| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/ebi-gxa/scmap_scmap_cell/scmap_scmap_cell/1.6.4+galaxy2 (this tool) |
| toolshed.g2.bx.psu.edu/repos/ebi-gxa/scmap_scmap_cell/scmap_scmap_cell/1.6.2+galaxy1 |
| toolshed.g2.bx.psu.edu/repos/ebi-gxa/scmap_scmap_cell/scmap_scmap_cell/1.6.2+galaxy0 |
| toolshed.g2.bx.psu.edu/repos/ebi-gxa/scmap_scmap_cell/scmap_scmap_cell/1.6.1+galaxy3 |
| toolshed.g2.bx.psu.edu/repos/ebi-gxa/scmap_scmap_cell/scmap_scmap_cell/1.6.1+galaxy2 |
| toolshed.g2.bx.psu.edu/repos/ebi-gxa/scmap_scmap_cell/scmap_scmap_cell/1.6.1+galaxy1 |
| toolshed.g2.bx.psu.edu/repos/ebi-gxa/scmap_scmap_cell/scmap_scmap_cell/1.6.0+galaxy1 |
| toolshed.g2.bx.psu.edu/repos/ebi-gxa/scmap_scmap_cell/scmap_scmap_cell/1.6.0+galaxy0 |
| scmap_scmap_cell |
| Requirements (dependencies defined in the <requirements> tag set) |
| name | version | type |
| scmap-cli | 0.1.0 | package |
| Additional information about this tool |
scmap-scmap-cell.R
-i '$index_single_cell_experiment'
-p '$project_single_cell_experiment'
--number-nearest-neighbours '$n_nearest_neighbours'
--nearest-neighbours-threshold '$nearest_neighbours_threshold'
--threshold '$threshold'
--cluster-col '${cluster_projection.cluster_col}'
--output-object-file '$output_single_cell_experiment'
--closest-cells-text-file '$closest_cells_text_file'
--closest-cells-similarities-text-file '$closest_cells_similarities_text_file'
#if $cluster_projection
--output-clusters-text-file '$clusters_text_file'
#end if
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
index_single_cell_experiment: index_cell.rds project_single_cell_experiment: test_sce_processed.rds cluster_projection|cluster_col: cell_type1 cluster_projection|do_cluster_projection: True |
name: value name: value name: value name: value |
index_cell.rds test_sce_processed.rds value |
| Test-2 |
index_single_cell_experiment: index_cell.rds project_single_cell_experiment: test_sce_processed.rds nearest_neighbours_threshold: 1 threshold: 0.2 cluster_projection|cluster_col: cell_type1 cluster_projection|do_cluster_projection: True |
name: value name: value name: value name: value |
index_cell.rds test_sce_processed.rds value |