# HG changeset patch
# User Jim Johnson <jj@umn.edu>
# Date 1392646413 21600
# Node ID 08bb52273ae1dbd6670f7ca5c319951e18a414e3
# Parent  001e77708ec982dfda1f41ead909f09ef97df2d8
Bjoern: remove unused repository dependency, cleanups

diff -r 001e77708ec9 -r 08bb52273ae1 TODO
--- a/TODO	Fri Jul 12 12:45:51 2013 -0400
+++ b/TODO	Mon Feb 17 08:13:33 2014 -0600
@@ -1,2 +1,1 @@
 Add precursorRefine option.
-Add peak picking options.
\ No newline at end of file
diff -r 001e77708ec9 -r 08bb52273ae1 msconvert2.xml
--- a/msconvert2.xml	Fri Jul 12 12:45:51 2013 -0400
+++ b/msconvert2.xml	Mon Feb 17 08:13:33 2014 -0600
@@ -1,8 +1,10 @@
-<tool id="msconvert2" name="msconvert2" version="0.2.0">
+<tool id="msconvert2" name="msconvert2" version="0.2.1">
   <!-- BEGIN_VERSION_DEFAULT -->
   <description>Convert and filter a mass spec peak list</description>
   <!-- END_VERSION_DEFAULT -->
-
+  <requirements>
+    <requirement type="package">proteowizard</requirement>
+  </requirements>
   <command interpreter="python">
     #set $ext = $input.ext
     #if $ext.startswith("m:")
@@ -292,11 +294,6 @@
       </change_format>
     </data>
   </outputs>
-
-  <requirements>
-    <requirement type="package">proteowizard</requirement>    
-  </requirements>
-
   <help>
 **What it does**
 
diff -r 001e77708ec9 -r 08bb52273ae1 msconvert2_raw.xml
--- a/msconvert2_raw.xml	Fri Jul 12 12:45:51 2013 -0400
+++ b/msconvert2_raw.xml	Mon Feb 17 08:13:33 2014 -0600
@@ -1,8 +1,13 @@
-<tool id="msconvert2_raw" name="msconvert2_raw" version="0.2.0">
+<tool id="msconvert2_raw" name="msconvert2_raw" version="0.2.1">
   <!-- BEGIN_VERSION_RAW -->
   <description>Convert and filter a Thermo Finnigan RAW file</description>
   <!-- END_VERSION_RAW -->
-
+  <requirements>
+    <requirement type="package">proteowizard</requirement>
+    <!-- BEGIN_VERSION_RAW -->
+    <requirement type="platform">windows</requirement>
+    <!-- END_VERSION_RAW -->
+  </requirements>
   <command interpreter="python">
     #set $ext = $input.ext
     #if $ext.startswith("m:")
@@ -273,14 +278,6 @@
       </change_format>
     </data>
   </outputs>
-
-  <requirements>
-    <requirement type="package">proteowizard</requirement>    
-    <!-- BEGIN_VERSION_RAW -->
-    <requirement type="platform">windows</requirement>
-    <!-- END_VERSION_RAW -->    
-  </requirements>
-
   <help>
 **What it does**
 
diff -r 001e77708ec9 -r 08bb52273ae1 msconvert3.xml
--- a/msconvert3.xml	Fri Jul 12 12:45:51 2013 -0400
+++ b/msconvert3.xml	Mon Feb 17 08:13:33 2014 -0600
@@ -1,8 +1,10 @@
-<tool id="msconvert3" name="msconvert3" version="0.2.0">
+<tool id="msconvert3" name="msconvert3" version="0.2.1">
   <!-- BEGIN_VERSION_DEFAULT -->
   <description>Convert and filter a mass spec peak list</description>
   <!-- END_VERSION_DEFAULT -->
-
+  <requirements>
+    <requirement type="package">proteowizard</requirement>
+  </requirements>
   <command interpreter="python">
     #set $ext = $input.ext
     #if $ext.startswith("m:")
@@ -14,7 +16,7 @@
     --input_name='${input.display_name}'
     #end if
     --output=${output} 
-    ## BEGIN_VERSION_DEFAULT    
+    ## BEGIN_VERSION_DEFAULT
     --fromextension=$ext
     ## END_VERSION_DEFAULT
 
