<?xml version="1.0" ?>
<tool id="qiime_gneiss_assign-ids" name="qiime gneiss assign-ids" version="2018.4">
	<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="2018.4">qiime2</requirement>
	</requirements>
	<command>
	<![CDATA[
	qiime gneiss assign-ids --i-input-table=$iinputtable --i-input-tree=$iinputtree

	#if str($cmdconfig) != 'None':
	 --cmd-config=$cmdconfig
	#end if
	 --o-output-tree=ooutputtree --o-output-table=ooutputtable;

	cp ooutputtree.qza $ooutputtree;
	cp ooutputtable.qza $ooutputtable;
	]]>
	</command>
	<inputs>
		<param format="qza,no_unzip.zip" label="--i-input-table: FeatureTable[Frequency] The input table of counts.  [required]" name="iinputtable" optional="False" type="data"/>
		<param format="qza,no_unzip.zip" label="--i-input-tree: Phylogeny[Rooted] The input tree with potential missing ids. [required]" name="iinputtree" optional="False" type="data"/>
		<param label="--cmd-config: Use config file for command options" name="cmdconfig" optional="True" type="data"/>
	</inputs>
	<outputs>
		<data format="qza" label="${tool.name} on ${on_string}: output-tree.qza" name="ooutputtree"/>
		<data format="qza" label="${tool.name} on ${on_string}: output-table.qza" name="ooutputtable"/>
	</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>