Mercurial > repos > galaxytrakr > aws_sra

annotate aws_sra.xml @ 30:73ee30eb273a draft

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planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit d0c08749588099d40db3c23bfd554800ac307a30
author galaxytrakr
date Tue, 24 Mar 2026 03:09:41 +0000
parents 569a598c7e68
children 90ae4d437133
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73ee30eb273a planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit d0c08749588099d40db3c23bfd554800ac307a30
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1 <tool id="aws_sra" name="NCBI SRA AWS Fetch" version="0.4.0+gt_0.50" profile="22.01">
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d7f68b3cde39 planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit e9adf514c1b6b341c9e5bf8cc5a41c79b738d48e
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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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3
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4 <requirements>
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5 <requirement type="package" version="3.1.1">sra-tools</requirement>
73ee30eb273a planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit d0c08749588099d40db3c23bfd554800ac307a30
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6 <requirement type="package" version="2.8">pigz</requirement>
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7 <requirement type="package" version="2.34.8">awscli</requirement>
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8 </requirements>
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9
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10 <version_command>fasterq-dump --version</version_command>
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11
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73ee30eb273a planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit d0c08749588099d40db3c23bfd554800ac307a30
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12 <command detect_errors="exit_code"><![CDATA[
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13 #if $input.input_select == "accession_number":
73ee30eb273a planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit d0c08749588099d40db3c23bfd554800ac307a30
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14 echo '${input.accession}' | sed -r 's/(\,|\;|__cn__)/\n/g' > accessions &&
73ee30eb273a planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit d0c08749588099d40db3c23bfd554800ac307a30
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15 #else:
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16 grep '^[[:space:]]*[ESD]RR[0-9]\{1,\}[[:space:]]*$' '${input.file_list}' > accessions &&
73ee30eb273a planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit d0c08749588099d40db3c23bfd554800ac307a30
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17 #end if
73ee30eb273a planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit d0c08749588099d40db3c23bfd554800ac307a30
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18 mkdir -p output &&
73ee30eb273a planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit d0c08749588099d40db3c23bfd554800ac307a30
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19 mkdir -p outputOther &&
73ee30eb273a planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit d0c08749588099d40db3c23bfd554800ac307a30
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20 for acc in \$(cat ./accessions);
73ee30eb273a planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit d0c08749588099d40db3c23bfd554800ac307a30
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21 do (
73ee30eb273a planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit d0c08749588099d40db3c23bfd554800ac307a30
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22 echo "Processing accession: \$acc" &&
73ee30eb273a planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit d0c08749588099d40db3c23bfd554800ac307a30
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23 mkdir -p sra_cache_\${acc} &&
73ee30eb273a planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit d0c08749588099d40db3c23bfd554800ac307a30
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24 aws s3 cp --no-sign-request "s3://sra-pub-run-odp/sra/\${acc}/\${acc}" ./sra_cache_\${acc}/\${acc} &&
73ee30eb273a planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit d0c08749588099d40db3c23bfd554800ac307a30
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25 fasterq-dump -e \${GALAXY_SLOTS:-4} -t . --split-3 ./sra_cache_\${acc}/\${acc} &&
73ee30eb273a planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit d0c08749588099d40db3c23bfd554800ac307a30
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26 rm -rf sra_cache_\${acc} &&
73ee30eb273a planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit d0c08749588099d40db3c23bfd554800ac307a30
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27 count="\$(ls \${acc}*.fastq 2>/dev/null | wc -l)" &&
73ee30eb273a planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit d0c08749588099d40db3c23bfd554800ac307a30
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28 echo "Found \$count fastq file(s) for \$acc" &&
73ee30eb273a planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit d0c08749588099d40db3c23bfd554800ac307a30
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29 data=(\$(ls \${acc}*.fastq 2>/dev/null)) &&
73ee30eb273a planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit d0c08749588099d40db3c23bfd554800ac307a30
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30 if [ "\$count" -eq 1 ]; then
73ee30eb273a planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit d0c08749588099d40db3c23bfd554800ac307a30
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31 pigz -cqp \${GALAXY_SLOTS:-4} "\${data[0]}" > output/"\${acc}".fastqsanger.gz &&
73ee30eb273a planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit d0c08749588099d40db3c23bfd554800ac307a30
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32 rm "\${data[0]}";
73ee30eb273a planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit d0c08749588099d40db3c23bfd554800ac307a30
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33 elif [ -e "\${acc}".fastq ]; then
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34 pigz -cqp \${GALAXY_SLOTS:-4} "\${acc}".fastq > outputOther/"\${acc}"__single.fastqsanger.gz &&
73ee30eb273a planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit d0c08749588099d40db3c23bfd554800ac307a30
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35 pigz -cqp \${GALAXY_SLOTS:-4} "\${acc}"_1.fastq > output/"\${acc}"_1.fastqsanger.gz &&
73ee30eb273a planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit d0c08749588099d40db3c23bfd554800ac307a30
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36 pigz -cqp \${GALAXY_SLOTS:-4} "\${acc}"_2.fastq > output/"\${acc}"_2.fastqsanger.gz &&
73ee30eb273a planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit d0c08749588099d40db3c23bfd554800ac307a30
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37 rm "\${acc}"*.fastq;
73ee30eb273a planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit d0c08749588099d40db3c23bfd554800ac307a30
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38 elif [ "\$count" -eq 2 ]; then
73ee30eb273a planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit d0c08749588099d40db3c23bfd554800ac307a30
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39 pigz -cqp \${GALAXY_SLOTS:-4} "\${acc}"_1.fastq > output/"\${acc}"_1.fastqsanger.gz &&
73ee30eb273a planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit d0c08749588099d40db3c23bfd554800ac307a30
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40 pigz -cqp \${GALAXY_SLOTS:-4} "\${acc}"_2.fastq > output/"\${acc}"_2.fastqsanger.gz &&
73ee30eb273a planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit d0c08749588099d40db3c23bfd554800ac307a30
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41 rm "\${acc}"*.fastq;
73ee30eb273a planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit d0c08749588099d40db3c23bfd554800ac307a30
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42 else
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43 for file in \${data[*]}; do
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44 pigz -cqp \${GALAXY_SLOTS:-4} "\$file" > outputOther/"\$file"sanger.gz &&
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45 rm "\$file";
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46 done;
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47 fi
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48 ); done;
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49 echo "Done with all accessions."
