| Previous changeset 6:a55510bb8478 (2019-05-14) Next changeset 8:9d6e7d2ddbb7 (2019-05-14) |
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Commit message:
Deleted selected files |
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removed:
annovar_yaml/YAML_annovar.yml annovar_yaml/YAML_arguments_annovar.yml annovar_yaml/annovar_yaml.pl annovar_yaml/annovar_yaml.xml |
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| diff -r a55510bb8478 -r 1119dc7a2f67 annovar_yaml/YAML_annovar.yml --- a/annovar_yaml/YAML_annovar.yml Tue May 14 05:07:34 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,66 +0,0 @@ -GENERAL: - - APPLICATION: 'annovar' - PATHSCRIPTS: '/hpc/cog_bioinf/pathologie/users/snouwens/Annovar_Moldia/Annovar/' - CODING_ANNOVAR: 'coding_annovar.pl' - TABLE_ANNOVAR: 'table_annovar.pl' - LOCATION_DATABASE: '/hpc/cog_bioinf/pathologie/users/snouwens/Annovar_Moldia/Annovar/' - DOT2UNDERLINE: 'yes' - NASTRING: '.' - OTHERINFO: 'yes' - POLISH: 'yes' - REMOVE: 'yes' - THREAD: '8' - INPUTFORMAT: 'vcfinput' - SPECIES: 'human' - BUILD: 'hg19' -ANALYSIS: - DATABASES: - - NAME: 'cosmic84' - PROTOCOL: 'cosmic' - VERSION: '84' - COMMENT: '20190221' - AVAILABLE: 'yes' - REQUIRED: 'yes' - OPERATION: 'f' - COLSWANTED: '4' - - NAME: 'refgene19' - PROTOCOL: 'refgene' - VERSION: '19' - AVAILABLE: 'yes' - REQUIRED: 'yes' - COMMENT: '20190210' - OPERATION: 'g' - HGVS: 'yes' - SPLICING: '6' - EXONSPLIC: 'yes' - - NAME: 'ncbiRefSeq_UMCU' - PROTOCOL: 'ncbiRefSeq' - VERSION: '_UMCU' - AVAILABLE: 'yes' - REQUIRED: 'yes' - COMMENT: "100519" - OPERATION: 'g' - HGVS: 'yes' - SPLICING: '6' - EXONSPLIC: 'yes' - - NAME: 'avsnp150' - PROTOCOL: 'avsnp' - VERSION: '150' - AVAILABLE: 'yes' - REQUIRED: 'yes' - OPERATION: 'f' - COLSWANTED: '1' - - NAME: 'clinvar_20180603' - PROTOCOL: 'clinvar' - VERSION: '_20180603' - AVAILABLE: 'yes' - REQUIRED: 'yes' - OPERATION: 'f' - COLSWANTED: '5' - - NAME: 'class100519' - PROTOCOL: 'class' - VERSION: '100519' - AVAILABLE: 'yes' - REQUIRED: 'yes' - OPERATION: 'f' - COLSWANTED: '1' |
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| diff -r a55510bb8478 -r 1119dc7a2f67 annovar_yaml/YAML_arguments_annovar.yml --- a/annovar_yaml/YAML_arguments_annovar.yml Tue May 14 05:07:34 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,111 +0,0 @@ -GENERAL: - - APPLICATION: 'annovar' - PATHSCRIPTS: '/hpc/cog_bioinf/pathologie/users/snouwens/Annovar_Moldia/Annovar/' - CODING_ANNOVAR: 'coding_annovar.pl ' - TABLE_ANNOVAR: 'table_annovar.pl ' - LOCATION_DATABASE: '/hpc/cog_bioinf/pathologie/users/snouwens/Annovar_Moldia/Annovar/' - DOT2UNDERLINE: - yes: '--dot2underline ' - no: '' - NASTRING: '--nastring . ' - OTHERINFO: - yes: '--otherinfo ' - no: '' - POLISH: - yes: '--polish ' - no: '' - REMOVE: - yes: '--remove ' - no: '' - THREAD: '--thread 8 ' - INPUTFORMAT: - vcfinput: '--vcfinput ' - SPECIES: - human: 'humandb ' - mouse: 'mousedb ' - BUILD: '--buildver hg19 ' -ANALYSIS: - DATABASES: - - NAME: 'cosmic84' - PROTOCOL: 'cosmic' - VERSION: '84' - COMMENT: '20190221' - AVAILABLE: - yes: '1' - no: '0' - REQUIRED: - yes: '1' - no: '0' - OPERATION: 'f' - COLSWANTED: '--colswanted 4 ' - - NAME: 'refgene19' - PROTOCOL: 'refgene' - VERSION: '19' - COMMENT: '20190210' - AVAILABLE: - yes: '1' - no: '0' - REQUIRED: - yes: '1' - no: '0' - OPERATION: 'g' - HGVS: - yes: '--hgvs ' - no: '' - SPLICING: '--splicing 6 ' - EXONSPLIC: - yes: '--exonicsplicing ' - no: '' - - NAME: 'ncbiRefSeq_UMCU' - PROTOCOL: 'ncbiRefSeq' - VERSION: '_UMCU' - AVAILABLE: - yes: '1' - no: '0' - REQUIRED: - yes: '1' - no: '0' - COMMENT: "100519" - OPERATION: 'g' - HGVS: - yes: '--hgvs ' - no: '' - SPLICING: '--splicing 6 ' - EXONSPLIC: - yes: '--exonicsplicing ' - no: '' - - NAME: 'avsnp150' - PROTOCOL: 'avsnp' - VERSION: '150' - AVAILABLE: - yes: '1' - no: '0' - REQUIRED: - yes: '1' - no: '0' - OPERATION: 'f' - COLSWANTED: '--colswanted 1 ' - - NAME: 'clinvar_20180603' - PROTOCOL: 'clinvar' - VERSION: '_20180603' - COMMENT: 'blah' - AVAILABLE: - yes: '1' - no: '0' - REQUIRED: - yes: '1' - no: '0' - OPERATION: 'f' - COLSWANTED: '--colswanted 5 ' - - NAME: 'class100519' - PROTOCOL: 'class' - VERSION: '100519' - AVAILABLE: - yes: '1' - no: '0' - REQUIRED: - yes: '1' - no: '0' - OPERATION: 'f' - COLSWANTED: '--colswanted 1 ' - |
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| diff -r a55510bb8478 -r 1119dc7a2f67 annovar_yaml/annovar_yaml.pl --- a/annovar_yaml/annovar_yaml.pl Tue May 14 05:07:34 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| b'@@ -1,1047 +0,0 @@\n-#/usr/bin/perl\n-\n-#perl modules use\n-use YAML;\n-use YAML::Tiny;\n-use YAML::XS \'LoadFile\';\n-use Data::Dumper;\n-#use Data::YAML::Writer;\n-use Getopt::Long;\n-use strict;\n-\n-#input required\n-#two modes run and edit\n-#Basis Yaml file [default required]\n-#Yaml out file [required in edit mode]\n-#species [default required]\n-#build [default required]\n-#protocol [default required]\n-#protocolversion [default required]\n-\n-#basic paramters\n-my $edit = "0";\n-my $run = "0";\n-my $application = "0";\n-my $parameter_yml = "YAML_arguments_annovar.yml";\n-my $inyml;\n-my $outyml;\n-my $invcf;\n-my $outvcf;\n-my $yml_hash_arguments;\n-my %yml_hash_arguments;\n-my $yml_hash;\n-my %yml_hash;\n-my $yml_hash_edit;\n-my %yml_hash_edit;\n-my $in;\n-my $in2;\n-my %in;\n-my %in2;\n-my $writer;\n-\n-#parameter applications\n-my %annovarparameters_array;\n-my %annovarparameters_single;\n-my $annovarparameters_array;\n-my $annovarparameters_single;\n-\n-#Strings used as input parameters\n-#my $input_general_location_database;\n-#my $input_general_dir_scripts;\n-#my $input_general_location_scripts_coding_annovar;\n-#my $input_general_location_scripts_table_annovar;\n-my $input_annovar_build;\n-my $input_annovar_species;\n-my $inprotocol;\n-my $inprotocolversion;\n-my @inprotocol;\n-my @inprotocolversion;\n-\n-my $input_general_settings_dot2underline;\n-my $input_general_settings_nastring;\n-my $input_general_settings_otherinfo;\n-my $input_general_settings_polish;\n-my $input_general_settings_remove;\n-my $input_general_settings_thread;\n-my $input_general_settings_inputformat;\n-\n-my $input_databases_available;\n-my $input_databases_required;\n-\n-my $input_databases_colswanted;\n-my $input_databases_exonicsplic;\n-my $input_databases_hgvs;\n-my $input_databases_operation;\n-my $input_databases_splicing;\n-my @input_databases_colswanted;\n-my @input_databases_exonicsplic;\n-my @input_databases_hgvs;\n-my @input_databases_operation;\n-my @input_databases_splicing;\n-\n-#other