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q2d2 committed Jan 29, 2024
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2 changes: 1 addition & 1 deletion tools/suite_qiime2__alignment/qiime2__alignment__mafft.xml
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<?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)
-->
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2 changes: 1 addition & 1 deletion tools/suite_qiime2__alignment/qiime2__alignment__mafft_add.xml
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<?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)
-->
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2 changes: 1 addition & 1 deletion tools/suite_qiime2__alignment/qiime2__alignment__mask.xml
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<?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)
-->
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2 changes: 1 addition & 1 deletion tools/suite_qiime2__composition/qiime2__composition__add_pseudocount.xml
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<?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)
-->
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2 changes: 1 addition & 1 deletion tools/suite_qiime2__composition/qiime2__composition__ancom.xml
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<?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)
-->
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2 changes: 1 addition & 1 deletion tools/suite_qiime2__composition/qiime2__composition__ancombc.xml
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<?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)
-->
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2 changes: 1 addition & 1 deletion tools/suite_qiime2__composition/qiime2__composition__da_barplot.xml
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<?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)
-->
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2 changes: 1 addition & 1 deletion tools/suite_qiime2__composition/qiime2__composition__tabulate.xml
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<?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)
-->
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2 changes: 1 addition & 1 deletion tools/suite_qiime2__cutadapt/qiime2__cutadapt__demux_paired.xml
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<?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)
-->
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2 changes: 1 addition & 1 deletion tools/suite_qiime2__cutadapt/qiime2__cutadapt__demux_single.xml
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<?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)
-->
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2 changes: 1 addition & 1 deletion tools/suite_qiime2__cutadapt/qiime2__cutadapt__trim_paired.xml
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<?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)
-->
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2 changes: 1 addition & 1 deletion tools/suite_qiime2__cutadapt/qiime2__cutadapt__trim_single.xml
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<?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)
-->
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2 changes: 1 addition & 1 deletion tools/suite_qiime2__dada2/qiime2__dada2__denoise_ccs.xml
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<?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)
-->
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2 changes: 1 addition & 1 deletion tools/suite_qiime2__dada2/qiime2__dada2__denoise_paired.xml
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<?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)
-->
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2 changes: 1 addition & 1 deletion tools/suite_qiime2__dada2/qiime2__dada2__denoise_pyro.xml
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<?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)
-->
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4 changes: 2 additions & 2 deletions tools/suite_qiime2__dada2/qiime2__dada2__denoise_single.xml
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<?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)
-->
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<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>
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4 changes: 2 additions & 2 deletions tools/suite_qiime2__deblur/qiime2__deblur__denoise_16S.xml
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<?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)
-->
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<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[SequencesWithQuality]"/>
<filter type="add_value" value="SampleData[PairedEndSequencesWithQuality]"/>
<filter type="add_value" value="SampleData[JoinedSequencesWithQuality]"/>
<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>
</param>
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4 changes: 2 additions & 2 deletions tools/suite_qiime2__deblur/qiime2__deblur__denoise_other.xml
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<?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)
-->
Expand All @@ -23,9 +23,9 @@ 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[SequencesWithQuality]"/>
<filter type="add_value" value="SampleData[PairedEndSequencesWithQuality]"/>
<filter type="add_value" value="SampleData[JoinedSequencesWithQuality]"/>
<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>
</param>
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2 changes: 1 addition & 1 deletion tools/suite_qiime2__deblur/qiime2__deblur__visualize_stats.xml
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<?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)
-->
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2 changes: 1 addition & 1 deletion tools/suite_qiime2__demux/qiime2__demux__emp_paired.xml
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<?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)
-->
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2 changes: 1 addition & 1 deletion tools/suite_qiime2__demux/qiime2__demux__emp_single.xml
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<?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)
-->
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4 changes: 2 additions & 2 deletions tools/suite_qiime2__demux/qiime2__demux__filter_samples.xml
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<?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)
-->
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<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>
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2 changes: 1 addition & 1 deletion tools/suite_qiime2__demux/qiime2__demux__subsample_paired.xml
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<?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)
-->
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4 changes: 2 additions & 2 deletions tools/suite_qiime2__demux/qiime2__demux__subsample_single.xml
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<?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)
-->
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<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>
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4 changes: 2 additions & 2 deletions tools/suite_qiime2__demux/qiime2__demux__summarize.xml
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<?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)
-->
Expand All @@ -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>
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2 changes: 1 addition & 1 deletion tools/suite_qiime2__diversity/qiime2__diversity__adonis.xml
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<?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)
-->
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4 changes: 2 additions & 2 deletions tools/suite_qiime2__diversity/qiime2__diversity__alpha.xml
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<?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)
-->
Expand All @@ -24,8 +24,8 @@ for:
<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[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>
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2 changes: 1 addition & 1 deletion tools/suite_qiime2__diversity/qiime2__diversity__alpha_correlation.xml
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<?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)
-->
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2 changes: 1 addition & 1 deletion tools/suite_qiime2__diversity/qiime2__diversity__alpha_group_significance.xml
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<?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)
-->
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4 changes: 2 additions & 2 deletions tools/suite_qiime2__diversity/qiime2__diversity__alpha_phylogenetic.xml
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<?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)
-->
Expand All @@ -24,8 +24,8 @@ for:
<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[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>
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2 changes: 1 addition & 1 deletion tools/suite_qiime2__diversity/qiime2__diversity__alpha_rarefaction.xml
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<?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)
-->
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4 changes: 2 additions & 2 deletions tools/suite_qiime2__diversity/qiime2__diversity__beta.xml
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<?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)
-->
Expand All @@ -24,8 +24,8 @@ for:
<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[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>
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2 changes: 1 addition & 1 deletion tools/suite_qiime2__diversity/qiime2__diversity__beta_correlation.xml
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<?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)
-->
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2 changes: 1 addition & 1 deletion tools/suite_qiime2__diversity/qiime2__diversity__beta_group_significance.xml
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<?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)
-->
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4 changes: 2 additions & 2 deletions tools/suite_qiime2__diversity/qiime2__diversity__beta_phylogenetic.xml
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<?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)
-->
Expand All @@ -24,8 +24,8 @@ for:
<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[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>
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2 changes: 1 addition & 1 deletion tools/suite_qiime2__diversity/qiime2__diversity__beta_rarefaction.xml
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<?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)
-->
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2 changes: 1 addition & 1 deletion tools/suite_qiime2__diversity/qiime2__diversity__bioenv.xml
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<?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)
-->
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