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comparison aws_sra.xml @ 9:40b61da6c6c5 draft

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planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit 270f1465bed97ea0f5ee3e7bce08f2793011dbce
author galaxytrakr
date Mon, 23 Mar 2026 18:55:11 +0000
parents ef51d44623c2
children 4bd2a27d3755
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8:ef51d44623c2 9:40b61da6c6c5
1 <tool id="aws_sra" name="NCBI SRA AWS Fetch" version="0.3.0+gt_0.8" profile="23.0"> 1 <tool id="aws_sra" name="NCBI SRA AWS Fetch" version="0.3.0+gt_0.9" 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>
47 47
48 ## ── FASTQ DUMP mode (sra-pub-run-odp only) ─────────────────────────────── 48 ## ── FASTQ DUMP mode (sra-pub-run-odp only) ───────────────────────────────
49 #elif $action.mode == 'fastq_dump' 49 #elif $action.mode == 'fastq_dump'
50 #set $acc = $action.accession.strip() 50 #set $acc = $action.accession.strip()
51 51
52 ## 1. Download the file from S3 52 ## 1. Download the file from S3 (CORRECTED: single line command)
53 mkdir -p sra_cache && 53 mkdir -p sra_cache &&
54 aws s3 cp \ 54 aws s3 cp --no-sign-request '${s3_base}/sra/${acc}/${acc}' ./sra_cache/${acc} &&
55 --no-sign-request \ 55
56 '${s3_base}/sra/${acc}/${acc}' \ 56 ## 2. Convert with fasterq-dump
57 ./sra_cache/${acc} &&
58
59 ## 2. Convert with fasterq-dump (CORRECTED: uses extensionless file)
60 mkdir -p fastq_out && 57 mkdir -p fastq_out &&
61 fasterq-dump \ 58 fasterq-dump \
62 ./sra_cache/${acc} \ 59 ./sra_cache/${acc} \
63 --outdir ./fastq_out \ 60 --outdir ./fastq_out \
64 --temp . \ 61 --temp . \
74 cp ./fastq_out/${acc}_1.fastq.gz '$output_r1' && 71 cp ./fastq_out/${acc}_1.fastq.gz '$output_r1' &&
75 cp ./fastq_out/${acc}_2.fastq.gz '$output_r2' 72 cp ./fastq_out/${acc}_2.fastq.gz '$output_r2'
76 #else 73 #else
77 cp ./fastq_out/${acc}.fastq.gz '$output_r1' 74 cp ./fastq_out/${acc}.fastq.gz '$output_r1'
78 #end if 75 #end if
79 #end if
80 ]]></command> 76 ]]></command>
81 77
82 <inputs> 78 <inputs>
83 <section name="source" title="Data Source" expanded="true"> 79 <section name="source" title="Data Source" expanded="true">
84 <param name="bucket" type="select" label="SRA S3 Bucket" 80 <param name="bucket" type="select" label="SRA S3 Bucket"