# HG changeset patch
# User q2d2
# Date 1746471939 0
# Node ID 37c6c368acdda04a467dfe84d2868c0a69a0f1f3
# Parent  c328a49a8ebf2778fba4f9543796b9f3f152eeb1
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch commit b1fccfb38b4873cd4699743033449014a2978e7d

diff -r c328a49a8ebf -r 37c6c368acdd qiime2__vsearch__uchime_denovo.xml
--- a/qiime2__vsearch__uchime_denovo.xml	Wed Oct 30 20:00:07 2024 +0000
+++ b/qiime2__vsearch__uchime_denovo.xml	Mon May 05 19:05:39 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 vsearch uchime-denovo" id="qiime2__vsearch__uchime_denovo" version="2024.10.0+q2galaxy.2024.10.0" profile="22.05" license="BSD-3-Clause">
-    <description>De novo chimera filtering with vsearch.</description>
+<tool name="qiime2 vsearch uchime-denovo" id="qiime2__vsearch__uchime_denovo" version="2025.4.0+q2galaxy.2025.4.0" profile="22.05" license="BSD-3-Clause">
+    <description>De novo chimera filtering.</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 vsearch</version_command>
     <command detect_errors="exit_code">q2galaxy run vsearch uchime_denovo '$inputs'</command>
@@ -37,10 +37,15 @@
             <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureTable[Frequency]']</validator>
         </param>
         <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">
+            <param name="method" type="select" label="method: Str % Choices('uchime', 'uchime2', 'uchime3')" display="radio">
+                <option value="uchime" selected="true">uchime</option>
+                <option value="uchime2">uchime2</option>
+                <option value="uchime3">uchime3</option>
+            </param>
             <param name="dn" type="float" min="0.0" value="1.4" label="dn: Float % Range(0.0, None)" help="[default: 1.4]  No vote pseudo-count, corresponding to the parameter n in the chimera scoring function."/>
-            <param name="mindiffs" type="integer" min="1" value="3" label="mindiffs: Int % Range(1, None)" help="[default: 3]  Minimum number of differences per segment."/>
-            <param name="mindiv" type="float" min="0.0" value="0.8" label="mindiv: Float % Range(0.0, None)" help="[default: 0.8]  Minimum divergence from closest parent."/>
-            <param name="minh" type="float" min="0.0" max="1.0" value="0.28" label="minh: Float % Range(0.0, 1.0, inclusive_end=True)" help="[default: 0.28]  Minimum score (h). Increasing this value tends to reduce the number of false positives and to decrease sensitivity."/>
+            <param name="mindiffs" type="integer" min="1" value="3" label="mindiffs: Int % Range(1, None)" help="[default: 3]  Minimum number of differences per segment. Ignored for uchime2 and uchime3."/>
+            <param name="mindiv" type="float" min="0.0" value="0.8" label="mindiv: Float % Range(0.0, None)" help="[default: 0.8]  Minimum divergence from closest parent. Ignored for uchime2 and uchime3."/>
+            <param name="minh" type="float" min="0.0" max="1.0" value="0.28" label="minh: Float % Range(0.0, 1.0, inclusive_end=True)" help="[default: 0.28]  Minimum score (h). Increasing this value tends to reduce the number of false positives and to decrease sensitivity. Ignored for uchime2 and uchime3."/>
             <param name="xn" type="float" min="1.000001" value="8.0" label="xn: Float % Range(1.0, None, inclusive_start=False)" help="[default: 8.0]  No vote weight, corresponding to the parameter beta in the scoring function."/>
         </section>
     </inputs>
@@ -53,7 +58,7 @@
     <help>
 QIIME 2: vsearch uchime-denovo
 ==============================
-De novo chimera filtering with vsearch.
+De novo chimera filtering.
 
 
 Outputs:
@@ -66,13 +71,42 @@
 
 Description:
 ------------
-Apply the vsearch uchime_denovo method to identify chimeric feature sequences. The results of this method can be used to filter chimeric features from the corresponding feature table. For more details, please refer to the vsearch documentation.
+Apply one of the vsearch uchime*_denovo methods to identify chimeric feature sequences. The results of these methods can be used to filter chimeric features from the corresponding feature table. For more details, please refer to the vsearch manual.
 
 
 |  
 
 </help>
     <citations>
+        <citation type="bibtex">@article{cite1,
+ author = {Edgar, Robert C and Haas, Brian J and Clemente, Jose C and Quince, Christopher and Knight, Rob},
+ journal = {Bioinformatics},
+ number = {16},
+ pages = {2194--2200},
+ publisher = {Oxford University Press},
+ title = {UCHIME improves sensitivity and speed of chimera detection},
+ volume = {27},
+ year = {2011}
+}
+</citation>
+        <citation type="bibtex">@article{cite2,
+ author = {Edgar, Robert C},
+ journal = {BioRxiv},
+ pages = {074252},
+ publisher = {Cold Spring Harbor Laboratory},
+ title = {UCHIME2: improved chimera prediction for amplicon sequencing},
+ year = {2016}
+}
+</citation>
+        <citation type="bibtex">@article{cite3,
+ author = {Edgar, Robert C},
+ journal = {BioRxiv},
+ pages = {081257},
+ publisher = {Cold Spring Harbor Laboratory},
+ title = {UNOISE2: improved error-correction for Illumina 16S and ITS amplicon sequencing},
+ year = {2016}
+}
+</citation>
         <citation type="doi">10.7717/peerj.2584</citation>
         <citation type="doi">10.1038/s41587-019-0209-9</citation>
     </citations>
diff -r c328a49a8ebf -r 37c6c368acdd test-data/cluster_features_de_novo.test0.seqs1.qza
Binary file test-data/cluster_features_de_novo.test0.seqs1.qza has changed
diff -r c328a49a8ebf -r 37c6c368acdd test-data/cluster_features_de_novo.test0.table1.qza
Binary file test-data/cluster_features_de_novo.test0.table1.qza has changed