| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_chicqualitycontrol/hicexplorer_chicqualitycontrol/3.6+galaxy1 (this tool) |
| toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_chicqualitycontrol/hicexplorer_chicqualitycontrol/3.6+galaxy0 |
| toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_chicqualitycontrol/hicexplorer_chicqualitycontrol/3.4.3.0 |
| toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_chicqualitycontrol/hicexplorer_chicqualitycontrol/3.4.2.0 |
| toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_chicqualitycontrol/hicexplorer_chicqualitycontrol/3.4.1.0 |
| toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_chicqualitycontrol/hicexplorer_chicqualitycontrol/3.3.1.0 |
| hicexplorer_chicqualitycontrol |
| 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) ])
chicQualityControl
--matrices $m
--referencePoints '$referencePoints'
--sparsity $sparsity
--fixateRange $fixateRange
--dpi $dpi
--threads \${GALAXY_SLOTS:-4}
--outFileName reference_points
--outFileNameHistogram histogram.$image_file_format
--outFileNameSparsity sparsity.$image_file_format
&& mv histogram.$image_file_format histogram
&& mv sparsity.$image_file_format sparsity
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
matrix_h5_cooler_multiple: ['cHi-C/FL-E13-5_chr1.cool', 'cHi-C/MB-E10-5_chr1.cool'] referencePoints: cHi-C/referencePoints.bed sparsity: 0.05 |
name: value name: value name: value name: value name: value name: value name: value |
cHi-C/FL-E13-5_chr1.cool cHi-C/MB-E10-5_chr1.cool cHi-C/referencePoints.bed value |