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comparison variant_annotator.xml @ 2:8bcc13094767 draft

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Uploaded
author iuc
date Sat, 18 Jan 2014 07:21:33 -0500
parents 340633249b3d
children f244b8209eb8
comparison
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1:f760c0de8e3a 2:8bcc13094767
49 49
50 #for $rod_binding in $comp_rod_bind: 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_${rod_binding.comp_rod_name}" 51 -d "--comp:${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 52 #end for
53 53
54 #if str( $dbsnp_rod_bind_type.dbsnp_rod_bind_type_selector ) == 'set_dbsnp': 54 @DBSNP_OPTIONS@
55 -d "--dbsnp:${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 55
59 #for $rod_binding in $resource_rod_bind: 56 #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_${rod_binding.resource_rod_name}" 57 -d "--resource:${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 58 #end for
62 59
134 131
135 <repeat name="comp_rod_bind" title="Binding for reference-ordered comparison data" help="-comp,--comp &amp;lt;comp&amp;gt;"> 132 <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" /> 133 <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"/> 134 <param name="comp_rod_name" type="text" value="Unnamed" label="ROD Name"/>
138 </repeat> 135 </repeat>
139 136 <expand macro="dbsnp_param" />
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>
153 137
154 <repeat name="resource_rod_bind" title="Binding for reference-ordered resource data" help="-resource,--resource &amp;lt;resource&amp;gt;"> 138 <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" /> 139 <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"/> 140 <param name="resource_rod_name" type="text" value="Unnamed" label="ROD Name"/>
157 </repeat> 141 </repeat>
208 <param name="annotations_type_selector" value="choose" /> 192 <param name="annotations_type_selector" value="choose" />
209 <param name="annotations" value="AlleleBalance,BaseQualityRankSumTest,DepthOfCoverage,HomopolymerRun,MappingQualityRankSumTest,MappingQualityZero,QualByDepth,RMSMappingQuality,SpanningDeletions,HaplotypeScore" /> 193 <param name="annotations" value="AlleleBalance,BaseQualityRankSumTest,DepthOfCoverage,HomopolymerRun,MappingQualityRankSumTest,MappingQualityZero,QualByDepth,RMSMappingQuality,SpanningDeletions,HaplotypeScore" />
210 <param name="additional_annotations" value="0" /> 194 <param name="additional_annotations" value="0" />
211 <param name="dbsnp_rod_bind_type_selector" value="set_dbsnp" /> 195 <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" /> 196 <param name="dbsnp_input_rod" value="gatk/fake_phiX_variant_locations.vcf" ftype="vcf" />
197 <param name="dbsnp_rod_name" value="dbsnp" />
213 <param name="snpEff_rod_bind_type_selector" value="exclude_snpEff" /> 198 <param name="snpEff_rod_bind_type_selector" value="exclude_snpEff" />
214 <param name="gatk_param_type_selector" value="basic" /> 199 <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" /> 200 <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" /> 201 <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" /> 202 <param name="comp_rod_bind" value="0" />