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annotate emboss_digest.xml @ 16:33381b9c268c draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 431486be049407b094d495ae4a68bf76d27fa522
author iuc
date Mon, 28 Jan 2019 14:49:47 -0500
parents 27c43fb015f0
children 21a9fb508031
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27c43fb015f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 9844cae766e7471d9fa6b2e8356e5194e77f6753
iuc
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1 <tool id="EMBOSS: digest23" name="digest" version="@VERSION@">
11
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2 <description>Protein proteolytic enzyme or reagent cleavage digest</description>
0e2484b6829b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
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3 <macros>
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iuc
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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>
0e2484b6829b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
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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">
0e2484b6829b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
iuc
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12 <option value="1">Trypsin</option>
0e2484b6829b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
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13 <option value="2">Lys-C</option>
0e2484b6829b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
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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>
0e2484b6829b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
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17 <option value="6">V8-phosph</option>
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18 <option value="7">Chymotrypsin</option>
0e2484b6829b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
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19 <option value="8">CNBr</option>
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20 </param>
0e2484b6829b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
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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">
0e2484b6829b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
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22 <option value="no">No</option>
0e2484b6829b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
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23 <option value="yes">Yes</option>
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24 </param>
0e2484b6829b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
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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">
0e2484b6829b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
iuc
parents: 10
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26 <option value="no">No</option>
0e2484b6829b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
iuc
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27 <option value="yes">Yes</option>
0e2484b6829b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
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28 </param>
0e2484b6829b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
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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">
0e2484b6829b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
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30 <option value="no">No</option>
0e2484b6829b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
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31 <option value="yes">Yes</option>
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32 </param>
0e2484b6829b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
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33 <param name="out_format1" type="select" label="Output report file format">
0e2484b6829b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
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34 <option value="seqtable">SeqTable</option>
0e2484b6829b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
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35 <option value="embl">EMBL</option>
0e2484b6829b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
iuc
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36 <option value="genbank">GENBANK</option>
0e2484b6829b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
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37 <option value="gff">GFF</option>
0e2484b6829b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
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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>
0e2484b6829b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
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41 <option value="diffseq">Diffseq</option>
0e2484b6829b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
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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>
10
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55 <help>
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56 You can view the original documentation here_.
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57
11
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58 .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/digest.html
10
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59 </help>
11
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60 <expand macro="citations" />
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61 </tool>