Ecoregionalization workflow (Part 1) Version 1
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Run on GalaxyPart 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 |
|
| ceamarc_env.tab | ceamarc_env.tab | Environment file |
|
| pivot_wider_jupytool_notebook.ipynb | pivot_wider_jupytool_notebook.ipynb | Jupyter Notebook 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 |
|
| occ_env_out | occ_env_out | n/a |
|
| info_out | info_out | n/a |
|
| coll_pred | coll_pred | n/a |
|
| coll_val | coll_val | n/a |
|
| coll_distri | coll_distri | n/a |
|
| coll_plots | coll_plots | n/a |
|
| summary | summary | n/a |
|
| taxa | taxa | n/a |
|
| taxa_clean | taxa_clean | n/a |
|
| SIH_index | SIH_index | n/a |
|
| data_to_clus | data_to_clus | n/a |
|
| databio_table | databio_table | n/a |
|
Version History
Version 1 (earliest) Created 18th Nov 2024 at 14:13 by Pauline Seguineau
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Views: 65 Downloads: 14 Runs: 0
Created: 18th Nov 2024 at 14:13
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