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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="2018.4">
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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="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 feature-classifier fit-classifier-sklearn --p-classifier-specification="$pclassifierspecification"
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10
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11 #if str( $id_to_taxonomy_fp.selector ) == 'history'
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12 #set $tax = $id_to_taxonomy_fp.taxonomy_fp
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13 --i-reference-taxonomy '$tax'
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14 #else:
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15 #set $tax = $id_to_taxonomy_fp.taxonomy_fp.fields.path
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16 --i-reference-taxonomy '$tax'
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17 #end if
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18
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19 --i-reference-reads=$ireferencereads
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20 #if str($iclassweight) != 'None':
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21 --i-class-weight=$iclassweight
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22 #end if
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23 --o-classifier=oclassifier
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24 #if str($cmdconfig) != 'None':
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25 --cmd-config=$cmdconfig
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26 #end if
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27 ;
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28 cp oclassifier.qza $oclassifier;
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29 ]]>
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30 </command>
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31 <inputs>
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32 <param format="qza,no_unzip.zip" label="--i-reference-reads: FeatureData[Sequence] [required]" name="ireferencereads" optional="False" type="data"/>
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33
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34 <conditional name="id_to_taxonomy_fp" optional="True">
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35 <param name="selector" type="select" label="Reference taxonomy to query">
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36 <option value="cached">Public databases</option>
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37 <option value="history">Databases from your history</option>
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38 </param>
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39 <when value="cached">
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40 <param argument="--taxonomy_fp" label="Reference taxonomy" type="select" optional="True">
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41 <options from_data_table="qiime_taxonomy" />
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42 </param>
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43 </when>
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44 <when value="history">
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45 <param argument="--taxonomy_fp" type="data" format="qza,no_unzip.zip" label="Reference databases" optional="True" />
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46 </when>
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47 </conditional>
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48
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49 <param format="qza,no_unzip.zip" label="--i-class-weight: FeatureTable[RelativeFrequency] [optional]" name="iclassweight" optional="True" type="data"/>
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50 <param label="--p-classifier-specification: [required]" name="pclassifierspecification" optional="False" type="text"/>
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51 <param label="--cmd-config: Use config file for command options" name="cmdconfig" 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>
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57 <![CDATA[
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58 Train an almost arbitrary scikit-learn classifier
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59 -------------------------------------------------
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60
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61 Train a scikit-learn classifier to classify reads.
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62
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63 Parameters
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64 ----------
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65 reference_reads : FeatureData[Sequence]
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66 \
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67 reference_taxonomy : FeatureData[Taxonomy]
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68 \
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69 class_weight : FeatureTable[RelativeFrequency], optional
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70 \
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71 classifier_specification : Str
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72 \
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73
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74 Returns
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75 -------
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76 classifier : TaxonomicClassifier
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77 \
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78 ]]>
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79 </help>
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80 </tool>
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