diff --git a/tools/suite_qiime2__alignment/qiime2__alignment__mafft.xml b/tools/suite_qiime2__alignment/qiime2__alignment__mafft.xml
index e8cbb40..664776a 100644
--- a/tools/suite_qiime2__alignment/qiime2__alignment__mafft.xml
+++ b/tools/suite_qiime2__alignment/qiime2__alignment__mafft.xml
@@ -1,6 +1,6 @@
 <?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)
 -->
diff --git a/tools/suite_qiime2__alignment/qiime2__alignment__mafft_add.xml b/tools/suite_qiime2__alignment/qiime2__alignment__mafft_add.xml
index b963158..b61f4c4 100644
--- a/tools/suite_qiime2__alignment/qiime2__alignment__mafft_add.xml
+++ b/tools/suite_qiime2__alignment/qiime2__alignment__mafft_add.xml
@@ -1,6 +1,6 @@
 <?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)
 -->
diff --git a/tools/suite_qiime2__alignment/qiime2__alignment__mask.xml b/tools/suite_qiime2__alignment/qiime2__alignment__mask.xml
index 46b5a43..2377643 100644
--- a/tools/suite_qiime2__alignment/qiime2__alignment__mask.xml
+++ b/tools/suite_qiime2__alignment/qiime2__alignment__mask.xml
@@ -1,6 +1,6 @@
 <?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)
 -->
diff --git a/tools/suite_qiime2__composition/qiime2__composition__add_pseudocount.xml b/tools/suite_qiime2__composition/qiime2__composition__add_pseudocount.xml
index a967a66..b630e89 100644
--- a/tools/suite_qiime2__composition/qiime2__composition__add_pseudocount.xml
+++ b/tools/suite_qiime2__composition/qiime2__composition__add_pseudocount.xml
@@ -1,6 +1,6 @@
 <?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)
 -->
diff --git a/tools/suite_qiime2__composition/qiime2__composition__ancom.xml b/tools/suite_qiime2__composition/qiime2__composition__ancom.xml
index 25866e7..d973563 100644
--- a/tools/suite_qiime2__composition/qiime2__composition__ancom.xml
+++ b/tools/suite_qiime2__composition/qiime2__composition__ancom.xml
@@ -1,6 +1,6 @@
 <?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)
 -->
diff --git a/tools/suite_qiime2__composition/qiime2__composition__ancombc.xml b/tools/suite_qiime2__composition/qiime2__composition__ancombc.xml
index 201ad67..e9d447d 100644
--- a/tools/suite_qiime2__composition/qiime2__composition__ancombc.xml
+++ b/tools/suite_qiime2__composition/qiime2__composition__ancombc.xml
@@ -1,6 +1,6 @@
 <?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)
 -->
diff --git a/tools/suite_qiime2__composition/qiime2__composition__da_barplot.xml b/tools/suite_qiime2__composition/qiime2__composition__da_barplot.xml
index c1317d0..2716cd0 100644
--- a/tools/suite_qiime2__composition/qiime2__composition__da_barplot.xml
+++ b/tools/suite_qiime2__composition/qiime2__composition__da_barplot.xml
@@ -1,6 +1,6 @@
 <?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)
 -->
diff --git a/tools/suite_qiime2__composition/qiime2__composition__tabulate.xml b/tools/suite_qiime2__composition/qiime2__composition__tabulate.xml
index d0e8176..941f300 100644
--- a/tools/suite_qiime2__composition/qiime2__composition__tabulate.xml
+++ b/tools/suite_qiime2__composition/qiime2__composition__tabulate.xml
@@ -1,6 +1,6 @@
 <?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)
 -->
diff --git a/tools/suite_qiime2__composition/test-data/ancombc.test0.table.qza b/tools/suite_qiime2__composition/test-data/ancombc.test0.table.qza
index ef17d69..e486c5c 100644
Binary files a/tools/suite_qiime2__composition/test-data/ancombc.test0.table.qza and b/tools/suite_qiime2__composition/test-data/ancombc.test0.table.qza differ
diff --git a/tools/suite_qiime2__composition/test-data/ancombc.test1.table.qza b/tools/suite_qiime2__composition/test-data/ancombc.test1.table.qza
index ef17d69..e486c5c 100644
Binary files a/tools/suite_qiime2__composition/test-data/ancombc.test1.table.qza and b/tools/suite_qiime2__composition/test-data/ancombc.test1.table.qza differ
diff --git a/tools/suite_qiime2__cutadapt/qiime2__cutadapt__demux_paired.xml b/tools/suite_qiime2__cutadapt/qiime2__cutadapt__demux_paired.xml
index c129c89..3a4e0b6 100644
--- a/tools/suite_qiime2__cutadapt/qiime2__cutadapt__demux_paired.xml
+++ b/tools/suite_qiime2__cutadapt/qiime2__cutadapt__demux_paired.xml
@@ -1,6 +1,6 @@
 <?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)
 -->
diff --git a/tools/suite_qiime2__cutadapt/qiime2__cutadapt__demux_single.xml b/tools/suite_qiime2__cutadapt/qiime2__cutadapt__demux_single.xml
index 4740785..7f5e05f 100644
--- a/tools/suite_qiime2__cutadapt/qiime2__cutadapt__demux_single.xml
+++ b/tools/suite_qiime2__cutadapt/qiime2__cutadapt__demux_single.xml
@@ -1,6 +1,6 @@
 <?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)
 -->
diff --git a/tools/suite_qiime2__cutadapt/qiime2__cutadapt__trim_paired.xml b/tools/suite_qiime2__cutadapt/qiime2__cutadapt__trim_paired.xml
index 80a5c28..5bb6f6d 100644
--- a/tools/suite_qiime2__cutadapt/qiime2__cutadapt__trim_paired.xml
+++ b/tools/suite_qiime2__cutadapt/qiime2__cutadapt__trim_paired.xml
@@ -1,6 +1,6 @@
 <?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)
 -->
diff --git a/tools/suite_qiime2__cutadapt/qiime2__cutadapt__trim_single.xml b/tools/suite_qiime2__cutadapt/qiime2__cutadapt__trim_single.xml
index b433286..e6c87dc 100644
--- a/tools/suite_qiime2__cutadapt/qiime2__cutadapt__trim_single.xml
+++ b/tools/suite_qiime2__cutadapt/qiime2__cutadapt__trim_single.xml
@@ -1,6 +1,6 @@
 <?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)
 -->
diff --git a/tools/suite_qiime2__cutadapt/test-data/demux_paired.test0.seqs.qza b/tools/suite_qiime2__cutadapt/test-data/demux_paired.test0.seqs.qza
index bc5e569..919a8fd 100644
Binary files a/tools/suite_qiime2__cutadapt/test-data/demux_paired.test0.seqs.qza and b/tools/suite_qiime2__cutadapt/test-data/demux_paired.test0.seqs.qza differ
diff --git a/tools/suite_qiime2__cutadapt/test-data/demux_single.test0.seqs.qza b/tools/suite_qiime2__cutadapt/test-data/demux_single.test0.seqs.qza
index 510c1fd..27b0c9d 100644
Binary files a/tools/suite_qiime2__cutadapt/test-data/demux_single.test0.seqs.qza and b/tools/suite_qiime2__cutadapt/test-data/demux_single.test0.seqs.qza differ
diff --git a/tools/suite_qiime2__dada2/qiime2__dada2__denoise_ccs.xml b/tools/suite_qiime2__dada2/qiime2__dada2__denoise_ccs.xml
index cae5b3f..53481ec 100644
--- a/tools/suite_qiime2__dada2/qiime2__dada2__denoise_ccs.xml
+++ b/tools/suite_qiime2__dada2/qiime2__dada2__denoise_ccs.xml
@@ -1,6 +1,6 @@
 <?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)
 -->
diff --git a/tools/suite_qiime2__dada2/qiime2__dada2__denoise_paired.xml b/tools/suite_qiime2__dada2/qiime2__dada2__denoise_paired.xml
index 51f4aad..371b97b 100644
--- a/tools/suite_qiime2__dada2/qiime2__dada2__denoise_paired.xml
+++ b/tools/suite_qiime2__dada2/qiime2__dada2__denoise_paired.xml
@@ -1,6 +1,6 @@
 <?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)
 -->
diff --git a/tools/suite_qiime2__dada2/qiime2__dada2__denoise_pyro.xml b/tools/suite_qiime2__dada2/qiime2__dada2__denoise_pyro.xml
index f938b6e..4fd9d0f 100644
--- a/tools/suite_qiime2__dada2/qiime2__dada2__denoise_pyro.xml
+++ b/tools/suite_qiime2__dada2/qiime2__dada2__denoise_pyro.xml
@@ -1,6 +1,6 @@
 <?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)
 -->
diff --git a/tools/suite_qiime2__dada2/qiime2__dada2__denoise_single.xml b/tools/suite_qiime2__dada2/qiime2__dada2__denoise_single.xml
index 234a738..62707c7 100644
--- a/tools/suite_qiime2__dada2/qiime2__dada2__denoise_single.xml
+++ b/tools/suite_qiime2__dada2/qiime2__dada2__denoise_single.xml
@@ -1,6 +1,6 @@
 <?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)
 -->
@@ -23,8 +23,8 @@ for:
     <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>
diff --git a/tools/suite_qiime2__dada2/test-data/denoise_paired.test0.demux-paired.qza b/tools/suite_qiime2__dada2/test-data/denoise_paired.test0.demux-paired.qza
index 6498d5e..d0971f0 100644
Binary files a/tools/suite_qiime2__dada2/test-data/denoise_paired.test0.demux-paired.qza and b/tools/suite_qiime2__dada2/test-data/denoise_paired.test0.demux-paired.qza differ
diff --git a/tools/suite_qiime2__dada2/test-data/denoise_single.test0.demux-single.qza b/tools/suite_qiime2__dada2/test-data/denoise_single.test0.demux-single.qza
index 56f218a..81f2e5d 100644
Binary files a/tools/suite_qiime2__dada2/test-data/denoise_single.test0.demux-single.qza and b/tools/suite_qiime2__dada2/test-data/denoise_single.test0.demux-single.qza differ
diff --git a/tools/suite_qiime2__deblur/qiime2__deblur__denoise_16S.xml b/tools/suite_qiime2__deblur/qiime2__deblur__denoise_16S.xml
index 44b925f..7620411 100644
--- a/tools/suite_qiime2__deblur/qiime2__deblur__denoise_16S.xml
+++ b/tools/suite_qiime2__deblur/qiime2__deblur__denoise_16S.xml
@@ -1,6 +1,6 @@
 <?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)
 -->
@@ -23,8 +23,8 @@ for:
     <inputs>
         <param name="demultiplexed_seqs" type="data" format="qza" label="demultiplexed_seqs: SampleData[SequencesWithQuality | PairedEndSequencesWithQuality | JoinedSequencesWithQuality]" help="[required]  The 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[JoinedSequencesWithQuality]"/>
+                <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[JoinedSequencesWithQuality]', 'SampleData[PairedEndSequencesWithQuality]', 'SampleData[SequencesWithQuality]']</validator>
diff --git a/tools/suite_qiime2__deblur/qiime2__deblur__denoise_other.xml b/tools/suite_qiime2__deblur/qiime2__deblur__denoise_other.xml
index 63af2fb..a8d23eb 100644
--- a/tools/suite_qiime2__deblur/qiime2__deblur__denoise_other.xml
+++ b/tools/suite_qiime2__deblur/qiime2__deblur__denoise_other.xml
@@ -1,6 +1,6 @@
 <?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)
 -->
@@ -23,8 +23,8 @@ for:
     <inputs>
         <param name="demultiplexed_seqs" type="data" format="qza" label="demultiplexed_seqs: SampleData[SequencesWithQuality | PairedEndSequencesWithQuality | JoinedSequencesWithQuality]" help="[required]  The 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[JoinedSequencesWithQuality]"/>
+                <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[JoinedSequencesWithQuality]', 'SampleData[PairedEndSequencesWithQuality]', 'SampleData[SequencesWithQuality]']</validator>
diff --git a/tools/suite_qiime2__deblur/qiime2__deblur__visualize_stats.xml b/tools/suite_qiime2__deblur/qiime2__deblur__visualize_stats.xml
index f855cff..5997a77 100644
--- a/tools/suite_qiime2__deblur/qiime2__deblur__visualize_stats.xml
+++ b/tools/suite_qiime2__deblur/qiime2__deblur__visualize_stats.xml
@@ -1,6 +1,6 @@
 <?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)
 -->
diff --git a/tools/suite_qiime2__deblur/test-data/denoise_16S.test0.demux-filtered.qza b/tools/suite_qiime2__deblur/test-data/denoise_16S.test0.demux-filtered.qza
index 0ff6e40..fb819c4 100644
Binary files a/tools/suite_qiime2__deblur/test-data/denoise_16S.test0.demux-filtered.qza and b/tools/suite_qiime2__deblur/test-data/denoise_16S.test0.demux-filtered.qza differ
diff --git a/tools/suite_qiime2__deblur/test-data/visualize_stats.test0.deblur-stats.qza b/tools/suite_qiime2__deblur/test-data/visualize_stats.test0.deblur-stats.qza
index 284bd27..79ad209 100644
Binary files a/tools/suite_qiime2__deblur/test-data/visualize_stats.test0.deblur-stats.qza and b/tools/suite_qiime2__deblur/test-data/visualize_stats.test0.deblur-stats.qza differ
diff --git a/tools/suite_qiime2__demux/qiime2__demux__emp_paired.xml b/tools/suite_qiime2__demux/qiime2__demux__emp_paired.xml
index d4c8904..905e270 100644
--- a/tools/suite_qiime2__demux/qiime2__demux__emp_paired.xml
+++ b/tools/suite_qiime2__demux/qiime2__demux__emp_paired.xml
@@ -1,6 +1,6 @@
 <?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)
 -->
diff --git a/tools/suite_qiime2__demux/qiime2__demux__emp_single.xml b/tools/suite_qiime2__demux/qiime2__demux__emp_single.xml
index ec71585..5b3db40 100644
--- a/tools/suite_qiime2__demux/qiime2__demux__emp_single.xml
+++ b/tools/suite_qiime2__demux/qiime2__demux__emp_single.xml
@@ -1,6 +1,6 @@
 <?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)
 -->
diff --git a/tools/suite_qiime2__demux/qiime2__demux__filter_samples.xml b/tools/suite_qiime2__demux/qiime2__demux__filter_samples.xml
index ff634e7..b029d2f 100644
--- a/tools/suite_qiime2__demux/qiime2__demux__filter_samples.xml
+++ b/tools/suite_qiime2__demux/qiime2__demux__filter_samples.xml
@@ -1,6 +1,6 @@
 <?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)
 -->
@@ -23,9 +23,9 @@ for:
     <inputs>
         <param name="demux" type="data" format="qza" label="demux: SampleData[SequencesWithQuality¹ | PairedEndSequencesWithQuality² | JoinedSequencesWithQuality³]" help="[required]  The demultiplexed data from which samples should be filtered.">
             <options options_filter_attribute="metadata.semantic_type">
-                <filter type="add_value" value="SampleData[PairedEndSequencesWithQuality]"/>
                 <filter type="add_value" value="SampleData[JoinedSequencesWithQuality]"/>
                 <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[JoinedSequencesWithQuality]', 'SampleData[PairedEndSequencesWithQuality]', 'SampleData[SequencesWithQuality]']</validator>
         </param>
diff --git a/tools/suite_qiime2__demux/qiime2__demux__subsample_paired.xml b/tools/suite_qiime2__demux/qiime2__demux__subsample_paired.xml
index 744804d..663d928 100644
--- a/tools/suite_qiime2__demux/qiime2__demux__subsample_paired.xml
+++ b/tools/suite_qiime2__demux/qiime2__demux__subsample_paired.xml
@@ -1,6 +1,6 @@
 <?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)
 -->
diff --git a/tools/suite_qiime2__demux/qiime2__demux__subsample_single.xml b/tools/suite_qiime2__demux/qiime2__demux__subsample_single.xml
index 069b847..40c809f 100644
--- a/tools/suite_qiime2__demux/qiime2__demux__subsample_single.xml
+++ b/tools/suite_qiime2__demux/qiime2__demux__subsample_single.xml
@@ -1,6 +1,6 @@
 <?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)
 -->
@@ -23,8 +23,8 @@ for:
     <inputs>
         <param name="sequences" type="data" format="qza" label="sequences: SampleData[SequencesWithQuality | PairedEndSequencesWithQuality]" help="[required]  The demultiplexed sequences to be subsampled.">
             <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>
diff --git a/tools/suite_qiime2__demux/qiime2__demux__summarize.xml b/tools/suite_qiime2__demux/qiime2__demux__summarize.xml
index 153fc1f..513913e 100644
--- a/tools/suite_qiime2__demux/qiime2__demux__summarize.xml
+++ b/tools/suite_qiime2__demux/qiime2__demux__summarize.xml
@@ -1,6 +1,6 @@
 <?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)
 -->
@@ -23,9 +23,9 @@ for:
     <inputs>
