[2] | 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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