# HG changeset patch
# User bgruening
# Date 1480943345 18000
# Node ID 1638c02b28b521a17b4193e1f634e4ffe01842bf
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
diff -r 000000000000 -r 1638c02b28b5 computeMatrixOperations.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/computeMatrixOperations.xml Mon Dec 05 08:09:05 2016 -0500
@@ -0,0 +1,179 @@
+
+ Modify or combine the output of computeMatrix in a variety of ways.
+
+ computeMatrixOperations
+ deepTools_macros.xml
+
+
+
+ $outFileTxt
+ #else if $submodule.command == "subset":
+ subset
+ -m $submodule.matrixFile
+ #if $submodule.groups is not None and str($submodule.groups) != '':
+ --groups $submodule.groups
+ #end if
+ #if $submodule.samples is not None and str($submodule.samples) != '':
+ --samples $submodule.samples
+ #end if
+ -o $outFileName
+ #else if $submodule.command == "filterStrand":
+ filterStrand
+ -m $submodule.matrixFile
+ --strand $submodule.strand
+ -o $outFileName
+ #else if $submodule.command == "rbind":
+ #set $files=[]
+ #for $f in $submodule.matrixFiles:
+ #silent $files.append(str($f.matrixFile))
+ #end for
+ rbind
+ -m '#echo "' '".join($files)#'
+ -o $outFileName
+ #else if $submodule.command == "cbind":
+ cbind
+ #set $files=[]
+ #for $f in $submodule.matrixFiles:
+ #silent $files.append(str($f.matrixFile))
+ #end for
+ -m '#echo "' '".join($files)#'
+ -o $outFileName
+ #else if $submodule.command == "sort":
+ sort
+ #set $files=[]
+ #for $f in $submodule.regionsFiles:
+ #silent $files.append(str($f.regionsFile))
+ #end for
+ -m $submodule.matrixFile
+ -R '#echo "' '".join($files)#'
+ -o $outFileName
+ #end if
+]]>
+
+
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+
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+
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+ ((
+ submodule['command'] != "info"
+ ))
+
+
+
+
+ ((
+ submodule['command'] == "info"
+ ))
+
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diff -r 000000000000 -r 1638c02b28b5 datatypes_conf.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/datatypes_conf.xml Mon Dec 05 08:09:05 2016 -0500
@@ -0,0 +1,7 @@
+
+
+
+
+
+
+
diff -r 000000000000 -r 1638c02b28b5 deepTools_macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/deepTools_macros.xml Mon Dec 05 08:09:05 2016 -0500
@@ -0,0 +1,811 @@
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ #if $advancedOpt.doExtendCustom.doExtend == 'custom':
+ --extendReads $advancedOpt.doExtendCustom.extendReadsValue
+ #else if $advancedOpt.doExtendCustom.doExtend == 'yes':
+ --extendReads
+ #end if
+ $advancedOpt.ignoreDuplicates
+ $advancedOpt.centerReads
+ #if $advancedOpt.minMappingQuality:
+ --minMappingQuality '$advancedOpt.minMappingQuality'
+ #end if
+ #if $advancedOpt.samFlagInclude:
+ --samFlagInclude $advancedOpt.samFlagInclude
+ #end if
+ #if $advancedOpt.samFlagExclude:
+ --samFlagExclude $advancedOpt.samFlagExclude
+ #end if
+ #if $advancedOpt.minFragmentLength:
+ --minFragmentLength $advancedOpt.minFragmentLength
+ #end if
+ #if $advancedOpt.maxFragmentLength:
+ --maxFragmentLength $advancedOpt.maxFragmentLength
+ #end if
+
+
+
+ $advancedOpt.metagene
+ #if $advancedOpt.transcriptID:
+ --transcriptID $advancedOpt.transcriptID
+ #end if
+ #if $advancedOpt.exonID:
+ --exonID $advancedOpt.exonID
+ #end if
+ #if $advancedOpt.transcript_id_designator:
+ --transcript_id_designator $advancedOpt.transcript_id_designator
+ #end if
+
+
+
+
+
+
+
+
+
+
+ #if str($plotting_type.zMin) != "":
+ --zMin $plotting_type.zMin
+ #end if
+ #if str($plotting_type.zMax) != "":
+ --zMax $plotting_type.zMax
+ #end if
+ --colorMap '$plotting_type.colorMap'
+ $plotting_type.plotNumbers
+ --plotTitle '$plotting_type.plotTitle'
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ --numberOfProcessors "\${GALAXY_SLOTS:-4}"
+ 2.4.1
+
+
+ python
+ deeptools
+
+
+
+ @BINARY@ --version
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
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+
+
+
+
+
+
+
+ #if $advancedOpt.used_multiple_regions.used_multiple_regions_options == 'no':
+ #if $advancedOpt.used_multiple_regions.clustering.clustering_options == 'kmeans':
+ #if int($advancedOpt.used_multiple_regions.clustering.k_kmeans) > 0:
+ --kmeans $advancedOpt.used_multiple_regions.clustering.k_kmeans
+ #end if
+ #end if
+ #if $advancedOpt.used_multiple_regions.clustering.clustering_options == 'hclust':
+ #if int($advancedOpt.used_multiple_regions.clustering.n_hclust) > 0:
+ --hclust $advancedOpt.used_multiple_regions.clustering.n_hclust
+ #end if
+ #end if
+ #end if
+
+
+
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+
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+
+
+
+
+
+
+.. class:: infomark
+
+For more information on the tools, please visit our `help site`_.
