# HG changeset patch
# User q2d2
# Date 1746470535 0
# Node ID 1eb5c20bf4cfe9f923b03a763be8fb9a7f25c545
# Parent  e73ff752eb455add18eec6c4a5f6e42122139258
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 commit b1fccfb38b4873cd4699743033449014a2978e7d

diff -r e73ff752eb45 -r 1eb5c20bf4cf qiime2__dada2__denoise_ccs.xml
--- a/qiime2__dada2__denoise_ccs.xml	Wed Oct 30 19:36:49 2024 +0000
+++ b/qiime2__dada2__denoise_ccs.xml	Mon May 05 18:42:15 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-ccs" id="qiime2__dada2__denoise_ccs" version="2024.10.0+q2galaxy.2024.10.0" profile="22.05" license="BSD-3-Clause">
+<tool name="qiime2 dada2 denoise-ccs" id="qiime2__dada2__denoise_ccs" version="2025.4.0+q2galaxy.2025.4.0" profile="22.05" license="BSD-3-Clause">
     <description>Denoise and dereplicate single-end Pacbio CCS</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_ccs '$inputs'</command>
@@ -65,10 +65,9 @@
                 <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="3.5" label="min_fold_parent_over_abundance: Float" help="[default: 3.5]  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). Suggest 3.5. 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."/>
@@ -106,6 +105,7 @@
 
 </help>
     <citations>
+        <citation type="doi">10.1093/nar/gkz569</citation>
         <citation type="doi">10.1038/nmeth.3869</citation>
         <citation type="doi">10.1038/s41587-019-0209-9</citation>
     </citations>
diff -r e73ff752eb45 -r 1eb5c20bf4cf test-data/denoise_paired.test0.demux-paired.qza
Binary file test-data/denoise_paired.test0.demux-paired.qza has changed
diff -r e73ff752eb45 -r 1eb5c20bf4cf test-data/denoise_single.test0.demux-single.qza
Binary file test-data/denoise_single.test0.demux-single.qza has changed