# HG changeset patch
# User bgruening
# Date 1409075336 14400
# Node ID 72d1d7c68bd37b00cdfb9761ad92c636c7ed67d9
# Parent 7d6d2f91843e89ecbd002d9666e168fa913def44
Uploaded
diff -r 7d6d2f91843e -r 72d1d7c68bd3 bamCompare.xml
--- a/bamCompare.xml Tue Apr 01 12:31:58 2014 -0400
+++ b/bamCompare.xml Tue Aug 26 13:48:56 2014 -0400
@@ -45,6 +45,8 @@
#end if
#end if
+ #elif $comparison.type in ['ratio','log2']:
+ --pseudocount $comparison.pseudocount
#end if
#if str($region).strip() != '':
@@ -117,8 +119,12 @@
-
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@@ -222,4 +228,5 @@
@REFERENCES@
+
diff -r 7d6d2f91843e -r 72d1d7c68bd3 bamCorrelate.xml
--- a/bamCorrelate.xml Tue Apr 01 12:31:58 2014 -0400
+++ b/bamCorrelate.xml Tue Aug 26 13:48:56 2014 -0400
@@ -185,4 +185,5 @@
@REFERENCES@
+
diff -r 7d6d2f91843e -r 72d1d7c68bd3 bamCoverage.xml
--- a/bamCoverage.xml Tue Apr 01 12:31:58 2014 -0400
+++ b/bamCoverage.xml Tue Aug 26 13:48:56 2014 -0400
@@ -158,4 +158,5 @@
@REFERENCES@
+
diff -r 7d6d2f91843e -r 72d1d7c68bd3 bamFingerprint.xml
--- a/bamFingerprint.xml Tue Apr 01 12:31:58 2014 -0400
+++ b/bamFingerprint.xml Tue Aug 26 13:48:56 2014 -0400
@@ -148,4 +148,5 @@
@REFERENCES@
+
diff -r 7d6d2f91843e -r 72d1d7c68bd3 bigwigCompare.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/bigwigCompare.xml Tue Aug 26 13:48:56 2014 -0400
@@ -0,0 +1,116 @@
+
+ normalizes and compares two bigWig files to obtain the ratio, log2ratio or difference
+
+
+
+ bigwigCompare
+ deepTools_macros.xml
+
+
+ bigwigCompare
+
+ @THREADS@
+
+ --bigwig1 '$bigwigFile1'
+ --bigwig2 '$bigwigFile2'
+
+ --outFileName '$outFileName'
+ --outFileFormat '$outFileFormat'
+
+ --ratio $comparison.type
+
+ #if $comparison.type in ['ratio','log2']:
+ --pseudocount $comparison.pseudocount
+ #end if
+
+ #if str($region).strip() != '':
+ --region '$region'
+ #end if
+
+ #if $advancedOpt.showAdvancedOpt == "yes":
+
+ --missingDataAsZero $advancedOpt.missingDataAsZero
+ --scaleFactors '$advancedOpt.scaleFactor1:$advancedOpt.scaleFactor2'
+ --binSize $advancedOpt.binSize
+
+ #end if
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+**What it does**
+
+This tool compares two bigwig files based on the number of mapped reads. To
+compare the bigwig files the genome is partitioned into bins of equal size,
+then the number of reads found in each BAM file are counted for such bins and
+finally a summarizing value is reported. This value can be the ratio of the
+number of reads per bin, the log2 of the ratio, the sum or the difference.
+
+
+-----
+
+@REFERENCES@
+
+
+
+
diff -r 7d6d2f91843e -r 72d1d7c68bd3 computeGCBias.xml
--- a/computeGCBias.xml Tue Apr 01 12:31:58 2014 -0400
+++ b/computeGCBias.xml Tue Aug 26 13:48:56 2014 -0400
@@ -152,4 +152,5 @@
@REFERENCES@
+
diff -r 7d6d2f91843e -r 72d1d7c68bd3 computeMatrix.xml
--- a/computeMatrix.xml Tue Apr 01 12:31:58 2014 -0400
+++ b/computeMatrix.xml Tue Aug 26 13:48:56 2014 -0400
@@ -219,4 +219,5 @@
@REFERENCES@
+
diff -r 7d6d2f91843e -r 72d1d7c68bd3 correctGCBias.xml
--- a/correctGCBias.xml Tue Apr 01 12:31:58 2014 -0400
+++ b/correctGCBias.xml Tue Aug 26 13:48:56 2014 -0400
@@ -105,4 +105,5 @@
@REFERENCES@
+
diff -r 7d6d2f91843e -r 72d1d7c68bd3 deepTools_macros.xml
--- a/deepTools_macros.xml Tue Apr 01 12:31:58 2014 -0400
+++ b/deepTools_macros.xml Tue Aug 26 13:48:56 2014 -0400
@@ -36,7 +36,7 @@
-
+
--numberOfProcessors "\${GALAXY_SLOTS:-4}"
