diff --git a/tools/droplet-barcode-plot/.shed.yml b/tools/droplet-barcode-plot/.shed.yml
index bde3123b..d8965cbf 100644
--- a/tools/droplet-barcode-plot/.shed.yml
+++ b/tools/droplet-barcode-plot/.shed.yml
@@ -1,7 +1,9 @@
-categories: [Sequence Analysis]
+categories:
+ - Single Cell
+ - Sequence Analysis
 description: Make a cell barcode plot for droplet single-cell RNA-seq QC
-homepage_url: https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary 
+homepage_url: https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary
 long_description: Given a barcode freqeuncy table or an MTX-format matrix from which one can be calculated, produces a barcode rank plot to assess distinctness of droplets with cells over those without.
-name: droplet_barcode_plot 
+name: droplet_barcode_plot
 owner: ebi-gxa
 remote_repository_url: https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/droplet-rank-plot/.shed.yml
diff --git a/tools/salmon-kallisto-mtx-to-10x/.shed.yml b/tools/salmon-kallisto-mtx-to-10x/.shed.yml
index e308f442..84ed1fbd 100644
--- a/tools/salmon-kallisto-mtx-to-10x/.shed.yml
+++ b/tools/salmon-kallisto-mtx-to-10x/.shed.yml
@@ -1,7 +1,9 @@
-categories: [Sequence Analysis]
+categories:
+ - Single Cell
+ - Sequence Analysis
 description: Transforms .mtx matrix and associated labels into a format compatible with tools expecting old-style 10X data
-homepage_url: https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary 
+homepage_url: https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary
 long_description: Kallisto and Alevin (and possibly other tools) output an MTX file and associated labels that are not consistent with the old-style 10X, meaning that routines designed to parse those files cannot be used. This tool transforms (in the mathematical sense) the matrix, and reformats the genes file (essentially duplicating the column) to match those earlier conventions.
-name: salmon_kallisto_mtx_to_10x 
+name: salmon_kallisto_mtx_to_10x
 owner: ebi-gxa
 remote_repository_url: https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/salmon-kallisto-mtx-to-10x/.shed.yml
diff --git a/tools/tertiary-analysis/cell-types-analysis/.shed.yml b/tools/tertiary-analysis/cell-types-analysis/.shed.yml
index d79a5ebe..fd8ec99b 100644
--- a/tools/tertiary-analysis/cell-types-analysis/.shed.yml
+++ b/tools/tertiary-analysis/cell-types-analysis/.shed.yml
@@ -1,4 +1,5 @@
 categories:
+ - Single Cell
  - Transcriptomics
  - RNA
  - Statistics
diff --git a/tools/tertiary-analysis/data-hca/.shed.yml b/tools/tertiary-analysis/data-hca/.shed.yml
index f8ebaf61..40d6bdee 100644
--- a/tools/tertiary-analysis/data-hca/.shed.yml
+++ b/tools/tertiary-analysis/data-hca/.shed.yml
@@ -1,4 +1,6 @@
 categories:
+ - Single Cell
+ - Spatial Omics
  - Transcriptomics
  - Sequence Analysis
 description: "Tools for interacting with the Human Cell Atlas resource https://prod.data.humancellatlas.org/explore/projects"
diff --git a/tools/tertiary-analysis/data-scxa/.shed.yml b/tools/tertiary-analysis/data-scxa/.shed.yml
index ebbe68f6..2ecf99ba 100644
--- a/tools/tertiary-analysis/data-scxa/.shed.yml
+++ b/tools/tertiary-analysis/data-scxa/.shed.yml
@@ -1,4 +1,5 @@
 categories:
+ - Single Cell
  - Transcriptomics
  - Sequence Analysis
 description: "Tools for interacting with the EMBL-EBI Expression Atlas resource https://www.ebi.ac.uk/gxa/home https://www.ebi.ac.uk/gxa/sc/home"
diff --git a/tools/tertiary-analysis/decoupler/.shed.yml b/tools/tertiary-analysis/decoupler/.shed.yml
index 480cd4ac..58d7a986 100644
--- a/tools/tertiary-analysis/decoupler/.shed.yml
+++ b/tools/tertiary-analysis/decoupler/.shed.yml
@@ -1,4 +1,5 @@
 categories:
+ - Single Cell
  - Transcriptomics
 description: "decoupler - Ensemble of methods to infer biological activities"
 long_description: |
@@ -23,4 +24,4 @@ suite:
     activities from omics data within a unified framework. It allows to flexibly test any
     method with any prior knowledge resource and incorporates methods that take into account
     the sign and weight. It can be used with any omic, as long as its features can be linked
-    to a biological process based on prior knowledge.  
