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comparison variant_eval.xml @ 4:e67da4f2c9bf draft

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author bgruening
date Sat, 18 Jan 2014 07:00:26 -0500
parents c8752e31f496
children b80301676614
comparison
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3:b7ef18eaa9c9 4:e67da4f2c9bf
30 #if str( $rod_binding.comp_known_names ): 30 #if str( $rod_binding.comp_known_names ):
31 -p '--known_names "${rod_binding.comp_rod_name}"' 31 -p '--known_names "${rod_binding.comp_rod_name}"'
32 #end if 32 #end if
33 #end for 33 #end for
34 34
35 #if str( $dbsnp_rod_bind_type.dbsnp_rod_bind_type_selector ) == 'set_dbsnp': 35 #if $dbsnp_rod_bind_type.dbsnp_rod_bind_type_selector == 'set_dbsnp'
36 -d "--dbsnp:${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_${dbsnp_rod_bind_type.dbsnp_rod_name}" 36 -d "--dbsnp:${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}"
37 #if str( $dbsnp_rod_bind_type.dbsnp_known_names ): 37 #if $dbsnp_rod_bind_type.dbsnp_known_names
38 -p '--known_names "${dbsnp_rod_bind_type.dbsnp_rod_name}"' 38 -p '--known_names "${dbsnp_rod_bind_type.dbsnp_rod_name}"'
39 #end if 39 #end if
40 #end if 40 #end if
41 41
42 #include source=$standard_gatk_options# 42 #include source=$standard_gatk_options#
120 </repeat> 120 </repeat>
121 <param name="ref_file" type="data" format="fasta" label="Using reference file" help="-R,--reference_sequence &amp;lt;reference_sequence&amp;gt;" /> 121 <param name="ref_file" type="data" format="fasta" label="Using reference file" help="-R,--reference_sequence &amp;lt;reference_sequence&amp;gt;" />
122 </when> 122 </when>
123 </conditional> 123 </conditional>
124 124
125 <repeat name="comp_rod_bind" title="Binding for reference-ordered comparison data" help="-comp,--comp &amp;lt;comp&amp;gt;"> 125 <repeat name="comp_rod_bind" title="Comparison Reference-Ordered Data (ROD) file" help="-comp,--comp &amp;lt;comp&amp;gt;">
126 <param name="comp_input_rod" type="data" format="vcf" label="Comparison ROD file" /> 126 <param name="comp_input_rod" type="data" format="vcf" label="Comparison ROD file" />
127 <param name="comp_rod_name" type="text" value="Unnamed" label="Comparison ROD Name"/> 127 <param name="comp_rod_name" type="text" value="" label="Comparison ROD name">
128 <param name="comp_known_names" type="boolean" truevalue="--known_names" falsevalue="" label="Use Comparison ROD as known_names" help="-knownName,--known_names &amp;lt;known_names&amp;gt;"/> 128 <validator type="regex" message="Value must be a not empty string composed by alphanumeric characters and underscores">^\w+$</validator>
129 </param>
130 <param name="comp_known_names" type="boolean" label="Use comparison ROD file as known_names" help="-knownName,--known_names &amp;lt;known_names&amp;gt;"/>
129 </repeat> 131 </repeat>
130
131 <conditional name="dbsnp_rod_bind_type"> 132 <conditional name="dbsnp_rod_bind_type">
132 <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;"> 133 <param name="dbsnp_rod_bind_type_selector" type="select" label="Provide a dbSNP Reference-Ordered Data (ROD) file" help="-D,--dbsnp &amp;lt;dbsnp&amp;gt;">
133 <option value="set_dbsnp" selected="True">Set dbSNP</option> 134 <option value="set_dbsnp" selected="True">Set dbSNP</option>
134 <option value="exclude_dbsnp">Don't set dbSNP</option> 135 <option value="exclude_dbsnp">Don't set dbSNP</option>
135 </param> 136 </param>
136 <when value="exclude_dbsnp"> 137 <when value="exclude_dbsnp" />
137 <!-- Do nothing here -->
138 </when>
139 <when value="set_dbsnp"> 138 <when value="set_dbsnp">
140 <param name="dbsnp_input_rod" type="data" format="vcf" label="dbSNP ROD file" /> 139 <param name="dbsnp_input_rod" type="data" format="vcf" label="dbSNP ROD file" />
141 <param name="dbsnp_rod_name" type="hidden" value="dbsnp" label="dbSNP ROD Name"/> 140 <param name="dbsnp_rod_name" type="text" value="dbsnp" label="dbsnp ROD name">
142 <param name="dbsnp_known_names" type="boolean" truevalue="--known_names" falsevalue="" label="Use dbSNP ROD as known_names" help="-knownName,--known_names &amp;lt;known_names&amp;gt;" /> 141 <validator type="regex" message="Value must be a not empty string composed by alphanumeric characters and underscores">^\w+$</validator>
142 </param>
143 <param name="dbsnp_known_names" type="boolean" label="Use dbSNP ROD file as known_names" help="-knownName,--known_names &amp;lt;known_names&amp;gt;" />
143 </when> 144 </when>
144 </conditional> 145 </conditional>
145 146
146 <expand macro="gatk_param_type_conditional" /> 147 <expand macro="gatk_param_type_conditional" />
147 148
226 <param name="reference_source_selector" value="history" /> 227 <param name="reference_source_selector" value="history" />
227 <param name="ref_file" value="phiX.fasta" ftype="fasta" /> 228 <param name="ref_file" value="phiX.fasta" ftype="fasta" />
228 <param name="input_variant" value="gatk/gatk_variant_annotator/gatk_variant_annotator_out_1.vcf" ftype="vcf" /> 229 <param name="input_variant" value="gatk/gatk_variant_annotator/gatk_variant_annotator_out_1.vcf" ftype="vcf" />
229 <param name="dbsnp_rod_bind_type_selector" value="set_dbsnp" /> 230 <param name="dbsnp_rod_bind_type_selector" value="set_dbsnp" />
230 <param name="dbsnp_input_rod" value="gatk/fake_phiX_variant_locations.vcf" ftype="vcf" /> 231 <param name="dbsnp_input_rod" value="gatk/fake_phiX_variant_locations.vcf" ftype="vcf" />
232 <param name="dbsnp_rod_name" value="dbsnp" />
231 <param name="dbsnp_known_names" value="True"/> 233 <param name="dbsnp_known_names" value="True"/>
232 <param name="comp_rod_bind" value="0" /> 234 <param name="comp_rod_bind" value="0" />
233 <param name="gatk_param_type_selector" value="basic" /> 235 <param name="gatk_param_type_selector" value="basic" />
234 <param name="analysis_param_type_selector" value="basic" /> 236 <param name="analysis_param_type_selector" value="basic" />
235 <output name="output_report" file="gatk/gatk_variant_eval/gatk_variant_eval_out_1.gatk_report" /> 237 <output name="output_report" file="gatk/gatk_variant_eval/gatk_variant_eval_out_1.gatk_report" />