Mercurial > repos > jjohnson > snpeff
changeset 18:36f3c82323e6
Use tool_data_table with key and version columns added to allow for multiple versions in a .loc file
| author | Jim Johnson <jj@umn.edu> |
|---|---|
| date | Tue, 13 Jan 2015 13:36:11 -0600 |
| parents | 13d81e5226cd |
| children | 2e37b58fc24d |
| files | readme.rst repository_dependencies.xml snpEff.xml snpEff_databases.xml snpEff_download.xml snpEff_macros.xml tool-data/snpeff4_annotations.loc.sample tool-data/snpeff4_databases.loc.sample tool-data/snpeff4_genomedb.loc.sample tool-data/snpeff4_regulationdb.loc.sample tool-data/snpeffv_annotations.loc.sample tool-data/snpeffv_databases.loc.sample tool-data/snpeffv_genomedb.loc.sample tool-data/snpeffv_regulationdb.loc.sample tool_data_table_conf.xml.sample |
| diffstat | 15 files changed, 146 insertions(+), 95 deletions(-) [+] |
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--- a/readme.rst Mon Nov 10 09:33:36 2014 -0600 +++ b/readme.rst Tue Jan 13 13:36:11 2015 -0600 @@ -1,20 +1,38 @@ -These are galaxy tools for SnpEff a variant annotation and effect prediction tool by Pablo Cingolani. +SnpEff wrappers +=============== + +These are galaxy tools for SnpEff_, a variant annotation and effect prediction tool by Pablo Cingolani. It annotates and predicts the effects of variants on genes (such as amino acid changes). -( http://snpeff.sourceforge.net/ ) + +.. _SnpEff: http://snpeff.sourceforge.net/ + + +This repository let you automatically install SnpEff and SnpSift. +This will use the default location for genome reference downloads from the ``snpEff.config`` file: -This repository contains a tool_dependencies.xml file that will attempt to automatically install SnpEff and SnpSift. + data_dir = ~/snpEff/data/ + +You can manually edit the installed ``snpEff.config`` file and change the location, or you can create a symbolic link to the desired data location from ``~/snpEff``. + +The genome reference options used by the tools "SnpEff" (snpEff.xml) and "SnpEff Download" (snpEff_download.xml) are taken from the ``tool-data/snpeffect_genomedb.loc`` file. +You can fill this file by running the following command: -The genome reference options used by the tools: - "SnpEff" snpEff.xml - "SnpEff Download" snpEff_download.xml -are taken from: tool-data/snpeffect_genomedb.loc + java -jar snpEff.jar databases | tail -n +3 | cut -f 1,2 | awk '{ gsub(/_/, " ", $2); printf "%s\\t%s : %s\\n", $1, $2, $1 }' | sort -k 2 > snpeffect_genomedb.loc + +There are 2 datamanagers to download and install prebuilt SnpEff genome databases: + +* data_manager_snpeff_databases: generates a list of available SnpEff genome databases into the ``tool-data/snpeff_databases.loc`` file +* data_manager_snpeff_download: downloads a SnpEff genome database selected from ``tool-data/snpeff_databases.loc`` and adds entries to ``snpeff_genomedb.loc``, ``snpeff_regulationdb.loc`` and ``snpeff_annotations.loc`` + +SnpEff citation: |Cingolani2012program|_. -There are 2 datamanagers to download and install prebuilt SnpEff Genome databases: - data_manager_snpeff_databases - generates a list of available SnpEff genome databases into the tool-data/snpeff_databases.loc - data_manager_snpeff_download - downloads a SnpEff genome database selected from: tool-data/snpeff_databases.loc and adds entries to snpeff_genomedb.loc,snpeff_regulationdb.loc,snpeff_annotations.loc +.. |Cingolani2012program| replace:: Cingolani, P., Platts, A., Wang, L. L., Coon, M., Nguyen, T., Wang, L., Land, S. J., Lu, X., Ruden, D. M. (2012) A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of *Drosophila melanogaster* strain w1118; iso-2; iso-3. *Fly* 6(2):80-92 +.. _Cingolani2012program: https://www.landesbioscience.com/journals/fly/article/19695/ + +SnpSift citation: |Cingolani2012using|_. -SnpEff citation: -"A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3.", Cingolani P, Platts A, Wang le L, Coon M, Nguyen T, Wang L, Land SJ, Lu X, Ruden DM. Fly (Austin). 