view vcfToXena.xml @ 55:1093078e7976

merge mutation data conform to new mutationVector data standard

<tool id="vcfToXena" name="vcfToXena" version="0.1">
    <description>Convert vcf To Xena ready mutation data</description>
    <command>
      java -Xmx4G -jar $__tool_directory__/snpEff/snpEff.jar  -c $__tool_directory__/snpEff/snpEff.config 
      -i vcf -upDownStreamLen 5000 $genome $input > $__tool_directory__/tmp_$input.name ;
      python $__tool_directory__/xenaHeader.py $snpeff_output;
      cat $__tool_directory__/tmp_$input.name | python $__tool_directory__/parseSnpEffVcf.py $input.name $snpeff_output;
      rm $__tool_directory__/tmp_$input.name
    </command>
    <inputs>
        <param format="vcf" name="input" type="data" label="Input VCF file"/>
	<param name="genome" type="select" label="Genome">
	  <option value="hg19">hg19</option>
	</param>

    </inputs>
    <outputs>
        <data format="tabular" name="snpeff_output" label="${input.name}.mutationVector" />
    </outputs>
    <help>
      This tool convert vcf files to xena ready positional mutation data files.
    </help>
</tool>