Mercurial > repos > galaxytrakr > aws_sra

annotate aws_sra.xml @ 28:8e6c35583761 draft

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planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit 133ce5adcf21338376fb8a1fa0003d97ffc8cbbb
author galaxytrakr
date Tue, 24 Mar 2026 01:35:38 +0000
parents 4f6a7017cbbb
children 569a598c7e68
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1 <tool id="aws_sra" name="NCBI SRA AWS Fetch" version="0.4.0+gt_0.7" profile="23.0">
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2 <description>Fetches one or more SRA runs from AWS S3 and converts them to FASTQ</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>fasterq-dump --version</version_command>
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12 <command detect_errors="aggressive"><![CDATA[
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13 ## Create a clean list of accessions from the user input
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14 echo "$accession" | sed 's/,/\n/g; s/ \+/\n/g' | grep . > accessions.txt &&
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16 ## Loop over each clean accession
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17 for acc in $(cat accessions.txt);
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18 do
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19 echo "Processing accession: $acc" &&
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21 ## 1. Create unique directories for this accession
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22 mkdir -p sra_cache_${acc} fastq_out_${acc} &&
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24 ## 2. Download the file from S3 using aws s3 cp
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25 aws s3 cp --no-sign-request "s3://sra-pub-run-odp/sra/${acc}/${acc}" ./sra_cache_${acc}/ &&
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27 ## 3. Convert with fasterq-dump
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28 fasterq-dump --outdir ./fastq_out_${acc} --temp . --threads \${GALAXY_SLOTS:-4} --split-files ./sra_cache_${acc}/${acc} &&
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30 ## 4. Compress with pigz
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31 pigz -p \${GALAXY_SLOTS:-4} ./fastq_out_${acc}/*.fastq &&
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33 ## 5. Move outputs for collection discovery
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34 #if str($layout) == 'paired'
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35 mv ./fastq_out_${acc}/${acc}_1.fastq.gz '$output_r1.files_path/${acc}_1.fastq.gz' &&
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36 mv ./fastq_out_${acc}/${acc}_2.fastq.gz '$output_r2.files_path/${acc}_2.fastq.gz'
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37 #else
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38 mv ./fastq_out_${acc}/${acc}.fastq.gz '$output_r1.files_path/${acc}.fastq.gz'
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39 #end if &&
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41 ## 6. Clean up
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42 rm -rf sra_cache_${acc} fastq_out_${acc}
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43 done
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44 ]]></command>
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46 <inputs>
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47 <param name="accession" type="text" label="SRA Accession(s)" value="" optional="false" help="Provide one or more accession numbers (separated by commas, spaces, or newlines)."/>
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48 <param name="layout" type="select" label="Read layout" optional="false" help="This setting is applied to all accessions.">
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49 <option value="paired" selected="true">Paired-end (R1 + R2)</option>
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50 <option value="single">Single-end</option>
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51 </param>
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52 </inputs>
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54 <outputs>
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55 <collection name="output_r1" type="list" label="FASTQ Reads (R1) for ${accession}">
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56 <discover_datasets pattern="(?P&lt;designation&gt;.+)_1\.fastq\.gz" format="fastqsanger.gz" />
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57 </collection>
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58 <collection name="output_r2" type="list" label="FASTQ Reads (R2) for ${accession}">
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59 <discover_datasets pattern="(?P&lt;designation&gt;.+)_2\.fastq\.gz" format="fastqsanger.gz" />
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60 <filter>layout == 'paired'</filter>
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61 </collection>
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62 </outputs>
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63
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64 <tests>
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65 <test expect_num_outputs="2">
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66 <param name="accession" value="SRR13333333"/>
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67 <param name="layout" value="paired"/>
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68 <output_collection name="output_r1" type="list" count="1">
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69 <element name="SRR13333333_1" ftype="fastqsanger.gz">
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70 <assert_contents>
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71 <has_text text="@SRR13333333"/>
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72 </assert_contents>
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73 </element>
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74 </output_collection>
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75 <output_collection name="output_r2" type="list" count="1">
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76 <element name="SRR13333333_2" ftype="fastqsanger.gz">
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77 <assert_contents>
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78 <has_text text="@SRR13333333"/>
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79 </assert_contents>
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80 </element>
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81 </output_collection>
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82 </test>
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83 </tests>
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84
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85 <help><![CDATA[
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86 **NCBI SRA AWS Fetch**
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87
23
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88 Fetches one or more SRA runs from the public `sra-pub-run-odp` S3 bucket and converts them to gzip-compressed FASTQ using `fasterq-dump`. This tool uses `aws s3 cp` for direct downloads within the AWS environment.
0
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89 ]]></help>
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90
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91 <citations>
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92 <citation type="bibtex">
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93 @misc{ncbi_sra_aws,
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94 title = {{NCBI} {SRA} on {AWS} Open Data},
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95 author = {{National Center for Biotechnology Information}},
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96 howpublished = {\\url{https://registry.opendata.aws/ncbi-sra/}},
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97 note = {Accessed via AWS S3 without credentials}
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98 }
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99 </citation>
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100 <citation type="bibtex">
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101 @article{sra_toolkit,
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102 title = {The {NCBI} {SRA} and portable data in biology},
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103 author = {Leinonen, Rasko and Sugawara, Hideaki and Shumway, Martin and
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104 {International Nucleotide Sequence Database Collaboration}},
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105 journal = {Nucleic Acids Research},
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106 volume = {39},
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107 number = {suppl\\\_1},
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108 pages = {D19--D21},
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109 year = {2011},
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110 doi = {10.1093/nar/gkq1019}
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111 }
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112 </citation>
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113 </citations>
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114 </tool>