diff --git a/communities/spoc/lab/sections/1_beginner.yml b/communities/spoc/lab/sections/1_beginner.yml
index ea4c4fd8..620491a8 100644
--- a/communities/spoc/lab/sections/1_beginner.yml
+++ b/communities/spoc/lab/sections/1_beginner.yml
@@ -41,13 +41,13 @@ tabs:
heading_md: >
Using public data is free! Learn how to retrieve data from common sources.
content:
- - title_md: Importing files from the Single Cell Expression Atlas
- description_md: >
- You can import data directly from the Single Cell Expression Atlas with one tool. You will need an **experiment accession** ID, which you can find by browsing experiments at the [EBI Atlas site](https://www.ebi.ac.uk/gxa/sc/experiments). Input that **experiment accession** ID in the *Tool Parameters* box when of the following tool. Then **Run tool** to get your matrix!
- EBI SCXA Data Retrieval
- button_link: "{{ galaxy_base_url }}/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Febi-gxa%2fretrieve_scxa%2fretrieve_scxa"
- button_icon: run
- button_tip: Run tool
+ # - title_md: Importing files from the Single Cell Expression Atlas
+ # description_md: >
+ # You can import data directly from the Single Cell Expression Atlas with one tool. You will need an **experiment accession** ID, which you can find by browsing experiments at the [EBI Atlas site](https://www.ebi.ac.uk/gxa/sc/experiments). Input that **experiment accession** ID in the *Tool Parameters* box when of the following tool. Then **Run tool** to get your matrix!
+ # EBI SCXA Data Retrieval
+ # button_link: "{{ galaxy_base_url }}/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Febi-gxa%2fretrieve_scxa%2fretrieve_scxa"
+ # button_icon: run
+ # button_tip: Run tool
- title_md: Importing from public atlases - Tutorial
description_md: >
You can learn more by following our dedicated to tutorial for importing files from public atlases.
@@ -60,25 +60,25 @@ tabs:
button_link: https://training.galaxyproject.org/training-material/topics/single-cell/tutorials/scrna-ncbi-anndata/tutorial.html
button_icon: tutorial
button_tip: View tutorial
- - title_md: Importing 10X Files
- description_md: >
- You can find many tools for importing 10X formatted data into target datatypes.
- Scanpy Read10x
- button_link: "{{ galaxy_base_url }}/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Febi-gxa%2fscanpy_read_10x%2fscanpy_read_10x"
- button_icon: run
- button_tip: Run tool
- - title_md: Seurat Read10x
- description_md: >
- Import 10X formatted data into a Seurat object. Seurat is an R package designed for QC, analysis, and exploration of single cell RNA-seq data.
- button_link: "{{ galaxy_base_url }}/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Febi-gxa%2fseurat_read10x%2fseurat_read10x"
- button_icon: run
- button_tip: Run tool
- - title_md: DropletUtils Read10x
- description_md: >
- DropletUtils provides a number of utility functions for handling single-cell (RNA-seq) data from droplet technologies such as 10X Genomics. This includes data loading, identification of cells from empty droplets, removal of barcode-swapped pseudo-cells, and downsampling of the count matrix.
- button_link: "{{ galaxy_base_url }}/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Febi-gxa%2fdropletutils_read_10x%2fdropletutils_read_10x"
- button_icon: run
- button_tip: Run tool
+ #- title_md: Importing 10X Files
+ # description_md: >
+ # You can find many tools for importing 10X formatted data into target datatypes.
+ # Scanpy Read10x
+ # button_link: "{{ galaxy_base_url }}/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Febi-gxa%2fscanpy_read_10x%2fscanpy_read_10x"
+ # button_icon: run
+ # button_tip: Run tool
+ #- title_md: Seurat Read10x
+ # description_md: >
+ # Import 10X formatted data into a Seurat object. Seurat is an R package designed for QC, analysis, and exploration of single cell RNA-seq data.
+ # button_link: "{{ galaxy_base_url }}/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Febi-gxa%2fseurat_read10x%2fseurat_read10x"
+ # button_icon: run
+ # button_tip: Run tool
+ #- title_md: DropletUtils Read10x
+ # description_md: >
+ # DropletUtils provides a number of utility functions for handling single-cell (RNA-seq) data from droplet technologies such as 10X Genomics. This includes data loading, identification of cells from empty droplets, removal of barcode-swapped pseudo-cells, and downsampling of the count matrix.
