<?xml version='1.0' encoding='utf-8'?>
<!--
Copyright (c) 2023, QIIME 2 development team.

Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause)
-->
<!--
This tool was automatically generated by:
    q2galaxy (version: 2022.11.1)
for:
    qiime2 (version: 2022.11.1)
-->
<tool name="qiime2 gneiss assign-ids" id="qiime2__gneiss__assign_ids" version="2022.11.1+q2galaxy.2022.11.1.2" profile="22.05" license="BSD-3-Clause">
    <description>Assigns ids on internal nodes in the tree, and makes sure that they are consistent with the table columns.</description>
    <requirements>
        <container type="docker">quay.io/qiime2/core:2022.11</container>
    </requirements>
    <version_command>q2galaxy version gneiss</version_command>
    <command detect_errors="exit_code">q2galaxy run gneiss assign_ids '$inputs'</command>
    <configfiles>
        <inputs name="inputs" data_style="paths"/>
    </configfiles>
    <inputs>
        <param name="input_table" type="data" format="qza" label="input_table: FeatureTable[Frequency]" help="[required]  The input table of counts.">
            <options options_filter_attribute="metadata.semantic_type">
                <filter type="add_value" value="FeatureTable[Frequency]"/>
            </options>
            <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureTable[Frequency]']</validator>
        </param>
        <param name="input_tree" type="data" format="qza" label="input_tree: Phylogeny[Rooted]" help="[required]  The input tree with potential missing ids.">
            <options options_filter_attribute="metadata.semantic_type">
                <filter type="add_value" value="Phylogeny[Rooted]"/>
            </options>
            <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['Phylogeny[Rooted]']</validator>
        </param>
    </inputs>
    <outputs>
        <data name="output_table" format="qza" label="${tool.name} on ${on_string}: output_table.qza" from_work_dir="output_table.qza"/>
        <data name="output_tree" format="qza" label="${tool.name} on ${on_string}: output_tree.qza" from_work_dir="output_tree.qza"/>
    </outputs>
    <tests/>
    <help>
QIIME 2: gneiss assign-ids
==========================
Assigns ids on internal nodes in the tree, and makes sure that they are consistent with the table columns.


Outputs:
--------
:output_table.qza: A table with features matching the tree tips.
:output_tree.qza: A tree with uniquely identifying ids.

|  

Description:
------------
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


|  

</help>
    <citations>
        <citation type="bibtex">@article{cite1,
 author = {Morton, James T and Sanders, Jon and Quinn, Robert A and McDonald, Daniel and Gonzalez, Antonio and Vázquez-Baeza, Yoshiki and Navas-Molina, Jose A and Song, Se Jin and Metcalf, Jessica L and Hyde, Embriette R and Lladser, Manuel and Dorrestein, Pieter C and Knight, Rob},
 journal = {MSystems},
 number = {1},
 pages = {e00162--16},
 publisher = {Am Soc Microbiol},
 title = {Balance trees reveal microbial niche differentiation},
 volume = {2},
 year = {2017}
}
</citation>
        <citation type="doi">10.1038/s41587-019-0209-9</citation>
    </citations>
</tool>