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date Sun, 21 Feb 2016 11:20:31 -0500
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1 <tool id="decoyfasta" name="Create Decoy Database (reverse)" version="0.2.0">
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2 <description>Creates a decoy search database by adding reverse
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3 sequences to an existing database</description>
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4 <requirements>
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5 <requirement type="package" version="4.8.0">trans_proteomic_pipeline</requirement>
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6 </requirements>
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7 <command>
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8 <![CDATA[
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9 decoyFASTA
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10 ${input}
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11 ${output}
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12 ${include_original}
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13 #if $freq_type.advanced == "yes"
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14 -t${frequency} ${tag}
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15 #for $extra_tag in $extra_tags
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16 -t${extra_tag.frequency} ${extra_tag.tag}
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17 #end for
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18 #else
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19 -t1 ${freq_type.tag}
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20 #end if
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21 ]]>
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22 </command>
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23 <inputs>
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24 <param format="fasta" name="input" type="data" label="FASTA Input" help="select input database from history in FASTA format" />
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25 <param name="include_original" type="boolean" truevalue="" falsevalue="-no_orig" label="Include original entries in output database" checked="True" help="(default) keep checked in all standard searches" />
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26 <conditional name="freq_type">
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27 <param name="advanced" type="select" label="Specify advanced decoy frequency options?" help="&quot;Decoy Prefix&quot; will name the prefix of each decoy sequence, &quot;Frequency&quot; will specify how many decoy sequences are created">
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28 <option value="no">No, just create database with one reversed sequence for every input sequence</option>
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29 <option value="yes">Yes, I want to specify multiple prefixes and specific frequencies</option>
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30 </param>
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31 <when value="no">
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32 <param name="tag" type="text" value="decoy_" label="Decoy Prefix"/>
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33 </when>
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34 <when value="yes">
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35 <param name="tag" type="text" value="decoy_" label="Decoy Prefix"/>
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36 <param name="frequency" type="integer" value="1" label="Decoy Frequency" />
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37 <repeat name="extra_tags" title="Additional Decoy Tags">
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38 <param name="tag" type="text" value="decoy_" label="Decoy Prefix"/>
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39 <param name="frequency" type="integer" value="1" label="Decoy Frequency" />
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40 </repeat>
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41 </when>
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42 </conditional>
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43 </inputs>
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44 <outputs>
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45 <data format="fasta" name="output" />
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46 </outputs>
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47 <help>
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48 <![CDATA[
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49 **What it does**
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50
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51 Given an input database, this tool will produce another database with
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52 reversed sequences to use as decoys for False Discovery Rate (FDR) estimation in protein search identification. This tool employs the decoyFASTA program from
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53 the Transproteomic Pipeline.
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54
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55 ------
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56
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57 **Citation**
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58
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59 If you use this tool in Galaxy, please cite Chilton J, et al. https://github.com/galaxyproteomics/
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60 ]]>
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61 </help>
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62 <citations>
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63 <citation type="doi">10.1002/pmic.200900375</citation>
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64 </citations>
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65 </tool>