annotate qiime2__feature_table__core_features.xml @ 1:3ab02629e494 draft

planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 69da7976573cc07a363ac66bdacc9269d7cd3732

<?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 core-features" id="qiime2__feature_table__core_features" version="2022.11.1+q2galaxy.2022.11.1.2" profile="22.05" license="BSD-3-Clause">
    <description>Identify core features in table</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 core_features '$inputs'</command>
    <configfiles>
        <inputs name="inputs" data_style="paths"/>
    </configfiles>
    <inputs>
        <param name="table" type="data" format="qza" label="table: FeatureTable[Frequency]" help="[required]  The feature table to use in core features calculations.">
            <options options_filter_attribute="metadata.semantic_type">
                <filter type="add_value" value="FeatureTable[Frequency]"/>
            </options>
            <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureTable[Frequency]']</validator>
        </param>
        <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">
            <param name="min_fraction" type="float" min="1e-06" max="0.999999" value="0.5" label="min_fraction: Float % Range(0.0, 1.0, inclusive_start=False)" help="[default: 0.5]  The minimum fraction of samples that a feature must be observed in for that feature to be considered a core feature."/>
            <param name="max_fraction" type="float" min="0.0" max="1.0" value="1.0" label="max_fraction: Float % Range(0.0, 1.0, inclusive_end=True)" help="[default: 1.0]  The maximum fraction of samples that a feature must be observed in for that feature to be considered a core feature."/>
            <param name="steps" type="integer" min="2" value="11" label="steps: Int % Range(2, None)" help="[default: 11]  The number of steps to take between `min_fraction` and `max_fraction` for core features calculations. This parameter has no effect if `min_fraction` and `max_fraction` are the same value."/>
        </section>
    </inputs>
    <outputs>
        <data name="visualization" format="qzv" label="${tool.name} on ${on_string}: visualization.qzv" from_work_dir="visualization.qzv"/>
    </outputs>
    <tests/>
    <help>
QIIME 2: feature-table core-features
====================================
Identify core features in table


Outputs:
--------
:visualization.qzv: &lt;no description&gt;

|  

Description:
------------
Identify "core" features, which are features observed in a user-defined fraction of the samples. Since the core features are a function of the fraction of samples that the feature must be observed in to be considered core, this is computed over a range of fractions defined by the `min_fraction`, `max_fraction`, and `steps` parameters.


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