| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/iuc/scanpy_inspect/scanpy_inspect/1.4.4.post1+galaxy1 |
| toolshed.g2.bx.psu.edu/repos/iuc/scanpy_inspect/scanpy_inspect/1.4.4.post1+galaxy0 (this tool) |
| toolshed.g2.bx.psu.edu/repos/iuc/scanpy_inspect/scanpy_inspect/1.4.4+galaxy0 |
| toolshed.g2.bx.psu.edu/repos/iuc/scanpy_inspect/scanpy_inspect/1.4+galaxy0 |
| scanpy_inspect |
| 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|expr_type: counts method|method: pp.calculate_qc_metrics method|qc_vars: mito,negative method|percent_top: method|var_type: genes adata: sparce_csr_matrix.h5ad |
attributes: name |
sparce_csr_matrix.h5ad name |
| Test-2 |
method|random_state: 0 method|method: pp.neighbors method|n_neighbors: 15 method|metric: euclidean method|knn: True adata: pp.recipe_weinreb17.paul15_subsample.h5ad method|pp_neighbors_method: umap |
attributes: name |
pp.recipe_weinreb17.paul15_subsample.h5ad name |
| Test-3 |
method|n_neighbors: 15 method|method: pp.neighbors method|metric: braycurtis method|knn: True adata: pp.recipe_weinreb17.paul15_subsample.h5ad method|pp_neighbors_method: gauss |
attributes: name |
pp.recipe_weinreb17.paul15_subsample.h5ad name |
| Test-4 |
method|random_state: 2 method|gene_list: Gata2, Fog1 method|method: tl.score_genes method|score_name: score method|n_bins: 2 method|use_raw: False adata: krumsiek11.h5ad method|ctrl_size: 2 |
attributes: name |
krumsiek11.h5ad name |
| Test-5 |
method|random_state: 1 method|g2m_genes|format: text method|method: tl.score_genes_cell_cycle method|g2m_genes|text: Gata2, Fog1, EgrNab method|s_genes|format: text method|n_bins: 2 method|use_raw: False method|s_genes|text: Gata2, Fog1, EgrNab adata: krumsiek11.h5ad |
attributes: name |
krumsiek11.h5ad name |
| Test-6 |
method|groupby: cell_type method|tl_rank_genes_groups_method|corr_method: benjamini-hochberg method|method: tl.rank_genes_groups method|use_raw: True method|ref|rest: rest method|n_genes: 100 method|tl_rank_genes_groups_method|method: t-test_overestim_var method|only_positive: True adata: krumsiek11.h5ad |
attributes: name |
krumsiek11.h5ad name |
| Test-7 |
method|groupby: louvain method|tl_rank_genes_groups_method|solver|solver: newton-cg method|method: tl.rank_genes_groups method|tl_rank_genes_groups_method|tol: 1e-4 method|use_raw: True method|ref|rest: rest method|tl_rank_genes_groups_method|solver|max_iter: 100 method|tl_rank_genes_groups_method|c: 1.0 method|n_genes: 100 method|tl_rank_genes_groups_method|method: logreg method|only_positive: True method|tl_rank_genes_groups_method|solver|fit_intercept: True method|tl_rank_genes_groups_method|solver|multi_class: auto adata: pbmc68k_reduced.h5ad |
attributes: name |
pbmc68k_reduced.h5ad name |
| Test-8 |
method|groupby: louvain method|tl_rank_genes_groups_method|solver|penalty|dual: False method|tl_rank_genes_groups_method|solver|solver: liblinear method|method: tl.rank_genes_groups adata: pbmc68k_reduced.h5ad method|tl_rank_genes_groups_method|tol: 1e-4 method|use_raw: True method|ref|rest: rest method|tl_rank_genes_groups_method|c: 1.0 method|n_genes: 100 method|tl_rank_genes_groups_method|method: logreg method|only_positive: True method|tl_rank_genes_groups_method|solver|penalty|penalty: l2 |
attributes: name |
pbmc68k_reduced.h5ad name |
| Test-9 |
adata: krumsiek11.h5ad method|method: pp.log1p |
attributes: name |
krumsiek11.h5ad name |
| Test-10 |
method|zero_center: True adata: krumsiek11.h5ad method|method: pp.scale |
attributes: name |
krumsiek11.h5ad name |
| Test-11 |
method|max_value: 10 adata: krumsiek11.h5ad method|zero_center: True method|method: pp.scale |
attributes: name |
krumsiek11.h5ad name |
| Test-12 |
adata: krumsiek11.h5ad method|method: pp.sqrt |
attributes: name |
krumsiek11.h5ad name |