Mercurial > repos > iuc > optdoe

annotate optdoe.xml @ 1:635ec9d1326f draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit 381e8b82419e6002c74849cc37f924bc8296b0b1
author iuc
date Fri, 10 Feb 2023 15:04:42 +0000
parents 8791140662dc
children
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8791140662dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
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1 <tool id="optdoe" name="Optimal Design of Experiment" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.09">
8791140662dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
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2 <description>Combine selected genetic parts and enzyme variants for the desired pathways</description>
8791140662dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
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3 <macros>
8791140662dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
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4 <token name="@VERSION_SUFFIX@">0</token>
1
635ec9d1326f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit 381e8b82419e6002c74849cc37f924bc8296b0b1
iuc
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5 <token name="@TOOL_VERSION@">v2.0.2</token>
0
8791140662dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
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6 </macros>
8791140662dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
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7 <requirements>
8791140662dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
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8 <requirement type="package" version="@TOOL_VERSION@">doebase</requirement>
8791140662dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
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9 </requirements>
8791140662dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
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10 <command detect_errors="exit_code"><![CDATA[
8791140662dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
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11 python -m doebase
8791140662dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
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12 --func doeGetSBOL
8791140662dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
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13 #if $adv.genes_sbol_file
8791140662dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
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14 --sbol_file '$adv.genes_sbol_file'
8791140662dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
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15 #end if
8791140662dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
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16 #if $adv.ref_parts_file
8791140662dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
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17 --ref_parts_file '$adv.ref_parts_file'
8791140662dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
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18 #end if
8791140662dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
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19 --libsize '$adv.libsize'
8791140662dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
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20 $adv.get_sequences
8791140662dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
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21 $adv.backtranslate
8791140662dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
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22 --codon_table '$adv.codon_table'
8791140662dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
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23 '$genes_file'
8791140662dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
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24 '$constructs'
8791140662dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
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25 ]]></command>
8791140662dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
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26 <inputs>
8791140662dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
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27 <param name="genes_file" type="data" format="csv" label="Genes" help="CSV file with header: Name,Type,Part,Step. Provided by the tool Selenzyme"/>
8791140662dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
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28 <section name="adv" title="Advanced Options" expanded="false">
8791140662dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
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29 <param name="genes_sbol_file" type="data" format="xml" optional="true" label="Optimised Genes" help="SBOL file with genes associated with different RBS. Provided by the tool PartsGenie"/>
8791140662dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
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30 <param argument="--ref_parts_file" type="data" format="csv" value="None" optional="true" label="Ref Parts (default: E. coli compliant)" help="Provide fixed parts"/>
8791140662dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
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31 <param argument="--libsize" type="integer" value="32" min="32" label="Maximal library size" help="Maximal number of contructs in the output"/>
8791140662dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
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32 <param argument="--get_sequences" type="boolean" truevalue="--get_sequences true" falsevalue="--get_sequences false" checked="true" label="Get sequences" help="Grab the sequence for each part of the SBOL output"/>
8791140662dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
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33 <param argument="--backtranslate" type="boolean" truevalue="--backtranslate true" falsevalue="--backtranslate false" checked="true" label="Back translate" help="Translate the protein sequence given by its Uniprot ID to a DNA sequence"/>
8791140662dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
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34 <param argument="--codon_table" type="select" label="Codon Table">
8791140662dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
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35 <option value="Eecoli.cut">Escherichia coli K12</option>
8791140662dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
