Mercurial > repos > galaxytrakr > aws_sra

annotate aws_sra.xml @ 0:a4afe551dfc9 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
author galaxytrakr
date Mon, 23 Mar 2026 14:09:35 +0000
parents
children ddfdc4c465e7
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
1 <tool id="aws_sra" name="NCBI SRA AWS Fetch" version="0.3.0+gt_0.1" profile="23.0">
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
2 <description>Fetch SRA data files from NCBI's public AWS S3 buckets</description>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
3
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
4 <requirements>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
5 <requirement type="package" version="2.34.8" channel="conda-forge">awscli</requirement>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
6 <requirement type="package" version="3.2.1" channel="bioconda">sra-tools</requirement>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
7 <requirement type="package" version="2.8" channel="conda-forge">pigz</requirement>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
8 </requirements>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
9
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
10 <version_command>aws --version</version_command>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
11
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
12 <command detect_errors="exit_code"><![CDATA[
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
13 ## ── Resolve bucket base URL ──────────────────────────────────────────────
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
14 #if $source.bucket == 'sra_pub_run_odp'
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
15 #set $s3_base = 's3://sra-pub-run-odp'
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
16 #elif $source.bucket == 'sra_pub_src_1'
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
17 #set $s3_base = 's3://sra-pub-src-1'
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
18 #elif $source.bucket == 'sra_pub_src_2'
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
19 #set $s3_base = 's3://sra-pub-src-2'
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
20 #elif $source.bucket == 'sra_pub_metadata'
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
21 #set $s3_base = 's3://sra-pub-metadata-us-east-1/sra/metadata'
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
22 #end if
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
23
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
24 ## ── LIST mode ────────────────────────────────────────────────────────────
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
25 #if $action.mode == 'list'
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
26 aws s3 ls
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
27 --no-sign-request
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
28 #if $source.prefix
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
29 '${s3_base}/${ $source.prefix.strip("/") }/'
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
30 #else
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
31 '${s3_base}/'
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
32 #end if
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
33 #if $action.recursive
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
34 --recursive
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
35 #end if
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
36 > '$output_list'
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
37
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
38 ## ── DOWNLOAD RAW mode ────────────────────────────────────────────────────
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
39 #elif $action.mode == 'copy'
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
40 aws s3 cp
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
41 --no-sign-request
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
42 #if $action.recursive
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
43 --recursive
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
44 #end if
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
45 '${s3_base}/${ $action.s3_key.strip("/") }'
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
46 '$output_data'
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
47
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
48 ## ── FASTQ DUMP mode (sra-pub-run-odp only) ───────────────────────────────
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
49 #elif $action.mode == 'fastq_dump'
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
50 #set $acc = $action.accession.strip()
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
51
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
52 ## 1. Download the .sra file from S3
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
53 mkdir -p sra_cache &&
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
54 aws s3 cp
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
55 --no-sign-request
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
56 '${s3_base}/sra/${acc}/${acc}.sra'
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
57 ./sra_cache/${acc}.sra &&
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
58
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
59 ## 2. Convert with fasterq-dump --split-files.
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
60 ## Paired runs → <acc>_1.fastq + <acc>_2.fastq
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
61 ## Single runs → <acc>.fastq (no _1/_2 suffix)
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
62 ## We always use --split-files; single-end runs simply produce one file.
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
63 mkdir -p fastq_out &&
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
64 fasterq-dump
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
65 ./sra_cache/${acc}.sra
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
66 --outdir ./fastq_out
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
67 --temp .
