diff data_manager/data_manager_snpEff_databases.xml @ 0:e1d9f6a0ad53

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/data_manager_snpEff_databases.xml	Thu Jul 04 10:43:55 2013 -0400
@@ -0,0 +1,29 @@
+<tool id="data_manager_snpeff_databases" name="SnpEff Databases" version="3.2" tool_type="manage_data">
+	<description>Read the list of available snpEff databases</description>
+	<requirements>
+		<requirement type="package" version="3.2">snpEff</requirement>
+	</requirements>
+	<command interpreter="python">
+        data_manager_snpEff_databases.py --jar_path \$JAVA_JAR_PATH/snpEff.jar "$out_file"
+        </command>
+	<inputs>
+	</inputs>
+	<outputs>
+           <data name="out_file" format="data_manager_json"/>
+	</outputs>
+        <stdio>
+          <exit_code range=":-1"  level="fatal"   description="Error: Cannot open file" />
+          <exit_code range="1:"  level="fatal"   description="Error" />
+        </stdio>
+
+	<help>
+
+This tool updatess the list of SnpEff databases for the SnpEff Download data manager.
+It should only need to be run once for a snpEff version, 
+since it populates the SnpEff Download data manager from the snpEff config file.
+
+For information about snpEff:    http://snpEff.sourceforge.net
+
+	</help>
+</tool>
+