# HG changeset patch
# User q2d2
# Date 1746470540 0
# Node ID 1e09dd637eb72dc896c9fe65fbcfcfb9780cf198
# Parent  354f63459d374530d2fc19d91172722257d5cf22
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 commit b1fccfb38b4873cd4699743033449014a2978e7d

diff -r 354f63459d37 -r 1e09dd637eb7 qiime2__dada2__denoise_single.xml
--- a/qiime2__dada2__denoise_single.xml	Wed Oct 30 19:36:55 2024 +0000
+++ b/qiime2__dada2__denoise_single.xml	Mon May 05 18:42:20 2025 +0000
@@ -1,22 +1,22 @@
 <?xml version='1.0' encoding='utf-8'?>
 <!--
-Copyright (c) 2024, QIIME 2 development team.
+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: 2024.10.0)
+    q2galaxy (version: 2025.4.0)
 for:
-    qiime2 (version: 2024.10.1)
+    qiime2 (version: 2025.4.0)
 -->
-<tool name="qiime2 dada2 denoise-single" id="qiime2__dada2__denoise_single" version="2024.10.0+q2galaxy.2024.10.0" profile="22.05" license="BSD-3-Clause">
+<tool name="qiime2 dada2 denoise-single" id="qiime2__dada2__denoise_single" version="2025.4.0+q2galaxy.2025.4.0" profile="22.05" license="BSD-3-Clause">
     <description>Denoise and dereplicate single-end sequences</description>
     <xrefs>
         <xref type="bio.tools">qiime2</xref>
     </xrefs>
     <requirements>
-        <container type="docker">quay.io/qiime2/amplicon:2024.10</container>
+        <container type="docker">quay.io/qiime2/amplicon:2025.4</container>
     </requirements>
     <version_command>q2galaxy version dada2</version_command>
     <command detect_errors="exit_code">q2galaxy run dada2 denoise_single '$inputs'</command>
@@ -26,8 +26,8 @@
     <inputs>
         <param name="demultiplexed_seqs" type="data" format="qza" label="demultiplexed_seqs: SampleData[SequencesWithQuality | PairedEndSequencesWithQuality]" help="[required]  The single-end demultiplexed sequences to be denoised.">
             <options options_filter_attribute="metadata.semantic_type">
+                <filter type="add_value" value="SampleData[PairedEndSequencesWithQuality]"/>
                 <filter type="add_value" value="SampleData[SequencesWithQuality]"/>
-                <filter type="add_value" value="SampleData[PairedEndSequencesWithQuality]"/>
             </options>
             <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['SampleData[PairedEndSequencesWithQuality]', 'SampleData[SequencesWithQuality]']</validator>
         </param>
@@ -40,10 +40,9 @@
                 <option value="independent" selected="true">independent</option>
                 <option value="pseudo">pseudo</option>
             </param>
-            <param name="chimera_method" type="select" label="chimera_method: Str % Choices('consensus', 'none', 'pooled')" display="radio">
+            <param name="chimera_method" type="select" label="chimera_method: Str % Choices('consensus', 'none')" display="radio">
                 <option value="consensus" selected="true">consensus</option>
                 <option value="none">none</option>
-                <option value="pooled">pooled</option>
             </param>
             <param name="min_fold_parent_over_abundance" type="float" value="1.0" label="min_fold_parent_over_abundance: Float" help="[default: 1.0]  The minimum abundance of potential parents of a sequence being tested as chimeric, expressed as a fold-change versus the abundance of the sequence being tested. Values should be greater than or equal to 1 (i.e. parents should be more abundant than the sequence being tested). This parameter has no effect if chimera_method is &quot;none&quot;."/>
             <param name="allow_one_off" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" label="allow_one_off: Bool" help="[default: No]  Bimeras that are one-off from exact are also identified if the `allow_one_off` argument is True.If True, a sequence will be identified as bimera if it is one mismatch or indel away from an exact bimera."/>
diff -r 354f63459d37 -r 1e09dd637eb7 test-data/denoise_paired.test0.demux-paired.qza
Binary file test-data/denoise_paired.test0.demux-paired.qza has changed
diff -r 354f63459d37 -r 1e09dd637eb7 test-data/denoise_single.test0.demux-single.qza
Binary file test-data/denoise_single.test0.demux-single.qza has changed