Mercurial > repos > galaxytrakr > aws_sra

annotate aws_sra.xml @ 10:4bd2a27d3755 draft

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planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit be05af327782763c7179b8b67ab5ee6a956c81a3
author galaxytrakr
date Mon, 23 Mar 2026 19:09:24 +0000
parents 40b61da6c6c5
children 696191ca014e
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4bd2a27d3755 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit be05af327782763c7179b8b67ab5ee6a956c81a3
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1 <tool id="aws_sra" name="NCBI SRA AWS Fetch" version="0.3.0+gt_0.10" profile="23.0">
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2 <description>Fetch SRA data files from NCBI's public AWS S3 buckets</description>
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4 <requirements>
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5 <requirement type="package" version="2.34.8">awscli</requirement>
83c923bd9da6 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit a95de952e58b29875b31e55f0ef06a83a18618fc
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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
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7 <requirement type="package" version="2.8">pigz</requirement>
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8 </requirements>
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10 <version_command>aws --version</version_command>
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12 <command detect_errors="exit_code"><![CDATA[
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13 ## ── Resolve bucket base URL ──────────────────────────────────────────────
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14 #if $source.bucket == 'sra_pub_run_odp'
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15 #set $s3_base = 's3://sra-pub-run-odp'
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16 #elif $source.bucket == 'sra_pub_src_1'
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17 #set $s3_base = 's3://sra-pub-src-1'
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18 #elif $source.bucket == 'sra_pub_src_2'
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19 #set $s3_base = 's3://sra-pub-src-2'
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20 #elif $source.bucket == 'sra_pub_metadata'
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21 #set $s3_base = 's3://sra-pub-metadata-us-east-1/sra/metadata'
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22 #end if
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24 ## ── LIST mode ────────────────────────────────────────────────────────────
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25 #if $action.mode == 'list'
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26 #set $s3_path = $s3_base
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27 #if $source.prefix
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28 #set $s3_path = $s3_path + '/' + $source.prefix.strip("/")
8c60cd4c0ca7 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit 69bae7a0b8011217f6c61fbc62344bcd6a445160
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29 #end if
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30 aws s3 ls
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31 --no-sign-request
0
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32 #if $action.recursive
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33 --recursive
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34 #end if
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35 $s3_path/
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36 > '$output_list'
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37
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38 ## ── DOWNLOAD RAW mode ────────────────────────────────────────────────────
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39 #elif $action.mode == 'copy'
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40 aws s3 cp
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41 --no-sign-request
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42 #if $action.recursive
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43 --recursive
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44 #end if
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45 '${s3_base}/${ $action.s3_key.strip("/") }'
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46 '$output_data'
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47
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48 ## ── FASTQ DUMP mode (sra-pub-run-odp only) ───────────────────────────────
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49 #elif $action.mode == 'fastq_dump'
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50 #set $acc = $action.accession.strip()
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52 mkdir -p sra_cache &&
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53 aws s3 cp --no-sign-request '${s3_base}/sra/${acc}/${acc}' ./sra_cache/${acc} &&
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54 mkdir -p fastq_out &&
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55 fasterq-dump --outdir ./fastq_out --temp . --threads \${GALAXY_SLOTS:-4} --split-files ./sra_cache/${acc} &&
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56 pigz -p \${GALAXY_SLOTS:-4} ./fastq_out/*.fastq &&
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57 #if $action.layout == 'paired'
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58 cp ./fastq_out/${acc}_1.fastq.gz '$output_r1' &&
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
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59 cp ./fastq_out/${acc}_2.fastq.gz '$output_r2'
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60 #else
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61 cp ./fastq_out/${acc}.fastq.gz '$output_r1'
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62 #end if
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63 #end if
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64 ]]></command>
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65
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66 <inputs>
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67 <section name="source" title="Data Source" expanded="true">
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68 <param name="bucket" type="select" label="SRA S3 Bucket"
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69 help="Select the NCBI SRA AWS Open Data bucket to access. FASTQ conversion is only available for sra-pub-run-odp.">
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70 <option value="sra_pub_run_odp" selected="true">
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71 sra-pub-run-odp — Open-access SRA runs (.sra format)
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72 </option>
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73 <option value="sra_pub_src_1">
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74 sra-pub-src-1 — Source submissions: BAM/CRAM/FASTQ (PacBio, ONT, 10X) [bucket 1]
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75 </option>
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76 <option value="sra_pub_src_2">
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77 sra-pub-src-2 — Source submissions: BAM/CRAM/FASTQ (PacBio, ONT, 10X) [bucket 2]
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78 </option>
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79 <option value="sra_pub_metadata">
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80 sra-pub-metadata-us-east-1 — SRA metadata (Parquet/CSV for Athena/Glue)
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81 </option>
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82 </param>
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83 <param name="prefix" type="text" value="" optional="true"
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84 label="S3 key prefix (optional)"
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85 help="Restrict listing to a sub-path, e.g. 'sra/SRR000001'. Used only in List mode.">
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86 <sanitizer invalid_char="">
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87 <valid initial="string.printable">
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
88 <remove value="'"/>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
89 <remove value='"'/>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
90 </valid>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
91 </sanitizer>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
92 </param>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
93 </section>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
94
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
95 <conditional name="action">
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
96 <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
97 <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
98 <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
99 <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
100 </param>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
101
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
102 <!-- ── LIST ── -->
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
103 <when value="list">
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
104 <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
105 checked="false" label="List recursively"
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
106 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
107 </when>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
108
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
109 <!-- ── COPY ── -->
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
110 <when value="copy">
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
111 <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
112 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
113 <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
114 <sanitizer invalid_char="">
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
115 <valid initial="string.printable">
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
116 <remove value="'"/>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
117 <remove value='"'/>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
118 </valid>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
119 </sanitizer>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
120 </param>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
121 <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
122 checked="false" label="Download recursively"
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
123 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
124 </when>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
125
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
126 <!-- ── FASTQ DUMP ── -->
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
127 <when value="fastq_dump">
