<?xml version="1.0" ?>
<tool id="qiime_fragment-insertion_classify-otus-experimental" name="qiime fragment-insertion classify-otus-experimental" version="2019.4">
	<description> - Experimental: Obtain taxonomic lineages, by finding closest OTU in reference phylogeny.</description>
	<requirements>
		<requirement type="package" version="2019.4">qiime2</requirement>
	</requirements>
	<command><![CDATA[
qiime fragment-insertion classify-otus-experimental

--i-representative-sequences=$irepresentativesequences
--i-tree=$itree --o-classification=oclassification


#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


;
cp oclassification.qza $oclassification
	]]></command>
	<inputs>
		<param format="qza,no_unzip.zip" label="--i-representative-sequences: ARTIFACT FeatureData[Sequence] The sequences used for a 'sepp' run to produce the 'tree'.                                      [required]" name="irepresentativesequences" optional="False" type="data"/>
		<param format="qza,no_unzip.zip" label="--i-tree: ARTIFACT    The tree resulting from inserting fragments into a Phylogeny[Rooted]  reference phylogeny, i.e. the output of function 'sepp' [required]" name="itree" 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>

	</inputs>
	<outputs>
		<data format="qza" label="${tool.name} on ${on_string}: classification.qza" name="oclassification"/>
	</outputs>
	<help><![CDATA[
Experimental: Obtain taxonomic lineages, by finding closest OTU in reference phylogeny.
#######################################################################################

Experimental: Use the resulting tree from 'sepp' and find closest OTU-ID
for every inserted fragment. Then, look up the reference lineage string in
the reference taxonomy.

Parameters
----------
representative_sequences : FeatureData[Sequence]
    The sequences used for a 'sepp' run to produce the 'tree'.
tree : Phylogeny[Rooted]
    The tree resulting from inserting fragments into a reference phylogeny,
    i.e. the output of function 'sepp'
reference_taxonomy : FeatureData[Taxonomy], optional
    Reference taxonomic table that maps every OTU-ID into a taxonomic
    lineage string.

Returns
-------
classification : FeatureData[Taxonomy]
    Taxonomic lineages for inserted fragments.
	]]></help>
<macros>
    <import>qiime_citation.xml</import>
</macros>
<expand macro="qiime_citation"/>
</tool>