Mercurial > repos > iuc > gatk2

comparison variant_annotator.xml @ 0:340633249b3d draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author bgruening
date Mon, 02 Dec 2013 06:18:36 -0500
parents
children 8bcc13094767
comparison
equal deleted inserted replaced
-1:000000000000 0:340633249b3d
1 <tool id="gatk2_variant_annotator" name="Variant Annotator" version="0.0.7">
2 <description></description>
3 <expand macro="requirements" />
4 <macros>
5 <import>gatk2_macros.xml</import>
6 </macros>
7 <command interpreter="python">
8 gatk2_wrapper.py
9 --stdout "${output_log}"
10 #if str( $reference_source.input_bam ) != "None":
11 -d "-I" "${reference_source.input_bam}" "${reference_source.input_bam.ext}" "gatk_input"
12 #if str( $reference_source.input_bam.metadata.bam_index ) != "None":
13 -d "" "${reference_source.input_bam.metadata.bam_index}" "bam_index" "gatk_input" ##hardcode galaxy ext type as bam_index
14 #end if
15 #end if
16 -d "--variant" "${reference_source.input_variant}" "${reference_source.input_variant.ext}" "input_variant"
17 -p '
18 @JAR_PATH@
19 -T "VariantAnnotator"
20 \$GATK2_SITE_OPTIONS
21
22 @THREADS@
23
24 #if $reference_source.reference_source_selector != "history":
25 -R "${reference_source.ref_file.fields.path}"
26 #end if
27 -o "${output_vcf}"
28 #if str( $annotations_type.annotations_type_selector ) == "use_all_annotations":
29 --useAllAnnotations
30 #else:
31 #if $annotations_type.annotations:
32 #for $annotation in str( $annotations_type.annotations.fields.gatk_value ).split( ',' ):
33 --annotation "${annotation}"
34 #end for
35 #end if
36 #end if
37 #if $exclude_annotations:
38 #for $annotation in str( $exclude_annotations.fields.gatk_value ).split( ',' ):
39 --excludeAnnotation "${annotation}"
40 #end for
41 #end if
42 #for $additional_annotation in $additional_annotations:
43 --annotation "${additional_annotation.additional_annotation_name}"
44 #end for
45 '
46 #if $reference_source.input_variant_bti:
47 -d "--intervals" "${reference_source.input_variant}" "${reference_source.input_variant.ext}" "input_variant_bti"
48 #end if
49
50 #for $rod_binding in $comp_rod_bind:
51 -d "--comp:${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}"
52 #end for
53
54 #if str( $dbsnp_rod_bind_type.dbsnp_rod_bind_type_selector ) == 'set_dbsnp':
55 -d "--dbsnp:${dbsnp_rod_bind_type.dbsnp_rod_name},%(file_type)s" "${dbsnp_rod_bind_type.dbsnp_input_rod}" "${dbsnp_rod_bind_type.dbsnp_input_rod.ext}" "input_dbsnp_${dbsnp_rod_bind_type.dbsnp_rod_name}"
56 #end if
57
58
59 #for $rod_binding in $resource_rod_bind:
60 -d "--resource:${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}"
61 #end for
62
63 #if str( $snpEff_rod_bind_type.snpEff_rod_bind_type_selector ) == 'set_snpEff':
64 -p '--annotation "SnpEff"'
65 -d "--snpEffFile:${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}"
66 #else:
67 -p '--excludeAnnotation "SnpEff"'
68 #end if
69
70 #for $expression in $expressions:
71 -p '--expression "${expression.expression}"'
72 #end for
73
74 #include source=$standard_gatk_options#
75
76 -p '
77 #if str( $annotation_group ) != "None":
78 #for $group in str( $annotation_group ).split( ',' ):
79 --group "${group}"
80 #end for
81 #end if
82 #if str( $family_string ) != "":
83 --family_string "${family_string}"
84 #end if
85 --MendelViolationGenotypeQualityThreshold "${mendel_violation_genotype_quality_threshold}"
86 '
87 </command>
88 <inputs>
89 <conditional name="reference_source">
90 <expand macro="reference_source_selector_param" />
91 <when value="cached">
92 <param name="input_variant" type="data" format="vcf" label="Variant file to annotate" help="-V,--variant &amp;lt;variant&amp;gt;"/>
93 <param name="input_variant_bti" type="boolean" truevalue="-BTI variant" falsevalue="" label="Increase efficiency for small variant files." help="-BTI variant"/>
94 <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;)" >
95 <validator type="unspecified_build" />
96 <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 -->
97 </param>
98 <param name="ref_file" type="select" label="Using reference genome" help="-R,--reference_sequence &amp;lt;reference_sequence&amp;gt;">
