Mercurial > repos > q2d2 > qiime2__dada2__denoise_single
changeset 8:1601b340fb81 draft default tip
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 commit 64ed09f1f1c680ad8373d261bd6be43a4f8a8d5b
| author | q2d2 |
|---|---|
| date | Sat, 01 Nov 2025 17:10:17 +0000 |
| parents | be83e72c1ee9 |
| children | |
| files | qiime2__dada2__denoise_single.xml test-data/denoise_paired.test0.demux-paired.qza test-data/denoise_single.test0.demux-single.qza |
| diffstat | 3 files changed, 15 insertions(+), 6 deletions(-) [+] |
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--- a/qiime2__dada2__denoise_single.xml Tue Jul 15 21:48:40 2025 +0000 +++ b/qiime2__dada2__denoise_single.xml Sat Nov 01 17:10:17 2025 +0000 @@ -6,17 +6,17 @@ --> <!-- This tool was automatically generated by: - q2galaxy (version: 2025.7.0) + q2galaxy (version: 2025.10.0) for: - qiime2 (version: 2025.7.0) + qiime2 (version: 2025.10.0) --> -<tool name="qiime2 dada2 denoise-single" id="qiime2__dada2__denoise_single" version="2025.7.0+q2galaxy.2025.7.0" profile="22.05" license="BSD-3-Clause"> +<tool name="qiime2 dada2 denoise-single" id="qiime2__dada2__denoise_single" version="2025.10.0+q2galaxy.2025.10.0" profile="22.05" license="BSD-3-Clause"> <description>Denoise and dereplicate single-end sequences</description> <xrefs> <xref type="bio.tools">qiime2</xref> </xrefs> <requirements> - <container type="docker">quay.io/qiime2/amplicon:2025.7</container> + <container type="docker">quay.io/qiime2/amplicon:2025.10</container> </requirements> <version_command>q2galaxy version dada2</version_command> <command detect_errors="exit_code">q2galaxy run dada2 denoise_single '$inputs'</command> @@ -26,8 +26,8 @@ <inputs> <param name="demultiplexed_seqs" type="data" format="qza" label="demultiplexed_seqs: SampleData[SequencesWithQuality | PairedEndSequencesWithQuality]" help="[required] The single-end demultiplexed sequences to be denoised."> <options options_filter_attribute="metadata.semantic_type"> + <filter type="add_value" value="SampleData[SequencesWithQuality]"/> <filter type="add_value" value="SampleData[PairedEndSequencesWithQuality]"/> - <filter type="add_value" value="SampleData[SequencesWithQuality]"/> </options> <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['SampleData[PairedEndSequencesWithQuality]', 'SampleData[SequencesWithQuality]']</validator> </param> @@ -55,6 +55,7 @@ <data name="table" format="qza" label="${tool.name} on ${on_string}: table.qza" from_work_dir="table.qza"/> <data name="representative_sequences" format="qza" label="${tool.name} on ${on_string}: representative_sequences.qza" from_work_dir="representative_sequences.qza"/> <data name="denoising_stats" format="qza" label="${tool.name} on ${on_string}: denoising_stats.qza" from_work_dir="denoising_stats.qza"/> + <data name="base_transition_stats" format="qza" label="${tool.name} on ${on_string}: base_transition_stats.qza" from_work_dir="base_transition_stats.qza"/> </outputs> <tests> <test> @@ -82,6 +83,13 @@ </has_archive_member> </assert_contents> </output> + <output name="base_transition_stats" ftype="qza"> + <assert_contents> + <has_archive_member path="[0-9a-f]{8}-[0-9a-f]{4}-[4][0-9a-f]{3}-[89ab][0-9a-f]{3}-[0-9a-f]{12}\/metadata.yaml"> + <has_line_matching expression="type: DADA2BaseTransitionStats"/> + </has_archive_member> + </assert_contents> + </output> </test> </tests> <help> @@ -94,7 +102,8 @@ -------- :table.qza: The resulting feature table. :representative_sequences.qza: The resulting feature sequences. Each feature in the feature table will be represented by exactly one sequence. -:denoising_stats.qza: <no description> +:denoising_stats.qza: A table listing per-sample read retention counts and percentages after each stage of the pipeline. +:base_transition_stats.qza: A table listing the transition rates of each ordered pair of nucleotides at each quality score. |