Workflows

These workflows are associated with Proteogenomics 2: Database Search

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 Proteogemics2 Database Search

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\nUniprot_cRAP_SAV_indel_translatedbed.FASTA"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Collection\nMGF Collection"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["ℹ️ Input Dataset\nReference Protein Accessions"];
  style 2 stroke:#2c3143,stroke-width:4px;
  3["Search GUI"];
  0 -->|output| 3;
  1 -->|output| 3;
  d14f9481-80db-4c15-8afc-6fa38ef61deb["Output\nSearch GUI on input dataset(s)"];
  3 --> d14f9481-80db-4c15-8afc-6fa38ef61deb;
  style d14f9481-80db-4c15-8afc-6fa38ef61deb stroke:#2c3143,stroke-width:4px;
  4["Peptide Shaker"];
  3 -->|searchgui_results| 4;
  afe0f1a5-28bb-44bd-b32b-c634aa2154f3["Output\nPeptide Shaker on input dataset(s): mzidentML file"];
  4 --> afe0f1a5-28bb-44bd-b32b-c634aa2154f3;
  style afe0f1a5-28bb-44bd-b32b-c634aa2154f3 stroke:#2c3143,stroke-width:4px;
  5["mz to sqlite"];
  4 -->|mzidentML| 5;
  1 -->|output| 5;
  0 -->|output| 5;
  b43a2136-cf59-4fb0-bb2b-0d5b446c8ba9["Output\nmz to sqlite on input dataset(s)"];
  5 --> b43a2136-cf59-4fb0-bb2b-0d5b446c8ba9;
  style b43a2136-cf59-4fb0-bb2b-0d5b446c8ba9 stroke:#2c3143,stroke-width:4px;
  6["Removing reference proteins"];
  4 -->|output_psm| 6;
  4 -->|output_psm| 6;
  2 -->|output| 6;
  a06ad5fa-9a00-4867-b976-3745c5e59c80["Output\nRemoving reference proteins"];
  6 --> a06ad5fa-9a00-4867-b976-3745c5e59c80;
  style a06ad5fa-9a00-4867-b976-3745c5e59c80 stroke:#2c3143,stroke-width:4px;
  7["Selecting sequence with length >6 and <30"];
  6 -->|output| 7;
  b71e5417-2864-4712-b5c1-c90725976baf["Output\nSelecting sequence with length >6 and <30"];
  7 --> b71e5417-2864-4712-b5c1-c90725976baf;
  style b71e5417-2864-4712-b5c1-c90725976baf stroke:#2c3143,stroke-width:4px;
  8["Peptides for BlastP analysis"];
  7 -->|output| 8;
  1ac3c776-8095-4db1-8518-3643dc081006["Output\nPeptides_for_BlastP_analysis"];
  8 --> 1ac3c776-8095-4db1-8518-3643dc081006;
  style 1ac3c776-8095-4db1-8518-3643dc081006 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