Mercurial > repos > galaxytrakr > aws_sra
changeset 40:04632fbfb752 draft
planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit ae8bd99f91b8f4bbf9a020c7a641425a2931106a
| author | galaxytrakr |
|---|---|
| date | Wed, 25 Mar 2026 11:02:25 +0000 |
| parents | bb993ca44098 |
| children | d91855b2a813 |
| files | aws_sra.xml |
| diffstat | 1 files changed, 2 insertions(+), 2 deletions(-) [+] |
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--- a/aws_sra.xml Wed Mar 25 10:35:36 2026 +0000 +++ b/aws_sra.xml Wed Mar 25 11:02:25 2026 +0000 @@ -1,4 +1,4 @@ -<tool id="aws_sra" name="NCBI SRA AWS Fetch" version="0.4.0+gt_1.8" profile="23.0"> +<tool id="aws_sra" name="NCBI SRA AWS Fetch" version="0.4.0+gt_1.9" profile="23.0"> <description>Fetches one or more SRA runs from AWS S3 and converts them to FASTQ</description> <requirements> @@ -29,7 +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]}" > outputSingle/"\${acc}__single.fastqsanger.gz && + pigz -cqp \${GALAXY_SLOTS:-4} "\${data[0]}" > outputSingle/"\${acc}"__single.fastqsanger.gz && rm "\${data[0]}"; elif [ "\$count" -eq 2 ]; then pigz -cqp \${GALAXY_SLOTS:-4} "\${acc}"_1.fastq > output/"\${acc}"_forward.fastqsanger.gz &&