Repository revision
29:10301d137111

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

plotProfile tool metadata
Miscellaneous
plotProfile
creates a profile plot for score distributions across genomic regions
deeptools_plot_profile
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_profile/deeptools_plot_profile/3.5.2+galaxy0
3.5.2+galaxy0
plotProfile --version
True
Version lineage of this tool (guids ordered most recent to oldest)
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_profile/deeptools_plot_profile/3.5.4+galaxy0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_profile/deeptools_plot_profile/3.5.2+galaxy0 (this tool)
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_profile/deeptools_plot_profile/3.5.1.0.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_profile/deeptools_plot_profile/3.3.2.0.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_profile/deeptools_plot_profile/3.3.0.0.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_profile/deeptools_plot_profile/3.2.1.0.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_profile/deeptools_plot_profile/3.2.0.0.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_profile/deeptools_plot_profile/3.1.2.0.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_profile/deeptools_plot_profile/3.1.0.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_profile/deeptools_plot_profile/3.0.2.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_profile/deeptools_plot_profile/3.0.1.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_profile/deeptools_plot_profile/3.0.0.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_profile/deeptools_plot_profile/2.5.7.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_profile/deeptools_plot_profile/2.5.1.1.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_profile/deeptools_plot_profile/2.5.1.0.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_profile/deeptools_plot_profile/2.5.0.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_profile/deeptools_plot_profile/2.4.2.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_profile/deeptools_plot_profile/2.4.1.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_profile/deeptools_plot_profile/2.3.6.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_profile/deeptools_plot_profile/2.3.5.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_profile/deeptools_plot_profile/2.2.3.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_profile/deeptools_plot_profile/2.2.2.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_profile/deeptools_plot_profile/2.1.0.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_profile/deeptools_plot_profile/2.0.1.0
deeptools_plot_profile
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
plotProfile
            --matrixFile "$matrixFile"
            --outFileName "$outFileName"

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

                #if $output.dpi:
                    --dpi '$output.dpi'
                #end if

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

            #if $scaleRegions.showScaleRegionsOpt == "yes":
                --startLabel '$scaleRegions.startLabel'
                --endLabel '$scaleRegions.endLabel'
            #end if

            #if $advancedOpt.showAdvancedOpt == "yes":
                #if $advancedOpt.averageType:
                    --averageType '$advancedOpt.averageType'
                #end if
                --plotHeight $advancedOpt.plotHeight
                --plotWidth $advancedOpt.plotWidth
                --plotType $advancedOpt.plotType
                #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).strip() != "":
                    --plotTitle '$advancedOpt.plotTitle'
                #end if

                #if str($advancedOpt.colors).strip() != "":
                    --colors #echo ' '.join( ["'%s'" % $color for $color in $advancedOpt.colors.split()] )#
                #end if

                --legendLocation '$advancedOpt.legendLocation'

                --labelRotation '$advancedOpt.labelRotation'

                $advancedOpt.perGroup

                #if str($advancedOpt.yMin):
                    --yMin $advancedOpt.yMin
                #end if
                #if str($advancedOpt.yMax):
                    --yMax $advancedOpt.yMax
                #end if

                #if $advancedOpt.outFileNameData:
                    --outFileNameData '$output_outFileNameData'
                #end if

                
        #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
scaleRegions|showScaleRegionsOpt: yes
advancedOpt|outFileNameData: True
advancedOpt|showAdvancedOpt: yes
name: value
name: value
computeMatrix_result1.gz
value