# HG changeset patch
# User q2d2
# Date 1746470548 0
# Node ID efafec3b4e06831cc2eec9a568393032e429f1b5
# Parent  933b92011b912c7b6d898a6806d9964c96979d90
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 commit b1fccfb38b4873cd4699743033449014a2978e7d

diff -r 933b92011b91 -r efafec3b4e06 qiime2__dada2__denoise_paired.xml
--- a/qiime2__dada2__denoise_paired.xml	Wed Oct 30 19:36:45 2024 +0000
+++ b/qiime2__dada2__denoise_paired.xml	Mon May 05 18:42:28 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-paired" id="qiime2__dada2__denoise_paired" version="2024.10.0+q2galaxy.2024.10.0" profile="22.05" license="BSD-3-Clause">
+<tool name="qiime2 dada2 denoise-paired" id="qiime2__dada2__denoise_paired" version="2025.4.0+q2galaxy.2025.4.0" profile="22.05" license="BSD-3-Clause">
     <description>Denoise and dereplicate paired-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_paired '$inputs'</command>
@@ -43,10 +43,9 @@
                 <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 TrueIf True, a sequence will be identified as bimera if it is one mismatch or indel away from an exact bimera."/>
diff -r 933b92011b91 -r efafec3b4e06 test-data/denoise_paired.test0.demux-paired.qza
Binary file test-data/denoise_paired.test0.demux-paired.qza has changed
diff -r 933b92011b91 -r efafec3b4e06 test-data/denoise_single.test0.demux-single.qza
Binary file test-data/denoise_single.test0.demux-single.qza has changed