Mercurial > repos > galaxytrakr > aws_sra

annotate aws_sra.xml @ 21:02f45c03c306 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 f72940592c22c9ba88f1dcb23ef8bb5199ce434e
author galaxytrakr
date Mon, 23 Mar 2026 23:33:12 +0000
parents 2b4efa539c71
children 5ecb94ab82c3
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
21
02f45c03c306 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit f72940592c22c9ba88f1dcb23ef8bb5199ce434e
galaxytrakr
parents: 20
diff changeset
1 <tool id="aws_sra" name="NCBI SRA AWS Fetch" version="1.3.0" profile="23.0">
02f45c03c306 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit f72940592c22c9ba88f1dcb23ef8bb5199ce434e
galaxytrakr
parents: 20
diff changeset
2 <description>Fetches a single SRA run from AWS and converts it to FASTQ</description>
02f45c03c306 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit f72940592c22c9ba88f1dcb23ef8bb5199ce434e
galaxytrakr
parents: 20
diff changeset
3
0
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
4 <requirements>
2
83c923bd9da6 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit a95de952e58b29875b31e55f0ef06a83a18618fc
galaxytrakr
parents: 1
diff changeset
5 <requirement type="package" version="2.34.8">awscli</requirement>
83c923bd9da6 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit a95de952e58b29875b31e55f0ef06a83a18618fc
galaxytrakr
parents: 1
diff changeset
6 <requirement type="package" version="3.2.1">sra-tools</requirement>
83c923bd9da6 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit a95de952e58b29875b31e55f0ef06a83a18618fc
galaxytrakr
parents: 1
diff changeset
7 <requirement type="package" version="2.8">pigz</requirement>
0
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
8 </requirements>
21
02f45c03c306 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit f72940592c22c9ba88f1dcb23ef8bb5199ce434e
galaxytrakr
parents: 20
diff changeset
9
13
2897d365dd62 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit 619ebd7e6a24be0ec6c2728511290f43b0bad89f
galaxytrakr
parents: 12
diff changeset
10 <version_command>fasterq-dump --version</version_command>
2897d365dd62 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit 619ebd7e6a24be0ec6c2728511290f43b0bad89f
galaxytrakr
parents: 12
diff changeset
11
2897d365dd62 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit 619ebd7e6a24be0ec6c2728511290f43b0bad89f
galaxytrakr
parents: 12
diff changeset
12 <command detect_errors="aggressive"><![CDATA[
21
02f45c03c306 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit f72940592c22c9ba88f1dcb23ef8bb5199ce434e
galaxytrakr
parents: 20
diff changeset
13 #set $acc = str($accession).strip()
02f45c03c306 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit f72940592c22c9ba88f1dcb23ef8bb5199ce434e
galaxytrakr
parents: 20
diff changeset
14
02f45c03c306 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit f72940592c22c9ba88f1dcb23ef8bb5199ce434e
galaxytrakr
parents: 20
diff changeset
15 echo "Processing single accession: $acc" &&
02f45c03c306 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit f72940592c22c9ba88f1dcb23ef8bb5199ce434e
galaxytrakr
parents: 20
diff changeset
16
02f45c03c306 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit f72940592c22c9ba88f1dcb23ef8bb5199ce434e
galaxytrakr
parents: 20
diff changeset
17 ## 1. Create temporary directories
02f45c03c306 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit f72940592c22c9ba88f1dcb23ef8bb5199ce434e
galaxytrakr
parents: 20
diff changeset
18 mkdir -p sra_cache fastq_out &&
02f45c03c306 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit f72940592c22c9ba88f1dcb23ef8bb5199ce434e
galaxytrakr
parents: 20
diff changeset
19
02f45c03c306 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit f72940592c22c9ba88f1dcb23ef8bb5199ce434e
galaxytrakr
parents: 20
diff changeset
20 ## 2. Download the file from S3 using the discovered path format (no .sra)
02f45c03c306 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit f72940592c22c9ba88f1dcb23ef8bb5199ce434e
galaxytrakr
parents: 20
diff changeset
21 aws s3 cp --no-sign-request 's3://sra-pub-run-odp/sra/${acc}/${acc}' ./sra_cache/ &&
13
2897d365dd62 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit 619ebd7e6a24be0ec6c2728511290f43b0bad89f
