Mercurial > repos > iuc > sra_tools

annotate fastq_dump.xml @ 21:494b2ec08162 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 1e2492fa4557ddc6ffefc16b249ed9ef0207d5e1"
author iuc
date Mon, 06 Jul 2020 19:46:26 -0400
parents 964579f93c54
children 751a694ec620
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21
494b2ec08162 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 1e2492fa4557ddc6ffefc16b249ed9ef0207d5e1"
iuc
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1 <tool id="fastq_dump" name="Download and Extract Reads in FASTA/Q" version="@VERSION@+galaxy1" profile="18.01">
7
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2 <description>format from NCBI SRA</description>
0
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3 <macros>
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4 <import>sra_macros.xml</import>
b723c120161a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
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5 </macros>
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6 <expand macro="requirements"/>
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7 <version_command>fastq-dump --version</version_command>
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8 <command detect_errors="exit_code"><![CDATA[
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9 @COPY_CONFIGFILE@
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10 @SET_ACCESSIONS@
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11
0
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12 #if $input.input_select == "file":
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13 fastq-dump --log-level fatal --accession '${input.file.name}'
b723c120161a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
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14 #else:
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15 ## Do not use prefetch if region is specified, to avoid downloading
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16 ## the complete sra file.
b723c120161a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
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17 #if ( str( $adv.region ) == "" ) and ( str( $adv.minID ) == "" ) and ( str( $adv.maxID ) == "" ):
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aad3885b3216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 2be63abd7e4db27fa32ecbbc10d48cacb0073115"
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18 prefetch -X 200000000 "\$acc" &&
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19 #end if
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20 fastq-dump --accession "\$acc"
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21 --split-files
0
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22 #end if
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23 --defline-seq '@\$sn[_\$rn]/\$ri'
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24 --defline-qual '+'
1
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25
0
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26 $adv.split
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27 #if str( $adv.alignments ) == "aligned":
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28 --aligned
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29 #end if
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30 #if str( $adv.alignments ) == "unaligned":
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31 --unaligned
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32 #end if
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33 #if str( $adv.minID ) != "":
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34 --minSpotId "$adv.minID"
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35 #end if
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36 #if str( $adv.maxID ) != "":
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37 --maxSpotId "$adv.maxID"
b723c120161a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
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38 #end if
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39 #if str( $adv.minlen ) != "":
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40 --minReadLen "$adv.minlen"
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41 #end if
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42 #if str( $adv.readfilter ) != "":
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43 --read-filter "$adv.readfilter"
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44 #end if
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45 #if str( $adv.region ) != "":
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46 --aligned-region "$adv.region"
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47 #end if
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48 #if str( $adv.spotgroups ) != "":
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49 --spot-groups "$adv.spotgroups"
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50 #end if
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51 #if str( $adv.matepairDist ) != "":
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52 --matepair-distance "$adv.matepairDist"
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53 #end if
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54 $adv.clip
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55 $adv.skip_technical
2
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56
7
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57 #if str( $outputformat ) == "fastqsanger.gz":
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58 --gzip
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59 #elif str( $outputformat ) == "fastqsanger.bz2":
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60 --bzip2
0
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61 #end if
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62
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
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63 #if str($adv.table) != "":
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
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64 --table $adv.table
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
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65 #end if
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66
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
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67
0
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68 #if $input.input_select=="file":
1
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69 --stdout
0
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70 "$input.file" > "$output_file"
7
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71
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72 #elif $input.input_select=="accession_number":
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73 --stdout
1
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74 "\$acc" > "$output_accession" )
0
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75 #end if
1
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76
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77 #if $input.input_select=="file_list":
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78 "\$acc"
7
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79 ) ; done
1
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80
7
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81 ;
1
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82
7
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83 for i in `ls *.fast* | cut -f 1 -d '_' | uniq` ; do
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84 count=`ls \$i* | wc -l` ;
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85 data=(\$(ls -d \$i*));
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86
7
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87 if [ "\$count" -eq 2 ]; then
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88 mv "\${data[0]}" "\${data[0]}"_forward.$outputformat; mv "\${data[1]}" "\${data[1]}"_reverse.$outputformat ;
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89 elif [ "\$count" -eq 1 ]; then
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90 mv "\${data[0]}" "\${data[0]}"__single.$outputformat ;
