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1 <?xml version="1.0" ?>
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2 <tool id="qiime_vsearch_uchime-ref" name="qiime vsearch uchime-ref" version="2019.4">
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3 <description> - Reference-based chimera filtering with vsearch.</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 vsearch uchime-ref
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9
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10 --i-sequences=$isequences
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11 --i-table=$itable
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12 --i-reference-sequences=$ireferencesequences
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13
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14 #if $pdn:
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15 --p-dn=$pdn
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16 #end if
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17
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18 #if $pmindiffs:
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19 --p-mindiffs=$pmindiffs
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20 #end if
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21
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22 #if $pmindiv:
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23 --p-mindiv=$pmindiv
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24 #end if
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25
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26 #if $pminh:
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27 --p-minh=$pminh
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28 #end if
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29
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30 #if $pxn:
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31 --p-xn=$pxn
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32 #end if
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33
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34 #set $pthreads = '${GALAXY_SLOTS:-4}'
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35 #if str($pthreads):
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36 --p-threads="$pthreads"
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37 #end if
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38
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39 --o-chimeras=ochimeras
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40 --o-nonchimeras=ononchimeras
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41 --o-stats=ostats
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42 ;
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43 cp ochimeras.qza $ochimeras;
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44 cp ononchimeras.qza $ononchimeras;
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45 cp ostats.qza $ostats
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46 ]]></command>
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47 <inputs>
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48 <param format="qza,no_unzip.zip" label="--i-sequences: ARTIFACT FeatureData[Sequence] The feature sequences to be chimera-checked. [required]" name="isequences" optional="False" type="data"/>
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49 <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Frequency] Feature table (used for computing total feature abundances). [required]" name="itable" optional="False" type="data"/>
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50 <param format="qza,no_unzip.zip" label="--i-reference-sequences: ARTIFACT FeatureData[Sequence] The non-chimeric reference sequences. [required]" name="ireferencesequences" optional="False" type="data"/>
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51 <param label="--p-dn: NUMBER No vote pseudo-count, corresponding to the Range(0.0, None) parameter n in the chimera scoring function. [default: 1.4]" name="pdn" optional="True" type="float" min="0" value="1.4"/>
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52 <param label="--p-mindiffs: INTEGER Minimum number of differences per segment. Range(1, None) [default: 3]" name="pmindiffs" optional="True" type="integer" min="1" value="3"/>
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53 <param label="--p-mindiv: NUMBER Minimum divergence from closest parent. Range(0.0, None) [default: 0.8]" name="pmindiv" optional="True" type="float" min="0" value="0.8"/>
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54 <param label="--p-minh: PROPORTION Range(0.0, 1.0, inclusive_end=True) Minimum score (h). Increasing this value tends to reduce the number of false positives and to decrease sensitivity. [default: 0.28]" name="pminh" optional="True" type="float" min="0" max="1" exclude_max="False" value="0.28"/>
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55 <param label="--p-xn: NUMBER Range(1.0, None, inclusive_start=False) No vote weight, corresponding to the parameter beta in the scoring function. [default: 8.0]" name="pxn" optional="True" type="float" min="1" exclude_min="True" value="8.0"/>
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56 </inputs>
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57 <outputs>
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58 <data format="qza" label="${tool.name} on ${on_string}: chimeras.qza" name="ochimeras"/>
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59 <data format="qza" label="${tool.name} on ${on_string}: nonchimeras.qza" name="ononchimeras"/>
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60 <data format="qza" label="${tool.name} on ${on_string}: stats.qza" name="ostats"/>
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61 </outputs>
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62 <help><![CDATA[
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63 Reference-based chimera filtering with vsearch.
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64 ###############################################
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65
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66 Apply the vsearch uchime_ref method to identify chimeric feature sequences.
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67 The results of this method can be used to filter chimeric features from the
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68 corresponding feature table. For additional details, please refer to the
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69 vsearch documentation.
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70
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71 Parameters
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72 ----------
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73 sequences : FeatureData[Sequence]
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74 The feature sequences to be chimera-checked.
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75 table : FeatureTable[Frequency]
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76 Feature table (used for computing total feature abundances).
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77 reference_sequences : FeatureData[Sequence]
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78 The non-chimeric reference sequences.
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79 dn : Float % Range(0.0, None), optional
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80 No vote pseudo-count, corresponding to the parameter n in the chimera
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81 scoring function.
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82 mindiffs : Int % Range(1, None), optional
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83 Minimum number of differences per segment.
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84 mindiv : Float % Range(0.0, None), optional
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85 Minimum divergence from closest parent.
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86 minh : Float % Range(0.0, 1.0, inclusive_end=True), optional
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87 Minimum score (h). Increasing this value tends to reduce the number of
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88 false positives and to decrease sensitivity.
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89 xn : Float % Range(1.0, None, inclusive_start=False), optional
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90 No vote weight, corresponding to the parameter beta in the scoring
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91 function.
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92 threads : Int % Range(0, 256, inclusive_end=True), optional
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93 The number of threads to use for computation. Passing 0 will launch one
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94 thread per CPU core.
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95
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96 Returns
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97 -------
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98 chimeras : FeatureData[Sequence]
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99 The chimeric sequences.
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100 nonchimeras : FeatureData[Sequence]
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101 The non-chimeric sequences.
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102 stats : UchimeStats
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103 Summary statistics from chimera checking.
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104 ]]></help>
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105 <macros>
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106 <import>qiime_citation.xml</import>
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107 </macros>
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108 <expand macro="qiime_citation"/>
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109 </tool>
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