Mercurial > repos > iuc > gatk2
comparison variant_eval.xml @ 2:8bcc13094767 draft
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author | iuc |
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date | Sat, 18 Jan 2014 07:21:33 -0500 |
parents | 340633249b3d |
children | f244b8209eb8 |
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1:f760c0de8e3a | 2:8bcc13094767 |
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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=$standard_gatk_options# |
120 </repeat> | 120 </repeat> |
121 <param name="ref_file" type="data" format="fasta" label="Using reference file" help="-R,--reference_sequence &lt;reference_sequence&gt;" /> | 121 <param name="ref_file" type="data" format="fasta" label="Using reference file" help="-R,--reference_sequence &lt;reference_sequence&gt;" /> |
122 </when> | 122 </when> |
123 </conditional> | 123 </conditional> |
124 | 124 |
125 <repeat name="comp_rod_bind" title="Binding for reference-ordered comparison data" help="-comp,--comp &lt;comp&gt;"> | 125 <repeat name="comp_rod_bind" title="Comparison Reference-Ordered Data (ROD) file" help="-comp,--comp &lt;comp&gt;"> |
126 <param name="comp_input_rod" type="data" format="vcf" label="Comparison ROD file" /> | 126 <param name="comp_input_rod" type="data" format="vcf" label="Comparison ROD file" /> |
127 <param name="comp_rod_name" type="text" value="Unnamed" label="Comparison ROD Name"/> | 127 <param name="comp_rod_name" type="text" value="" label="Comparison ROD name"> |
128 <param name="comp_known_names" type="boolean" truevalue="--known_names" falsevalue="" label="Use Comparison ROD as known_names" help="-knownName,--known_names &lt;known_names&gt;"/> | 128 <validator type="regex" message="Value must be a not empty string composed by alphanumeric characters and underscores">^\w+$</validator> |
129 </param> | |
130 <param name="comp_known_names" type="boolean" label="Use comparison ROD file as known_names" help="-knownName,--known_names &lt;known_names&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 &lt;dbsnp&gt;"> | 133 <param name="dbsnp_rod_bind_type_selector" type="select" label="Provide a dbSNP Reference-Ordered Data (ROD) file" help="-D,--dbsnp &lt;dbsnp&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 &lt;known_names&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 &lt;known_names&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" /> |