comparison qiime_feature-classifier_fit-classifier-sklearn.xml @ 0:09b7bcb72fa7 draft

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0:09b7bcb72fa7

<?xml version="1.0" ?>
<tool id="qiime_feature-classifier_fit-classifier-sklearn" name="qiime feature-classifier fit-classifier-sklearn" version="2018.4">
	<description>- Train an almost arbitrary scikit-learn classifier</description>
	<requirements>
		<requirement type="package" version="2018.4">qiime2</requirement>
	</requirements>
	<command>
		<![CDATA[
	qiime feature-classifier fit-classifier-sklearn --p-classifier-specification="$pclassifierspecification"

	#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

		--i-reference-reads=$ireferencereads
	#if str($iclassweight) != 'None':
	 --i-class-weight=$iclassweight
	#end if
	 --o-classifier=oclassifier
	#if str($cmdconfig) != 'None':
	 --cmd-config=$cmdconfig
	#end if
	;
	cp oclassifier.qza $oclassifier;
]]>
	</command>
	<inputs>
		<param format="qza,no_unzip.zip" label="--i-reference-reads: 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 format="qza,no_unzip.zip" label="--i-class-weight: FeatureTable[RelativeFrequency] [optional]" name="iclassweight" optional="True" type="data"/>
		<param label="--p-classifier-specification: [required]" name="pclassifierspecification" optional="False" type="text"/>
		<param label="--cmd-config: Use config file for command options" name="cmdconfig" optional="True" type="data"/>
	</inputs>
	<outputs>
		<data format="qza" label="${tool.name} on ${on_string}: classifier.qza" name="oclassifier"/>
	</outputs>
	<help>
		<![CDATA[
Train an almost arbitrary scikit-learn classifier
-------------------------------------------------

Train a scikit-learn classifier to classify reads.

Parameters
----------
reference_reads : FeatureData[Sequence]
		\
reference_taxonomy : FeatureData[Taxonomy]
		\
class_weight : FeatureTable[RelativeFrequency], optional
		\
classifier_specification : Str
		\

Returns
-------
classifier : TaxonomicClassifier
		\
		]]>
	</help>
</tool>