analyze_screen

imaging-hela-screen-analysis/analyze-screen

Author(s)
Till Korten
Version
5
Last updated
Dec 5, 2023
License
MIT
Tags

Features
Tutorial
Analyse HeLa fluorescence siRNA screen
Other workflows associated with this material
Workflow Testing
Tests: ✅
Results: Not yet automated
FAIRness PURL
https://gxy.io/GTN:W00101
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 Collection\ninput images"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nrules"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["🛠️ Subworkflow\nfeature_extraction"];
  style 2 fill:#edd,stroke:#900,stroke-width:4px;
  0 -->|output| 2;
  1 -->|output| 2;
  3["merge_table"];
  2 -->|output| 3;
  3fc2324d-233b-4785-9fb7-9c30b2daaef4["Output\noutput"];
  3 --> 3fc2324d-233b-4785-9fb7-9c30b2daaef4;
  style 3fc2324d-233b-4785-9fb7-9c30b2daaef4 stroke:#2c3143,stroke-width:4px;

Inputs

Input Label
Input dataset collection input images
Input dataset rules

Outputs

From Output Label
toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0 Collapse Collection merge_table

Tools

Tool Links
toolshed.g2.bx.psu.edu/repos/imgteam/2d_auto_threshold/ip_threshold/0.0.5 View in ToolShed
toolshed.g2.bx.psu.edu/repos/imgteam/2d_feature_extraction/ip_2d_feature_extraction/0.1.1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/imgteam/2d_filter_segmentation_by_features/ip_2d_filter_segmentation_by_features/0.0.1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/imgteam/2d_simple_filter/ip_filter_standard/0.0.3 View in ToolShed
toolshed.g2.bx.psu.edu/repos/imgteam/2d_split_binaryimage_by_watershed/ip_2d_split_binaryimage_by_watershed/0.0.1
toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0 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
7 d1e807a66 2023-11-08 10:56:10 fixed json syntax
6 e34767b4a 2023-11-08 10:48:59 added `creator` and `license` fields
5 fab15d8bf 2023-11-07 17:02:31 updated analyze_screen.ga
4 667ff3de9 2020-01-22 10:59:29 annotation
3 eb4d724e0 2020-01-15 10:41:35 Workflow renaming
2 faf6d298a 2019-12-12 13:02:33 unflatten workflows
1 96462d6dc 2019-08-06 12:50:14 added second tutorial

For Admins

Installing the workflow tools

wget https://training.galaxyproject.org/training-material/topics/imaging/tutorials/hela-screen-analysis/workflows/analyze_screen.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