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
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 galaxy-upload 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