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38
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1 <tool id="coordinatesToSequence" name="coordinates to sequence">
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2 <description>Coordinates to Sequences: Extract the sequences from a list of 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/coordinatesToSequence.py -i $formatType.inputFileName1
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8 #if $formatType.FormatInputFileName1 == 'bed':
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9 -f bed
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10 #elif $formatType.FormatInputFileName1 == 'gff':
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11 -f gff
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12 #elif $formatType.FormatInputFileName1 == 'gff2':
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13 -f gff2
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14 #elif $formatType.FormatInputFileName1 == 'gff3':
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15 -f gff3
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16 #elif $formatType.FormatInputFileName1 == 'sam':
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17 -f sam
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18 #elif $formatType.FormatInputFileName1 == '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 -s $sequence
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23 -o $outputFileFasta
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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="FormatInputFileName1" 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="inputFileName1" 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="inputFileName1" 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="inputFileName1" 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="inputFileName1" 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="inputFileName1" 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="inputFileName1" 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="sequence" type="data" label="Reference fasta File" format="fasta"/>
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58
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59 </inputs>
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60
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61 <outputs>
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62 <data name="outputFileFasta" format="fasta" label="coordinates to sequences output"/>
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63 </outputs>
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64
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65 <help>
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66 You can use this tool, if you just want to convert your mapping data to genomic coordinates, without any filtering. It requires a genomic coordinates file together with its format, an output format (GFF3, BED, etc...), the genome, and prints you the corresponding file.
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67 </help>
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68 </tool>
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