@@ -116,7 +118,7 @@
 
     <!-- BEGIN_VERSION_DEFAULT -->
     <conditional name="type">
-      <param name="input_type" type="select" label="Input Type" help="select file type of input data from history- mzml, mzXML, mgf or ms2. then select appropriate input file from drop down menu depending on input in history">
+      <param name="input_type" type="select" label="Input Type">
         <option value="mzml">mzML</option>
         <option value="mzxml">mzXML</option>
         <option value="mgf">mgf</option>
@@ -136,7 +138,7 @@
       </when>
     </conditional>
     <!-- END_VERSION_DEFAULT -->    
-    <param name="output_type" type="select" label="Output Type" help="select file type of output. mzXML is an open, generic XML file type. mzml is The standard file extension for most search engines. ms2 displays a header followed by scan data. mgf is the format for use with MASCOT, OMSSA, ProteinPilot search engines (See MGF Formatter for details).">
+    <param name="output_type" type="select" label="Output Type">
       <option value="mzML">mzML (indexed)</option>
       <option value="unindexed_mzML">mzML (unindexed)</option>
       <option value="mzXML">mzXML (indexed)</option>      
@@ -145,7 +147,7 @@
       <option value="ms2">ms2</option>  
     </param>    
     <conditional name="filtering">
-      <param name="filtering_use" type="boolean" label="Use Filtering?" help="" truevalue="true" falsevalue="false" help="incorporates algorithm that separates noisy peaks from actual ion peaks (see also peaklist processing)" />
+      <param name="filtering_use" type="boolean" label="Use Filtering?" truevalue="true" falsevalue="false" />
       <when value="false" />
       <when value="true">
         <param type="boolean" name="precursor_recalculation" label="Recalculate Precursor?" />
@@ -355,11 +357,6 @@
       </change_format>
     </data>
   </outputs>
-
-  <requirements>
-    <requirement type="package">proteowizard</requirement>    
-  </requirements>
-
   <help>
 **What it does**
 
diff -r 001e77708ec9 -r 08bb52273ae1 msconvert3_raw.xml
--- a/msconvert3_raw.xml	Fri Jul 12 12:45:51 2013 -0400
+++ b/msconvert3_raw.xml	Mon Feb 17 08:13:33 2014 -0600
@@ -1,8 +1,13 @@
-<tool id="msconvert3_raw" name="msconvert3_raw" version="0.2.0">
+<tool id="msconvert3_raw" name="msconvert3_raw" version="0.2.1">
   <!-- BEGIN_VERSION_RAW -->
   <description>Convert and filter a Thermo Finnigan RAW file</description>
   <!-- END_VERSION_RAW -->
-
+  <requirements>
+    <requirement type="package">proteowizard</requirement>
+    <!-- BEGIN_VERSION_RAW -->
+    <requirement type="platform">windows</requirement>
+    <!-- END_VERSION_RAW -->
+  </requirements>
   <command interpreter="python">
     #set $ext = $input.ext
     #if $ext.startswith("m:")
@@ -117,7 +122,7 @@
     <param format="RAW" name="input" type="data" label="Thermo Finnigan RAW Input" help="select input file in RAW format"/>
     <!-- END_VERSION_RAW -->
 
