diff variant_annotator.xml @ 2:8bcc13094767 draft

Uploaded

--- a/variant_annotator.xml	Mon Dec 02 10:36:02 2013 -0500
+++ b/variant_annotator.xml	Sat Jan 18 07:21:33 2014 -0500
@@ -51,10 +51,7 @@
         -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}"
     #end for
     
-    #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@
     
     #for $rod_binding in $resource_rod_bind:
         -d "--resource:${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}"
@@ -136,20 +133,7 @@
       <param name="comp_input_rod" type="data" format="vcf" label="ROD file" />
       <param name="comp_rod_name" type="text" value="Unnamed" label="ROD Name"/>
     </repeat>
-    
-    <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" />
     
     <repeat name="resource_rod_bind" title="Binding for reference-ordered resource data" help="-resource,--resource &amp;lt;resource&amp;gt;">
       <param name="resource_input_rod" type="data" format="vcf" label="ROD file" />
@@ -210,6 +194,7 @@
           <param name="additional_annotations" value="0" />
           <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="snpEff_rod_bind_type_selector" value="exclude_snpEff" />
           <param name="gatk_param_type_selector" value="basic" />
           <output name="output_vcf" file="gatk/gatk_variant_annotator/gatk_variant_annotator_out_1.vcf" lines_diff="4" />