Galaxy |

hicFindTADs tool metadata

Miscellaneous

Name: hicFindTADs

Description: identify TAD boundaries by computing the degree of separation of each Hi-C matrix bin

Id: hicexplorer_hicfindtads

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

Version: 3.6+galaxy0

Version command string: hicFindTADs --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_hicfindtads/hicexplorer_hicfindtads/3.6+galaxy1

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

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

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

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

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

toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hicfindtads/hicexplorer_hicfindtads/2.1.4.0

toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hicfindtads/hicexplorer_hicfindtads/2.1.2.0

toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hicfindtads/hicexplorer_hicfindtads/2.1.0

toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hicfindtads/hicexplorer_hicfindtads/2.0.0

toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hicfindtads/hicexplorer_hicfindtads/1.8.1.0

toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hicfindtads/hicexplorer_hicfindtads/1.8.0

toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hicfindtads/hicexplorer_hicfindtads/1.7.2.0

toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hicfindtads/hicexplorer_hicfindtads/1.7.1.0

hicexplorer_hicfindtads

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

matrix_h5_cooler: small_test_matrix.h5
precomputedZscore_conditional|minDepth: 15000
precomputedZscore_conditional|maxDepth: 30000
precomputedZscore_conditional|step: 15000
precomputedZscore_conditional|precomputedZscore_selector: scratch
multiple_comparison_conditional|threshold: 0.8
multiple_comparison_conditional|multiple_comparison_selector: fdr
minBoundaryDistance: 5000

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

small_test_matrix.h5
value

Test-2

matrix_h5_cooler: small_test_matrix.h5
precomputedZscore_conditional|scoreFile: find_TADs/multiFDR_tad_score.bm
precomputedZscore_conditional|zscoreMatrix: find_TADs/multiFDR_zscore_matrix.h5
precomputedZscore_conditional|precomputedZscore_selector: precomputed
multiple_comparison_conditional|threshold: 0.1
multiple_comparison_conditional|multiple_comparison_selector: fdr
minBoundaryDistance: 5000

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

small_test_matrix.h5
find_TADs/multiFDR_tad_score.bm
find_TADs/multiFDR_zscore_matrix.h5
value