Galaxy |

chicExportData tool metadata

Miscellaneous

Name: chicExportData

Description: exports data of hdf to txt based files

Id: hicexplorer_chicexportdata

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

Version: 3.7.2+galaxy0

Version command string: chicExportData --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_chicexportdata/hicexplorer_chicexportdata/3.7.2+galaxy0 (this tool)

hicexplorer_chicexportdata

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

Requirements:

name

version

type

hicexplorer

3.7.2

package

Additional information about this tool

Command:

#import re
        mkdir exportFolder && 
        chicExportData
            --file '$file'

            #if $fileType_conditional.fileType_selector == 'interaction':
                #if $fileType_conditional.txtBigwig_conditional.txtBigwig_selector == 'txt':
                    --outputFileType txt
                #else:
                    --outputFileType bigwig 
                    --outputValueBigwig $fileType_conditional.txtBigwig_conditional.column_selector
                    --chromosomeSizes '$fileType_conditional.txtBigwig_conditional.chromosomeSize'
                    --range $fileType_conditional.txtBigwig_conditional.rangeUpstream $fileType_conditional.txtBigwig_conditional.rangeDownstream
                    --backgroundModelFile '$fileType_conditional.txtBigwig_conditional.backgroundModelFile'
                #end if
            #else if $fileType_conditional.fileType_selector == 'target':
                $fileType_conditional.oneTargetFile
            #end if
            #if $fileType_conditional.fileType_selector != 'interaction':
                --outputFileType txt
            #end if

            --outputMode $outputMode_conditional.outputMode_selector
            #if $outputMode_conditional.outputMode_selector == 'geneName':
                --outputModeName $outputMode_conditional.outputModeName
            #end if
            --decimalPlaces $decimalPlaces
            
            --outFileName exportFolder/export.tar.gz
            --threads \${GALAXY_SLOTS:-4}

Interpreter: None

Forces a history refresh: False

Functional tests

name

inputs

outputs

required files

Test-1

file: cHi-C/chicAggregateStatistic/aggregate.hdf5
fileType_conditional|fileType_selector: aggregate
outputMode_conditional|outputMode_selector: all

name: value

cHi-C/chicAggregateStatistic/aggregate.hdf5
value

Test-2

file: cHi-C/chicViewpoint/two_matrices.hdf5
fileType_conditional|txtBigwig_conditional|backgroundModelFile: cHi-C/background.txt
fileType_conditional|txtBigwig_conditional|chromosomeSize: cHi-C/hg19.chrom.sizes
fileType_conditional|txtBigwig_conditional|txtBigwig_selector: bigwig
fileType_conditional|fileType_selector: interaction
outputMode_conditional|outputModeName: Eya1
outputMode_conditional|outputMode_selector: geneName

cHi-C/chicViewpoint/two_matrices.hdf5
cHi-C/background.txt
cHi-C/hg19.chrom.sizes

Test-3

file: cHi-C/chicViewpoint/two_matrices.hdf5
fileType_conditional|txtBigwig_conditional|txtBigwig_selector: txt
fileType_conditional|fileType_selector: interaction
outputMode_conditional|outputModeName: Eya1
outputMode_conditional|outputMode_selector: geneName

cHi-C/chicViewpoint/two_matrices.hdf5