Repository revision
29:2c66e43f1c86

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

plotCorrelation tool metadata
Miscellaneous
Create a heatmap or scatterplot of correlation scores between different samples
deeptools_plot_correlation
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_correlation/deeptools_plot_correlation/3.5.2+galaxy0
3.5.2+galaxy0
plotCorrelation --version
True
Version lineage of this tool (guids ordered most recent to oldest)
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_correlation/deeptools_plot_correlation/3.5.4+galaxy0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_correlation/deeptools_plot_correlation/3.5.2+galaxy0 (this tool)
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_correlation/deeptools_plot_correlation/3.5.1.0.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_correlation/deeptools_plot_correlation/3.3.2.0.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_correlation/deeptools_plot_correlation/3.3.0.0.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_correlation/deeptools_plot_correlation/3.2.1.0.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_correlation/deeptools_plot_correlation/3.2.0.0.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_correlation/deeptools_plot_correlation/3.1.2.0.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_correlation/deeptools_plot_correlation/3.1.0.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_correlation/deeptools_plot_correlation/3.0.2.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_correlation/deeptools_plot_correlation/3.0.1.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_correlation/deeptools_plot_correlation/3.0.0.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_correlation/deeptools_plot_correlation/2.5.7.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_correlation/deeptools_plot_correlation/2.5.1.1.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_correlation/deeptools_plot_correlation/2.5.1.0.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_correlation/deeptools_plot_correlation/2.5.0.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_correlation/deeptools_plot_correlation/2.4.2.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_correlation/deeptools_plot_correlation/2.4.1.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_correlation/deeptools_plot_correlation/2.3.6.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_correlation/deeptools_plot_correlation/2.3.5.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_correlation/deeptools_plot_correlation/2.2.3.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_correlation/deeptools_plot_correlation/2.2.2.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_correlation/deeptools_plot_correlation/2.1.0.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_correlation/deeptools_plot_correlation/2.0.1.0
deeptools_plot_correlation
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
plotCorrelation
            --corData '$corData'
            --plotFile '$outFileName'
            --corMethod '$corMethod'
            --whatToPlot '$plotting_type.whatToPlot'
            #if str($plotting_type.whatToPlot) == 'heatmap':
                
        #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'
    
                --plotWidth $plotting_type.plotWidth
                --plotHeight $plotting_type.plotHeight
            #else:
                --plotTitle '$plotting_type.plotTitle'
                #if str($plotting_type.xrange_conditional.xrange_select) == 'yes':
                    --xRange $plotting_type.xrange_conditional.xRange_min $plotting_type.xrange_conditional.xRange_max
                #end if
                #if str($plotting_type.yrange_conditional.yrange_select) == 'yes':
                    --yRange $plotting_type.yrange_conditional.yRange_min $plotting_type.yrange_conditional.yRange_max
                #end if
                $plotting_type.log1p
            #end if
            $skipZeros
            --plotFileFormat '$outFileFormat'
            $removeOutliers
            #if $outFileCorMatrix:
                --outFileCorMatrix '$matrix'
            #end if


    
None
False
Functional tests
name inputs outputs required files
Test-1 corData: multiBamSummary_result1.npz
outFileFormat: png
outFileCorMatrix: True
name: value
name: value
multiBamSummary_result1.npz
value
Test-2 corData: multiBamSummary_result1.npz
plotting_type|plotTitle: Test Plot
plotting_type|whatToPlot: scatterplot
outFileFormat: png
removeOutliers: True
name: value
multiBamSummary_result1.npz
value