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36 <option value="Ehuman.cut">Homo sapiens</option>
8791140662dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
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37 <option value="Eacica.cut">Acinetobacter calcoaceticus</option>
8791140662dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
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38 <option value="Eagrtu.cut">Agrobacterium tumefaciens str C58</option>
8791140662dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
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39 <option value="Eanasp.cut">Anabaena sp</option>
8791140662dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
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40 <option value="Earath.cut">Arabidopsis thaliana</option>
8791140662dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
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41 <option value="Eazovi.cut">Azotobacter vinelandii</option>
8791140662dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
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42 <option value="Ebacme.cut">Bacillus megaterium</option>
8791140662dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
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43 <option value="Ebacst.cut">Geobacillus stearothermophilus</option>
8791140662dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
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44 <option value="Ebacsu.cut">Bacillus subtilis</option>
8791140662dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
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45 <option value="Ebacsu_high.cut">Bacillus subtilis (high)</option>
8791140662dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
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46 <option value="Ebommo.cut">Bombyx mori (silkmoth)</option>
8791140662dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
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47 <option value="Ebovin.cut">Bos taurus</option>
8791140662dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
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48 <option value="Ebpphx.cut">Bacteriophage phi-X174</option>
8791140662dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
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49 <option value="Ebraja.cut">Bradyrhizobium japonicum USDA 110</option>
8791140662dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
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50 <option value="Ebrana.cut">Brassica napus (rape)</option>
8791140662dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
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51 <option value="Ebrare.cut">Brachydanio rerio (zebrafish)</option>
8791140662dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
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52 <option value="Ecaeel.cut">Caenorhabditis elegans (nematode)</option>
8791140662dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
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53 <option value="Ecanal.cut">Candida albicans</option>
8791140662dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
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54 <option value="Ecanfa.cut">Canis familiaris (dog)</option>
8791140662dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
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55 <option value="Ecaucr.cut">Caulobacter crescentus CB15</option>
8791140662dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
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56 <option value="Echick.cut">Gallus gallus (chicken)</option>
8791140662dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
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57 <option value="Echlre.cut">Chlamydomonas reinhardtii</option>
8791140662dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
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58 <option value="Echltr.cut">Chlamydia trachomatis D UW-3 CX</option>
8791140662dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
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59 <option value="Ecloab.cut">Clostridium acetobutylicum ATCC 824</option>
8791140662dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
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60 <option value="Ecrigr.cut">Cricetulus greseus (hamster)</option>
8791140662dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
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61 <option value="Ecyapa.cut">Cyanophora paradoxa</option>
8791140662dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
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62 <option value="Edicdi.cut">Dictyostelium discoideum</option>
8791140662dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
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63 <option value="Edicdi_high.cut">Dictyostelium discoideum (high)</option>
8791140662dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
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64 <option value="Edrome.cut">Drosophila melanogaster</option>
8791140662dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
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65 <option value="Edrome_high.cut">Drosophila melanogaster (high)</option>
8791140662dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
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66 <option value="Eecoli_high.cut">Escherichia coli K12 (high)</option>
8791140662dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
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67 <option value="Eemeni.cut">Emericella nidulans</option>
8791140662dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
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68 <option value="Eemeni_mit.cut">Emericella nidulans mitochondrion</option>
8791140662dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
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69 <option value="Eemeni_high.cut">Emericella nidulans highly expressed</option>
8791140662dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
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70 <option value="Eerwct.cut">Erwinia carotovora subsp atroseptica SCRI1043</option>
8791140662dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
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71 <option value="Ehaein.cut">Haemophilus influenzae Rd KW20</option>
8791140662dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
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72 <option value="Ehalma.cut">Haloarcula marismortui ATCC 43049 (Halobacterium marismortui)</option>
