Mercurial > repos > galaxytrakr > aws_sra

annotate aws_sra.xml @ 8:ef51d44623c2 draft

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planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit 37694a2c524c1c5124f0da25ee49077717438a59
author galaxytrakr
date Mon, 23 Mar 2026 18:42:57 +0000
parents 3529ce6bcde7
children 40b61da6c6c5
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ef51d44623c2 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit 37694a2c524c1c5124f0da25ee49077717438a59
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1 <tool id="aws_sra" name="NCBI SRA AWS Fetch" version="0.3.0+gt_0.8" 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>
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6 <requirement type="package" version="3.2.1">sra-tools</requirement>
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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("/")
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29 #end if
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30 aws s3 ls \
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31 --no-sign-request \
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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 = $action.accession.strip()
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51
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52 ## 1. Download the file from S3
0
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53 mkdir -p sra_cache &&
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54 aws s3 cp \
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55 --no-sign-request \
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56 '${s3_base}/sra/${acc}/${acc}' \
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57 ./sra_cache/${acc} &&
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58
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59 ## 2. Convert with fasterq-dump (CORRECTED: uses extensionless file)
0
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60 mkdir -p fastq_out &&
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61 fasterq-dump \
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62 ./sra_cache/${acc} \
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63 --outdir ./fastq_out \
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64 --temp . \
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65 --threads \${GALAXY_SLOTS:-4} \
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66 --split-files
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67 &&
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68
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69 ## 3. Compress with pigz
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70 pigz -p \${GALAXY_SLOTS:-4} ./fastq_out/*.fastq &&
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71
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72 ## 4. Stage outputs
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73 #if $action.layout == 'paired'
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74 cp ./fastq_out/${acc}_1.fastq.gz '$output_r1' &&
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75 cp ./fastq_out/${acc}_2.fastq.gz '$output_r2'
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76 #else
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77 cp ./fastq_out/${acc}.fastq.gz '$output_r1'
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78 #end if
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79 #end if
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80 ]]></command>
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81
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82 <inputs>
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83 <section name="source" title="Data Source" expanded="true">
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84 <param name="bucket" type="select" label="SRA S3 Bucket"
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85 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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86 <option value="sra_pub_run_odp" selected="true">
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87 sra-pub-run-odp — Open-access SRA runs (.sra format)
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88 </option>
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89 <option value="sra_pub_src_1">
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
90 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
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_2">
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
93 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
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_metadata">
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
96 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
97 </option>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
98 </param>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
99 <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
100 label="S3 key prefix (optional)"
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
101 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
102 <sanitizer invalid_char="">
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
103 <valid initial="string.printable">
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
104 <remove value="'"/>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
105 <remove value='"'/>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
106 </valid>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
107 </sanitizer>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
108 </param>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
109 </section>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
110
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
111 <conditional name="action">
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
112 <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
113 <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
114 <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
115 <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
116 </param>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
117
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
118 <!-- ── LIST ── -->
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
119 <when value="list">
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
120 <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
121 checked="false" label="List recursively"
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
122 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
123 </when>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
124
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
125 <!-- ── COPY ── -->
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
126 <when value="copy">
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
127 <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
128 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
129 <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
130 <sanitizer invalid_char="">
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
131 <valid initial="string.printable">
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
132 <remove value="'"/>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
133 <remove value='"'/>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
134 </valid>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
135 </sanitizer>
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 <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
138 checked="false" label="Download recursively"
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
139 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
140 </when>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
141
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
142 <!-- ── FASTQ DUMP ── -->
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
143 <when value="fastq_dump">
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
144 <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
145 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
146 <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
147 </param>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
148 <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
149 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
150 <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
151 <option value="single">Single-end</option>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
152 </param>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
153 </when>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
154 </conditional>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
155 </inputs>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
156
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
157 <outputs>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
158 <!-- List output -->
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
159 <data name="output_list" format="txt"
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
160 label="SRA S3 listing: ${source.prefix}">
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
161 <filter>action['mode'] == 'list'</filter>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
162 </data>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
163
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
164 <!-- Raw download -->
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
165 <data name="output_data" format="auto"
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
166 label="SRA download: ${action.s3_key}">
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
167 <filter>action['mode'] == 'copy'</filter>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
168 </data>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
169
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
170 <!-- FASTQ R1 / single.
