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1 <?xml version='1.0' encoding='UTF-8'?>
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2 <tool id="DecoyDatabase" name="DecoyDatabase" version="1.12.0">
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3 <description>Create decoy peptide databases from normal ones.</description>
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4 <macros>
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5 <token name="@EXECUTABLE@">DecoyDatabase</token>
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6 <import>macros.xml</import>
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7 </macros>
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8 <expand macro="stdio"/>
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9 <expand macro="requirements"/>
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10 <command>DecoyDatabase
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11
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12 -in ${param_in}
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13 -out ${param_out}
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14 -decoy_string ${param_decoy_string}
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15 -decoy_string_position ${param_decoy_string_position}
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16 ${param_append}
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17 ${param_shuffle}
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18 -threads \${GALAXY_SLOTS:-24}
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19 </command>
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20 <inputs>
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21 <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)"/>
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22 <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)"/>
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23 <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)">
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24 <option value="prefix">prefix</option>
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25 <option value="suffix">suffix</option>
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26 </param>
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27 <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)"/>
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28 <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)"/>
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29 </inputs>
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30 <outputs>
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31 <data name="param_out" label="Output FASTA file where the decoy database will be written to." format="fasta"/>
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32 </outputs>
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33 <help>**What it does**
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34
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35 Create decoy peptide databases from normal ones.
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36
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37
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38 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_DecoyDatabase.html
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39
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40 @REFERENCES@
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41 </help>
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42 </tool>
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