# HG changeset patch
# User bgruening
# Date 1397301947 14400
# Node ID 89dd3b8129060d4dbace473c078ed3b8c1d593bd
# Parent  00a775971820797422f0784ea8b3df066a56728d
Uploaded

diff -r 00a775971820 -r 89dd3b812906 peptide_shaker.xml
--- a/peptide_shaker.xml	Fri Apr 11 18:14:57 2014 -0400
+++ b/peptide_shaker.xml	Sat Apr 12 07:25:47 2014 -0400
@@ -1,8 +1,8 @@
 <tool id="peptide_shaker" name="Peptide Shaker" version="0.1.0">
      <!-- TODO: Set defaults for weights correctly -->
     <requirements>
-        <requirement type="package" version="0.20.1">peptide_shaker</requirement>
-        <requirement type="package" version="1.14.4">searchgui</requirement>
+        <requirement type="package" version="0.28.0">peptide_shaker</requirement>
+        <requirement type="package" version="1.18.0">searchgui</requirement>
     </requirements>
     <description>
         Peform protein identification combining X! Tandem and OMSSA (using SearchGUI) and PeptideShaker pipeline.
diff -r 00a775971820 -r 89dd3b812906 reverse.py
--- a/reverse.py	Fri Apr 11 18:14:57 2014 -0400
+++ b/reverse.py	Sat Apr 12 07:25:47 2014 -0400
@@ -19,9 +19,9 @@
     _exec(command)
 
 
-def _run_dbtoolkit(java_class, args):
+def _run_dbtoolkit(java_class, command, args):
     command_prefix = "java -cp %s" % _dbtoolkit_jar_path( args.script_path )
-    _exec("%s %s %s" % (command_prefix, java_class, args))
+    _exec("%s %s %s" % (command_prefix, java_class, command))
 
 
 def _dbtoolkit_jar_path( script_path ):
diff -r 00a775971820 -r 89dd3b812906 tool_dependencies.xml
--- a/tool_dependencies.xml	Fri Apr 11 18:14:57 2014 -0400
+++ b/tool_dependencies.xml	Sat Apr 12 07:25:47 2014 -0400
@@ -3,10 +3,10 @@
     <set_environment version="1.0">
         <environment_variable action="set_to" name="PEPTIDESHAKER_SCRIPT_PATH">$REPOSITORY_INSTALL_DIR</environment_variable>
     </set_environment>
-    <package name="searchgui" version="1.14.4">
-      <repository changeset_revision="0692ca995a01" name="package_searchgui_1_14_4" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+    <package name="searchgui" version="1.18.0">
+      <repository changeset_revision="3bcfc0d7275b" name="package_searchgui_1_18" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu" />
     </package>
-    <package name="peptide_shaker" version="0.20.1">
-      <repository changeset_revision="c661fad47f03" name="package_peptideshaker_0_20_1" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+    <package name="peptide_shaker" version="0.28.0">
+      <repository changeset_revision="aa0a836dfaa9" name="package_peptideshaker_0_28" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu" />
     </package>
 </tool_dependency>