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95 lines
3.8 KiB
XML
95 lines
3.8 KiB
XML
<tool id="EMBOSS_fuzztran39" name="fuzztran">
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<description>Protein pattern search after translation</description>
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<command>fuzztran -sequence $input1 -outfile $out_file1 -pattern "$pattern" -pmismatch $mismatch -frame $frame -table $table -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="frame" type="select">
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<label>Frame(s) to translate</label>
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<option value="1">Frame 1</option>
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<option value="2">Frame 2</option>
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<option value="3">Frame 3</option>
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<option value="F">Forward three frames</option>
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<option value="-1">Frame -1</option>
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<option value="-2">Frame -2</option>
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<option value="-3">Frame -3</option>
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<option value="R">Reverse three frames</option>
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<option value="6">All six frames</option>
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</param>
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<param name="table" type="select">
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<label>Code to use</label>
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<option value="0">Standard</option>
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<option value="1">Standard (with alternative initiation codons)</option>
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<option value="2">Vertebrate Mitochondrial</option>
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<option value="3">Yeast Mitochondrial</option>
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<option value="4">Mold, Protozoan, Coelenterate Mitochondrial and Mycoplasma/Spiroplasma</option>
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<option value="5">Invertebrate Mitochondrial</option>
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<option value="6">Ciliate Macronuclear and Dasycladacean</option>
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<option value="9">Echinoderm Mitochondrial</option>
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<option value="10">Euplotid Nuclear</option>
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<option value="11">Bacterial</option>
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<option value="12">Alternative Yeast Nuclear</option>
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<option value="13">Ascidian Mitochondrial</option>
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<option value="14">Flatworm Mitochondrial</option>
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<option value="15">Blepharisma Macronuclear</option>
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<option value="16">Chlorophycean Mitochondrial</option>
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<option value="21">Trematode Mitochondrial</option>
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<option value="22">Scenedesmus obliquus</option>
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<option value="23">Thraustochytrium Mitochondrial</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="table">Table</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="seqtable">SeqTable</option>
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<option value="simple">SRS Simple</option>
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<option value="srs">SRS</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="fuzztran" 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="1.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="frame" value="6"/>
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<param name="table" value="0"/>
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<param name="out_format1" value="excel"/>
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<output name="out_file1" file="emboss_fuzztran_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/fuzztran.html
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</help>
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</tool>
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