Mercurial > repos > iuc > sra_tools

annotate fasterq_dump.xml @ 31:734abc7ac21d draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 3a7f854e8ebfb2bed11198fb83181f305af633f7
author iuc
date Thu, 14 Sep 2023 07:38:02 +0000
parents 4317d3cb6cba
children 1ec814014652
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
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9a776b080193 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
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1 <tool id="fasterq_dump" name="Faster Download and Extract Reads in FASTQ" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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2 <description>format from NCBI SRA</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="edam_ontology"/>
9a776b080193 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
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7 <expand macro="bio_tools"/>
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8 <expand macro="requirements"/>
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9 <version_command>fasterq-dump --version | tr -d $'\n'</version_command>
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10 <command detect_errors="exit_code"><![CDATA[
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11 set -o | grep -q pipefail && set -o pipefail;
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12 @COPY_CONFIGFILE@
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13 @CONFIGURE_RETRY@
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14 @SET_ACCESSIONS@
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15 while [ \$SRA_PREFETCH_ATTEMPT -le \$SRA_PREFETCH_RETRIES ] ; do
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16 fasterq-dump "\$acc" -e \${GALAXY_SLOTS:-1}
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17 --seq-defline '$adv.seq_defline'
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18 --qual-defline '+'
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19 $adv.split
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20 #if str( $adv.minlen ) != "":
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21 --min-read-len "$adv.minlen"
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22 #end if
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23 $adv.skip_technical 2>&1 | tee -a '$log';
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24 if [ \$? == 0 ] && [ \$(ls *.fastq | wc -l) -ge 1 ]; then
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25 break ;
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26 else
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27 echo "Prefetch attempt \$SRA_PREFETCH_ATTEMPT of \$SRA_PREFETCH_RETRIES exited with code \$?" ;
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28 SRA_PREFETCH_ATTEMPT=`expr \$SRA_PREFETCH_ATTEMPT + 1` ;
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29 sleep 1 ;
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30 fi ;
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31 done &&
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32 mkdir -p output &&
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33 mkdir -p outputOther &&
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34 count="\$(ls *.fastq | wc -l)" &&
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35 echo "There are \$count fastq files" &&
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36 data=(\$(ls *.fastq)) &&
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37 if [ "\$count" -eq 1 ]; then
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38 @COMPRESS@ "\${data[0]}" > output/"\${acc}"__single.fastqsanger.gz &&
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39 rm "\${data[0]}";
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40 elif [ "$adv.split" = "--split-3" ]; then
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41 if [ -e "\${acc}".fastq ]; then
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42 @COMPRESS@ "\${acc}".fastq > outputOther/"\${acc}"__single.fastqsanger.gz;
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43 fi &&
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44 @COMPRESS@ "\${acc}"_1.fastq > output/"\${acc}"_forward.fastqsanger.gz &&
c441583adae5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit e00e33a3405201e8decbbb641ad0a8c3e16c8bef"
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45 @COMPRESS@ "\${acc}"_2.fastq > output/"\${acc}"_reverse.fastqsanger.gz &&
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46 rm "\${acc}"*.fastq;
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47 elif [ "\$count" -eq 2 ]; then
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48 #if $adv.skip_technical:
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49 @COMPRESS@ "\${data[0]}" > output/"\${acc}"_forward.fastqsanger.gz &&
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50 @COMPRESS@ "\${data[1]}" > output/"\${acc}"_reverse.fastqsanger.gz &&
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51 #else
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52 @COMPRESS@ "\${data[0]}" > outputOther/"\${data[0]}"sanger.gz &&
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53 @COMPRESS@ "\${data[1]}" > outputOther/"\${data[1]}"sanger.gz &&
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54 #end if
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55 rm "\${data[0]}" &&
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56 rm "\${data[1]}";
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57 else
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58 for file in \${data[*]}; do
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59 @COMPRESS@ "\$file" > outputOther/"\$file"sanger.gz &&
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60 rm "\$file";
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61 done;
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62 fi;
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63
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64 #if $input.input_select != "sra_file":
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65 ); done;
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66 #end if
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67 echo "Done with all accessions."
