<?xml version='1.0' encoding='utf-8'?>
<!--
Copyright (c) 2025, 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: 2025.10.0)
for:
    qiime2 (version: 2025.10.0)
-->
<tool name="qiime2 boots resample" id="qiime2__boots__resample" version="2025.10.0+q2galaxy.2025.10.0" profile="22.05" license="BSD-3-Clause">
    <description>Resample feature table, returning `n` feature tables.</description>
    <xrefs>
        <xref type="bio.tools">qiime2</xref>
    </xrefs>
    <requirements>
        <container type="docker">quay.io/qiime2/amplicon:2025.10</container>
    </requirements>
    <version_command>q2galaxy version boots</version_command>
    <command detect_errors="exit_code">q2galaxy run boots resample '$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]  The input feature table.">
            <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="sampling_depth" type="integer" min="1" value="" label="sampling_depth: Int % Range(1, None)" help="[required]  The total number of observations that each sample in `table` should be resampled to. Samples where the total number of observations in `table` is less than `sampling_depth` will be not be included in the output tables."/>
        <param name="n" type="integer" min="1" value="" label="n: Int % Range(1, None)" help="[required]  The number of resampled tables that should be generated."/>
        <param name="replacement" type="select" label="replacement: Bool" help="[required]  Resample `table` with replacement (i.e., bootstrap) or without replacement (i.e., rarefaction)." display="radio">
            <option value="__q2galaxy__::literal::None">Selection required</option>
            <option value="__q2galaxy__::literal::True">Yes</option>
            <option value="__q2galaxy__::literal::False">No</option>
            <validator type="expression" message="Please verify this parameter.">value != '__q2galaxy__::literal::None'</validator>
        </param>
    </inputs>
    <outputs>
        <collection name="resampled_tables" type="list">
            <discover_datasets directory="resampled_tables" pattern="__name_and_ext__"/>
        </collection>
    </outputs>
    <tests>
        <test>
            <param name="table" value="resample.test0.table.qza" ftype="qza"/>
            <param name="sampling_depth" value="20"/>
            <param name="n" value="10"/>
            <param name="replacement" value="__q2galaxy__::literal::True"/>
            <output_collection name="resampled_tables" type="list"/>
        </test>
        <test>
            <param name="table" value="resample.test1.table.qza" ftype="qza"/>
            <param name="sampling_depth" value="20"/>
            <param name="n" value="10"/>
            <param name="replacement" value="__q2galaxy__::literal::False"/>
            <output_collection name="resampled_tables" type="list"/>
        </test>
    </tests>
    <help>
QIIME 2: boots resample
=======================
Resample feature table, returning `n` feature tables.


Outputs:
--------
:resampled_tables.qza: The `n` resampled tables.

|  

Description:
------------
Resample `table` to `sampling_depth` total observations with replacement (i.e., bootstrapping) or without replacement (i.e., rarefaction) `n` times, to generate `n` resampled feature tables.

Examples:
---------

Generate 10 bootstrapped tables.
********************************
Using the ``qiime2 boots resample`` tool:
 #. Set *"table"* to ``#: table.qza``
 #. Set *"sampling_depth"* to ``20``
 #. Set *"n"* to ``10``
 #. Set *"replacement"* to ``Yes``
 #. 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 boots resample [...] : resampled_tables.qza``
      - ``bootstrapped-tables/``

Generate 10 rarefied tables.
****************************
Using the ``qiime2 boots resample`` tool:
 #. Set *"table"* to ``#: table.qza``
 #. Set *"sampling_depth"* to ``20``
 #. Set *"n"* to ``10``
 #. Set *"replacement"* to ``No``
 #. 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 boots resample [...] : resampled_tables.qza``
      - ``rarefaction-tables/``


|  

</help>
    <citations>
        <citation type="doi">https://doi.org/10.12688/f1000research.156295.1</citation>
        <citation type="doi">10.1038/s41587-019-0209-9</citation>
    </citations>
</tool>