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Changeset 0:105b9da2445c (2016-01-25)

Next changeset 1:e237a134059a (2016-02-15)

Commit message:
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty

diff -r 000000000000 -r 105b9da2445c bamCompare.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/bamCompare.xml Mon Jan 25 20:25:37 2016 -0500

[

b'@@ -0,0 +1,234 @@\n+<tool id="deeptools_bam_compare" name="bamCompare" version="@WRAPPER_VERSION@.0">\n+ <description>normalizes and compares two BAM files to obtain the ratio, log2ratio or difference between them</description>\n+ <macros>\n+ <token name="@BINARY@">bamCompare</token>\n+ <import>deepTools_macros.xml</import>\n+ </macros>\n+ <expand macro="requirements" />\n+ <command>\n+<![CDATA[\n+ ln -s \'$bamFile1\' one.bam &&\n+ ln -s \'${bamFile1.metadata.bam_index}\' one.bam.bai &&\n+ ln -s \'$bamFile2\' two.bam &&\n+ ln -s \'${bamFile2.metadata.bam_index}\' two.bam.bai &&\n+\n+ @BINARY@\n+ @THREADS@\n+ --bamfile1 one.bam\n+ --bamfile2 two.bam\n+\n+ --outFileName \'$outFileName\'\n+ --outFileFormat \'$outFileFormat\'\n+\n+ --binSize $binSize\n+\n+ #if $scaling.method == \'SES\':\n+ --scaleFactorsMethod SES\n+ --sampleLength $scaling.sampleLength\n+ --numberOfSamples $scaling.numberOfSamples\n+ #elif $scaling.method == \'readCount\':\n+ --scaleFactorsMethod readCount\n+ #elif $scaling.method == \'own\':\n+ --scaleFactors \'$scaling.scaleFactor1:$scaling.scaleFactor2\'\n+ #end if\n+\n+ --ratio $comparison.type\n+\n+ #if $comparison.type == \'subtract\':\n+ #if $comparison.normalization.type == \'rpkm\':\n+ --normalizeUsingRPKM\n+ #elif $comparison.normalization.type == \'1x\':\n+\n+ #if $comparison.normalization.effectiveGenomeSize.effectiveGenomeSize_opt == "specific":\n+ --normalizeTo1x $comparison.normalization.effectiveGenomeSize.effectiveGenomeSize\n+ #else:\n+ --normalizeTo1x $comparison.normalization.effectiveGenomeSize.effectiveGenomeSize_opt\n+ #end if\n+\n+ #end if\n+ #elif $comparison.type in [\'ratio\',\'log2\']:\n+ --pseudocount $comparison.pseudocount\n+ #end if\n+\n+ #if str($region).strip() != \'\':\n+ --region \'$region\'\n+ #end if\n+\n+ #if $advancedOpt.showAdvancedOpt == "yes":\n+ #if $advancedOpt.smoothLength:\n+ --smoothLength \'$advancedOpt.smoothLength\'\n+ #end if\n+\n+ @ADVANCED_OPTS_READ_PROCESSING@\n+ $advancedOpt.skipNAs\n+\n+ #if str($advancedOpt.ignoreForNormalization).strip() != \'\':\n+ --ignoreForNormalization \'$advancedOpt.ignoreForNormalization\'\n+ #end if\n+ #end if\n+]]>\n+ </command>\n+ <inputs>\n+ <param argument="--bamFile1" format="bam" type="data" label="First BAM file (e.g. treated sample)"\n+ help="The BAM file must be sorted."/>\n+ <param argument="--bamFile2" format="bam" type="data" label="Second BAM file (e.g. control sample)"\n+ help="The BAM file must be sorted."/>\n+\n+ <param argument="--binSize" type="integer" value="50" min="1"\n+ label="Bin size in bases"\n+ help="The genome will be divided into bins of the specified size. For each bin, the overlaping number of fragments (or reads) will be reported.\n+ If only half a fragment overlaps then this fraction will be reported."/>\n+\n+ <conditional name="scaling">\n+ <param name="method" type="select"\n+ label="Method to use for scaling the largest sample to the smallest">\n+ <option value="readCount" selected="true">read count</option>\n+ <option value="SES">signal extraction scaling (SES), check with plotFingerprint before using it!