8791140662dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
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73 <option value="Ehalsa.cut">Halobacterium salinarum NRC-1 (Halobacterium halobium)</option>
8791140662dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
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74 <option value="Ehorvu.cut">Hordeum vulgare subsp vulgare (Barley)</option>
8791140662dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
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75 <option value="Eklepn.cut">Klebsiella pneumoniae</option>
8791140662dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
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76 <option value="Eklula.cut">Kluyveromyces lactis NRRL Y-1140</option>
8791140662dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
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77 <option value="Elacdl.cut">Lactococcus lactis subsp lactis Il1403 L. delbrueckii subsp lactis</option>
8791140662dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
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78 <option value="Elyces.cut">Lycopersicon esculentum (tomato)</option>
8791140662dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
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79 <option value="Emacfa.cut">Macaca fascicularis</option>
8791140662dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
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80 <option value="Emaize.cut">Zea mays</option>
8791140662dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
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diff changeset
81 <option value="Emaize_chl.cut">Zea mays chloroplast</option>
8791140662dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
82 <option value="Emammal_high.cut">Mammalian species (high)</option>
8791140662dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
83 <option value="Emanse.cut">Manduca sexta</option>
8791140662dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
84 <option value="Emarpo_chl.cut">Marchantia polymorpha chloroplast (liverwort)</option>
8791140662dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
85 <option value="Emedsa.cut">Medicago sativa</option>
8791140662dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
86 <option value="Emetth.cut">Methanothermobacter thermautotrophicus str Delta H</option>
8791140662dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
87 <option value="Emouse.cut">Mus musculus</option>
8791140662dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
88 <option value="Emyctu.cut">Mycobacterium tuberculosis H37Rv</option>
8791140662dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
89 <option value="Eneigo.cut">Neisseria gonorrhoeae</option>
8791140662dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
90 <option value="Eneucr.cut">Neurospora crassa</option>
8791140662dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
91 <option value="Eoncmy.cut">Oncorhynchus mykiss (rainbow trout)</option>
8791140662dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
92 <option value="Eorysa.cut">Oryza sativa (rice)</option>
8791140662dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
93 <option value="Eorysa_chl.cut">Oryza sativa chloroplast (rice)</option>
8791140662dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
94 <option value="Epea.cut">Pisum sativum (pea)</option>
8791140662dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
95 <option value="Epethy.cut">Petunia x hybrida</option>
8791140662dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
96 <option value="Ephavu.cut">Phaseolus vulgaris</option>
8791140662dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
97 <option value="Epig.cut">Sus scrofa (pig)</option>
8791140662dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
98 <option value="Eplafa.cut">Plasmodium falciparum 3D7</option>
8791140662dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
99 <option value="Eprovu.cut">Proteus vulgaris</option>
8791140662dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
100 <option value="Epseae.cut">Pseudomonas aeruginosa PAO1</option>
8791140662dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
101 <option value="Epsepu.cut">Pseudomonas putida KT2440</option>
8791140662dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
102 <option value="Epsesm.cut">Pseudomonas syringae pv tomato str DC3000</option>
8791140662dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
103 <option value="Erabit.cut">Oryctolagus cuniculus (rabbit)</option>
8791140662dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
104 <option value="Erat.cut">Rattus norvegicus</option>
8791140662dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
105 <option value="Erhile.cut">Rhizobium leguminosarum</option>
8791140662dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
106 <option value="Erhime.cut">Sinorhizobium meliloti 1021</option>
8791140662dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
107 <option value="Erhoca.cut">Rhodobacter capsulatus</option>
8791140662dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
108 <option value="Erhosh.cut">Rhodobacter sphaeroides</option>
8791140662dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
109 <option value="Esalsa.cut">Salmo salar (Atlantic salmon)</option>
8791140662dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
110 <option value="Esalty.cut">Salmonella typhimurium LT2</option>
8791140662dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
111 <option value="Eschma.cut">Schistosoma mansoni</option>
8791140662dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
112 <option value="Eschpo.cut">Schizosaccharomyces pombe</option>
8791140662dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
113 <option value="Eschpo_cai.cut">Schizosaccharomyces pombe (CAI equivalent)</option>
8791140662dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
114 <option value="Eschpo_high.cut">Schizosaccharomyces pombe (high)</option>
8791140662dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
115 <option value="Eserma.cut">Serratia marcescens</option>
8791140662dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
116 <option value="Esheep.cut">Ovis aries (sheep)</option>
8791140662dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
117 <option value="Esoltu.cut">Solanum tuberosum (potato)</option>
8791140662dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
118 <option value="Esoybn.cut">Glycine max (soybean)</option>
8791140662dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
119 <option value="Espiol.cut">Spinacia oleracea (spinach)</option>
