changeset 0:ded55fcb6253 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__scrape_collection.xml	Sat Nov 01 17:25:15 2025 +0000
@@ -0,0 +1,83 @@
+<?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 scrape-collection" id="qiime2__fondue__scrape_collection" version="2025.10.0+q2galaxy.2025.10.0" profile="22.05" license="BSD-3-Clause">
+    <description>Scrape Zotero collection for run, study, BioProject, experiment and sample IDs, and associated DOI names.</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 scrape_collection '$inputs'</command>
+    <configfiles>
+        <inputs name="inputs" data_style="staging_path_and_source_path"/>
+    </configfiles>
+    <inputs>
+        <param name="collection_name" type="text" label="collection_name: Str" help="[required]  Name of the collection to be scraped.">
+            <sanitizer>
+                <valid initial="string.printable"/>
+            </sanitizer>
+            <validator type="expression" message="Please verify this parameter.">value is not None and len(value) &gt; 0</validator>
+        </param>
+        <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">
+            <param name="on_no_dois" type="select" label="on_no_dois: Str % Choices('ignore', 'error')" display="radio">
+                <option value="ignore" selected="true">ignore</option>
+                <option value="error">error</option>
+            </param>
+            <param name="log_level" type="select" label="log_level: Str % Choices('DEBUG', 'INFO', 'WARNING', 'ERROR')" display="radio">
+                <option value="DEBUG">DEBUG</option>
+                <option value="INFO" selected="true">INFO</option>
+                <option value="WARNING">WARNING</option>
+                <option value="ERROR">ERROR</option>
+            </param>
+        </section>
+    </inputs>
+    <outputs>
+        <data name="run_ids" format="qza" label="${tool.name} on ${on_string}: run_ids.qza" from_work_dir="run_ids.qza"/>
+        <data name="study_ids" format="qza" label="${tool.name} on ${on_string}: study_ids.qza" from_work_dir="study_ids.qza"/>
+        <data name="bioproject_ids" format="qza" label="${tool.name} on ${on_string}: bioproject_ids.qza" from_work_dir="bioproject_ids.qza"/>
+        <data name="experiment_ids" format="qza" label="${tool.name} on ${on_string}: experiment_ids.qza" from_work_dir="experiment_ids.qza"/>
+        <data name="sample_ids" format="qza" label="${tool.name} on ${on_string}: sample_ids.qza" from_work_dir="sample_ids.qza"/>
+    </outputs>
+    <tests/>
+    <help>
+QIIME 2: fondue scrape-collection
+=================================
+Scrape Zotero collection for run, study, BioProject, experiment and sample IDs, and associated DOI names.
+
+
+Outputs:
+--------
+:run_ids.qza: Artifact containing all run IDs scraped from a Zotero collection and associated DOI names.
+:study_ids.qza: Artifact containing all study IDs scraped from a Zotero collection and associated DOI names.
+:bioproject_ids.qza: Artifact containing all BioProject IDs scraped from a Zotero collection and associated DOI names.
+:experiment_ids.qza: Artifact containing all experiment IDs scraped from a Zotero collection and associated DOI names.
+:sample_ids.qza: Artifact containing all sample IDs scraped from a Zotero collection and associated DOI names.
+
+|  
+
+Description:
+------------
+Scrape attachment files of a Zotero collection for run, study, BioProject, experiment and sample IDs, and associated DOI names.
+
+
+|  
+
+</help>
+    <citations>
+        <citation type="doi">10.5281/zenodo.2917290</citation>
+        <citation type="doi">10.1093/bioinformatics/btac639</citation>
+        <citation type="doi">10.1038/s41587-019-0209-9</citation>
+    </citations>
+</tool>