Mercurial > repos > iuc > sra_tools

annotate fastq_dump.xml @ 0:b723c120161a draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
author iuc
date Sun, 06 Dec 2015 09:04:37 -0500
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children 462ee06c9358
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b723c120161a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
iuc
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1 <tool id="fastq_dump" name="Extract reads" version="1.2.5">
b723c120161a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
iuc
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2 <description>in FASTQ/A format from NCBI SRA.</description>
b723c120161a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
iuc
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3 <macros>
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iuc
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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
iuc
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5 </macros>
b723c120161a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
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6 <expand macro="requirements"/>
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7 <stdio>
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iuc
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8 <exit_code range="127" level="fatal" description="Could not locate fastq-dump binary"/>
b723c120161a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
iuc
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9 </stdio>
b723c120161a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
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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[
b723c120161a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
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13 ## Need to set the home directory to the current working directory,
b723c120161a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
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14 ## else the tool tries to write to home/.ncbi and fails when used
b723c120161a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
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15 ## with a cluster manager.
b723c120161a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
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16 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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17 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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18 #if $input.input_select == "file":
b723c120161a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
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19 fastq-dump --log-level fatal --accession '${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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20 #else:
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21 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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22 ## 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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23 ## 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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24 #if ( str( $adv.region ) == "" ) and ( str( $adv.minID ) == "" ) and ( str( $adv.maxID ) == "" ):
b723c120161a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
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25 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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26 ASCP_KEY=`dirname \$ASCP_PATH`/asperaweb_id_dsa.openssh || true &&
b723c120161a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
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27 prefetch --ascp-path "\$ASCP_PATH|\$ASCP_KEY" $input.accession &&
b723c120161a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
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28 ## Duplicate vdb-config, in case settings changed between prefetch and
b723c120161a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
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29 ## dump command.
b723c120161a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
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30 vdb-config -s "/repository/user/main/public/root=\$PWD" &&
b723c120161a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
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31 #end if
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32 fastq-dump --accession "$input.accession"
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33 #end if
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34 --defline-seq '@\$sn[_\$rn]/\$ri'
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35 --stdout
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36 $adv.split
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37 #if str( $adv.alignments ) == "aligned":
b723c120161a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
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38 --aligned
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39 #end if
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40 #if str( $adv.alignments ) == "unaligned":
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41 --unaligned
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42 #end if
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43 #if str( $adv.minID ) != "":
b723c120161a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
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44 --minSpotId "$adv.minID"
b723c120161a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
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45 #end if
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46 #if str( $adv.maxID ) != "":
b723c120161a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
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47 --maxSpotId "$adv.maxID"
b723c120161a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
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48 #end if
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49 #if str( $adv.minlen ) != "":
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50 --minReadLen "$adv.minlen"
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51 #end if
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52 #if str( $adv.readfilter ) != "":
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53 --read-filter "$adv.readfilter"
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54 #end if
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55 #if str( $adv.region ) != "":
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56 --aligned-region "$adv.region"
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57 #end if
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58 #if str( $adv.spotgroups ) != "":
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59 --spot-groups "$adv.spotgroups"
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60 #end if
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61 #if str( $adv.matepairDist ) != "":
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62 --matepair-distance "$adv.matepairDist"
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63 #end if
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64 $adv.clip
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65 $adv.skip_technical
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66 #if str( $outputformat ) == "fasta":
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67 --fasta
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68 #end if
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69 #if $input.input_select=="file":
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70 "$input.file" > "$output_file"
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71 #else:
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72 "$input.accession" > "$output_accession"
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73 #end if
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74 ]]>
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75 </command>
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76 <inputs>
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77 <expand macro="input_conditional"/>
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78 <param name="outputformat" type="select" label="select output format">
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79 <option value="fastqsanger">fastq</option>
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80 <option value="fasta">fasta</option>
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81 </param>
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82 <section name="adv" title="Advanced Options" expanded="False">
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83 <param name="minID" type="integer" label="minimum spot ID" optional="true"/>
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84 <param name="maxID" type="integer" label="maximum spot ID" optional="true"/>
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85 <param name="minlen" type="integer" label="minimum read length" optional="true"/>
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86 <param name="split" type="boolean" checked="true" truevalue="--split-spot" falsevalue="">
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87 <label>split spot by read pairs</label>
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88 </param>
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89 <expand macro="alignments"/>
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90 <expand macro="region"/>
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91 <expand macro="matepairDist"/>
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92 <param name="readfilter" type="select" value="">
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93 <label>filter by value</label>
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94 <option value="">None</option>
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95 <option value="pass">pass</option>
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96 <option value="reject">reject</option>
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97 <option value="criteria">criteria</option>
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98 <option value="redacted">redacted</option>
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99 </param>
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100 <param name="spotgroups" type="text" label="filter by spot-groups" optional="true"/>
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101 <param name="clip" type="boolean" truevalue="--clip" falsevalue="">
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102 <label>apply left and right clips</label>
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103 </param>
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104 <param name="skip_technical" type="boolean" truevalue="--skip-technical" falsevalue="" checked="False" label="Dump only biological reads"/>
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105 </section>
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106 </inputs>
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107 <outputs>
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108 <data format="fastq" name="output_accession" label="${input.accession}.${outputformat}">
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109 <filter>input['input_select'] == "accession_number"</filter>
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110 <change_format>
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111 <when input="outputformat" value="fasta" format="fasta"/>
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112 </change_format>
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113 </data>
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114 <data format="fastq" name="output_file" label="${input.file.name}.${outputformat}">
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115 <filter>input['input_select'] == "file"</filter>
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116 <change_format>
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117 <when input="outputformat" value="fasta" format="fasta"/>
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118 </change_format>
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119 </data>
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120 </outputs>
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121 <tests>
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122 <test>
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123 <param name="input_select" value="accession_number"/>
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124 <param name="outputformat" value="fastqsanger"/>
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125 <param name="accession" value="SRR044777"/>
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126 <param name="skip_technical" value="True"/>
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127 <output name="output_accession">
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128 <assert_contents>
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129 <not_has_text text="rRNA_primer"/>
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130 <has_text text="F47USSH02GNP1D" />
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131 </assert_contents>
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132 </output>
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133 </test>
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134 <test>
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135 <param name="input_select" value="accession_number"/>
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136 <param name="outputformat" value="fastqsanger"/>
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137 <param name="accession" value="SRR925743"/>
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138 <param name="maxID" value="5"/>
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139 <output name="output_accession" file="fastq_dump_result.fastq" ftype="fastq"/>
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140 </test>
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141 </tests>
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142 <help>
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143 This tool extracts reads from SRA archives using fastq-dump.
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144 The fastq-dump program is developed at NCBI, and is available at
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145 http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software.
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146 @SRATOOLS_ATTRRIBUTION@
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147 </help>
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148 <expand macro="citation"/>
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149 </tool>