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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"
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3 version="2020.8">
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4 <description>Join paired-end reads.</description>
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5 <requirements>
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6 <requirement type="package" version="2020.8">qiime2</requirement>
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7 </requirements>
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8 <command><![CDATA[
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9 qiime vsearch join-pairs
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10
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11 --i-demultiplexed-seqs=$idemultiplexedseqs
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12
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13 #if str($ptruncqual):
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14 --p-truncqual=$ptruncqual
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15 #end if
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16 --p-minlen=$pminlen
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17
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18 #if str($pmaxns):
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19 --p-maxns=$pmaxns
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20 #end if
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21 #if $pallowmergestagger:
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22 --p-allowmergestagger
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23 #end if
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24
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25 --p-minovlen=$pminovlen
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26
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27 --p-maxdiffs=$pmaxdiffs
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28
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29 #if str($pminmergelen):
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30 --p-minmergelen=$pminmergelen
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31 #end if
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32 #if str($pmaxmergelen):
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33 --p-maxmergelen=$pmaxmergelen
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34 #end if
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35 #if str($pmaxee):
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36 --p-maxee=$pmaxee
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37 #end if
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38 --p-qmin=$pqmin
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39
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40 --p-qminout=$pqminout
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41
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42 --p-qmax=$pqmax
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43
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44 --p-qmaxout=$pqmaxout
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45
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46 --p-threads=$pthreads
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47
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48 --o-joined-sequences=ojoinedsequences
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49
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50 #if str($examples) != 'None':
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51 --examples=$examples
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52 #end if
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53
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54 ;
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55 cp ojoinedsequences.qza $ojoinedsequences
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56
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57 ]]></command>
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58 <inputs>
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59 <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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60 <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="False" type="text" />
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61 <param label="--p-minlen: INTEGER Sequences shorter than minlen after truncation are Range(0, None) discarded. [default: 1]" min="0" name="pminlen" optional="True" type="integer" value="1" />
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62 <param label="--p-maxns: INTEGER Sequences with more than maxns N characters are Range(0, None) discarded. [optional]" name="pmaxns" optional="False" type="text" />
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63 <param label="--p-allowmergestagger: --p-allowmergestagger: / --p-no-allowmergestagger Allow joining of staggered read pairs. [default: False]" name="pallowmergestagger" selected="False" type="boolean" />
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64 <param label="--p-minovlen: INTEGER Minimum overlap length of forward and reverse reads Range(0, None) for joining. [default: 10]" min="0" name="pminovlen" optional="True" type="integer" value="10" />
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65 <param label="--p-maxdiffs: INTEGER Maximum number of mismatches in the forward/reverse Range(0, None) read overlap for joining. [default: 10]" min="0" name="pmaxdiffs" optional="True" type="integer" value="10" />
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66 <param label="--p-minmergelen: INTEGER Range(0, None) Minimum length of the joined read to be retained. [optional]" name="pminmergelen" optional="False" type="text" />
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67 <param label="--p-maxmergelen: INTEGER Range(0, None) Maximum length of the joined read to be retained. [optional]" name="pmaxmergelen" optional="False" type="text" />
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68 <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="False" type="text" />
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69 <param exclude_max="False" label="--p-qmin: INTEGER Range(-5, 2, inclusive_end=True) The minimum allowed quality score in the input. [default: 0]" max="2" min="-5" name="pqmin" optional="True" type="integer" value="0" />
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70 <param exclude_max="False" label="--p-qminout: INTEGER Range(-5, 2, inclusive_end=True) The minimum allowed quality score to use in output. [default: 0]" max="2" min="-5" name="pqminout" optional="True" type="integer" value="0" />
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71 <param exclude_max="False" label="--p-qmax: INTEGER Range(40, 41, inclusive_end=True) The maximum allowed quality score in the input. [default: 41]" max="41" min="40" name="pqmax" optional="True" type="integer" value="41" />
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72 <param exclude_max="False" label="--p-qmaxout: INTEGER Range(40, 41, inclusive_end=True) The maximum allowed quality score to use in output. [default: 41]" max="41" min="40" name="pqmaxout" optional="True" type="integer" value="41" />
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73 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
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74
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75 </inputs>
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76
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77 <outputs>
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78 <data format="qza" label="${tool.name} on ${on_string}: joinedsequences.qza" name="ojoinedsequences" />
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79
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80 </outputs>
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81
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82 <help><![CDATA[
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83 Join paired-end reads.
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84 ###############################################################
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85
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86 Join paired-end sequence reads using vsearch's merge_pairs function. The
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87 qmin, qminout, qmax, and qmaxout parameters should only need to be modified
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88 when working with older fastq sequence data. See the vsearch documentation
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89 for details on how paired-end joining is performed, and for more
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90 information on the parameters to this method.
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91
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92 Parameters
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93 ----------
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94 demultiplexed_seqs : SampleData[PairedEndSequencesWithQuality]
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95 The demultiplexed paired-end sequences to be joined.
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96 truncqual : Int % Range(0, None), optional
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97 Truncate sequences at the first base with the specified quality score
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98 value or lower.
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99 minlen : Int % Range(0, None), optional
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100 Sequences shorter than minlen after truncation are discarded.
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101 maxns : Int % Range(0, None), optional
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102 Sequences with more than maxns N characters are discarded.
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103 allowmergestagger : Bool, optional
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104 Allow joining of staggered read pairs.
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105 minovlen : Int % Range(0, None), optional
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106 Minimum overlap length of forward and reverse reads for joining.
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107 maxdiffs : Int % Range(0, None), optional
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108 Maximum number of mismatches in the forward/reverse read overlap for
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109 joining.
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110 minmergelen : Int % Range(0, None), optional
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111 Minimum length of the joined read to be retained.
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112 maxmergelen : Int % Range(0, None), optional
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113 Maximum length of the joined read to be retained.
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114 maxee : Float % Range(0.0, None), optional
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115 Maximum number of expected errors in the joined read to be retained.
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116 qmin : Int % Range(-5, 2, inclusive_end=True), optional
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117 The minimum allowed quality score in the input.
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118 qminout : Int % Range(-5, 2, inclusive_end=True), optional
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119 The minimum allowed quality score to use in output.
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120 qmax : Int % Range(40, 41, inclusive_end=True), optional
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121 The maximum allowed quality score in the input.
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122 qmaxout : Int % Range(40, 41, inclusive_end=True), optional
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123 The maximum allowed quality score to use in output.
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124 threads : Int % Range(0, 8, inclusive_end=True), optional
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125 The number of threads to use for computation. Does not scale much past
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126 4 threads.
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127
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128 Returns
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129 -------
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130 joined_sequences : SampleData[JoinedSequencesWithQuality]
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131 The joined sequences.
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132 ]]></help>
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133 <macros>
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134 <import>qiime_citation.xml</import>
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135 </macros>
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136 <expand macro="qiime_citation"/>
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137 </tool> |
