Workflow Constructed From History 'IWTomics Workflow'

statistics-iwtomics/iwtomics-workflow

Author(s)

Version
5
Last updated
Oct 21, 2021
License
None Specified, defaults to CC-BY-4.0
Tags
genomics
iwtomics
statistics

Features
Tutorial
Interval-Wise Testing for omics data
Workflow Testing
Tests: ❌
Results: Not yet automated
FAIRness PURL
https://gxy.io/GTN:W00227
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 Dataset\nETn_fixed.bed"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nControl.bed"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["ℹ️ Input Dataset\nfeatures_header.tabular"];
  style 2 stroke:#2c3143,stroke-width:4px;
  3["ℹ️ Input Dataset\nregions_header.tabular"];
  style 3 stroke:#2c3143,stroke-width:4px;
  4["ℹ️ Input Dataset\nRecombination_hotspots.txt"];
  style 4 stroke:#2c3143,stroke-width:4px;
  5["IWTomics Load"];
  4 -->|output| 5;
  2 -->|output| 5;
  0 -->|output| 5;
  1 -->|output| 5;
  3 -->|output| 5;
  6["IWTomics Test"];
  5 -->|outfeatures| 6;
  5 -->|outrdata| 6;
  5 -->|outregions| 6;
  7["IWTomics Plot with Threshold"];
  6 -->|iwtomicsselectedfeatures| 7;
  6 -->|iwtomicsrdata| 7;
  6 -->|iwtomicstests| 7;

Inputs

Input Label
Input dataset ETn_fixed.bed
Input dataset Control.bed
Input dataset features_header.tabular
Input dataset regions_header.tabular
Input dataset Recombination_hotspots.txt

Outputs

From Output Label

Tools

Tool Links
toolshed.g2.bx.psu.edu/repos/iuc/iwtomics_loadandplot/iwtomics_loadandplot/1.0.0.0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/iwtomics_plotwithscale/iwtomics_plotwithscale/1.0.0.0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/iwtomics_testandplot/iwtomics_testandplot/1.0.0.0 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
6 b97fcf8db 2021-10-21 14:03:55 Updating IWTomics data
5 667ff3de9 2020-01-22 10:59:29 annotation
4 eb4d724e0 2020-01-15 10:41:35 Workflow renaming
3 361236c41 2019-04-04 09:00:14 Changed format of workflows
2 251bebcf1 2018-06-13 13:06:36 workflow fixed
1 5752bb6b9 2018-06-13 11:32:26 IWTomics Workflow

For Admins

Installing the workflow tools

wget https://training.galaxyproject.org/training-material/topics/statistics/tutorials/iwtomics/workflows/IWTomics_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