Mercurial > repos > galaxytrakr > aws_sra

annotate aws_sra.xml @ 16:58cc45662c63 draft

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planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit 98b1c300d492ffb675d64e6c64484c681b277369
author galaxytrakr
date Mon, 23 Mar 2026 20:23:58 +0000
parents 25cf81d65cb8
children 9fb80e0392ce
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58cc45662c63 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit 98b1c300d492ffb675d64e6c64484c681b277369
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1 <tool id="aws_sra" name="NCBI SRA AWS Fetch" version="0.3.0+gt_0.16" profile="23.0">
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2 <description>Fetches SRA runs from AWS 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 ## This loop handles both 'single' and 'batch' modes.
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14 #for $acc_line in $run_type.mode == 'single' and str($run_type.accession).split() or $run_type.accession_list.lines:
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15 #set $acc = $acc_line.strip()
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16 #if $acc:
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18 echo "Processing accession: $acc" &&
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20 ## 1. Create unique directories for this accession
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21 mkdir -p sra_cache_${acc} fastq_out_${acc} &&
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23 ## 2. Download the file from S3 using the discovered path format
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24 aws s3 cp --no-sign-request 's3://sra-pub-run-odp/sra/${acc}/${acc}' ./sra_cache_${acc}/ &&
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26 ## 3. Convert with fasterq-dump, using the correct argument order
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27 fasterq-dump --outdir ./fastq_out_${acc} --temp . --threads \${GALAXY_SLOTS:-4} --split-files ./sra_cache_${acc}/${acc} &&
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29 ## 4. Compress with pigz
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30 pigz -p \${GALAXY_SLOTS:-4} ./fastq_out_${acc}/*.fastq &&
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32 ## 5. Move outputs to special directories Galaxy can discover
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33 #if $layout == 'paired'
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34 mv ./fastq_out_${acc}/${acc}_1.fastq.gz '$output_r1.files_path/${acc}_1.fastq.gz' &&
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35 mv ./fastq_out_${acc}/${acc}_2.fastq.gz '$output_r2.files_path/${acc}_2.fastq.gz'
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36 #else
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37 mv ./fastq_out_${acc}/*.fastq.gz '$output_r1.files_path/${acc}.fastq.gz'
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38 #end if &&
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40 ## 6. Clean up temporary files
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41 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 ]]></command>
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47 <inputs>
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48 <!-- This conditional allows the user to choose a single run or a list of runs -->
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49 <conditional name="run_type">
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50 <param name="mode" type="select" label="Execution Mode" help="Run on a single accession or a list of accessions from a file.">
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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" help="e.g., SRR13333333"/>
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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" help="A plain text file with one SRA accession per line."/>
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59 </when>
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60 </conditional>
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62 <!-- This layout parameter is always required -->
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63 <param name="layout" type="select" label="Read layout" help="Check the SRA record to confirm layout before running.">
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64 <option value="paired" selected="true">Paired-end (R1 + R2)</option>
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65 <option value="single">Single-end</option>
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66 </param>
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67 </inputs>
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69 <outputs>
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70 <!-- These collections will gather all the files produced by the loop -->
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71 <collection name="output_r1" type="list" label="${run_type.accession or 'FASTQ Reads (R1)'}">
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72 <discover_datasets pattern="(?P&lt;designation&gt;.+)_1\.fastq\.gz" format="fastqsanger.gz" />
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73 </collection>
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74 <collection name="output_r2" type="list" label="${run_type.accession or 'FASTQ Reads (R2)'}">
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75 <discover_datasets pattern="(?P&lt;designation&gt;.+)_2\.fastq\.gz" format="fastqsanger.gz" />
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76 <filter>layout == 'paired'</filter>
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77 </collection>
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78 </outputs>
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80 <tests>
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81 <test expect_num_outputs="2">
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82 <param name="mode" value="single"/>
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83 <param name="accession" value="SRR13333333"/>
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84 <param name="layout" value="paired"/>
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85 <output_collection name="output_r1" type="list" count="1">
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86 <element name="SRR13333333_1" ftype="fastqsanger.gz">
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87 <assert_contents>
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88 <has_text text="@SRR13333333"/>
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89 </assert_contents>
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90 </element>
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91 </output_collection>
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92 <output_collection name="output_r2" type="list" count="1">
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93 <element name="SRR13333333_2" ftype="fastqsanger.gz">
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94 <assert_contents>
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95 <has_text text="@SRR13333333"/>
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96 </assert_contents>
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97 </element>
13
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98 </output_collection>
0
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99 </test>
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100 </tests>
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101
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102 <help><![CDATA[
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103 **NCBI SRA AWS Fetch**
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104
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105 Fetches SRA runs from the public `sra-pub-run-odp` bucket on Amazon S3 and converts them to gzip-compressed FASTQ using `fasterq-dump`.
0
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106
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107 This tool can be run on a single SRA accession or a list of accessions provided as a text file (one per line).
0
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108
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109 Outputs are automatically organized into collections suitable for downstream analysis.
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110 ]]></help>
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111
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112 <citations>
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113 <citation type="bibtex">
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114 @misc{ncbi_sra_aws,
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115 title = {{NCBI} {SRA} on {AWS} Open Data},
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116 author = {{National Center for Biotechnology Information}},
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117 howpublished = {\\url{https://registry.opendata.aws/ncbi-sra/}},
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118 note = {Accessed via AWS S3 without credentials}
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119 }
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120 </citation>
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121 <citation type="bibtex">
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122 @article{sra_toolkit,
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123 title = {The {NCBI} {SRA} and portable data in biology},
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124 author = {Leinonen, Rasko and Sugawara, Hideaki and Shumway, Martin and
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125 {International Nucleotide Sequence Database Collaboration}},
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126 journal = {Nucleic Acids Research},
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127 volume = {39},
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128 number = {suppl\\\_1},
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129 pages = {D19--D21},
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130 year = {2011},
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131 doi = {10.1093/nar/gkq1019}
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132 }
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133 </citation>
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134 </citations>
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135 </tool>