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annotate emboss_digest.xml @ 10:9b98d3d903c6 draft

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author devteam
date Fri, 12 Aug 2016 19:17:10 -0400
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10
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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
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65 ------
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66
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67 **Citation**
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68
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69 For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. &lt;http://www.ncbi.nlm.nih.gov/pubmed/10827456&gt;`_
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70
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71 If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. &lt;http://www.ncbi.nlm.nih.gov/pubmed/17568012&gt;`_
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72 </help>
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73 </tool>