flowchart TD
0["Expression matrix"];
1["Metadata"];
2["annotateMyIDs"];
0 -->|output_tabular| 2;
8415bac0-6beb-467d-a0fa-fb6465987ff7["Output\nannotateMyIDs on input dataset(s): Annotated IDs"];
2 --> 8415bac0-6beb-467d-a0fa-fb6465987ff7;
style 8415bac0-6beb-467d-a0fa-fb6465987ff7 stroke:#2c3143,stroke-width:4px;
3["Regex Find And Replace"];
1 -->|output| 3;
4["🛠️ Subworkflow\nCopy of Convert from Ensembl to GeneSymbol, summing duplicate genes"];
style 4 fill:#edd,stroke:#900,stroke-width:4px;
2 -->|out_tab| 4;
0 -->|output_tabular| 4;
5["Construct Expression Set Object"];
4 -->|Gene Symbol Count Matrix| 5;
3 -->|out_file1| 5;
6["Manipulate Expression Set Object"];
5 -->|out_rds| 6;
88196d0b-7254-4794-b08a-5409f19c8323["Output\nManipulate Expression Set Object on input dataset(s): ExpressionSet Object"];
6 --> 88196d0b-7254-4794-b08a-5409f19c8323;
style 88196d0b-7254-4794-b08a-5409f19c8323 stroke:#2c3143,stroke-width:4px;
7["Manipulate Expression Set Object"];
5 -->|out_rds| 7;
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-uploadImport 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:
Download Workflow RO-Crate
View on WorkflowHub