Workflow 'Biodiversity data exploration tuto'

ecology-biodiversity-data-exploration/main-workflow

Author(s)

Version
1
Last updated
Mar 1, 2022
License
None Specified, defaults to CC-BY-4.0
Tags
ecology

Features
Tutorial
Biodiversity data exploration
Workflow Testing
Tests: ❌
Results: Not yet automated
FAIRness PURL
https://gxy.io/GTN:W00045
RO-Crate logo with flask Download Workflow RO-Crate Workflowhub cloud with gears logo View on WorkflowHub
Launch in Tutorial Mode
Download 
flowchart TD
  0["ℹ️ Input Dataset\nReel_life_survey_fish_modif.tabular"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["Spatial coordinates anonymization"];
  0 -->|output| 1;
  2["Homoscedasticity and normality"];
  0 -->|output| 2;
  3["Variables exploration"];
  0 -->|output| 3;
  4["Presence-absence and abundance"];
  0 -->|output| 4;
  5["Statistics on presence-absence"];
  0 -->|output| 5;
  6["Local Contributions to Beta Diversity LCBD"];
  0 -->|output| 6;

Inputs

Input Label
Input dataset Reel_life_survey_fish_modif.tabular

Outputs

From Output Label
Input dataset Reel_life_survey_fish_modif.tabular
toolshed.g2.bx.psu.edu/repos/ecology/tool_anonymization/tool_anonymization/0.0.0 Spatial coordinates anonymization
toolshed.g2.bx.psu.edu/repos/ecology/ecology_homogeneity_normality/ecology_homogeneity_normality/0.0.0 Homoscedasticity and normality
toolshed.g2.bx.psu.edu/repos/ecology/ecology_link_between_var/ecology_link_between_var/0.0.0 Variables exploration
toolshed.g2.bx.psu.edu/repos/ecology/ecology_presence_abs_abund/ecology_presence_abs_abund/0.0.0 Presence-absence and abundance
toolshed.g2.bx.psu.edu/repos/ecology/ecology_stat_presence_abs/ecology_stat_presence_abs/0.0.0 Statistics on presence-absence
toolshed.g2.bx.psu.edu/repos/ecology/ecology_beta_diversity/ecology_beta_diversity/0.0.0 Local Contributions to Beta Diversity (LCBD)

Tools

Tool Links
toolshed.g2.bx.psu.edu/repos/ecology/ecology_beta_diversity/ecology_beta_diversity/0.0.0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/ecology/ecology_homogeneity_normality/ecology_homogeneity_normality/0.0.0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/ecology/ecology_link_between_var/ecology_link_between_var/0.0.0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/ecology/ecology_presence_abs_abund/ecology_presence_abs_abund/0.0.0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/ecology/ecology_stat_presence_abs/ecology_stat_presence_abs/0.0.0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/ecology/tool_anonymization/tool_anonymization/0.0.0 View in ToolShed

To use these workflows in Galaxy you can either click the links to download the workflows, or you can right-click and copy the link to the workflow which can be used in the Galaxy form to import workflows.

Importing into Galaxy

Below are the instructions for importing these workflows directly into your Galaxy server of choice to start using them!
Hands-on: Importing a workflow
  • Click on Workflow on the top menu bar of Galaxy. You will see a list of all your workflows.
  • Click on Import at the top-right of the screen
  • Provide your workflow
    • Option 1: Paste the URL of the workflow into the box labelled “Archived Workflow URL”
    • Option 2: Upload the workflow file in the box labelled “Archived Workflow File”
  • Click the Import workflow button

Below is a short video demonstrating how to import a workflow from GitHub using this procedure:

Video: Importing a workflow from URL

Version History

Version Commit Time Comments
1 00c1aaba1 2022-03-01 10:05:23 Make some renames for the gtn

For Admins

Installing the workflow tools

wget https://training.galaxyproject.org/training-material/topics/ecology/tutorials/biodiversity-data-exploration/workflows/main_workflow.ga -O workflow.ga
workflow-to-tools -w workflow.ga -o tools.yaml
shed-tools install -g GALAXY -a API_KEY -t tools.yaml
workflow-install -g GALAXY -a API_KEY -w workflow.ga --publish-workflows