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hicAdjustMatrix tool metadata

Miscellaneous

Name: hicAdjustMatrix

Description: adjust the shape of a Hi-C matrix

Id: hicexplorer_hicadjustmatrix

Guid: toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hicadjustmatrix/hicexplorer_hicadjustmatrix/3.7.2+galaxy0

Version: 3.7.2+galaxy0

Version command string: hicAdjustMatrix --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_hicadjustmatrix/hicexplorer_hicadjustmatrix/3.7.2+galaxy0 (this tool)

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

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

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

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

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

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

hicexplorer_hicadjustmatrix

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

Requirements:

name

version

type

hicexplorer

3.7.2

package

Additional information about this tool

Command:

#set matrix_name = 'matrix_in.' + str($matrix_h5_cooler.ext)
        #set matrix_file_out = 'matrix_out.' + str($matrix_h5_cooler.ext)

        ln -s '$matrix_h5_cooler' 'matrix_name.$matrix_h5_cooler.ext' &&
        hicAdjustMatrix --matrix 'matrix_name.$matrix_h5_cooler.ext'
        --action $action_selector
        --outFileName '$matrix_file_out'
        #if $chromosomeOrRegionFile_conditional.chromosomeOrRegionFile_selector == "optionChromosomes":
            ## special: --chromosomeOrder is optional, but if given it needs at least one argument
            #set chroms = '\' \''.join([ str($var.chromosome) for $var in $chromosomeOrRegionFile_conditional.chromosomeOrder ])
            #if chroms:
                --chromosomes '$chroms'
            #end if
        #end if

        #if $chromosomeOrRegionFile_conditional.chromosomeOrRegionFile_selector == "optionRegionFile":
            --regions '$chromosomeOrRegionFile_conditional.regions'
        #end if

        #if not $interIntra_selector == 'keep':
            --interIntraHandling $interIntra_selector
        #end if
        && mv '$matrix_file_out' matrix

Interpreter: None

Forces a history refresh: False

Functional tests

name

inputs

outputs

required files

Test-1

matrix_h5_cooler: small_test_matrix.h5
action_selector: keep
chromosomeOrRegionFile_conditional|chromosomeOrder_0|chromosome: chr3R
chromosomeOrRegionFile_conditional|chromosomeOrRegionFile_selector: optionChromosomes

name: value

small_test_matrix.h5
value

Test-2

matrix_h5_cooler: small_test_matrix.h5
action_selector: mask
chromosomeOrRegionFile_conditional|regions: regions.bed
chromosomeOrRegionFile_conditional|chromosomeOrRegionFile_selector: optionRegionFile

name: value

small_test_matrix.h5
regions.bed
value