         <param name="data" type="data" format="qza" label="data: SampleData[SequencesWithQuality | PairedEndSequencesWithQuality | JoinedSequencesWithQuality]" help="[required]  The demultiplexed sequences to be summarized.">
             <options options_filter_attribute="metadata.semantic_type">
-                <filter type="add_value" value="SampleData[PairedEndSequencesWithQuality]"/>
                 <filter type="add_value" value="SampleData[JoinedSequencesWithQuality]"/>
                 <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[JoinedSequencesWithQuality]', 'SampleData[PairedEndSequencesWithQuality]', 'SampleData[SequencesWithQuality]']</validator>
         </param>
diff --git a/tools/suite_qiime2__demux/test-data/emp_single.test0.sequences.qza b/tools/suite_qiime2__demux/test-data/emp_single.test0.sequences.qza
index 0a8be34..05023a3 100644
Binary files a/tools/suite_qiime2__demux/test-data/emp_single.test0.sequences.qza and b/tools/suite_qiime2__demux/test-data/emp_single.test0.sequences.qza differ
diff --git a/tools/suite_qiime2__demux/test-data/summarize.test0.demux.qza b/tools/suite_qiime2__demux/test-data/summarize.test0.demux.qza
index a04aab3..8dc3c76 100644
Binary files a/tools/suite_qiime2__demux/test-data/summarize.test0.demux.qza and b/tools/suite_qiime2__demux/test-data/summarize.test0.demux.qza differ
diff --git a/tools/suite_qiime2__diversity/qiime2__diversity__adonis.xml b/tools/suite_qiime2__diversity/qiime2__diversity__adonis.xml
index 73d7939..418d67a 100644
--- a/tools/suite_qiime2__diversity/qiime2__diversity__adonis.xml
+++ b/tools/suite_qiime2__diversity/qiime2__diversity__adonis.xml
@@ -1,6 +1,6 @@
 <?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)
 -->
diff --git a/tools/suite_qiime2__diversity/qiime2__diversity__alpha.xml b/tools/suite_qiime2__diversity/qiime2__diversity__alpha.xml
index 3fd54b2..1e82777 100644
--- a/tools/suite_qiime2__diversity/qiime2__diversity__alpha.xml
+++ b/tools/suite_qiime2__diversity/qiime2__diversity__alpha.xml
@@ -1,6 +1,6 @@
 <?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)
 -->
@@ -23,9 +23,9 @@ for:
     <inputs>
         <param name="table" type="data" format="qza" label="table: FeatureTable[Frequency | RelativeFrequency | PresenceAbsence]" help="[required]  The feature table containing the samples for which alpha diversity should be computed.">
             <options options_filter_attribute="metadata.semantic_type">
-                <filter type="add_value" value="FeatureTable[RelativeFrequency]"/>
                 <filter type="add_value" value="FeatureTable[PresenceAbsence]"/>
                 <filter type="add_value" value="FeatureTable[Frequency]"/>
+                <filter type="add_value" value="FeatureTable[RelativeFrequency]"/>
             </options>
             <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureTable[Frequency]', 'FeatureTable[PresenceAbsence]', 'FeatureTable[RelativeFrequency]']</validator>
         </param>
diff --git a/tools/suite_qiime2__diversity/qiime2__diversity__alpha_correlation.xml b/tools/suite_qiime2__diversity/qiime2__diversity__alpha_correlation.xml
index 00495f3..b0b14b6 100644
--- a/tools/suite_qiime2__diversity/qiime2__diversity__alpha_correlation.xml
+++ b/tools/suite_qiime2__diversity/qiime2__diversity__alpha_correlation.xml
@@ -1,6 +1,6 @@
 <?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)
 -->
diff --git a/tools/suite_qiime2__diversity/qiime2__diversity__alpha_group_significance.xml b/tools/suite_qiime2__diversity/qiime2__diversity__alpha_group_significance.xml
index e13143d..ae9f7b2 100644
--- a/tools/suite_qiime2__diversity/qiime2__diversity__alpha_group_significance.xml
+++ b/tools/suite_qiime2__diversity/qiime2__diversity__alpha_group_significance.xml
@@ -1,6 +1,6 @@
 <?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)
 -->
diff --git a/tools/suite_qiime2__diversity/qiime2__diversity__alpha_phylogenetic.xml b/tools/suite_qiime2__diversity/qiime2__diversity__alpha_phylogenetic.xml
index 15e08b9..aca93c6 100644
--- a/tools/suite_qiime2__diversity/qiime2__diversity__alpha_phylogenetic.xml
+++ b/tools/suite_qiime2__diversity/qiime2__diversity__alpha_phylogenetic.xml
@@ -1,6 +1,6 @@
 <?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)
 -->
@@ -23,9 +23,9 @@ for:
     <inputs>
         <param name="table" type="data" format="qza" label="table: FeatureTable[Frequency | RelativeFrequency | PresenceAbsence]" help="[required]  The feature table containing the samples for which alpha diversity should be computed.">
             <options options_filter_attribute="metadata.semantic_type">
-                <filter type="add_value" value="FeatureTable[RelativeFrequency]"/>
                 <filter type="add_value" value="FeatureTable[PresenceAbsence]"/>
                 <filter type="add_value" value="FeatureTable[Frequency]"/>
+                <filter type="add_value" value="FeatureTable[RelativeFrequency]"/>
             </options>
             <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureTable[Frequency]', 'FeatureTable[PresenceAbsence]', 'FeatureTable[RelativeFrequency]']</validator>
         </param>
diff --git a/tools/suite_qiime2__diversity/qiime2__diversity__alpha_rarefaction.xml b/tools/suite_qiime2__diversity/qiime2__diversity__alpha_rarefaction.xml
index 460e9a2..0174cda 100644
--- a/tools/suite_qiime2__diversity/qiime2__diversity__alpha_rarefaction.xml
+++ b/tools/suite_qiime2__diversity/qiime2__diversity__alpha_rarefaction.xml
@@ -1,6 +1,6 @@
 <?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)
 -->
diff --git a/tools/suite_qiime2__diversity/qiime2__diversity__beta.xml b/tools/suite_qiime2__diversity/qiime2__diversity__beta.xml
index d157ba7..146c282 100644
--- a/tools/suite_qiime2__diversity/qiime2__diversity__beta.xml
+++ b/tools/suite_qiime2__diversity/qiime2__diversity__beta.xml
@@ -1,6 +1,6 @@
 <?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)
 -->
@@ -23,9 +23,9 @@ for:
     <inputs>
         <param name="table" type="data" format="qza" label="table: FeatureTable[Frequency | RelativeFrequency | PresenceAbsence]" help="[required]  The feature table containing the samples over which beta diversity should be computed.">
             <options options_filter_attribute="metadata.semantic_type">
-                <filter type="add_value" value="FeatureTable[RelativeFrequency]"/>
                 <filter type="add_value" value="FeatureTable[PresenceAbsence]"/>
                 <filter type="add_value" value="FeatureTable[Frequency]"/>
+                <filter type="add_value" value="FeatureTable[RelativeFrequency]"/>
             </options>
             <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureTable[Frequency]', 'FeatureTable[PresenceAbsence]', 'FeatureTable[RelativeFrequency]']</validator>
         </param>
diff --git a/tools/suite_qiime2__diversity/qiime2__diversity__beta_correlation.xml b/tools/suite_qiime2__diversity/qiime2__diversity__beta_correlation.xml
index f04f47d..fc76fd2 100644
--- a/tools/suite_qiime2__diversity/qiime2__diversity__beta_correlation.xml
+++ b/tools/suite_qiime2__diversity/qiime2__diversity__beta_correlation.xml
@@ -1,6 +1,6 @@
 <?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)
 -->
diff --git a/tools/suite_qiime2__diversity/qiime2__diversity__beta_group_significance.xml b/tools/suite_qiime2__diversity/qiime2__diversity__beta_group_significance.xml
index 7d2f406..5a745c2 100644
--- a/tools/suite_qiime2__diversity/qiime2__diversity__beta_group_significance.xml
+++ b/tools/suite_qiime2__diversity/qiime2__diversity__beta_group_significance.xml
@@ -1,6 +1,6 @@
 <?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)
 -->
diff --git a/tools/suite_qiime2__diversity/qiime2__diversity__beta_phylogenetic.xml b/tools/suite_qiime2__diversity/qiime2__diversity__beta_phylogenetic.xml
index a26d6ab..b12cccf 100644
--- a/tools/suite_qiime2__diversity/qiime2__diversity__beta_phylogenetic.xml
+++ b/tools/suite_qiime2__diversity/qiime2__diversity__beta_phylogenetic.xml
@@ -1,6 +1,6 @@
 <?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)
 -->
@@ -23,9 +23,9 @@ for:
     <inputs>
         <param name="table" type="data" format="qza" label="table: FeatureTable[Frequency | RelativeFrequency | PresenceAbsence]" help="[required]  The feature table containing the samples over which beta diversity should be computed.">
             <options options_filter_attribute="metadata.semantic_type">
-                <filter type="add_value" value="FeatureTable[RelativeFrequency]"/>
                 <filter type="add_value" value="FeatureTable[PresenceAbsence]"/>
                 <filter type="add_value" value="FeatureTable[Frequency]"/>
+                <filter type="add_value" value="FeatureTable[RelativeFrequency]"/>
             </options>
             <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureTable[Frequency]', 'FeatureTable[PresenceAbsence]', 'FeatureTable[RelativeFrequency]']</validator>
         </param>
diff --git a/tools/suite_qiime2__diversity/qiime2__diversity__beta_rarefaction.xml b/tools/suite_qiime2__diversity/qiime2__diversity__beta_rarefaction.xml
index cd0822e..077095c 100644
--- a/tools/suite_qiime2__diversity/qiime2__diversity__beta_rarefaction.xml
+++ b/tools/suite_qiime2__diversity/qiime2__diversity__beta_rarefaction.xml
@@ -1,6 +1,6 @@
 <?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)
 -->
diff --git a/tools/suite_qiime2__diversity/qiime2__diversity__bioenv.xml b/tools/suite_qiime2__diversity/qiime2__diversity__bioenv.xml
index 3693d78..cdcf565 100644
--- a/tools/suite_qiime2__diversity/qiime2__diversity__bioenv.xml
+++ b/tools/suite_qiime2__diversity/qiime2__diversity__bioenv.xml
@@ -1,6 +1,6 @@
 <?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)
 -->
diff --git a/tools/suite_qiime2__diversity/qiime2__diversity__core_metrics.xml b/tools/suite_qiime2__diversity/qiime2__diversity__core_metrics.xml
index 8634327..11137e7 100644
--- a/tools/suite_qiime2__diversity/qiime2__diversity__core_metrics.xml
+++ b/tools/suite_qiime2__diversity/qiime2__diversity__core_metrics.xml
@@ -1,6 +1,6 @@
 <?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)
 -->
diff --git a/tools/suite_qiime2__diversity/qiime2__diversity__core_metrics_phylogenetic.xml b/tools/suite_qiime2__diversity/qiime2__diversity__core_metrics_phylogenetic.xml
index 8046572..4f2273a 100644
--- a/tools/suite_qiime2__diversity/qiime2__diversity__core_metrics_phylogenetic.xml
+++ b/tools/suite_qiime2__diversity/qiime2__diversity__core_metrics_phylogenetic.xml
@@ -1,6 +1,6 @@
 <?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)
 -->
diff --git a/tools/suite_qiime2__diversity/qiime2__diversity__filter_distance_matrix.xml b/tools/suite_qiime2__diversity/qiime2__diversity__filter_distance_matrix.xml
index 6ce315a..c7edd18 100644
--- a/tools/suite_qiime2__diversity/qiime2__diversity__filter_distance_matrix.xml
+++ b/tools/suite_qiime2__diversity/qiime2__diversity__filter_distance_matrix.xml
@@ -1,6 +1,6 @@
 <?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)
 -->
diff --git a/tools/suite_qiime2__diversity/qiime2__diversity__mantel.xml b/tools/suite_qiime2__diversity/qiime2__diversity__mantel.xml
index 17f5644..9ff8041 100644
--- a/tools/suite_qiime2__diversity/qiime2__diversity__mantel.xml
+++ b/tools/suite_qiime2__diversity/qiime2__diversity__mantel.xml
@@ -1,6 +1,6 @@
 <?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)
 -->
diff --git a/tools/suite_qiime2__diversity/qiime2__diversity__pcoa.xml b/tools/suite_qiime2__diversity/qiime2__diversity__pcoa.xml
index 7dbbe24..becd7bf 100644
--- a/tools/suite_qiime2__diversity/qiime2__diversity__pcoa.xml
+++ b/tools/suite_qiime2__diversity/qiime2__diversity__pcoa.xml
@@ -1,6 +1,6 @@
 <?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)
 -->
diff --git a/tools/suite_qiime2__diversity/qiime2__diversity__pcoa_biplot.xml b/tools/suite_qiime2__diversity/qiime2__diversity__pcoa_biplot.xml
index 4ddfad2..86fc479 100644
--- a/tools/suite_qiime2__diversity/qiime2__diversity__pcoa_biplot.xml
+++ b/tools/suite_qiime2__diversity/qiime2__diversity__pcoa_biplot.xml
@@ -1,6 +1,6 @@
 <?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)
 -->
diff --git a/tools/suite_qiime2__diversity/qiime2__diversity__procrustes_analysis.xml b/tools/suite_qiime2__diversity/qiime2__diversity__procrustes_analysis.xml
index f5bb4c0..ab16f40 100644
--- a/tools/suite_qiime2__diversity/qiime2__diversity__procrustes_analysis.xml
+++ b/tools/suite_qiime2__diversity/qiime2__diversity__procrustes_analysis.xml
@@ -1,6 +1,6 @@
 <?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)
 -->
diff --git a/tools/suite_qiime2__diversity/qiime2__diversity__tsne.xml b/tools/suite_qiime2__diversity/qiime2__diversity__tsne.xml
index fea9060..2e4f2d5 100644
--- a/tools/suite_qiime2__diversity/qiime2__diversity__tsne.xml
+++ b/tools/suite_qiime2__diversity/qiime2__diversity__tsne.xml
@@ -1,6 +1,6 @@
 <?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)
 -->
diff --git a/tools/suite_qiime2__diversity/qiime2__diversity__umap.xml b/tools/suite_qiime2__diversity/qiime2__diversity__umap.xml
index 01c361e..6085b00 100644
--- a/tools/suite_qiime2__diversity/qiime2__diversity__umap.xml
+++ b/tools/suite_qiime2__diversity/qiime2__diversity__umap.xml
@@ -1,6 +1,6 @@
 <?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)
 -->
diff --git a/tools/suite_qiime2__diversity/test-data/alpha_correlation.test0.alpha-div-faith-pd.qza b/tools/suite_qiime2__diversity/test-data/alpha_correlation.test0.alpha-div-faith-pd.qza
index 3dc4240..539ddf2 100644
Binary files a/tools/suite_qiime2__diversity/test-data/alpha_correlation.test0.alpha-div-faith-pd.qza and b/tools/suite_qiime2__diversity/test-data/alpha_correlation.test0.alpha-div-faith-pd.qza differ
diff --git a/tools/suite_qiime2__diversity/test-data/alpha_group_significance.test0.alpha-div-faith-pd.qza b/tools/suite_qiime2__diversity/test-data/alpha_group_significance.test0.alpha-div-faith-pd.qza
index 3dc4240..539ddf2 100644
Binary files a/tools/suite_qiime2__diversity/test-data/alpha_group_significance.test0.alpha-div-faith-pd.qza and b/tools/suite_qiime2__diversity/test-data/alpha_group_significance.test0.alpha-div-faith-pd.qza differ
diff --git a/tools/suite_qiime2__diversity_lib/qiime2__diversity_lib__alpha_passthrough.xml b/tools/suite_qiime2__diversity_lib/qiime2__diversity_lib__alpha_passthrough.xml
index cd85bb6..b95702e 100644
--- a/tools/suite_qiime2__diversity_lib/qiime2__diversity_lib__alpha_passthrough.xml
+++ b/tools/suite_qiime2__diversity_lib/qiime2__diversity_lib__alpha_passthrough.xml
@@ -1,6 +1,6 @@
 <?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)
 -->
diff --git a/tools/suite_qiime2__diversity_lib/qiime2__diversity_lib__beta_passthrough.xml b/tools/suite_qiime2__diversity_lib/qiime2__diversity_lib__beta_passthrough.xml
index 996f1ab..ad93bab 100644
--- a/tools/suite_qiime2__diversity_lib/qiime2__diversity_lib__beta_passthrough.xml
+++ b/tools/suite_qiime2__diversity_lib/qiime2__diversity_lib__beta_passthrough.xml
@@ -1,6 +1,6 @@
 <?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)
 -->
diff --git a/tools/suite_qiime2__diversity_lib/qiime2__diversity_lib__beta_phylogenetic_meta_passthrough.xml b/tools/suite_qiime2__diversity_lib/qiime2__diversity_lib__beta_phylogenetic_meta_passthrough.xml
index 055ba09..ec7cbda 100644
--- a/tools/suite_qiime2__diversity_lib/qiime2__diversity_lib__beta_phylogenetic_meta_passthrough.xml
+++ b/tools/suite_qiime2__diversity_lib/qiime2__diversity_lib__beta_phylogenetic_meta_passthrough.xml
@@ -1,6 +1,6 @@
 <?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)
 -->
diff --git a/tools/suite_qiime2__diversity_lib/qiime2__diversity_lib__beta_phylogenetic_passthrough.xml b/tools/suite_qiime2__diversity_lib/qiime2__diversity_lib__beta_phylogenetic_passthrough.xml
index 3c01949..fc44dc7 100644
--- a/tools/suite_qiime2__diversity_lib/qiime2__diversity_lib__beta_phylogenetic_passthrough.xml
+++ b/tools/suite_qiime2__diversity_lib/qiime2__diversity_lib__beta_phylogenetic_passthrough.xml
@@ -1,6 +1,6 @@
 <?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)
 -->
diff --git a/tools/suite_qiime2__diversity_lib/qiime2__diversity_lib__bray_curtis.xml b/tools/suite_qiime2__diversity_lib/qiime2__diversity_lib__bray_curtis.xml
index fddd2ae..7c248c8 100644
--- a/tools/suite_qiime2__diversity_lib/qiime2__diversity_lib__bray_curtis.xml
+++ b/tools/suite_qiime2__diversity_lib/qiime2__diversity_lib__bray_curtis.xml
@@ -1,6 +1,6 @@
 <?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)
 -->
diff --git a/tools/suite_qiime2__diversity_lib/qiime2__diversity_lib__faith_pd.xml b/tools/suite_qiime2__diversity_lib/qiime2__diversity_lib__faith_pd.xml
index efd2cad..59b47e6 100644
--- a/tools/suite_qiime2__diversity_lib/qiime2__diversity_lib__faith_pd.xml
+++ b/tools/suite_qiime2__diversity_lib/qiime2__diversity_lib__faith_pd.xml
@@ -1,6 +1,6 @@
 <?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)
 -->
@@ -23,9 +23,9 @@ for:
     <inputs>
         <param name="table" type="data" format="qza" label="table: FeatureTable[Frequency | RelativeFrequency | PresenceAbsence]" help="[required]  The feature table containing the samples for which Faith's phylogenetic diversity should be computed. Table values will be converted to presence/absence.">
             <options options_filter_attribute="metadata.semantic_type">
-                <filter type="add_value" value="FeatureTable[RelativeFrequency]"/>
                 <filter type="add_value" value="FeatureTable[Frequency]"/>
                 <filter type="add_value" value="FeatureTable[PresenceAbsence]"/>
+                <filter type="add_value" value="FeatureTable[RelativeFrequency]"/>
             </options>
             <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureTable[Frequency]', 'FeatureTable[PresenceAbsence]', 'FeatureTable[RelativeFrequency]']</validator>
         </param>
diff --git a/tools/suite_qiime2__diversity_lib/qiime2__diversity_lib__jaccard.xml b/tools/suite_qiime2__diversity_lib/qiime2__diversity_lib__jaccard.xml
index 2dbd5a8..0a8553f 100644
--- a/tools/suite_qiime2__diversity_lib/qiime2__diversity_lib__jaccard.xml
+++ b/tools/suite_qiime2__diversity_lib/qiime2__diversity_lib__jaccard.xml
@@ -1,6 +1,6 @@
 <?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)
 -->
@@ -23,9 +23,9 @@ for:
     <inputs>
         <param name="table" type="data" format="qza" label="table: FeatureTable[Frequency | RelativeFrequency | PresenceAbsence]" help="[required]  The feature table containing the samples for which Jaccard distance should be computed.">
             <options options_filter_attribute="metadata.semantic_type">
-                <filter type="add_value" value="FeatureTable[RelativeFrequency]"/>
                 <filter type="add_value" value="FeatureTable[Frequency]"/>
                 <filter type="add_value" value="FeatureTable[PresenceAbsence]"/>
+                <filter type="add_value" value="FeatureTable[RelativeFrequency]"/>
             </options>
             <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureTable[Frequency]', 'FeatureTable[PresenceAbsence]', 'FeatureTable[RelativeFrequency]']</validator>
         </param>
diff --git a/tools/suite_qiime2__diversity_lib/qiime2__diversity_lib__observed_features.xml b/tools/suite_qiime2__diversity_lib/qiime2__diversity_lib__observed_features.xml
index d1d9594..393d138 100644
--- a/tools/suite_qiime2__diversity_lib/qiime2__diversity_lib__observed_features.xml
+++ b/tools/suite_qiime2__diversity_lib/qiime2__diversity_lib__observed_features.xml
@@ -1,6 +1,6 @@
 <?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)
 -->
@@ -23,9 +23,9 @@ for:
     <inputs>
         <param name="table" type="data" format="qza" label="table: FeatureTable[Frequency | RelativeFrequency | PresenceAbsence]" help="[required]  The feature table containing the samples for which the number of observed features should be calculated. Table values will be converted to presence/absence.">
             <options options_filter_attribute="metadata.semantic_type">
-                <filter type="add_value" value="FeatureTable[RelativeFrequency]"/>
                 <filter type="add_value" value="FeatureTable[Frequency]"/>
                 <filter type="add_value" value="FeatureTable[PresenceAbsence]"/>
+                <filter type="add_value" value="FeatureTable[RelativeFrequency]"/>
             </options>
             <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureTable[Frequency]', 'FeatureTable[PresenceAbsence]', 'FeatureTable[RelativeFrequency]']</validator>
         </param>
diff --git a/tools/suite_qiime2__diversity_lib/qiime2__diversity_lib__pielou_evenness.xml b/tools/suite_qiime2__diversity_lib/qiime2__diversity_lib__pielou_evenness.xml
index f5af92f..cbe02d4 100644
--- a/tools/suite_qiime2__diversity_lib/qiime2__diversity_lib__pielou_evenness.xml
+++ b/tools/suite_qiime2__diversity_lib/qiime2__diversity_lib__pielou_evenness.xml
@@ -1,6 +1,6 @@
 <?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)
 -->
@@ -23,8 +23,8 @@ for:
     <inputs>
         <param name="table" type="data" format="qza" label="table: FeatureTable[Frequency | RelativeFrequency]" help="[required]  The feature table containing the samples for which Pielou's evenness should be computed.">
             <options options_filter_attribute="metadata.semantic_type">
-                <filter type="add_value" value="FeatureTable[RelativeFrequency]"/>
                 <filter type="add_value" value="FeatureTable[Frequency]"/>
+                <filter type="add_value" value="FeatureTable[RelativeFrequency]"/>
             </options>
             <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureTable[Frequency]', 'FeatureTable[RelativeFrequency]']</validator>
         </param>
diff --git a/tools/suite_qiime2__diversity_lib/qiime2__diversity_lib__shannon_entropy.xml b/tools/suite_qiime2__diversity_lib/qiime2__diversity_lib__shannon_entropy.xml
index 430b778..9c8ddae 100644
--- a/tools/suite_qiime2__diversity_lib/qiime2__diversity_lib__shannon_entropy.xml
+++ b/tools/suite_qiime2__diversity_lib/qiime2__diversity_lib__shannon_entropy.xml
@@ -1,6 +1,6 @@
 <?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)
 -->
@@ -23,8 +23,8 @@ for:
     <inputs>
         <param name="table" type="data" format="qza" label="table: FeatureTable[Frequency | RelativeFrequency]" help="[required]  The feature table containing the samples for which Shannon's Entropy should be computed.">
             <options options_filter_attribute="metadata.semantic_type">
-                <filter type="add_value" value="FeatureTable[RelativeFrequency]"/>
                 <filter type="add_value" value="FeatureTable[Frequency]"/>
+                <filter type="add_value" value="FeatureTable[RelativeFrequency]"/>
             </options>
             <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureTable[Frequency]', 'FeatureTable[RelativeFrequency]']</validator>
         </param>
diff --git a/tools/suite_qiime2__diversity_lib/qiime2__diversity_lib__unweighted_unifrac.xml b/tools/suite_qiime2__diversity_lib/qiime2__diversity_lib__unweighted_unifrac.xml
index 8771430..272a606 100644
--- a/tools/suite_qiime2__diversity_lib/qiime2__diversity_lib__unweighted_unifrac.xml
+++ b/tools/suite_qiime2__diversity_lib/qiime2__diversity_lib__unweighted_unifrac.xml
@@ -1,6 +1,6 @@
 <?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)
 -->
@@ -23,9 +23,9 @@ for:
     <inputs>
         <param name="table" type="data" format="qza" label="table: FeatureTable[Frequency | RelativeFrequency | PresenceAbsence]" help="[required]  The feature table containing the samples for which Unweighted Unifrac should be computed.">
             <options options_filter_attribute="metadata.semantic_type">
-                <filter type="add_value" value="FeatureTable[RelativeFrequency]"/>
                 <filter type="add_value" value="FeatureTable[Frequency]"/>
                 <filter type="add_value" value="FeatureTable[PresenceAbsence]"/>
+                <filter type="add_value" value="FeatureTable[RelativeFrequency]"/>
             </options>
             <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureTable[Frequency]', 'FeatureTable[PresenceAbsence]', 'FeatureTable[RelativeFrequency]']</validator>
         </param>
diff --git a/tools/suite_qiime2__diversity_lib/qiime2__diversity_lib__weighted_unifrac.xml b/tools/suite_qiime2__diversity_lib/qiime2__diversity_lib__weighted_unifrac.xml
index 37edf74..efdef28 100644
--- a/tools/suite_qiime2__diversity_lib/qiime2__diversity_lib__weighted_unifrac.xml
+++ b/tools/suite_qiime2__diversity_lib/qiime2__diversity_lib__weighted_unifrac.xml
@@ -1,6 +1,6 @@
 <?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)
 -->
@@ -23,8 +23,8 @@ for:
     <inputs>
         <param name="table" type="data" format="qza" label="table: FeatureTable[Frequency | RelativeFrequency]" help="[required]  The feature table containing the samples for which Weighted Unifrac should be computed.">
             <options options_filter_attribute="metadata.semantic_type">
-                <filter type="add_value" value="FeatureTable[RelativeFrequency]"/>
                 <filter type="add_value" value="FeatureTable[Frequency]"/>
+                <filter type="add_value" value="FeatureTable[RelativeFrequency]"/>
             </options>
             <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureTable[Frequency]', 'FeatureTable[RelativeFrequency]']</validator>
         </param>
diff --git a/tools/suite_qiime2__diversity_lib/test-data/alpha_passthrough.test0.feature-table.qza b/tools/suite_qiime2__diversity_lib/test-data/alpha_passthrough.test0.feature-table.qza
index 07997c8..0d393f8 100644
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diff --git a/tools/suite_qiime2__diversity_lib/test-data/beta_passthrough.test0.feature-table.qza b/tools/suite_qiime2__diversity_lib/test-data/beta_passthrough.test0.feature-table.qza
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diff --git a/tools/suite_qiime2__feature_classifier/qiime2__feature_classifier__classify_consensus_blast.xml b/tools/suite_qiime2__feature_classifier/qiime2__feature_classifier__classify_consensus_blast.xml
index e5c55d2..8f25211 100644
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diff --git a/tools/suite_qiime2__feature_classifier/qiime2__feature_classifier__classify_consensus_vsearch.xml b/tools/suite_qiime2__feature_classifier/qiime2__feature_classifier__classify_consensus_vsearch.xml
index fb5440c..d8dfd17 100644
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diff --git a/tools/suite_qiime2__feature_classifier/qiime2__feature_classifier__classify_hybrid_vsearch_sklearn.xml b/tools/suite_qiime2__feature_classifier/qiime2__feature_classifier__classify_hybrid_vsearch_sklearn.xml
index 7348dde..b151d8e 100644
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index 2d47ec2..ca91eeb 100644
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diff --git a/tools/suite_qiime2__feature_classifier/qiime2__feature_classifier__extract_reads.xml b/tools/suite_qiime2__feature_classifier/qiime2__feature_classifier__extract_reads.xml
index ac712cc..3cfc127 100644
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diff --git a/tools/suite_qiime2__feature_classifier/qiime2__feature_classifier__find_consensus_annotation.xml b/tools/suite_qiime2__feature_classifier/qiime2__feature_classifier__find_consensus_annotation.xml
index 392e17f..1ef787d 100644
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index 2d27e28..559f7f3 100644
--- a/tools/suite_qiime2__feature_classifier/qiime2__feature_classifier__fit_classifier_naive_bayes.xml
+++ b/tools/suite_qiime2__feature_classifier/qiime2__feature_classifier__fit_classifier_naive_bayes.xml
@@ -1,6 +1,6 @@
 <?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)
 -->
diff --git a/tools/suite_qiime2__feature_classifier/qiime2__feature_classifier__fit_classifier_sklearn.xml b/tools/suite_qiime2__feature_classifier/qiime2__feature_classifier__fit_classifier_sklearn.xml
index b5965ca..0ed9f61 100644
--- a/tools/suite_qiime2__feature_classifier/qiime2__feature_classifier__fit_classifier_sklearn.xml
+++ b/tools/suite_qiime2__feature_classifier/qiime2__feature_classifier__fit_classifier_sklearn.xml
@@ -1,6 +1,6 @@
 <?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)
 -->
diff --git a/tools/suite_qiime2__feature_classifier/qiime2__feature_classifier__vsearch_global.xml b/tools/suite_qiime2__feature_classifier/qiime2__feature_classifier__vsearch_global.xml
index a8c7a86..5d40347 100644
--- a/tools/suite_qiime2__feature_classifier/qiime2__feature_classifier__vsearch_global.xml
+++ b/tools/suite_qiime2__feature_classifier/qiime2__feature_classifier__vsearch_global.xml
@@ -1,6 +1,6 @@
 <?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)
 -->
diff --git a/tools/suite_qiime2__feature_table/qiime2__feature_table__core_features.xml b/tools/suite_qiime2__feature_table/qiime2__feature_table__core_features.xml
index dba670f..b6fd368 100644
--- a/tools/suite_qiime2__feature_table/qiime2__feature_table__core_features.xml
+++ b/tools/suite_qiime2__feature_table/qiime2__feature_table__core_features.xml
@@ -1,6 +1,6 @@
 <?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)
 -->
diff --git a/tools/suite_qiime2__feature_table/qiime2__feature_table__filter_features.xml b/tools/suite_qiime2__feature_table/qiime2__feature_table__filter_features.xml
index 39bac63..088b898 100644
--- a/tools/suite_qiime2__feature_table/qiime2__feature_table__filter_features.xml
+++ b/tools/suite_qiime2__feature_table/qiime2__feature_table__filter_features.xml
@@ -1,6 +1,6 @@
 <?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)
 -->
diff --git a/tools/suite_qiime2__feature_table/qiime2__feature_table__filter_features_conditionally.xml b/tools/suite_qiime2__feature_table/qiime2__feature_table__filter_features_conditionally.xml
index b24a786..f7f84b6 100644
--- a/tools/suite_qiime2__feature_table/qiime2__feature_table__filter_features_conditionally.xml
+++ b/tools/suite_qiime2__feature_table/qiime2__feature_table__filter_features_conditionally.xml
@@ -1,6 +1,6 @@
 <?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)
 -->
@@ -25,8 +25,8 @@ for:
             <options options_filter_attribute="metadata.semantic_type">
                 <filter type="add_value" value="FeatureTable[Frequency]"/>
                 <filter type="add_value" value="FeatureTable[Composition]"/>
-                <filter type="add_value" value="FeatureTable[PresenceAbsence]"/>
                 <filter type="add_value" value="FeatureTable[RelativeFrequency]"/>
+                <filter type="add_value" value="FeatureTable[PresenceAbsence]"/>
             </options>
             <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureTable[Composition]', 'FeatureTable[Frequency]', 'FeatureTable[PresenceAbsence]', 'FeatureTable[RelativeFrequency]']</validator>
         </param>
diff --git a/tools/suite_qiime2__feature_table/qiime2__feature_table__filter_samples.xml b/tools/suite_qiime2__feature_table/qiime2__feature_table__filter_samples.xml
index 82d14af..3f2b984 100644
--- a/tools/suite_qiime2__feature_table/qiime2__feature_table__filter_samples.xml
+++ b/tools/suite_qiime2__feature_table/qiime2__feature_table__filter_samples.xml
@@ -1,6 +1,6 @@
 <?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)
 -->
@@ -25,8 +25,8 @@ for:
             <options options_filter_attribute="metadata.semantic_type">
                 <filter type="add_value" value="FeatureTable[Frequency]"/>
                 <filter type="add_value" value="FeatureTable[Composition]"/>
-                <filter type="add_value" value="FeatureTable[PresenceAbsence]"/>
                 <filter type="add_value" value="FeatureTable[RelativeFrequency]"/>
+                <filter type="add_value" value="FeatureTable[PresenceAbsence]"/>
             </options>
             <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureTable[Composition]', 'FeatureTable[Frequency]', 'FeatureTable[PresenceAbsence]', 'FeatureTable[RelativeFrequency]']</validator>
         </param>
diff --git a/tools/suite_qiime2__feature_table/qiime2__feature_table__filter_seqs.xml b/tools/suite_qiime2__feature_table/qiime2__feature_table__filter_seqs.xml
index 7949514..edaf4f9 100644
--- a/tools/suite_qiime2__feature_table/qiime2__feature_table__filter_seqs.xml
+++ b/tools/suite_qiime2__feature_table/qiime2__feature_table__filter_seqs.xml
@@ -1,6 +1,6 @@
 <?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)
 -->
@@ -23,8 +23,8 @@ for:
     <inputs>
         <param name="data" type="data" format="qza" label="data: FeatureData[Sequence¹ | AlignedSequence²]" help="[required]  The sequences from which features should be filtered.">
             <options options_filter_attribute="metadata.semantic_type">
-                <filter type="add_value" value="FeatureData[Sequence]"/>
                 <filter type="add_value" value="FeatureData[AlignedSequence]"/>
+                <filter type="add_value" value="FeatureData[Sequence]"/>
             </options>
             <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureData[AlignedSequence]', 'FeatureData[Sequence]']</validator>
         </param>
diff --git a/tools/suite_qiime2__feature_table/qiime2__feature_table__group.xml b/tools/suite_qiime2__feature_table/qiime2__feature_table__group.xml
index 9cfd667..0cf6c41 100644
--- a/tools/suite_qiime2__feature_table/qiime2__feature_table__group.xml
+++ b/tools/suite_qiime2__feature_table/qiime2__feature_table__group.xml
@@ -1,6 +1,6 @@
 <?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)
 -->
diff --git a/tools/suite_qiime2__feature_table/qiime2__feature_table__heatmap.xml b/tools/suite_qiime2__feature_table/qiime2__feature_table__heatmap.xml
index 15a90f7..164ed29 100644
--- a/tools/suite_qiime2__feature_table/qiime2__feature_table__heatmap.xml
+++ b/tools/suite_qiime2__feature_table/qiime2__feature_table__heatmap.xml
@@ -1,6 +1,6 @@
 <?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)
 -->
diff --git a/tools/suite_qiime2__feature_table/qiime2__feature_table__merge.xml b/tools/suite_qiime2__feature_table/qiime2__feature_table__merge.xml
index bd47590..68d7629 100644
--- a/tools/suite_qiime2__feature_table/qiime2__feature_table__merge.xml
+++ b/tools/suite_qiime2__feature_table/qiime2__feature_table__merge.xml
@@ -1,6 +1,6 @@
 <?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)
 -->
diff --git a/tools/suite_qiime2__feature_table/qiime2__feature_table__merge_seqs.xml b/tools/suite_qiime2__feature_table/qiime2__feature_table__merge_seqs.xml
index 31b2a72..a0df4c8 100644
--- a/tools/suite_qiime2__feature_table/qiime2__feature_table__merge_seqs.xml
+++ b/tools/suite_qiime2__feature_table/qiime2__feature_table__merge_seqs.xml
@@ -1,6 +1,6 @@
 <?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)
 -->
diff --git a/tools/suite_qiime2__feature_table/qiime2__feature_table__merge_taxa.xml b/tools/suite_qiime2__feature_table/qiime2__feature_table__merge_taxa.xml
index ff4c27f..eb142bd 100644
--- a/tools/suite_qiime2__feature_table/qiime2__feature_table__merge_taxa.xml
+++ b/tools/suite_qiime2__feature_table/qiime2__feature_table__merge_taxa.xml
@@ -1,6 +1,6 @@
 <?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)
 -->
diff --git a/tools/suite_qiime2__feature_table/qiime2__feature_table__presence_absence.xml b/tools/suite_qiime2__feature_table/qiime2__feature_table__presence_absence.xml
index 729b91d..3a95485 100644
--- a/tools/suite_qiime2__feature_table/qiime2__feature_table__presence_absence.xml
+++ b/tools/suite_qiime2__feature_table/qiime2__feature_table__presence_absence.xml
@@ -1,6 +1,6 @@
 <?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)
 -->
diff --git a/tools/suite_qiime2__feature_table/qiime2__feature_table__rarefy.xml b/tools/suite_qiime2__feature_table/qiime2__feature_table__rarefy.xml
index d5f47d5..af1feae 100644
--- a/tools/suite_qiime2__feature_table/qiime2__feature_table__rarefy.xml
+++ b/tools/suite_qiime2__feature_table/qiime2__feature_table__rarefy.xml
@@ -1,6 +1,6 @@
 <?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)
 -->
diff --git a/tools/suite_qiime2__feature_table/qiime2__feature_table__relative_frequency.xml b/tools/suite_qiime2__feature_table/qiime2__feature_table__relative_frequency.xml
index 375f469..f0e2e0c 100644
--- a/tools/suite_qiime2__feature_table/qiime2__feature_table__relative_frequency.xml
+++ b/tools/suite_qiime2__feature_table/qiime2__feature_table__relative_frequency.xml
@@ -1,6 +1,6 @@
 <?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)
 -->
diff --git a/tools/suite_qiime2__feature_table/qiime2__feature_table__rename_ids.xml b/tools/suite_qiime2__feature_table/qiime2__feature_table__rename_ids.xml
index 1fda834..f2f4c89 100644
--- a/tools/suite_qiime2__feature_table/qiime2__feature_table__rename_ids.xml
+++ b/tools/suite_qiime2__feature_table/qiime2__feature_table__rename_ids.xml
@@ -1,6 +1,6 @@
 <?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)
 -->
@@ -25,8 +25,8 @@ for:
             <options options_filter_attribute="metadata.semantic_type">
                 <filter type="add_value" value="FeatureTable[Frequency]"/>
                 <filter type="add_value" value="FeatureTable[Composition]"/>
-                <filter type="add_value" value="FeatureTable[PresenceAbsence]"/>
                 <filter type="add_value" value="FeatureTable[RelativeFrequency]"/>
+                <filter type="add_value" value="FeatureTable[PresenceAbsence]"/>
             </options>
             <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureTable[Composition]', 'FeatureTable[Frequency]', 'FeatureTable[PresenceAbsence]', 'FeatureTable[RelativeFrequency]']</validator>
         </param>
diff --git a/tools/suite_qiime2__feature_table/qiime2__feature_table__subsample.xml b/tools/suite_qiime2__feature_table/qiime2__feature_table__subsample.xml
index 1fd3d85..5e4dd8b 100644
--- a/tools/suite_qiime2__feature_table/qiime2__feature_table__subsample.xml
+++ b/tools/suite_qiime2__feature_table/qiime2__feature_table__subsample.xml
@@ -1,6 +1,6 @@
 <?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)
 -->
diff --git a/tools/suite_qiime2__feature_table/qiime2__feature_table__summarize.xml b/tools/suite_qiime2__feature_table/qiime2__feature_table__summarize.xml
index 36041df..80c36a2 100644
--- a/tools/suite_qiime2__feature_table/qiime2__feature_table__summarize.xml
+++ b/tools/suite_qiime2__feature_table/qiime2__feature_table__summarize.xml
@@ -1,6 +1,6 @@
 <?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)
 -->
@@ -24,8 +24,8 @@ for:
         <param name="table" type="data" format="qza" label="table: FeatureTable[Frequency | RelativeFrequency | PresenceAbsence]" help="[required]  The feature table to be summarized.">
             <options options_filter_attribute="metadata.semantic_type">
                 <filter type="add_value" value="FeatureTable[Frequency]"/>
-                <filter type="add_value" value="FeatureTable[PresenceAbsence]"/>
                 <filter type="add_value" value="FeatureTable[RelativeFrequency]"/>
+                <filter type="add_value" value="FeatureTable[PresenceAbsence]"/>
             </options>
             <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureTable[Frequency]', 'FeatureTable[PresenceAbsence]', 'FeatureTable[RelativeFrequency]']</validator>
         </param>
diff --git a/tools/suite_qiime2__feature_table/qiime2__feature_table__tabulate_seqs.xml b/tools/suite_qiime2__feature_table/qiime2__feature_table__tabulate_seqs.xml
index 8aceccc..135c3c7 100644
--- a/tools/suite_qiime2__feature_table/qiime2__feature_table__tabulate_seqs.xml
+++ b/tools/suite_qiime2__feature_table/qiime2__feature_table__tabulate_seqs.xml
@@ -1,6 +1,6 @@
 <?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)
 -->
@@ -23,8 +23,8 @@ for:
     <inputs>
         <param name="data" type="data" format="qza" label="data: FeatureData[Sequence | AlignedSequence]" help="[required]  The feature sequences to be tabulated.">
             <options options_filter_attribute="metadata.semantic_type">
-                <filter type="add_value" value="FeatureData[Sequence]"/>
                 <filter type="add_value" value="FeatureData[AlignedSequence]"/>
+                <filter type="add_value" value="FeatureData[Sequence]"/>
             </options>
             <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureData[AlignedSequence]', 'FeatureData[Sequence]']</validator>
         </param>
diff --git a/tools/suite_qiime2__feature_table/qiime2__feature_table__transpose.xml b/tools/suite_qiime2__feature_table/qiime2__feature_table__transpose.xml
index f88cc4c..cd0f27c 100644
--- a/tools/suite_qiime2__feature_table/qiime2__feature_table__transpose.xml
+++ b/tools/suite_qiime2__feature_table/qiime2__feature_table__transpose.xml
@@ -1,6 +1,6 @@
 <?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)
 -->
@@ -25,8 +25,8 @@ for:
             <options options_filter_attribute="metadata.semantic_type">
                 <filter type="add_value" value="FeatureTable[Frequency]"/>
                 <filter type="add_value" value="FeatureTable[Composition]"/>
-                <filter type="add_value" value="FeatureTable[PresenceAbsence]"/>
                 <filter type="add_value" value="FeatureTable[RelativeFrequency]"/>
+                <filter type="add_value" value="FeatureTable[PresenceAbsence]"/>
             </options>
             <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureTable[Composition]', 'FeatureTable[Frequency]', 'FeatureTable[PresenceAbsence]', 'FeatureTable[RelativeFrequency]']</validator>
         </param>
diff --git a/tools/suite_qiime2__feature_table/test-data/filter_features.test0.feature-table.qza b/tools/suite_qiime2__feature_table/test-data/filter_features.test0.feature-table.qza
index be1ba00..736da1e 100644
Binary files a/tools/suite_qiime2__feature_table/test-data/filter_features.test0.feature-table.qza and b/tools/suite_qiime2__feature_table/test-data/filter_features.test0.feature-table.qza differ
diff --git a/tools/suite_qiime2__feature_table/test-data/filter_features_conditionally.test0.feature-table.qza b/tools/suite_qiime2__feature_table/test-data/filter_features_conditionally.test0.feature-table.qza
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diff --git a/tools/suite_qiime2__feature_table/test-data/filter_samples.test0.feature-table.qza b/tools/suite_qiime2__feature_table/test-data/filter_samples.test0.feature-table.qza
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diff --git a/tools/suite_qiime2__feature_table/test-data/filter_samples.test2.feature-table.qza b/tools/suite_qiime2__feature_table/test-data/filter_samples.test2.feature-table.qza
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diff --git a/tools/suite_qiime2__feature_table/test-data/merge.test1.feature-table1.qza b/tools/suite_qiime2__feature_table/test-data/merge.test1.feature-table1.qza
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diff --git a/tools/suite_qiime2__feature_table/test-data/merge.test1.feature-table3.qza b/tools/suite_qiime2__feature_table/test-data/merge.test1.feature-table3.qza
index a734b16..d724467 100644
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diff --git a/tools/suite_qiime2__feature_table/test-data/merge_seqs.test0.seqs1.qza b/tools/suite_qiime2__feature_table/test-data/merge_seqs.test0.seqs1.qza
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diff --git a/tools/suite_qiime2__feature_table/test-data/merge_seqs.test0.seqs2.qza b/tools/suite_qiime2__feature_table/test-data/merge_seqs.test0.seqs2.qza
index 4444c19..63e1a8c 100644
