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1 <?xml version="1.0"?>
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2 <tool id="patman_1" name="search for patterns in DNA using PatMaN">
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3 <description>search for approximate patterns in DNA libraries</description>
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4 <command>patman -a -e $edits -g $gaps -D $inputfastaFile -P $inputPatfile | sort | uniq > $patman_outputfile </command>
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5 <inputs>
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6 <param name="edits" type="integer" label="max N mismatches and or gaps" value="0" size="1" />
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7 <param name="gaps" type="integer" label="max N gaps" value="0" size="1"/>
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8 <param format="fasta" name="inputfastaFile" type="data" label="Multifasta target file" />
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9 <param format="fasta" name="inputPatfile" type="data" label="Pattern fasta" />
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10
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11 </inputs>
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12 <outputs>
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13 <data format="tabular" name="patman_outputfile" />
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14 </outputs>
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15 <help>
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16
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17
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18
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19 This is a Galaxy wrapper for PatMaN: a DNA pattern matcher for short sequences
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20
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21 * Website https://bioinf.eva.mpg.de/patman/
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22 * PubMed Citation_
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23
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24 *Inputs*
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25
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26 * Patterns in fasta format (create from tabular using tabular-to-fasta tool)
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27 * Multifasta file of target sequences
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28
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29 *Output*
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30
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31 * 6 Column tabular interval data
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32 * Columns Chrom, Pattern Name, Start, End, strand, N mismatches
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33
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34 ::
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35
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36 isotig05934 ACP818 368 389 + 0
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37 isotig05934 ACP859 377 396 + 0
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38 isotig06765 ACP822 448 468 + 0
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39 isotig07088 ACP825 49 75 + 0
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40 isotig07652 ACP830 199 218 + 0
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41 isotig07652 ACP831 257 276 + 0
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42 isotig10333 ACP837 474 497 + 0
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43 isotig10393 ACP838 10 34 + 0
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44
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45
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46
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47 .. _Citation: http://www.ncbi.nlm.nih.gov/pubmed/18467344?dopt=Abstract
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48
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49
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50 </help>
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51 </tool>
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