Find exons with the highest number of features

introduction-galaxy-intro-101/galaxy-intro-101-workflow

Author(s)
Anton Nekrutenko, Helena Rasche
Version
5
Last updated
Mar 21, 2024
License
CC-BY-4.0
Tags
introduction

Features
Tutorial
Galaxy Basics for genomics
Workflow Testing
Tests: ✅
Results:
FAIRness PURL
https://gxy.io/GTN:W00108
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\nExons"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nFeatures"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["bedtools Intersect intervals"];
  0 -->|output| 2;
  1 -->|output| 2;
  3["Datamash"];
  2 -->|output| 3;
  4["Sort"];
  3 -->|out_file| 4;
  5["Select first"];
  4 -->|outfile| 5;
  6["Compare two Datasets"];
  0 -->|output| 6;
  5 -->|outfile| 6;
  565e3d76-0230-4a5e-87c1-9c36ce0b7df8["Output\ntop_5_exons"];
  6 --> 565e3d76-0230-4a5e-87c1-9c36ce0b7df8;
  style 565e3d76-0230-4a5e-87c1-9c36ce0b7df8 stroke:#2c3143,stroke-width:4px;

Inputs

Input Label
Input dataset Exons
Input dataset Features

Outputs

From Output Label
comp1 Compare two Datasets

Tools

Tool Links
comp1
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_head_tool/1.1.0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/1.1.1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.30.0+galaxy1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.1.0 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
8 a448d3356 2024-03-20 16:33:47 added modified workflow
7 f90859e9d 2023-05-18 17:25:14 Fix workflow for planemo
6 553ea8e51 2022-04-13 16:26:45 Rename workflow
5 a49d7d1a4 2022-04-13 16:24:48 Include modifications
4 222c554db 2021-07-20 16:47:36 workflow annotation wteaks
3 43d15ed0c 2021-07-20 16:08:52 Refresh for galaxy101
2 d0f7b8009 2020-10-18 17:31:54 Added workflow test.
1 bffe460ee 2020-10-18 16:42:47 Added workflow.

For Admins

Installing the workflow tools

wget https://training.galaxyproject.org/training-material/topics/introduction/tutorials/galaxy-intro-101/workflows/galaxy-intro-101-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