Miscellaneous |
Version lineage of this tool (guids ordered most recent to oldest) |
toolshed.g2.bx.psu.edu/repos/iuc/scanpy_filter/scanpy_filter/1.4.4.post1+galaxy3 |
toolshed.g2.bx.psu.edu/repos/iuc/scanpy_filter/scanpy_filter/1.4.4.post1+galaxy2 (this tool) |
toolshed.g2.bx.psu.edu/repos/iuc/scanpy_filter/scanpy_filter/1.4.4.post1+galaxy1 |
toolshed.g2.bx.psu.edu/repos/iuc/scanpy_filter/scanpy_filter/1.4.4.post1+galaxy0 |
toolshed.g2.bx.psu.edu/repos/iuc/scanpy_filter/scanpy_filter/1.4.4+galaxy0 |
toolshed.g2.bx.psu.edu/repos/iuc/scanpy_filter/scanpy_filter/1.4+galaxy0 |
scanpy_filter |
Requirements (dependencies defined in the <requirements> tag set) |
name | version | type |
scanpy | 1.4.4.post1 | package |
loompy | 2.0.17 | package |
h5py | 2.9.0 | package |
leidenalg | 0.7.0 | package |
Functional tests |
name | inputs | outputs | required files |
Test-1 |
method|filter|min_counts: 3 method|filter|filter: min_counts adata: krumsiek11.h5ad advanced_common|show_log: True method|method: pp.filter_cells |
attributes: name attributes: name |
krumsiek11.h5ad name |
Test-2 |
method|filter|max_genes: 100 advanced_common|show_log: True method|filter|filter: max_genes adata: krumsiek11.h5ad method|method: pp.filter_cells |
attributes: name attributes: name |
krumsiek11.h5ad name |
Test-3 |
method|filter|min_counts: 3 method|filter|filter: min_counts adata: krumsiek11.h5ad advanced_common|show_log: True method|method: pp.filter_genes |
attributes: name attributes: name |
krumsiek11.h5ad name |
Test-4 |
advanced_common|show_log: True method|flavor|max_mean: 3 method|method: pp.highly_variable_genes method|flavor|min_disp: 0.5 method|n_bins: 20 method|flavor|min_mean: 0.0125 method|flavor|flavor: seurat adata: blobs.h5ad method|subset: False |
attributes: name attributes: name |
blobs.h5ad name |
Test-5 |
advanced_common|show_log: True method|method: pp.highly_variable_genes method|n_bins: 20 method|flavor|flavor: cell_ranger method|flavor|n_top_genes: 2 adata: krumsiek11.h5ad method|subset: True |
attributes: name attributes: name |
krumsiek11.h5ad name |
Test-6 |
method|random_state: 0 advanced_common|show_log: True method|method: pp.subsample method|type|fraction: 0.5 method|type|type: fraction adata: krumsiek11.h5ad |
attributes: name attributes: name |
krumsiek11.h5ad name |
Test-7 |
method|random_state: 0 advanced_common|show_log: True method|method: pp.subsample method|type|n_obs: 10 method|type|type: n_obs adata: krumsiek11.h5ad |
attributes: name attributes: name |
krumsiek11.h5ad name |
Test-8 |
method|random_state: 0 advanced_common|show_log: True method|method: pp.downsample_counts method|replace: False adata: random-randint.h5ad method|total_counts: 20000 |
attributes: name attributes: name |
random-randint.h5ad name |