Workflows

These workflows are associated with EncyclopeDIA

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.

EncyclopeDIA-GTN
GalaxyP

Last updated Sep 4, 2024

Launch in Tutorial Mode
License: CC-BY-4.0
Tests: ✅ Results: Not yet automated

Download Galaxy Workflow.ga Galaxy Europe Galaxy France Galaxy Main Galaxy Australia Import to another server (≥23.0+ only!) 
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;

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