diff qiime2-2020.8/qiime_feature-classifier_fit-classifier-naive-bayes.xml @ 20:d93d8888f0b0 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2-2020.8/qiime_feature-classifier_fit-classifier-naive-bayes.xml	Fri Sep 04 12:44:24 2020 +0000
@@ -0,0 +1,208 @@
+<?xml version="1.0" ?>
+<tool id="qiime_feature-classifier_fit-classifier-naive-bayes" name="qiime feature-classifier fit-classifier-naive-bayes"
+      version="2020.8">
+  <description>Train the naive_bayes classifier</description>
+  <requirements>
+    <requirement type="package" version="2020.8">qiime2</requirement>
+  </requirements>
+  <command><![CDATA[
+qiime feature-classifier fit-classifier-naive-bayes
+
+--i-reference-reads=$ireferencereads
+
+--i-reference-taxonomy=$ireferencetaxonomy
+
+#if str($iclassweight) != 'None':
+--i-class-weight=$iclassweight
+#end if
+
+--p-classify--alpha=$pclassifyalpha
+
+--p-classify--chunk-size=$pclassifychunksize
+
+#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 $pnofeatextlowercase:
+ --p-no-feat-ext--lowercase
+#end if
+
+--p-feat-ext--n-features=$pfeatextnfeatures
+
+#if '__ob__' in str($pfeatextngramrange):
+  #set $pfeatextngramrange_temp = $pfeatextngramrange.replace('__ob__', '[')
+  #set $pfeatextngramrange = $pfeatextngramrange_temp
+#end if
+#if '__cb__' in str($pfeatextngramrange):
+  #set $pfeatextngramrange_temp = $pfeatextngramrange.replace('__cb__', ']')
+  #set $pfeatextngramrange = $pfeatextngramrange_temp
+#end if
+#if 'X' in str($pfeatextngramrange):
+  #set $pfeatextngramrange_temp = $pfeatextngramrange.replace('X', '\\')
+  #set $pfeatextngramrange = $pfeatextngramrange_temp
+#end if
+#if '__sq__' in str($pfeatextngramrange):
+  #set $pfeatextngramrange_temp = $pfeatextngramrange.replace('__sq__', "'")
+  #set $pfeatextngramrange = $pfeatextngramrange_temp
+#end if
+#if '__db__' in str($pfeatextngramrange):
+  #set $pfeatextngramrange_temp = $pfeatextngramrange.replace('__db__', '"')
+  #set $pfeatextngramrange = $pfeatextngramrange_temp
+#end if
+
+#if str($pfeatextngramrange):
+  --p-feat-ext--ngram-range=$pfeatextngramrange
+#end if
+
+#if str($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 = $pfeatexttokenpattern_temp
+#end if
+#if '__cb__' in str($pfeatexttokenpattern):
+  #set $pfeatexttokenpattern_temp = $pfeatexttokenpattern.replace('__cb__', ']')
+  #set $pfeatexttokenpattern = $pfeatexttokenpattern_temp
+#end if
+#if 'X' in str($pfeatexttokenpattern):
+  #set $pfeatexttokenpattern_temp = $pfeatexttokenpattern.replace('X', '\\')
+  #set $pfeatexttokenpattern = $pfeatexttokenpattern_temp
+#end if
+#if '__sq__' in str($pfeatexttokenpattern):
+  #set $pfeatexttokenpattern_temp = $pfeatexttokenpattern.replace('__sq__', "'")
+  #set $pfeatexttokenpattern = $pfeatexttokenpattern_temp
+#end if
+#if '__db__' in str($pfeatexttokenpattern):
+  #set $pfeatexttokenpattern_temp = $pfeatexttokenpattern.replace('__db__', '"')
+  #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
+#if $pverbose:
+ --p-verbose
+#end if
+
+--o-classifier=oclassifier
+
+#if str($examples) != 'None':
+--examples=$examples
+#end if
+
+;
+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-reference-taxonomy: ARTIFACT FeatureData[Taxonomy] [required]" name="ireferencetaxonomy" optional="False" type="data" />
+    <param format="qza,no_unzip.zip" label="--i-class-weight: ARTIFACT FeatureTable[RelativeFrequency] [optional]" name="iclassweight" optional="False" type="data" />
+    <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="False" type="text" value="\'null\'" />
+    <param label="--p-classify--fit-prior: --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-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="False" type="text" value="\'char_wb\'" />
+    <param label="--p-feat-ext--binary: --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="False" type="text" value="\'strict\'" />
+    <param label="--p-feat-ext--encoding: TEXT [default: \'utf-8\']" name="pfeatextencoding" optional="False" type="text" value="\'utf-8\'" />
+    <param label="--p-feat-ext--input: TEXT [default: \'content\']" name="pfeatextinput" optional="False" type="text" value="\'content\'" />
+    <param label="--p-no-feat-ext--lowercase: Do not [default: True]" 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="False" type="text" value="\'[7, 7]" />
+    <param label="--p-feat-ext--norm: TEXT [default: \'l2\']" name="pfeatextnorm" optional="False" type="text" value="\'l2\'" />
+    <param label="--p-feat-ext--preprocessor: TEXT [default: \'null\']" name="pfeatextpreprocessor" optional="False" type="text" value="\'null\'" />
+    <param label="--p-feat-ext--stop-words: TEXT [default: \'null\']" name="pfeatextstopwords" optional="False" type="text" value="\'null\'" />
+    <param label="--p-feat-ext--strip-accents: TEXT [default: \'null\']" name="pfeatextstripaccents" optional="False" type="text" value="\'null\'" />
+    <param label="--p-feat-ext--token-pattern: TEXT [default: \'(?u)\\\\b\\\\w\\\\w+\\\\b\']" name="pfeatexttokenpattern" optional="False" type="text" value="\'(?u)\\\\b\\\\w\\\\w+\\\\b\'" />
+    <param label="--p-feat-ext--tokenizer: TEXT [default: \'null\']" name="pfeatexttokenizer" optional="False" type="text" value="\'null\'" />
+    <param label="--p-verbose: --p-verbose: / --p-no-verbose [default: False]" name="pverbose" selected="False" type="boolean" />
+    <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
+    
+  </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__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
+verbose : Bool, optional
+
+Returns
+-------
+classifier : TaxonomicClassifier
+  ]]></help>
+  <macros>
+    <import>qiime_citation.xml</import>
+  </macros>
+  <expand macro="qiime_citation"/>
+</tool>
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