WF3_VERIFICATION_WORKFLOW

Run Workflow in Galaxy

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

flowchart TD
  0["Human UniProt+Isoforms FASTA"];
  4bdae9fb-eb48-4821-a806-e7dd3a8c7101["Output\nHuman UniProt+Isoforms FASTA"];
  0 --> 4bdae9fb-eb48-4821-a806-e7dd3a8c7101;
  style 4bdae9fb-eb48-4821-a806-e7dd3a8c7101 stroke:#2c3143,stroke-width:4px;
  1["cRAP"];
  13ddaf34-d346-4cc4-b5b6-fee2b5e0c1aa["Output\ncRAP"];
  1 --> 13ddaf34-d346-4cc4-b5b6-fee2b5e0c1aa;
  style 13ddaf34-d346-4cc4-b5b6-fee2b5e0c1aa stroke:#2c3143,stroke-width:4px;
  2["ℹ️ Input Collection\nInput MGFs Dataset Collection"];
  style 2 stroke:#2c3143,stroke-width:4px;
  3["ℹ️ Input Dataset\nSGPS_peptide-report"];
  style 3 stroke:#2c3143,stroke-width:4px;
  4["ℹ️ Input Dataset\nDistinct Peptides for PepQuery"];
  style 4 stroke:#2c3143,stroke-width:4px;
  5["ℹ️ Input Dataset\nMaxQuant-peptide-report"];
  style 5 stroke:#2c3143,stroke-width:4px;
  6["Human UniProt+Isoforms+cRAP FASTA"];
  0 -->|output_database| 6;
  1 -->|output_database| 6;
  62c376eb-85a3-4976-8024-bd72ac528af3["Output\nHuman UniProt+Isoforms+cRAP FASTA"];
  6 --> 62c376eb-85a3-4976-8024-bd72ac528af3;
  style 62c376eb-85a3-4976-8024-bd72ac528af3 stroke:#2c3143,stroke-width:4px;
  7["Cut"];
  3 -->|output| 7;
  8["Cut"];
  5 -->|output| 8;
  9["PepQuery2"];
  6 -->|output| 9;
  4 -->|output| 9;
  2 -->|output| 9;
  10["Remove beginning"];
  7 -->|out_file1| 10;
  11["Remove beginning"];
  8 -->|out_file1| 11;
  12["Collapse Collection"];
  9 -->|psm_rank_txt| 12;
  13["Concatenate datasets"];
  10 -->|out_file1| 13;
  11 -->|out_file1| 13;
  14["Filter"];
  12 -->|output| 14;
  15["Remove beginning"];
  14 -->|out_file1| 15;
  16["Cut"];
  15 -->|out_file1| 16;
  17["Peptide and Protein from Peptide reports"];
  16 -->|out_file1| 17;
  13 -->|out_file1| 17;
  bc4e33da-4064-4b78-bb15-5732b08b9316["Output\nPeptide and Protein from Peptide reports"];
  17 --> bc4e33da-4064-4b78-bb15-5732b08b9316;
  style bc4e33da-4064-4b78-bb15-5732b08b9316 stroke:#2c3143,stroke-width:4px;
  18["Remove beginning"];
  17 -->|output| 18;
  19["Group"];
  18 -->|out_file1| 19;
  20["Uniprot-ID from verified Peptides"];
  19 -->|out_file1| 20;
  cd6c81d8-1f44-4129-b505-2ee4dde10cd2["Output\nUniprot-ID from verified Peptides"];
  20 --> cd6c81d8-1f44-4129-b505-2ee4dde10cd2;
  style cd6c81d8-1f44-4129-b505-2ee4dde10cd2 stroke:#2c3143,stroke-width:4px;
  21["UniProt"];
  20 -->|output| 21;
  22["Quantitation Database for MaxQuant"];
  0 -->|output_database| 22;
  1 -->|output_database| 22;
  21 -->|proteome| 22;
  a52b5136-db74-496f-9b66-ec1064f2301d["Output\nQuantitation Database for MaxQuant"];
  22 --> a52b5136-db74-496f-9b66-ec1064f2301d;
  style a52b5136-db74-496f-9b66-ec1064f2301d 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-3-verification/workflows/WF3_Verification_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