| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/iuc/scanpy_cluster_reduce_dimension/scanpy_cluster_reduce_dimension/1.4.4.post1+galaxy1 |
| toolshed.g2.bx.psu.edu/repos/iuc/scanpy_cluster_reduce_dimension/scanpy_cluster_reduce_dimension/1.4.4.post1+galaxy0 (this tool) |
| toolshed.g2.bx.psu.edu/repos/iuc/scanpy_cluster_reduce_dimension/scanpy_cluster_reduce_dimension/1.4.4+galaxy0 |
| toolshed.g2.bx.psu.edu/repos/iuc/scanpy_cluster_reduce_dimension/scanpy_cluster_reduce_dimension/1.4+galaxy0 |
| scanpy_cluster_reduce_dimension |
| 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 |
| louvain | 0.6.1 | package |
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
method|random_state: 10 method|method: tl.louvain method|directed: True method|key_added: louvain method|flavor|flavor: vtraag adata: pp.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad method|flavor|resolution: 1.0 method|use_weights: False |
attributes: name |
pp.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad name |
| Test-2 |
method|random_state: 10 method|method: tl.leiden method|key_added: leiden method|n_iterations: -1 adata: pp.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad method|use_weights: False |
attributes: name |
pp.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad name |
| Test-3 |
method|pca|chunked: False method|method: pp.pca method|dtype: float32 method|n_comps: 50 method|pca|svd_solver: auto method|pca|zero_center: True method|use_highly_variable: False adata: krumsiek11.h5ad method|pca|random_state: 0 |
attributes: name |
krumsiek11.h5ad name |
| Test-4 |
method|pca|chunked: False method|method: tl.pca method|dtype: float32 method|n_comps: 50 method|pca|svd_solver: auto method|pca|zero_center: True method|use_highly_variable: False adata: krumsiek11.h5ad method|pca|random_state: 0 |
attributes: name |
krumsiek11.h5ad name |
| Test-5 |
adata: pp.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad method|n_comps: 15 method|method: tl.diffmap |
attributes: name |
pp.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad name |
| Test-6 |
method|learning_rate: 1000 method|random_state: 0 method|early_exaggeration: 12.0 method|method: tl.tsne method|use_fast_tsne: True method|n_pcs: 10 adata: krumsiek11.h5ad method|perplexity: 30 |
attributes: name |
krumsiek11.h5ad name |
| Test-7 |
method|random_state: 0 method|min_dist: 0.5 method|method: tl.umap method|n_components: 2 method|negative_sample_rate: 5 method|alpha: 1.0 method|spread: 1.0 method|gamma: 1.0 method|maxiter: 2 adata: pp.neighbors_umap_euclidean.recipe_weinreb17.paul15_subsample.h5ad method|init_pos: spectral |
attributes: name |
pp.neighbors_umap_euclidean.recipe_weinreb17.paul15_subsample.h5ad name |
| Test-8 |
method|random_state: 0 method|layout: fa adata: pp.neighbors_umap_euclidean.recipe_weinreb17.paul15_subsample.h5ad method|method: tl.draw_graph |
attributes: name |
pp.neighbors_umap_euclidean.recipe_weinreb17.paul15_subsample.h5ad name |
| Test-9 |
method|groups: paul15_clusters method|model: v1.2 method|use_rna_velocity: True adata: pp.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad method|method: tl.paga |
attributes: name |
pp.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad name |
| Test-10 |
method|allow_kendall_tau_shift: True method|n_branchings: 1 method|method: tl.dpt method|min_group_size: 0.01 method|n_dcs: 15 adata: tl.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad |
attributes: name |
tl.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad name |