diff --git a/test/functional/tools/sam_to_bam_native.xml b/test/functional/tools/sam_to_bam_native.xml
index b960bb4c87a..aed8f24892c 100644
--- a/test/functional/tools/sam_to_bam_native.xml
+++ b/test/functional/tools/sam_to_bam_native.xml
@@ -8,30 +8,39 @@
             -b
             -h
             -@ \${GALAXY_SLOTS:-2}
-            -o '${output}'
+            -o '$bam_native_output'
             '$input1'
-    #else
-        cp '$input2' '$output'
+    #elif $input2:
+        cp '$input2' '$bam_native_output'
+    #elif $input3:
+        cp '$input3' '$bam_output'
     #end if
     ]]>
     </command>
     <inputs>
         <param name="input1" type="data" format="sam" label="SAM file" optional="true"/>
         <param name="input2" type="data" format="bam_native" label="Unsorted BAM file" optional="true"/>
+        <param name="input3" type="data" format="bam" label="Sorted BAM file" optional="true"/>
     </inputs>
     <outputs>
-        <data name="output" format="bam_native"/>
+        <data name="bam_native_output" format="bam_native"/>
+        <data name="bam_output" format="bam"/>
     </outputs>
     <tests>
         <!-- Test that bam native output won't be sorted-->
         <test>
             <param name="input1" value="sam_with_header.sam" ftype="sam"/>
-            <output name="output" file="bam_native_from_sam.bam" ftype="bam_native"/>
+            <output name="bam_native_output" file="bam_native_from_sam.bam" ftype="bam_native"/>
         </test>
         <!-- Test that sam input is properly converted to bam native -->
         <test>
             <param name="input2" value="sam_with_header.sam" ftype="sam"/>
-            <output name="output" file="bam_native_from_sam.bam" ftype="bam_native"/>
+            <output name="bam_native_output" file="bam_native_from_sam.bam" ftype="bam_native"/>
+        </test>
+        <!-- Test that sam input is properly converted to bam -->
+        <test>
+            <param name="input3" value="sam_with_header.sam" ftype="sam"/>
+            <output name="bam_output" file="bam_from_sam.bam" ftype="bam"/>
         </test>
     </tests>
     <help>