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1 <?xml version="1.0" ?>
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2 <tool id="qiime_dada2_denoise-single" name="qiime dada2 denoise-single" version="2019.4">
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3 <description> - Denoise and dereplicate single-end sequences</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 dada2 denoise-single
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9
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10 --i-demultiplexed-seqs=$idemultiplexedseqs
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11 --p-trunc-len="$ptrunclen"
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12
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13 #if $ptrimleft:
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14 --p-trim-left=$ptrimleft
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15 #end if
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16
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17 #if $pmaxee:
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18 --p-max-ee=$pmaxee
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19 #end if
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20
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21 #if $ptruncq:
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22 --p-trunc-q=$ptruncq
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23 #end if
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24
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25 #if str($pchimeramethod) != 'None':
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26 --p-chimera-method=$pchimeramethod
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27 #end if
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28
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29 #if $pminfoldparentoverabundance:
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30 --p-min-fold-parent-over-abundance=$pminfoldparentoverabundance
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31 #end if
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32
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33 #set $pnthreads = '${GALAXY_SLOTS:-4}'
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34 #if str($pnthreads):
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35 --p-n-threads="$pnthreads"
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36 #end if
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37
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38
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39 #if $pnreadslearn:
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40 --p-n-reads-learn=$pnreadslearn
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41 #end if
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42
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43 #if $pnohashedfeatureids:
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44 --p-no-hashed-feature-ids
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45 #end if
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46
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47 --o-table=otable
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48 --o-representative-sequences=orepresentativesequences
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49 --o-denoising-stats=odenoisingstats
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50 ;
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51 cp otable.qza $otable;
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52 cp orepresentativesequences.qza $orepresentativesequences;
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53 cp odenoisingstats.qza $odenoisingstats
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54 ]]></command>
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55 <inputs>
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56 <param format="qza,no_unzip.zip" label="--i-demultiplexed-seqs: ARTIFACT SampleData[SequencesWithQuality | PairedEndSequencesWithQuality] The single-end demultiplexed sequences to be denoised. [required]" name="idemultiplexedseqs" optional="False" type="data"/>
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57 <param label="--p-trunc-len: INTEGER Position at which sequences should be truncated due to decrease in quality. This truncates the 3' end of the of the input sequences, which will be the bases that were sequenced in the last cycles. Reads that are shorter than this value will be discarded. If 0 is provided, no truncation or length filtering will be performed [required]" name="ptrunclen" optional="False" value="" type="integer"/>
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58 <param label="--p-trim-left: INTEGER Position at which sequences should be trimmed due to low quality. This trims the 5' end of the of the input sequences, which will be the bases that were sequenced in the first cycles. [default: 0]" name="ptrimleft" optional="True" type="integer" value="0"/>
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59 <param label="--p-max-ee: NUMBER Reads with number of expected errors higher than this value will be discarded. [default: 2.0]" name="pmaxee" optional="True" type="float" value="2.0"/>
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60 <param label="--p-trunc-q: INTEGER Reads are truncated at the first instance of a quality score less than or equal to this value. If the resulting read is then shorter than `trunc-len`, it is discarded. [default: 2]" name="ptruncq" optional="True" type="integer" value="2"/>
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61 <param label="--p-chimera-method: " name="pchimeramethod" optional="True" type="select">
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62 <option selected="True" value="None">Selection is Optional</option>
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63 <option value="consensus">consensus</option>
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64 <option value="pooled">pooled</option>
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65 <option value="none">none</option>
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66 </param>
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67 <param label="--p-min-fold-parent-over-abundance: NUMBER The minimum abundance of potential parents of a sequence being tested as chimeric, expressed as a fold-change versus the abundance of the sequence being tested. Values should be greater than or equal to 1 (i.e. parents should be more abundant than the sequence being tested). This parameter has no effect if chimera-method is 'none'. [default: 1.0]" name="pminfoldparentoverabundance" optional="True" type="float" value="1.0"/>
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68 <param label="--p-n-reads-learn: INTEGER The number of reads to use when training the error model. Smaller numbers will result in a shorter run time but a less reliable error model. [default: 1000000]" name="pnreadslearn" optional="True" type="integer" value="1000000"/>
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4
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69 <param label="--p-no-hashed-feature-ids: If false, the feature ids in the resulting table will be presented as hashes of the sequences defining each feature. The hash will always be the same for the same sequence so this allows feature tables to be merged across runs of this method. You should only merge tables if the exact same parameters are used for each run. [default: False]" name="pnohashedfeatureids" selected="False" type="boolean"/>
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70 </inputs>
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71 <outputs>
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72 <data format="qza" label="${tool.name} on ${on_string}: table.qza" name="otable"/>
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73 <data format="qza" label="${tool.name} on ${on_string}: representativesequences.qza" name="orepresentativesequences"/>
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74 <data format="qza" label="${tool.name} on ${on_string}: denoisingstats.qza" name="odenoisingstats"/>
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75 </outputs>
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76 <help><![CDATA[
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77 Denoise and dereplicate single-end sequences
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78 ############################################
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79
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80 This method denoises single-end sequences, dereplicates them, and filters
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81 chimeras.
