comparison qiime2/qiime_feature-classifier_fit-classifier-sklearn.xml @ 2:149432539226 draft

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2:149432539226

<?xml version="1.0" ?>
<tool id="qiime_feature-classifier_fit-classifier-sklearn" name="qiime feature-classifier fit-classifier-sklearn" version="2019.4">
	<description> - Train an almost arbitrary scikit-learn classifier</description>
	<requirements>
		<requirement type="package" version="2019.4">qiime2</requirement>
	</requirements>
	<command><![CDATA[
qiime feature-classifier fit-classifier-sklearn

--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


--p-classifier-specification="$pclassifierspecification"

#if str($iclassweight) != 'None':
 --i-class-weight=$iclassweight
#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"/>
		
		<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-classifier-specification: TEXT [required]" name="pclassifierspecification" optional="False" type="text"/>
		<param format="qza,no_unzip.zip" label="--i-class-weight: ARTIFACT FeatureTable[RelativeFrequency] [optional]" name="iclassweight" optional="True" type="data"/>
	</inputs>
	<outputs>
		<data format="qza" label="${tool.name} on ${on_string}: classifier.qza" name="oclassifier"/>
	</outputs>
	<help><![CDATA[
rain an almost arbitrary scikit-learn classifier
################################################

Train a scikit-learn classifier to classify reads.

Parameters
----------
reference_reads : FeatureData[Sequence]
	\

reference_taxonomy : FeatureData[Taxonomy]
	\

classifier_specification : Str
	\

class_weight : FeatureTable[RelativeFrequency], optional
	\

Returns
-------
classifier : TaxonomicClassifier
	\

	]]></help>
<macros>
    <import>qiime_citation.xml</import>
</macros>
<expand macro="qiime_citation"/>
</tool>