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/1.9.6+galaxy4 |
toolshed.g2.bx.psu.edu/repos/iuc/scanpy_cluster_reduce_dimension/scanpy_cluster_reduce_dimension/1.9.6+galaxy3 (this tool) |
toolshed.g2.bx.psu.edu/repos/iuc/scanpy_cluster_reduce_dimension/scanpy_cluster_reduce_dimension/1.9.6+galaxy2 |
toolshed.g2.bx.psu.edu/repos/iuc/scanpy_cluster_reduce_dimension/scanpy_cluster_reduce_dimension/1.9.6+galaxy1 |
toolshed.g2.bx.psu.edu/repos/iuc/scanpy_cluster_reduce_dimension/scanpy_cluster_reduce_dimension/1.9.6+galaxy0 |
toolshed.g2.bx.psu.edu/repos/iuc/scanpy_cluster_reduce_dimension/scanpy_cluster_reduce_dimension/1.7.1+galaxy0 |
toolshed.g2.bx.psu.edu/repos/iuc/scanpy_cluster_reduce_dimension/scanpy_cluster_reduce_dimension/1.4.4.post1+galaxy3 |
toolshed.g2.bx.psu.edu/repos/iuc/scanpy_cluster_reduce_dimension/scanpy_cluster_reduce_dimension/1.4.4.post1+galaxy2 |
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 |
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 | 1.9.6 | package |
loompy | 3.0.6 | package |
leidenalg | 0.10.1 | package |
louvain | 0.8.1 | package |
pandas | 1.5.3 | package |
matplotlib | 3.7 | package |
seaborn | 0.12.2 | package |
magic-impute | 3.0.0 | package |
Functional tests |
name | inputs | outputs | required files |
Test-1 |
adata: pp.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad method|flavor|resolution: 1.0 method|flavor|flavor: vtraag method|random_state: 10 method|key_added: louvain method|directed: True method|use_weights: False method|method: tl.louvain advanced_common|show_log: True |
name: value name: value |
pp.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad value |
Test-2 |
adata: pp.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad method|random_state: 10 method|key_added: leiden method|use_weights: False method|n_iterations: -1 method|method: tl.leiden advanced_common|show_log: True |
name: value name: value |
pp.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad value |
Test-3 |
adata: krumsiek11.h5ad method|n_comps: 50 method|dtype: float32 method|pca|zero_center: True method|pca|svd_solver: auto method|pca|random_state: 0 method|pca|chunked: False method|use_highly_variable: False method|method: pp.pca advanced_common|show_log: True |
name: value name: value |
krumsiek11.h5ad value |
Test-4 |
adata: krumsiek11.h5ad method|n_comps: 20 method|dtype: float32 method|pca|chunk_size: 50 method|pca|chunked: True method|use_highly_variable: False method|method: pp.pca advanced_common|show_log: True |
name: value name: value |
krumsiek11.h5ad value |
Test-5 |
adata: krumsiek11.h5ad method|n_comps: 50 method|dtype: float32 method|pca|zero_center: True method|pca|svd_solver: auto method|pca|random_state: 0 method|pca|chunked: False method|use_highly_variable: False method|method: tl.pca advanced_common|show_log: True |
name: value name: value |
krumsiek11.h5ad value |
Test-6 |
adata: pp.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad method|n_comps: 15 method|method: tl.diffmap advanced_common|show_log: True |
name: value name: value |
pp.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad value |
Test-7 |
adata: krumsiek11.h5ad method|n_pcs: 10 method|perplexity: 30 method|early_exaggeration: 12.0 method|learning_rate: 1000 method|random_state: 0 method|use_fast_tsne: True method|method: tl.tsne advanced_common|show_log: True |
name: value name: value |
krumsiek11.h5ad value |
Test-8 |
adata: pp.neighbors_umap_euclidean.recipe_weinreb17.paul15_subsample.h5ad method|min_dist: 0.5 method|spread: 1.0 method|n_components: 2 method|maxiter: 2 method|alpha: 1.0 method|gamma: 1.0 method|negative_sample_rate: 5 method|init_pos: spectral method|random_state: 0 method|method: tl.umap advanced_common|show_log: True |
name: value name: value |
pp.neighbors_umap_euclidean.recipe_weinreb17.paul15_subsample.h5ad value |
Test-9 |
adata: pp.neighbors_umap_euclidean.recipe_weinreb17.paul15_subsample.h5ad method|layout: fa method|random_state: 0 method|method: tl.draw_graph advanced_common|show_log: True |
name: value name: value |
pp.neighbors_umap_euclidean.recipe_weinreb17.paul15_subsample.h5ad value |
Test-10 |
adata: pp.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad method|groups: paul15_clusters method|use_rna_velocity: False method|model: v1.2 method|method: tl.paga advanced_common|show_log: True |
name: value name: value |
pp.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad value |
Test-11 |
adata: tl.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad method|n_dcs: 15 method|n_branchings: 1 method|min_group_size: 0.01 method|allow_kendall_tau_shift: True method|method: tl.dpt advanced_common|show_log: True |
name: value name: value |
tl.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad value |
Test-12 |
adata: tl.umap.neighbors_umap_euclidean.recipe_weinreb17.paul15_subsample.h5ad method|basis: umap method|key_added: umap_density method|method: tl.embedding_density advanced_common|show_log: True |
name: value name: value |
tl.umap.neighbors_umap_euclidean.recipe_weinreb17.paul15_subsample.h5ad value |