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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/3.7.2+galaxy0

Version: 3.7.2+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/3.7.2+galaxy0 (this tool)

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

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

3.7.2

package

Additional information about this tool

Command:

ln -s '$matrix_h5_cooler' 'matrix.$matrix_h5_cooler.ext' &&

        #if $precomputedZscore_conditional.precomputedZscore_selector == 'precomputed':
            ln -s '$precomputedZscore_conditional.scoreFile' 'prefix_tad_score.bm' &&
            ln -s '$precomputedZscore_conditional.zscoreMatrix' 'prefix_zscore_matrix.h5' &&
        #end if
        hicFindTADs
            --matrix 'matrix.$matrix_h5_cooler.ext'
            --delta $delta
            #if $minBoundaryDistance:
            --minBoundaryDistance $minBoundaryDistance
            #end if

            #if $precomputedZscore_conditional.precomputedZscore_selector == 'scratch':
                --minDepth $precomputedZscore_conditional.minDepth
                --maxDepth $precomputedZscore_conditional.maxDepth
                --step $precomputedZscore_conditional.step
            #elif $precomputedZscore_conditional.precomputedZscore_selector == 'precomputed':
                --TAD_sep_score_prefix prefix
            #end if
            #if $multiple_comparison_conditional.multiple_comparison_selector == 'fdr':
                --correctForMultipleTesting fdr
                --threshold $multiple_comparison_conditional.threshold
            #elif $multiple_comparison_conditional.multiple_comparison_selector == 'bonferroni':
                --correctForMultipleTesting bonferroni
                --threshold $multiple_comparison_conditional.threshold
            #else:
                --multipleComparisons None
            #end if

            --numberOfProcessors \${GALAXY_SLOTS:-4}
            --outPrefix galaxy_tad_prefix
            #if $chromosomes:
                --chromosomes #echo "' '".join([ "'%s'" % $chrom.chromosome for $chrom in $chromosomes ])#
            #end if
        #if $precomputedZscore_conditional.precomputedZscore_selector == 'scratch':
            #if $matrix_h5_cooler.ext == 'cool':
                && mv galaxy_tad_prefix*.cool matrix
            #elif $matrix_h5_cooler.ext == 'h5':
                && mv galaxy_tad_prefix*.h5 matrix
            #end if
        #end if

Interpreter: None

Forces a history refresh: False

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