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68 ]]>
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69 </command>
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70 <expand macro="configfile_hack"/>
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71 <inputs>
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72 <expand macro="input_conditional"/>
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73 <section name="adv" title="Advanced Options" expanded="False">
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74 <expand macro="defline" defline_param="--seq-defline" defline_default="@$sn/$ri"/>
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75 <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="--min-read-len"/>
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76 <param name="split" type="select" display="radio" label="Select how to split the spots" help="This option will only be used when there are multiple reads per spot (for example paired-end).">
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77 <option value="--split-3">--split-3: write properly paired biological reads into different files and single reads in another file</option>
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78 <option value="--split-files">--split-files: write reads into different files (forward and reverse may not match if one read is empty)</option>
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79 <option value="--split-spot">--split-spot: split spots into reads (only one output file)</option>
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80 <option value="--concatenate-reads">--concatenate-reads: writes whole spots into one file</option>
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
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81 </param>
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82 <param name="skip_technical" type="boolean" truevalue="--skip-technical" falsevalue="--include-technical" checked="True" label="Dump only biological reads" help="Will not be used if --split-3 is selected." argument="--skip-technical/--include-technical"/>
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
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83 </section>
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84 </inputs>
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85 <outputs>
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86 <data name="log" format="txt" label="fasterq-dump log"/>
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87 <collection name="list_paired" type="list:paired" label="Pair-end data (fasterq-dump)">
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88
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89 <!-- Use named regex group to grab pattern
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90 <identifier_0>_<identifier_1>.fq. Here identifier_0 is the list
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91 identifier in the nested collection and identifier_1 is either
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92 forward or reverse (for instance samp1_forward.fq).
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93 -->
17
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94
15
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95 <discover_datasets pattern="(?P&lt;identifier_0&gt;[^_]+)_(?P&lt;identifier_1&gt;[^_]+)\.fastqsanger.gz" directory="output" ext="fastqsanger.gz" />
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
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96 </collection>
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97 <collection name="output_collection" type='list' label="Single-end data (fasterq-dump)">
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
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98 <discover_datasets pattern="(?P&lt;designation&gt;.+)__single\.fastqsanger.gz" directory="output" ext='fastqsanger.gz'/>
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99 </collection>
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100 <collection name="output_collection_other" type='list' label="Other data (fasterq-dump)">
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
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101 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.fastqsanger\.gz" directory="outputOther" format="fastqsanger.gz"/>
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102 </collection>
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103 </outputs>
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104 <tests>
25
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105 <test expect_num_outputs="4">
15
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106 <param name="input_select" value="accession_number"/>
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107 <param name="accession" value="ERR086330"/>
25
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108 <output_collection name="list_paired" type="list:paired" count="1">
15
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109 <element name="ERR086330">
27
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110 <element name="forward" file="ERR086330_1.fastq.gz" ftype="fastqsanger.gz" decompress="True"/>
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111 <element name="reverse" file="ERR086330_2.fastq.gz" ftype="fastqsanger.gz" decompress="True"/>
15
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
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112 </element>
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113 </output_collection>
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114 </test>
25
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115 <test expect_num_outputs="4">
15
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116 <param name="input_select" value="accession_number"/>
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117 <param name="accession" value="SRR002702"/>
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
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118 <param name="split" value="--split-files"/>
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119 <param name="skip_technical" value="False"/>
25
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120 <output_collection name="output_collection_other" type="list" count="2">
15
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121 <element name="SRR002702_1" file="SRR002702_1.fastq.gz" ftype="fastqsanger.gz" decompress="True"/>
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
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122 <element name="SRR002702_2" file="SRR002702_2.fastq.gz" ftype="fastqsanger.gz" decompress="True"/>
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
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123 </output_collection>
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124 </test>
25
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diff changeset
125 <test expect_num_outputs="4">
27
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126 <param name="input_select" value="accession_number"/>
