Mercurial > repos > galaxytrakr > aws_sra

changeset 36:4632b9e5e884 draft

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planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit 2233d6d0b755c3cec6bfc718372d7ea8fc9192bc
author galaxytrakr
date Tue, 24 Mar 2026 15:18:10 +0000
parents b67fb757d585
children cf03db9460f8
files aws_sra.xml
diffstat 1 files changed, 5 insertions(+), 5 deletions(-) [+]
line wrap: on
line diff
--- a/aws_sra.xml	Tue Mar 24 14:56:17 2026 +0000
+++ b/aws_sra.xml	Tue Mar 24 15:18:10 2026 +0000
@@ -1,4 +1,4 @@
-<tool id="aws_sra" name="NCBI SRA AWS Fetch" version="0.4.0+gt_1.4" profile="23.0">
+<tool id="aws_sra" name="NCBI SRA AWS Fetch" version="0.4.0+gt_1.5" profile="23.0">
     <description>Fetches one or more SRA runs from AWS S3 and converts them to FASTQ</description>
 
     <requirements>
@@ -33,12 +33,12 @@
             rm "\${data[0]}";
         elif [ -e "\${acc}".fastq ]; then
             pigz -cqp \${GALAXY_SLOTS:-4} "\${acc}".fastq > outputOther/"\${acc}"__single.fastqsanger.gz &&
-            pigz -cqp \${GALAXY_SLOTS:-4} "\${acc}"_1.fastq > output/"\${acc}"_1.fastqsanger.gz &&
-            pigz -cqp \${GALAXY_SLOTS:-4} "\${acc}"_2.fastq > output/"\${acc}"_2.fastqsanger.gz &&
+            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}"_1.fastqsanger.gz &&
-            pigz -cqp \${GALAXY_SLOTS:-4} "\${acc}"_2.fastq > output/"\${acc}"_2.fastqsanger.gz &&
+            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;
         else
             for file in \${data[*]}; do