99 <options from_data_table="gatk2_picard_indexes">
100 <filter type="data_meta" key="dbkey" ref="input_variant" column="dbkey"/>
101 </options>
102 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
103 </param>
104 </when>
105 <when value="history"> <!-- FIX ME!!!! -->
106 <param name="input_variant" type="data" format="vcf" label="Variant file to annotate" help="-V,--variant &amp;lt;variant&amp;gt;"/>
107 <param name="input_variant_bti" type="boolean" truevalue="-BTI variant" falsevalue="" label="Increase efficiency for small variant files." help="-BTI variant"/>
108 <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;)" />
109 <param name="ref_file" type="data" format="fasta" label="Using reference file" help="-R,--reference_sequence &amp;lt;reference_sequence&amp;gt;" />
110 </when>
111 </conditional>
112 <conditional name="annotations_type">
113 <param name="annotations_type_selector" type="select" label="Use all possible annotations">
114 <option value="use_all_annotations">Use all</option>
115 <option value="choose" selected="True">Use selected</option>
116 </param>
117 <when value="use_all_annotations">
118 <!-- no extra options here -->
119 </when>
120 <when value="choose">
121 <param name="annotations" type="select" multiple="True" display="checkboxes" label="Annotations to apply" help="-A,--annotation &amp;lt;annotation&amp;gt;" >
122 <!-- load the available annotations from an external configuration file, since additional ones can be added to local installs -->
123 <options from_data_table="gatk2_annotations">
124 <filter type="multiple_splitter" column="tools_valid_for" separator=","/>
125 <filter type="static_value" value="VariantAnnotator" column="tools_valid_for"/>
126 </options>
127 </param>
128 </when>
129 </conditional>
130
131 <repeat name="additional_annotations" title="Additional annotation" help="-A,--annotation &amp;lt;annotation&amp;gt;">
132 <param name="additional_annotation_name" type="text" value="" label="Annotation name" />
133 </repeat>
134
135 <repeat name="comp_rod_bind" title="Binding for reference-ordered comparison data" help="-comp,--comp &amp;lt;comp&amp;gt;">
136 <param name="comp_input_rod" type="data" format="vcf" label="ROD file" />
137 <param name="comp_rod_name" type="text" value="Unnamed" label="ROD Name"/>
138 </repeat>
139
140 <conditional name="dbsnp_rod_bind_type">
141 <param name="dbsnp_rod_bind_type_selector" type="select" label="Provide a dbSNP reference-ordered data file" help="-D,--dbsnp &amp;lt;dbsnp&amp;gt;">
142 <option value="set_dbsnp" selected="True">Set dbSNP</option>
143 <option value="exclude_dbsnp">Don't set dbSNP</option>
144 </param>
145 <when value="exclude_dbsnp">
146 <!-- Do nothing here -->
147 </when>
148 <when value="set_dbsnp">
149 <param name="dbsnp_input_rod" type="data" format="vcf" label="ROD file" />
150 <param name="dbsnp_rod_name" type="hidden" value="dbsnp" label="ROD Name"/>
151 </when>
152 </conditional>
153
154 <repeat name="resource_rod_bind" title="Binding for reference-ordered resource data" help="-resource,--resource &amp;lt;resource&amp;gt;">
155 <param name="resource_input_rod" type="data" format="vcf" label="ROD file" />
156 <param name="resource_rod_name" type="text" value="Unnamed" label="ROD Name"/>
157 </repeat>
158
159 <conditional name="snpEff_rod_bind_type">
160 <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;">
161 <option value="set_snpEff">Set snpEff</option>
162 <option value="exclude_snpEff" selected="True">Don't set snpEff</option>
163 </param>
164 <when value="exclude_snpEff">
165 <!-- Do nothing here -->
166 </when>
167 <when value="set_snpEff">
168 <param name="snpEff_input_rod" type="data" format="vcf" label="ROD file" />
169 <param name="snpEff_rod_name" type="hidden" value="snpEff" label="ROD Name"/>
170 </when>
171 </conditional>
172
173 <repeat name="expressions" title="Expression" help="-E,--expression &amp;lt;expression&amp;gt;">
174 <param name="expression" type="text" value="" label="Expression"/>
175 </repeat>
176
