feat(app-panel): improve capsule parameter UI (#2)

* Update boolean parameters to TRUE/FALSE list options

* Update count_type to list with raw and clean options (default: clean)

* Move count_type to first position in Basic category

* Split visualization parameters by plot type

* Move group-based filtering first

* Update changelog for parameter UI changes

* docs: Update changelog with contributor mention

Added contributor mention in the changelog for clarity.

---------

Co-authored-by: Kelly Sovacool, PhD <kelly-sovacool@users.noreply.github.com>

Author: phoman14

.codeocean/app-panel.json

@@ -16,27 +16,41 @@
 			"id": "gDLmTU36PrmD13RK",
 			"name": "Input Data Parameters",
 			"description": "Options for defining input data",
-			"icon": "📁"
+			"icon": "\ud83d\udcc1"
 		},
 		{
 			"id": "gn9FXwemlVazWQIo",
 			"name": "Basic",
-			"icon": "📂"
+			"icon": "\ud83d\udcc2"
 		},
 		{
 			"id": "rT9kLmPqRsUvWxYz",
-			"name": "Visualization",
-			"description": "Visualization and plotting options",
-			"icon": "📊"
+			"name": "Visualization: General",
+			"description": "General visualization and plotting options",
+			"icon": "\ud83d\udcca"
 		},
 		{
 			"id": "XqgPq28Eo5VCFSZu",
 			"name": "Advanced",
 			"description": "Advanced parameters",
-			"icon": "📂"
+			"icon": "\ud83d\udcc2"
 		}
 	],
 	"parameters": [
+		{
+			"id": "vJvArGM6rjelGp9u",
+			"category": "gn9FXwemlVazWQIo",
+			"name": "Count type",
+			"param_name": "count_type",
+			"description": "Type of counts to filter. Must be a count type in names(moo@counts)",
+			"type": "list",
+			"value_type": "string",
+			"default_value": "clean",
+			"extra_data": [
+				"raw",
+				"clean"
+			]
+		},
 		{
 			"id": "vJvArGM6rjelGp9v",
 			"category": "gn9FXwemlVazWQIo",
@@ -74,10 +88,13 @@
 			"param_name": "use_cpm_counts_to_filter",
 			"description": "Transform raw counts to CPM before filtering",
 			"help_text": "Set TRUE for raw counts, FALSE if counts are already normalized/transformed",
-			"type": "text",
+			"type": "list",
 			"value_type": "string",
 			"default_value": "TRUE",
-			"pattern": "TRUE|FALSE|T|F"
+			"extra_data": [
+				"TRUE",
+				"FALSE"
+			]
 		},
 		{
 			"id": "vJvArGM6rjelGp9c",
@@ -96,10 +113,13 @@
 			"param_name": "plot_corr_matrix_heatmap",
 			"description": "Create a correlation matrix heatmap for sample similarity",
 			"help_text": "Set to FALSE for datasets with many samples to avoid long run times",
-			"type": "text",
+			"type": "list",
 			"value_type": "string",
 			"default_value": "TRUE",
-			"pattern": "TRUE|FALSE|T|F"
+			"extra_data": [
+				"TRUE",
+				"FALSE"
+			]
 		},
 		{
 			"id": "vJvArGM6rjelGp9g",
@@ -108,41 +128,37 @@
 			"param_name": "interactive_plots",
 			"description": "Create interactive plots with plotly (PCA and histogram)",
 			"help_text": "Interactive plots allow hovering to view sample information, but correlation heatmap will not display",
-			"type": "text",
+			"type": "list",
 			"value_type": "string",
 			"default_value": "FALSE",
-			"pattern": "TRUE|FALSE|T|F"
-		},
-		{
-			"id": "vJvArGM6rjelGp9d",
-			"category": "XqgPq28Eo5VCFSZu",
-			"name": "Minimum samples per group with nonzero counts",
-			"param_name": "minimum_number_of_samples_with_nonzero_counts_in_a_group",
-			"description": "Only keeps genes that have at least this number of samples with nonzero counts in at least one group",
-			"type": "text",
-			"value_type": "integer",
-			"default_value": "3"
+			"extra_data": [
+				"TRUE",
+				"FALSE"
+			]
 		},
 		{
 			"id": "vJvArGM6rjelGp9e",
 			"category": "XqgPq28Eo5VCFSZu",
 			"name": "Use group-based filtering",
 			"param_name": "use_group_based_filtering",
 			"description": "If TRUE, only keeps features that have sufficient nonzero counts in at least one group",
-			"type": "text",
+			"type": "list",
 			"value_type": "string",
 			"default_value": "FALSE",
-			"pattern": "TRUE|FALSE|T|F"
+			"extra_data": [
+				"TRUE",
+				"FALSE"
+			]
 		},
 		{
-			"id": "vJvArGM6rjelGp9u",
+			"id": "vJvArGM6rjelGp9d",
 			"category": "XqgPq28Eo5VCFSZu",
-			"name": "Count type",
-			"param_name": "count_type",
-			"description": "Type of counts to filter. Must be a count type in names(moo@counts)",
+			"name": "Minimum samples per group with nonzero counts",
+			"param_name": "minimum_number_of_samples_with_nonzero_counts_in_a_group",
+			"description": "Only keeps genes that have at least this number of samples with nonzero counts in at least one group",
 			"type": "text",
-			"value_type": "string",
-			"default_value": "clean"
+			"value_type": "integer",
+			"default_value": "3"
 		},
 		{
 			"id": "vJvArGM6rjelGp9w",
@@ -176,4 +192,4 @@
 			"file_name": "figures/filt/pca.png"
 		}
 	]
-}
+}

CHANGELOG.md

@@ -1,5 +1,9 @@
 # Code Ocean capsule - MOSuite - filter low counts
 
+## Development version
+
+- Improved the Code Ocean parameter UI by using list controls for key options and reorganizing related filtering and visualization settings. (#2, @phoman14)
+
 ## v3.0
 
 - Use MOSuite v0.3.0.
@@ -15,4 +19,4 @@
 
 Initial release
 
-<https://poc-nci.codeocean.io/capsule/4565215/tree/v1> (`7ee2ff0`)
+<https://poc-nci.codeocean.io/capsule/4565215/tree/v1> (`7ee2ff0`)