Mercurial > repos > galaxytrakr > aws_sra

comparison aws_sra.xml @ 35:b67fb757d585 draft

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planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c3ad6628d856e66db87f4ad2f21484f4b759544a
author galaxytrakr
date Tue, 24 Mar 2026 14:56:17 +0000
parents 4c1ff0d60937
children 4632b9e5e884
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34:4c1ff0d60937 35:b67fb757d585
1 <tool id="aws_sra" name="NCBI SRA AWS Fetch" version="0.4.0+gt_1.3" profile="23.0"> 1 <tool id="aws_sra" name="NCBI SRA AWS Fetch" version="0.4.0+gt_1.4" 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;designation&gt;.+)_(?P&lt;pair_identifier&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