Mercurial > repos > melissacline > ucsc_cancer_utilities
comparison vcfToXena.xml @ 49:986bca7bc318
multiple files
| author | jingchunzhu |
|---|---|
| date | Fri, 14 Aug 2015 00:17:55 -0700 |
| parents | a38cc72edd75 |
| children |
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| 48:a38cc72edd75 | 49:986bca7bc318 |
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| 1 <tool id="vcfToXena" name="vcfToXena" version="0.1"> | 1 <tool id="vcfToXena" name="vcfToXena" version="0.1"> |
| 2 <description>Convert vcf To Xena ready mutation data</description> | 2 <description>Convert vcf To Xena ready mutation data</description> |
| 3 <command> | 3 <command> |
| 4 java -Xmx4G -jar $__tool_directory__/snpEff/snpEff.jar -c $__tool_directory__/snpEff/snpEff.config | 4 java -Xmx4G -jar $__tool_directory__/snpEff/snpEff.jar -c $__tool_directory__/snpEff/snpEff.config |
| 5 -i vcf -upDownStreamLen 5000 $genome | 5 -i vcf -upDownStreamLen 5000 $genome $input > $__tool_directory__/tmp_$input.name ; |
| 6 $input > $__tool_directory__/tmp ; | |
| 7 python $__tool_directory__/xenaHeader.py $snpeff_output; | 6 python $__tool_directory__/xenaHeader.py $snpeff_output; |
| 8 cat $__tool_directory__/tmp | python $__tool_directory__/parseSnpEffVcf.py $input.name $snpeff_output | 7 cat $__tool_directory__/tmp_$input.name | python $__tool_directory__/parseSnpEffVcf.py $input.name $snpeff_output; |
| 8 rm $__tool_directory__/tmp_$input.name | |
| 9 </command> | 9 </command> |
| 10 <inputs> | 10 <inputs> |
| 11 <param format="vcf" name="input" type="data" label="Input VCF file"/> | 11 <param format="vcf" name="input" type="data" label="Input VCF file"/> |
| 12 <param name="genome" type="select" label="Genome"> | 12 <param name="genome" type="select" label="Genome"> |
| 13 <option value="hg19">hg19</option> | 13 <option value="hg19">hg19</option> |