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1 <tool id="EMBOSS: supermatcher95" name="supermatcher" version="5.0.0">
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2 <!-- puts file information in output report -->
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3 <description>Match large sequences against one or more other sequences</description>
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4 <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
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5 <command>supermatcher -asequence $input1 -bsequence $input2 -gapopen "$gapopen" -gapextend "$gapextend" -width "$width" -wordlen "$wordlen" -outfile $ofile1 -errorfile $ofile2 -aformat3
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6 $out_format1 -auto</command>
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7 <inputs>
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8 <param format="fasta" name="input1" type="data">
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9 <label>Large sequences</label>
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10 </param>
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11 <param format="data" name="input2" type="data">
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12 <label>Sequences to match</label>
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13 </param>
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14 <param name="gapopen" size="4" type="text" value="10.0">
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15 <label>Gap opening penalty</label>
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16 </param>
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17 <param name="gapextend" size="4" type="text" value="0.5">
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18 <label>Gap extension penalty</label>
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19 </param>
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20 <param name="width" size="4" type="text" value="16">
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21 <label>Alignment width</label>
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22 </param>
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23 <param name="wordlen" size="4" type="text" value="6">
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24 <label>Word length for initial matching</label>
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25 </param>
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26 <param name="out_format1" type="select">
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27 <label>Output Alignment File Format</label>
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28 <option value="simple">Simple (m)</option>
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29 <option value="fasta">FASTA (m)</option>
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30 <option value="msf">MSF (m)</option>
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31 <option value="srs">SRS (m)</option>
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32 <option value="pair">Pair (p)</option>
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33 <option value="markx0">Markx0 (p)</option>
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34 <option value="markx1">Markx1 (p)</option>
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35 <option value="markx2">Markx2 (p)</option>
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36 <option value="markx3">Markx3 (p)</option>
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37 <option value="markx10">Markx10 (p)</option>
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38 <option value="srspair">SRS pair (p)</option>
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39 <option value="score">Score (p)</option>
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40 </param>
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41 </inputs>
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42 <outputs>
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43 <data format="simple" name="ofile1" />
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44 <data format="supermatcher" name="ofile2" />
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45 </outputs>
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46 <!-- <tests>
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47 <test>
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48 <param name="input1" value="2.fasta"/>
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49 <param name="input2" value="1.fasta"/>
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50 <param name="gapopen" value="10.0"/>
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51 <param name="gapextend" value="0.5"/>
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52 <param name="width" value="16"/>
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53 <param name="wordlen" value="6"/>
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54 <param name="out_format1" value="fasta"/>
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55 <output name="ofile1" file="emboss_supermatcher_out.fasta"/>
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56 </test>
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57 </tests> -->
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58 <code file="emboss_format_corrector.py" />
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59 <help>
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60 You can view the original documentation here_.
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61
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62 .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/supermatcher.html
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63 </help>
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64 </tool>
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