177 <expand macro="gatk_param_type_conditional" />
178
179 <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;">
180 <option value="RodRequiringAnnotation">RodRequiringAnnotation</option>
181 <option value="Standard">Standard</option>
182 <option value="Experimental">Experimental</option>
183 <option value="WorkInProgress">WorkInProgress</option>
184 <option value="RankSumTest">RankSumTest</option>
185 </param>
186 <param name="family_string" type="text" value="" label="Family String" help="--family_string"/>
187 <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;"/>
188 <param name="exclude_annotations" type="select" multiple="True" display="checkboxes" label="Annotations to exclude" help="-XA,--excludeAnnotation &amp;lt;excludeAnnotation&amp;gt;" >
189 <!-- load the available annotations from an external configuration file, since additional ones can be added to local installs -->
190 <options from_data_table="gatk2_annotations">
191 <filter type="multiple_splitter" column="tools_valid_for" separator=","/>
192 <filter type="static_value" value="VariantAnnotator" column="tools_valid_for"/>
193 </options>
194 </param>
195
196 </inputs>
197 <outputs>
198 <data format="vcf" name="output_vcf" label="${tool.name} on ${on_string} (Variant File)" />
199 <data format="txt" name="output_log" label="${tool.name} on ${on_string} (log)" />
200 </outputs>
201 <tests>
202 <test>
203 <param name="reference_source_selector" value="history" />
204 <param name="ref_file" value="phiX.fasta" ftype="fasta" />
205 <param name="input_bam" value="gatk/gatk_table_recalibration/gatk_table_recalibration_out_1.bam" ftype="bam" />
206 <param name="input_variant" value="gatk/gatk_unified_genotyper/gatk_unified_genotyper_out_1.vcf" ftype="vcf" />
207 <param name="input_variant_bti" />
208 <param name="annotations_type_selector" value="choose" />
209 <param name="annotations" value="AlleleBalance,BaseQualityRankSumTest,DepthOfCoverage,HomopolymerRun,MappingQualityRankSumTest,MappingQualityZero,QualByDepth,RMSMappingQuality,SpanningDeletions,HaplotypeScore" />
210 <param name="additional_annotations" value="0" />
211 <param name="dbsnp_rod_bind_type_selector" value="set_dbsnp" />
212 <param name="dbsnp_input_rod" value="gatk/fake_phiX_variant_locations.vcf" ftype="vcf" />
213 <param name="snpEff_rod_bind_type_selector" value="exclude_snpEff" />
214 <param name="gatk_param_type_selector" value="basic" />
215 <output name="output_vcf" file="gatk/gatk_variant_annotator/gatk_variant_annotator_out_1.vcf" lines_diff="4" />
216 <output name="output_log" file="gatk/gatk_variant_annotator/gatk_variant_annotator_out_1.log.contains" compare="contains" />
217 <param name="comp_rod_bind" value="0" />
218 <param name="resource_rod_bind" value="0" />
219 <param name="expressions" value="0" />
220 <!-- <param name="annotation_group" /> -->
221 </test>
222 </tests>
223 <help>
224 **What it does**
225
226 Annotates variant calls with context information. Users can specify which of the available annotations to use.
227
228 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;`_.
229
230 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;`_.
231
232 If you encounter errors, please view the `GATK FAQ &lt;http://www.broadinstitute.org/gatk/guide/topic?name=faqs&gt;`_.
233
234 ------
235
236
237 **Inputs**
238
239 GenomeAnalysisTK: VariantAnnotator accepts a variant input file.
240
241
242 **Outputs**
243
244 The output is in VCF format.
245
246
247 Go `here &lt;http://www.broadinstitute.org/gatk/guide/topic?name=intro&gt;`_ for details on GATK file formats.
248
249 -------
250
251 **Settings**::
252
253
254 sampleName The sample (NA-ID) corresponding to the variant input (for non-VCF input only)
255 annotation One or more specific annotations to apply to variant calls
256 group One or more classes/groups of annotations to apply to variant calls
257 expression One or more specific expressions to apply to variant calls; see documentation for more details
258 useAllAnnotations Use all possible annotations (not for the faint of heart)
259
260 @CITATION_SECTION@
261 </help>
262 </tool>