Proteomics: MaxQuant workflow
proteomics-maxquant-label-free/maxquant-label-free
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flowchart TD 0["ℹ️ Input Dataset\nProtein_database"]; style 0 stroke:#2c3143,stroke-width:4px; 1["ℹ️ Input Dataset\nSample1"]; style 1 stroke:#2c3143,stroke-width:4px; 2["ℹ️ Input Dataset\nSample2"]; style 2 stroke:#2c3143,stroke-width:4px; 3["MaxQuant"]; 0 -->|output| 3; 1 -->|output| 3; 2 -->|output| 3; 4["Filter"]; 3 -->|proteinGroups| 4; 5["Select"]; 4 -->|out_file1| 5; 6["Cut"]; 5 -->|out_file1| 6; 7["Sort"]; 6 -->|out_file1| 7; 8["Compute"]; 6 -->|out_file1| 8; 9["Sort"]; 7 -->|outfile| 9; 10["Compute"]; 8 -->|out_file1| 10; 11["Cut"]; 10 -->|out_file1| 11; 12["Compute"]; 10 -->|out_file1| 12; 13["Histogram"]; 12 -->|out_file1| 13;
Inputs
Input | Label |
---|---|
Input dataset | Protein_database |
Input dataset | Sample1 |
Input dataset | Sample2 |
Outputs
From | Output | Label |
---|---|---|
Input dataset | Protein_database | |
Input dataset | Sample1 | |
Input dataset | Sample2 | |
toolshed.g2.bx.psu.edu/repos/galaxyp/maxquant/maxquant/1.6.10.43+galaxy3 | MaxQuant | |
Filter1 | Filter | |
Grep1 | Select | |
Cut1 | Cut | |
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/1.1.1 | Sort | |
toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/1.3.0 | Compute | |
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/1.1.1 | Sort | |
toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/1.3.0 | Compute | |
Cut1 | Cut | |
toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/1.3.0 | Compute | |
toolshed.g2.bx.psu.edu/repos/devteam/histogram/histogram_rpy/1.0.4 | Histogram |
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 |
---|---|---|---|
8 | 1a316efff | 2020-11-15 23:35:58 | update wf parameter |
7 | dffe67cc1 | 2020-10-31 19:54:12 | Updating figure and workflow |
6 | 3fd8e24d1 | 2020-10-22 11:42:53 | Adding steps to workflow |
5 | cf8b1cb05 | 2020-08-31 01:11:11 | Update some workflow names for consistency |
4 | cdab43efb | 2020-08-03 04:07:53 | update maxquant workflow histogram version to 1.0.4, add test |
3 | ba67a0dfe | 2020-06-07 22:01:16 | Adding a few more follow up steps and improving some older training content |
2 | 5d041fcf7 | 2020-04-29 16:49:34 | adding more stuff to the workflow |
1 | 83de9bde8 | 2020-04-29 15:54:56 | Adding MaxQuant training and levels for other proteomics tutorials |
For Admins
Installing the workflow tools
wget https://training.galaxyproject.org/training-material/topics/proteomics/tutorials/maxquant-label-free/workflows/maxquant_label_free.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