Mercurial > repos > iuc > sra_tools

annotate fastq_dump.xml @ 3:4732693f4661 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit f30369bef4e2cef17395cdd62ce81768c93f5edd
author iuc
date Tue, 18 Oct 2016 14:54:40 -0400
parents f256cb398262
children 62e4d56ebb6f
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3
4732693f4661 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit f30369bef4e2cef17395cdd62ce81768c93f5edd
iuc
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1 <tool id="fastq_dump" name="Extract reads" version="@VERSION@">
0
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2 <description>in FASTQ/A format from NCBI SRA.</description>
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3 <macros>
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4 <import>sra_macros.xml</import>
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5 </macros>
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6 <expand macro="requirements"/>
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7 <stdio>
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8 <exit_code range="127" level="fatal" description="Could not locate fastq-dump binary"/>
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9 </stdio>
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10 <version_command>fastq-dump --version</version_command>
b723c120161a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
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11 <command>
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12 <![CDATA[
1
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13
462ee06c9358 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 4defaa3ff1c21e2ec39033bfe63ee69471104ede
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14 #if $input.input_select=="file_list":
462ee06c9358 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 4defaa3ff1c21e2ec39033bfe63ee69471104ede
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15 for acc in `cat $input.file_list` ;
462ee06c9358 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 4defaa3ff1c21e2ec39033bfe63ee69471104ede
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16 do
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17 #elif $input.input_select=="accession_number":
462ee06c9358 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 4defaa3ff1c21e2ec39033bfe63ee69471104ede
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18 acc="$input.accession" &&
462ee06c9358 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 4defaa3ff1c21e2ec39033bfe63ee69471104ede
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19 #end if
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21 #if $input.input_select=="file_list" or $input.input_select=="accession_number":
462ee06c9358 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 4defaa3ff1c21e2ec39033bfe63ee69471104ede
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22 [ ""\$acc" =~ ^[E|S|D]RR[0-9]{1,}$" ] && (
462ee06c9358 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 4defaa3ff1c21e2ec39033bfe63ee69471104ede
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23 #end if
2
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24
0
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25 ## Need to set the home directory to the current working directory,
2
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26 ## else the tool tries to write to home/.ncbi and fails when used
f256cb398262 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 4e83a7f6d542cd3129eb14a142f74c127f91d026
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27 ## with a cluster manager.
0
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28 export HOME=\$PWD &&
b723c120161a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
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29 vdb-config --restore-defaults &&
b723c120161a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
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30 #if $input.input_select == "file":
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31 fastq-dump --log-level fatal --accession '${input.file.name}'
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32 #else:
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33 vdb-config -s "/repository/user/main/public/root=\$PWD" &&
b723c120161a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
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34 ## Do not use prefetch if region is specified, to avoid downloading
b723c120161a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
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35 ## the complete sra file.
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36 #if ( str( $adv.region ) == "" ) and ( str( $adv.minID ) == "" ) and ( str( $adv.maxID ) == "" ):
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37 ASCP_PATH=`command -v ascp` &&
b723c120161a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
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38 ASCP_KEY=`dirname \$ASCP_PATH`/asperaweb_id_dsa.openssh || true &&
3
4732693f4661 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit f30369bef4e2cef17395cdd62ce81768c93f5edd
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39 prefetch -X 200G --ascp-path "\$ASCP_PATH|\$ASCP_KEY" "\$acc" &&
0
b723c120161a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
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40 ## Duplicate vdb-config, in case settings changed between prefetch and
b723c120161a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
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41 ## dump command.
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42 vdb-config -s "/repository/user/main/public/root=\$PWD" &&
1
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43 #end if
462ee06c9358 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 4defaa3ff1c21e2ec39033bfe63ee69471104ede
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44 fastq-dump --accession "\$acc"
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45 --split-files
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46 #end if
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47 --defline-seq '@\$sn[_\$rn]/\$ri'
1
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48
0
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49 $adv.split
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50 #if str( $adv.alignments ) == "aligned":
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51 --aligned
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52 #end if
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53 #if str( $adv.alignments ) == "unaligned":
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54 --unaligned
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55 #end if
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56 #if str( $adv.minID ) != "":
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57 --minSpotId "$adv.minID"
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58 #end if
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59 #if str( $adv.maxID ) != "":
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60 --maxSpotId "$adv.maxID"
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61 #end if
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62 #if str( $adv.minlen ) != "":
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63 --minReadLen "$adv.minlen"
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64 #end if
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65 #if str( $adv.readfilter ) != "":
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66 --read-filter "$adv.readfilter"
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67 #end if
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68 #if str( $adv.region ) != "":
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69 --aligned-region "$adv.region"
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70 #end if
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71 #if str( $adv.spotgroups ) != "":
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72 --spot-groups "$adv.spotgroups"
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73 #end if
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74 #if str( $adv.matepairDist ) != "":
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75 --matepair-distance "$adv.matepairDist"
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76 #end if
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77 $adv.clip
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78 $adv.skip_technical
2
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79
0
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80 #if str( $outputformat ) == "fasta":
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81 --fasta
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82 #end if
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83 #if $input.input_select=="file":
1
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84 --stdout
0
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85 "$input.file" > "$output_file"
1
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86 #elif $input.input_select=="file_list":
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87 "\$acc"
0
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88 #else:
1
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89 --stdout
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90 "\$acc" > "$output_accession" )
0
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91 #end if
1
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92
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93 #if $input.input_select=="file_list":
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94 ) ; done
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95
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96 ;
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97
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98
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99 #if str( $outputformat ) == "fasta":
2
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100
1
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101 for f in *_2.fasta ; do mv "\$f" "`basename \$f _2.fasta`_reverse.fasta" ; mv "`basename \$f _2.fasta`_1.fasta" "`basename \$f _2.fasta`_forward.fasta" ; done &&
462ee06c9358 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 4defaa3ff1c21e2ec39033bfe63ee69471104ede
