <option value="binary_r">binary reversed</option>\n+ <option value="pink_r">pink reversed</option>\n+ <option value="gray_r">gray reversed</option>\n+ <option value="copper_r">copper reversed</option>\n+ <option value="BrBG_r">BrBG reversed</option>\n+ <option value="BuGn_r">BuGn reversed</option>\n+ <option value="BuPu_r">BuPu reversed</option>\n+ <option value="GnBu_r">GnBu reversed</option>\n+ <option value="OrRd_r">OrRd reversed</option>\n+ <option value="PiYG_r">PiYG reversed</option>\n+ <option value="PRGn_r">PRGn reversed</option>\n+ <option value="PuOr_r">PuOr reversed</option>\n+ <option value="PuRd_r">PuRd reversed</option>\n+ <option value="PuBu_r">PuBu reversed</option>\n+ <option value="RdBu_r">RdBu reversed</option>\n+ <option value="RdGy_r">RdGy reversed</option>\n+ <option value="RdPu_r">RdPu reversed</option>\n+ <option value="YlGn_r">YlGn reversed</option>\n+ <option value="PuBuGn_r">PuBuGn reversed</option>\n+ <option value="RdYlBu_r">RdYlBu reversed</option>\n+ <option value="RdYlGn_r">RdYlGn reversed</option>\n+ <option value="YlGnBu_r">YlGnBu reversed</option>\n+ <option value="YlOrBr_r">YlOrBr reversed</option>\n+ <option value="YlOrRd_r">YlOrRd reversed</option>\n+ <option value="gist_gray_r">gist_gray reversed</option>\n+ <option value="gist_stern_r">gist_stern reversed</option>\n+ <option value="gist_earth_r">gist_earth reversed</option>\n+ <option value="gist_yarg_r">gist_yarg reversed</option>\n+ <option value="gist_ncar_r">gist_ncar reversed</option>\n+ <option value="gist_rainbow_r">gist_rainbow reversed</option>\n+ <option value="gist_heat_r">gist_heat reversed</option>\n+ <option value="gnuplot_r">gnuplot reversed</option>\n+ <option value="gnuplot2_r">gnuplot2 reversed</option>\n+ <option value="CMRmap_r">CMRmap reversed</option>\n+ <option value="bwr_r">bwr reversed</option>\n+ <option value="hsv_r">hsv reversed</option>\n+ <option value="brg_r">brg reversed</option>\n+ <option value="jet_r">jet reversed</option>\n+ <option value="afmhot_r">afmhot reversed</option>\n+ </param>\n+\n+ </xml>\n+\n+</macros>\n'

diff -r 000000000000 -r dfc5a344e2c2 readme.rst
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/readme.rst Thu Feb 15 08:13:20 2018 -0500

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

diff -r 000000000000 -r dfc5a344e2c2 repository_dependencies.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/repository_dependencies.xml Thu Feb 15 08:13:20 2018 -0500

@@ -0,0 +1,4 @@
+<?xml version="1.0"?>
+<repositories>
+ <repository changeset_revision="9946bc39c834" name="data_manager_twobit_builder" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" />
+</repositories>

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+++ b/test-data/alignmentSieve.bed Thu Feb 15 08:13:20 2018 -0500

b'@@ -0,0 +1,4261 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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 000000000000 -r dfc5a344e2c2 test-data/alignmentSieve.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/alignmentSieve.txt Thu Feb 15 08:13:20 2018 -0500

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

diff -r 000000000000 -r dfc5a344e2c2 test-data/alignmentSieve2.bam

Binary file test-data/alignmentSieve2.bam has changed

diff -r 000000000000 -r dfc5a344e2c2 test-data/alignmentSieve3.bam

Binary file test-data/alignmentSieve3.bam has changed

diff -r 000000000000 -r dfc5a344e2c2 test-data/bamCompare_result1.bg
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/bamCompare_result1.bg Thu Feb 15 08:13:20 2018 -0500

@@ -0,0 +1,1 @@
+chrM 0 16569 1

diff -r 000000000000 -r dfc5a344e2c2 test-data/bamCompare_result2.bw

Binary file test-data/bamCompare_result2.bw has changed

diff -r 000000000000 -r dfc5a344e2c2 test-data/bamCoverage_result1.bw

Binary file test-data/bamCoverage_result1.bw has changed

diff -r 000000000000 -r dfc5a344e2c2 test-data/bamCoverage_result2.bw

Binary file test-data/bamCoverage_result2.bw has changed

diff -r 000000000000 -r dfc5a344e2c2 test-data/bamCoverage_result3.bg
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/bamCoverage_result3.bg Thu Feb 15 08:13:20 2018 -0500

@@ -0,0 +1,7 @@
+chrM 0 210 9.76876e+06
+chrM 210 220 9.56092e+06
+chrM 220 230 7.6903e+06
+chrM 230 240 5.19615e+06
+chrM 240 250 3.32554e+06
+chrM 250 260 623538
+chrM 260 16569 0

diff -r 000000000000 -r dfc5a344e2c2 test-data/bamCoverage_result4.bg
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/bamCoverage_result4.bg Thu Feb 15 08:13:20 2018 -0500

b'@@ -0,0 +1,472 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diff -r 000000000000 -r dfc5a344e2c2 test-data/bamCoverage_result4.bw

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diff -r 000000000000 -r dfc5a344e2c2 test-data/bamCoverage_result6.bw

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diff -r 000000000000 -r dfc5a344e2c2 test-data/bamPEFragmentSize_histogram_result1.png

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diff -r 000000000000 -r dfc5a344e2c2 test-data/bamPEFragmentSize_lengths1.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/bamPEFragmentSize_lengths1.txt Thu Feb 15 08:13:20 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

diff -r 000000000000 -r dfc5a344e2c2 test-data/bamPEFragmentSize_result1.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/bamPEFragmentSize_result1.txt Thu Feb 15 08:13:20 2018 -0500

@@ -0,0 +1,46 @@
+
+
+Sample label: bowtie2 test1.bam
+Sample size: 3
+
+Fragment lengths:
+Min.: 241.0
+1st Qu.: 241.5
+Mean: 244.66666666666666
+Median: 242.0
+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
+Median: 251.0
+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 000000000000 -r dfc5a344e2c2 test-data/bamPEFragmentSize_table1.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/bamPEFragmentSize_table1.txt Thu Feb 15 08:13:20 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

diff -r 000000000000 -r dfc5a344e2c2 test-data/bigwigCompare_result1.bw

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diff -r 000000000000 -r dfc5a344e2c2 test-data/bigwigCompare_result2.bg
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/bigwigCompare_result2.bg Thu Feb 15 08:13:20 2018 -0500

