MSI Finding Diff Analytes
metabolomics-msi-finding-nglycans/msi-finding-diff-analytes
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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
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