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
171 Label matches fasterq-dump's native _1 suffix so Galaxy's
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
172 "Build List of Dataset Pairs" can auto-detect pairings. -->
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
173 <data name="output_r1" format="fastqsanger.gz"
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
174 label="${action.accession}_1">
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
175 <filter>action['mode'] == 'fastq_dump'</filter>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
176 </data>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
177
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
178 <!-- FASTQ R2 (paired-end only) -->
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
179 <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
180 label="${action.accession}_2">
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
181 <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
182 </data>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
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183 </outputs>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
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184
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
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185 <tests>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
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186 <!-- Test 1: list mode -->
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
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187 <test expect_num_outputs="1">
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
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diff changeset
188 <section name="source">
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
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189 <param name="bucket" value="sra_pub_run_odp"/>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
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190 <param name="prefix" value="sra/SRR000001"/>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
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191 </section>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
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diff changeset
192 <conditional name="action">
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
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193 <param name="mode" value="list"/>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
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194 <param name="recursive" value="false"/>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
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195 </conditional>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
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196 <output name="output_list">
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
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197 <assert_contents>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
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198 <has_text text="SRR000001"/>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
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199 </assert_contents>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
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200 </output>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
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201 </test>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
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202
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
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203 <!-- Test 2: fastq_dump paired -->
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
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204 <test expect_num_outputs="2">
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
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205 <section name="source">
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
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206 <param name="bucket" value="sra_pub_run_odp"/>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
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207 </section>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
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208 <conditional name="action">
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
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209 <param name="mode" value="fastq_dump"/>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
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210 <param name="accession" value="SRR000001"/>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
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211 <param name="layout" value="paired"/>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
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212 </conditional>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
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213 <output name="output_r1">
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
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214 <assert_contents>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
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215 <has_text text="@SRR000001"/>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
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216 </assert_contents>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
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217 </output>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
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218 <output name="output_r2">
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
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219 <assert_contents>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
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220 <has_text text="@SRR000001"/>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
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221 </assert_contents>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
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222 </output>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
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223 </test>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
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224
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
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225 <!-- Test 3: fastq_dump single-end -->
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
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226 <test expect_num_outputs="1">
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
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227 <section name="source">
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
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228 <param name="bucket" value="sra_pub_run_odp"/>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
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229 </section>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
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230 <conditional name="action">
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
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231 <param name="mode" value="fastq_dump"/>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
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232 <param name="accession" value="SRR000001"/>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
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233 <param name="layout" value="single"/>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
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234 </conditional>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
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235 <output name="output_r1">
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
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236 <assert_contents>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
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237 <has_text text="@SRR000001"/>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
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238 </assert_contents>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
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239 </output>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
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240 </test>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
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241 </tests>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
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242
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
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243 <help><![CDATA[
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
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244 **NCBI SRA AWS Fetch**
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
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245
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
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246 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
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247 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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248
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
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249 -----
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
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250
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
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251 **Available Buckets**
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 +------------------------------+------------------------------------------------------------+
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
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254 | Bucket | Contents |
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
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255 +==============================+============================================================+
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
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256 | 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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257 | | Supports FASTQ conversion via this tool. |
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
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258 +------------------------------+------------------------------------------------------------+
2
83c923bd9da6 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit a95de952e58b29875b31e55f0ef06a83a18618fc
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259 | 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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260 +------------------------------+------------------------------------------------------------+
2
83c923bd9da6 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit a95de952e58b29875b31e55f0ef06a83a18618fc
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261 | 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
galaxytrakr
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262 +------------------------------+------------------------------------------------------------+
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
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263 | 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
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264 +------------------------------+------------------------------------------------------------+
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
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265
2
83c923bd9da6 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit a95de952e58b29875b31e55f0ef06a83a18618fc
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266
0
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
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267 -----
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
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268
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
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269 **Listing objects**
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
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270
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
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271 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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272 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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273
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
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274 -----
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
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275
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
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276 **Downloading raw files**
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
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277
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
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278 Select **Download raw file(s)** and provide the full S3 key, e.g.::
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279
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280 sra/SRR000001/SRR000001.sra
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281
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282 -----
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283
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284 **Download and convert to FASTQ**
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285
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286 Fetches a single SRA run from ``sra-pub-run-odp`` and converts it to gzip-compressed
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287 FASTQ using ``fasterq-dump``.
