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1 <?xml version="1.0" ?>
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2 <tool id="qiime_feature-classifier_classify-sklearn" name="qiime feature-classifier classify-sklearn" version="2019.7">
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3 <description> - Pre-fitted sklearn-based taxonomy classifier</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 feature-classifier classify-sklearn
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9
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6
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10
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11 #if str( $id_to_classifier_fp.selector ) == 'history'
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12 #set $classifier = $id_to_classifier_fp.classifier_fp
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13 --i-classifier '$classifier'
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14 #else:
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15 #set $classifier = $id_to_classifier_fp.classifier_fp.fields.path
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16 --i-classifier '$classifier'
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17 #end if
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18
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19
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20 --i-reads=$ireads
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21
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22 #set $pnjobs = '${GALAXY_SLOTS:-4}'
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23
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24 #if str($pnjobs):
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25 --p-n-jobs="$pnjobs"
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26 #end if
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27
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28
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29 #if str($pconfidence) != '':
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30 #if float($pconfidence) >= 0.0:
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31 --p-confidence=$pconfidence
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32 #end if
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0
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33 #end if
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34
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35 #if str($preadorientation) != 'None':
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36 --p-read-orientation=$preadorientation
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37 #end if
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38
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39 --o-classification=oclassification
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40 ;
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41 cp oclassification.qza $oclassification
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42 ]]></command>
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43 <inputs>
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44 <conditional name="id_to_classifier_fp" optional="True">
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45 <param name="selector" type="select" label="Reference classifier to query">
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46 <option value="cached">Public classifiers</option>
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47 <option value="history">Classifiers from your history</option>
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48 </param>
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49 <when value="cached">
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50 <param name="classifier_fp" label="Reference classifier" type="select" optional="True">
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51 <options from_data_table="qiime_rep_set" />
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52 </param>
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53 </when>
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54 <when value="history">
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55 <param name="classifier_fp" type="data" format="qza,no_unzip.zip" label="Reference classifier" optional="True" />
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56 </when>
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57 </conditional>
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58
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59 <param format="qza,no_unzip.zip" label="--i-reads: ARTIFACT FeatureData[Sequence] The feature data to be classified. [required]" name="ireads" optional="False" type="data"/>
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60 <param label="--p-confidence: NUMBER Confidence threshold for limiting taxonomic depth. Provide -1 to disable confidence calculation, or 0 to calculate confidence but not apply it to limit the taxonomic depth of the assignments. [default: 0.7]" name="pconfidence" optional="True" type="float" value="0.7"/>
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61 <param label="--p-read-orientation: " name="preadorientation" optional="True" type="select">
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62 <option selected="True" value="None">Selection is Optional</option>
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63 <option value="same">same</option>
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64 <option value="reverse-complement">reverse-complement</option>
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65 </param>
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66 </inputs>
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67 <outputs>
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68 <data format="qza" label="${tool.name} on ${on_string}: classification.qza" name="oclassification"/>
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69 </outputs>
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70 <help><![CDATA[
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71 Pre-fitted sklearn-based taxonomy classifier
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72 ############################################
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73
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74 Classify reads by taxon using a fitted classifier.
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75
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76 Parameters
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77 ----------
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78 reads : FeatureData[Sequence]
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79 The feature data to be classified.
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80 classifier : TaxonomicClassifier
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81 The taxonomic classifier for classifying the reads.
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82 reads_per_batch : Int % Range(0, None), optional
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83 Number of reads to process in each batch. If 0, this parameter is
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84 autoscaled to min( number of query sequences / n_jobs, 20000).
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85 pre_dispatch : Str, optional
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86 "all" or expression, as in "3*n_jobs". The number of batches (of tasks)
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87 to be pre-dispatched.
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88 confidence : Float, optional
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89 Confidence threshold for limiting taxonomic depth. Provide -1 to
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90 disable confidence calculation, or 0 to calculate confidence but not
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91 apply it to limit the taxonomic depth of the assignments.
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92 read_orientation : Str % Choices('same', 'reverse-complement'), optional
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93 Direction of reads with respect to reference sequences. same will cause
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94 reads to be classified unchanged; reverse-complement will cause reads
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95 to be reversed and complemented prior to classification. Default is to
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96 autodetect based on the confidence estimates for the first 100 reads.
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97
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98 Returns
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99 -------
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100 classification : FeatureData[Taxonomy]
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101 ]]></help>
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102 <macros>
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103 <import>qiime_citation.xml</import>
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104 </macros>
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105 <expand macro="qiime_citation"/>
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106 </tool>
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