CS2_Combining datasets after pre-processing
Version 1

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Workflow Type: Galaxy

Galaxy workflow

SEEK ID: https://dev.workflowhub.eu/workflows/1023?version=1

Inputs

ID Name Description Type
N701 #main/N701 n/a
  • File
N702 #main/N702 n/a
  • File
N703 #main/N703 n/a
  • File
N704 #main/N704 n/a
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N705 #main/N705 n/a
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N706 #main/N706 n/a
  • File
N707 #main/N707 n/a
  • File

Steps

ID Name Description
7 EBI SCXA Data Retrieval toolshed.g2.bx.psu.edu/repos/ebi-gxa/retrieve_scxa/retrieve_scxa/v0.0.2+galaxy2
8 Concatenating Datasets toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.7.5+galaxy1
9 Scanpy Read10x toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_read_10x/scanpy_read_10x/1.8.1+galaxy0
10 Inspect AnnData toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.7.5+galaxy1
11 Inspect AnnData toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.7.5+galaxy1
12 Inspect AnnData toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.7.5+galaxy1
13 Replace Text toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/1.1.3
14 Replace Text toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/1.1.3
15 Cut Cut1
16 Cut Cut1
17 Paste Paste1
18 Adding in cell metadata toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.7.5+galaxy1
19 Batching Cell Metadata toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.7.5+galaxy1
20 Calculating mitochondrial toolshed.g2.bx.psu.edu/repos/ebi-gxa/anndata_ops/anndata_ops/1.8.1+galaxy0

Outputs

ID Name Description Type
AnnData with Cell Metadata #main/AnnData with Cell Metadata n/a
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Annotated AnnData #main/Annotated AnnData n/a
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Batched AnnData #main/Batched AnnData n/a
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Cell metadata #main/Cell metadata n/a
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Combined AnnData #main/Combined AnnData n/a
  • File
Genotype metadata #main/Genotype metadata n/a
  • File
Scanpy Read10x on input dataset(s): anndata_h5ad AnnData #main/Scanpy Read10x on input dataset(s): anndata_h5ad AnnData n/a
  • File
Sex metadata #main/Sex metadata n/a
  • File
_anonymous_output_1 #main/_anonymous_output_1 n/a
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_anonymous_output_2 #main/_anonymous_output_2 n/a
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_anonymous_output_3 #main/_anonymous_output_3 n/a
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_anonymous_output_4 #main/_anonymous_output_4 n/a
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_anonymous_output_5 #main/_anonymous_output_5 n/a
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_anonymous_output_6 #main/_anonymous_output_6 n/a
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_anonymous_output_7 #main/_anonymous_output_7 n/a
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_anonymous_output_8 #main/_anonymous_output_8 n/a
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_anonymous_output_9 #main/_anonymous_output_9 n/a
  • File

Version History

1 (earliest) Created 22nd Apr 2024 at 11:21 by Helena Rasche

Added/updated 3 files


Open master c869032
help Creators and Submitter
Creators
Not specified
Submitter
Tool
SCANPY
License
Creative Commons Attribution 4.0 International
Activity

Views: 31

Created: 22nd Apr 2024 at 11:21

Last updated: 22nd Apr 2024 at 11:21

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Total size: 39.3 KB
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