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annotate combine_variants.xml @ 0:b80ff7f43ad1 draft default tip

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author avowinkel
date Thu, 24 Sep 2015 12:10:01 -0400
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1 <macros>
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2 <xml name="CombineVariantsParameters" tokens="tag">
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4 <expand macro="macro_vcf_input" tag="@TAG@" />
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6 <expand macro="macro_optional_parameters">
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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;">
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9 <option value="">No Selection</option>
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10 <option value="KEEP_IF_ANY_UNFILTERED">KEEP_IF_ANY_UNFILTERED</option>
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11 <option value="KEEP_IF_ALL_UNFILTERED">KEEP_IF_ALL_UNFILTERED</option>
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12 <option value="KEEP_UNCONDITIONAL">KEEP_UNCONDITIONAL</option>
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13 </param>
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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;">
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16 <option value="">No Selection</option>
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17 <option value="UNIQUIFY">UNIQUIFY</option>
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18 <option value="PRIORITIZE">PRIORITIZE</option>
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19 <option value="UNSORTED">UNSORTED</option>
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20 <option value="REQUIRE_UNIQUE">REQUIRE_UNIQUE</option>
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21 </param>
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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;" />
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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;" />
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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;" />
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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" />
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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" />
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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" />
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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" />
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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" />
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39 <param name="printComplexMerges" type="boolean" truevalue="--printComplexMerges" falsevalue="" label="Print out interesting sites requiring complex compatibility merging" help="-printComplexMerges,&#8209;&#8209;printComplexMerges" />
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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" />
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43 </expand>
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45 </xml>
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47 <xml name="CombineVariantsOutput">
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48 <data format="vcf" name="cv_output_vcf" label="${tool.name} - ${analysis_type.analysis_type_selector} on ${on_string} (VCF)">
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49 <yield />
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50 </data>
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51 </xml>
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53 <template name="CombineVariantsPreprocessing">
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54 <![CDATA[
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55 @token_vcf_input_pre@
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56 ]]>
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57 </template>
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59 <template name="CombineVariantsOptions">
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60 <![CDATA[
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61 --out ${cv_output_vcf}
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63 @token_vcf_input@
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65 #set $optionals = $analysis_type.optional_parameters
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66 #if $optionals.optional_parameters_enabled
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68 #if $optionals.filteredRecordsMergeType
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69 --filteredRecordsMergeType $optionals.filteredRecordsMergeType
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70 #end if
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71 #if $optionals.genotypeMergeOptions
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72 --genotypeMergeOptions $optionals.genotypeMergeOptions
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73 #end if
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74 #if $optionals.minimumN != 1
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75 --minimumN $optionals.minimumN
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76 #end if
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77 #if $optionals.rod_priority_list
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78 --rod_priority_list $optionals.rod_priority_list
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79 #end if
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81 $optionals.assumeIdenticalSamples
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82 $optionals.excludeNonVariants
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83 $optionals.filteredAreUncalled
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84 $optionals.mergeInfoWithMaxAC
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85 $optionals.minimalVCF
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86 $optionals.printComplexMerges
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87 $optionals.suppressCommandLineHeader
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88
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89 #end if
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90 ]]>
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91 </template>
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92
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93
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94 </macros>
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95
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96