'Biomarkers4Paris' Workflow

proteomics-biomarker_selection/main-workflow

Author(s)

Version
3
Last updated
Jan 23, 2020
License
None Specified, defaults to CC-BY-4.0
Tags
proteomics

Features
Tutorial
Biomarker candidate identification
Workflow Testing
Tests: ❌
Results: Not yet automated
FAIRness PURL
https://gxy.io/GTN:W00152
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["Build tissue-specific expression dataset"];
  1["Build tissue-specific expression dataset"];
  2["Filter by keywords and/or numerical value"];
  1 -->|output| 2;
  3["Venn diagram"];
  0 -->|output| 3;
  2 -->|kept_lines| 3;
  4["Cut"];
  3 -->|output_text| 4;
  5["Filter by keywords and/or numerical value"];
  4 -->|output| 5;
  6["Add expression data"];
  5 -->|kept_lines| 6;
  7["Filter by keywords and/or numerical value"];
  6 -->|output| 7;
  8["ID Converter"];
  7 -->|kept_lines| 8;
  9["Add protein features"];
  8 -->|output| 9;
  10["Filter by keywords and/or numerical value"];
  9 -->|output| 10;
  11["Get MS/MS observations in tissue/fluid"];
  10 -->|kept_lines| 11;
  12["Filter by keywords and/or numerical value"];
  11 -->|output| 12;

Inputs

Input Label

Outputs

From Output Label

Tools

Tool Links
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/1.0.0 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/2019.03.05 View in ToolShed
toolshed.g2.bx.psu.edu/repos/proteore/proteore_id_converter/IDconverter/2019.01.28 View in ToolShed
toolshed.g2.bx.psu.edu/repos/proteore/proteore_ms_observation_pepatlas/retr_pepatlas1/2019.02.01.1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/proteore/proteore_prot_features/prot_features/2019.01.18 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/2018.12.18 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
3 667ff3de9 2020-01-22 10:59:29 annotation
2 eb4d724e0 2020-01-15 10:41:35 Workflow renaming
1 efe112854 2019-04-26 08:38:08 Add first version of biomarker selection tutorial

For Admins

Installing the workflow tools

wget https://training.galaxyproject.org/training-material/topics/proteomics/tutorials/biomarker_selection/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