Mercurial > repos > geert-vandeweyer > vcf_to_variantdb
changeset 9:3b27cae9b359 draft
New Version. VariantDB checks for Genome Build matching using the Galaxy dbkey variable.
| author | geert-vandeweyer |
|---|---|
| date | Mon, 14 Jul 2014 03:24:28 -0400 |
| parents | db44ff975de8 |
| children | d5040a542e9d |
| files | VCF_to_VariantDB.pl VCF_to_VariantDB.xml |
| diffstat | 2 files changed, 8 insertions(+), 6 deletions(-) [+] |
line wrap: on
line diff
--- 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");
--- 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