+    to a biological process based on prior knowledge.
diff --git a/tools/tertiary-analysis/dropletutils/.shed.yml b/tools/tertiary-analysis/dropletutils/.shed.yml
index 18783732..5908a0ce 100644
--- a/tools/tertiary-analysis/dropletutils/.shed.yml
+++ b/tools/tertiary-analysis/dropletutils/.shed.yml
@@ -1,4 +1,5 @@
 categories:
+ - Single Cell
  - Transcriptomics
  - RNA
  - Statistics
diff --git a/tools/tertiary-analysis/garnett/.shed.yml b/tools/tertiary-analysis/garnett/.shed.yml
index c08b215d..07d7ac8c 100644
--- a/tools/tertiary-analysis/garnett/.shed.yml
+++ b/tools/tertiary-analysis/garnett/.shed.yml
@@ -1,4 +1,5 @@
 categories:
+ - Single Cell
  - Transcriptomics
  - RNA
  - Statistics
diff --git a/tools/tertiary-analysis/monocle3/.shed.yml b/tools/tertiary-analysis/monocle3/.shed.yml
index 89c85b5c..968f51d8 100644
--- a/tools/tertiary-analysis/monocle3/.shed.yml
+++ b/tools/tertiary-analysis/monocle3/.shed.yml
@@ -1,4 +1,5 @@
 categories:
+ - Single Cell
  - Transcriptomics
  - RNA
  - Statistics
@@ -17,4 +18,4 @@ suite:
   name: "suite_monocle3"
   description: "De-composed monocle3 functionality tools, based on https://github.com/ebi-gene-expression-group/monocle-scripts and monocle3 0.1.2."
   long_description: |
-    monocle3: A tool for trajectory analysis of single cell RNA-seq data  
+    monocle3: A tool for trajectory analysis of single cell RNA-seq data
diff --git a/tools/tertiary-analysis/pyscenic/.shed.yml b/tools/tertiary-analysis/pyscenic/.shed.yml
index f4c05268..dbedd2f1 100644
--- a/tools/tertiary-analysis/pyscenic/.shed.yml
+++ b/tools/tertiary-analysis/pyscenic/.shed.yml
@@ -1,10 +1,11 @@
 categories:
+ - Single Cell
  - Transcriptomics
  - RNA
  - Sequence Analysis
 description: "PySCENIC scripts based on usage at https://pyscenic.readthedocs.io/"
 long_description: |
-        pySCENIC is a lightning-fast python implementation of the SCENIC pipeline (Single-Cell rEgulatory Network Inference and Clustering) 
+        pySCENIC is a lightning-fast python implementation of the SCENIC pipeline (Single-Cell rEgulatory Network Inference and Clustering)
         which enables biologists to infer transcription factors, gene regulatory networks and cell types from single-cell RNA-seq data.
 name: suite_pyscenic
 owner: ebi-gxa
@@ -17,5 +18,5 @@ suite:
   name: "suite_pyscenic"
   description: "PySCENIC scripts based on usage at https://pyscenic.readthedocs.io/"
   long_description: |
-    pySCENIC is a lightning-fast python implementation of the SCENIC pipeline (Single-Cell rEgulatory Network Inference and Clustering) 
+    pySCENIC is a lightning-fast python implementation of the SCENIC pipeline (Single-Cell rEgulatory Network Inference and Clustering)
     which enables biologists to infer transcription factors, gene regulatory networks and cell types from single-cell RNA-seq data.
