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comparison variant_combine.xml @ 6:35c00763cb5c draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit cf399638ebca4250bcc15f468238a9964de97b33
author iuc
date Mon, 04 Jun 2018 05:38:15 -0400
parents f244b8209eb8
children
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5:84584664264c 6:35c00763cb5c
1 <tool id="gatk2_variant_combine" name="Combine Variants" version="@VERSION@.0"> 1 <tool id="gatk2_variant_combine" name="Combine Variants" version="@VERSION@.0">
2 <description></description> 2 <description></description>
3 <expand macro="requirements" />
4 <macros> 3 <macros>
5 <import>gatk2_macros.xml</import> 4 <import>gatk2_macros.xml</import>
6 </macros> 5 </macros>
6 <expand macro="requirements" />
7 <expand macro="version_command" />
7 <command interpreter="python"> 8 <command interpreter="python">
8 gatk2_wrapper.py 9 gatk2_wrapper.py
9 --stdout "${output_log}" 10 --stdout "${output_log}"
10 11
11 #set $priority_order = [] 12 #set $priority_order = []
27 -R "${reference_source.ref_file.fields.path}" 28 -R "${reference_source.ref_file.fields.path}"
28 #end if 29 #end if
29 --genotypemergeoption "${genotype_merge_option}" 30 --genotypemergeoption "${genotype_merge_option}"
30 --rod_priority_list "${ ','.join( $priority_order ) }" 31 --rod_priority_list "${ ','.join( $priority_order ) }"
31 ' 32 '
32 33
33 #include source=$standard_gatk_options# 34 #include source=$standard_gatk_options#
34 35
35
36 ##start analysis specific options 36 ##start analysis specific options
37 #if $analysis_param_type.analysis_param_type_selector == "advanced": 37 #if $analysis_param_type.analysis_param_type_selector == "advanced":
38 -p ' 38 -p '
39 --filteredrecordsmergetype "${analysis_param_type.filtered_records_merge_type}" 39 --filteredrecordsmergetype "${analysis_param_type.filtered_records_merge_type}"
40 ${analysis_param_type.print_complex_merges} 40 ${analysis_param_type.print_complex_merges}
41 ${analysis_param_type.filtered_are_uncalled} 41 ${analysis_param_type.filtered_are_uncalled}
42 ${analysis_param_type.minimal_vcf} 42 ${analysis_param_type.minimal_vcf}
43 ${analysis_param_type.assume_identical_samples} 43 ${analysis_param_type.assume_identical_samples}
44 44
45 #if str( $analysis_param_type.set_key ): 45 #if str( $analysis_param_type.set_key ):
46 --setKey "${analysis_param_type.set_key}" 46 --setKey "${analysis_param_type.set_key}"
47 #end if 47 #end if
48 48
49 --minimumN "${analysis_param_type.minimum_n}" 49 --minimumN "${analysis_param_type.minimum_n}"
50 ' 50 '
51 #end if 51 #end if
52 </command> 52 </command>
53 <inputs> 53 <inputs>
54 54
55 <conditional name="reference_source"> 55 <conditional name="reference_source">
56 <expand macro="reference_source_selector_param" /> 56 <expand macro="reference_source_selector_param" />
57 <when value="cached"> 57 <when value="cached">
58 <repeat min="1" name="input_variants" title="Variants to Merge" help="Records will be prioritized in the order that you list them here (-V,--variant &amp;lt;variant&amp;gt;)"> 58 <repeat min="1" name="input_variants" title="Variants to Merge" help="Records will be prioritized in the order that you list them here (-V,--variant &amp;lt;variant&amp;gt;)">
59 <param name="input_variant" type="data" format="vcf" label="Input variant file" /> 59 <param name="input_variant" type="data" format="vcf" label="Input variant file" />
76 </param> 76 </param>
77 </repeat> 77 </repeat>
78 <param name="ref_file" type="data" format="fasta" label="Using reference file" help="-R,--reference_sequence &amp;lt;reference_sequence&amp;gt;" /> 78 <param name="ref_file" type="data" format="fasta" label="Using reference file" help="-R,--reference_sequence &amp;lt;reference_sequence&amp;gt;" />
79 </when> 79 </when>
80 </conditional> 80 </conditional>
81 81
82 <param name="genotype_merge_option" type="select" label="How should we merge genotype records across records for samples shared across the ROD files" help="-genotypeMergeOptions,--genotypemergeoption &amp;lt;genotypemergeoption&amp;gt;" > 82 <param name="genotype_merge_option" type="select" label="How should we merge genotype records across records for samples shared across the ROD files" help="-genotypeMergeOptions,--genotypemergeoption &amp;lt;genotypemergeoption&amp;gt;" >
83 <option value="UNIQUIFY" /> 83 <option value="UNIQUIFY" />
84 <option value="PRIORITIZE" selected="true"/> 84 <option value="PRIORITIZE" selected="true"/>
85 <option value="UNSORTED" /> 85 <option value="UNSORTED" />
86 <option value="REQUIRE_UNIQUE" /> 86 <option value="REQUIRE_UNIQUE" />
