--- a/arriba.xml	Mon Sep 26 09:30:22 2022 +0000
+++ b/arriba.xml	Fri Mar 24 08:12:15 2023 +0000
@@ -154,7 +154,7 @@
     $options.duplicate_marking
     $options.fill_discarded_columns
     $options.fill_the_gaps
-#if str($visualization.do_viz) == "yes"
+#if $output_fusion_bams or str($visualization.do_viz) == "yes"
     && samtools sort -@ \${GALAXY_SLOTS:-1} -m 4G -T tmp -O bam '$input' > Aligned.sortedByCoord.out.bam
     && samtools index Aligned.sortedByCoord.out.bam
 #end if
@@ -441,16 +441,13 @@
             <discover_datasets pattern="(?P&lt;name&gt;fusion_\d+\.bam)$" format="bam" directory="fusion_bams" visible="false"/>
             <filter>output_fusion_bams == True</filter>
         </collection>
-        <data name="aligned_bam" format="bam" label="${tool.name} on ${on_string}: Aligned.bam" from_work_dir="Aligned.sortedByCoord.out.bam">
-            <filter>input_params['input_source'] == "use_fastq"</filter>
-        </data> 
         <data name="fusions_pdf" format="pdf" label="${tool.name} on ${on_string}: fusions.pdf" from_work_dir="fusions.pdf">
             <filter>visualization['do_viz'] == "yes"</filter>
         </data> 
     </outputs>
     <tests>
         <!-- Test 1 - From exisitng BAM -->
-        <test> 
+        <test expect_num_outputs="3"> 
             <param name="input" ftype="sam" value="Aligned.out.sam"/>
             <conditional name="genome">
                 <param name="genome_source" value="history"/>
@@ -472,7 +469,7 @@
             </output>
         </test>
         <!-- Test 2 - From exisitng BAM with protein_domains and visualization -->
-        <test> 
+        <test expect_num_outputs="4"> 
             <param name="input" ftype="sam" value="Aligned.out.sam"/>
             <conditional name="genome">
                 <param name="genome_source" value="history"/>