Workflows

These workflows are associated with Annotating a protein list identified by LC-MS/MS experiments

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.

flowchart TD
  0["ℹ️ Input Dataset\nInput dataset"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nInput dataset"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["ℹ️ Input Dataset\nInput dataset"];
  style 2 stroke:#2c3143,stroke-width:4px;
  3["Build tissue-specific expression dataset"];
  4["Filter by keywords and/or numerical value"];
  1 -->|output| 4;
  5["ID Converter"];
  3 -->|output| 5;
  6["ID Converter"];
  4 -->|kept_lines| 6;
  7["Venn diagram"];
  4 -->|kept_lines| 7;
  0 -->|output| 7;
  2 -->|output| 7;
  8["Add expression data"];
  6 -->|output| 8;
  9["Filter by keywords and/or numerical value"];
  8 -->|output| 9;
  10["GO terms classification and enrichment analysis"];
  5 -->|output| 10;
  9 -->|kept_lines| 10;
  11["Query pathway database"];
  9 -->|kept_lines| 11;
	

flowchart TD
  0["ℹ️ Input Dataset\nLacombe_et_al_2017.txt"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nBredberg.txt"];
  style 1 stroke:#2c3143,stroke-width:4px;
  10["View proteins on Reactome maps"];
  9 -->|kept_lines| 10;
  11["GO terms classification and enrichment analysis"];
  5 -->|output| 11;
  9 -->|kept_lines| 11;
  2["ℹ️ Input Dataset\nMucilli.txt"];
  style 2 stroke:#2c3143,stroke-width:4px;
  3["Build a lung proteome as a background "];
  4["Filter technical contaminants"];
  0 -->|output| 4;
  5["ID Converter"];
  3 -->|output| 5;
  6["ID mapping UniProt <-> ENSG ID"];
  4 -->|kept_lines| 6;
  7["MS/MS datasets comparison"];
  4 -->|kept_lines| 7;
  1 -->|output| 7;
  2 -->|output| 7;
  8["Add expression data"];
  6 -->|output| 8;
  9["Filter biological contaminants"];
  8 -->|output| 9;
	

Importing into Galaxy

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: