Galaxy |

Export AnnData and loom files tool metadata

Miscellaneous

Name: Export AnnData and loom files

Description: Interconvert AnnData and Loom formats

Id: anndata_export

Guid: toolshed.g2.bx.psu.edu/repos/iuc/anndata_export/anndata_export/0.10.3+galaxy0

Version: 0.10.3+galaxy0

Version command string: python -c "import anndata as ad;print('anndata version: %s' % ad.__version__); import loompy;print('\nloompy version: %s' % loompy.__version__)"

Display in tool panel: True

Version lineage of this tool (guids ordered most recent to oldest)

toolshed.g2.bx.psu.edu/repos/iuc/anndata_export/anndata_export/0.10.3+galaxy0 (this tool)

toolshed.g2.bx.psu.edu/repos/iuc/anndata_export/anndata_export/0.7.5+galaxy1

toolshed.g2.bx.psu.edu/repos/iuc/anndata_export/anndata_export/0.7.5+galaxy0

toolshed.g2.bx.psu.edu/repos/iuc/anndata_export/anndata_export/0.7.4+galaxy1

toolshed.g2.bx.psu.edu/repos/iuc/anndata_export/anndata_export/0.6.22.post1+galaxy4

toolshed.g2.bx.psu.edu/repos/iuc/anndata_export/anndata_export/0.6.22.post1+galaxy3

toolshed.g2.bx.psu.edu/repos/iuc/anndata_export/anndata_export/0.6.22.post1+galaxy2

toolshed.g2.bx.psu.edu/repos/iuc/anndata_export/anndata_export/0.6.22.post1+galaxy1

toolshed.g2.bx.psu.edu/repos/iuc/anndata_export/anndata_export/0.6.22.post1+galaxy0

toolshed.g2.bx.psu.edu/repos/iuc/anndata_export/anndata_export/0.6.19+galaxy0

anndata_export

Requirements (dependencies defined in the <requirements> tag set)

Requirements:

name

version

type

anndata

0.10.3

package

loompy

3.0.6

package

Additional information about this tool

Command:

#if $hd5_format.filetype == 'anndata':
    
cat '$script_file' &&
python '$script_file'
    
    
#else:
    
mkdir ./output &&
mkdir ./attributes &&
python '$__tool_directory__/loompy_to_tsv.py' -f '${hd5_format.input}'
    
    
#end if

Interpreter: None

Forces a history refresh: False

Functional tests

name

inputs

outputs

required files

Test-1

hd5_format|input: krumsiek11.h5ad
hd5_format|output_format: loom
hd5_format|filetype: anndata

name: value

krumsiek11.h5ad
value

Test-2

hd5_format|input: krumsiek11.h5ad
hd5_format|output_format: tabular
hd5_format|filetype: anndata

name: value
name: value
name: value
name: value
name: value

krumsiek11.h5ad
value

Test-3

hd5_format|input: loomtest.loom
hd5_format|filetype: loom

loomtest.loom