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2 <!-- Flexbar tool definition for Galaxy, version 2.5 -->
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3 <!-- Author: Johannes Roehr -->
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4 <!-- Modified by Daniel Maticzka as specialized tool for splitting binary barcodes. -->
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5
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6
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7 <tool id="flexbar_split_RYYR_bcs" name="Split by binary barcodes" version="2.5">
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8
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9 <description>using RYYR IUPAC pattern.</description>
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10
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11 <requirements>
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12 <requirement type="package" version="2.5">flexbar</requirement>
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13
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13 </requirements>
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14
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15 <version_command>flexbar --version</version_command>
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16
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58
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17 <command><![CDATA[
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18
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19 flexbar
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20
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21 --threads \${GALAXY_SLOTS:-1}
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22
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23 --reads $reads
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24
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25 --reads2 $reads2
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26
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27 #if $reads.ext == "fastqsanger":
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28 --format sanger
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29 #end if
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30 #if $reads.ext == "fastqsolexa":
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31 --format solexa
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32 #end if
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33 #if $reads.ext == "fastqillumina":
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34 --format i1.3
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35 #end if
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36 #if $reads.ext == "csfasta":
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37 --color-space
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38 #end if
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39 #if $reads.ext == "fastqcssanger":
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40 --color-space
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41 #end if
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42
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43 --barcodes $__tool_directory__/RYYR_bcs.fa
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44
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45 --barcode-reads $bReads
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46
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47 --barcode-threshold $bThresh
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48
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49 --max-uncalled $maxUncalled
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50 --min-read-length $minReadLen
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51
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52 > $output
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53
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54 && mv flexbar_barcode_repA_1.fastq $output_repA_1
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55 && mv flexbar_barcode_repA_2.fastq $output_repA_2
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56 && mv flexbar_barcode_repB_1.fastq $output_repB_1
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57 && mv flexbar_barcode_repB_2.fastq $output_repB_2
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10
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58
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58
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59 && sleep 20
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60
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61 ]]></command>
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62
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63
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64 <inputs>
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65
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66 <param format="fasta,fastq,fastqsanger,fastqsolexa,fastqillumina,csfasta,fastqcssanger" name="reads" type="data" label="Sequencing reads" optional="false"/>
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67
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68 <param format="fasta,fastq,fastqsanger,fastqsolexa,fastqillumina,csfasta,fastqcssanger" name="reads2" type="data" label="Reads 2" optional="false" help="same format as first read set"/>
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69
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70 <param format="fasta,fastq,fastqsanger,fastqsolexa,fastqillumina,csfasta,fastqcssanger" name="bReads" type="data" label="Separate barcode reads" optional="false"/>
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71
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72 <param name="bThresh" size="4" type="integer" value="1" label="Threshold" optional="false" help="allowed mismatches and indels per 10 bases"/>
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73
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74 <param name="maxUncalled" size="4" type="integer" value="0" label="Max uncalled" optional="false" help="allowed uncalled bases per read"/>
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75
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76 <param name="minReadLen" size="4" type="integer" value="18" label="Minimum read length" optional="false" help="shorter reads are discarded"/>
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77
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78 </inputs>
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79
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80 <stdio>
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81 <exit_code range="1:" level="fatal" description="Error!" />
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82 </stdio>
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83
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84 <outputs>
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85 <data format="txt" name="output" metadata_source="reads"/>
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86 <data format="fastq" name="output_repA_1"/>
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87 <data format="fastq" name="output_repA_2"/>
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88 <data format="fastq" name="output_repB_1"/>
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89 <data format="fastq" name="output_repB_2"/>
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90 </outputs>
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91
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92
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93 <help>
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94
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95 **Description**
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96
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97 This tool splits paired-end reads according to an external set of barcode reads in RY IUPAC format according to patterns RYYR (replicate A) and YRRY (replicate B) using Flexbar.
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98
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99 .. _project: https://github.com/seqan/flexbar
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100
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101 ------
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102
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103 **Reference**
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104
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105 Matthias Dodt, Johannes T. Roehr, Rina Ahmed, Christoph Dieterich: Flexbar — flexible barcode and adapter processing for next-generation sequencing platforms. Biology 2012, 1(3):895-905.
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106
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107 </help>
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108
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109 </tool>
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