Workflows

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 28, 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\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;
  88461c74-1312-41d5-bd54-e7d7297ccd76["Output\nBLASTP_results"];
  5 --> 88461c74-1312-41d5-bd54-e7d7297ccd76;
  style 88461c74-1312-41d5-bd54-e7d7297ccd76 stroke:#2c3143,stroke-width:4px;
  6["PSM_Novel_Peptides"];
  5 -->|output1| 6;
  2 -->|output| 6;
  29c9a368-a7e6-4e8b-81ca-131f63293093["Output\nPSM_Novel_Peptides"];
  6 --> 29c9a368-a7e6-4e8b-81ca-131f63293093;
  style 29c9a368-a7e6-4e8b-81ca-131f63293093 stroke:#2c3143,stroke-width:4px;
  7["Novel_Peptides"];
  6 -->|output| 7;
  56954668-7aac-423a-89af-aecf2b405b94["Output\nNovel_Peptides"];
  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;
  9["PepPointer"];
  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;
  10["Final_Summary_Novel_Peptides"];
  9 -->|classified| 10;
  6 -->|output| 10;
  50e64c95-cd68-47cb-9e0c-b3714b2f2431["Output\nFinal_Summary_Novel_Peptides"];
  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 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