<?xml version="1.0" ?>
<tool id="qiime_fragment-insertion_classify-otus-experimental" name="qiime fragment-insertion classify-otus-experimental"
      version="2020.8">
  <description>Experimental: Obtain taxonomic lineages, by finding closest OTU in reference phylogeny.</description>
  <requirements>
    <requirement type="package" version="2020.8">qiime2</requirement>
  </requirements>
  <command><![CDATA[
qiime fragment-insertion classify-otus-experimental

--i-representative-sequences=$irepresentativesequences

--i-tree=$itree

--i-reference-taxonomy=$ireferencetaxonomy

--o-classification=oclassification

#if str($examples) != 'None':
--examples=$examples
#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" />
    <param format="qza,no_unzip.zip" label="--i-reference-taxonomy: ARTIFACT FeatureData[Taxonomy] Reference taxonomic table that maps every OTU-ID into a taxonomic lineage string.                  [required]" name="ireferencetaxonomy" optional="False" type="data" />
    <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}: 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]
    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>