Comment out tools for Single-cell GalaxyLab

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!
-          <code>EBI SCXA Data Retrieval</code>
-        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!
+      #    <code>EBI SCXA Data Retrieval</code>
+      #  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.
@@ -60,128 +60,128 @@ 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.
-          <code>Scanpy Read10x</code>
-        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: <code>Seurat Read10x</code>
-        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: <code>DropletUtils Read10x</code>
-        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.
+      #    <code>Scanpy Read10x</code>
+      #  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: <code>Seurat Read10x</code>
+      #  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: <code>DropletUtils Read10x</code>
+      #  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
     heading_md: >
       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: <code>SCEasy Converter</code>
-        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: <code>SCEasy Converter</code>
+      #  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: <code>Manipulate AnnData</code>
         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: <code>AnnData Operations</code>
-        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: <code>AnnData Operations</code>
+#        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.
         button_link: "https://training.galaxyproject.org/training-material/topics/single-cell/tutorials/scrna-data-ingest/tutorial.html"
         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: <code>Plot with Scanpy</code>
-        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: <code>Scanpy PlotEmbed</code>
-        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: <code>Scanpy PlotTrajectory</code>
-        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: <code>Scanpy Plot dimension reduction</code>
-        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: <code>Plot with Seurat</code>
-        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: <code>Plot with Scanpy</code>
+#        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: <code>Scanpy PlotEmbed</code>
+#        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: <code>Scanpy PlotTrajectory</code>
+      #   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: <code>Scanpy Plot dimension reduction</code>
+      #   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: <code>Plot with Seurat</code>
+      #   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