WF3_VERIFICATION_WORKFLOW

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

Author(s)
Subina Mehta
Version
0
Last updated
Jun 21, 2025
License
CC-BY-4.0
Tags
name:clinicalMP

Features
Tutorial
Clinical Metaproteomics 3: Verification
Workflow Testing
Tests: ❌
Results: Not yet automated
FAIRness PURL
https://gxy.io/GTN:
RO-Crate logo with flask Download Workflow RO-Crate Workflowhub cloud with gears logo View on WorkflowHub
Launch in Tutorial Mode
Download 
output_database
output_database
output
output
output
output
output
out_file1
out_file1
psm_rank_txt
out_file1
out_file1
output
out_file1
out_file1
out_file1
out_file1
output
out_file1
out_file1
output
output_database
output_database
proteome
Human UniProt+Isoforms FASTA
cRAP
ℹ️ Input Collection
Input MGFs Dataset Collection
ℹ️ Input Dataset
SGPS_peptide-report
ℹ️ Input Dataset
Distinct Peptides for PepQuery
ℹ️ Input Dataset
MaxQuant-peptide-report
Human UniProt+Isoforms+cRAP FASTA
Cut
Cut
PepQuery2
Remove beginning
Remove beginning
Collapse Collection
Concatenate datasets
Filter
Remove beginning
Cut
Peptide and Protein from Peptide reports
Remove beginning
Group
Uniprot-ID from verified Peptides
UniProt
Quantitation Database for MaxQuant
Output
Human UniProt+Isoforms FASTA
Output
cRAP
Output
Human UniProt+Isoforms+cRAP FASTA
Output
Peptide and Protein from Peptide reports
Output
Uniprot-ID from verified Peptides
Output
Quantitation Database for MaxQuant

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
  1. Click on Workflows in the Galaxy activity bar (on the left side of the screen, or in the top menu bar of older Galaxy instances). You will see a list of all your workflows
  2. Click on Import at the top-right of the screen
  3. 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”
  4. 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