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1 <tool id="findTss" name="findTss">
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2 <description>Find the transcription start site of a list of transcripts.</description>
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3 <command interpreter="python">
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4 ../Java/Python/findTss.py -i $formatType.inputFileName
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5 #if $formatType.FormatInputFileName == 'bed':
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6 -f bed
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7 #elif $formatType.FormatInputFileName == 'gff':
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8 -f gff
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9 #elif $formatType.FormatInputFileName == 'gff2':
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10 -f gff2
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11 #elif $formatType.FormatInputFileName == 'gff3':
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12 -f gff3
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13 #end if
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14
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15
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16 -o $outputFileGff
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17 $colinear
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18 $normalize
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19 -d $distance
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20 $excel $excelOutput
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21
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22 </command>
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23
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24 <inputs>
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25 <conditional name="formatType">
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26 <param name="FormatInputFileName" type="select" label="Input File Format">
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27 <option value="bed">bed</option>
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28 <option value="gff">gff</option>
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29 <option value="gff2">gff2</option>
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30 <option value="gff3">gff3</option>
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31 </param>
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32 <when value="bed">
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33 <param name="inputFileName" format="bed" type="data" label="Input File"/>
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34 </when>
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35 <when value="gff">
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36 <param name="inputFileName" format="gff" type="data" label="Input File"/>
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37 </when>
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38 <when value="gff2">
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39 <param name="inputFileName" format="gff2" type="data" label="Input File"/>
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40 </when>
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41 <when value="gff3">
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42 <param name="inputFileName" format="gff3" type="data" label="Input File"/>
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43 </when>
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44 </conditional>
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45
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46 <param name="colinear" type="boolean" truevalue="-e" falsevalue="" checked="false" label="colinear option" help="This option clusterizes only the same strand reads"/>
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47 <param name="normalize" type="boolean" truevalue="-n" falsevalue="" checked="false" label="normalize option for only GFF3 file format" help="This option normalize (Warning!! Only for GFF3 file!!!!!)"/>
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48 <param name="distance" type="text" value="10" label="distance option" help="Limit the maximum distance between two reads"/>
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49 <param name="excel" type="boolean" truevalue="-c" falsevalue="" checked="false" label="excel option" help="This option creates a csv file."/>
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50 </inputs>
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51
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52 <outputs>
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53 <data name="outputFileGff" format="gff3" label="[findTss] Output File"/>
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54 <data name="excelOutput" format="csv" label="[findTss] CSV File">
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55 <filter>excel</filter>
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56 </data>
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57 </outputs>
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58
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59 </tool>
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