Ecoregionalization workflow (Part 1)
Version 1

Workflow Type: Galaxy

Part 1 of ecoregionalization workflow

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 first part.

Inputs

ID Name Description Type
0030809-240506114902167.zip 0030809-240506114902167.zip Gbif downloaded zip file
  • File
ceamarc_env.tab ceamarc_env.tab Environment file
  • File
pivot_wider_jupytool_notebook.ipynb pivot_wider_jupytool_notebook.ipynb Jupyter Notebook file
  • File

Steps

ID Name Description
3 Unzip Unzipped file toolshed.g2.bx.psu.edu/repos/imgteam/unzip/unzip/6.0+galaxy0
4 Advanced Cut 1 Advanced Cut toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/9.3+galaxy2
5 Column Regex Find And Replace 1 Column Regex Find And Replace toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regexColumn1/1.0.3
6 Column Regex Find And Replace 2 Column Regex Find And Replace toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regexColumn1/1.0.3
7 Column Regex Find And Replace 3 Column Regex Find And Replace toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regexColumn1/1.0.3
8 Column Regex Find And Replace 4 Column Regex Find And Replace toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regexColumn1/1.0.3
9 Filter Tabular Filter toolshed.g2.bx.psu.edu/repos/iuc/filter_tabular/filter_tabular/3.3.1
10 Column Regex Find And Replace 5 Column Regex Find And Replace toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regexColumn1/1.0.3
11 Column Regex Find And Replace 6 Column Regex Find And Replace toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regexColumn1/1.0.3
12 Column Regex Find And Replace 7 Column Regex Find And Replace toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regexColumn1/1.0.3
13 Column Regex Find And Replace 8 Column Regex Find And Replace toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regexColumn1/1.0.3
14 Column Regex Find And Replace 9 Column Regex Find And Replace toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regexColumn1/1.0.3
15 Merge Columns Merge file toolshed.g2.bx.psu.edu/repos/devteam/merge_cols/mergeCols1/1.0.2
16 Advanced Cut 2 Advanced Cut toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/9.3+galaxy2
17 Interactive JupyterLab Notebook Interactive tool jupyter notebook interactive_tool_jupyter_notebook
18 GeoNearestNeighbor GeoNearestNeighbor to merge environemental file and occurrence file toolshed.g2.bx.psu.edu/repos/ecology/ecoregion_geonearestneighbor/ecoregion_GeoNearestNeighbor/0.1.0+galaxy0
19 BRT tool prediction BRT predictions toolshed.g2.bx.psu.edu/repos/ecology/ecoregion_brt_analysis/ecoregion_brt_analysis/0.1.0+galaxy0
20 TaxaSeeker Retrive taxa toolshed.g2.bx.psu.edu/repos/ecology/ecoregion_taxa_seeker/ecoregion_taxa_seeker/0.1.0+galaxy0
21 ClusterEstimate Estimate the number of cluster toolshed.g2.bx.psu.edu/repos/ecology/ecoregion_cluster_estimate/ecoregion_cluster_estimate/0.1.0+galaxy0

Outputs

ID Name Description Type
occ_out occ_out n/a
  • File
occ_env_out occ_env_out n/a
  • File
info_out info_out n/a
  • File
coll_pred coll_pred n/a
  • File
coll_val coll_val n/a
  • File
coll_distri coll_distri n/a
  • File
coll_plots coll_plots n/a
  • File
summary summary n/a
  • File
taxa taxa n/a
  • File
taxa_clean taxa_clean n/a
  • File
SIH_index SIH_index n/a
  • File
data_to_clus data_to_clus n/a
  • File
databio_table databio_table n/a
  • File

Version History

Version 1 (earliest) Created 18th Nov 2024 at 14:13 by Pauline Seguineau

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Citation
Seguineau, P. (2024). Ecoregionalization workflow (Part 1). WorkflowHub. https://doi.org/10.48546/WORKFLOWHUB.WORKFLOW.1208.1
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Created: 18th Nov 2024 at 14:13

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