<?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="2.0.0">
    <description>Create decoy peptide databases from normal ones.</description>
    <macros>
      <token name="@EXECUTABLE@">DecoyDatabase</token>
      <import>macros.xml</import>
    </macros>
    <expand macro="references"/>
    <expand macro="stdio"/>
    <expand macro="requirements"/>
    <command>DecoyDatabase

-in
  #for token in $param_in:
    $token
  #end for
#if $param_out:
  -out $param_out
#end if
#if $param_decoy_string:
  -decoy_string     &quot;$param_decoy_string&quot;
#end if
#if $param_decoy_string_position:
  -decoy_string_position
  #if &quot; &quot; in str($param_decoy_string_position):
    &quot;$param_decoy_string_position&quot;
  #else
    $param_decoy_string_position
  #end if
#end if
#if $param_append:
  -append
#end if
#if $param_shuffle:
  -shuffle
#end if
-threads \${GALAXY_SLOTS:-24}
#if $adv_opts.adv_opts_selector=='advanced':
    #if $adv_opts.param_force:
  -force
#end if
#end if
</command>
    <inputs>
      <param format="fasta" help="(-in) It is recommended to include a contaminant database as well" label="Input FASTA file(s), each containing a database" multiple="true" name="param_in" optional="False" size="30" type="data">
        <sanitizer>
          <valid initial="string.printable">
            <remove value="'"/>
            <remove value="&quot;"/>
          </valid>
        </sanitizer>
      </param>
      <param help="(-decoy_string) " label="String that is appended to the accession of the protein database to indicate a decoy protein" name="param_decoy_string" size="30" type="text" value="_rev">
        <sanitizer>
          <valid initial="string.printable">
            <remove value="'"/>
            <remove value="&quot;"/>
          </valid>
        </sanitizer>
      </param>
      <param help="(-decoy_string_position) " label="Should the 'decoy_string' be prepended (prefix) or appended (suffix) to the protein accession?" name="param_decoy_string_position" optional="True" type="select" value="suffix">
        <option value="prefix">prefix</option>
        <option value="suffix">suffix</option>
      </param>
      <param checked="false" falsevalue="" help="(-append) " label="If this flag is used, the decoy database is appended to the target database, allowing combined target decoy searches" name="param_append" optional="True" truevalue="-append" type="boolean"/>
      <param checked="false" falsevalue="" help="(-shuffle) " label="If 'true' then the decoy hit are shuffled from the target sequences, otherwise they are reversed" name="param_shuffle" optional="True" truevalue="-shuffle" type="boolean"/>
      <expand macro="advanced_options">
        <param checked="false" falsevalue="" help="(-force) " label="Overwrite tool specific checks" name="param_force" optional="True" truevalue="-force" type="boolean"/>
      </expand>
    </inputs>
    <outputs>
      <data format="fasta" name="param_out"/>
    </outputs>
    <help>Create decoy peptide databases from normal ones.


For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_DecoyDatabase.html</help>
  </tool>