# HG changeset patch
# User Ira Cooke <iracooke@gmail.com>
# Date 1370783971 18000
# Node ID 50eb60757ca59d4f6b01e541d18f06327d2f73d0
# Parent  16080891c80d0a380ebe663de6892e4185602929
Update

diff -r 16080891c80d -r 50eb60757ca5 repository_dependencies.xml
--- a/repository_dependencies.xml	Tue Mar 05 00:48:00 2013 -0500
+++ b/repository_dependencies.xml	Sun Jun 09 08:19:31 2013 -0500
@@ -1,16 +1,5 @@
 <?xml version="1.0"?>
-<!-- <repositories description="X!Tandem requires Proteomics Datatypes as well the trans proteomic pipeline">
-     <repository toolshed="http://10.211.55.28:9009" name="proteomics_datatypes" owner="iracooke" changeset_revision="699a890a9d99"/>
- </repositories>
- -->
 <repositories description="Proteomics datatypes and the TPP">
- 
-     <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="dac478a72c1d"/>
- -->
-     <repository toolshed="http://toolshed.g2.bx.psu.edu" name="protk_trans_proteomic_pipeline" owner="iracooke" changeset_revision="cedd5e884349"/>
-
-
+     <repository toolshed="http://toolshed.g2.bx.psu.edu" name="proteomics_datatypes" owner="iracooke" changeset_revision="09b89b345de2"/>
+     <repository toolshed="http://toolshed.g2.bx.psu.edu" name="protk_trans_proteomic_pipeline" owner="iracooke" changeset_revision="e85a18371516"/>
  </repositories>
-
diff -r 16080891c80d -r 50eb60757ca5 tandem.xml
--- a/tandem.xml	Tue Mar 05 00:48:00 2013 -0500
+++ b/tandem.xml	Sun Jun 09 08:19:31 2013 -0500
@@ -1,7 +1,7 @@
 <tool id="proteomics_search_tandem_1" name="X!Tandem MSMS Search" version="1.0.1">
 
    <requirements>
-    <requirement type="package" version="1.2.0">galaxy_protk</requirement>
+    <requirement type="package" version="1.2.2">galaxy_protk</requirement>
     <requirement type="package" version="4.6.1">trans_proteomic_pipeline</requirement>
    </requirements>
 
@@ -9,8 +9,8 @@
 
 	<command>
 		#if $database.source_select=="built_in":
-		rvm 1.9.3@protk-1.2.0 do tandem_search.rb -d $database.dbkey 
-		#else #rvm 1.9.3@protk-1.2.0 do tandem_search.rb -d $database.fasta_file
+		rvm 1.9.3@protk-1.2.2 do tandem_search.rb -d $database.dbkey 
+		#else #rvm 1.9.3@protk-1.2.2 do tandem_search.rb -d $database.fasta_file
 		#end if
 
 		--var-mods='
@@ -121,7 +121,7 @@
       		<param name="variable_mods" value="15.994915@M"/>
       		<param name="fixed_mods" value="57.021464@C"/>
       		<param name="allow_multi_isotope_search" value="false"/>
-      		<output name="output" file="bsa.pepXML" compare="sim_size" delta="100" /> 
+      		<output name="output" file="bsa.pepXML" compare="sim_size" delta="600" /> 
     	</test>
   	</tests>
 
diff -r 16080891c80d -r 50eb60757ca5 tool_dependencies.xml
--- a/tool_dependencies.xml	Tue Mar 05 00:48:00 2013 -0500
+++ b/tool_dependencies.xml	Sun Jun 09 08:19:31 2013 -0500
@@ -1,21 +1,10 @@
 <?xml version="1.0"?>
 <tool_dependency>
-<!--     <package name="galaxy_protk" version="1.2.0">
-	     <repository toolshed="http://10.211.55.28:9009" name="galaxy_protk" owner="iracooke" changeset_revision="5610168f3b53"/>
+    <package name="galaxy_protk" version="1.2.2">
+	     <repository toolshed="http://toolshed.g2.bx.psu.edu" name="galaxy_protk" owner="iracooke" changeset_revision="c25df71f7b68" prior_installation_required="True"/>
     </package>
 
     <package name="trans_proteomic_pipeline" version="4.6.1">
-        <repository toolshed="http://10.211.55.28:9009" name="protk_tpp" owner="iracooke" changeset_revision="e44f0d3bb9dd" />
-    </package>
- -->
-    <package name="galaxy_protk" version="1.2.0">
-	     <repository toolshed="http://toolshed.g2.bx.psu.edu" name="galaxy_protk" owner="iracooke" changeset_revision="dac478a72c1d"/>
+        <repository toolshed="http://toolshed.g2.bx.psu.edu" name="protk_trans_proteomic_pipeline" owner="iracooke" changeset_revision="e85a18371516"/>
     </package>
-
-    <package name="trans_proteomic_pipeline" version="4.6.1">
-        <repository toolshed="http://toolshed.g2.bx.psu.edu" name="protk_trans_proteomic_pipeline" owner="iracooke" changeset_revision="cedd5e884349" />
-    </package>
-
-
-
-</tool_dependency>
\ No newline at end of file
+</tool_dependency>