diff data_manager/data_manager_gemini_download.xml @ 3:172815da3d41 draft

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

--- a/data_manager/data_manager_gemini_download.xml	Thu Feb 18 08:49:06 2016 -0500
+++ b/data_manager/data_manager_gemini_download.xml	Tue Apr 04 18:09:05 2017 -0400
@@ -3,12 +3,8 @@
     <requirements>
         <requirement type="package" version="0.18.1">gemini</requirement>
     </requirements>
-    <stdio>
-        <exit_code range=":-1"  level="fatal" description="Error: Cannot open file" />
-        <exit_code range="1:"  level="fatal" description="Error" />
-    </stdio>
-    <command interpreter="python">
-        data_manager_gemini_download.py "$out_file"
+    <command detect_errors="exit_code">
+        python '$__tool_directory__/data_manager_gemini_download.py' '$out_file'
     </command>
     <inputs>
         <param name="cadd" type="boolean" truevalue="--extra cadd_score" falsevalue="" checked="True"
@@ -17,20 +13,17 @@
             label="Download GERP for GEMINI database annotation" help="(--extra gerp_bp)"/>
     </inputs>
     <outputs>
-           <data name="out_file" format="data_manager_json" label="${tool.name}"/>
+        <data name="out_file" format="data_manager_json" label="${tool.name}"/>
     </outputs>
     <tests>
     </tests>
     <help>
-
 This tool downloads the GEMINI databases.
 
 For details about this tool, please go to http://gemini.readthedocs.org
-
     </help>
     <citations>
         <citation type="doi">10.1371/journal.pcbi.1003153</citation>
-        <yield />
     </citations>
 </tool>