- 1.1
+ 1.5.8.2
@BINARY@
samtools
deepTools
ucsc_tools
- deepTools
+ deepTools
ucsc_tools
numpy
pysam
@@ -109,6 +109,9 @@
+
+
+
.. class:: infomark
@@ -119,12 +122,22 @@
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://www3.ie-freiburg.mpg.de/facilities/research-facilities/bioinformatics-and-deep-sequencing-unit/
.. _Max Planck Institute for Immunobiology and Epigenetics: http://www3.ie-freiburg.mpg.de
.. _help site: https://github.com/fidelram/deepTools/wiki/
+**References**
+
+If you use this Galaxy tool in work leading to a scientific publication please
+cite the following paper:
+
+
+
+ 10.1093/nar/gku365
+
+
+
diff -r 7d6d2f91843e -r 72d1d7c68bd3 heatmapper.xml
--- a/heatmapper.xml Tue Apr 01 12:31:58 2014 -0400
+++ b/heatmapper.xml Tue Aug 26 13:48:56 2014 -0400
@@ -1,210 +1,211 @@
-
- creates a heatmap for a score associated to genomic regions
-
-
-
- heatmapper
- deepTools_macros.xml
-
-
- heatmapper
-
- --matrixFile $matrixFile
- --outFileName $outFileName
-
- #if $output.showOutputSettings == "yes"
- --plotFileFormat $output.outFileFormat
- #if $outFileNameData:
- --outFileNameData '$outFileNameData'
- #end if
-
- #if $outFileNameMatrix:
- --outFileNameMatrix '$outFileNameMatrix'
- #end if
-
- #if $outFileSortedRegions:
- --outFileSortedRegions '$outFileSortedRegions'
- #end if
- #else
- --plotFileFormat 'png'
- #end if
-
- #if $advancedOpt.showAdvancedOpt == "yes"
- #if $advancedOpt.sortRegions:
- --sortRegions '$advancedOpt.sortRegions'
- #end if
-
- #if $advancedOpt.sortUsing:
- --sortUsing '$advancedOpt.sortUsing'
- #end if
-
- #if $advancedOpt.averageTypeSummaryPlot:
- --averageTypeSummaryPlot '$advancedOpt.averageTypeSummaryPlot'
- #end if
-
- #if str($advancedOpt.missingDataColor.value) != "None":
- --missingDataColor '$advancedOpt.missingDataColor'
- #end if
-
- --colorMap '$advancedOpt.colorMap'
-
- #if $advancedOpt.zMin:
- --zMin $advancedOpt.zMin
- #end if
- #if $advancedOpt.zMax:
- --zMax $advancedOpt.zMax
- #end if
-
- #if $advancedOpt.yMin:
- --yMin $advancedOpt.yMin
- #end if
- #if $advancedOpt.yMax:
- --yMax $advancedOpt.yMax
- #end if
-
- --xAxisLabel '$advancedOpt.xAxisLabel'
- --yAxisLabel '$advancedOpt.yAxisLabel'
-
- --heatmapWidth $advancedOpt.heatmapWidth
- --heatmapHeight $advancedOpt.heatmapHeight
-
- --whatToShow '$advancedOpt.whatToShow'
-
- --startLabel '$advancedOpt.startLabel'
- --endLabel '$advancedOpt.endLabel'
- --refPointLabel '$advancedOpt.referencePointLabel'
- --regionsLabel '$advancedOpt.regionsLabel'
-
- #if str($advancedOpt.plotTitle.value) != "None":
- --plotTitle '$advancedOpt.plotTitle'
- #end if
-
- $advancedOpt.onePlotPerGroup
-
- @kmeans_clusterin@
-
- #end if
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-**What it does**
-
-The heatmapper visualizes scores associated with genomic regions, for example ChIP enrichment values around the TSS of genes.
-Like profiler, it requires that computeMatrix was run first to calculate the values.
-
-We implemented vast optional parameters to optimize the visual output and we encourage you to play around with the min/max values displayed in the heatmap as well as
-with the different coloring options. The most powerful option is the k-means clustering where you simply need to indicate the number of
-groups with similar read distributions that you expect and the algorithm will do the sorting for you.