8791140662dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
120 <option value="Estaau.cut">Staphylococcus aureus</option>
8791140662dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
121 <option value="Estrco.cut">Streptomyces coelicolor A3 2</option>
8791140662dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
122 <option value="Estrmu.cut">Streptococcus mutans UA159</option>
8791140662dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
123 <option value="Estrpn.cut">Streptococcus pneumoniae R6</option>
8791140662dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
124 <option value="Estrpu.cut">Strongylocentrotus purpuratus (sea urchin)</option>
8791140662dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
125 <option value="Esv40.cut">Simian Virus 40</option>
8791140662dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
126 <option value="Esynco.cut">Synechococcus sp WH 8102</option>
8791140662dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
127 <option value="Esyncy.cut">Synechocystis sp PCC 6803</option>
8791140662dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
128 <option value="Etetth.cut">Tetrahymena thermophila</option>
8791140662dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
129 <option value="Etheth.cut">Thermus thermophilus HB8</option>
8791140662dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
130 <option value="Etobac.cut">Nicotiana tabacum (tobacco)</option>
8791140662dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
131 <option value="Etobac_chl.cut">Nicotiana tabacum chloroplast (tobacco)</option>
8791140662dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
132 <option value="Etrybr.cut">Trypanosoma brucei</option>
8791140662dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
133 <option value="Etrycr.cut">Trypanosoma cruzi</option>
8791140662dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
134 <option value="Evibch.cut">Vibrio cholerae O1 biovar eltor str N16961</option>
8791140662dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
135 <option value="Ewheat.cut">Triticum aestivum (wheat)</option>
8791140662dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
136 <option value="Exenla.cut">Xenopus laevis</option>
8791140662dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
137 <option value="Eyeast.cut">Saccharomyces cerevisiae</option>
8791140662dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
138 <option value="Eyeast_cai.cut">Saccharomyces cerevisiae original CAI set</option>
8791140662dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
139 <option value="Eyeast_high.cut">Saccharomyces cerevisiae (high)</option>
8791140662dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
140 <option value="Eyeast_mit.cut">Saccharomyces cerevisiae mitochondrion</option>
8791140662dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
141 <option value="Eyeren.cut">Yersinia enterocolitica</option>
8791140662dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
142 </param>
8791140662dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
143 </section>
8791140662dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
144 </inputs>
8791140662dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
145 <outputs>
8791140662dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
146 <data name="constructs" format="xml" label="Constructs" />
8791140662dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
147 </outputs>
8791140662dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
148 <tests>
8791140662dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
149 <test>
8791140662dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
150 <!-- test 1: check if identical outputs are produced with default parameters -->
8791140662dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
151 <param name="genes_file" value="genes_lycopene.csv" />
8791140662dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
152 <output name="constructs" >
8791140662dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
153 <assert_contents>
8791140662dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
154 <is_valid_xml />
8791140662dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
155 <has_text text='rdf:RDF xmlns:owl="http://www.w3.org/2002/07/owl#" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" xmlns:xsd="http://www.w3.org/2001/XMLSchema#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:prov="http://www.w3.org/ns/prov#" xmlns:sbol="http://sbols.org/v2#" xmlns:xsd1="http://www.w3.org/2001/XMLSchema#dateTime/" xmlns:om="http://www.ontology-of-units-of-measure.org/resource/om-2/" xmlns:synbiohub="http://synbiohub.org#" xmlns:sbh="http://wiki.synbiohub.org/wiki/Terms/synbiohub#" xmlns:sybio="http://www.sybio.ncl.ac.uk#" xmlns:ncbi="http://www.ncbi.nlm.nih.gov#" xmlns:igem="http://wiki.synbiohub.org/wiki/Terms/igem#" xmlns:genbank="http://www.ncbi.nlm.nih.gov/genbank#" xmlns:gbconv="http://sbols.org/genBankConversion#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:obo="http://purl.obolibrary.org/obo/"'/>
8791140662dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
156 </assert_contents>
8791140662dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
157 </output>
8791140662dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
158 </test>
8791140662dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
159 </tests>
8791140662dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
160 <help><![CDATA[
8791140662dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
161 OptDoE
8791140662dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
diff changeset
162 ===========
8791140662dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit ef03bd3baa194ea25b29a8e87d0cb0faab56f913
iuc
parents:
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163
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164 An optimal design of experiments is performed by using OptBioDes based on logistic regression analysis with an assumed linear model for the response. The design is evaluated by its D-efficiency, defined as:
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166 .. math:: D_{eff} = \frac{1}{n}\abs{X^{T}X}^{\frac{1}{p}}
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168 |
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169
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170 Where n is the number of experimental runs or library size, p is the number of independent variables, and X is the model matrix, i.e., a row for each experimental run and a column for each term in the model. The library size n can be selected and should be above a minimal threshold depending on the number of combinatorial complexity of the library.