2012 Apr-Jun;6(2):80-92. PMID: 22728672 [PubMed - in process] +.. |Cingolani2012using| replace:: Cingolani, P., Patel, V. M., Coon, M., Nguyen, T., Land, S. J., Ruden, D. M., Lu, X. (2012) Using *Drosophila melanogaster* as a model for genotoxic chemical mutational studies with a new program, SnpSift. *Front. Genet.* 3:35 +.. _Cingolani2012using: http://journal.frontiersin.org/Journal/10.3389/fgene.2012.00035/ -SnpSift citation: -"Using Drosophila melanogaster as a model for genotoxic chemical mutational studies with a new program, SnpSift", Cingolani, P., et. al., Frontiers in Genetics, 3, 2012. +Wrapper authors: Jim Johnson +
--- a/repository_dependencies.xml Mon Nov 10 09:33:36 2014 -0600 +++ b/repository_dependencies.xml Tue Jan 13 13:36:11 2015 -0600 @@ -1,4 +1,5 @@ <?xml version="1.0"?> <repositories description="This requires the SnpEff datatype definitions."> - <repository name="snpeff_datatypes" owner="jjohnson" changeset_revision="b33911fdbac4" toolshed="http://testtoolshed.g2.bx.psu.edu/" /> + <repository name="snpeff_datatypes" owner="jjohnson" changeset_revision="9efd0d32fe8a" toolshed="http://testtoolshed.g2.bx.psu.edu/" /> + <repository name="snpeff_datatype_v4_0" owner="jjohnson" changeset_revision="dc8dfd3f9da8" toolshed="http://testtoolshed.g2.bx.psu.edu/" /> </repositories>
--- a/snpEff.xml Mon Nov 10 09:33:36 2014 -0600 +++ b/snpEff.xml Tue Jan 13 13:36:11 2015 -0600 @@ -1,13 +1,14 @@ -<tool id="snpEff" name="SnpEff" version="4.0.1"> +<tool id="snpEff" name="SnpEff" version="@WRAPPER_VERSION@.2"> <description>Variant effect and annotation</description> <expand macro="requirements" /> <macros> <import>snpEff_macros.xml</import> </macros> <command> +<![CDATA[ java -Xmx6G -jar \$SNPEFF_JAR_PATH/snpEff.jar eff -c \$SNPEFF_JAR_PATH/snpEff.config - -i $inputFormat -o $outputFormat -upDownStreamLen $udLength + -i $inputFormat -o ${outputConditional.outputFormat} -upDownStreamLen $udLength #if $spliceSiteSize and $spliceSiteSize.__str__ != '': -spliceSiteSize $spliceSiteSize #end if @@ -32,7 +33,7 @@ -interval $intervals #end if #if $statsFile: - -stats snpeff_report + -stats $statsFile #end if #if $offset.__str__ != 'default': ${offset} @@ -66,10 +67,19 @@ -download $snpDb.genome_version #end if - $input > $snpeff_output + $input > $snpeff_output ; #if $statsFile: - && mkdir $statsFile.extra_files_path && cp snpeff_report.genes.txt $statsFile.extra_files_path + #import os + #set $genes_file = str($statsFile) + '.genes.txt' + #set $genes_file_name = os.path.split($genes_file)[-1] + mkdir $statsFile.files_path; + mv $genes_file #echo os.path.join($statsFile.files_path, $genes_file_name)#; #end if + #if $outputConditional.outputFormat == 'gatk' and $outputConditional.gatk_v1 + ## Replace real SnpEff version with 2.0.5 to prevent this GATK 1.x error: "The version of SnpEff used to generate the SnpEff input file (x.x) is not currently supported by the GATK. Supported versions are: [2.0.5]" + sed -i 's/^\#\#SnpEffVersion="\(\S*\s\)/\#\#SnpEffVersion="2.0.5 - real is \1/' $snpeff_output + #end if +]]> </command> <inputs> <param format="vcf,tabular,pileup,bed" name="input" type="data" label="Sequence changes (SNPs, MNPs, InDels)"/> @@ -81,12 +91,22 @@ <option value="bed">BED (Deprecated)</option> </param> - <param name="outputFormat" type="select" label="Output format"> - <option value="vcf" selected="true">VCF (only if input is VCF)</option> - <option value="txt">Tabular</option> - <option value="bed">BED</option> - <option value="bedAnn">BED Annotations</option> - </param> + <conditional name="outputConditional"> + <param name="outputFormat" type="select" label="Output format"> + <option value="vcf" selected="true">VCF (only if input is VCF)</option> + <option value="gatk">GATK-compatible