diff DecoyDatabase.xml @ 3:178e00cf12d7 draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 9a14ed1f2d3c9abdfb080251b3419dd9e0c52a14

--- a/DecoyDatabase.xml	Thu Apr 27 13:17:58 2017 -0400
+++ b/DecoyDatabase.xml	Wed Aug 09 08:58:49 2017 -0400
@@ -1,8 +1,8 @@
 <?xml version='1.0' encoding='UTF-8'?>
 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.-->
 <!--Proposed Tool Section: [Utilities]-->
-<tool id="DecoyDatabase" name="DecoyDatabase" version="2.1.0">
-  <description>Create decoy peptide databases from normal ones.</description>
+<tool id="DecoyDatabase" name="DecoyDatabase" version="2.2.0">
+  <description>Create decoy protein DB from forward protein DB.</description>
   <macros>
     <token name="@EXECUTABLE@">DecoyDatabase</token>
     <import>macros.xml</import>
@@ -30,13 +30,8 @@
     $param_decoy_string_position
   #end if
 #end if
-#if $param_append:
-  -append
-  #if " " in str($param_append):
-    "$param_append"
-  #else
-    $param_append
-  #end if
+#if $param_only_decoy:
+  -only_decoy
 #end if
 #if $param_method:
   -method
@@ -73,10 +68,7 @@
       <option value="prefix" selected="true">prefix</option>
       <option value="suffix">suffix</option>
     </param>
-    <param name="param_append" display="radio" type="select" optional="False" value="true" label="If this flag is used, the decoy database is appended to the target database, allowing combined target decoy searches" help="(-append) ">
-      <option value="true" selected="true">true</option>
-      <option value="false">false</option>
-    </param>
+    <param name="param_only_decoy" display="radio" type="boolean" truevalue="-only_decoy" falsevalue="" checked="false" optional="True" label="Write only decoy proteins to the output database instead of a combined database" help="(-only_decoy) "/>
     <param name="param_method" display="radio" type="select" optional="False" value="reverse" label="Method by which decoy sequences are generated from target sequences" help="(-method) ">
       <option value="reverse" selected="true">reverse</option>
       <option value="shuffle">shuffle</option>
@@ -94,7 +86,7 @@
         <output name="param_out" file="DecoyDatabase_output.fasta"/>
     </test>
   </tests>
-  <help>Create decoy peptide databases from normal ones.
+  <help>Create decoy protein DB from forward protein DB.
 
 
 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_DecoyDatabase.html</help>