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1 <tool id="removeIntrons" name="remove introns">
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2 <description>Removes the introns of the transcript files.</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"> ../Java/Python/RemoveExons.py -i $formatType.inputFileName -f $formatType.FormatInputFileName -o $outputFile </command>
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7 <inputs>
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8 <conditional name="formatType">
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9 <param name="FormatInputFileName1" type="select" label="query File Format">
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10 <option value="bed">bed</option>
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11 <option value="gff">gff</option>
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12 <option value="gff2">gff2</option>
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13 <option value="gff3">gff3</option>
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14 <option value="sam">sam</option>
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15 <option value="gtf">gtf</option>
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16 </param>
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17 <when value="bed">
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18 <param name="inputFileName" format="bed" type="data" label="Input File 1"/>
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19 </when>
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20 <when value="gff">
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21 <param name="inputFileName" format="gff" type="data" label="Input File 1"/>
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22 </when>
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23 <when value="gff2">
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24 <param name="inputFileName" format="gff2" type="data" label="Input File 1"/>
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25 </when>
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26 <when value="gff3">
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27 <param name="inputFileName" format="gff3" type="data" label="Input File 1"/>
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28 </when>
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29 <when value="sam">
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30 <param name="inputFileName" format="sam" type="data" label="Input File 1"/>
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31 </when>
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32 <when value="gtf">
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33 <param name="inputFileName" format="gtf" type="data" label="Input File 1"/>
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34 </when>
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35 </conditional>
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36 </inputs>
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37
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38 <outputs>
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39 <data format="gff3" name="outputFile" label="[remove introns] output file"/>
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40 </outputs>
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41
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42 <help>
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43 Simply remove the introns of the input file, thus getting the unmatured transcript.
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44 </help>
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45 </tool>
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