# HG changeset patch
# User geert-vandeweyer
# Date 1405322668 14400
# Node ID 3b27cae9b359c8cd8b8f7542b2ed7624066f67ef
# Parent  db44ff975de8aa746557cf224571df9c66f51da7
New Version. VariantDB checks for Genome Build matching using the Galaxy dbkey variable.

diff -r db44ff975de8 -r 3b27cae9b359 VCF_to_VariantDB.pl
--- a/VCF_to_VariantDB.pl	Tue Jun 10 06:01:18 2014 -0400
+++ b/VCF_to_VariantDB.pl	Mon Jul 14 03:24:28 2014 -0400
@@ -20,9 +20,9 @@
 # S = (S)erver addrress to send data to.
 # R = (r)oot of galaxy web server (/home/galaxyuser/galaxy-dist)
 # H = (H)ost of the galaxy web server (http://my.galaxy.server/galaxy/)
+# G = Genome build (dbkey)
 # F = (F)ormat of input file 
-getopts('v:u:n:a:g:o:b:B:V:c:S:R:H:F:', \%opts);  # option are in %opts
-
+getopts('v:u:n:a:g:o:b:B:V:c:S:R:H:G:F:', \%opts);  # option are in %opts
 $|++;
 #################
 ## CHECK INPUT ##
@@ -75,11 +75,12 @@
 ## TEST USER ID ##
 ##################
 $email = $opts{'u'};
-my $response = $conn->post( $url, {'CheckUser' => $email} );
+$dbkey = $opts{'G'};
+my $response = $conn->post( $url, {'CheckUser' => $email,'dbkey' => $dbkey} );
 my $content = $response->decoded_content();
 
 if ($content eq 'OK') {
-	print OUT "Testing User-existence : OK.\n";
+	print OUT "Testing User-existence and Genome Build: OK.\n";
 }
 else {
 	die("ERROR: $content");
diff -r db44ff975de8 -r 3b27cae9b359 VCF_to_VariantDB.xml
--- a/VCF_to_VariantDB.xml	Tue Jun 10 06:01:18 2014 -0400
+++ b/VCF_to_VariantDB.xml	Mon Jul 14 03:24:28 2014 -0400
@@ -1,4 +1,4 @@
-<tool id="VCF_to_DB_rev" name="VCF to VariantDB" version="0.1.2">
+<tool id="VCF_to_DB_rev" name="VCF to VariantDB" version="0.1.3">
   <description></description>
   <expand macro="requirements" />
   <macros>
@@ -13,7 +13,8 @@
       -V $__app__.security.encode_id( '%s' % $input1.id )
       ## user email, for identification in DataBase
       -u $__user_email__
-      
+      ## source file dbkey ( match against variantdb genome build)
+      -G ${input1.dbkey} 
       ## OUTPUT FILE 
 	-o $output1