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comparison vt_normalize.xml @ 5:b425a93b4da6 draft

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Uploaded
author bgruening
date Thu, 14 Aug 2014 10:44:32 -0400
parents bb468ee178d8
children d67bfd79bf6c
comparison
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4:bb468ee178d8 5:b425a93b4da6
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 -o "${ outfile }" 12 #if $output_format == 'bcf':
13 -o normalised.bcf
14 #else:
15 -o normalised.vcf
16 #end if
13 ##-q do not print options and summary [] 17 ##-q do not print options and summary []
14 -w $window 18 -w $window
15 19
16 #if str( $intervals_file ) != 'None': 20 #if str( $intervals_file ) != 'None':
17 -I "${intervals_file}" 21 -I "${intervals_file}"
23 -r "${reference_source.reference_genome.fields.path}" 27 -r "${reference_source.reference_genome.fields.path}"
24 #else: 28 #else:
25 -r "${reference_source.reference_genome}" 29 -r "${reference_source.reference_genome}"
26 #end if 30 #end if
27 31
28 "${ infile }" 32 "${ infile }";
33
34 #if $output_format == 'bcf':
35 mv normalised.bcf "${ outfile }";
36 #else:
37 mv normalised.vcf "${ outfile }";
38 #end if
39
29 ]]> 40 ]]>
30 </command> 41 </command>
31 <expand macro="stdio" /> 42 <expand macro="stdio" />
32 <inputs> 43 <inputs>
33 <param name="infile" type="data" format="vcf" label="VCF file to be normalised" /> 44 <param name="infile" type="data" format="vcf" label="VCF file to be normalised" />
55 <param name="window" type="integer" value="10000" size="10" label="Window size for local sorting of variants" 66 <param name="window" type="integer" value="10000" size="10" label="Window size for local sorting of variants"
56 help="(-w)"> 67 help="(-w)">
57 <validator type="in_range" min="0"/> 68 <validator type="in_range" min="0"/>
58 </param> 69 </param>
59 70
71 <param name="output_format" type="select" label="Choose the output format" help="">
72 <option value="bcf">BCF</option>
73 <option value="vcf" selected="true">VCF</option>
74 </param>
75
60 </inputs> 76 </inputs>
61 <outputs> 77 <outputs>
62 <data name="outfile" format="vcf" label="${tool.name} on ${on_string}" /> 78 <data name="outfile" format="vcf" label="${tool.name} on ${on_string}">
79 <change_format>
80 <when input="output_format" value="bcf" format="bcf" />
81 </change_format>
82 </data>
63 </outputs> 83 </outputs>
64 <tests> 84 <tests>
65 <test> 85 <test>
66 </test> 86 </test>
67 </tests> 87 </tests>