--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_feature-classifier_fit-classifier-naive-bayes.xml	Wed Jul 17 03:05:17 2019 -0400
@@ -0,0 +1,260 @@
+<?xml version="1.0" ?>
+<tool id="qiime_feature-classifier_fit-classifier-naive-bayes" name="qiime feature-classifier fit-classifier-naive-bayes" version="2019.4">
+	<description> - Train the naive_bayes classifier</description>
+	<requirements>
+		<requirement type="package" version="2019.4">qiime2</requirement>
+	</requirements>
+	<command><![CDATA[
+qiime feature-classifier fit-classifier-naive-bayes
+
+--i-reference-reads=$ireferencereads
+
+
+#if str( $id_to_taxonomy_fp.selector ) == 'history'
+	#set $tax = $id_to_taxonomy_fp.taxonomy_fp
+	--i-reference-taxonomy '$tax'
+#else:
+	#set $tax = $id_to_taxonomy_fp.taxonomy_fp.fields.path
+	--i-reference-taxonomy '$tax'
+#end if
+
+
+#if str($iclassweight) != 'None':
+ --i-class-weight=$iclassweight
+#end if
+
+#if $pclassifyalpha:
+ --p-classify--alpha=$pclassifyalpha
+#end if
+
+#if $pclassifychunksize:
+ --p-classify--chunk-size=$pclassifychunksize
+#end if
+
+#if str($pclassifyclassprior):
+ --p-classify--class-prior="$pclassifyclassprior"
+#end if
+
+#if $pclassifyfitprior:
+ --p-classify--fit-prior
+#end if
+
+#if $pfeatextalternatesign:
+ --p-feat-ext--alternate-sign
+#end if
+
+#if str($pfeatextanalyzer):
+ --p-feat-ext--analyzer="$pfeatextanalyzer"
+#end if
+
+#if $pfeatextbinary:
+ --p-feat-ext--binary
+#end if
+
+#if str($pfeatextdecodeerror):
+ --p-feat-ext--decode-error="$pfeatextdecodeerror"
+#end if
+
+#if str($pfeatextencoding):
+ --p-feat-ext--encoding="$pfeatextencoding"
+#end if
+
+#if str($pfeatextinput):
+ --p-feat-ext--input="$pfeatextinput"
+#end if
+
+#if $pnofeatextlowercase:
+ --p-no-feat-ext--lowercase
+#end if
+
+#if $pfeatextnfeatures:
+ --p-feat-ext--n-features=$pfeatextnfeatures
+#end if
+
+#if '__ob__' in str($pfeatextngramrange):
+  #set $pfeatextngramrange_temp = $pfeatextngramrange.replace('__ob__', '[')
+  #set $pfeatextngramrange = $pfeatextngramrange_temp
+#end if
+#if 'X' in str($pfeatextngramrange):
+  #set $pfeatextngramrange_temp = $pfeatextngramrange.replace('X', '\\')
+  #set $pfeatextngramrange = $pfeatextngramrange_temp
+#end if
+
+#if str($pfeatextngramrange):
+ --p-feat-ext--ngram-range="$pfeatextngramrange"
+#end if
+
+
+#if $pfeatextnonnegative:
+ --p-feat-ext--non-negative
+#end if
+
+#if str($pfeatextnorm):
+ --p-feat-ext--norm="$pfeatextnorm"
+#end if
+
+#if str($pfeatextpreprocessor):
+ --p-feat-ext--preprocessor="$pfeatextpreprocessor"
+#end if
+
+#if str($pfeatextstopwords):
+ --p-feat-ext--stop-words="$pfeatextstopwords"
+#end if
+
+#if str($pfeatextstripaccents):
+ --p-feat-ext--strip-accents="$pfeatextstripaccents"
+#end if
+
+#if '__ob__' in str($pfeatexttokenpattern):
+  #set $pfeatexttokenpattern_temp = $pfeatexttokenpattern.replace('__ob__', '[')
+  #set $pfeatexttokenpattern = $pfeatexttokenpattern_temp
+#end if
+#if 'X' in str($pfeatexttokenpattern):
+  #set $pfeatexttokenpattern_temp = $pfeatexttokenpattern.replace('X', '\\')
+  #set $pfeatexttokenpattern = $pfeatexttokenpattern_temp
+#end if
+
+#if str($pfeatexttokenpattern):
+ --p-feat-ext--token-pattern="$pfeatexttokenpattern"
+#end if
+
+
+#if str($pfeatexttokenizer):
+ --p-feat-ext--tokenizer="$pfeatexttokenizer"
+#end if
+
+--o-classifier=oclassifier
+;
+cp oclassifier.qza $oclassifier
+	]]></command>
+	<inputs>
+		<param format="qza,no_unzip.zip" label="--i-reference-reads: ARTIFACT FeatureData[Sequence] [required]" name="ireferencereads" optional="False" type="data"/>
+		<param format="qza,no_unzip.zip" label="--i-class-weight: ARTIFACT FeatureTable[RelativeFrequency] [optional]" name="iclassweight" optional="True" type="data"/>
+
+		<conditional name="id_to_taxonomy_fp" optional="True">
+		   <param name="selector" type="select" label="Reference taxonomy to query">
+			  <option value="cached">Public databases</option>
+			  <option value="history">Databases from your history</option>
+		   </param>
+		   <when value="cached">
+			  <param argument="--taxonomy_fp" label="Reference taxonomy" type="select" optional="True">
+				 <options from_data_table="qiime_taxonomy" />
+			  </param>
+		   </when>
+		   <when value="history">
+			  <param argument="--taxonomy_fp" type="data" format="qza,no_unzip.zip" label="Reference databases" optional="True" />
+		   </when>
