diff msconvert3.xml @ 5:08bb52273ae1

Bjoern: remove unused repository dependency, cleanups

--- 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**