</option>\n+ <option value="own">enter own scaling factors</option>\n+ </param>\n+ <when value="SES">\n+ <param argument="--sampleLength" type="integer" value="1000" min="1'..b'd="true">no</option>\n+ <option value="yes">yes</option>\n+ </param>\n+ <when value="no" />\n+ <when value="yes">\n+ <expand macro="smoothLength" />\n+ <expand macro="read_processing_options" />\n+\n+ <expand macro="skipNAs" />\n+ <param argument="--ignoreForNormalization" type="text" value="" size="50"\n+ label="regions that should be excluded for calculating the scaling factor"\n+ help="Sometimes it makes sense to exclude certain regions when calculating the scaling factor.\n+ For example, if you know of copy number variations between samples then you may want to exclude these.\n+ Another typical example is the difference in chromosome X copies between males and females in many species.\n+ Example inputs are chrX,chrY,chr3 or chr10:12220-128932" />\n+ </when>\n+ </conditional>\n+ </inputs>\n+ <outputs>\n+ <data format="bigwig" name="outFileName">\n+ <change_format>\n+ <when input="outFileFormat" value="bigwig" format="bigwig" />\n+ <when input="outFileFormat" value="bedgraph" format="bedgraph" />\n+ </change_format>\n+ </data>\n+ </outputs>\n+ <tests>\n+ <test>\n+ <param name="bamFile1" value="bowtie2-test1.bam" ftype="bam" />\n+ <param name="bamFile2" value="bowtie2-test1.bam" ftype="bam" />\n+ <param name="showAdvancedOpt" value="no" />\n+ <param name="outFileFormat" value="bigwig" />\n+ <param name="outFileFormat" value="bedgraph" />\n+ <param name="binSize" value="5" />\n+ <param name="type" value="ratio" />\n+ <output name="outFileName" file="bamCompare_result1.bg" ftype="bedgraph" />\n+ </test>\n+ <test>\n+ <param name="bamFile1" value="bowtie2-test1.bam" ftype="bam" />\n+ <param name="bamFile2" value="bowtie2-test1.bam" ftype="bam" />\n+ <param name="showAdvancedOpt" value="yes" />\n+ <param name="outFileFormat" value="bigwig" />\n+ <param name="outFileFormat" value="bigwig" />\n+ <param name="binSize" value="10" />\n+ <param name="type" value="ratio" />\n+ <output name="outFileName" file="bamCompare_result2.bw" ftype="bigwig" />\n+ </test>\n+ </tests>\n+ <help>\n+<![CDATA[\n+\n+**What it does**\n+\n+This tool compares two BAM files based on the number of mapped reads. To\n+compare the BAM files, the genome is partitioned into bins of equal size, then\n+the number of reads found in each BAM file is counted per bin and\n+finally a summary value reported. This value can be the ratio of the\n+number of reads per bin, the log2 of the ratio or the difference. This tool\n+can normalize the number of reads in each BAM file using the SES method\n+proposed in Diaz et al. (2012). "Normalization, bias correction, and peak\n+calling for ChIP-seq". Statistical applications in genetics and molecular\n+biology, 11(3). Normalization based on read counts is also available. The\n+output is either a bedgraph or a bigwig file containing the bin location and\n+the resulting comparison values. By default, if reads are mated, the fragment\n+length reported in the BAM file is used. In the case of paired-end mapping,\n+each read mate is treated independently to avoid a bias when a mixture of\n+concordant and discordant pairs are present. This means that *each end* will be\n+extended to match the fragment length.\n+\n+\n+.. image:: $PATH_TO_IMAGES/norm_IGVsnapshot_indFiles.png\n+\n+\n+You can find more details on the bamCompare doc page: https://deeptools.readthedocs.org/en/master/content/tools/bamCompare.html\n+\n+\n+**Output files**:\n+\n+- same as for bamCoverage, except that you now obtain 1 coverage file that is based on 2 BAM files.\n+\n+-----\n+\n+@REFERENCES@\n+]]>\n+ </help>\n+ <expand macro="citations" />\n+</tool>\n'

diff -r 000000000000 -r 105b9da2445c datatypes_conf.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/datatypes_conf.xml Mon Jan 25 20:25:37 2016 -0500

