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1 <?xml version="1.0" ?>
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2 <tool id="qiime_feature-classifier_extract-reads" name="qiime feature-classifier extract-reads"
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3 version="2020.8">
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4 <description>Extract reads from reference sequences.</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 feature-classifier extract-reads
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10
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11 --i-sequences=$isequences
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12
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13 --p-f-primer=$pfprimer
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15 --p-r-primer=$prprimer
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16
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17 --p-trim-right=$ptrimright
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18
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19 --p-trunc-len=$ptrunclen
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20
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21 --p-trim-left=$ptrimleft
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22
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23 --p-identity=$pidentity
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24
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25 --p-min-length=$pminlength
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26
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27 --p-max-length=$pmaxlength
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28
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29 --p-n-jobs=$pnjobs
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30
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31 #if str($preadorientation) != 'None':
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32 --p-read-orientation=$preadorientation
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33 #end if
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34
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35 --o-reads=oreads
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36
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37 #if str($examples) != 'None':
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38 --examples=$examples
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39 #end if
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40
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41 ;
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42 cp oreads.qza $oreads
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43
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44 ]]></command>
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45 <inputs>
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46 <param format="qza,no_unzip.zip" label="--i-sequences: ARTIFACT FeatureData[Sequence] [required]" name="isequences" optional="False" type="data" />
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47 <param label="--p-f-primer: TEXT forward primer sequence (5\' -> 3\'). [required]" name="pfprimer" optional="False" type="text" />
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48 <param label="--p-r-primer: TEXT reverse primer sequence (5\' -> 3\'). Do not use reverse-complemented primer sequence. [required]" name="prprimer" optional="False" type="text" />
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49 <param label="--p-trim-right: INTEGER trim-right nucleotides are removed from the 3\' end if trim-right is positive. Applied before trunc-len and trim-left. [default: 0]" name="ptrimright" optional="True" type="integer" value="0" />
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50 <param label="--p-trunc-len: INTEGER read is cut to trunc-len if trunc-len is positive. Applied after trim-right but before trim-left. [default: 0]" name="ptrunclen" optional="True" type="integer" value="0" />
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51 <param label="--p-trim-left: INTEGER trim-left nucleotides are removed from the 5\' end if trim-left is positive. Applied after trim-right and trunc-len. [default: 0]" name="ptrimleft" optional="True" type="integer" value="0" />
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52 <param label="--p-identity: NUMBER minimum combined primer match identity threshold. [default: 0.8]" name="pidentity" optional="True" type="float" value="0.8" />
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53 <param label="--p-min-length: INTEGER Minimum amplicon length. Shorter amplicons are Range(0, None) discarded. Applied after trimming and truncation, so be aware that trimming may impact sequence retention. Set to zero to disable min length filtering. [default: 50]" min="0" name="pminlength" optional="True" type="integer" value="50" />
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54 <param label="--p-max-length: INTEGER Maximum amplicon length. Longer amplicons are Range(0, None) discarded. Applied before trimming and truncation, so plan accordingly. Set to zero (default) to disable max length filtering. [default: 0]" min="0" name="pmaxlength" optional="True" type="integer" value="0" />
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55 <param label="--p-read-orientation: " name="preadorientation" optional="True" type="select">
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56 <option selected="True" value="None">Selection is Optional</option>
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57 <option value="both">both</option>
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58 <option value="forward">forward</option>
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59 <option value="reverse">reverse</option>
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60 </param>
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61 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
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62
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63 </inputs>
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64
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65 <outputs>
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66 <data format="qza" label="${tool.name} on ${on_string}: reads.qza" name="oreads" />
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67
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68 </outputs>
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69
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70 <help><![CDATA[
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71 Extract reads from reference sequences.
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72 ###############################################################
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73
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74 Extract simulated amplicon reads from a reference database. Performs in-
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75 silico PCR to extract simulated amplicons from reference sequences that
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76 match the input primer sequences (within the mismatch threshold specified
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77 by `identity`). Both primer sequences must be in the 5' -> 3' orientation.
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78 Sequences that fail to match both primers will be excluded. Reads are
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79 extracted, trimmed, and filtered in the following order: 1. reads are
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80 extracted in specified orientation; 2. primers are removed; 3. reads longer
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81 than `max_length` are removed; 4. reads are trimmed with `trim_right`; 5.
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82 reads are truncated to `trunc_len`; 6. reads are trimmed with `trim_left`;
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83 7. reads shorter than `min_length` are removed.
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84
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85 Parameters
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86 ----------
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87 sequences : FeatureData[Sequence]
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88 f_primer : Str
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89 forward primer sequence (5' -> 3').
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90 r_primer : Str
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91 reverse primer sequence (5' -> 3'). Do not use reverse-complemented
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92 primer sequence.
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93 trim_right : Int, optional
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94 trim_right nucleotides are removed from the 3' end if trim_right is
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95 positive. Applied before trunc_len and trim_left.
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96 trunc_len : Int, optional
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97 read is cut to trunc_len if trunc_len is positive. Applied after
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98 trim_right but before trim_left.
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99 trim_left : Int, optional
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100 trim_left nucleotides are removed from the 5' end if trim_left is
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101 positive. Applied after trim_right and trunc_len.
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102 identity : Float, optional
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103 minimum combined primer match identity threshold.
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104 min_length : Int % Range(0, None), optional
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105 Minimum amplicon length. Shorter amplicons are discarded. Applied after
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106 trimming and truncation, so be aware that trimming may impact sequence
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107 retention. Set to zero to disable min length filtering.
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108 max_length : Int % Range(0, None), optional
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109 Maximum amplicon length. Longer amplicons are discarded. Applied before
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110 trimming and truncation, so plan accordingly. Set to zero (default) to
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111 disable max length filtering.
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112 n_jobs : Int % Range(1, None), optional
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113 Number of seperate processes to run.
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114 batch_size : Int % Range(1, None) | Str % Choices('auto'), optional
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115 Number of sequences to process in a batch. The `auto` option is
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116 calculated from the number of sequences and number of jobs specified.
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117 read_orientation : Str % Choices('both', 'forward', 'reverse'), optional
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118 Orientation of primers relative to the sequences: "forward" searches
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119 for primer hits in the forward direction, "reverse" searches reverse-
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120 complement, and "both" searches both directions.
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121
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122 Returns
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123 -------
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124 reads : FeatureData[Sequence]
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125 ]]></help>
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126 <macros>
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127 <import>qiime_citation.xml</import>
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128 </macros>
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129 <expand macro="qiime_citation"/>
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130 </tool> |