VCF (only if input is VCF)</option> + <option value="txt">Tabular</option> + <option value="bed">BED</option> + <option value="bedAnn">BED annotations</option> + </param> + <when value="vcf" /> + <when value="gatk"> + <param name="gatk_v1" type="boolean" checked="true" label="Compatible with GATK 1.x" /> + </when> + <when value="txt" /> + <when value="bed" /> + <when value="bedAnn" /> + </conditional> <conditional name="snpDb"> <param name="genomeSrc" type="select" label="Genome source"> @@ -97,35 +117,36 @@ <when value="cached"> <param name="genomeVersion" type="select" label="Genome"> <!--GENOME DESCRIPTION--> - <options from_data_table="snpeff4_genomedb"> - <filter type="unique_value" column="0" /> + <options from_data_table="snpeffv_genomedb"> + <filter type="static_value" name="snpeff_version" value="SnpEff4.1" column="1"/> + <filter type="unique_value" column="2" /> </options> </param> - <param name="extra_annotations" type="select" display="checkboxes" multiple="true" label="Additional Annotations"> + <param name="extra_annotations" type="select" display="checkboxes" multiple="true" label="Additional annotations"> <help>These are available for only a few genomes</help> - <options from_data_table="snpeff4_annotations"> - <filter type="param_value" ref="genomeVersion" key="genome" column="0" /> + <options from_data_table="snpeffv_annotations"> + <filter type="param_value" ref="genomeVersion" key="genome" column="2" /> <filter type="unique_value" column="1" /> </options> </param> - <param name="regulation" type="select" display="checkboxes" multiple="true" label="Non-coding and regulatory Annotation"> + <param name="regulation" type="select" display="checkboxes" multiple="true" label="Non-coding and regulatory annotation"> <help>These are available for only a few genomes</help> - <options from_data_table="snpeff4_regulationdb"> - <filter type="param_value" ref="genomeVersion" key="genome" column="0" /> + <options from_data_table="snpeffv_regulationdb"> + <filter type="param_value" ref="genomeVersion" key="genome" column="2" /> <filter type="unique_value" column="1" /> </options> </param> </when> <when value="history"> - <param format="snpeffdbv4" name="snpeff_db" type="data" label="SnpEff Genome Version Data"/> + <param format="snpeffdbv41" name="snpeff_db" type="data" label="SnpEff Genome Version Data"/> <!-- From metadata --> - <param name="extra_annotations" type="select" display="checkboxes" multiple="true" label="Additional Annotations"> + <param name="extra_annotations" type="select" display="checkboxes" multiple="true" label="Additional annotations"> <help>These are available for only a few genomes</help> <options> <filter type="data_meta" ref="snpeff_db" key="annotation" /> </options> </param> - <param name="regulation" type="select" display="checkboxes" multiple="true" label="Non-coding and regulatory Annotation"> + <param name="regulation" type="select" display="checkboxes" multiple="true" label="Non-coding and regulatory annotation"> <help>These are available for only a few genomes</help> <options> <filter type="data_meta" ref="snpeff_db" key="regulation" /> @@ -134,7 +155,7 @@ </when> <when value="named"> <param name="genome_version" type="text" size="40" value="" label="Snpff Genome Version Name (e.g. GRCh38.76)"> - <help>http://sourceforge.net/projects/snpeff/files/databases/v4_0/</help> + <help>@SNPEFF_DATABASE_URL@</help> <validator type="regex" message="A genome version name is required">\S+</validator> </param> </when> @@ -153,7 +174,7 @@ <param name="spliceSiteSize" type="select" optional="true" label="Set size for splice sites (donor and acceptor) in bases" help="Default: 2"> <option value="1">1 base</option> - <option value="2">2 bases</option> + <option value="2" selected="true">2 bases</option> <option value="3">3 bases</option> <option value="4">4 bases</option> <option value="5">5 bases</option> @@ -165,24 +186,24 @@ <param name="filterHomHet" type="select" display="radio" label="Filter homozygous / heterozygous changes"> <option value="no_filter" selected="true">No filter (analyze everything)</option> - <option value="-hom">Analyze homozygous sequence changes only </option> - <option value="-het">Analyze heterozygous sequence changes only </option> + <option value="-hom">Analyze homozygous sequence changes only</option> + <option value="-het">Analyze heterozygous sequence changes only</option> </param> <!