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1 <macros>
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2 <token name="@WRAPPER_VERSION@">2014.11.03.0</token>
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3 <xml name="stdio">
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4 <stdio>
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5 <!-- Anything other than zero is an error -->
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6 <exit_code range="1:" />
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7 <exit_code range=":-1" />
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8 <!-- In case the return code has not been set propery check stderr too -->
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9 <regex match="Error:" />
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10 <regex match="Exception:" />
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11 </stdio>
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12 </xml>
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13 <xml name="aln">
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14 <param type="boolean" label="output ALN alignment file (-a)" name="aln"
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15 truevalue="-a" falsevalue="" />
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16 </xml>
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17 <xml name="sam">
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18 <param type="boolean" label="output SAM alignment file (-s)" name="sam"
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19 truevalue="-s" falsevalue="" />
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20 </xml>
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21
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22 <xml name="rndSeed">
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23 <param label="specify a fixed, random seed for the simulation"
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24 help="Use -1 to request a random seed (-r)" name="rndSeed"
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25 type="integer" value="-1" optional="true" />
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26 </xml>
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27
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28 <xml name="citation">
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29 <citations>
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30 <citation type="doi">10.1093/bioinformatics/btr708</citation>
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31 </citations>
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32 </xml>
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33
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34 <xml name="amplicon">
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35 <conditional name="amplicon">
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36 <param name="use_amplicon" type="boolean" label="Run Amplicon Sequencing Simulation" truevalue="amplicon_true" falsevalue="amplicon_false" />
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37 <when value="amplicon_true">
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38 <param label="number of reads per amplicon (for 5'end amplicon sequencing)" name="reads_per_amplicon" type="integer" value="0"/>
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39 </when>
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40 <when value="amplicon_false">
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41 </when>
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42 </conditional>
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43 </xml>
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44
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45 <xml name="amplicon_pair">
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46 <conditional name="amplicon">
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47 <param name="use_amplicon" type="boolean" label="Run Amplicon Sequencing Simulation" truevalue="amplicon_true" falsevalue="amplicon_false" />
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48 <when value="amplicon_true">
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49 <param label="number of read pairs per amplicon (for two-end amplicon sequencing)" name="read_pairs_per_amplicon" type="integer" value="0"/>
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50 </when>
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51 <when value="amplicon_false">
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52 </when>
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53 </conditional>
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54 </xml>
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55
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56 <xml name="frag_len_sd">
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57 <param label="the average DNA fragment size"
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58 name="fragment_size" type="integer" value="200" minimum="101" />
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59 <param label="the standard deviation of the DNA fragment size"
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60 name="fragment_sd" type="integer" value="0"/>
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61 </xml>
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62 </macros>
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