diff variant_validate.xml @ 2:8bcc13094767 draft

Uploaded

--- a/variant_validate.xml	Mon Dec 02 10:36:02 2013 -0500
+++ b/variant_validate.xml	Sat Jan 18 07:21:33 2014 -0500
@@ -14,18 +14,13 @@
     
     \$GATK2_SITE_OPTIONS
 
-    @THREADS@
-
     #if $reference_source.reference_source_selector != "history":
         -R "${reference_source.ref_file.fields.path}"
     #end if
     ${warn_on_errors}
     ${do_not_validate_filtered_records}
    '
-   
-    #if str( $dbsnp_rod_bind_type.dbsnp_rod_bind_type_selector ) == 'set_dbsnp':
-        -d "--dbsnp:${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}"
-    #end if
+    @DBSNP_OPTIONS@
    
     #include source=$standard_gatk_options#
   </command>
@@ -47,20 +42,7 @@
         <param name="ref_file" type="data" format="fasta" label="Using reference file" help="-R,--reference_sequence &amp;lt;reference_sequence&amp;gt;" />
       </when>
     </conditional>
-    
-    <conditional name="dbsnp_rod_bind_type">
-      <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;">
-        <option value="set_dbsnp" selected="True">Set dbSNP</option>
-        <option value="exclude_dbsnp">Don't set dbSNP</option>
-      </param>
-      <when value="exclude_dbsnp">
-        <!-- Do nothing here -->
-      </when>
-      <when value="set_dbsnp">
-        <param name="dbsnp_input_rod" type="data" format="vcf" label="ROD file" />
-        <param name="dbsnp_rod_name" type="hidden" value="dbsnp" label="ROD Name"/>
-      </when>
-    </conditional>
+    <expand macro="dbsnp_param" />
     
     <param name="warn_on_errors" type="boolean" checked="False" truevalue="-warnOnErrors" falsevalue="" label="instead of terminating the run at the first error, print warning messages for each error seen." help="-warnOnErrors,--warnOnErrors"/>
     <param name="do_not_validate_filtered_records" type="boolean" checked="False" truevalue="-doNotValidateFilteredRecords" falsevalue="" label="do not try to validate records that are FILTERed." help="-doNotValidateFilteredRecords,--doNotValidateFilteredRecords"/>
@@ -78,6 +60,7 @@
           <param name="input_variant" value="gatk/gatk_variant_annotator/gatk_variant_annotator_out_1.vcf" ftype="vcf" />
           <param name="dbsnp_rod_bind_type_selector" value="set_dbsnp" />
           <param name="dbsnp_input_rod" value="gatk/fake_phiX_variant_locations.vcf" ftype="vcf" />
+          <param name="dbsnp_rod_name" value="dbsnp" />
           <param name="warn_on_errors" value="True"/>
           <param name="do_not_validate_filtered_records" />
           <param name="gatk_param_type_selector" value="basic" />