GO Enrichment Workflow

transcriptomics-goenrichment/goenrichment-workflow

Author(s)

version Version
3
last_modification Last updated
Jan 17, 2020
license License
None Specified, defaults to CC-BY-4.0
galaxy-tags Tags
transcriptomics

Features

Tutorial
hands_on GO Enrichment Analysis

Workflow Testing
Tests: ❌
Results: Not yet automated
FAIRness purl PURL
https://gxy.io/GTN:W00238
RO-Crate logo with flask Download Workflow RO-Crate Workflowhub cloud with gears logo View on WorkflowHub
Launch in Tutorial Mode question
galaxy-download Download
flowchart TD
  0["ℹ️ Input Dataset\nGO annotations Drosophila melanogaster"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nGO"];
  style 1 stroke:#2c3143,stroke-width:4px;
  10["Filter"];
  2 -->|output| 10;
  11["GOEnrichment"];
  3 -->|output| 11;
  1 -->|output| 11;
  4 -->|output| 11;
  5 -->|output| 11;
  12["GOEnrichment"];
  3 -->|output| 12;
  1 -->|output| 12;
  4 -->|output| 12;
  5 -->|output| 12;
  13["GOSlimmer"];
  3 -->|output| 13;
  1 -->|output| 13;
  6 -->|output| 13;
  14["GOEnrichment"];
  3 -->|output| 14;
  1 -->|output| 14;
  4 -->|output| 14;
  7 -->|output| 14;
  15["GOEnrichment"];
  3 -->|output| 15;
  1 -->|output| 15;
  4 -->|output| 15;
  8 -->|output| 15;
  16["GOEnrichment"];
  0 -->|output| 16;
  1 -->|output| 16;
  2 -->|output| 16;
  9 -->|out_file1| 16;
  17["GOEnrichment"];
  0 -->|output| 17;
  1 -->|output| 17;
  10 -->|out_file1| 17;
  9 -->|out_file1| 17;
  18["GOEnrichment"];
  13 -->|output| 18;
  6 -->|output| 18;
  4 -->|output| 18;
  5 -->|output| 18;
  2["ℹ️ Input Dataset\ntrapnellPopulation.tab"];
  style 2 stroke:#2c3143,stroke-width:4px;
  3["ℹ️ Input Dataset\nGO annotations Mus musculus"];
  style 3 stroke:#2c3143,stroke-width:4px;
  4["ℹ️ Input Dataset\nMouse population"];
  style 4 stroke:#2c3143,stroke-width:4px;
  5["ℹ️ Input Dataset\nMouse diff"];
  style 5 stroke:#2c3143,stroke-width:4px;
  6["ℹ️ Input Dataset\nGO Slim"];
  style 6 stroke:#2c3143,stroke-width:4px;
  7["ℹ️ Input Dataset\nmouseUnderexpressed.txt"];
  style 7 stroke:#2c3143,stroke-width:4px;
  8["ℹ️ Input Dataset\nmouseOverexpressed.txt"];
  style 8 stroke:#2c3143,stroke-width:4px;
  9["Filter"];
  2 -->|output| 9;

Inputs

Input Label
Input dataset GO annotations Drosophila melanogaster
Input dataset GO
Input dataset trapnellPopulation.tab
Input dataset GO annotations Mus musculus
Input dataset Mouse population
Input dataset Mouse diff
Input dataset GO Slim
Input dataset mouseUnderexpressed.txt
Input dataset mouseOverexpressed.txt

Outputs

From Output Label

Tools

Tool Links
Filter1
toolshed.g2.bx.psu.edu/repos/iuc/goenrichment/goenrichment/2.0.1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/goslimmer/goslimmer/1.0.1 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 galaxy-upload 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
3 eb4d724e0 2020-01-15 10:41:35 Workflow renaming
2 361236c41 2019-04-04 09:00:14 Changed format of workflows
1 79f4dd991 2019-02-14 21:26:21 Create goenrichment-workflow.ga

For Admins

Installing the workflow tools

wget https://training.galaxyproject.org/training-material/topics/transcriptomics/tutorials/goenrichment/workflows/goenrichment-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