-- The tool testing code can not handle select,radio,check boxes values that start with '-', so the '-' is added in the command generation --> <param name="filterIn" type="select" display="radio" label="Filter sequence changes"> <option value="no_filter" selected="true">No filter (analyze everything)</option> - <option value="-del">Analyze deletions only </option> - <option value="-ins">Analyze insertions only </option> - <option value="-mnp">Only MNPs (multiple nucleotide polymorphisms) </option> - <option value="-snp">Only SNPs (single nucleotide polymorphisms) </option> + <option value="-del">Analyze deletions only</option> + <option value="-ins">Analyze insertions only</option> + <option value="-mnp">Only MNPs (multiple nucleotide polymorphisms)</option> + <option value="-snp">Only SNPs (single nucleotide polymorphisms)</option> </param> <param name="annotations" type="select" display="checkboxes" multiple="true" label="Annotation options"> - <option value="-cancer">Perform 'cancer' comparissons (Somatic vs Germline)</option> + <option value="-cancer">Perform 'cancer' comparisons (somatic vs. germline)</option> <option value="-canon">Only use canonical transcripts</option> <option value="-geneId">Use gene ID instead of gene name (VCF output)</option> - <option value="-lof">Add loss of function (LOF) and Nonsense mediated decay (NMD) tags</option> + <option value="-lof">Add loss of function (LOF) and nonsense mediated decay (NMD) tags</option> <option value="-oicr">Add OICR tag in VCF file</option> <option value="-onlyReg">Only use regulation tracks</option> <option value="-classic">Use Classic Effect names and amino acid variant annotations (NON_SYNONYMOUS_CODING vs missense_variant and G180R vs p.Gly180Arg/c.538G>C)</option> @@ -217,13 +238,12 @@ <outputs> <data format="vcf" name="snpeff_output" > <change_format> - <when input="outputFormat" value="vcf" format="vcf" /> - <when input="outputFormat" value="txt" format="tabular" /> - <when input="outputFormat" value="bed" format="bed" /> - <when input="outputFormat" value="bedAnn" format="bed" /> + <when input="outputConditional.outputFormat" value="txt" format="tabular" /> + <when input="outputConditional.outputFormat" value="bed" format="bed" /> + <when input="outputConditional.outputFormat" value="bedAnn" format="bed" /> </change_format> </data> - <data format="html" name="statsFile" label="{tool.name} on ${on_string} Summary Report" from_work_dir="snpeff_report"> + <data format="html" name="statsFile" label="${tool.name} on ${on_string} - stats"> <filter>generate_stats == True</filter> </data> </outputs> @@ -287,7 +307,7 @@ <param name="genome_version" value="testCase"/> <param name="udLength" value="0"/> <param name="filterHomHet" value="no_filter"/> - <param name="filterIn" value="del"/> + <param name="filterIn" value="+-del"/> <!-- <param name="filterOut" value=""/> --> @@ -333,5 +353,6 @@ @CITATION_SECTION@ </help> + <expand macro="citations" /> </tool>
--- a/snpEff_databases.xml Mon Nov 10 09:33:36 2014 -0600 +++ b/snpEff_databases.xml Tue Jan 13 13:36:11 2015 -0600 @@ -1,11 +1,13 @@ -<tool id="snpEff_databases" name="SnpEff Available Databases" version="4.0.0"> +<tool id="snpEff_databases" name="SnpEff Available Databases" version="@WRAPPER_VERSION@.0"> <description></description> <expand macro="requirements" /> <macros> <import>snpEff_macros.xml</import> </macros> <command> +<![CDATA[ java -jar \$SNPEFF_JAR_PATH/snpEff.jar databases | grep -v '^---' | sed 's/^Genome/#Genome/' | sed 's/ *//g' > $snpeff_dbs +]]> </command> <inputs> </inputs>
