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1 <tool id="EMBOSS: matcher52" name="matcher" version="5.0.0">
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2 <description>Finds the best local alignments between two sequences</description>
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3 <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
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4 <command>matcher -asequence $input1 -bsequence $input2 -outfile $out_file1 -alternatives $alternatives -gapopen $gapopen -gapextend $gapextend -aformat3 $out_format1 -auto</command>
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5 <inputs>
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6 <param format="data" name="input1" type="data">
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7 <label>Sequence 1</label>
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8 </param>
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9 <param format="data" name="input2" type="data">
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10 <label>Sequence 2</label>
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11 </param>
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12 <param name="alternatives" size="4" type="text" value="1">
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13 <label>Number of alternative matches</label>
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14 </param>
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15 <param name="gapopen" size="4" type="text" value="16">
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16 <label>Gap penalty</label>
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17 </param>
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18 <param name="gapextend" size="4" type="text" value="4">
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19 <label>Gap length (extension) penalty</label>
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20 </param>
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21 <param name="out_format1" type="select">
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22 <label>Output Alignment File Format</label>
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23 <option value="markx0">Markx0 (p)</option>
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24 <option value="simple">Simple (m)</option>
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25 <option value="fasta">FASTA (m)</option>
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26 <option value="msf">MSF (m)</option>
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27 <option value="srs">SRS (m)</option>
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28 <option value="pair">Pair (p)</option>
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29 <option value="markx1">Markx1 (p)</option>
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30 <option value="markx2">Markx2 (p)</option>
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31 <option value="markx3">Markx3 (p)</option>
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32 <option value="markx10">Markx10 (p)</option>
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33 <option value="srspair">SRS pair (p)</option>
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34 <option value="score">Score (p)</option>
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35 </param>
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36 </inputs>
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37 <outputs>
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38 <data format="markx0" name="out_file1" />
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39 </outputs>
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40 <tests>
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41 <test>
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42 <param name="input1" value="2.fasta"/>
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43 <param name="input2" value="1.fasta"/>
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44 <param name="alternatives" value="1"/>
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45 <param name="gapopen" value="16"/>
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46 <param name="gapextend" value="4"/>
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47 <param name="out_format1" value="fasta"/>
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48 <output name="out_file1" file="emboss_matcher_out.fasta"/>
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49 </test>
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50 </tests>
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51 <code file="emboss_format_corrector.py" />
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52 <help>
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53 You can view the original documentation here_.
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54
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55 .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/matcher.html
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56 </help>
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57 </tool> |
