Workflow 3: Functional Information (quick)
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Run on GalaxyMetatranscriptomics analysis using microbiome RNA-seq data (short)
Associated Tutorial
This workflows is part of the tutorial Metatranscriptomics analysis using microbiome RNA-seq data (short), available in the GTN
Features
- Includes Galaxy Workflow Tests
Thanks to...
Workflow Author(s): Bérénice Batut, Pratik Jagtap, Subina Mehta, Ray Sajulga, Emma Leith, Praveen Kumar, Saskia Hiltemann, Paul Zierep
Tutorial Author(s): Pratik Jagtap, Subina Mehta, Ray Sajulga, Bérénice Batut, Emma Leith, Praveen Kumar, Saskia Hiltemann, Paul Zierep, Engy Nasr
Tutorial Contributor(s): Christine Oger, Bérénice Batut, Helena Rasche, Saskia Hiltemann, Paul Zierep, Björn Grüning
Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| Gene Family abundance | Gene Family abundance | n/a |
|
| Pathway abundance | Pathway abundance | n/a |
|
| Predicted taxon relative abundances | Predicted taxon relative abundances | n/a |
|
Steps
| ID | Name | Description |
|---|---|---|
| 3 | Cut | Cut1 |
| 4 | Renormalize | toolshed.g2.bx.psu.edu/repos/iuc/humann_renorm_table/humann_renorm_table/3.9+galaxy0 |
| 5 | Regroup | toolshed.g2.bx.psu.edu/repos/iuc/humann_regroup_table/humann_regroup_table/3.9+galaxy0 |
| 6 | Renormalize | toolshed.g2.bx.psu.edu/repos/iuc/humann_renorm_table/humann_renorm_table/3.9+galaxy0 |
| 7 | Replace | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.4 |
| 8 | Rename features | toolshed.g2.bx.psu.edu/repos/iuc/humann_rename_table/humann_rename_table/3.9+galaxy0 |
| 9 | Split a HUMAnN table | toolshed.g2.bx.psu.edu/repos/iuc/humann_split_stratified_table/humann_split_stratified_table/3.9+galaxy0 |
| 10 | Unpack pathway abundances | toolshed.g2.bx.psu.edu/repos/iuc/humann_unpack_pathways/humann_unpack_pathways/3.9+galaxy0 |
| 11 | Combination of taxonomic and metabolic assignations for gene families | toolshed.g2.bx.psu.edu/repos/bebatut/combine_metaphlan2_humann2/combine_metaphlan2_humann2/0.2.0 |
| 12 | Select | Grep1 |
| 13 | Select | Grep1 |
| 14 | Select | Grep1 |
Outputs
| ID | Name | Description | Type |
|---|---|---|---|
| _anonymous_output_1 | _anonymous_output_1 | n/a |
|
| _anonymous_output_2 | _anonymous_output_2 | n/a |
|
| _anonymous_output_3 | _anonymous_output_3 | n/a |
|
| _anonymous_output_4 | _anonymous_output_4 | n/a |
|
| Split a HUMAnN table on input dataset(s): Stratified table | Split a HUMAnN table on input dataset(s): Stratified table | n/a |
|
| Split a HUMAnN table on input dataset(s): Unstratified table | Split a HUMAnN table on input dataset(s): Unstratified table | n/a |
|
| _anonymous_output_5 | _anonymous_output_5 | n/a |
|
| species abundances | Combine MetaPhlAn2 and HUMAnN2 outputs on input dataset(s): Gene family abundances related to genus/species abundances | n/a |
|
| _anonymous_output_6 | _anonymous_output_6 | n/a |
|
| _anonymous_output_7 | _anonymous_output_7 | n/a |
|
| _anonymous_output_8 | _anonymous_output_8 | n/a |
|
Version History
master
1.0
Creators and Submitter
Views: 410 Downloads: 59 Runs: 0
Created: 2nd Jun 2025 at 10:53
Last updated: 14th Jul 2025 at 14:14
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