diff qiime2__rescript__get_gtdb_data.xml @ 0:421308ae47cf draft

planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 389df0134cd0763dcf02aac6e623fc15f8861c1e

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2__rescript__get_gtdb_data.xml	Thu Apr 25 21:25:08 2024 +0000
@@ -0,0 +1,74 @@
+<?xml version='1.0' encoding='utf-8'?>
+<!--
+Copyright (c) 2024, 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: 2024.2.1)
+for:
+    qiime2 (version: 2024.2.0)
+-->
+<tool name="qiime2 rescript get-gtdb-data" id="qiime2__rescript__get_gtdb_data" version="2024.2.2+q2galaxy.2024.2.1" profile="22.05" license="BSD-3-Clause">
+    <description>Download, parse, and import SSU GTDB reference data.</description>
+    <requirements>
+        <container type="docker">quay.io/qiime2/amplicon:2024.2</container>
+    </requirements>
+    <version_command>q2galaxy version rescript</version_command>
+    <command detect_errors="exit_code">q2galaxy run rescript get_gtdb_data '$inputs'</command>
+    <configfiles>
+        <inputs name="inputs" data_style="staging_path_and_source_path"/>
+    </configfiles>
+    <inputs>
+        <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">
+            <param name="version" type="select" label="version: Str % Choices('202.0', '207.0', '214.0', '214.1')" display="radio">
+                <option value="202.0">202.0</option>
+                <option value="207.0">207.0</option>
+                <option value="214.0">214.0</option>
+                <option value="214.1" selected="true">214.1</option>
+            </param>
+            <param name="domain" type="select" label="domain: Str % Choices('Both', 'Bacteria', 'Archaea')" display="radio">
+                <option value="Both" selected="true">Both</option>
+                <option value="Bacteria">Bacteria</option>
+                <option value="Archaea">Archaea</option>
+            </param>
+            <param name="db_type" type="select" label="db_type: Str % Choices('All', 'SpeciesReps')" display="radio">
+                <option value="All">All</option>
+                <option value="SpeciesReps" selected="true">SpeciesReps</option>
+            </param>
+        </section>
+    </inputs>
+    <outputs>
+        <data name="gtdb_taxonomy" format="qza" label="${tool.name} on ${on_string}: gtdb_taxonomy.qza" from_work_dir="gtdb_taxonomy.qza"/>
+        <data name="gtdb_sequences" format="qza" label="${tool.name} on ${on_string}: gtdb_sequences.qza" from_work_dir="gtdb_sequences.qza"/>
+    </outputs>
+    <tests/>
+    <help>
+QIIME 2: rescript get-gtdb-data
+===============================
+Download, parse, and import SSU GTDB reference data.
+
+
+Outputs:
+--------
+:gtdb_taxonomy.qza: SSU GTDB reference taxonomy.
+:gtdb_sequences.qza: SSU GTDB reference sequences.
+
+|  
+
+Description:
+------------
+Download, parse, and import SSU GTDB files, given a version number. Downloads data directly from GTDB, parses the taxonomy files, and outputs ready-to-use sequence and taxonomy artifacts. REQUIRES STABLE INTERNET CONNECTION. NOTE: THIS ACTION ACQUIRES DATA FROM GTDB. SEE https://gtdb.ecogenomic.org/about FOR MORE INFORMATION and be aware that earlier versions may be released under a different license.
+
+
+|  
+
+</help>
+    <citations>
+        <citation type="doi">10.1038/s41587-020-0501-8</citation>
+        <citation type="doi">10.1093/nar/gkab776</citation>
+        <citation type="doi">10.1371/journal.pcbi.1009581</citation>
+        <citation type="doi">10.1038/s41587-019-0209-9</citation>
+    </citations>
+</tool>