# HG changeset patch
# User galaxytrakr
# Date 1774434936 0
# Node ID bb993ca440981fc3a14115c4a58f7031827f632d
# Parent  980bb8758ff477cc03e4db7e6857b1c484b568dc
planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit 5c4ba2cc27bc718393cb3b267e6fccb0ab48038a

diff -r 980bb8758ff4 -r bb993ca44098 aws_sra.xml
--- a/aws_sra.xml	Wed Mar 25 01:50:22 2026 +0000
+++ b/aws_sra.xml	Wed Mar 25 10:35:36 2026 +0000
@@ -1,4 +1,4 @@
-<tool id="aws_sra" name="NCBI SRA AWS Fetch" version="0.4.0+gt_1.7" profile="23.0">
+<tool id="aws_sra" name="NCBI SRA AWS Fetch" version="0.4.0+gt_1.8" profile="23.0">
     <description>Fetches one or more SRA runs from AWS S3 and converts them to FASTQ</description>
 
     <requirements>
@@ -29,16 +29,16 @@
         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]}" > outputSingle/"\${acc}".fastqsanger.gz &&
+            pigz -cqp \${GALAXY_SLOTS:-4} "\${data[0]}" > outputSingle/"\${acc}__single.fastqsanger.gz &&
             rm "\${data[0]}";
-        elif [ -e "\${acc}".fastq ]; then
-            pigz -cqp \${GALAXY_SLOTS:-4} "\${acc}".fastq > outputOther/"\${acc}"__single.fastqsanger.gz &&
+        elif [ "\$count" -eq 2 ]; then
             pigz -cqp \${GALAXY_SLOTS:-4} "\${acc}"_1.fastq > output/"\${acc}"_forward.fastqsanger.gz &&
             pigz -cqp \${GALAXY_SLOTS:-4} "\${acc}"_2.fastq > output/"\${acc}"_reverse.fastqsanger.gz &&
             rm "\${acc}"*.fastq;
-        elif [ "\$count" -eq 2 ]; then
-            pigz -cqp \${GALAXY_SLOTS:-4} "\${acc}"_1.fastq > output/"\${acc}"_forward.fastqsanger.gz &&
-            pigz -cqp \${GALAXY_SLOTS:-4} "\${acc}"_2.fastq > output/"\${acc}"_reverse.fastqsanger.gz &&
+        elif [ -e "\${acc}".fastq ]; then
+            pigz -cqp \${GALAXY_SLOTS:-4} "\${acc}".fastq > outputSingle/"\${acc}"__single.fastqsanger.gz &&
+            pigz -cqp \${GALAXY_SLOTS:-4} "\${acc}"_forward.fastq > output/"\${acc}"_forward.fastqsanger.gz &&
+            pigz -cqp \${GALAXY_SLOTS:-4} "\${acc}"_reverse.fastq > output/"\${acc}"_reverse.fastqsanger.gz &&
             rm "\${acc}"*.fastq;
         else
             for file in \${data[*]}; do
@@ -80,13 +80,13 @@
     <outputs>
         <collection name="list_paired" type="list:paired" label="Paired-end FASTQ (aws_sra)">
             <discover_datasets
-                pattern="(?P&lt;identifier_0&gt;[^_]+)_(?P&lt;identifier_1&gt;[^_]+)\.fastqsanger.gz" 
+                pattern="(?P&lt;identifier_0&gt;[^_]+)_(?P&lt;identifier_1&gt;[^_]+)\.fastqsanger.gz"
                 directory="output"
                 ext="fastqsanger.gz"/>
         </collection>
         <collection name="output_single" type="list" label="Single-end FASTQ (aws_sra)">
             <discover_datasets
-                pattern="(?P&lt;designation&gt;.+)\.fastqsanger\.gz"
+                pattern="(?P&lt;designation&gt;.+)__single\.fastqsanger.gz"
                 directory="outputSingle"
                 ext="fastqsanger.gz"/>
         </collection>
@@ -94,7 +94,7 @@
             <discover_datasets
                 pattern="(?P&lt;designation&gt;.+)\.fastqsanger\.gz"
                 directory="outputOther"
-                ext="fastqsanger.gz"/>
+                format="fastqsanger.gz"/>
         </collection>
     </outputs>