# 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 @@ - - + + + + + + @@ -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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +**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 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -**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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +**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 @@ - + - + - + - + - + - + @@ -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. - + git clone --recursive https://github.com/fidelram/deepTools.git - + - + - + - + - + - git reset --hard 09023018b96c23f922aa2ea553090e9df8ecf41e + git reset --hard ae9c18b3b7e79d0d1077f636168ac24baeb7b184 $INSTALL_DIR/lib/python export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python &&