<?xml version="1.0" ?>
<tool id="qiime_gneiss_ilr-phylogenetic" name="qiime gneiss ilr-phylogenetic"
      version="2020.8">
  <description>Isometric Log-ratio Transform applied to a phylogenetic tree</description>
  <requirements>
    <requirement type="package" version="2020.8">qiime2</requirement>
  </requirements>
  <command><![CDATA[
qiime gneiss ilr-phylogenetic

--i-table=$itable

--i-tree=$itree

--p-pseudocount=$ppseudocount

--o-balances=obalances

--o-hierarchy=ohierarchy

#if str($examples) != 'None':
--examples=$examples
#end if

;
cp ohierarchy.qza $ohierarchy

  ]]></command>
  <inputs>
    <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Frequency | Composition] The feature table containing the samples in which the ilr transform will be performed.      [required]" name="itable" optional="False" type="data" />
    <param format="qza,no_unzip.zip" label="--i-tree: ARTIFACT       A rooted phylogeny of feature identifiers that Phylogeny[Rooted]     defines the partitions of features.  Each tip in the hierarchycorresponds to the feature identifiers in the table. This tree can contain tip ids that are not present in the table, but all feature ids in the table must be present in this tree.  This assumes that all of the internal nodes in the tree have labels. This tree may contain polytomic nodes (i.e., nodes with more than two children), in which case they will be bifurcated.                  [required]" name="itree" optional="False" type="data" />
    <param label="--p-pseudocount: NUMBER  The value to add to zero counts in the feature table.                                [default: 0.5]" name="ppseudocount" optional="True" type="float" value="0.5" />
    <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
    
  </inputs>

  <outputs>
    <data format="qza" label="${tool.name} on ${on_string}: balances.qza" name="obalances" />
    <data format="qza" label="${tool.name} on ${on_string}: hierarchy.qza" name="ohierarchy" />
    
  </outputs>

  <help><![CDATA[
Isometric Log-ratio Transform applied to a phylogenetic tree
###############################################################

Calculate balances given a rooted phylogeny.

Parameters
----------
table : FeatureTable[Frequency | Composition]
    The feature table containing the samples in which the ilr transform
    will be performed.
tree : Phylogeny[Rooted]
    A rooted phylogeny of feature identifiers that defines the partitions
    of features.  Each tip in the hierarchycorresponds to the feature
    identifiers in the table. This tree can contain tip ids that are not
    present in the table, but all feature ids in the table must be present
    in this tree.  This assumes that all of the internal nodes in the tree
    have labels. This tree may contain polytomic nodes (i.e., nodes with
    more than two children), in which case they will be bifurcated.
pseudocount : Float, optional
    The value to add to zero counts in the feature table.

Returns
-------
balances : FeatureTable[Balance]
    The resulting balances from the ilr transform.
hierarchy : Hierarchy
    Hierarchy from bifurcated phylogeny
  ]]></help>
  <macros>
    <import>qiime_citation.xml</import>
  </macros>
  <expand macro="qiime_citation"/>
</tool>