Add Seurat v5 tools

communities/spoc/lab/tool_panel/hca-seurat.yml

@@ -0,0 +1,28 @@
+tool_panel_section_label: HCA-Seurat
+tools:
+- name: seurat_create_seurat_object
+  owner: ebi-gxa
+- name: seurat_export_cellbrowser
+  owner: ebi-gxa
+- name: seurat_filter_cells
+  owner: ebi-gxa
+- name: seurat_find_clusters
+  owner: ebi-gxa
+- name: seurat_find_markers
+  owner: ebi-gxa
+- name: seurat_find_neighbours
+  owner: ebi-gxa
+- name: seurat_find_variable_genes
+  owner: ebi-gxa
+- name: seurat_normalise_data
+  owner: ebi-gxa
+- name: seurat_dim_plot
+  owner: ebi-gxa
+- name: seurat_read10x
+  owner: ebi-gxa
+- name: seurat_run_pca
+  owner: ebi-gxa
+- name: seurat_run_tsne
+  owner: ebi-gxa
+- name: seurat_scale_data
+  owner: ebi-gxa

communities/spoc/lab/tool_panel/hca-seurat.yml.lock

@@ -0,0 +1,83 @@
+install_repository_dependencies: true
+install_resolver_dependencies: false
+install_tool_dependencies: false
+tool_panel_section_label: HCA-Seurat
+tools:
+- name: seurat_create_seurat_object
+  owner: ebi-gxa
+  revisions:
+  - f8865ae30723
+  tool_panel_section_id: seurat
+  tool_panel_section_label: Seurat
+- name: seurat_export_cellbrowser
+  owner: ebi-gxa
+  revisions:
+  - 36221da750e8
+  tool_panel_section_id: seurat
+  tool_panel_section_label: Seurat
+- name: seurat_filter_cells
+  owner: ebi-gxa
+  revisions:
+  - cd9f564bd63f
+  tool_panel_section_id: seurat
+  tool_panel_section_label: Seurat
+- name: seurat_find_clusters
+  owner: ebi-gxa
+  revisions:
+  - d541e9e62beb
+  tool_panel_section_id: seurat
+  tool_panel_section_label: Seurat
+- name: seurat_find_markers
+  owner: ebi-gxa
+  revisions:
+  - 07fc9f4841b3
+  tool_panel_section_id: seurat
+  tool_panel_section_label: Seurat
+- name: seurat_find_neighbours
+  owner: ebi-gxa
+  revisions:
+  - ba897c57bdd9
+  tool_panel_section_id: seurat
+  tool_panel_section_label: Seurat
+- name: seurat_find_variable_genes
+  owner: ebi-gxa
+  revisions:
+  - 948fc0276b4f
+  tool_panel_section_id: seurat
+  tool_panel_section_label: Seurat
+- name: seurat_normalise_data
+  owner: ebi-gxa
+  revisions:
+  - 3f49bc9c9213
+  tool_panel_section_id: seurat
+  tool_panel_section_label: Seurat
+- name: seurat_dim_plot
+  owner: ebi-gxa
+  revisions:
+  - 64174ac50d78
+  tool_panel_section_id: seurat
+  tool_panel_section_label: Seurat
+- name: seurat_read10x
+  owner: ebi-gxa
+  revisions:
+  - f5db0e853f57
+  tool_panel_section_id: seurat
+  tool_panel_section_label: Seurat
+- name: seurat_run_pca
+  owner: ebi-gxa
+  revisions:
+  - 8ded486b0014
+  tool_panel_section_id: seurat
+  tool_panel_section_label: Seurat
+- name: seurat_run_tsne
+  owner: ebi-gxa
+  revisions:
+  - 0db997e4a81d
+  tool_panel_section_id: seurat
+  tool_panel_section_label: Seurat
+- name: seurat_scale_data
+  owner: ebi-gxa
+  revisions:
+  - 5e9ba303f9e1
+  tool_panel_section_id: seurat
+  tool_panel_section_label: Seurat

