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1 <tool id="MergingDataClusterize" name="Clusterize">
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2 <description>Clusterizes the reads when their genomic intervals overlap.</description>
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3 <command interpreter="python">
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4 ../Java/Python/clusterize.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 #elif $formatType.FormatInputFileName == 'csv':
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14 -f csv
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15 #elif $formatType.FormatInputFileName == 'sam':
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16 -f sam
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17 #end if
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18 -o $outputFileGff
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19 $colinear
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20 $normalize
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21 -d $distance
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22 $log $outputFileLog
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23 </command>
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24
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25 <inputs>
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26 <conditional name="formatType">
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27 <param name="FormatInputFileName" type="select" label="Input File Format">
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28 <option value="bed">bed</option>
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29 <option value="gff">gff</option>
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30 <option value="gff2">gff2</option>
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31 <option value="gff3">gff3</option>
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32 <option value="csv">csv</option>
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33 <option value="sam">sam</option>
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34 </param>
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35 <when value="bed">
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36 <param name="inputFileName" format="bed" type="data" label="Input File"/>
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37 </when>
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38 <when value="gff">
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39 <param name="inputFileName" format="gff" type="data" label="Input File"/>
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40 </when>
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41 <when value="gff2">
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42 <param name="inputFileName" format="gff2" type="data" label="Input File"/>
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43 </when>
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44 <when value="gff3">
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45 <param name="inputFileName" format="gff3" type="data" label="Input File"/>
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46 </when>
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47 <when value="csv">
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48 <param name="inputFileName" format="csv" type="data" label="Input File"/>
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49 </when>
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50 <when value="sam">
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51 <param name="inputFileName" format="sam" type="data" label="Input File"/>
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52 </when>
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53 </conditional>
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54
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55 <param name="colinear" type="boolean" truevalue="-c" falsevalue="" checked="false" label="colinear option" help="This option clusterizes only the same strand reads"/>
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56 <param name="normalize" type="boolean" truevalue="-n" falsevalue="" checked="false" label="normalize option for only GFF3 file format" help="This option normalize (attention!! Only for GFF3 file!!!!!)"/>
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57 <param name="log" type="boolean" truevalue="-l" falsevalue="" checked="false" label="log option" help="This option create a log file"/>
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58 <param name="distance" type="integer" value="0" label="distance option" help="Limit the maximum distance between two reads"/>
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59 </inputs>
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60
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61 <outputs>
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62 <data name="outputFileGff" format="gff3" label="[clusterize]output file"/>
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63 <data name="outputFileLog" format="txt" label="[clusterize]output file">
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64 <filter>log</filter>
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65 </data>
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66 </outputs>
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67 </tool>
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