@@ -0,0 +1,3 @@
+ch1 0 400 1
+ch2 0 400 1
+ch3 0 400 1

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diff -r 000000000000 -r dfc5a344e2c2 test-data/computeGCBias_result1.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/computeGCBias_result1.tabular Thu Feb 15 08:13:20 2018 -0500

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diff -r 000000000000 -r dfc5a344e2c2 test-data/computeMatrix1.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/computeMatrix1.bed Thu Feb 15 08:13:20 2018 -0500

@@ -0,0 +1,8 @@
+phiX174 1000 1500 CG11023 0 +
+phiX174 150 1750 cda5 0 -
+phiX174 150 177 cda8 0 -
+phiX174 75 1500 cda9 0 +
+phiX174 101 175 C11023 0 +
+phiX174 125 150 ca5 0 -
+phiX174 450 1750 ca8 0 +
+phiX174 80 1500 cda9 0 +

diff -r 000000000000 -r dfc5a344e2c2 test-data/computeMatrix2.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/computeMatrix2.bed Thu Feb 15 08:13:20 2018 -0500

@@ -0,0 +1,6 @@
+ch1 100 150 CG11023 0 +
+ch2 150 175 cda5 0 -
+ch3 100 125 cda8 0 +
+ch1 75 125 C11023 0 +
+ch2 125 150 ca5 0 -
+ch3 75 100 ca8 0 +

diff -r 000000000000 -r dfc5a344e2c2 test-data/computeMatrix2.bw

Binary file test-data/computeMatrix2.bw has changed

diff -r 000000000000 -r dfc5a344e2c2 test-data/computeMatrixOperations.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/computeMatrixOperations.txt Thu Feb 15 08:13:20 2018 -0500

@@ -0,0 +1,4 @@
+Groups:
+ genes
+Samples:
+ bamCoverage_result4_bw_0

diff -r 000000000000 -r dfc5a344e2c2 test-data/computeMatrixOperations_result2.mat.gz

Binary file test-data/computeMatrixOperations_result2.mat.gz has changed

diff -r 000000000000 -r dfc5a344e2c2 test-data/computeMatrix_result1.gz

Binary file test-data/computeMatrix_result1.gz has changed

diff -r 000000000000 -r dfc5a344e2c2 test-data/computeMatrix_result2.gz

Binary file test-data/computeMatrix_result2.gz has changed

diff -r 000000000000 -r dfc5a344e2c2 test-data/computeMatrix_result3.gz

Binary file test-data/computeMatrix_result3.gz has changed

diff -r 000000000000 -r dfc5a344e2c2 test-data/correctGCBias_result1.bam

Binary file test-data/correctGCBias_result1.bam has changed

diff -r 000000000000 -r dfc5a344e2c2 test-data/estimateReadFiltering.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/estimateReadFiltering.txt Thu Feb 15 08:13:20 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

diff -r 000000000000 -r dfc5a344e2c2 test-data/heatmapper_result1.png

Binary file test-data/heatmapper_result1.png has changed

diff -r 000000000000 -r dfc5a344e2c2 test-data/heatmapper_result2.png

Binary file test-data/heatmapper_result2.png has changed

diff -r 000000000000 -r dfc5a344e2c2 test-data/heatmapper_result2.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/heatmapper_result2.tabular Thu Feb 15 08:13:20 2018 -0500

@@ -0,0 +1,3 @@
+bin labels -0.0Kb 0.0Kb
+bins 1 2
+file_0 genes 2477942.34473 2610259.65234

diff -r 000000000000 -r dfc5a344e2c2 test-data/multiBamSummary_regions.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/multiBamSummary_regions.bed Thu Feb 15 08:13:20 2018 -0500

@@ -0,0 +1,3 @@
+chrM 1 10
+chrM 5 15
+chrM 10 20

diff -r 000000000000 -r dfc5a344e2c2 test-data/multiBamSummary_result1.npz

Binary file test-data/multiBamSummary_result1.npz has changed

diff -r 000000000000 -r dfc5a344e2c2 test-data/multiBamSummary_result2.npz

Binary file test-data/multiBamSummary_result2.npz has changed

diff -r 000000000000 -r dfc5a344e2c2 test-data/multiBamSummary_result2b.npz

Binary file test-data/multiBamSummary_result2b.npz has changed

diff -r 000000000000 -r dfc5a344e2c2 test-data/multiBigwigSummary_result1.npz

Binary file test-data/multiBigwigSummary_result1.npz has changed

diff -r 000000000000 -r dfc5a344e2c2 test-data/multiBigwigSummary_result1.png

Binary file test-data/multiBigwigSummary_result1.png has changed

diff -r 000000000000 -r dfc5a344e2c2 test-data/paired_chr2L.bam

Binary file test-data/paired_chr2L.bam has changed

diff -r 000000000000 -r dfc5a344e2c2 test-data/paired_chr2L.cram

Binary file test-data/paired_chr2L.cram has changed

diff -r 000000000000 -r dfc5a344e2c2 test-data/phiX.2bit

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

diff -r 000000000000 -r dfc5a344e2c2 test-data/phiX.bam

Binary file test-data/phiX.bam has changed

diff -r 000000000000 -r dfc5a344e2c2 test-data/phiX.bam.bai

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

diff -r 000000000000 -r dfc5a344e2c2 test-data/phiX.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/phiX.fasta Thu Feb 15 08:13:20 2018 -0500

