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author q2d2
date Wed, 28 Jan 2026 16:26:14 +0000
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36f8db68eca4 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit b1fccfb38b4873cd4699743033449014a2978e7d
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1 <?xml version='1.0' encoding='utf-8'?>
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2 <!--
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3 Copyright (c) 2026, QIIME 2 development team.
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5 Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause)
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6 -->
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7 <!--
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8 This tool was automatically generated by:
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9 q2galaxy (version: 2026.1.0)
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10 for:
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11 qiime2 (version: 2026.1.0)
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12 -->
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13 <tool name="qiime2 feature-table normalize" id="qiime2__feature_table__normalize" version="2026.1.0+q2galaxy.2026.1.0" profile="22.05" license="BSD-3-Clause">
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14 <description>Normalize FeatureTable</description>
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15 <xrefs>
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16 <xref type="bio.tools">qiime2</xref>
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17 </xrefs>
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18 <requirements>
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19 <container type="docker">quay.io/qiime2/amplicon:2026.1</container>
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20 </requirements>
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21 <version_command>q2galaxy version feature_table</version_command>
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22 <command detect_errors="exit_code">q2galaxy run feature_table normalize '$inputs'</command>
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23 <configfiles>
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24 <inputs name="inputs" data_style="staging_path_and_source_path"/>
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25 </configfiles>
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26 <inputs>
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27 <param name="table" type="data" format="qza" label="table: FeatureTable[Frequency]" help="[required] Feature table with gene counts.">
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28 <options options_filter_attribute="metadata.semantic_type">
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29 <filter type="add_value" value="FeatureTable[Frequency]"/>
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30 </options>
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31 <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureTable[Frequency]']</validator>
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32 </param>
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33 <param name="method" type="select" label="method: Str % (Choices('tpm')¹ | Choices('fpkm')² | Choices('tmm')³ | Choices('uq')⁴ | Choices('cuf')⁵ | Choices('ctf')⁶ | 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.">
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34 <option value="__q2galaxy__::literal::None" selected="true">Selection required</option>
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35 <validator type="expression" message="Please verify this parameter.">value != '__q2galaxy__::literal::None'</validator>
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36 </param>
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37 <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">
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38 <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.">
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39 <options options_filter_attribute="metadata.semantic_type">
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40 <filter type="add_value" value="FeatureData[SequenceCharacteristics % Properties('length')]"/>
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41 </options>
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42 <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ["FeatureData[SequenceCharacteristics % Properties('length')]"]</validator>
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43 </param>
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44 <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)"/>
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45 <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)"/>
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46 </section>
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47 </inputs>
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48 <outputs>
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49 <data name="normalized_table" format="qza" label="${tool.name} on ${on_string}: normalized_table.qza" from_work_dir="normalized_table.qza"/>
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50 </outputs>
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51 <tests/>
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52 <help>
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53 QIIME 2: feature-table normalize
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54 ================================
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55 Normalize FeatureTable
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56
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57
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58 Outputs:
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59 --------
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60 :normalized_table.qza: Feature table normalized with specified method.
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61
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62 |
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63
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64 Description:
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65 ------------
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66 Normalize FeatureTable by gene length, library size and composition with common methods for RNA-seq.
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67
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69 |
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71 </help>
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72 <citations>
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73 <citation type="bibtex">@misc{cite1,
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74 author = {Zmrzlikar, Jure and Žganec, Matjaž and Ausec, Luka and Štajdohar, Miha},
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75 month = {July},
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76 title = {RNAnorm: RNA-seq data normalization in Python},
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77 url = {https://github.com/genialis/RNAnorm},
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78 version = {2.1.0},
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79 year = {2023}
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80 }
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81 </citation>
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82 <citation type="doi">10.1038/s41587-019-0209-9</citation>
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83 </citations>
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84 </tool>