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91 fi;
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92 done
1
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93
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94
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95 #end if
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96
2
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97
0
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98 ]]>
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99 </command>
18
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100 <expand macro="configfile_hack"/>
0
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101 <inputs>
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102 <expand macro="input_conditional"/>
7
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103 <param name="outputformat" type="select" display="radio" label="Select output format" help="Compression will greatly reduce the amount of space occupied by downloaded data. Downstream applications such as a short-read mappers will accept compressed data as input. Consider this example: an uncoimpressed 400 Mb fastq datasets compresses to 100 Mb or 80 Mb by gzip or bzip2, respectively. " argument="--gzip --bzip2">
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104 <option value="fastqsanger.gz">gzip compressed fastq</option>
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105 <option value="fastqsanger">Uncompressed fastq</option>
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106 <option value="fastqsanger.bz2">bzip2 compressed fastq</option>
0
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107 </param>
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108 <section name="adv" title="Advanced Options" expanded="False">
7
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109 <param name="minID" type="integer" label="Minimum spot ID" optional="true" help="Minimum spot id to be dumped." argument="--minSpotId"/>
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110 <param name="maxID" type="integer" label="Maximum spot ID" optional="true" help="Maximum spot id to be dumped." argument="--maxSpotId"/>
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111 <param name="minlen" type="integer" label="Minimum read length" optional="true" help="Filter by sequence length. Will dump only reads longer or equal to this value." argument="--minReadLen"/>
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112 <param name="split" type="boolean" checked="true" truevalue="--split-spot" falsevalue="" label="Split spot by read pairs" help="Split spots into individual reads." argument="--split-spot"/>
0
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113 <expand macro="alignments"/>
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114 <expand macro="region"/>
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115 <expand macro="matepairDist"/>
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116 <param name="readfilter" type="select" value="" label="filter by value" argument="--read-filter">
0
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117 <option value="">None</option>
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118 <option value="pass">pass</option>
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119 <option value="reject">reject</option>
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120 <option value="criteria">criteria</option>
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121 <option value="redacted">redacted</option>
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122 </param>
7
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123 <param name="spotgroups" type="text" label="Filter by spot-groups" optional="true" argument="--spot-groups"/>
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124 <param name="clip" type="boolean" truevalue="--clip" falsevalue="" argument="--clip" label="Apply left and right clips" />
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125 <param name="skip_technical" type="boolean" truevalue="--skip-technical" falsevalue="" checked="False" label="Dump only biological reads" argument="--skip-technical"/>
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126 <param name="table" label="Table name within cSRA object" type="text" value="" optional="true" help="For SRA of noisy long-reads put SEQUENCE" argument="--table"/>
0
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127 </section>
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128 </inputs>
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129 <outputs>
7
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130 <collection name="list_paired" type="list:paired" label="Pair-end data (fastq-dump)">
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131 <filter>input['input_select'] == "file_list"</filter>
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132
1
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133 <!-- Use named regex group to grab pattern
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134 <identifier_0>_<identifier_1>.fq. Here identifier_0 is the list
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135 identifier in the nested collection and identifier_1 is either
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136 forward or reverse (for instance samp1_forward.fq).
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137 -->
7
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138
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139 <discover_datasets pattern="(?P&lt;identifier_0&gt;[^_]+)_\d+.fastq_(?P&lt;identifier_1&gt;[^_]+)\.fastqsanger" ext="fastqsanger" />
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140 <discover_datasets pattern="(?P&lt;identifier_0&gt;[^_]+)_\d+.fastq.gz_(?P&lt;identifier_1&gt;[^_]+)\.fastqsanger.gz" ext="fastqsanger.gz" />
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141 <discover_datasets pattern="(?P&lt;identifier_0&gt;[^_]+)_\d+.fastq.bz2_(?P&lt;identifier_1&gt;[^_]+)\.fastqsanger.bz2" ext="fastqsanger.bz2" />
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142 </collection>
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143 <collection name="output_collection" type='list' label="Single-end data (fastq-dump)">
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144 <filter>input['input_select'] == "file_list"</filter>
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145 <discover_datasets pattern="(?P&lt;designation&gt;.+)_\d+.fastq__single\.fastqsanger" directory="." ext='fastqsanger'/>
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146 <discover_datasets pattern="(?P&lt;designation&gt;.+)_\d+.fastq.gz__single\.fastqsanger.gz" directory="." ext='fastqsanger.gz'/>
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147 <discover_datasets pattern="(?P&lt;designation&gt;.+)_\d+.fastq.bz2__single\.fastqsanger.bz2" directory="." ext='fastqsanger.bz2'/>
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148 </collection>
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149 <data format="fastqsanger" name="output_accession" label="${input.accession} (fastq-dump)">
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150 <filter>input['input_select'] == "accession_number"</filter>
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151 <change_format>
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152 <when input="outputformat" value="fastqsanger.gz" format="fastqsanger.gz"/>
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153 <when input="outputformat" value="fastqsanger.bz2" format="fastqsanger.bz2"/>
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154 </change_format>
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155 </data>
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156 <data format="fastqsanger" name="output_file" label="${input.file.name} (fastq-dump)">
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157 <filter>input['input_select'] == "file"</filter>
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158 <change_format>
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159 <when input="outputformat" value="fastqsanger.gz" format="fastqsanger.gz"/>
