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1 <tool id="changeName" name="changeName">
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2 <description>Change the chromosome name or gene name of a singla fasta, gff or sam file. For this tool, it can not treat mutiple-chromosome, gene files.</description>
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3 <command interpreter="python">
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4 changeName.py
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5 #if $optionFasta.fastaFile == 'Yes':
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6 --input1 $optionFasta.fasta --output1 $outputFasta
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7 #end if
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8 #if $optionGff.gffFile == 'Yes':
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9 --input2 $optionGff.gff --output2 $outputGff
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10 #end if
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11 #if $optionSam.samFile == 'Yes':
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12 --input3 $optionSam.sam --output3 $outputSam
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13 #end if
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14 #if $optionName.name == 'Yes':
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15 --name $optionName.nameValue
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16 #end if
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17 </command>
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18
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19 <inputs>
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20 <conditional name="optionFasta">
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21 <param name="fastaFile" type="select" label="You can choose a fasta input file to change the name." >
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22 <option value="Yes">Yes</option>
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23 <option value="No" selected="true">No</option>
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24 </param>
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25 <when value="Yes">
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26 <param name="fasta" format="fasta" type="data" label="Identify you fasta input file."/>
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27 </when>
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28 <when value="No">
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29 </when>
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30 </conditional>
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31
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32 <conditional name="optionGff">
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33 <param name="gffFile" type="select" label="You can choose a supplementary gff input file to change the name." >
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34 <option value="Yes">Yes</option>
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35 <option value="No" selected="true">No</option>
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36 </param>
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37 <when value="Yes">
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38 <param name="gff" format="gff" type="data" label="Identify you gff input file."/>
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39 </when>
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40 <when value="No">
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41 </when>
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42 </conditional>
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43
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44 <conditional name="optionSam">
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45 <param name="samFile" type="select" label="You can choose a supplementary sam input file to change the name." >
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46 <option value="Yes">Yes</option>
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47 <option value="No" selected="true">No</option>
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48 </param>
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49 <when value="Yes">
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50 <param name="sam" format="sam" type="data" label="Identify you sam input file."/>
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51 </when>
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52 <when value="No">
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53 </when>
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54 </conditional>
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55
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56 <conditional name="optionName">
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57 <param name="name" type="select" label="Identify a new name to change." >
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58 <option value="Yes">Yes</option>
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59 <option value="No" selected="true">No</option>
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60 </param>
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61 <when value="Yes">
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62 <param name="nameValue" type="text" value="None" label="Identify the new name."/>
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63 </when>
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64 <when value="No">
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65 </when>
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66 </conditional>
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67 </inputs>
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68
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69 <outputs>
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70 <data name="outputFasta" format="fasta">
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71 <filter>optionFasta['fastaFile'] == 'Yes'</filter>
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72 </data>
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73 <data format="gff" name="outputGff" >
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74 <filter>optionGff['gffFile'] == 'Yes'</filter>
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75 </data>
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76 <data format="sam" name="outputSam" >
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77 <filter>optionSam['samFile'] == 'Yes'</filter>
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78 </data>
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79 </outputs>
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80 </tool>
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