Mercurial > repos > galaxytrakr > aws_sra

comparison aws_sra.xml @ 33:4dbb8753a569 draft

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planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit 569b20847bf87de3c298edf3d2435d198b8805ba
author galaxytrakr
date Tue, 24 Mar 2026 14:28:21 +0000
parents 8b8a63786853
children 4c1ff0d60937
comparison
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32:8b8a63786853 33:4dbb8753a569
1 <tool id="aws_sra" name="NCBI SRA AWS Fetch" version="0.4.0+gt_1.1" profile="23.0"> 1 <tool id="aws_sra" name="NCBI SRA AWS Fetch" version="0.4.0+gt_1.2" 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>
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;[12])\.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;.+?)(?&lt;!_[12])\\.fastqsanger\\.gz" 89 pattern="(?P&lt;designation&gt;.+)\\.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