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
68 --threads \${GALAXY_SLOTS:-4}
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
69 --split-files
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
70 &&
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
71
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
72 ## 3. Compress with pigz (fasterq-dump does not gzip natively)
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
73 pigz -p \${GALAXY_SLOTS:-4} ./fastq_out/*.fastq &&
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
74
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
75 ## 4. Stage outputs
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
76 #if $action.layout == 'paired'
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
77 cp ./fastq_out/${acc}_1.fastq.gz '$output_r1' &&
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
78 cp ./fastq_out/${acc}_2.fastq.gz '$output_r2'
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
79 #else
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
80 cp ./fastq_out/${acc}.fastq.gz '$output_r1'
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
81 #end if
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
82 #end if
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
83 ]]></command>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
84
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
85 <inputs>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
86 <section name="source" title="Data Source" expanded="true">
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
87 <param name="bucket" type="select" label="SRA S3 Bucket"
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
88 help="Select the NCBI SRA AWS Open Data bucket to access. FASTQ conversion is only available for sra-pub-run-odp.">
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
89 <option value="sra_pub_run_odp" selected="true">
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
90 sra-pub-run-odp — Open-access SRA runs (.sra format)
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
91 </option>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
92 <option value="sra_pub_src_1">
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
93 sra-pub-src-1 — Source submissions: BAM/CRAM/FASTQ (PacBio, ONT, 10X) [bucket 1]
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
94 </option>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
95 <option value="sra_pub_src_2">
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
96 sra-pub-src-2 — Source submissions: BAM/CRAM/FASTQ (PacBio, ONT, 10X) [bucket 2]
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
97 </option>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
98 <option value="sra_pub_metadata">
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
99 sra-pub-metadata-us-east-1 — SRA metadata (Parquet/CSV for Athena/Glue)
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
100 </option>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
101 </param>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
102 <param name="prefix" type="text" value="" optional="true"
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
103 label="S3 key prefix (optional)"
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
104 help="Restrict listing to a sub-path, e.g. 'sra/SRR000001'. Used only in List mode.">
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
105 <sanitizer invalid_char="">
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
106 <valid initial="string.printable">
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
107 <remove value="'"/>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
108 <remove value='"'/>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
109 </valid>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
110 </sanitizer>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
111 </param>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
112 </section>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
113
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
114 <conditional name="action">
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
115 <param name="mode" type="select" label="Action">
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
116 <option value="list" selected="true">List objects</option>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
117 <option value="copy">Download raw file(s)</option>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
118 <option value="fastq_dump">Download and convert to FASTQ (sra-pub-run-odp only)</option>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
119 </param>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
120
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
121 <!-- ── LIST ── -->
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
122 <when value="list">
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
123 <param name="recursive" type="boolean" truevalue="--recursive" falsevalue=""
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
124 checked="false" label="List recursively"
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
125 help="List all objects under the prefix, not just the immediate level."/>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
126 </when>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
127
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
128 <!-- ── COPY ── -->
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
129 <when value="copy">
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
130 <param name="s3_key" type="text" label="S3 key to download"
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
131 help="Full key of the object to download, e.g. 'sra/SRR000001/SRR000001.sra'.">
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
132 <validator type="empty_field" message="An S3 key is required for download."/>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
133 <sanitizer invalid_char="">
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
134 <valid initial="string.printable">
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
135 <remove value="'"/>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
136 <remove value='"'/>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
137 </valid>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
138 </sanitizer>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
139 </param>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
140 <param name="recursive" type="boolean" truevalue="--recursive" falsevalue=""
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
141 checked="false" label="Download recursively"
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
142 help="Download all objects with this prefix rather than a single object."/>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
143 </when>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
144
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
145 <!-- ── FASTQ DUMP ── -->
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
146 <when value="fastq_dump">
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
147 <param name="accession" type="text" label="SRA Accession"
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
148 help="SRA run accession to fetch and convert, e.g. SRR000001. Must be present in sra-pub-run-odp.">
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
149 <validator type="empty_field" message="An SRA accession is required."/>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
150 <validator type="regex"
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
151 message="Must be a valid SRA run accession (SRR, ERR, or DRR followed by digits)."
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
152 expression="^[SED]RR[0-9]+$"/>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
153 </param>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
154 <param name="layout" type="select" label="Read layout"
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
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.">
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
156 <option value="paired" selected="true">Paired-end (R1 + R2)</option>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
157 <option value="single">Single-end</option>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
158 </param>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
159 </when>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
160 </conditional>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
161 </inputs>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
162
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
163 <outputs>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
164 <!-- List output -->
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
165 <data name="output_list" format="txt"
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
166 label="SRA S3 listing: ${source.prefix}">
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
167 <filter>action['mode'] == 'list'</filter>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
168 </data>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
169
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
170 <!-- Raw download -->
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
171 <data name="output_data" format="auto"
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
172 label="SRA download: ${action.s3_key}">
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
173 <filter>action['mode'] == 'copy'</filter>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
174 </data>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
175
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
176 <!-- FASTQ R1 / single.
