Mercurial > repos > q2d2 > qiime2__rescript__get_pr2_data
changeset 0:b37a81a7d407 draft
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit b1fccfb38b4873cd4699743033449014a2978e7d
author | q2d2 |
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date | Mon, 05 May 2025 19:02:13 +0000 |
parents | |
children | 528198f12435 |
files | qiime2__rescript__get_pr2_data.xml test-data/.gitkeep |
diffstat | 1 files changed, 80 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2__rescript__get_pr2_data.xml Mon May 05 19:02:13 2025 +0000 @@ -0,0 +1,80 @@ +<?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: 2025.4.0) +for: + qiime2 (version: 2025.4.0) +--> +<tool name="qiime2 rescript get-pr2-data" id="qiime2__rescript__get_pr2_data" version="2025.4.0+q2galaxy.2025.4.0" profile="22.05" license="BSD-3-Clause"> + <description>Download, parse, and import SSU PR2 reference data.</description> + <xrefs> + <xref type="bio.tools">qiime2</xref> + </xrefs> + <requirements> + <container type="docker">quay.io/qiime2/amplicon:2025.4</container> + </requirements> + <version_command>q2galaxy version rescript</version_command> + <command detect_errors="exit_code">q2galaxy run rescript get_pr2_data '$inputs'</command> + <configfiles> + <inputs name="inputs" data_style="staging_path_and_source_path"/> + </configfiles> + <inputs> + <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options"> + <param name="version" type="select" label="version: Str % Choices('5.0.0', '4.14.0')" display="radio"> + <option value="5.0.0" selected="true">5.0.0</option> + <option value="4.14.0">4.14.0</option> + </param> + <repeat name="ranks" help="[optional] List of taxonomic ranks for building a taxonomy from the PR2 Taxonomy database. Ranks can be provided as multiple separate flags, e.g.: `--p-ranks genus --p-ranks species`, or with a single flag delimited by a space: `--p-ranks genus species`. [default: 'domain', 'supergroup', 'division', 'subdivision', 'class', 'order', 'family', 'genus', 'species']" title="ranks: List[Str % Choices('domain', 'supergroup', 'division', 'subdivision', 'class', 'order', 'family', 'genus', 'species')]"> + <param name="element" type="select" label="element: Str % Choices('domain', 'supergroup', 'division', 'subdivision', 'class', 'order', 'family', 'genus', 'species')"> + <option value="__q2galaxy__::literal::None">Selection required</option> + <option value="domain">domain</option> + <option value="supergroup">supergroup</option> + <option value="division">division</option> + <option value="subdivision">subdivision</option> + <option value="class">class</option> + <option value="order">order</option> + <option value="family">family</option> + <option value="genus">genus</option> + <option value="species">species</option> + <validator type="expression" message="Please verify this parameter.">value != '__q2galaxy__::literal::None'</validator> + </param> + </repeat> + </section> + </inputs> + <outputs> + <data name="pr2_sequences" format="qza" label="${tool.name} on ${on_string}: pr2_sequences.qza" from_work_dir="pr2_sequences.qza"/> + <data name="pr2_taxonomy" format="qza" label="${tool.name} on ${on_string}: pr2_taxonomy.qza" from_work_dir="pr2_taxonomy.qza"/> + </outputs> + <tests/> + <help> +QIIME 2: rescript get-pr2-data +============================== +Download, parse, and import SSU PR2 reference data. + + +Outputs: +-------- +:pr2_sequences.qza: SSU PR2 reference sequences. +:pr2_taxonomy.qza: SSU PR2 reference taxonomy. + +| + +Description: +------------ +Download, parse, and import SSU PR2 files, given a version number. Downloads data directly from PR2, and outputs ready-to-use sequence and taxonomy artifacts. REQUIRES STABLE INTERNET CONNECTION. NOTE: THIS ACTION ACQUIRES DATA FROM PR2, which is licensed under MIT. To learn more, please visit https://pr2-database.org/ and https://github.com/pr2database/. + + +| + +</help> + <citations> + <citation type="doi">10.1093/nar/gks1160</citation> + <citation type="doi">10.1371/journal.pcbi.1009581</citation> + <citation type="doi">10.1038/s41587-019-0209-9</citation> + </citations> +</tool>