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288
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289 Outputs are labelled ``<accession>_1`` (R1 / forward) and ``<accession>_2`` (R2 / reverse)
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290 for paired-end runs, matching ``fasterq-dump``'s native ``--split-files`` naming.
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291 Single-end runs produce only ``<accession>_1``.
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292
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293 *Fetching multiple accessions and building a paired collection*
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294
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295 Run this tool **once per accession** — either manually or by using Galaxy's dataset
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296 collection mapping to fan out over a list of accession identifiers. Keeping one job per
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297 accession means a failed download does not affect the others.
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298
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299 Once all jobs are complete your history will contain datasets labelled::
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300
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301 SRR000001_1 SRR000001_2
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302 SRR000002_1 SRR000002_2
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303 ...
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304
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305 Use **Galaxy's "Build List of Dataset Pairs"** tool to assemble these into a
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306 ``list:paired`` collection. Galaxy will auto-detect the ``_1`` / ``_2`` suffixes
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307 and propose pairings — confirm and name the collection, then pass it directly to
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308 any downstream tool that accepts a paired collection (aligners, QC tools, etc.).
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309
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310 .. warning::
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311
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312 This tool cannot auto-detect read layout from the accession. Check the SRA record
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313 at https://www.ncbi.nlm.nih.gov/sra before running. Selecting the wrong layout will
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314 produce incorrect output.
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315
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316 -----
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317
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318 **Notes**
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319
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320 - All S3 requests are made without AWS credentials (``--no-sign-request``).
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321 - There is typically a **1–2 day lag** between an accession appearing in SRA Search and
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322 being available in the S3 buckets.
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323 - Controlled-access dbGaP data (``sra-ca-run-odp``) requires AWS credentials and is
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324 **not** supported by this tool.
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325 - ``fasterq-dump`` and ``pigz`` both use ``\${GALAXY_SLOTS}`` threads. Allocate more
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326 cores in your job configuration to speed up conversion of large runs.
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327
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328 .. _NCBI Sequence Read Archive (SRA): https://www.ncbi.nlm.nih.gov/sra
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329 ]]></help>
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330
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331 <citations>
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332 <citation type="bibtex">
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333 @misc{ncbi_sra_aws,
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334 title = {{NCBI} {SRA} on {AWS} Open Data},
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335 author = {{National Center for Biotechnology Information}},
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336 howpublished = {\url{https://registry.opendata.aws/ncbi-sra/}},
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337 note = {Accessed via AWS S3 without credentials}
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338 }
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339 </citation>
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340 <citation type="bibtex">
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341 @article{sra_toolkit,
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342 title = {The {NCBI} {SRA} and portable data in biology},
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343 author = {Leinonen, Rasko and Sugawara, Hideaki and Shumway, Martin and
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344 {International Nucleotide Sequence Database Collaboration}},
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345 journal = {Nucleic Acids Research},
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346 volume = {39},
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347 number = {suppl\_1},
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348 pages = {D19--D21},
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349 year = {2011},
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350 doi = {10.1093/nar/gkq1019}
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351 }
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352 </citation>
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353 </citations>
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354
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355 </tool>