Mercurial > repos > q2d2 > qiime2__rescript__get_bv_brc_genome_features
changeset 0:c735738cecca 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 19:55:30 +0000 |
| parents | |
| children | |
| files | qiime2__rescript__get_bv_brc_genome_features.xml test-data/.gitkeep |
| diffstat | 1 files changed, 172 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2__rescript__get_bv_brc_genome_features.xml Wed Oct 30 19:55:30 2024 +0000 @@ -0,0 +1,172 @@ +<?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-genome-features" id="qiime2__rescript__get_bv_brc_genome_features" version="2024.10.0+q2galaxy.2024.10.0" profile="22.05" license="BSD-3-Clause"> + <description>Fetch genome features from BV-BRC.</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_genome_features '$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> + <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 data type "genome_feature". This parameter can only be used in conjunction with the "ids" parameter. Retrieves all data associated with the IDs/values specified in parameter "ids" in this data field. Check https://www.bv-brc.org/api/doc/genome_feature for allowed 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="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> + <repeat name="ranks" help="[optional] List of taxonomic ranks for building a taxonomy [default: 'kingdom, phylum, class, order, family, genus, species']" title="ranks: List[Str % Choices('domain', 'superkingdom', 'kingdom', 'subkingdom', 'superphylum', 'phylum', 'subphylum', 'infraphylum', 'superclass', 'class', 'subclass', 'infraclass', 'cohort', 'superorder', 'order', 'suborder', 'infraorder', 'parvorder', 'superfamily', 'family', 'subfamily', 'tribe', 'subtribe', 'genus', 'subgenus', 'species group', 'species subgroup', 'species', 'subspecies', 'forma')]"> + <param name="element" type="select" label="element: Str % Choices('domain', 'superkingdom', 'kingdom', 'subkingdom', 'superphylum', 'phylum', 'subphylum', 'infraphylum', 'superclass', 'class', 'subclass', 'infraclass', 'cohort', 'superorder', 'order', 'suborder', 'infraorder', 'parvorder', 'superfamily', 'family', 'subfamily', 'tribe', 'subtribe', 'genus', 'subgenus', 'species group', 'species subgroup', 'species', 'subspecies', 'forma')"> + <option value="__q2galaxy__::literal::None">Selection required</option> + <option value="domain">domain</option> + <option value="superkingdom">superkingdom</option> + <option value="kingdom">kingdom</option> + <option value="subkingdom">subkingdom</option> + <option value="superphylum">superphylum</option> + <option value="phylum">phylum</option> + <option value="subphylum">subphylum</option> + <option value="infraphylum">infraphylum</option> + <option value="superclass">superclass</option> + <option value="class">class</option> + <option value="subclass">subclass</option> + <option value="infraclass">infraclass</option> + <option value="cohort">cohort</option> + <option value="superorder">superorder</option> + <option value="order">order</option> + <option value="suborder">suborder</option> + <option value="infraorder">infraorder</option> + <option value="parvorder">parvorder</option> + <option value="superfamily">superfamily</option> + <option value="family">family</option> + <option value="subfamily">subfamily</option> + <option value="tribe">tribe</option> + <option value="subtribe">subtribe</option> + <option value="genus">genus</option> + <option value="subgenus">subgenus</option> + <option value="species group">species group</option> + <option value="species subgroup">species subgroup</option> + <option value="species">species</option> + <option value="subspecies">subspecies</option> + <option value="forma">forma</option> + <validator type="expression" message="Please verify this parameter.">value != '__q2galaxy__::literal::None'</validator> + </param> + </repeat> + <param name="rank_propagation" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" checked="true" label="rank_propagation: Bool" help="[default: Yes] If a rank has no taxonomy associated with it, the taxonomy from the upper-level rank of that lineage, will be propagated downward. For example, if we are missing the genus label for 'f__Pasteurellaceae; g__'then the 'f__' rank will be propagated to become: 'f__Pasteurellaceae; g__Pasteurellaceae'."/> + </section> + </inputs> + <outputs> + <data name="genes" format="qza" label="${tool.name} on ${on_string}: genes.qza" from_work_dir="genes.qza"/> + <data name="proteins" format="qza" label="${tool.name} on ${on_string}: proteins.qza" from_work_dir="proteins.qza"/> + <data name="taxonomy" format="qza" label="${tool.name} on ${on_string}: taxonomy.qza" from_work_dir="taxonomy.qza"/> + <data name="loci" format="qza" label="${tool.name} on ${on_string}: loci.qza" from_work_dir="loci.qza"/> + </outputs> + <tests/> + <help> +QIIME 2: rescript get-bv-brc-genome-features +============================================ +Fetch genome features from BV-BRC. + + +Outputs: +-------- +:genes.qza: Gene +:proteins.qza: proteins +:taxonomy.qza: Taxonomy data for all sequences. +:loci.qza: loci + +| + +Description: +------------ +Fetch DNA and protein sequences of genome features from BV-BRC. 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 features. By providing IDs/values and a corresponding data field, you can retrieve all features associated with those specific values in that data field. And as a third option a metadata column can be provided, to use metadata obtained with the action get-bv-brc-metadata 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>