Scanpy Parameter Iterator workflow full (imported from URL)

single-cell-scanpy_parameter_iterator/scanpy-parameter-iterator-workflow-full

Author(s)
Julia Jakiela
version Version
1
last_modification Last updated
Jul 19, 2023
license License
CC-BY-4.0
galaxy-tags Tags

Features

Tutorial
hands_on Scanpy Parameter Iterator

Workflow Testing
Tests: ✅
Results: Not yet automated
FAIRness purl PURL
https://gxy.io/GTN:W00191
RO-Crate logo with flask Download Workflow RO-Crate Workflowhub cloud with gears logo View on (Dev) WorkflowHub
Launch in Tutorial Mode question
galaxy-download Download
output
parameter_iteration
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parameter_iteration
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parameter_iteration
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output_h5ad
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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

Inputs

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

Tools

Tool Links
toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_compute_graph/scanpy_compute_graph/1.8.1+galaxy9 View in ToolShed
toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_find_cluster/scanpy_find_cluster/1.8.1+galaxy9 View in ToolShed
toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_parameter_iterator/scanpy_parameter_iterator/0.0.1+galaxy9 View in ToolShed
toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_plot_embed/scanpy_plot_embed/1.8.1+galaxy9 View in ToolShed
toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_run_tsne/scanpy_run_tsne/1.8.1+galaxy9 View in ToolShed
toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_run_umap/scanpy_run_umap/1.8.1+galaxy9 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
  1. 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
  2. Click on galaxy-upload Import at the top-right of the screen
  3. 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”
  4. 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

Installing the workflow tools

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