Add Single Cell and Spatial Omics shed categories

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

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

tools/tertiary-analysis/cell-types-analysis/.shed.yml

@@ -1,4 +1,5 @@
 categories:
+ - Single Cell
  - Transcriptomics
  - RNA
  - Statistics

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"

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"

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.

tools/tertiary-analysis/dropletutils/.shed.yml

@@ -1,4 +1,5 @@
 categories:
+ - Single Cell
  - Transcriptomics
  - RNA
  - Statistics

tools/tertiary-analysis/garnett/.shed.yml

@@ -1,4 +1,5 @@
 categories:
+ - Single Cell
  - Transcriptomics
  - RNA
  - Statistics

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

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.

tools/tertiary-analysis/sc3/.shed.yml

@@ -1,4 +1,5 @@
 categories:
+ - Single Cell
  - Transcriptomics
  - RNA
  - Statistics

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 }}"

tools/tertiary-analysis/scater/.shed.yml

@@ -1,4 +1,5 @@
 categories:
+ - Single Cell
  - Transcriptomics
  - RNA
  - Statistics

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 }}"

tools/tertiary-analysis/sceasy/.shed.yml

@@ -1,4 +1,5 @@
 categories:
+ - Single Cell
  - Transcriptomics
 description: "Convert scRNA data object between popular formats"
 long_description: |

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

tools/tertiary-analysis/scpred/.shed.yml

@@ -1,4 +1,5 @@
 categories:
+ - Single Cell
  - Transcriptomics
  - RNA
  - Statistics

tools/tertiary-analysis/seurat/.shed.yml

@@ -1,4 +1,5 @@
-categories: 
+categories:
+ - Single Cell
  - Transcriptomics
  - RNA
  - Statistics

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