[2] | 1 | <tool id="EMBOSS: digest23" name="digest" version="5.0.0">
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| 2 | <description>Protein proteolytic enzyme or reagent cleavage digest</description>
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| 3 | <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
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| 4 | <command>digest -seqall $input1 -outfile $out_file1 -menu $menu -unfavoured $unfavoured -overlap $overlap -allpartials $allpartials -rformat2 $out_format1 -auto</command>
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| 5 | <inputs>
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| 6 | <param format="data" name="input1" type="data">
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| 7 | <label>Sequence</label>
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| 8 | </param>
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| 9 | <param name="menu" type="select">
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| 10 | <label>Enzyme/Reagent</label>
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| 11 | <option value="1">Trypsin</option>
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| 12 | <option value="2">Lys-C</option>
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| 13 | <option value="3">Arg-C</option>
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| 14 | <option value="4">Asp-N</option>
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| 15 | <option value="5">V8-bicarb</option>
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| 16 | <option value="6">V8-phosph</option>
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| 17 | <option value="7">Chymotrypsin</option>
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| 18 | <option value="8">CNBr</option>
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| 19 | </param>
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| 20 | <param name="unfavoured" type="select">
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| 21 | <label>Trypsin will not normally cut after a K if it is followed by (e.g.) another K or a P. Specifying this shows those cuts, as well as the favoured ones.</label>
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| 22 | <option value="no">No</option>
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| 23 | <option value="yes">Yes</option>
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| 24 | </param>
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| 25 | <param name="overlap" type="select">
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| 26 | <label>Used for partial digestion. Shows all cuts from favoured cut sites plus 1..3, 2..4, 3..5 etc but not (e.g.) 2..5. Overlaps are therefore fragments with exactly one potential cut site
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| 27 | within it.</label>
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| 28 | <option value="no">No</option>
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| 29 | <option value="yes">Yes</option>
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| 30 | </param>
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| 31 | <param name="allpartials" type="select">
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| 32 | <label>As for overlap but fragments containing more than one potential cut site are included.</label>
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| 33 | <option value="no">No</option>
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| 34 | <option value="yes">Yes</option>
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| 35 | </param>
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| 36 | <param name="out_format1" type="select">
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| 37 | <label>Output Report File Format</label>
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| 38 | <option value="seqtable">SeqTable</option>
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| 39 | <option value="embl">EMBL</option>
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| 40 | <option value="genbank">GENBANK</option>
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| 41 | <option value="gff">GFF</option>
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| 42 | <option value="pir">PIR</option>
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| 43 | <option value="swiss">SwissProt</option>
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| 44 | <option value="dbmotif">DbMotif</option>
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| 45 | <option value="diffseq">Diffseq</option>
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| 46 | <option value="excel">Excel (tab delimited)</option>
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| 47 | <option value="feattable">FeatTable</option>
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| 48 | <option value="motif">Motif</option>
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| 49 | <option value="regions">Regions</option>
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| 50 | <option value="simple">SRS Simple</option>
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| 51 | <option value="srs">SRS</option>
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| 52 | <option value="table">Table</option>
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| 53 | <option value="tagseq">TagSeq</option>
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| 54 | </param>
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| 55 | </inputs>
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| 56 | <outputs>
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| 57 | <data format="digest" name="out_file1" />
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| 58 | </outputs>
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| 59 | <code file="emboss_format_corrector.py" />
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| 60 | <help> |
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| 61 | You can view the original documentation here_. |
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| 62 | |
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| 63 | .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/digest.html |
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| 64 | </help> |
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| 65 | </tool> |
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