From 459e1a720927efa4747990b443969cd879687a59 Mon Sep 17 00:00:00 2001
From: phoman14 <Philip.homan@nih.gov>
Date: Tue, 30 Jun 2026 03:34:04 -0400
Subject: [PATCH 1/3] Convert volcano summary booleans to lists

---
 .codeocean/app-panel.json | 56 +++++++++++++++++++++++++++++----------
 1 file changed, 42 insertions(+), 14 deletions(-)

diff --git a/.codeocean/app-panel.json b/.codeocean/app-panel.json
index 50be09f..5e9d739 100644
--- a/.codeocean/app-panel.json
+++ b/.codeocean/app-panel.json
@@ -102,9 +102,13 @@
 			"name": "Add custom features to labels",
 			"param_name": "add_features",
 			"description": "Add custom_gene_list to default labels",
-			"type": "text",
+			"type": "list",
 			"value_type": "string",
-			"default_value": "FALSE"
+			"default_value": "FALSE",
+			"extra_data": [
+				"TRUE",
+				"FALSE"
+			]
 		},
 		{
 			"id": "label_features_id",
@@ -112,9 +116,13 @@
 			"name": "Label only custom features",
 			"param_name": "label_features",
 			"description": "Label ONLY features from custom_gene_list",
-			"type": "text",
+			"type": "list",
 			"value_type": "string",
-			"default_value": "FALSE"
+			"default_value": "FALSE",
+			"extra_data": [
+				"TRUE",
+				"FALSE"
+			]
 		},
 		{
 			"id": "custom_gene_list_id",
@@ -201,9 +209,13 @@
 			"name": "Displace specific labels",
 			"param_name": "displace_feature_labels",
 			"description": "Displace specific feature labels",
-			"type": "text",
+			"type": "list",
 			"value_type": "string",
-			"default_value": "FALSE"
+			"default_value": "FALSE",
+			"extra_data": [
+				"TRUE",
+				"FALSE"
+			]
 		},
 		{
 			"id": "custom_gene_list_special_label_displacement_id",
@@ -290,9 +302,13 @@
 			"name": "Flip volcano plot",
 			"param_name": "flip_vplot",
 			"description": "Flip fold change values",
-			"type": "text",
+			"type": "list",
 			"value_type": "string",
-			"default_value": "FALSE"
+			"default_value": "FALSE",
+			"extra_data": [
+				"TRUE",
+				"FALSE"
+			]
 		},
 		{
 			"id": "use_default_x_axis_limit_id",
@@ -300,9 +316,13 @@
 			"name": "Use default X-axis limit",
 			"param_name": "use_default_x_axis_limit",
 			"description": "Use default X-axis limit",
-			"type": "text",
+			"type": "list",
 			"value_type": "string",
-			"default_value": "TRUE"
+			"default_value": "TRUE",
+			"extra_data": [
+				"TRUE",
+				"FALSE"
+			]
 		},
 		{
 			"id": "x_axis_limit_id",
@@ -320,9 +340,13 @@
 			"name": "Use default Y-axis limit",
 			"param_name": "use_default_y_axis_limit",
 			"description": "Use default Y-axis limit",
-			"type": "text",
+			"type": "list",
 			"value_type": "string",
-			"default_value": "TRUE"
+			"default_value": "TRUE",
+			"extra_data": [
+				"TRUE",
+				"FALSE"
+			]
 		},
 		{
 			"id": "y_axis_limit_id",
@@ -390,9 +414,13 @@
 			"name": "Use default grid layout",
 			"param_name": "use_default_grid_layout",
 			"description": "Use default grid layout for multiple plots",
-			"type": "text",
+			"type": "list",
 			"value_type": "string",
-			"default_value": "TRUE"
+			"default_value": "TRUE",
+			"extra_data": [
+				"TRUE",
+				"FALSE"
+			]
 		},
 		{
 			"id": "number_of_rows_in_grid_layout_id",

From b55420ac568d9bc707575af7197acd3d30c4acf8 Mon Sep 17 00:00:00 2001
From: phoman14 <Philip.homan@nih.gov>
Date: Tue, 30 Jun 2026 13:41:14 -0400
Subject: [PATCH 2/3] Update changelog for parameter UI changes

---
 CHANGELOG.md | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index e477074..cee27bd 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,5 +1,9 @@
 # Code Ocean capsule - MOSuite - Plot Volcano Summary
 
+## Development version
+
+- Improved the Code Ocean parameter UI for the plot volcano summary capsule (#2).
+
 ## v4.0
 
 - The MOSuite package is now available in `code/MOSuite`. (#1)
@@ -20,4 +24,4 @@ Save summarized dataframe to `results/moo/volcano_summary_data.csv`.
 
 Initial release
 
-<https://poc-nci.codeocean.io/capsule/6849617/tree/v1> `0a5bebc`
\ No newline at end of file
+<https://poc-nci.codeocean.io/capsule/6849617/tree/v1> `0a5bebc`

From da16526e03aa6f87eff437bc562eb76e7ef2c44d Mon Sep 17 00:00:00 2001
From: phoman14 <Philip.homan@nih.gov>
Date: Tue, 30 Jun 2026 14:11:06 -0400
Subject: [PATCH 3/3] Add author handle to changelog entry

---
 CHANGELOG.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index cee27bd..dfc6967 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -2,7 +2,7 @@
 
 ## Development version
 
-- Improved the Code Ocean parameter UI for the plot volcano summary capsule (#2).
+- Improved the Code Ocean parameter UI for the plot volcano summary capsule (#2, @phoman14).
 
 ## v4.0