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1 <tool id="cnvnator" name="cnvnator" version="0.3">
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2 <description></description>
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3
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3
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4 <requirements>
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5 <requirement type="package" version="0.3">cnvnator</requirement>
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6 </requirements>
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7
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8 <command interpreter="python">
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9 cnvnator.py
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10 -r $inputFastaFile
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11 -b $inputBamFile
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12 -s $binSize
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13 -o1 $outputRawFile
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14 -o2 $outputVcfFile
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15 $outputRaw
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16 </command>
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17
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18 <inputs>
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19 <param format="fasta" name="inputFastaFile" type="data" label="reference file" help="" />
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20 <param format="bam" name="inputBamFile" type="data" label="bam file" help="" />
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21 <param name="binSize" type="integer" label="bin size" help="" value="100" />
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22 <!-- <conditional name="outputChoice">
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23 <param name="outputChoiceSelect" type="select" label="Conditional output">
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24 <option value="yes">Yes</option>
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25 <option value="no">No</option>
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26 </param>
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27 </condition> -->
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28 <param name="outputRaw" type="boolean" label="output raw?" checked="false" />
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29 <param name="outputVcf" type="boolean" label="output vcf?" checked="true" />
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30 </inputs>
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31
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32 <outputs>
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33 <data format="tabular" name="outputRawFile" >
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34 <filter>outputRaw == false</filter>
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35 </data>
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36 <data format="vcf" name="outputVcfFile" />
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37 </outputs>
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38
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39 <help>
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40
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41
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42 </help>
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43
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44 </tool> |
