diff --git a/lib/galaxy/tool_util/verify/__init__.py b/lib/galaxy/tool_util/verify/__init__.py
index b3b1abda323..5414d31ac75 100644
--- a/lib/galaxy/tool_util/verify/__init__.py
+++ b/lib/galaxy/tool_util/verify/__init__.py
@@ -184,12 +184,12 @@ def _bam_to_sam(local_name, temp_name):
     temp_local = tempfile.NamedTemporaryFile(suffix='.sam', prefix='local_bam_converted_to_sam_')
     with tempfile.NamedTemporaryFile(suffix='.sam', prefix='history_bam_converted_to_sam_', delete=False) as temp:
         try:
-            pysam.view('-h', '-o%s' % temp_local.name, local_name)
+            pysam.view('-h', '--no-PG', '-o', temp_local.name, local_name, catch_stdout=False)
         except Exception as e:
             msg = "Converting local (test-data) BAM to SAM failed: %s" % unicodify(e)
             raise Exception(msg)
         try:
-            pysam.view('-h', '-o%s' % temp.name, temp_name)
+            pysam.view('-h', '--no-PG', '-o', temp.name, temp_name, catch_stdout=False)
         except Exception as e:
             msg = "Converting history BAM to SAM failed: %s" % unicodify(e)
             raise Exception(msg)
diff --git a/test/functional/tools/sam_to_bam.xml b/test/functional/tools/sam_to_bam.xml
index b01152a7670..3420ed73ec9 100644
--- a/test/functional/tools/sam_to_bam.xml
+++ b/test/functional/tools/sam_to_bam.xml
@@ -11,7 +11,7 @@ cat '$input1' > '$out_file1'
     <tests>
         <test>
             <param name="input1" value="sam_with_header.sam" ftype="sam"/>
-            <output name="out_file1" file="bam_from_sam.bam"/>
+            <output name="out_file1" file="bam_from_sam.bam" ftype="bam"/>
         </test>
     </tests>
     <help>