diff data_manager/motus_db_fetcher.xml @ 0:0370fe3cf518 draft default tip

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/ commit f42263c2875a78500f141027803a38606ecb0f14

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/motus_db_fetcher.xml	Thu Oct 10 11:00:40 2024 +0000
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+<?xml version="1.0"?>
+<tool id="motus_db_fetcher" name="mOTUs DB fetcher" tool_type="manage_data" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
+    <description>Fetches the DB required for mOTUs</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="biotools" />
+    <expand macro="requirements" />
+    <!-- <expand macro="version" /> -->
+
+    <command detect_errors="exit_code">
+    <![CDATA[
+        python '$__tool_directory__/data_manager_fetch_motus_db.py' --out '${out_file}' --version '${version}' 
+        $test_data_manager
+    ]]>
+    </command>
+    <inputs>
+    <param name="test_data_manager" type="hidden" truevalue="--test" falsevalue="" checked="False" label="Copy minimal test DB and create mock data table entry." />
+
+    <!-- <param name="test_data_manager" type="text" value=""/> -->
+    <param argument="--version" type="select" multiple="false" label="Database Version" help="Check https://zenodo.org/records/7778108 for current version. The default value is recommended.">
+        <option value="3.1.0">3.1.0</option>
+        <option value="3.0.1">3.0.1</option>
+        <option value="3.0.0">3.0.0</option>
+    </param>
+
+    </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="3.1.0"/>
+        <output name="out_file">
+                <assert_contents>
+                    <has_text text="mOTUs DB version 3.1.0 downloaded at"/>
+                </assert_contents>
+        </output>
+    </test>
+    </tests>
+    <help><![CDATA[
+mOTUs
+=====
+
+The mOTUs profiler is a tool designed for taxonomic profiling of metagenomic and metatranscriptomic data.
+It allows for the identification and quantification of microbial community composition directly from sequencing reads. 
+mOTUs utilizes a database of marker genes identified across a wide range of microbial taxa, enabling the detection of known and unknown microorganisms in your sample data.
+
+Additional Resources
+====================
+
+For a more comprehensive understanding of mOTUs and detailed usage instructions, please visit the mOTUs GitHub repository:
+
+mOTUs GitHub Repository: [https://github.com/motu-tool/mOTUs](https://github.com/motu-tool/mOTUs)
+        
+Data Manager
+============
+
+This DM download the available DBs from: https://zenodo.org/records/5012106
+            ]]></help>
+    <expand macro="citations" />
+    <expand macro="creator" />
+</tool>
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