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

diff -r 000000000000 -r 105b9da2445c deepTools_macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/deepTools_macros.xml Mon Jan 25 20:25:37 2016 -0500

b'@@ -0,0 +1,615 @@\n+<macros>\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="@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 $advancedOpt.samFlagExclude\n+ #end if\n+ </token>\n+\n+ <xml name="heatmap_options">\n+ <expand macro="zMin_zMax" />\n+ <expand macro="colorMap" />\n+ <expand macro="plotTitle" />\n+ <expand macro="plotNumbers" />\n+ </xml>\n+\n+ <token name="@HEATMAP_OPTIONS@">\n+ #if str($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 files are included. The default behavior is to ignore such regions." />\n+ </xml>\n+\n+ <xml name="zMin_zMax">\n+ <param argument="--zMin" type="float" value="" optional="true" label="Minimum value for the heatmap intensities"\n+ help="If not specified the value is set automatically."/>\n+ <param argument="--zMax" type="float" value="" optional="true" label="Maximum value for the heatmap intensities"\n+ help="If not specified the value is set automatically."/>\n+ </xml>\n+\n+ <xml name="region_limit_operation">\n+ <param argument="--region" type="text" value=""\n+ label="Region of the genome to limit the operation to"\n+ help="This is useful when testing parameters to reduce the time required. The format is chr:start:end, for example "chr10" or "chr10:456700:891000"." />\n+ </xml>\n+\n+ <token name="@THREADS@">--numberOfProcessors "\\${GALAXY_SLOTS:-4}"</token>\n+ <token name="@WRAPPER_VERSION@">2.0.1</token>\n+ <xml name="requirements">\n+ <requirements>\n+ <requirement type="package" version="2.7.10">python</requirement>\n+ <requirement type="binary">@BINARY@</requirement>\n+ <requirement type="package" version="2.0.1">deepTools</requirement>\n+ <yield />\n+ </requirements>\n+ <expand macro="stdio" />\n+ <version_command>@BINARY@ --version</version_command>\n+ </xml>\n+\n+ <xml name="smoothLength">\n+ <param argument="--smoothLength" type="integer" value="" optional="True" min="1"\n+ label="Smooth values using the following length (in bases)"\n+ help ="The smooth length defines a window, larger than the bin size, over which the number of reads is to be averaged. For example, if the bin size is set to 20 and the smooth length is 60, then, for each bin, its value is set to the average of it and its left and right neighbors. Any'..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 105b9da2445c readme.rst
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/readme.rst Mon Jan 25 20:25:37 2016 -0500

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

diff -r 000000000000 -r 105b9da2445c repository_dependencies.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/repository_dependencies.xml Mon Jan 25 20:25:37 2016 -0500

@@ -0,0 +1,4 @@
+<?xml version="1.0"?>
+<repositories>
+ <repository changeset_revision="74b09c8e5f6e" name="data_manager_twobit_builder" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" />
+</repositories>

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diff -r 000000000000 -r 105b9da2445c test-data/bamCompare_result1.bg
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/bamCompare_result1.bg Mon Jan 25 20:25:37 2016 -0500

@@ -0,0 +1,1 @@
+chrM 0 16569 1.0

diff -r 000000000000 -r 105b9da2445c test-data/bamCompare_result2.bw

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diff -r 000000000000 -r 105b9da2445c test-data/bamCoverage_result3.bg
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/bamCoverage_result3.bg Mon Jan 25 20:25:37 2016 -0500

