| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hicaverageregions/hicexplorer_hicaverageregions/3.7.2+galaxy0 (this tool) |
| toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hicaverageregions/hicexplorer_hicaverageregions/3.6+galaxy1 |
| toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hicaverageregions/hicexplorer_hicaverageregions/3.6+galaxy0 |
| toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hicaverageregions/hicexplorer_hicaverageregions/3.4.3.0 |
| toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hicaverageregions/hicexplorer_hicaverageregions/3.4.2.0 |
| toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hicaverageregions/hicexplorer_hicaverageregions/3.4.1.0 |
| toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hicaverageregions/hicexplorer_hicaverageregions/3.3.1.0 |
| hicexplorer_hicaverageregions |
| Requirements (dependencies defined in the <requirements> tag set) |
| name | version | type |
| hicexplorer | 3.7.2 | package |
| Additional information about this tool |
ln -s '$matrix_h5_cooler' 'matrix_name.$matrix_h5_cooler.ext' &&
hicAverageRegions --matrix 'matrix_name.$matrix_h5_cooler.ext'
--regions '$regions'
#if $rangeFormat_conditional.rangeFormat_selector == 'optionGenomicUnits':
--range '$rangeFormat_conditional.upstreamRange' '$rangeFormat_conditional.downstreamRange'
#else:
--rangeInBins '$rangeFormat_conditional.upstreamRange' '$rangeFormat_conditional.downstreamRange'
#end if
--coordinatesToBinMapping $coordinatesToBinMapping_selector
$considerStrandDirection
--outFileName output_matrix.npz
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
matrix_h5_cooler: small_test_matrix.cool regions: hicAverageRegions/regions.bed rangeFormat_conditional|upstreamRange: 100000 rangeFormat_conditional|downstreamRange: 100000 rangeFormat_conditional|rangeFormat_selector: optionGenomicUnits |
name: value |
small_test_matrix.cool hicAverageRegions/regions.bed value |
| Test-2 |
matrix_h5_cooler: small_test_matrix.cool regions: hicAverageRegions/regions.bed rangeFormat_conditional|upstreamRange: 100 rangeFormat_conditional|downstreamRange: 100 rangeFormat_conditional|rangeFormat_selector: optionBinUnits |
name: value |
small_test_matrix.cool hicAverageRegions/regions.bed value |