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comparison aws_sra.xml @ 10:4bd2a27d3755 draft

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planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit be05af327782763c7179b8b67ab5ee6a956c81a3
author galaxytrakr
date Mon, 23 Mar 2026 19:09:24 +0000
parents 40b61da6c6c5
children 696191ca014e
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9:40b61da6c6c5 10:4bd2a27d3755
1 <tool id="aws_sra" name="NCBI SRA AWS Fetch" version="0.3.0+gt_0.9" profile="23.0"> 1 <tool id="aws_sra" name="NCBI SRA AWS Fetch" version="0.3.0+gt_0.10" 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>
25 #if $action.mode == 'list' 25 #if $action.mode == 'list'
26 #set $s3_path = $s3_base 26 #set $s3_path = $s3_base
27 #if $source.prefix 27 #if $source.prefix
28 #set $s3_path = $s3_path + '/' + $source.prefix.strip("/") 28 #set $s3_path = $s3_path + '/' + $source.prefix.strip("/")
29 #end if 29 #end if
30 aws s3 ls \ 30 aws s3 ls
31 --no-sign-request \ 31 --no-sign-request
32 #if $action.recursive 32 #if $action.recursive
33 --recursive 33 --recursive
34 #end if \ 34 #end if
35 $s3_path/ \ 35 $s3_path/
36 > '$output_list' 36 > '$output_list'
37 37
38 ## ── DOWNLOAD RAW mode ──────────────────────────────────────────────────── 38 ## ── DOWNLOAD RAW mode ────────────────────────────────────────────────────
39 #elif $action.mode == 'copy' 39 #elif $action.mode == 'copy'
40 aws s3 cp 40 aws s3 cp
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 = $action.accession.strip()
51 51
52 ## 1. Download the file from S3 (CORRECTED: single line command)
53 mkdir -p sra_cache && 52 mkdir -p sra_cache &&
54 aws s3 cp --no-sign-request '${s3_base}/sra/${acc}/${acc}' ./sra_cache/${acc} && 53 aws s3 cp --no-sign-request '${s3_base}/sra/${acc}/${acc}' ./sra_cache/${acc} &&
55
56 ## 2. Convert with fasterq-dump
57 mkdir -p fastq_out && 54 mkdir -p fastq_out &&
58 fasterq-dump \ 55 fasterq-dump --outdir ./fastq_out --temp . --threads \${GALAXY_SLOTS:-4} --split-files ./sra_cache/${acc} &&
59 ./sra_cache/${acc} \
60 --outdir ./fastq_out \
61 --temp . \
62 --threads \${GALAXY_SLOTS:-4} \
63 --split-files
64 &&
65
66 ## 3. Compress with pigz
67 pigz -p \${GALAXY_SLOTS:-4} ./fastq_out/*.fastq && 56 pigz -p \${GALAXY_SLOTS:-4} ./fastq_out/*.fastq &&
68
69 ## 4. Stage outputs
70 #if $action.layout == 'paired' 57 #if $action.layout == 'paired'
71 cp ./fastq_out/${acc}_1.fastq.gz '$output_r1' && 58 cp ./fastq_out/${acc}_1.fastq.gz '$output_r1' &&
72 cp ./fastq_out/${acc}_2.fastq.gz '$output_r2' 59 cp ./fastq_out/${acc}_2.fastq.gz '$output_r2'
73 #else 60 #else
74 cp ./fastq_out/${acc}.fastq.gz '$output_r1' 61 cp ./fastq_out/${acc}.fastq.gz '$output_r1'
75 #end if 62 #end if
63 #end if
76 ]]></command> 64 ]]></command>
77 65
78 <inputs> 66 <inputs>
79 <section name="source" title="Data Source" expanded="true"> 67 <section name="source" title="Data Source" expanded="true">
80 <param name="bucket" type="select" label="SRA S3 Bucket" 68 <param name="bucket" type="select" label="SRA S3 Bucket"