diff picard_macros.xml @ 19:5053a18d9bc8 draft

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

--- a/picard_macros.xml	Sat Jan 20 08:28:24 2018 -0500
+++ b/picard_macros.xml	Mon Apr 16 21:27:29 2018 -0400
@@ -7,11 +7,11 @@
         </param>
     </xml>
 
-    <token name="@TOOL_VERSION@">2.7.1</token>
+    <token name="@TOOL_VERSION@">2.18.2</token>
 
     <xml name="requirements">
         <requirements>
-            <requirement type="package" version="2.7.1">picard</requirement>
+            <requirement type="package" version="@TOOL_VERSION@">picard</requirement>
             <yield/>
         </requirements>
     </xml>
@@ -27,6 +27,14 @@
     export _JAVA_OPTIONS &&
     ]]></token>
 
+    <token name="@handle_reference_source@"><![CDATA[
+    #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
+    ]]></token>
+
     <token name="@more_info@">
 ------
 
@@ -96,5 +104,18 @@
 
     </token>
 
+    <xml name="citations">
+        <citations>
+            <citation type="bibtex">@misc{Picard,
+                  author = {Broad Institute},
+                  title = {Picard},
+                  publisher = {GitHub},
+                  journal = { Broad Institute, GitHub repository},
+                  url = {http://broadinstitute.github.io/picard/}
+                }
+            </citation>
+        </citations>
+    </xml>
+
 
 </macros>