Repository revision
30:25d830337d31

Repository 'deeptools_plot_heatmap'
hg clone https://toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_heatmap

plotHeatmap tool metadata
Miscellaneous
plotHeatmap
creates a heatmap for score distributions across genomic regions
deeptools_plot_heatmap
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_heatmap/deeptools_plot_heatmap/3.5.2+galaxy0
3.5.2+galaxy0
plotHeatmap --version
True
Version lineage of this tool (guids ordered most recent to oldest)
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_heatmap/deeptools_plot_heatmap/3.5.4+galaxy0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_heatmap/deeptools_plot_heatmap/3.5.2+galaxy0 (this tool)
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_heatmap/deeptools_plot_heatmap/3.5.1.0.1
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_heatmap/deeptools_plot_heatmap/3.3.2.0.1
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_heatmap/deeptools_plot_heatmap/3.3.0.0.1
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_heatmap/deeptools_plot_heatmap/3.2.1.0.1
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_heatmap/deeptools_plot_heatmap/3.2.0.0.1
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_heatmap/deeptools_plot_heatmap/3.1.2.0.1
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_heatmap/deeptools_plot_heatmap/3.1.2.0.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_heatmap/deeptools_plot_heatmap/3.1.0.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_heatmap/deeptools_plot_heatmap/3.0.2.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_heatmap/deeptools_plot_heatmap/3.0.1.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_heatmap/deeptools_plot_heatmap/3.0.0.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_heatmap/deeptools_plot_heatmap/2.5.7.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_heatmap/deeptools_plot_heatmap/2.5.1.1.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_heatmap/deeptools_plot_heatmap/2.5.1.0.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_heatmap/deeptools_plot_heatmap/2.5.0.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_heatmap/deeptools_plot_heatmap/2.4.2.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_heatmap/deeptools_plot_heatmap/2.4.1.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_heatmap/deeptools_plot_heatmap/2.3.6.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_heatmap/deeptools_plot_heatmap/2.3.5.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_heatmap/deeptools_plot_heatmap/2.2.3.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_heatmap/deeptools_plot_heatmap/2.2.2.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_heatmap/deeptools_plot_heatmap/2.1.0.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_heatmap/deeptools_plot_heatmap/2.0.1.0
deeptools_plot_heatmap
Requirements (dependencies defined in the <requirements> tag set)
name version type
deeptools 3.5.2 package
samtools 1.9 package
Additional information about this tool
plotHeatmap
            --matrixFile '$matrixFile'
            --outFileName '$outFileName'

            #if $output.showOutputSettings == "yes"
                --plotFileFormat '$output.outFileFormat'

                #if $outFileNameMatrix:
                    --outFileNameMatrix '$outFileNameMatrix'
                #end if

                #if $outFileSortedRegions:
                    --outFileSortedRegions '$outFileSortedRegions'
                #end if

                #if $output.dpi:
                    --dpi '$output.dpi'
                #end if
            #else
                --plotFileFormat 'png'
            #end if

            #if $advancedOpt.showAdvancedOpt == "yes"
                #if $advancedOpt.sortRegions:
                    --sortRegions '$advancedOpt.sortRegions'
                #end if

                #if $advancedOpt.linesAtTickMarks:
                    --linesAtTickMarks
                #end if

                #if $advancedOpt.sortUsing:
                    --sortUsing '$advancedOpt.sortUsing'
                #end if

                #if $advancedOpt.averageTypeSummaryPlot:
                    --averageTypeSummaryPlot '$advancedOpt.averageTypeSummaryPlot'
                #end if

                --plotType '$advancedOpt.plotType'

                #if str($advancedOpt.missingDataColor.value) != "None":
                    --missingDataColor '$advancedOpt.missingDataColor'
                #end if

                #set colorMap = []
                #for $cmap in $advancedOpt.colorMapRepeat:
                    #silent $colorMap.append(str($cmap.colorMap))
                #end for
                #if len($colorMap) > 0:
                    --colorMap #echo " ".join($colorMap)#
                #end if

                --alpha '$advancedOpt.alpha'
                #if str($advancedOpt.colorList).strip() != "":
                    --colorList $advancedOpt.colorList
                #end if

                #if str($advancedOpt.zMin).strip() != "":
                    --zMin $advancedOpt.zMin
                #end if
                #if str($advancedOpt.zMax).strip() != "":
                    --zMax $advancedOpt.zMax
                #end if

                #if str($advancedOpt.yMin).strip() != "":
                    --yMin $advancedOpt.yMin
                #end if
                #if str($advancedOpt.yMax).strip() != "":
                    --yMax $advancedOpt.yMax
                #end if
                #if str($advancedOpt.sortUsingSamples).strip() != "":
                    --sortUsingSamples $advancedOpt.sortUsingSamples
                #end if
                #if str($advancedOpt.clusterUsingSamples).strip() != "":
                    --clusterUsingSamples $advancedOpt.clusterUsingSamples
                #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'

                #if $advancedOpt.samplesLabel and str($advancedOpt.samplesLabel).strip() != "":
                    --samplesLabel $advancedOpt.samplesLabel
                #end if

                #if $advancedOpt.regionsLabel and str($advancedOpt.regionsLabel).strip() != "":
                    --regionsLabel $advancedOpt.regionsLabel
                #end if

                #if $advancedOpt.plotTitle and str($advancedOpt.plotTitle.value) != "":
                    --plotTitle '$advancedOpt.plotTitle'
                #end if

                --legendLocation '$advancedOpt.legendLocation'

                --labelRotation '$advancedOpt.labelRotation'

                $advancedOpt.perGroup

                
        #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
            $advancedOpt.used_multiple_regions.silhouette
        #end if
    

            #end if

    
None
False
Functional tests
name inputs outputs required files
Test-1 matrixFile: computeMatrix_result1.gz
name: value
computeMatrix_result1.gz
value
Test-2 matrixFile: computeMatrix_result1.gz
advancedOpt|whatToShow: heatmap and colorbar
advancedOpt|showAdvancedOpt: yes
name: value
computeMatrix_result1.gz
value