Fix spanorm install, config, and test input

Author: LouisK92

src/methods_normalization/spanorm/config.vsh.yaml

@@ -1,14 +1,14 @@
 __merge__: /src/api/comp_method_normalization.yaml
 
 name: spanorm
-label: "Spatially-aware normalisation for spatial transcriptomics data"
+label: "SpaNorm normalization"
 summary: "Spatially-aware normalisation for spatial transcriptomics data"
 description: "Spatially-aware normalisation for spatial transcriptomics data"
 links:
   documentation: "https://github.com/openproblems-bio/task_ist_preprocessing"
   repository: "https://github.com/bhuvad/SpaNorm/tree/master"
 references:
-  doi: "https://doi.org/10.1101/2024.05.31.596908"
+  doi: "10.1101/2024.05.31.596908"
 
 resources:
   - type: r_script
@@ -19,7 +19,7 @@ engines:
     image: openproblems/base_r:1.0.0
     setup:
       - type: r
-        bioc: SpaNorm, zellkonverter
+        bioc: [SpaNorm, zellkonverter]
   - type: native
 
 runners:

src/methods_normalization/spanorm/script.R

@@ -3,12 +3,14 @@ library(SingleCellExperiment)
 library(SpatialExperiment)
 library(zellkonverter)
 
+## VIASH START
 par <- list(
-  "input" = 'resources_test/task_ist_preprocessing/mouse_brain_combined/spatial_aggregated_counts.h5ad',
+  "input_spatial_aggregated_counts" = 'resources_test/task_ist_preprocessing/mouse_brain_combined/spatial_aggregated_counts.h5ad',
   "output" = 'tmp/spatial_spanormed_counts.h5ad'
 )
+## VIASH END
 
-sce <- readH5AD(par$input)
+sce <- readH5AD(par$input_spatial_aggregated_counts)
 sce <- as(sce, "SpatialExperiment")
 
 centroid_x <- colData(sce)$centroid_x