# HG changeset patch
# User q2d2
# Date 1730318118 0
# Node ID 9dd05f5c60b9b1f7f6a44be07a3bd586f7cf63ca

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

diff -r 000000000000 -r 9dd05f5c60b9 qiime2__rescript__get_bv_brc_genomes.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2__rescript__get_bv_brc_genomes.xml	Wed Oct 30 19:55:18 2024 +0000
@@ -0,0 +1,168 @@
+<?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-genomes" id="qiime2__rescript__get_bv_brc_genomes" version="2024.10.0+q2galaxy.2024.10.0" profile="22.05" license="BSD-3-Clause">
+    <description>Get genome sequences from the BV-BRC database.</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_genomes '$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 &quot;224308.43&quot; and &quot;2030927.4755&quot;, the RQL query looks like this: &quot;in(genome_id,(224308.43,2030927.4755))&quot;. While &quot;in&quot; is an RQL operator, &quot;genome_id&quot; is a data field and &quot;224308.43,2030927.4755&quot; are the values. It is important to percent encode values if they contain illegal characters like spaces. The values &quot;Bacillus subtilis&quot; and &quot;Bacteroidales bacterium&quot; have to be provided with percent encoded quotes (%22) and spaces (%20) like this: &quot;in(species,(%22Bacillus%20subtilis%22,%22Bacteroidales%20bacterium%22))&quot;. 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 &quot;genome_sequence&quot;. This parameter can only be used in conjunction with the &quot;ids&quot; parameter. Retrieves all genomes associated with the IDs/values specified in parameter &quot;ids&quot; in this data field. Check https://www.bv-brc.org/api/doc/genome_sequence 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 &quot;data-field&quot; 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) &gt; 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="genomes" format="qza" label="${tool.name} on ${on_string}: genomes.qza" from_work_dir="genomes.qza"/>
+        <data name="taxonomy" format="qza" label="${tool.name} on ${on_string}: taxonomy.qza" from_work_dir="taxonomy.qza"/>
+    </outputs>
+    <tests/>
+    <help>
+QIIME 2: rescript get-bv-brc-genomes
+====================================
+Get genome sequences from the BV-BRC database.
+
+
+Outputs:
+--------
+:genomes.qza: Genome sequences for specified query.
+:taxonomy.qza: Taxonomy data for all sequences.
+
+|  
+
+Description:
+------------
+Fetch genome sequences 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 genomes. By providing IDs/values and a corresponding data field, you can retrieve all genomes 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>
diff -r 000000000000 -r 9dd05f5c60b9 test-data/.gitkeep