Repository revision
5:32e547223c9e

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

Import Anndata and loom tool metadata
Miscellaneous
from different format
anndata_import
toolshed.g2.bx.psu.edu/repos/iuc/anndata_import/anndata_import/0.6.22.post1+galaxy3
0.6.22.post1+galaxy3
python -c "import anndata as ad;print('anndata version: %s' % ad.__version__); import loompy;print('\nloompy version: %s' % loompy.__version__)"
True
Version lineage of this tool (guids ordered most recent to oldest)
toolshed.g2.bx.psu.edu/repos/iuc/anndata_import/anndata_import/0.6.22.post1+galaxy4
toolshed.g2.bx.psu.edu/repos/iuc/anndata_import/anndata_import/0.6.22.post1+galaxy3 (this tool)
toolshed.g2.bx.psu.edu/repos/iuc/anndata_import/anndata_import/0.6.22.post1+galaxy2
toolshed.g2.bx.psu.edu/repos/iuc/anndata_import/anndata_import/0.6.22.post1+galaxy1
toolshed.g2.bx.psu.edu/repos/iuc/anndata_import/anndata_import/0.6.22.post1+galaxy0
toolshed.g2.bx.psu.edu/repos/iuc/anndata_import/anndata_import/0.6.19+galaxy0
anndata_import
Requirements (dependencies defined in the <requirements> tag set)
name version type
anndata 0.6.22.post1 package
loompy 2.0.17 package
h5py 2.9.0 package
scanpy 1.4.4.post1 package
Functional tests
name inputs outputs required files
Test-1 hd5_format|in|obs_names: CellID
hd5_format|in|input: krumsiek11.loom
hd5_format|in|sparse: True
hd5_format|in|var_names: Gene
hd5_format|in|cleanup: False
hd5_format|in|x_name: spliced
hd5_format|in|adata_format: loom
attributes: name
krumsiek11.loom
name
Test-2 hd5_format|in|first_column_names: True
hd5_format|in|input: adata.csv
hd5_format|in|adata_format: tabular
attributes: name
adata.csv
name
Test-3 hd5_format|in|first_column_names: True
hd5_format|in|input: adata.tsv
hd5_format|in|adata_format: tabular
attributes: name
adata.tsv
name
Test-4 hd5_format|in|input: umi_tools.tsv
hd5_format|filetype: anndata
hd5_format|in|adata_format: umi_tools
attributes: name
umi_tools.tsv
name
Test-5 hd5_format|other_files: secondlayer.tsv
hd5_format|mainmatrix: firstlayer.tsv
hd5_format|coldata: cols.tsv
hd5_format|filetype: loom
hd5_format|rowdata: rows.tsv
attributes: name
firstlayer.tsv
secondlayer.tsv
cols.tsv
rows.tsv
name
Test-6 hd5_format|in|input: dropletutils_input.h5
hd5_format|filetype: anndata
hd5_format|in|adata_format: 10x_h5
attributes: name
dropletutils_input.h5
name