DIA_analysis_MSstats

proteomics-DIA_Analysis_MSstats/galaxy-workflow-dia-msstats-training-msstats-input-tabular

Author(s)

Version
2
Last updated
Jan 21, 2022
License
None Specified, defaults to CC-BY-4.0
Tags
proteomics

Features
Tutorial
Statistical analysis of DIA data
Other workflows associated with this material
Workflow Testing
Tests: ✅
Results: Not yet automated
FAIRness PURL
https://gxy.io/GTN:W00149
RO-Crate logo with flask Download Workflow RO-Crate Workflowhub cloud with gears logo View on (Dev) WorkflowHub
Launch in Tutorial Mode
Download 
flowchart TD
  0["ℹ️ Input Dataset\nPyProphet MSstats input"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nComparison matrix"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["MSstats"];
  1 -->|output| 2;
  0 -->|output| 2;
  3["Select"];
  2 -->|comparison_result| 3;
  6e8589bd-13fd-4a97-a9c3-ea0a5a0e2326["Output\nSelect_Ecoli"];
  3 --> 6e8589bd-13fd-4a97-a9c3-ea0a5a0e2326;
  style 6e8589bd-13fd-4a97-a9c3-ea0a5a0e2326 stroke:#2c3143,stroke-width:4px;
  4["Filter"];
  3 -->|out_file1| 4;
  6997a43a-a17b-418b-bb6d-7d32a6c277ae["Output\nFilter_Ecoli"];
  4 --> 6997a43a-a17b-418b-bb6d-7d32a6c277ae;
  style 6997a43a-a17b-418b-bb6d-7d32a6c277ae stroke:#2c3143,stroke-width:4px;
  5["Histogram"];
  4 -->|out_file1| 5;
  cf3abac3-8227-4af8-a551-6aeae154a0e4["Output\nHistogram_Ecoli"];
  5 --> cf3abac3-8227-4af8-a551-6aeae154a0e4;
  style cf3abac3-8227-4af8-a551-6aeae154a0e4 stroke:#2c3143,stroke-width:4px;

Inputs

Input Label
Input dataset PyProphet MSstats input
Input dataset Comparison matrix

Outputs

From Output Label
Input dataset PyProphet MSstats input
Input dataset Comparison matrix
toolshed.g2.bx.psu.edu/repos/galaxyp/msstats/msstats/3.20.1.0 MSstats
Grep1 Select
Filter1 Filter
toolshed.g2.bx.psu.edu/repos/devteam/histogram/histogram_rpy/1.0.4 Histogram

Tools

Tool Links
Filter1
Grep1
toolshed.g2.bx.psu.edu/repos/devteam/histogram/histogram_rpy/1.0.4 View in ToolShed
toolshed.g2.bx.psu.edu/repos/galaxyp/msstats/msstats/3.20.1.0 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 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 bef209fa8 2022-01-21 03:48:50 Add workflow tests to DIA_MSstats_Training tutorial
2 15a13c366 2020-12-02 17:50:43 updated workflow annotation and name
1 e8f20c190 2020-12-02 17:31:58 generated three tutorials on DIA data analysis in galaxy

For Admins

Installing the workflow tools

wget https://training.galaxyproject.org/training-material/topics/proteomics/tutorials/DIA_Analysis_MSstats/workflows/Galaxy-Workflow-DIA_MSstats_Training_msstats_input_tabular.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