@@ -0,0 +1,8 @@
+chrM 0 10 18498299.57
+chrM 10 200 9768764.94
+chrM 200 210 10184457.07
+chrM 210 220 9976611.00
+chrM 220 230 7690304.31
+chrM 230 240 6027535.81
+chrM 240 250 3325537.00
+chrM 250 260 623538.19

diff -r 000000000000 -r 105b9da2445c test-data/bamCoverage_result4.bg
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/bamCoverage_result4.bg Mon Jan 25 20:25:37 2016 -0500

b'@@ -0,0 +1,472 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diff -r 000000000000 -r 105b9da2445c test-data/bamCoverage_result4.bw

Binary file test-data/bamCoverage_result4.bw has changed

diff -r 000000000000 -r 105b9da2445c test-data/bamPEFragmentSize_histogram_result1.png

Binary file test-data/bamPEFragmentSize_histogram_result1.png has changed

diff -r 000000000000 -r 105b9da2445c test-data/bamPEFragmentSize_result1.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/bamPEFragmentSize_result1.txt Mon Jan 25 20:25:37 2016 -0500

@@ -0,0 +1,20 @@
+Sample size: 3
+
+
+Fragment lengths:
+Min.: 241
+1st Qu.: 241.5
+Mean: 244.666666667
+Median: 242.0
+3rd Qu.: 246.5
+Max.: 251
+Std: 4.49691252108
+
+Read lengths:
+Min.: 251
+1st Qu.: 251.0
+Mean: 251.0
+Median: 251.0
+3rd Qu.: 251.0
+Max.: 251
+Std: 0.0

diff -r 000000000000 -r 105b9da2445c test-data/bigwigCompare_result1.bw

Binary file test-data/bigwigCompare_result1.bw has changed

diff -r 000000000000 -r 105b9da2445c test-data/bigwigCompare_result2.bg
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/bigwigCompare_result2.bg Mon Jan 25 20:25:37 2016 -0500

@@ -0,0 +1,3 @@
+ch1 0 400 1.0
+ch2 0 400 1.0
+ch3 0 400 1.0

diff -r 000000000000 -r 105b9da2445c test-data/bowtie2-test1.bam

Binary file test-data/bowtie2-test1.bam has changed

diff -r 000000000000 -r 105b9da2445c test-data/computeGCBias_result1.png

Binary file test-data/computeGCBias_result1.png has changed

diff -r 000000000000 -r 105b9da2445c test-data/computeGCBias_result1.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/computeGCBias_result1.tabular Mon Jan 25 20:25:37 2016 -0500

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diff -r 000000000000 -r 105b9da2445c test-data/computeMatrix1.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/computeMatrix1.bed Mon Jan 25 20:25:37 2016 -0500

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

diff -r 000000000000 -r 105b9da2445c test-data/computeMatrix2.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/computeMatrix2.bed Mon Jan 25 20:25:37 2016 -0500

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

diff -r 000000000000 -r 105b9da2445c test-data/computeMatrix2.bw

Binary file test-data/computeMatrix2.bw has changed

diff -r 000000000000 -r 105b9da2445c test-data/computeMatrix_result1.gz

Binary file test-data/computeMatrix_result1.gz has changed

diff -r 000000000000 -r 105b9da2445c test-data/computeMatrix_result2.gz

Binary file test-data/computeMatrix_result2.gz has changed

diff -r 000000000000 -r 105b9da2445c test-data/computeMatrix_result3.gz

Binary file test-data/computeMatrix_result3.gz has changed

diff -r 000000000000 -r 105b9da2445c test-data/correctGCBias_result1.bam

Binary file test-data/correctGCBias_result1.bam has changed

diff -r 000000000000 -r 105b9da2445c test-data/heatmapper_result1.png

Binary file test-data/heatmapper_result1.png has changed

diff -r 000000000000 -r 105b9da2445c test-data/heatmapper_result2.png

Binary file test-data/heatmapper_result2.png has changed

diff -r 000000000000 -r 105b9da2445c test-data/multiBamSummary_regions.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/multiBamSummary_regions.bed Mon Jan 25 20:25:37 2016 -0500

