Launch in Tutorial Mode
question
Run Workflow in Galaxy
galaxy-download
Download
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parameter_iteration
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parameter_iteration
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parameter_iteration
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ℹ️ Input Dataset Scanpy RunPCA: AnnData object
ParameterIterator n-neighbors
ℹ️ Input Dataset Scanpy ComputeGraph on data X and data Y: Graph object AnnData
ParameterIterator perplexity
ℹ️ Input Dataset Scanpy RunUMAP on data X: UMAP object AnnData
ParameterIterator resolution
Scanpy ComputeGraph
Scanpy RunTSNE
Scanpy FindCluster
Scanpy RunTSNE
Scanpy RunUMAP
Scanpy PlotEmbed
Scanpy PlotEmbed
Scanpy PlotEmbed
Scanpy RunUMAP
Scanpy FindCluster
Scanpy FindCluster
Scanpy PlotEmbed
Scanpy PlotEmbed
Output Scanpy ComputeGraph on collection X: Graph object AnnData (n-neighbours)
Output Scanpy RunTSNE on collection X: tSNE object AnnData (perplexity)
Output Scanpy FindCluster on collection X: Clusters AnnData (resolution)
Output Scanpy RunTSNE on collection X: tSNE object AnnData (n-neighbours)
Output Scanpy RunUMAP on collection X: UMAP object AnnData (perplexity)
Output resolution_pca_plots
Output resolution_umap_plots
Output resolution_tsne_plots
Output Scanpy RunUMAP on collection X: UMAP object AnnData (n-neighbours)
Output Scanpy FindCluster on collection X: Clusters AnnData (perplexity)
Output Scanpy FindCluster on collection X: Clusters AnnData (n-neighbours)
Output perplexity_plots
Output n-neighbors_plots
Input
Label
Input dataset
Scanpy RunPCA: AnnData object
Input dataset
Scanpy ComputeGraph on data X and data Y: Graph object AnnData
Input dataset
Scanpy RunUMAP on data X: UMAP object AnnData
Outputs
From
Output
Label
toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_compute_graph/scanpy_compute_graph/1.8.1+galaxy9
Scanpy ComputeGraph
toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_run_tsne/scanpy_run_tsne/1.8.1+galaxy9
Scanpy RunTSNE
toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_find_cluster/scanpy_find_cluster/1.8.1+galaxy9
Scanpy FindCluster
toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_run_tsne/scanpy_run_tsne/1.8.1+galaxy9
Scanpy RunTSNE
toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_run_umap/scanpy_run_umap/1.8.1+galaxy9
Scanpy RunUMAP
toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_plot_embed/scanpy_plot_embed/1.8.1+galaxy9
Scanpy PlotEmbed
toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_plot_embed/scanpy_plot_embed/1.8.1+galaxy9
Scanpy PlotEmbed
toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_plot_embed/scanpy_plot_embed/1.8.1+galaxy9
Scanpy PlotEmbed
toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_run_umap/scanpy_run_umap/1.8.1+galaxy9
Scanpy RunUMAP
toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_find_cluster/scanpy_find_cluster/1.8.1+galaxy9
Scanpy FindCluster
toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_find_cluster/scanpy_find_cluster/1.8.1+galaxy9
Scanpy FindCluster
toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_plot_embed/scanpy_plot_embed/1.8.1+galaxy9
Scanpy PlotEmbed
toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_plot_embed/scanpy_plot_embed/1.8.1+galaxy9
Scanpy PlotEmbed
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 galaxy-workflows-activity Workflows in the Galaxy activity bar (on the left side of the screen, or in the top menu bar of older Galaxy instances). 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
2
331d2c1b5
2023-07-14 04:11:29
updated workflow tests
1
68fc015a7
2023-06-08 07:12:29
add workflow tests
For Admins
wget https://training.galaxyproject.org/training-material/topics/single-cell/tutorials/scanpy_parameter_iterator/workflows/Scanpy-Parameter-Iterator-workflow-full.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