Workflows
These workflows are associated with Clinical Metaproteomics 3: Verification
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.
WF3_VERIFICATION_WORKFLOW
Subina Mehta
Last updated Nov 21, 2024
Launch in Tutorial Mode
License:
CC-BY-4.0
Tests: ❌
Results: Not yet automated
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;
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: