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1 <tool id="getExons" name="get exons">
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2 <description>Get the exons of a set of transcripts.</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/getExons.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 == 'gtf':
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19 -f gtf
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20 #end if
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21
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22 #if $optionSelect.Value == "Yes":
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23 -s $optionSelect.selectValue
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24 #end if
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25
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26 -o $outputFileGff
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27 </command>
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28
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29 <inputs>
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30 <conditional name="formatType">
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31 <param name="FormatInputFileName" type="select" label="Input File Format">
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32 <option value="bed">bed</option>
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33 <option value="gff">gff</option>
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34 <option value="gff2">gff2</option>
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35 <option value="gff3">gff3</option>
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36 <option value="sam">sam</option>
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37 <option value="gtf">gtf</option>
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38 </param>
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39 <when value="bed">
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40 <param name="inputFileName" format="bed" type="data" label="Input File"/>
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41 </when>
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42 <when value="gff">
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43 <param name="inputFileName" format="gff" type="data" label="Input File"/>
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44 </when>
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45 <when value="gff2">
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46 <param name="inputFileName" format="gff2" type="data" label="Input File"/>
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47 </when>
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48 <when value="gff3">
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49 <param name="inputFileName" format="gff3" type="data" label="Input File"/>
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50 </when>
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51 <when value="sam">
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52 <param name="inputFileName" format="sam" type="data" label="Input File"/>
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53 </when>
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54 <when value="gtf">
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55 <param name="inputFileName" format="gtf" type="data" label="Input File"/>
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56 </when>
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57 </conditional>
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58
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59 <conditional name="optionSelect">
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60 <param name="Value" type="select" label="select some of the exons (like '1,2,5..-3,-1')">
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61 <option value="Yes">Yes</option>
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62 <option value="No" selected="true">No</option>
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63 </param>
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64 <when value="Yes">
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65 <param name="selectValue" type="text" value="None" label="select option" help="like '1,2,5..-3,-1'"/>
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66 </when>
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67 <when value="No">
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68 </when>
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69 </conditional>
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70 </inputs>
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71
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72 <outputs>
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73 <data format="gff3" name="outputFileGff" label="[get exons] output file"/>
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74 </outputs>
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75 <tests>
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76 <test>
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77 <param name="FormatInputFileName" value="gtf" />
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78 <param name="inputFileName" value="genes.gtf" />
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79 <param name="Value" value="No"/>
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80 <output name="outputFileGff" file="exp_getExons.gff3" />
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81 </test>
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82 </tests>
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83
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84 <help>
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85 Provide all the exons of an annotation file.
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86 </help>
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87 </tool>
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