WF2_Discovery-Workflow

Run Workflow in Galaxy

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

flowchart TD
  0["ℹ️ Input Dataset\nHuman UniProt Microbial Proteins from MetaNovo and cRAP "];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["Identification Parameters: PAR file"];
  2["ℹ️ Input Collection\nRAW files Dataset Collection"];
  style 2 stroke:#2c3143,stroke-width:4px;
  3["Human SwissProt reviewed only"];
  e0de9f90-a710-4b55-af62-41ba1c2d8e1f["Output\nHuman SwissProt (reviewed only)"];
  3 --> e0de9f90-a710-4b55-af62-41ba1c2d8e1f;
  style e0de9f90-a710-4b55-af62-41ba1c2d8e1f stroke:#2c3143,stroke-width:4px;
  4["Contaminants cRAP"];
  5["ℹ️ Input Dataset\nExperimental Design Discovery MaxQuant"];
  style 5 stroke:#2c3143,stroke-width:4px;
  6["FastaCLI__MetaNovo_Human_SwissProt_cRAP_with_decoys_on_data_1_MetaNovo_Human_SwissProt_cRAP_concatenated_target_decoy.fasta"];
  0 -->|output| 6;
  7["msconvert"];
  2 -->|output| 7;
  8["Human SwissProt+cRAP"];
  3 -->|output_database| 8;
  4 -->|output_database| 8;
  2f14902f-b005-4c08-b6d1-6d7ee0b4b199["Output\nHuman SwissProt+cRAP"];
  8 --> 2f14902f-b005-4c08-b6d1-6d7ee0b4b199;
  style 2f14902f-b005-4c08-b6d1-6d7ee0b4b199 stroke:#2c3143,stroke-width:4px;
  9["MaxQuant"];
  0 -->|output| 9;
  2 -->|output| 9;
  5 -->|output| 9;
  10["Search GUI"];
  6 -->|input_database_concatenated_target_decoy| 10;
  1 -->|Identification_Parameters_File| 10;
  7 -->|output| 10;
  11["FASTA-to-Tabular"];
  8 -->|output| 11;
  12["Select microbial peptides MQ"];
  9 -->|peptides| 12;
  d7718bab-9e75-4729-bfb6-03bc3112a0e2["Output\nSelect microbial peptides (MQ)"];
  12 --> d7718bab-9e75-4729-bfb6-03bc3112a0e2;
  style d7718bab-9e75-4729-bfb6-03bc3112a0e2 stroke:#2c3143,stroke-width:4px;
  13["Peptide Shaker"];
  10 -->|searchgui_results| 13;
  14["Filter Tabular"];
  11 -->|output| 14;
  15["MQ Peptide Sequences"];
  12 -->|out_file1| 15;
  16["Select microbial peptides SGPS"];
  13 -->|output_peptides| 16;
  14fd9080-df92-4c61-b1f1-3f700a166700["Output\nSelect microbial peptides (SGPS)"];
  16 --> 14fd9080-df92-4c61-b1f1-3f700a166700;
  style 14fd9080-df92-4c61-b1f1-3f700a166700 stroke:#2c3143,stroke-width:4px;
  17["Select microbial PSMs"];
  13 -->|output_psm| 17;
  18["Remove beginning"];
  15 -->|out_file1| 18;
  19["Filter confident microbial peptides"];
  16 -->|out_file1| 19;
  1c6c953f-d192-4953-938a-9f401315bc0d["Output\nFilter confident microbial peptides"];
  19 --> 1c6c953f-d192-4953-938a-9f401315bc0d;
  style 1c6c953f-d192-4953-938a-9f401315bc0d stroke:#2c3143,stroke-width:4px;
  20["Filter confident microbial PSMs"];
  17 -->|out_file1| 20;
  d8ec7f0c-7ba1-4733-a3dc-74a9ef298dc2["Output\nFilter confident microbial PSMs"];
  20 --> d8ec7f0c-7ba1-4733-a3dc-74a9ef298dc2;
  style d8ec7f0c-7ba1-4733-a3dc-74a9ef298dc2 stroke:#2c3143,stroke-width:4px;
  21["MQ Distinct Peptides"];
  18 -->|out_file1| 21;
  07cae017-0b39-4065-b83e-b5f2e27fe740["Output\nMQ Peptides"];
  21 --> 07cae017-0b39-4065-b83e-b5f2e27fe740;
  style 07cae017-0b39-4065-b83e-b5f2e27fe740 stroke:#2c3143,stroke-width:4px;
  22["Query Tabular"];
  20 -->|out_file1| 22;
  20 -->|out_file1| 22;
  14 -->|output| 22;
  23["Cut"];
  22 -->|output| 23;
  24["SGPS Distinct Peptides"];
  23 -->|out_file1| 24;
  b6c61697-ff52-43c0-8fb4-765d7b4204cc["Output\nSGPS Distinct Peptides"];
  24 --> b6c61697-ff52-43c0-8fb4-765d7b4204cc;
  style b6c61697-ff52-43c0-8fb4-765d7b4204cc stroke:#2c3143,stroke-width:4px;
  25["SGPS-MQ Peptides"];
  21 -->|out_file1| 25;
  24 -->|out_file1| 25;
  a8c2de2e-e322-4830-9d28-2f79bf937013["Output\nSGPS-MQ Peptides"];
  25 --> a8c2de2e-e322-4830-9d28-2f79bf937013;
  style a8c2de2e-e322-4830-9d28-2f79bf937013 stroke:#2c3143,stroke-width:4px;
  26["Distinct Peptides"];
  25 -->|out_file1| 26;
  ef0d91b1-042f-4a9f-a2b6-bf73d82f24f7["Output\nDistinct Peptides"];
  26 --> ef0d91b1-042f-4a9f-a2b6-bf73d82f24f7;
  style ef0d91b1-042f-4a9f-a2b6-bf73d82f24f7 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/clinical-mp-2-discovery/workflows/WF2_Discovery-Workflow.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