These workflows are associated with Proteogenomics 3: Novel peptide analysis

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.

GTN Proteogemics3 Novel Peptide Analysis

Last updated Jan 27, 2021

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

flowchart TD
  0["ℹ️ Input Dataset\nEdited_Mus_Musculus.GRCm38.86"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\npeptides for blast"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["ℹ️ Input Dataset\nPSM Report"];
  style 2 stroke:#2c3143,stroke-width:4px;
  3["ℹ️ Input Dataset\nmz_sqlite"];
  style 3 stroke:#2c3143,stroke-width:4px;
  4["ℹ️ Input Dataset\ngenomic mapping sqlite db"];
  style 4 stroke:#2c3143,stroke-width:4px;
  5["NCBI BLAST+ blastp"];
  1 -->|output| 5;
  5 --> 88461c74-1312-41d5-bd54-e7d7297ccd76;
  style 88461c74-1312-41d5-bd54-e7d7297ccd76 stroke:#2c3143,stroke-width:4px;
  5 -->|output1| 6;
  2 -->|output| 6;
  6 --> 29c9a368-a7e6-4e8b-81ca-131f63293093;
  style 29c9a368-a7e6-4e8b-81ca-131f63293093 stroke:#2c3143,stroke-width:4px;
  6 -->|output| 7;
  7 --> 56954668-7aac-423a-89af-aecf2b405b94;
  style 56954668-7aac-423a-89af-aecf2b405b94 stroke:#2c3143,stroke-width:4px;
  8["Peptide Genomic Coodinate"];
  4 -->|output| 8;
  3 -->|output| 8;
  7 -->|output| 8;
  60fd3e41-8cb7-4a49-b585-2a43117e9cf8["Output\nPeptide Genomic Coodinate on input dataset(s)"];
  8 --> 60fd3e41-8cb7-4a49-b585-2a43117e9cf8;
  style 60fd3e41-8cb7-4a49-b585-2a43117e9cf8 stroke:#2c3143,stroke-width:4px;
  8 -->|peptide_bed| 9;
  0 -->|output| 9;
  3c410bed-ff79-4774-b75c-48659d291160["Output\nPepPointer on input dataset(s)"];
  9 --> 3c410bed-ff79-4774-b75c-48659d291160;
  style 3c410bed-ff79-4774-b75c-48659d291160 stroke:#2c3143,stroke-width:4px;
  9 -->|classified| 10;
  6 -->|output| 10;
  10 --> 50e64c95-cd68-47cb-9e0c-b3714b2f2431;
  style 50e64c95-cd68-47cb-9e0c-b3714b2f2431 stroke:#2c3143,stroke-width:4px;

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 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: