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13
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1 <tool id="match" name="match">
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2 <description>find short motif occurrences</description>
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3 <command> match $motif $seq $output $nmismatch $rc $bed > $log</command>
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4 <inputs>
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5
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6 <param name="motif" type="data" format="fasta" label="Search occurances of the following motifs" help="one or multiple sequences, FASTA format"/>
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7 <param name="seq" type="data" format="fasta" label="in sequences" help="one or multiple sequences, FASTA format"/>
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8 <param name="nmismatch" size="10" type="integer" value="0" label="number of mismatches allowed"/>
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9 <param name="rc" label="Do not score the reverse complement DNA strand. Both strands are scored by default" type="boolean" truevalue="norc" falsevalue="rc" checked="False"/>
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10 <param name="bed" label="output BED format" help="Default is tabular file (see example below). Please only check this if your sequence identifier looks like: hg18_chr6_122208322_122209078_+ (true for galaxy tool extracted sequences)" type="boolean" truevalue="bed" falsevalue="nobed" checked="False"/>
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11 </inputs>
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12 <outputs>
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13 <data format="txt" name="log" label="${tool.name} on ${on_string} (log)"/>
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14 <data format="bed" name="output" label="${tool.name} on ${on_string} (bed)"/>
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15 </outputs>
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16 <help>
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17
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18 **What it does**
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19
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20 This tool searches occurrences of a short nucleotide seuqences (allowing mismatches) in a set of longer sequences.
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21
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22 Example motif file::
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23
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24 >motif1
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25 CAGGTAAGT
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26 >motif2
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27 GTTTGGGGGCC
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28
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29 Example sequence file::
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30
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31 >hg18_chr6_122208322_122209078_+
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32 CGTCGTAGCTACTAGCTACGTACGTACGTAGCTAGCATGCATGCTACGTA
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33 CGTAGCTAGCTAAAAAAAAAAAAAAACTGCGGCTAGCTAGCTAGCTACGT
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34 CGATCGTAGCTAC...
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35 >hg18_chr6_1208322_122209023_+
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36 CGATGCTAGCTAGCTAGCTACGTAGCTAGCTAGTCGATGCTAGCTAGCTA
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37 ATGCTAGCTAGC....
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38
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39 Output (bed)::
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40
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41 chr11 72790893 72790902 ACTTAACTG 1 - antisense 5ss,G4T:CAGTTAAGT-rc hg18_chr11_72790846_72791902_+ 47
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42 chr11 72791880 72791889 CAGGTAAGA 1 + sense 5ss,T9A:CAGGTAAGA hg18_chr11_72790846_72791902_+ 1034
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43
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44
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45 Output (tab)::
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46
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47 Tmod4 802 5ss:CAGGTAAGT-rc ACTTACCTG
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48 Atp7b 77 5ss:CAGGTAAGT CAGGTAAGT
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49 Fnta 665 5ss:CAGGTAAGT CAGGTAAGT
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50
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51
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52
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53 </help>
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54 </tool>
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