diff data_manager/recetox_metabolite_fetcher.xml @ 0:953dd78a34d3 draft default tip

"planemo upload commit be4b24b2dacc3f23538068d5a6082bca246f6887"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/recetox_metabolite_fetcher.xml	Tue Aug 25 11:15:49 2020 +0000
@@ -0,0 +1,35 @@
+<tool id="recetox_metabolite_fetcher" name="Metabolite Fetcher" version="1.0.0" tool_type="manage_data">
+    <requirements>
+        <requirement type="package" version="3.7">python</requirement>
+    </requirements>
+
+    <command detect_errors="exit_code"><![CDATA[
+        python '${__tool_directory__}/recetox_metabolite_fetcher.py'
+            --tool_data_dir '${__tool_directory__}'
+            --database_url '${url}'
+            --data_manager_json '${out_file}'
+    ]]></command>
+    
+    <inputs>
+        <param name="url" type="text" label="Database url" help="Type custom url or select url from a predefined list a metabolite databases.">
+            <option value="https://hmdb.ca/system/downloads/3.6/hmdb_metabolites.zip">HMDB 3.6</option>
+            <option value="https://hmdb.ca/system/downloads/current/hmdb_metabolites.zip">HMDB 4.0</option>
+            <option value="http://www.t3db.ca/system/downloads/current/toxins.xml.zip">T3DB</option>
+        </param>
+    </inputs>
+    
+    <outputs>
+        <data name="out_file" format="data_manager_json"/>
+    </outputs>
+    
+    <help><![CDATA[
+        Downloads a snapshot of a specified metabolite database and stores it withing the whole Galaxy instance.
+    ]]></help>
+    
+    <citations>
+        <citation type="doi">https://doi.org/10.1093/nar/gkl923</citation>
+        <citation type="doi">https://doi.org/10.1093/nar/gkn810</citation>
+        <citation type="doi">https://doi.org/10.1093/nar/gks1065</citation>
+        <citation type="doi">https://doi.org/10.1093/nar/gkx1089</citation>
+    </citations>
+</tool>
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