Mercurial > repos > elixir-it > covacs_annovar
changeset 0:a28564bf926a draft
Uploaded
author | elixir-it |
---|---|
date | Thu, 08 Nov 2018 12:13:56 -0500 |
parents | |
children | ab0933ba7535 |
files | covacs_annovar.xml mv_untar_annovar.sh tool-data/annovar.loc.sample tool_data_table_conf.xml.sample |
diffstat | 4 files changed, 128 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/covacs_annovar.xml Thu Nov 08 12:13:56 2018 -0500 @@ -0,0 +1,102 @@ +<tool id="annovar_elixir" name="annovar" version="1"> + <description> annovar, annotate variants using specified gene annotations, regions, and filtering databases</description> + <requirements> + <requirement type="package" >perl</requirement> + </requirements> + <command> <![CDATA[ + ### call the .sh to untar the package + sh $__tool_directory__/mv_untar_annovar.sh && + + ## Variant annotation; make sure to include entry in indexes table for build database. + + #set protocol = [] + #set operation = [] + + ## Add gene annotations. + #if $gene_anns: + #silent protocol.append( str( $gene_anns ) ) + #silent operation.append( ','.join( ['g' for t in range( str($gene_anns).count(',') + 1 )] ) ) + #end if + + ## Add filters. + #if $filters: + #silent protocol.append( str( $filters ) ) + #silent operation.append( ','.join( ['f' for t in range( str($filters).count(',') + 1 )] ) ) + #end if + ##add resions. + #if $regions: + #silent protocol.append( str( $regions ) ) + #silent operation.append( ','.join( ['r' for t in range( str($filters).count(',') + 1 )] ) ) + #end if + + + #set protocol = ','.join( $protocol ) + #set operation = ','.join( $operation ) + + ## Annotate variants. + perl \$CONDA_PREFIX/annovar/table_annovar.pl $input1 $location_db.fields.path --buildver $assembly --out annovarAnnotation --protocol $protocol --operation $operation --nastring $NA --vcfinput + ]]> + </command> + <inputs> + <param name="assembly" type="select" label="Genome_assembly" multiple="no"> + <option value="hg18" >hg18</option> + <option value="hg19" selected="true">hg19</option> + <option value="hg38" >hg38</option> + </param> + <param name="NA" type="text" label="substitute NA with:"/> + <param format="vcf" name="input1" type="data" label="VCF" help="vcf input file"/> + <param name="gene_anns" type="select" multiple="yes" optional="true"> + <options from_data_table="annovar"> + <filter type="static_value" name="type" value="gene_ann" column="1"/> + <filter type="sort_by" column="0"/> + </options> + </param> + <param name="filters" type="select" multiple="yes" optional="true"> + <options from_data_table="annovar"> + <filter type="static_value" name="type" value="filter" column="1"/> + <filter type="sort_by" column="0"/> + </options> + </param> + <param name="regions" type="select" multiple="yes" optional="true"> + <options from_data_table="annovar"> + <filter type="static_value" name="type" value="regions" column="1"/> + <filter type="sort_by" column="0"/> + </options> + </param> + <param name="location_db" type="select" display="radio"> + <options from_data_table="annovar"> + <filter type="static_value" name="type" value="location" column="1"/> + <filter type="sort_by" column="0"/> + </options> + </param> + </inputs> + <outputs> + <data format="vcf" name="output" from_work_dir="annovarAnnotation.????_multianno.vcf" label="${tool.name} on ${on_string}"/> + </outputs> + <stdio> + <regex match=".*" source="both" level="log" description="tool progress"/> + </stdio> + <tests> + <test> + </test> + </tests> + <help> +**What it does** + +This tool will annotate variants using specified gene annotations, regions, and filtering databases. Input is a VCF dataset, and output is a table of annotations for each variant in the +VCF dataset or a VCF dataset with the annotations in INFO fields. + + +**Important Usage Note** + +ANNOVAR is open-source and free for non-profit use. If you use it for commercial purposes, please contact BIOBASE (info@biobase-international.com) directly for license related issues. Also see http://www.openbioinformatics.org/annovar/annovar_faq.html#license + +**IMPORTANT** to get the wrapper ready to start the admin user have to download annovar."version".tar.gz and then move it in the conda_prefix folder, the path of the conda_prefix is written in the galaxy.ini(or .yml) file + + + </help> + <citations> + <citation type="doi">10.1093/nar/gkq603</citation> + <citation type="doi">10.1186/s12864-018-4508-1</citation> + </citations> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mv_untar_annovar.sh Thu Nov 08 12:13:56 2018 -0500 @@ -0,0 +1,11 @@ +#!/bin/bash +# if the symbolic link is not present in the annovar conda virtual environment the script search for the tar.gz in the conda_prefix, +# untar the archive and make a symbolic link to the $CONDA_PREFIX of the conda virtual environment +if [[ ! -d $CONDA_PREFIX/annovar ]] ; then + tar -zxvf $CONDA_PREFIX/../../annovar.*.tar.gz -C $CONDA_PREFIX/../../ && + echo start untar && + ln -s $CONDA_PREFIX/../../annovar $CONDA_PREFIX && + echo all done +else + echo annovar was present +fi
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/annovar.loc.sample Thu Nov 08 12:13:56 2018 -0500 @@ -0,0 +1,10 @@ + +#location of humandb the fields are tab delimited +db location /export/_conda/annovar/humandb + + + +#definition of present db name + type(gene_ann, region, filter) the fields are tab delimited +refGene gene_ann +prova gene_ann +exac03 filter
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Thu Nov 08 12:13:56 2018 -0500 @@ -0,0 +1,5 @@ +<!-- Location of annovar_elixir loc file --> +<table name="annovar" comment_char="#"> + <columns> value, type, path</columns> + <file path="tool-data/annovar.loc" /> +</table>