diff variant_validate.xml @ 11:0d369d08ad6e draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit 344140b8df53b8b7024618bb04594607a045c03a

--- a/variant_validate.xml	Tue Apr 28 22:56:25 2015 -0400
+++ b/variant_validate.xml	Mon May 04 22:47:06 2015 -0400
@@ -1,10 +1,10 @@
 <tool id="gatk2_variant_validate" name="Validate Variants" version="@VERSION@.0">
   <description></description>
-  <expand macro="requirements" />
-  <expand macro="version_command" />
   <macros>
     <import>gatk2_macros.xml</import>
   </macros>
+  <expand macro="requirements" />
+  <expand macro="version_command" />
   <command interpreter="python">
     gatk2_wrapper.py
    --stdout "${output_log}"
@@ -12,7 +12,7 @@
    -p '
    @JAR_PATH@
     -T "ValidateVariants"
-    
+
     \$GATK2_SITE_OPTIONS
 
     #if $reference_source.reference_source_selector != "history":
@@ -22,11 +22,11 @@
     ${do_not_validate_filtered_records}
    '
     @DBSNP_OPTIONS@
-   
+
     #include source=$standard_gatk_options#
   </command>
   <inputs>
-    
+
     <conditional name="reference_source">
       <expand macro="reference_source_selector_param" />
       <when value="cached">
@@ -44,12 +44,12 @@
       </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"/>
-    
+
     <expand macro="gatk_param_type_conditional" />
-    
+
   </inputs>
   <outputs>
     <data format="txt" name="output_log" label="${tool.name} on ${on_string} (log)" />