WF1_Database_Generation_Workflow

proteomics-clinical-mp-1-database-generation/wf1-database-generation-workflow

Author(s)
Subina Mehta
Version
1
Last updated
Aug 8, 2024
License
CC-BY-4.0
Tags
name:clinicalMP

Features
Tutorial
Clinical Metaproteomics 1: Database-Generation
Workflow Testing
Tests: ❌
Results: Not yet automated
FAIRness PURL
https://gxy.io/GTN:W00277
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\nHUMAN SwissProt Protein Database"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Collection\nInput MGF files Dataset Collection"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["ℹ️ Input Dataset\nSpecies_UniProt_FASTA"];
  style 2 stroke:#2c3143,stroke-width:4px;
  3["ℹ️ Input Dataset\nContaminants cRAP Protein Database "];
  style 3 stroke:#2c3143,stroke-width:4px;
  4["Human UniProt Microbial Proteins cRAP for MetaNovo"];
  0 -->|output| 4;
  2 -->|output| 4;
  3 -->|output| 4;
  286f5bd4-fb0d-4649-8dac-f191acc72722["Output\nHuman UniProt Microbial Proteins cRAP for MetaNovo"];
  4 --> 286f5bd4-fb0d-4649-8dac-f191acc72722;
  style 286f5bd4-fb0d-4649-8dac-f191acc72722 stroke:#2c3143,stroke-width:4px;
  5["MetaNovo"];
  4 -->|output| 5;
  1 -->|output| 5;
  6["FASTA Merge Files and Filter Unique Sequences"];
  0 -->|output| 6;
  5 -->|output_fasta| 6;
  3 -->|output| 6;
  de57cd9d-ac05-4397-9d44-e65620913447["Output\nHuman UniProt Microbial Proteins (from MetaNovo) and cRAP "];
  6 --> de57cd9d-ac05-4397-9d44-e65620913447;
  style de57cd9d-ac05-4397-9d44-e65620913447 stroke:#2c3143,stroke-width:4px;

Inputs

Input Label
Input dataset HUMAN SwissProt Protein Database
Input dataset collection Input MGF files (Dataset Collection)
Input dataset Species_UniProt_FASTA
Input dataset Contaminants (cRAP) Protein Database

Outputs

From Output Label
toolshed.g2.bx.psu.edu/repos/galaxyp/fasta_merge_files_and_filter_unique_sequences/fasta_merge_files_and_filter_unique_sequences/1.2.0 FASTA Merge Files and Filter Unique Sequences Human UniProt Microbial Proteins cRAP for MetaNovo
toolshed.g2.bx.psu.edu/repos/galaxyp/metanovo/metanovo/1.9.4+galaxy4 MetaNovo
toolshed.g2.bx.psu.edu/repos/galaxyp/fasta_merge_files_and_filter_unique_sequences/fasta_merge_files_and_filter_unique_sequences/1.2.0 FASTA Merge Files and Filter Unique Sequences

Tools

Tool Links
toolshed.g2.bx.psu.edu/repos/galaxyp/fasta_merge_files_and_filter_unique_sequences/fasta_merge_files_and_filter_unique_sequences/1.2.0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/galaxyp/metanovo/metanovo/1.9.4+galaxy4 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 9a94b97ce 2024-08-08 11:22:48 add workflow

For Admins

Installing the workflow tools

wget https://training.galaxyproject.org/training-material/topics/proteomics/tutorials/clinical-mp-1-database-generation/workflows/WF1_Database_Generation_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