MSI Finding Diff Analytes

metabolomics-msi-finding-nglycans/msi-finding-diff-analytes

Author(s)

version Version
4
last_modification Last updated
Jan 23, 2020
license License
None Specified, defaults to CC-BY-4.0
galaxy-tags Tags
metabolomics

Features

Tutorial
hands_on Mass spectrometry imaging: Finding differential analytes

Workflow Testing
Tests: ❌
Results: Not yet automated
FAIRness purl PURL
https://gxy.io/GTN:W00120
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\ntreated"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\ncontrol"];
  style 1 stroke:#2c3143,stroke-width:4px;
  10["MSI classification"];
  9 -->|outfile_imzml| 10;
  4 -->|pixel_annotations| 10;
  11["MSI segmentation"];
  9 -->|outfile_imzml| 11;
  12["Filter"];
  10 -->|mzfeatures| 12;
  13["Join two files"];
  12 -->|out_file1| 13;
  2 -->|output| 13;
  14["Summary Statistics"];
  13 -->|merged_file| 14;
  15["MSI mz images"];
  13 -->|merged_file| 15;
  3 -->|output| 15;
  16["Select"];
  13 -->|merged_file| 16;
  17["MSI mz images"];
  16 -->|out_file1| 17;
  3 -->|output| 17;
  2["ℹ️ Input Dataset\nGlycan_IDs"];
  style 2 stroke:#2c3143,stroke-width:4px;
  3["ℹ️ Input Dataset\nall_files"];
  style 3 stroke:#2c3143,stroke-width:4px;
  4["MSI combine"];
  1 -->|output| 4;
  0 -->|output| 4;
  5["MSI preprocessing"];
  4 -->|outfile_imzml| 5;
  6["MSI Qualitycontrol"];
  4 -->|outfile_imzml| 6;
  4 -->|pixel_annotations| 6;
  7["MALDIquant preprocessing"];
  5 -->|outfile_imzml| 7;
  8["MALDIquant peak detection"];
  7 -->|outfile_imzml| 8;
  4 -->|pixel_annotations| 8;
  9["MSI preprocessing"];
  5 -->|outfile_imzml| 9;
  8 -->|intensity_matrix| 9;

Inputs

Input Label
Input dataset treated
Input dataset control
Input dataset Glycan_IDs
Input dataset all_files

Outputs

From Output Label
Input dataset treated
Input dataset control
toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_classification/cardinal_classification/1.12.1.3 MSI classification
toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_segmentations/cardinal_segmentations/1.12.1.3 MSI segmentation
toolshed.g2.bx.psu.edu/repos/bgruening/join_files_on_column_fuzzy/join_files_on_column_fuzzy/1.0.1 Join two files
Summary_Statistics1 Summary Statistics
toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_mz_images/cardinal_mz_images/1.12.1.2 MSI mz images
Grep1 Select
toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_mz_images/cardinal_mz_images/1.12.1.2 MSI mz images
Input dataset Glycan_IDs
Input dataset all_files
toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_combine/cardinal_combine/1.12.1.3 MSI combine
toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_preprocessing/cardinal_preprocessing/1.12.1.3 MSI preprocessing
toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_quality_report/cardinal_quality_report/1.12.1.3 MSI Qualitycontrol
toolshed.g2.bx.psu.edu/repos/galaxyp/maldi_quant_preprocessing/maldi_quant_preprocessing/1.18.0.3 MALDIquant preprocessing

Tools

Tool Links
Filter1
Grep1
Summary_Statistics1
toolshed.g2.bx.psu.edu/repos/bgruening/join_files_on_column_fuzzy/join_files_on_column_fuzzy/1.0.1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_classification/cardinal_classification/1.12.1.3 View in ToolShed
toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_combine/cardinal_combine/1.12.1.3 View in ToolShed
toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_mz_images/cardinal_mz_images/1.12.1.2 View in ToolShed
toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_preprocessing/cardinal_preprocessing/1.12.1.3 View in ToolShed
toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_quality_report/cardinal_quality_report/1.12.1.3 View in ToolShed
toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_segmentations/cardinal_segmentations/1.12.1.3 View in ToolShed
toolshed.g2.bx.psu.edu/repos/galaxyp/maldi_quant_peak_detection/maldi_quant_peak_detection/1.18.0.4 View in ToolShed
toolshed.g2.bx.psu.edu/repos/galaxyp/maldi_quant_preprocessing/maldi_quant_preprocessing/1.18.0.3 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
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 6b3331c23 2019-04-13 15:52:01 Adding MSI N-glycan training and small updates for the other MSI trainings (#1333)

For Admins

Installing the workflow tools

wget https://training.galaxyproject.org/training-material/topics/metabolomics/tutorials/msi-finding-nglycans/workflows/msi-finding-diff-analytes.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