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comparison combine_gvcfs.xml @ 0:b80ff7f43ad1 draft default tip

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planemo upload for repository https://github.com/kaktus42/galaxytools/tree/master/tools/gatk commit 8764cef47529f6285678af4ca24b66d0fe516b88-dirty
author avowinkel
date Thu, 24 Sep 2015 12:10:01 -0400
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-1:000000000000 0:b80ff7f43ad1
1 <macros>
2 <xml name="CombineGVCFsParameters" tokens="tag">
3
4 <expand macro="macro_gvcf_input" tag="@TAG@" />
5
6 <expand macro="macro_optional_parameters">
7
8 <param name="breakBandsAtMultiplesOf" type="integer" value="0" label="If > 0, reference bands will be broken up at genomic positions that are multiples of this number" help="-breakBandsAtMultiplesOf,&#8209;&#8209;breakBandsAtMultiplesOf &amp;lt;breakBandsAtMultiplesOf&amp;gt;" />
9
10 </expand>
11
12 </xml>
13
14 <xml name="CombineGVCFsOutput">
15 <data format="vcf" name="cg_output_vcf" label="${tool.name} - ${analysis_type.analysis_type_selector} on ${on_string} (VCF)">
16 <yield />
17 </data>
18 </xml>
19
20 <template name="CombineGVCFsPreprocessing">
21 <![CDATA[
22 @token_gvcf_input_pre@
23 ]]>
24 </template>
25
26 <template name="CombineGVCFsOptions">
27 <![CDATA[
28 --out ${cg_output_vcf}
29
30 @token_gvcf_input@
31
32 #set $optionals = $analysis_type.optional_parameters
33 #if $optionals.optional_parameters_enabled
34 #if $optionals.breakBandsAtMultiplesOf > 0
35 --breakBandsAtMultiplesOf $optionals.breakBandsAtMultiplesOf
36 #end if
37 #end if
38 ]]>
39 </template>
40
41
42 </macros>
43
44