changeset 0:9099f71beb46 draft default tip

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

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2__fondue__combine_seqs.xml	Sat Nov 01 17:25:33 2025 +0000
@@ -0,0 +1,68 @@
+<?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 combine-seqs" id="qiime2__fondue__combine_seqs" version="2025.10.0+q2galaxy.2025.10.0" profile="22.05" license="BSD-3-Clause">
+    <description>Combine sequences from multiple artifacts.</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 combine_seqs '$inputs'</command>
+    <configfiles>
+        <inputs name="inputs" data_style="staging_path_and_source_path"/>
+    </configfiles>
+    <inputs>
+        <param name="seqs" type="data" format="qza" label="seqs: List[SampleData[SequencesWithQuality¹ | PairedEndSequencesWithQuality²]]" help="[required]  Sequence artifacts to be combined together." multiple="true">
+            <options options_filter_attribute="metadata.semantic_type">
+                <filter type="add_value" value="SampleData[PairedEndSequencesWithQuality]"/>
+                <filter type="add_value" value="SampleData[SequencesWithQuality]"/>
+            </options>
+        </param>
+        <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">
+            <param name="on_duplicates" type="select" label="on_duplicates: Str % Choices('error', 'warn')" display="radio">
+                <option value="error" selected="true">error</option>
+                <option value="warn">warn</option>
+            </param>
+        </section>
+    </inputs>
+    <outputs>
+        <data name="combined_seqs" format="qza" label="${tool.name} on ${on_string}: combined_seqs.qza" from_work_dir="combined_seqs.qza"/>
+    </outputs>
+    <tests/>
+    <help>
+QIIME 2: fondue combine-seqs
+============================
+Combine sequences from multiple artifacts.
+
+
+Outputs:
+--------
+:combined_seqs.qza: Sequences combined from all input artifacts.
+
+|  
+
+Description:
+------------
+Combine paired- or single-end sequences from multiple artifacts, for example obtained by re-fetching failed downloads.
+
+
+|  
+
+</help>
+    <citations>
+        <citation type="doi">10.1093/bioinformatics/btac639</citation>
+        <citation type="doi">10.1038/s41587-019-0209-9</citation>
+    </citations>
+</tool>