diff variant_apply_recalibration.xml @ 11:0d369d08ad6e draft

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

--- a/variant_apply_recalibration.xml	Tue Apr 28 22:56:25 2015 -0400
+++ b/variant_apply_recalibration.xml	Mon May 04 22:47:06 2015 -0400
@@ -1,10 +1,10 @@
 <tool id="gatk2_variant_apply_recalibration" name="Apply Variant Recalibration" 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 "${output_log}"
@@ -25,13 +25,13 @@
     --tranches_file "${reference_source.input_tranches}"
     --out "${output_variants}"
    '
-    
+
     #include source=$standard_gatk_options#
-    
+
     ##start analysis specific options
     -p '
     --mode "${mode}"
-    
+
     #for $ignore_filter in $ignore_filters:
         #set $ignore_filter_name = str( $ignore_filter.ignore_filter_type.ignore_filter_type_selector )
         #if $ignore_filter_name == "custom":
@@ -67,9 +67,9 @@
         <param name="ref_file" type="data" format="fasta" label="Using reference file" help="-R,--reference_sequence &amp;lt;reference_sequence&amp;gt;" />
       </when>
     </conditional>
-    
+
     <expand macro="gatk_param_type_conditional" />
-    
+
         <param name="mode" type="select" label="Recalibration mode" help="-mode,--mode &amp;lt;mode&amp;gt;">
           <option value="SNP" selected="True">SNP</option>
           <option value="INDEL">INDEL</option>