chicViewpoint tool metadata

Miscellaneous

Name: chicViewpoint

Description: computes viewpoints with the given reference points and a background model.

Id: hicexplorer_chicviewpoint

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

Version: 3.7.6+galaxy1

Version command string: chicViewpoint --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_chicviewpoint/hicexplorer_chicviewpoint/3.7.6+galaxy1 (this tool)

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

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

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

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

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

toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_chicviewpoint/hicexplorer_chicviewpoint/3.4.3.1

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

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

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

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

hicexplorer_chicviewpoint

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

Requirements:

name

version

type

hicexplorer

3.7.6

package

Additional information about this tool

Command:

#import re

        #for $m in $matrix_h5_cooler_multiple:
            #set identifier = re.sub('[^\s\w\-\.]', '_', str($m.element_identifier))
            ln -s '$m' '$identifier' &&
        #end for
        #set $m = ' '.join([ '\'%s\'' % re.sub('[^\s\w\-\.]', '_', str($matrix.element_identifier)) for $matrix in $matrix_h5_cooler_multiple ])

        chicViewpoint
            --matrices $m
            --range $rangeUpstream $rangeDownstream
            --referencePoints '$referencePoints'
            --averageContactBin $averageContactBin
            --fixateRange $fixateRange
            --threads \${GALAXY_SLOTS:-4}
            --backgroundModelFile '$backgroundModelFile'
            --outFileName interactionFiles.hdf5

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_chicViewpoint.bed
rangeUpstream: 200000
rangeDownstream: 200000
backgroundModelFile: cHi-C/background.txt
fixateRange: 500000

name: value

cHi-C/FL-E13-5_chr1.cool
cHi-C/MB-E10-5_chr1.cool
cHi-C/referencePoints_chicViewpoint.bed
cHi-C/background.txt
value