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diff qiime2/qiime_feature-classifier_fit-classifier-naive-bayes.xml @ 14:a0a8d77a991c draft

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Uploaded
author florianbegusch
date Thu, 03 Sep 2020 09:51:29 +0000
parents 21c7954105a9
children
line wrap: on
line diff
--- a/qiime2/qiime_feature-classifier_fit-classifier-naive-bayes.xml	Thu Sep 03 09:46:00 2020 +0000
+++ b/qiime2/qiime_feature-classifier_fit-classifier-naive-bayes.xml	Thu Sep 03 09:51:29 2020 +0000
@@ -1,56 +1,28 @@
 <?xml version="1.0" ?>
-<tool id="qiime_feature-classifier_fit-classifier-naive-bayes" name="qiime feature-classifier fit-classifier-naive-bayes" version="2019.7">
-	<description> - Train the naive_bayes classifier</description>
-	<requirements>
-		<requirement type="package" version="2019.7">qiime2</requirement>
-	</requirements>
-	<command><![CDATA[
-
-
-#if str( $id_to_taxonomy_fp.selector ) == 'history'
-	#set $tax = $id_to_taxonomy_fp.taxonomy_fp
-#else:
-	#set $tax_path = $id_to_taxonomy_fp.taxonomy_fp.fields.path
-	qiime tools import --type 'FeatureData[Taxonomy]'  --input-format HeaderlessTSVTaxonomyFormat --input-path $tax_path --output-path ref-taxonomy.qza;
-	#set $tax='ref-taxonomy.qza'
-#end if
-
-
+<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-taxonomy '$tax'
-
-
 --i-reference-reads=$ireferencereads
 
-#if str($iclassweight) != 'None':
- --i-class-weight=$iclassweight
-#end if
+--i-reference-taxonomy=$ireferencetaxonomy
 
-#if str($pclassifyalpha):
- --p-classify--alpha=$pclassifyalpha
-#end if
-
-#if str($pclassifychunksize):
- --p-classify--chunk-size=$pclassifychunksize
+#if str($iclassweight) != 'None':
+--i-class-weight=$iclassweight
 #end if
 
-
-
+--p-classify--alpha=$pclassifyalpha
 
-#if '__sq__' in str($pclassifyclassprior):
-  #set $pclassifyclassprior_temp = $pclassifyclassprior.replace('__sq__', "'")
-  #set $pclassifyclassprior = $pclassifyclassprior_temp
-#end if
+--p-classify--chunk-size=$pclassifychunksize
 
 #if str($pclassifyclassprior):
- --p-classify--class-prior="$pclassifyclassprior"
+  --p-classify--class-prior=$pclassifyclassprior
 #end if
-
-
-
-
 #if $pclassifyfitprior:
  --p-classify--fit-prior
 #end if
@@ -59,320 +31,178 @@
  --p-feat-ext--alternate-sign
 #end if
 
-
-
-
-
-#if '__sq__' in str($pfeatextanalyzer):
-  #set $pfeatextanalyzer_temp = $pfeatextanalyzer.replace('__sq__', "'")
-  #set $pfeatextanalyzer = $pfeatextanalyzer_temp
+#if str($pfeatextanalyzer):
+  --p-feat-ext--analyzer=$pfeatextanalyzer
 #end if
-
-#if str($pfeatextanalyzer):
- --p-feat-ext--analyzer="$pfeatextanalyzer"
-#end if
-
-
-
-
-
 #if $pfeatextbinary:
  --p-feat-ext--binary
 #end if
 
-
-
-#if '__sq__' in str($pfeatextdecodeerror):
-  #set $pfeatextdecodeerror_temp = $pfeatextdecodeerror.replace('__sq__', "'")
-  #set $pfeatextdecodeerror = $pfeatextdecodeerror_temp
-#end if
-
 #if str($pfeatextdecodeerror):
- --p-feat-ext--decode-error="$pfeatextdecodeerror"
-#end if
-
-
-
-
-
-#if '__sq__' in str($pfeatextencoding):
-  #set $pfeatextencoding_temp = $pfeatextencoding.replace('__sq__', "'")
-  #set $pfeatextencoding = $pfeatextencoding_temp
+  --p-feat-ext--decode-error=$pfeatextdecodeerror
 #end if
-
 #if str($pfeatextencoding):
- --p-feat-ext--encoding="$pfeatextencoding"
+  --p-feat-ext--encoding=$pfeatextencoding
 #end if
-
-
-
-
-
-#if '__sq__' in str($pfeatextinput):
-  #set $pfeatextinput_temp = $pfeatextinput.replace('__sq__', "'")
-  #set $pfeatextinput = $pfeatextinput_temp
+#if str($pfeatextinput):
+  --p-feat-ext--input=$pfeatextinput
 #end if
-
-#if str($pfeatextinput):
- --p-feat-ext--input="$pfeatextinput"
-#end if
-
-
-
-
 #if $pnofeatextlowercase:
  --p-no-feat-ext--lowercase
 #end if
 
