# HG changeset patch
# User q2d2
# Date 1752616116 0
# Node ID 53a7856cfafc125d13340f1ff25c5056cff0364a
# Parent  efafec3b4e06831cc2eec9a568393032e429f1b5
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 commit 9436cc47c72b58a6a3d3a5c2ee075689c2926ef0

diff -r efafec3b4e06 -r 53a7856cfafc qiime2__dada2__denoise_paired.xml
--- a/qiime2__dada2__denoise_paired.xml	Mon May 05 18:42:28 2025 +0000
+++ b/qiime2__dada2__denoise_paired.xml	Tue Jul 15 21:48:36 2025 +0000
@@ -6,17 +6,17 @@
 -->
 <!--
 This tool was automatically generated by:
-    q2galaxy (version: 2025.4.0)
+    q2galaxy (version: 2025.7.0)
 for:
-    qiime2 (version: 2025.4.0)
+    qiime2 (version: 2025.7.0)
 -->
-<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">
+<tool name="qiime2 dada2 denoise-paired" id="qiime2__dada2__denoise_paired" version="2025.7.0+q2galaxy.2025.7.0" 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:2025.4</container>
+        <container type="docker">quay.io/qiime2/amplicon:2025.7</container>
     </requirements>
     <version_command>q2galaxy version dada2</version_command>
     <command detect_errors="exit_code">q2galaxy run dada2 denoise_paired '$inputs'</command>
@@ -39,6 +39,8 @@
             <param name="max_ee_r" type="float" value="2.0" label="max_ee_r: Float" help="[default: 2.0]  Reverse reads with number of expected errors higher than this value will be discarded."/>
             <param name="trunc_q" type="integer" value="2" label="trunc_q: Int" help="[default: 2]  Reads are truncated at the first instance of a quality score less than or equal to this value. If the resulting read is then shorter than `trunc_len_f` or `trunc_len_r` (depending on the direction of the read) it is discarded."/>
             <param name="min_overlap" type="integer" min="4" value="12" label="min_overlap: Int % Range(4, None)" help="[default: 12]  The minimum length of the overlap required for merging the forward and reverse reads."/>
+            <param name="max_merge_mismatch" type="integer" value="0" label="max_merge_mismatch: Int" help="[default: 0]  The maximum number of mismatches allowed in the overlap region when merging reads. If 0, only exact overlaps are allowed."/>
+            <param name="trim_overhang" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" label="trim_overhang: Bool" help="[default: No]  If TRUE, &quot;overhangs&quot; in the alignment after merging are trimmed off. &quot;Overhangs&quot; are when the reverse read extends past the start of the forward read, and vice-versa, as can happen when reads are longer than the amplicon and read into the other-direction primer region."/>
             <param name="pooling_method" type="select" label="pooling_method: Str % Choices('independent', 'pseudo')" display="radio">
                 <option value="independent" selected="true">independent</option>
                 <option value="pseudo">pseudo</option>
diff -r efafec3b4e06 -r 53a7856cfafc test-data/denoise_paired.test0.demux-paired.qza
Binary file test-data/denoise_paired.test0.demux-paired.qza has changed
diff -r efafec3b4e06 -r 53a7856cfafc test-data/denoise_single.test0.demux-single.qza
Binary file test-data/denoise_single.test0.demux-single.qza has changed