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67 lines
2.4 KiB
XML
67 lines
2.4 KiB
XML
<tool id="EMBOSS: fuzznuc37" name="fuzznuc" version="5.0.0">
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<description>Nucleic acid pattern search</description>
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<command>fuzznuc -sequence $input1 -outfile $out_file1 -pattern "$pattern" -pmismatch $mismatch -complement $complement -rformat2 $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>Sequences</label>
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</param>
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<param name="pattern" size="5" type="text" value="">
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<label>Search pattern</label>
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</param>
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<param name="mismatch" size="5" type="text" value="0">
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<label>Number of mismatches</label>
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</param>
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<param name="complement" type="select">
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<label>Search complementary strand</label>
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<option value="no">No</option>
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<option value="yes">Yes</option>
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</param>
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<param name="out_format1" type="select">
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<label>Output Report File Format</label>
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<option value="seqtable">SeqTable</option>
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<option value="embl">EMBL</option>
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<option value="genbank">GENBANK</option>
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<option value="gff">GFF</option>
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<option value="pir">PIR</option>
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<option value="swiss">SwissProt</option>
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<option value="dbmotif">DbMotif</option>
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<option value="diffseq">Diffseq</option>
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<option value="excel">Excel (tab delimited)</option>
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<option value="feattable">FeatTable</option>
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<option value="motif">Motif</option>
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<option value="regions">Regions</option>
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<option value="simple">SRS Simple</option>
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<option value="fuzznuc">Fuzznuc Output File</option>
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<option value="srs">SRS</option>
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<option value="table">Table</option>
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<option value="tagseq">TagSeq</option>
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</param>
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</inputs>
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<outputs>
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<data format="fuzznuc" name="out_file1" />
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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="pattern" value="AA"/>
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<param name="mismatch" value="0"/>
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<param name="complement" value="no"/>
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<param name="out_format1" value="excel"/>
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<output name="out_file1" file="emboss_fuzznuc_out.tabular"/>
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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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.. class:: warningmark
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The input dataset needs 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/5.0/emboss/apps/fuzznuc.html
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</help>
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</tool>
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