# HG changeset patch
# User q2d2
# Date 1730317009 0
# Node ID e73ff752eb455add18eec6c4a5f6e42122139258
# Parent  a22807aaff34af70059fdc57289d4158648ba345
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 commit 5f71b597c9495eae67a447744fded834f56ca1f7

diff -r a22807aaff34 -r e73ff752eb45 qiime2__dada2__denoise_ccs.xml
--- a/qiime2__dada2__denoise_ccs.xml	Mon Jun 03 23:17:30 2024 +0000
+++ b/qiime2__dada2__denoise_ccs.xml	Wed Oct 30 19:36:49 2024 +0000
@@ -6,14 +6,17 @@
 -->
 <!--
 This tool was automatically generated by:
-    q2galaxy (version: 2024.5.0)
+    q2galaxy (version: 2024.10.0)
 for:
-    qiime2 (version: 2024.5.0)
+    qiime2 (version: 2024.10.1)
 -->
-<tool name="qiime2 dada2 denoise-ccs" id="qiime2__dada2__denoise_ccs" version="2024.5.0+q2galaxy.2024.5.0" profile="22.05" license="BSD-3-Clause">
+<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">
     <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:2024.5</container>
+        <container type="docker">quay.io/qiime2/amplicon:2024.10</container>
     </requirements>
     <version_command>q2galaxy version dada2</version_command>
     <command detect_errors="exit_code">q2galaxy run dada2 denoise_ccs '$inputs'</command>
@@ -33,13 +36,23 @@
             </sanitizer>
             <validator type="expression" message="Please verify this parameter.">value is not None and len(value) &gt; 0</validator>
         </param>
-        <param name="adapter" type="text" label="adapter: Str" help="[required]  Sequence of an adapter ligated to the 3' end. The adapter and any preceding bases are trimmed. Can contain IUPAC ambiguous nucleotide codes. Note, primer direction is 5' to 3'. Primers are removed before trim and filter step. Reads that do not contain the primer are discarded.">
-            <sanitizer>
-                <valid initial="string.printable"/>
-            </sanitizer>
-            <validator type="expression" message="Please verify this parameter.">value is not None and len(value) &gt; 0</validator>
-        </param>
         <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">
+            <conditional name="__q2galaxy__GUI__conditional__adapter__" label="adapter: Str">
+                <param name="__q2galaxy__GUI__select__" type="select" label="adapter: Str" help="[optional]  Sequence of an adapter ligated to the 3' end. The adapter and any preceding bases are trimmed. Can contain IUPAC ambiguous nucleotide codes. Note, primer direction is 5' to 3'. Primers are removed before trim and filter step. Reads that do not contain the primer are discarded.">
+                    <option value="__q2galaxy__::control::default" selected="true">None (Use default behavior)</option>
+                    <option value="__q2galaxy__::control::provide">Provide a value</option>
+                </param>
+                <when value="__q2galaxy__::control::default">
+                    <param name="adapter" type="hidden" value="__q2galaxy__::literal::None"/>
+                </when>
+                <when value="__q2galaxy__::control::provide">
+                    <param name="adapter" type="text">
+                        <sanitizer>
+                            <valid initial="string.printable"/>
+                        </sanitizer>
+                    </param>
+                </when>
+            </conditional>
             <param name="max_mismatch" type="integer" value="2" label="max_mismatch: Int" help="[default: 2]  The number of mismatches to tolerate when matching reads to primer sequences - see http://benjjneb.github.io/dada2/ for complete details."/>
             <param name="indels" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" label="indels: Bool" help="[default: No]  Allow insertions or deletions of bases when matching adapters. Note that primer matching can be significantly slower, currently about 4x slower"/>
             <param name="trunc_len" type="integer" value="0" label="trunc_len: Int" help="[default: 0]  Position at which sequences should be truncated due to decrease in quality. This truncates the 3' end of the of the input sequences, which will be the bases that were sequenced in the last cycles. Reads that are shorter than this value will be discarded. If 0 is provided, no truncation or length filtering will be performed. Note: Since Pacbio CCS sequences were normally with very high quality scores, there is no need to truncate the Pacbio CCS sequences."/>
diff -r a22807aaff34 -r e73ff752eb45 test-data/denoise_paired.test0.demux-paired.qza
Binary file test-data/denoise_paired.test0.demux-paired.qza has changed
diff -r a22807aaff34 -r e73ff752eb45 test-data/denoise_single.test0.demux-single.qza
Binary file test-data/denoise_single.test0.demux-single.qza has changed