communities/spoc/lab/tool_panel/seurat.yml

@@ -1,28 +1,16 @@
 tool_panel_section_label: Seurat
 tools:
-- name: seurat_create_seurat_object
-  owner: ebi-gxa
-- name: seurat_export_cellbrowser
-  owner: ebi-gxa
-- name: seurat_filter_cells
-  owner: ebi-gxa
-- name: seurat_find_clusters
-  owner: ebi-gxa
-- name: seurat_find_markers
-  owner: ebi-gxa
-- name: seurat_find_neighbours
-  owner: ebi-gxa
-- name: seurat_find_variable_genes
-  owner: ebi-gxa
-- name: seurat_normalise_data
-  owner: ebi-gxa
-- name: seurat_dim_plot
-  owner: ebi-gxa
-- name: seurat_read10x
-  owner: ebi-gxa
-- name: seurat_run_pca
-  owner: ebi-gxa
-- name: seurat_run_tsne
-  owner: ebi-gxa
-- name: seurat_scale_data
-  owner: ebi-gxa
+- name: create_seurat
+  owner: iuc
+- name: inspect_and_manipulate
+  owner: iuc
+- name: integrate
+  owner: iuc
+- name: normalize_select_features_scale
+  owner: iuc
+- name: reduce_dimensions
+  owner: iuc
+- name: neighbors_clusters_markers
+  owner: iuc
+- name: plot
+  owner: iuc

communities/spoc/lab/tool_panel/seurat.yml.lock

@@ -3,81 +3,49 @@ install_resolver_dependencies: false
 install_tool_dependencies: false
 tool_panel_section_label: Seurat
 tools:
-- name: seurat_create_seurat_object
-  owner: ebi-gxa
+- name: create_seurat
+  owner: iuc
   revisions:
-  - f8865ae30723
-  tool_panel_section_id: seurat
+  -
+  tool_panel_section_id: Seurat
   tool_panel_section_label: Seurat
-- name: seurat_export_cellbrowser
-  owner: ebi-gxa
+- name: inspect_and_manipulate
+  owner: iuc
   revisions:
-  - 36221da750e8
-  tool_panel_section_id: seurat
+  -
+  tool_panel_section_id: Seurat
   tool_panel_section_label: Seurat
-- name: seurat_filter_cells
-  owner: ebi-gxa
+- name: integrate
+  owner: iuc
   revisions:
-  - cd9f564bd63f
-  tool_panel_section_id: seurat
+  -
+  tool_panel_section_id: Seurat
   tool_panel_section_label: Seurat
-- name: seurat_find_clusters
-  owner: ebi-gxa
+- name: neighbors_clusters_markers
+  owner: iuc
   revisions:
-  - d541e9e62beb
-  tool_panel_section_id: seurat
+  -
+  tool_panel_section_id: Seurat
   tool_panel_section_label: Seurat
-- name: seurat_find_markers
-  owner: ebi-gxa
+- name: normalize_select_features_scale
+  owner: iuc
   revisions:
-  - 07fc9f4841b3
-  tool_panel_section_id: seurat
+  -
+  tool_panel_section_id: Seurat
   tool_panel_section_label: Seurat
-- name: seurat_find_neighbours
-  owner: ebi-gxa
+- name: plot
+  owner: iuc
   revisions:
-  - ba897c57bdd9
-  tool_panel_section_id: seurat
+  -
+  tool_panel_section_id: Seurat
   tool_panel_section_label: Seurat
-- name: seurat_find_variable_genes
-  owner: ebi-gxa
+- name: reduce_dimensions
+  owner: iuc
   revisions:
-  - 948fc0276b4f
-  tool_panel_section_id: seurat
-  tool_panel_section_label: Seurat
-- name: seurat_normalise_data
-  owner: ebi-gxa
-  revisions:
-  - 3f49bc9c9213
-  tool_panel_section_id: seurat
-  tool_panel_section_label: Seurat
-- name: seurat_dim_plot
-  owner: ebi-gxa
-  revisions:
-  - 64174ac50d78
-  tool_panel_section_id: seurat
-  tool_panel_section_label: Seurat
-- name: seurat_read10x
-  owner: ebi-gxa
-  revisions:
-  - f5db0e853f57
-  tool_panel_section_id: seurat
-  tool_panel_section_label: Seurat
-- name: seurat_run_pca
-  owner: ebi-gxa
-  revisions:
-  - 8ded486b0014
-  tool_panel_section_id: seurat
-  tool_panel_section_label: Seurat
-- name: seurat_run_tsne
-  owner: ebi-gxa
-  revisions:
-  - 0db997e4a81d
-  tool_panel_section_id: seurat
-  tool_panel_section_label: Seurat
-- name: seurat_scale_data
-  owner: ebi-gxa
-  revisions:
-  - 5e9ba303f9e1
-  tool_panel_section_id: seurat
+  - 0cb889db0910
+  - 32c5c85cbc12
+  - c0b037b12765
+  - c5ac926c838f
+  - e1c3c2f2a834
+  tool_panel_section_id: Seurat
   tool_panel_section_label: Seurat

