Repository revision
10:b409c2486353

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

Filter tool metadata
Miscellaneous
Filter
with scanpy
scanpy_filter
toolshed.g2.bx.psu.edu/repos/iuc/scanpy_filter/scanpy_filter/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_filter/scanpy_filter/1.9.6+galaxy0
toolshed.g2.bx.psu.edu/repos/iuc/scanpy_filter/scanpy_filter/1.7.1+galaxy0 (this tool)
toolshed.g2.bx.psu.edu/repos/iuc/scanpy_filter/scanpy_filter/1.4.4.post1+galaxy3
toolshed.g2.bx.psu.edu/repos/iuc/scanpy_filter/scanpy_filter/1.4.4.post1+galaxy2
toolshed.g2.bx.psu.edu/repos/iuc/scanpy_filter/scanpy_filter/1.4.4.post1+galaxy1
toolshed.g2.bx.psu.edu/repos/iuc/scanpy_filter/scanpy_filter/1.4.4.post1+galaxy0
toolshed.g2.bx.psu.edu/repos/iuc/scanpy_filter/scanpy_filter/1.4.4+galaxy0
toolshed.g2.bx.psu.edu/repos/iuc/scanpy_filter/scanpy_filter/1.4+galaxy0
scanpy_filter
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
Functional tests
name inputs outputs required files
Test-1 adata: krumsiek11.h5ad
method|filter|min_counts: 3
method|filter|filter: min_counts
method|method: pp.filter_cells
advanced_common|show_log: True
name: value
name: value
krumsiek11.h5ad
value
Test-2 adata: krumsiek11.h5ad
method|filter|max_genes: 100
method|filter|filter: max_genes
method|method: pp.filter_cells
advanced_common|show_log: True
name: value
name: value
krumsiek11.h5ad
value
Test-3 adata: krumsiek11.h5ad
method|filter|min_counts: 3
method|filter|filter: min_counts
method|method: pp.filter_genes
advanced_common|show_log: True
name: value
name: value
krumsiek11.h5ad
value
Test-4 adata: blobs.h5ad
method|flavor|min_mean: 0.0125
method|flavor|max_mean: 3
method|flavor|min_disp: 0.5
method|flavor|flavor: seurat
method|n_bins: 20
method|subset: False
method|method: pp.highly_variable_genes
advanced_common|show_log: True
name: value
name: value
blobs.h5ad
value
Test-5 adata: krumsiek11.h5ad
method|flavor|n_top_genes: 2
method|flavor|flavor: cell_ranger
method|n_bins: 20
method|subset: True
method|method: pp.highly_variable_genes
advanced_common|show_log: True
name: value
name: value
krumsiek11.h5ad
value
Test-6 adata: krumsiek11.h5ad
method|type|fraction: 0.5
method|type|type: fraction
method|random_state: 0
method|method: pp.subsample
advanced_common|show_log: True
name: value
name: value
krumsiek11.h5ad
value
Test-7 adata: krumsiek11.h5ad
method|type|n_obs: 10
method|type|type: n_obs
method|random_state: 0
method|method: pp.subsample
advanced_common|show_log: True
name: value
name: value
krumsiek11.h5ad
value
Test-8 adata: random-randint.h5ad
method|total_counts: 20000
method|random_state: 0
method|replace: False
method|method: pp.downsample_counts
advanced_common|show_log: True
name: value
name: value
random-randint.h5ad
value