Mercurial > repos > galaxytrakr > aws_sra

comparison aws_sra.xml @ 8:ef51d44623c2 draft

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planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit 37694a2c524c1c5124f0da25ee49077717438a59
author galaxytrakr
date Mon, 23 Mar 2026 18:42:57 +0000
parents 3529ce6bcde7
children 40b61da6c6c5
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7:3529ce6bcde7 8:ef51d44623c2
1 <tool id="aws_sra" name="NCBI SRA AWS Fetch" version="0.3.0+gt_0.7" profile="23.0"> 1 <tool id="aws_sra" name="NCBI SRA AWS Fetch" version="0.3.0+gt_0.8" 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>
142 <!-- ── FASTQ DUMP ── --> 142 <!-- ── FASTQ DUMP ── -->
143 <when value="fastq_dump"> 143 <when value="fastq_dump">
144 <param name="accession" type="text" label="SRA Accession" 144 <param name="accession" type="text" label="SRA Accession"
145 help="SRA run accession to fetch and convert, e.g. SRR000001. Must be present in sra-pub-run-odp."> 145 help="SRA run accession to fetch and convert, e.g. SRR000001. Must be present in sra-pub-run-odp.">
146 <validator type="empty_field" message="An SRA accession is required."/> 146 <validator type="empty_field" message="An SRA accession is required."/>
147 <validator type="regex" message="Must be a valid SRA run accession (SRR, ERR, or DRR followed by digits).">^[SED]RR[0-9]+$</validator>
148 </param> 147 </param>
149 <param name="layout" type="select" label="Read layout" 148 <param name="layout" type="select" label="Read layout"
150 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."> 149 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.">
151 <option value="paired" selected="true">Paired-end (R1 + R2)</option> 150 <option value="paired" selected="true">Paired-end (R1 + R2)</option>
152 <option value="single">Single-end</option> 151 <option value="single">Single-end</option>