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

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

--- a/variant_combine.xml	Mon Aug 25 17:44:53 2014 -0400
+++ b/variant_combine.xml	Mon Jun 04 05:38:15 2018 -0400
@@ -1,9 +1,10 @@
 <tool id="gatk2_variant_combine" name="Combine Variants" 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 "${output_log}"
@@ -29,10 +30,9 @@
    --genotypemergeoption "${genotype_merge_option}"
    --rod_priority_list "${ ','.join( $priority_order ) }"
    '
-   
+
     #include source=$standard_gatk_options#
-    
-    
+
     ##start analysis specific options
     #if $analysis_param_type.analysis_param_type_selector == "advanced":
         -p '
@@ -41,17 +41,17 @@
         ${analysis_param_type.filtered_are_uncalled}
         ${analysis_param_type.minimal_vcf}
         ${analysis_param_type.assume_identical_samples}
-        
+
         #if str( $analysis_param_type.set_key ):
             --setKey "${analysis_param_type.set_key}"
         #end if
-        
+
         --minimumN "${analysis_param_type.minimum_n}"
         '
     #end if
   </command>
   <inputs>
-    
+
     <conditional name="reference_source">
       <expand macro="reference_source_selector_param" />
       <when value="cached">
@@ -78,34 +78,31 @@
         <param name="ref_file" type="data" format="fasta" label="Using reference file" help="-R,--reference_sequence &amp;lt;reference_sequence&amp;gt;" />
       </when>
     </conditional>
-    
+
     <param name="genotype_merge_option" type="select" label="How should we merge genotype records across records for samples shared across the ROD files" help="-genotypeMergeOptions,--genotypemergeoption &amp;lt;genotypemergeoption&amp;gt;" >
       <option value="UNIQUIFY" />
       <option value="PRIORITIZE" selected="true"/>
       <option value="UNSORTED" />
       <option value="REQUIRE_UNIQUE" />
     </param>
-    
+
     <expand macro="gatk_param_type_conditional" />
-    
-    
+
     <expand macro="analysis_type_conditional">
         <param name="filtered_records_merge_type" type="select" label="How should we deal with records seen at the same site in the VCF, but with different FILTER fields?" help="-filteredRecordsMergeType,--filteredrecordsmergetype &amp;lt;filteredrecordsmergetype&amp;gt;" >
           <option value="KEEP_IF_ANY_UNFILTERED" selected="true"/>
           <option value="KEEP_IF_ALL_UNFILTERED" />
         </param>
-        
+
         <param name="print_complex_merges" checked="false" type="boolean" truevalue="--printComplexMerges" falsevalue="" label="Print out interesting sites requiring complex compatibility merging" help="-printComplexMerges,--printComplexMerges" />
         <param name="filtered_are_uncalled" checked="false" type="boolean" truevalue="--filteredAreUncalled" falsevalue="" label="If true, then filtered VCFs are treated as uncalled, so that filtered set annotation don't appear in the combined VCF" help="-filteredAreUncalled,--filteredAreUncalled" />
         <param name="minimal_vcf" checked="false" type="boolean" truevalue="--minimalVCF" falsevalue="" label="If true, then the output VCF will contain no INFO or genotype INFO field" help="-minimalVCF,--minimalVCF" />
-        
+
         <param name="set_key" type="text" value="" label="Key, by default set, in the INFO key=value tag emitted describing which set the combined VCF record came from." help="-setKey,--setKey &amp;lt;setKey&amp;gt;"/>
         <param name="assume_identical_samples" checked="false" type="boolean" truevalue="--assumeIdenticalSamples" falsevalue="" label="If true, assume input VCFs have identical sample sets and disjoint calls so that one can simply perform a merge sort to combine the VCFs into one, drastically reducing the runtime." help="-assumeIdenticalSamples,--assumeIdenticalSamples" />
         <param name="minimum_n" type="integer" value="1" label="Combine variants and output site only if variant is present in at least N input files." help="-minN,--minimumN &amp;lt;minimumN&amp;gt;"/>
-        
     </expand>
-    
-    
+
   </inputs>
   <outputs>
     <data format="vcf" name="output_variants" label="${tool.name} on ${on_string} (variants)" />