view DecoyDatabase.xml @ 3:75537a09e9fa draft

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<?xml version='1.0' encoding='UTF-8'?>
<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="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 $param_decoy_string_position:
  -decoy_string_position
  #if " " in str($param_decoy_string_position):
    "$param_decoy_string_position"
  #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 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="_rev" label="String that is appended to the accession of the protein database 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" type="select" optional="True" value="suffix" label="Should the 'decoy_string' be prepended (prefix) or appended (suffix) to the protein accession?" help="(-decoy_string_position) ">
      <option value="prefix">prefix</option>
      <option value="suffix">suffix</option>
    </param>
    <param name="param_append" type="boolean" truevalue="-append" falsevalue="" checked="false" optional="True" label="If this flag is used, the decoy database is appended to the target database, allowing combined target decoy searches" help="(-append) "/>
    <param name="param_shuffle" type="boolean" truevalue="-shuffle" falsevalue="" checked="false" optional="True" label="If 'true' then the decoy hit are shuffled from the target sequences, otherwise they are reversed" help="(-shuffle) "/>
    <expand macro="advanced_options">
      <param name="param_force" 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>
  <help>**What it does**

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>
  <expand macro="references"/>
</tool>