--- a/fasterq_dump.xml	Fri Jun 23 21:31:47 2023 +0000
+++ b/fasterq_dump.xml	Mon Aug 26 14:59:07 2024 +0000
@@ -13,8 +13,10 @@
     @CONFIGURE_RETRY@
     @SET_ACCESSIONS@
     while [ \$SRA_PREFETCH_ATTEMPT -le \$SRA_PREFETCH_RETRIES ] ; do
-        fasterq-dump "\$acc" -e \${GALAXY_SLOTS:-1}
-        --seq-defline '@\$sn/\$ri'
+        fasterq-dump "\$acc"
+        -e \${GALAXY_SLOTS:-1}
+        -t \${TMPDIR}
+        --seq-defline '$adv.seq_defline'
         --qual-defline '+'
         $adv.split
         #if str( $adv.minlen ) != "":
@@ -71,6 +73,7 @@
     <inputs>
         <expand macro="input_conditional"/>
         <section name="adv" title="Advanced Options" expanded="False">
+            <expand macro="defline" defline_param="--seq-defline" defline_default="@$ac.$sn/$ri"/>
             <param name="minlen" type="integer" label="Minimum read length" optional="true" help="Filter by sequence length. Will dump only reads longer or equal to this value." argument="--min-read-len"/>
             <param name="split" type="select" display="radio" label="Select how to split the spots" help="This option will only be used when there are multiple reads per spot (for example paired-end).">
                 <option value="--split-3">--split-3: write properly paired biological reads into different files and single reads in another file</option>
@@ -186,6 +189,30 @@
                 </element>
             </output_collection>
         </test>
+        <test expect_num_outputs="4">
+            <param name="input_select" value="file_list"/>
+            <param name="file_list" value="sra_manifest.tabular" ftype="sra_manifest.tabular"/>
+            <section name="adv">
+                <param name="seq_defline" value="@$ac.$si/$ri $sn length=$rl"/>
+            </section>
+            <output_collection name="list_paired" type="list:paired" count="1">
+                <element name="SRR11953971">
+                    <element name="forward" ftype="fastqsanger.gz" decompress="True">
+                        <assert_contents>
+                            <!-- TODO replace has_size by has_line -->
+                            <has_size min="56206"/>
+                            <!-- <has_line line="@SRR11953971.2053/1 2053 length=101"/> -->
+                        </assert_contents>
+                    </element>
+                    <element name="reverse" ftype="fastqsanger.gz" decompress="True">
+                        <assert_contents>
+                            <has_size min="59843"/>
+                            <!-- <has_line line="@SRR11953971.2053/2 2053 length=101"/> -->
+                        </assert_contents>
+                    </element>
+                </element>
+            </output_collection>
+        </test>
     </tests>
     <help><![CDATA[
 **What it does?**