variables\n-my $script;\n-my $type;\n-my $count;\n-my $column_build;\n-my $column_species;\n-my @column_build;\n-my @column_species;\n-my $pattern;\n-my $pattern2;\n-my $match;\n-my $match_value;\n-my @match_value;\n-my @readonly;\n-my %editinyml;\n-\n-#Fixed values for searching hashes\n-my $level5 = "DATABASES";\n-\n-#parameters to build command\n-my $protocol;\n-my @protocol;\n-my $operation;\n-my $argument;\n-\n-GetOptions (\n-\t#Required input\n-\t\'protocol=s\' => \\$inprotocol,\n-\t\'protocolversion=s\' => \\$inprotocolversion,\n-\t\'script=s\' => \\$script,\n-\t\'invcf=s\' => \\$invcf,\n-\t\'outvcf=s\' => \\$outvcf,\n-\t\'application=s\' => \\$application,\n- \'inyml=s\' => \\$inyml,\n- \'outyml=s\' => \\$outyml,\n- \'build=s\' => \\$input_annovar_build,\n- \'species=s\' => \\$input_annovar_species,\n-\t#Optional input\n-\t\'edit\' => \\$edit,\n-\t\'run\' => \\$run,\n-\t#variables in GENERAL\n-\t\'dot2underline=s\' => \\$input_general_settings_dot2underline,\n-\t\'nastring=s\' => \\$input_general_settings_nastring,\n-\t\'otherinfo=s\' => \\$input_general_settings_otherinfo,\n-\t\'polish=s\' => \\$input_general_settings_polish,\n-\t\'remove=s\' => \\$input_general_settings_remove,\n-\t\'thread=s\' => \\$input_general_settings_thread,\n-\t\'inputformat=s\' => \\$input_general_settings_inputformat,\n-\t#variables in DATABASES\n-\t\'colswanted=s\' => \\$input_databases_colswanted,\n-\t\'exonicsplic=s\' => \\$input_databases_exonicsplic,\n-\t\'hgvs=s\' => \\$input_databases_hgvs,\n-\t\'operation=s\' => \\$input_databases_operation,\n-\t\'splicing=s\' => \\$input_databases_splicing,\n-);\n-\n-\n-#inactive options\n-# \'drequired=s\' => \\$input_databases_required,\n-# \'davail=s\' => \\$input_databases_available,\n-\n-# \'gpathdatabase=s\' => \\$input_general_location_database,\n-#\t\'gpathscripts=s\' => \\$input_general_dir_scripts,\n-# \'gpathcodannovar=s\' => \\$input_general_location_scripts_coding_annovar,\n-# \'gpathtabannovar=s\' => \\$input_general_location_scripts_table_annovar,\n-\n-#Check input parameters\n-#Do some checks whether all required arguments are given\n-\n-#some code\n-\n-#arrays w'..b':$key2:$key3:$key4:$key5:$key6:$key7:$key8 $yml_hash->{$key1}{$key2}{$key3}{$key4}{$key5}{$key6}{$key7}{$key8}\\n";\n- }\n-\t\t\t\t\t\t }\n- } else {\n-\t\t\t\t\t\tmy $value = "$key1:$key2:$key3:$key4:$key5:$key6:$key7 $yml_hash->{$key1}{$key2}{$key3}{$key4}{$key5}{$key6}{$key7}";\n-\t\t\t\t\t\tif ( $value =~ /$pattern/ ) {\n-\t\t\t\t\t\t $match++;\n-\t\t\t\t\t\t $match_value = "$key1:$key2:$key3:$key4:$key5:$key6:$key7:$yml_hash->{$key1}{$key2}{$key3}{$key4}{$key5}{$key6}{$key7}";\n- #print "value: $key1:$key2:$key3:$key4:$key5:$key6:$key7 $yml_hash->{$key1}{$key2}{$key3}{$key4}{$key5}{$key6}{$key7}\\n";\n-\t\t\t\t\t\t}\n-\t\t\t\t\t\t#print "value: $key1:$key2:$key3:$key4:$key5:$key6:$key7 $yml_hash->{$key1}{$key2}{$key3}{$key4}{$key5}{$key6}{$key7}\\n";\n- }\n- }\n- } else {\n-\t\t\t\t\t my $value = "$key1:$key2:$key3:$key4:$key5:$key6 $yml_hash->{$key1}{$key2}{$key3}{$key4}{$key5}{$key6}";\n-\t\t\t\t\t if ( $value =~ /$pattern/ ) {\n-\t\t\t\t\t $match++;\n-\t\t\t\t\t $match_value = "$key1:$key2:$key3:$key4:$key5:$key6:$yml_hash->{$key1}{$key2}{$key3}{$key4}{$key5}{$key6}";\n- #print "value: $key1:$key2:$key3:$key4:$key5:$key6 $yml_hash->{$key1}{$key2}{$key3}{$key4}{$key5}{$key6}\\n";\n-\t\t\t\t\t }\n-\t\t\t\t\t #print "value: $key1:$key2:$key3:$key4:$key5:$key6 $yml_hash->{$key1}{$key2}{$key3}{$key4}{$key5}{$key6}\\n";\n- }\n- }\n- } else {\n-\t\t\t\t my $value = "$key1:$key2:$key3:$key4:$key5 $yml_hash->{$key1}{$key2}{$key3}{$key4}{$key5}";\n-\t\t\t\t if ( $value =~ /$pattern/ ) {\n-\t\t\t\t $match++;\n-\t\t\t\t $match_value = "$key1:$key2:$key3:$key4:$key5:$yml_hash->{$key1}{$key2}{$key3}{$key4}{$key5}";\n- #print "value: $key1:$key2:$key3:$key4:$key5 $yml_hash->{$key1}{$key2}{$key3}{$key4}{$key5}\\n";\n-\t\t\t\t }\n-\t\t\t\t #print "value: $key1:$key2:$key3:$key4:$key5 $yml_hash->{$key1}{$key2}{$key3}{$key4}{$key5}\\n";\n- }\n- }\n- } else {\n-\t\t\t my $value = "$key1:$key2:$key3:$key4 $yml_hash->{$key1}{$key2}{$key3}{$key4}";\n-\t\t\t if ( $value =~ /$pattern/ ) {\n-\t\t\t $match++;\n-\t\t\t $match_value = "$key1:$key2:$key3:$key4:$yml_hash->{$key1}{$key2}{$key3}{$key4}";\n- #print "value: $key1:$key2:$key3:$key4 $yml_hash->{$key1}{$key2}{$key3}{$key4}\\n";\n-\t\t\t }\n-\t\t\t #print "value: $key1:$key2:$key3:$key4 $yml_hash->{$key1}{$key2}{$key3}{$key4}\\n";\n- }\n- }\n- } else {\n-\t\t my $value = "$key1:$key2:$key3 $yml_hash->{$key1}{$key2}{$key3}";\n-\t\t if ( $value =~ /$pattern/ ) {\n-\t\t\t$match++;\n-\t\t\t$match_value = "$key1:$key2:$key3:$yml_hash->{$key1}{$key2}{$key3}";\n- #print "value: $key1:$key2:$key3 $yml_hash->{$key1}{$key2}{$key3}\\n";\n-\t\t }\n-\t\t #print "value: $key1:$key2:$key3 $yml_hash->{$key1}{$key2}{$key3}\\n";\n- }\n- }\n- } else {\n-\t my $value = "$key1:$key2 $yml_hash->{$key1}{$key2}";\n-\t if ( $value =~ /$pattern/ ) {\n-\t\t$match++;\n-\t\t$match_value = "$key1:$key2:$yml_hash->{$key1}{$key2}";\n- #print "value: $key1:$key2 $yml_hash->{$key1}{$key2}\\n";\n-\t }\n-\t #print "value: $key1:$key2 $yml_hash->{$key1}{$key2}\\n";\n- }\n- }\n- } else {\n- my $value = "$key1 $yml_hash->{$key1}";\n- if ( $value =~ /$pattern/ ) {\n-\t$match++;\n-\t$match_value = "$key1:$yml_hash->{$key1}";\n- #print "value: $key1 $yml_hash->{$key1}\\n";\n- }\n- #print "value: $key1 $yml_hash->{$key1}\\n";\n- }\n-}\n-\n-print "Match: $match\\n";\n-\n-return $match;\n-return $match_value;\n-} \n' |
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| diff -r a55510bb8478 -r 1119dc7a2f67 annovar_yaml/annovar_yaml.xml --- a/annovar_yaml/annovar_yaml.xml Tue May 14 05:07:34 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,26 +0,0 @@ -<tool id="annovar_yaml" name="Annovar YAML" version="0.1.0"> - <requirements> - <requirement type="package" version="5.22">perl</requirement> - <requirement type="package" version="1.27">perl-yaml</requirement> - <requirement type="package" version="1.73">perl-yaml-tiny</requirement> - <requirement type="package" version="0.74">perl-yaml-xs</requirement> - <requirement type="package" version="2.173">perl-data-dumper</requirement> - <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 - ]]></command> - - <inputs> - - <param type="data" name="yaml" format="txt" /> - <param type="data" name="vcf" format="vcf" /> - - </inputs> - <outputs> - <data name="output" format="vcf"/> - </outputs> - <help><![CDATA[ - TODO: Fill in help for Annovar YAML tool. perl 5.22 - ]]></help> -</tool> |