From 7db3dcf713446f98bd68ce232540bb79f79c31d7 Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Mon, 24 Aug 2026 18:49:02 +0300
Subject: [PATCH 1/2] Treat multiple selects as optional by default in the tool
 parameter model

---
 lib/galaxy/tool_util/parameters/factory.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/galaxy/tool_util/parameters/factory.py b/lib/galaxy/tool_util/parameters/factory.py
index bdd7be88920..56f13b3517c 100644
--- a/lib/galaxy/tool_util/parameters/factory.py
+++ b/lib/galaxy/tool_util/parameters/factory.py
@@ -246,10 +246,10 @@ def _from_input_source_galaxy(input_source: InputSource, profile: float) -> Tool
             )
         elif param_type == "select":
             # Function... example in devteam cummeRbund.
-            optional = input_source.parse_optional()
             dynamic_options_config = input_source.parse_dynamic_options()
             is_static = dynamic_options_config is None
             multiple = input_source.get_bool("multiple", False)
+            optional = input_source.parse_optional(multiple)
             options: list[LabelValue] | None = None
             if is_static:
                 options = []

From 022812ed60923982ad5efaa48eae9015500fb475 Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Mon, 24 Aug 2026 19:26:35 +0300
Subject: [PATCH 2/2] Cover multiple selects with a no_options validator

---
 ..._select_multiple_no_options_validation.xml | 20 +++++++++++++++++++
 .../tool_util/parameter_specification.yml     | 15 ++++++++++++--
 2 files changed, 33 insertions(+), 2 deletions(-)
 create mode 100644 test/functional/tools/parameters/gx_select_multiple_no_options_validation.xml

diff --git a/test/functional/tools/parameters/gx_select_multiple_no_options_validation.xml b/test/functional/tools/parameters/gx_select_multiple_no_options_validation.xml
new file mode 100644
index 00000000000..67ac26a60f3
--- /dev/null
+++ b/test/functional/tools/parameters/gx_select_multiple_no_options_validation.xml
@@ -0,0 +1,20 @@
+<tool id="gx_select_multiple_no_options_validation" name="gx_select_multiple_no_options_validation" version="1.0.0">
+    <command><![CDATA[
+echo '$parameter' >> '$output'
+    ]]></command>
+    <inputs>
+        <param name="parameter" type="select" multiple="true">
+            <option value="--ex1">Ex1</option>
+            <option value="ex2">Ex2</option>
+            <option value="--ex3">Ex3</option>
+            <option value="--ex4">Ex4</option>
+            <option value="ex5">Ex5</option>
+            <validator type="no_options" />
+        </param>
+    </inputs>
+    <outputs>
+        <data name="output" format="txt" />
+    </outputs>
+    <tests>
+    </tests>
+</tool>
diff --git a/test/unit/tool_util/parameter_specification.yml b/test/unit/tool_util/parameter_specification.yml
index 7b1b125c0ae..59bea6b472c 100644
--- a/test/unit/tool_util/parameter_specification.yml
+++ b/test/unit/tool_util/parameter_specification.yml
@@ -729,7 +729,7 @@ gx_select_multiple:
   request_valid:
   - parameter: ["--ex1"]
   - parameter: ["ex2"]
-  # ugh... but these aren't optional...
+  # multiple selects are optional by default
   - parameter: null
   - {}
   request_invalid:
@@ -754,7 +754,6 @@ gx_select_multiple:
   - parameter: ["--ex1"]
   - parameter: ["ex2"]
   - {}  # could come in linked...
-  # ... hmmm? this should maybe be invalid right?
   - parameter: null
   job_internal_valid:
   - parameter: ["--ex1"]
@@ -822,6 +821,18 @@ gx_select_no_options_validation:
   job_runtime_invalid:
   - {}
 
+gx_select_multiple_no_options_validation:
+  job_internal_valid:
+  - parameter: ["--ex1"]
+  - parameter: null
+  job_internal_invalid:
+  - {}
+  job_runtime_valid:
+  - parameter: ["--ex1"]
+  - parameter: null
+  job_runtime_invalid:
+  - {}
+
 gx_genomebuild:
   request_valid:
   - parameter: hg19