annotate emboss_digest.xml @ 18:63dd26468588 draft default tip

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 18de4aa9ba00124b1b3e3afe14219e46931e58a9"
author iuc
date Fri, 09 Jul 2021 18:36:34 +0000
parents 8992d258e42f
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8992d258e42f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 9844cae766e7471d9fa6b2e8356e5194e77f6753
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1 <tool id="EMBOSS: digest23" name="digest" version="@VERSION@">
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2 <description>Protein proteolytic enzyme or reagent cleavage digest</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements" />
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7 <code file="emboss_format_corrector.py" />
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8 <command>digest -seqall '$input1' -outfile '$out_file1' -menu $menu -unfavoured $unfavoured -overlap $overlap -allpartials $allpartials -rformat2 $out_format1 -auto</command>
d49956b87f7e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
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9 <inputs>
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10 <param name="input1" type="data" format="data" label="Sequence" />
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11 <param name="menu" type="select" label="Enzyme/Reagent">
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12 <option value="1">Trypsin</option>
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13 <option value="2">Lys-C</option>
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14 <option value="3">Arg-C</option>
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15 <option value="4">Asp-N</option>
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16 <option value="5">V8-bicarb</option>
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17 <option value="6">V8-phosph</option>
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18 <option value="7">Chymotrypsin</option>
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19 <option value="8">CNBr</option>
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20 </param>
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21 <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">
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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" 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">
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26 <option value="no">No</option>
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27 <option value="yes">Yes</option>
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28 </param>
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29 <param name="allpartials" type="select" label="As for overlap but fragments containing more than one potential cut site are included">
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30 <option value="no">No</option>
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31 <option value="yes">Yes</option>
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32 </param>
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33 <param name="out_format1" type="select" label="Output report file format">
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34 <option value="seqtable">SeqTable</option>
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35 <option value="embl">EMBL</option>
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36 <option value="genbank">GENBANK</option>
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37 <option value="gff">GFF</option>
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38 <option value="pir">PIR</option>
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39 <option value="swiss">SwissProt</option>
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40 <option value="dbmotif">DbMotif</option>
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41 <option value="diffseq">Diffseq</option>
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42 <option value="excel">Excel (tab delimited)</option>
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43 <option value="feattable">FeatTable</option>
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44 <option value="motif">Motif</option>
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45 <option value="regions">Regions</option>
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46 <option value="simple">SRS Simple</option>
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47 <option value="srs">SRS</option>
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48 <option value="table">Table</option>
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49 <option value="tagseq">TagSeq</option>
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50 </param>
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51 </inputs>
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52 <outputs>
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53 <data name="out_file1" format="digest" />
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54 </outputs>
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55 <help>
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56 You can view the original documentation here_.
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57
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58 .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/digest.html
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59 </help>
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60 <expand macro="citations" />
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61 </tool>