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63 lines
2.6 KiB
XML
63 lines
2.6 KiB
XML
<tool id="EMBOSS: diffseq22" name="diffseq" version="4.0.0">
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<description>Find differences between nearly identical sequences</description>
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<command>diffseq -asequence $input1 -bsequence $input2 -outfile $out_file1 -aoutfeat $out_file2 -boutfeat $out_file3 -wordsize $wordsize -globaldifferences $globaldifferences -rformat3
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$out_format1 -offormat4 $out_format2 -offormat5 $out_format3 -auto</command>
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<inputs>
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<param format="data" name="input1" type="data">
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<label>Sequence 1</label>
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</param>
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<param format="data" 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="4" type="text" value="20">
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<label>Wordsize</label>
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</param>
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<param name="globaldifferences" type="select">
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<label>Report differences at the ends</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="diffseq">Diffseq</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="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="table">Table</option>
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<option value="tagseq">TagSeq</option>
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</param>
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<param name="out_format2" type="select">
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<label>Sequence 1 Output Feature 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>Sequence 2 Output Feature 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="diffseq" 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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You can view the original documentation here_.
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.. _here: http://emboss.sourceforge.net/apps/release/4.0/emboss/apps/diffseq.html
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</help>
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</tool> |