annotate qiime2__feature_table__filter_features.xml @ 0:5585d004e609 draft

planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1

<?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 feature-table filter-features" id="qiime2__feature_table__filter_features" version="2022.8.0+q2galaxy.2022.8.1.2" profile="22.05" license="BSD-3-Clause">
    <description>Filter features from table</description>
    <requirements>
        <container type="docker">quay.io/qiime2/core:2022.8</container>
    </requirements>
    <version_command>q2galaxy version feature_table</version_command>
    <command detect_errors="aggressive">q2galaxy run feature_table filter_features '$inputs'</command>
    <configfiles>
        <inputs name="inputs" data_style="paths"/>
    </configfiles>
    <inputs>
        <param name="table" type="data" format="qza" label="table: FeatureTable[Frequency]" help="[required]  The feature table from which features should be filtered.">
            <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>
        <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">
            <param name="min_frequency" type="integer" value="0" label="min_frequency: Int" help="[default: 0]  The minimum total frequency that a feature must have to be retained."/>
            <param name="max_frequency" type="integer" optional="true" label="max_frequency: Int" help="[optional]  The maximum total frequency that a feature can have to be retained. If no value is provided this will default to infinity (i.e., no maximum frequency filter will be applied)."/>
            <param name="min_samples" type="integer" value="0" label="min_samples: Int" help="[default: 0]  The minimum number of samples that a feature must be observed in to be retained."/>
            <param name="max_samples" type="integer" optional="true" label="max_samples: Int" help="[optional]  The maximum number of samples that a feature can be observed in to be retained. If no value is provided this will default to infinity (i.e., no maximum sample filter will be applied)."/>
            <repeat name="metadata" help="[optional]  Feature metadata used with `where` parameter when selecting features to retain, or with `exclude_ids` when selecting features to discard." title="metadata: Metadata">
                <conditional name="__q2galaxy__GUI__conditional__metadata__">
                    <param name="type" type="select" label="metadata: Metadata">
                        <option value="tsv" selected="true">Metadata from TSV</option>
                        <option value="qza">Metadata from Artifact</option>
                    </param>
                    <when value="tsv">
                        <param name="source" type="data" format="tabular,qiime2.tabular" label="Metadata Source"/>
                    </when>
                    <when value="qza">
                        <param name="source" type="data" format="qza" label="Metadata Source"/>
                    </when>
                </conditional>
            </repeat>
            <conditional name="__q2galaxy__GUI__conditional__where__" label="where: Str">
                <param name="__q2galaxy__GUI__select__" type="select" label="where: Str" help="[optional]  SQLite WHERE clause specifying feature metadata criteria that must be met to be included in the filtered feature table. If not provided, all features in `metadata` that are also in the feature table will be retained.">
                    <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="where" type="hidden" value="__q2galaxy__::literal::None"/>
                </when>
                <when value="__q2galaxy__::control::provide">
                    <param name="where" type="text">
                        <sanitizer>
                            <valid initial="string.printable"/>
                        </sanitizer>
                    </param>
                </when>
            </conditional>
            <param name="exclude_ids" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" label="exclude_ids: Bool" help="[default: No]  If true, the features selected by `metadata` or `where` parameters will be excluded from the filtered table instead of being retained."/>
            <param name="filter_empty_samples" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" checked="true" label="filter_empty_samples: Bool" help="[default: Yes]  If true, drop any samples where none of the retained features are present."/>
        </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: feature-table filter-features
======================================
Filter features from table


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

|  

Description:
------------
Filter features from table based on frequency and/or metadata. Any samples with a frequency of zero after feature filtering will also be removed. See the filtering tutorial on https://docs.qiime2.org for additional details.


|  

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