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38
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1 <tool id="changeTagName" name="change tag name">
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2 <description>Change the name of a tag in a GFF file.</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/changeTagName.py -i $formatType.inputFileName
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39
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8 #if $formatType.FormatInputFileName == 'gff':
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38
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9 -f gff
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10 #elif $formatType.FormatInputFileName == 'gff2':
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11 -f gff2
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12 #elif $formatType.FormatInputFileName == 'gff3':
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13 -f gff3
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14 #end if
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15
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16 -t $Tag
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17 -n $name
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18
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19 -o $outputFileGff
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20 </command>
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21
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22 <inputs>
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23 <conditional name="formatType">
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24 <param name="FormatInputFileName" type="select" label="Input File Format">
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25 <option value="gff">gff</option>
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26 <option value="gff2">gff2</option>
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27 <option value="gff3">gff3</option>
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28 </param>
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29 <when value="gff">
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30 <param name="inputFileName" format="gff" type="data" label="Input File"/>
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31 </when>
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32 <when value="gff2">
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33 <param name="inputFileName" format="gff2" type="data" label="Input File"/>
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34 </when>
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35 <when value="gff3">
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36 <param name="inputFileName" format="gff3" type="data" label="Input File"/>
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37 </when>
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38 </conditional>
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39
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40 <param name="Tag" type="text" label="tag option" help="The tag you want to change"/>
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41 <param name="name" type="text" label="name option" help="A new name for the tag"/>
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42 </inputs>
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43
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44 <outputs>
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45 <data name="outputFileGff" format="gff3" label="[change tag name] Output File"/>
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46 </outputs>
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47
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48 <help>
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49 Change the name of a tag in the 9th field of a GFF3 file (please consult http://www.sequenceontology.org/gff3.shtml to know more about this format).
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50 </help>
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51 </tool>
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