-#if str($pfeatextnfeatures):
- --p-feat-ext--n-features=$pfeatextnfeatures
-#end if
-
-
-
-
-#if '__sq__' in str($pfeatextngramrange):
-  #set $pfeatextngramrange_temp = $pfeatextngramrange.replace('__sq__', "'")
-  #set $pfeatextngramrange = $pfeatextngramrange_temp
-#end if
+--p-feat-ext--n-features=$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 = $pfeatextngramrange_temp
 #end if
-
-#if str($pfeatextngramrange):
- --p-feat-ext--ngram-range="$pfeatextngramrange"
+#if '__sq__' in str($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 $pfeatextnonnegative:
- --p-feat-ext--non-negative
-#end if
-
-
-#if '__sq__' in str($pfeatextnorm):
-  #set $pfeatextnorm_temp = $pfeatextnorm.replace('__sq__', "'")
-  #set $pfeatextnorm = $pfeatextnorm_temp
+#if str($pfeatextngramrange):
+  --p-feat-ext--ngram-range=$pfeatextngramrange
 #end if
 
 #if str($pfeatextnorm):
- --p-feat-ext--norm="$pfeatextnorm"
+  --p-feat-ext--norm=$pfeatextnorm
 #end if
-
-
-
-
-#if '__sq__' in str($pfeatextpreprocessor):
-  #set $pfeatextpreprocessor_temp = $pfeatextpreprocessor.replace('__sq__', "'")
-  #set $pfeatextpreprocessor = $pfeatextpreprocessor_temp
-#end if
-
 #if str($pfeatextpreprocessor):
- --p-feat-ext--preprocessor="$pfeatextpreprocessor"
+  --p-feat-ext--preprocessor=$pfeatextpreprocessor
 #end if
-
-
-
-
-#if '__sq__' in str($pfeatextstopwords):
-  #set $pfeatextstopwords_temp = $pfeatextstopwords.replace('__sq__', "'")
-  #set $pfeatextstopwords = $pfeatextstopwords_temp
-#end if
-
 #if str($pfeatextstopwords):
- --p-feat-ext--stop-words="$pfeatextstopwords"
+  --p-feat-ext--stop-words=$pfeatextstopwords
 #end if
-
-
-
-
-
-#if '__sq__' in str($pfeatextstripaccents):
-  #set $pfeatextstripaccents_temp = $pfeatextstripaccents.replace('__sq__', "'")
-  #set $pfeatextstripaccents = $pfeatextstripaccents_temp
-#end if
-
 #if str($pfeatextstripaccents):
- --p-feat-ext--strip-accents="$pfeatextstripaccents"
+  --p-feat-ext--strip-accents=$pfeatextstripaccents
 #end if
-
-
-
-
-
-
-#if '__sq__' in str($pfeatexttokenpattern):
-  #set $pfeatexttokenpattern_temp = $pfeatexttokenpattern.replace('__sq__', "'")
-  #set $pfeatexttokenpattern = $pfeatexttokenpattern_temp
-#end if
-
 #if '__ob__' in str($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 '__sq__' in str($pfeatexttokenizer):
-  #set $pfeatexttokenizer_temp = $pfeatexttokenizer.replace('__sq__', "'")
-  #set $pfeatexttokenizer = $pfeatexttokenizer_temp
+  --p-feat-ext--token-pattern=$pfeatexttokenpattern
 #end if
 
 #if str($pfeatexttokenizer):
- --p-feat-ext--tokenizer="$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-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[
+  ]]></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__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
-	\
+verbose : Bool, optional
 
 Returns
 -------
 classifier : TaxonomicClassifier
-	\
-
-	]]></help>
-<macros>
+  ]]></help>
+  <macros>
     <import>qiime_citation.xml</import>
-</macros>
-<expand macro="qiime_citation"/>
-</tool>
+  </macros>
+  <expand macro="qiime_citation"/>
+</tool>
\ No newline at end of file