diff data_manager/ncbi_taxonomy_fetcher.xml @ 1:926847693e4d draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_ncbi_taxonomy/ commit 8652f36a3a3838dca989426961561e81432acf4f

--- a/data_manager/ncbi_taxonomy_fetcher.xml	Thu Oct 08 12:14:42 2015 -0400
+++ b/data_manager/ncbi_taxonomy_fetcher.xml	Tue Apr 04 18:08:21 2017 -0400
@@ -1,25 +1,22 @@
 <?xml version="1.0"?>
 <tool id="ncbi_taxonomy_fetcher" name="NCBI" tool_type="manage_data" version="1.0.0">
     <description>taxonomy downloader</description>
-    <stdio>
-        <exit_code description="Error" level="fatal" range="1:" />
-    </stdio>
-    <command interpreter="python">
+    <command detect_errors="exit_code">
     <![CDATA[
-        data_manager.py --out "${out_file}"
+        python '$__tool_directory__/data_manager.py' --out '${out_file}'
         #if $taxonomy_url:
-            --url "${taxonomy_url}"
+            --url '${taxonomy_url}'
         #end if
         #if $database_name:
-            --name "${database_name}"
+            --name '${database_name}'
         #end if
     ]]>
     </command>
     <inputs>
-        <param help="Enter a unique identifier, or leave blank for today's date" label="Name for this database" name="database_name" type="text" optional="True" />
-        <param label="Enter URL for taxonomy files" name="taxonomy_url" type="text" />
+        <param name="database_name" type="text" optional="true" label="Name for this database" help="Enter a unique identifier, or leave blank for today's date" />
+        <param name="taxonomy_url" type="text" label="Enter URL for taxonomy files" />
     </inputs>
     <outputs>
-        <data format="data_manager_json" name="out_file" />
+        <data name="out_file" format="data_manager_json" />
     </outputs>
 </tool>