+		</conditional>
+
+		<param label="--p-classify--alpha: NUMBER [default: 0.001]" name="pclassifyalpha" optional="True" type="float" value="0.001"/>
+		<param label="--p-classify--chunk-size: INTEGER [default: 20000]" name="pclassifychunksize" optional="True" type="integer" value="20000"/>
+		<param label="--p-classify--class-prior: TEXT [default: 'null']" name="pclassifyclassprior" optional="True" type="text" value="'null'"/>
+		<param label="--p-classify--fit-prior: --p-no-classify--fit-prior [default: False]" name="pclassifyfitprior" selected="False" type="boolean"/>
+		<param label="--p-feat-ext--alternate-sign: --p-no-feat-ext--alternate-sign [default: False]" name="pfeatextalternatesign" selected="False" type="boolean"/>
+		<param label="--p-feat-ext--analyzer: TEXT [default: 'char_wb']" name="pfeatextanalyzer" optional="True" type="text" value="'char_wb'"/>
+		<param label="--p-feat-ext--binary: --p-no-feat-ext--binary [default: False]" name="pfeatextbinary" selected="False" type="boolean"/>
+		<param label="--p-feat-ext--decode-error: TEXT [default: 'strict']" name="pfeatextdecodeerror" optional="True" type="text" value="'strict'"/>
+		<param label="--p-feat-ext--encoding: TEXT [default: 'utf-8']" name="pfeatextencoding" optional="True" type="text" value="'utf-8'"/>
+		<param label="--p-feat-ext--input: TEXT [default: 'content']" name="pfeatextinput" optional="True" type="text" value="'content'"/>
+		<param label="--p-no-feat-ext--lowercase:  [default: False]" name="pnofeatextlowercase" selected="False" type="boolean"/>
+		<param label="--p-feat-ext--n-features: INTEGER [default: 8192]" name="pfeatextnfeatures" optional="True" type="integer" value="8192"/>
+		<param label="--p-feat-ext--ngram-range: TEXT [default: '[7, 7]']" name="pfeatextngramrange" optional="True" type="text" value="'[7, 7]"/>
+		<param label="--p-feat-ext--non-negative: --p-no-feat-ext--non-negative [default: False]" name="pfeatextnonnegative" selected="False" type="boolean"/>
+		<param label="--p-feat-ext--norm: TEXT [default: 'l2']" name="pfeatextnorm" optional="True" type="text" value="'l2'"/>
+		<param label="--p-feat-ext--preprocessor: TEXT [default: 'null']" name="pfeatextpreprocessor" optional="True" type="text" value="'null'"/>
+		<param label="--p-feat-ext--stop-words: TEXT [default: 'null']" name="pfeatextstopwords" optional="True" type="text" value="'null'"/>
+		<param label="--p-feat-ext--strip-accents: TEXT [default: 'null']" name="pfeatextstripaccents" optional="True" type="text" value="'null'"/>
+		<param label="--p-feat-ext--token-pattern: TEXT [default: '(?u)\\b\\w\\w+\\b']" name="pfeatexttokenpattern" optional="True" type="text" value="'(?u)\\b\\w\\w+\\b'"/>
+		<param label="--p-feat-ext--tokenizer: TEXT [default: 'null']" name="pfeatexttokenizer" optional="True" type="text" value="'null'"/>
+	</inputs>
+	<outputs>
+		<data format="qza" label="${tool.name} on ${on_string}: classifier.qza" name="oclassifier"/>
+	</outputs>
+	<help><![CDATA[
+Train the naive_bayes classifier
+################################
+
+Create a scikit-learn naive_bayes classifier for reads
+
+Parameters
+----------
+reference_reads : FeatureData[Sequence]
+	\
+
+reference_taxonomy : FeatureData[Taxonomy]
+	\
+
+class_weight : FeatureTable[RelativeFrequency], optional
+	\
+
+classify__alpha : Float, optional
+	\
+
+classify__chunk_size : Int, optional
+	\
+
+classify__class_prior : Str, optional
+	\
+
+classify__fit_prior : Bool, optional
+	\
+
+feat_ext__alternate_sign : Bool, optional
+	\
+
+feat_ext__analyzer : Str, optional
+	\
+
+feat_ext__binary : Bool, optional
+	\
+
+feat_ext__decode_error : Str, optional
+	\
+
+feat_ext__encoding : Str, optional
+	\
+
+feat_ext__input : Str, optional
+	\
+
+feat_ext__lowercase : Bool, optional
+	\
+
+feat_ext__n_features : Int, optional
+	\
+
+feat_ext__ngram_range : Str, optional
+	\
+
+feat_ext__non_negative : Bool, optional
+	\
+
+feat_ext__norm : Str, optional
+	\
+
+feat_ext__preprocessor : Str, optional
+	\
+
+feat_ext__stop_words : Str, optional
+	\
+
+feat_ext__strip_accents : Str, optional
+	\
+
+feat_ext__token_pattern : Str, optional
+	\
+
+feat_ext__tokenizer : Str, optional
+	\
+
+Returns
+-------
+classifier : TaxonomicClassifier
+	\
+
+	]]></help>
+<macros>
+    <import>qiime_citation.xml</import>
+</macros>
+<expand macro="qiime_citation"/>
+</tool>