annotate qiime2__feature_table__normalize.xml @ 0:36f8db68eca4 draft default tip

planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit b1fccfb38b4873cd4699743033449014a2978e7d

<?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: 2025.4.0)
for:
    qiime2 (version: 2025.4.0)
-->
<tool name="qiime2 feature-table normalize" id="qiime2__feature_table__normalize" version="2025.4.0+q2galaxy.2025.4.0" profile="22.05" license="BSD-3-Clause">
    <description>Normalize FeatureTable</description>
    <xrefs>
        <xref type="bio.tools">qiime2</xref>
    </xrefs>
    <requirements>
        <container type="docker">quay.io/qiime2/amplicon:2025.4</container>
    </requirements>
    <version_command>q2galaxy version feature_table</version_command>
    <command detect_errors="exit_code">q2galaxy run feature_table normalize '$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]  Feature table with gene counts.">
            <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="method" type="select" label="method: Str % Choices('tpm')¹ | Str % Choices('fpkm')² | Str % Choices('tmm')³ | Str % Choices('uq')⁴ | Str % Choices('cuf')⁵ | Str % Choices('ctf')⁶ | Str % Choices('cpm')⁷" help="[required]  Specify the normalization method to be used. Use FPKM or TPM for within comparisons and TMM, UQ, CUF or CTF for between sample camparisons. Check https://www.genialis.com/wp-content/uploads/2023/12/2023-Normalizing-RNA-seq-data-in-Python-with-RNAnorm.pdf for more information on the methods.">
            <option value="__q2galaxy__::literal::None" selected="true">Selection required</option>
            <option value="tpm">tpm (Str)</option>
            <option value="fpkm">fpkm (Str)</option>
            <option value="tmm">tmm (Str)</option>
            <option value="uq">uq (Str)</option>
            <option value="cuf">cuf (Str)</option>
            <option value="ctf">ctf (Str)</option>
            <option value="cpm">cpm (Str)</option>
            <validator type="expression" message="Please verify this parameter.">value != '__q2galaxy__::literal::None'</validator>
        </param>
        <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">
            <param name="gene_length" type="data" format="qza" optional="true" label="gene_length: FeatureData[SequenceCharacteristics % Properties('length')]" help="[optional]  Gene lengths of all genes in the feature table.">
                <options options_filter_attribute="metadata.semantic_type">
                    <filter type="add_value" value="FeatureData[SequenceCharacteristics % Properties('length')]"/>
                </options>
                <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ["FeatureData[SequenceCharacteristics % Properties('length')]"]</validator>
            </param>
            <param name="m_trim" type="float" min="0" max="1" optional="true" label="m_trim: Float % Range(0, 1, inclusive_end=True)" help="[optional]  Two sided cutoff for M-values. Can only be used for methods TMM and CTF. (default = 0.3)"/>
            <param name="a_trim" type="float" min="0" max="1" optional="true" label="a_trim: Float % Range(0, 1, inclusive_end=True)" help="[optional]  Two sided cutoff for A-values. Can only be used for methods TMM and CTF. (default = 0.05)"/>
        </section>
    </inputs>
    <outputs>
        <data name="normalized_table" format="qza" label="${tool.name} on ${on_string}: normalized_table.qza" from_work_dir="normalized_table.qza"/>
    </outputs>
    <tests/>
    <help>
QIIME 2: feature-table normalize
================================
Normalize FeatureTable


Outputs:
--------
:normalized_table.qza: Feature table normalized with specified method.

|  

Description:
------------
Normalize FeatureTable by gene length, library size and composition with common methods for RNA-seq.


|  

</help>
    <citations>
        <citation type="bibtex">@misc{cite1,
 author = {Zmrzlikar, Jure and Žganec, Matjaž and Ausec, Luka and Štajdohar, Miha},
 month = {July},
 title = {RNAnorm: RNA-seq data normalization in Python},
 url = {https://github.com/genialis/RNAnorm},
 version = {2.1.0},
 year = {2023}
}
</citation>
        <citation type="doi">10.1038/s41587-019-0209-9</citation>
    </citations>
</tool>