Workflows

These workflows are associated with Secretome Prediction

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.

Secreted Proteins Via GO Annotation And WoLF PSORT For shCTSB Paper

Last updated Jan 17, 2020

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

flowchart TD
  0["ℹ️ Input Dataset\nInput dataset"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nInput dataset"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["ℹ️ Input Dataset\nInput dataset"];
  style 2 stroke:#2c3143,stroke-width:4px;
  3["UniProt"];
  0 -->|output| 3;
  4["Select"];
  1 -->|output| 4;
  5["Get subontology from a given OBO term"];
  2 -->|output| 5;
  6["Get subontology from a given OBO term"];
  2 -->|output| 6;
  7["Get subontology from a given OBO term"];
  2 -->|output| 7;
  8["Get subontology from a given OBO term"];
  2 -->|output| 8;
  9["Get subontology from a given OBO term"];
  2 -->|output| 9;
  10["WoLF PSORT"];
  3 -->|outfile_retrieve_fasta| 10;
  11["Join"];
  0 -->|output| 11;
  4 -->|out_file1| 11;
  12["Get all the term IDs and term names of a given OBO ontology"];
  5 -->|output| 12;
  13["Get all the term IDs and term names of a given OBO ontology"];
  6 -->|output| 13;
  14["Get all the term IDs and term names of a given OBO ontology"];
  7 -->|output| 14;
  15["Get all the term IDs and term names of a given OBO ontology"];
  8 -->|output| 15;
  16["Get all the term IDs and term names of a given OBO ontology"];
  9 -->|output| 16;
  17["Filter"];
  10 -->|tabular_file| 17;
  18["Filter"];
  10 -->|tabular_file| 18;
  19["Join"];
  12 -->|output| 19;
  13 -->|output| 19;
  20["Join"];
  14 -->|output| 20;
  15 -->|output| 20;
  21["Join"];
  17 -->|out_file1| 21;
  18 -->|out_file1| 21;
  22["Join"];
  19 -->|output| 22;
  20 -->|output| 22;
  23["Convert"];
  21 -->|output| 23;
  24["Join"];
  22 -->|output| 24;
  16 -->|output| 24;
  25["Cut"];
  23 -->|out_file1| 25;
  26["Compare two Datasets"];
  11 -->|output| 26;
  24 -->|output| 26;
  27["Unique"];
  26 -->|out_file1| 27;
  28["Cut"];
  27 -->|outfile| 28;
  29["Join"];
  25 -->|output| 29;
  28 -->|output| 29;
  30["Unique"];
  29 -->|output| 30;
  14e0c6dc-436b-4c4c-9292-d5e00cca8c92["Output\nSecretome proteins"];
  30 --> 14e0c6dc-436b-4c4c-9292-d5e00cca8c92;
  style 14e0c6dc-436b-4c4c-9292-d5e00cca8c92 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:

Video: Importing a workflow from URL