Secreted Proteins Via GO Annotation And WoLF PSORT For shCTSB Paper

Run Workflow in Galaxy

• Galaxy France
• Galaxy Europe
• Galaxy Main
• Galaxy Australia
• Import to another server (≥23.0+ only!)

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;

Inputs

Outputs

Tools

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.

Importing into Galaxy

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:

Version History

For Admins

Installing the workflow tools

wget https://training.galaxyproject.org/training-material/topics/proteomics/tutorials/secretome-prediction/workflows/WF_secretomePrediction_goWolfpsort.ga -O workflow.ga
workflow-to-tools -w workflow.ga -o tools.yaml
shed-tools install -g GALAXY -a API_KEY -t tools.yaml
workflow-install -g GALAXY -a API_KEY -w workflow.ga --publish-workflows