<?xml version="1.0" ?>
<tool id="qiime_gneiss_assign-ids" name="qiime gneiss assign-ids" version="2019.7">
	<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="2019.7">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
;
cp ooutputtable.qza $ooutputtable;
cp ooutputtree.qza $ooutputtree
	]]></command>
	<inputs>
		<param format="qza,no_unzip.zip" label="--i-input-table: ARTIFACT FeatureTable[Frequency] The input table of counts.                   [required]" name="iinputtable" optional="False" type="data"/>
		<param format="qza,no_unzip.zip" label="--i-input-tree: ARTIFACT Phylogeny[Rooted]  The input tree with potential missing ids.   [required]" name="iinputtree" optional="False" type="data"/>
	</inputs>
	<outputs>
		<data format="qza" label="${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>