# HG changeset patch
# User q2d2
# Date 1752617049 0
# Node ID 826e62af85a9e0a15b4a9a7d3c9402e7a12662da

planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 9436cc47c72b58a6a3d3a5c2ee075689c2926ef0

diff -r 000000000000 -r 826e62af85a9 qiime2__rescript__get_midori2_data.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2__rescript__get_midori2_data.xml	Tue Jul 15 22:04:09 2025 +0000
@@ -0,0 +1,100 @@
+<?xml version='1.0' encoding='utf-8'?>
+<!--
+Copyright (c) 2025, 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: 2025.7.0)
+for:
+    qiime2 (version: 2025.7.0)
+-->
+<tool name="qiime2 rescript get-midori2-data" id="qiime2__rescript__get_midori2_data" version="2025.7.0+q2galaxy.2025.7.0" profile="22.05" license="BSD-3-Clause">
+    <description>Download and import MIDORI 2 reference data.</description>
+    <xrefs>
+        <xref type="bio.tools">qiime2</xref>
+    </xrefs>
+    <requirements>
+        <container type="docker">quay.io/qiime2/amplicon:2025.7</container>
+    </requirements>
+    <version_command>q2galaxy version rescript</version_command>
+    <command detect_errors="exit_code">q2galaxy run rescript get_midori2_data '$inputs'</command>
+    <configfiles>
+        <inputs name="inputs" data_style="staging_path_and_source_path"/>
+    </configfiles>
+    <inputs>
+        <repeat name="mito_gene" min="1" help="[required]  Download the mitochondrial gene(s) of interest. Specify the respective gene(s), or download all genes using 'all'." title="mito_gene: List[Str % Choices('A6', 'A8', 'CO1', 'CO2', 'CO3', 'Cytb', 'ND1', 'ND2', 'ND3', 'ND4L', 'ND4', 'ND5', 'ND6', 'lrRNA', 'srRNA', 'all')]">
+            <param name="element" type="select" label="element: Str % Choices('A6', 'A8', 'CO1', 'CO2', 'CO3', 'Cytb', 'ND1', 'ND2', 'ND3', 'ND4L', 'ND4', 'ND5', 'ND6', 'lrRNA', 'srRNA', 'all')">
+                <option value="__q2galaxy__::literal::None">Selection required</option>
+                <option value="A6">A6</option>
+                <option value="A8">A8</option>
+                <option value="CO1">CO1</option>
+                <option value="CO2">CO2</option>
+                <option value="CO3">CO3</option>
+                <option value="Cytb">Cytb</option>
+                <option value="ND1">ND1</option>
+                <option value="ND2">ND2</option>
+                <option value="ND3">ND3</option>
+                <option value="ND4L">ND4L</option>
+                <option value="ND4">ND4</option>
+                <option value="ND5">ND5</option>
+                <option value="ND6">ND6</option>
+                <option value="lrRNA">lrRNA</option>
+                <option value="srRNA">srRNA</option>
+                <option value="all">all</option>
+                <validator type="expression" message="Please verify this parameter.">value != '__q2galaxy__::literal::None'</validator>
+            </param>
+        </repeat>
+        <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">
+            <param name="version" type="select" label="version: Str % Choices('GenBank265_2025-03-08', 'GenBank264_2024-12-14', 'GenBank263_2024-10-13', 'GenBank262_2024-08-16', 'GenBank261_2024-06-15', 'GenBank260_2024-04-15')">
+                <option value="GenBank265_2025-03-08" selected="true">GenBank265_2025-03-08</option>
+                <option value="GenBank264_2024-12-14">GenBank264_2024-12-14</option>
+                <option value="GenBank263_2024-10-13">GenBank263_2024-10-13</option>
+                <option value="GenBank262_2024-08-16">GenBank262_2024-08-16</option>
+                <option value="GenBank261_2024-06-15">GenBank261_2024-06-15</option>
+                <option value="GenBank260_2024-04-15">GenBank260_2024-04-15</option>
+            </param>
+            <param name="ref_seq_type" type="select" label="ref_seq_type: Str % Choices('uniq', 'longest')" display="radio">
+                <option value="uniq" selected="true">uniq</option>
+                <option value="longest">longest</option>
+            </param>
+            <param name="unspecified_species" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" label="unspecified_species: Bool" help="[default: No]  Download reference sequences that contain species that are left unspecified. That is, any reference sequences that lack binomial species-level description."/>
+        </section>
+    </inputs>
+    <outputs>
+        <collection name="midori2_sequences" type="list">
+            <discover_datasets directory="midori2_sequences" pattern="__name_and_ext__"/>
+        </collection>
+        <collection name="midori2_taxonomy" type="list">
+            <discover_datasets directory="midori2_taxonomy" pattern="__name_and_ext__"/>
+        </collection>
+    </outputs>
+    <tests/>
+    <help>
+QIIME 2: rescript get-midori2-data
+==================================
+Download and import MIDORI 2 reference data.
+
+
+Outputs:
+--------
+:midori2_sequences.qza: MIDORI 2 reference sequence output directory.
+:midori2_taxonomy.qza: MIDORI 2 reference taxonomy output directory.
+
+|  
+
+Description:
+------------
+Download and import a variety of mitochonrial DNA gene sequences along with their associated taxonomy from the MIDORI 2 database. Simply provide the database version, the mitochondrial gene of interest, the reference sequence type, and if reference sequences with unspecified species information should be downloaded. NOTE: THIS ACTION ACQUIRES DATA FROM MIDORI2. To learn more, please visit https://www.reference-midori.info/.
+
+
+|  
+
+</help>
+    <citations>
+        <citation type="doi">10.1002/edn3.303</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 826e62af85a9 test-data/.gitkeep