WF3_VERIFICATION_WORKFLOW

microbiome-clinical-mp-3-verification/wf3-verification-workflow

Author(s)
Subina Mehta
version Version
0
last_modification Last updated
Dec 11, 2024
license License
CC-BY-4.0
galaxy-tags Tags
name:clinicalMP

Features

Tutorial
hands_on Clinical Metaproteomics 3: Verification

Workflow Testing
Tests: ❌
Results: Not yet automated
FAIRness purl PURL
https://gxy.io/GTN:
RO-Crate logo with flask Download Workflow RO-Crate Workflowhub cloud with gears logo View on (Dev) WorkflowHub
Launch in Tutorial Mode question
galaxy-download Download
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

Input Label
Input dataset collection Input MGFs Dataset Collection
Input dataset SGPS_peptide-report
Input dataset Distinct Peptides for PepQuery
Input dataset MaxQuant-peptide-report

Outputs

From Output Label
toolshed.g2.bx.psu.edu/repos/galaxyp/dbbuilder/dbbuilder/0.3.4 Protein Database Downloader Human UniProt+Isoforms FASTA
toolshed.g2.bx.psu.edu/repos/galaxyp/dbbuilder/dbbuilder/0.3.4 Protein Database Downloader cRAP
toolshed.g2.bx.psu.edu/repos/galaxyp/fasta_merge_files_and_filter_unique_sequences/fasta_merge_files_and_filter_unique_sequences/1.2.0 FASTA Merge Files and Filter Unique Sequences Human UniProt+Isoforms+cRAP FASTA
toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.0 Query Tabular Peptide and Protein from Peptide reports
toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.0 Query Tabular Uniprot-ID from verified Peptides
toolshed.g2.bx.psu.edu/repos/galaxyp/fasta_merge_files_and_filter_unique_sequences/fasta_merge_files_and_filter_unique_sequences/1.2.0 FASTA Merge Files and Filter Unique Sequences Quantitation Database for MaxQuant

Tools

Tool Links
Cut1
Filter1
Grouping1
Remove beginning1
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/galaxyp/dbbuilder/dbbuilder/0.3.4 View in ToolShed
toolshed.g2.bx.psu.edu/repos/galaxyp/fasta_merge_files_and_filter_unique_sequences/fasta_merge_files_and_filter_unique_sequences/1.2.0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/galaxyp/pepquery2/pepquery2/2.0.2+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/galaxyp/uniprotxml_downloader/uniprotxml_downloader/2.4.0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0 View in ToolShed

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

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

Version History

Version Commit Time Comments

For Admins

Installing the workflow tools

wget https://training.galaxyproject.org/training-material/topics/microbiome/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