@@ -0,0 +1,79 @@
+>phiX174
+GAGTTTTATCGCTTCCATGACGCAGAAGTTAACACTTTCGGATATTTCTGATGAGTCGAAAAATTATCTT
+GATAAAGCAGGAATTACTACTGCTTGTTTACGAATTAAATCGAAGTGGACTGCTGGCGGAAAATGAGAAA
+ATTCGACCTATCCTTGCGCAGCTCGAGAAGCTCTTACTTTGCGACCTTTCGCCATCAACTAACGATTCTG
+TCAAAAACTGACGCGTTGGATGAGGAGAAGTGGCTTAATATGCTTGGCACGTTCGTCAAGGACTGGTTTA
+GATATGAGTCACATTTTGTTCATGGTAGAGATTCTCTTGTTGACATTTTAAAAGAGCGTGGATTACTATC
+TGAGTCCGATGCTGTTCAACCACTAATAGGTAAGAAATCATGAGTCAAGTTACTGAACAATCCGTACGTT
+TCCAGACCGCTTTGGCCTCTATTAAGCTCATTCAGGCTTCTGCCGTTTTGGATTTAACCGAAGATGATTT
+CGATTTTCTGACGAGTAACAAAGTTTGGATTGCTACTGACCGCTCTCGTGCTCGTCGCTGCGTTGAGGCT
+TGCGTTTATGGTACGCTGGACTTTGTGGGATACCCTCGCTTTCCTGCTCCTGTTGAGTTTATTGCTGCCG
+TCATTGCTTATTATGTTCATCCCGTCAACATTCAAACGGCCTGTCTCATCATGGAAGGCGCTGAATTTAC
+GGAAAACATTATTAATGGCGTCGAGCGTCCGGTTAAAGCCGCTGAATTGTTCGCGTTTACCTTGCGTGTA
+CGCGCAGGAAACACTGACGTTCTTACTGACGCAGAAGAAAACGTGCGTCAAAAATTACGTGCAGAAGGAG
+TGATGTAATGTCTAAAGGTAAAAAACGTTCTGGCGCTCGCCCTGGTCGTCCGCAGCCGTTGCGAGGTACT
+AAAGGCAAGCGTAAAGGCGCTCGTCTTTGGTATGTAGGTGGTCAACAATTTTAATTGCAGGGGCTTCGGC
+CCCTTACTTGAGGATAAATTATGTCTAATATTCAAACTGGCGCCGAGCGTATGCCGCATGACCTTTCCCA
+TCTTGGCTTCCTTGCTGGTCAGATTGGTCGTCTTATTACCATTTCAACTACTCCGGTTATCGCTGGCGAC
+TCCTTCGAGATGGACGCCGTTGGCGCTCTCCGTCTTTCTCCATTGCGTCGTGGCCTTGCTATTGACTCTA
+CTGTAGACATTTTTACTTTTTATGTCCCTCATCGTCACGTTTATGGTGAACAGTGGATTAAGTTCATGAA
+GGATGGTGTTAATGCCACTCCTCTCCCGACTGTTAACACTACTGGTTATATTGACCATGCCGCTTTTCTT
+GGCACGATTAACCCTGATACCAATAAAATCCCTAAGCATTTGTTTCAGGGTTATTTGAATATCTATAACA
+ACTATTTTAAAGCGCCGTGGATGCCTGACCGTACCGAGGCTAACCCTAATGAGCTTAATCAAGATGATGC
+TCGTTATGGTTTCCGTTGCTGCCATCTCAAAAACATTTGGACTGCTCCGCTTCCTCCTGAGACTGAGCTT
+TCTCGCCAAATGACGACTTCTACCACATCTATTGACATTATGGGTCTGCAAGCTGCTTATGCTAATTTGC
+ATACTGACCAAGAACGTGATTACTTCATGCAGCGTTACCGTGATGTTATTTCTTCATTTGGAGGTAAAAC
+CTCTTATGACGCTGACAACCGTCCTTTACTTGTCATGCGCTCTAATCTCTGGGCATCTGGCTATGATGTT
+GATGGAACTGACCAAACGTCGTTAGGCCAGTTTTCTGGTCGTGTTCAACAGACCTATAAACATTCTGTGC
+CGCGTTTCTTTGTTCCTGAGCATGGCACTATGTTTACTCTTGCGCTTGTTCGTTTTCCGCCTACTGCGAC
+TAAAGAGATTCAGTACCTTAACGCTAAAGGTGCTTTGACTTATACCGATATTGCTGGCGACCCTGTTTTG
+TATGGCAACTTGCCGCCGCGTGAAATTTCTATGAAGGATGTTTTCCGTTCTGGTGATTCGTCTAAGAAGT
+TTAAGATTGCTGAGGGTCAGTGGTATCGTTATGCGCCTTCGTATGTTTCTCCTGCTTATCACCTTCTTGA
+AGGCTTCCCATTCATTCAGGAACCGCCTTCTGGTGATTTGCAAGAACGCGTACTTATTCGCCACCATGAT
+TATGACCAGTGTTTCCAGTCCGTTCAGTTGTTGCAGTGGAATAGTCAGGTTAAATTTAATGTGACCGTTT
+ATCGCAATCTGCCGACCACTCGCGATTCAATCATGACTTCGTGATAAAAGATTGAGTGTGAGGTTATAAC
+GCCGAAGCGGTAAAAATTTTAATTTTTGCCGCTGAGGGGTTGACCAAGCGAAGCGCGGTAGGTTTTCTGC
+TTAGGAGTTTAATCATGTTTCAGACTTTTATTTCTCGCCATAATTCAAACTTTTTTTCTGATAAGCTGGT
+TCTCACTTCTGTTACTCCAGCTTCTTCGGCACCTGTTTTACAGACACCTAAAGCTACATCGTCAACGTTA
+TATTTTGATAGTTTGACGGTTAATGCTGGTAATGGTGGTTTTCTTCATTGCATTCAGATGGATACATCTG
+TCAACGCCGCTAATCAGGTTGTTTCTGTTGGTGCTGATATTGCTTTTGATGCCGACCCTAAATTTTTTGC
