ProteoRE ProteomeAnnotation Tutorial (release 2.0)

proteomics-proteome_annotation/main-workflow

Author(s)

Version
4
Last updated
Jan 23, 2020
License
None Specified, defaults to CC-BY-4.0
Tags
proteomics

Features
Tutorial
Annotating a protein list identified by LC-MS/MS experiments
Other workflows associated with this material
Workflow Testing
Tests: ❌
Results: Not yet automated
FAIRness PURL
https://gxy.io/GTN:W00176
RO-Crate logo with flask Download Workflow RO-Crate Workflowhub cloud with gears logo View on WorkflowHub
Launch in Tutorial Mode
Download 
flowchart TD
  0["ℹ️ Input Dataset\nLacombe_et_al_2017.txt"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nBredberg.txt"];
  style 1 stroke:#2c3143,stroke-width:4px;
  10["View proteins on Reactome maps"];
  9 -->|kept_lines| 10;
  11["GO terms classification and enrichment analysis"];
  5 -->|output| 11;
  9 -->|kept_lines| 11;
  2["ℹ️ Input Dataset\nMucilli.txt"];
  style 2 stroke:#2c3143,stroke-width:4px;
  3["Build a lung proteome as a background "];
  4["Filter technical contaminants"];
  0 -->|output| 4;
  5["ID Converter"];
  3 -->|output| 5;
  6["ID mapping UniProt <-> ENSG ID"];
  4 -->|kept_lines| 6;
  7["MS/MS datasets comparison"];
  4 -->|kept_lines| 7;
  1 -->|output| 7;
  2 -->|output| 7;
  8["Add expression data"];
  6 -->|output| 8;
  9["Filter biological contaminants"];
  8 -->|output| 9;

Inputs

Input Label
Input dataset Lacombe_et_al_2017.txt
Input dataset Bredberg.txt
Input dataset Mucilli.txt

Outputs

From Output Label

Tools

Tool Links
toolshed.g2.bx.psu.edu/repos/proteore/proteore_clusterprofiler/cluter_profiler/2019.02.18 View in ToolShed
toolshed.g2.bx.psu.edu/repos/proteore/proteore_expression_rnaseq_abbased/rna_abbased_data/2019.03.07 View in ToolShed
toolshed.g2.bx.psu.edu/repos/proteore/proteore_filter_keywords_values/MQoutputfilter/2019.03.11 View in ToolShed
toolshed.g2.bx.psu.edu/repos/proteore/proteore_id_converter/IDconverter/2019.03.07 View in ToolShed
toolshed.g2.bx.psu.edu/repos/proteore/proteore_reactome/reactome_analysis/2018.12.12 View in ToolShed
toolshed.g2.bx.psu.edu/repos/proteore/proteore_tissue_specific_expression_data/retrieve_from_hpa/2019.02.27 View in ToolShed
toolshed.g2.bx.psu.edu/repos/proteore/proteore_venn_diagram/Jvenn/2019.02.21 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 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
4 667ff3de9 2020-01-22 10:59:29 annotation
3 eb4d724e0 2020-01-15 10:41:35 Workflow renaming
2 faf6d298a 2019-12-12 13:02:33 unflatten workflows
1 a853f1694 2019-04-26 12:28:48 First draft of proteome annotation tutorial

For Admins

Installing the workflow tools

wget https://training.galaxyproject.org/training-material/topics/proteomics/tutorials/proteome_annotation/workflows/main_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