view DecoyDatabase.xml @ 1:17e8c91b70d5 draft

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<?xml version='1.0' encoding='UTF-8'?>
<tool id="DecoyDatabase" name="DecoyDatabase" version="1.12.0">
  <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 ${param_in}
-out ${param_out}
-decoy_string ${param_decoy_string}
-decoy_string_position ${param_decoy_string_position}
${param_append}
${param_shuffle}
-threads \${GALAXY_SLOTS:-24} 
</command>
  <inputs>
    <param name="param_in" type="data" format="fasta" optional="False" size="20" label="Input FASTA file(s), each containing a database. It is recommended to include a contaminant database as well." help="(-in)"/>
    <param name="param_decoy_string" type="text" size="20" value="_rev" label="String that is appended to the accession of the protein database to indicate a decoy protein." help="(-decoy_string)"/>
    <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 true" falsevalue="-append false" 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 true" falsevalue="-shuffle false" checked="false" optional="True" label="If 'true' then the decoy hit are shuffled from the target sequences, otherwise they are reversed" help="(-shuffle)"/>
  </inputs>
  <outputs>
    <data name="param_out" label="Output FASTA file where the decoy database will be written to." 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

@REFERENCES@
</help>
</tool>