diff mapseq_db_fetcher.xml @ 0:dbf2735e8480 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/ commit 66e797aaa79b92c282a8127260cdfd5702207e35

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mapseq_db_fetcher.xml	Wed Sep 13 19:54:19 2023 +0000
@@ -0,0 +1,54 @@
+<?xml version="1.0"?>
+<tool id="mapseq_db_fetcher" name="Mapseq DB fetcher" tool_type="manage_data" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
+    <description>Fetches the DB required for mapseq</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <expand macro="version" />
+    <command detect_errors="exit_code">
+    <![CDATA[
+        python '$__tool_directory__/data_manager_fetch_mapseq_db.py' 
+        --out '${out_file}' 
+        --version '${version}' 
+        --database-type '${database_type}'
+        $test_data_manager
+    ]]>
+    </command>
+    <inputs>
+    <!-- <param name="test_data_manager" type="hidden" /> -->
+    <param name="test_data_manager" type="boolean" truevalue="--test" falsevalue="" checked="False" label="Download minimal test DB and create mock data table entry." />
+
+    <param name="database_type" type="select" multiple="false" label="Database Type">
+        <option value="mgnify_lsu">MGnify LSU (v5.0.7)</option>
+        <option value="mgnify_ssu">MGnify SSU (v5.0.7)</option>
+        <option value="mgnify_its_itsonedb">MGnify ITS ITSonedb (v5.0.7)</option>
+        <option value="mgnify_its_unite">MGnify ITS UNITE (v5.0.7)</option>
+    </param>
+
+    <!-- <param name="test_data_manager" type="text" value=""/> -->
+    <param argument="--version" type="text" value="5.0.7" help="Check MGnify GitHub (https://github.com/EBI-Metagenomics/pipeline-v5/releases) for the version."/> 
+    </inputs>
+    <outputs>
+        <data format="data_manager_json" name="out_file" />
+    </outputs>
+    <tests>
+    <test expect_num_outputs="1">
+        <param name="test_data_manager" value="--test"/>
+        <param name="version" value="5.0.7"/>
+        <param name="database_type" value="mgnify_lsu"/>
+        <output name="out_file">
+                <assert_contents>
+                    <has_text text="mgnify_lsu"/>
+                    <has_text text="5.0.7"/>
+                </assert_contents>
+        </output>
+    </test>
+    </tests>
+    <help>
+    Downloads preformatted DBs form MGnify that can be used for mapseq. 
+    The download paths were taken from: https://github.com/EBI-Metagenomics/pipeline-v5/
+    </help>
+    <expand macro="citations" />
+    <expand macro="creator" />
+</tool>
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