| Previous changeset 0:4218e3146518 (2022-08-29) Next changeset 2:06bacd08bb47 (2023-06-08) |
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Commit message:
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 commit 69da7976573cc07a363ac66bdacc9269d7cd3732 |
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modified:
qiime2__dada2__denoise_paired.xml |
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added:
test-data/denoise_paired.test0.demux-paired.qza test-data/denoise_single.test0.demux-single.qza |
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removed:
test-data/.gitkeep |
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| diff -r 4218e3146518 -r bbaba1707475 qiime2__dada2__denoise_paired.xml --- a/qiime2__dada2__denoise_paired.xml Mon Aug 29 19:23:50 2022 +0000 +++ b/qiime2__dada2__denoise_paired.xml Fri Jan 13 22:42:24 2023 +0000 |
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| @@ -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-paired" id="qiime2__dada2__denoise_paired" version="2022.8.0+q2galaxy.2022.8.1.2" profile="22.05" license="BSD-3-Clause"> +<tool name="qiime2 dada2 denoise-paired" id="qiime2__dada2__denoise_paired" version="2022.11.2+q2galaxy.2022.11.1.2" profile="22.05" license="BSD-3-Clause"> <description>Denoise and dereplicate paired-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_paired '$inputs'</command> + <command detect_errors="exit_code">q2galaxy run dada2 denoise_paired '$inputs'</command> <configfiles> <inputs name="inputs" data_style="paths"/> </configfiles> @@ -57,7 +57,34 @@ <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_paired.test0.demux-paired.qza" ftype="qza"/> + <param name="trunc_len_f" value="150"/> + <param name="trunc_len_r" value="140"/> + <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-paired ============================= @@ -76,6 +103,18 @@ ------------ This method denoises paired-end sequences, dereplicates them, and filters chimeras. +Examples: +--------- + +denoise_paired +************** +Using the ``qiime2 dada2 denoise-paired`` tool: + #. Set *"demultiplexed_seqs"* to ``#: demux-paired.qza`` + #. Set *"trunc_len_f"* to ``150`` + #. Set *"trunc_len_r"* to ``140`` + #. Press the ``Execute`` button. + + | |
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| diff -r 4218e3146518 -r bbaba1707475 test-data/denoise_single.test0.demux-single.qza |
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