Mercurial > repos > galaxytrakr > aws_sra

comparison aws_sra.xml @ 39:bb993ca44098 draft

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planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit 5c4ba2cc27bc718393cb3b267e6fccb0ab48038a
author galaxytrakr
date Wed, 25 Mar 2026 10:35:36 +0000
parents 980bb8758ff4
children 04632fbfb752
comparison
equal deleted inserted replaced
38:980bb8758ff4 39:bb993ca44098
1 <tool id="aws_sra" name="NCBI SRA AWS Fetch" version="0.4.0+gt_1.7" profile="23.0"> 1 <tool id="aws_sra" name="NCBI SRA AWS Fetch" version="0.4.0+gt_1.8" 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}".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 [ -e "\${acc}".fastq ]; then 34 elif [ "\$count" -eq 2 ]; then
35 pigz -cqp \${GALAXY_SLOTS:-4} "\${acc}".fastq > outputOther/"\${acc}"__single.fastqsanger.gz &&
36 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 &&
37 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 &&
38 rm "\${acc}"*.fastq; 37 rm "\${acc}"*.fastq;
39 elif [ "\$count" -eq 2 ]; then 38 elif [ -e "\${acc}".fastq ]; then
40 pigz -cqp \${GALAXY_SLOTS:-4} "\${acc}"_1.fastq > output/"\${acc}"_forward.fastqsanger.gz && 39 pigz -cqp \${GALAXY_SLOTS:-4} "\${acc}".fastq > outputSingle/"\${acc}"__single.fastqsanger.gz &&
41 pigz -cqp \${GALAXY_SLOTS:-4} "\${acc}"_2.fastq > output/"\${acc}"_reverse.fastqsanger.gz && 40 pigz -cqp \${GALAXY_SLOTS:-4} "\${acc}"_forward.fastq > output/"\${acc}"_forward.fastqsanger.gz &&
41 pigz -cqp \${GALAXY_SLOTS:-4} "\${acc}"_reverse.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;.+)\.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
95 pattern="(?P&lt;designation&gt;.+)\.fastqsanger\.gz" 95 pattern="(?P&lt;designation&gt;.+)\.fastqsanger\.gz"
96 directory="outputOther" 96 directory="outputOther"
97 ext="fastqsanger.gz"/> 97 format="fastqsanger.gz"/>
98 </collection> 98 </collection>
99 </outputs> 99 </outputs>
100 100
101 <tests> 101 <tests>
102 <test expect_num_outputs="3"> 102 <test expect_num_outputs="3">