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127 <param name="accession" value="ERR086330, SRR11953971"/>
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128 <output_collection name="list_paired" type="list:paired" count="2">
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129 <element name="ERR086330">
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130 <element name="forward" file="ERR086330_1.fastq.gz" ftype="fastqsanger.gz" decompress="True"/>
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131 <element name="reverse" file="ERR086330_2.fastq.gz" ftype="fastqsanger.gz" decompress="True"/>
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diff changeset
132 </element>
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diff changeset
133 <element name="SRR11953971">
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134 <element name="forward" file="SRR11953971_1.fastq.gz" ftype="fastqsanger.gz" decompress="True"/>
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135 <element name="reverse" file="SRR11953971_2.fastq.gz" ftype="fastqsanger.gz" decompress="True"/>
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136 </element>
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137 </output_collection>
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138 </test>
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139 <test expect_num_outputs="4">
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140 <param name="input_select" value="sra_file"/>
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141 <param name="sra_file" value="SRR522874.sra"/>
15
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142 <param name="split" value="--split-files"/>
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143 <param name="skip_technical" value="True"/>
25
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144 <output_collection name="list_paired" type="list:paired" count="1">
15
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145 <element name="SRR522874.sra">
27
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146 <element name="forward" file="SRR522874.sra_2.fastq.gz" ftype="fastqsanger.gz" decompress="True"/>
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147 <element name="reverse" file="SRR522874.sra_4.fastq.gz" ftype="fastqsanger.gz" decompress="True"/>
15
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148 </element>
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149 </output_collection>
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150 </test>
25
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diff changeset
151 <test expect_num_outputs="4">
27
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152 <param name="input_select" value="sra_file"/>
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153 <param name="sra_file" value="SRR522874.sra"/>
15
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154 <param name="split" value="--split-files"/>
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155 <param name="skip_technical" value="False"/>
25
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diff changeset
156 <output_collection name="output_collection_other" type="list" count="4">
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157 <element name="SRR522874_1" file="SRR522874.sra_1.fastq.gz" ftype="fastqsanger.gz" decompress="True"/>
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158 <element name="SRR522874_2" file="SRR522874.sra_2.fastq.gz" ftype="fastqsanger.gz" decompress="True"/>
69ebb7f46e45 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit a464017f4a599697101dbd26cf5eb902588359b5"
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159 <element name="SRR522874_3" file="SRR522874.sra_3.fastq.gz" ftype="fastqsanger.gz" decompress="True"/>
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160 <element name="SRR522874_4" file="SRR522874.sra_4.fastq.gz" ftype="fastqsanger.gz" decompress="True"/>
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161 </output_collection>
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162 </test>
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163 <test expect_num_outputs="4">
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164 <param name="input_select" value="file_list"/>
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165 <param name="file_list" value="list_sra"/>
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166 <param name="minlen" value="21"/>
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167 <output_collection name="output_collection_other" type="list" count="1">
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168 <element name="SRR522874__single" file="SRR522874.fastq.gz" ftype="fastqsanger.gz" decompress="True"/>
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169 </output_collection>
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170 <output_collection name="list_paired" type="list:paired" count="1">
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171 <element name="SRR522874">
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172 <element name="forward" file="SRR522874_1.fastq.gz" ftype="fastqsanger.gz" decompress="True"/>
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173 <element name="reverse" file="SRR522874_2.fastq.gz" ftype="fastqsanger.gz" decompress="True"/>
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174 </element>
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175 </output_collection>
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176 <output_collection name="output_collection" type="list" count="1">
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177 <element name="SRR002702" file="SRR002702_2.fastq.gz" ftype="fastqsanger.gz" decompress="True"/>
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178 </output_collection>
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179 </test>
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180 <test expect_num_outputs="4">
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181 <param name="input_select" value="file_list"/>
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182 <param name="file_list" value="sra_manifest.tabular" ftype="sra_manifest.tabular"/>
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183 <output_collection name="list_paired" type="list:paired" count="1">
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184 <element name="SRR11953971">
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185 <element name="forward" file="SRR11953971_1.fastq.gz" ftype="fastqsanger.gz" decompress="True"/>
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186 <element name="reverse" file="SRR11953971_2.fastq.gz" ftype="fastqsanger.gz" decompress="True"/>
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187 </element>
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188 </output_collection>
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189 </test>
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190 <test expect_num_outputs="4">
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191 <param name="input_select" value="file_list"/>
