Mercurial > repos > galaxytrakr > aws_sra

comparison aws_sra.xml @ 40:04632fbfb752 draft

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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
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39:bb993ca44098 40:04632fbfb752
1 <tool id="aws_sra" name="NCBI SRA AWS Fetch" version="0.4.0+gt_1.8" profile="23.0"> 1 <tool id="aws_sra" name="NCBI SRA AWS Fetch" version="0.4.0+gt_1.9" 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>
27 rm -rf sra_cache_\${acc} && 27 rm -rf sra_cache_\${acc} &&
28 count="\$(ls \${acc}*.fastq 2>/dev/null | wc -l)" && 28 count="\$(ls \${acc}*.fastq 2>/dev/null | wc -l)" &&
29 echo "Found \$count fastq file(s) for \$acc" && 29 echo "Found \$count fastq file(s) for \$acc" &&
30 data=(\$(ls \${acc}*.fastq 2>/dev/null)) && 30 data=(\$(ls \${acc}*.fastq 2>/dev/null)) &&
31 if [ "\$count" -eq 1 ]; then 31 if [ "\$count" -eq 1 ]; then
32 pigz -cqp \${GALAXY_SLOTS:-4} "\${data[0]}" > outputSingle/"\${acc}__single.fastqsanger.gz && 32 pigz -cqp \${GALAXY_SLOTS:-4} "\${data[0]}" > outputSingle/"\${acc}"__single.fastqsanger.gz &&
33 rm "\${data[0]}"; 33 rm "\${data[0]}";
34 elif [ "\$count" -eq 2 ]; then 34 elif [ "\$count" -eq 2 ]; then
35 pigz -cqp \${GALAXY_SLOTS:-4} "\${acc}"_1.fastq > output/"\${acc}"_forward.fastqsanger.gz && 35 pigz -cqp \${GALAXY_SLOTS:-4} "\${acc}"_1.fastq > output/"\${acc}"_forward.fastqsanger.gz &&
36 pigz -cqp \${GALAXY_SLOTS:-4} "\${acc}"_2.fastq > output/"\${acc}"_reverse.fastqsanger.gz && 36 pigz -cqp \${GALAXY_SLOTS:-4} "\${acc}"_2.fastq > output/"\${acc}"_reverse.fastqsanger.gz &&
37 rm "\${acc}"*.fastq; 37 rm "\${acc}"*.fastq;