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diff --git a/tools/suite_qiime2__feature_table/test-data/merge_taxa.test0.tax1.qza b/tools/suite_qiime2__feature_table/test-data/merge_taxa.test0.tax1.qza
index 18c5bc9..c2dfea2 100644
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diff --git a/tools/suite_qiime2__feature_table/test-data/merge_taxa.test0.tax2.qza b/tools/suite_qiime2__feature_table/test-data/merge_taxa.test0.tax2.qza
index 18c5bc9..c2dfea2 100644
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diff --git a/tools/suite_qiime2__feature_table/test-data/summarize.test0.feature-table.qza b/tools/suite_qiime2__feature_table/test-data/summarize.test0.feature-table.qza
index be1ba00..736da1e 100644
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diff --git a/tools/suite_qiime2__feature_table/test-data/tabulate_seqs.test0.rep-seqs.qza b/tools/suite_qiime2__feature_table/test-data/tabulate_seqs.test0.rep-seqs.qza
index 7f057e3..9c8b648 100644
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diff --git a/tools/suite_qiime2__fragment_insertion/qiime2__fragment_insertion__classify_otus_experimental.xml b/tools/suite_qiime2__fragment_insertion/qiime2__fragment_insertion__classify_otus_experimental.xml
index 834e8f3..79ce12e 100644
--- a/tools/suite_qiime2__fragment_insertion/qiime2__fragment_insertion__classify_otus_experimental.xml
+++ b/tools/suite_qiime2__fragment_insertion/qiime2__fragment_insertion__classify_otus_experimental.xml
@@ -1,6 +1,6 @@
 <?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)
 -->
diff --git a/tools/suite_qiime2__fragment_insertion/qiime2__fragment_insertion__filter_features.xml b/tools/suite_qiime2__fragment_insertion/qiime2__fragment_insertion__filter_features.xml
index 6923d53..c1adc5e 100644
--- a/tools/suite_qiime2__fragment_insertion/qiime2__fragment_insertion__filter_features.xml
+++ b/tools/suite_qiime2__fragment_insertion/qiime2__fragment_insertion__filter_features.xml
@@ -1,6 +1,6 @@
 <?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)
 -->
diff --git a/tools/suite_qiime2__fragment_insertion/qiime2__fragment_insertion__sepp.xml b/tools/suite_qiime2__fragment_insertion/qiime2__fragment_insertion__sepp.xml
index bab6ec8..b142b3d 100644
--- a/tools/suite_qiime2__fragment_insertion/qiime2__fragment_insertion__sepp.xml
+++ b/tools/suite_qiime2__fragment_insertion/qiime2__fragment_insertion__sepp.xml
@@ -1,6 +1,6 @@
 <?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)
 -->
diff --git a/tools/suite_qiime2__gneiss/qiime2__gneiss__assign_ids.xml b/tools/suite_qiime2__gneiss/qiime2__gneiss__assign_ids.xml
index 17961ed..06ef2fc 100644
--- a/tools/suite_qiime2__gneiss/qiime2__gneiss__assign_ids.xml
+++ b/tools/suite_qiime2__gneiss/qiime2__gneiss__assign_ids.xml
@@ -1,6 +1,6 @@
 <?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)
 -->
diff --git a/tools/suite_qiime2__gneiss/qiime2__gneiss__correlation_clustering.xml b/tools/suite_qiime2__gneiss/qiime2__gneiss__correlation_clustering.xml
index e72dd8f..9a89316 100644
--- a/tools/suite_qiime2__gneiss/qiime2__gneiss__correlation_clustering.xml
+++ b/tools/suite_qiime2__gneiss/qiime2__gneiss__correlation_clustering.xml
@@ -1,6 +1,6 @@
 <?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)
 -->
diff --git a/tools/suite_qiime2__gneiss/qiime2__gneiss__dendrogram_heatmap.xml b/tools/suite_qiime2__gneiss/qiime2__gneiss__dendrogram_heatmap.xml
index 3b8c2cf..0e3e5c2 100644
--- a/tools/suite_qiime2__gneiss/qiime2__gneiss__dendrogram_heatmap.xml
+++ b/tools/suite_qiime2__gneiss/qiime2__gneiss__dendrogram_heatmap.xml
@@ -1,6 +1,6 @@
 <?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)
 -->
diff --git a/tools/suite_qiime2__gneiss/qiime2__gneiss__gradient_clustering.xml b/tools/suite_qiime2__gneiss/qiime2__gneiss__gradient_clustering.xml
index 2a693d3..c900b26 100644
--- a/tools/suite_qiime2__gneiss/qiime2__gneiss__gradient_clustering.xml
+++ b/tools/suite_qiime2__gneiss/qiime2__gneiss__gradient_clustering.xml
@@ -1,6 +1,6 @@
 <?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)
 -->
@@ -24,8 +24,8 @@ for:
         <param name="table" type="data" format="qza" label="table: FeatureTable[Frequency | RelativeFrequency | Composition]" help="[required]  The feature table containing the samples in which the columns will be clustered.">
             <options options_filter_attribute="metadata.semantic_type">
                 <filter type="add_value" value="FeatureTable[Composition]"/>
-                <filter type="add_value" value="FeatureTable[RelativeFrequency]"/>
                 <filter type="add_value" value="FeatureTable[Frequency]"/>
+                <filter type="add_value" value="FeatureTable[RelativeFrequency]"/>
             </options>
             <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureTable[Composition]', 'FeatureTable[Frequency]', 'FeatureTable[RelativeFrequency]']</validator>
         </param>
diff --git a/tools/suite_qiime2__gneiss/qiime2__gneiss__ilr_hierarchical.xml b/tools/suite_qiime2__gneiss/qiime2__gneiss__ilr_hierarchical.xml
index dfd3c22..0afab77 100644
--- a/tools/suite_qiime2__gneiss/qiime2__gneiss__ilr_hierarchical.xml
+++ b/tools/suite_qiime2__gneiss/qiime2__gneiss__ilr_hierarchical.xml
@@ -1,6 +1,6 @@
 <?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)
 -->
diff --git a/tools/suite_qiime2__gneiss/qiime2__gneiss__ilr_phylogenetic.xml b/tools/suite_qiime2__gneiss/qiime2__gneiss__ilr_phylogenetic.xml
index 7277e82..f87fe40 100644
--- a/tools/suite_qiime2__gneiss/qiime2__gneiss__ilr_phylogenetic.xml
+++ b/tools/suite_qiime2__gneiss/qiime2__gneiss__ilr_phylogenetic.xml
@@ -1,6 +1,6 @@
 <?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)
 -->
diff --git a/tools/suite_qiime2__gneiss/qiime2__gneiss__ilr_phylogenetic_differential.xml b/tools/suite_qiime2__gneiss/qiime2__gneiss__ilr_phylogenetic_differential.xml
index 9f30ae7..c7cb1a8 100644
--- a/tools/suite_qiime2__gneiss/qiime2__gneiss__ilr_phylogenetic_differential.xml
+++ b/tools/suite_qiime2__gneiss/qiime2__gneiss__ilr_phylogenetic_differential.xml
@@ -1,6 +1,6 @@
 <?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)
 -->
diff --git a/tools/suite_qiime2__gneiss/qiime2__gneiss__ilr_phylogenetic_ordination.xml b/tools/suite_qiime2__gneiss/qiime2__gneiss__ilr_phylogenetic_ordination.xml
index 8f86f5b..f5e6fe0 100644
--- a/tools/suite_qiime2__gneiss/qiime2__gneiss__ilr_phylogenetic_ordination.xml
+++ b/tools/suite_qiime2__gneiss/qiime2__gneiss__ilr_phylogenetic_ordination.xml
@@ -1,6 +1,6 @@
 <?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)
 -->
diff --git a/tools/suite_qiime2__longitudinal/qiime2__longitudinal__anova.xml b/tools/suite_qiime2__longitudinal/qiime2__longitudinal__anova.xml
index 377322d..328a7c6 100644
--- a/tools/suite_qiime2__longitudinal/qiime2__longitudinal__anova.xml
+++ b/tools/suite_qiime2__longitudinal/qiime2__longitudinal__anova.xml
@@ -1,6 +1,6 @@
 <?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)
 -->
diff --git a/tools/suite_qiime2__longitudinal/qiime2__longitudinal__feature_volatility.xml b/tools/suite_qiime2__longitudinal/qiime2__longitudinal__feature_volatility.xml
index fc4705f..0d29425 100644
--- a/tools/suite_qiime2__longitudinal/qiime2__longitudinal__feature_volatility.xml
+++ b/tools/suite_qiime2__longitudinal/qiime2__longitudinal__feature_volatility.xml
@@ -1,6 +1,6 @@
 <?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)
 -->
diff --git a/tools/suite_qiime2__longitudinal/qiime2__longitudinal__first_differences.xml b/tools/suite_qiime2__longitudinal/qiime2__longitudinal__first_differences.xml
index 9bcdbfe..b623ec9 100644
--- a/tools/suite_qiime2__longitudinal/qiime2__longitudinal__first_differences.xml
+++ b/tools/suite_qiime2__longitudinal/qiime2__longitudinal__first_differences.xml
@@ -1,6 +1,6 @@
 <?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)
 -->
diff --git a/tools/suite_qiime2__longitudinal/qiime2__longitudinal__first_distances.xml b/tools/suite_qiime2__longitudinal/qiime2__longitudinal__first_distances.xml
index 453a4d4..3e22bcc 100644
--- a/tools/suite_qiime2__longitudinal/qiime2__longitudinal__first_distances.xml
+++ b/tools/suite_qiime2__longitudinal/qiime2__longitudinal__first_distances.xml
@@ -1,6 +1,6 @@
 <?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)
 -->
diff --git a/tools/suite_qiime2__longitudinal/qiime2__longitudinal__linear_mixed_effects.xml b/tools/suite_qiime2__longitudinal/qiime2__longitudinal__linear_mixed_effects.xml
index 88debc6..8b96f69 100644
--- a/tools/suite_qiime2__longitudinal/qiime2__longitudinal__linear_mixed_effects.xml
+++ b/tools/suite_qiime2__longitudinal/qiime2__longitudinal__linear_mixed_effects.xml
@@ -1,6 +1,6 @@
 <?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)
 -->
diff --git a/tools/suite_qiime2__longitudinal/qiime2__longitudinal__maturity_index.xml b/tools/suite_qiime2__longitudinal/qiime2__longitudinal__maturity_index.xml
index 7ffe4d5..3bf8135 100644
--- a/tools/suite_qiime2__longitudinal/qiime2__longitudinal__maturity_index.xml
+++ b/tools/suite_qiime2__longitudinal/qiime2__longitudinal__maturity_index.xml
@@ -1,6 +1,6 @@
 <?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)
 -->
diff --git a/tools/suite_qiime2__longitudinal/qiime2__longitudinal__nmit.xml b/tools/suite_qiime2__longitudinal/qiime2__longitudinal__nmit.xml
index 255d442..a50998b 100644
--- a/tools/suite_qiime2__longitudinal/qiime2__longitudinal__nmit.xml
+++ b/tools/suite_qiime2__longitudinal/qiime2__longitudinal__nmit.xml
@@ -1,6 +1,6 @@
 <?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)
 -->
diff --git a/tools/suite_qiime2__longitudinal/qiime2__longitudinal__pairwise_differences.xml b/tools/suite_qiime2__longitudinal/qiime2__longitudinal__pairwise_differences.xml
index 4282dda..342e6dd 100644
--- a/tools/suite_qiime2__longitudinal/qiime2__longitudinal__pairwise_differences.xml
+++ b/tools/suite_qiime2__longitudinal/qiime2__longitudinal__pairwise_differences.xml
@@ -1,6 +1,6 @@
 <?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)
 -->
diff --git a/tools/suite_qiime2__longitudinal/qiime2__longitudinal__pairwise_distances.xml b/tools/suite_qiime2__longitudinal/qiime2__longitudinal__pairwise_distances.xml
index 3e16edc..0a4dd34 100644
--- a/tools/suite_qiime2__longitudinal/qiime2__longitudinal__pairwise_distances.xml
+++ b/tools/suite_qiime2__longitudinal/qiime2__longitudinal__pairwise_distances.xml
@@ -1,6 +1,6 @@
 <?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)
 -->
diff --git a/tools/suite_qiime2__longitudinal/qiime2__longitudinal__plot_feature_volatility.xml b/tools/suite_qiime2__longitudinal/qiime2__longitudinal__plot_feature_volatility.xml
index 4b1fd69..4f2d7d0 100644
--- a/tools/suite_qiime2__longitudinal/qiime2__longitudinal__plot_feature_volatility.xml
+++ b/tools/suite_qiime2__longitudinal/qiime2__longitudinal__plot_feature_volatility.xml
@@ -1,6 +1,6 @@
 <?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)
 -->
diff --git a/tools/suite_qiime2__longitudinal/qiime2__longitudinal__volatility.xml b/tools/suite_qiime2__longitudinal/qiime2__longitudinal__volatility.xml
index c3bf7ee..7d92265 100644
--- a/tools/suite_qiime2__longitudinal/qiime2__longitudinal__volatility.xml
+++ b/tools/suite_qiime2__longitudinal/qiime2__longitudinal__volatility.xml
@@ -1,6 +1,6 @@
 <?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)
 -->
diff --git a/tools/suite_qiime2__metadata/qiime2__metadata__distance_matrix.xml b/tools/suite_qiime2__metadata/qiime2__metadata__distance_matrix.xml
index 7f02f39..6ee9070 100644
--- a/tools/suite_qiime2__metadata/qiime2__metadata__distance_matrix.xml
+++ b/tools/suite_qiime2__metadata/qiime2__metadata__distance_matrix.xml
@@ -1,6 +1,6 @@
 <?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)
 -->
diff --git a/tools/suite_qiime2__metadata/qiime2__metadata__shuffle_groups.xml b/tools/suite_qiime2__metadata/qiime2__metadata__shuffle_groups.xml
index 56585ec..d5a3911 100644
--- a/tools/suite_qiime2__metadata/qiime2__metadata__shuffle_groups.xml
+++ b/tools/suite_qiime2__metadata/qiime2__metadata__shuffle_groups.xml
@@ -1,6 +1,6 @@
 <?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)
 -->
diff --git a/tools/suite_qiime2__metadata/qiime2__metadata__tabulate.xml b/tools/suite_qiime2__metadata/qiime2__metadata__tabulate.xml
index 1c6e84f..4de7ef1 100644
--- a/tools/suite_qiime2__metadata/qiime2__metadata__tabulate.xml
+++ b/tools/suite_qiime2__metadata/qiime2__metadata__tabulate.xml
@@ -1,6 +1,6 @@
 <?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)
 -->
diff --git a/tools/suite_qiime2__phylogeny/qiime2__phylogeny__align_to_tree_mafft_fasttree.xml b/tools/suite_qiime2__phylogeny/qiime2__phylogeny__align_to_tree_mafft_fasttree.xml
index 2038876..2fc294a 100644
--- a/tools/suite_qiime2__phylogeny/qiime2__phylogeny__align_to_tree_mafft_fasttree.xml
+++ b/tools/suite_qiime2__phylogeny/qiime2__phylogeny__align_to_tree_mafft_fasttree.xml
@@ -1,6 +1,6 @@
 <?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)
 -->
diff --git a/tools/suite_qiime2__phylogeny/qiime2__phylogeny__align_to_tree_mafft_iqtree.xml b/tools/suite_qiime2__phylogeny/qiime2__phylogeny__align_to_tree_mafft_iqtree.xml
index 5cdd27e..3429180 100644
--- a/tools/suite_qiime2__phylogeny/qiime2__phylogeny__align_to_tree_mafft_iqtree.xml
+++ b/tools/suite_qiime2__phylogeny/qiime2__phylogeny__align_to_tree_mafft_iqtree.xml
@@ -1,6 +1,6 @@
 <?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)
 -->
diff --git a/tools/suite_qiime2__phylogeny/qiime2__phylogeny__align_to_tree_mafft_raxml.xml b/tools/suite_qiime2__phylogeny/qiime2__phylogeny__align_to_tree_mafft_raxml.xml
index 21a1f75..18c421b 100644
--- a/tools/suite_qiime2__phylogeny/qiime2__phylogeny__align_to_tree_mafft_raxml.xml
+++ b/tools/suite_qiime2__phylogeny/qiime2__phylogeny__align_to_tree_mafft_raxml.xml
@@ -1,6 +1,6 @@
 <?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)
 -->
diff --git a/tools/suite_qiime2__phylogeny/qiime2__phylogeny__fasttree.xml b/tools/suite_qiime2__phylogeny/qiime2__phylogeny__fasttree.xml
index 752cbaf..232c440 100644
--- a/tools/suite_qiime2__phylogeny/qiime2__phylogeny__fasttree.xml
+++ b/tools/suite_qiime2__phylogeny/qiime2__phylogeny__fasttree.xml
@@ -1,6 +1,6 @@
 <?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)
 -->
diff --git a/tools/suite_qiime2__phylogeny/qiime2__phylogeny__filter_table.xml b/tools/suite_qiime2__phylogeny/qiime2__phylogeny__filter_table.xml
index 9c26692..385a96c 100644
--- a/tools/suite_qiime2__phylogeny/qiime2__phylogeny__filter_table.xml
+++ b/tools/suite_qiime2__phylogeny/qiime2__phylogeny__filter_table.xml
@@ -1,6 +1,6 @@
 <?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)
 -->
diff --git a/tools/suite_qiime2__phylogeny/qiime2__phylogeny__filter_tree.xml b/tools/suite_qiime2__phylogeny/qiime2__phylogeny__filter_tree.xml
index 2c7168a..08c0eaf 100644
--- a/tools/suite_qiime2__phylogeny/qiime2__phylogeny__filter_tree.xml
+++ b/tools/suite_qiime2__phylogeny/qiime2__phylogeny__filter_tree.xml
@@ -1,6 +1,6 @@
 <?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)
 -->
diff --git a/tools/suite_qiime2__phylogeny/qiime2__phylogeny__iqtree.xml b/tools/suite_qiime2__phylogeny/qiime2__phylogeny__iqtree.xml
index 4c04ed2..e9ff093 100644
--- a/tools/suite_qiime2__phylogeny/qiime2__phylogeny__iqtree.xml
+++ b/tools/suite_qiime2__phylogeny/qiime2__phylogeny__iqtree.xml
@@ -1,6 +1,6 @@
 <?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)
 -->
diff --git a/tools/suite_qiime2__phylogeny/qiime2__phylogeny__iqtree_ultrafast_bootstrap.xml b/tools/suite_qiime2__phylogeny/qiime2__phylogeny__iqtree_ultrafast_bootstrap.xml
index 7ed4512..c5a2e08 100644
--- a/tools/suite_qiime2__phylogeny/qiime2__phylogeny__iqtree_ultrafast_bootstrap.xml
+++ b/tools/suite_qiime2__phylogeny/qiime2__phylogeny__iqtree_ultrafast_bootstrap.xml
@@ -1,6 +1,6 @@
 <?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)
 -->
diff --git a/tools/suite_qiime2__phylogeny/qiime2__phylogeny__midpoint_root.xml b/tools/suite_qiime2__phylogeny/qiime2__phylogeny__midpoint_root.xml
index ede6666..9be4bf6 100644
--- a/tools/suite_qiime2__phylogeny/qiime2__phylogeny__midpoint_root.xml
+++ b/tools/suite_qiime2__phylogeny/qiime2__phylogeny__midpoint_root.xml
@@ -1,6 +1,6 @@
 <?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)
 -->
diff --git a/tools/suite_qiime2__phylogeny/qiime2__phylogeny__raxml.xml b/tools/suite_qiime2__phylogeny/qiime2__phylogeny__raxml.xml
index 4e7ccb9..5cd0960 100644
--- a/tools/suite_qiime2__phylogeny/qiime2__phylogeny__raxml.xml
+++ b/tools/suite_qiime2__phylogeny/qiime2__phylogeny__raxml.xml
@@ -1,6 +1,6 @@
 <?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)
 -->
diff --git a/tools/suite_qiime2__phylogeny/qiime2__phylogeny__raxml_rapid_bootstrap.xml b/tools/suite_qiime2__phylogeny/qiime2__phylogeny__raxml_rapid_bootstrap.xml
index dc75ad6..f10abc5 100644
--- a/tools/suite_qiime2__phylogeny/qiime2__phylogeny__raxml_rapid_bootstrap.xml
+++ b/tools/suite_qiime2__phylogeny/qiime2__phylogeny__raxml_rapid_bootstrap.xml
@@ -1,6 +1,6 @@
 <?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)
 -->
diff --git a/tools/suite_qiime2__phylogeny/qiime2__phylogeny__robinson_foulds.xml b/tools/suite_qiime2__phylogeny/qiime2__phylogeny__robinson_foulds.xml
index 6f9a21b..37a9efc 100644
--- a/tools/suite_qiime2__phylogeny/qiime2__phylogeny__robinson_foulds.xml
+++ b/tools/suite_qiime2__phylogeny/qiime2__phylogeny__robinson_foulds.xml
@@ -1,6 +1,6 @@
 <?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)
 -->
diff --git a/tools/suite_qiime2__phylogeny/test-data/align_to_tree_mafft_fasttree.test0.rep-seqs.qza b/tools/suite_qiime2__phylogeny/test-data/align_to_tree_mafft_fasttree.test0.rep-seqs.qza
index b5836dd..d0f768a 100644
Binary files a/tools/suite_qiime2__phylogeny/test-data/align_to_tree_mafft_fasttree.test0.rep-seqs.qza and b/tools/suite_qiime2__phylogeny/test-data/align_to_tree_mafft_fasttree.test0.rep-seqs.qza differ
diff --git a/tools/suite_qiime2__quality_control/qiime2__quality_control__bowtie2_build.xml b/tools/suite_qiime2__quality_control/qiime2__quality_control__bowtie2_build.xml
index 0c9d1dd..ce818d7 100644
--- a/tools/suite_qiime2__quality_control/qiime2__quality_control__bowtie2_build.xml
+++ b/tools/suite_qiime2__quality_control/qiime2__quality_control__bowtie2_build.xml
@@ -1,6 +1,6 @@
 <?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)
 -->
diff --git a/tools/suite_qiime2__quality_control/qiime2__quality_control__decontam_identify.xml b/tools/suite_qiime2__quality_control/qiime2__quality_control__decontam_identify.xml
index 9aee021..3239f13 100644
--- a/tools/suite_qiime2__quality_control/qiime2__quality_control__decontam_identify.xml
+++ b/tools/suite_qiime2__quality_control/qiime2__quality_control__decontam_identify.xml
@@ -1,6 +1,6 @@
 <?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)
 -->
diff --git a/tools/suite_qiime2__quality_control/qiime2__quality_control__decontam_remove.xml b/tools/suite_qiime2__quality_control/qiime2__quality_control__decontam_remove.xml
index b825ba3..f9ffd9a 100644
--- a/tools/suite_qiime2__quality_control/qiime2__quality_control__decontam_remove.xml
+++ b/tools/suite_qiime2__quality_control/qiime2__quality_control__decontam_remove.xml
@@ -1,6 +1,6 @@
 <?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)
 -->
diff --git a/tools/suite_qiime2__quality_control/qiime2__quality_control__decontam_score_viz.xml b/tools/suite_qiime2__quality_control/qiime2__quality_control__decontam_score_viz.xml
index 80d64e2..a753edb 100644
--- a/tools/suite_qiime2__quality_control/qiime2__quality_control__decontam_score_viz.xml
+++ b/tools/suite_qiime2__quality_control/qiime2__quality_control__decontam_score_viz.xml
@@ -1,6 +1,6 @@
 <?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)
 -->
diff --git a/tools/suite_qiime2__quality_control/qiime2__quality_control__evaluate_composition.xml b/tools/suite_qiime2__quality_control/qiime2__quality_control__evaluate_composition.xml
index 919f93d..4e1a7cc 100644
--- a/tools/suite_qiime2__quality_control/qiime2__quality_control__evaluate_composition.xml
+++ b/tools/suite_qiime2__quality_control/qiime2__quality_control__evaluate_composition.xml
@@ -1,6 +1,6 @@
 <?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)
 -->
diff --git a/tools/suite_qiime2__quality_control/qiime2__quality_control__evaluate_seqs.xml b/tools/suite_qiime2__quality_control/qiime2__quality_control__evaluate_seqs.xml
index 8c4cfe8..13c0e05 100644
--- a/tools/suite_qiime2__quality_control/qiime2__quality_control__evaluate_seqs.xml
+++ b/tools/suite_qiime2__quality_control/qiime2__quality_control__evaluate_seqs.xml
@@ -1,6 +1,6 @@
 <?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)
 -->
diff --git a/tools/suite_qiime2__quality_control/qiime2__quality_control__evaluate_taxonomy.xml b/tools/suite_qiime2__quality_control/qiime2__quality_control__evaluate_taxonomy.xml
index 38ff7cd..44807a8 100644
--- a/tools/suite_qiime2__quality_control/qiime2__quality_control__evaluate_taxonomy.xml
+++ b/tools/suite_qiime2__quality_control/qiime2__quality_control__evaluate_taxonomy.xml
@@ -1,6 +1,6 @@
 <?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)
 -->
diff --git a/tools/suite_qiime2__quality_control/qiime2__quality_control__exclude_seqs.xml b/tools/suite_qiime2__quality_control/qiime2__quality_control__exclude_seqs.xml
index dc08004..7f0f44e 100644
--- a/tools/suite_qiime2__quality_control/qiime2__quality_control__exclude_seqs.xml
+++ b/tools/suite_qiime2__quality_control/qiime2__quality_control__exclude_seqs.xml
@@ -1,6 +1,6 @@
 <?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)
 -->
diff --git a/tools/suite_qiime2__quality_control/qiime2__quality_control__filter_reads.xml b/tools/suite_qiime2__quality_control/qiime2__quality_control__filter_reads.xml
index 3869250..bfd423b 100644
--- a/tools/suite_qiime2__quality_control/qiime2__quality_control__filter_reads.xml
+++ b/tools/suite_qiime2__quality_control/qiime2__quality_control__filter_reads.xml
@@ -1,6 +1,6 @@
 <?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)
 -->
@@ -23,8 +23,8 @@ for:
     <inputs>
         <param name="demultiplexed_sequences" type="data" format="qza" label="demultiplexed_sequences: SampleData[SequencesWithQuality¹ | PairedEndSequencesWithQuality²]" help="[required]  The sequences to be trimmed.">
             <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>
diff --git a/tools/suite_qiime2__quality_filter/qiime2__quality_filter__q_score.xml b/tools/suite_qiime2__quality_filter/qiime2__quality_filter__q_score.xml
index 5f1cbe0..bcd85ab 100644
--- a/tools/suite_qiime2__quality_filter/qiime2__quality_filter__q_score.xml
+++ b/tools/suite_qiime2__quality_filter/qiime2__quality_filter__q_score.xml
@@ -1,6 +1,6 @@
 <?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)
 -->
@@ -23,11 +23,10 @@ for:
     <inputs>
         <param name="demux" type="data" format="qza" label="demux: SampleData[SequencesWithQuality | PairedEndSequencesWithQuality]¹ | SampleData[JoinedSequencesWithQuality]²" help="[required]  The demultiplexed sequence data to be quality filtered.">
             <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 | PairedEndSequencesWithQuality]"/>
                 <filter type="add_value" value="SampleData[JoinedSequencesWithQuality]"/>
             </options>
-            <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['SampleData[JoinedSequencesWithQuality]', 'SampleData[SequencesWithQuality]', 'SampleData[PairedEndSequencesWithQuality]']</validator>
+            <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['SampleData[JoinedSequencesWithQuality]', 'SampleData[SequencesWithQuality | PairedEndSequencesWithQuality]']</validator>
         </param>
         <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">
             <param name="min_quality" type="integer" value="4" label="min_quality: Int" help="[default: 4]  The minimum acceptable PHRED score. All PHRED scores less that this value are considered to be low PHRED scores."/>
diff --git a/tools/suite_qiime2__quality_filter/test-data/q_score.test0.demuxed-seqs.qza b/tools/suite_qiime2__quality_filter/test-data/q_score.test0.demuxed-seqs.qza
index 347e642..b997b18 100644
Binary files a/tools/suite_qiime2__quality_filter/test-data/q_score.test0.demuxed-seqs.qza and b/tools/suite_qiime2__quality_filter/test-data/q_score.test0.demuxed-seqs.qza differ
diff --git a/tools/suite_qiime2__sample_classifier/qiime2__sample_classifier__classify_samples.xml b/tools/suite_qiime2__sample_classifier/qiime2__sample_classifier__classify_samples.xml
index f6adaa1..921b4d8 100644
--- a/tools/suite_qiime2__sample_classifier/qiime2__sample_classifier__classify_samples.xml
+++ b/tools/suite_qiime2__sample_classifier/qiime2__sample_classifier__classify_samples.xml
@@ -1,6 +1,6 @@
 <?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)
 -->
diff --git a/tools/suite_qiime2__sample_classifier/qiime2__sample_classifier__classify_samples_from_dist.xml b/tools/suite_qiime2__sample_classifier/qiime2__sample_classifier__classify_samples_from_dist.xml
index b984bec..7ad36d8 100644
--- a/tools/suite_qiime2__sample_classifier/qiime2__sample_classifier__classify_samples_from_dist.xml
+++ b/tools/suite_qiime2__sample_classifier/qiime2__sample_classifier__classify_samples_from_dist.xml
@@ -1,6 +1,6 @@
 <?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)
 -->
diff --git a/tools/suite_qiime2__sample_classifier/qiime2__sample_classifier__classify_samples_ncv.xml b/tools/suite_qiime2__sample_classifier/qiime2__sample_classifier__classify_samples_ncv.xml
index 1a865ba..522485d 100644
--- a/tools/suite_qiime2__sample_classifier/qiime2__sample_classifier__classify_samples_ncv.xml
+++ b/tools/suite_qiime2__sample_classifier/qiime2__sample_classifier__classify_samples_ncv.xml
@@ -1,6 +1,6 @@
 <?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)
 -->
diff --git a/tools/suite_qiime2__sample_classifier/qiime2__sample_classifier__confusion_matrix.xml b/tools/suite_qiime2__sample_classifier/qiime2__sample_classifier__confusion_matrix.xml
index 3e350a9..6f2ece3 100644
--- a/tools/suite_qiime2__sample_classifier/qiime2__sample_classifier__confusion_matrix.xml
+++ b/tools/suite_qiime2__sample_classifier/qiime2__sample_classifier__confusion_matrix.xml
@@ -1,6 +1,6 @@
 <?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)
 -->
diff --git a/tools/suite_qiime2__sample_classifier/qiime2__sample_classifier__fit_classifier.xml b/tools/suite_qiime2__sample_classifier/qiime2__sample_classifier__fit_classifier.xml
index dbae394..4227b27 100644
--- a/tools/suite_qiime2__sample_classifier/qiime2__sample_classifier__fit_classifier.xml
+++ b/tools/suite_qiime2__sample_classifier/qiime2__sample_classifier__fit_classifier.xml
@@ -1,6 +1,6 @@
 <?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)
 -->
diff --git a/tools/suite_qiime2__sample_classifier/qiime2__sample_classifier__fit_regressor.xml b/tools/suite_qiime2__sample_classifier/qiime2__sample_classifier__fit_regressor.xml
index d458a9b..395205d 100644
--- a/tools/suite_qiime2__sample_classifier/qiime2__sample_classifier__fit_regressor.xml
+++ b/tools/suite_qiime2__sample_classifier/qiime2__sample_classifier__fit_regressor.xml
@@ -1,6 +1,6 @@
 <?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)
 -->
diff --git a/tools/suite_qiime2__sample_classifier/qiime2__sample_classifier__heatmap.xml b/tools/suite_qiime2__sample_classifier/qiime2__sample_classifier__heatmap.xml
index 32d99c3..099e234 100644
--- a/tools/suite_qiime2__sample_classifier/qiime2__sample_classifier__heatmap.xml
+++ b/tools/suite_qiime2__sample_classifier/qiime2__sample_classifier__heatmap.xml
@@ -1,6 +1,6 @@
 <?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)
 -->
diff --git a/tools/suite_qiime2__sample_classifier/qiime2__sample_classifier__metatable.xml b/tools/suite_qiime2__sample_classifier/qiime2__sample_classifier__metatable.xml
index b18a155..1b08f25 100644
--- a/tools/suite_qiime2__sample_classifier/qiime2__sample_classifier__metatable.xml
+++ b/tools/suite_qiime2__sample_classifier/qiime2__sample_classifier__metatable.xml
@@ -1,6 +1,6 @@
 <?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)
 -->
diff --git a/tools/suite_qiime2__sample_classifier/qiime2__sample_classifier__predict_classification.xml b/tools/suite_qiime2__sample_classifier/qiime2__sample_classifier__predict_classification.xml
index 2459d43..2572af4 100644
--- a/tools/suite_qiime2__sample_classifier/qiime2__sample_classifier__predict_classification.xml
+++ b/tools/suite_qiime2__sample_classifier/qiime2__sample_classifier__predict_classification.xml
@@ -1,6 +1,6 @@
 <?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)
 -->
diff --git a/tools/suite_qiime2__sample_classifier/qiime2__sample_classifier__predict_regression.xml b/tools/suite_qiime2__sample_classifier/qiime2__sample_classifier__predict_regression.xml
index 724343d..eaac067 100644
--- a/tools/suite_qiime2__sample_classifier/qiime2__sample_classifier__predict_regression.xml
+++ b/tools/suite_qiime2__sample_classifier/qiime2__sample_classifier__predict_regression.xml
@@ -1,6 +1,6 @@
 <?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)
 -->
diff --git a/tools/suite_qiime2__sample_classifier/qiime2__sample_classifier__regress_samples.xml b/tools/suite_qiime2__sample_classifier/qiime2__sample_classifier__regress_samples.xml
