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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"
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3 version="2020.8">
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4 <description>Reference-based chimera filtering with vsearch.</description>
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5 <requirements>
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6 <requirement type="package" version="2020.8">qiime2</requirement>
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7 </requirements>
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8 <command><![CDATA[
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9 qiime vsearch uchime-ref
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10
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11 --i-sequences=$isequences
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12
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13 --i-table=$itable
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14
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15 --i-reference-sequences=$ireferencesequences
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16
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17 --p-dn=$pdn
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18
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19 --p-mindiffs=$pmindiffs
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20
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21 --p-mindiv=$pmindiv
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22
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23 --p-minh=$pminh
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24
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25 --p-xn=$pxn
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26
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27 --p-threads=$pthreads
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28
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29 --o-chimeras=ochimeras
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30
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31 --o-nonchimeras=ononchimeras
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32
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33 --o-stats=ostats
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34
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35 #if str($examples) != 'None':
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36 --examples=$examples
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37 #end if
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38
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39 ;
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40 cp ostats.qza $ostats
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41
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42 ]]></command>
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43 <inputs>
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44 <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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45 <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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46 <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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47 <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]" min="0.0" name="pdn" optional="True" type="float" value="1.4" />
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48 <param label="--p-mindiffs: INTEGER Minimum number of differences per segment. Range(1, None) [default: 3]" min="1" name="pmindiffs" optional="True" type="integer" value="3" />
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49 <param label="--p-mindiv: NUMBER Minimum divergence from closest parent. Range(0.0, None) [default: 0.8]" min="0.0" name="pmindiv" optional="True" type="float" value="0.8" />
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50 <param exclude_max="False" 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]" max="1.0" min="0.0" name="pminh" optional="True" type="float" value="0.28" />
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51 <param exclude_min="True" 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]" max="20.0" min="1.0" name="pxn" optional="True" type="float" value="8.0" />
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52 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
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53
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54 </inputs>
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55
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56 <outputs>
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57 <data format="qza" label="${tool.name} on ${on_string}: chimeras.qza" name="ochimeras" />
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58 <data format="qza" label="${tool.name} on ${on_string}: nonchimeras.qza" name="ononchimeras" />
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59 <data format="qza" label="${tool.name} on ${on_string}: stats.qza" name="ostats" />
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60
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61 </outputs>
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62
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63 <help><![CDATA[
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64 Reference-based chimera filtering with vsearch.
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65 ###############################################################
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66
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67 Apply the vsearch uchime_ref method to identify chimeric feature sequences.
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68 The results of this method can be used to filter chimeric features from the
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69 corresponding feature table. For additional details, please refer to the
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70 vsearch documentation.
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71
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72 Parameters
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73 ----------
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74 sequences : FeatureData[Sequence]
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75 The feature sequences to be chimera-checked.
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76 table : FeatureTable[Frequency]
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77 Feature table (used for computing total feature abundances).
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78 reference_sequences : FeatureData[Sequence]
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79 The non-chimeric reference sequences.
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80 dn : Float % Range(0.0, None), optional
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81 No vote pseudo-count, corresponding to the parameter n in the chimera
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82 scoring function.
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83 mindiffs : Int % Range(1, None), optional
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84 Minimum number of differences per segment.
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85 mindiv : Float % Range(0.0, None), optional
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86 Minimum divergence from closest parent.
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87 minh : Float % Range(0.0, 1.0, inclusive_end=True), optional
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88 Minimum score (h). Increasing this value tends to reduce the number of
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89 false positives and to decrease sensitivity.
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90 xn : Float % Range(1.0, None, inclusive_start=False), optional
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91 No vote weight, corresponding to the parameter beta in the scoring
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92 function.
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93 threads : Int % Range(0, 256, inclusive_end=True), optional
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94 The number of threads to use for computation. Passing 0 will launch one
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95 thread per CPU core.
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96
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97 Returns
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98 -------
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99 chimeras : FeatureData[Sequence]
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100 The chimeric sequences.
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101 nonchimeras : FeatureData[Sequence]
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102 The non-chimeric sequences.
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103 stats : UchimeStats
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104 Summary statistics from chimera checking.
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105 ]]></help>
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106 <macros>
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107 <import>qiime_citation.xml</import>
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108 </macros>
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109 <expand macro="qiime_citation"/>
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110 </tool> |