galaxytrakr
parents: 12
diff changeset
22
21
02f45c03c306 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit f72940592c22c9ba88f1dcb23ef8bb5199ce434e
galaxytrakr
parents: 20
diff changeset
23 ## 3. Convert with fasterq-dump, using the correct argument order
02f45c03c306 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit f72940592c22c9ba88f1dcb23ef8bb5199ce434e
galaxytrakr
parents: 20
diff changeset
24 fasterq-dump --outdir ./fastq_out --temp . --threads \${GALAXY_SLOTS:-4} --split-files ./sra_cache/${acc} &&
02f45c03c306 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit f72940592c22c9ba88f1dcb23ef8bb5199ce434e
galaxytrakr
parents: 20
diff changeset
25
02f45c03c306 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit f72940592c22c9ba88f1dcb23ef8bb5199ce434e
galaxytrakr
parents: 20
diff changeset
26 ## 4. Compress with pigz
02f45c03c306 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit f72940592c22c9ba88f1dcb23ef8bb5199ce434e
galaxytrakr
parents: 20
diff changeset
27 pigz -p \${GALAXY_SLOTS:-4} ./fastq_out/*.fastq &&
02f45c03c306 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit f72940592c22c9ba88f1dcb23ef8bb5199ce434e
galaxytrakr
parents: 20
diff changeset
28
02f45c03c306 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit f72940592c22c9ba88f1dcb23ef8bb5199ce434e
galaxytrakr
parents: 20
diff changeset
29 ## 5. Move the final outputs to their Galaxy dataset paths
02f45c03c306 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit f72940592c22c9ba88f1dcb23ef8bb5199ce434e
galaxytrakr
parents: 20
diff changeset
30 #if str($layout) == 'paired'
02f45c03c306 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit f72940592c22c9ba88f1dcb23ef8bb5199ce434e
galaxytrakr
parents: 20
diff changeset
31 mv ./fastq_out/${acc}_1.fastq.gz '$output_r1' &&
02f45c03c306 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit f72940592c22c9ba88f1dcb23ef8bb5199ce434e
galaxytrakr
parents: 20
diff changeset
32 mv ./fastq_out/${acc}_2.fastq.gz '$output_r2'
17
9fb80e0392ce planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit 9707fa5e3ca6db5b58f271d133484d078cf65390
galaxytrakr
parents: 16
diff changeset
33 #else
21
02f45c03c306 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit f72940592c22c9ba88f1dcb23ef8bb5199ce434e
galaxytrakr
parents: 20
diff changeset
34 # Be explicit about the single-end filename, removing the wildcard
02f45c03c306 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit f72940592c22c9ba88f1dcb23ef8bb5199ce434e
galaxytrakr
parents: 20
diff changeset
35 mv ./fastq_out/${acc}.fastq.gz '$output_r1'
17
9fb80e0392ce planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit 9707fa5e3ca6db5b58f271d133484d078cf65390
galaxytrakr
parents: 16
diff changeset
36 #end if
0
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
37 ]]></command>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
38
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
39 <inputs>
21
02f45c03c306 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit f72940592c22c9ba88f1dcb23ef8bb5199ce434e
galaxytrakr
parents: 20
diff changeset
40 <param name="accession" type="text" label="SRA Accession" help="e.g., SRR13333333"/>
02f45c03c306 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit f72940592c22c9ba88f1dcb23ef8bb5199ce434e
galaxytrakr
parents: 20
diff changeset
41 <param name="layout" type="select" label="Read layout" help="Check the SRA record to confirm layout before running.">
13
2897d365dd62 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit 619ebd7e6a24be0ec6c2728511290f43b0bad89f
galaxytrakr
parents: 12
diff changeset
42 <option value="paired" selected="true">Paired-end (R1 + R2)</option>
2897d365dd62 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit 619ebd7e6a24be0ec6c2728511290f43b0bad89f
galaxytrakr
parents: 12
diff changeset
43 <option value="single">Single-end</option>
2897d365dd62 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit 619ebd7e6a24be0ec6c2728511290f43b0bad89f
galaxytrakr
parents: 12
diff changeset
44 </param>
0
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
45 </inputs>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
46
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
