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chicQualityControl tool metadata

Miscellaneous

Name: chicQualityControl

Description: generates an estimate of the quality of each viewpoint

Id: hicexplorer_chicqualitycontrol

Guid: toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_chicqualitycontrol/hicexplorer_chicqualitycontrol/3.7.5+galaxy0

Version: 3.7.5+galaxy0

Version command string: chicQualityControl --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_chicqualitycontrol/hicexplorer_chicqualitycontrol/3.7.5+galaxy1

toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_chicqualitycontrol/hicexplorer_chicqualitycontrol/3.7.5+galaxy0 (this tool)

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

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

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

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

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

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

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

hicexplorer_chicqualitycontrol

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

Requirements:

name

version

type

hicexplorer

3.7.5

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) ])

        chicQualityControl
            --matrices $m
            --referencePoints '$referencePoints'
            --sparsity $sparsity
            --fixateRange $fixateRange
            --dpi $dpi
            --threads \${GALAXY_SLOTS:-4}
            --outFileName reference_points
            --outFileNameHistogram histogram.$image_file_format
            --outFileNameSparsity sparsity.$image_file_format

            && mv histogram.$image_file_format histogram
            && mv sparsity.$image_file_format sparsity

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
sparsity: 0.05

name: value
name: value
name: value
name: value
name: value
name: value
name: value

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