chicViewpointBackgroundModel tool metadata

Miscellaneous

Name: chicViewpointBackgroundModel

Description: compute a background model for cHi-C / HiChIP data

Id: hicexplorer_chicviewpointbackgroundmodel

Guid: toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_chicviewpointbackgroundmodel/hicexplorer_chicviewpointbackgroundmodel/3.7.6+galaxy1

Version: 3.7.6+galaxy1

Version command string: chicViewpointBackgroundModel --version

Display in tool panel: True

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

toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_chicviewpointbackgroundmodel/hicexplorer_chicviewpointbackgroundmodel/3.7.6+galaxy1 (this tool)

toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_chicviewpointbackgroundmodel/hicexplorer_chicviewpointbackgroundmodel/3.7.5+galaxy1

toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_chicviewpointbackgroundmodel/hicexplorer_chicviewpointbackgroundmodel/3.7.5+galaxy0

toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_chicviewpointbackgroundmodel/hicexplorer_chicviewpointbackgroundmodel/3.7.2+galaxy0

toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_chicviewpointbackgroundmodel/hicexplorer_chicviewpointbackgroundmodel/3.6+galaxy1

toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_chicviewpointbackgroundmodel/hicexplorer_chicviewpointbackgroundmodel/3.6+galaxy0

toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_chicviewpointbackgroundmodel/hicexplorer_chicviewpointbackgroundmodel/3.4.3.0

toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_chicviewpointbackgroundmodel/hicexplorer_chicviewpointbackgroundmodel/3.4.2.0

toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_chicviewpointbackgroundmodel/hicexplorer_chicviewpointbackgroundmodel/3.4.1.0

toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_chicviewpointbackgroundmodel/hicexplorer_chicviewpointbackgroundmodel/3.3.1.0

hicexplorer_chicviewpointbackgroundmodel

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

Requirements:

name

version

type

hicexplorer

3.7.6

package

Additional information about this tool

Command:

#for $counter, $m in enumerate($matrix_h5_cooler_multiple):
            ln -s '$m' '${counter}_matrix.$m.ext' &&
        #end for
        #set $m = ' '.join([ '\'%s_matrix.%s\'' % ($counter, $matrix.ext) for $counter, $matrix in enumerate($matrix_h5_cooler_multiple) ])

        chicViewpointBackgroundModel
            --matrices $m
            --averageContactBin $averageContactBin
            --fixateRange $fixateRange
            --referencePoints '$referencePoints'
            $truncateZeros
            --threads \${GALAXY_SLOTS:-4}
            --outFileName background.txt

Interpreter: None

Forces a history refresh: False

Functional tests

name

inputs

outputs

required files

Test-1

matrix_h5_cooler_multiple: ['cHi-C/FL-E13-5_chr1.cool', 'cHi-C/MB-E10-5_chr1.cool']
referencePoints: cHi-C/referencePoints.bed

name: value

cHi-C/FL-E13-5_chr1.cool
cHi-C/MB-E10-5_chr1.cool
cHi-C/referencePoints.bed
value

Test-2

matrix_h5_cooler_multiple: ['cHi-C/FL-E13-5_chr1.cool', 'cHi-C/MB-E10-5_chr1.cool']
referencePoints: cHi-C/referencePoints.bed
truncateZeros: True

name: value

cHi-C/FL-E13-5_chr1.cool
cHi-C/MB-E10-5_chr1.cool
cHi-C/referencePoints.bed
value