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

Uploaded

--- a/qiime2/qiime_feature-classifier_fit-classifier-sklearn.xml	Thu Sep 03 09:46:00 2020 +0000
+++ b/qiime2/qiime_feature-classifier_fit-classifier-sklearn.xml	Thu Sep 03 09:51:29 2020 +0000
@@ -1,86 +1,66 @@
 <?xml version="1.0" ?>
-<tool id="qiime_feature-classifier_fit-classifier-sklearn" name="qiime feature-classifier fit-classifier-sklearn" version="2019.7">
-	<description> - Train an almost arbitrary scikit-learn classifier</description>
-	<requirements>
-		<requirement type="package" version="2019.7">qiime2</requirement>
-	</requirements>
-	<command><![CDATA[
+<tool id="qiime_feature-classifier_fit-classifier-sklearn" name="qiime feature-classifier fit-classifier-sklearn"
+      version="2020.8">
+  <description>Train an almost arbitrary scikit-learn classifier</description>
+  <requirements>
+    <requirement type="package" version="2020.8">qiime2</requirement>
+  </requirements>
+  <command><![CDATA[
 qiime feature-classifier fit-classifier-sklearn
 
 --i-reference-reads=$ireferencereads
 
+--i-reference-taxonomy=$ireferencetaxonomy
 
-#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'
+#if str($iclassweight) != 'None':
+--i-class-weight=$iclassweight
 #end if
 
-
---p-classifier-specification="$pclassifierspecification"
+--p-classifier-specification=$pclassifierspecification
 
-#if str($iclassweight) != 'None':
- --i-class-weight=$iclassweight
+--o-classifier=oclassifier
+
+#if str($examples) != 'None':
+--examples=$examples
 #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 ${on_string}: classifier.qza" name="oclassifier"/>
-	</outputs>
-	<help><![CDATA[
-rain an almost arbitrary scikit-learn classifier
-################################################
+
+  ]]></command>
+  <inputs>
+    <param format="qza,no_unzip.zip" label="--i-reference-reads: ARTIFACT FeatureData[Sequence] [required]" name="ireferencereads" optional="False" type="data" />
+    <param format="qza,no_unzip.zip" label="--i-reference-taxonomy: ARTIFACT FeatureData[Taxonomy] [required]" name="ireferencetaxonomy" optional="False" type="data" />
+    <param format="qza,no_unzip.zip" label="--i-class-weight: ARTIFACT FeatureTable[RelativeFrequency] [optional]" name="iclassweight" optional="False" type="data" />
+    <param label="--p-classifier-specification: TEXT [required]" name="pclassifierspecification" optional="False" type="text" />
+    <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
+    
+  </inputs>
+
+  <outputs>
+    <data format="qza" label="${tool.name} on ${on_string}: classifier.qza" name="oclassifier" />
+    
+  </outputs>
+
+  <help><![CDATA[
+Train 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>
+  ]]></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