<?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 feature-table filter-features-conditionally" id="qiime2__feature_table__filter_features_conditionally" version="2022.11.1+q2galaxy.2022.11.1.2" profile="22.05" license="BSD-3-Clause">
    <description>Filter features from a table based on abundance and prevalence</description>
    <requirements>
        <container type="docker">quay.io/qiime2/core:2022.11</container>
    </requirements>
    <version_command>q2galaxy version feature_table</version_command>
    <command detect_errors="exit_code">q2galaxy run feature_table filter_features_conditionally '$inputs'</command>
    <configfiles>
        <inputs name="inputs" data_style="paths"/>
    </configfiles>
    <inputs>
        <param name="table" type="data" format="qza" label="table: FeatureTable[Frequency¹ | RelativeFrequency² | PresenceAbsence³ | Composition⁴]" help="[required]  The feature table from which features should be filtered.">
            <options options_filter_attribute="metadata.semantic_type">
                <filter type="add_value" value="FeatureTable[RelativeFrequency]"/>
                <filter type="add_value" value="FeatureTable[Composition]"/>
                <filter type="add_value" value="FeatureTable[Frequency]"/>
                <filter type="add_value" value="FeatureTable[PresenceAbsence]"/>
            </options>
            <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureTable[Composition]', 'FeatureTable[Frequency]', 'FeatureTable[PresenceAbsence]', 'FeatureTable[RelativeFrequency]']</validator>
        </param>
        <param name="abundance" type="float" min="0" max="0.999999" value="" label="abundance: Float % Range(0, 1)" help="[required]  The minimum relative abundance for a feature to be retained."/>
        <param name="prevalence" type="float" min="0" max="0.999999" value="" label="prevalence: Float % Range(0, 1)" help="[required]  The minimum portion of samples that a feature must have a relative abundance of at least `abundance` to be retained."/>
    </inputs>
    <outputs>
        <data name="filtered_table" format="qza" label="${tool.name} on ${on_string}: filtered_table.qza" from_work_dir="filtered_table.qza"/>
    </outputs>
    <tests>
        <test>
            <param name="table" value="filter_features_conditionally.test0.feature-table.qza" ftype="qza"/>
            <param name="abundance" value="0.01"/>
            <param name="prevalence" value="0.34"/>
            <output name="filtered_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: feature-table filter-features-conditionally
====================================================
Filter features from a table based on abundance and prevalence


Outputs:
--------
:filtered_table.qza: The resulting feature table filtered by feature.

|  

Description:
------------
Filter features based on the relative abundance in a certain portion of samples (i.e., features must have a relative abundance of at least `abundance` in at least `prevalence` number of samples). Any samples with a frequency of zero after feature filtering will also be removed.

Examples:
---------

feature_table_filter_features_conditionally
*******************************************
| Retain only features with at least 1%% abundance in at least 34%% of samples.
Using the ``qiime2 feature-table filter-features-conditionally`` tool:
 #. Set *"table"* to ``#: feature-table.qza``
 #. Set *"abundance"* to ``0.01``
 #. Set *"prevalence"* to ``0.34``
 #. Press the ``Execute`` button.



|  

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