GTN Training: Workflow Reports
galaxy-interface-workflow-reports/workflow-reports-final-workflow
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flowchart TD 0["ℹ️ Input Dataset\nIris Dataset"]; style 0 stroke:#2c3143,stroke-width:4px; 1["Convert CSV to tabular"]; 0 -->|output| 1; 2["Datamash"]; 1 -->|tabular| 2; 5381f9b0-5170-484c-828e-4469ec27ab3e["Output\ndatamash_output"]; 2 --> 5381f9b0-5170-484c-828e-4469ec27ab3e; style 5381f9b0-5170-484c-828e-4469ec27ab3e stroke:#2c3143,stroke-width:4px; 3["Remove beginning"]; 1 -->|tabular| 3; 4["Cut"]; 3 -->|out_file1| 4; 5["Group"]; 3 -->|out_file1| 5; 836a57b3-3657-435b-b396-869af7e2f35e["Output\ngroup1"]; 5 --> 836a57b3-3657-435b-b396-869af7e2f35e; style 836a57b3-3657-435b-b396-869af7e2f35e stroke:#2c3143,stroke-width:4px; 6["Group"]; 3 -->|out_file1| 6; 82e163a4-8fc5-4b8e-8186-9fc66cd75b1d["Output\ngroup2"]; 6 --> 82e163a4-8fc5-4b8e-8186-9fc66cd75b1d; style 82e163a4-8fc5-4b8e-8186-9fc66cd75b1d stroke:#2c3143,stroke-width:4px; 7["Scatterplot with ggplot2"]; 3 -->|out_file1| 7; bbbac6ca-64fb-46ad-8798-6c7c5369ccaf["Output\nSepal Plot (PNG)"]; 7 --> bbbac6ca-64fb-46ad-8798-6c7c5369ccaf; style bbbac6ca-64fb-46ad-8798-6c7c5369ccaf stroke:#2c3143,stroke-width:4px; 8["Scatterplot with ggplot2"]; 3 -->|out_file1| 8; 74ee0c3c-53c2-44cf-b0e8-2a10c24166c9["Output\nPetal Plot (PNG)"]; 8 --> 74ee0c3c-53c2-44cf-b0e8-2a10c24166c9; style 74ee0c3c-53c2-44cf-b0e8-2a10c24166c9 stroke:#2c3143,stroke-width:4px; 9["Unique"]; 4 -->|out_file1| 9; 6bcc2f96-255e-48f5-a37b-7d6a2c123493["Output\nIris Species"]; 9 --> 6bcc2f96-255e-48f5-a37b-7d6a2c123493; style 6bcc2f96-255e-48f5-a37b-7d6a2c123493 stroke:#2c3143,stroke-width:4px;
Inputs
Input | Label |
---|---|
Input dataset | Iris Dataset |
Outputs
From | Output | Label |
---|---|---|
toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.1.0 | Datamash | |
Grouping1 | Group | |
Grouping1 | Group | |
toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_point/ggplot2_point/3.3.5+galaxy0 | Scatterplot with ggplot2 | |
toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_point/ggplot2_point/3.3.5+galaxy0 | Scatterplot with ggplot2 | |
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sorted_uniq/1.1.0 | Unique |
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 |
---|---|---|---|
1 | a8cea912f | 2022-06-01 14:08:14 | add final workflow with report |
For Admins
Installing the workflow tools
wget https://training.galaxyproject.org/training-material/topics/galaxy-interface/tutorials/workflow-reports/workflows/workflow_reports_final_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