Mercurial > repos > q2d2 > qiime2__rescript__get_gtdb_data
changeset 0:421308ae47cf draft
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
| author | q2d2 |
|---|---|
| date | Thu, 25 Apr 2024 21:25:08 +0000 |
| parents | |
| children | 27f4edc4dd8d |
| files | qiime2__rescript__get_gtdb_data.xml test-data/.gitkeep |
| diffstat | 1 files changed, 74 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2__rescript__get_gtdb_data.xml Thu Apr 25 21:25:08 2024 +0000 @@ -0,0 +1,74 @@ +<?xml version='1.0' encoding='utf-8'?> +<!-- +Copyright (c) 2024, 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: 2024.2.1) +for: + qiime2 (version: 2024.2.0) +--> +<tool name="qiime2 rescript get-gtdb-data" id="qiime2__rescript__get_gtdb_data" version="2024.2.2+q2galaxy.2024.2.1" profile="22.05" license="BSD-3-Clause"> + <description>Download, parse, and import SSU GTDB reference data.</description> + <requirements> + <container type="docker">quay.io/qiime2/amplicon:2024.2</container> + </requirements> + <version_command>q2galaxy version rescript</version_command> + <command detect_errors="exit_code">q2galaxy run rescript get_gtdb_data '$inputs'</command> + <configfiles> + <inputs name="inputs" data_style="staging_path_and_source_path"/> + </configfiles> + <inputs> + <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options"> + <param name="version" type="select" label="version: Str % Choices('202.0', '207.0', '214.0', '214.1')" display="radio"> + <option value="202.0">202.0</option> + <option value="207.0">207.0</option> + <option value="214.0">214.0</option> + <option value="214.1" selected="true">214.1</option> + </param> + <param name="domain" type="select" label="domain: Str % Choices('Both', 'Bacteria', 'Archaea')" display="radio"> + <option value="Both" selected="true">Both</option> + <option value="Bacteria">Bacteria</option> + <option value="Archaea">Archaea</option> + </param> + <param name="db_type" type="select" label="db_type: Str % Choices('All', 'SpeciesReps')" display="radio"> + <option value="All">All</option> + <option value="SpeciesReps" selected="true">SpeciesReps</option> + </param> + </section> + </inputs> + <outputs> + <data name="gtdb_taxonomy" format="qza" label="${tool.name} on ${on_string}: gtdb_taxonomy.qza" from_work_dir="gtdb_taxonomy.qza"/> + <data name="gtdb_sequences" format="qza" label="${tool.name} on ${on_string}: gtdb_sequences.qza" from_work_dir="gtdb_sequences.qza"/> + </outputs> + <tests/> + <help> +QIIME 2: rescript get-gtdb-data +=============================== +Download, parse, and import SSU GTDB reference data. + + +Outputs: +-------- +:gtdb_taxonomy.qza: SSU GTDB reference taxonomy. +:gtdb_sequences.qza: SSU GTDB reference sequences. + +| + +Description: +------------ +Download, parse, and import SSU GTDB files, given a version number. Downloads data directly from GTDB, parses the taxonomy files, and outputs ready-to-use sequence and taxonomy artifacts. REQUIRES STABLE INTERNET CONNECTION. NOTE: THIS ACTION ACQUIRES DATA FROM GTDB. SEE https://gtdb.ecogenomic.org/about FOR MORE INFORMATION and be aware that earlier versions may be released under a different license. + + +| + +</help> + <citations> + <citation type="doi">10.1038/s41587-020-0501-8</citation> + <citation type="doi">10.1093/nar/gkab776</citation> + <citation type="doi">10.1371/journal.pcbi.1009581</citation> + <citation type="doi">10.1038/s41587-019-0209-9</citation> + </citations> +</tool>