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1 <tool id="changeTagName" name="change tag name">
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2 <description>Changes the name of tag of a list of transcripts.</description>
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3 <command interpreter="python">
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4 ../Java/Python/changeTagName.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 #end if
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14
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15 -t $Tag
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16 -n $name
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17
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18 -o $outputFileGff
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19 </command>
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20
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21 <inputs>
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22 <conditional name="formatType">
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23 <param name="FormatInputFileName" type="select" label="Input File Format">
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24 <option value="bed">bed</option>
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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="bed">
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30 <param name="inputFileName" format="bed" type="data" label="Input File"/>
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31 </when>
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32 <when value="gff">
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33 <param name="inputFileName" format="gff" type="data" label="Input File"/>
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34 </when>
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35 <when value="gff2">
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36 <param name="inputFileName" format="gff2" type="data" label="Input File"/>
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37 </when>
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38 <when value="gff3">
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39 <param name="inputFileName" format="gff3" type="data" label="Input File"/>
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40 </when>
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41 </conditional>
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42
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43 <param name="Tag" type="text" value="None" label="tag option" help="A given tag, you must choose a tag."/>
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44 <param name="name" type="text" value="None" label="name option" help="new name for the tag, you must choose a new name."/>
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45
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46
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47
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48 </inputs>
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49
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50 <outputs>
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51 <data name="outputFileGff" format="gff3" label="[changeTagName] Output File"/>
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52 </outputs>
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53
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54 </tool>
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