# HG changeset patch
# User q2d2
# Date 1762017017 0
# Node ID 1601b340fb81080e2007f97b849f608bca4e269d
# Parent  be83e72c1ee98dc78b77b49fd627fcc858547b88
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 commit 64ed09f1f1c680ad8373d261bd6be43a4f8a8d5b

diff -r be83e72c1ee9 -r 1601b340fb81 qiime2__dada2__denoise_single.xml
--- a/qiime2__dada2__denoise_single.xml	Tue Jul 15 21:48:40 2025 +0000
+++ b/qiime2__dada2__denoise_single.xml	Sat Nov 01 17:10:17 2025 +0000
@@ -6,17 +6,17 @@
 -->
 <!--
 This tool was automatically generated by:
-    q2galaxy (version: 2025.7.0)
+    q2galaxy (version: 2025.10.0)
 for:
-    qiime2 (version: 2025.7.0)
+    qiime2 (version: 2025.10.0)
 -->
-<tool name="qiime2 dada2 denoise-single" id="qiime2__dada2__denoise_single" version="2025.7.0+q2galaxy.2025.7.0" profile="22.05" license="BSD-3-Clause">
+<tool name="qiime2 dada2 denoise-single" id="qiime2__dada2__denoise_single" version="2025.10.0+q2galaxy.2025.10.0" 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:2025.7</container>
+        <container type="docker">quay.io/qiime2/amplicon:2025.10</container>
     </requirements>
     <version_command>q2galaxy version dada2</version_command>
     <command detect_errors="exit_code">q2galaxy run dada2 denoise_single '$inputs'</command>
@@ -26,8 +26,8 @@
     <inputs>
         <param name="demultiplexed_seqs" type="data" format="qza" label="demultiplexed_seqs: SampleData[SequencesWithQuality | PairedEndSequencesWithQuality]" help="[required]  The single-end demultiplexed sequences to be denoised.">
             <options options_filter_attribute="metadata.semantic_type">
+                <filter type="add_value" value="SampleData[SequencesWithQuality]"/>
                 <filter type="add_value" value="SampleData[PairedEndSequencesWithQuality]"/>
-                <filter type="add_value" value="SampleData[SequencesWithQuality]"/>
             </options>
             <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['SampleData[PairedEndSequencesWithQuality]', 'SampleData[SequencesWithQuality]']</validator>
         </param>
@@ -55,6 +55,7 @@
         <data name="table" format="qza" label="${tool.name} on ${on_string}: table.qza" from_work_dir="table.qza"/>
         <data name="representative_sequences" format="qza" label="${tool.name} on ${on_string}: representative_sequences.qza" from_work_dir="representative_sequences.qza"/>
         <data name="denoising_stats" format="qza" label="${tool.name} on ${on_string}: denoising_stats.qza" from_work_dir="denoising_stats.qza"/>
+        <data name="base_transition_stats" format="qza" label="${tool.name} on ${on_string}: base_transition_stats.qza" from_work_dir="base_transition_stats.qza"/>
     </outputs>
     <tests>
         <test>
@@ -82,6 +83,13 @@
                     </has_archive_member>
                 </assert_contents>
             </output>
+            <output name="base_transition_stats" ftype="qza">
+                <assert_contents>
+                    <has_archive_member path="[0-9a-f]{8}-[0-9a-f]{4}-[4][0-9a-f]{3}-[89ab][0-9a-f]{3}-[0-9a-f]{12}\/metadata.yaml">
+                        <has_line_matching expression="type: DADA2BaseTransitionStats"/>
+                    </has_archive_member>
+                </assert_contents>
+            </output>
         </test>
     </tests>
     <help>
@@ -94,7 +102,8 @@
 --------
 :table.qza: The resulting feature table.
 :representative_sequences.qza: The resulting feature sequences. Each feature in the feature table will be represented by exactly one sequence.
-:denoising_stats.qza: &lt;no description&gt;
+:denoising_stats.qza: A table listing per-sample read retention counts and percentages after each stage of the pipeline.
+:base_transition_stats.qza: A table listing the transition rates of each ordered pair of nucleotides at each quality score.
 
 |  
 
diff -r be83e72c1ee9 -r 1601b340fb81 test-data/denoise_paired.test0.demux-paired.qza
Binary file test-data/denoise_paired.test0.demux-paired.qza has changed
diff -r be83e72c1ee9 -r 1601b340fb81 test-data/denoise_single.test0.demux-single.qza
Binary file test-data/denoise_single.test0.demux-single.qza has changed