Repository revision
7:6ef732512682

Repository 'hicexplorer_chicsignificantinteractions'
hg clone https://toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_chicsignificantinteractions

chicSignificantInteractions tool metadata
Miscellaneous
computes viewpoints with the given reference points and a background model
hicexplorer_chicsignificantinteractions
toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_chicsignificantinteractions/hicexplorer_chicsignificantinteractions/3.6+galaxy1
3.6+galaxy1
chicSignificantInteractions --version
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)
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 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
tar: True
name: value
name: value
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-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