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1 <tool id="trimAdaptor" name="trim adaptors">
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2 <description>Remove the 3' adaptor of a list of reads.</description>
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3 <command interpreter="python"> ../Java/Python/trimAdaptor.py -i $inputFile -f fastq
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4 -a $adaptor
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5 #if $OptionError.Error == "Yes":
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6 -e $OptionError.ErrorVal
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7 #end if
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8 $noAdaptor $noAdaptorFile
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9 -o $outputFile
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10 </command>
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11
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12
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13 <inputs>
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14 <param name="inputFile" type="data" label="Input fastq File" format="fastq"/>
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15 <param name="adaptor" type="text" value="None" label="adaptor [compulsory option]"/>
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16 <conditional name="OptionError">
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17 <param name="Error" type="select" label="number of errors in percent">
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18 <option value="Yes">Yes</option>
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19 <option value="No" selected="true">No</option>
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20 </param>
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21 <when value="Yes">
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22 <param name="ErrorVal" type="integer" value="0" />
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23 </when>
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24 <when value="No">
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25 </when>
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26 </conditional>
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27 <param name="noAdaptor" type="boolean" truevalue="-n" falsevalue="" checked="false" label="log option" help="file name where to print sequences with no adaptor"/>
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28 </inputs>
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29
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30 <outputs>
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31 <data format="fastq" name="outputFile" label="[trimAdaptor] Output File"/>
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32 <data name="noAdaptorFile" format="fastq" label="[trimAdaptor] Log File">
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33 <filter>noAdaptor</filter>
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34 </data>
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35 </outputs>
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36 <tests>
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37 <test>
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38 <param name="inputFile" value="short_fastq.fastq" />
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39 <param name="adaptor" value="AAAA" />
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40 <param name ="Error" value="No"/>
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41 <param name ="noAdaptor" value="False"/>
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42 <output name="outputFile" file="exp_trimadaptator_short_fastq.fastq" />
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43 </test>
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44 </tests>
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45 <help>
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46 </help>
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47 </tool>
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