+
+If you would like to give us feedback or you run into any trouble, please send an email to deeptools@googlegroups.com
+
+This tool is developed by the `Bioinformatics and Deep-Sequencing Unit`_ at the `Max Planck Institute for Immunobiology and Epigenetics`_.
+
+.. _Bioinformatics and Deep-Sequencing Unit: http://www.ie-freiburg.mpg.de/bioinformaticsfac
+.. _Max Planck Institute for Immunobiology and Epigenetics: http://www3.ie-freiburg.mpg.de
+.. _help site: https://deeptools.readthedocs.org/
+
+
+
+
+ 10.1093/nar/gkw257
+
+
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+ 0:
+ --BED #echo ' '.join($files)#
+ --regionLabels #echo ' '.join($labels)#
+ #end if
+]]>
+
+
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+
+ #if $source.ref_source=="history":
+ --genome $source.input1
+ #else:
+ --genome "$source.input1_2bit.fields.path"
+ #end if
+
+
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+ ((
+ output['showOutputSettings'] == 'yes' and
+ output['saveMatrix'] is True
+ ))
+
+
+
+
+
+
+
+ ((
+ output['showOutputSettings'] == 'yes' and
+ output['saveSortedRegions'] is True
+ ))
+
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diff -r 000000000000 -r 1638c02b28b5 deepTools_macros.xml.orig
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/deepTools_macros.xml.orig Mon Dec 05 08:09:05 2016 -0500
@@ -0,0 +1,639 @@
+
+
+
+
+
+
+
+
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+
+
+
+
+
+
+ #if $advancedOpt.doExtendCustom.doExtend == 'custom':
+ --extendReads $advancedOpt.doExtendCustom.extendReadsValue
+ #else if $advancedOpt.doExtendCustom.doExtend == 'yes':
+ --extendReads
+ #end if
+ $advancedOpt.ignoreDuplicates
+ $advancedOpt.centerReads
+ #if $advancedOpt.minMappingQuality:
+ --minMappingQuality '$advancedOpt.minMappingQuality'
+ #end if
+ #if $advancedOpt.samFlagInclude:
+ --samFlagInclude $advancedOpt.samFlagInclude
+ #end if
+ #if $advancedOpt.samFlagExclude:
+ --samFlagExclude $advancedOpt.samFlagExclude
+ #end if
+
+
+
+
+
+
+
+
+
+
+ #if str($plotting_type.zMin) != "":
+ --zMin $plotting_type.zMin
+ #end if
+ #if str($plotting_type.zMax) != "":
+ --zMax $plotting_type.zMax
+ #end if
+ --colorMap '$plotting_type.colorMap'
+ $plotting_type.plotNumbers
+ --plotTitle '$plotting_type.plotTitle'
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ --numberOfProcessors "\${GALAXY_SLOTS:-4}"
+<<<<<<< HEAD
+ 2.0.1.0
+=======
+ 2.1.0
+>>>>>>> d56067f86089e75354a2fad266002db3730766d9
+
+
+ python
+ @BINARY@
+<<<<<<< HEAD
+ deepTools
+=======
+ deepTools
+>>>>>>> d56067f86089e75354a2fad266002db3730766d9
+
+
+
+ @BINARY@ --version
+
+
+
+
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+
+ #if $advancedOpt.used_multiple_regions.used_multiple_regions_options == 'no':
+ #if $advancedOpt.used_multiple_regions.clustering.clustering_options == 'kmeans':
+ #if int($advancedOpt.used_multiple_regions.clustering.k_kmeans) > 0:
+ --kmeans $advancedOpt.used_multiple_regions.clustering.k_kmeans
+ #end if
+ #end if
+ #if $advancedOpt.used_multiple_regions.clustering.clustering_options == 'hclust':
+ #if int($advancedOpt.used_multiple_regions.clustering.n_hclust) > 0:
+ --hclust $advancedOpt.used_multiple_regions.clustering.n_hclust
+ #end if
+ #end if
+ #end if
+
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+
+
+
+
+
+
+.. class:: infomark
+
+For more information on the tools, please visit our `help site`_.
