Repository revision
29:00d869ea03a1

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

plotPCA tool metadata
Miscellaneous
plotPCA
Generate principal component analysis (PCA) plots from multiBamSummary or multiBigwigSummary output
deeptools_plot_pca
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_pca/deeptools_plot_pca/3.5.2+galaxy0
3.5.2+galaxy0
plotPCA --version
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
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_pca/deeptools_plot_pca/3.5.2+galaxy0 (this tool)
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)
name version type
deeptools 3.5.2 package
samtools 1.9 package
Additional information about this tool
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

    
None
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