--- a/snpEff_download.xml Mon Nov 10 09:33:36 2014 -0600 +++ b/snpEff_download.xml Tue Jan 13 13:36:11 2015 -0600 @@ -1,21 +1,22 @@ -<tool id="snpEff_download" name="SnpEff Download" version="4.0.1"> +<tool id="snpEff_download" name="SnpEff Download" version="@WRAPPER_VERSION@.2"> <description>Download a new database</description> <expand macro="requirements" /> <macros> <import>snpEff_macros.xml</import> </macros> <command> - java -jar \$SNPEFF_JAR_PATH/snpEff.jar download -c \$SNPEFF_JAR_PATH/snpEff.config -dataDir $snpeff_db.extra_files_path -v $genome_version > $logfile +<![CDATA[ + java -jar \$SNPEFF_JAR_PATH/snpEff.jar download -c \$SNPEFF_JAR_PATH/snpEff.config -dataDir $snpeff_db.files_path -v $genome_version +]]> </command> <inputs> - <param name="genome_version" type="text" size="40" value="" label="Snpff Genome Version Name (e.g. GRCh37.74)"> - <help>http://sourceforge.net/projects/snpeff/files/databases/</help> + <param name="genome_version" type="text" size="40" value="" label="Select the genome version you want to download (e.g. GRCh37.74)"> + <help>@SNPEFF_DATABASE_URL@</help> <validator type="regex" message="A genome version name is required">\S+</validator> </param> </inputs> <outputs> - <data format="txt" name="logfile" /> - <data format="snpeffdbv4" name="snpeff_db" label="${tool.name} ${genome_version}" /> + <data format="snpeffdbv41" name="snpeff_db" label="${tool.name} ${genome_version}" /> </outputs> <expand macro="stdio" /> <help> @@ -25,5 +26,6 @@ @CITATION_SECTION@ </help> + <expand macro="citations" /> </tool>
--- a/snpEff_macros.xml Mon Nov 10 09:33:36 2014 -0600 +++ b/snpEff_macros.xml Tue Jan 13 13:36:11 2015 -0600 @@ -10,6 +10,8 @@ <exit_code range="1:" level="fatal" description="Error" /> </stdio> </xml> + <token name="@WRAPPER_VERSION@">4.0</token> + <token name="@SNPEFF_DATABASE_URL@">http://sourceforge.net/projects/snpeff/files/databases/v4_1/</token> <token name="@EXTERNAL_DOCUMENTATION@"> For details about this tool, please go to: @@ -23,10 +25,13 @@ For the underlying tool, please cite the following two publications: SnpEff citation: -"A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3.", Cingolani P, Platts A, Wang le L, Coon M, Nguyen T, Wang L, Land SJ, Lu X, Ruden DM. Fly (Austin). 2012 Apr-Jun;6(2):80-92. PMID: 22728672 [PubMed - in process] - -SnpSift citation: -"Using Drosophila melanogaster as a model for genotoxic chemical mutational studies with a new program, SnpSift", Cingolani, P., et. al., Frontiers in Genetics, 3, 2012. +"A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3.", Cingolani P, Platts A, Wang le L, Coon M, Nguyen T, Wang L, Land SJ, Lu X, Ruden DM. Fly 6(2):80-92, 2012 </token> + <xml name="citations"> + <citations> + <citation type="doi">10.4161/fly.19695</citation> + <yield /> + </citations> + </xml> </macros>
--- a/tool-data/snpeff4_annotations.loc.sample Mon Nov 10 09:33:36 2014 -0600 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,5 +0,0 @@ -## Regulation Databases for SnpEff -## These are from the list on: http://snpeff.sourceforge.net/download.html -#genome annotation_name description -#GRCh37.71 nextprot nextprot -#GRCh37.71 motif motif
--- a/tool-data/snpeff4_databases.loc.sample Mon Nov 10 09:33:36 2014 -0600 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,5 +0,0 @@ -## Available Databases for SnpEff -## These are from the list on: http://snpeff.sourceforge.net/download.html -## the Description field in this sample is "Genome : Version" -#Version Description -#GRCh37.68 Homo sapiens : GRCh37.68
