Mercurial > repos > iuc > sra_tools

annotate fasterq_dump.xml @ 36:1ec814014652 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cb858cbf5d9e307b663105f674f1acaa4f90a1fb
author iuc
date Thu, 14 Mar 2024 15:21:59 +0000
parents 734abc7ac21d
children f8054ea1c365
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9a776b080193 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
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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>
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
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3 <macros>
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4 <import>macros.xml</import>
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5 <token name="VERSION_SUFFIX">1</token>
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6 </macros>
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7 <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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8 <expand macro="bio_tools"/>
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9 <expand macro="requirements"/>
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10 <version_command>fasterq-dump --version | tr -d $'\n'</version_command>
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11 <command detect_errors="exit_code"><![CDATA[
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12 set -o | grep -q pipefail && set -o pipefail;
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13 @COPY_CONFIGFILE@
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14 @CONFIGURE_RETRY@
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15 @SET_ACCESSIONS@
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16 while [ \$SRA_PREFETCH_ATTEMPT -le \$SRA_PREFETCH_RETRIES ] ; do
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17 fasterq-dump "\$acc"
1ec814014652 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cb858cbf5d9e307b663105f674f1acaa4f90a1fb
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18 -e \${GALAXY_SLOTS:-1}
1ec814014652 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cb858cbf5d9e307b663105f674f1acaa4f90a1fb
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19 -t \${TMPDIR}
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20 --seq-defline '$adv.seq_defline'
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21 --qual-defline '+'
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22 $adv.split
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23 #if str( $adv.minlen ) != "":
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24 --min-read-len "$adv.minlen"
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25 #end if
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26 $adv.skip_technical 2>&1 | tee -a '$log';
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27 if [ \$? == 0 ] && [ \$(ls *.fastq | wc -l) -ge 1 ]; then
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28 break ;
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29 else
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30 echo "Prefetch attempt \$SRA_PREFETCH_ATTEMPT of \$SRA_PREFETCH_RETRIES exited with code \$?" ;
c441583adae5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit e00e33a3405201e8decbbb641ad0a8c3e16c8bef"
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31 SRA_PREFETCH_ATTEMPT=`expr \$SRA_PREFETCH_ATTEMPT + 1` ;
c441583adae5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit e00e33a3405201e8decbbb641ad0a8c3e16c8bef"
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32 sleep 1 ;
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33 fi ;
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34 done &&
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35 mkdir -p output &&
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36 mkdir -p outputOther &&
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37 count="\$(ls *.fastq | wc -l)" &&
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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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38 echo "There are \$count fastq files" &&
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39 data=(\$(ls *.fastq)) &&
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
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40 if [ "\$count" -eq 1 ]; then
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41 @COMPRESS@ "\${data[0]}" > output/"\${acc}"__single.fastqsanger.gz &&
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42 rm "\${data[0]}";
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43 elif [ "$adv.split" = "--split-3" ]; then
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44 if [ -e "\${acc}".fastq ]; then
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45 @COMPRESS@ "\${acc}".fastq > outputOther/"\${acc}"__single.fastqsanger.gz;
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46 fi &&
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47 @COMPRESS@ "\${acc}"_1.fastq > output/"\${acc}"_forward.fastqsanger.gz &&
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48 @COMPRESS@ "\${acc}"_2.fastq > output/"\${acc}"_reverse.fastqsanger.gz &&
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49 rm "\${acc}"*.fastq;
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50 elif [ "\$count" -eq 2 ]; then
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51 #if $adv.skip_technical:
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52 @COMPRESS@ "\${data[0]}" > output/"\${acc}"_forward.fastqsanger.gz &&
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53 @COMPRESS@ "\${data[1]}" > output/"\${acc}"_reverse.fastqsanger.gz &&
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54 #else
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55 @COMPRESS@ "\${data[0]}" > outputOther/"\${data[0]}"sanger.gz &&
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56 @COMPRESS@ "\${data[1]}" > outputOther/"\${data[1]}"sanger.gz &&
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57 #end if
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58 rm "\${data[0]}" &&
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59 rm "\${data[1]}";
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60 else
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61 for file in \${data[*]}; do
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62 @COMPRESS@ "\$file" > outputOther/"\$file"sanger.gz &&
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63 rm "\$file";
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64 done;
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
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65 fi;
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66
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67 #if $input.input_select != "sra_file":
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68 ); done;
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69 #end if
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70 echo "Done with all accessions."