0
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50 ]]></command>
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51
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52 <inputs>
30
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53 <conditional name="input">
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54 <param name="input_select" type="select" label="Select input type">
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55 <option value="accession_number">SRA Accession number(s)</option>
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56 <option value="file_list">File containing accession list</option>
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57 </param>
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58 <when value="accession_number">
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59 <param name="accession" type="text" label="SRA Accession(s)"
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60 help="One or more SRA run accessions (SRR, ERR, or DRR), separated by commas or spaces.">
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61 <validator type="empty_field" message="At least one SRA accession is required."/>
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62 <sanitizer>
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63 <valid initial="string.printable">
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64 <remove value="&apos;"/>
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65 </valid>
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66 <mapping initial="none">
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67 <add source="&apos;" target="&apos;&quot;&apos;&quot;&apos;"/>
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68 </mapping>
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69 </sanitizer>
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70 </param>
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71 </when>
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72 <when value="file_list">
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73 <param name="file_list" type="data" format="txt,tabular" label="Accession list file"
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74 help="A text file with one SRA accession (SRR, ERR, or DRR) per line."/>
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75 </when>
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76 </conditional>
0
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77 </inputs>
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78
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79 <outputs>
30
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80 <collection name="list_paired" type="list:paired" label="Paired-end FASTQ (aws_sra)">
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81 <discover_datasets
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82 pattern="(?P&lt;identifier_0&gt;[^_]+)_(?P&lt;identifier_1&gt;[12])\.fastqsanger\.gz"
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83 directory="output"
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84 ext="fastqsanger.gz"/>
23
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85 </collection>
30
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86 <collection name="output_single" type="list" label="Single-end FASTQ (aws_sra)">
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87 <discover_datasets
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88 pattern="(?P&lt;designation&gt;.+)\.fastqsanger\.gz"
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89 directory="output"
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90 ext="fastqsanger.gz"/>
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91 </collection>
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92 <collection name="output_other" type="list" label="Other FASTQ (aws_sra)">
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93 <discover_datasets
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94 pattern="(?P&lt;designation&gt;.+)\.fastqsanger\.gz"
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95 directory="outputOther"
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96 format="fastqsanger.gz"/>
23
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97 </collection>
21
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98 </outputs>
17
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99
21
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100 <tests>
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101 <test expect_num_outputs="3">
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102 <conditional name="input">
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103 <param name="input_select" value="accession_number"/>
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104 <param name="accession" value="SRR13333333"/>
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105 </conditional>
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106 <output_collection name="list_paired" type="list:paired" count="1">
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107 <element name="SRR13333333">
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108 <element name="forward" ftype="fastqsanger.gz">
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109 <assert_contents>
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110 <has_text text="@SRR13333333"/>
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111 </assert_contents>
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112 </element>
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113 <element name="reverse" ftype="fastqsanger.gz">
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114 <assert_contents>
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115 <has_text text="@SRR13333333"/>
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116 </assert_contents>
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117 </element>
24
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118 </element>
23
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119 </output_collection>
21
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120 </test>
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121
21
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122 </tests>
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123
0
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124 <help><![CDATA[
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125 **NCBI SRA AWS Fetch**
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126
30
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127 Fetches one or more SRA runs from the public ``sra-pub-run-odp`` S3 bucket and converts them to
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128 gzip-compressed FASTQ using ``fasterq-dump``. Downloads use ``aws s3 cp`` with no credentials
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129 required (public bucket).
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130
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131 **Inputs**
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132
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133 - **SRA Accession number(s)**: Type one or more accessions (SRR, ERR, or DRR) directly, comma- or space-separated.
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134 - **File containing accession list**: A text file with one accession per line. This option is connectable as a workflow input.
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135
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136 **Outputs**
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137
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138 Three collections are always created (some may be empty depending on the data):
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139
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140 - **Paired-end FASTQ**: A nested ``list:paired`` collection — each accession contains a forward/reverse pair.
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141 - **Single-end FASTQ**: A flat list for reads confirmed single-end by ``--split-3``.
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142 - **Other FASTQ**: Reads that could not be cleanly classified.
0
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143 ]]></help>
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144
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145 <citations>
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146 <citation type="bibtex">
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147 @misc{ncbi_sra_aws,
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148 title = {{NCBI} {SRA} on {AWS} Open Data},
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149 author = {{National Center for Biotechnology Information}},
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150 howpublished = {\url{https://registry.opendata.aws/ncbi-sra/}},
0
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151 note = {Accessed via AWS S3 without credentials}
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152 }
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153 </citation>
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154 <citation type="doi">10.1093/nar/gkq1019</citation>
0
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155 </citations>
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156 </tool>