annotate qiime2__taxa__filter_table.xml @ 4:a8972ecf15c1 draft default tip

planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa commit c7e80dcda727ce63b42aa8a946e9330310929797

<?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: 2024.5.0)
for:
    qiime2 (version: 2024.5.0)
-->
<tool name="qiime2 taxa filter-table" id="qiime2__taxa__filter_table" version="2024.5.0+q2galaxy.2024.5.0" profile="22.05" license="BSD-3-Clause">
    <description>Taxonomy-based feature table filter.</description>
    <requirements>
        <container type="docker">quay.io/qiime2/amplicon:2024.5</container>
    </requirements>
    <version_command>q2galaxy version taxa</version_command>
    <command detect_errors="exit_code">q2galaxy run taxa filter_table '$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[Frequency¹ | PresenceAbsence²]" help="[required]  Feature table to be filtered.">
            <options options_filter_attribute="metadata.semantic_type">
                <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[Frequency]', 'FeatureTable[PresenceAbsence]']</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 for features 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>
        <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">
            <conditional name="__q2galaxy__GUI__conditional__include__" label="include: Str">
                <param name="__q2galaxy__GUI__select__" type="select" label="include: Str" help="[optional]  One or more search terms that indicate which taxa should be included in the resulting table. If providing more than one term, terms should be delimited by the query-delimiter character. By default, all taxa will be included.">
                    <option value="__q2galaxy__::control::default" selected="true">None (Use default behavior)</option>
                    <option value="__q2galaxy__::control::provide">Provide a value</option>
                </param>
                <when value="__q2galaxy__::control::default">
                    <param name="include" type="hidden" value="__q2galaxy__::literal::None"/>
                </when>
                <when value="__q2galaxy__::control::provide">
                    <param name="include" type="text">
                        <sanitizer>
                            <valid initial="string.printable"/>
                        </sanitizer>
                    </param>
                </when>
            </conditional>
            <conditional name="__q2galaxy__GUI__conditional__exclude__" label="exclude: Str">
                <param name="__q2galaxy__GUI__select__" type="select" label="exclude: Str" help="[optional]  One or more search terms that indicate which taxa should be excluded from the resulting table. If providing more than one term, terms should be delimited by the query-delimiter character. By default, no taxa will be excluded.">
                    <option value="__q2galaxy__::control::default" selected="true">None (Use default behavior)</option>
                    <option value="__q2galaxy__::control::provide">Provide a value</option>
                </param>
                <when value="__q2galaxy__::control::default">
                    <param name="exclude" type="hidden" value="__q2galaxy__::literal::None"/>
                </when>
                <when value="__q2galaxy__::control::provide">
                    <param name="exclude" type="text">
                        <sanitizer>
                            <valid initial="string.printable"/>
                        </sanitizer>
                    </param>
                </when>
            </conditional>
            <param name="query_delimiter" type="text" value="," label="query_delimiter: Str" help="[default: ',']  The string used to delimit multiple search terms provided to include or exclude. This parameter should only need to be modified if the default delimiter (a comma) is used in the provided taxonomic annotations.">
                <sanitizer>
                    <valid initial="string.printable"/>
                </sanitizer>
            </param>
            <param name="mode" type="select" label="mode: Str % Choices('exact', 'contains')" display="radio">
                <option value="exact">exact</option>
                <option value="contains" selected="true">contains</option>
            </param>
        </section>
    </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/>
    <help>
QIIME 2: taxa filter-table
==========================
Taxonomy-based feature table filter.


Outputs:
--------
:filtered_table.qza: The taxonomy-filtered feature table.

|  

Description:
------------
This method filters features from a table based on their taxonomic annotations. Features can be retained in the resulting table by specifying one or more include search terms, and can be filtered out of the resulting table by specifying one or more exclude search terms. If both include and exclude are provided, the inclusion critera will be applied before the exclusion critera. Either include or exclude terms (or both) must be provided. Any samples that have a total frequency of zero after filtering will be removed from the resulting table.


|  

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