MSI Workflow: spatial distribution

metabolomics-msi-analyte-distribution/wf-msi-distribution

Author(s)

version Version
1
last_modification Last updated
Nov 1, 2020
license License
None Specified, defaults to CC-BY-4.0
galaxy-tags Tags
metabolomics

Features

Tutorial
hands_on Mass spectrometry imaging: Examining the spatial distribution of analytes

Workflow Testing
Tests: ❌
Results: Not yet automated
FAIRness purl PURL
https://gxy.io/GTN:W00119
RO-Crate logo with flask Download Workflow RO-Crate Workflowhub cloud with gears logo View on WorkflowHub
Launch in Tutorial Mode question
galaxy-download Download
flowchart TD
  0["ℹ️ Input Dataset\nUploaded Composite Dataset imzml"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nAnnotation"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["ℹ️ Input Dataset\nm/z features"];
  style 2 stroke:#2c3143,stroke-width:4px;
  3["MSI Qualitycontrol"];
  0 -->|output| 3;
  4["MSI plot spectra"];
  0 -->|output| 4;
  5["MSI filtering"];
  0 -->|output| 5;
  6["MSI plot spectra"];
  0 -->|output| 6;
  1 -->|output| 6;
  7["MSI data exporter"];
  5 -->|outfile_imzml| 7;
  8["MSI mz images"];
  2 -->|output| 8;
  5 -->|outfile_imzml| 8;
  9["Filter"];
  7 -->|feature_output| 9;
  10["MSI mz images"];
  9 -->|out_file1| 10;
  5 -->|outfile_imzml| 10;

Inputs

Input Label
Input dataset Uploaded Composite Dataset (imzml)
Input dataset Annotation
Input dataset m/z features

Outputs

From Output Label
Input dataset Uploaded Composite Dataset (imzml)
Input dataset Annotation
Input dataset m/z features
toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_quality_report/cardinal_quality_report/2.6.0.1 MSI Qualitycontrol
toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_spectra_plots/cardinal_spectra_plots/2.6.0.0 MSI plot spectra
toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_filtering/cardinal_filtering/2.6.0.0 MSI filtering
toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_spectra_plots/cardinal_spectra_plots/2.6.0.0 MSI plot spectra
toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_data_exporter/cardinal_data_exporter/2.6.0.0 MSI data exporter
toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_mz_images/cardinal_mz_images/2.6.0.0 MSI mz images
Filter1 Filter
toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_mz_images/cardinal_mz_images/2.6.0.0 MSI mz images

Tools

Tool Links
Filter1
toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_data_exporter/cardinal_data_exporter/2.6.0.0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_filtering/cardinal_filtering/2.6.0.0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_mz_images/cardinal_mz_images/2.6.0.0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_quality_report/cardinal_quality_report/2.6.0.1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_spectra_plots/cardinal_spectra_plots/2.6.0.0 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
1 a46d3c7f2 2020-10-31 19:23:05 small updates in figures, tutorial and workflow

For Admins

Installing the workflow tools

wget https://training.galaxyproject.org/training-material/topics/metabolomics/tutorials/msi-analyte-distribution/workflows/wf_MSI_distribution.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