diff --git a/lib/galaxy/tool_util/linters/output.py b/lib/galaxy/tool_util/linters/output.py
index e9ab7c4aaf4e..b1d48fd2a60d 100644
--- a/lib/galaxy/tool_util/linters/output.py
+++ b/lib/galaxy/tool_util/linters/output.py
@@ -83,9 +83,9 @@ def lint(cls, tool_source: "ToolSource", lint_ctx: "LintContext"):
         tool_xml = getattr(tool_source, "xml_tree", None)
         if not tool_xml:
             return
-        for filter in tool_xml.findall("./outputs//filter"):
+        for filter in tool_xml.findall("./outputs/*/filter"):
             try:
-                ast.parse(filter.text, mode="eval")
+                ast.parse(filter.text.strip(), mode="eval")
             except Exception as e:
                 lint_ctx.warn(
                     f"Filter '{filter.text}' is no valid expression: {str(e)}",
diff --git a/test/unit/tool_util/test_tool_linters.py b/test/unit/tool_util/test_tool_linters.py
index ea7f4cd8d5d5..867e85dc2ba3 100644
--- a/test/unit/tool_util/test_tool_linters.py
+++ b/test/unit/tool_util/test_tool_linters.py
@@ -656,7 +656,7 @@
     <outputs>
         <data name="another_valid_name" format="fasta" label="a label">
             <filter>an invalid condition</filter>
-            <filter>an and condition</filter>
+            <filter> an and condition </filter>
         </data>
         <collection name="yet_another_valid_name" type="list" format="fasta" label="another label">
             <filter>another invalid condition</filter>