Metaproteomics_GTN

Run Workflow in Galaxy

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

flowchart TD
  0["ℹ️ Input Dataset\nSixgill generated protein FASTA File"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Collection\nDataset Collection of Bering Strait MGF Files"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["ℹ️ Input Dataset\nGene Ontology Terms Selected"];
  style 2 stroke:#2c3143,stroke-width:4px;
  3["Search GUI"];
  0 -->|output| 3;
  1 -->|output| 3;
  7516674a-b5aa-45b5-b2e8-38c1889ad2e9["Output\nSearch GUI on input dataset(s)"];
  3 --> 7516674a-b5aa-45b5-b2e8-38c1889ad2e9;
  style 7516674a-b5aa-45b5-b2e8-38c1889ad2e9 stroke:#2c3143,stroke-width:4px;
  4["Peptide Shaker"];
  3 -->|searchgui_results| 4;
  ddfe8d62-a7b7-4e30-a84d-91c92fc60bd0["Output\nPeptide Shaker on input dataset(s): mzidentML file"];
  4 --> ddfe8d62-a7b7-4e30-a84d-91c92fc60bd0;
  style ddfe8d62-a7b7-4e30-a84d-91c92fc60bd0 stroke:#2c3143,stroke-width:4px;
  5["Query Tabular Select Peptides"];
  4 -->|output_psm| 5;
  6["Unipept pept2prot"];
  5 -->|output| 6;
  7["Unipept lca"];
  5 -->|output| 7;
  8["Go Pop2Prot DB"];
  2 -->|output| 8;
  6 -->|output_tsv| 8;
  6 -->|output_tsv| 8;
  4 -->|output_psm| 8;
  9["Genera | PSMs | Peptides"];
  4 -->|output_psm| 9;
  7 -->|output_tsv| 9;
  10["GO Terms: Biological Processes"];
  8 -->|sqlitedb| 10;
  11["GO Terms: Molecular Functions"];
  8 -->|sqlitedb| 11;
  12["GO Terms: Cellular Localization"];
  8 -->|sqlitedb| 12;

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/metaproteomics/workflows/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