# HG changeset patch
# User Ira Cooke <iracooke@gmail.com>
# Date 1370783910 18000
# Node ID 54b870eaca8d3c8cb8d83ce8ecc720fe6cf06672
# Parent  155b6449fdf3aabec71436023989b3ffcefd7066
Update

diff -r 155b6449fdf3 -r 54b870eaca8d omssa.xml
--- a/omssa.xml	Tue Mar 05 00:25:34 2013 -0500
+++ b/omssa.xml	Sun Jun 09 08:18:30 2013 -0500
@@ -1,17 +1,20 @@
 <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="2.1.8">omssa</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>
 
 
 	<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 155b6449fdf3 -r 54b870eaca8d repository_dependencies.xml
--- a/repository_dependencies.xml	Tue Mar 05 00:25:34 2013 -0500
+++ b/repository_dependencies.xml	Sun Jun 09 08:18:30 2013 -0500
@@ -1,18 +1,12 @@
 <?xml version="1.0"?>
-<!-- <repositories description="Requires Proteomics Datatypes">
-     <repository toolshed="http://10.211.55.28:9009" name="proteomics_datatypes" owner="iracooke" changeset_revision="699a890a9d99"/>
- </repositories>
- -->
+<repositories description="Proteomics datatypes, omssa and blast executables">
+
+	<repository toolshed="http://toolshed.g2.bx.psu.edu" name="proteomics_datatypes" owner="iracooke" changeset_revision="09b89b345de2"/>
 
- 
-  <repositories description="Proteomics datatypes, omssa and blast executables">
-     <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="galaxy_protk" owner="iracooke" changeset_revision="c25df71f7b68" prior_installation_required="True"/>
 
-	<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="protk_blast" owner="iracooke" changeset_revision="e34365cd29fa"/>
 
-  	<repository toolshed="http://toolshed.g2.bx.psu.edu" name="protk_blast" owner="iracooke" changeset_revision="0d86d29aaed6" />
+    <repository toolshed="http://toolshed.g2.bx.psu.edu" name="protk_omssa" owner="iracooke" changeset_revision="8f3813e7b0a6"/>
 
-    <repository toolshed="http://toolshed.g2.bx.psu.edu" name="protk_omssa" owner="iracooke" changeset_revision="f77532db59b6" />
-
-
-</repositories>
\ No newline at end of file
+</repositories>
diff -r 155b6449fdf3 -r 54b870eaca8d tool_dependencies.xml
--- a/tool_dependencies.xml	Tue Mar 05 00:25:34 2013 -0500
+++ b/tool_dependencies.xml	Sun Jun 09 08:18:30 2013 -0500
@@ -1,29 +1,18 @@
 <?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="blast" version="2.2.27">
-        <repository toolshed="http://10.211.55.28:9009" name="protk_blast" owner="iracooke" changeset_revision="0f3b7bbdfdd4" />
+        <repository toolshed="http://toolshed.g2.bx.psu.edu" name="protk_blast" owner="iracooke" changeset_revision="e34365cd29fa"/>
     </package>
 
-    <package name="omssa" version="2.1.8">
-        <repository toolshed="http://10.211.55.28:9009" name="protk_omssa" owner="iracooke" changeset_revision="117faa58df2a" />
-    </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"/>
-    </package>
-
-    <package name="blast" version="2.2.27">
-        <repository toolshed="http://toolshed.g2.bx.psu.edu" name="protk_blast" owner="iracooke" changeset_revision="0d86d29aaed6" />
-    </package>
-
-    <package name="omssa" version="2.1.8">
-        <repository toolshed="http://toolshed.g2.bx.psu.edu" name="protk_omssa" owner="iracooke" changeset_revision="f77532db59b6" />
+    <package name="omssa" version="2.1.9">
+        <repository toolshed="http://toolshed.g2.bx.psu.edu" name="protk_omssa" owner="iracooke" changeset_revision="8f3813e7b0a6"/>
     </package>
 
 
 
-</tool_dependency>
\ No newline at end of file
+</tool_dependency>