[2] | 1 | <tool id="EMBOSS: diffseq22" name="diffseq" version="5.0.0">
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| 2 | <description>Find differences between nearly identical sequences</description>
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| 3 | <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
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| 4 | <command>diffseq -asequence $input1 -bsequence $input2 -outfile $out_file1 -aoutfeat $out_file2 -boutfeat $out_file3 -wordsize $wordsize -globaldifferences $globaldifferences -rformat3
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| 5 | $out_format1 -offormat4 $out_format2 -offormat5 $out_format3 -auto</command>
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| 6 | <inputs>
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| 7 | <param format="data" name="input1" type="data">
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| 8 | <label>Sequence 1</label>
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| 9 | </param>
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| 10 | <param format="data" name="input2" type="data">
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| 11 | <label>Sequence 2</label>
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| 12 | </param>
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| 13 | <param name="wordsize" size="4" type="text" value="20">
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| 14 | <label>Wordsize</label>
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| 15 | </param>
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| 16 | <param name="globaldifferences" type="select">
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| 17 | <label>Report differences at the ends</label>
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| 18 | <option value="no">No</option>
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| 19 | <option value="yes">Yes</option>
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| 20 | </param>
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| 21 | <param name="out_format1" type="select">
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| 22 | <label>Output Report File Format</label>
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| 23 | <option value="diffseq">Diffseq</option>
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| 24 | <option value="embl">EMBL</option>
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| 25 | <option value="genbank">GENBANK</option>
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| 26 | <option value="gff">GFF</option>
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| 27 | <option value="pir">PIR</option>
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| 28 | <option value="swiss">SwissProt</option>
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| 29 | <option value="dbmotif">DbMotif</option>
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| 30 | <option value="excel">Excel (tab delimited)</option>
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| 31 | <option value="feattable">FeatTable</option>
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| 32 | <option value="motif">Motif</option>
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| 33 | <option value="regions">Regions</option>
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| 34 | <option value="seqtable">SeqTable</option>
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| 35 | <option value="simple">SRS Simple</option>
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| 36 | <option value="srs">SRS</option>
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| 37 | <option value="table">Table</option>
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| 38 | <option value="tagseq">TagSeq</option>
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| 39 | </param>
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| 40 | <param name="out_format2" type="select">
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| 41 | <label>Sequence 1 Output Feature File Format</label>
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| 42 | <option value="gff">GFF</option>
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| 43 | <option value="embl">EMBL</option>
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| 44 | <option value="swiss">SwissProt</option>
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| 45 | </param>
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| 46 | <param name="out_format3" type="select">
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| 47 | <label>Sequence 2 Output Feature File Format</label>
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| 48 | <option value="gff">GFF</option>
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| 49 | <option value="embl">EMBL</option>
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| 50 | <option value="swiss">SwissProt</option>
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| 51 | </param>
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| 52 | </inputs>
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| 53 | <outputs>
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| 54 | <data format="diffseq" name="out_file1" />
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| 55 | <data format="gff" name="out_file2" />
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| 56 | <data format="gff" name="out_file3" />
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| 57 | </outputs>
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| 58 | <code file="emboss_format_corrector.py" />
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| 59 | <help> |
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| 60 | You can view the original documentation here_. |
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| 61 | |
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| 62 | .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/diffseq.html |
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| 63 | </help> |
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| 64 | </tool> |
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