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
177 Label matches fasterq-dump's native _1 suffix so Galaxy's
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
178 "Build List of Dataset Pairs" can auto-detect pairings. -->
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
179 <data name="output_r1" format="fastqsanger.gz"
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
180 label="${action.accession}_1">
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
181 <filter>action['mode'] == 'fastq_dump'</filter>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
182 </data>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
183
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
184 <!-- FASTQ R2 (paired-end only) -->
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
185 <data name="output_r2" format="fastqsanger.gz"
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
186 label="${action.accession}_2">
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
187 <filter>action['mode'] == 'fastq_dump' and action['layout'] == 'paired'</filter>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
188 </data>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
189 </outputs>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
190
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
191 <tests>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
192 <!-- Test 1: list mode -->
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
193 <test expect_num_outputs="1">
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
194 <section name="source">
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
195 <param name="bucket" value="sra_pub_run_odp"/>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
196 <param name="prefix" value="sra/SRR000001"/>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
197 </section>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
198 <conditional name="action">
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
199 <param name="mode" value="list"/>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
200 <param name="recursive" value="false"/>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
201 </conditional>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
202 <output name="output_list">
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
203 <assert_contents>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
204 <has_text text="SRR000001"/>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
205 </assert_contents>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
206 </output>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
207 </test>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
208
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
209 <!-- Test 2: fastq_dump paired -->
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
210 <test expect_num_outputs="2">
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
211 <section name="source">
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
212 <param name="bucket" value="sra_pub_run_odp"/>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
213 </section>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
214 <conditional name="action">
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
215 <param name="mode" value="fastq_dump"/>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
216 <param name="accession" value="SRR000001"/>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
217 <param name="layout" value="paired"/>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
218 </conditional>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
219 <output name="output_r1">
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
220 <assert_contents>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
221 <has_text text="@SRR000001"/>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
222 </assert_contents>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
223 </output>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
224 <output name="output_r2">
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
225 <assert_contents>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
226 <has_text text="@SRR000001"/>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
227 </assert_contents>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
228 </output>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
229 </test>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
230
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
231 <!-- Test 3: fastq_dump single-end -->
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
232 <test expect_num_outputs="1">
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
233 <section name="source">
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
234 <param name="bucket" value="sra_pub_run_odp"/>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
235 </section>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
236 <conditional name="action">
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
237 <param name="mode" value="fastq_dump"/>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
238 <param name="accession" value="SRR000001"/>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
239 <param name="layout" value="single"/>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
240 </conditional>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
241 <output name="output_r1">
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
242 <assert_contents>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
243 <has_text text="@SRR000001"/>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
244 </assert_contents>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
245 </output>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
246 </test>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
247 </tests>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
248
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
249 <help><![CDATA[
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
250 **NCBI SRA AWS Fetch**
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
251
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
252 This tool fetches data from the `NCBI Sequence Read Archive (SRA)`_ hosted on Amazon S3
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
253 as part of the AWS Open Data program. No AWS account is required.
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
254
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
255 -----
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
256
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
257 **Available Buckets**
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
258
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
259 +------------------------------+------------------------------------------------------------+
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
260 | Bucket | Contents |
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
261 +==============================+============================================================+
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
262 | sra-pub-run-odp | All open-access SRA runs in SRA Normalized format (.sra). |
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
263 | | Supports FASTQ conversion via this tool. |
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
264 +------------------------------+------------------------------------------------------------+
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
265 | sra-pub-src-1 | Source BAM, CRAM, and FASTQ files from PacBio, ONT, 10X. |
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
266 +------------------------------+------------------------------------------------------------+
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
267 | sra-pub-src-2 | Same as above (second bucket for source submissions). |
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
268 +------------------------------+------------------------------------------------------------+
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
269 | sra-pub-metadata-us-east-1 | SRA metadata in Parquet/CSV format (for Athena / Glue). |
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
270 +------------------------------+------------------------------------------------------------+
