Combining datasets after pre-processing
1.0

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Workflow Type: Galaxy

Updated March 2024

Associated Tutorial

This workflows is part of the tutorial Combining datasets after pre-processing, available in the GTN

Features

Includes Galaxy Workflow Tests

Thanks to...

Tutorial Author(s): Wendi Bacon, Jonathan Manning

Tutorial Contributor(s): Helena Rasche, Julia Jakiela

Workflow Author(s): Julia Jakiela, Wendi Bacon

SEEK ID: https://dev.workflowhub.eu/workflows/1225?version=1

Inputs

ID	Name	Description	Type
N701	N701	Dataset to be combined	File
N702	N702	Dataset to be combined	File
N703	N703	Dataset to be combined	File
N704	N704	Dataset to be combined	File
N705	N705	Dataset to be combined	File
N706	N706	Dataset to be combined	File
N707	N707	Dataset to be combined	File

Steps

ID	Name	Description
7	Concatenating Datasets	toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.10.3+galaxy0
8	Inspect AnnData	toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.10.3+galaxy0
9	Inspect AnnData	toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.10.3+galaxy0
10	Inspect AnnData	toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.10.3+galaxy0
11	Replace Text	toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/9.3+galaxy0
12	Replace Text	toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/9.3+galaxy0
13	Cut	Cut1
14	Cut	Cut1
15	Paste	Paste1
16	Adding in cell metadata	toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.10.3+galaxy0
17	Batching Cell Metadata	toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.10.3+galaxy0
18	Calculating mitochondrial	toolshed.g2.bx.psu.edu/repos/ebi-gxa/anndata_ops/anndata_ops/1.9.3+galaxy0

Outputs

ID	Name	Description	Type
Combined Object	Combined Object	n/a	File
Sex metadata	Sex metadata	n/a	File
Genotype metadata	Genotype metadata	n/a	File
Cell metadata	Cell metadata	n/a	File
AnnData with Cell Metadata	AnnData with Cell Metadata	n/a	File
Batched Object	Batched Object	n/a	File
Annotated AnnData	Annotated AnnData	n/a	File

Version History

1.0 (earliest) Created 25th Jun 2024 at 11:12 by Helena Rasche

Added/updated 4 files

Open master c82edc1

Creators and Submitter

Creators

Not specified

Submitter

Helena Rasche

Discussion Channel

GTN Matrix

License

Creative Commons Attribution 4.0 International

Activity

Views: 355 Downloads: 83

Created: 25th Jun 2024 at 11:12

Last updated: 25th Jun 2024 at 11:12

Combining datasets after pre-processing 1.0