Mercurial > repos > galaxytrakr > aws_sra

comparison aws_sra.xml @ 6:8c60cd4c0ca7 draft

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planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit 69bae7a0b8011217f6c61fbc62344bcd6a445160
author galaxytrakr
date Mon, 23 Mar 2026 18:17:47 +0000
parents 313a1e088e09
children 3529ce6bcde7
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5:313a1e088e09 6:8c60cd4c0ca7
1 <tool id="aws_sra" name="NCBI SRA AWS Fetch" version="0.3.0+gt_0.5" profile="23.0"> 1 <tool id="aws_sra" name="NCBI SRA AWS Fetch" version="0.3.0+gt_0.6" 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>
21 #set $s3_base = 's3://sra-pub-metadata-us-east-1/sra/metadata' 21 #set $s3_base = 's3://sra-pub-metadata-us-east-1/sra/metadata'
22 #end if 22 #end if
23 23
24 ## ── LIST mode ──────────────────────────────────────────────────────────── 24 ## ── LIST mode ────────────────────────────────────────────────────────────
25 #if $action.mode == 'list' 25 #if $action.mode == 'list'
26 aws s3 ls 26 #set $s3_path = $s3_base
27 --no-sign-request 27 #if $source.prefix
28 #if $source.prefix 28 #set $s3_path = $s3_path + '/' + $source.prefix.strip("/")
29 '${s3_base}/${ $source.prefix.strip("/") }/' 29 #end if
30 #else 30 aws s3 ls \
31 '${s3_base}/' 31 --no-sign-request \
32 #end if
33 #if $action.recursive 32 #if $action.recursive
34 --recursive 33 --recursive
35 #end if 34 #end if \
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