# HG changeset patch
# User iracooke
# Date 1362446245 18000
# Node ID 50002ff2c1f339b4430ba0d68c82d3e8c86f5d3e
# Parent  1049de3f4aedb82752d5d9fb16c7aa344741bc1f
Uploaded

diff -r 1049de3f4aed -r 50002ff2c1f3 README
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/README	Mon Mar 04 20:17:25 2013 -0500
@@ -0,0 +1,6 @@
+This package is an installer for the MSGF+ search tool.
+
+System Requirements. Ensure that you have the following packages installed on your system
+- unzip
+- java runtime 6 or higher
+
diff -r 1049de3f4aed -r 50002ff2c1f3 msgfplus_search.xml
--- a/msgfplus_search.xml	Sun Jan 06 20:06:08 2013 -0500
+++ b/msgfplus_search.xml	Mon Mar 04 20:17:25 2013 -0500
@@ -1,11 +1,28 @@
 <tool id="proteomics_search_msgfplus_1" name="MSGF+ MSMS Search" version="1.0.0">
-	<requirements><requirement type="package">protkgem</requirement></requirements>
+
+	<requirements>
+    	<requirement type="package" version="1.1.9">galaxy_protk</requirement>
+    	<requirement type="package" version="20121116">protk_msgfplus</requirement>
+   	</requirements>
+
+
 	<description>Run an MSGF+ Search</description>
 
+
+
+	<description>Run an X!Tandem Search</description>
+
 	<command>
 		#if $database.source_select=="built_in":
-		msgfplus_search.rb --galaxy -d $database.dbkey --java-mem 8000M
-		#else #msgfplus_search.rb -d $database.fasta_file
+		rvm 1.9.3@protk-1.1.9 do tandem_search.rb -d $database.dbkey 
+		#else #rvm 1.9.3@protk-1.1.9 do tandem_search.rb -d $database.fasta_file
+		#end if
+
+
+	<command>
+		#if $database.source_select=="built_in":
+		rvm 1.9.3@protk-1.1.9 do msgfplus_search.rb --galaxy -d $database.dbkey
+		#else #rvm 1.9.3@protk-1.1.9 do msgfplus_search.rb -d $database.fasta_file
 		#end if
 
 		--var-mods='
diff -r 1049de3f4aed -r 50002ff2c1f3 repository_dependencies.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/repository_dependencies.xml	Mon Mar 04 20:17:25 2013 -0500
@@ -0,0 +1,10 @@
+<?xml version="1.0"?>
+<repositories description="Proteomics datatypes, MSGF+ and Protk">
+
+     <repository toolshed="http://toolshed.g2.bx.psu.edu" name="proteomics_datatypes" owner="iracooke" changeset_revision="463328a6967f"/>
+
+	<repository toolshed="http://toolshed.g2.bx.psu.edu" name="galaxy_protk" owner="iracooke" changeset_revision="51f7c347c955"/>
+
+     <repository toolshed="http://toolshed.g2.bx.psu.edu" name="protk_msgfplus" owner="iracooke" changeset_revision="528bcbb94199"/>
+
+ </repositories>
diff -r 1049de3f4aed -r 50002ff2c1f3 tool_dependencies.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Mon Mar 04 20:17:25 2013 -0500
@@ -0,0 +1,13 @@
+<?xml version="1.0"?>
+<tool_dependency>
+
+    <package name="galaxy_protk" version="1.1.9">
+	     <repository toolshed="http://toolshed.g2.bx.psu.edu" name="galaxy_protk" owner="iracooke" changeset_revision="51f7c347c955"/>
+    </package>
+
+    <package name="msgfplus" version="20130227">
+	     <repository toolshed="http://toolshed.g2.bx.psu.edu" name="protk_msgfplus" owner="iracooke" changeset_revision="528bcbb94199"/>
+    </package>
+
+
+</tool_dependency>
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