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71 ]]>
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72 </command>
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73 <expand macro="configfile_hack"/>
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74 <inputs>
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75 <expand macro="input_conditional"/>
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76 <section name="adv" title="Advanced Options" expanded="False">
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77 <expand macro="defline" defline_param="--seq-defline" defline_default="@$sn/$ri"/>
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78 <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"/>
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
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79 <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).">
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
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80 <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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81 <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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82 <option value="--split-spot">--split-spot: split spots into reads (only one output file)</option>
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
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83 <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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84 </param>
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85 <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"/>
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86 </section>
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87 </inputs>
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88 <outputs>
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89 <data name="log" format="txt" label="fasterq-dump log"/>
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90 <collection name="list_paired" type="list:paired" label="Pair-end data (fasterq-dump)">
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91
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92 <!-- Use named regex group to grab pattern
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93 <identifier_0>_<identifier_1>.fq. Here identifier_0 is the list
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94 identifier in the nested collection and identifier_1 is either
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95 forward or reverse (for instance samp1_forward.fq).
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96 -->
17
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97
15
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98 <discover_datasets pattern="(?P&lt;identifier_0&gt;[^_]+)_(?P&lt;identifier_1&gt;[^_]+)\.fastqsanger.gz" directory="output" ext="fastqsanger.gz" />
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99 </collection>
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100 <collection name="output_collection" type='list' label="Single-end data (fasterq-dump)">
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101 <discover_datasets pattern="(?P&lt;designation&gt;.+)__single\.fastqsanger.gz" directory="output" ext='fastqsanger.gz'/>
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102 </collection>
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103 <collection name="output_collection_other" type='list' label="Other data (fasterq-dump)">
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104 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.fastqsanger\.gz" directory="outputOther" format="fastqsanger.gz"/>
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105 </collection>
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106 </outputs>
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107 <tests>
25
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108 <test expect_num_outputs="4">
15
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109 <param name="input_select" value="accession_number"/>
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110 <param name="accession" value="ERR086330"/>
25
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111 <output_collection name="list_paired" type="list:paired" count="1">
15
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112 <element name="ERR086330">
27
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113 <element name="forward" file="ERR086330_1.fastq.gz" ftype="fastqsanger.gz" decompress="True"/>
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114 <element name="reverse" file="ERR086330_2.fastq.gz" ftype="fastqsanger.gz" decompress="True"/>
15
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115 </element>
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116 </output_collection>
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117 </test>
25
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118 <test expect_num_outputs="4">
15
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119 <param name="input_select" value="accession_number"/>
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120 <param name="accession" value="SRR002702"/>
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121 <param name="split" value="--split-files"/>
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122 <param name="skip_technical" value="False"/>
25
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123 <output_collection name="output_collection_other" type="list" count="2">
15
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124 <element name="SRR002702_1" file="SRR002702_1.fastq.gz" ftype="fastqsanger.gz" decompress="True"/>
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125 <element name="SRR002702_2" file="SRR002702_2.fastq.gz" ftype="fastqsanger.gz" decompress="True"/>
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126 </output_collection>
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127 </test>
25
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128 <test expect_num_outputs="4">
27
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129 <param name="input_select" value="accession_number"/>
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130 <param name="accession" value="ERR086330, SRR11953971"/>
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131 <output_collection name="list_paired" type="list:paired" count="2">
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132 <element name="ERR086330">
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133 <element name="forward" file="ERR086330_1.fastq.gz" ftype="fastqsanger.gz" decompress="True"/>
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134 <element name="reverse" file="ERR086330_2.fastq.gz" ftype="fastqsanger.gz" decompress="True"/>
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135 </element>
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136 <element name="SRR11953971">
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137 <element name="forward" file="SRR11953971_1.fastq.gz" ftype="fastqsanger.gz" decompress="True"/>
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138 <element name="reverse" file="SRR11953971_2.fastq.gz" ftype="fastqsanger.gz" decompress="True"/>
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139 </element>
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140 </output_collection>
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141 </test>
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142 <test expect_num_outputs="4">
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143 <param name="input_select" value="sra_file"/>
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144 <param name="sra_file" value="SRR522874.sra"/>
15
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145 <param name="split" value="--split-files"/>
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146 <param name="skip_technical" value="True"/>
25
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147 <output_collection name="list_paired" type="list:paired" count="1">
15
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148 <element name="SRR522874.sra">
27
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149 <element name="forward" file="SRR522874.sra_2.fastq.gz" ftype="fastqsanger.gz" decompress="True"/>
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150 <element name="reverse" file="SRR522874.sra_4.fastq.gz" ftype="fastqsanger.gz" decompress="True"/>
15
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151 </element>
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152 </output_collection>
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153 </test>
25
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154 <test expect_num_outputs="4">
27
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155 <param name="input_select" value="sra_file"/>
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156 <param name="sra_file" value="SRR522874.sra"/>
15
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157 <param name="split" value="--split-files"/>
