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1 <tool id="uniqprimer" name="Uniqprimer" version="0.5.0">
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2 <description>Design specific primers of sequences</description>
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3 <requirements>
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4 <requirement type="package" version="6.6.0">emboss</requirement>
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5 <requirement type="package" version="3.23">mummer</requirement>
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6 <requirement type="package" version="2.5.0">primer3</requirement>
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7 </requirements>
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8 <command>$__tool_directory__/uniqprimer.sh $include $exclude $product_size_range $primer_size $min_size $max_size $crossvalidate $outfile $log $fasta
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9 #for $i in $inputs
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10 -i ${i.input}
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11 #end for
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12
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13 </command>
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14 <inputs>
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15 <param format="fasta" name="include" type="data" label="FASTA file to include" help="Sequences for which you want design specific primer"/>
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16 <repeat name="inputs" title="Include FASTA file">
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17 <param name="input" label="Add FASTA file to include" type="data" format="fasta" />
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18 </repeat>
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19 <param format="fasta" name="exclude" type="data" label="FASTA file to exclude" help="Primers will not match these sequences"/>
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20 <param type="text" name="product_size_range" label="Product size range" value="100-300"/>
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21 <param type="text" name="primer_size" label="Optimal primer size" value="20"/>
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22 <param type="text" name="min_size" label="Min primer size" value="18"/>
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23 <param type="text" name="max_size" label="Max primer size" value="27"/>
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24 <param name="crossvalidate" type="select" label="Cross validate primers against exclude files for extra certainty">
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25 <option value="Yes">Yes</option>
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26 <option value="No">No</option>
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27 </param>
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28 </inputs>
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29 <outputs>
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30 <data format="txt" name="outfile" label="Primer list"/>
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31 <data format="fasta" name="fasta" label="Fasta for Primer3"/>
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32 <data format="txt" name="log" label="Logfile"/>
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33 </outputs>
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34 <help>
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35
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36
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37 .. class:: infomark
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38
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39 **Program encapsulated in Galaxy by IRRI (International Rice Reasearch Institute) and South Green bioinformatics platform**
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40
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41 .. class:: infomark
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42
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43 **UniqPrimer version 0.5.0**
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44
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45 -----
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46
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47 ==============
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48 Please cite:
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49 ==============
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50
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51 "".
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52
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53 -----
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54
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55 ===========
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56 Overview:
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57 ===========
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58
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59 Uniqprimer designs specific primers of sequences. The goal of this tool is to accept a number of "include" FASTA files of diagnostic target genomes (draft or complete) and "exclude" files of non-target genomes, and output a list of PCR primers that will amplify target genomes but not non-target genomes.
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60
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61 </help>
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62
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63 </tool>
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