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1 <tool id="getNumber" name="get number">
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2 <description>Get the distribution of exons per transcripts, or mapping per read, or transcript per cluster.</description>
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3 <command interpreter="python">
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4 ../Java/Python/getNb.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 == 'sam':
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14 -f sam
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15 #elif $formatType.FormatInputFileName == 'gtf':
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16 -f gtf
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17 #end if
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18 -o $outputFilePNG
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19 -q $query
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20 $barPlot
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21 #if $optionXMAX.XMAX == 'Yes':
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22 -x $optionXMAX.xMaxValue
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23 #end if
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24
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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="gtf">gtf</option>
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36 </param>
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37 <when value="bed">
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38 <param name="inputFileName" format="bed" type="data" label="Input File"/>
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39 </when>
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40 <when value="gff">
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41 <param name="inputFileName" format="gff" type="data" label="Input File"/>
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42 </when>
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43 <when value="gff2">
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44 <param name="inputFileName" format="gff2" type="data" label="Input File"/>
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45 </when>
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46 <when value="gff3">
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47 <param name="inputFileName" format="gff3" type="data" label="Input File"/>
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48 </when>
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49 <when value="sam">
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50 <param name="inputFileName" format="sam" type="data" label="Input File"/>
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51 </when>
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52 <when value="gtf">
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53 <param name="inputFileName" format="gtf" type="data" label="Input File"/>
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54 </when>
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55 </conditional>
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56
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57 <param name="query" type="text" value="None" label="compulsory option, choice (exon, transcript, cluster)" />
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58 <param name="barPlot" type="boolean" truevalue="-b" falsevalue="" checked="false" label="use barplot representation"/>
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59
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60 <conditional name="optionXMAX">
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61 <param name="XMAX" type="select" label="maximum value on the x-axis to plot ">
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62 <option value="Yes">Yes</option>
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63 <option value="No" selected="true">No</option>
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64 </param>
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65 <when value="Yes">
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66 <param name="xMaxValue" type="integer" value="0" />
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67 </when>
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68 <when value="No">
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69 </when>
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70 </conditional>
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71
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72 </inputs>
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73
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74 <outputs>
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75 <data name="outputFilePNG" format="png" label="[getNB]out file"/>
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76 </outputs>
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77
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78 </tool>
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