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comparison combine_variants.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="CombineVariantsParameters" tokens="tag">
3
4 <expand macro="macro_vcf_input" tag="@TAG@" />
5
6 <expand macro="macro_optional_parameters">
7
8 <param name="filteredRecordsMergeType" type="select" label="Determines how we should handle records seen at the same site in the VCF, but with different FILTER fields" help="-filteredRecordsMergeType,&#8209;&#8209;filteredrecordsmergetype &amp;lt;filteredrecordsmergetype&amp;gt;">
9 <option value="">No Selection</option>
10 <option value="KEEP_IF_ANY_UNFILTERED">KEEP_IF_ANY_UNFILTERED</option>
11 <option value="KEEP_IF_ALL_UNFILTERED">KEEP_IF_ALL_UNFILTERED</option>
12 <option value="KEEP_UNCONDITIONAL">KEEP_UNCONDITIONAL</option>
13 </param>
14
15 <param name="genotypeMergeOptions" type="select" label="Determines how we should merge genotype records for samples shared across the ROD files" help="-genotypeMergeOptions,&#8209;&#8209;genotypemergeoption &amp;lt;genotypemergeoption&amp;gt;">
16 <option value="">No Selection</option>
17 <option value="UNIQUIFY">UNIQUIFY</option>
18 <option value="PRIORITIZE">PRIORITIZE</option>
19 <option value="UNSORTED">UNSORTED</option>
20 <option value="REQUIRE_UNIQUE">REQUIRE_UNIQUE</option>
21 </param>
22
23 <param name="minimumN" type="integer" value="1" optional="true" label="Combine variants and output site only if the variant is present in at least N input files" help="-minN,&#8209;&#8209;minimumN &amp;lt;minimumN&amp;gt;" />
24
25 <param name="rod_priority_list" type="text" value="" optional="true" label="A comma-separated string describing the priority ordering for the genotypes as far as which record gets emitted" help="-priority,&#8209;&#8209;rod_priority_list &amp;lt;rod_priority_list&amp;gt;" />
26
27 <param name="setKey" type="text" value="" optional="true" label="Key used in the INFO key=value tag emitted describing which set the combined VCF record came from" help="-setKey,&#8209;&#8209;setKey &amp;lt;setKey&amp;gt;" />
28
29 <param name="assumeIdenticalSamples" type="boolean" truevalue="--assumeIdenticalSamples" falsevalue="" label="If true, assume input VCFs have identical sample sets and disjoint calls" help="-assumeIdenticalSamples,&#8209;&#8209;assumeIdenticalSamples" />
30
31 <param name="excludeNonVariants" type="boolean" truevalue="--excludeNonVariants" falsevalue="" label="Don't include loci found to be non-variant after the combining procedure" help="-env,&#8209;&#8209;excludeNonVariants" />
32
33 <param name="filteredAreUncalled" type="boolean" truevalue="--filteredAreUncalled" falsevalue="" label="If true, then filtered VCFs are treated as uncalled, so that filtered set annotations don't appear in the combined VCF" help="-filteredAreUncalled,&#8209;&#8209;filteredAreUncalled" />
34
35 <param name="mergeInfoWithMaxAC" type="boolean" truevalue="--mergeInfoWithMaxAC" falsevalue="" label="If true, when VCF records overlap the info field is taken from the one with the max AC instead of only taking the fields which are identical across the overlapping records." help="-mergeInfoWithMaxAC,&#8209;&#8209;mergeInfoWithMaxAC" />
36
37 <param name="minimalVCF" type="boolean" truevalue="--minimalVCF" falsevalue="" label="If true, then the output VCF will contain no INFO or genotype FORMAT fields" help="-minimalVCF,&#8209;&#8209;minimalVCF" />
38
39 <param name="printComplexMerges" type="boolean" truevalue="--printComplexMerges" falsevalue="" label="Print out interesting sites requiring complex compatibility merging" help="-printComplexMerges,&#8209;&#8209;printComplexMerges" />
40
41 <param name="suppressCommandLineHeader" type="boolean" truevalue="--suppressCommandLineHeader" falsevalue="" label="If true, do not output the header containing the command line used" help="-suppressCommandLineHeader,&#8209;&#8209;suppressCommandLineHeader" />
42
43 </expand>
44
45 </xml>
46
47 <xml name="CombineVariantsOutput">
48 <data format="vcf" name="cv_output_vcf" label="${tool.name} - ${analysis_type.analysis_type_selector} on ${on_string} (VCF)">
49 <yield />
50 </data>
51 </xml>
52
53 <template name="CombineVariantsPreprocessing">
54 <![CDATA[
55 @token_vcf_input_pre@
56 ]]>
57 </template>
58
59 <template name="CombineVariantsOptions">
60 <![CDATA[
61 --out ${cv_output_vcf}
62
63 @token_vcf_input@
64
65 #set $optionals = $analysis_type.optional_parameters
66 #if $optionals.optional_parameters_enabled
67
68 #if $optionals.filteredRecordsMergeType
69 --filteredRecordsMergeType $optionals.filteredRecordsMergeType
70 #end if
71 #if $optionals.genotypeMergeOptions
72 --genotypeMergeOptions $optionals.genotypeMergeOptions
73 #end if
74 #if $optionals.minimumN != 1
75 --minimumN $optionals.minimumN
76 #end if
77 #if $optionals.rod_priority_list
78 --rod_priority_list $optionals.rod_priority_list
79 #end if
80
81 $optionals.assumeIdenticalSamples
82 $optionals.excludeNonVariants
83 $optionals.filteredAreUncalled
84 $optionals.mergeInfoWithMaxAC
85 $optionals.minimalVCF
86 $optionals.printComplexMerges
87 $optionals.suppressCommandLineHeader
88
89 #end if
90 ]]>
91 </template>
92
93
94 </macros>
95
96