Mercurial > repos > q2d2 > qiime2__dada2__denoise_single
changeset 1:3c8340e400df draft
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 commit 69da7976573cc07a363ac66bdacc9269d7cd3732
| author | q2d2 |
|---|---|
| date | Fri, 13 Jan 2023 22:42:17 +0000 |
| parents | dba6cccafa22 |
| children | e7812ca89033 |
| files | qiime2__dada2__denoise_single.xml test-data/.gitkeep test-data/denoise_paired.test0.demux-paired.qza test-data/denoise_single.test0.demux-single.qza |
| diffstat | 3 files changed, 49 insertions(+), 7 deletions(-) [+] |
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--- a/qiime2__dada2__denoise_single.xml Mon Aug 29 19:24:35 2022 +0000 +++ b/qiime2__dada2__denoise_single.xml Fri Jan 13 22:42:17 2023 +0000 @@ -1,22 +1,22 @@ <?xml version='1.0' encoding='utf-8'?> <!-- -Copyright (c) 2022, QIIME 2 development team. +Copyright (c) 2023, QIIME 2 development team. Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> <!-- This tool was automatically generated by: - q2galaxy (version: 2022.8.1) + q2galaxy (version: 2022.11.1) for: - qiime2 (version: 2022.8.1) + qiime2 (version: 2022.11.1) --> -<tool name="qiime2 dada2 denoise-single" id="qiime2__dada2__denoise_single" version="2022.8.0+q2galaxy.2022.8.1.2" profile="22.05" license="BSD-3-Clause"> +<tool name="qiime2 dada2 denoise-single" id="qiime2__dada2__denoise_single" version="2022.11.2+q2galaxy.2022.11.1.2" profile="22.05" license="BSD-3-Clause"> <description>Denoise and dereplicate single-end sequences</description> <requirements> - <container type="docker">quay.io/qiime2/core:2022.8</container> + <container type="docker">quay.io/qiime2/core:2022.11</container> </requirements> <version_command>q2galaxy version dada2</version_command> - <command detect_errors="aggressive">q2galaxy run dada2 denoise_single '$inputs'</command> + <command detect_errors="exit_code">q2galaxy run dada2 denoise_single '$inputs'</command> <configfiles> <inputs name="inputs" data_style="paths"/> </configfiles> @@ -54,7 +54,34 @@ <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"/> </outputs> - <tests/> + <tests> + <test> + <param name="demultiplexed_seqs" value="denoise_single.test0.demux-single.qza" ftype="qza"/> + <param name="trunc_len" value="120"/> + <param name="trim_left" value="0"/> + <output name="representative_sequences" 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: FeatureData\[Sequence\]"/> + </has_archive_member> + </assert_contents> + </output> + <output name="table" 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: FeatureTable\[Frequency\]"/> + </has_archive_member> + </assert_contents> + </output> + <output name="denoising_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: SampleData\[DADA2Stats\]"/> + </has_archive_member> + </assert_contents> + </output> + </test> + </tests> <help> QIIME 2: dada2 denoise-single ============================= @@ -73,6 +100,21 @@ ------------ This method denoises single-end sequences, dereplicates them, and filters chimeras. +Examples: +--------- + +denoise_single +************** +Using the ``qiime2 dada2 denoise-single`` tool: + #. Set *"demultiplexed_seqs"* to ``#: demux-single.qza`` + #. Set *"trunc_len"* to ``120`` + #. Expand the ``additional options`` section + + - Leave *"trim_left"* as its default value of ``0`` + + #. Press the ``Execute`` button. + + |