--- a/aws_sra.xml	Tue Mar 24 03:14:28 2026 +0000
+++ b/aws_sra.xml	Tue Mar 24 14:12:59 2026 +0000
@@ -1,4 +1,4 @@
-<tool id="aws_sra" name="NCBI SRA AWS Fetch" version="0.4.0+gt_1.0" profile="23.0">
+<tool id="aws_sra" name="NCBI SRA AWS Fetch" version="0.4.0+gt_1.1" profile="23.0">
     <description>Fetches one or more SRA runs from AWS S3 and converts them to FASTQ</description>
 
     <requirements>
@@ -17,6 +17,7 @@
     #end if
     mkdir -p output &&
     mkdir -p outputOther &&
+    mkdir -p outputSingle &&  
     for acc in \$(cat ./accessions);
     do (
         echo "Processing accession: \$acc" &&
@@ -28,7 +29,7 @@
         echo "Found \$count fastq file(s) for \$acc" &&
         data=(\$(ls \${acc}*.fastq 2>/dev/null)) &&
         if [ "\$count" -eq 1 ]; then
-            pigz -cqp \${GALAXY_SLOTS:-4} "\${data[0]}" > output/"\${acc}".fastqsanger.gz &&
+            pigz -cqp \${GALAXY_SLOTS:-4} "\${data[0]}" > outputSingle/"\${acc}".fastqsanger.gz &&
             rm "\${data[0]}";
         elif [ -e "\${acc}".fastq ]; then
             pigz -cqp \${GALAXY_SLOTS:-4} "\${acc}".fastq > outputOther/"\${acc}"__single.fastqsanger.gz &&
@@ -85,8 +86,8 @@
         </collection>
         <collection name="output_single" type="list" label="Single-end FASTQ (aws_sra)">
             <discover_datasets
-                pattern="(?P&lt;designation&gt;.+)\.fastqsanger\.gz"
-                directory="output"
+                pattern="(?P&lt;designation&gt;.+?)(?&lt;!_[12])\\.fastqsanger\\.gz"
+                directory="outputSingle"
                 ext="fastqsanger.gz"/>
         </collection>
         <collection name="output_other" type="list" label="Other FASTQ (aws_sra)">