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64 lines
2.5 KiB
XML
64 lines
2.5 KiB
XML
<tool id="EMBOSS: supermatcher95" name="supermatcher" version="5.0.0">
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<!-- puts file information in output report -->
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<description>Match large sequences against one or more other sequences</description>
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<command>supermatcher -asequence $input1 -bsequence $input2 -gapopen "$gapopen" -gapextend "$gapextend" -width "$width" -wordlen "$wordlen" -outfile $ofile1 -errorfile $ofile2 -aformat3
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$out_format1 -auto</command>
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<inputs>
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<param format="fasta" name="input1" type="data">
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<label>Large sequences</label>
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</param>
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<param format="data" name="input2" type="data">
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<label>Sequences to match</label>
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</param>
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<param name="gapopen" size="4" type="text" value="10.0">
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<label>Gap opening penalty</label>
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</param>
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<param name="gapextend" size="4" type="text" value="0.5">
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<label>Gap extension penalty</label>
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</param>
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<param name="width" size="4" type="text" value="16">
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<label>Alignment width</label>
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</param>
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<param name="wordlen" size="4" type="text" value="6">
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<label>Word length for initial matching</label>
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</param>
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<param name="out_format1" type="select">
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<label>Output Alignment File Format</label>
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<option value="simple">Simple (m)</option>
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<option value="fasta">FASTA (m)</option>
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<option value="msf">MSF (m)</option>
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<option value="srs">SRS (m)</option>
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<option value="pair">Pair (p)</option>
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<option value="markx0">Markx0 (p)</option>
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<option value="markx1">Markx1 (p)</option>
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<option value="markx2">Markx2 (p)</option>
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<option value="markx3">Markx3 (p)</option>
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<option value="markx10">Markx10 (p)</option>
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<option value="srspair">SRS pair (p)</option>
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<option value="score">Score (p)</option>
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</param>
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</inputs>
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<outputs>
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<data format="simple" name="ofile1" />
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<data format="supermatcher" name="ofile2" />
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</outputs>
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<!-- <tests>
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<test>
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<param name="input1" value="2.fasta"/>
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<param name="input2" value="1.fasta"/>
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<param name="gapopen" value="10.0"/>
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<param name="gapextend" value="0.5"/>
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<param name="width" value="16"/>
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<param name="wordlen" value="6"/>
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<param name="out_format1" value="fasta"/>
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<output name="ofile1" file="emboss_supermatcher_out.fasta"/>
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</test>
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</tests> -->
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<code file="emboss_format_corrector.py" />
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<help>
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You can view the original documentation here_.
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.. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/supermatcher.html
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</help>
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</tool>
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