Ecoregionalization workflow

Associated Tutorial

This workflows is part of the tutorial Ecoregionalization workflow tutorial, available in the GTN

Features

Includes Galaxy Workflow Tests
Uses Galaxy Workflow Comments

Thanks to...

Workflow Author(s): Seguineau Pauline

Tutorial Author(s): Pauline Seguineau

Tutorial Contributor(s): Yvan Le Bras, Marie Josse, Ankerl Yassine, Coline Royaux, Helena Rasche, Saskia Hiltemann, Björn Grüning

Funder(s): Pôle National de Données de Biodiversité, Antarctic and Southern Ocean Coalition

Inputs

ID	Name	Description	Type
ceamarc_env.tsv	ceamarc_env.tsv	n/a	File
occurrence.txt	occurrence.txt	n/a	File
pivot_wider_jupytool_notebook.ipynb	pivot_wider_jupytool_notebook.ipynb	n/a	File

Steps

ID	Name	Description
3	Advanced Cut	toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/9.3+galaxy1
4	Column Regex Find And Replace	toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regexColumn1/1.0.3
5	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	toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regexColumn1/1.0.3
7	Column Regex Find And Replace	toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regexColumn1/1.0.3
8	Filter Tabular	toolshed.g2.bx.psu.edu/repos/iuc/filter_tabular/filter_tabular/3.3.0
9	Column Regex Find And Replace	toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regexColumn1/1.0.3
10	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	toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regexColumn1/1.0.3
12	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	toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regexColumn1/1.0.3
14	Merge Columns	toolshed.g2.bx.psu.edu/repos/devteam/merge_cols/mergeCols1/1.0.2
15	Advanced Cut	toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/9.3+galaxy1
16	Interactive JupyTool and notebook	interactive_tool_jupyter_notebook
17	GeoNearestNeighbor	toolshed.g2.bx.psu.edu/repos/ecology/ecoregion_geonearestneighbor/ecoregion_GeoNearestNeighbor/0.1.0+galaxy0
18	BRT tool prediction	toolshed.g2.bx.psu.edu/repos/ecology/ecoregion_brt_analysis/ecoregion_brt_analysis/0.1.0+galaxy0
19	TaxaSeeker	toolshed.g2.bx.psu.edu/repos/ecology/ecoregion_taxa_seeker/ecoregion_taxa_seeker/0.1.0+galaxy0
20	ClusterEstimate	toolshed.g2.bx.psu.edu/repos/ecology/ecoregion_cluster_estimate/ecoregion_cluster_estimate/0.1.0+galaxy0
21	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
22	EcoMap	toolshed.g2.bx.psu.edu/repos/ecology/ecoregion_eco_map/ecoregion_eco_map/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
SIH_plot	SIH_plot	n/a	File
cluster_points	cluster_points	n/a	File
cluster_info	cluster_info	n/a	File
eco_map	eco_map	n/a	File

Ecoregionalization workflow
1.0

Associated Tutorial

Features

Thanks to...

Inputs

Steps

Outputs

Version History

1.0 (earliest) Created 2nd Jun 2025 at 11:04 by GTN Bot

Creators

Submitter

Ecoregionalization workflow 1.0

Associated Tutorial

Features

Thanks to...

Inputs

Steps

Outputs

Version History

1.0 (earliest) Created 2nd Jun 2025 at 11:04 by GTN Bot

Creators

Submitter

Related items

Ecoregionalization workflow
1.0