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160 <when input="outputformat" value="fastqsanger.bz2" format="fastqsanger.bz2"/>
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161 </change_format>
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162 </data>
0
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163 </outputs>
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164 <tests>
7
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165 <test>
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166 <param name="input_select" value="accession_number"/>
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167 <param name="outputformat" value="fastqsanger"/>
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168 <param name="accession" value="SRR044777"/>
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169 <param name="skip_technical" value="True"/>
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170 <output name="output_accession">
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171 <assert_contents>
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172 <not_has_text text="rRNA_primer"/>
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173 <has_text text="F47USSH02GNP1D" />
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174 </assert_contents>
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175 </output>
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176 </test>
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177 <test>
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178 <param name="input_select" value="accession_number"/>
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179 <param name="outputformat" value="fastqsanger.gz"/>
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180 <param name="accession" value="SRR925743"/>
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181 <param name="maxID" value="5"/>
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182 <output name="output_accession" file="fastq_dump_result.fastq.gz" decompress="True"/>
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183 </test>
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184 <test>
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185 <param name="input_select" value="accession_number"/>
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186 <param name="outputformat" value="fastqsanger"/>
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187 <param name="accession" value="SRR925743"/>
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188 <param name="maxID" value="5"/>
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189 <output name="output_accession" file="fastq_dump_result.fastq" ftype="fastqsanger"/>
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190 </test>
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191 <test>
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192 <param name="input_select" value="file_list"/>
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193 <param name="outputformat" value="fastqsanger"/>
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194 <param name="file_list" value="list_pe"/>
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195 <param name="maxID" value="5"/>
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196 <output_collection name="list_paired" type="list:paired">
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197 <element name="DRR015708">
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198 <element name="forward" file="DRR015708_forward.fastqsanger">
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199 </element>
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200 <element name="reverse" file="DRR015708_reverse.fastqsanger">
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201 </element>
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202 </element>
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203 </output_collection>
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204 </test>
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205 <test>
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206 <param name="input_select" value="file_list"/>
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207 <param name="outputformat" value="fastqsanger"/>
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208 <param name="file_list" value="list_pe2"/>
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209 <param name="maxID" value="5"/>
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210 <output_collection name="list_paired" type="list:paired">
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211 <element name="ERR027433">
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212 <element name="forward" file="ERR027433_forward.fastqsanger">
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213 </element>
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214 <element name="reverse" file="ERR027433_reverse.fastqsanger">
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215 </element>
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216 </element>
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217 </output_collection>
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218 </test>
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219 <test>
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220 <param name="input_select" value="file_list"/>
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221 <param name="outputformat" value="fastqsanger"/>
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222 <param name="file_list" value="list_se"/>
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223 <param name="maxID" value="5"/>
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224 <output_collection name="output_collection" type="list">
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225 <element name="SRR1993644" file="SRR1993644.fastqsanger"/>
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226 </output_collection>
15
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227 </test>
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228 <test>
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229 <param name="input_select" value="accession_number"/>
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230 <param name="outputformat" value="fastqsanger.gz"/>
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231 <param name="accession" value="SRR6982805"/>
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232 <param name="maxID" value="2"/>
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233 <param name="table" value="SEQUENCE"/>
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234 <output name="output_accession" file="SRR6982805.fastqsanger.gz" ftype="fastqsanger.gz" decompress="True"/>
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235 </test>
0
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236 </tests>
7
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237 <help><![CDATA[
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238 **What it does?**
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239
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240 This tool extracts data (in fastq_ format) from the Short Read Archive (SRA) at the National Center for Biotechnology Information (NCBI). It is based on the fastq-dump_ utility of the SRA Toolkit.
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241
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242 **How to use it?**
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243
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244 There are three ways in which you can download data:
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245
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246 1. Data for single accession
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247 2. Multiple datasets using a list of accessions
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248 3. Extract data from already uploaded SRA dataset
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249
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250 Below we discuss each in detail.