+ # button_link: "{{ galaxy_base_url }}/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Febi-gxa%2fdropletutils_read_10x%2fdropletutils_read_10x"
+ # button_icon: run
+ # button_tip: Run tool
- id: data_convert
title: Converting datatypes
@@ -86,34 +86,34 @@ tabs:
Single-cell data comes in many formats.
Here we show a few key tools in Galaxy for converting and manipulating objects in Galaxy.
content:
- - title_md: SCEasy Converter
- description_md: >
- This tool allows you to convert between the following formats:
-
- - `hdf5` (AnnData/Loom)
- - `rds` (Seurat)
- - `rdata.sce` (Single Cell Experiment)
- - `h5` (Seurat)
- button_link: "{{ galaxy_base_url }}/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc/sceasy_convert%2fsceasy_convert"
- button_icon: run
- button_tip: Run tool
+ #- title_md: SCEasy Converter
+ # description_md: >
+ # This tool allows you to convert between the following formats:
+#
+# - `hdf5` (AnnData/Loom)
+# - `rds` (Seurat)
+# - `rdata.sce` (Single Cell Experiment)
+# - `h5` (Seurat)
+# button_link: "{{ galaxy_base_url }}/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc/sceasy_convert%2fsceasy_convert"
+# button_icon: run
+# button_tip: Run tool
- title_md: Manipulate AnnData
description_md: >
- Under the parameter `Function to manipulate the object` you'll find key manipulations for AnnData, such as:
-
- - `Concatenate along the observations axis` for combining AnnData objects together
- - `Transpose the data matrix` for help with converting formats
- - `Filter observations or variables` for refining or subsetting your dataset
- - `Adding annotations` and `Rename categories` for manipulating metadata
- button_link: "{{ galaxy_base_url }}/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc/anndata_manipulate%2fanndata_manipulate"
- button_icon: run
- button_tip: Run tool
- - title_md: AnnData Operations
- description_md: >
- This tool allows you to flag genes (such as mitochondrial genes) as well as change names in the metadata.
- button_link: "{{ galaxy_base_url }}/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Febi-gxa%2fanndata_ops%2fanndata_ops"
- button_icon: run
- button_tip: Run tool
+# Under the parameter `Function to manipulate the object` you'll find key manipulations for AnnData, such as:
+#
+# - `Concatenate along the observations axis` for combining AnnData objects together
+# - `Transpose the data matrix` for help with converting formats
+# - `Filter observations or variables` for refining or subsetting your dataset
+# - `Adding annotations` and `Rename categories` for manipulating metadata
+# button_link: "{{ galaxy_base_url }}/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc/anndata_manipulate%2fanndata_manipulate"
+# button_icon: run
+# button_tip: Run tool
+# - title_md: AnnData Operations
+# description_md: >
+# This tool allows you to flag genes (such as mitochondrial genes) as well as change names in the metadata.
+# button_link: "{{ galaxy_base_url }}/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Febi-gxa%2fanndata_ops%2fanndata_ops"
+# button_icon: run
+# button_tip: Run tool
- title_md: Data conversion training
description_md: >
You can also explore our dedicated tutorial on single-cell data conversion.
@@ -121,67 +121,67 @@ tabs:
button_icon: tutorial
button_tip: View tutorial
- - id: data_viz
- title: Visualising Data
- heading_md: >
- There are a few key tools for visualising single-cell data in Galaxy.
- content:
- - title_md: Plot with Scanpy
- description_md: >
- This tool allows you to generate many plots, from scatterplots, to violin plots, to gene heatplots.
- inputs:
- - label: Single cell data
- datatypes:
- - hdf5 (AnnData)
- button_link: "{{ galaxy_base_url }}/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc/scanpy_plot%2fscanpy_plot"
- button_icon: run
- button_tip: Run tool
- - title_md: Scanpy PlotEmbed
- description_md: >
- This tool allows you to plot embeddings like UMAPs.
- inputs:
- - label: Single cell data
- datatypes:
- - hdf5 (AnnData)
- button_link: "{{ galaxy_base_url }}/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Febi-gxa%2fscanpy_plot_embed%2fscanpy_plot_embed"
- button_icon: run
- button_tip: Run tool
- - title_md: Scanpy PlotTrajectory
- description_md: >
- This tool allows you to plot trajectory data, such as PAGA, pre-calculated in an AnnData object.
