| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/iuc/scater_filter/scater_filter/1.22.0 (this tool) |
| toolshed.g2.bx.psu.edu/repos/iuc/scater_filter/scater_filter/1.20.0 |
| toolshed.g2.bx.psu.edu/repos/iuc/scater_filter/scater_filter/1.12.2 |
| toolshed.g2.bx.psu.edu/repos/iuc/scater_filter/scater_filter/1.10.1 |
| scater_filter |
| Requirements (dependencies defined in the <requirements> tag set) |
| name | version | type |
| bioconductor-scater | 1.22.0 | package |
| r-optparse | 1.7.1 | package |
| r-workflowscriptscommon | 0.0.7 | package |
| bioconductor-loomexperiment | 1.12.0 | package |
| r-robustbase | 0.93_9 | package |
| Additional information about this tool |
#if $filter_type.filter_type_selector == 'manual':
Rscript '$__tool_directory__/scater-manual-filter.R'
-i '$input_loom'
#if str($filter_type.library_size):
--library-size ${filter_type.library_size}
#end if
#if str($filter_type.percent_counts_MT):
--percent-counts-MT ${filter_type.percent_counts_MT}
#end if
#if str($filter_type.expressed_features):
--expressed-features ${filter_type.expressed_features}
#end if
#if str($filter_type.detection_limit):
--detection-limit ${filter_type.detection_limit}
#end if
#if str($filter_type.min_cells_expressed):
--min-cells-expressed ${filter_type.min_cells_expressed}
#end if
#else:
Rscript '$__tool_directory__/scater-pca-filter.R'
-i '$input_loom'
#end if
-o '$output_loom'
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
input_loom: scater_qcready.loom filter_type|library_size: 100000 filter_type|percent_counts_MT: 33.0 filter_type|detection_limit: 4 filter_type|min_cells_expressed: 3 filter_type|filter_type_selector: manual |
name: value |
scater_qcready.loom value |
| Test-2 |
input_loom: scater_qcready.loom filter_type|filter_type_selector: pca |
name: value |
scater_qcready.loom value |