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102 for f in *_1.fasta; do mv "\$f" "`basename \$f _1.fasta`__single.fasta"; done
2
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103
1
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104 #else:
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105
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106 for f in *_2.fastq ; do mv "\$f" "`basename \$f _2.fastq`_reverse.fastq" ; mv "`basename \$f _2.fastq`_1.fastq" "`basename \$f _2.fastq`_forward.fastq" ; done &&
462ee06c9358 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 4defaa3ff1c21e2ec39033bfe63ee69471104ede
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107 for f in *_1.fastq; do mv "\$f" "`basename \$f _1.fastq`__single.fastq"; done
2
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108
1
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109 #end if
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110
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111
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112
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113
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114
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115 #end if
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116
2
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117
0
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118 ]]>
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119 </command>
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120 <inputs>
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121 <expand macro="input_conditional"/>
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122 <param name="outputformat" type="select" label="select output format">
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123 <option value="fastqsanger">fastq</option>
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124 <option value="fasta">fasta</option>
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125 </param>
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126 <section name="adv" title="Advanced Options" expanded="False">
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127 <param name="minID" type="integer" label="minimum spot ID" optional="true"/>
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128 <param name="maxID" type="integer" label="maximum spot ID" optional="true"/>
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129 <param name="minlen" type="integer" label="minimum read length" optional="true"/>
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130 <param name="split" type="boolean" checked="true" truevalue="--split-spot" falsevalue="">
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131 <label>split spot by read pairs</label>
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132 </param>
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133 <expand macro="alignments"/>
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134 <expand macro="region"/>
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135 <expand macro="matepairDist"/>
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136 <param name="readfilter" type="select" value="">
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137 <label>filter by value</label>
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138 <option value="">None</option>
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139 <option value="pass">pass</option>
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140 <option value="reject">reject</option>
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141 <option value="criteria">criteria</option>
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142 <option value="redacted">redacted</option>
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143 </param>
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144 <param name="spotgroups" type="text" label="filter by spot-groups" optional="true"/>
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145 <param name="clip" type="boolean" truevalue="--clip" falsevalue="">
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146 <label>apply left and right clips</label>
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147 </param>
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148 <param name="skip_technical" type="boolean" truevalue="--skip-technical" falsevalue="" checked="False" label="Dump only biological reads"/>
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149 </section>
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150 </inputs>
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151 <outputs>
1
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152 <collection name="list_paired" type="list:paired" label="Pair-end Fast(q|a)">
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153 <filter>input['input_select'] == "file_list"</filter>
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154 <!-- Use named regex group to grab pattern
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155 <identifier_0>_<identifier_1>.fq. Here identifier_0 is the list
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156 identifier in the nested collection and identifier_1 is either
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157 forward or reverse (for instance samp1_forward.fq).
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158 -->
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159 <discover_datasets pattern="(?P&lt;identifier_0&gt;[^_]+)_(?P&lt;identifier_1&gt;[^_]+)\.fastq" ext="fastqsanger" visible="false" />
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160 <discover_datasets pattern="(?P&lt;identifier_0&gt;[^_]+)_(?P&lt;identifier_1&gt;[^_]+)\.fasta" ext="fasta" visible="false" />
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161 </collection>
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162 <collection name="output_collection" type='list' label="Single-end Fast(q|a)">
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163 <filter>input['input_select'] == "file_list"</filter>
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164 <discover_datasets pattern="(?P&lt;designation&gt;.+)__single\.fastq" directory="." ext='fastqsanger'/>
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165 <discover_datasets pattern="(?P&lt;designation&gt;.+)__single\.fasta" directory="." ext='fasta'/>
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166 </collection>
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167 <data format="fastqsanger" name="output_accession" >
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168 <filter>input['input_select'] == "accession_number"</filter>
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169 <change_format>
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170 <when input="outputformat" value="fasta" format="fasta"/>
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171 </change_format>
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172 </data>
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173 <data format="fastqsanger" name="output_file" label="${input.file.name}.${outputformat}">
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174 <filter>input['input_select'] == "file"</filter>
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175 <change_format>
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176 <when input="outputformat" value="fasta" format="fasta"/>
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177 </change_format>
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178 </data>
0
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179 </outputs>
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180 <tests>
1
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181 <test>
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182 <param name="input_select" value="accession_number"/>
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183 <param name="outputformat" value="fastqsanger"/>
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184 <param name="accession" value="SRR044777"/>
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185 <param name="skip_technical" value="True"/>
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186 <output name="output_accession">
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187 <assert_contents>
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188 <not_has_text text="rRNA_primer"/>
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189 <has_text text="F47USSH02GNP1D" />
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190 </assert_contents>
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191 </output>
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192 </test>
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193 <test>
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194 <param name="input_select" value="accession_number"/>
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195 <param name="outputformat" value="fastqsanger"/>
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196 <param name="accession" value="SRR925743"/>
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197 <param name="maxID" value="5"/>
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198 <output name="output_accession" file="fastq_dump_result.fastq" ftype="fastqsanger"/>
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199 </test>
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200 </tests>
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201 <help>
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202 This tool extracts reads from SRA archives using fastq-dump.
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203 The fastq-dump program is developed at NCBI, and is available at
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204 http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software.
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205
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206 NB: Single-end or pair-end collections may be empty if given SRRs LibraryLayout contains only either SINGLE or PAIRED respectively
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207 @SRATOOLS_ATTRRIBUTION@
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208 </help>
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209 <expand macro="citation"/>
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210 </tool>