Mercurial > repos > q2d2 > qiime2__rescript__get_bv_brc_metadata
changeset 0:f3cd42768927 draft default tip
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 5f71b597c9495eae67a447744fded834f56ca1f7
| author | q2d2 |
|---|---|
| date | Wed, 30 Oct 2024 19:54:52 +0000 |
| parents | |
| children | |
| files | qiime2__rescript__get_bv_brc_metadata.xml test-data/.gitkeep |
| diffstat | 1 files changed, 166 insertions(+), 0 deletions(-) [+] |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2__rescript__get_bv_brc_metadata.xml Wed Oct 30 19:54:52 2024 +0000 @@ -0,0 +1,166 @@ +<?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: 2024.10.0) +for: + qiime2 (version: 2024.10.1) +--> +<tool name="qiime2 rescript get-bv-brc-metadata" id="qiime2__rescript__get_bv_brc_metadata" version="2024.10.0+q2galaxy.2024.10.0" profile="22.05" license="BSD-3-Clause"> + <description>Fetch BV-BCR metadata.</description> + <xrefs> + <xref type="bio.tools">qiime2</xref> + </xrefs> + <requirements> + <container type="docker">quay.io/qiime2/amplicon:2024.10</container> + </requirements> + <version_command>q2galaxy version rescript</version_command> + <command detect_errors="exit_code">q2galaxy run rescript get_bv_brc_metadata '$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"> + <conditional name="ids_metadata"> + <param name="type" type="select" label="ids_metadata: MetadataColumn[Numeric | Categorical]" help="[optional] A metadata column obtained with the action get-bv-brc-metadata that can be used as a query."> + <option value="none" selected="true">None (default)</option> + <option value="tsv">Metadata from TSV</option> + <option value="qza">Metadata from Artifact</option> + </param> + <when value="none"/> + <when value="tsv"> + <param name="source" type="data" format="tabular,qiime2.tabular" label="Metadata Source"/> + <param name="column" type="data_column" label="Column Name" data_ref="source" use_header_names="true"> + <validator type="expression" message="The first column cannot be selected (they are IDs).">value != "1"</validator> + </param> + </when> + <when value="qza"> + <param name="source" type="data" format="qza" label="Metadata Source"/> + <param name="column" type="text" label="Column Name"> + <validator type="empty_field"/> + </param> + </when> + </conditional> + <param name="data_type" type="select" label="data_type: Str % Choices('antibiotics', 'enzyme_class_ref', 'epitope', 'epitope_assay', 'experiment', 'bioset', 'bioset_result', 'gene_ontology_ref', 'genome', 'strain', 'genome_amr', 'feature_sequence', 'genome_feature', 'genome_sequence', 'id_ref', 'misc_niaid_sgc', 'pathway', 'pathway_ref', 'ppi', 'protein_family_ref', 'sequence_feature', 'sequence_feature_vt', 'sp_gene', 'sp_gene_ref', 'spike_lineage', 'spike_variant', 'structured_assertion', 'subsystem', 'subsystem_ref', 'taxonomy', 'protein_structure', 'protein_feature', 'surveillance', 'serology')"> + <option value="__q2galaxy__::literal::None" selected="true">None (Use default behavior)</option> + <option value="antibiotics">antibiotics</option> + <option value="enzyme_class_ref">enzyme_class_ref</option> + <option value="epitope">epitope</option> + <option value="epitope_assay">epitope_assay</option> + <option value="experiment">experiment</option> + <option value="bioset">bioset</option> + <option value="bioset_result">bioset_result</option> + <option value="gene_ontology_ref">gene_ontology_ref</option> + <option value="genome">genome</option> + <option value="strain">strain</option> + <option value="genome_amr">genome_amr</option> + <option value="feature_sequence">feature_sequence</option> + <option value="genome_feature">genome_feature</option> + <option value="genome_sequence">genome_sequence</option> + <option value="id_ref">id_ref</option> + <option value="misc_niaid_sgc">misc_niaid_sgc</option> + <option value="pathway">pathway</option> + <option value="pathway_ref">pathway_ref</option> + <option value="ppi">ppi</option> + <option value="protein_family_ref">protein_family_ref</option> + <option value="sequence_feature">sequence_feature</option> + <option value="sequence_feature_vt">sequence_feature_vt</option> + <option value="sp_gene">sp_gene</option> + <option value="sp_gene_ref">sp_gene_ref</option> + <option value="spike_lineage">spike_lineage</option> + <option value="spike_variant">spike_variant</option> + <option value="structured_assertion">structured_assertion</option> + <option value="subsystem">subsystem</option> + <option value="subsystem_ref">subsystem_ref</option> + <option value="taxonomy">taxonomy</option> + <option value="protein_structure">protein_structure</option> + <option value="protein_feature">protein_feature</option> + <option value="surveillance">surveillance</option> + <option