Repository revision
7:43cb7b5a6fe7

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

Manipulate AnnData tool metadata
Miscellaneous
object
anndata_manipulate
toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.6.22.post1+galaxy4
0.6.22.post1+galaxy4
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_manipulate/anndata_manipulate/0.7.4+galaxy1
toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.6.22.post1+galaxy4 (this tool)
toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.6.22.post1+galaxy3
toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.6.22.post1+galaxy2
toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.6.22.post1+galaxy1
toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.6.22.post1+galaxy0
toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.6.19+galaxy0
anndata_manipulate
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
Functional tests
name inputs outputs required files
Test-1 manipulate|index_unique: -
manipulate|join: inner
manipulate|batch_key: batch
manipulate|other_adatas: import.csv.h5ad
input: krumsiek11.h5ad
manipulate|function: concatenate
attributes: name
krumsiek11.h5ad
import.csv.h5ad
name
Test-2 input: krumsiek11.h5ad
manipulate|function: obs_names_make_unique
manipulate|join: -
attributes: name
krumsiek11.h5ad
name
Test-3 input: krumsiek11.h5ad
manipulate|function: var_names_make_unique
manipulate|join: -
attributes: name
krumsiek11.h5ad
name
Test-4 input: krumsiek11.h5ad
manipulate|key: cell_type
manipulate|function: rename_categories
manipulate|categories: Er,Ml,Mt, Ne, pr
attributes: name
krumsiek11.h5ad
name
Test-5 input: krumsiek11.h5ad
manipulate|function: strings_to_categoricals
attributes: name
krumsiek11.h5ad
name
Test-6 input: krumsiek11.h5ad
manipulate|function: transpose
attributes: name
krumsiek11.h5ad
name
Test-7 input: krumsiek11.h5ad
manipulate|function: add_annotation
manipulate|var_obs: var
manipulate|new_annot: var_add_annotation.tabular
attributes: name
krumsiek11.h5ad
var_add_annotation.tabular
name
Test-8 input: krumsiek11.h5ad
manipulate|function: add_annotation
manipulate|var_obs: obs
manipulate|new_annot: obs_add_annotation.tabular
attributes: name
krumsiek11.h5ad
obs_add_annotation.tabular
name
Test-9 manipulate|var_obs: var
manipulate|filter|index|text: Gata2,EKLF
manipulate|filter|filter: index
input: krumsiek11.h5ad
manipulate|filter|index|format: text
manipulate|function: filter
attributes: name
krumsiek11.h5ad
name
Test-10 manipulate|var_obs: obs
manipulate|filter|key: cell_type
manipulate|filter|filter: key
manipulate|filter|filter_key|value: progenitor
input: krumsiek11.h5ad
manipulate|filter|filter_key|filter: equal
manipulate|function: filter
manipulate|filter|filter_key|type: text
attributes: name
krumsiek11.h5ad
name
Test-11 input: krumsiek11.h5ad
manipulate|function: save_raw
attributes: name
krumsiek11.h5ad
name