47 <outputs>
21
02f45c03c306 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit f72940592c22c9ba88f1dcb23ef8bb5199ce434e
galaxytrakr
parents: 20
diff changeset
48 <data name="output_r1" format="fastqsanger.gz" label="${accession}_1.fastq.gz"/>
02f45c03c306 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit f72940592c22c9ba88f1dcb23ef8bb5199ce434e
galaxytrakr
parents: 20
diff changeset
49 <data name="output_r2" format="fastqsanger.gz" label="${accession}_2.fastq.gz">
02f45c03c306 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit f72940592c22c9ba88f1dcb23ef8bb5199ce434e
galaxytrakr
parents: 20
diff changeset
50 <filter>layout == 'paired'</filter>
17
9fb80e0392ce planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit 9707fa5e3ca6db5b58f271d133484d078cf65390
galaxytrakr
parents: 16
diff changeset
51 </data>
21
02f45c03c306 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit f72940592c22c9ba88f1dcb23ef8bb5199ce434e
galaxytrakr
parents: 20
diff changeset
52 </outputs>
17
9fb80e0392ce planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit 9707fa5e3ca6db5b58f271d133484d078cf65390
galaxytrakr
parents: 16
diff changeset
53
21
02f45c03c306 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit f72940592c22c9ba88f1dcb23ef8bb5199ce434e
galaxytrakr
parents: 20
diff changeset
54 <tests>
02f45c03c306 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit f72940592c22c9ba88f1dcb23ef8bb5199ce434e
galaxytrakr
parents: 20
diff changeset
55 <test expect_num_outputs="2">
02f45c03c306 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit f72940592c22c9ba88f1dcb23ef8bb5199ce434e
galaxytrakr
parents: 20
diff changeset
56 <param name="accession" value="SRR13333333"/>
02f45c03c306 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit f72940592c22c9ba88f1dcb23ef8bb5199ce434e
galaxytrakr
parents: 20
diff changeset
57 <param name="layout" value="paired"/>
02f45c03c306 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit f72940592c22c9ba88f1dcb23ef8bb5199ce434e
galaxytrakr
parents: 20
diff changeset
58 <output name="output_r1" ftype="fastqsanger.gz">
02f45c03c306 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit f72940592c22c9ba88f1dcb23ef8bb5199ce434e
galaxytrakr
parents: 20
diff changeset
59 <assert_contents>
02f45c03c306 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit f72940592c22c9ba88f1dcb23ef8bb5199ce434e
galaxytrakr
parents: 20
diff changeset
60 <has_text text="@SRR13333333"/>
02f45c03c306 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit f72940592c22c9ba88f1dcb23ef8bb5199ce434e
galaxytrakr
parents: 20
diff changeset
61 </assert_contents>
02f45c03c306 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit f72940592c22c9ba88f1dcb23ef8bb5199ce434e
galaxytrakr
parents: 20
diff changeset
62 </output>
02f45c03c306 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit f72940592c22c9ba88f1dcb23ef8bb5199ce434e
galaxytrakr
parents: 20
diff changeset
63 <output name="output_r2" ftype="fastqsanger.gz">
02f45c03c306 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit f72940592c22c9ba88f1dcb23ef8bb5199ce434e
galaxytrakr
parents: 20
diff changeset
64 <assert_contents>
02f45c03c306 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit f72940592c22c9ba88f1dcb23ef8bb5199ce434e
galaxytrakr
parents: 20
diff changeset
65 <has_text text="@SRR13333333"/>
02f45c03c306 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit f72940592c22c9ba88f1dcb23ef8bb5199ce434e
galaxytrakr
parents: 20
diff changeset
66 </assert_contents>
02f45c03c306 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit f72940592c22c9ba88f1dcb23ef8bb5199ce434e
galaxytrakr
parents: 20
diff changeset
67 </output>
02f45c03c306 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit f72940592c22c9ba88f1dcb23ef8bb5199ce434e
galaxytrakr
parents: 20
diff changeset
68 </test>
02f45c03c306 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit f72940592c22c9ba88f1dcb23ef8bb5199ce434e
galaxytrakr
parents: 20
diff changeset
69 <test expect_num_outputs="1">
02f45c03c306 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit f72940592c22c9ba88f1dcb23ef8bb5199ce434e
galaxytrakr
parents: 20
diff changeset
70 <param name="accession" value="SRR11181815"/> <!-- A known single-end run -->