communities/spoc/lab/tool_panel/tool_panel_view.yml

@@ -109,38 +109,6 @@ items:
     id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/monocle3_reducedim/monocle3_reduceDim
   - type: tool
     id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/monocle3_topmarkers/monocle3_topmarkers
-- id: seurat
-  type: section
-  name: Seurat
-  items:
-  - type: tool
-    id: toolshed.g2.bx.psu.edu/repos/iuc/seurat/seurat
-  - type: tool
-    id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_create_seurat_object/seurat_create_seurat_object
-  - type: tool
-    id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_export_cellbrowser/seurat_export_cellbrowser
-  - type: tool
-    id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_filter_cells/seurat_filter_cells
-  - type: tool
-    id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_find_clusters/seurat_find_clusters
-  - type: tool
-    id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_find_markers/seurat_find_markers
-  - type: tool
-    id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_find_neighbours/seurat_find_neighbours
-  - type: tool
-    id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_find_variable_genes/seurat_find_variable_genes
-  - type: tool
-    id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_normalise_data/seurat_normalise_data
-  - type: tool
-    id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_dim_plot/seurat_dim_plot
-  - type: tool
-    id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_read10x/seurat_read10x
-  - type: tool
-    id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_run_pca/seurat_run_pca
-  - type: tool
-    id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_run_tsne/seurat_run_tsne
-  - type: tool
-    id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_scale_data/seurat_scale_data
 - id: inference
   type: section
   name: Inference
@@ -186,7 +154,7 @@ items:
 - id: hca-scanpy
   type: section
   name: HCA-Scanpy
-  items: 
+  items:
   - type: tool
     id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/anndata_ops/anndata_ops
   - type: tool
@@ -245,10 +213,42 @@ items:
     id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_multiplet_scrublet/scanpy_multiplet_scrublet
   - type: tool
     id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_run_umap/seurat_run_umap
+- id: seurat
+  type: section
+  name: Seurat
+  items:
+  - type: tool
+    id: toolshed.g2.bx.psu.edu/repos/iuc/seurat/seurat
+  - type: tool
+    id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_create_seurat_object/seurat_create_seurat_object
+  - type: tool
+    id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_export_cellbrowser/seurat_export_cellbrowser
+  - type: tool
+    id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_filter_cells/seurat_filter_cells
+  - type: tool
+    id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_find_clusters/seurat_find_clusters
+  - type: tool
+    id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_find_markers/seurat_find_markers
+  - type: tool
+    id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_find_neighbours/seurat_find_neighbours
+  - type: tool
+    id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_find_variable_genes/seurat_find_variable_genes
+  - type: tool
+    id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_normalise_data/seurat_normalise_data
+  - type: tool
+    id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_dim_plot/seurat_dim_plot
+  - type: tool
+    id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_read10x/seurat_read10x
+  - type: tool
+    id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_run_pca/seurat_run_pca
+  - type: tool
+    id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_run_tsne/seurat_run_tsne
+  - type: tool
+    id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_scale_data/seurat_scale_data
 - id: raceid
   type: section
   name: RaceID
-  items: 
+  items:
   - type: tool
     id: toolshed.g2.bx.psu.edu/repos/iuc/raceid_inspectclusters/raceid_inspectclusters
   - type: tool