diff 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

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2__feature_table__normalize.xml	Mon May 05 18:54:07 2025 +0000
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+<?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>