| Previous changeset 7:1119dc7a2f67 (2019-05-14) Next changeset 9:4939ab9e935b (2019-05-14) |
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Commit message:
Uploaded new version of xml file containing dependency for perl 5.22 |
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added:
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 1119dc7a2f67 -r 9d6e7d2ddbb7 annovar_yaml/YAML_annovar.yml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/annovar_yaml/YAML_annovar.yml Tue May 14 05:08:45 2019 -0400 |
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| @@ -0,0 +1,66 @@ +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 1119dc7a2f67 -r 9d6e7d2ddbb7 annovar_yaml/YAML_arguments_annovar.yml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/annovar_yaml/YAML_arguments_annovar.yml Tue May 14 05:08:45 2019 -0400 |
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| @@ -0,0 +1,111 @@ +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 1119dc7a2f67 -r 9d6e7d2ddbb7 annovar_yaml/annovar_yaml.pl --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/annovar_yaml/annovar_yaml.pl Tue May 14 05:08:45 2019 -0400 |
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| b'@@ -0,0 +1,1047 @@\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 1119dc7a2f67 -r 9d6e7d2ddbb7 annovar_yaml/annovar_yaml.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/annovar_yaml/annovar_yaml.xml Tue May 14 05:08:45 2019 -0400 |
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| @@ -0,0 +1,26 @@ +<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> |