Mercurial > repos > galaxytrakr > aws_sra

annotate aws_sra.xml @ 20:2b4efa539c71 draft

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planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit fd13e80a4e6b713b4b7a90ab45dd38ff0889cb3c
author galaxytrakr
date Mon, 23 Mar 2026 22:09:06 +0000
parents a4186132e1c4
children 02f45c03c306
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2b4efa539c71 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit fd13e80a4e6b713b4b7a90ab45dd38ff0889cb3c
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1 <tool id="aws_sra" name="NCBI SRA AWS Fetch" version="0.3.0+gt_0.20" profile="23.0">
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2 <description>Fetches SRA runs from AWS and converts them to FASTQ</description>
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3 <requirements>
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4 <requirement type="package" version="2.34.8">awscli</requirement>
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5 <requirement type="package" version="3.2.1">sra-tools</requirement>
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6 <requirement type="package" version="2.8">pigz</requirement>
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7 </requirements>
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8 <version_command>fasterq-dump --version</version_command>
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10 <command detect_errors="aggressive"><![CDATA[
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11 ## Single Run Mode
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12 #if $run_type.mode == 'single'
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13 #set $acc = str($run_type.accession).strip()
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14 echo "Processing single accession: $acc" &&
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15 mkdir -p sra_cache fastq_out &&
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16 aws s3 cp --no-sign-request 's3://sra-pub-run-odp/sra/${acc}/${acc}' ./sra_cache/ &&
9fb80e0392ce planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit 9707fa5e3ca6db5b58f271d133484d078cf65390
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17 fasterq-dump --outdir ./fastq_out --temp . --threads \${GALAXY_SLOTS:-4} --split-files ./sra_cache/${acc} &&
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18 pigz -p \${GALAXY_SLOTS:-4} ./fastq_out/*.fastq &&
9fb80e0392ce planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit 9707fa5e3ca6db5b58f271d133484d078cf65390
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19 #if str($layout) == 'paired'
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20 mv ./fastq_out/${acc}_1.fastq.gz '$output_r1_single' &&
9fb80e0392ce planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit 9707fa5e3ca6db5b58f271d133484d078cf65390
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21 mv ./fastq_out/${acc}_2.fastq.gz '$output_r2_single'
9fb80e0392ce planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit 9707fa5e3ca6db5b58f271d133484d078cf65390
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22 #else
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23 mv ./fastq_out/*.fastq.gz '$output_r1_single'
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24 #end if
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25
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26 ## Batch Run Mode
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27 #else
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28 #for $acc in $run_type.accession_list.lines:
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29 #set $acc = $acc.strip()
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30 #if $acc:
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31 echo "Processing batch accession: $acc" &&
9fb80e0392ce planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit 9707fa5e3ca6db5b58f271d133484d078cf65390
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32 mkdir -p sra_cache_${acc} fastq_out_${acc} &&
9fb80e0392ce planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit 9707fa5e3ca6db5b58f271d133484d078cf65390
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33 aws s3 cp --no-sign-request 's3://sra-pub-run-odp/sra/${acc}/${acc}' ./sra_cache_${acc}/ &&
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34 fasterq-dump --outdir ./fastq_out_${acc} --temp . --threads \${GALAXY_SLOTS:-4} --split-files ./sra_cache_${acc}/${acc} &&
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35 pigz -p \${GALAXY_SLOTS:-4} ./fastq_out_${acc}/*.fastq &&
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36 #if str($layout) == 'paired'
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37 mv ./fastq_out_${acc}/${acc}_1.fastq.gz '$output_r1_batch.files_path/${acc}_1.fastq.gz' &&
2b4efa539c71 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit fd13e80a4e6b713b4b7a90ab45dd38ff0889cb3c
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38 mv ./fastq_out_${acc}/${acc}_2.fastq.gz '$output_r2_batch.files_path/${acc}_2.fastq.gz'
2b4efa539c71 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit fd13e80a4e6b713b4b7a90ab45dd38ff0889cb3c
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39 #else
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40 mv ./fastq_out_${acc}/${acc}.fastq.gz '$output_r1_batch.files_path/${acc}.fastq.gz'
2b4efa539c71 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit fd13e80a4e6b713b4b7a90ab45dd38ff0889cb3c
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41 #end if &&
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42 rm -rf sra_cache_${acc} fastq_out_${acc}
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43 #end if
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44 # end for
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45 #end if
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46 ]]></command>
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48 <inputs>
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49 <conditional name="run_type">
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50 <param name="mode" type="select" label="Execution Mode">
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51 <option value="single" selected="true">Single Accession</option>
