Calculating diversity from microbiome taxonomic data

microbiome-diversity/workflow

Author(s)
Paul Zierep, Sophia Hampe, Bérénice Batut
Version
1
Last updated
Aug 6, 2024
License
MIT
Tags
name:GTN

Features
Tutorial
Calculating α and β diversity from microbiome taxonomic data
Workflow Testing
Tests: ✅
Results: Not yet automated
FAIRness PURL
https://gxy.io/GTN:W00276
RO-Crate logo with flask Download Workflow RO-Crate Workflowhub cloud with gears logo View on (Dev) WorkflowHub
Launch in Tutorial Mode
Download 
flowchart TD
  0["ℹ️ Input Collection\nInput Dataset Collection"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["Krakentools: Calculates alpha diversity"];
  0 -->|output| 1;
  2["Krakentools: Calculates alpha diversity"];
  0 -->|output| 2;
  3["Krakentools: Calculates alpha diversity"];
  0 -->|output| 3;
  4["Krakentools: Calculates alpha diversity"];
  0 -->|output| 4;
  5["Krakentools: Calculates alpha diversity"];
  0 -->|output| 5;
  6["Krakentools: calculates beta diversity Bray-Curtis dissimilarity"];
  0 -->|output| 6;

Inputs

Input Label
Input dataset collection Input Dataset Collection

Outputs

From Output Label

Tools

Tool Links
toolshed.g2.bx.psu.edu/repos/iuc/krakentools_alpha_diversity/krakentools_alpha_diversity/1.2+galaxy1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/krakentools_beta_diversity/krakentools_beta_diversity/1.2+galaxy1 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
5 e548ec8fc 2024-08-05 07:30:23 add orcid to WF
4 7e3938070 2024-08-05 07:08:44 add license, fix alpha div formula, add subsections
3 d448f8052 2024-08-05 06:32:59 update wf creator
2 c0ff830e1 2024-08-01 13:32:54 fix workflow
1 cd4066fc9 2024-08-01 13:18:03 add workflow

For Admins

Installing the workflow tools

wget https://training.galaxyproject.org/training-material/topics/microbiome/tutorials/diversity/workflows/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