Mercurial > repos > galaxytrakr > aws_sra

comparison aws_sra.xml @ 32:8b8a63786853 draft

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planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit 5be25e80679a5df7d0ee7526e85d727024e78920
author galaxytrakr
date Tue, 24 Mar 2026 14:12:59 +0000
parents 90ae4d437133
children 4dbb8753a569
comparison
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31:90ae4d437133 32:8b8a63786853
1 <tool id="aws_sra" name="NCBI SRA AWS Fetch" version="0.4.0+gt_1.0" profile="23.0"> 1 <tool id="aws_sra" name="NCBI SRA AWS Fetch" version="0.4.0+gt_1.1" 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>
15 #else: 15 #else:
16 grep '^[[:space:]]*[ESD]RR[0-9]\{1,\}[[:space:]]*$' '${input.file_list}' > accessions && 16 grep '^[[:space:]]*[ESD]RR[0-9]\{1,\}[[:space:]]*$' '${input.file_list}' > accessions &&
17 #end if 17 #end if
18 mkdir -p output && 18 mkdir -p output &&
19 mkdir -p outputOther && 19 mkdir -p outputOther &&
20 mkdir -p outputSingle &&
20 for acc in \$(cat ./accessions); 21 for acc in \$(cat ./accessions);
21 do ( 22 do (
22 echo "Processing accession: \$acc" && 23 echo "Processing accession: \$acc" &&
23 mkdir -p sra_cache_\${acc} && 24 mkdir -p sra_cache_\${acc} &&
24 aws s3 cp --no-sign-request "s3://sra-pub-run-odp/sra/\${acc}/\${acc}" ./sra_cache_\${acc}/\${acc} && 25 aws s3 cp --no-sign-request "s3://sra-pub-run-odp/sra/\${acc}/\${acc}" ./sra_cache_\${acc}/\${acc} &&
26 rm -rf sra_cache_\${acc} && 27 rm -rf sra_cache_\${acc} &&
27 count="\$(ls \${acc}*.fastq 2>/dev/null | wc -l)" && 28 count="\$(ls \${acc}*.fastq 2>/dev/null | wc -l)" &&
28 echo "Found \$count fastq file(s) for \$acc" && 29 echo "Found \$count fastq file(s) for \$acc" &&
29 data=(\$(ls \${acc}*.fastq 2>/dev/null)) && 30 data=(\$(ls \${acc}*.fastq 2>/dev/null)) &&
30 if [ "\$count" -eq 1 ]; then 31 if [ "\$count" -eq 1 ]; then
31 pigz -cqp \${GALAXY_SLOTS:-4} "\${data[0]}" > output/"\${acc}".fastqsanger.gz && 32 pigz -cqp \${GALAXY_SLOTS:-4} "\${data[0]}" > outputSingle/"\${acc}".fastqsanger.gz &&
32 rm "\${data[0]}"; 33 rm "\${data[0]}";
33 elif [ -e "\${acc}".fastq ]; then 34 elif [ -e "\${acc}".fastq ]; then
34 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 &&
35 pigz -cqp \${GALAXY_SLOTS:-4} "\${acc}"_1.fastq > output/"\${acc}"_1.fastqsanger.gz && 36 pigz -cqp \${GALAXY_SLOTS:-4} "\${acc}"_1.fastq > output/"\${acc}"_1.fastqsanger.gz &&
36 pigz -cqp \${GALAXY_SLOTS:-4} "\${acc}"_2.fastq > output/"\${acc}"_2.fastqsanger.gz && 37 pigz -cqp \${GALAXY_SLOTS:-4} "\${acc}"_2.fastq > output/"\${acc}"_2.fastqsanger.gz &&
83 directory="output" 84 directory="output"
84 ext="fastqsanger.gz"/> 85 ext="fastqsanger.gz"/>
85 </collection> 86 </collection>
86 <collection name="output_single" type="list" label="Single-end FASTQ (aws_sra)"> 87 <collection name="output_single" type="list" label="Single-end FASTQ (aws_sra)">
87 <discover_datasets 88 <discover_datasets
88 pattern="(?P&lt;designation&gt;.+)\.fastqsanger\.gz" 89 pattern="(?P&lt;designation&gt;.+?)(?&lt;!_[12])\\.fastqsanger\\.gz"
89 directory="output" 90 directory="outputSingle"
90 ext="fastqsanger.gz"/> 91 ext="fastqsanger.gz"/>
91 </collection> 92 </collection>
92 <collection name="output_other" type="list" label="Other FASTQ (aws_sra)"> 93 <collection name="output_other" type="list" label="Other FASTQ (aws_sra)">
93 <discover_datasets 94 <discover_datasets
94 pattern="(?P&lt;designation&gt;.+)\.fastqsanger\.gz" 95 pattern="(?P&lt;designation&gt;.+)\.fastqsanger\.gz"