+CTGTTTGGTTCGCTTTGAGTCTTCTTCGGTTCCGACTACCCTCCCGACTGCCTATGATGTTTATCCTTTG
+AATGGTCGCCATGATGGTGGTTATTATACCGTCAAGGACTGTGTGACTATTGACGTCCTTCCCCGTACGC
+CGGGCAATAATGTTTATGTTGGTTTCATGGTTTGGTCTAACTTTACCGCTACTAAATGCCGCGGATTGGT
+TTCGCTGAATCAGGTTATTAAAGAGATTATTTGTCTCCAGCCACTTAAGTGAGGTGATTTATGTTTGGTG
+CTATTGCTGGCGGTATTGCTTCTGCTCTTGCTGGTGGCGCCATGTCTAAATTGTTTGGAGGCGGTCAAAA
+AGCCGCCTCCGGTGGCATTCAAGGTGATGTGCTTGCTACCGATAACAATACTGTAGGCATGGGTGATGCT
+GGTATTAAATCTGCCATTCAAGGCTCTAATGTTCCTAACCCTGATGAGGCCGCCCCTAGTTTTGTTTCTG
+GTGCTATGGCTAAAGCTGGTAAAGGACTTCTTGAAGGTACGTTGCAGGCTGGCACTTCTGCCGTTTCTGA
+TAAGTTGCTTGATTTGGTTGGACTTGGTGGCAAGTCTGCCGCTGATAAAGGAAAGGATACTCGTGATTAT
+CTTGCTGCTGCATTTCCTGAGCTTAATGCTTGGGAGCGTGCTGGTGCTGATGCTTCCTCTGCTGGTATGG
+TTGACGCCGGATTTGAGAATCAAAAAGAGCTTACTAAAATGCAACTGGACAATCAGAAAGAGATTGCCGA
+GATGCAAAATGAGACTCAAAAAGAGATTGCTGGCATTCAGTCGGCGACTTCACGCCAGAATACGAAAGAC
+CAGGTATATGCACAAAATGAGATGCTTGCTTATCAACAGAAGGAGTCTACTGCTCGCGTTGCGTCTATTA
+TGGAAAACACCAATCTTTCCAAGCAACAGCAGGTTTCCGAGATTATGCGCCAAATGCTTACTCAAGCTCA
+AACGGCTGGTCAGTATTTTACCAATGACCAAATCAAAGAAATGACTCGCAAGGTTAGTGCTGAGGTTGAC
+TTAGTTCATCAGCAAACGCAGAATCAGCGGTATGGCTCTTCTCATATTGGCGCTACTGCAAAGGATATTT
+CTAATGTCGTCACTGATGCTGCTTCTGGTGTGGTTGATATTTTTCATGGTATTGATAAAGCTGTTGCCGA
+TACTTGGAACAATTTCTGGAAAGACGGTAAAGCTGATGGTATTGGCTCTAATTTGTCTAGGAAATAACCG
+TCAGGATTGACACCCTCCCAATTGTATGTTTTCATGCCTCCAAATCTTGGAGGCTTTTTTATGGTTCGTT
+CTTATTACCCTTCTGAATGTCACGCTGATTATTTTGACTTTGAGCGTATCGAGGCTCTTAAACCTGCTAT
+TGAGGCTTGTGGCATTTCTACTCTTTCTCAATCCCCAATGCTTGGCTTCCATAAGCAGATGGATAACCGC
+ATCAAGCTCTTGGAAGAGATTCTGTCTTTTCGTATGCAGGGCGTTGAGTTCGATAATGGTGATATGTATG
+TTGACGGCCATAAGGCTGCTTCTGACGTTCGTGATGAGTTTGTATCTGTTACTGAGAAGTTAATGGATGA
+ATTGGCACAATGCTACAATGTGCTCCCCCAACTTGATATTAATAACACTATAGACCACCGCCCCGAAGGG
+GACGAAAAATGGTTTTTAGAGAACGAGAAGACGGTTACGCAGTTTTGCCGCAAGCTGGCTGCTGAACGCC
+CTCTTAAGGATATTCGCGATGAGTATAATTACCCCAAAAAGAAAGGTATTAAGGATGAGTGTTCAAGATT
+GCTGGAGGCCTCCACTATGAAATCGCGTAGAGGCTTTACTATTCAGCGTTTGATGAATGCAATGCGACAG
+GCTCATGCTGATGGTTGGTTTATCGTTTTTGACACTCTCACGTTGGCTGACGACCGATTAGAGGCGTTTT
+ATGATAATCCCAATGCTTTGCGTGACTATTTTCGTGATATTGGTCGTATGGTTCTTGCTGCCGAGGGTCG
+CAAGGCTAATGATTCACACGCCGACTGCTATCAGTATTTTTGTGTGCCTGAGTATGGTACAGCTAATGGC
+CGTCTTCATTTCCATGCGGTGCATTTTATGCGGACACTTCCTACAGGTAGCGTTGACCCTAATTTTGGTC
+GTCGGGTACGCAATCGCCGCCAGTTAAATAGCTTGCAAAATACGTGGCCTTATGGTTACAGTATGCCCAT
+CGCAGTTCGCTACACGCAGGACGCTTTTTCACGTTCTGGTTGGTTGTGGCCTGTTGATGCTAAAGGTGAG
+CCGCTTAAAGCTACCAGTTATATGGCTGTTGGTTTCTATGTGGCTAAATACGTTAACAAAAAGTCAGATA
+TGGACCTTGCTGCTAAAGGTCTAGGAGCTAAAGAATGGAACAACTCACTAAAAACCAAGCTGTCGCTACT
+TCCCAAGAAGCTGTTCAGAATCAGAATGAGCCGCAACTTCGGGATGAAAATGCTCACAATGACAAATCTG
+TCCACGGAGTGCTTAATCCAACTTACCAAGCTGGGTTACGACGCGACGCCGTTCAACCAGATATTGAAGC
+AGAACGCAAAAAGAGAGATGAGATTGAGGCTGGGAAAAGTTACTGTAGCCGACGTTTTGGCGGCGCAACC
+TGTGACGACAAATCTGCTCAAATTTATGCGCGCTTCGATAAAAATGATTGGCGTATCCAACCTGCA
+