+
+If you would like to give us feedback or you run into any trouble, please send an email to deeptools@googlegroups.com
+
+This tool is developed by the `Bioinformatics and Deep-Sequencing Unit`_ at the `Max Planck Institute for Immunobiology and Epigenetics`_.
+
+.. _Bioinformatics and Deep-Sequencing Unit: http://www.ie-freiburg.mpg.de/bioinformaticsfac
+.. _Max Planck Institute for Immunobiology and Epigenetics: http://www3.ie-freiburg.mpg.de
+.. _help site: https://deeptools.readthedocs.org/
+
+
+
+
+ 10.1093/nar/gku365
+
+
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+ #if $source.ref_source=="history":
+ --genome $source.input1
+ #else:
+ --genome "$source.input1_2bit.fields.path"
+ #end if
+
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+ ((
+ output['showOutputSettings'] == 'yes' and
+ output['saveMatrix'] is True
+ ))
+
+
+
+
+
+
+
+ ((
+ output['showOutputSettings'] == 'yes' and
+ output['saveSortedRegions'] is True
+ ))
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diff -r 000000000000 -r 1638c02b28b5 readme.rst
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/readme.rst Mon Dec 05 08:09:05 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 1638c02b28b5 repository_dependencies.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/repository_dependencies.xml Mon Dec 05 08:09:05 2016 -0500
@@ -0,0 +1,4 @@
+
+
+
+
diff -r 000000000000 -r 1638c02b28b5 static/images/GC_bias_simulated_reads_2L.png
Binary file static/images/GC_bias_simulated_reads_2L.png has changed
diff -r 000000000000 -r 1638c02b28b5 static/images/QC_GCplots_input.png
Binary file static/images/QC_GCplots_input.png has changed
diff -r 000000000000 -r 1638c02b28b5 static/images/QC_fingerprint.png
Binary file static/images/QC_fingerprint.png has changed
diff -r 000000000000 -r 1638c02b28b5 static/images/QC_multiBamSummary_humanSamples.png
Binary file static/images/QC_multiBamSummary_humanSamples.png has changed
diff -r 000000000000 -r 1638c02b28b5 static/images/QC_plotCoverage.png
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diff -r 000000000000 -r 1638c02b28b5 static/images/bamCompare_output.png
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diff -r 000000000000 -r 1638c02b28b5 static/images/bamCoverage_output.png
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diff -r 000000000000 -r 1638c02b28b5 static/images/bamFP_galaxy_output.png
Binary file static/images/bamFP_galaxy_output.png has changed
diff -r 000000000000 -r 1638c02b28b5 static/images/bamPEFragmentSize_output.png
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diff -r 000000000000 -r 1638c02b28b5 static/images/bigwigCompare_output.png
Binary file static/images/bigwigCompare_output.png has changed
diff -r 000000000000 -r 1638c02b28b5 static/images/computeGCBias_output.png
Binary file static/images/computeGCBias_output.png has changed
diff -r 000000000000 -r 1638c02b28b5 static/images/computeMatrix_advancedOutput.png
Binary file static/images/computeMatrix_advancedOutput.png has changed
diff -r 000000000000 -r 1638c02b28b5 static/images/computeMatrix_output.png
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diff -r 000000000000 -r 1638c02b28b5 static/images/computeMatrix_overview.png
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diff -r 000000000000 -r 1638c02b28b5 static/images/computeMatrix_selectRegions.png
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diff -r 000000000000 -r 1638c02b28b5 static/images/computeMatrix_selectScores.png
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diff -r 000000000000 -r 1638c02b28b5 test-data/multiBamSummary_regions.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/multiBamSummary_regions.bed Mon Dec 05 08:09:05 2016 -0500
@@ -0,0 +1,3 @@
+chrM 1 10
+chrM 5 15
+chrM 10 20
diff -r 000000000000 -r 1638c02b28b5 test-data/multiBamSummary_result1.npz
Binary file test-data/multiBamSummary_result1.npz has changed
diff -r 000000000000 -r 1638c02b28b5 test-data/multiBamSummary_result2.npz
Binary file test-data/multiBamSummary_result2.npz has changed
diff -r 000000000000 -r 1638c02b28b5 test-data/multiBigwigSummary_result1.npz
Binary file test-data/multiBigwigSummary_result1.npz has changed
