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1 <tool id="fastq_dump" name="Extract reads" version="1.1.1">
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2 <description> from NCBI SRA.</description>
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3 <command>
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4 fastq-dump --log-level fatal
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5 #if $input.input_select == "file":
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6 --accession '${input.file.name}'
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7 #else:
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8 --accession $input.accession
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9 #end if
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10 --defline-seq '@\$sn[_\$rn]/\$ri'
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11 --stdout
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12 #if $split == "yes":
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13 --split-spot
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14 #end if
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15 #if str( $alignments ) == "aligned":
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16 --aligned
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17 #end if
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18 #if str( $alignments ) == "unaligned":
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19 --unaligned
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20 #end if
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21 #if str( $minID ) != "":
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22 --minSpotId $minID
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23 #end if
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24 #if str( $maxID ) != "":
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25 --maxSpotId $maxID
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26 #end if
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27 #if str( $minlen ) != "":
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28 --minReadLen $minlen
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29 #end if
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30 #if str( $readfilter ) != "":
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31 --read-filter $readfilter
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32 #end if
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33 #if str( $region ) != "":
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34 --aligned-region $region
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35 #end if
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36 #if str( $spotgroups ) != "":
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37 --spot-groups $spotgroups
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38 #end if
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39 #if str( $matepairDist ) != "":
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40 --matepair-distance $matepairDist
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41 #end if
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42 #if $clip == "yes":
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43 --clip
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44 #end if
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45 #if str( $outputformat ) == "fasta":
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46 --fasta
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47 #end if
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48 #if $input.input_select=="file":
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49 $input.file
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50 #else:
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51 $input.accession
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52 #end if
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53 > $output
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54 </command>
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55 <version_string>fastq-dump --version</version_string>
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56 <inputs>
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57 <conditional name="input">
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58 <param name="input_select" type="select" label="select input type">
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59 <option value="accession_number">SRR accession</option>
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60 <option value="file">SRA archive in current history</option>
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61 </param>
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62 <when value="file">
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63 <param format="sra" name="file" type="data" label="sra archive"/>
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64 </when>
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65 <when value="accession_number">
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66 <param format="text" name="accession" type="text" label="accession"/>
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67 </when>
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68 </conditional>
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69 <param format="text" name="minID" type="text" label="minimum spot ID"/>
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70 <param format="text" name="maxID" type="text" label="maximum spot ID"/>
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71 <param format="text" name="minlen" type="text" label="minimum read length"/>
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72 <param format="text" name="split" type="select" value="yes">
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73 <label>split spot by read pairs</label>
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74 <option value="yes">Yes</option>
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75 <option value="no">No</option>
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76 </param>
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77 <param format="text" name="alignments" type="select" value="both">
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78 <label>aligned or unaligned reads</label>
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79 <option value="both">both</option>
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80 <option value="aligned">aligned only</option>
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81 <option value="unaligned">unaligned only</option>
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82 </param>
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83 <param format="text" name="region" type="text" label="aligned region"/>
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84 <param format="text" name="matepairDist" type="text" label="mate-pair distance (from-to|unknown)"/>
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85 <param format="text" name="readfilter" type="select" value="">
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86 <label>filter by value</label>
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87 <option value="">None</option>
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88 <option value="pass">pass</option>
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89 <option value="reject">reject</option>
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90 <option value="criteria">criteria</option>
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91 <option value="redacted">redacted</option>
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92 </param>
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93 <param name="outputformat" type="select" label="select output format">
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94 <option value="fastqsanger">fastq</option>
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95 <option value="fasta">fasta</option>
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96 </param>
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97 <param format="text" name="spotgroups" type="text" label="filter by spot-groups"/>
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98 <param format="text" name="clip" type="select" value="no">
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99 <label>apply left and right clips</label>
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100 <option value="no">No</option>
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101 <option value="yes">Yes</option>
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102 </param>
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103 </inputs>
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104 <outputs>
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105 <data format="fastq" name="output">
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106 <change_format>
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107 <when input="outputformat" value="fasta" format="fasta" />
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108 </change_format>
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109 </data>
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110 </outputs>
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111 <stdio>
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112 <exit_code range="127" level="fatal" description="Could not locate fastq-dump binary"/>
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113 </stdio>
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114 <requirements>
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115 <requirement type="package" version="2.3.3-3">sra_toolkit</requirement>
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116 </requirements>
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117 <help>
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118 This tool extracts reads from SRA archives using fastq-dump.
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119 Browse the NCBI SRA for SRR accessions at http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=studies.
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120 The fastq-dump program is developed at NCBI, and is available at: http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software.
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121 Contact Matt Shirley at mdshw5@gmail.com for support and bug reports.
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122 </help>
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123 </tool>
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