# HG changeset patch
# User galaxytrakr
# Date 1774303284 0
# Node ID a4186132e1c46d323fb8e8e1afa1aa5141139e34
# Parent  5680c31cd031aba504fc50217022710ab5770e08
planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit ba119cea4881b4ff3a27470d8b426902977290b3

diff -r 5680c31cd031 -r a4186132e1c4 aws_sra.xml
--- a/aws_sra.xml	Mon Mar 23 20:51:03 2026 +0000
+++ b/aws_sra.xml	Mon Mar 23 22:01:24 2026 +0000
@@ -1,4 +1,4 @@
-<tool id="aws_sra" name="NCBI SRA AWS Fetch" version="0.3.0+gt_0.18" profile="23.0">
+<tool id="aws_sra" name="NCBI SRA AWS Fetch" version="0.3.0+gt_0.19" profile="23.0">
     <description>Fetches SRA runs from AWS and converts them to FASTQ</description>
     <requirements>
         <requirement type="package" version="2.34.8">awscli</requirement>
@@ -33,13 +33,14 @@
                     aws s3 cp --no-sign-request 's3://sra-pub-run-odp/sra/${acc}/${acc}' ./sra_cache_${acc}/ &&
                     fasterq-dump --outdir ./fastq_out_${acc} --temp . --threads \${GALAXY_SLOTS:-4} --split-files ./sra_cache_${acc}/${acc} &&
                     pigz -p \${GALAXY_SLOTS:-4} ./fastq_out_${acc}/*.fastq &&
-                    #if str($layout) == 'paired'
-                        # Move files to the special path for collection discovery
-                        mv ./fastq_out_${acc}/${acc}_1.fastq.gz '$output_r1_batch.files_path/${acc}_1.fastq.gz' &&
-                        mv ./fastq_out_${acc}/${acc}_2.fastq.gz '$output_r2_batch.files_path/${acc}_2.fastq.gz'
-                    #else
-                        mv ./fastq_out_${acc}/*.fastq.gz '$output_r1_batch.files_path/${acc}.fastq.gz'
-                    #end if &&
+                    (
+                        #if str($layout) == 'paired'
+                            mv ./fastq_out_${acc}/${acc}_1.fastq.gz '$output_r1_batch.files_path/${acc}_1.fastq.gz' &&
+                            mv ./fastq_out_${acc}/${acc}_2.fastq.gz '$output_r2_batch.files_path/${acc}_2.fastq.gz'
+                        #else
+                            mv ./fastq_out_${acc}/*.fastq.gz '$output_r1_batch.files_path/${acc}.fastq.gz'
+                        #end if
+                    ) &&
                     rm -rf sra_cache_${acc} fastq_out_${acc}
                 #end if
             #end for