Mercurial > repos > galaxytrakr > aws_sra

comparison aws_sra.xml @ 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
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35:b67fb757d585 36:4632b9e5e884
1 <tool id="aws_sra" name="NCBI SRA AWS Fetch" version="0.4.0+gt_1.4" profile="23.0"> 1 <tool id="aws_sra" name="NCBI SRA AWS Fetch" version="0.4.0+gt_1.5" profile="23.0">
2 <description>Fetches one or more SRA runs from AWS S3 and converts them to FASTQ</description> 2 <description>Fetches one or more SRA runs from AWS S3 and converts them to FASTQ</description>
3 3
4 <requirements> 4 <requirements>
5 <requirement type="package" version="3.1.1">sra-tools</requirement> 5 <requirement type="package" version="3.1.1">sra-tools</requirement>
6 <requirement type="package" version="2.8">pigz</requirement> 6 <requirement type="package" version="2.8">pigz</requirement>
31 if [ "\$count" -eq 1 ]; then 31 if [ "\$count" -eq 1 ]; then
32 pigz -cqp \${GALAXY_SLOTS:-4} "\${data[0]}" > outputSingle/"\${acc}".fastqsanger.gz && 32 pigz -cqp \${GALAXY_SLOTS:-4} "\${data[0]}" > outputSingle/"\${acc}".fastqsanger.gz &&
33 rm "\${data[0]}"; 33 rm "\${data[0]}";
34 elif [ -e "\${acc}".fastq ]; then 34 elif [ -e "\${acc}".fastq ]; then
35 pigz -cqp \${GALAXY_SLOTS:-4} "\${acc}".fastq > outputOther/"\${acc}"__single.fastqsanger.gz && 35 pigz -cqp \${GALAXY_SLOTS:-4} "\${acc}".fastq > outputOther/"\${acc}"__single.fastqsanger.gz &&
36 pigz -cqp \${GALAXY_SLOTS:-4} "\${acc}"_1.fastq > output/"\${acc}"_1.fastqsanger.gz && 36 pigz -cqp \${GALAXY_SLOTS:-4} "\${acc}"_1.fastq > output/"\${acc}"_forward.fastqsanger.gz &&
37 pigz -cqp \${GALAXY_SLOTS:-4} "\${acc}"_2.fastq > output/"\${acc}"_2.fastqsanger.gz && 37 pigz -cqp \${GALAXY_SLOTS:-4} "\${acc}"_2.fastq > output/"\${acc}"_reverse.fastqsanger.gz &&
38 rm "\${acc}"*.fastq; 38 rm "\${acc}"*.fastq;
39 elif [ "\$count" -eq 2 ]; then 39 elif [ "\$count" -eq 2 ]; then
40 pigz -cqp \${GALAXY_SLOTS:-4} "\${acc}"_1.fastq > output/"\${acc}"_1.fastqsanger.gz && 40 pigz -cqp \${GALAXY_SLOTS:-4} "\${acc}"_1.fastq > output/"\${acc}"_forward.fastqsanger.gz &&
41 pigz -cqp \${GALAXY_SLOTS:-4} "\${acc}"_2.fastq > output/"\${acc}"_2.fastqsanger.gz && 41 pigz -cqp \${GALAXY_SLOTS:-4} "\${acc}"_2.fastq > output/"\${acc}"_reverse.fastqsanger.gz &&
42 rm "\${acc}"*.fastq; 42 rm "\${acc}"*.fastq;
43 else 43 else
44 for file in \${data[*]}; do 44 for file in \${data[*]}; do
45 pigz -cqp \${GALAXY_SLOTS:-4} "\$file" > outputOther/"\$file"sanger.gz && 45 pigz -cqp \${GALAXY_SLOTS:-4} "\$file" > outputOther/"\$file"sanger.gz &&
46 rm "\$file"; 46 rm "\$file";