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comparison vt_normalize.xml @ 3:6e073fc99d9c draft default tip

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author iuc
date Thu, 14 Aug 2014 12:36:27 -0400
parents e76f203fc135
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2:e76f203fc135 3:6e073fc99d9c
7 <token name="@BINARY@">normalize</token> 7 <token name="@BINARY@">normalize</token>
8 </macros> 8 </macros>
9 <command> 9 <command>
10 <![CDATA[ 10 <![CDATA[
11 vt @BINARY@ 11 vt @BINARY@
12 #if $output_format == 'bcf': 12 #if str($output_format) == 'bcf':
13 -o normalised.bcf 13 -o normalised.bcf
14 #else: 14 #else:
15 -o normalised.vcf 15 -o normalised.vcf
16 #end if 16 #end if
17 ##-q do not print options and summary [] 17 ##-q do not print options and summary []
27 -r "${reference_source.reference_genome.fields.path}" 27 -r "${reference_source.reference_genome.fields.path}"
28 #else: 28 #else:
29 -r "${reference_source.reference_genome}" 29 -r "${reference_source.reference_genome}"
30 #end if 30 #end if
31 31
32 "${ infile }"; 32 "${ infile }"
33 33
34 #if $output_format == 'bcf': 34 &&
35
36 #if str($output_format) == 'bcf':
35 mv normalised.bcf "${ outfile }"; 37 mv normalised.bcf "${ outfile }";
36 #else: 38 #else:
37 mv normalised.vcf "${ outfile }"; 39 mv normalised.vcf "${ outfile }";
38 #end if 40 #end if
39 41