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<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 
	bash $__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 $NA --vcfinput
    ]]>
  </command>
  <inputs>
    <param name="assembly" type="select" label="Genome_assembly" multiple="no">
      <option value="hg18" >hg18</option>
      <option value="hg19" selected="true">hg19</option>
      <option value="hg38" >hg38</option>
    </param>
    <param name="NA" type="text" value="." label="substitute NA with:"/>
    <param format="vcf" name="input1" type="data" label="VCF" help="vcf input file"/>
    <param name="gene_anns" type="select" multiple="yes" optional="true">
      <options from_data_table="annovar">
	<filter type="static_value" name="type" value="gene_ann" column="1"/>
	<filter type="sort_by" column="0"/>
      </options>
    </param>
    <param name="filters" type="select" multiple="yes" optional="true">
      <options from_data_table="annovar">
	<filter type="static_value" name="type" value="filter" column="1"/>
        <filter type="sort_by" column="0"/>
      </options>
    </param>
    <param name="regions" type="select" multiple="yes" optional="true">
      <options from_data_table="annovar">
	<filter type="static_value" name="type" value="regions" column="1"/>
        <filter type="sort_by" column="0"/>
      </options>
    </param>
    <param name="location_db" type="select" display="radio">
      <options from_data_table="annovar">
        <filter type="static_value" name="type" value="location" column="1"/>
        <filter type="sort_by" column="0"/>
      </options>
    </param> 
  </inputs>
  <outputs>
    <data format="vcf" name="output" from_work_dir="annovarAnnotation.????_multianno.vcf" label="${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 ([e-mail]) 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>