annotate qiime2/qiime_vsearch_uchime-denovo.xml @ 0:51b9b6b57732 draft

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author florianbegusch
date Thu, 24 May 2018 05:21:07 -0400
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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="2018.4">
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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="2018.4">qiime2</requirement>
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6 </requirements>
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7 <command>
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8 <![CDATA[
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9 qiime vsearch uchime-denovo --i-table=$itable --i-sequences=$isequences
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10
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11 #if $pdn:
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12 --p-dn=$pdn
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13 #end if
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14 --o-nonchimeras=ononchimeras --o-stats=ostats --o-chimeras=ochimeras
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15 #if $pmindiffs:
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16 --p-mindiffs=$pmindiffs
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17 #end if
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18
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19 #if $pminh:
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20 --p-minh=$pminh
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21 #end if
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22
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23 #if str($cmdconfig) != 'None':
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24 --cmd-config=$cmdconfig
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25 #end if
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26
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27 #if $pmindiv:
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28 --p-mindiv=$pmindiv
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29 #end if
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30
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31 #if $pxn:
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32 --p-xn=$pxn
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33 #end if
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34 ;
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35 cp ononchimeras.qza $ononchimeras;
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36 cp ostats.qza $ostats;
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37 cp ochimeras.qza $ochimeras;
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38 ]]>
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39 </command>
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40 <inputs>
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41 <param format="qza,no_unzip.zip" label="--i-sequences: FeatureData[Sequence] The feature sequences to be chimera-checked. [required]" name="isequences" optional="False" type="data"/>
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42 <param format="qza,no_unzip.zip" label="--i-table: FeatureTable[Frequency] Feature table (used for computing total feature abundances). [required]" name="itable" optional="False" type="data"/>
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43
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44 <param label="--p-dn: No vote pseudo-count, corresponding to the parameter n in the chimera scoring function. [default: 1.4]" name="pdn" optional="True" type="float" value="1.4"/>
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45
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46 <param label="--p-mindiffs: Minimum number of differences per segment. [default: 3]" name="pmindiffs" optional="True" type="integer" value="3"/>
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47 <param label="--p-mindiv: Minimum divergence from closest parent. [default: 0.8]" name="pmindiv" optional="True" type="float" value="0.8"/>
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48 <param label="--p-minh: 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" value="0.28"/>
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49
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50 <param label="--p-xn: No vote weight, corresponding to the parameter beta in the scoring function. [default: 8.0]" name="pxn" optional="True" type="float" value="8.0"/>
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51
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52 <param label="--cmd-config: Use config file for command options" name="cmdconfig" optional="True" type="data"/>
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53 </inputs>
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54 <outputs>
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55 <data format="qza" label="${tool.name} on ${on_string}: non-chimeras.qza" name="ononchimeras"/>
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56 <data format="qza" label="${tool.name} on ${on_string}: stats.qza" name="ostats"/>
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57 <data format="qza" label="${tool.name} on ${on_string}: chimeras.qza" name="ochimeras"/>
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58 </outputs>
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59 <help>
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60 <![CDATA[
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61 De novo chimera filtering with vsearch.
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62 ----------------------------------------
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63
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64 Apply the vsearch uchime_denovo method to identify chimeric feature
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65 sequences. The results of this method can be used to filter chimeric
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66 features from the corresponding feature table. For additional details,
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67 please refer to the vsearch documentation.
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68
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69 Parameters
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70 ----------
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71 sequences : FeatureData[Sequence]
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72 The feature sequences to be chimera-checked.
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73 table : FeatureTable[Frequency]
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74 Feature table (used for computing total feature abundances).
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75 dn : Float % Range(0.0, None), optional
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76 No vote pseudo-count, corresponding to the parameter n in the chimera
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77 scoring function.
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78 mindiffs : Int % Range(1, None), optional
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79 Minimum number of differences per segment.
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80 mindiv : Float % Range(0.0, None), optional
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81 Minimum divergence from closest parent.
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82 minh : Float % Range(0.0, 1.0, inclusive_end=True), optional
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83 Minimum score (h). Increasing this value tends to reduce the number of
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84 false positives and to decrease sensitivity.
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85 xn : Float % Range(1.0, None, inclusive_start=False), optional
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86 No vote weight, corresponding to the parameter beta in the scoring
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87 function.
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88
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89 Returns
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90 -------
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91 chimeras : FeatureData[Sequence]
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92 The chimeric sequences.
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93 nonchimeras : FeatureData[Sequence]
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94 The non-chimeric sequences.
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95 stats : UchimeStats
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96 Summary statistics from chimera checking.
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97 ]]>
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98 </help>
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99 <macros>
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100 <import>qiime_citation.xml</import>
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101 </macros>
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102 <expand macro="qiime_citation" />
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103 </tool>