Mercurial > repos > galaxytrakr > aws_sra

comparison aws_sra.xml @ 12:76192dc490d2 draft

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planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit 72fa1e46c3eaa5b7e8ed1461e3d5ecb4d65c0a1c
author galaxytrakr
date Mon, 23 Mar 2026 19:52:43 +0000
parents 696191ca014e
children 2897d365dd62
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11:696191ca014e 12:76192dc490d2
1 <tool id="aws_sra" name="NCBI SRA AWS Fetch" version="0.3.0+gt_0.11" profile="23.0"> 1 <tool id="aws_sra" name="NCBI SRA AWS Fetch" version="0.3.0+gt_0.12" profile="23.0">
2 <description>Fetch SRA data files from NCBI's public AWS S3 buckets</description> 2 <description>Fetch SRA data files from NCBI's public AWS S3 buckets</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>
125 125
126 <!-- ── FASTQ DUMP ── --> 126 <!-- ── FASTQ DUMP ── -->
127 <when value="fastq_dump"> 127 <when value="fastq_dump">
128 <param name="accession" type="text" label="SRA Accession" 128 <param name="accession" type="text" label="SRA Accession"
129 help="SRA run accession to fetch and convert, e.g. SRR000001. Must be present in sra-pub-run-odp."> 129 help="SRA run accession to fetch and convert, e.g. SRR000001. Must be present in sra-pub-run-odp.">
130 <validator type="empty_field" message="An SRA accession is required."/>
131 </param> 130 </param>
132 <param name="layout" type="select" label="Read layout" 131 <param name="layout" type="select" label="Read layout"
133 help="Paired-end produces two datasets labelled accession_1 and accession_2. Single-end produces one dataset. Check the SRA record to confirm layout before running."> 132 help="Paired-end produces two datasets labelled accession_1 and accession_2. Single-end produces one dataset. Check the SRA record to confirm layout before running.">
134 <option value="paired" selected="true">Paired-end (R1 + R2)</option> 133 <option value="paired" selected="true">Paired-end (R1 + R2)</option>
135 <option value="single">Single-end</option> 134 <option value="single">Single-end</option>