- inputs:
- - label: Single cell data
- datatypes:
- - hdf5 (AnnData)
- button_link: "{{ galaxy_base_url }}/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Febi-gxi%2fscanpy_plot_trajectory/scanpy_plot_trajectory"
- button_icon: run
- button_tip: Run tool
- - title_md: Scanpy Plot dimension reduction
- description_md: >
- This tool allows you to plot embeddings such as PCA, UMAP, and tSNE.
- inputs:
- - label: Single cell data
- datatypes:
- - rds (Seurat object)
- - rdata.sce (Single Cell Experiment)
- - h5 (Seurat)
- - hdf5 (Loom/AnnData)
- button_link: "{{ galaxy_base_url }}/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Febi-gxa%2fseurat_dim_plot%2fseurat_dim_plot"
- button_icon: run
- button_tip: Run tool
- - title_md: Plot with Seurat
- description_md: >
- This tool allows you to plot gene expressions, such as with Violin Plots.
- inputs:
- - label: Single cell data
- datatypes:
- - rds (Seurat object)
- - rdata.sce (Single Cell Experiment)
- - h5 (Seurat)
- - hdf5 (Loom/AnnData)
- button_link: "{{ galaxy_base_url }}/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Febi-gxa%2fseurat_plot%2fseurat_plot"
- button_icon: run
- button_tip: Run tool
+# - id: data_viz
+# title: Visualising Data
+# heading_md: >
+# There are a few key tools for visualising single-cell data in Galaxy.
+# content:
+# - title_md: Plot with Scanpy
+# description_md: >
+# This tool allows you to generate many plots, from scatterplots, to violin plots, to gene heatplots.
+# inputs:
+# - label: Single cell data
+# datatypes:
+# - hdf5 (AnnData)
+# button_link: "{{ galaxy_base_url }}/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc/scanpy_plot%2fscanpy_plot"
+# button_icon: run
+# button_tip: Run tool
+# - title_md: Scanpy PlotEmbed
+# description_md: >
+# This tool allows you to plot embeddings like UMAPs.
+# inputs:
+# - label: Single cell data
+# datatypes:
+# - hdf5 (AnnData)
+# button_link: "{{ galaxy_base_url }}/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Febi-gxa%2fscanpy_plot_embed%2fscanpy_plot_embed"
+# button_icon: run
+# button_tip: Run tool
+ # - title_md: Scanpy PlotTrajectory
+ # description_md: >
+ # This tool allows you to plot trajectory data, such as PAGA, pre-calculated in an AnnData object.
+ # inputs:
+ # - label: Single cell data
+ # datatypes:
+ # - hdf5 (AnnData)
+ # button_link: "{{ galaxy_base_url }}/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Febi-gxi%2fscanpy_plot_trajectory/scanpy_plot_trajectory"
+ # button_icon: run
+ # button_tip: Run tool
+ # - title_md: Scanpy Plot dimension reduction
+ # description_md: >
+ # This tool allows you to plot embeddings such as PCA, UMAP, and tSNE.
+ # inputs:
+ # - label: Single cell data
+ # datatypes:
+ # - rds (Seurat object)
+ # - rdata.sce (Single Cell Experiment)
+ # - h5 (Seurat)
+ # - hdf5 (Loom/AnnData)
+ # button_link: "{{ galaxy_base_url }}/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Febi-gxa%2fseurat_dim_plot%2fseurat_dim_plot"
+ # button_icon: run
+ # button_tip: Run tool
+ # - title_md: Plot with Seurat
+ # description_md: >
+ # This tool allows you to plot gene expressions, such as with Violin Plots.
+ # inputs:
+ # - label: Single cell data
+ # datatypes:
+ # - rds (Seurat object)
+ # - rdata.sce (Single Cell Experiment)
+ # - h5 (Seurat)
+ # - hdf5 (Loom/AnnData)
+ # button_link: "{{ galaxy_base_url }}/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Febi-gxa%2fseurat_plot%2fseurat_plot"
+ # button_icon: run
+ # button_tip: Run tool
- id: help
title: Help