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2 <tool id="pairScan" name="Scan paired-end reads for overlap" version="1.0.0">
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3 <description> Scan paired-end reads for overlap </description>
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3
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4 <requirements>
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5 <requirement type="package">python-levenshtein</requirement>
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6 </requirements>
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7 <command interpreter="python">
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8 pairScan.py -f $fasta_input -o $min_overlap -m $max_mismatch -p $pass -b $bad -s $offset
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9 </command>
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10
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11 <inputs>
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12 <param format="fasta" type="data" name="fasta_input" label="Reads in FASTA format" />
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13 <param name="min_overlap" type="integer" size="3" value="30" min="20" max="100" label="Minimum overlap length [nt] " />
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14 <param name="max_mismatch" type="select" label="Maximum number of mismatches per 100 bp">
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15 <option value="0">0</option>
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16 <option value="1" selected="true">1</option>
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17 <option value="2">2</option>
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18 <option value="3">3</option>
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19 <option value="4">4</option>
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20 </param>
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21 <param name="offset" type="select" label="Maximum offset">
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22 <option value="0">0</option>
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23 <option value="1">1</option>
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24 <option value="2">2</option>
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25 <option value="3">3</option>
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26 <option value="4">4</option>
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27 <option value="5" selected="true" >5</option>
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28 <option value="6">6</option>
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29 <option value="7">7</option>
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30 <option value="8">8</option>
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31 <option value="9">9</option>
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32 <option value="10">10</option>
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33 </param>
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34
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35
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36
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37 </inputs>
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38
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39
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40 <outputs>
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41 <data format="fasta" name="pass" label="Pairs with no overlap from dataset ${fasta_input.hid}"/>
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42 <data format="fasta" name="bad" label="Overlaping pairs from dataset ${fasta_input.hid}"/>
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43 </outputs>
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44
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45 <help>
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46 **Scan paired reads for overlap**
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47
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48 </help>
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49
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50
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51 </tool>
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