diff picard_CollectAlignmentSummaryMetrics.xml @ 14:486d7500da69 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 7036343b9ac0a0ffc2ce4f6db465b9298ef05e73

--- a/picard_CollectAlignmentSummaryMetrics.xml	Sat Jan 20 08:28:02 2018 -0500
+++ b/picard_CollectAlignmentSummaryMetrics.xml	Mon Apr 16 21:27:09 2018 -0400
@@ -1,7 +1,8 @@
-<tool name="Collect Alignment Summary Metrics" id="picard_CASM" version="@TOOL_VERSION@.1">
+<tool name="Collect Alignment Summary Metrics" id="picard_CASM" version="@TOOL_VERSION@.@WRAPPER_VERSION@">
   <description>writes a file containing summary alignment metrics</description>
   <macros>
     <import>picard_macros.xml</import>
+    <token name="@WRAPPER_VERSION@">0</token>
   </macros>
   <expand macro="requirements" />
   <command detect_errors="exit_code"><![CDATA[
@@ -11,11 +12,7 @@
 
     #set $reference_fasta_filename = "localref.fa"
 
-    #if str( $reference_source.reference_source_selector ) == "history":
-        ln -s "${reference_source.ref_file}" "${reference_fasta_filename}" &&
-    #else:
-        #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path )
-    #end if
+    @handle_reference_source@
 
     picard
     CollectAlignmentSummaryMetrics
@@ -122,6 +119,5 @@
 @more_info@
 
   </help>
+  <expand macro="citations" />
 </tool>
-
-