# HG changeset patch
# User niels
# Date 1560167599 14400
# Node ID ce16079341bfb4762f90dbb92067cdabbe2544a8
# Parent  ee5053b5e72b76a81cfb5b0b86a3727e8261bb08
Uploaded

diff -r ee5053b5e72b -r ce16079341bf annovar_yaml.zip
Binary file annovar_yaml.zip has changed
diff -r ee5053b5e72b -r ce16079341bf annovar_yaml/annovar_yaml.pl
--- a/annovar_yaml/annovar_yaml.pl	Mon Jun 10 07:25:08 2019 -0400
+++ b/annovar_yaml/annovar_yaml.pl	Mon Jun 10 07:53:19 2019 -0400
@@ -37,7 +37,8 @@
 my $run = "0";
 my $application = "0";
 #arguments yaml file is fixed!
-my $parameter_yml = "YAML_arguments_annovar.yml";
+#my $paryml = "YAML_arguments_annovar.yml";
+my $paryml;
 my $inyml;
 my $outyml;
 my $invcf;
@@ -131,6 +132,7 @@
 	'script=s' => \$script,
 	'invcf=s' => \$invcf,
 	'outvcf=s' => \$outvcf,
+        'paryml=s' => \$paryml,
 	'application=s' => \$application,
         'inyml=s' => \$inyml,
         'outyml=s' => \$outyml,
@@ -371,18 +373,18 @@
 #print "Finished loading second yml...\n";
 
 #Load ymlhash with arguments
-#$in = $parameter_yml;
+#$in = $paryml;
 #openyml_read($in);
-#$in = $parameter_yml;
+#$in = $paryml;
 #load_arguments($in);
 #print "Finished loading arguments...\n";
 
 
 #Fill hashes with input yaml files as defined in input and fixed arguments yaml
-openyml_read ($parameter_yml);
+openyml_read ($paryml);
 openyml_read ($inyml);
 load ($inyml, %yml_hash, $yml_hash);
-load_arguments ($parameter_yml, %yml_hash_arguments, $yml_hash_arguments);
+load_arguments ($paryml, %yml_hash_arguments, $yml_hash_arguments);
 
 ##Check input yaml files format
 ##Pickup arguments from YAML to run command
@@ -460,7 +462,7 @@
 
   foreach (@symlinkfolder_building_blocks) {
     $in = $inyml;
-    $in2 = $parameter_yml;
+    $in2 = $paryml;
     #print "loop1:$_\n";
     my @values = split /\,/, $_;
     foreach (@values) {
@@ -594,7 +596,7 @@
 #Start building command to run
 foreach (@command_building_blocks) {
   $in = $inyml;
-  $in2 = $parameter_yml;
+  $in2 = $paryml;
   #print "loop1:$_\n";
   if ( $_ =~ /^,$/ ) {
     print "[NOT YAML] $_ is separator and does not require matching!\n";
@@ -650,7 +652,7 @@
   #Use parse_lookup to find argument and create symlinks in analysis database folder
   foreach (@softlink_building_blocks) {
     $in = $inyml;
-    $in2 = $parameter_yml;
+    $in2 = $paryml;
     my @values = split /\,/, $_;
     foreach (@values) {
       if ( $_ !~ /^parse[12]$/ ) { 
diff -r ee5053b5e72b -r ce16079341bf annovar_yaml/annovar_yaml.xml
--- a/annovar_yaml/annovar_yaml.xml	Mon Jun 10 07:25:08 2019 -0400
+++ b/annovar_yaml/annovar_yaml.xml	Mon Jun 10 07:53:19 2019 -0400
@@ -7,7 +7,7 @@
         <requirement type="package" version="2.50">perl-getopt-long</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
-        perl $__tool_directory__/annovar_yaml.pl --invcf $vcf --inyml $yaml --outvcf $output
+        perl $__tool_directory__/annovar_yaml.pl --paryml /data/annovar/YAML_arguments_annovar.yml --invcf $vcf --inyml $yaml --outvcf $output
     ]]></command>
 
     <inputs>