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

diff -r 000000000000 -r 105b9da2445c test-data/multiBamSummary_result1.npz

Binary file test-data/multiBamSummary_result1.npz has changed

diff -r 000000000000 -r 105b9da2445c test-data/multiBamSummary_result2.npz

Binary file test-data/multiBamSummary_result2.npz has changed

diff -r 000000000000 -r 105b9da2445c test-data/multiBigwigSummary_result1.npz

Binary file test-data/multiBigwigSummary_result1.npz has changed

diff -r 000000000000 -r 105b9da2445c test-data/multiBigwigSummary_result1.png

Binary file test-data/multiBigwigSummary_result1.png has changed

diff -r 000000000000 -r 105b9da2445c test-data/paired_chr2L.bam

Binary file test-data/paired_chr2L.bam has changed

diff -r 000000000000 -r 105b9da2445c test-data/phiX.2bit

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

diff -r 000000000000 -r 105b9da2445c test-data/phiX.bam

Binary file test-data/phiX.bam has changed

diff -r 000000000000 -r 105b9da2445c test-data/phiX.bam.bai

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

diff -r 000000000000 -r 105b9da2445c test-data/phiX.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/phiX.fasta Mon Jan 25 20:25:37 2016 -0500

@@ -0,0 +1,79 @@
+>phiX174
+GAGTTTTATCGCTTCCATGACGCAGAAGTTAACACTTTCGGATATTTCTGATGAGTCGAAAAATTATCTT
+GATAAAGCAGGAATTACTACTGCTTGTTTACGAATTAAATCGAAGTGGACTGCTGGCGGAAAATGAGAAA
+ATTCGACCTATCCTTGCGCAGCTCGAGAAGCTCTTACTTTGCGACCTTTCGCCATCAACTAACGATTCTG
+TCAAAAACTGACGCGTTGGATGAGGAGAAGTGGCTTAATATGCTTGGCACGTTCGTCAAGGACTGGTTTA
+GATATGAGTCACATTTTGTTCATGGTAGAGATTCTCTTGTTGACATTTTAAAAGAGCGTGGATTACTATC
+TGAGTCCGATGCTGTTCAACCACTAATAGGTAAGAAATCATGAGTCAAGTTACTGAACAATCCGTACGTT
+TCCAGACCGCTTTGGCCTCTATTAAGCTCATTCAGGCTTCTGCCGTTTTGGATTTAACCGAAGATGATTT
+CGATTTTCTGACGAGTAACAAAGTTTGGATTGCTACTGACCGCTCTCGTGCTCGTCGCTGCGTTGAGGCT
+TGCGTTTATGGTACGCTGGACTTTGTGGGATACCCTCGCTTTCCTGCTCCTGTTGAGTTTATTGCTGCCG
+TCATTGCTTATTATGTTCATCCCGTCAACATTCAAACGGCCTGTCTCATCATGGAAGGCGCTGAATTTAC
+GGAAAACATTATTAATGGCGTCGAGCGTCCGGTTAAAGCCGCTGAATTGTTCGCGTTTACCTTGCGTGTA
+CGCGCAGGAAACACTGACGTTCTTACTGACGCAGAAGAAAACGTGCGTCAAAAATTACGTGCAGAAGGAG
+TGATGTAATGTCTAAAGGTAAAAAACGTTCTGGCGCTCGCCCTGGTCGTCCGCAGCCGTTGCGAGGTACT
+AAAGGCAAGCGTAAAGGCGCTCGTCTTTGGTATGTAGGTGGTCAACAATTTTAATTGCAGGGGCTTCGGC
+CCCTTACTTGAGGATAAATTATGTCTAATATTCAAACTGGCGCCGAGCGTATGCCGCATGACCTTTCCCA
+TCTTGGCTTCCTTGCTGGTCAGATTGGTCGTCTTATTACCATTTCAACTACTCCGGTTATCGCTGGCGAC
+TCCTTCGAGATGGACGCCGTTGGCGCTCTCCGTCTTTCTCCATTGCGTCGTGGCCTTGCTATTGACTCTA
+CTGTAGACATTTTTACTTTTTATGTCCCTCATCGTCACGTTTATGGTGAACAGTGGATTAAGTTCATGAA
+GGATGGTGTTAATGCCACTCCTCTCCCGACTGTTAACACTACTGGTTATATTGACCATGCCGCTTTTCTT
+GGCACGATTAACCCTGATACCAATAAAATCCCTAAGCATTTGTTTCAGGGTTATTTGAATATCTATAACA
+ACTATTTTAAAGCGCCGTGGATGCCTGACCGTACCGAGGCTAACCCTAATGAGCTTAATCAAGATGATGC
+TCGTTATGGTTTCCGTTGCTGCCATCTCAAAAACATTTGGACTGCTCCGCTTCCTCCTGAGACTGAGCTT
+TCTCGCCAAATGACGACTTCTACCACATCTATTGACATTATGGGTCTGCAAGCTGCTTATGCTAATTTGC
+ATACTGACCAAGAACGTGATTACTTCATGCAGCGTTACCGTGATGTTATTTCTTCATTTGGAGGTAAAAC
+CTCTTATGACGCTGACAACCGTCCTTTACTTGTCATGCGCTCTAATCTCTGGGCATCTGGCTATGATGTT
+GATGGAACTGACCAAACGTCGTTAGGCCAGTTTTCTGGTCGTGTTCAACAGACCTATAAACATTCTGTGC
+CGCGTTTCTTTGTTCCTGAGCATGGCACTATGTTTACTCTTGCGCTTGTTCGTTTTCCGCCTACTGCGAC
+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 105b9da2445c test-data/plotCorrelation_result1.png

