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18
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1 <tool id="usearch_fastq_mergepairs" name="usearch fastq_mergepairs" version="0.0.2">
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2
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2 <description>merging of paired reads</description>
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3 <version_command>usearch -version</version_command>
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12
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4 <command interpreter='bash'>usearch_wrapper.sh
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5 usearch
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6 -quiet
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7
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7 -fastq_mergepairs '$input_forward'
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8 -reverse '$input_reverse'
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17
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9 #if $minovlen.value != 0
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13
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10 -fastq_minovlen $minovlen
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7
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11 #end if
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22
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12 #if $minmergelen.value != 0
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13 -fastq_minmergelen $minmergelen
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14 #end if
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24
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15 #if $maxmergelen.value != 0
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16 -fastq_maxmergelen $maxmergelen
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17 #end if
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18 #if $maxdiffs.value != 0
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19 -fastq_maxdiffs $maxdiffs
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20 #end if
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21 #if $truncqual.value != 0
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22 -fastq_truncqual $truncqual
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23 #end if
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24 #if $minlen.value != 0
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25 -fastq_minlen $minlen
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26 #end if
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25
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27 $allowmergestagger
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28 -fastq_ascii $ascii
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29 -fastq_qmin $qmin
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7
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30 -fastq_qmax $qmax
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25
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31 -fastq_qmaxout $qmaxout
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26
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32 #if $output_format.format == "fastq"
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33 -fastqout $output
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34 #else
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35 -fastaout $output
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36 #end if
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2
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37 </command>
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38 <inputs>
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17
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39 <!-- INPUT OPTIONS -->
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27
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40 <param name="input_forward" type="data" format="fastq,fastqsanger,fastqcssanger" label="1. File with forward reads" />
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41 <param name="input_reverse" type="data" format="fastq,fastqsanger,fastqcssanger" label="2. File with reverse reads" />
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42 <param name="minovlen" type="integer" value="0" label="3. Minimum length of the overlap" help="'0' means no minimum." />
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43 <param name="minmergelen" type="integer" value="0" label="4. Minimum length of the merged read" help="'0' means no minimum." />
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44 <param name="maxmergelen" type="integer" value="0" label="5. Maximum length of the merged read" help="'0' means no maximum." />
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30
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45 <param name="maxdiffs" type="integer" value="0" label="6. Maximum number of mismatches allowed in the overlap region" help="'0' means any number of mismatches allowed." />
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46 <param name="truncqual" type="integer" value="0" label="7. Truncate the forward and reverse reads at the first Q that is equal or less than this value, if present"
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29
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47 help="'0' means no quality truncation. This truncation is performed before aligning the pair. With Illumina paired reads, it is recommended to set this to 2 or higher, as low-quality tails will otherwise often cause alignment of the pair to fail." />
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28
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48 <param name="minlen" type="integer" value="0" label="8. Minimum length of the forward and reverse read, after truncating per option 7 if applicable" help="'0' means no minimum." />
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27
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49 <param name="allowmergestagger" type="boolean" truevalue="-fastq_allowmergestagger" falsevalue="" checked="false" label="9. Allow merge of a pair where the alignment is staggered" help="By default, pairs with staggered alignments are discarded." />
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50 <param name="ascii" type="integer" value="33" label="10. ASCII_BASE constant" help="See http://drive5.com/usearch/manual/fastq_params.html" />
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51 <param name="qmin" type="integer" value="0" label="11. Minimum Q score" />
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52 <param name="qmax" type="integer" value="41" label="12. Maximum Q score for input files" />
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53 <param name="qmaxout" type="integer" value="41" label="13. Maximum Q score for output files" />
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17
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54
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55 <!-- OUTPUT OPTIONS -->
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56 <conditional name="output_format">
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19
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57 <param name="format" type="select" label="Output format">
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58 <option value="fastq" selected="true">FASTQ</option>
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17
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59 <option value="fasta">FASTA</option>
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60 </param>
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61 <when value="fastq"></when>
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62 <when value="fasta"></when>
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63 </conditional>
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64 </inputs>
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2
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65 <outputs>
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28
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66 <data format="fastq" name="output" label="Merge output">
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67 <change_format>
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68 <when input="format" value="fasta" format="fasta" />
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69 </change_format>
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70 </data>
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2
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71 </outputs>
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72 <tests>
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73 <test>
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74 <param name="input_forward" value="fastq_mergepairs_input1.fq" ftype="fastqsanger" />
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75 <param name="input_reverse" value="fastq_mergepairs_input2.fq" ftype="fastqsanger" />
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5
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76 <param name="qmax" value="65" />
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2
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77 <output name="output" file="fastq_mergepairs_output.fq" />
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78 </test>
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79 </tests>
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80 <help>
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81 **What it Does**
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82
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83 Performs merging of paired reads.
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84
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85 The FASTQ filename for the forward reads is specified by the -fastq_mergepairs option, and the reverse read filename is specified by the -reverse option. Output files are specified by -fastqout (for FASTQ) and / or -fastaout (for FASTA).
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86
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87 Forward and reverse must be in 1:1 correspondence and must appear in the same order in both files. The labels for the forward and reverse read in a given pair must be identical except for a single position where a '1' appears in the forward read label and a '2' appears in the reverse read label.
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88
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89 -----
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90
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91 **Input formats**
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92
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93 Forward read::
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94
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95 @IRIS:7:1:29:952#0/1
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96 TGAGAAGCAAGAAGAAGGTTGGTTAGTGTTTTGGAG
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97 +IRIS:7:1:29:952#0/1
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98 aaabaaaaaaaaaaa`aaY`aa^aaa^a_a_`aa``
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99
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100 Reverse read::
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101
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102 @IRIS:7:1:29:952#0/2
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103 GACTCCAAAACACTAACCAACCTTCTTCTTGCTTCT
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104 +IRIS:7:1:29:952#0/2
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105 aaaabaaaabaaaabbaaaa````__`__^__``__
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106
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107 -----
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108
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109 **Output**
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110
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111 A multiple-fastq file, for example::
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112
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113 @IRIS:7:1:29:952#0/1
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114 TGAGAAGCAAGAAGAAGGTTGGTTAGTGTTTTGGAGTC
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115 +
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116 aaJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJaa
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117
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118 ------
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119
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120 **Manual**
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121
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30
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122 * USEARCH fastq_mergepairs command options: http://drive5.com/usearch/manual/fastq_mergepairs.html
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123 * FASTQ format options: http://drive5.com/usearch/manual/fastq_params.html
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2
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124
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125 **Citation**
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126
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127 Please cite one of these papers if you use USEARCH in published work.
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128
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129 Edgar,RC (2010) Search and clustering orders of magnitude faster than BLAST, Bioinformatics 26(19), 2460-2461.
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130 doi: 10.1093/bioinformatics/btq461
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131 </help>
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132 </tool>
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