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192 <param name="file_list" value="sra_manifest.tabular" ftype="sra_manifest.tabular"/>
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193 <section name="adv">
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194 <param name="seq_defline" value="@$ac.$si/$ri $sn length=$rl"/>
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195 </section>
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196 <output_collection name="list_paired" type="list:paired" count="1">
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197 <element name="SRR11953971">
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198 <element name="forward" ftype="fastqsanger.gz" decompress="True">
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199 <assert_contents>
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200 <!-- TODO replace has_size by has_line -->
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201 <has_size min="56206"/>
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202 <!-- <has_line line="@SRR11953971.2053/1 2053 length=101"/> -->
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203 </assert_contents>
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204 </element>
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205 <element name="reverse" ftype="fastqsanger.gz" decompress="True">
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206 <assert_contents>
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207 <has_size min="59843"/>
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208 <!-- <has_line line="@SRR11953971.2053/2 2053 length=101"/> -->
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209 </assert_contents>
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210 </element>
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211 </element>
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212 </output_collection>
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213 </test>
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214 </tests>
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215 <help><![CDATA[
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216 **What it does?**
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217
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218 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 fasterq-dump_ utility of the SRA Toolkit. The following applies:
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219
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220 - if data is paired-ended (or mate-pair) the tool will generate a collection of file pairs, in which each element will be a pair of fastq_ files containing forward and reverse mates.
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221 - if data is single ended, each element of the collection will be a single fastq_ dataset.
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222
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223
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224 @HOW_TO_USE_IT@
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225
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226 -----
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227
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228 **Output**
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229
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230 In every case, fastq datasets produced will be saved in Galaxy's history as a collection_ - a single history element containing multiple datasets. In fact, regardless of the experimental design, three collections will be produced: one containing paired-end data, another containing single-end data, and a third one which contains reads which could not be classified.
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231 Some collections may be empty if the accessions provided in the list do not contain one of the type of data.
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232
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233 .. class:: warningmark
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234
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235 When you decide to dump technical reads (in Advanced Options Dump only biological reads is set to No), you will probably find your PAIRED data in the other data collection as it is impossible to determine if it was 2 biological reads or one biological and one technical.
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236
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237 .. class:: warningmark
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238
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239 By default, only biological reads are dumped and in case of PAIRED dataset only the spots which have both reads will be in the paired-end collection. The remaining single reads will be in the other colletion.
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240 To keep all reads, and potentially not have the same number of reads in forward and reverse use the --split-files option in Advanced Options, Select how to split the spots.
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241
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242 @ACCESSION_LIST_HOWTO@
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
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243
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
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244 -----
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
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245
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
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246
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
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247 .. _fastq: https://en.wikipedia.org/wiki/FASTQ_format
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
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248 .. _fasterq-dump: https://github.com/ncbi/sra-tools/wiki/HowTo:-fasterq-dump
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
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249 .. _collection: https://galaxyproject.org/tutorials/collections/
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250 .. _link: https://trace.ncbi.nlm.nih.gov/Traces/index.html?view=run_browser&display=reads
15
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
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251
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
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252 @SRATOOLS_ATTRRIBUTION@
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
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253 ]]>
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
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254 </help>
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
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255 <expand macro="citation"/>
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256 </tool>