Mercurial > repos > xuebing > sharplabtool
comparison tools/emboss_5/emboss_digest.xml @ 0:9071e359b9a3
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| author | xuebing |
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| date | Fri, 09 Mar 2012 19:37:19 -0500 |
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| -1:000000000000 | 0:9071e359b9a3 |
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| 1 <tool id="EMBOSS: digest23" name="digest" version="5.0.0"> | |
| 2 <description>Protein proteolytic enzyme or reagent cleavage digest</description> | |
| 3 <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> | |
| 4 <command>digest -seqall $input1 -outfile $out_file1 -menu $menu -unfavoured $unfavoured -overlap $overlap -allpartials $allpartials -rformat2 $out_format1 -auto</command> | |
| 5 <inputs> | |
| 6 <param format="data" name="input1" type="data"> | |
| 7 <label>Sequence</label> | |
| 8 </param> | |
| 9 <param name="menu" type="select"> | |
| 10 <label>Enzyme/Reagent</label> | |
| 11 <option value="1">Trypsin</option> | |
| 12 <option value="2">Lys-C</option> | |
| 13 <option value="3">Arg-C</option> | |
| 14 <option value="4">Asp-N</option> | |
| 15 <option value="5">V8-bicarb</option> | |
| 16 <option value="6">V8-phosph</option> | |
| 17 <option value="7">Chymotrypsin</option> | |
| 18 <option value="8">CNBr</option> | |
| 19 </param> | |
| 20 <param name="unfavoured" type="select"> | |
| 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> | |
| 22 <option value="no">No</option> | |
| 23 <option value="yes">Yes</option> | |
| 24 </param> | |
| 25 <param name="overlap" type="select"> | |
| 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 | |
| 27 within it.</label> | |
| 28 <option value="no">No</option> | |
| 29 <option value="yes">Yes</option> | |
| 30 </param> | |
| 31 <param name="allpartials" type="select"> | |
| 32 <label>As for overlap but fragments containing more than one potential cut site are included.</label> | |
| 33 <option value="no">No</option> | |
| 34 <option value="yes">Yes</option> | |
| 35 </param> | |
| 36 <param name="out_format1" type="select"> | |
| 37 <label>Output Report File Format</label> | |
| 38 <option value="seqtable">SeqTable</option> | |
| 39 <option value="embl">EMBL</option> | |
| 40 <option value="genbank">GENBANK</option> | |
| 41 <option value="gff">GFF</option> | |
| 42 <option value="pir">PIR</option> | |
| 43 <option value="swiss">SwissProt</option> | |
| 44 <option value="dbmotif">DbMotif</option> | |
| 45 <option value="diffseq">Diffseq</option> | |
| 46 <option value="excel">Excel (tab delimited)</option> | |
| 47 <option value="feattable">FeatTable</option> | |
| 48 <option value="motif">Motif</option> | |
| 49 <option value="regions">Regions</option> | |
| 50 <option value="simple">SRS Simple</option> | |
| 51 <option value="srs">SRS</option> | |
| 52 <option value="table">Table</option> | |
| 53 <option value="tagseq">TagSeq</option> | |
| 54 </param> | |
| 55 </inputs> | |
| 56 <outputs> | |
| 57 <data format="digest" name="out_file1" /> | |
| 58 </outputs> | |
| 59 <code file="emboss_format_corrector.py" /> | |
| 60 <help> | |
| 61 You can view the original documentation here_. | |
| 62 | |
| 63 .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/digest.html | |
| 64 </help> | |
| 65 </tool> |