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comparison aws_sra.xml @ 41:d91855b2a813 draft default tip

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planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit 936065a7ceffa42a7c2f1b8b752a62b419575bd4
author galaxytrakr
date Wed, 25 Mar 2026 11:56:49 +0000
parents 04632fbfb752
children
comparison
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40:04632fbfb752 41:d91855b2a813
1 <tool id="aws_sra" name="NCBI SRA AWS Fetch" version="0.4.0+gt_1.9" profile="23.0"> 1 <tool id="aws_sra" name="NCBI SRA AWS Fetch" version="0.4.0+gt_2.00" 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>
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;
38 elif [ -e "\${acc}".fastq ]; then 38 elif [ "\$count" -eq 3 ]; then
39 pigz -cqp \${GALAXY_SLOTS:-4} "\${acc}".fastq > outputSingle/"\${acc}"__single.fastqsanger.gz && 39 pigz -cqp \${GALAXY_SLOTS:-4} "\${acc}".fastq > outputSingle/"\${acc}"__single.fastqsanger.gz &&
40 pigz -cqp \${GALAXY_SLOTS:-4} "\${acc}"_forward.fastq > output/"\${acc}"_forward.fastqsanger.gz && 40 pigz -cqp \${GALAXY_SLOTS:-4} "\${acc}"_1.fastq > output/"\${acc}"_forward.fastqsanger.gz &&
41 pigz -cqp \${GALAXY_SLOTS:-4} "\${acc}"_reverse.fastq > output/"\${acc}"_reverse.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";
78 </inputs> 78 </inputs>
79 79
80 <outputs> 80 <outputs>
81 <collection name="list_paired" type="list:paired" label="Paired-end FASTQ (aws_sra)"> 81 <collection name="list_paired" type="list:paired" label="Paired-end FASTQ (aws_sra)">
82 <discover_datasets 82 <discover_datasets
83 pattern="(?P&lt;identifier_0&gt;[^_]+)_(?P&lt;identifier_1&gt;[^_]+)\.fastqsanger.gz" 83 pattern="(?P&lt;identifier_0&gt;[^_]+)_(?P&lt;identifier_1&gt;[^_]+)\.fastqsanger\.gz"
84 directory="output" 84 directory="output"
85 ext="fastqsanger.gz"/> 85 ext="fastqsanger.gz"/>
86 </collection> 86 </collection>
87 <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)">
88 <discover_datasets 88 <discover_datasets
89 pattern="(?P&lt;designation&gt;.+)__single\.fastqsanger.gz" 89 pattern="(?P&lt;designation&gt;.+)__single\.fastqsanger\.gz"
90 directory="outputSingle" 90 directory="outputSingle"
91 ext="fastqsanger.gz"/> 91 ext="fastqsanger.gz"/>
92 </collection> 92 </collection>
93 <collection name="output_other" type="list" label="Other FASTQ (aws_sra)"> 93 <collection name="output_other" type="list" label="Other FASTQ (aws_sra)">
94 <discover_datasets 94 <discover_datasets