Mercurial > repos > galaxytrakr > aws_sra

comparison aws_sra.xml @ 15:25cf81d65cb8 draft

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planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit fd740a9434d21f68658fe261b1b043033e491b05
author galaxytrakr
date Mon, 23 Mar 2026 20:18:33 +0000
parents 27569ff426e0
children 58cc45662c63
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14:27569ff426e0 15:25cf81d65cb8
1 <tool id="aws_sra" name="NCBI SRA AWS Fetch" version="0.3.0+gt_0.14" profile="23.0"> 1 <tool id="aws_sra" name="NCBI SRA AWS Fetch" version="0.3.0+gt_0.15" profile="23.0">
2 <description>Fetches SRA runs from AWS and converts them to FASTQ</description> 2 <description>Fetches SRA runs from AWS and converts them to FASTQ</description>
3 3
4 <requirements> 4 <requirements>
5 <requirement type="package" version="2.34.8">awscli</requirement> 5 <requirement type="package" version="2.34.8">awscli</requirement>
6 <requirement type="package" version="3.2.1">sra-tools</requirement> 6 <requirement type="package" version="3.2.1">sra-tools</requirement>
67 </inputs> 67 </inputs>
68 68
69 <outputs> 69 <outputs>
70 <!-- These collections will gather all the files produced by the loop --> 70 <!-- These collections will gather all the files produced by the loop -->
71 <collection name="output_r1" type="list" label="${run_type.accession or 'FASTQ Reads (R1)'}"> 71 <collection name="output_r1" type="list" label="${run_type.accession or 'FASTQ Reads (R1)'}">
72 <discover_datasets pattern="(?P<designation>.+)_1\.fastq\.gz" format="fastqsanger.gz" /> 72 <discover_datasets pattern="(?P&lt;designation&gt;.+)_1\.fastq\.gz" format="fastqsanger.gz" />
73 </collection> 73 </collection>
74 <collection name="output_r2" type="list" label="${run_type.accession or 'FASTQ Reads (R2)'}"> 74 <collection name="output_r2" type="list" label="${run_type.accession or 'FASTQ Reads (R2)'}">
75 <discover_datasets pattern="(?P<designation>.+)_2\.fastq\.gz" format="fastqsanger.gz" /> 75 <discover_datasets pattern="(?P&lt;designation&gt;.+)_2\.fastq\.gz" format="fastqsanger.gz" />
76 <filter>layout == 'paired'</filter> 76 <filter>layout == 'paired'</filter>
77 </collection> 77 </collection>
78 </outputs> 78 </outputs>
79 79
80 <tests> 80 <tests>