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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" version="2019.4">
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3 <description> - Extract reads from reference</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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6
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8
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9
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10 #if str( $input_sequences.selector ) == 'history'
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11 #set $seq = $input_sequences.i_sequences
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12
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13 #else:
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14 qiime tools import --type 'FeatureData[Sequence]' --input-path '$input_sequences.i_sequences.fields.path' --output-path database.qza;
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15 #set $seq = 'database.qza'
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16 #end if
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17
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18
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19 qiime feature-classifier extract-reads
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20
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21 --i-sequences=$seq
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22
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23 --p-f-primer="$pfprimer"
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24 --p-r-primer="$prprimer"
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25
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26 #if str($ptrunclen):
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27 --p-trunc-len=$ptrunclen
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28 #end if
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29
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30 #if str($ptrimleft):
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31 --p-trim-left=$ptrimleft
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32 #end if
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33
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34 #if str($pidentity):
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35 --p-identity=$pidentity
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36 #end if
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37
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38 #if str($pminlength):
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39 --p-min-length=$pminlength
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40 #end if
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41
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42 #if str($pmaxlength):
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43 --p-max-length=$pmaxlength
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44 #end if
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45
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46 --o-reads=oreads
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47 ;
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48 cp oreads.qza $oreads
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49 ]]></command>
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50 <inputs>
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51 <conditional name="input_sequences" optional="False">
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52 <param name="selector" type="select" label="--i-sequences: FeatureData[Sequence] [required] - Reference sequences to query">
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53 <option value="cached">Public databases</option>
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54 <option value="history">Databases from your history</option>
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55 </param>
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56 <when value="cached">
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57 <param name="i_sequences" label="--i-sequences: FeatureData[Sequence] [required] - Reference sequences" type="select" optional="True">
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58 <options from_data_table="qiime_rep_set" />
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59 </param>
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60 </when>
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61 <when value="history">
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62 <param name="i_sequences" type="data" format="qza,no_unzip.zip" label="Reference databases" optional="True" />
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63 </when>
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64 </conditional>
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65
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66 <param label="--p-f-primer: TEXT forward primer sequence [required]" name="pfprimer" optional="False" type="text"/>
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67 <param label="--p-r-primer: TEXT reverse primer sequence [required]" name="prprimer" optional="False" type="text"/>
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68 <param label="--p-trunc-len: INTEGER read is cut to trunc-len if trunc-len is positive. Applied before trim-left. [default: 0]" name="ptrunclen" optional="True" type="integer" value="0"/>
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69 <param label="--p-trim-left: INTEGER trim-left nucleotides are removed from the 5' end if trim-left is positive. Applied after trunc-len. [default: 0]" name="ptrimleft" optional="True" type="integer" value="0"/>
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70 <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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71 <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]" name="pminlength" optional="True" type="integer" min="0" value="50"/>
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72 <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]" name="pmaxlength" optional="True" type="integer" min="0" value="0"/>
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73 </inputs>
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74 <outputs>
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75 <data format="qza" label="${tool.name} on ${on_string}: reads.qza" name="oreads"/>
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76 </outputs>
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77 <help><![CDATA[
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78 Extract reads from reference
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79 ############################
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80
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81 Extract sequencing-like reads from a reference database.
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82
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83 Parameters
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84 ----------
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85 sequences : FeatureData[Sequence]
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86 \
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87
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88 f_primer : Str
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89 forward primer sequence
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90 r_primer : Str
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91 reverse primer sequence
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92 trunc_len : Int, optional
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93 read is cut to trunc_len if trunc_len is positive. Applied before
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94 trim_left.
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95 trim_left : Int, optional
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96 trim_left nucleotides are removed from the 5' end if trim_left is
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97 positive. Applied after trunc_len.
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98 identity : Float, optional
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99 minimum combined primer match identity threshold.
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100 min_length : Int % Range(0, None), optional
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101 Minimum amplicon length. Shorter amplicons are discarded. Applied after
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102 trimming and truncation, so be aware that trimming may impact sequence
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103 retention. Set to zero to disable min length filtering.
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104 max_length : Int % Range(0, None), optional
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105 Maximum amplicon length. Longer amplicons are discarded. Applied before
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106 trimming and truncation, so plan accordingly. Set to zero (default) to
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107 disable max length filtering.
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108
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109 Returns
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110 -------
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111 reads : FeatureData[Sequence]
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112 ]]></help>
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113 <macros>
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114 <import>qiime_citation.xml</import>
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115 </macros>
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116 <expand macro="qiime_citation"/>
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117 </tool>
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