--- a/fastq_dump.xml	Thu Sep 14 07:38:02 2023 +0000
+++ b/fastq_dump.xml	Wed Oct 25 07:10:06 2023 +0000
@@ -12,7 +12,7 @@
     @SET_ACCESSIONS@
 
     #if $input.input_select == "sra_file":
-        fastq-dump --log-level fatal --accession '${input.file.name}'
+        fastq-dump --log-level fatal --accession "\$acc"
     #else:
         ## Do not use prefetch if region is specified, to avoid downloading
         ## the complete sra file.
@@ -20,8 +20,8 @@
             prefetch -X 200000000 "\$acc" &&
         #end if
         fastq-dump --accession "\$acc"
-        --split-files
     #end if
+    --split-files
     --defline-seq '$adv.defline_seq'
     --defline-qual '+'
 
@@ -269,6 +269,21 @@
                 </element>
             </output_collection>
         </test>
+        <test expect_num_outputs="2">
+            <param name="input_select" value="sra_file"/>
+            <param name="sra_file" value="SRR522874.sra"/>
+            <param name="split" value="True"/>
+            <param name="skip_technical" value="True"/>
+            <section name="adv">
+                <param name="defline_seq" value="@$sn/$ri"/>
+            </section>
+            <output_collection name="list_paired" type="list:paired" count="1">
+                <element name="SRR522874.sra">
+                    <element name="forward" file="SRR522874.sra_2.fastq.gz" ftype="fastqsanger.gz" decompress="True"/>
+                    <element name="reverse" file="SRR522874.sra_4.fastq.gz" ftype="fastqsanger.gz" decompress="True"/>
+                </element>
+            </output_collection>
+        </test>
     </tests>
     <help><![CDATA[
 **What it does?**