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comparison variant_annotator.xml @ 15:01ff8dd37d4d draft default tip

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author lz_hust
date Sat, 01 Jun 2019 07:20:41 -0400
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14:68426930d59c 15:01ff8dd37d4d
1 <tool id="gatk2_variant_annotator" name="Variant Annotator" version="@VERSION@.0">
2 <description></description>
3 <macros>
4 <import>gatk2_macros.xml</import>
5 </macros>
6 <expand macro="requirements" />
7 <expand macro="version_command" />
8 <command interpreter="python">
9 gatk2_wrapper.py
10 --stdout "${output_log}"
11 #if str( $reference_source.input_bam ) != "None":
12 -d "-I" "${reference_source.input_bam}" "${reference_source.input_bam.ext}" "gatk_input"
13 #if str( $reference_source.input_bam.metadata.bam_index ) != "None":
14 -d "" "${reference_source.input_bam.metadata.bam_index}" "bam_index" "gatk_input" ##hardcode galaxy ext type as bam_index
15 #end if
16 #end if
17 -d "--variant" "${reference_source.input_variant}" "${reference_source.input_variant.ext}" "input_variant"
18 -p '
19 @JAR_PATH@
20 -T "VariantAnnotator"
21 \$GATK2_SITE_OPTIONS
22
23 @THREADS@
24
25 #if $reference_source.reference_source_selector != "history":
26 -R "${reference_source.ref_file.fields.path}"
27 #end if
28 -o "${output_vcf}"
29 #if str( $annotations_type.annotations_type_selector ) == "use_all_annotations":
30 --useAllAnnotations
31 #else:
32 #if $annotations_type.annotations:
33 #for $annotation in str( $annotations_type.annotations.fields.gatk_value ).split( ',' ):
34 --annotation "${annotation}"
35 #end for
36 #end if
37 #end if
38 #if $exclude_annotations:
39 #for $annotation in str( $exclude_annotations.fields.gatk_value ).split( ',' ):
40 --excludeAnnotation "${annotation}"
41 #end for
42 #end if
43 #for $additional_annotation in $additional_annotations:
44 --annotation "${additional_annotation.additional_annotation_name}"
45 #end for
46 '
47 #if $reference_source.input_variant_bti:
48 -d "--intervals" "${reference_source.input_variant}" "${reference_source.input_variant.ext}" "input_variant_bti"
49 #end if
50
51 #for $rod_binding in $comp_rod_bind:
52 -d "--comp:${rod_binding.comp_rod_name},%(file_type)s" "${rod_binding.comp_input_rod}" "${rod_binding.comp_input_rod.ext}" "input_comp_${rod_binding.comp_rod_name}"
53 #end for
54
55 @DBSNP_OPTIONS@
56
57 #for $rod_binding in $resource_rod_bind:
58 -d "--resource:${rod_binding.resource_rod_name},%(file_type)s" "${rod_binding.resource_input_rod}" "${rod_binding.resource_input_rod.ext}" "input_resource_${rod_binding.resource_rod_name}"
59 #end for
60
61 #if str( $snpEff_rod_bind_type.snpEff_rod_bind_type_selector ) == 'set_snpEff':
62 -p '--annotation "SnpEff"'
63 -d "--snpEffFile:${snpEff_rod_bind_type.snpEff_rod_name},%(file_type)s" "${snpEff_rod_bind_type.snpEff_input_rod}" "${snpEff_rod_bind_type.snpEff_input_rod.ext}" "input_snpEff_${snpEff_rod_bind_type.snpEff_rod_name}"
64 #else:
65 -p '--excludeAnnotation "SnpEff"'
66 #end if
67
68 #for $expression in $expressions:
69 -p '--expression "${expression.expression}"'
70 #end for
71
72 #include source=$standard_gatk_options#
73
74 -p '
75 #if str( $annotation_group ) != "None":
76 #for $group in str( $annotation_group ).split( ',' ):
77 --group "${group}"
78 #end for
79 #end if
80 #if str( $family_string ) != "":
81 --family_string "${family_string}"
82 #end if
83 --MendelViolationGenotypeQualityThreshold "${mendel_violation_genotype_quality_threshold}"
84 '
85 </command>
86 <inputs>
87 <conditional name="reference_source">
88 <expand macro="reference_source_selector_param" />
89 <when value="cached">
90 <param name="input_variant" type="data" format="vcf" label="Variant file to annotate" help="-V,--variant &amp;lt;variant&amp;gt;"/>
91 <param name="input_variant_bti" type="boolean" truevalue="-BTI variant" falsevalue="" label="Increase efficiency for small variant files." help="-BTI variant"/>
92 <param name="input_bam" type="data" format="bam" label="BAM file" optional="True" help="Not needed for all annotations. (-I,--input_file &amp;lt;input_file&amp;gt;)" >
93 <validator type="unspecified_build" />
94 <validator type="dataset_metadata_in_data_table" table_name="gatk2_picard_indexes" metadata_name="dbkey" metadata_column="dbkey" message="Sequences are not currently available for the specified build." /> <!-- fixme!!! this needs to be a select -->
