Mercurial > repos > galaxytrakr > aws_sra

annotate aws_sra.xml @ 6:8c60cd4c0ca7 draft

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planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit 69bae7a0b8011217f6c61fbc62344bcd6a445160
author galaxytrakr
date Mon, 23 Mar 2026 18:17:47 +0000
parents 313a1e088e09
children 3529ce6bcde7
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8c60cd4c0ca7 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit 69bae7a0b8011217f6c61fbc62344bcd6a445160
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1 <tool id="aws_sra" name="NCBI SRA AWS Fetch" version="0.3.0+gt_0.6" 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>
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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a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
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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'
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
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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
8c60cd4c0ca7 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit 69bae7a0b8011217f6c61fbc62344bcd6a445160
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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
8c60cd4c0ca7 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit 69bae7a0b8011217f6c61fbc62344bcd6a445160
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30 aws s3 ls \
8c60cd4c0ca7 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit 69bae7a0b8011217f6c61fbc62344bcd6a445160
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31 --no-sign-request \
0
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
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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 = $action.accession.strip()
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51
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52 ## 1. Download the .sra file from S3
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53 mkdir -p sra_cache &&
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54 aws s3 cp
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55 --no-sign-request
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56 '${s3_base}/sra/${acc}/${acc}.sra'
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57 ./sra_cache/${acc}.sra &&
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58
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59 ## 2. Convert with fasterq-dump --split-files.
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60 ## Paired runs → <acc>_1.fastq + <acc>_2.fastq
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61 ## Single runs → <acc>.fastq (no _1/_2 suffix)
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62 ## We always use --split-files; single-end runs simply produce one file.
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63 mkdir -p fastq_out &&
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64 fasterq-dump
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65 ./sra_cache/${acc}.sra
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66 --outdir ./fastq_out
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67 --temp .
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68 --threads \${GALAXY_SLOTS:-4}
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69 --split-files
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70 &&
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71
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72 ## 3. Compress with pigz (fasterq-dump does not gzip natively)
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73 pigz -p \${GALAXY_SLOTS:-4} ./fastq_out/*.fastq &&
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74
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75 ## 4. Stage outputs
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76 #if $action.layout == 'paired'
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77 cp ./fastq_out/${acc}_1.fastq.gz '$output_r1' &&
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
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78 cp ./fastq_out/${acc}_2.fastq.gz '$output_r2'
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79 #else
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80 cp ./fastq_out/${acc}.fastq.gz '$output_r1'
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81 #end if
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82 #end if
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83 ]]></command>
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84
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85 <inputs>
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86 <section name="source" title="Data Source" expanded="true">
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87 <param name="bucket" type="select" label="SRA S3 Bucket"
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
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88 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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89 <option value="sra_pub_run_odp" selected="true">
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
90 sra-pub-run-odp — Open-access SRA runs (.sra format)
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
91 </option>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
92 <option value="sra_pub_src_1">
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
93 sra-pub-src-1 — Source submissions: BAM/CRAM/FASTQ (PacBio, ONT, 10X) [bucket 1]
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
94 </option>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
95 <option value="sra_pub_src_2">
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
96 sra-pub-src-2 — Source submissions: BAM/CRAM/FASTQ (PacBio, ONT, 10X) [bucket 2]
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
97 </option>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
98 <option value="sra_pub_metadata">
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
99 sra-pub-metadata-us-east-1 — SRA metadata (Parquet/CSV for Athena/Glue)
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
100 </option>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
101 </param>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
102 <param name="prefix" type="text" value="" optional="true"
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
103 label="S3 key prefix (optional)"
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
104 help="Restrict listing to a sub-path, e.g. 'sra/SRR000001'. Used only in List mode.">
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
105 <sanitizer invalid_char="">
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
106 <valid initial="string.printable">
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
107 <remove value="'"/>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
108 <remove value='"'/>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
109 </valid>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
110 </sanitizer>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
111 </param>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
112 </section>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
113
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
114 <conditional name="action">
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
115 <param name="mode" type="select" label="Action">
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
116 <option value="list" selected="true">List objects</option>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
117 <option value="copy">Download raw file(s)</option>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
118 <option value="fastq_dump">Download and convert to FASTQ (sra-pub-run-odp only)</option>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
119 </param>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
120
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
121 <!-- ── LIST ── -->
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
122 <when value="list">
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
123 <param name="recursive" type="boolean" truevalue="--recursive" falsevalue=""
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
124 checked="false" label="List recursively"
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
125 help="List all objects under the prefix, not just the immediate level."/>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
126 </when>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
127
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
128 <!-- ── COPY ── -->
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
129 <when value="copy">
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
130 <param name="s3_key" type="text" label="S3 key to download"
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
131 help="Full key of the object to download, e.g. 'sra/SRR000001/SRR000001.sra'.">
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
132 <validator type="empty_field" message="An S3 key is required for download."/>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
133 <sanitizer invalid_char="">
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
134 <valid initial="string.printable">
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
135 <remove value="'"/>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
136 <remove value='"'/>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
137 </valid>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
138 </sanitizer>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
139 </param>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
140 <param name="recursive" type="boolean" truevalue="--recursive" falsevalue=""
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
141 checked="false" label="Download recursively"
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
142 help="Download all objects with this prefix rather than a single object."/>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
143 </when>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
144
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
145 <!-- ── FASTQ DUMP ── -->
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
146 <when value="fastq_dump">
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
147 <param name="accession" type="text" label="SRA Accession"
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
148 help="SRA run accession to fetch and convert, e.g. SRR000001. Must be present in sra-pub-run-odp.">
2
83c923bd9da6 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit a95de952e58b29875b31e55f0ef06a83a18618fc
galaxytrakr
parents: 1
diff changeset
149 <validator type="empty_field" message="An SRA accession is required."/>
83c923bd9da6 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit a95de952e58b29875b31e55f0ef06a83a18618fc
galaxytrakr
parents: 1
diff changeset
150 <validator type="regex" message="Must be a valid SRA run accession (SRR, ERR, or DRR followed by digits).">^\[SED\]RR\[0-9\]+$</validator>
0
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
151 </param>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
152 <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
153 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
154 <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
