Mercurial > repos > iuc > gatk2
annotate variant_annotator.xml @ 6:35c00763cb5c draft default tip
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 |
| rev | line source |
|---|---|
| 4 | 1 <tool id="gatk2_variant_annotator" name="Variant Annotator" version="@VERSION@.0"> |
| 0 | 2 <description></description> |
| 3 <macros> | |
| 4 <import>gatk2_macros.xml</import> | |
| 5 </macros> | |
|
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35c00763cb5c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit cf399638ebca4250bcc15f468238a9964de97b33
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6 <expand macro="requirements" /> |
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35c00763cb5c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit cf399638ebca4250bcc15f468238a9964de97b33
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7 <expand macro="version_command" /> |
| 0 | 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 | |
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6
35c00763cb5c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit cf399638ebca4250bcc15f468238a9964de97b33
iuc
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50 |
| 0 | 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 | |
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6
35c00763cb5c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit cf399638ebca4250bcc15f468238a9964de97b33
iuc
parents:
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|
54 |
| 2 | 55 @DBSNP_OPTIONS@ |
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6
35c00763cb5c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit cf399638ebca4250bcc15f468238a9964de97b33
iuc
parents:
4
diff
changeset
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56 |
| 0 | 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 | |
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6
35c00763cb5c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit cf399638ebca4250bcc15f468238a9964de97b33
iuc
parents:
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diff
changeset
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60 |
| 0 | 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 | |
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6
35c00763cb5c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit cf399638ebca4250bcc15f468238a9964de97b33
iuc
parents:
4
diff
changeset
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67 |
| 0 | 68 #for $expression in $expressions: |
| 69 -p '--expression "${expression.expression}"' | |
| 70 #end for | |
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6
35c00763cb5c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit cf399638ebca4250bcc15f468238a9964de97b33
iuc
parents:
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diff
changeset
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71 |
| 0 | 72 #include source=$standard_gatk_options# |
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6
35c00763cb5c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit cf399638ebca4250bcc15f468238a9964de97b33
iuc
parents:
4
diff
changeset
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73 |
| 0 | 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 &lt;variant&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 &lt;input_file&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 &lt;reference_sequence&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 &lt;variant&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 &lt;input_file&gt;)" /> | |
| 107 <param name="ref_file" type="data" format="fasta" label="Using reference file" help="-R,--reference_sequence &lt;reference_sequence&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 &lt;annotation&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> | |
|
6
35c00763cb5c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit cf399638ebca4250bcc15f468238a9964de97b33
iuc
parents:
4
diff
changeset
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128 |
| 0 | 129 <repeat name="additional_annotations" title="Additional annotation" help="-A,--annotation &lt;annotation&gt;"> |
| 130 <param name="additional_annotation_name" type="text" value="" label="Annotation name" /> | |
| 131 </repeat> | |
|
6
35c00763cb5c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit cf399638ebca4250bcc15f468238a9964de97b33
iuc
parents:
4
diff
changeset
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132 |
| 0 | 133 <repeat name="comp_rod_bind" title="Binding for reference-ordered comparison data" help="-comp,--comp &lt;comp&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> | |
| 2 | 137 <expand macro="dbsnp_param" /> |
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6
35c00763cb5c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit cf399638ebca4250bcc15f468238a9964de97b33
iuc
parents:
4
diff
changeset
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138 |
| 0 | 139 <repeat name="resource_rod_bind" title="Binding for reference-ordered resource data" help="-resource,--resource &lt;resource&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> | |
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6
35c00763cb5c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit cf399638ebca4250bcc15f468238a9964de97b33
iuc
parents:
4
diff
changeset
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143 |
| 0 | 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 &lt;snpEffFile&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> | |
|
6
35c00763cb5c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit cf399638ebca4250bcc15f468238a9964de97b33
iuc
parents:
4
diff
changeset
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157 |
| 0 | 158 <repeat name="expressions" title="Expression" help="-E,--expression &lt;expression&gt;"> |
| 159 <param name="expression" type="text" value="" label="Expression"/> | |
| 160 </repeat> | |
|
6
35c00763cb5c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit cf399638ebca4250bcc15f468238a9964de97b33
iuc
parents:
4
diff
changeset
|
161 |
| 0 | 162 <expand macro="gatk_param_type_conditional" /> |
|
6
35c00763cb5c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit cf399638ebca4250bcc15f468238a9964de97b33
iuc
parents:
4
diff
changeset
|
163 |
| 0 | 164 <param name="annotation_group" type="select" multiple="True" display="checkboxes" label="annotation interfaces/groups to apply to variant calls" help="-G,--group &lt;group&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 &lt;MendelViolationGenotypeQualityThreshold&gt;"/> | |
| 173 <param name="exclude_annotations" type="select" multiple="True" display="checkboxes" label="Annotations to exclude" help="-XA,--excludeAnnotation &lt;excludeAnnotation&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> | |
|
6
35c00763cb5c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit cf399638ebca4250bcc15f468238a9964de97b33
iuc
parents:
4
diff
changeset
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180 |
| 0 | 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" /> | |
| 2 | 198 <param name="dbsnp_rod_name" value="dbsnp" /> |
| 0 | 199 <param name="snpEff_rod_bind_type_selector" value="exclude_snpEff" /> |
| 200 <param name="gatk_param_type_selector" value="basic" /> | |
|
6
35c00763cb5c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit cf399638ebca4250bcc15f468238a9964de97b33
iuc
parents:
4
diff
changeset
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201 <output name="output_vcf" file="gatk/gatk_variant_annotator/gatk_variant_annotator_out_1.vcf" lines_diff="4" /> |
| 0 | 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 <http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_gatk_walkers_annotator_VariantAnnotator.html>`_. | |
| 215 | |
| 216 To learn about best practices for variant detection using GATK, see this `overview <http://www.broadinstitute.org/gatk/guide/topic?name=best-practices>`_. | |
| 217 | |
| 218 If you encounter errors, please view the `GATK FAQ <http://www.broadinstitute.org/gatk/guide/topic?name=faqs>`_. | |
| 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 <http://www.broadinstitute.org/gatk/guide/topic?name=intro>`_ 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> | |
| 4 | 248 <expand macro="citations" /> |
| 0 | 249 </tool> |