95 </param>
96 <param name="ref_file" type="select" label="Using reference genome" help="-R,--reference_sequence &amp;lt;reference_sequence&amp;gt;">
97 <options from_data_table="gatk2_picard_indexes">
98 <filter type="data_meta" key="dbkey" ref="input_variant" column="dbkey"/>
99 </options>
100 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
101 </param>
102 </when>
103 <when value="history"> <!-- FIX ME!!!! -->
104 <param name="input_variant" type="data" format="vcf" label="Variant file to annotate" help="-V,--variant &amp;lt;variant&amp;gt;"/>
105 <param name="input_variant_bti" type="boolean" truevalue="-BTI variant" falsevalue="" label="Increase efficiency for small variant files." help="-BTI variant"/>
106 <param name="input_bam" type="data" format="bam" label="BAM file" optional="True" help="Not needed for all annotations. (-I,--input_file &amp;lt;input_file&amp;gt;)" />
107 <param name="ref_file" type="data" format="fasta" label="Using reference file" help="-R,--reference_sequence &amp;lt;reference_sequence&amp;gt;" />
108 </when>
109 </conditional>
110 <conditional name="annotations_type">
111 <param name="annotations_type_selector" type="select" label="Use all possible annotations">
112 <option value="use_all_annotations">Use all</option>
113 <option value="choose" selected="True">Use selected</option>
114 </param>
115 <when value="use_all_annotations">
116 <!-- no extra options here -->
117 </when>
118 <when value="choose">
119 <param name="annotations" type="select" multiple="True" display="checkboxes" label="Annotations to apply" help="-A,--annotation &amp;lt;annotation&amp;gt;" >
120 <!-- load the available annotations from an external configuration file, since additional ones can be added to local installs -->
121 <options from_data_table="gatk2_annotations">
122 <filter type="multiple_splitter" column="tools_valid_for" separator=","/>
123 <filter type="static_value" value="VariantAnnotator" column="tools_valid_for"/>
124 </options>
125 </param>
126 </when>
127 </conditional>
128
129 <repeat name="additional_annotations" title="Additional annotation" help="-A,--annotation &amp;lt;annotation&amp;gt;">
130 <param name="additional_annotation_name" type="text" value="" label="Annotation name" />
131 </repeat>
132
133 <repeat name="comp_rod_bind" title="Binding for reference-ordered comparison data" help="-comp,--comp &amp;lt;comp&amp;gt;">
134 <param name="comp_input_rod" type="data" format="vcf" label="ROD file" />
135 <param name="comp_rod_name" type="text" value="Unnamed" label="ROD Name"/>
136 </repeat>
137 <expand macro="dbsnp_param" />
138
139 <repeat name="resource_rod_bind" title="Binding for reference-ordered resource data" help="-resource,--resource &amp;lt;resource&amp;gt;">
140 <param name="resource_input_rod" type="data" format="vcf" label="ROD file" />
141 <param name="resource_rod_name" type="text" value="Unnamed" label="ROD Name"/>
142 </repeat>
143
144 <conditional name="snpEff_rod_bind_type">
145 <param name="snpEff_rod_bind_type_selector" type="select" label="Provide a snpEff reference-ordered data file (VCF)" help="-snpEffFile,--snpEffFile &amp;lt;snpEffFile&amp;gt;">
146 <option value="set_snpEff">Set snpEff</option>
147 <option value="exclude_snpEff" selected="True">Don't set snpEff</option>
148 </param>
149 <when value="exclude_snpEff">
150 <!-- Do nothing here -->
151 </when>
152 <when value="set_snpEff">
153 <param name="snpEff_input_rod" type="data" format="vcf" label="ROD file" />
154 <param name="snpEff_rod_name" type="hidden" value="snpEff" label="ROD Name"/>
155 </when>
156 </conditional>
157
158 <repeat name="expressions" title="Expression" help="-E,--expression &amp;lt;expression&amp;gt;">
159 <param name="expression" type="text" value="" label="Expression"/>
160 </repeat>
161
162 <expand macro="gatk_param_type_conditional" />
163
164 <param name="annotation_group" type="select" multiple="True" display="checkboxes" label="annotation interfaces/groups to apply to variant calls" help="-G,--group &amp;lt;group&amp;gt;">
165 <option value="RodRequiringAnnotation">RodRequiringAnnotation</option>
166 <option value="Standard">Standard</option>
167 <option value="Experimental">Experimental</option>