155 <option value="single">Single-end</option>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
156 </param>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
157 </when>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
158 </conditional>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
159 </inputs>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
160
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
161 <outputs>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
162 <!-- List output -->
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
163 <data name="output_list" format="txt"
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
164 label="SRA S3 listing: ${source.prefix}">
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
165 <filter>action['mode'] == 'list'</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
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
168 <!-- Raw download -->
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
169 <data name="output_data" format="auto"
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
170 label="SRA download: ${action.s3_key}">
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
171 <filter>action['mode'] == 'copy'</filter>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
172 </data>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
173
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
174 <!-- FASTQ R1 / single.
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
175 Label matches fasterq-dump's native _1 suffix so Galaxy's
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
176 "Build List of Dataset Pairs" can auto-detect pairings. -->
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
177 <data name="output_r1" format="fastqsanger.gz"
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
178 label="${action.accession}_1">
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
parents:
diff changeset
179 <filter>action['mode'] == 'fastq_dump'</filter>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
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diff changeset
180 </data>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
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181
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182 <!-- FASTQ R2 (paired-end only) -->
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
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183 <data name="output_r2" format="fastqsanger.gz"
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
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184 label="${action.accession}_2">
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
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185 <filter>action['mode'] == 'fastq_dump' and action['layout'] == 'paired'</filter>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
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186 </data>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
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187 </outputs>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
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188
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
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189 <tests>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
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190 <!-- Test 1: list mode -->
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
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191 <test expect_num_outputs="1">
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
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192 <section name="source">
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
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193 <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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194 <param name="prefix" value="sra/SRR000001"/>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
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195 </section>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
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196 <conditional name="action">
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
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197 <param name="mode" value="list"/>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
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198 <param name="recursive" value="false"/>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
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199 </conditional>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
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200 <output name="output_list">
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
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201 <assert_contents>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
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202 <has_text text="SRR000001"/>
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 </output>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
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205 </test>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
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206
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
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207 <!-- Test 2: fastq_dump paired -->
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
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208 <test expect_num_outputs="2">
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
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209 <section name="source">
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
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210 <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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211 </section>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
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212 <conditional name="action">
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
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213 <param name="mode" value="fastq_dump"/>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
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214 <param name="accession" value="SRR000001"/>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
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215 <param name="layout" value="paired"/>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
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216 </conditional>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
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217 <output name="output_r1">
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
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218 <assert_contents>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
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219 <has_text text="@SRR000001"/>
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 </output>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
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222 <output name="output_r2">
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
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223 <assert_contents>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
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224 <has_text text="@SRR000001"/>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
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225 </assert_contents>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
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226 </output>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
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227 </test>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
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228
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
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229 <!-- Test 3: fastq_dump single-end -->
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
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230 <test expect_num_outputs="1">
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
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231 <section name="source">
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
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232 <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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233 </section>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
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234 <conditional name="action">
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
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235 <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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236 <param name="accession" value="SRR000001"/>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
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237 <param name="layout" value="single"/>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
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238 </conditional>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
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239 <output name="output_r1">
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
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240 <assert_contents>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
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241 <has_text text="@SRR000001"/>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
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242 </assert_contents>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
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243 </output>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
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244 </test>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
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245 </tests>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
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246
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
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247 <help><![CDATA[
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
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248 **NCBI SRA AWS Fetch**
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
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249
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
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250 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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251 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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252
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
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253 -----
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
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254
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
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255 **Available Buckets**
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
