Mercurial > repos > galaxyp > msconvert

changeset 3:7e41529ee90c

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added repo and tool dependencies
author galaxyp
date Thu, 20 Jun 2013 16:08:23 -0400
parents 50e30fb68be2
children 001e77708ec9
files msconvert.xml.template msconvert2.xml msconvert2_raw.xml msconvert3.xml msconvert3_raw.xml repository_dependencies.xml tool_dependencies.xml
diffstat 7 files changed, 43 insertions(+), 3 deletions(-) [+]
line wrap: on
line diff
--- 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>
--- 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
 
 
--- 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>
--- 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
 
 
--- 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>
--- /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>
--- /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>