| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/iuc/scanpy_filter/scanpy_filter/1.7.1+galaxy0 (this tool) |
| 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 |
| 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 | 1.7.1 | package |
| loompy | 2.0.17 | package |
| leidenalg | 0.8.3 | package |
| Additional information about this tool |
cp '$adata' 'anndata.h5ad' &&
cat '$script_file' > '$hidden_output' &&
python '$script_file' >> '$hidden_output' &&
ls . >> '$hidden_output' &&
touch 'anndata_info.txt' &&
cat 'anndata_info.txt' | sed -r '1 s|AnnData object with (.+) = (.*)\s*|\1: \2|g' | sed "s|'||g" | sed -r 's|^\s*(.*):\s(.*)|[\1]\n- \2|g' | sed 's|, |\n- |g'
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
adata: krumsiek11.h5ad method|filter|min_counts: 3 method|filter|filter: min_counts method|method: pp.filter_cells advanced_common|show_log: True |
name: value name: value |
krumsiek11.h5ad value |
| Test-2 |
adata: krumsiek11.h5ad method|filter|max_genes: 100 method|filter|filter: max_genes method|method: pp.filter_cells advanced_common|show_log: True |
name: value name: value |
krumsiek11.h5ad value |
| Test-3 |
adata: krumsiek11.h5ad method|filter|min_counts: 3 method|filter|filter: min_counts method|method: pp.filter_genes advanced_common|show_log: True |
name: value name: value |
krumsiek11.h5ad value |
| Test-4 |
adata: blobs.h5ad method|flavor|min_mean: 0.0125 method|flavor|max_mean: 3 method|flavor|min_disp: 0.5 method|flavor|flavor: seurat method|n_bins: 20 method|subset: False method|method: pp.highly_variable_genes advanced_common|show_log: True |
name: value name: value |
blobs.h5ad value |
| Test-5 |
adata: krumsiek11.h5ad method|flavor|n_top_genes: 2 method|flavor|flavor: cell_ranger method|n_bins: 20 method|subset: True method|method: pp.highly_variable_genes advanced_common|show_log: True |
name: value name: value |
krumsiek11.h5ad value |
| Test-6 |
adata: krumsiek11.h5ad method|type|fraction: 0.5 method|type|type: fraction method|random_state: 0 method|method: pp.subsample advanced_common|show_log: True |
name: value name: value |
krumsiek11.h5ad value |
| Test-7 |
adata: krumsiek11.h5ad method|type|n_obs: 10 method|type|type: n_obs method|random_state: 0 method|method: pp.subsample advanced_common|show_log: True |
name: value name: value |
krumsiek11.h5ad value |
| Test-8 |
adata: random-randint.h5ad method|total_counts: 20000 method|random_state: 0 method|replace: False method|method: pp.downsample_counts advanced_common|show_log: True |
name: value name: value |
random-randint.h5ad value |