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52 <option value="batch">Batch of Accessions</option>
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53 </param>
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54 <when value="single">
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55 <param name="accession" type="text" label="SRA Accession"/>
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56 </when>
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57 <when value="batch">
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58 <param name="accession_list" type="data" format="txt" label="List of SRA Accessions"/>
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59 </when>
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60 </conditional>
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61 <param name="layout" type="select" label="Read layout">
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62 <option value="paired" selected="true">Paired-end (R1 + R2)</option>
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63 <option value="single">Single-end</option>
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64 </param>
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65 </inputs>
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67 <outputs>
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68 <!-- Outputs for Single Run Mode -->
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69 <data name="output_r1_single" format="fastqsanger.gz" label="${run_type.accession}_1.fastq.gz">
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70 <filter>run_type['mode'] == 'single'</filter>
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71 </data>
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72 <data name="output_r2_single" format="fastqsanger.gz" label="${run_type.accession}_2.fastq.gz">
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73 <filter>run_type['mode'] == 'single' and layout == 'paired'</filter>
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74 </data>
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75
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76 <!-- Outputs for Batch Mode -->
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77 <collection name="output_r1_batch" type="list" label="FASTQ Reads (R1)">
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78 <discover_datasets pattern="(?P&lt;designation&gt;.+)_1\.fastq\.gz" format="fastqsanger.gz" />
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79 <filter>run_type['mode'] == 'batch'</filter>
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80 </collection>
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81 <collection name="output_r2_batch" type="list" label="FASTQ Reads (R2)">
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82 <discover_datasets pattern="(?P&lt;designation&gt;.+)_2\.fastq\.gz" format="fastqsanger.gz" />
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83 <filter>run_type['mode'] == 'batch' and layout == 'paired'</filter>
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84 </collection>
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85 </outputs>
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86
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87 <help><![CDATA[
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88 **NCBI SRA AWS Fetch**
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89
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90 Fetches SRA runs from the public `sra-pub-run-odp` bucket on Amazon S3 and converts them to gzip-compressed FASTQ using `fasterq-dump`.
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91
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92 This tool can be run on a single SRA accession or a list of accessions provided as a text file (one per line).
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93
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94 Outputs are automatically organized into collections suitable for downstream analysis.
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95 ]]></help>
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96
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97 <citations>
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98 <citation type="bibtex">
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99 @misc{ncbi_sra_aws,
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100 title = {{NCBI} {SRA} on {AWS} Open Data},
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101 author = {{National Center for Biotechnology Information}},
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102 howpublished = {\\url{https://registry.opendata.aws/ncbi-sra/}},
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103 note = {Accessed via AWS S3 without credentials}
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104 }
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105 </citation>
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106 <citation type="bibtex">
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107 @article{sra_toolkit,
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108 title = {The {NCBI} {SRA} and portable data in biology},
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109 author = {Leinonen, Rasko and Sugawara, Hideaki and Shumway, Martin and
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110 {International Nucleotide Sequence Database Collaboration}},
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111 journal = {Nucleic Acids Research},
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112 volume = {39},
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113 number = {suppl\\\_1},
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114 pages = {D19--D21},
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115 year = {2011},
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116 doi = {10.1093/nar/gkq1019}
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117 }
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118 </citation>
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119 </citations>
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120 </tool>