Binary file test-data/plotCorrelation_result1.png has changed

diff -r 000000000000 -r 105b9da2445c test-data/plotCorrelation_result1.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/plotCorrelation_result1.tabular Mon Jan 25 20:25:37 2016 -0500

@@ -0,0 +1,3 @@
+ 'bowtie2-test1.bam' 'bowtie2-test1.bam'
+'bowtie2-test1.bam' 1.0000 1.0000
+'bowtie2-test1.bam' 1.0000 1.0000

diff -r 000000000000 -r 105b9da2445c test-data/plotCorrelation_result2.png

Binary file test-data/plotCorrelation_result2.png has changed

diff -r 000000000000 -r 105b9da2445c test-data/plotCoverage_result1.png

Binary file test-data/plotCoverage_result1.png has changed

diff -r 000000000000 -r 105b9da2445c test-data/plotCoverage_result1.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/plotCoverage_result1.tabular Mon Jan 25 20:25:37 2016 -0500

b"@@ -0,0 +1,16570 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diff -r 000000000000 -r 105b9da2445c test-data/plotFingerprint_result1.png

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diff -r 000000000000 -r 105b9da2445c test-data/plotFingerprint_result2.png

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diff -r 000000000000 -r 105b9da2445c test-data/plotFingerprint_result2.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/plotFingerprint_result2.tabular Mon Jan 25 20:25:37 2016 -0500

b"@@ -0,0 +1,16071 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diff -r 000000000000 -r 105b9da2445c tool-data/deepTools_seqs.loc.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/deepTools_seqs.loc.sample Mon Jan 25 20:25:37 2016 -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 105b9da2445c tool-data/lastz_seqs.loc.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/lastz_seqs.loc.sample Mon Jan 25 20:25:37 2016 -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 105b9da2445c tool_data_table_conf.xml.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample Mon Jan 25 20:25:37 2016 -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>

diff -r 000000000000 -r 105b9da2445c tool_dependencies.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml Mon Jan 25 20:25:37 2016 -0500

@@ -0,0 +1,9 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="python" version="2.7.10">
+        <repository changeset_revision="0339c4a9b87b" name="package_python_2_7_10" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="deepTools" version="2.0.1">
+        <repository changeset_revision="1fb61fa32733" name="package_python_2_7_deeptools_2_0_1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
+    </package>
+</tool_dependency>