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158 <param name="skip_technical" value="False"/>
25
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159 <output_collection name="output_collection_other" type="list" count="4">
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160 <element name="SRR522874_1" file="SRR522874.sra_1.fastq.gz" ftype="fastqsanger.gz" decompress="True"/>
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161 <element name="SRR522874_2" file="SRR522874.sra_2.fastq.gz" ftype="fastqsanger.gz" decompress="True"/>
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162 <element name="SRR522874_3" file="SRR522874.sra_3.fastq.gz" ftype="fastqsanger.gz" decompress="True"/>
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163 <element name="SRR522874_4" file="SRR522874.sra_4.fastq.gz" ftype="fastqsanger.gz" decompress="True"/>
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164 </output_collection>
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165 </test>
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166 <test expect_num_outputs="4">
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167 <param name="input_select" value="file_list"/>
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168 <param name="file_list" value="list_sra"/>
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169 <param name="minlen" value="21"/>
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170 <output_collection name="output_collection_other" type="list" count="1">
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171 <element name="SRR522874__single" file="SRR522874.fastq.gz" ftype="fastqsanger.gz" decompress="True"/>
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172 </output_collection>
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173 <output_collection name="list_paired" type="list:paired" count="1">
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174 <element name="SRR522874">
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175 <element name="forward" file="SRR522874_1.fastq.gz" ftype="fastqsanger.gz" decompress="True"/>
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176 <element name="reverse" file="SRR522874_2.fastq.gz" ftype="fastqsanger.gz" decompress="True"/>
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177 </element>
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178 </output_collection>
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179 <output_collection name="output_collection" type="list" count="1">
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180 <element name="SRR002702" file="SRR002702_2.fastq.gz" ftype="fastqsanger.gz" decompress="True"/>
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181 </output_collection>
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182 </test>
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183 <test expect_num_outputs="4">
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184 <param name="input_select" value="file_list"/>
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185 <param name="file_list" value="sra_manifest.tabular" ftype="sra_manifest.tabular"/>
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186 <output_collection name="list_paired" type="list:paired" count="1">
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187 <element name="SRR11953971">
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188 <element name="forward" file="SRR11953971_1.fastq.gz" ftype="fastqsanger.gz" decompress="True"/>
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189 <element name="reverse" file="SRR11953971_2.fastq.gz" ftype="fastqsanger.gz" decompress="True"/>
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190 </element>
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191 </output_collection>
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192 </test>
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193 <test expect_num_outputs="4">
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194 <param name="input_select" value="file_list"/>
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195 <param name="file_list" value="sra_manifest.tabular" ftype="sra_manifest.tabular"/>
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196 <section name="adv">
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197 <param name="seq_defline" value="@$ac.$si/$ri $sn length=$rl"/>
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198 </section>
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199 <output_collection name="list_paired" type="list:paired" count="1">
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200 <element name="SRR11953971">
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201 <element name="forward" ftype="fastqsanger.gz" decompress="True">
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202 <assert_contents>
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203 <!-- TODO replace has_size by has_line -->
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204 <has_size min="56206"/>
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205 <!-- <has_line line="@SRR11953971.2053/1 2053 length=101"/> -->
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206 </assert_contents>
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207 </element>
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208 <element name="reverse" ftype="fastqsanger.gz" decompress="True">
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209 <assert_contents>
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210 <has_size min="59843"/>
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211 <!-- <has_line line="@SRR11953971.2053/2 2053 length=101"/> -->
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212 </assert_contents>
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213 </element>
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214 </element>
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215 </output_collection>
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216 </test>
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217 </tests>
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218 <help><![CDATA[
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219 **What it does?**
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220
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221 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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222
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223 - 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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224 - if data is single ended, each element of the collection will be a single fastq_ dataset.
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225
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226
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227 @HOW_TO_USE_IT@
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228
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229 -----
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230
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231 **Output**
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232
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233 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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234 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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235
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236 .. class:: warningmark
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237
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238 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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239
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240 .. class:: warningmark
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241
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242 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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243 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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245 @ACCESSION_LIST_HOWTO@
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247 -----
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250 .. _fastq: https://en.wikipedia.org/wiki/FASTQ_format
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251 .. _fasterq-dump: https://github.com/ncbi/sra-tools/wiki/HowTo:-fasterq-dump
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252 .. _collection: https://galaxyproject.org/tutorials/collections/
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253 .. _link: https://trace.ncbi.nlm.nih.gov/Traces/index.html?view=run_browser&display=reads
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255 @SRATOOLS_ATTRRIBUTION@
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256 ]]>
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257 </help>
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258 <expand macro="citation"/>
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259 </tool>