MAPseq to ampvis2 1.0
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Run on GalaxyThe MAPseq to Ampvis workflow processes MAPseq OTU tables and associated metadata for analysis in Ampvis2. This workflow involves reformatting MAPseq output datasets to produce structured output files suitable for Ampvis2.
Associated Tutorial
This workflows is part of the tutorial MGnify v5.0 Amplicon Pipeline, available in the GTN
Features
- Includes a Galaxy Workflow Report
- Uses Galaxy Workflow Comments
Thanks to...
Workflow Author(s): Rand Zoabi, Mara Besemer
Tutorial Author(s): Rand Zoabi
Tutorial Contributor(s): Paul Zierep, Saskia Hiltemann
Funder(s): German Competence Center Cloud Technologies for Data Management and Processing (de.KCD)
Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| MAPseq OTU tables | #main/MAPseq OTU tables | A dataset collection containing the tab-separated OTU outputs of MAPseq. |
|
| OTU table metadata | #main/OTU table metadata | Contextual information associated with the data from the OTU tables. |
|
Steps
| ID | Name | Description |
|---|---|---|
| 2 | Query Tabular | toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.2 |
| 3 | Text reformatting | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.5+galaxy0 |
| 4 | Text reformatting | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.5+galaxy0 |
| 5 | Collapse Collection | toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0 |
| 6 | Column join | toolshed.g2.bx.psu.edu/repos/iuc/collection_column_join/collection_column_join/0.0.3 |
| 7 | Text reformatting | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.5+galaxy0 |
| 8 | Text reformatting | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.5+galaxy0 |
| 9 | Query Tabular | toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.2 |
| 10 | ampvis2 load | toolshed.g2.bx.psu.edu/repos/iuc/ampvis2_load/ampvis2_load/2.8.9+galaxy0 |
Outputs
| ID | Name | Description | Type |
|---|---|---|---|
| Ampvis2 metadata table | #main/Ampvis2 metadata table | n/a |
|
| Ampvis2 object | #main/Ampvis2 object | n/a |
|
| Ampvis2 taxonomy table | #main/Ampvis2 taxonomy table | n/a |
|
| OTU table | #main/OTU table | n/a |
|
| Taxonomy table | #main/Taxonomy table | n/a |
|
Version History
master
Creators and Submitter
Views: 42 Downloads: 6 Runs: 0
Created: 11th Aug 2025 at 14:15
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