# HG changeset patch
# User Jim Johnson <jj@umn.edu>
# Date 1385648171 21600
# Node ID eb394dd65c98852429ff3aa4269b8611aeeb24a1
# Parent  8952990fcab9243efea248154795d5e766a0a8d1
Add mutli-select to data managers from Bjoern, filter unique database options in snpEff_download.xml snpEff.xml

diff -r 8952990fcab9 -r eb394dd65c98 data_manager/data_manager_snpEff_databases.py
--- a/data_manager/data_manager_snpEff_databases.py	Wed Nov 27 09:11:32 2013 -0600
+++ b/data_manager/data_manager_snpEff_databases.py	Thu Nov 28 08:16:11 2013 -0600
@@ -44,11 +44,14 @@
             fields = line.split('\t')
             if len(fields) >= 2:
                 genome_version = fields[0].strip()
-                if genome_version.startswith("Genome") or  genome_version.startswith("-"):
+                if genome_version.startswith("Genome") or genome_version.startswith("-"):
+                    continue
+                #snpeff test genome
+                if genome_version == '30c2c903' or fields[1].strip() == 'TestCase' or fields[1].strip().startswith('Test_'):
                     continue
                 description = fields[1].strip() + ' : ' + genome_version
                 data_table_entries.append(dict(value=genome_version, name=description))
-        data_manager_dict['data_tables']['snpeff_databases'] = data_table_entries   
+        data_manager_dict['data_tables']['snpeff_databases'] = data_table_entries
     except Exception, e:
         stop_err( 'Error parsing %s %s\n' % (config,str( e )) )
     else:
diff -r 8952990fcab9 -r eb394dd65c98 data_manager/data_manager_snpEff_download.py
--- a/data_manager/data_manager_snpEff_download.py	Wed Nov 27 09:11:32 2013 -0600
+++ b/data_manager/data_manager_snpEff_download.py	Thu Nov 28 08:16:11 2013 -0600
@@ -104,7 +104,8 @@
 
 
     #Create SnpEff Reference Data
-    download_database(data_manager_dict, target_directory, options.jar_path,options.config,options.genome_version,options.organism)
+    for genome_version, organism in zip(options.genome_version.split(','), options.organism.split(',')):
+        download_database( data_manager_dict, target_directory, options.jar_path, options.config, genome_version, organism )
 
     #save info to json file
     open( filename, 'wb' ).write( to_json_string( data_manager_dict ) )
diff -r 8952990fcab9 -r eb394dd65c98 data_manager/data_manager_snpEff_download.xml
--- a/data_manager/data_manager_snpEff_download.xml	Wed Nov 27 09:11:32 2013 -0600
+++ b/data_manager/data_manager_snpEff_download.xml	Thu Nov 28 08:16:11 2013 -0600
@@ -10,7 +10,7 @@
         "$out_file"
         </command>
     <inputs>
-        <param name="genome_databases" type="select" label="Genome Version">
+        <param name="genome_databases" type="select" display="checkboxes" multiple="true" label="Genome Version">
             <options from_data_table="snpeff_databases">
                 <filter type="sort_by" column="0" />
             </options>
diff -r 8952990fcab9 -r eb394dd65c98 snpEff.xml
--- a/snpEff.xml	Wed Nov 27 09:11:32 2013 -0600
+++ b/snpEff.xml	Thu Nov 28 08:16:11 2013 -0600
@@ -93,7 +93,9 @@
             <when value="cached">
                 <param name="genomeVersion" type="select" label="Genome">
                     <!--GENOME    DESCRIPTION-->
-                    <options from_data_table="snpeff_genomedb"/>
+                    <options from_data_table="snpeff_genomedb">
+                           <filter type="unique_value" column="0" />
+                    </options>
                 </param>
                 <param name="extra_annotations" type="select" display="checkboxes" multiple="true" label="Additional Annotations">
                        <help>These are available for only a few genomes</help>
diff -r 8952990fcab9 -r eb394dd65c98 snpEff_download.xml
--- a/snpEff_download.xml	Wed Nov 27 09:11:32 2013 -0600
+++ b/snpEff_download.xml	Thu Nov 28 08:16:11 2013 -0600
@@ -9,7 +9,9 @@
     </command>
     <inputs>
         <param name="genomeVersion" type="select" label="Genome Version">
-            <options from_data_table="snpeff_databases"/>
+            <options from_data_table="snpeff_databases">
+                <filter type="sort_by" column="0" />
+            </options>
         </param>
     </inputs>
     <outputs>