plotPCA tool metadata

Miscellaneous

Name: plotPCA

Description: Generate principal component analysis (PCA) plots from multiBamSummary or multiBigwigSummary output

Id: deeptools_plot_pca

Guid: toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_pca/deeptools_plot_pca/3.5.4+galaxy0

Version: 3.5.4+galaxy0

Version command string: plotPCA --version

Display in tool panel: True

Version lineage of this tool (guids ordered most recent to oldest)

toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_pca/deeptools_plot_pca/3.5.4+galaxy0 (this tool)

toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_pca/deeptools_plot_pca/3.5.2+galaxy0

toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_pca/deeptools_plot_pca/3.5.1.0.0

toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_pca/deeptools_plot_pca/3.3.2.0.0

toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_pca/deeptools_plot_pca/3.3.0.0.0

toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_pca/deeptools_plot_pca/3.2.1.0.0

toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_pca/deeptools_plot_pca/3.2.0.0.0

toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_pca/deeptools_plot_pca/3.1.2.0.0

toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_pca/deeptools_plot_pca/3.1.0.0

toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_pca/deeptools_plot_pca/3.0.2.0

toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_pca/deeptools_plot_pca/3.0.1.0

toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_pca/deeptools_plot_pca/3.0.0.0

toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_pca/deeptools_plot_pca/2.5.7.0

toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_pca/deeptools_plot_pca/2.5.1.1.0

toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_pca/deeptools_plot_pca/2.5.1.0.0

toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_pca/deeptools_plot_pca/2.5.0.0

toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_pca/deeptools_plot_pca/2.4.2.0

toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_pca/deeptools_plot_pca/2.4.1.0

toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_pca/deeptools_plot_pca/2.3.6.0

toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_pca/deeptools_plot_pca/2.3.5.0

toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_pca/deeptools_plot_pca/2.2.3.0

toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_pca/deeptools_plot_pca/2.2.2.0

toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_pca/deeptools_plot_pca/2.1.0.0

toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_pca/deeptools_plot_pca/2.0.1.0

deeptools_plot_pca

Requirements (dependencies defined in the <requirements> tag set)

Requirements:

name

version

type

deeptools

3.5.4

package

samtools

1.9

package

Additional information about this tool

Command:

plotPCA
            --corData '$corData'
            --plotTitle '$plotTitle'
            --plotFile '$outFileName'
            --plotFileFormat '$outFileFormat'
            #if str($advancedOpt.showAdvancedOpt) == 'yes':
                
        --plotWidth '$advancedOpt.plotWidth'
        --plotHeight '$advancedOpt.plotHeight'
    
                $advancedOpt.log2
                --PCs $advancedOpt.PCs
                --ntop $advancedOpt.ntop
                $advancedOpt.transpose
                $advancedOpt.rowCenter
                #if $advancedOpt.colors:
                    --colors $advancedOpt.colors
                #end if
                #if $advancedOpt.markers:
                    --markers $advancedOpt.markers
                #end if
            #end if
            #if $outFileNameData
                --outFileNameData '$output_outFileNameData'
            #end if

Interpreter: None

Forces a history refresh: False

Functional tests

name

inputs

outputs

required files

Test-1

corData: multiBamSummary_result2b.npz
outFileFormat: png
plotTitle: Test Plot
advancedOpt|showAdvancedOpt: yes

name: value

multiBamSummary_result2b.npz
value

Test-2

corData: multiBamSummary_result2b.npz
outFileFormat: png
plotTitle: Test Plot
outFileNameData: True

name: value
name: value

multiBamSummary_result2b.npz
value