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
128 <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
129 help="SRA run accession to fetch and convert, e.g. SRR000001. Must be present in sra-pub-run-odp.">
2
83c923bd9da6 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit a95de952e58b29875b31e55f0ef06a83a18618fc
galaxytrakr
parents: 1
diff changeset
130 <validator type="empty_field" message="An SRA accession is required."/>
0
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
131 </param>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
132 <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
133 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
134 <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
135 <option value="single">Single-end</option>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
136 </param>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
137 </when>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
138 </conditional>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
139 </inputs>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
140
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
141 <outputs>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
142 <!-- List output -->
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
143 <data name="output_list" format="txt"
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
144 label="SRA S3 listing: ${source.prefix}">
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
145 <filter>action['mode'] == 'list'</filter>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
146 </data>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
147
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
148 <!-- Raw download -->
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
149 <data name="output_data" format="auto"
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
150 label="SRA download: ${action.s3_key}">
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
151 <filter>action['mode'] == 'copy'</filter>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
152 </data>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
153
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
154 <!-- FASTQ R1 / single.
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
155 Label matches fasterq-dump's native _1 suffix so Galaxy's
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
156 "Build List of Dataset Pairs" can auto-detect pairings. -->
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
157 <data name="output_r1" format="fastqsanger.gz"
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
158 label="${action.accession}_1">
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
159 <filter>action['mode'] == 'fastq_dump'</filter>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
160 </data>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
161
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
162 <!-- FASTQ R2 (paired-end only) -->
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
163 <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
164 label="${action.accession}_2">
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
165 <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
166 </data>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
167 </outputs>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
168
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
169 <tests>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
170 <!-- Test 1: list mode -->
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
171 <test expect_num_outputs="1">
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
172 <section name="source">
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
173 <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
174 <param name="prefix" value="sra/SRR000001"/>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
175 </section>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
176 <conditional name="action">
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
177 <param name="mode" value="list"/>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
178 <param name="recursive" value="false"/>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
179 </conditional>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
180 <output name="output_list">
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
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181 <assert_contents>
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182 <has_text text="SRR000001"/>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
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183 </assert_contents>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
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184 </output>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
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185 </test>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
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186
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187 <!-- Test 2: fastq_dump paired -->
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
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188 <test expect_num_outputs="2">
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
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189 <section name="source">
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
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190 <param name="bucket" value="sra_pub_run_odp"/>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
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191 </section>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
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192 <conditional name="action">
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
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193 <param name="mode" value="fastq_dump"/>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
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194 <param name="accession" value="SRR000001"/>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
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195 <param name="layout" value="paired"/>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
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196 </conditional>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
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197 <output name="output_r1">
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
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198 <assert_contents>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
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199 <has_text text="@SRR000001"/>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
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200 </assert_contents>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
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201 </output>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
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202 <output name="output_r2">
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
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203 <assert_contents>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
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204 <has_text text="@SRR000001"/>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
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205 </assert_contents>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
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206 </output>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
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207 </test>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
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208
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
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209 <!-- Test 3: fastq_dump single-end -->
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
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210 <test expect_num_outputs="1">
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
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211 <section name="source">
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
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212 <param name="bucket" value="sra_pub_run_odp"/>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
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213 </section>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
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214 <conditional name="action">
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
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215 <param name="mode" value="fastq_dump"/>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
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216 <param name="accession" value="SRR000001"/>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
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217 <param name="layout" value="single"/>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
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218 </conditional>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
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219 <output name="output_r1">
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
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220 <assert_contents>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
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221 <has_text text="@SRR000001"/>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
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222 </assert_contents>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
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223 </output>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
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224 </test>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
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225 </tests>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
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226
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
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227 <help><![CDATA[
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
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228 **NCBI SRA AWS Fetch**
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
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229
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
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230 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
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231 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
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232
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
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233 -----
