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chicSignificantInteractions tool metadata

Miscellaneous

Name: chicSignificantInteractions

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

Id: hicexplorer_chicsignificantinteractions

Guid: toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_chicsignificantinteractions/hicexplorer_chicsignificantinteractions/3.6+galaxy1

Version: 3.6+galaxy1

Version command string: chicSignificantInteractions --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_chicsignificantinteractions/hicexplorer_chicsignificantinteractions/3.7.2+galaxy0

toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_chicsignificantinteractions/hicexplorer_chicsignificantinteractions/3.6+galaxy1 (this tool)

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

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

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

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

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

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

hicexplorer_chicsignificantinteractions

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

Requirements:

name

version

type

hicexplorer

3.6

package

Functional tests

name

inputs

outputs

required files

Test-1

tar_input_conditional|interactionFiles: ['cHi-C/chicViewpoint/output_3/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.txt', 'cHi-C/chicViewpoint/output_3/FL-E13-5_chr1_chr1_4487435_4487435_Sox17.txt', 'cHi-C/chicViewpoint/output_3/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d.txt', 'cHi-C/chicViewpoint/output_3/MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d.txt', 'cHi-C/chicViewpoint/output_3/MB-E10-5_chr1_chr1_14300280_14300280_Eya1.txt', 'cHi-C/chicViewpoint/output_3/MB-E10-5_chr1_chr1_4487435_4487435_Sox17.txt']
tar_input_conditional|tar_input_selector: interval_input
batchmode_conditional|interactionFilesOrderFile: cHi-C/chicViewpoint/fileNames_two_matrices.txt
batchmode_conditional|computeSampleNumber: 2
batchmode_conditional|batchmode_selector: optionBatchmode
pvalue: 0.2
filter_conditional|loosePvalue: 0.5
filter_conditional|filter_selector: optionLoosePvalue
backgroundModelFile: cHi-C/background.txt
rangeUpstream: 200000
rangeDownstream: 200000

name: value
name: value

cHi-C/chicViewpoint/output_3/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.txt
cHi-C/chicViewpoint/output_3/FL-E13-5_chr1_chr1_4487435_4487435_Sox17.txt
cHi-C/chicViewpoint/output_3/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d.txt
cHi-C/chicViewpoint/output_3/MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d.txt
cHi-C/chicViewpoint/output_3/MB-E10-5_chr1_chr1_14300280_14300280_Eya1.txt
cHi-C/chicViewpoint/output_3/MB-E10-5_chr1_chr1_4487435_4487435_Sox17.txt
cHi-C/chicViewpoint/fileNames_two_matrices.txt
cHi-C/background.txt
value

Test-2

tar_input_conditional|interactionFiles: ['cHi-C/chicViewpoint/output_1/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.txt', 'cHi-C/chicViewpoint/output_1/MB-E10-5_chr1_chr1_14300280_14300280_Eya1.txt']
tar_input_conditional|tar_input_selector: interval_input
batchmode_conditional|computeSampleNumber: 1
batchmode_conditional|batchmode_selector: optionSinglemode
pvalue: 0.2
filter_conditional|xfold: 1.5
filter_conditional|filter_selector: optionXfold
backgroundModelFile: cHi-C/background.txt
rangeUpstream: 200000
rangeDownstream: 200000

cHi-C/chicViewpoint/output_1/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.txt
cHi-C/chicViewpoint/output_1/MB-E10-5_chr1_chr1_14300280_14300280_Eya1.txt
cHi-C/background.txt

Test-3

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

Test-4

tar_input_conditional|interactionFiles: cHi-C/chicViewpoint/viewpoints.tar
tar_input_conditional|tar_input_selector: tar_input
batchmode_conditional|interactionFilesOrderFile: cHi-C/chicViewpoint/fileNames_two_matrices.txt
batchmode_conditional|computeSampleNumber: 2
batchmode_conditional|batchmode_selector: optionBatchmode
pvalue: 0.2
filter_conditional|loosePvalue: 0.5
filter_conditional|filter_selector: optionLoosePvalue
backgroundModelFile: cHi-C/background.txt
rangeUpstream: 200000
rangeDownstream: 200000
tar: True

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

cHi-C/chicViewpoint/viewpoints.tar
cHi-C/chicViewpoint/fileNames_two_matrices.txt
cHi-C/background.txt
value