#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 ))