Mercurial > repos > q2d2 > qiime2__feature_table__normalize

comparison qiime2__feature_table__normalize.xml @ 3:706e4624a7fa draft default tip

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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 36ec48f8c55799a0c963733df13da30f19b1bdf3
author q2d2
date Wed, 28 Jan 2026 16:26:14 +0000
parents 88ba945ca47b
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2:88ba945ca47b 3:706e4624a7fa
1 <?xml version='1.0' encoding='utf-8'?> 1 <?xml version='1.0' encoding='utf-8'?>
2 <!-- 2 <!--
3 Copyright (c) 2025, QIIME 2 development team. 3 Copyright (c) 2026, QIIME 2 development team.
4 4
5 Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) 5 Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause)
6 --> 6 -->
7 <!-- 7 <!--
8 This tool was automatically generated by: 8 This tool was automatically generated by:
9 q2galaxy (version: 2025.10.0) 9 q2galaxy (version: 2026.1.0)
10 for: 10 for:
11 qiime2 (version: 2025.10.0) 11 qiime2 (version: 2026.1.0)
12 --> 12 -->
13 <tool name="qiime2 feature-table normalize" id="qiime2__feature_table__normalize" version="2025.10.0+q2galaxy.2025.10.0" profile="22.05" license="BSD-3-Clause"> 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">
14 <description>Normalize FeatureTable</description> 14 <description>Normalize FeatureTable</description>
15 <xrefs> 15 <xrefs>
16 <xref type="bio.tools">qiime2</xref> 16 <xref type="bio.tools">qiime2</xref>
17 </xrefs> 17 </xrefs>
18 <requirements> 18 <requirements>
19 <container type="docker">quay.io/qiime2/amplicon:2025.10</container> 19 <container type="docker">quay.io/qiime2/amplicon:2026.1</container>
20 </requirements> 20 </requirements>
21 <version_command>q2galaxy version feature_table</version_command> 21 <version_command>q2galaxy version feature_table</version_command>
22 <command detect_errors="exit_code">q2galaxy run feature_table normalize '$inputs'</command> 22 <command detect_errors="exit_code">q2galaxy run feature_table normalize '$inputs'</command>
23 <configfiles> 23 <configfiles>
24 <inputs name="inputs" data_style="staging_path_and_source_path"/> 24 <inputs name="inputs" data_style="staging_path_and_source_path"/>
28 <options options_filter_attribute="metadata.semantic_type"> 28 <options options_filter_attribute="metadata.semantic_type">
29 <filter type="add_value" value="FeatureTable[Frequency]"/> 29 <filter type="add_value" value="FeatureTable[Frequency]"/>
30 </options> 30 </options>
31 <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureTable[Frequency]']</validator> 31 <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureTable[Frequency]']</validator>
32 </param> 32 </param>
33 <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."> 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.">
34 <option value="__q2galaxy__::literal::None" selected="true">Selection required</option> 34 <option value="__q2galaxy__::literal::None" selected="true">Selection required</option>
35 <option value="tpm">tpm (Str)</option>
36 <option value="fpkm">fpkm (Str)</option>
37 <option value="tmm">tmm (Str)</option>
38 <option value="uq">uq (Str)</option>
39 <option value="cuf">cuf (Str)</option>
40 <option value="ctf">ctf (Str)</option>
41 <option value="cpm">cpm (Str)</option>
42 <validator type="expression" message="Please verify this parameter.">value != '__q2galaxy__::literal::None'</validator> 35 <validator type="expression" message="Please verify this parameter.">value != '__q2galaxy__::literal::None'</validator>
43 </param> 36 </param>
44 <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options"> 37 <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">
45 <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."> 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.">
46 <options options_filter_attribute="metadata.semantic_type"> 39 <options options_filter_attribute="metadata.semantic_type">