Repository revision
10:aaa5da8e73a9

Repository 'scanpy_cluster_reduce_dimension'
hg clone https://toolshed.g2.bx.psu.edu/repos/iuc/scanpy_cluster_reduce_dimension

Cluster, infer trajectories and embed tool metadata
Miscellaneous
with scanpy
scanpy_cluster_reduce_dimension
toolshed.g2.bx.psu.edu/repos/iuc/scanpy_cluster_reduce_dimension/scanpy_cluster_reduce_dimension/1.7.1+galaxy0
1.7.1+galaxy0
python -c "import scanpy as sc;print('scanpy version: %s' % sc.__version__)"
True
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+galaxy0
toolshed.g2.bx.psu.edu/repos/iuc/scanpy_cluster_reduce_dimension/scanpy_cluster_reduce_dimension/1.7.1+galaxy0 (this tool)
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 1.7.1 package
loompy 2.0.17 package
leidenalg 0.8.3 package
louvain 0.7.0 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: 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-5 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-6 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-7 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-8 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-9 adata: pp.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad
method|groups: paul15_clusters
method|use_rna_velocity: True
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-10 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