DIA_lib_OSW

proteomics-DIA_lib_OSW/galaxy-workflow-dia-lib-training-hek-ecoli-3-eg-data

Author(s)

Version
2
Last updated
Dec 2, 2020
License
None Specified, defaults to CC-BY-4.0
Tags
proteomics

Features
Tutorial
Library Generation for DIA Analysis
Workflow Testing
Tests: ❌
Results: Not yet automated
FAIRness PURL
https://gxy.io/GTN:W00151
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\nHEK_Ecoli_exp_design.txt"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\niRTassays.tsv"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["ℹ️ Input Collection\nFASTA collection"];
  style 2 stroke:#2c3143,stroke-width:4px;
  3["ℹ️ Input Collection\nDDA_data collection"];
  style 3 stroke:#2c3143,stroke-width:4px;
  4["MaxQuant"];
  2 -->|output| 4;
  3 -->|output| 4;
  0 -->|output| 4;
  5["Filter"];
  4 -->|evidence| 5;
  6["Filter"];
  4 -->|msms| 6;
  7["diapysef library generation"];
  5 -->|out_file1| 7;
  1 -->|output| 7;
  6 -->|out_file1| 7;
  8["OpenSwathAssayGenerator"];
  7 -->|output_tabular| 8;
  9["OpenSwathDecoyGenerator"];
  8 -->|out| 9;
  10["TargetedFileConverter"];
  9 -->|out| 10;

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
2 15a13c366 2020-12-02 17:50:43 updated workflow annotation and name
1 e8f20c190 2020-12-02 17:31:58 generated three tutorials on DIA data analysis in galaxy

For Admins

Installing the workflow tools

wget https://training.galaxyproject.org/training-material/topics/proteomics/tutorials/DIA_lib_OSW/workflows/Galaxy-Workflow-DIA_lib_Training_HEK_Ecoli_3_EG_data.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