# HG changeset patch
# User q2d2
# Date 1714078474 0
# Node ID 20a297ae45057f0ff61c7a7071914860007cf681
# Parent  e7812ca89033268fa412a6e8ce55506607eac948
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 commit 389df0134cd0763dcf02aac6e623fc15f8861c1e

diff -r e7812ca89033 -r 20a297ae4505 qiime2__dada2__denoise_single.xml
--- a/qiime2__dada2__denoise_single.xml	Thu Jun 08 19:35:16 2023 +0000
+++ b/qiime2__dada2__denoise_single.xml	Thu Apr 25 20:54:34 2024 +0000
@@ -1,30 +1,30 @@
 <?xml version='1.0' encoding='utf-8'?>
 <!--
-Copyright (c) 2023, QIIME 2 development team.
+Copyright (c) 2024, 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: 2023.5.0)
+    q2galaxy (version: 2024.2.1)
 for:
-    qiime2 (version: 2023.5.1)
+    qiime2 (version: 2024.2.0)
 -->
-<tool name="qiime2 dada2 denoise-single" id="qiime2__dada2__denoise_single" version="2023.5.0+q2galaxy.2023.5.0.2" profile="22.05" license="BSD-3-Clause">
+<tool name="qiime2 dada2 denoise-single" id="qiime2__dada2__denoise_single" version="2024.2.0+q2galaxy.2024.2.1" profile="22.05" license="BSD-3-Clause">
     <description>Denoise and dereplicate single-end sequences</description>
     <requirements>
-        <container type="docker">quay.io/qiime2/core:2023.5</container>
+        <container type="docker">quay.io/qiime2/amplicon:2024.2</container>
     </requirements>
     <version_command>q2galaxy version dada2</version_command>
     <command detect_errors="exit_code">q2galaxy run dada2 denoise_single '$inputs'</command>
     <configfiles>
-        <inputs name="inputs" data_style="paths"/>
+        <inputs name="inputs" data_style="staging_path_and_source_path"/>
     </configfiles>
     <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[PairedEndSequencesWithQuality]"/>
                 <filter type="add_value" value="SampleData[SequencesWithQuality]"/>
-                <filter type="add_value" value="SampleData[PairedEndSequencesWithQuality]"/>
             </options>
             <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['SampleData[PairedEndSequencesWithQuality]', 'SampleData[SequencesWithQuality]']</validator>
         </param>
@@ -44,9 +44,9 @@
             </param>
             <param name="min_fold_parent_over_abundance" type="float" value="1.0" label="min_fold_parent_over_abundance: Float" help="[default: 1.0]  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). 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."/>
-            <param name="n_threads" type="integer" value="1" label="n_threads: Int" help="[default: 1]  The number of threads to use for multithreaded processing. If 0 is provided, all available cores will be used."/>
             <param name="n_reads_learn" type="integer" value="1000000" label="n_reads_learn: Int" help="[default: 1000000]  The number of reads to use when training the error model. Smaller numbers will result in a shorter run time but a less reliable error model."/>
             <param name="hashed_feature_ids" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" checked="true" label="hashed_feature_ids: Bool" help="[default: Yes]  If true, the feature ids in the resulting table will be presented as hashes of the sequences defining each feature. The hash will always be the same for the same sequence so this allows feature tables to be merged across runs of this method. You should only merge tables if the exact same parameters are used for each run."/>
+            <param name="retain_all_samples" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" checked="true" label="retain_all_samples: Bool" help="[default: Yes]  If True all samples input to dada2 will be retained in the output of dada2, if false samples with zero total frequency are removed from the table."/>
         </section>
     </inputs>
     <outputs>
diff -r e7812ca89033 -r 20a297ae4505 test-data/denoise_paired.test0.demux-paired.qza
Binary file test-data/denoise_paired.test0.demux-paired.qza has changed
diff -r e7812ca89033 -r 20a297ae4505 test-data/denoise_single.test0.demux-single.qza
Binary file test-data/denoise_single.test0.demux-single.qza has changed