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comparison aws_sra.xml @ 2:83c923bd9da6 draft

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planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit a95de952e58b29875b31e55f0ef06a83a18618fc
author galaxytrakr
date Mon, 23 Mar 2026 14:53:10 +0000
parents ddfdc4c465e7
children 6e7f066ba7fc
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1:ddfdc4c465e7 2:83c923bd9da6
1 <tool id="aws_sra" name="NCBI SRA AWS Fetch" version="0.3.0+gt_0.2" profile="23.0"> 1 <tool id="aws_sra" name="NCBI SRA AWS Fetch" version="0.3.0+gt_0.3" 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" channel="conda-forge">awscli</requirement> 5 <requirement type="package" version="2.34.8">awscli</requirement>
6 <requirement type="package" version="3.2.1" channel="bioconda">sra-tools</requirement> 6 <requirement type="package" version="3.2.1">sra-tools</requirement>
7 <requirement type="package" version="2.8" channel="conda-forge">pigz</requirement> 7 <requirement type="package" version="2.8">pigz</requirement>
8 </requirements> 8 </requirements>
9 9
10 <version_command>aws --version</version_command> 10 <version_command>aws --version</version_command>
11 11
12 <command detect_errors="exit_code"><![CDATA[ 12 <command detect_errors="exit_code"><![CDATA[
144 144
145 <!-- ── FASTQ DUMP ── --> 145 <!-- ── FASTQ DUMP ── -->
146 <when value="fastq_dump"> 146 <when value="fastq_dump">
147 <param name="accession" type="text" label="SRA Accession" 147 <param name="accession" type="text" label="SRA Accession"
148 help="SRA run accession to fetch and convert, e.g. SRR000001. Must be present in sra-pub-run-odp."> 148 help="SRA run accession to fetch and convert, e.g. SRR000001. Must be present in sra-pub-run-odp.">
149 <validator type="empty_field" message="An SRA accession is required."/> 149 <validator type="empty_field" message="An SRA accession is required."/>
150 <validator type="regex" 150 <validator type="regex" message="Must be a valid SRA run accession (SRR, ERR, or DRR followed by digits).">^\[SED\]RR\[0-9\]+$</validator>
151 message="Must be a valid SRA run accession (SRR, ERR, or DRR followed by digits)."
152 expression="^[SED]RR[0-9]+$"/>
153 </param> 151 </param>
154 <param name="layout" type="select" label="Read layout" 152 <param name="layout" type="select" label="Read layout"
155 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."> 153 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.">
156 <option value="paired" selected="true">Paired-end (R1 + R2)</option> 154 <option value="paired" selected="true">Paired-end (R1 + R2)</option>
157 <option value="single">Single-end</option> 155 <option value="single">Single-end</option>
260 | Bucket | Contents | 258 | Bucket | Contents |
261 +==============================+============================================================+ 259 +==============================+============================================================+
262 | sra-pub-run-odp | All open-access SRA runs in SRA Normalized format (.sra). | 260 | sra-pub-run-odp | All open-access SRA runs in SRA Normalized format (.sra). |
263 | | Supports FASTQ conversion via this tool. | 261 | | Supports FASTQ conversion via this tool. |
264 +------------------------------+------------------------------------------------------------+ 262 +------------------------------+------------------------------------------------------------+
265 | sra-pub-src-1 | Source BAM, CRAM, and FASTQ files from PacBio, ONT, 10X. | 263 | sra-pub-src-1 | Source BAM, CRAM, and FASTQ files from PacBio, ONT, 10X. |
266 +------------------------------+------------------------------------------------------------+ 264 +------------------------------+------------------------------------------------------------+
267 | sra-pub-src-2 | Same as above (second bucket for source submissions). | 265 | sra-pub-src-2 | Same as above (second bucket for source submissions). |
268 +------------------------------+------------------------------------------------------------+ 266 +------------------------------+------------------------------------------------------------+
269 | sra-pub-metadata-us-east-1 | SRA metadata in Parquet/CSV format (for Athena / Glue). | 267 | sra-pub-metadata-us-east-1 | SRA metadata in Parquet/CSV format (for Athena / Glue). |
270 +------------------------------+------------------------------------------------------------+ 268 +------------------------------+------------------------------------------------------------+
269
271 270
272 ----- 271 -----
273 272
274 **Listing objects** 273 **Listing objects**
275 274