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1 <tool id="openms_decoy_database" version="0.1.0" name="Decoy Database Creator">
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2 <description>
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3 Create decoy protein/peptide databases from normal ones.
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4 </description>
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5 <macros>
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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="requires" />
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10 <command interpreter="python">
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11 openms_wrapper.py --executable 'DecoyDatabase' --config $config
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12 </command>
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13 <configfiles>
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14 <configfile name="config">[simple_options]
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15 in=${in}
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16 out=${out}
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17 decoy_string=${decoy_string}
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18 decoy_string_position=${decoy_string_position}
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19 append=${append}
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20 shuffle=${shuffle}
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21 </configfile>
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22 </configfiles>
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23 <inputs>
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24 <param format="fasta" name="in" type="data" label="Input database"/>
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25 <param name="decoy_string" type="text" value="_rev" label="Decoy string"/>
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26 <param name="decoy_string_position" type="select" label="Decoy Position">
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27 <option value="suffix" selected="true">Suffix</option>
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28 <option value="prefix">Prefix</option>
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29 </param>
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30 <param type="boolean" name="append" label="Append to original database" checked="true" />
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31 <param type="select" name="shuffle" label="Decoy type">
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32 <option value="false" selected="true">Reverse</option>
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33 <option value="true">Shuffle</option>
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34 </param>
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35 </inputs>
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36 <outputs>
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37 <data format="fasta" name="out" />
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38 </outputs>
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39 <stdio>
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40 <exit_code range="1:" level="fatal" description="Error creating decoy database." />
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41 </stdio>
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42 <help>
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43 **What it does**
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44
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45 Create decoy protein/peptide databases from normal ones.
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46
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47 **Citation**
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48
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49 For the underlying tool, please cite ``Marc Sturm, Andreas Bertsch, Clemens Gröpl, Andreas Hildebrandt, Rene Hussong, Eva Lange, Nico Pfeifer, Ole Schulz-Trieglaff, Alexandra Zerck, Knut Reinert, and Oliver Kohlbacher, 2008. OpenMS – an Open-Source Software Framework for Mass Spectrometry. BMC Bioinformatics 9: 163. doi:10.1186/1471-2105-9-163.``
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50
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51 If you use this tool in Galaxy, please cite Chilton J, et al. https://bitbucket.org/galaxyp/galaxyp-toolshed-openms
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52 </help>
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53 </tool>
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