Galaxy |

Changeset 0:f3cd42768927 (2024-10-30)

Commit message:
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 5f71b597c9495eae67a447744fded834f56ca1f7

added:
qiime2__rescript__get_bv_brc_metadata.xml
test-data/.gitkeep

diff -r 000000000000 -r f3cd42768927 qiime2__rescript__get_bv_brc_metadata.xml
--- /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

[

b'@@ -0,0 +1,166 @@\n+<?xml version=\'1.0\' encoding=\'utf-8\'?>\n+\n+\n+<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">\n+ <description>Fetch BV-BCR metadata.</description>\n+ <xrefs>\n+ <xref type="bio.tools">qiime2</xref>\n+ </xrefs>\n+ <requirements>\n+ <container type="docker">quay.io/qiime2/amplicon:2024.10</container>\n+ </requirements>\n+ <version_command>q2galaxy version rescript</version_command>\n+ <command detect_errors="exit_code">q2galaxy run rescript get_bv_brc_metadata \'$inputs\'</command>\n+ <configfiles>\n+ <inputs name="inputs" data_style="staging_path_and_source_path"/>\n+ </configfiles>\n+ <inputs>\n+ <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">\n+ <conditional name="ids_metadata">\n+ <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.">\n+ <option value="none" selected="true">None (default)</option>\n+ <option value="tsv">Metadata from TSV</option>\n+ <option value="qza">Metadata from Artifact</option>\n+ </param>\n+ <when value="none"/>\n+ <when value="tsv">\n+ <param name="source" type="data" format="tabular,qiime2.tabular" label="Metadata Source"/>\n+ <param name="column" type="data_column" label="Column Name" data_ref="source" use_header_names="true">\n+ <validator type="expression" message="The first column cannot be selected (they are IDs).">value != "1"</validator>\n+ </param>\n+ </when>\n+ <when value="qza">\n+ <param name="source" type="data" format="qza" label="Metadata Source"/>\n+ <param name="column" type="text" label="Column Name">\n+ <validator type="empty_field"/>\n+ </param>\n+ </when>\n+ </conditional>\n+ <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\')">\n+ <option value="__q2galaxy__::literal::None" selected="true">None (Use default behavior)</option>\n+ <option value="antibiotics">antibiotics</option>\n+ <option value="enzyme_class_ref">enzyme_class_ref</option>\n+ <option value="epitope">epitope</option>\n+ <option value="epitope_assay">epitope_assay</option>\n+ <option value="experiment">experiment</option>\n+ <option value="bioset">bioset</option>\n+ <option value="bioset_result">bioset_result</option>\n+ <option value="gene_ontology_ref">gene_ontology_ref</option>\n+ <option value="genome">genome</option>\n+ <option value="strain">strain</option>\n+ <option value="genome_amr">genome_amr</option>\n+ <option value="fea'..b'id initial="string.printable"/>\n+ </sanitizer>\n+ </param>\n+ </when>\n+ </conditional>\n+ <conditional name="__q2galaxy__GUI__conditional__data_field__" label="data_field: Str">\n+ <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".">\n+ <option value="__q2galaxy__::control::default" selected="true">None (Use default behavior)</option>\n+ <option value="__q2galaxy__::control::provide">Provide a value</option>\n+ </param>\n+ <when value="__q2galaxy__::control::default">\n+ <param name="data_field" type="hidden" value="__q2galaxy__::literal::None"/>\n+ </when>\n+ <when value="__q2galaxy__::control::provide">\n+ <param name="data_field" type="text">\n+ <sanitizer>\n+ <valid initial="string.printable"/>\n+ </sanitizer>\n+ </param>\n+ </when>\n+ </conditional>\n+ <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]">\n+ <param name="element" type="text" label="element: Str" help="[required]">\n+ <sanitizer>\n+ <valid initial="string.printable"/>\n+ </sanitizer>\n+ <validator type="expression" message="Please verify this parameter.">value is not None and len(value) > 0</validator>\n+ </param>\n+ </repeat>\n+ </section>\n+ </inputs>\n+ <outputs>\n+ <data name="metadata" format="qza" label="${tool.name} on ${on_string}: metadata.qza" from_work_dir="metadata.qza"/>\n+ </outputs>\n+ <tests/>\n+ <help>\n+QIIME 2: rescript get-bv-brc-metadata\n+=====================================\n+Fetch BV-BCR metadata.\n+\n+\n+Outputs:\n+--------\n+:metadata.qza: BV-BCR metadata of specified data type.\n+\n+| \n+\n+Description:\n+------------\n+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.\n+\n+\n+| \n+\n+</help>\n+ <citations>\n+ <citation type="bibtex">@article{cite1,\n+ 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},\n+ journal = {Nucleic acids research},\n+ number = {D1},\n+ pages = {D678--D689},\n+ publisher = {Oxford University Press},\n+ title = {Introducing the bacterial and viral bioinformatics resource center (BV-BRC): a resource combining PATRIC, IRD and ViPR},\n+ volume = {51},\n+ year = {2023}\n+}\n+</citation>\n+ <citation type="doi">10.1371/journal.pcbi.1009581</citation>\n+ <citation type="doi">10.1038/s41587-019-0209-9</citation>\n+ </citations>\n+</tool>\n'