| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hiccompartmentspolarization/hicexplorer_hiccompartmentspolarization/3.6+galaxy1 (this tool) |
| toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hiccompartmentspolarization/hicexplorer_hiccompartmentspolarization/3.6+galaxy0 |
| toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hiccompartmentspolarization/hicexplorer_hiccompartmentspolarization/3.4.3.0 |
| toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hiccompartmentspolarization/hicexplorer_hiccompartmentspolarization/3.4.2.0 |
| toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hiccompartmentspolarization/hicexplorer_hiccompartmentspolarization/3.4.1.0 |
| toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hiccompartmentspolarization/hicexplorer_hiccompartmentspolarization/3.3.1.0 |
| hicexplorer_hiccompartmentspolarization |
| Requirements (dependencies defined in the <requirements> tag set) |
| name | version | type |
| hicexplorer | 3.6 | package |
| Additional information about this tool |
#for $counter, $m in enumerate($matrix_h5_cooler_multiple):
ln -s '$m' '${counter}_matrix.$m.ext' &&
#end for
#set $m = ' '.join([ '\'%s_matrix.%s\'' % ($counter, $matrix.ext) for $counter, $matrix in enumerate($matrix_h5_cooler_multiple) ])
hicCompartmentalization
--obsexp_matrices $m
--pca '$pca'
--quantile $quantile
#if $set_offset_value:
#set $offset_array = $set_offset_value.split(' ')
#set $offset = ' '.join([ '%s' % int($value) for $value in $offset_array ])
--offset $offset
#end if
--outliers $outliers
--outputFileName plot.$image_file_format
&& mv plot.$image_file_format plot
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
matrix_h5_cooler_multiple: hicTransform/obs_exp_norm.h5 pca: hicCompartmentsPolarization/pca1.bedgraph |
name: value |
hicTransform/obs_exp_norm.h5 hicCompartmentsPolarization/pca1.bedgraph value |
| Test-2 |
matrix_h5_cooler_multiple: hicTransform/obs_exp_norm.h5 pca: hicCompartmentsPolarization/pca1.bedgraph quantile: 30 |
name: value |
hicTransform/obs_exp_norm.h5 hicCompartmentsPolarization/pca1.bedgraph value |
| Test-3 |
matrix_h5_cooler_multiple: hicTransform/obs_exp_norm.h5 pca: hicCompartmentsPolarization/pca1.bedgraph outliers: 1.0 |
name: value |
hicTransform/obs_exp_norm.h5 hicCompartmentsPolarization/pca1.bedgraph value |