-    <param name="output_type" type="select" label="Output Type" help="select file type of output. mzXML is an open, generic XML file type. mzml is the standard file extension for most search engines. ms2 displays a header followed by scan data. mgf is the format for use with MASCOT, OMSSA, ProteinPilot search engines (See MGF Formatter for details)">
+    <param name="output_type" type="select" label="Output Type">
       <option value="mzML">mzML (indexed)</option>
       <option value="unindexed_mzML">mzML (unindexed)</option>
       <option value="mzXML">mzXML (indexed)</option>      
@@ -126,7 +131,7 @@
       <option value="ms2">ms2</option>  
     </param>    
     <conditional name="filtering">
-      <param name="filtering_use" type="boolean" label="Use Filtering?" help="" truevalue="true" falsevalue="false" help="incorporates algorithm that separates noisy peaks from actual ion peaks (also called as peaklist processing)" />
+      <param name="filtering_use" type="boolean" label="Use Filtering?" help="" truevalue="true" falsevalue="false" />
       <when value="false" />
       <when value="true">
         <param type="boolean" name="precursor_recalculation" label="Recalculate Precursor?" />
@@ -336,14 +341,6 @@
       </change_format>
     </data>
   </outputs>
-
-  <requirements>
-    <requirement type="package">proteowizard</requirement>    
-    <!-- BEGIN_VERSION_RAW -->
-    <requirement type="platform">windows</requirement>
-    <!-- END_VERSION_RAW -->    
-  </requirements>
-
   <help>
 **What it does**
 
@@ -353,21 +350,6 @@
     
 .. _here: http://proteowizard.sourceforge.net/tools/msconvert.html
 
-**Recommended**
-
-For X!tandem searches: Use mzml format generated from RAW file.
-
-                                       RAW → mzml
-
-For ProteinPilot searches: Use MGF format generated from mzml file using MGF formatter.
-
-                                       RAW → mzml → MGF (ProteinPilot)
-
-For MaxQuant searches: Use RAW file as an input.
-
-For OMSSA : Use MGF format generated from mzml file using MGF formatter.
-
-                                       RAW → mzml → MGF (Mascot)
 ------
 
 **Citation**
diff -r 001e77708ec9 -r 08bb52273ae1 msconvert_subset.xml
--- a/msconvert_subset.xml	Fri Jul 12 12:45:51 2013 -0400
+++ b/msconvert_subset.xml	Mon Feb 17 08:13:33 2014 -0600
@@ -1,5 +1,8 @@
-<tool id="msconvert_subset" name="Subset Peak List" version="0.2.0">
+<tool id="msconvert_subset" name="Subset Peak List" version="0.2.1">
   <description>against list of scan numbers or indices.</description>
+  <requirements>
+    <requirement type="package">proteowizard</requirement>
+  </requirements>
   <command interpreter="python">
     msconvert_wrapper.py 
     --input=${input} 
@@ -95,11 +98,6 @@
       </change_format>
     </data>
   </outputs>
-
-  <requirements>
-    <requirement type="package">proteowizard</requirement>    
-  </requirements>
-
   <help>
   </help>
 </tool>
diff -r 001e77708ec9 -r 08bb52273ae1 repository_dependencies.xml
--- a/repository_dependencies.xml	Fri Jul 12 12:45:51 2013 -0400
+++ b/repository_dependencies.xml	Mon Feb 17 08:13:33 2014 -0600
@@ -1,5 +1,4 @@
 <?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" />
+    <repository name="proteomics_datatypes" owner="iracooke" />
 </repositories>
diff -r 001e77708ec9 -r 08bb52273ae1 tool_dependencies.xml
--- a/tool_dependencies.xml	Fri Jul 12 12:45:51 2013 -0400
+++ b/tool_dependencies.xml	Mon Feb 17 08:13:33 2014 -0600
@@ -1,6 +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>
+    <package name="proteowizard" version="3_0_4388">
+        <repository name="protk_proteowizard" owner="iracooke"/>
+    </package>
 </tool_dependency>
diff -r 001e77708ec9 -r 08bb52273ae1 version
--- a/version	Fri Jul 12 12:45:51 2013 -0400
+++ b/version	Mon Feb 17 08:13:33 2014 -0600
@@ -1,1 +1,1 @@
-0.2.0
\ No newline at end of file
+0.2.1