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1 <?xml version="1.0" ?>
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2 <tool id="qiime_feature-classifier_fit-classifier-sklearn" name="qiime feature-classifier fit-classifier-sklearn" version="2019.4">
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3 <description> - Train an almost arbitrary scikit-learn classifier</description>
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4 <requirements>
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5 <requirement type="package" version="2019.4">qiime2</requirement>
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6 </requirements>
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7 <command><![CDATA[
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8 qiime feature-classifier fit-classifier-sklearn
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9
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10 --i-reference-reads=$ireferencereads
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11
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12
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13 #if str( $id_to_taxonomy_fp.selector ) == 'history'
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14 #set $tax = $id_to_taxonomy_fp.taxonomy_fp
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15 --i-reference-taxonomy '$tax'
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16 #else:
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17 #set $tax = $id_to_taxonomy_fp.taxonomy_fp.fields.path
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18 --i-reference-taxonomy '$tax'
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19 #end if
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20
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21
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22 --p-classifier-specification="$pclassifierspecification"
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23
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24 #if str($iclassweight) != 'None':
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25 --i-class-weight=$iclassweight
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26 #end if
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27
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28 --o-classifier=oclassifier
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29 ;
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30 cp oclassifier.qza $oclassifier
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31 ]]></command>
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32 <inputs>
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33 <param format="qza,no_unzip.zip" label="--i-reference-reads: ARTIFACT FeatureData[Sequence] [required]" name="ireferencereads" optional="False" type="data"/>
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34
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35 <conditional name="id_to_taxonomy_fp" optional="True">
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36 <param name="selector" type="select" label="Reference taxonomy to query">
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37 <option value="cached">Public databases</option>
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38 <option value="history">Databases from your history</option>
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39 </param>
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40 <when value="cached">
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41 <param argument="--taxonomy_fp" label="Reference taxonomy" type="select" optional="True">
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42 <options from_data_table="qiime_taxonomy" />
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43 </param>
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44 </when>
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45 <when value="history">
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46 <param argument="--taxonomy_fp" type="data" format="qza,no_unzip.zip" label="Reference databases" optional="True" />
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47 </when>
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48 </conditional>
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49
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50 <param label="--p-classifier-specification: TEXT [required]" name="pclassifierspecification" optional="False" type="text"/>
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51 <param format="qza,no_unzip.zip" label="--i-class-weight: ARTIFACT FeatureTable[RelativeFrequency] [optional]" name="iclassweight" optional="True" type="data"/>
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52 </inputs>
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53 <outputs>
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54 <data format="qza" label="${tool.name} on ${on_string}: classifier.qza" name="oclassifier"/>
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55 </outputs>
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56 <help><![CDATA[
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57 rain an almost arbitrary scikit-learn classifier
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58 ################################################
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59
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60 Train a scikit-learn classifier to classify reads.
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61
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62 Parameters
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63 ----------
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64 reference_reads : FeatureData[Sequence]
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65 \
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66
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67 reference_taxonomy : FeatureData[Taxonomy]
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68 \
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69
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70 classifier_specification : Str
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71 \
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72
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73 class_weight : FeatureTable[RelativeFrequency], optional
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74 \
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75
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76 Returns
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77 -------
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78 classifier : TaxonomicClassifier
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79 \
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80
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81 ]]></help>
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82 <macros>
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83 <import>qiime_citation.xml</import>
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84 </macros>
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85 <expand macro="qiime_citation"/>
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86 </tool>
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