Mercurial > repos > florianbegusch > qiime2_suite

<?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>
author	florianbegusch
date	Fri, 04 Sep 2020 12:44:24 +0000
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