diff picard_CollectBaseDistributionByCycle.xml @ 19:5053a18d9bc8 draft

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

--- a/picard_CollectBaseDistributionByCycle.xml	Sat Jan 20 08:28:24 2018 -0500
+++ b/picard_CollectBaseDistributionByCycle.xml	Mon Apr 16 21:27:29 2018 -0400
@@ -1,10 +1,11 @@
-<tool name="CollectBaseDistributionByCycle" id="picard_CollectBaseDistributionByCycle" version="@TOOL_VERSION@.0">
+<tool name="CollectBaseDistributionByCycle" id="picard_CollectBaseDistributionByCycle" version="@TOOL_VERSION@.@WRAPPER_VERSION@">
   <description>charts the nucleotide distribution per cycle in a SAM or BAM dataset</description>
   <macros>
     <import>picard_macros.xml</import>
+    <token name="@WRAPPER_VERSION@">0</token>
   </macros>
   <expand macro="requirements">
-    <requirement type="package" version="3.3.1">r</requirement>
+    <requirement type="package" version="3.4.1">r-base</requirement>
   </expand>
   <command detect_errors="exit_code"><![CDATA[
     @java_options@
@@ -13,11 +14,7 @@
 
     #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
     CollectBaseDistributionByCycle
@@ -107,6 +104,5 @@
 @more_info@
 
   </help>
+  <expand macro="citations" />
 </tool>
-
-