diff -r 000000000000 -r dfc5a344e2c2 test-data/plotCorrelation_result1.png

Binary file test-data/plotCorrelation_result1.png has changed

diff -r 000000000000 -r dfc5a344e2c2 test-data/plotCorrelation_result1.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/plotCorrelation_result1.tabular Thu Feb 15 08:13:20 2018 -0500

@@ -0,0 +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 000000000000 -r dfc5a344e2c2 test-data/plotCorrelation_result2.png

Binary file test-data/plotCorrelation_result2.png has changed

diff -r 000000000000 -r dfc5a344e2c2 test-data/plotCoverage_result1.png

Binary file test-data/plotCoverage_result1.png has changed

diff -r 000000000000 -r dfc5a344e2c2 test-data/plotCoverage_result1.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/plotCoverage_result1.tabular Thu Feb 15 08:13:20 2018 -0500

b"@@ -0,0 +1,16571 @@\n+#plotCoverage --outRawCounts\n+#'chr'\t'start'\t'end'\t'bowtie2 test1.bam'\t'bowtie2 test1.bam'\n+chrM\t0\t1\t23.0\t23.0\n+chrM\t1\t2\t35.0\t35.0\n+chrM\t2\t3\t35.0\t35.0\n+chrM\t3\t4\t35.0\t35.0\n+chrM\t4\t5\t35.0\t35.0\n+chrM\t5\t6\t35.0\t35.0\n+chrM\t6\t7\t35.0\t35.0\n+chrM\t7\t8\t35.0\t35.0\n+chrM\t8\t9\t35.0\t35.0\n+chrM\t9\t10\t35.0\t35.0\n+chrM\t10\t11\t35.0\t35.0\n+chrM\t11\t12\t35.0\t35.0\n+chrM\t12\t13\t35.0\t35.0\n+chrM\t13\t14\t35.0\t35.0\n+chrM\t14\t15\t35.0\t35.0\n+chrM\t15\t16\t35.0\t35.0\n+chrM\t16\t17\t35.0\t35.0\n+chrM\t17\t18\t35.0\t35.0\n+chrM\t18\t19\t35.0\t35.0\n+chrM\t19\t20\t35.0\t35.0\n+chrM\t20\t21\t35.0\t35.0\n+chrM\t21\t22\t35.0\t35.0\n+chrM\t22\t23\t35.0\t35.0\n+chrM\t23\t24\t35.0\t35.0\n+chrM\t24\t25\t35.0\t35.0\n+chrM\t25\t26\t35.0\t35.0\n+chrM\t26\t27\t35.0\t35.0\n+chrM\t27\t28\t35.0\t35.0\n+chrM\t28\t29\t35.0\t35.0\n+chrM\t29\t30\t35.0\t35.0\n+chrM\t30\t31\t35.0\t35.0\n+chrM\t31\t32\t35.0\t35.0\n+chrM\t32\t33\t35.0\t35.0\n+chrM\t33\t34\t35.0\t35.0\n+chrM\t34\t35\t35.0\t35.0\n+chrM\t35\t36\t35.0\t35.0\n+chrM\t36\t37\t35.0\t35.0\n+chrM\t37\t38\t35.0\t35.0\n+chrM\t38\t39\t35.0\t35.0\n+chrM\t39\t40\t35.0\t35.0\n+chrM\t40\t41\t35.0\t35.0\n+chrM\t41\t42\t35.0\t35.0\n+chrM\t42\t43\t35.0\t35.0\n+chrM\t43\t44\t35.0\t35.0\n+chrM\t44\t45\t35.0\t35.0\n+chrM\t45\t46\t35.0\t35.0\n+chrM\t46\t47\t35.0\t35.0\n+chrM\t47\t48\t35.0\t35.0\n+chrM\t48\t49\t35.0\t35.0\n+chrM\t49\t50\t35.0\t35.0\n+chrM\t50\t51\t35.0\t35.0\n+chrM\t51\t52\t35.0\t35.0\n+chrM\t52\t53\t35.0\t35.0\n+chrM\t53\t54\t35.0\t35.0\n+chrM\t54\t55\t35.0\t35.0\n+chrM\t55\t56\t35.0\t35.0\n+chrM\t56\t57\t35.0\t35.0\n+chrM\t57\t58\t35.0\t35.0\n+chrM\t58\t59\t35.0\t35.0\n+chrM\t59\t60\t35.0\t35.0\n+chrM\t60\t61\t35.0\t35.0\n+chrM\t61\t62\t35.0\t35.0\n+chrM\t62\t63\t35.0\t35.0\n+chrM\t63\t64\t35.0\t35.0\n+chrM\t64\t65\t35.0\t35.0\n+chrM\t65\t66\t35.0\t35.0\n+chrM\t66\t67\t35.0\t35.0\n+chrM\t67\t68\t35.0\t35.0\n+chrM\t68\t69\t35.0\t35.0\n+chrM\t69\t70\t35.0\t35.0\n+chrM\t70\t71\t35.0\t35.0\n+chrM\t71\t72\t35.0\t35.0\n+chrM\t72\t73\t35.0\t35.0\n+chrM\t73\t74\t35.0\t35.0\n+chrM\t74\t75\t35.0\t35.0\n+chrM\t75\t76\t35.0\t35.0\n+chrM\t76\t77\t35.0\t35.0\n+chrM\t77\t78\t35.0\t35.0\n+chrM\t78\t79\t35.0\t35.0\n+chrM\t79\t80\t35.0\t35.0\n+chrM\t80\t81\t35.0\t35.0\n+chrM\t81\t82\t35.0\t35.0\n+chrM\t82\t83\t35.0\t35.0\n+chrM\t83\t84\t35.0\t35.0\n+chrM\t84\t85\t35.0\t35.0\n+chrM\t85\t86\t35.0\t35.0\n+chrM\t86\t87\t35.0\t35.0\n+chrM\t87\t88\t35.0\t35.0\n+chrM\t88\t89\t35.0\t35.0\n+chrM\t89\t90\t35.0\t35.0\n+chrM\t90\t91\t35.0\t35.0\n+chrM\t91\t92\t35.0\t35.0\n+chrM\t92\t93\t35.0\t35.0\n+chrM\t93\t94\t35.0\t35.0\n+chrM\t94\t95\t