Mercurial > repos > xuebing > sharplabtool
diff 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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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/emboss_5/emboss_digest.xml Fri Mar 09 19:37:19 2012 -0500 @@ -0,0 +1,65 @@ +<tool id="EMBOSS: digest23" name="digest" version="5.0.0"> + <description>Protein proteolytic enzyme or reagent cleavage digest</description> + <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> + <command>digest -seqall $input1 -outfile $out_file1 -menu $menu -unfavoured $unfavoured -overlap $overlap -allpartials $allpartials -rformat2 $out_format1 -auto</command> + <inputs> + <param format="data" name="input1" type="data"> + <label>Sequence</label> + </param> + <param name="menu" type="select"> + <label>Enzyme/Reagent</label> + <option value="1">Trypsin</option> + <option value="2">Lys-C</option> + <option value="3">Arg-C</option> + <option value="4">Asp-N</option> + <option value="5">V8-bicarb</option> + <option value="6">V8-phosph</option> + <option value="7">Chymotrypsin</option> + <option value="8">CNBr</option> + </param> + <param name="unfavoured" type="select"> + <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> + <option value="no">No</option> + <option value="yes">Yes</option> + </param> + <param name="overlap" type="select"> + <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 + within it.</label> + <option value="no">No</option> + <option value="yes">Yes</option> + </param> + <param name="allpartials" type="select"> + <label>As for overlap but fragments containing more than one potential cut site are included.</label> + <option value="no">No</option> + <option value="yes">Yes</option> + </param> + <param name="out_format1" type="select"> + <label>Output Report File Format</label> + <option value="seqtable">SeqTable</option> + <option value="embl">EMBL</option> + <option value="genbank">GENBANK</option> + <option value="gff">GFF</option> + <option value="pir">PIR</option> + <option value="swiss">SwissProt</option> + <option value="dbmotif">DbMotif</option> + <option value="diffseq">Diffseq</option> + <option value="excel">Excel (tab delimited)</option> + <option value="feattable">FeatTable</option> + <option value="motif">Motif</option> + <option value="regions">Regions</option> + <option value="simple">SRS Simple</option> + <option value="srs">SRS</option> + <option value="table">Table</option> + <option value="tagseq">TagSeq</option> + </param> + </inputs> + <outputs> + <data format="digest" name="out_file1" /> + </outputs> + <code file="emboss_format_corrector.py" /> + <help> + You can view the original documentation here_. + + .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/digest.html + </help> +</tool> \ No newline at end of file