# HG changeset patch
# User q2d2
# Date 1762017946 0
# Node ID f67bc93fd333b56af3f523873c6834981d42ae74

planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__fondue commit 64ed09f1f1c680ad8373d261bd6be43a4f8a8d5b

diff -r 000000000000 -r f67bc93fd333 qiime2__fondue__get_ids_from_query.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2__fondue__get_ids_from_query.xml	Sat Nov 01 17:25:46 2025 +0000
@@ -0,0 +1,77 @@
+<?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: 2025.10.0)
+for:
+    qiime2 (version: 2025.10.0)
+-->
+<tool name="qiime2 fondue get-ids-from-query" id="qiime2__fondue__get_ids_from_query" version="2025.10.0+q2galaxy.2025.10.0" profile="22.05" license="BSD-3-Clause">
+    <description>Find SRA run accession IDs based on a search query.</description>
+    <xrefs>
+        <xref type="bio.tools">qiime2</xref>
+    </xrefs>
+    <requirements>
+        <container type="docker">quay.io/qiime2/amplicon:2025.10</container>
+    </requirements>
+    <version_command>q2galaxy version fondue</version_command>
+    <command detect_errors="exit_code">q2galaxy run fondue get_ids_from_query '$inputs'</command>
+    <configfiles>
+        <inputs name="inputs" data_style="staging_path_and_source_path"/>
+    </configfiles>
+    <inputs>
+        <param name="query" type="text" label="query: Str" help="[required]  Search query to retrieve SRA run IDs from the BioSample database.">
+            <sanitizer>
+                <valid initial="string.printable"/>
+            </sanitizer>
+            <validator type="expression" message="Please verify this parameter.">value is not None and len(value) &gt; 0</validator>
+        </param>
+        <param name="email" type="text" label="email: Str" help="[required]  Your e-mail address (required by NCBI).">
+            <sanitizer>
+                <valid initial="string.printable"/>
+            </sanitizer>
+            <validator type="expression" message="Please verify this parameter.">value is not None and len(value) &gt; 0</validator>
+        </param>
+        <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">
+            <param name="threads" type="integer" min="1" value="1" label="threads: Int % Range(1, None)" help="[default: 1]  Number of threads to be used for parallelization of the data download from NCBI. Not to be confused with the number of parsl workers which can be configured through the parsl configuration file."/>
+            <param name="log_level" type="select" label="log_level: Str % Choices('DEBUG', 'INFO', 'WARNING', 'ERROR')" display="radio">
+                <option value="DEBUG">DEBUG</option>
+                <option value="INFO" selected="true">INFO</option>
+                <option value="WARNING">WARNING</option>
+                <option value="ERROR">ERROR</option>
+            </param>
+        </section>
+    </inputs>
+    <outputs>
+        <data name="ids" format="qza" label="${tool.name} on ${on_string}: ids.qza" from_work_dir="ids.qza"/>
+    </outputs>
+    <tests/>
+    <help>
+QIIME 2: fondue get-ids-from-query
+==================================
+Find SRA run accession IDs based on a search query.
+
+
+Outputs:
+--------
+:ids.qza: Table containing metadata for all the requested IDs.
+
+|  
+
+Description:
+------------
+Find SRA run accession IDs in the BioSample database using a text search query.
+
+
+|  
+
+</help>
+    <citations>
+        <citation type="doi">10.1093/bioinformatics/btac639</citation>
+        <citation type="doi">10.1038/s41587-019-0209-9</citation>
+    </citations>
+</tool>
diff -r 000000000000 -r f67bc93fd333 test-data/.gitkeep