# HG changeset patch
# User refinery-platform
# Date 1537800716 14400
# Node ID afcccc536c1d41336d8681a62ff50b82ba41478e
# Parent  28f273969b5eb29eb74cb4806f24639f89a6cd74
planemo upload for repository https://github.com/scottx611x/picard_MergeSamFiles commit 18b5e06ecfca32bbeed3306c4576ddb500d71cc1

diff -r 28f273969b5e -r afcccc536c1d picard_MergeSamFiles.xml
--- a/picard_MergeSamFiles.xml	Mon Dec 04 10:52:59 2017 -0500
+++ b/picard_MergeSamFiles.xml	Mon Sep 24 10:51:56 2018 -0400
@@ -1,17 +1,14 @@
 <tool name="MergeSamFiles" id="picard_MergeSamFiles" version="@TOOL_VERSION@.0">
   <description>merges multiple SAM/BAM datasets into one</description>
-  <requirements>
-    <requirement type="package" version="1.126.0">picard</requirement>
-  </requirements>
-  
   <macros>
     <import>picard_macros.xml</import>
   </macros>
+  <expand macro="requirements" />
   <command detect_errors="exit_code"><![CDATA[
     @java_options@
     #for $index, $listCollection in enumerate($inputList):
       && 
-      java -jar \$JAVA_JAR_PATH/picard.jar 
+      picard
       MergeSamFiles
 
       #for $element in $listCollection:
diff -r 28f273969b5e -r afcccc536c1d picard_macros.xml
--- a/picard_macros.xml	Mon Dec 04 10:52:59 2017 -0500
+++ b/picard_macros.xml	Mon Sep 24 10:51:56 2018 -0400
@@ -9,6 +9,13 @@
 
     <token name="@TOOL_VERSION@">2.7.1</token>
 
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="2.7.1">picard</requirement>
+            <yield/>
+        </requirements>
+    </xml>
+
     <token name="@symlink_element_identifier@"><![CDATA[
     #import re
     #set escaped_element_identifier = re.sub('[^\w\-]', '_', str($inputFile.element_identifier))
diff -r 28f273969b5e -r afcccc536c1d tool_dependencies.xml
--- a/tool_dependencies.xml	Mon Dec 04 10:52:59 2017 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,22 +0,0 @@
-<?xml version="1.0"?>
-<tool_dependency>
-    <package name="picard" version="1.126.0">
-        <install version="1.0">
-            <actions_group>
-                <actions architecture="x86_64" os="linux">
-                    <action type="download_by_url">https://github.com/broadinstitute/picard/releases/download/1.126/picard-tools-1.126.zip</action>
-                    <action type="move_directory_files">
-                        <source_directory>.</source_directory>
-                        <destination_directory>$INSTALL_DIR</destination_directory>
-                    </action>       
-                </actions>                
-                <action type="set_environment">
-                    <environment_variable name="JAVA_JAR_PATH" action="set_to">$INSTALL_DIR</environment_variable>
-                </action>
-            </actions_group>
-        </install>
-        <readme>
-This picard package dependency is retrieved directly from https://github.com/broadinstitute/picard/releases
-        </readme>
-    </package>
-</tool_dependency>
\ No newline at end of file