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1 <?xml version="1.0" ?>
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2 <tool id="qiime_vsearch_uchime-denovo" name="qiime vsearch uchime-denovo" version="2019.7">
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3 <description> - De novo chimera filtering with vsearch.</description>
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4 <requirements>
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5 <requirement type="package" version="2019.7">qiime2</requirement>
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6 </requirements>
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7 <command><![CDATA[
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8 qiime vsearch uchime-denovo
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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
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13 #if str($pdn):
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14 --p-dn=$pdn
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15 #end if
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16
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17 #if str($pmindiffs):
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18 --p-mindiffs=$pmindiffs
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19 #end if
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20
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21 #if str($pmindiv):
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22 --p-mindiv=$pmindiv
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23 #end if
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24
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25 #if str($pminh):
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26 --p-minh=$pminh
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27 #end if
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28
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29 #if str($pxn):
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30 --p-xn=$pxn
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31 #end if
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32
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33 --o-chimeras=ochimeras
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34 --o-nonchimeras=ononchimeras
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35 --o-stats=ostats
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36 ;
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37 cp ochimeras.qza $ochimeras;
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38 cp ononchimeras.qza $ononchimeras;
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39 cp ostats.qza $ostats
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40 ]]></command>
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41 <inputs>
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42 <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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43 <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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44
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45 <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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46 <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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47 <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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48 <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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49 <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_max="True" value="8.0"/>
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50 </inputs>
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51 <outputs>
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52 <data format="qza" label="${tool.name} on ${on_string}: chimeras.qza" name="ochimeras"/>
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53 <data format="qza" label="${tool.name} on ${on_string}: nonchimeras.qza" name="ononchimeras"/>
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54 <data format="qza" label="${tool.name} on ${on_string}: stats.qza" name="ostats"/>
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55 </outputs>
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56 <help><![CDATA[
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57 De novo chimera filtering with vsearch.
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58 #######################################
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59
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60 Apply the vsearch uchime_denovo method to identify chimeric feature
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61 sequences. The results of this method can be used to filter chimeric
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62 features from the corresponding feature table. For additional details,
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63 please refer to the vsearch documentation.
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64
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65 Parameters
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66 ----------
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67 sequences : FeatureData[Sequence]
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68 The feature sequences to be chimera-checked.
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69 table : FeatureTable[Frequency]
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70 Feature table (used for computing total feature abundances).
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71 dn : Float % Range(0.0, None), optional
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72 No vote pseudo-count, corresponding to the parameter n in the chimera
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73 scoring function.
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74 mindiffs : Int % Range(1, None), optional
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75 Minimum number of differences per segment.
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76 mindiv : Float % Range(0.0, None), optional
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77 Minimum divergence from closest parent.
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78 minh : Float % Range(0.0, 1.0, inclusive_end=True), optional
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79 Minimum score (h). Increasing this value tends to reduce the number of
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80 false positives and to decrease sensitivity.
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81 xn : Float % Range(1.0, None, inclusive_start=False), optional
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82 No vote weight, corresponding to the parameter beta in the scoring
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83 function.
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84
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85 Returns
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86 -------
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87 chimeras : FeatureData[Sequence]
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88 The chimeric sequences.
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89 nonchimeras : FeatureData[Sequence]
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90 The non-chimeric sequences.
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91 stats : UchimeStats
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92 Summary statistics from chimera checking.
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93 ]]></help>
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94 <macros>
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95 <import>qiime_citation.xml</import>
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96 </macros>
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97 <expand macro="qiime_citation"/>
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98 </tool>
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