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82
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83 Parameters
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84 ----------
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85 demultiplexed_seqs : SampleData[SequencesWithQuality | PairedEndSequencesWithQuality]
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86 The single-end demultiplexed sequences to be denoised.
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87 trunc_len : Int
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88 Position at which sequences should be truncated due to decrease in
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89 quality. This truncates the 3' end of the of the input sequences, which
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90 will be the bases that were sequenced in the last cycles. Reads that
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91 are shorter than this value will be discarded. If 0 is provided, no
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92 truncation or length filtering will be performed
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93 trim_left : Int, optional
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94 Position at which sequences should be trimmed due to low quality. This
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95 trims the 5' end of the of the input sequences, which will be the bases
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96 that were sequenced in the first cycles.
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97 max_ee : Float, optional
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98 Reads with number of expected errors higher than this value will be
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99 discarded.
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100 trunc_q : Int, optional
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101 Reads are truncated at the first instance of a quality score less than
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102 or equal to this value. If the resulting read is then shorter than
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103 `trunc_len`, it is discarded.
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104 chimera_method : Str % Choices('consensus', 'pooled', 'none'), optional
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105 The method used to remove chimeras. "none": No chimera removal is
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106 performed. "pooled": All reads are pooled prior to chimera detection.
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107 "consensus": Chimeras are detected in samples individually, and
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108 sequences found chimeric in a sufficient fraction of samples are
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109 removed.
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110 min_fold_parent_over_abundance : Float, optional
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111 The minimum abundance of potential parents of a sequence being tested
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112 as chimeric, expressed as a fold-change versus the abundance of the
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113 sequence being tested. Values should be greater than or equal to 1
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114 (i.e. parents should be more abundant than the sequence being tested).
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115 This parameter has no effect if chimera_method is "none".
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116 n_reads_learn : Int, optional
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117 The number of reads to use when training the error model. Smaller
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118 numbers will result in a shorter run time but a less reliable error
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119 model.
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120 hashed_feature_ids : Bool, optional
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121 If true, the feature ids in the resulting table will be presented as
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122 hashes of the sequences defining each feature. The hash will always be
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123 the same for the same sequence so this allows feature tables to be
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124 merged across runs of this method. You should only merge tables if the
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125 exact same parameters are used for each run.
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126
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127 Returns
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128 -------
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129 table : FeatureTable[Frequency]
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130 The resulting feature table.
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131 representative_sequences : FeatureData[Sequence]
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132 The resulting feature sequences. Each feature in the feature table will
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133 be represented by exactly one sequence.
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134 denoising_stats : SampleData[DADA2Stats]
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135 ]]></help>
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136 <macros>
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137 <import>qiime_citation.xml</import>
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138 </macros>
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139 <expand macro="qiime_citation"/>
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140 </tool>
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