diff --git a/tools/htseq_count/htseq-count.xml b/tools/htseq_count/htseq-count.xml
index 77c26204db7..446cc25004e 100644
--- a/tools/htseq_count/htseq-count.xml
+++ b/tools/htseq_count/htseq-count.xml
@@ -31,10 +31,12 @@
     ##set up input files
     #set $name_sorted_alignment_filename = "name_sorted.bam"
     #set $ref_index = "ref.fai"
-    #if str($reference_source.reference_source_selector) == "history":
-        samtools faidx --fai-idx $ref_index '${reference_source.ref_file}' 2>&1 || echo "Error running samtools faidx for htseq-count" >&2 &&
-    #elif str($reference_source.reference_source_selector) == "cached":
-        ln -s '${reference_source.ref_file.fields.path}.fai' $ref_index
+    #if $samfile.extension == 'sam':
+        #if str($reference_source.reference_source_selector) == "history":
+            samtools faidx --fai-idx $ref_index '${reference_source.ref_file}' 2>&1 || echo "Error running samtools faidx for htseq-count" >&2 &&
+        #elif str($reference_source.reference_source_selector) == "cached":
+            ln -s '${reference_source.ref_file.fields.path}.fai' $ref_index
+        #end if
     #end if
 
     #if $samfile.extension == 'sam' and str($reference_source.reference_source_selector):
@@ -130,7 +132,7 @@
             </when>
         </conditional>
         <conditional name="reference_source">
-            <param name="reference_source_selector" type="select" label="Provide a reference sequence?" help="Required for SAM input without @SQ headers, not necessary otherwise.">
+            <param name="reference_source_selector" type="select" label="Provide a reference sequence?" help="Required for SAM input without @SQ headers, not necessary otherwise and ignored for BAM input.">
                 <option value="">No</option>
                 <option value="cached">Locally cached</option>
                 <option value="history">History</option>