-
-Do check the examples on our help page with step-by-step protocols: https://github.com/fidelram/deepTools/wiki/Example-workflows
-
-
-.. image:: $PATH_TO_IMAGES/visual_hm_DmelPolII.png
- :alt: Heatmap of RNA Polymerase II ChIP-seq
-
-
-You can find more details on the tool itself on the heatmapper wiki page: https://github.com/fidelram/deepTools/wiki/Visualizations#wiki-heatmapper
-
-
------
-
-@REFERENCES@
-
-
-
+
+ creates a heatmap for a score associated to genomic regions
+
+
+
+ heatmapper
+ deepTools_macros.xml
+
+
+ heatmapper
+
+ --matrixFile $matrixFile
+ --outFileName $outFileName
+
+ #if $output.showOutputSettings == "yes"
+ --plotFileFormat $output.outFileFormat
+ #if $outFileNameData:
+ --outFileNameData '$outFileNameData'
+ #end if
+
+ #if $outFileNameMatrix:
+ --outFileNameMatrix '$outFileNameMatrix'
+ #end if
+
+ #if $outFileSortedRegions:
+ --outFileSortedRegions '$outFileSortedRegions'
+ #end if
+ #else
+ --plotFileFormat 'png'
+ #end if
+
+ #if $advancedOpt.showAdvancedOpt == "yes"
+ #if $advancedOpt.sortRegions:
+ --sortRegions '$advancedOpt.sortRegions'
+ #end if
+
+ #if $advancedOpt.sortUsing:
+ --sortUsing '$advancedOpt.sortUsing'
+ #end if
+
+ #if $advancedOpt.averageTypeSummaryPlot:
+ --averageTypeSummaryPlot '$advancedOpt.averageTypeSummaryPlot'
+ #end if
+
+ #if str($advancedOpt.missingDataColor.value) != "None":
+ --missingDataColor '$advancedOpt.missingDataColor'
+ #end if
+
+ --colorMap '$advancedOpt.colorMap'
+
+ #if str($advancedOpt.zMin).strip() != "":
+ --zMin $advancedOpt.zMin
+ #end if
+ #if $advancedOpt.zMax:
+ --zMax $advancedOpt.zMax
+ #end if
+
+ #if str($advancedOpt.yMin).strip() != "":
+ --yMin $advancedOpt.yMin
+ #end if
+ #if $advancedOpt.yMax:
+ --yMax $advancedOpt.yMax
+ #end if
+
+ --xAxisLabel '$advancedOpt.xAxisLabel'
+ --yAxisLabel '$advancedOpt.yAxisLabel'
+
+ --heatmapWidth $advancedOpt.heatmapWidth
+ --heatmapHeight $advancedOpt.heatmapHeight
+
+ --whatToShow '$advancedOpt.whatToShow'
+
+ --startLabel '$advancedOpt.startLabel'
+ --endLabel '$advancedOpt.endLabel'
+ --refPointLabel '$advancedOpt.referencePointLabel'
+ --regionsLabel '$advancedOpt.regionsLabel'
+
+ #if str($advancedOpt.plotTitle.value) != "None":
+ --plotTitle '$advancedOpt.plotTitle'
+ #end if
+
+ $advancedOpt.onePlotPerGroup
+
+ @kmeans_clusterin@
+
+ #end if
+
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+**What it does**
+
+The heatmapper visualizes scores associated with genomic regions, for example ChIP enrichment values around the TSS of genes.
+Like profiler, it requires that computeMatrix was run first to calculate the values.
+
+We implemented vast optional parameters to optimize the visual output and we encourage you to play around with the min/max values displayed in the heatmap as well as
+with the different coloring options. The most powerful option is the k-means clustering where you simply need to indicate the number of
+groups with similar read distributions that you expect and the algorithm will do the sorting for you.
+
+Do check the examples on our help page with step-by-step protocols: https://github.com/fidelram/deepTools/wiki/Example-workflows
+
+
+.. image:: $PATH_TO_IMAGES/visual_hm_DmelPolII.png
+ :alt: Heatmap of RNA Polymerase II ChIP-seq
+
+
+You can find more details on the tool itself on the heatmapper wiki page: https://github.com/fidelram/deepTools/wiki/Visualizations#wiki-heatmapper
+
+
+-----
+
+@REFERENCES@
+
+
+
+
diff -r 7d6d2f91843e -r 72d1d7c68bd3 profiler.xml
--- a/profiler.xml Tue Apr 01 12:31:58 2014 -0400
+++ b/profiler.xml Tue Aug 26 13:48:56 2014 -0400
@@ -160,4 +160,5 @@
@REFERENCES@
+
diff -r 7d6d2f91843e -r 72d1d7c68bd3 readme.rst
--- a/readme.rst Tue Apr 01 12:31:58 2014 -0400
+++ b/readme.rst Tue Aug 26 13:48:56 2014 -0400
@@ -48,7 +48,8 @@
History
=======
-- v1.0: Initial public release
+ * 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)
diff -r 7d6d2f91843e -r 72d1d7c68bd3 tool_dependencies.xml
--- a/tool_dependencies.xml Tue Apr 01 12:31:58 2014 -0400
+++ b/tool_dependencies.xml Tue Aug 26 13:48:56 2014 -0400
@@ -1,22 +1,22 @@
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@@ -57,29 +57,29 @@
The tools downloaded by this dependency definition are free for academic use. TODO: UCSC tools are only available with their latest version. That is not good for reproducibility.
-
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git clone --recursive https://github.com/fidelram/deepTools.git
-
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- git reset --hard 09023018b96c23f922aa2ea553090e9df8ecf41e
+ git reset --hard ae9c18b3b7e79d0d1077f636168ac24baeb7b184
$INSTALL_DIR/lib/python
export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python &&