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chicPlotViewpoint tool metadata

Miscellaneous

Name: chicPlotViewpoint

Description: creates plots for viewpoints

Id: hicexplorer_chicplotviewpoint

Guid: toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_chicplotviewpoint/hicexplorer_chicplotviewpoint/3.6+galaxy0

Version: 3.6+galaxy0

Version command string: chicPlotViewpoint --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_chicplotviewpoint/hicexplorer_chicplotviewpoint/3.6+galaxy1

toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_chicplotviewpoint/hicexplorer_chicplotviewpoint/3.6+galaxy0 (this tool)

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

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

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

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

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

hicexplorer_chicplotviewpoint

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_1/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.txt', 'cHi-C/chicViewpoint/output_1/FL-E13-5_chr1_chr1_4487435_4487435_Sox17.txt', 'cHi-C/chicViewpoint/output_1/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d.txt', 'cHi-C/chicViewpoint/output_1/MB-E10-5_chr1_chr1_4487435_4487435_Sox17.txt', 'cHi-C/chicViewpoint/output_1/MB-E10-5_chr1_chr1_14300280_14300280_Eya1.txt', 'cHi-C/chicViewpoint/output_1/MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d.txt']
tar_input_conditional|differentialFiles: ['cHi-C/chicDifferentialTest/batch_mode_fisher_outfile/FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_H0_rejected.txt', 'cHi-C/chicDifferentialTest/batch_mode_fisher_outfile/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_H0_rejected.txt', 'cHi-C/chicDifferentialTest/batch_mode_fisher_outfile/FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_H0_rejected.txt']
tar_input_conditional|significantFiles: ['cHi-C/chicSignificantInteractions/output_5/FL-E13-5_chr1_chr1_4487435_4487435_Sox17_significant_interactions.txt', 'cHi-C/chicSignificantInteractions/output_5/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_significant_interactions.txt', 'cHi-C/chicSignificantInteractions/output_5/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d_significant_interactions.txt', 'cHi-C/chicSignificantInteractions/output_5/MB-E10-5_chr1_chr1_4487435_4487435_Sox17_significant_interactions.txt', 'cHi-C/chicSignificantInteractions/output_5/MB-E10-5_chr1_chr1_14300280_14300280_Eya1_significant_interactions.txt', 'cHi-C/chicSignificantInteractions/output_5/MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_significant_interactions.txt']
tar_input_conditional|tar_input_selector: interval_input
backgroundModelFile: cHi-C/background.txt
batchmode_conditional|interactionFilesOrderFile: cHi-C/chicViewpoint/fileNames_two_matrices.txt
batchmode_conditional|differentialFilesOrderFile: cHi-C/chicDifferentialTest/rejectedFilesList.txt
batchmode_conditional|significantInteractionFilesOrderFile: cHi-C/chicSignificantInteractions/output_5_significant_files.txt
batchmode_conditional|computeSampleNumber: 2
batchmode_conditional|batchmode_selector: optionBatchmode
pvalue: True
xFold: 1.5
truncateZeroPvalues: True

cHi-C/chicViewpoint/output_1/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.txt
cHi-C/chicViewpoint/output_1/FL-E13-5_chr1_chr1_4487435_4487435_Sox17.txt
cHi-C/chicViewpoint/output_1/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d.txt
cHi-C/chicViewpoint/output_1/MB-E10-5_chr1_chr1_4487435_4487435_Sox17.txt
cHi-C/chicViewpoint/output_1/MB-E10-5_chr1_chr1_14300280_14300280_Eya1.txt
cHi-C/chicViewpoint/output_1/MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d.txt
cHi-C/chicDifferentialTest/batch_mode_fisher_outfile/FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_H0_rejected.txt
cHi-C/chicDifferentialTest/batch_mode_fisher_outfile/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_H0_rejected.txt
cHi-C/chicDifferentialTest/batch_mode_fisher_outfile/FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_H0_rejected.txt
cHi-C/chicSignificantInteractions/output_5/FL-E13-5_chr1_chr1_4487435_4487435_Sox17_significant_interactions.txt
cHi-C/chicSignificantInteractions/output_5/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_significant_interactions.txt
cHi-C/chicSignificantInteractions/output_5/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d_significant_interactions.txt
cHi-C/chicSignificantInteractions/output_5/MB-E10-5_chr1_chr1_4487435_4487435_Sox17_significant_interactions.txt
cHi-C/chicSignificantInteractions/output_5/MB-E10-5_chr1_chr1_14300280_14300280_Eya1_significant_interactions.txt
cHi-C/chicSignificantInteractions/output_5/MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_significant_interactions.txt
cHi-C/background.txt
cHi-C/chicViewpoint/fileNames_two_matrices.txt
cHi-C/chicDifferentialTest/rejectedFilesList.txt
cHi-C/chicSignificantInteractions/output_5_significant_files.txt

Test-2

tar_input_conditional|interactionFiles: cHi-C/chicViewpoint/output_1/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.txt
tar_input_conditional|tar_input_selector: interval_input
batchmode_conditional|batchmode_selector: optionSinglemode

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

Test-3

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

Test-4

name: value

Test-5

tar_input_conditional|interactionFiles: cHi-C/chicViewpoint/output_1.tar
tar_input_conditional|differentialFiles: cHi-C/chicDifferentialTest/batch_mode_fisher_outfile.tar
tar_input_conditional|significantFiles: cHi-C/chicSignificantInteractions/significantFilesFolder.tar
tar_input_conditional|tar_input_selector: tar_input
backgroundModelFile: cHi-C/background.txt
batchmode_conditional|interactionFilesOrderFile: cHi-C/chicViewpoint/fileNames_two_matrices.txt
batchmode_conditional|differentialFilesOrderFile: cHi-C/chicDifferentialTest/rejectedFilesList.txt
batchmode_conditional|significantInteractionFilesOrderFile: cHi-C/chicSignificantInteractions/output_5_significant_files.txt
batchmode_conditional|computeSampleNumber: 2
batchmode_conditional|batchmode_selector: optionBatchmode
pvalue: True
xFold: 1.5
truncateZeroPvalues: True
tar: True

name: value

cHi-C/chicViewpoint/output_1.tar
cHi-C/chicDifferentialTest/batch_mode_fisher_outfile.tar
cHi-C/chicSignificantInteractions/significantFilesFolder.tar
cHi-C/background.txt
cHi-C/chicViewpoint/fileNames_two_matrices.txt
cHi-C/chicDifferentialTest/rejectedFilesList.txt
cHi-C/chicSignificantInteractions/output_5_significant_files.txt
value