Repository revision
8:013e53ccc7ac

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

chicPlotViewpoint tool metadata
Miscellaneous
creates plots for viewpoints
hicexplorer_chicplotviewpoint
toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_chicplotviewpoint/hicexplorer_chicplotviewpoint/3.7.2+galaxy0
3.7.2+galaxy0
chicPlotViewpoint --version
True
Version lineage of this tool (guids ordered most recent to oldest)
toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_chicplotviewpoint/hicexplorer_chicplotviewpoint/3.7.2+galaxy0 (this tool)
toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_chicplotviewpoint/hicexplorer_chicplotviewpoint/3.6+galaxy1
toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_chicplotviewpoint/hicexplorer_chicplotviewpoint/3.6+galaxy0
toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_chicplotviewpoint/hicexplorer_chicplotviewpoint/3.4.3.1
toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_chicplotviewpoint/hicexplorer_chicplotviewpoint/3.4.3.0
toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_chicplotviewpoint/hicexplorer_chicplotviewpoint/3.4.2.0
toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_chicplotviewpoint/hicexplorer_chicplotviewpoint/3.4.1.0
toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_chicplotviewpoint/hicexplorer_chicplotviewpoint/3.3.1.0
hicexplorer_chicplotviewpoint
Requirements (dependencies defined in the <requirements> tag set)
name version type
hicexplorer 3.7.2 package
Additional information about this tool
#import re

        chicPlotViewpoint
          
            --interactionFile '$interactionFile'
            #if $differentialFile:
                --differentialTestResult '$differentialFile'
            #end if

            #if $significantInteractionFile:
                --significantInteractions '$significantInteractionFile'
                $plotSignificantInteractions
            #end if

            --range $rangeUpstream $rangeDownstream
            #if $backgroundModelFile:
                --backgroundModelFile '$backgroundModelFile'
            #end if
            
            --combinationMode $combinationMode_conditional.combinationMode_selector

            #if $combinationMode_conditional.combinationMode_selector == 'oneGene':
                --combinationName $combinationMode_conditional.geneName
            #end if

            #if $dpi:
                --dpi $dpi
            #end if

            #if $maxPValue:
                --maxPValue $maxPValue
            #end if

            #if $minPValue:
                --minPValue $minPValue
            #end if

            
            #if $colormap:
                --colorMapPvalue $colormap
            #end if

            $pvalue
            #if $xFold:
                --xFold $xFold
            #end if
            --colorList $colorList
            --threads \${GALAXY_SLOTS:-4}
            $truncateZeroPvalues
           
            -o plots.tar.gz
          
        
None
False
Functional tests
name inputs outputs required files
Test-1 interactionFile: cHi-C/chicViewpoint/two_matrices.hdf5
differentialFile: cHi-C/chicDifferentialTest/differential.hdf5
significantInteractionFile: cHi-C/chicSignificantInteractions/significantInteractions_dual.hdf5
backgroundModelFile: cHi-C/background.txt
combinationMode_conditional|combinationMode_selector: dual
pvalue: True
xFold: 1.5
truncateZeroPvalues: True
name: value
cHi-C/chicViewpoint/two_matrices.hdf5
cHi-C/chicDifferentialTest/differential.hdf5
cHi-C/chicSignificantInteractions/significantInteractions_dual.hdf5
cHi-C/background.txt
value