hicPlotMatrix tool metadata

Miscellaneous

Name: hicPlotMatrix

Description: plot a Hi-C contact matrix heatmap

Id: hicexplorer_hicplotmatrix

Guid: toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hicplotmatrix/hicexplorer_hicplotmatrix/3.4.3.0

Version: 3.4.3.0

Version command string: hicPlotMatrix --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_hicplotmatrix/hicexplorer_hicplotmatrix/3.6+galaxy0

toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hicplotmatrix/hicexplorer_hicplotmatrix/3.4.3.0 (this tool)

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

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

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

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

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

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

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

toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hicplotmatrix/hicexplorer_hicplotmatrix/1.8.1.1

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

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

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

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

hicexplorer_hicplotmatrix

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

Requirements:

name

version

type

hicexplorer

3.4.3

package

Functional tests

name

inputs

outputs

required files

Test-1

matrix_h5_cooler: small_test_matrix.h5
clearMaskedBins: True
region: chr2L:3000000-3500000
region2: chr2L:3100000-3600000
log1p: True
pca_conditional|pca_type:
image_file_format: png
dpi: 10

name: value

small_test_matrix.h5
value

Test-2

matrix_h5_cooler: small_test_matrix.cool
region: chr2L:3000000-3500000
pca_conditional|pca_type:
image_file_format: pdf
dpi: 10

name: value

small_test_matrix.cool
value

Test-3

matrix_h5_cooler: small_test_matrix.cool
region: chr2L:3000000-3500000
colormap: hot
pca_conditional|pca_bigwig: hicPCA/pca1_test1.bw
pca_conditional|vMinBigwig: 10
pca_conditional|vMaxBigwig: 20
pca_conditional|flipBigwigSign: True
pca_conditional|scaleFactorBigwig: 2000
pca_conditional|pca_type: bigwig
image_file_format: svg
dpi: 10

name: value