metaQuantome_datacreation_workflow

Run Workflow in Galaxy

• Galaxy France
• Galaxy Main
• Galaxy Australia
• Galaxy Europe
• Import to another server (≥23.0+ only!)

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;

Inputs

Outputs

Tools

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

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:

Version History

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