diff --git a/tools/tertiary-analysis/sc3/.shed.yml b/tools/tertiary-analysis/sc3/.shed.yml
index 4006c4f3..36cfab97 100644
--- a/tools/tertiary-analysis/sc3/.shed.yml
+++ b/tools/tertiary-analysis/sc3/.shed.yml
@@ -1,4 +1,5 @@
 categories:
+ - Single Cell
  - Transcriptomics
  - RNA
  - Statistics
diff --git a/tools/tertiary-analysis/scanpy/.shed.yml b/tools/tertiary-analysis/scanpy/.shed.yml
index a46e310d..602d17be 100644
--- a/tools/tertiary-analysis/scanpy/.shed.yml
+++ b/tools/tertiary-analysis/scanpy/.shed.yml
@@ -10,9 +10,11 @@ homepage_url: https://scanpy.readthedocs.io
 remote_repository_url: https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy
 type: unrestricted
 categories:
-- Transcriptomics
-- Sequence Analysis
-- RNA
+  - Single Cell
+  - Spatial Omics
+  - Transcriptomics
+  - Sequence Analysis
+  - RNA
 auto_tool_repositories:
     name_template: "{{ tool_id }}"
     description_template: "Wrapper for the scanpy-scripts tool suite: {{ tool_name }}"
diff --git a/tools/tertiary-analysis/scater/.shed.yml b/tools/tertiary-analysis/scater/.shed.yml
index 28d4f9e7..d0923307 100644
--- a/tools/tertiary-analysis/scater/.shed.yml
+++ b/tools/tertiary-analysis/scater/.shed.yml
@@ -1,4 +1,5 @@
 categories:
+ - Single Cell
  - Transcriptomics
  - RNA
  - Statistics
diff --git a/tools/tertiary-analysis/sccaf/.shed.yml b/tools/tertiary-analysis/sccaf/.shed.yml
index 70ee4a8e..69e1a5ba 100644
--- a/tools/tertiary-analysis/sccaf/.shed.yml
+++ b/tools/tertiary-analysis/sccaf/.shed.yml
@@ -15,7 +15,8 @@ homepage_url: https://github.com/sccaf/sccaf
 remote_repository_url: https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf
 type: unrestricted
 categories:
-- Transcriptomics
+ - Single Cell
+ - Transcriptomics
 auto_tool_repositories:
     name_template: "{{ tool_id }}"
     description_template: "Wrapper for the SCCAF tool: {{ tool_name }}"
diff --git a/tools/tertiary-analysis/sceasy/.shed.yml b/tools/tertiary-analysis/sceasy/.shed.yml
index e16ba551..af50f8ab 100644
--- a/tools/tertiary-analysis/sceasy/.shed.yml
+++ b/tools/tertiary-analysis/sceasy/.shed.yml
@@ -1,4 +1,5 @@
 categories:
+ - Single Cell
  - Transcriptomics
 description: "Convert scRNA data object between popular formats"
 long_description: |
diff --git a/tools/tertiary-analysis/scmap/.shed.yml b/tools/tertiary-analysis/scmap/.shed.yml
index 6799a600..12743549 100644
--- a/tools/tertiary-analysis/scmap/.shed.yml
+++ b/tools/tertiary-analysis/scmap/.shed.yml
@@ -1,4 +1,5 @@
 categories:
+ - Single Cell
  - Transcriptomics
  - RNA
  - Statistics
@@ -17,4 +18,4 @@ suite:
   name: "suite_scmap"
   description: "De-composed scmap functionality tools, based on https://github.com/ebi-gene-expression-group/scmap-cli and scmap 1.6.0."
   long_description: |
-    scmap: A tool for unsupervised projection of single cell RNA-seq data  
+    scmap: A tool for unsupervised projection of single cell RNA-seq data
diff --git a/tools/tertiary-analysis/scpred/.shed.yml b/tools/tertiary-analysis/scpred/.shed.yml
index 0dcc7f88..b053a61c 100644
--- a/tools/tertiary-analysis/scpred/.shed.yml
+++ b/tools/tertiary-analysis/scpred/.shed.yml
@@ -1,4 +1,5 @@
 categories:
+ - Single Cell
  - Transcriptomics
  - RNA
  - Statistics
diff --git a/tools/tertiary-analysis/seurat/.shed.yml b/tools/tertiary-analysis/seurat/.shed.yml
index d76804a2..794b3a77 100644
--- a/tools/tertiary-analysis/seurat/.shed.yml
+++ b/tools/tertiary-analysis/seurat/.shed.yml
@@ -1,4 +1,5 @@
-categories: 
+categories:
+ - Single Cell
  - Transcriptomics
  - RNA
  - Statistics
diff --git a/tools/tertiary-analysis/ucsc-cell-browser/.shed.yml b/tools/tertiary-analysis/ucsc-cell-browser/.shed.yml
index c349a3b0..2282c971 100644
--- a/tools/tertiary-analysis/ucsc-cell-browser/.shed.yml
+++ b/tools/tertiary-analysis/ucsc-cell-browser/.shed.yml
@@ -1,4 +1,6 @@
-categories: [Transcriptomics]
+categories:
+ - Single Cell
+ - Transcriptomics
 description: Python pipeline and Javascript scatter plot library for single-cell datasets
 homepage_url: https://cells.ucsc.edu/
 long_description: The UCSC Cell Browser is a viewer for single cell data. You can