<?xml version="1.0" encoding="UTF-8"?>
<tool ctdVersion="1.7" version="2.1.0" name="DecoyDatabase" docurl="http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_DecoyDatabase.html" category="Utilities" >
<description><![CDATA[Create decoy peptide databases from normal ones.]]></description>
<manual><![CDATA[Create decoy peptide databases from normal ones.]]></manual>
<PARAMETERS version="1.6.2" xsi:noNamespaceSchemaLocation="http://open-ms.sourceforge.net/schemas/Param_1_6_2.xsd" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
  <NODE name="DecoyDatabase" description="Create decoy peptide databases from normal ones.">
    <ITEM name="version" value="2.1.0" type="string" description="Version of the tool that generated this parameters file." required="false" advanced="true" />
    <NODE name="1" description="Instance &apos;1&apos; section for &apos;DecoyDatabase&apos;">
      <ITEMLIST name="in" type="input-file" description="Input FASTA file(s), each containing a database. It is recommended to include a contaminant database as well." required="true" advanced="false" supported_formats="*.fasta">
      </ITEMLIST>
      <ITEM name="out" value="" type="output-file" description="Output FASTA file where the decoy database will be written to." required="true" advanced="false" supported_formats="*.fasta" />
      <ITEM name="decoy_string" value="DECOY_" type="string" description="String that is combined with the accession of the protein identifier to indicate a decoy protein." required="false" advanced="false" />
      <ITEM name="decoy_string_position" value="prefix" type="string" description="Should the &apos;decoy_string&apos; be prepended (prefix) or appended (suffix) to the protein accession?" required="false" advanced="false" restrictions="prefix,suffix" />
      <ITEM name="append" value="true" type="string" description="If this flag is used, the decoy database is appended to the target database, allowing combined target decoy searches." required="false" advanced="false" restrictions="true,false" />
      <ITEM name="method" value="reverse" type="string" description="Method by which decoy sequences are generated from target sequences." required="false" advanced="false" restrictions="reverse,shuffle" />
      <ITEM name="log" value="" type="string" description="Name of log file (created only when specified)" required="false" advanced="true" />
      <ITEM name="debug" value="0" type="int" description="Sets the debug level" required="false" advanced="true" />
      <ITEM name="threads" value="1" type="int" description="Sets the number of threads allowed to be used by the TOPP tool" required="false" advanced="false" />
      <ITEM name="no_progress" value="false" type="string" description="Disables progress logging to command line" required="false" advanced="true" restrictions="true,false" />
      <ITEM name="force" value="false" type="string" description="Overwrite tool specific checks." required="false" advanced="true" restrictions="true,false" />
      <ITEM name="test" value="false" type="string" description="Enables the test mode (needed for internal use only)" required="false" advanced="true" restrictions="true,false" />
    </NODE>
  </NODE>
</PARAMETERS>
</tool>
