Zauberkugel

computational-chemistry-zauberkugel/main-workflow

Author(s)
Aurélien F. A. Moumbock, Albert-Ludwigs-Universität Freiburg
Version
1
Last updated
Feb 15, 2022
License
MIT
Tags
cheminformatics
computational-chemistry

Features
Tutorial
Protein target prediction of a bioactive ligand with Align-it and ePharmaLib
Workflow Testing
Tests: ❌
Results: Not yet automated
FAIRness PURL
https://gxy.io/GTN:W00039
RO-Crate logo with flask Download Workflow RO-Crate Workflowhub cloud with gears logo View on (Dev) WorkflowHub
Launch in Tutorial Mode
Download 
flowchart TD
  0["ℹ️ Input Dataset\nQuery ligand"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nPharmacophore library"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["Ligand ionization state generation"];
  0 -->|output| 2;
  3["Splitting ePharmaLib into individual pharmacophores"];
  1 -->|output| 3;
  4[" Low-energy ligand conformer search"];
  2 -->|outfile| 4;
  5["Pharmacophore alignment"];
  4 -->|outfile| 5;
  3 -->|list_output_generic| 5;
  6["Concatenating the pharmacophore alignment scores"];
  5 -->|score_result_file| 6;
  7["Ranking the predicted protein targets according to the Tversky index 10th column"];
  6 -->|out_file1| 7;

Inputs

Input Label
Input dataset Query ligand
Input dataset Pharmacophore library

Outputs

From Output Label
toolshed.g2.bx.psu.edu/repos/bgruening/openbabel_addh/openbabel_addh/3.1.1+galaxy1 Add hydrogen atoms Ligand ionization state generation
toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.0 Split file Splitting ePharmaLib into individual pharmacophores
toolshed.g2.bx.psu.edu/repos/bgruening/rdconf/rdconf/2020.03.4+galaxy0 RDConf: Low-energy ligand conformer search Low-energy ligand conformer search
toolshed.g2.bx.psu.edu/repos/bgruening/align_it/ctb_alignit/1.0.4+galaxy0 Pharmacophore alignment
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.1 Concatenate datasets Concatenating the pharmacophore alignment scores
sort1 Sort Ranking the predicted protein targets according to the Tversky index (10th column)

Tools

Tool Links
sort1
toolshed.g2.bx.psu.edu/repos/bgruening/align_it/ctb_alignit/1.0.4+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/bgruening/openbabel_addh/openbabel_addh/3.1.1+galaxy1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/bgruening/rdconf/rdconf/2020.03.4+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.1 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
3 b70afe303 2022-02-15 13:25:54 annotate workflow for gtn linting
2 506069da4 2022-02-11 12:36:16 pretty print pharmacophore workflow
1 fdd280bcf 2022-02-08 20:03:56 Add files via upload

For Admins

Installing the workflow tools

wget https://training.galaxyproject.org/training-material/topics/computational-chemistry/tutorials/zauberkugel/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