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256
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
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257 +------------------------------+------------------------------------------------------------+
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
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258 | Bucket | Contents |
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
galaxytrakr
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260 | 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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261 | | Supports FASTQ conversion via this tool. |
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
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262 +------------------------------+------------------------------------------------------------+
2
83c923bd9da6 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit a95de952e58b29875b31e55f0ef06a83a18618fc
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263 | 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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264 +------------------------------+------------------------------------------------------------+
2
83c923bd9da6 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit a95de952e58b29875b31e55f0ef06a83a18618fc
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265 | 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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266 +------------------------------+------------------------------------------------------------+
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
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267 | 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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268 +------------------------------+------------------------------------------------------------+
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
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269
2
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270
0
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galaxytrakr
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271 -----
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 **Listing objects**
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 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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276 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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277
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278 -----
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279
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280 **Downloading raw files**
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281
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282 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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283
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284 sra/SRR000001/SRR000001.sra
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285
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286 -----
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287
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288 **Download and convert to FASTQ**
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289
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galaxytrakr
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290 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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291 FASTQ using ``fasterq-dump``.
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292
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293 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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294 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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295 Single-end runs produce only ``<accession>_1``.
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296
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297 *Fetching multiple accessions and building a paired collection*
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298
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299 Run this tool **once per accession** — either manually or by using Galaxy's dataset
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300 collection mapping to fan out over a list of accession identifiers. Keeping one job per
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
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301 accession means a failed download does not affect the others.
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302
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303 Once all jobs are complete your history will contain datasets labelled::
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
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304
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305 SRR000001_1 SRR000001_2
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
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306 SRR000002_1 SRR000002_2
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307 ...
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
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308
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309 Use **Galaxy's "Build List of Dataset Pairs"** tool to assemble these into a
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
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310 ``list:paired`` collection. Galaxy will auto-detect the ``_1`` / ``_2`` suffixes
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
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311 and propose pairings — confirm and name the collection, then pass it directly to
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312 any downstream tool that accepts a paired collection (aligners, QC tools, etc.).
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313
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314 .. warning::
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315
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316 This tool cannot auto-detect read layout from the accession. Check the SRA record
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
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317 at https://www.ncbi.nlm.nih.gov/sra before running. Selecting the wrong layout will
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
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318 produce incorrect output.
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319
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320 -----
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321
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322 **Notes**
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
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323
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324 - All S3 requests are made without AWS credentials (``--no-sign-request``).
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325 - There is typically a **1–2 day lag** between an accession appearing in SRA Search and
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
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326 being available in the S3 buckets.
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327 - Controlled-access dbGaP data (``sra-ca-run-odp``) requires AWS credentials and is
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
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328 **not** supported by this tool.
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
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329 - ``fasterq-dump`` and ``pigz`` both use ``\${GALAXY_SLOTS}`` threads. Allocate more
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
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330 cores in your job configuration to speed up conversion of large runs.
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331
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332 .. _NCBI Sequence Read Archive (SRA): https://www.ncbi.nlm.nih.gov/sra
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
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333 ]]></help>
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334
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335 <citations>
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336 <citation type="bibtex">
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337 @misc{ncbi_sra_aws,
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338 title = {{NCBI} {SRA} on {AWS} Open Data},
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339 author = {{National Center for Biotechnology Information}},
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340 howpublished = {\url{https://registry.opendata.aws/ncbi-sra/}},
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
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341 note = {Accessed via AWS S3 without credentials}
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342 }
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
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343 </citation>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
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344 <citation type="bibtex">
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345 @article{sra_toolkit,
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
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346 title = {The {NCBI} {SRA} and portable data in biology},
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
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347 author = {Leinonen, Rasko and Sugawara, Hideaki and Shumway, Martin and
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
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348 {International Nucleotide Sequence Database Collaboration}},
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galaxytrakr
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349 journal = {Nucleic Acids Research},
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
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350 volume = {39},
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
galaxytrakr
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351 number = {suppl\_1},
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galaxytrakr
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352 pages = {D19--D21},
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
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353 year = {2011},
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
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354 doi = {10.1093/nar/gkq1019}
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355 }
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
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356 </citation>
a4afe551dfc9 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit c55c06b92c0ee0429047bcff1992bf2ec293284a
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357 </citations>
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358
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359 </tool>