diff variant_annotator.xml @ 6:35c00763cb5c draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit cf399638ebca4250bcc15f468238a9964de97b33

--- a/variant_annotator.xml	Mon Aug 25 17:44:53 2014 -0400
+++ b/variant_annotator.xml	Mon Jun 04 05:38:15 2018 -0400
@@ -1,9 +1,10 @@
 <tool id="gatk2_variant_annotator" name="Variant Annotator" version="@VERSION@.0">
   <description></description>
-  <expand macro="requirements" />
   <macros>
     <import>gatk2_macros.xml</import>
   </macros>
+  <expand macro="requirements" />
+  <expand macro="version_command" />
   <command interpreter="python">
     gatk2_wrapper.py
     --stdout "${output_log}"
@@ -46,30 +47,30 @@
     #if $reference_source.input_variant_bti:
         -d "--intervals" "${reference_source.input_variant}" "${reference_source.input_variant.ext}" "input_variant_bti"
     #end if
-    
+
     #for $rod_binding in $comp_rod_bind:
         -d "--comp:${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
-    
+
     @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}"
     #end for
-    
+
     #if str( $snpEff_rod_bind_type.snpEff_rod_bind_type_selector ) == 'set_snpEff':
         -p '--annotation "SnpEff"'
         -d "--snpEffFile:${snpEff_rod_bind_type.snpEff_rod_name},%(file_type)s" "${snpEff_rod_bind_type.snpEff_input_rod}" "${snpEff_rod_bind_type.snpEff_input_rod.ext}" "input_snpEff_${snpEff_rod_bind_type.snpEff_rod_name}"
     #else:
         -p '--excludeAnnotation "SnpEff"'
     #end if
-    
+
     #for $expression in $expressions:
         -p '--expression "${expression.expression}"'
     #end for
-    
+
     #include source=$standard_gatk_options#
-    
+
     -p '
     #if str( $annotation_group ) != "None":
         #for $group in str( $annotation_group ).split( ',' ):
@@ -124,22 +125,22 @@
         </param>
       </when>
     </conditional>
-    
+
     <repeat name="additional_annotations" title="Additional annotation" help="-A,--annotation &amp;lt;annotation&amp;gt;">
       <param name="additional_annotation_name" type="text" value="" label="Annotation name" />
     </repeat>
-    
+
     <repeat name="comp_rod_bind" title="Binding for reference-ordered comparison data" help="-comp,--comp &amp;lt;comp&amp;gt;">
       <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>
     <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" />
       <param name="resource_rod_name" type="text" value="Unnamed" label="ROD Name"/>
     </repeat>
-    
+
     <conditional name="snpEff_rod_bind_type">
       <param name="snpEff_rod_bind_type_selector" type="select" label="Provide a snpEff reference-ordered data file (VCF)" help="-snpEffFile,--snpEffFile &amp;lt;snpEffFile&amp;gt;">
         <option value="set_snpEff">Set snpEff</option>
@@ -153,13 +154,13 @@
         <param name="snpEff_rod_name" type="hidden" value="snpEff" label="ROD Name"/>
       </when>
     </conditional>
-    
+
     <repeat name="expressions" title="Expression" help="-E,--expression &amp;lt;expression&amp;gt;">
       <param name="expression" type="text" value="" label="Expression"/>
     </repeat>
-    
+
     <expand macro="gatk_param_type_conditional" />
-    
+
     <param name="annotation_group" type="select" multiple="True" display="checkboxes" label="annotation interfaces/groups to apply to variant calls" help="-G,--group &amp;lt;group&amp;gt;">
       <option value="RodRequiringAnnotation">RodRequiringAnnotation</option>
       <option value="Standard">Standard</option>
@@ -176,7 +177,7 @@
         <filter type="static_value" value="VariantAnnotator" column="tools_valid_for"/>
       </options>
     </param>
-    
+
   </inputs>
   <outputs>
     <data format="vcf" name="output_vcf" label="${tool.name} on ${on_string} (Variant File)" />
@@ -197,7 +198,7 @@
           <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" /> 
+          <output name="output_vcf" file="gatk/gatk_variant_annotator/gatk_variant_annotator_out_1.vcf" lines_diff="4" />
           <output name="output_log" file="gatk/gatk_variant_annotator/gatk_variant_annotator_out_1.log.contains" compare="contains" />
           <param name="comp_rod_bind" value="0" />
           <param name="resource_rod_bind" value="0" />