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
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234
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
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235 **Available Buckets**
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
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236
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
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237 +------------------------------+------------------------------------------------------------+
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238 | Bucket | Contents |
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
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239 +==============================+============================================================+
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
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240 | 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
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241 | | Supports FASTQ conversion via this tool. |
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
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242 +------------------------------+------------------------------------------------------------+
2
83c923bd9da6 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit a95de952e58b29875b31e55f0ef06a83a18618fc
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243 | sra-pub-src-1 | Source BAM, CRAM, and FASTQ files from PacBio, ONT, 10X. |
0
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
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244 +------------------------------+------------------------------------------------------------+
2
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245 | sra-pub-src-2 | Same as above (second bucket for source submissions). |
0
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
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246 +------------------------------+------------------------------------------------------------+
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247 | 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
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248 +------------------------------+------------------------------------------------------------+
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249
2
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250
0
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
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251 -----
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
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252
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
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253 **Listing objects**
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254
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
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255 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
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256 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
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257
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258 -----
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
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259
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
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260 **Downloading raw files**
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
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261
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
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262 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
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263
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
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264 sra/SRR000001/SRR000001.sra
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
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265
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266 -----
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
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267
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
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268 **Download and convert to FASTQ**
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
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269
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270 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
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271 FASTQ using ``fasterq-dump``.
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
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272
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
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273 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
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274 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
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275 Single-end runs produce only ``<accession>_1``.
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
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276
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277 *Fetching multiple accessions and building a paired collection*
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278
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279 Run this tool **once per accession** — either manually or by using Galaxy's dataset
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280 collection mapping to fan out over a list of accession identifiers. Keeping one job per
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281 accession means a failed download does not affect the others.
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282
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283 Once all jobs are complete your history will contain datasets labelled::
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284
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285 SRR000001_1 SRR000001_2
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286 SRR000002_1 SRR000002_2
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287 ...
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288
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289 Use **Galaxy's "Build List of Dataset Pairs"** tool to assemble these into a
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290 ``list:paired`` collection. Galaxy will auto-detect the ``_1`` / ``_2`` suffixes
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291 and propose pairings — confirm and name the collection, then pass it directly to
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292 any downstream tool that accepts a paired collection (aligners, QC tools, etc.).
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293
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294 .. warning::
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295
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296 This tool cannot auto-detect read layout from the accession. Check the SRA record
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297 at https://www.ncbi.nlm.nih.gov/sra before running. Selecting the wrong layout will
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298 produce incorrect output.
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299
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300 -----
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301
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302 **Notes**
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303
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304 - All S3 requests are made without AWS credentials (``--no-sign-request``).
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305 - There is typically a **1–2 day lag** between an accession appearing in SRA Search and
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306 being available in the S3 buckets.
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307 - Controlled-access dbGaP data (``sra-ca-run-odp``) requires AWS credentials and is
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308 **not** supported by this tool.
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309 - ``fasterq-dump`` and ``pigz`` both use ``\${GALAXY_SLOTS}`` threads. Allocate more
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310 cores in your job configuration to speed up conversion of large runs.
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311
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312 .. _NCBI Sequence Read Archive (SRA): https://www.ncbi.nlm.nih.gov/sra
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313 ]]></help>
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314
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315 <citations>
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316 <citation type="bibtex">
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317 @misc{ncbi_sra_aws,
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318 title = {{NCBI} {SRA} on {AWS} Open Data},
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319 author = {{National Center for Biotechnology Information}},
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320 howpublished = {\url{https://registry.opendata.aws/ncbi-sra/}},
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321 note = {Accessed via AWS S3 without credentials}
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322 }
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323 </citation>
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324 <citation type="bibtex">
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325 @article{sra_toolkit,
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326 title = {The {NCBI} {SRA} and portable data in biology},
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327 author = {Leinonen, Rasko and Sugawara, Hideaki and Shumway, Martin and
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328 {International Nucleotide Sequence Database Collaboration}},
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329 journal = {Nucleic Acids Research},
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330 volume = {39},
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331 number = {suppl\_1},
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332 pages = {D19--D21},
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333 year = {2011},
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334 doi = {10.1093/nar/gkq1019}
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335 }
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336 </citation>
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337 </citations>
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338
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339 </tool>