index b81165b..be7b5f9 100644
--- a/tools/suite_qiime2__sample_classifier/qiime2__sample_classifier__regress_samples.xml
+++ b/tools/suite_qiime2__sample_classifier/qiime2__sample_classifier__regress_samples.xml
@@ -1,6 +1,6 @@
 <?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)
 -->
diff --git a/tools/suite_qiime2__sample_classifier/qiime2__sample_classifier__regress_samples_ncv.xml b/tools/suite_qiime2__sample_classifier/qiime2__sample_classifier__regress_samples_ncv.xml
index 1578d71..6ecbf01 100644
--- a/tools/suite_qiime2__sample_classifier/qiime2__sample_classifier__regress_samples_ncv.xml
+++ b/tools/suite_qiime2__sample_classifier/qiime2__sample_classifier__regress_samples_ncv.xml
@@ -1,6 +1,6 @@
 <?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)
 -->
diff --git a/tools/suite_qiime2__sample_classifier/qiime2__sample_classifier__scatterplot.xml b/tools/suite_qiime2__sample_classifier/qiime2__sample_classifier__scatterplot.xml
index b6af4a2..e4c1d53 100644
--- a/tools/suite_qiime2__sample_classifier/qiime2__sample_classifier__scatterplot.xml
+++ b/tools/suite_qiime2__sample_classifier/qiime2__sample_classifier__scatterplot.xml
@@ -1,6 +1,6 @@
 <?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)
 -->
diff --git a/tools/suite_qiime2__sample_classifier/qiime2__sample_classifier__split_table.xml b/tools/suite_qiime2__sample_classifier/qiime2__sample_classifier__split_table.xml
index 9fbe097..83e4eaa 100644
--- a/tools/suite_qiime2__sample_classifier/qiime2__sample_classifier__split_table.xml
+++ b/tools/suite_qiime2__sample_classifier/qiime2__sample_classifier__split_table.xml
@@ -1,6 +1,6 @@
 <?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)
 -->
@@ -23,11 +23,11 @@ for:
     <inputs>
         <param name="table" type="data" format="qza" label="table: FeatureTable[Frequency¹ | RelativeFrequency² | PresenceAbsence³ | Balance⁴ | PercentileNormalized⁵ | Design⁶]" help="[required]  Feature table containing all features that should be used for target prediction.">
             <options options_filter_attribute="metadata.semantic_type">
-                <filter type="add_value" value="FeatureTable[Balance]"/>
-                <filter type="add_value" value="FeatureTable[PercentileNormalized]"/>
-                <filter type="add_value" value="FeatureTable[Design]"/>
                 <filter type="add_value" value="FeatureTable[RelativeFrequency]"/>
                 <filter type="add_value" value="FeatureTable[PresenceAbsence]"/>
+                <filter type="add_value" value="FeatureTable[Balance]"/>
+                <filter type="add_value" value="FeatureTable[Design]"/>
+                <filter type="add_value" value="FeatureTable[PercentileNormalized]"/>
                 <filter type="add_value" value="FeatureTable[Frequency]"/>
             </options>
             <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureTable[Balance]', 'FeatureTable[Design]', 'FeatureTable[Frequency]', 'FeatureTable[PercentileNormalized]', 'FeatureTable[PresenceAbsence]', 'FeatureTable[RelativeFrequency]']</validator>
diff --git a/tools/suite_qiime2__sample_classifier/qiime2__sample_classifier__summarize.xml b/tools/suite_qiime2__sample_classifier/qiime2__sample_classifier__summarize.xml
index b400100..7dbc86b 100644
--- a/tools/suite_qiime2__sample_classifier/qiime2__sample_classifier__summarize.xml
+++ b/tools/suite_qiime2__sample_classifier/qiime2__sample_classifier__summarize.xml
@@ -1,6 +1,6 @@
 <?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)
 -->
diff --git a/tools/suite_qiime2__taxa/qiime2__taxa__barplot.xml b/tools/suite_qiime2__taxa/qiime2__taxa__barplot.xml
index 2ae1716..23a0d02 100644
--- a/tools/suite_qiime2__taxa/qiime2__taxa__barplot.xml
+++ b/tools/suite_qiime2__taxa/qiime2__taxa__barplot.xml
@@ -1,6 +1,6 @@
 <?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)
 -->
diff --git a/tools/suite_qiime2__taxa/qiime2__taxa__collapse.xml b/tools/suite_qiime2__taxa/qiime2__taxa__collapse.xml
index ec2797f..481e975 100644
--- a/tools/suite_qiime2__taxa/qiime2__taxa__collapse.xml
+++ b/tools/suite_qiime2__taxa/qiime2__taxa__collapse.xml
@@ -1,6 +1,6 @@
 <?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)
 -->
diff --git a/tools/suite_qiime2__taxa/qiime2__taxa__filter_seqs.xml b/tools/suite_qiime2__taxa/qiime2__taxa__filter_seqs.xml
index e4aacc7..6a4e68e 100644
--- a/tools/suite_qiime2__taxa/qiime2__taxa__filter_seqs.xml
+++ b/tools/suite_qiime2__taxa/qiime2__taxa__filter_seqs.xml
@@ -1,6 +1,6 @@
 <?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)
 -->
diff --git a/tools/suite_qiime2__taxa/qiime2__taxa__filter_table.xml b/tools/suite_qiime2__taxa/qiime2__taxa__filter_table.xml
index b9c6599..4e3c642 100644
--- a/tools/suite_qiime2__taxa/qiime2__taxa__filter_table.xml
+++ b/tools/suite_qiime2__taxa/qiime2__taxa__filter_table.xml
@@ -1,6 +1,6 @@
 <?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)
 -->
diff --git a/tools/suite_qiime2__taxa/test-data/barplot.test0.table.qza b/tools/suite_qiime2__taxa/test-data/barplot.test0.table.qza
index 233a916..9b0cba8 100644
Binary files a/tools/suite_qiime2__taxa/test-data/barplot.test0.table.qza and b/tools/suite_qiime2__taxa/test-data/barplot.test0.table.qza differ
diff --git a/tools/suite_qiime2__taxa/test-data/barplot.test0.taxonomy.qza b/tools/suite_qiime2__taxa/test-data/barplot.test0.taxonomy.qza
index 0cfe9a2..8cd6030 100644
Binary files a/tools/suite_qiime2__taxa/test-data/barplot.test0.taxonomy.qza and b/tools/suite_qiime2__taxa/test-data/barplot.test0.taxonomy.qza differ
diff --git a/tools/suite_qiime2__taxa/test-data/collapse.test0.table.qza b/tools/suite_qiime2__taxa/test-data/collapse.test0.table.qza
index 233a916..9b0cba8 100644
Binary files a/tools/suite_qiime2__taxa/test-data/collapse.test0.table.qza and b/tools/suite_qiime2__taxa/test-data/collapse.test0.table.qza differ
diff --git a/tools/suite_qiime2__taxa/test-data/collapse.test0.taxonomy.qza b/tools/suite_qiime2__taxa/test-data/collapse.test0.taxonomy.qza
index 0cfe9a2..8cd6030 100644
Binary files a/tools/suite_qiime2__taxa/test-data/collapse.test0.taxonomy.qza and b/tools/suite_qiime2__taxa/test-data/collapse.test0.taxonomy.qza differ
diff --git a/tools/suite_qiime2__vsearch/qiime2__vsearch__cluster_features_closed_reference.xml b/tools/suite_qiime2__vsearch/qiime2__vsearch__cluster_features_closed_reference.xml
index 80fc621..d120be6 100644
--- a/tools/suite_qiime2__vsearch/qiime2__vsearch__cluster_features_closed_reference.xml
+++ b/tools/suite_qiime2__vsearch/qiime2__vsearch__cluster_features_closed_reference.xml
@@ -1,6 +1,6 @@
 <?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)
 -->
diff --git a/tools/suite_qiime2__vsearch/qiime2__vsearch__cluster_features_de_novo.xml b/tools/suite_qiime2__vsearch/qiime2__vsearch__cluster_features_de_novo.xml
index df7d1f2..c858d67 100644
--- a/tools/suite_qiime2__vsearch/qiime2__vsearch__cluster_features_de_novo.xml
+++ b/tools/suite_qiime2__vsearch/qiime2__vsearch__cluster_features_de_novo.xml
@@ -1,6 +1,6 @@
 <?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)
 -->
diff --git a/tools/suite_qiime2__vsearch/qiime2__vsearch__cluster_features_open_reference.xml b/tools/suite_qiime2__vsearch/qiime2__vsearch__cluster_features_open_reference.xml
index e34fab1..5aeea17 100644
--- a/tools/suite_qiime2__vsearch/qiime2__vsearch__cluster_features_open_reference.xml
+++ b/tools/suite_qiime2__vsearch/qiime2__vsearch__cluster_features_open_reference.xml
@@ -1,6 +1,6 @@
 <?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)
 -->
diff --git a/tools/suite_qiime2__vsearch/qiime2__vsearch__dereplicate_sequences.xml b/tools/suite_qiime2__vsearch/qiime2__vsearch__dereplicate_sequences.xml
index e07a5f1..b877e7a 100644
--- a/tools/suite_qiime2__vsearch/qiime2__vsearch__dereplicate_sequences.xml
+++ b/tools/suite_qiime2__vsearch/qiime2__vsearch__dereplicate_sequences.xml
@@ -1,6 +1,6 @@
 <?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)
 -->
diff --git a/tools/suite_qiime2__vsearch/qiime2__vsearch__fastq_stats.xml b/tools/suite_qiime2__vsearch/qiime2__vsearch__fastq_stats.xml
index 18cffff..4152c19 100644
--- a/tools/suite_qiime2__vsearch/qiime2__vsearch__fastq_stats.xml
+++ b/tools/suite_qiime2__vsearch/qiime2__vsearch__fastq_stats.xml
@@ -1,6 +1,6 @@
 <?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)
 -->
diff --git a/tools/suite_qiime2__vsearch/qiime2__vsearch__merge_pairs.xml b/tools/suite_qiime2__vsearch/qiime2__vsearch__merge_pairs.xml
index 2dfaaa9..5ddde83 100644
--- a/tools/suite_qiime2__vsearch/qiime2__vsearch__merge_pairs.xml
+++ b/tools/suite_qiime2__vsearch/qiime2__vsearch__merge_pairs.xml
@@ -1,6 +1,6 @@
 <?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)
 -->
diff --git a/tools/suite_qiime2__vsearch/qiime2__vsearch__uchime_denovo.xml b/tools/suite_qiime2__vsearch/qiime2__vsearch__uchime_denovo.xml
index e1a68d8..bbc4b25 100644
--- a/tools/suite_qiime2__vsearch/qiime2__vsearch__uchime_denovo.xml
+++ b/tools/suite_qiime2__vsearch/qiime2__vsearch__uchime_denovo.xml
@@ -1,6 +1,6 @@
 <?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)
 -->
diff --git a/tools/suite_qiime2__vsearch/qiime2__vsearch__uchime_ref.xml b/tools/suite_qiime2__vsearch/qiime2__vsearch__uchime_ref.xml
index 5a939fa..4085fe9 100644
--- a/tools/suite_qiime2__vsearch/qiime2__vsearch__uchime_ref.xml
+++ b/tools/suite_qiime2__vsearch/qiime2__vsearch__uchime_ref.xml
@@ -1,6 +1,6 @@
 <?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)
 -->
diff --git a/tools/suite_qiime2_core__tools/qiime2_core__tools__export.xml b/tools/suite_qiime2_core__tools/qiime2_core__tools__export.xml
index 1ba40fc..6cb2d54 100644
--- a/tools/suite_qiime2_core__tools/qiime2_core__tools__export.xml
+++ b/tools/suite_qiime2_core__tools/qiime2_core__tools__export.xml
@@ -1,6 +1,6 @@
 <?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)
 -->
@@ -448,7 +448,7 @@ for:
     </inputs>
     <outputs>
         <collection name="exported" type="list" label="${tool.name} on ${on_string} as ${fmt_peek}">
-            <filter>fmt_finder['output_format'] == 'None' and fmt_peek not in {'QIIME1DemuxFormat', 'DNAFASTAFormat', 'PlacementsDirFmt', 'ImmutableMetadataFormat', 'Bowtie2IndexDirFmt', 'QIIME1DemuxDirFmt', 'AlignedDNASequencesDirectoryFormat', 'DADA2StatsDirFmt', 'AlignedRNASequencesDirectoryFormat', 'OrdinationFormat', 'ProteinFASTAFormat', 'LSMatFormat', 'PairedRNASequencesDirectoryFormat', 'DifferentialFormat', 'MultiplexedPairedEndBarcodeInSequenceDirFmt', 'AlignedProteinFASTAFormat', 'ArtificialGroupingDirectoryFormat', 'RNAFASTAFormat', 'SeppReferenceDirFmt', 'FastqGzFormat', 'ProcrustesStatisticsDirFmt', 'SingleLanePerSampleSingleEndFastqDirFmt', 'QualityFilterStatsFmt', 'PlacementsFormat', 'ProbabilitiesDirectoryFormat', 'ImportanceDirectoryFormat', 'FirstDifferencesFormat', 'TrueTargetsDirectoryFormat', 'ImmutableMetadataDirectoryFormat', 'UchimeStatsDirFmt', 'NewickDirectoryFormat', 'DADA2StatsFormat', 'AlignedDNAFASTAFormat', 'PredictionsDirectoryFormat', 'AlphaDiversityDirectoryFormat', 'MultiplexedSingleEndBarcodeInSequenceDirFmt', 'DeblurStatsDirFmt', 'DNASequencesDirectoryFormat', 'SingleLanePerSamplePairedEndFastqDirFmt', 'UchimeStatsFmt', 'CasavaOneEightSingleLanePerSampleDirFmt', 'ErrorCorrectionDetailsDirFmt', 'BLAST6DirectoryFormat', 'DecontamScoreDirFmt', 'SampleEstimatorDirFmt', 'FirstDifferencesDirectoryFormat', 'QualityFilterStatsDirFmt', 'DistanceMatrixDirectoryFormat', 'DecontamScoreFormat', 'EMPSingleEndDirFmt', 'EMPPairedEndDirFmt', 'DataLoafPackageDirFmt', 'PairedDNASequencesDirectoryFormat', 'BIOMV210DirFmt', 'AlignedRNAFASTAFormat', 'OrdinationDirectoryFormat', 'BIOMV210Format', 'AlphaDiversityFormat', 'ArtificialGroupingFormat', 'DeblurStatsFmt', 'TSVTaxonomyDirectoryFormat', 'PredictionsFormat', 'BooleanSeriesFormat', 'DifferentialDirectoryFormat', 'ProcrustesStatisticsFmt', 'BooleanSeriesDirectoryFormat', 'AlignedProteinSequencesDirectoryFormat', 'TSVTaxonomyFormat', 'NewickFormat', 'ProteinSequencesDirectoryFormat', 'BLAST6Format', 'ImportanceFormat', 'RNASequencesDirectoryFormat', 'TaxonomicClassiferTemporaryPickleDirFmt', 'ProbabilitiesFormat'}</filter>
+            <filter>fmt_finder['output_format'] == 'None' and fmt_peek not in {'NewickDirectoryFormat', 'TrueTargetsDirectoryFormat', 'QIIME1DemuxDirFmt', 'QualityFilterStatsFmt', 'ArtificialGroupingFormat', 'DeblurStatsFmt', 'PlacementsDirFmt', 'DeblurStatsDirFmt', 'DADA2StatsDirFmt', 'AlignedRNAFASTAFormat', 'RNAFASTAFormat', 'ErrorCorrectionDetailsDirFmt', 'DistanceMatrixDirectoryFormat', 'AlignedProteinSequencesDirectoryFormat', 'AlignedProteinFASTAFormat', 'ProteinSequencesDirectoryFormat', 'FirstDifferencesFormat', 'ImportanceDirectoryFormat', 'PairedRNASequencesDirectoryFormat', 'ProbabilitiesFormat', 'ArtificialGroupingDirectoryFormat', 'MultiplexedSingleEndBarcodeInSequenceDirFmt', 'DecontamScoreDirFmt', 'UchimeStatsFmt', 'OrdinationFormat', 'SingleLanePerSampleSingleEndFastqDirFmt', 'AlignedRNASequencesDirectoryFormat', 'PlacementsFormat', 'ProcrustesStatisticsFmt', 'OrdinationDirectoryFormat', 'BLAST6Format', 'DecontamScoreFormat', 'BIOMV210DirFmt', 'PredictionsFormat', 'SampleEstimatorDirFmt', 'DifferentialDirectoryFormat', 'BIOMV210Format', 'Bowtie2IndexDirFmt', 'ImmutableMetadataFormat', 'QIIME1DemuxFormat', 'SingleLanePerSamplePairedEndFastqDirFmt', 'TSVTaxonomyFormat', 'PredictionsDirectoryFormat', 'NewickFormat', 'ProteinFASTAFormat', 'DNAFASTAFormat', 'AlignedDNASequencesDirectoryFormat', 'MultiplexedPairedEndBarcodeInSequenceDirFmt', 'AlphaDiversityFormat', 'TSVTaxonomyDirectoryFormat', 'QualityFilterStatsDirFmt', 'LSMatFormat', 'ProbabilitiesDirectoryFormat', 'AlphaDiversityDirectoryFormat', 'DADA2StatsFormat', 'DNASequencesDirectoryFormat', 'PairedDNASequencesDirectoryFormat', 'DifferentialFormat', 'FirstDifferencesDirectoryFormat', 'ImportanceFormat', 'SeppReferenceDirFmt', 'EMPSingleEndDirFmt', 'TaxonomicClassiferTemporaryPickleDirFmt', 'EMPPairedEndDirFmt', 'CasavaOneEightSingleLanePerSampleDirFmt', 'BooleanSeriesDirectoryFormat', 'AlignedDNAFASTAFormat', 'BooleanSeriesFormat', 'FastqGzFormat', 'DataLoafPackageDirFmt', 'BLAST6DirectoryFormat', 'UchimeStatsDirFmt', 'ProcrustesStatisticsDirFmt', 'RNASequencesDirectoryFormat', 'ImmutableMetadataDirectoryFormat'}</filter>
             <discover_datasets pattern="__designation_and_ext__" visible="false"/>
         </collection>
         <data name="AlignedDNAFASTAFormat" label="${tool.name} on ${on_string} as AlignedDNAFASTAFormat">
@@ -862,78 +862,78 @@ A gzipped fastq file.
