# HG changeset patch # User bgruening # Date 1455549900 18000 # Node ID 011ea45dda075577c1d80ec85592775b82d6b2d0 # Parent bb2b0ad44c0eaf82c0381404b5acabd4fe9f3389 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 diff -r bb2b0ad44c0e -r 011ea45dda07 bamPEFragmentSize.xml --- a/bamPEFragmentSize.xml Mon Jan 25 20:14:03 2016 -0500 +++ b/bamPEFragmentSize.xml Mon Feb 15 10:25:00 2016 -0500 @@ -1,5 +1,5 @@ - Estimate the paired-end fragment length in a BAM file + Estimate the predominant cDNA fragment length from a paired-end sequenced BAM file bamPEFragmentSize deepTools_macros.xml @@ -16,6 +16,10 @@ --histogram ./hist.png #end if --plotTitle "$plotTitle" + #if $advancedOpt.showAdvancedOpt == 'yes' + --binSize '$advancedOpt.binSize' + --distanceBetweenBins '$advancedOpt.distanceBetweenBins' + #end if one.bam > $outfile ]]> @@ -27,6 +31,21 @@ label="Get the distribution of fragment lengths as a histogram" help=""/> + + + + + + + + + + + + @@ -45,10 +64,24 @@ --numberOfProcessors "\${GALAXY_SLOTS:-4}" - 2.0.1 + 2.1.0 python @BINARY@ - deepTools + deepTools @@ -104,6 +104,7 @@ + + + + @@ -126,6 +136,11 @@ --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 @@ -293,6 +308,12 @@ + + + + @@ -310,6 +331,7 @@ help="Title of the plot, to be printed on top of the generated image." /> + + + + + + + + + + + + + + + + + #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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + #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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +.. 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + #if $source.ref_source=="history": + --genome $source.input1 + #else: + --genome "$source.input1_2bit.fields.path" + #end if + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + (( + output['showOutputSettings'] == 'yes' and + output['saveMatrix'] is True + )) + + + + + + + + (( + output['showOutputSettings'] == 'yes' and + output['saveSortedRegions'] is True + )) + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff -r bb2b0ad44c0e -r 011ea45dda07 readme.rst diff -r bb2b0ad44c0e -r 011ea45dda07 static/images/GC_bias_simulated_reads_2L.png Binary file static/images/GC_bias_simulated_reads_2L.png has changed diff -r bb2b0ad44c0e -r 011ea45dda07 static/images/QC_plotCoverage.png Binary file static/images/QC_plotCoverage.png has changed diff -r bb2b0ad44c0e -r 011ea45dda07 static/images/bamCompare_output.png Binary file static/images/bamCompare_output.png has changed diff -r bb2b0ad44c0e -r 011ea45dda07 static/images/bamCoverage_output.png Binary file static/images/bamCoverage_output.png has changed diff -r bb2b0ad44c0e -r 011ea45dda07 static/images/bamPEFragmentSize_output.png Binary file static/images/bamPEFragmentSize_output.png has changed diff -r bb2b0ad44c0e -r 011ea45dda07 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bb2b0ad44c0e -r 011ea45dda07 tool-data/deepTools_seqs.loc.sample diff -r bb2b0ad44c0e -r 011ea45dda07 tool_dependencies.xml --- a/tool_dependencies.xml Mon Jan 25 20:14:03 2016 -0500 +++ b/tool_dependencies.xml Mon Feb 15 10:25:00 2016 -0500 @@ -1,9 +1,9 @@ - + - - + + diff -r bb2b0ad44c0e -r 011ea45dda07 tool_dependencies.xml.orig --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml.orig Mon Feb 15 10:25:00 2016 -0500 @@ -0,0 +1,76 @@ + + + + + + + + + + + + + + +<<<<<<< HEAD + + +======= + + + + + + + + +>>>>>>> d56067f86089e75354a2fad266002db3730766d9 + + + + + + + + + + + + + + + + + + + + + + + + + + + https://pypi.python.org/packages/source/d/deepTools/deepTools-2.1.0.tar.gz + + + + $INSTALL_DIR/bin + $INSTALL_DIR + $INSTALL_DIR + $INSTALL_DIR + $INSTALL_DIR/bin + + $ENV[LIBPNG_LIB_PATH] + $ENV[LIBPNG_LIB_PATH] + + TRUE + + + + + Installation of deepTools from Fidel Ramirez. + https://github.com/fidelram/deepTools + + +