| Previous changeset 17:ee5053b5e72b (2019-06-10) Next changeset 19:0044b989f60f (2019-06-10) |
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Commit message:
Uploaded |
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modified:
annovar_yaml/annovar_yaml.pl annovar_yaml/annovar_yaml.xml |
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removed:
annovar_yaml.zip |
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| diff -r ee5053b5e72b -r ce16079341bf annovar_yaml.zip |
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| Binary file annovar_yaml.zip has changed |
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| 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 |
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| @@ -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 ( $_ !~ /^parse[12]$/ ) { |
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| 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 |
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| @@ -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> |