# HG changeset patch
# User iuc
# Date 1491344117 14400
# Node ID 47f276ffcbfcc3e49f9d0a44167b071a90571c29
# Parent  0e9624bcd70798655f49b2e35475791f57176c6c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 8652f36a3a3838dca989426961561e81432acf4f

diff -r 0e9624bcd707 -r 47f276ffcbfc data_manager/data_manager_snpsift_dbnsfp.py
--- a/data_manager/data_manager_snpsift_dbnsfp.py	Mon Oct 31 08:13:28 2016 -0400
+++ b/data_manager/data_manager_snpsift_dbnsfp.py	Tue Apr 04 18:15:17 2017 -0400
@@ -197,5 +197,6 @@
     # save info to json file
     open(filename, 'wb').write(json.dumps(data_manager_dict))
 
+
 if __name__ == "__main__":
     main()
diff -r 0e9624bcd707 -r 47f276ffcbfc data_manager/data_manager_snpsift_dbnsfp.xml
--- a/data_manager/data_manager_snpsift_dbnsfp.xml	Mon Oct 31 08:13:28 2016 -0400
+++ b/data_manager/data_manager_snpsift_dbnsfp.xml	Tue Apr 04 18:15:17 2017 -0400
@@ -4,30 +4,30 @@
         <requirement type="package" version="0.8.3">pysam</requirement>
     </requirements>
     <stdio>
-        <exit_code range=":-1" level="fatal" description="Error: Cannot open file" />
-        <exit_code range="1:" level="fatal" description="Error" />
+        <exit_code range=":-1"  level="fatal"   description="Error: Cannot open file" />
+        <exit_code range="1:"  level="fatal"   description="Error" />
     </stdio>
-    <command><![CDATA[
-        python '$__tool_directory__/data_manager_snpsift_dbnsfp.py' 
+    <command interpreter="python">
+        #import re
+        data_manager_snpsift_dbnsfp.py
         #if $db.src == 'softgenetics':
-            --softgenetics '$db.softgenetics_name'
+            --softgenetics "$db.softgenetics_name"
         #elif $db.src == 'history':
-            #if $db.snpsiftdbnsfp.ext == 'snpsiftdbnsfp':
+            #if $db.snpsiftdbnsfp.is_of_type('snpsiftdbnsfp'):
                 #import os.path
-                --snpsiftdbnsfp '$os.path.join($db.snpsiftdbnsfp.extra_files_path, $db.snpsiftdbnsfp.metadata.bgzip)'
-            #else 
-                --dbnsfp_tabular '$db.snpsiftdbnsfp'
+                --snpsiftdbnsfp "$os.path.join($db.snpsiftdbnsfp.extra_files_path, $db.snpsiftdbnsfp.metadata.bgzip)"
+            #else
+                --dbnsfp_tabular "$db.snpsiftdbnsfp"
             #end if
-            --db_name '$db.db_name'
-            #if str($db.dbkey).strip() != '': 
-                --dbkey '$db.dbkey'
+            --db_name "$db.db_name"
+            #if str($db.dbkey).strip() != '':
+                --dbkey "$db.dbkey"
             #elif str($db.snpsiftdbnsfp.metadata.dbkey) != '?':
-                --dbkey '$db.snpsiftdbnsfp.metadata.dbkey' 
+                --dbkey "$db.snpsiftdbnsfp.metadata.dbkey"
             #end if
         #end if
-        '$out_file'
-        ]]>
-    </command>
+        "$out_file"
+        </command>
     <inputs>
         <conditional name="db">
             <param name="src" type="select" label="Source for dbNSFP file">
@@ -43,7 +43,7 @@
                 </param>
             </when>
             <when value="history">
-                <param name="snpsiftdbnsfp" type="data" format="snpsiftdbnsfp,dbnsfp.tabular" label="A snpsift dbnsfp from your history" 
+                <param name="snpsiftdbnsfp" type="data" format="snpsiftdbnsfp,dbnsfp.tabular" label="A snpsift dbnsfp from your history"
                  help="This can can be generated by converting a tabular file set to type: dbnsfp.tabular"/>
                 <param name="db_name" type="text" value="" label="The unique name to give this dbnsfp database">
                   <validator type="length" min="3" max="20" message="Must have between 3 and 20 chracters"/>
@@ -72,7 +72,7 @@
 It populates data table: snpsift_dbnsfps
 
 .. _dbNSFP: https://sites.google.com/site/jpopgen/dbNSFP
-.. _SnpSift_dbNSFP: http://snpefIf.sourceforge.net/SnpSift.html#dbNSFP 
+.. _SnpSift_dbNSFP: http://snpefIf.sourceforge.net/SnpSift.html#dbNSFP
 
 Please refer to https://sites.google.com/site/jpopgen/dbNSFP for which citations to use with specific dbNSFP database versions.
 
diff -r 0e9624bcd707 -r 47f276ffcbfc tool_data_table_conf.xml.sample
--- a/tool_data_table_conf.xml.sample	Mon Oct 31 08:13:28 2016 -0400
+++ b/tool_data_table_conf.xml.sample	Tue Apr 04 18:15:17 2017 -0400
@@ -1,5 +1,5 @@
 <tables>
-    <table name="snpsift_dbnsfps" comment_char="#">
+    <table name="snpsift_dbnsfps" comment_char="#" allow_duplicate_entries="False">
         <columns>key, build, name, value, annotations</columns>
         <file path="tool-data/snpsift_dbnsfps.loc" />
     </table>