--- a/tool-data/snpeff4_genomedb.loc.sample Mon Nov 10 09:33:36 2014 -0600 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,5 +0,0 @@ -## Downloaded Databases for SnpEff -## These are from the list on: http://snpeff.sourceforge.net/download.html -## the Description field in this sample is "Genome : Version" -#Version Description data_dir path -#GRCh37.68 Homo sapiens : GRCh37.68 /home/galaxy/snpEff/data
--- a/tool-data/snpeff4_regulationdb.loc.sample Mon Nov 10 09:33:36 2014 -0600 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,4 +0,0 @@ -## Regulation Databases for SnpEff -## These are from the list on: http://snpeff.sourceforge.net/download.html -#genome regulation_name description -#GRCh37.70 CD4 CD4
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/snpeffv_annotations.loc.sample Tue Jan 13 13:36:11 2015 -0600 @@ -0,0 +1,5 @@ +## Regulation Databases for SnpEff +## These are from the list on: http://snpeff.sourceforge.net/download.html +#key snpeff_version genome annotation_name description +#SnpEff4.0_GRCh37.75 SnpEff4.0 GRCh37.75 nextprot nextprot +#SnpEff4.0_GRCh38.76 SnpEff4.1 GRCh38.76 motif motif
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/snpeffv_databases.loc.sample Tue Jan 13 13:36:11 2015 -0600 @@ -0,0 +1,5 @@ +## Available Databases for SnpEff +## These are from the list on: http://snpeff.sourceforge.net/download.html +## the Description field in this sample is "Genome : Version" +#key snpeff_version Version Description +#SnpEff4.0_GRCh37.75 SnpEff4.0 GRCh37.75 Homo sapiens : GRCh37.75
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/snpeffv_genomedb.loc.sample Tue Jan 13 13:36:11 2015 -0600 @@ -0,0 +1,6 @@ +## Downloaded Databases for SnpEff +## These are from the list on: http://snpeff.sourceforge.net/download.html +## the Description field in this sample is "Genome : Version" +#Key snpeff_version Version Description data_dir path +#SnpEff4.0_GRCh37.74 SnpEff4.0 GRCh37.74 Homo sapiens : GRCh37.74 /home/galaxy/snpEff/v4_0/data +#SnpEff4.1_GRCh38.76 SnpEff4.1 GRCh38.76 Homo sapiens : GRCh38.76 /home/galaxy/snpEff/v4_1/data
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/snpeffv_regulationdb.loc.sample Tue Jan 13 13:36:11 2015 -0600 @@ -0,0 +1,5 @@ +## Regulation Databases for SnpEff +## These are from the list on: http://snpeff.sourceforge.net/download.html +#Key snpeff_version genome regulation_name description +#SnpEff4.0_GRCh37.74 SnpEff4.0 GRCh37.74 CD4 CD4 +#SnpEff4.1_GRCh38.76 SnpEff4.1 GRCh38.76 CD4 CD4
--- a/tool_data_table_conf.xml.sample Mon Nov 10 09:33:36 2014 -0600 +++ b/tool_data_table_conf.xml.sample Tue Jan 13 13:36:11 2015 -0600 @@ -1,19 +1,19 @@ <tables> - <table name="snpeff4_databases" comment_char="#"> - <columns>value, name</columns> - <file path="tool-data/snpeff4_databases.loc" /> + <table name="snpeffv_databases" comment_char="#"> + <columns>key, version, value, name</columns> + <file path="tool-data/snpeffv_databases.loc" /> </table> - <table name="snpeff4_genomedb" comment_char="#"> - <columns>value, name, path</columns> - <file path="tool-data/snpeff4_genomedb.loc" /> + <table name="snpeffv_genomedb" comment_char="#"> + <columns>key, version, value, name, path</columns> + <file path="tool-data/snpeffv_genomedb.loc" /> </table> - <table name="snpeff4_regulationdb" comment_char="#"> - <columns>genome, value, name</columns> - <file path="tool-data/snpeff4_regulationdb.loc" /> + <table name="snpeffv_regulationdb" comment_char="#"> + <columns>key, version, genome, value, name</columns> + <file path="tool-data/snpeffv_regulationdb.loc" /> </table> - <table name="snpeff4_annotations" comment_char="#"> - <columns>genome, value, name</columns> - <file path="tool-data/snpeff4_annotations.loc" /> + <table name="snpeffv_annotations" comment_char="#"> + <columns>key, version, genome, value, name</columns> + <file path="tool-data/snpeffv_annotations.loc" /> </table> </tables>