35.0\t35.0\n+chrM\t95\t96\t35.0\t35.0\n+chrM\t96\t97\t35.0\t35.0\n+chrM\t97\t98\t35.0\t35.0\n+chrM\t98\t99\t35.0\t35.0\n+chrM\t99\t100\t35.0\t35.0\n+chrM\t100\t101\t35.0\t35.0\n+chrM\t101\t102\t35.0\t35.0\n+chrM\t102\t103\t35.0\t35.0\n+chrM\t103\t104\t35.0\t35.0\n+chrM\t104\t105\t35.0\t35.0\n+chrM\t105\t106\t35.0\t35.0\n+chrM\t106\t107\t35.0\t35.0\n+chrM\t107\t108\t35.0\t35.0\n+chrM\t108\t109\t35.0\t35.0\n+chrM\t109\t110\t35.0\t35.0\n+chrM\t110\t111\t35.0\t35.0\n+chrM\t111\t112\t35.0\t35.0\n+chrM\t112\t113\t35.0\t35.0\n+chrM\t113\t114\t35.0\t35.0\n+chrM\t114\t115\t35.0\t35.0\n+chrM\t115\t116\t35.0\t35.0\n+chrM\t116\t117\t35.0\t35.0\n+chrM\t117\t118\t35.0\t35.0\n+chrM\t118\t119\t35.0\t35.0\n+chrM\t119\t120\t35.0\t35.0\n+chrM\t120\t121\t35.0\t35.0\n+chrM\t121\t122\t35.0\t35.0\n+chrM\t122\t123\t35.0\t35.0\n+chrM\t123\t124\t35.0\t35.0\n+chrM\t124\t125\t35.0\t35.0\n+chrM\t125\t126\t35.0\t35.0\n+chrM\t126\t127\t35.0\t35.0\n+chrM\t127\t128\t35.0\t35.0\n+chrM\t128\t129\t35.0\t35.0\n+chrM\t129\t130\t35.0\t35.0\n+chrM\t130\t131\t35.0\t35.0\n+chrM\t131\t132\t35.0\t35.0\n+chrM\t132\t133\t35.0\t35.0\n+chrM\t133\t134\t35.0\t35.0\n+chrM\t134\t135\t35.0\t35.0\n+chrM\t135\t136\t35.0\t35.0\n+chrM\t136\t137\t35.0\t35.0\n+chrM\t137\t138\t35.0\t35.0\n+chrM\t138\t139\t35.0\t35.0\n+chrM\t139\t140\t35.0\t35.0\n+chrM\t140\t141\t35.0\t35.0\n+chrM\t141\t142\t35.0\t35.0\n+chrM\t142\t143\t35.0\t35.0\n+chrM\t143\t144\t35.0\t35.0\n+chrM\t144\t145\t35.0\t35.0\n+chrM\t145\t146\t35.0\t35.0\n+chrM\t146\t147\t35.0\t35.0\n+chrM\t147\t148\t35.0\t35.0\n+chrM\t148\t149\t35.0\t35.0\n+chrM\t149\t150\t35.0\t35.0\n+chrM\t150\t151\t35.0\t35.0\n+chrM\t151\t152\t35.0\t35.0\n+chrM\t152\t153\t35.0\t35.0\n+chrM\t153\t154\t35.0\t35.0\n+chrM\t154\t155\t35.0\t35.0\n+chrM\t155\t156\t35.0\t35.0\n+chrM\t156\t157\t35.0\t35.0\n+chrM\t157\t158\t35.0\t35.0\n+chrM\t158\t159\t35.0\t35.0\n+chrM\t159\t160\t35.0\t35.0\n+chrM\t160\t161\t35.0\t35.0\n+chrM\t161\t162\t35.0\t35.0\n+chrM\t162\t163\t35.0\t35.0\n+chrM\t163\t164\t35.0\t35.0\n+chrM\t164\t165\t35.0\t35.0\n+chrM\t165\t166\t35.0\t35.0\n+chrM\t166\t167\t35.0\t35.0\n+chrM\t167\t168\t35.0\t35.0\n+chrM\t168\t169\t35.0\t35.0\n+chrM\t169\t170\t35.0\t35.0\n+chrM\t170\t171\t35.0\t35.0\n+"..b'\t16415\t16416\t0.0\t0.0\n+chrM\t16416\t16417\t0.0\t0.0\n+chrM\t16417\t16418\t0.0\t0.0\n+chrM\t16418\t16419\t0.0\t0.0\n+chrM\t16419\t16420\t0.0\t0.0\n+chrM\t16420\t16421\t0.0\t0.0\n+chrM\t16421\t16422\t0.0\t0.0\n+chrM\t16422\t16423\t0.0\t0.0\n+chrM\t16423\t16424\t0.0\t0.0\n+chrM\t16424\t16425\t0.0\t0.0\n+chrM\t16425\t16426\t0.0\t0.0\n+chrM\t16426\t16427\t0.0\t0.0\n+chrM\t16427\t16428\t0.0\t0.0\n+chrM\t16428\t16429\t0.0\t0.0\n+chrM\t16429\t16430\t0.0\t0.0\n+chrM\t16430\t16431\t0.0\t0.0\n+chrM\t16431\t16432\t0.0\t0.0\n+chrM\t16432\t16433\t0.0\t0.0\n+chrM\t16433\t16434\t0.0\t0.0\n+chrM\t16434\t16435\t0.0\t0.0\n+chrM\t16435\t16436\t0.0\t0.0\n+chrM\t16436\t16437\t0.0\t0.0\n+chrM\t16437\t16438\t0.0\t0.0\n+chrM\t16438\t16439\t0.0\t0.0\n+chrM\t16439\t16440\t0.0\t0.0\n+chrM\t16440\t16441\t0.0\t0.0\n+chrM\t16441\t16442\t0.0\t0.0\n+chrM\t16442\t16443\t0.0\t0.0\n+chrM\t16443\t16444\t0.0\t0.0\n+chrM\t16444\t16445\t0.0\t0.0\n+chrM\t16445\t16446\t0.0\t0.0\n+chrM\t16446\t16447\t0.0\t0.0\n+chrM\t16447\t16448\t0.0\t0.0\n+chrM\t16448\t16449\t0.0\t0.0\n+chrM\t16449\t16450\t0.0\t0.0\n+chrM\t16450\t16451\t0.0\t0.0\n+chrM\t16451\t16452\t0.0\t0.0\n+chrM\t16452\t16453\t0.0\t0.0\n+chrM\t16453\t16454\t0.0\t0.0\n+chrM\t16454\t16455\t0.0\t0.0\n+chrM\t16455\t16456\t0.0\t0.0\n+chrM\t16456\