metaQuantome_datacreation_workflow

proteomics-metaquantome-data-creation/main-workflow

Author(s)

Version
13
Last updated
Nov 10, 2021
License
None Specified, defaults to CC-BY-4.0
Tags
proteomics

Features
Tutorial
metaQuantome 1: Data creation
Workflow Testing
Tests: ✅
Results: Not yet automated
FAIRness PURL
https://gxy.io/GTN:W00161
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 dataset collection"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nExperiment_Design"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["ℹ️ Input Dataset\nFASTA_db"];
  style 2 stroke:#2c3143,stroke-width:4px;
  3["mzml to mgf"];
  0 -->|output| 3;
  4["Search GUI"];
  2 -->|output| 4;
  3 -->|output| 4;
  5["Peptide Shaker"];
  4 -->|searchgui_results| 5;
  6["Replace Text"];
  5 -->|output_psm| 6;
  7["Remove beginning"];
  5 -->|output_peptides| 7;
  8["Unipept_lca"];
  5 -->|output_peptides| 8;
  9["FlashLFQ"];
  1 -->|output| 9;
  6 -->|outfile| 9;
  0 -->|output| 9;
  10["Unipept_peptinfo"];
  7 -->|out_file1| 10;
  11["Replace Text"];
  8 -->|output_tsv| 11;
  12["Regex Find And Replace"];
  9 -->|quantifiedPeptides| 12;
  13["selecting EC column"];
  10 -->|output_ec_tsv| 13;
  14["filter 5% All_funct"];
  10 -->|output_go_tsv| 14;
  15["GO_EC"];
  13 -->|out_file1| 15;
  16["GO_BP"];
  14 -->|output| 16;
  17["GO_CC"];
  14 -->|output| 17;
  18["GO_MF"];
  14 -->|output| 18;

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
14 72e53ea9a 2021-11-10 18:44:34 Rename workflow.ga to main_workflow.ga
13 b63d3bd07 2021-11-10 18:06:54 Rename main_workflow.ga to workflow.ga
12 02a2548ec 2021-11-09 16:10:35 Update main_workflow.ga
11 d4a710e9f 2021-11-09 16:04:54 Update main_workflow.ga
10 d0478e7ff 2021-11-09 16:00:03 Update main_workflow.ga
9 2c4ad397f 2020-10-16 19:41:28 Fixed tool_state.
8 f81d5946b 2020-10-16 18:41:38 Added collection to test.
7 70b86ecbf 2020-10-16 17:52:11 Updated workflow.
6 b8a5ce3d4 2020-10-15 23:04:35 Update main_workflow.ga
5 71d516d05 2020-10-15 19:30:59 Update main_workflow.ga
4 aa695993e 2020-10-12 12:59:36 Update main_workflow.ga
3 dadb44fb5 2020-10-12 02:21:26 Update main_workflow.ga
2 a45af5ea9 2020-10-12 02:20:38 Update main_workflow.ga
1 c042f2b71 2020-09-17 15:49:53 planemo workflow-to-tutorial

For Admins

Installing the workflow tools

wget https://training.galaxyproject.org/training-material/topics/proteomics/tutorials/metaquantome-data-creation/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