Simtext training workflow

statistics-text-mining_simtext/main-workflow

Author(s)

Version
1
Last updated
Apr 5, 2021
License
None Specified, defaults to CC-BY-4.0
Tags
text-mining
statistics
visualisation
PubMed
PubTator

Features
Tutorial
Text-mining with the SimText toolset
Workflow Testing
Tests: ❌
Results: Not yet automated
FAIRness PURL
https://gxy.io/GTN:W00230
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\nInput dataset"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["PubMed query"];
  0 -->|output| 1;
  2["PMIDs to PubTator"];
  1 -->|output| 2;
  3["simtext_app"];
  0 -->|output| 3;
  2 -->|output| 3;

Inputs

Input Label
Input dataset

Outputs

From Output Label
toolshed.g2.bx.psu.edu/repos/iuc/pubmed_by_queries/pubmed_by_queries/0.0.2 PubMed query
toolshed.g2.bx.psu.edu/repos/iuc/pmids_to_pubtator_matrix/pmids_to_pubtator_matrix/0.0.2 PMIDs to PubTator
interactive_tool_simtext_app simtext_app

Tools

Tool Links
interactive_tool_simtext_app
toolshed.g2.bx.psu.edu/repos/iuc/pmids_to_pubtator_matrix/pmids_to_pubtator_matrix/0.0.2 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/pubmed_by_queries/pubmed_by_queries/0.0.2 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 9ac4bf8f2 2021-03-31 09:54:54 Change topic of training to statistics

For Admins

Installing the workflow tools

wget https://training.galaxyproject.org/training-material/topics/statistics/tutorials/text-mining_simtext/workflows/main_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