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251
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252 ------
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253
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254 **Uploading data for a single accession**
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255
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256 When you type a single accession number (e.g., `SRR1582967`) into **Accession** box and click **Execute** the tool will fetch data for you. It is important to keep the following in mind:
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257
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258 - if data is paired-ended (or mate-paired) the tool will generate a single *interleaved* dataset, in which forward and reverse mates are alternating (see an example dataset below)
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259 - if data is single ended, a standard single fastq dataset will be produced
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260
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261 -----
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262
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263 **Uploading multiple datasets using a list of accessions**
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264
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265 A more realistic scenario is when you want to upload a number of datasets at once. To do this you need a list of accession, where there is only one accession per line (see below for information on how to generate such a file). Once you have this file:
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266
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267 1. Upload it into your history using Galaxy's upload tool
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268 2. Once the list of accessions is uploaded choose *List of SRA accessions, one per line* from **select input type** dropdown
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269 3. Choose uploaded file within the **sra accession list** field
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270 4. Click **Execute**
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271
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272 .. class:: warningmark
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273
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274 Fastq datasets produced by this option will be saved in Galaxy's history as a collection_ - a single history element containing multiple datasets. In fact, two collections will be produced: one containing paired-end data and another containing single-end data. Single-end or pair-end collections may be empty if the accessions provided in the list contain only SINGLE or PAIRED data, respectively.
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275
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276 -----
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277
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278 **Extract data from already uploaded SRA dataset**
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279
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280 If a SRA dataset is present in the history, it can be converted into fastq dataset by setting **select input type** drop-down to *SRA archive in current history*. Just like in the case of extracting data for single accession number the following applies:
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281
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282 - if data is paired-ended (or mate-pair) the tool will generate a single *interleaved* dataset, in which forward and reverse mates are alternating (see example below).
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283 - if data is single ended, a standard fastq dataset will be produced
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284
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285 @ACCESSION_LIST_HOWTO@
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286
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287 -----
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288
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289 **Paired-end (and mate-pair) data in fastq format**
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290
7
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291 Paired end datasets can be represented as two individual datasets:
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292
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293 First dataset::
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294
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295 @1/1
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296 AGGGATGTGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTA
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297 +
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298 EGGEGGGDFGEEEAEECGDEGGFEEGEFGBEEDDECFEFDD@CDD<ED
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299 @2/1
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300 AGGGATGTGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTA
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301 +
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302 HHHHHHEGFHEEFEEHEEHHGGEGGGGEFGFGGGGHHHHFBEEEEEFG
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303
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304 Second dataset::
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305
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306 @1/2
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307 CCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAAC
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308 +
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309 GHHHDFDFGFGEGFBGEGGEGEGGGHGFGHFHFHHHHHHHEF?EFEFF
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310 @2/2
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311 CCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAAC
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312 +
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313 HHHHHHHHHHHHHGHHHHHHGHHHHHHHHHHHFHHHFHHHHHHHHHHH
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314
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315 Or a single *interleaved* dataset::
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316
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317 @1/1
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318 AGGGATGTGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTA
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319 +
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320 EGGEGGGDFGEEEAEECGDEGGFEEGEFGBEEDDECFEFDD@CDD<ED
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321 @1/2
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322 CCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAAC
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323 +
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324 GHHHDFDFGFGEGFBGEGGEGEGGGHGFGHFHFHHHHHHHEF?EFEFF
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325 @2/1
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326 AGGGATGTGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTA
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327 +
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328 HHHHHHEGFHEEFEEHEEHHGGEGGGGEFGFGGGGHHHHFBEEEEEFG
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329 @2/2
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330 CCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAAC
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331 +
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332 HHHHHHHHHHHHHGHHHHHHGHHHHHHHHHHHFHHHFHHHHHHHHHHH
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333
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334 ----
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335
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336
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337 .. _fastq: https://en.wikipedia.org/wiki/FASTQ_format
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338 .. _fastq-dump: https://ncbi.github.io/sra-tools/fastq-dump.html
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339 .. _collection: https://galaxyproject.org/tutorials/collections/
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7068f48d0ef9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d22c001db39b52ebaa54837bebe2765c17b5c876"
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340 .. _link: https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=studies
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341
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342 @SRATOOLS_ATTRRIBUTION@
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343
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344 ]]>
0
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345 </help>
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346 <expand macro="citation"/>
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347 </tool>