Repository revision
6:77b91b9bdf52

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/1.4.4.post1+galaxy2
1.4.4.post1+galaxy2
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/1.4.4.post1+galaxy3
toolshed.g2.bx.psu.edu/repos/iuc/scanpy_cluster_reduce_dimension/scanpy_cluster_reduce_dimension/1.4.4.post1+galaxy2 (this tool)
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 1.4.4.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
advanced_common|show_log: True
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
attributes: name
pp.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad
name
Test-2 method|random_state: 10
advanced_common|show_log: True
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
attributes: name
pp.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad
name
Test-3 advanced_common|show_log: True
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
attributes: name
krumsiek11.h5ad
name
Test-4 advanced_common|show_log: True
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
attributes: name
krumsiek11.h5ad
name
Test-5 advanced_common|show_log: True
adata: pp.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad
method|n_comps: 15
method|method: tl.diffmap
attributes: name
attributes: name
pp.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad
name
Test-6 method|learning_rate: 1000
method|random_state: 0
advanced_common|show_log: True
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
attributes: name
krumsiek11.h5ad
name
Test-7 method|random_state: 0
advanced_common|show_log: True
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
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
advanced_common|show_log: True
method|method: tl.draw_graph
attributes: name
attributes: name
pp.neighbors_umap_euclidean.recipe_weinreb17.paul15_subsample.h5ad
name
Test-9 method|groups: paul15_clusters
method|model: v1.2
advanced_common|show_log: True
method|use_rna_velocity: True
method|method: tl.paga
adata: pp.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad
attributes: name
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
advanced_common|show_log: True
method|n_dcs: 15
adata: tl.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad
attributes: name
attributes: name
tl.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad
name