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1 <tool id="rna_probing_preprocessing" version="1.0.0" name="Preprocessing" force_history_refresh="True">
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2 <description>RNA probing data</description>
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3
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4 <requirements>
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5 <requirement type="package" version="4.1.0">gnu_awk</requirement>
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6 <requirement type="set_environment">RNA_RPOBING_SCRIPT_PATH</requirement>
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7 </requirements>
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8
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9 <command interpreter="bash">
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10 preprocessing.sh
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11
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12 ## check if paired-end
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13 #if str( $library.type ) == "paired"
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14 -2 $library.input2
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15 #end if
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16
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17 ## Inputs
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18 -1 $library.input1
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19
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20 ## Barcode sequence
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21 -b '$library.barcode_seq'
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22
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23 ## Trimming length
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24 -t $trim
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25 </command>
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26
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27 <inputs>
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28 <!-- single/paired -->
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29 <conditional name="library">
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30 <param name="type" type="select" label="Is this single or paired-end sequencing?">
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31 <option value="single">Single-end</option>
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32 <option value="paired">Paired-end</option>
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33 </param>
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34 <when value="single">
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35 <param format="fastqsanger" name="input1" type="data" label="FASTQ file" help="Must have Sanger-scaled quality values (fastqsanger)." />
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36 <param name="barcode_seq" type="text" size="20" label="Barcode sequence" help="Reads that do not start with the signature will be removed. Use IUPAC alphabet, e.g. NNNNXRTYNN as in the randomized part of the ligation adapter." >
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37 <!-- <validator type="empty_field" message="Specify the Barcode sequence" /> -->
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38 </param>
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39 </when>
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40 <when value="paired">
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41 <param format="fastqsanger" name="input1" type="data" label="FASTQ file (read 1)" help="Must have Sanger-scaled quality values (fastqsanger)." />
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42 <param format="fastqsanger" name="input2" type="data" label="FASTQ file (read 2)" help="Must have Sanger-scaled quality values (fastqsanger)." />
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43 <param name="barcode_seq" type="text" size="20" label="Barcode sequence" help="Reads that do not start with the signature will be removed. Use IUPAC alphabet, e.g. NNNNXRTYNN as in the randomized part of the ligation adapter." >
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44 <!-- <validator type="empty_field" message="Specify the Barcode sequence" /> -->
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45 </param>
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46 </when>
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47 </conditional>
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48 <param name="trim" type="integer" min="0" optional="true" value="15" label="3' trimming length" help="Number of random bases for random priming, will be removed as they are likely to differ from a template." />
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49
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50 </inputs>
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51
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52 <outputs>
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53 <data format="fastqsanger" name="output1" label="${tool.name} on ${on_string}: Read 1" from_work_dir="output_dir/read1.fastq" />
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54 <data format="fastqsanger" name="output2" label="${tool.name} on ${on_string}: Read 2" from_work_dir="output_dir/read2.fastq" >
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55 <filter> library['type'] == "paired"</filter>
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56 </data>
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57 <data format="tabular" name="barcodes" label="${tool.name} on ${on_string}: Barcodes" from_work_dir="output_dir/barcodes.txt">
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58 <filter> library['barcode_seq'] != '' </filter>
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59 </data>
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60 </outputs>
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61
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62 <tests>
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63 <test>
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64 <param name="input1" value="reads1.fastq"/>
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65 <param name="input2" value="reads2.fastq"/>
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66 <param name="barcode_seq" value="NNNNNNN"/>
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67 <param name="trim" value="15"/>
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68 <output name="output1" file="reads1_preprocessed.fastq"/>
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69 <output name="output2" file="reads2_preprocessed.fastq"/>
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70 <output name="barcodes" file="barcodes.txt"/>
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71 </test>
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72 </tests>
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73
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74 <help>
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75 **What it does**
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76
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77 *Preprocessing* tool removes and saves the random barcodes sequences, if they were ligated to 3’ ends of cDNA, in a separate dataset to be used in downstream analysis. Additionally to debarcoding, it trims 1) the 5’ end of the second-in-pair reads to remove the reverse transcription primer derived sequence and 2) 3’ end of both reads to remove possible random barcode incorporation in the second-in-pair read and random primer in first-in-pair read.
