--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2__fondue___get_sequences.xml	Sat Nov 01 17:25:53 2025 +0000
@@ -0,0 +1,84 @@
+<?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-sequences" id="qiime2__fondue___get_sequences" version="2025.10.0+q2galaxy.2025.10.0" profile="22.05" license="BSD-3-Clause">
+    <description>Fetch sequences based on run ID.</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_sequences '$inputs'</command>
+    <configfiles>
+        <inputs name="inputs" data_style="staging_path_and_source_path"/>
+    </configfiles>
+    <inputs>
+        <param name="accession_id" type="text" label="accession_id: Str" help="[required]  Run ID to fetch sequences for.">
+            <sanitizer>
+                <valid initial="string.printable"/>
+            </sanitizer>
+            <validator type="expression" message="Please verify this parameter.">value is not None and len(value) &gt; 0</validator>
+        </param>
+        <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">
+            <param name="retries" type="integer" min="0" value="2" label="retries: Int % Range(0, None)" help="[default: 2]  Number of retries to fetch sequences."/>
+            <param name="threads" type="integer" min="1" value="1" label="threads: Int % Range(1, None)" help="[default: 1]  Number of threads to be used for parallelization of the data download from NCBI. Not to be confused with the number of parsl workers which can be configured through the parsl configuration file."/>
+            <param name="log_level" type="select" label="log_level: Str % Choices('DEBUG', 'INFO', 'WARNING', 'ERROR')" display="radio">
+                <option value="DEBUG">DEBUG</option>
+                <option value="INFO" selected="true">INFO</option>
+                <option value="WARNING">WARNING</option>
+                <option value="ERROR">ERROR</option>
+            </param>
+            <param name="restricted_access" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" label="restricted_access: Bool" help="[default: No]  If sequence fetch requires dbGaP repository key."/>
+        </section>
+    </inputs>
+    <outputs>
+        <data name="single_reads" format="qza" label="${tool.name} on ${on_string}: single_reads.qza" from_work_dir="single_reads.qza"/>
+        <data name="paired_reads" format="qza" label="${tool.name} on ${on_string}: paired_reads.qza" from_work_dir="paired_reads.qza"/>
+        <data name="failed_runs" format="qza" label="${tool.name} on ${on_string}: failed_runs.qza" from_work_dir="failed_runs.qza"/>
+    </outputs>
+    <tests/>
+    <help>
+QIIME 2: fondue -get-sequences
+==============================
+Fetch sequences based on run ID.
+
+
+Outputs:
+--------
+:single_reads.qza: Artifact containing single-read fastq.gz files for all the requested IDs.
+:paired_reads.qza: Artifact containing paired-end fastq.gz files for all the requested IDs.
+:failed_runs.qza: List of all run IDs for which fetching sequences failed, with their corresponding error messages.
+
+|  
+
+Description:
+------------
+Fetch sequence data of all run IDs.
+
+
+|  
+
+</help>
+    <citations>
+        <citation type="bibtex">@misc{cite1,
+ author = {SRA Toolkit Development Team},
+ name = {SRA Toolkit},
+ url = {https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software},
+ version = {2.9.6}
+}
+</citation>
+        <citation type="doi">10.1093/bioinformatics/btac639</citation>
+        <citation type="doi">10.1038/s41587-019-0209-9</citation>
+    </citations>
+</tool>