02f45c03c306 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit f72940592c22c9ba88f1dcb23ef8bb5199ce434e
galaxytrakr
parents: 20
diff changeset
71 <param name="layout" value="single"/>
02f45c03c306 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit f72940592c22c9ba88f1dcb23ef8bb5199ce434e
galaxytrakr
parents: 20
diff changeset
72 <output name="output_r1" ftype="fastqsanger.gz">
02f45c03c306 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit f72940592c22c9ba88f1dcb23ef8bb5199ce434e
galaxytrakr
parents: 20
diff changeset
73 <assert_contents>
02f45c03c306 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit f72940592c22c9ba88f1dcb23ef8bb5199ce434e
galaxytrakr
parents: 20
diff changeset
74 <has_text text="@SRR11181815"/>
02f45c03c306 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit f72940592c22c9ba88f1dcb23ef8bb5199ce434e
galaxytrakr
parents: 20
diff changeset
75 </assert_contents>
02f45c03c306 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit f72940592c22c9ba88f1dcb23ef8bb5199ce434e
galaxytrakr
parents: 20
diff changeset
76 </output>
02f45c03c306 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit f72940592c22c9ba88f1dcb23ef8bb5199ce434e
galaxytrakr
parents: 20
diff changeset
77 </test>
02f45c03c306 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit f72940592c22c9ba88f1dcb23ef8bb5199ce434e
galaxytrakr
parents: 20
diff changeset
78 </tests>
02f45c03c306 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit f72940592c22c9ba88f1dcb23ef8bb5199ce434e
galaxytrakr
parents: 20
diff changeset
79
0
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
80 <help><![CDATA[
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
81 **NCBI SRA AWS Fetch**
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
82
21
02f45c03c306 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit f72940592c22c9ba88f1dcb23ef8bb5199ce434e
galaxytrakr
parents: 20
diff changeset
83 Fetches a single SRA run from the public `sra-pub-run-odp` bucket on Amazon S3 and converts it to gzip-compressed FASTQ using `fasterq-dump`.
0
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
84 ]]></help>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
85
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
86 <citations>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
87 <citation type="bibtex">
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
88 @misc{ncbi_sra_aws,
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
89 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
90 author = {{National Center for Biotechnology Information}},
13
2897d365dd62 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit 619ebd7e6a24be0ec6c2728511290f43b0bad89f
galaxytrakr
parents: 12
diff changeset
91 howpublished = {\\url{https://registry.opendata.aws/ncbi-sra/}},
0
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
92 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
93 }
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
94 </citation>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
95 <citation type="bibtex">
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
96 @article{sra_toolkit,
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
97 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
98 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
99 {International Nucleotide Sequence Database Collaboration}},
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
100 journal = {Nucleic Acids Research},
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
101 volume = {39},
13
2897d365dd62 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit 619ebd7e6a24be0ec6c2728511290f43b0bad89f
galaxytrakr
parents: 12
diff changeset
102 number = {suppl\\\_1},
0
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
103 pages = {D19--D21},
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
104 year = {2011},
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
105 doi = {10.1093/nar/gkq1019}
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
106 }
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
107 </citation>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
108 </citations>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
109 </tool>