EncyclopeDIA-GTN
proteomics-encyclopedia/main-workflow
Launch in Tutorial Mode
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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
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 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
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