 
 Additional formats without documentation:
 *****************************************
- - FirstDifferencesFormat
+ - PairedRNASequencesDirectoryFormat
+ - BooleanSeriesDirectoryFormat
+ - NewickDirectoryFormat
+ - PredictionsFormat
+ - CasavaOneEightSingleLanePerSampleDirFmt
+ - AlignedProteinSequencesDirectoryFormat
+ - DistanceMatrixDirectoryFormat
+ - DeblurStatsDirFmt
+ - DifferentialFormat
+ - ProteinSequencesDirectoryFormat
+ - RNASequencesDirectoryFormat
  - DecontamScoreDirFmt
- - OrdinationDirectoryFormat
+ - MultiplexedPairedEndBarcodeInSequenceDirFmt
+ - AlphaDiversityFormat
+ - DADA2StatsDirFmt
+ - DADA2StatsFormat
  - EMPPairedEndDirFmt
+ - QualityFilterStatsFmt
+ - ArtificialGroupingDirectoryFormat
+ - FirstDifferencesDirectoryFormat
+ - BLAST6DirectoryFormat
+ - TrueTargetsDirectoryFormat
+ - AlignedRNAFASTAFormat
+ - DNASequencesDirectoryFormat
+ - ProcrustesStatisticsDirFmt
+ - QualityFilterStatsDirFmt
+ - ArtificialGroupingFormat
+ - ProbabilitiesFormat
+ - OrdinationDirectoryFormat
+ - SingleLanePerSamplePairedEndFastqDirFmt
  - ImmutableMetadataFormat
- - PredictionsDirectoryFormat
+ - ImportanceFormat
  - AlphaDiversityDirectoryFormat
- - DataLoafPackageDirFmt
  - AlignedDNAFASTAFormat
- - DADA2StatsDirFmt
- - TrueTargetsDirectoryFormat
+ - PredictionsDirectoryFormat
+ - UchimeStatsDirFmt
  - UchimeStatsFmt
  - BLAST6Format
  - PairedDNASequencesDirectoryFormat
+ - NewickFormat
  - QIIME1DemuxDirFmt
- - QualityFilterStatsFmt
- - DADA2StatsFormat
+ - TaxonomicClassiferTemporaryPickleDirFmt
+ - TSVTaxonomyDirectoryFormat
  - AlignedProteinFASTAFormat
- - PlacementsFormat
- - NewickFormat
- - ProbabilitiesDirectoryFormat
- - ErrorCorrectionDetailsDirFmt
+ - DeblurStatsFmt
+ - LSMatFormat
+ - DecontamScoreFormat
  - ProteinFASTAFormat
  - RNAFASTAFormat
+ - EMPSingleEndDirFmt
  - MultiplexedSingleEndBarcodeInSequenceDirFmt
- - BooleanSeriesFormat
- - LSMatFormat
- - ImportanceDirectoryFormat
- - DeblurStatsFmt
+ - FirstDifferencesFormat
+ - DataLoafPackageDirFmt
+ - SeppReferenceDirFmt
  - AlignedRNASequencesDirectoryFormat
- - QualityFilterStatsDirFmt
- - TaxonomicClassiferTemporaryPickleDirFmt
- - BooleanSeriesDirectoryFormat
+ - BIOMV210DirFmt
+ - PlacementsFormat
+ - BooleanSeriesFormat
+ - ProbabilitiesDirectoryFormat
+ - ErrorCorrectionDetailsDirFmt
+ - PlacementsDirFmt
  - DifferentialDirectoryFormat
  - DNAFASTAFormat
  - ProcrustesStatisticsFmt
- - PlacementsDirFmt
- - EMPSingleEndDirFmt
- - DecontamScoreFormat
- - BIOMV210DirFmt
+ - BIOMV210Format
+ - SampleEstimatorDirFmt
  - ImmutableMetadataDirectoryFormat
+ - ImportanceDirectoryFormat
  - AlignedDNASequencesDirectoryFormat
- - TSVTaxonomyDirectoryFormat
  - OrdinationFormat
- - FirstDifferencesDirectoryFormat
- - Bowtie2IndexDirFmt
- - BIOMV210Format
  - SingleLanePerSampleSingleEndFastqDirFmt
- - SampleEstimatorDirFmt
- - PairedRNASequencesDirectoryFormat
- - CasavaOneEightSingleLanePerSampleDirFmt
- - AlignedProteinSequencesDirectoryFormat
- - UchimeStatsDirFmt
- - NewickDirectoryFormat
- - SingleLanePerSamplePairedEndFastqDirFmt
- - DifferentialFormat
- - ProteinSequencesDirectoryFormat
- - RNASequencesDirectoryFormat
- - MultiplexedPairedEndBarcodeInSequenceDirFmt
- - AlphaDiversityFormat
- - DistanceMatrixDirectoryFormat
- - ArtificialGroupingFormat
- - ArtificialGroupingDirectoryFormat
- - ProbabilitiesFormat
- - DeblurStatsDirFmt
- - SeppReferenceDirFmt
- - ImportanceFormat
- - BLAST6DirectoryFormat
- - AlignedRNAFASTAFormat
- - DNASequencesDirectoryFormat
- - ProcrustesStatisticsDirFmt
- - PredictionsFormat
+ - Bowtie2IndexDirFmt
 </help>
     <citations>
         <citation type="doi">10.1038/s41587-019-0209-9</citation>
diff --git a/tools/suite_qiime2_core__tools/qiime2_core__tools__import.xml b/tools/suite_qiime2_core__tools/qiime2_core__tools__import.xml
index c05ed24..84f43a8 100644
--- a/tools/suite_qiime2_core__tools/qiime2_core__tools__import.xml
+++ b/tools/suite_qiime2_core__tools/qiime2_core__tools__import.xml
@@ -1,6 +1,6 @@
 <?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)
 -->
@@ -10,7 +10,7 @@ This tool was automatically generated by:
 for:
     qiime2 (version: 2023.5.1)
 -->
-<tool name="qiime2 tools import" id="qiime2_core__tools__import" version="2023.5.0+dist.h193f7cc9.3" profile="22.05" license="BSD-3-Clause">
+<tool name="qiime2 tools import" id="qiime2_core__tools__import" version="2023.5.0+dist.h193f7cc9.2" profile="22.05" license="BSD-3-Clause">
     <description>Import data into a QIIME 2 artifact</description>
     <requirements>
         <container type="docker">quay.io/qiime2/core:2023.5</container>
@@ -20,7 +20,6 @@ for:
         <configfile name="inputs">&lt;%
 # This is an exercise in cheating the Cheetah
 import json
-from collections.abc import MutableMapping
 
 def expand_collection(collection):
     # All of this work is just to extract the
@@ -29,7 +28,7 @@ def expand_collection(collection):
             for d in collection]
 
 def stringify(obj):
-    if isinstance(obj, MutableMapping):
+    if type(obj) is dict:
         new = {}
         for key, value in obj.items():
             if (key.startswith('__') and key.endswith('__')
@@ -970,7 +969,7 @@ write(json.dumps(inputs))
                                     <option value="individual">Associate individual files</option>
                                 </param>
                                 <when value="collection">
-                                    <param name="elements" type="data_collection" collection_type="list" help="This data should be formatted as a FastqGzFormat. See the documentation below for more information. Elements must match regex: .+_.+_L[0-9][0-9][0-9]_R[12]_001\.fastq\.gz"/>
+                                    <param name="elements" type="data_collection" help="This data should be formatted as a FastqGzFormat. See the documentation below for more information. Elements must match regex: .+_.+_L[0-9][0-9][0-9]_R[12]_001\.fastq\.gz"/>
                                     <conditional name="__q2galaxy__GUI__cond__add_ext__">
                                         <param name="__q2galaxy__GUI__select__ext_pick__" type="select" label="Append an extension?" help="This is needed if your element identifiers lack one.">
                                             <option value="no">No, use element identifiers as is</option>
@@ -1147,7 +1146,7 @@ write(json.dumps(inputs))
                                     <option value="individual">Associate individual files</option>
                                 </param>
                                 <when value="collection">
-                                    <param name="elements" type="data_collection" collection_type="list" help="This data should be formatted as a FastqGzFormat. See the documentation below for more information. Elements must match regex: .+_.+_R[12]_001\.fastq\.gz"/>
+                                    <param name="elements" type="data_collection" help="This data should be formatted as a FastqGzFormat. See the documentation below for more information. Elements must match regex: .+_.+_R[12]_001\.fastq\.gz"/>
                                     <conditional name="__q2galaxy__GUI__cond__add_ext__">
                                         <param name="__q2galaxy__GUI__select__ext_pick__" type="select" label="Append an extension?" help="This is needed if your element identifiers lack one.">
                                             <option value="no">No, use element identifiers as is</option>
@@ -1658,64 +1657,6 @@ write(json.dumps(inputs))
     <outputs>
         <data name="imported_data" format="qza" from_work_dir="imported_data.qza"/>
     </outputs>
-    <tests>
-        <test>
-            <conditional name="import_root">
-                <param name="type" value="SampleData__ob__PairedEndSequencesWithQuality__cb__"/>
-                <conditional name="__q2galaxy__GUI__cond__format__">
-                    <param name="format" value="CasavaOneEightLanelessPerSampleDirFmt"/>
-                    <section name="import_sequences">
-                    <conditional name="__q2galaxy__GUI__cond__sequences__">
-                        <param name="__q2galaxy__GUI__select__picker__" value="collection"/>
-                        <param name="elements">
-                            <collection type="list">
-                                <element name="YY_S49_R1_001.fastq.gz" ftype="fastqsanger.gz" value="YY/YY_S49_R1_001.fastq.gz" />
-                                <element name="YY_S49_R2_001.fastq.gz" ftype="fastqsanger.gz" value="YY/YY_S49_R2_001.fastq.gz" />
-                            </collection>
-                        </param>
-                        <conditional name="__q2galaxy__GUI__cond__add_ext__">
-                            <param name="__q2galaxy__GUI__select__ext_pick__" value="yes"/>
-                            <param name="ext" label="fastq.gz"/>
-                        </conditional>
-                    </conditional>
-                </section>
-                </conditional>
-            </conditional>
-            <output name="imported_data">
-                <assert_contents>
-                    <has_size min="1"/>
-                </assert_contents>
-            </output>
-        </test>
-        <test>
-            <conditional name="import_root">
-                <param name="type" value="SampleData__ob__PairedEndSequencesWithQuality__cb__"/>
-                <conditional name="__q2galaxy__GUI__cond__format__">
-                    <param name="format" value="CasavaOneEightSingleLanePerSampleDirFmt"/>
-                    <section name="import_sequences">
-                    <conditional name="__q2galaxy__GUI__cond__sequences__">
-                        <param name="__q2galaxy__GUI__select__picker__" value="collection"/>
-                        <param name="elements">
-                            <collection type="list">
-                                <element name="YY_S49_L001_R1_001.fastq.gz" ftype="fastqsanger.gz" value="YY/YY_S49_R1_001.fastq.gz" />
-                                <element name="YY_S49_L001_R2_001.fastq.gz" ftype="fastqsanger.gz" value="YY/YY_S49_R2_001.fastq.gz" />
-                            </collection>
-                        </param>
-                        <conditional name="__q2galaxy__GUI__cond__add_ext__">
-                            <param name="__q2galaxy__GUI__select__ext_pick__" value="yes"/>
-                            <param name="ext" label="fastq.gz"/>
-                        </conditional>
-                    </conditional>
-                </section>
-                </conditional>
-            </conditional>
-            <output name="imported_data">
-                <assert_contents>
-                    <has_size min="1"/>
-                </assert_contents>
-            </output>
-        </test>
-    </tests>
     <help>
 QIIME 2: tools import
 =====================
@@ -1747,6 +1688,16 @@ Formats:
 --------
 These formats have documentation available.
 
+SampleIdIndexedSingleEndPerSampleDirFmt
+***************************************
+Single-end reads in fastq.gz files where base filename is the sample id
+
+    The full file name, minus the extension (`.fastq.gz`) is the sample id.
+    For example, the sample id for the file:
+     * `sample-1.fastq.gz` is `sample-1`
+     * `xyz.fastq.gz` is `xyz`
+     * `sample-42_S1_L001_R1_001.fastq.gz` is `sample-42_S1_L001_R1_001`
+
 QIIME1DemuxFormat
 *****************
 QIIME 1 demultiplexed FASTA format.
@@ -1809,76 +1760,66 @@ FastqGzFormat
 A gzipped fastq file.
 
 
-SampleIdIndexedSingleEndPerSampleDirFmt
-***************************************
-Single-end reads in fastq.gz files where base filename is the sample id
-
-    The full file name, minus the extension (`.fastq.gz`) is the sample id.
-    For example, the sample id for the file:
-     * `sample-1.fastq.gz` is `sample-1`
-     * `xyz.fastq.gz` is `xyz`
-     * `sample-42_S1_L001_R1_001.fastq.gz` is `sample-42_S1_L001_R1_001`
-
 Additional formats without documentation:
 *****************************************
- - FirstDifferencesFormat
+ - PairedRNASequencesDirectoryFormat
+ - PredictionsFormat
+ - CasavaOneEightSingleLanePerSampleDirFmt
+ - SingleEndFastqManifestPhred64V2
+ - MultiplexedFastaQualDirFmt
+ - DifferentialFormat
+ - AlphaDiversityFormat
+ - DADA2StatsFormat
+ - MultiplexedPairedEndBarcodeInSequenceDirFmt
+ - PairedEndFastqManifestPhred33
+ - MixedCaseAlignedRNAFASTAFormat
+ - ErrorCorrectionDetailsFmt
+ - EMPPairedEndDirFmt
+ - QualityFilterStatsFmt
+ - SingleEndFastqManifestPhred33
+ - AlignedRNAFASTAFormat
+ - ArtificialGroupingFormat
+ - ProbabilitiesFormat
+ - EMPSingleEndCasavaDirFmt
  - MixedCaseAlignedDNAFASTAFormat
+ - BIOMV100Format
  - SingleLanePerSamplePairedEndFastqDirFmt
- - EMPPairedEndDirFmt
  - ImmutableMetadataFormat
  - PairedEndFastqManifestPhred64V2
- - DataLoafPackageDirFmt
+ - ImportanceFormat
  - AlignedDNAFASTAFormat
- - BIOMV100Format
  - UchimeStatsFmt
  - BLAST6Format
  - PairedDNASequencesDirectoryFormat
+ - NewickFormat
  - SingleEndFastqManifestPhred33V2
- - QualityFilterStatsFmt
- - DADA2StatsFormat
+ - TaxonomicClassiferTemporaryPickleDirFmt
  - AlignedProteinFASTAFormat
  - MixedCaseRNAFASTAFormat
- - PlacementsFormat
- - NewickFormat
+ - LSMatFormat
+ - DeblurStatsFmt
  - PairedEndFastqManifestPhred64
+ - DecontamScoreFormat
  - ProteinFASTAFormat
  - RNAFASTAFormat
- - BooleanSeriesFormat
+ - EMPSingleEndDirFmt
  - SingleEndFastqManifestPhred64
- - LSMatFormat
- - DeblurStatsFmt
- - ErrorCorrectionDetailsFmt
+ - FirstDifferencesFormat
+ - DataLoafPackageDirFmt
+ - SeppReferenceDirFmt
  - MixedCaseDNAFASTAFormat
- - TaxonomicClassiferTemporaryPickleDirFmt
+ - PlacementsFormat
+ - BooleanSeriesFormat
+ - PairedEndFastqManifestPhred33V2
  - DNAFASTAFormat
  - ProcrustesStatisticsFmt
+ - BIOMV210Format
  - CasavaOneEightLanelessPerSampleDirFmt
- - EMPSingleEndDirFmt
- - DecontamScoreFormat
+ - SampleEstimatorDirFmt
  - OrdinationFormat
  - SingleLanePerSampleSingleEndFastqDirFmt
  - Bowtie2IndexDirFmt
- - BIOMV210Format
- - PairedEndFastqManifestPhred33V2
- - SampleEstimatorDirFmt
- - EMPSingleEndCasavaDirFmt
- - PairedRNASequencesDirectoryFormat
  - EMPPairedEndCasavaDirFmt
- - CasavaOneEightSingleLanePerSampleDirFmt
- - SingleEndFastqManifestPhred64V2
- - MultiplexedFastaQualDirFmt
- - DifferentialFormat
- - AlphaDiversityFormat
- - MultiplexedPairedEndBarcodeInSequenceDirFmt
- - PairedEndFastqManifestPhred33
- - ArtificialGroupingFormat
- - ProbabilitiesFormat
- - SeppReferenceDirFmt
- - MixedCaseAlignedRNAFASTAFormat
- - SingleEndFastqManifestPhred33
- - ImportanceFormat
- - AlignedRNAFASTAFormat
- - PredictionsFormat
 </help>
     <citations>
         <citation type="doi">10.1038/s41587-019-0209-9</citation>
diff --git a/tools/suite_qiime2_core__tools/test-data/YY/YY_S49_R1_001.fastq.gz b/tools/suite_qiime2_core__tools/test-data/YY/YY_S49_R1_001.fastq.gz
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diff --git a/tools/suite_qiime2_core__tools/test-data/YY/YY_S49_R2_001.fastq.gz b/tools/suite_qiime2_core__tools/test-data/YY/YY_S49_R2_001.fastq.gz
deleted file mode 100644
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