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comparison aws_sra.xml @ 27:4f6a7017cbbb draft

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planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit e6b9f977f309c34ba98baa46a25f3460418607f0
author galaxytrakr
date Tue, 24 Mar 2026 00:34:13 +0000
parents 0694c136356f
children 8e6c35583761
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26:0694c136356f 27:4f6a7017cbbb
1 <tool id="aws_sra" name="NCBI SRA AWS Fetch" version="0.4.0+gt_0.5" profile="23.0"> 1 <tool id="aws_sra" name="NCBI SRA AWS Fetch" version="0.4.0+gt_0.6" 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="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>
42 rm -rf sra_cache_${acc} fastq_out_${acc} 42 rm -rf sra_cache_${acc} fastq_out_${acc}
43 done 43 done
44 ]]></command> 44 ]]></command>
45 45
46 <inputs> 46 <inputs>
47 <param name="accession" type="data" format="text"multiple="true" label="SRA Accession(s)" help="Provide one or more accession numbers (separated by commas, spaces, or newlines). This field accepts a dataset list of accessions in a workflow."/> 47 <param name="accession" type="data" format="txt" multiple="true" label="SRA Accession(s)" help="Provide one or more accession numbers (separated by commas, spaces, or newlines). This field accepts a dataset list of accessions in a workflow."/>
48 <param name="layout" type="select" label="Read layout" help="This setting is applied to all accessions."> 48 <param name="layout" type="select" label="Read layout" help="This setting is applied to all accessions.">
49 <option value="paired" selected="true">Paired-end (R1 + R2)</option> 49 <option value="paired" selected="true">Paired-end (R1 + R2)</option>
50 <option value="single">Single-end</option> 50 <option value="single">Single-end</option>
51 </param> 51 </param>
52 </inputs> 52 </inputs>