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

Download Workflow RO-Crate

View on 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 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
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