168 <option value="WorkInProgress">WorkInProgress</option>
169 <option value="RankSumTest">RankSumTest</option>
170 </param>
171 <param name="family_string" type="text" value="" label="Family String" help="--family_string"/>
172 <param name="mendel_violation_genotype_quality_threshold" type="float" value="0.0" label="genotype quality treshold in order to annotate mendelian violation ratio." help="-mvq,--MendelViolationGenotypeQualityThreshold &amp;lt;MendelViolationGenotypeQualityThreshold&amp;gt;"/>
173 <param name="exclude_annotations" type="select" multiple="True" display="checkboxes" label="Annotations to exclude" help="-XA,--excludeAnnotation &amp;lt;excludeAnnotation&amp;gt;" >
174 <!-- load the available annotations from an external configuration file, since additional ones can be added to local installs -->
175 <options from_data_table="gatk2_annotations">
176 <filter type="multiple_splitter" column="tools_valid_for" separator=","/>
177 <filter type="static_value" value="VariantAnnotator" column="tools_valid_for"/>
178 </options>
179 </param>
180
181 </inputs>
182 <outputs>
183 <data format="vcf" name="output_vcf" label="${tool.name} on ${on_string} (Variant File)" />
184 <data format="txt" name="output_log" label="${tool.name} on ${on_string} (log)" />
185 </outputs>
186 <tests>
187 <test>
188 <param name="reference_source_selector" value="history" />
189 <param name="ref_file" value="phiX.fasta" ftype="fasta" />
190 <param name="input_bam" value="gatk/gatk_table_recalibration/gatk_table_recalibration_out_1.bam" ftype="bam" />
191 <param name="input_variant" value="gatk/gatk_unified_genotyper/gatk_unified_genotyper_out_1.vcf" ftype="vcf" />
192 <param name="input_variant_bti" />
193 <param name="annotations_type_selector" value="choose" />
194 <param name="annotations" value="AlleleBalance,BaseQualityRankSumTest,DepthOfCoverage,HomopolymerRun,MappingQualityRankSumTest,MappingQualityZero,QualByDepth,RMSMappingQuality,SpanningDeletions,HaplotypeScore" />
195 <param name="additional_annotations" value="0" />
196 <param name="dbsnp_rod_bind_type_selector" value="set_dbsnp" />
197 <param name="dbsnp_input_rod" value="gatk/fake_phiX_variant_locations.vcf" ftype="vcf" />
198 <param name="dbsnp_rod_name" value="dbsnp" />
199 <param name="snpEff_rod_bind_type_selector" value="exclude_snpEff" />
200 <param name="gatk_param_type_selector" value="basic" />
201 <output name="output_vcf" file="gatk/gatk_variant_annotator/gatk_variant_annotator_out_1.vcf" lines_diff="4" />
202 <output name="output_log" file="gatk/gatk_variant_annotator/gatk_variant_annotator_out_1.log.contains" compare="contains" />
203 <param name="comp_rod_bind" value="0" />
204 <param name="resource_rod_bind" value="0" />
205 <param name="expressions" value="0" />
206 <!-- <param name="annotation_group" /> -->
207 </test>
208 </tests>
209 <help>
210 **What it does**
211
212 Annotates variant calls with context information. Users can specify which of the available annotations to use.
213
214 For more information on using the VariantAnnotator, see this `tool specific page &lt;http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_gatk_walkers_annotator_VariantAnnotator.html&gt;`_.
215
216 To learn about best practices for variant detection using GATK, see this `overview &lt;http://www.broadinstitute.org/gatk/guide/topic?name=best-practices&gt;`_.
217
218 If you encounter errors, please view the `GATK FAQ &lt;http://www.broadinstitute.org/gatk/guide/topic?name=faqs&gt;`_.
219
220 ------
221
222
223 **Inputs**
224
225 GenomeAnalysisTK: VariantAnnotator accepts a variant input file.
226
227
228 **Outputs**
229
230 The output is in VCF format.
231
232
233 Go `here &lt;http://www.broadinstitute.org/gatk/guide/topic?name=intro&gt;`_ for details on GATK file formats.
234
235 -------
236
237 **Settings**::
238
239
240 sampleName The sample (NA-ID) corresponding to the variant input (for non-VCF input only)
241 annotation One or more specific annotations to apply to variant calls
242 group One or more classes/groups of annotations to apply to variant calls
243 expression One or more specific expressions to apply to variant calls; see documentation for more details
244 useAllAnnotations Use all possible annotations (not for the faint of heart)
245
246 @CITATION_SECTION@
247 </help>
248 <expand macro="citations" />
249 </tool>