Ecoregionalization workflow (Part 2)
Version 1

Workflow Type: Galaxy

Second 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
  • File
Data_to_cluster.tabular #main/Data_to_cluster.tabular Prediction matrix
  • File
ceamarc_env.tabular #main/ceamarc_env.tabular Environmental file
  • 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
  • File
cluster_info #main/cluster_info n/a
  • File
cluster_points #main/cluster_points n/a
  • File
eco_map #main/eco_map n/a
  • File

Version History

Version 1 (earliest) Created 18th Nov 2024 at 14:23 by Pauline Seguineau

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Seguineau, P. (2024). Ecoregionalization workflow (Part 2). WorkflowHub. https://doi.org/10.48546/WORKFLOWHUB.WORKFLOW.1209.1
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Created: 18th Nov 2024 at 14:23

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