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1 <tool id="EMBOSS: ktrnascan_se" name="ktrnascan_se" version="1.0.2">
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2 <description>Finds tRNA genes using tRNAscan-SE</description>
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3 <command>ktrnascan_se -seqall $input1 -title $title -mode $mode -source $source -gcode $gcode -pesudogene $pesudogene -origin $origin -ace $ace -codons $codons -fpos $fpos -breakdown $breakdown -covescore $covescore -euparams $euparams -euscore $euscore -auto -outfile $out_file1</command>
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4 <inputs>
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5 <param format="data" name="input1" type="data">
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6 <label>Sequence</label>
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7 </param>
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8 <param name="title" size="4" type="text" value="">
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9 <label>Title of your job</label>
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10 </param>
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11 <param name="mode" size="4" type="text" value="Default">
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12 <label>Search mode</label>
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13 </param>
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14 <param name="source" size="4" type="text" value="Mixed (general tRNA model)">
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15 <label>Training data set</label>
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16 </param>
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17 <param name="gcode" size="4" type="text" value="Universal">
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18 <label>Genetic Code for tRNA Isotype Prediction</label>
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19 </param>
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20 <param name="pesudogene" type="select" value="">
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21 <label>Disable pseudo gene checking</label>
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22 <option value="no">No</option>
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23 <option value="yes">Yes</option>
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24 </param>
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25 <param name="origin" type="select" value="">
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26 <label>Show origin of first-pass hits</label>
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27 <option value="no">No</option>
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28 <option value="yes">Yes</option>
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29 </param>
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30 <param name="ace" type="select" value="">
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31 <label>Display results in ACeDB format</label>
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32 <option value="no">No</option>
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33 <option value="yes">Yes</option>
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34 </param>
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35 <param name="codons" type="select" value="">
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36 <label>Show codons instead of tRNA anticodons</label>
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37 <option value="no">No</option>
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38 <option value="yes">Yes</option>
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39 </param>
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40 <param name="fpos" type="select" value="">
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41 <label>Show false positives from tRNAscan/EufindtRNA</label>
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42 <option value="no">No</option>
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43 <option value="yes">Yes</option>
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44 </param>
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45 <param name="breakdown" type="select" value="">
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46 <label>Show primary and secondary structure components to Cove scores</label>
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47 <option value="no">No</option>
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48 <option value="yes">Yes</option>
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49 </param>
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50 <param name="covescore" size="4" type="text" value="">
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51 <label>Cove score cutoff</label>
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52 </param>
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53 <param name="euparams" size="4" type="text" value="Default">
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54 <label>EufindtRNA search parameters</label>
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55 </param>
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56 <param name="euscore" size="4" type="text" value="">
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57 <label>Intermediate score cutoff</label>
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58 </param>
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59
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60 </inputs>
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61 <outputs>
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62 <data format="txt" name="out_file1" label="${tool.name} for ${input1.name}" />
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63 </outputs>
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64 </tool>
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