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1 <tool id="getReadDistribution" name="get read distribution">
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2 <description>Get Read Distribution v1.0.1: Plot the number of identical reads and give the most represented.</description>
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18
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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
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6 <command interpreter="python">
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7 ../Java/Python/WrappGetReadDistribution.py -i $formatType.inputFileName
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8 #if $formatType.FormatInputFileName == 'fasta':
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9 -f fasta
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10 #elif $formatType.FormatInputFileName == 'fastq':
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11 -f fastq
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12 #end if
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13
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14 #if $optionnumber.number == 'Yes':
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15 -n $optionnumber.bestNumber
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16 #end if
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17 #if $optionpercent.percent == 'Yes':
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18 -p $optionpercent.percentage
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19 #end if
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20 -o $outputFile
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21 </command>
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22
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23 <inputs>
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24 <conditional name="formatType">
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25 <param name="FormatInputFileName" type="select" label="Sequence input File Format ">
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26 <option value="fasta">fasta</option>
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27 <option value="fastq">fastq</option>
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28 </param>
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29 <when value="fasta">
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30 <param name="inputFileName" format="fasta" type="data" label="Sequence input File"/>
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31 </when>
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32 <when value="fastq">
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33 <param name="inputFileName" format="fastq" type="data" label="Sequence input File"/>
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34 </when>
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35 </conditional>
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36
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37 <conditional name="optionnumber">
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38 <param name="number" type="select" label="keep the best n">
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39 <option value="Yes">Yes</option>
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40 <option value="No" selected="true">No</option>
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41 </param>
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42 <when value="Yes">
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43 <param name="bestNumber" type="integer" value="0" />
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44 </when>
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45 <when value="No">
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46 </when>
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47 </conditional>
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48
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49 <conditional name="optionpercent">
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50 <param name="percent" type="select" label="keep the best n percentage">
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51 <option value="Yes">Yes</option>
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52 <option value="No" selected="true">No</option>
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53 </param>
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54 <when value="Yes">
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55 <param name="percentage" type="integer" value="0" />
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56 </when>
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57 <when value="No">
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58 </when>
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59 </conditional>
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60
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61 </inputs>
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62
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63 <outputs>
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64 <data name="outputFile" format="tar" label="[get read distribution] tar out file" help="You can not see the results directly from galaxy, but you can download this tar output file."/>
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6
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65 </outputs>
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66
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67 <help>
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68 This script gives a .tar out file, if you want to take look at the results, you have to download it.
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69 </help>
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70 </tool>
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