# HG changeset patch
# User Ira Cooke <iracooke@gmail.com>
# Date 1370497042 -36000
# Node ID cd0d5e6b9a92446aff1cee47996f25d83ae051d3
# Parent  18bf78e49e88a6c0c9b00283472cf94342a41203
Fix

diff -r 18bf78e49e88 -r cd0d5e6b9a92 omssa.xml
--- a/omssa.xml	Thu Jun 06 01:33:45 2013 -0400
+++ b/omssa.xml	Thu Jun 06 15:37:22 2013 +1000
@@ -1,7 +1,7 @@
 <tool id="proteomics_search_omssa_1" name="OMSSA 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="2.1.9">omssa</requirement>
     	<requirement type="package" version="2.2.27">blast</requirement>
    </requirements>
@@ -9,9 +9,12 @@
 
 	<description>Run an OMSSA MS/MS Search</description>
 		
-	<command>#if $database.source_select=="built_in":
-		rvm 1.9.3@protk-1.2.0 do omssa_search.rb -d $database.dbkey 
-		#else #rvm 1.9.3@protk-1.2.0 do omssa_search.rb -d $database.fasta_file
+	<command>rvm 1.9.3@protk-1.2.2 do omssa_search.rb
+
+		#if $database.source_select=="built_in":
+		-d $database.dbkey 
+		#else
+		-d $database.fasta_file
 		#end if
 		
 		--var-mods='
@@ -26,7 +29,28 @@
 		$searched_ions
 		'
 		
-		$input_file -o $output -r --enzyme=$enzyme --precursor-ion-tol-units=$precursor_tolu -v $missed_cleavages -f $fragment_ion_tol -p $precursor_ion_tol --num-peaks-for-multi-isotope-search $multi_isotope $use_average_mass $respect_precursor_charges --max-hit-expect $max_hit_expect --intensity-cut-off $intensity_cut_off
+		$input_file 
+		-o $output 
+		-r 
+
+		--enzyme=$enzyme 
+
+		--precursor-ion-tol-units=$precursor_tolu 
+
+		-v $missed_cleavages 
+
+		-f $fragment_ion_tol 
+
+		-p $precursor_ion_tol 
+
+		--num-peaks-for-multi-isotope-search $multi_isotope 
+
+		$use_average_mass 
+		$respect_precursor_charges 
+
+		--max-hit-expect $max_hit_expect 
+
+		--intensity-cut-off $intensity_cut_off
 
 	</command>
 	
diff -r 18bf78e49e88 -r cd0d5e6b9a92 repository_dependencies.xml
--- a/repository_dependencies.xml	Thu Jun 06 01:33:45 2013 -0400
+++ b/repository_dependencies.xml	Thu Jun 06 15:37:22 2013 +1000
@@ -1,12 +1,12 @@
 <?xml version="1.0"?>
 <repositories description="Proteomics datatypes, omssa and blast executables">
 
-	<repository toolshed="http://10.211.55.35:9009" name="proteomics_datatypes" owner="iracooke" changeset_revision="7049ac401bf6"/>
+	<repository toolshed="http://testtoolshed.g2.bx.psu.edu" name="proteomics_datatypes" owner="iracooke" changeset_revision="7101f7e4b00b"/>
 
-    <repository toolshed="http://10.211.55.35:9009" name="galaxy_protk" owner="iracooke" changeset_revision="0a2b3dcc986c" prior_installation_required="True"/>
+    <repository toolshed="http://testtoolshed.g2.bx.psu.edu" name="galaxy_protk" owner="iracooke" changeset_revision="32c643142290" prior_installation_required="True"/>
 
-    <repository toolshed="http://10.211.55.35:9009" name="protk_blast" owner="iracooke" changeset_revision="c685c193e5fe"/>
+    <repository toolshed="http://testtoolshed.g2.bx.psu.edu" name="protk_blast" owner="iracooke" changeset_revision="a1b21b3844c8"/>
 
-    <repository toolshed="http://10.211.55.35:9009" name="protk_omssa" owner="iracooke" changeset_revision="5fefcc853388"/>
+    <repository toolshed="http://testtoolshed.g2.bx.psu.edu" name="protk_omssa" owner="iracooke" changeset_revision="b386c6c95d0e"/>
 
 </repositories>
diff -r 18bf78e49e88 -r cd0d5e6b9a92 tool_dependencies.xml
--- a/tool_dependencies.xml	Thu Jun 06 01:33:45 2013 -0400
+++ b/tool_dependencies.xml	Thu Jun 06 15:37:22 2013 +1000
@@ -1,16 +1,16 @@
 <?xml version="1.0"?>
 <tool_dependency>
 
-    <package name="galaxy_protk" version="1.2.0">
-         <repository toolshed="http://10.211.55.35:9009" name="galaxy_protk" owner="iracooke" changeset_revision="0a2b3dcc986c" prior_installation_required="True"/>
+    <package name="galaxy_protk" version="1.2.2">
+         <repository toolshed="http://testtoolshed.g2.bx.psu.edu" name="galaxy_protk" owner="iracooke" changeset_revision="32c643142290" prior_installation_required="True"/>
     </package>
 
     <package name="blast" version="2.2.27">
-        <repository toolshed="http://10.211.55.35:9009" name="protk_blast" owner="iracooke" changeset_revision="c685c193e5fe"/>
+        <repository toolshed="http://testtoolshed.g2.bx.psu.edu" name="protk_blast" owner="iracooke" changeset_revision="a1b21b3844c8"/>
     </package>
 
     <package name="omssa" version="2.1.9">
-        <repository toolshed="http://10.211.55.35:9009" name="protk_omssa" owner="iracooke" changeset_revision="5fefcc853388"/>
+        <repository toolshed="http://testtoolshed.g2.bx.psu.edu" name="protk_omssa" owner="iracooke" changeset_revision="b386c6c95d0e"/>
     </package>