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1 <?xml version="1.0" ?>
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2 <tool id="qiime_deblur_denoise-other" name="qiime deblur denoise-other" version="2019.4">
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3 <description> - Deblur sequences using a user-specified positive filter.</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 deblur denoise-other
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9
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10 --i-demultiplexed-seqs=$idemultiplexedseqs
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11 --i-reference-seqs=$ireferenceseqs
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12 --p-trim-length="$ptrimlength"
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13
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14 #if $plefttrimlen:
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15 --p-left-trim-len=$plefttrimlen
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16 #end if
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17
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18 #if $psamplestats:
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19 --p-sample-stats
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20 #end if
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21
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22 #if $pmeanerror:
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23 --p-mean-error=$pmeanerror
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24 #end if
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25
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26 #if $pindelprob:
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27 --p-indel-prob=$pindelprob
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28 #end if
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29
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30 #if $pindelmax:
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31 --p-indel-max=$pindelmax
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32 #end if
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33
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34 #if $pminreads:
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35 --p-min-reads=$pminreads
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36 #end if
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37
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38 #if $pminsize:
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39 --p-min-size=$pminsize
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40 #end if
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41
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42 #set $pjobstostart = '${GALAXY_SLOTS:-4}'
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43
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44 #if str($pjobstostart):
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45 --p-jobs-to-start="$pjobstostart"
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46 #end if
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47
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48
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49 #if $pnohashedfeatureids:
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50 --p-no-hashed-feature-ids
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51 #end if
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52
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53 --o-table=otable
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54 --o-representative-sequences=orepresentativesequences
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55 --o-stats=ostats
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56 ;
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57 cp otable.qza $otable;
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58 cp orepresentativesequences.qza $orepresentativesequences;
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59 cp ostats.qza $ostats
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60 ]]></command>
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61 <inputs>
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62 <param format="qza,no_unzip.zip" label="--i-demultiplexed-seqs: ARTIFACT SampleData[SequencesWithQuality | PairedEndSequencesWithQuality | JoinedSequencesWithQuality] The demultiplexed sequences to be denoised. [required]" name="idemultiplexedseqs" optional="False" type="data"/>
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63 <param format="qza,no_unzip.zip" label="--i-reference-seqs: ARTIFACT FeatureData[Sequence] Positive filtering database. Keep all sequences aligning to these sequences. [required]" name="ireferenceseqs" optional="False" type="data"/>
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64 <param label="--p-trim-length: INTEGER Sequence trim length, specify -1 to disable trimming. [required]" name="ptrimlength" optional="False" value="" type="integer"/>
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65 <param label="--p-left-trim-len: INTEGER Range(0, None) Sequence trimming from the 5' end. A value of 0 will disable this trim. [default: 0]" name="plefttrimlen" optional="True" type="integer" min="0" value="0"/>
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66 <param label="--p-sample-stats: --p-no-sample-stats If true, gather stats per sample. [default: False]" name="psamplestats" selected="False" type="boolean"/>
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67 <param label="--p-mean-error: NUMBER The mean per nucleotide error, used for original sequence estimate. [default: 0.005]" name="pmeanerror" optional="True" type="float" value="0.005"/>
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68 <param label="--p-indel-prob: NUMBER Insertion/deletion (indel) probability (same for N indels). [default: 0.01]" name="pindelprob" optional="True" type="float" value="0.01"/>
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69 <param label="--p-indel-max: INTEGER Maximum number of insertion/deletions. [default: 3]" name="pindelmax" optional="True" type="integer" value="3"/>
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70 <param label="--p-min-reads: INTEGER Retain only features appearing at least min-reads times across all samples in the resulting feature table. [default: 10]" name="pminreads" optional="True" type="integer" value="10"/>
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71 <param label="--p-min-size: INTEGER In each sample, discard all features with an abundance less than min-size. [default: 2]" name="pminsize" optional="True" type="integer" value="2"/>
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72 <param label="--p-no-hashed-feature-ids: If false, hash the feature IDs. [default: False]" name="pnohashedfeatureids" selected="False" type="boolean"/>
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73 </inputs>
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74 <outputs>
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75 <data format="qza" label="${tool.name} on ${on_string}: table.qza" name="otable"/>
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76 <data format="qza" label="${tool.name} on ${on_string}: representativesequences.qza" name="orepresentativesequences"/>
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77 <data format="qza" label="${tool.name} on ${on_string}: stats.qza" name="ostats"/>
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78 </outputs>
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79 <help><![CDATA[
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80 Deblur sequences using a user-specified positive filter.
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81 ########################################################
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82
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83 Perform sequence quality control for Illumina data using the Deblur
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84 workflow, including positive alignment-based filtering. Only forward reads
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85 are supported at this time. This mode of execution is particularly useful
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86 when operating on non-16S data. For example, to apply Deblur to 18S data,
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87 you would want to specify a reference composed of 18S sequences in order to
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88 filter out sequences which do not appear to be 18S. The assessment is
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89 performed by local alignment using SortMeRNA with a permissive e-value
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90 threshold.
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91
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92 Parameters
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93 ----------
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94 demultiplexed_seqs : SampleData[SequencesWithQuality | PairedEndSequencesWithQuality | JoinedSequencesWithQuality]
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95 The demultiplexed sequences to be denoised.
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96 reference_seqs : FeatureData[Sequence]
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97 Positive filtering database. Keep all sequences aligning to these
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98 sequences.
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99 trim_length : Int
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100 Sequence trim length, specify -1 to disable trimming.
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101 left_trim_len : Int % Range(0, None), optional
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102 Sequence trimming from the 5' end. A value of 0 will disable this trim.
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103 sample_stats : Bool, optional
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104 If true, gather stats per sample.
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105 mean_error : Float, optional
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106 The mean per nucleotide error, used for original sequence estimate.
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107 indel_prob : Float, optional
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108 Insertion/deletion (indel) probability (same for N indels).
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109 indel_max : Int, optional
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110 Maximum number of insertion/deletions.
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111 min_reads : Int, optional
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112 Retain only features appearing at least min_reads times across all
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113 samples in the resulting feature table.
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114 min_size : Int, optional
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115 In each sample, discard all features with an abundance less than
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116 min_size.
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117 hashed_feature_ids : Bool, optional
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118 If true, hash the feature IDs.
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119
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120 Returns
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121 -------
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122 table : FeatureTable[Frequency]
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123 The resulting denoised feature table.
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124 representative_sequences : FeatureData[Sequence]
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125 The resulting feature sequences.
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126 stats : DeblurStats
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127 Per-sample stats if requested.
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128 ]]></help>
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129 <macros>
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130 <import>qiime_citation.xml</import>
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131 </macros>
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132 <expand macro="qiime_citation"/>
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133 </tool>
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