Mercurial > repos > q2d2 > qiime2__rescript__get_midori2_data
changeset 0:826e62af85a9 draft default tip
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 9436cc47c72b58a6a3d3a5c2ee075689c2926ef0
| author | q2d2 |
|---|---|
| date | Tue, 15 Jul 2025 22:04:09 +0000 |
| parents | |
| children | |
| files | qiime2__rescript__get_midori2_data.xml test-data/.gitkeep |
| diffstat | 1 files changed, 100 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2__rescript__get_midori2_data.xml Tue Jul 15 22:04:09 2025 +0000 @@ -0,0 +1,100 @@ +<?xml version='1.0' encoding='utf-8'?> +<!-- +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: 2025.7.0) +for: + qiime2 (version: 2025.7.0) +--> +<tool name="qiime2 rescript get-midori2-data" id="qiime2__rescript__get_midori2_data" version="2025.7.0+q2galaxy.2025.7.0" profile="22.05" license="BSD-3-Clause"> + <description>Download and import MIDORI 2 reference data.</description> + <xrefs> + <xref type="bio.tools">qiime2</xref> + </xrefs> + <requirements> + <container type="docker">quay.io/qiime2/amplicon:2025.7</container> + </requirements> + <version_command>q2galaxy version rescript</version_command> + <command detect_errors="exit_code">q2galaxy run rescript get_midori2_data '$inputs'</command> + <configfiles> + <inputs name="inputs" data_style="staging_path_and_source_path"/> + </configfiles> + <inputs> + <repeat name="mito_gene" min="1" help="[required] Download the mitochondrial gene(s) of interest. Specify the respective gene(s), or download all genes using 'all'." title="mito_gene: List[Str % Choices('A6', 'A8', 'CO1', 'CO2', 'CO3', 'Cytb', 'ND1', 'ND2', 'ND3', 'ND4L', 'ND4', 'ND5', 'ND6', 'lrRNA', 'srRNA', 'all')]"> + <param name="element" type="select" label="element: Str % Choices('A6', 'A8', 'CO1', 'CO2', 'CO3', 'Cytb', 'ND1', 'ND2', 'ND3', 'ND4L', 'ND4', 'ND5', 'ND6', 'lrRNA', 'srRNA', 'all')"> + <option value="__q2galaxy__::literal::None">Selection required</option> + <option value="A6">A6</option> + <option value="A8">A8</option> + <option value="CO1">CO1</option> + <option value="CO2">CO2</option> + <option value="CO3">CO3</option> + <option value="Cytb">Cytb</option> + <option value="ND1">ND1</option> + <option value="ND2">ND2</option> + <option value="ND3">ND3</option> + <option value="ND4L">ND4L</option> + <option value="ND4">ND4</option> + <option value="ND5">ND5</option> + <option value="ND6">ND6</option> + <option value="lrRNA">lrRNA</option> + <option value="srRNA">srRNA</option> + <option value="all">all</option> + <validator type="expression" message="Please verify this parameter.">value != '__q2galaxy__::literal::None'</validator> + </param> + </repeat> + <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options"> + <param name="version" type="select" label="version: Str % Choices('GenBank265_2025-03-08', 'GenBank264_2024-12-14', 'GenBank263_2024-10-13', 'GenBank262_2024-08-16', 'GenBank261_2024-06-15', 'GenBank260_2024-04-15')"> + <option value="GenBank265_2025-03-08" selected="true">GenBank265_2025-03-08</option> + <option value="GenBank264_2024-12-14">GenBank264_2024-12-14</option> + <option value="GenBank263_2024-10-13">GenBank263_2024-10-13</option> + <option value="GenBank262_2024-08-16">GenBank262_2024-08-16</option> + <option value="GenBank261_2024-06-15">GenBank261_2024-06-15</option> + <option value="GenBank260_2024-04-15">GenBank260_2024-04-15</option> + </param> + <param name="ref_seq_type" type="select" label="ref_seq_type: Str % Choices('uniq', 'longest')" display="radio"> + <option value="uniq" selected="true">uniq</option> + <option value="longest">longest</option> + </param> + <param name="unspecified_species" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" label="unspecified_species: Bool" help="[default: No] Download reference sequences that contain species that are left unspecified. That is, any reference sequences that lack binomial species-level description."/> + </section> + </inputs> + <outputs> + <collection name="midori2_sequences" type="list"> + <discover_datasets directory="midori2_sequences" pattern="__name_and_ext__"/> + </collection> + <collection name="midori2_taxonomy" type="list"> + <discover_datasets directory="midori2_taxonomy" pattern="__name_and_ext__"/> + </collection> + </outputs> + <tests/> + <help> +QIIME 2: rescript get-midori2-data +================================== +Download and import MIDORI 2 reference data. + + +Outputs: +-------- +:midori2_sequences.qza: MIDORI 2 reference sequence output directory. +:midori2_taxonomy.qza: MIDORI 2 reference taxonomy output directory. + +| + +Description: +------------ +Download and import a variety of mitochonrial DNA gene sequences along with their associated taxonomy from the MIDORI 2 database. Simply provide the database version, the mitochondrial gene of interest, the reference sequence type, and if reference sequences with unspecified species information should be downloaded. NOTE: THIS ACTION ACQUIRES DATA FROM MIDORI2. To learn more, please visit https://www.reference-midori.info/. + + +| + +</help> + <citations> + <citation type="doi">10.1002/edn3.303</citation> + <citation type="doi">10.1371/journal.pcbi.1009581</citation> + <citation type="doi">10.1038/s41587-019-0209-9</citation> + </citations> +</tool>