<?xml version='1.0' encoding='utf-8'?>
<!--
Copyright (c) 2024, 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: 2024.10.0)
for:
    qiime2 (version: 2024.10.1)
-->
<tool name="qiime2 taxa collapse" id="qiime2__taxa__collapse" version="2024.10.0+q2galaxy.2024.10.0" profile="22.05" license="BSD-3-Clause">
    <description>Collapse features by their taxonomy at the specified level</description>
    <xrefs>
        <xref type="bio.tools">qiime2</xref>
    </xrefs>
    <requirements>
        <container type="docker">quay.io/qiime2/amplicon:2024.10</container>
    </requirements>
    <version_command>q2galaxy version taxa</version_command>
    <command detect_errors="exit_code">q2galaxy run taxa collapse '$inputs'</command>
    <configfiles>
        <inputs name="inputs" data_style="staging_path_and_source_path"/>
    </configfiles>
    <inputs>
        <param name="table" type="data" format="qza" label="table: FeatureTable[Frequency]" help="[required]  Feature table to be collapsed.">
            <options options_filter_attribute="metadata.semantic_type">
                <filter type="add_value" value="FeatureTable[Frequency]"/>
            </options>
            <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureTable[Frequency]']</validator>
        </param>
        <param name="taxonomy" type="data" format="qza" label="taxonomy: FeatureData[Taxonomy]" help="[required]  Taxonomic annotations for features in the provided feature table. All features in the feature table must have a corresponding taxonomic annotation. Taxonomic annotations that are not present in the feature table will be ignored.">
            <options options_filter_attribute="metadata.semantic_type">
                <filter type="add_value" value="FeatureData[Taxonomy]"/>
            </options>
            <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureData[Taxonomy]']</validator>
        </param>
        <param name="level" type="integer" value="" label="level: Int" help="[required]  The taxonomic level at which the features should be collapsed. All ouput features will have exactly this many levels of taxonomic annotation."/>
    </inputs>
    <outputs>
        <data name="collapsed_table" format="qza" label="${tool.name} on ${on_string}: collapsed_table.qza" from_work_dir="collapsed_table.qza"/>
    </outputs>
    <tests>
        <test>
            <param name="table" value="collapse.test0.table.qza" ftype="qza"/>
            <param name="taxonomy" value="collapse.test0.taxonomy.qza" ftype="qza"/>
            <param name="level" value="6"/>
            <output name="collapsed_table" ftype="qza">
                <assert_contents>
                    <has_archive_member path="[0-9a-f]{8}-[0-9a-f]{4}-[4][0-9a-f]{3}-[89ab][0-9a-f]{3}-[0-9a-f]{12}\/metadata.yaml">
                        <has_line_matching expression="type: FeatureTable\[Frequency\]"/>
                    </has_archive_member>
                </assert_contents>
            </output>
        </test>
    </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.

Examples:
---------

collapse
********
Using the ``qiime2 taxa collapse`` tool:
 #. Set *"table"* to ``#: table.qza``
 #. Set *"taxonomy"* to ``#: taxonomy.qza``
 #. Set *"level"* to ``6``
 #. Press the ``Execute`` button.

Once completed, for the new entry in your history, use the ``Edit`` button to set the name as follows:
 (Renaming is optional, but it will make any subsequent steps easier to complete.)

 .. list-table::
    :align: left
    :header-rows: 1

    * - History Name
      - *"Name"* to set (be sure to press ``Save``)
    * - ``#: qiime2 taxa collapse [...] : collapsed_table.qza``
      - ``collapsed-table-l6.qza``


|  

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