Mercurial > repos > iuc > vt_variant_tools
diff vt_normalize.xml @ 2:e76f203fc135 draft
Uploaded
author | iuc |
---|---|
date | Thu, 14 Aug 2014 10:45:02 -0400 |
parents | 16f7587ab084 |
children | 6e073fc99d9c |
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--- a/vt_normalize.xml Thu Aug 14 09:58:02 2014 -0400 +++ b/vt_normalize.xml Thu Aug 14 10:45:02 2014 -0400 @@ -9,7 +9,11 @@ <command> <![CDATA[ vt @BINARY@ - -o "${ outfile }" + #if $output_format == 'bcf': + -o normalised.bcf + #else: + -o normalised.vcf + #end if ##-q do not print options and summary [] -w $window @@ -25,7 +29,14 @@ -r "${reference_source.reference_genome}" #end if - "${ infile }" + "${ infile }"; + + #if $output_format == 'bcf': + mv normalised.bcf "${ outfile }"; + #else: + mv normalised.vcf "${ outfile }"; + #end if + ]]> </command> <expand macro="stdio" /> @@ -57,9 +68,18 @@ <validator type="in_range" min="0"/> </param> + <param name="output_format" type="select" label="Choose the output format" help=""> + <option value="bcf">BCF</option> + <option value="vcf" selected="true">VCF</option> + </param> + </inputs> <outputs> - <data name="outfile" format="vcf" label="${tool.name} on ${on_string}" /> + <data name="outfile" format="vcf" label="${tool.name} on ${on_string}"> + <change_format> + <when input="output_format" value="bcf" format="bcf" /> + </change_format> + </data> </outputs> <tests> <test>