Mercurial > repos > galaxytrakr > aws_sra
diff aws_sra.xml @ 36:4632b9e5e884 draft
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 |
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