# HG changeset patch
# User galaxyp
# Date 1371758903 14400
# Node ID 7e41529ee90cc193fe276152964c127f8b6f121c
# Parent  50e30fb68be2ce81b5713bf0ccb8843ee7077993
added repo and tool dependencies

diff -r 50e30fb68be2 -r 7e41529ee90c msconvert.xml.template
--- a/msconvert.xml.template	Fri May 10 17:24:56 2013 -0400
+++ b/msconvert.xml.template	Thu Jun 20 16:08:23 2013 -0400
@@ -7,6 +7,10 @@
   <!-- END_VERSION_DEFAULT -->
 
   <command interpreter="python">
+    #set $ext = $input.ext
+    #if $ext.startswith("m:")
+    #set $ext = $ext[len("m:"):]
+    #end if
     msconvert_wrapper.py 
     --input=${input}
     #if hasattr($input, 'display_name')
@@ -14,7 +18,7 @@
     #end if
     --output=${output} 
     ## BEGIN_VERSION_DEFAULT    
-    --fromextension=${input.ext} 
+    --fromextension=$ext
     ## END_VERSION_DEFAULT
 
     ## BEGIN_VERSION_RAW
@@ -363,6 +367,9 @@
 
   <requirements>
     <requirement type="package">proteowizard</requirement>    
+    <!-- BEGIN_VERSION_RAW -->
+    <requirement type="platform">windows</requirement>
+    <!-- END_VERSION_RAW -->    
   </requirements>
 
   <help>
diff -r 50e30fb68be2 -r 7e41529ee90c msconvert2.xml
--- a/msconvert2.xml	Fri May 10 17:24:56 2013 -0400
+++ b/msconvert2.xml	Thu Jun 20 16:08:23 2013 -0400
@@ -4,6 +4,10 @@
   <!-- END_VERSION_DEFAULT -->
 
   <command interpreter="python">
+    #set $ext = $input.ext
+    #if $ext.startswith("m:")
+    #set $ext = $ext[len("m:"):]
+    #end if
     msconvert_wrapper.py 
     --input=${input}
     #if hasattr($input, 'display_name')
@@ -11,7 +15,7 @@
     #end if
     --output=${output} 
     ## BEGIN_VERSION_DEFAULT    
-    --fromextension=${input.ext} 
+    --fromextension=$ext
     ## END_VERSION_DEFAULT
 
 
diff -r 50e30fb68be2 -r 7e41529ee90c msconvert2_raw.xml
--- a/msconvert2_raw.xml	Fri May 10 17:24:56 2013 -0400
+++ b/msconvert2_raw.xml	Thu Jun 20 16:08:23 2013 -0400
@@ -4,6 +4,10 @@
   <!-- END_VERSION_RAW -->
 
   <command interpreter="python">
+    #set $ext = $input.ext
+    #if $ext.startswith("m:")
+    #set $ext = $ext[len("m:"):]
+    #end if
     msconvert_wrapper.py 
     --input=${input}
     #if hasattr($input, 'display_name')
@@ -272,6 +276,9 @@
 
   <requirements>
     <requirement type="package">proteowizard</requirement>    
+    <!-- BEGIN_VERSION_RAW -->
+    <requirement type="platform">windows</requirement>
+    <!-- END_VERSION_RAW -->    
   </requirements>
 
   <help>
diff -r 50e30fb68be2 -r 7e41529ee90c msconvert3.xml
--- a/msconvert3.xml	Fri May 10 17:24:56 2013 -0400
+++ b/msconvert3.xml	Thu Jun 20 16:08:23 2013 -0400
@@ -4,6 +4,10 @@
   <!-- END_VERSION_DEFAULT -->
 
   <command interpreter="python">
+    #set $ext = $input.ext
+    #if $ext.startswith("m:")
+    #set $ext = $ext[len("m:"):]
+    #end if
     msconvert_wrapper.py 
     --input=${input}
     #if hasattr($input, 'display_name')
@@ -11,7 +15,7 @@
     #end if
     --output=${output} 
     ## BEGIN_VERSION_DEFAULT    
-    --fromextension=${input.ext} 
+    --fromextension=$ext
     ## END_VERSION_DEFAULT
 
 
diff -r 50e30fb68be2 -r 7e41529ee90c msconvert3_raw.xml
--- a/msconvert3_raw.xml	Fri May 10 17:24:56 2013 -0400
+++ b/msconvert3_raw.xml	Thu Jun 20 16:08:23 2013 -0400
@@ -4,6 +4,10 @@
   <!-- END_VERSION_RAW -->
 
   <command interpreter="python">
+    #set $ext = $input.ext
+    #if $ext.startswith("m:")
+    #set $ext = $ext[len("m:"):]
+    #end if
     msconvert_wrapper.py 
     --input=${input}
     #if hasattr($input, 'display_name')
@@ -335,6 +339,9 @@
 
   <requirements>
     <requirement type="package">proteowizard</requirement>    
+    <!-- BEGIN_VERSION_RAW -->
+    <requirement type="platform">windows</requirement>
+    <!-- END_VERSION_RAW -->    
   </requirements>
 
   <help>
diff -r 50e30fb68be2 -r 7e41529ee90c repository_dependencies.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/repository_dependencies.xml	Thu Jun 20 16:08:23 2013 -0400
@@ -0,0 +1,5 @@
+<?xml version="1.0"?>
+<repositories description="Required proteomics dependencies.">
+  <repository toolshed="http://toolshed.g2.bx.psu.edu" name="proteomics_datatypes" owner="iracooke" changeset_revision="f74290b136fc" />
+  <repository toolshed="http://toolshed.g2.bx.psu.edu" name="protk_proteowizard" owner="iracooke" changeset_revision="863462ea0187" />
+</repositories>
diff -r 50e30fb68be2 -r 7e41529ee90c tool_dependencies.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Thu Jun 20 16:08:23 2013 -0400
@@ -0,0 +1,6 @@
+<?xml version="1.0"?>
+<tool_dependency>
+  <package name="proteowizard" version="3_0_4388">
+    <repository toolshed="http://toolshed.g2.bx.psu.edu" name="protk_proteowizard" owner="iracooke" changeset_revision="6ead3520e93a"/>
+  </package>
+</tool_dependency>