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
271
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
272 -----
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
273
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
274 **Listing objects**
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
275
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
276 Select **List objects** to see what files are available under a given prefix, e.g. ``sra/SRR000001``.
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
277 Leave the prefix blank to browse the bucket root (may return a very large listing).
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
278
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
279 -----
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
280
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
281 **Downloading raw files**
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
282
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
283 Select **Download raw file(s)** and provide the full S3 key, e.g.::
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
284
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
285 sra/SRR000001/SRR000001.sra
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
286
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
287 -----
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
288
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
289 **Download and convert to FASTQ**
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
290
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
291 Fetches a single SRA run from ``sra-pub-run-odp`` and converts it to gzip-compressed
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
292 FASTQ using ``fasterq-dump``.
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
293
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
294 Outputs are labelled ``<accession>_1`` (R1 / forward) and ``<accession>_2`` (R2 / reverse)
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
295 for paired-end runs, matching ``fasterq-dump``'s native ``--split-files`` naming.
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
296 Single-end runs produce only ``<accession>_1``.
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
297
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
298 *Fetching multiple accessions and building a paired collection*
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
299
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
300 Run this tool **once per accession** — either manually or by using Galaxy's dataset
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
301 collection mapping to fan out over a list of accession identifiers. Keeping one job per
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
302 accession means a failed download does not affect the others.
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
303
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
304 Once all jobs are complete your history will contain datasets labelled::
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
305
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
306 SRR000001_1 SRR000001_2
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
307 SRR000002_1 SRR000002_2
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
308 ...
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
309
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
310 Use **Galaxy's "Build List of Dataset Pairs"** tool to assemble these into a
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
311 ``list:paired`` collection. Galaxy will auto-detect the ``_1`` / ``_2`` suffixes
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
312 and propose pairings — confirm and name the collection, then pass it directly to
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
313 any downstream tool that accepts a paired collection (aligners, QC tools, etc.).
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
314
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
315 .. warning::
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
316
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
317 This tool cannot auto-detect read layout from the accession. Check the SRA record
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
318 at https://www.ncbi.nlm.nih.gov/sra before running. Selecting the wrong layout will
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
319 produce incorrect output.
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
320
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
321 -----
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
322
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
323 **Notes**
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
324
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
325 - All S3 requests are made without AWS credentials (``--no-sign-request``).
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
326 - There is typically a **1–2 day lag** between an accession appearing in SRA Search and
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
327 being available in the S3 buckets.
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
328 - Controlled-access dbGaP data (``sra-ca-run-odp``) requires AWS credentials and is
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
329 **not** supported by this tool.
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
330 - ``fasterq-dump`` and ``pigz`` both use ``\${GALAXY_SLOTS}`` threads. Allocate more
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
331 cores in your job configuration to speed up conversion of large runs.
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
332
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
333 .. _NCBI Sequence Read Archive (SRA): https://www.ncbi.nlm.nih.gov/sra
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
334 ]]></help>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
335
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
336 <citations>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
337 <citation type="bibtex">
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
338 @misc{ncbi_sra_aws,
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
339 title = {{NCBI} {SRA} on {AWS} Open Data},
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
340 author = {{National Center for Biotechnology Information}},
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
341 howpublished = {\url{https://registry.opendata.aws/ncbi-sra/}},
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
342 note = {Accessed via AWS S3 without credentials}
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
343 }
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
344 </citation>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
345 <citation type="bibtex">
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
346 @article{sra_toolkit,
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
347 title = {The {NCBI} {SRA} and portable data in biology},
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
348 author = {Leinonen, Rasko and Sugawara, Hideaki and Shumway, Martin and
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
349 {International Nucleotide Sequence Database Collaboration}},
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
350 journal = {Nucleic Acids Research},
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
351 volume = {39},
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
352 number = {suppl\_1},
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
353 pages = {D19--D21},
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
354 year = {2011},
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
355 doi = {10.1093/nar/gkq1019}
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
356 }
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
357 </citation>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
358 </citations>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
359
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
360 </tool>