Mercurial > repos > q2d2 > qiime2__dada2__denoise_ccs
changeset 6:1eb5c20bf4cf draft default tip
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 commit b1fccfb38b4873cd4699743033449014a2978e7d
| author | q2d2 |
|---|---|
| date | Mon, 05 May 2025 18:42:15 +0000 (2 days ago) |
| parents | e73ff752eb45 |
| children | |
| files | qiime2__dada2__denoise_ccs.xml test-data/denoise_paired.test0.demux-paired.qza test-data/denoise_single.test0.demux-single.qza |
| diffstat | 3 files changed, 7 insertions(+), 7 deletions(-) [+] |
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--- a/qiime2__dada2__denoise_ccs.xml Wed Oct 30 19:36:49 2024 +0000 +++ b/qiime2__dada2__denoise_ccs.xml Mon May 05 18:42:15 2025 +0000 @@ -1,22 +1,22 @@ <?xml version='1.0' encoding='utf-8'?> <!-- -Copyright (c) 2024, QIIME 2 development team. +Copyright (c) 2025, 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: 2024.10.0) + q2galaxy (version: 2025.4.0) for: - qiime2 (version: 2024.10.1) + qiime2 (version: 2025.4.0) --> -<tool name="qiime2 dada2 denoise-ccs" id="qiime2__dada2__denoise_ccs" version="2024.10.0+q2galaxy.2024.10.0" profile="22.05" license="BSD-3-Clause"> +<tool name="qiime2 dada2 denoise-ccs" id="qiime2__dada2__denoise_ccs" version="2025.4.0+q2galaxy.2025.4.0" profile="22.05" license="BSD-3-Clause"> <description>Denoise and dereplicate single-end Pacbio CCS</description> <xrefs> <xref type="bio.tools">qiime2</xref> </xrefs> <requirements> - <container type="docker">quay.io/qiime2/amplicon:2024.10</container> + <container type="docker">quay.io/qiime2/amplicon:2025.4</container> </requirements> <version_command>q2galaxy version dada2</version_command> <command detect_errors="exit_code">q2galaxy run dada2 denoise_ccs '$inputs'</command> @@ -65,10 +65,9 @@ <option value="independent" selected="true">independent</option> <option value="pseudo">pseudo</option> </param> - <param name="chimera_method" type="select" label="chimera_method: Str % Choices('consensus', 'none', 'pooled')" display="radio"> + <param name="chimera_method" type="select" label="chimera_method: Str % Choices('consensus', 'none')" display="radio"> <option value="consensus" selected="true">consensus</option> <option value="none">none</option> - <option value="pooled">pooled</option> </param> <param name="min_fold_parent_over_abundance" type="float" value="3.5" label="min_fold_parent_over_abundance: Float" help="[default: 3.5] The minimum abundance of potential parents of a sequence being tested as chimeric, expressed as a fold-change versus the abundance of the sequence being tested. Values should be greater than or equal to 1 (i.e. parents should be more abundant than the sequence being tested). Suggest 3.5. This parameter has no effect if chimera_method is "none"."/> <param name="allow_one_off" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" label="allow_one_off: Bool" help="[default: No] Bimeras that are one-off from exact are also identified if the `allow_one_off` argument is True. If True, a sequence will be identified as bimera if it is one mismatch or indel away from an exact bimera."/> @@ -106,6 +105,7 @@ </help> <citations> + <citation type="doi">10.1093/nar/gkz569</citation> <citation type="doi">10.1038/nmeth.3869</citation> <citation type="doi">10.1038/s41587-019-0209-9</citation> </citations>