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1 <?xml version="1.0" ?>
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2 <tool id="qiime_vsearch_join-pairs" name="qiime vsearch join-pairs" version="2019.4">
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3 <description> - Join paired-end reads.</description>
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4 <requirements>
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5 <requirement type="package" version="2019.4">qiime2</requirement>
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6 </requirements>
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7 <command><![CDATA[
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8 qiime vsearch join-pairs
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9
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10 --i-demultiplexed-seqs=$idemultiplexedseqs
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11
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12 #if str($ptruncqual):
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13 --p-truncqual="$ptruncqual"
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14 #end if
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15
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16 #if $pminlen:
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17 --p-minlen=$pminlen
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18 #end if
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19
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20 #if str($pmaxns):
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21 --p-maxns="$pmaxns"
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22 #end if
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23
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24 #if $pallowmergestagger:
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25 --p-allowmergestagger
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26 #end if
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27
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28 #if $pminovlen:
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29 --p-minovlen=$pminovlen
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30 #end if
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31
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32 #if $pmaxdiffs:
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33 --p-maxdiffs=$pmaxdiffs
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34 #end if
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35
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36 #if str($pminmergelen):
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37 --p-minmergelen="$pminmergelen"
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38 #end if
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39
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40 #if str($pmaxmergelen):
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41 --p-maxmergelen="$pmaxmergelen"
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42 #end if
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43
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44 #if str($pmaxee):
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45 --p-maxee="$pmaxee"
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46 #end if
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47
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48 #if $pqmin:
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49 --p-qmin=$pqmin
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50 #end if
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51
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52 #if $pqminout:
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53 --p-qminout=$pqminout
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54 #end if
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55
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56 #if $pqmax:
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57 --p-qmax=$pqmax
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58 #end if
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59
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60 #if $pqmaxout:
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61 --p-qmaxout=$pqmaxout
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62 #end if
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63
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64 --o-joined-sequences=ojoinedsequences
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65 ;
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66 cp ojoinedsequences.qza $ojoinedsequences
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67 ]]></command>
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68 <inputs>
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69 <param format="qza,no_unzip.zip" label="--i-demultiplexed-seqs: ARTIFACT SampleData[PairedEndSequencesWithQuality] The demultiplexed paired-end sequences to be joined. [required]" name="idemultiplexedseqs" optional="False" type="data"/>
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70 <param label="--p-truncqual: INTEGER Truncate sequences at the first base with the Range(0, None) specified quality score value or lower. [optional]" name="ptruncqual" optional="True" min="0" type="integer"/>
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71 <param label="--p-minlen: INTEGER Sequences shorter than minlen after truncation are Range(0, None) discarded. [default: 1]" name="pminlen" optional="True" type="integer" min="0" value="1"/>
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72 <param label="--p-maxns: INTEGER Sequences with more than maxns N characters are Range(0, None) discarded. [optional]" name="pmaxns" optional="True" min="0" type="integer"/>
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73 <param label="--p-allowmergestagger: --p-no-allowmergestagger Allow joining of staggered read pairs. [default: False]" name="pallowmergestagger" selected="False" type="boolean"/>
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74 <param label="--p-minovlen: INTEGER Minimum overlap length of forward and reverse reads Range(0, None) for joining. [default: 10]" name="pminovlen" optional="True" type="integer" min="0" value="10"/>
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75 <param label="--p-maxdiffs: INTEGER Maximum number of mismatches in the forward/reverse Range(0, None) read overlap for joining. [default: 10]" name="pmaxdiffs" optional="True" type="integer" min="0" value="10"/>
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76 <param label="--p-minmergelen: INTEGER Range(0, None) Minimum length of the joined read to be retained. [optional]" name="pminmergelen" optional="True" min="0" type="integer"/>
