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1 <tool id="collapseReads" name="collapse reads">
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2 <description>Merges two genomic features if they have exactly the same genomic coordinates.</description>
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3 <requirements>
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4 <requirement type="set_environment">PYTHONPATH</requirement>
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5 </requirements>
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6 <command interpreter="python">
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7 ../Java/Python/CollapseReads.py -i $formatType.inputFileName
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8 #if $formatType.FormatInputFileName == 'bed':
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9 -f bed
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10 #elif $formatType.FormatInputFileName == 'gff':
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11 -f gff
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12 #elif $formatType.FormatInputFileName == 'gff2':
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13 -f gff2
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14 #elif $formatType.FormatInputFileName == 'gff3':
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15 -f gff3
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16 #elif $formatType.FormatInputFileName == 'sam':
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17 -f sam
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18 #elif $formatType.FormatInputFileName == 'bam':
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19 -f bam
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20 #elif $formatType.FormatInputFileName == 'gtf':
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21 -f gtf
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22 #end if
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23 -$strand
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24 -o $outputFileGff
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25 </command>
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26
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27 <inputs>
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28 <conditional name="formatType">
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29 <param name="FormatInputFileName" type="select" label="Input File Format">
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30 <option value="bed">bed</option>
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31 <option value="gff">gff</option>
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32 <option value="gff2">gff2</option>
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33 <option value="gff3">gff3</option>
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34 <option value="sam">sam</option>
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35 <option value="bam">bam</option>
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36 <option value="gtf">gtf</option>
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37 </param>
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38 <when value="bed">
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39 <param name="inputFileName" format="bed" type="data" label="Input File"/>
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40 </when>
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41 <when value="gff">
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42 <param name="inputFileName" format="gff" type="data" label="Input File"/>
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43 </when>
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44 <when value="gff2">
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45 <param name="inputFileName" format="gff2" type="data" label="Input File"/>
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46 </when>
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47 <when value="gff3">
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48 <param name="inputFileName" format="gff3" 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 <when value="bam">
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54 <param name="inputFileName" format="bam" type="data" label="Input File"/>
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55 </when>
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56 <when value="gtf">
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57 <param name="inputFileName" format="gtf" type="data" label="Input File"/>
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58 </when>
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59 </conditional>
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60
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61 <param name="strand" type="boolean" truevalue="-s" falsevalue="" checked="false" label="Merges features even if they are on different strands."/>
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62 </inputs>
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63
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64 <outputs>
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65 <data name="outputFileGff" format="gff3"/>
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66 </outputs>
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67
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68 <help>
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69 Merge two input genomic coordinates iff they are exactly the same. If two or more genomic coordinates are merged, the tag **nbElements** is updated accordingly. As a consequence, all the reads which are exactly the same appear as one genomic coordinate.
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70
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71 This is especially useful for short RNA sequencing (where you want to count the number of read per miRNA, siRNA, etc.) or 5' capped short reads.
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72 </help>
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73 </tool>
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