diff -r 000000000000 -r 1638c02b28b5 test-data/multiBigwigSummary_result1.png
Binary file test-data/multiBigwigSummary_result1.png has changed
diff -r 000000000000 -r 1638c02b28b5 test-data/paired_chr2L.bam
Binary file test-data/paired_chr2L.bam has changed
diff -r 000000000000 -r 1638c02b28b5 test-data/phiX.2bit
Binary file test-data/phiX.2bit has changed
diff -r 000000000000 -r 1638c02b28b5 test-data/phiX.bam
Binary file test-data/phiX.bam has changed
diff -r 000000000000 -r 1638c02b28b5 test-data/phiX.bam.bai
Binary file test-data/phiX.bam.bai has changed
diff -r 000000000000 -r 1638c02b28b5 test-data/phiX.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/phiX.fasta Mon Dec 05 08:09:05 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 1638c02b28b5 test-data/plotCorrelation_result1.png
Binary file test-data/plotCorrelation_result1.png has changed
diff -r 000000000000 -r 1638c02b28b5 test-data/plotCorrelation_result1.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/plotCorrelation_result1.tabular Mon Dec 05 08:09:05 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 1638c02b28b5 test-data/plotCorrelation_result2.png
Binary file test-data/plotCorrelation_result2.png has changed
diff -r 000000000000 -r 1638c02b28b5 test-data/plotCoverage_result1.png
Binary file test-data/plotCoverage_result1.png has changed
diff -r 000000000000 -r 1638c02b28b5 test-data/plotCoverage_result1.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/plotCoverage_result1.tabular Mon Dec 05 08:09:05 2016 -0500
@@ -0,0 +1,16570 @@
+#'chr' 'start' 'end' 'bowtie2 test1.bam' 'bowtie2 test1.bam'
+chrM 0 1 23.0 23.0
+chrM 1 2 35.0 35.0
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+chrM 12 13 35.0 35.0
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000
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diff -r 000000000000 -r 1638c02b28b5 test-data/plotFingerprint_result1.png
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diff -r 000000000000 -r 1638c02b28b5 test-data/plotPCA_result1.png
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diff -r 000000000000 -r 1638c02b28b5 test-data/plotPCA_result2.png
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diff -r 000000000000 -r 1638c02b28b5 test-data/plotPCA_result2.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/plotPCA_result2.tabular Mon Dec 05 08:09:05 2016 -0500
@@ -0,0 +1,3 @@
+Component bowtie2-test1.bam bowtie2-test1.bam Eigenvalue
+1 -0.707106781187 -0.707106781187 6.0
+2 -0.707106781187 0.707106781187 1.23259516441e-32
diff -r 000000000000 -r 1638c02b28b5 test-data/profiler_result1.png
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diff -r 000000000000 -r 1638c02b28b5 test-data/profiler_result2.png
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diff -r 000000000000 -r 1638c02b28b5 test-data/profiler_result2.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/profiler_result2.tabular Mon Dec 05 08:09:05 2016 -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 1638c02b28b5 test-data/sequence.2bit
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diff -r 000000000000 -r 1638c02b28b5 test-data/test.bw
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diff -r 000000000000 -r 1638c02b28b5 tool-data/deepTools_seqs.loc.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/deepTools_seqs.loc.sample Mon Dec 05 08:09:05 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:
+#
+#
+#
+#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 is also used as "Species name abbreviation".
diff -r 000000000000 -r 1638c02b28b5 tool-data/lastz_seqs.loc.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/lastz_seqs.loc.sample Mon Dec 05 08:09:05 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:
+#
+#
+#
+#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 is also used as "Species name abbreviation".
diff -r 000000000000 -r 1638c02b28b5 tool_data_table_conf.xml.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample Mon Dec 05 08:09:05 2016 -0500
@@ -0,0 +1,8 @@
+
+
+
+
+
diff -r 000000000000 -r 1638c02b28b5 tool_dependencies.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml Mon Dec 05 08:09:05 2016 -0500
@@ -0,0 +1,9 @@
+
+
+
+
+
+
+
+
+