<?xml version="1.0" ?>
<tool id="qiime_gneiss_assign-ids" name="qiime gneiss assign-ids"
      version="2020.8">
  <description>Assigns ids on internal nodes in the tree, and makes sure that they are consistent with the table columns.</description>
  <requirements>
    <requirement type="package" version="2020.8">qiime2</requirement>
  </requirements>
  <command><![CDATA[
qiime gneiss assign-ids

--i-input-table=$iinputtable

--i-input-tree=$iinputtree

--o-output-table=ooutputtable

--o-output-tree=ooutputtree

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

;
cp ooutputtree.qza $ooutputtree

  ]]></command>
  <inputs>
    <param format="qza,no_unzip.zip" label="--i-input-table: ARTIFACT FeatureTable[Frequency] The input table of counts.                   [required]" name="iinputtable" optional="False" type="data" />
    <param format="qza,no_unzip.zip" label="--i-input-tree: ARTIFACT Phylogeny[Rooted]  The input tree with potential missing ids.   [required]" name="iinputtree" 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 ${on_string}: outputtable.qza" name="ooutputtable" />
    <data format="qza" label="${tool.name} on ${on_string}: outputtree.qza" name="ooutputtree" />
    
  </outputs>

  <help><![CDATA[
Assigns ids on internal nodes in the tree, and makes sure that they are consistent with the table columns.
###############################################################


Assigns UUIDs to uniquely identify internal nodes in the tree.  Also
corrects for polytomies to create strictly bifurcating trees and aligns the
table columns with the tree tip names

Parameters
----------
input_table : FeatureTable[Frequency]
    The input table of counts.
input_tree : Phylogeny[Rooted]
    The input tree with potential missing ids.

Returns
-------
output_table : FeatureTable[Frequency]
    A table with features matching the tree tips.
output_tree : Hierarchy
    A tree with uniquely identifying ids.
  ]]></help>
  <macros>
    <import>qiime_citation.xml</import>
  </macros>
  <expand macro="qiime_citation"/>
</tool>