87 </param> 87 </param>
88 88
89 <expand macro="gatk_param_type_conditional" /> 89 <expand macro="gatk_param_type_conditional" />
90 90
91
92 <expand macro="analysis_type_conditional"> 91 <expand macro="analysis_type_conditional">
93 <param name="filtered_records_merge_type" type="select" label="How should we deal with records seen at the same site in the VCF, but with different FILTER fields?" help="-filteredRecordsMergeType,--filteredrecordsmergetype &amp;lt;filteredrecordsmergetype&amp;gt;" > 92 <param name="filtered_records_merge_type" type="select" label="How should we deal with records seen at the same site in the VCF, but with different FILTER fields?" help="-filteredRecordsMergeType,--filteredrecordsmergetype &amp;lt;filteredrecordsmergetype&amp;gt;" >
94 <option value="KEEP_IF_ANY_UNFILTERED" selected="true"/> 93 <option value="KEEP_IF_ANY_UNFILTERED" selected="true"/>
95 <option value="KEEP_IF_ALL_UNFILTERED" /> 94 <option value="KEEP_IF_ALL_UNFILTERED" />
96 </param> 95 </param>
97 96
98 <param name="print_complex_merges" checked="false" type="boolean" truevalue="--printComplexMerges" falsevalue="" label="Print out interesting sites requiring complex compatibility merging" help="-printComplexMerges,--printComplexMerges" /> 97 <param name="print_complex_merges" checked="false" type="boolean" truevalue="--printComplexMerges" falsevalue="" label="Print out interesting sites requiring complex compatibility merging" help="-printComplexMerges,--printComplexMerges" />
99 <param name="filtered_are_uncalled" checked="false" type="boolean" truevalue="--filteredAreUncalled" falsevalue="" label="If true, then filtered VCFs are treated as uncalled, so that filtered set annotation don't appear in the combined VCF" help="-filteredAreUncalled,--filteredAreUncalled" /> 98 <param name="filtered_are_uncalled" checked="false" type="boolean" truevalue="--filteredAreUncalled" falsevalue="" label="If true, then filtered VCFs are treated as uncalled, so that filtered set annotation don't appear in the combined VCF" help="-filteredAreUncalled,--filteredAreUncalled" />
100 <param name="minimal_vcf" checked="false" type="boolean" truevalue="--minimalVCF" falsevalue="" label="If true, then the output VCF will contain no INFO or genotype INFO field" help="-minimalVCF,--minimalVCF" /> 99 <param name="minimal_vcf" checked="false" type="boolean" truevalue="--minimalVCF" falsevalue="" label="If true, then the output VCF will contain no INFO or genotype INFO field" help="-minimalVCF,--minimalVCF" />
101 100
102 <param name="set_key" type="text" value="" label="Key, by default set, in the INFO key=value tag emitted describing which set the combined VCF record came from." help="-setKey,--setKey &amp;lt;setKey&amp;gt;"/> 101 <param name="set_key" type="text" value="" label="Key, by default set, in the INFO key=value tag emitted describing which set the combined VCF record came from." help="-setKey,--setKey &amp;lt;setKey&amp;gt;"/>
103 <param name="assume_identical_samples" checked="false" type="boolean" truevalue="--assumeIdenticalSamples" falsevalue="" label="If true, assume input VCFs have identical sample sets and disjoint calls so that one can simply perform a merge sort to combine the VCFs into one, drastically reducing the runtime." help="-assumeIdenticalSamples,--assumeIdenticalSamples" /> 102 <param name="assume_identical_samples" checked="false" type="boolean" truevalue="--assumeIdenticalSamples" falsevalue="" label="If true, assume input VCFs have identical sample sets and disjoint calls so that one can simply perform a merge sort to combine the VCFs into one, drastically reducing the runtime." help="-assumeIdenticalSamples,--assumeIdenticalSamples" />
104 <param name="minimum_n" type="integer" value="1" label="Combine variants and output site only if variant is present in at least N input files." help="-minN,--minimumN &amp;lt;minimumN&amp;gt;"/> 103 <param name="minimum_n" type="integer" value="1" label="Combine variants and output site only if variant is present in at least N input files." help="-minN,--minimumN &amp;lt;minimumN&amp;gt;"/>
105
106 </expand> 104 </expand>
107 105
108
109 </inputs> 106 </inputs>
110 <outputs> 107 <outputs>
111 <data format="vcf" name="output_variants" label="${tool.name} on ${on_string} (variants)" /> 108 <data format="vcf" name="output_variants" label="${tool.name} on ${on_string} (variants)" />
112 <data format="txt" name="output_log" label="${tool.name} on ${on_string} (log)" /> 109 <data format="txt" name="output_log" label="${tool.name} on ${on_string} (log)" />
113 </outputs> 110 </outputs>