EncyclopeDIA-GTN

proteomics-encyclopedia/main-workflow

Author(s)
GalaxyP
Version
2
Last updated
Sep 4, 2024
License
CC-BY-4.0
Tags
proteomics

Features
Tutorial
EncyclopeDIA
Workflow Testing
Tests: ✅
Results: Not yet automated
FAIRness PURL
https://gxy.io/GTN:W00155
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 Collection\nGPF DIA RAW Files Dataset collection"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Collection\nEXPERIMENTAL DIA RAW FILES WIDE"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["ℹ️ Input Dataset\nSPECTRAL OR PROSIT LIBRARY"];
  style 2 stroke:#2c3143,stroke-width:4px;
  3["ℹ️ Input Dataset\nBACKGROUND PROTEIN FASTA FILE"];
  style 3 stroke:#2c3143,stroke-width:4px;
  4["Converting RAW to mzml "];
  0 -->|output| 4;
  ee41b00e-11e5-4943-96d0-bb64a0dd976c["Output\nGPF_MZML"];
  4 --> ee41b00e-11e5-4943-96d0-bb64a0dd976c;
  style ee41b00e-11e5-4943-96d0-bb64a0dd976c stroke:#2c3143,stroke-width:4px;
  5["msconvert"];
  1 -->|output| 5;
  982b3988-74ff-4755-b03f-564fd72adad9["Output\nExperimental-dataset-MZML"];
  5 --> 982b3988-74ff-4755-b03f-564fd72adad9;
  style 982b3988-74ff-4755-b03f-564fd72adad9 stroke:#2c3143,stroke-width:4px;
  6["Library searching"];
  3 -->|output| 6;
  2 -->|output| 6;
  4 -->|output| 6;
  a6ae2431-c813-408e-b67f-4df16f4d9816["Output\nCHROMATOGRAM LIBRARY"];
  6 --> a6ae2431-c813-408e-b67f-4df16f4d9816;
  style a6ae2431-c813-408e-b67f-4df16f4d9816 stroke:#2c3143,stroke-width:4px;
  1c3b0d2e-8786-4f81-8ac5-a932fe3759c6["Output\nLOG"];
  6 --> 1c3b0d2e-8786-4f81-8ac5-a932fe3759c6;
  style 1c3b0d2e-8786-4f81-8ac5-a932fe3759c6 stroke:#2c3143,stroke-width:4px;
  7["EncyclopeDIA Quantify"];
  3 -->|output| 7;
  6 -->|elib| 7;
  5 -->|output| 7;
  6fcebd60-0aa2-4833-ab18-bf3fad5f2e34["Output\nQuant-LOG"];
  7 --> 6fcebd60-0aa2-4833-ab18-bf3fad5f2e34;
  style 6fcebd60-0aa2-4833-ab18-bf3fad5f2e34 stroke:#2c3143,stroke-width:4px;
  31f9b9fa-9e6c-4531-b207-e6a4547f96a0["Output\nQUANT LIBRARY"];
  7 --> 31f9b9fa-9e6c-4531-b207-e6a4547f96a0;
  style 31f9b9fa-9e6c-4531-b207-e6a4547f96a0 stroke:#2c3143,stroke-width:4px;
  a6d58aaf-fd7b-4d14-92ce-c217e2fbad18["Output\nPEPTIDE QUANTITATION OUTPUT"];
  7 --> a6d58aaf-fd7b-4d14-92ce-c217e2fbad18;
  style a6d58aaf-fd7b-4d14-92ce-c217e2fbad18 stroke:#2c3143,stroke-width:4px;
  5cc9b38b-8355-4367-ab3e-382333a73eff["Output\nPROTEIN QUANTITATION OUTPUT"];
  7 --> 5cc9b38b-8355-4367-ab3e-382333a73eff;
  style 5cc9b38b-8355-4367-ab3e-382333a73eff stroke:#2c3143,stroke-width:4px;

Inputs

Input Label
Input dataset collection GPF DIA RAW Files (Dataset collection)
Input dataset collection EXPERIMENTAL DIA RAW FILES (WIDE)
Input dataset SPECTRAL OR PROSIT LIBRARY
Input dataset BACKGROUND PROTEIN FASTA FILE

Outputs

From Output Label
toolshed.g2.bx.psu.edu/repos/galaxyp/msconvert/msconvert/3.0.20287.2 msconvert Converting RAW to mzml
toolshed.g2.bx.psu.edu/repos/galaxyp/msconvert/msconvert/3.0.20287.2 msconvert
toolshed.g2.bx.psu.edu/repos/galaxyp/encyclopedia_searchtolib/encyclopedia_searchtolib/1.2.2+galaxy0 SearchToLib Library searching
toolshed.g2.bx.psu.edu/repos/galaxyp/encyclopedia_quantify/encyclopedia_quantify/1.2.2+galaxy0 EncyclopeDIA Quantify

Tools

Tool Links
toolshed.g2.bx.psu.edu/repos/galaxyp/encyclopedia_quantify/encyclopedia_quantify/1.2.2+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/galaxyp/encyclopedia_searchtolib/encyclopedia_searchtolib/1.2.2+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/galaxyp/msconvert/msconvert/3.0.20287.2 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
7 dec1b6f1d 2024-08-29 21:42:21 remove ga
6 cb6a5053b 2024-08-28 15:34:57 Update main_workflow.ga
5 3a53b7e1d 2024-08-28 15:24:46 Update main_workflow.ga
4 9126f68f0 2021-06-16 16:09:53 Update main_workflow.ga
3 0a1ee8353 2021-06-16 16:07:10 Rename Workflow-May19_EncyclopeDIA_raw_inputs.ga to main_workflow.ga
2 c07e80f5e 2021-06-16 16:06:53 Delete main_workflow.ga
1 34e20aef0 2020-12-14 16:52:55 add tutorial skeleton

For Admins

Installing the workflow tools

wget https://training.galaxyproject.org/training-material/topics/proteomics/tutorials/encyclopedia/workflows/main_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