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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="2018.4">
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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="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-ref --i-table=$itable --i-sequences=$isequences --i-reference-sequences=$ireferencesequences --o-nonchimeras=ononchimeras --o-stats=ostats
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10
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11 #if $pmindiffs:
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12 --p-mindiffs=$pmindiffs
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13 #end if
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14
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15 #set $pthreads = '${GALAXY_SLOTS:-4}'
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16
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17 #if str($pthreads):
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18 --p-threads="$pthreads"
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19 #end if
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20
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21
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22 #if $pdn:
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23 --p-dn=$pdn
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24 #end if
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25 --o-chimeras=ochimeras
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26 #if str($cmdconfig) != 'None':
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27 --cmd-config=$cmdconfig
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28 #end if
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29
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30 #if $pminh:
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31 --p-minh=$pminh
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32 #end if
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33
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34 #if $pmindiv:
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35 --p-mindiv=$pmindiv
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36 #end if
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37
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38 #if $pxn:
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39 --p-xn=$pxn
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40 #end if
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41 ;
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42 cp ononchimeras.qza $ononchimeras;
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43 cp ostats.qza $ostats;
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44 cp ochimeras.qza $ochimeras
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45 ]]>
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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: 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: 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: FeatureData[Sequence] The non-chimeric reference sequences. [required]" name="ireferencesequences" optional="False" type="data"/>
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51
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52 <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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53
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54 <param label="--p-mindiffs: Minimum number of differences per segment. [default: 3]" name="pmindiffs" optional="True" type="integer" value="3"/>
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55 <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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56 <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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57
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58 <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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59
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60 <param label="--cmd-config: Use config file for command options" name="cmdconfig" optional="True" type="data"/>
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61 </inputs>
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62 <outputs>
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63 <data format="qza" label="${tool.name} on ${on_string}: non-chimeras.qza" name="ononchimeras"/>
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64 <data format="qza" label="${tool.name} on ${on_string}: stats.qza" name="ostats"/>
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65 <data format="qza" label="${tool.name} on ${on_string}: chimeras.qza" name="ochimeras"/>
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66 </outputs>
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67 <help>
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68 <![CDATA[
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69 Reference-based chimera filtering with vsearch.
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70 ------------------------------------------------
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71
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72 Apply the vsearch uchime_ref method to identify chimeric feature sequences.
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73 The results of this method can be used to filter chimeric features from the
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74 corresponding feature table. For additional details, please refer to the
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75 vsearch documentation.
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76
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77 Parameters
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78 ----------
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79 sequences : FeatureData[Sequence]
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80 The feature sequences to be chimera-checked.
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81 table : FeatureTable[Frequency]
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82 Feature table (used for computing total feature abundances).
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83 reference_sequences : FeatureData[Sequence]
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84 The non-chimeric reference sequences.
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85 dn : Float % Range(0.0, None), optional
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86 No vote pseudo-count, corresponding to the parameter n in the chimera
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87 scoring function.
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88 mindiffs : Int % Range(1, None), optional
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89 Minimum number of differences per segment.
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90 mindiv : Float % Range(0.0, None), optional
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91 Minimum divergence from closest parent.
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92 minh : Float % Range(0.0, 1.0, inclusive_end=True), optional
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93 Minimum score (h). Increasing this value tends to reduce the number of
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94 false positives and to decrease sensitivity.
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95 xn : Float % Range(1.0, None, inclusive_start=False), optional
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96 No vote weight, corresponding to the parameter beta in the scoring
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97 function.
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98
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99 Returns
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100 -------
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101 chimeras : FeatureData[Sequence]
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102 The chimeric sequences.
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103 nonchimeras : FeatureData[Sequence]
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104 The non-chimeric sequences.
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105 stats : UchimeStats
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106 Summary statistics from chimera checking.
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107 ]]>
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108 </help>
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109 </tool>
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