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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="2018.4">
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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="2018.4">qiime2</requirement>
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6 </requirements>
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7 <command>
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8 <![CDATA[
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9 qiime vsearch join-pairs --i-demultiplexed-seqs=$idemultiplexedseqs
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10
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11 #if $pminovlen:
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12 --p-minovlen=$pminovlen
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13 #end if
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14
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15 #if str($ptruncqual):
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16 --p-truncqual="$ptruncqual"
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17 #end if
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18
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19 #if str($cmdconfig) != 'None':
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20 --cmd-config=$cmdconfig
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21 #end if
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22
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23 #if str($pminmergelen):
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24 --p-minmergelen="$pminmergelen"
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25 #end if
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26
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27 #if $pmaxdiffs:
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28 --p-maxdiffs=$pmaxdiffs
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29 #end if
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30
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31 #if str($pqminout):
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32 --p-qminout="$pqminout"
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33 #end if
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34
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35 #if str($pmaxmergelen):
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36 --p-maxmergelen="$pmaxmergelen"
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37 #end if
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38
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39 #if str($pmaxns):
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40 --p-maxns="$pmaxns"
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41 #end if
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42
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43 #if $pallowmergestagger:
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44 --p-allowmergestagger
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45 #else
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46 --p-no-allowmergestagger
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47 #end if
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48
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49 #if $pminlen:
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50 --p-minlen=$pminlen
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51 #end if
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52
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53 #if $pqmax:
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54 --p-qmax=$pqmax
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55 #end if
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56
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57 #if str($pmaxee):
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58 --p-maxee="$pmaxee"
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59 #end if
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60
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61 #if str($pqmin):
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62 --p-qmin="$pqmin"
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63 #end if
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64
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65 #if $pqmaxout:
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66 --p-qmaxout=$pqmaxout
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67 #end if
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68 --o-joined-sequences=ojoinedsequences;
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69
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70 cp ojoinedsequences.qza $ojoinedsequences;
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71 ]]>
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72 </command>
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73 <inputs>
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74 <param format="qza,no_unzip.zip" label="--i-demultiplexed-seqs: SampleData[PairedEndSequencesWithQuality] The demultiplexed paired-end sequences to be joined. [required]" name="idemultiplexedseqs" optional="False" type="data"/>
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75
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76 <param label="--p-truncqual: Truncate sequences at the first base with the specified quality score value or lower. [optional]" name="ptruncqual" optional="True" type="text"/>
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77
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78 <param label="--p-minlen: Sequences shorter than minlen after truncation are discarded. [default: 1]" name="pminlen" optional="True" type="integer" value="1"/>
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79 <param label="--p-maxns: Sequences with more than maxns N characters are discarded. [optional]" name="pmaxns" optional="True" type="text"/>
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80
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81 <param label="--p-allowmergestagger: --p-no-allowmergestagger Allow joining of staggered read pairs. [default: False]" name="pallowmergestagger" checked="False" type="boolean"/>
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82
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83 <param label="--p-minovlen: Minimum overlap length of forward and reverse reads for joining. [default: 10]" name="pminovlen" optional="True" type="integer" value="10"/>
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84 <param label="--p-maxdiffs: Maximum number of mismatches in the forward/reverse read overlap for joining. [default: 10]" name="pmaxdiffs" optional="True" type="integer" value="10"/>
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85
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86 <param label="--p-minmergelen: Minimum length of the joined read to be retained. [optional]" name="pminmergelen" optional="True" type="text"/>
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87 <param label="--p-maxmergelen: Maximum length of the joined read to be retained. [optional]" name="pmaxmergelen" optional="True" type="text"/>
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88
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89 <param label="--p-maxee: Maximum number of expected errors in the joined read to be retained. [optional]" name="pmaxee" optional="True" type="text"/>
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90
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91 <param label="--p-qmin: The minimum allowed quality score in the input. [default: 0]" name="pqmin" optional="True" type="text" value="0"/>
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92 <param label="--p-qminout: The minimum allowed quality score to use in output. [default: 0]" name="pqminout" optional="True" type="text" value="0"/>
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93
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94 <param label="--p-qmax: The maximum allowed quality score in the input. [default: 41]" name="pqmax" optional="True" type="integer" value="41"/>
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95 <param label="--p-qmaxout: The maximum allowed quality score to use in output. [default: 41]" name="pqmaxout" optional="True" type="integer" value="41"/>
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96
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97 <param label="--cmd-config: Use config file for command options" name="cmdconfig" optional="True" type="data"/>
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98 </inputs>
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99 <outputs>
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100 <data format="qza" label="${tool.name} on ${on_string}: joined-sequences.qza" name="ojoinedsequences"/>
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101 </outputs>
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102 <help>
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103 <![CDATA[
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104 Join paired-end reads.
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105 -----------------------
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106
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107 Join paired-end sequence reads using vsearch's merge_pairs function. The
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108 qmin, qminout, qmax, and qmaxout parameters should only need to be modified
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109 when working with older fastq sequence data. See the vsearch documentation
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110 for details on how paired-end joining is performed, and for more
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111 information on the parameters to this method.
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112
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113 Parameters
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114 ----------
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115 demultiplexed_seqs : SampleData[PairedEndSequencesWithQuality]
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116 The demultiplexed paired-end sequences to be joined.
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117 truncqual : Int % Range(0, None), optional
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118 Truncate sequences at the first base with the specified quality score
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119 value or lower.
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120 minlen : Int % Range(0, None), optional
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121 Sequences shorter than minlen after truncation are discarded.
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122 maxns : Int % Range(0, None), optional
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123 Sequences with more than maxns N characters are discarded.
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124 allowmergestagger : Bool, optional
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125 Allow joining of staggered read pairs.
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126 minovlen : Int % Range(0, None), optional
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127 Minimum overlap length of forward and reverse reads for joining.
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128 maxdiffs : Int % Range(0, None), optional
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129 Maximum number of mismatches in the forward/reverse read overlap for
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130 joining.
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131 minmergelen : Int % Range(0, None), optional
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132 Minimum length of the joined read to be retained.
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133 maxmergelen : Int % Range(0, None), optional
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134 Maximum length of the joined read to be retained.
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135 maxee : Float % Range(0.0, None), optional
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136 Maximum number of expected errors in the joined read to be retained.
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137 qmin : Int % Range(-5, 2, inclusive_end=True), optional
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138 The minimum allowed quality score in the input.
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139 qminout : Int % Range(-5, 2, inclusive_end=True), optional
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140 The minimum allowed quality score to use in output.
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141 qmax : Int % Range(40, 41, inclusive_end=True), optional
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142 The maximum allowed quality score in the input.
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143 qmaxout : Int % Range(40, 41, inclusive_end=True), optional
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144 The maximum allowed quality score to use in output.
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145
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146 Returns
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147 -------
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148 joined_sequences : SampleData[JoinedSequencesWithQuality]
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149 The joined sequences.
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150 ]]>
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151 </help>
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152 </tool>
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