<?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>
  <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 $param_decoy_string:
  -decoy_string     "$param_decoy_string"
#end if
#if $param_decoy_string_position:
  -decoy_string_position $param_decoy_string_position
#end if
#if $param_append:
  -append $param_append
#end if
#if $param_method:
  -method $param_method
#end if
#if $adv_opts.adv_opts_selector=='advanced':
    #if $adv_opts.param_force:
  -force
#end if
#end if
</command>
  <inputs>
    <param name="param_in" type="data" format="fasta" multiple="true" optional="False" size="30" label="Input FASTA file(s), each containing a database" help="(-in) It is recommended to include a contaminant database as well">
      <sanitizer>
        <valid initial="string.printable">
          <remove value="'"/>
          <remove value="&quot;"/>
        </valid>
      </sanitizer>
    </param>
    <param name="param_decoy_string" type="text" size="30" value="DECOY_" label="String that is combined with the accession of the protein identifier to indicate a decoy protein" help="(-decoy_string) ">
      <sanitizer>
        <valid initial="string.printable">
          <remove value="'"/>
          <remove value="&quot;"/>
        </valid>
      </sanitizer>
    </param>
    <param name="param_decoy_string_position" display="radio" type="select" optional="False" value="prefix" label="Should the 'decoy_string' be prepended (prefix) or appended (suffix) to the protein accession?" help="(-decoy_string_position) ">
      <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_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>
    </param>
    <expand macro="advanced_options">
      <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
    </expand>
  </inputs>
  <outputs>
    <data name="param_out" format="fasta"/>
  </outputs>

   <tests>
        <test>
            <param name="param_in" value="DecoyDatabase_input.fasta"/>
            <output name="param_out" file="DecoyDatabase_output.fasta"/>
        </test>
    </tests>

  <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>