<?xml version='1.0' encoding='utf-8'?>
<!--
Copyright (c) 2022, 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: 2022.8.1)
for:
    qiime2 (version: 2022.8.1)
-->
<tool name="qiime2 taxa collapse" id="qiime2__taxa__collapse" version="2022.8.0+q2galaxy.2022.8.1.2" profile="22.05" license="BSD-3-Clause">
    <description>Collapse features by their taxonomy at the specified level</description>
    <requirements>
        <container type="docker">quay.io/qiime2/core:2022.8</container>
    </requirements>
    <version_command>q2galaxy version taxa</version_command>
    <command detect_errors="aggressive">q2galaxy run taxa collapse '$inputs'</command>
    <configfiles>
        <inputs name="inputs" data_style="paths"/>
    </configfiles>
    <inputs>
        <param name="table" type="data" format="qza" label="table: FeatureTable[Frequency]" help="[required]  Feature table to be collapsed.">
            <options options_filter_attribute="metadata.semantic_type">
                <filter type="add_value" value="FeatureTable[Frequency]"/>
            </options>
            <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureTable[Frequency]']</validator>
        </param>
        <param name="taxonomy" type="data" format="qza" label="taxonomy: FeatureData[Taxonomy]" help="[required]  Taxonomic annotations for features in the provided feature table. All features in the feature table must have a corresponding taxonomic annotation. Taxonomic annotations that are not present in the feature table will be ignored.">
            <options options_filter_attribute="metadata.semantic_type">
                <filter type="add_value" value="FeatureData[Taxonomy]"/>
            </options>
            <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureData[Taxonomy]']</validator>
        </param>
        <param name="level" type="integer" value="" label="level: Int" help="[required]  The taxonomic level at which the features should be collapsed. All ouput features will have exactly this many levels of taxonomic annotation."/>
    </inputs>
    <outputs>
        <data name="collapsed_table" format="qza" label="${tool.name} on ${on_string}: collapsed_table.qza" from_work_dir="collapsed_table.qza"/>
    </outputs>
    <tests/>
    <help>
QIIME 2: taxa collapse
======================
Collapse features by their taxonomy at the specified level


Outputs:
--------
:collapsed_table.qza: The resulting feature table, where all features are now taxonomic annotations with the user-specified number of levels.

|  

Description:
------------
Collapse groups of features that have the same taxonomic assignment through the specified level. The frequencies of all features will be summed when they are collapsed.


|  

</help>
    <citations>
        <citation type="doi">10.1038/s41587-019-0209-9</citation>
    </citations>
</tool>