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63 lines
2.3 KiB
XML
63 lines
2.3 KiB
XML
<tool id="EMBOSS: wordmatch110" name="wordmatch">
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<description>Finds all exact matches of a given size between 2 sequences</description>
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<command>wordmatch -asequence $input1 -bsequence $input2 -outfile $out_file1 -aoutfeat $out_file2 -boutfeat $out_file3 -wordsize "$wordsize" -aformat3 $out_format1 -offormat4 $out_format2
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-offormat5 $out_format3 -auto</command>
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<inputs>
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<param format="fasta" name="input1" type="data">
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<label>Sequence 1</label>
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</param>
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<param format="fasta" name="input2" type="data">
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<label>Sequence 2</label>
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</param>
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<param name="wordsize" size="5" type="text" value="4">
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<label>Word size</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="match">Match (m)</option>
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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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<param name="out_format2" type="select">
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<label>Output Feature 1 File Format</label>
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<option value="gff">GFF</option>
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<option value="embl">EMBL</option>
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<option value="swiss">SwissProt</option>
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</param>
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<param name="out_format3" type="select">
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<label>Output Feature 2 File Format</label>
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<option value="gff">GFF</option>
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<option value="embl">EMBL</option>
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<option value="swiss">SwissProt</option>
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</param>
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</inputs>
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<outputs>
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<data format="match" name="out_file1" />
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<data format="gff" name="out_file2" />
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<data format="gff" name="out_file3" />
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</outputs>
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<code file="emboss_format_corrector.py" />
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<help>
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.. class:: warningmark
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The input datasets need to be sequences.
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-----
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You can view the original documentation here_.
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.. _here: http://emboss.sourceforge.net/apps/release/4.0/emboss/apps/wordmatch.html
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</help>
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</tool>
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