t16457\t0.0\t0.0\n+chrM\t16457\t16458\t0.0\t0.0\n+chrM\t16458\t16459\t0.0\t0.0\n+chrM\t16459\t16460\t0.0\t0.0\n+chrM\t16460\t16461\t0.0\t0.0\n+chrM\t16461\t16462\t0.0\t0.0\n+chrM\t16462\t16463\t0.0\t0.0\n+chrM\t16463\t16464\t0.0\t0.0\n+chrM\t16464\t16465\t0.0\t0.0\n+chrM\t16465\t16466\t0.0\t0.0\n+chrM\t16466\t16467\t0.0\t0.0\n+chrM\t16467\t16468\t0.0\t0.0\n+chrM\t16468\t16469\t0.0\t0.0\n+chrM\t16469\t16470\t0.0\t0.0\n+chrM\t16470\t16471\t0.0\t0.0\n+chrM\t16471\t16472\t0.0\t0.0\n+chrM\t16472\t16473\t0.0\t0.0\n+chrM\t16473\t16474\t0.0\t0.0\n+chrM\t16474\t16475\t0.0\t0.0\n+chrM\t16475\t16476\t0.0\t0.0\n+chrM\t16476\t16477\t0.0\t0.0\n+chrM\t16477\t16478\t0.0\t0.0\n+chrM\t16478\t16479\t0.0\t0.0\n+chrM\t16479\t16480\t0.0\t0.0\n+chrM\t16480\t16481\t0.0\t0.0\n+chrM\t16481\t16482\t0.0\t0.0\n+chrM\t16482\t16483\t0.0\t0.0\n+chrM\t16483\t16484\t0.0\t0.0\n+chrM\t16484\t16485\t0.0\t0.0\n+chrM\t16485\t16486\t0.0\t0.0\n+chrM\t16486\t16487\t0.0\t0.0\n+chrM\t16487\t16488\t0.0\t0.0\n+chrM\t16488\t16489\t0.0\t0.0\n+chrM\t16489\t16490\t0.0\t0.0\n+chrM\t16490\t16491\t0.0\t0.0\n+chrM\t16491\t16492\t0.0\t0.0\n+chrM\t16492\t16493\t0.0\t0.0\n+chrM\t16493\t16494\t0.0\t0.0\n+chrM\t16494\t16495\t0.0\t0.0\n+chrM\t16495\t16496\t0.0\t0.0\n+chrM\t16496\t16497\t0.0\t0.0\n+chrM\t16497\t16498\t0.0\t0.0\n+chrM\t16498\t16499\t0.0\t0.0\n+chrM\t16499\t16500\t0.0\t0.0\n+chrM\t16500\t16501\t0.0\t0.0\n+chrM\t16501\t16502\t0.0\t0.0\n+chrM\t16502\t16503\t0.0\t0.0\n+chrM\t16503\t16504\t0.0\t0.0\n+chrM\t16504\t16505\t0.0\t0.0\n+chrM\t16505\t16506\t0.0\t0.0\n+chrM\t16506\t16507\t0.0\t0.0\n+chrM\t16507\t16508\t0.0\t0.0\n+chrM\t16508\t16509\t0.0\t0.0\n+chrM\t16509\t16510\t0.0\t0.0\n+chrM\t16510\t16511\t0.0\t0.0\n+chrM\t16511\t16512\t0.0\t0.0\n+chrM\t16512\t16513\t0.0\t0.0\n+chrM\t16513\t16514\t0.0\t0.0\n+chrM\t16514\t16515\t0.0\t0.0\n+chrM\t16515\t16516\t0.0\t0.0\n+chrM\t16516\t16517\t0.0\t0.0\n+chrM\t16517\t16518\t0.0\t0.0\n+chrM\t16518\t16519\t0.0\t0.0\n+chrM\t16519\t16520\t0.0\t0.0\n+chrM\t16520\t16521\t0.0\t0.0\n+chrM\t16521\t16522\t0.0\t0.0\n+chrM\t16522\t16523\t0.0\t0.0\n+chrM\t16523\t16524\t0.0\t0.0\n+chrM\t16524\t16525\t0.0\t0.0\n+chrM\t16525\t16526\t0.0\t0.0\n+chrM\t16526\t16527\t0.0\t0.0\n+chrM\t16527\t16528\t0.0\t0.0\n+chrM\t16528\t16529\t0.0\t0.0\n+chrM\t16529\t16530\t0.0\t0.0\n+chrM\t16530\t16531\t0.0\t0.0\n+chrM\t16531\t16532\t0.0\t0.0\n+chrM\t16532\t16533\t0.0\t0.0\n+chrM\t16533\t16534\t0.0\t0.0\n+chrM\t16534\t16535\t0.0\t0.0\n+chrM\t16535\t16536\t0.0\t0.0\n+chrM\t16536\t16537\t0.0\t0.0\n+chrM\t16537\t16538\t0.0\t0.0\n+chrM\t16538\t16539\t0.0\t0.0\n+chrM\t16539\t16540\t0.0\t0.0\n+chrM\t16540\t16541\t0.0\t0.0\n+chrM\t16541\t16542\t0.0\t0.0\n+chrM\t16542\t16543\t0.0\t0.0\n+chrM\t16543\t16544\t0.0\t0.0\n+chrM\t16544\t16545\t0.0\t0.0\n+chrM\t16545\t16546\t0.0\t0.0\n+chrM\t16546\t16547\t0.0\t0.0\n+chrM\t16547\t16548\t0.0\t0.0\n+chrM\t16548\t16549\t0.0\t0.0\n+chrM\t16549\t16550\t0.0\t0.0\n+chrM\t16550\t16551\t0.0\t0.0\n+chrM\t16551\t16552\t0.0\t0.0\n+chrM\t16552\t16553\t0.0\t0.0\n+chrM\t16553\t16554\t0.0\t0.0\n+chrM\t16554\t16555\t0.0\t0.0\n+chrM\t16555\t16556\t0.0\t0.0\n+chrM\t16556\t16557\t0.0\t0.0\n+chrM\t16557\t16558\t0.0\t0.0\n+chrM\t16558\t16559\t0.0\t0.0\n+chrM\t16559\t16560\t0.0\t0.0\n+chrM\t16560\t16561\t0.0\t0.0\n+chrM\t16561\t16562\t0.0\t0.0\n+chrM\t16562\t16563\t0.0\t0.0\n+chrM\t16563\t16564\t0.0\t0.0\n+chrM\t16564\t16565\t0.0\t0.0\n+chrM\t16565\t16566\t0.0\t0.0\n+chrM\t16566\t16567\t0.0\t0.0\n+chrM\t16567\t16568\t0.0\t0.0\n+chrM\t16568\t16569\t0.0\t0.0\n'