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77 <param label="--p-maxmergelen: INTEGER Range(0, None) Maximum length of the joined read to be retained. [optional]" name="pmaxmergelen" optional="True" min="0" type="integer"/>
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78 <param label="--p-maxee: NUMBER Maximum number of expected errors in the joined read Range(0.0, None) to be retained. [optional]" name="pmaxee" optional="True" min="0" type="float"/>
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79 <param label="--p-qmin: INTEGER Range(-5, 2, inclusive_end=True) The minimum allowed quality score in the input. [default: 0]" name="pqmin" optional="True" type="integer" min="-5" max="2" exclude_max="False" value="0"/>
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80 <param label="--p-qminout: INTEGER Range(-5, 2, inclusive_end=True) The minimum allowed quality score to use in output. [default: 0]" name="pqminout" optional="True" type="integer" min="-5" max="2" exclude_max="False" value="0"/>
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81 <param label="--p-qmax: INTEGER Range(40, 41, inclusive_end=True) The maximum allowed quality score in the input. [default: 41]" name="pqmax" optional="True" type="integer" min="40" max="41" exclude_max="False" value="41"/>
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82 <param label="--p-qmaxout: INTEGER Range(40, 41, inclusive_end=True) The maximum allowed quality score to use in output. [default: 41]" name="pqmaxout" optional="True" type="integer" min="40" max="41" exclude_max="False" value="41"/>
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83 </inputs>
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84 <outputs>
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85 <data format="qza" label="${tool.name} on ${on_string}: joinedsequences.qza" name="ojoinedsequences"/>
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86 </outputs>
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87 <help><![CDATA[
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88 Join paired-end reads.
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89 ######################
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90
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91 Join paired-end sequence reads using vsearch's merge_pairs function. The
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92 qmin, qminout, qmax, and qmaxout parameters should only need to be modified
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93 when working with older fastq sequence data. See the vsearch documentation
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94 for details on how paired-end joining is performed, and for more
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95 information on the parameters to this method.
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96
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97 Parameters
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98 ----------
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99 demultiplexed_seqs : SampleData[PairedEndSequencesWithQuality]
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100 The demultiplexed paired-end sequences to be joined.
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101 truncqual : Int % Range(0, None), optional
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102 Truncate sequences at the first base with the specified quality score
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103 value or lower.
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104 minlen : Int % Range(0, None), optional
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105 Sequences shorter than minlen after truncation are discarded.
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106 maxns : Int % Range(0, None), optional
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107 Sequences with more than maxns N characters are discarded.
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108 allowmergestagger : Bool, optional
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109 Allow joining of staggered read pairs.
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110 minovlen : Int % Range(0, None), optional
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111 Minimum overlap length of forward and reverse reads for joining.
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112 maxdiffs : Int % Range(0, None), optional
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113 Maximum number of mismatches in the forward/reverse read overlap for
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114 joining.
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115 minmergelen : Int % Range(0, None), optional
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116 Minimum length of the joined read to be retained.
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117 maxmergelen : Int % Range(0, None), optional
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118 Maximum length of the joined read to be retained.
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119 maxee : Float % Range(0.0, None), optional
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120 Maximum number of expected errors in the joined read to be retained.
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121 qmin : Int % Range(-5, 2, inclusive_end=True), optional
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122 The minimum allowed quality score in the input.
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123 qminout : Int % Range(-5, 2, inclusive_end=True), optional
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124 The minimum allowed quality score to use in output.
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125 qmax : Int % Range(40, 41, inclusive_end=True), optional
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126 The maximum allowed quality score in the input.
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127 qmaxout : Int % Range(40, 41, inclusive_end=True), optional
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128 The maximum allowed quality score to use in output.
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129
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130 Returns
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131 -------
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132 joined_sequences : SampleData[JoinedSequencesWithQuality]
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133 The joined sequences.
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134 ]]></help>
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135 <macros>
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136 <import>qiime_citation.xml</import>
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137 </macros>
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138 <expand macro="qiime_citation"/>
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139 </tool>
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