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78
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79 ------
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80
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81 **Examples**
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82
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83 Sample input files (quality scores omited)::
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84
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85 * Read1
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86 @DJG83KN1:255:C3U57ACXX:3:1101:1215:2296 1:N:0:ATCACG
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87 TTCGCACAACATNATGGAGGCTTCACGGTACAGAACGAGGCCAGCAAATACCAAGTCTCAGTGAACAAATACAAAGGGACGGCTGGCAACGCCCTCAT
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88 @DJG83KN1:255:C3U57ACXX:3:1101:1142:2461 1:N:0:ATCACG
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89 ACCCCGCATCAAATTGGGAACTACTTCCAGCAGTTGTTAGACTTGGGCTCTGGCAGCCCCTTGGAGTGGAGGGACTTGCAGCCCTTCTTATCAGGTCT
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90
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91 * Read2
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92 @DJG83KN1:255:C3U57ACXX:3:1101:1215:2296 2:N:0:ATCACG
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93 CACAAATCTGCCGTTTGGATTGGCTGCATGGCATCTGTTATACCACCAGCCACCACCATCTTCTTTGGAGCACTGTTTTCTTGGATCCGTAGTTACCC
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94 @DJG83KN1:255:C3U57ACXX:3:1101:1142:2461 2:N:0:ATCACG
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95 GTTGGGGGTGTGGGGAAAAAAATAAAAATCGTGAGAAGTTTTAAGACTATGTCACAAAAATGGCTTTAATTATACCATCAAACAGAAACCACCAATTG
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96
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97 Run 1 - Barcode Sequence = '', Trimming length = 10::
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98
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99 * Read1
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100 @DJG83KN1:255:C3U57ACXX:3:1101:1215:2296
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101 TTCGCACAACATNATGGAGGCTTCACGGTACAGAACGAGGCCAGCAAATACCAAGTCTCAGTGAACAAATACAAAGGGACGGCTGGCA
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102 @DJG83KN1:255:C3U57ACXX:3:1101:1142:2461
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103 ACCCCGCATCAAATTGGGAACTACTTCCAGCAGTTGTTAGACTTGGGCTCTGGCAGCCCCTTGGAGTGGAGGGACTTGCAGCCCTTCT
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104
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105 * Read2
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106 @DJG83KN1:255:C3U57ACXX:3:1101:1215:2296
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107 CCGTTTGGATTGGCTGCATGGCATCTGTTATACCACCAGCCACCACCATCTTCTTTGGAGCACTGTTTTCTTGGATCCGTAGTTACCC
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108 @DJG83KN1:255:C3U57ACXX:3:1101:1142:2461
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109 TGGGGAAAAAAATAAAAATCGTGAGAAGTTTTAAGACTATGTCACAAAAATGGCTTTAATTATACCATCAAACAGAAACCACCAATTG
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110
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111 Run 2 - Barcode Sequence = 'NNNNNNN', Trimming length = 10::
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112
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113 * Read1
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114 @DJG83KN1:255:C3U57ACXX:3:1101:1215:2296
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115 AACATNATGGAGGCTTCACGGTACAGAACGAGGCCAGCAAATACCAAGTCTCAGTGAACAAATACAAAGGGACGGCTGGCA
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116 @DJG83KN1:255:C3U57ACXX:3:1101:1142:2461
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117 ATCAAATTGGGAACTACTTCCAGCAGTTGTTAGACTTGGGCTCTGGCAGCCCCTTGGAGTGGAGGGACTTGCAGCCCTTCT
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118
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119 * Read2
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120 @DJG83KN1:255:C3U57ACXX:3:1101:1215:2296
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121 CCGTTTGGATTGGCTGCATGGCATCTGTTATACCACCAGCCACCACCATCTTCTTTGGAGCACTGTTTTCTTGGATCCGTA
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122 @DJG83KN1:255:C3U57ACXX:3:1101:1142:2461
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123 TGGGGAAAAAAATAAAAATCGTGAGAAGTTTTAAGACTATGTCACAAAAATGGCTTTAATTATACCATCAAACAGAAACCA
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124
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125 * Barcodes
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126
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127 @DJG83KN1:255:C3U57ACXX:3:1101:1215:2296 TTCGCAC
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128 @DJG83KN1:255:C3U57ACXX:3:1101:1142:2461 ACCCCGC
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129
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130 </help>
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131
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132 <citations>
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133 <citation type="doi">10.1093/nar/gku167</citation>
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134 </citations>
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135
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136 </tool>
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