value="serology">serology</option> + </param> + <conditional name="__q2galaxy__GUI__conditional__rql_query__" label="rql_query: Str"> + <param name="__q2galaxy__GUI__select__" type="select" label="rql_query: Str" help="[optional] Query in RQL format. To download all data for genome_ids "224308.43" and "2030927.4755", the RQL query looks like this: "in(genome_id,(224308.43,2030927.4755))". While "in" is an RQL operator, "genome_id" is a data field and "224308.43,2030927.4755" are the values. It is important to percent encode values if they contain illegal characters like spaces. The values "Bacillus subtilis" and "Bacteroidales bacterium" have to be provided with percent encoded quotes (%22) and spaces (%20) like this: "in(species,(%22Bacillus%20subtilis%22,%22Bacteroidales%20bacterium%22))". Check https://www.bv-brc.org/api/doc/ for documentation on data types and corresponding data fields."> + <option value="__q2galaxy__::control::default" selected="true">None (Use default behavior)</option> + <option value="__q2galaxy__::control::provide">Provide a value</option> + </param> + <when value="__q2galaxy__::control::default"> + <param name="rql_query" type="hidden" value="__q2galaxy__::literal::None"/> + </when> + <when value="__q2galaxy__::control::provide"> + <param name="rql_query" type="text"> + <sanitizer> + <valid initial="string.printable"/> + </sanitizer> + </param> + </when> + </conditional> + <conditional name="__q2galaxy__GUI__conditional__data_field__" label="data_field: Str"> + <param name="__q2galaxy__GUI__select__" type="select" label="data_field: Str" help="[optional] Data field of the specified "data-type". This parameter can only be used in conjunction with the "ids" parameter. Retrieves metadata associated with the IDs/values specified in parameter "ids" in this data field. Check https://www.bv-brc.org/api/doc/ for allowed data fields in the specified "data-type"."> + <option value="__q2galaxy__::control::default" selected="true">None (Use default behavior)</option> + <option value="__q2galaxy__::control::provide">Provide a value</option> + </param> + <when value="__q2galaxy__::control::default"> + <param name="data_field" type="hidden" value="__q2galaxy__::literal::None"/> + </when> + <when value="__q2galaxy__::control::provide"> + <param name="data_field" type="text"> + <sanitizer> + <valid initial="string.printable"/> + </sanitizer> + </param> + </when> + </conditional> + <repeat name="ids" help="[optional] IDs/values of the corresponding data field. This parameter can only be used in conjunction with the "data-field" parameter. Retrieves all data associated with these IDs/values in the specified data field." title="ids: List[Str]"> + <param name="element" type="text" label="element: Str" help="[required]"> + <sanitizer> + <valid initial="string.printable"/> + </sanitizer> + <validator type="expression" message="Please verify this parameter.">value is not None and len(value) > 0</validator> + </param> + </repeat> + </section> + </inputs> + <outputs> + <data name="metadata" format="qza" label="${tool.name} on ${on_string}: metadata.qza" from_work_dir="metadata.qza"/> + </outputs> + <tests/> + <help> +QIIME 2: rescript get-bv-brc-metadata +===================================== +Fetch BV-BCR metadata. + + +Outputs: +-------- +:metadata.qza: BV-BCR metadata of specified data type. + +| + +Description: +------------ +Fetch BV-BCR metadata for a specific data type. BV-BRC (Bacterial and Viral Bioinformatics Resource Center) is a database for bacterial and viral genomes, annotations, and metadata. There are three ways to query data: You can use an RQL query to refine your search and get targeted results. By providing IDs/values and a corresponding data field, you can retrieve all metadata associated with those specific values in that data field. And as a third option a metadata column can be provided, to use the results from other data types as a new query. Check https://www.bv-brc.org/api/doc/ for documentation. + + +| + +</help> + <citations> + <citation type="bibtex">@article{cite1, + author = {Olson, Robert D and Assaf, Rida and Brettin, Thomas and Conrad, Neal and Cucinell, Clark and Davis, James J and Dempsey, Donald M and Dickerman, Allan and Dietrich, Emily M and Kenyon, Ronald W and others}, + journal = {Nucleic acids research}, + number = {D1}, + pages = {D678--D689}, + publisher = {Oxford University Press}, + title = {Introducing the bacterial and viral bioinformatics resource center (BV-BRC): a resource combining PATRIC, IRD and ViPR}, + volume = {51}, + year = {2023} +} +</citation> + <citation type="doi">10.1371/journal.pcbi.1009581</citation> + <citation type="doi">10.1038/s41587-019-0209-9</citation> + </citations> +</tool>