Ecoregionalization workflow (Part 2) Version 1
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Run on GalaxySecond part of the ecoregionalization
This workflow allows you to create an ecoregionalization map from occurrences and environmental data using a boosted regression trees model for predictions.
The workflow is intended for processing occurrence data, which should include latitude, longitude and species presence or absence. You can use example test data available with the workflow, highlighting a use case centered on the Dumont d'Urville sea region and benthic invertebrates. The primary goal of this workflow is to generate species distribution maps and identify ecoregions within the study area. The project's objective is to offer accessible, reproducible, and transparent IT solutions for processing and analyzing species occurrence data.
This workflow is linked to the Galaxy training ecoregionalization tutorial. (https://ecology.usegalaxy.eu/training-material/topics/ecology/tutorials/Ecoregionalization_tutorial/tutorial.html)
For practical use the ecoregionalization workflow is split in two worklows and this is the second part. You can find the first part here : https://workflowhub.eu/workflows/1208?version=1
Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| Data.bio_table.tabular | #main/Data.bio_table.tabular | Prediction table |
|
| Data_to_cluster.tabular | #main/Data_to_cluster.tabular | Prediction matrix |
|
| ceamarc_env.tabular | #main/ceamarc_env.tabular | Environmental file |
|
Steps
| ID | Name | Description |
|---|---|---|
| 3 | ClaraClust | Please ensure that the parameter 'Number of Clusters Wanted' reflects your actual desired number. To determine this parameter, refer to your SIH index plot from the ClusterEstimate step. toolshed.g2.bx.psu.edu/repos/ecology/ecoregion_clara_cluster/ecoregion_clara_cluster/0.1.0+galaxy0 |
| 4 | EcoMap | Tool for mapping ecoregions toolshed.g2.bx.psu.edu/repos/ecology/ecoregion_eco_map/ecoregion_eco_map/0.1.0+galaxy0 |
Outputs
| ID | Name | Description | Type |
|---|---|---|---|
| SIH_plot | #main/SIH_plot | n/a |
|
| cluster_info | #main/cluster_info | n/a |
|
| cluster_points | #main/cluster_points | n/a |
|
| eco_map | #main/eco_map | n/a |
|
Version History
Version 1 (earliest) Created 18th Nov 2024 at 14:23 by Pauline Seguineau
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Created: 18th Nov 2024 at 14:23
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