Workflows

These workflows are associated with Metaproteomics tutorial

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.

Metaproteomics_GTN

Last updated Feb 9, 2021

Launch in Tutorial Mode
License: None Specified, defaults to CC-BY-4.0
Tests: ❌ Results: Not yet automated

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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;

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: