<?xml version="1.0" ?>
<tool id="qiime_phylogeny_robinson-foulds" name="qiime phylogeny robinson-foulds"
      version="2020.8">
  <description>Calculate Robinson-Foulds distance between phylogenetic trees.</description>
  <requirements>
    <requirement type="package" version="2020.8">qiime2</requirement>
  </requirements>
  <command><![CDATA[
qiime phylogeny robinson-foulds

--i-trees=$itrees

#if str($plabels):
  --p-labels=$plabels
#end if
#if str($pmissingtips) != 'None':
--p-missing-tips=$pmissingtips
#end if

--o-distance-matrix=odistancematrix

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

;
cp odistancematrix.qza $odistancematrix

  ]]></command>
  <inputs>
    <param format="qza,no_unzip.zip" label="--i-trees: ARTIFACTS... List[Phylogeny[Rooted | Unrooted]] Phylogenetic trees to compare with Robinson-Foulds. Rooting information and branch lengths are ignored by this metric.                           [required]" name="itrees" optional="False" type="data" />
    <param label="--p-labels: TEXT...      Labels to use for the tree names in the distance List[Str]             matrix. If ommited, labels will be \'tree_n\' where \'n\' ranges from 1..N. The number of labels must match the number of trees.                [optional]" name="plabels" optional="False" type="text" />
    <param label="--p-missing-tips: " name="pmissingtips" optional="True" type="select">
      <option selected="True" value="None">Selection is Optional</option>
      <option value="error">error</option>
      <option value="intersect-all">intersect-all</option>
    </param>
    <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}: distancematrix.qza" name="odistancematrix" />
    
  </outputs>

  <help><![CDATA[
Calculate Robinson-Foulds distance between phylogenetic trees.
###############################################################

Calculate the Robinson-Foulds symmetric difference metric between two or
more phylogenetic trees.

Parameters
----------
trees : List[Phylogeny[Rooted | Unrooted]]
    Phylogenetic trees to compare with Robinson-Foulds. Rooting information
    and branch lengths are ignored by this metric.
labels : List[Str], optional
    Labels to use for the tree names in the distance matrix. If ommited,
    labels will be "tree_n" where "n" ranges from 1..N. The number of
    labels must match the number of trees.
missing_tips : Str % Choices('error', 'intersect-all'), optional
    How to handle tips that are not shared between trees. "error" will
    raise an error if the set of tips is not identical between all input
    trees. "intersect-all" will remove tips that are not shared between all
    trees before computing distances beteen trees.

Returns
-------
distance_matrix : DistanceMatrix
    The distances between trees as a symmetric matrix.
  ]]></help>
  <macros>
    <import>qiime_citation.xml</import>
  </macros>
  <expand macro="qiime_citation"/>
</tool>