GTN Training: Workflow Reports

galaxy-interface-workflow-reports/workflow-reports-final-workflow

Author(s)

Version
1
Last updated
Jun 2, 2022
License
None Specified, defaults to CC-BY-4.0
Tags
galaxy-interface

Features
Tutorial
Workflow Reports
Other workflows associated with this material
Workflow Testing
Tests: ❌
Results: Not yet automated
FAIRness PURL
https://gxy.io/GTN:W00084
RO-Crate logo with flask Download Workflow RO-Crate Workflowhub cloud with gears logo View on WorkflowHub
Launch in Tutorial Mode
Download 
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

Tool Links
Cut1
Grouping1
Remove beginning1
csv_to_tabular
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sorted_uniq/1.1.0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.1.0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_point/ggplot2_point/3.3.5+galaxy0 View in ToolShed

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 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