diff -r 000000000000 -r dfc5a344e2c2 test-data/plotEnrichment_output.png

Binary file test-data/plotEnrichment_output.png has changed

diff -r 000000000000 -r dfc5a344e2c2 test-data/plotEnrichment_output.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/plotEnrichment_output.txt Thu Feb 15 08:13:20 2018 -0500

@@ -0,0 +1,5 @@
+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 000000000000 -r dfc5a344e2c2 test-data/plotFingerprint_quality_metrics.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/plotFingerprint_quality_metrics.tabular Thu Feb 15 08:13:20 2018 -0500

@@ -0,0 +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 0.00493632029863651 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 000000000000 -r dfc5a344e2c2 test-data/plotFingerprint_result1.png

Binary file test-data/plotFingerprint_result1.png has changed

diff -r 000000000000 -r dfc5a344e2c2 test-data/plotFingerprint_result2.png

Binary file test-data/plotFingerprint_result2.png has changed

diff -r 000000000000 -r dfc5a344e2c2 test-data/plotFingerprint_result2.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/plotFingerprint_result2.tabular Thu Feb 15 08:13:20 2018 -0500

b"@@ -0,0 +1,16072 @@\n+#plotFingerprint --outRawCounts\n+'bowtie2 test1.bam'\t'bowtie2 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diff -r 000000000000 -r dfc5a344e2c2 test-data/plotPCA_result1.png

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diff -r 000000000000 -r dfc5a344e2c2 test-data/plotPCA_result2.png

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diff -r 000000000000 -r dfc5a344e2c2 test-data/plotPCA_result2.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/plotPCA_result2.tabular Thu Feb 15 08:13:20 2018 -0500

@@ -0,0 +1,4 @@
+#plotPCA --outFileNameData
+Component bowtie2-test1.bam bowtie2-test1.bam Eigenvalue
+1 -0.7071067811865476 -0.7071067811865475 4.0
+2 -0.7071067811865475 0.7071067811865476 1.2325951644078315e-32

diff -r 000000000000 -r dfc5a344e2c2 test-data/profiler_result1.png

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diff -r 000000000000 -r dfc5a344e2c2 test-data/profiler_result2.png

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diff -r 000000000000 -r dfc5a344e2c2 test-data/profiler_result2.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/profiler_result2.tabular Thu Feb 15 08:13:20 2018 -0500

@@ -0,0 +1,3 @@
+bin labels -0.0Kb 0.0Kb
+bins 1.0 2.0
+bamCoverage_result4_bw_0 genes 2477942.875 2610260.125

diff -r 000000000000 -r dfc5a344e2c2 test-data/sequence.2bit

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diff -r 000000000000 -r dfc5a344e2c2 test-data/test.bw

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diff -r 000000000000 -r dfc5a344e2c2 tool-data/deepTools_seqs.loc.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/deepTools_seqs.loc.sample Thu Feb 15 08:13:20 2018 -0500

@@ -0,0 +1,27 @@
+#This is a sample file distributed with Galaxy that enables tools
+#to use a directory of 2bit genome files for use with deepTools. You will
+#need to supply these files and then create a deepTools_seqs.loc file
+#similar to this one (store it in this directory) that points to
+#the directories in which those files are stored. The deepTools_seqs.loc
+#file has this format:
+#
+#<unique_build_id> <display_name> <file_path>
+#
+#So, for example, if your deepTools_seqs.loc began like this:
+#
+#hg18 Human (Homo sapiens): hg18 /depot/data2/galaxy/twobit/hg18.2bit
+#hg19 Human (Homo sapiens): hg19 /depot/data2/galaxy/twobit/hg19.2bit
+#mm9 Mouse (Mus musculus): mm9 /depot/data2/galaxy/twobit/mm9.2bit
+#
+#then your /depot/data2/galaxy/twobit/ directory
+#would need to contain the following 2bit files:
+#
+#-rw-r--r--  1 james    universe 830134 2005-09-13 10:12 hg18.2bit
+#-rw-r--r--  1 james    universe 527388 2005-09-13 10:12 hg19.2bit
+#-rw-r--r--  1 james    universe 269808 2005-09-13 10:12 mm9.2bit
+#
+#Your deepTools_seqs.loc file should include an entry per line for
+#each file you have stored that you want to be available. Note that
+#your files should all have the extension '2bit'.
+#
+#Please note that the <unique_build_id> is also used as "Species name abbreviation".

diff -r 000000000000 -r dfc5a344e2c2 tool-data/lastz_seqs.loc.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/lastz_seqs.loc.sample Thu Feb 15 08:13:20 2018 -0500

@@ -0,0 +1,29 @@
+#This is a sample file distributed with Galaxy that enables tools
+#to use a directory of 2bit genome files for use with deepTools.
+#This file is named lastz_seqs.loc file to make use of an already existing loc
+#file from the lastz tool that is created by the twobit data-manager.
+#You will need to supply these files and then create a lastz_seqs.loc file
+#similar to this one (store it in this directory) that points to
+#the directories in which those files are stored. The lastz_seqs.loc
+#file has this format:
+#
+#<unique_build_id> <display_name> <file_path>
+#
+#So, for example, if your lastz_seqs.loc began like this:
+#
+#hg18 Human (Homo sapiens): hg18 /depot/data2/galaxy/twobit/hg18.2bit
+#hg19 Human (Homo sapiens): hg19 /depot/data2/galaxy/twobit/hg19.2bit
+#mm9 Mouse (Mus musculus): mm9 /depot/data2/galaxy/twobit/mm9.2bit
+#
+#then your /depot/data2/galaxy/twobit/ directory
+#would need to contain the following 2bit files:
+#
+#-rw-r--r--  1 james    universe 830134 2005-09-13 10:12 hg18.2bit
+#-rw-r--r--  1 james    universe 527388 2005-09-13 10:12 hg19.2bit
+#-rw-r--r--  1 james    universe 269808 2005-09-13 10:12 mm9.2bit
+#
+#Your lastz_seqs.loc file should include an entry per line for
+#each file you have stored that you want to be available. Note that
+#your files should all have the extension '2bit'.
+#
+#Please note that the <unique_build_id> is also used as "Species name abbreviation".

diff -r 000000000000 -r dfc5a344e2c2 tool_data_table_conf.xml.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample Thu Feb 15 08:13:20 2018 -0500

@@ -0,0 +1,8 @@
+
+<tables>
+    
+    <table name="lastz_seqs" comment_char="#">
+        <columns>value, name, path</columns>
+        <file path="tool-data/lastz_seqs.loc" />
+    </table>
+</tables>