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171 The experimental design can be evaluated through the provided diagnostics for D-efficiency, power analysis, and relative prediction variance, allowing the optimal selection of library size.
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172 The resulting design is provided as an SBOL collection containing the definition of each DNA component and the combinatorial library of constructs.
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173
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174 .. image:: https://raw.githubusercontent.com/brsynth/synbiocad-galaxy-wrappers/master/optdoe/img/image3.png
0
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175 :width: 80 %
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176 :align: center
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178
1
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179 .. image:: https://raw.githubusercontent.com/brsynth/synbiocad-galaxy-wrappers/master/optdoe/img/image46.png
0
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180 :width: 80 %
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181 :align: center
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182
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183 |
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184
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185 Above are examples of two constructs generated through optimal combinatorial design and represented using SBOL Visual in SynBioHub.
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186 Note: if advanced parameter "input_parts" is left empty, the following parts are used:
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187
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188
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189 +---------+------------+--------------------------------------------------+
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190 | Name | Type | SynBioHub |
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191 +=========+============+==================================================+
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192 | PlacUV5 | Promoter | https://synbiohub.org/public/igem/BBa_K1847014/1 |
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193 +---------+------------+--------------------------------------------------+
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194 | Ptrc | Promoter | https://synbiohub.org/public/igem/BBa_J56012/1 |
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195 +---------+------------+--------------------------------------------------+
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196 | BBR1 | Origin | https://synbiohub.org/public/igem/BBa_I50041/1 |
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197 +---------+------------+--------------------------------------------------+
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198 | p15A | Origin | https://synbiohub.org/public/igem/BBa_I50032/1 |
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199 +---------+------------+--------------------------------------------------+
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200 | ColE1 | Origin | https://synbiohub.org/public/igem/BBa_J64101/1 |
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201 +---------+------------+--------------------------------------------------+
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202 | res1 | Resistance | https://synbiohub.org/public/igem/BBa_I13800/1 |
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203 +---------+------------+--------------------------------------------------+
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204 | Ter | Terminator | https://synbiohub.org/public/igem/BBa_B1006/1 |
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205 +---------+------------+--------------------------------------------------+
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206
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207 The source of this file can be found here as a model: https://raw.githubusercontent.com/pablocarb/doebase/master/doebase/data/ref_parts.csv
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208
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209 Input
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210 -----
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211
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212 Required:
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213
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214 * **Genes**\ : Output of Selenzyme. The CSV file contains four columnds: Name,Type,Part,Step. The column "Name" contains the Uniprot ID found by Selenzyme. The column "Type" represents the type of the "Part", a *gene*. The column "Part" has the same information as the column "Name". The column "Step" contains the order of the position in the pathway of the gene.
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215
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216 Advanced options:
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217
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218 * **Optimised Genes**\ : SBOL file containing optimized versions of the genes associated with different RBS. Output of the PartsGenie tool.
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219 * **Ref Parts**\ : CSV with the genetic parts. Default (if left empty) is the above table. To generate a new compatible CSV file, please use the "OptDoE Parts Reference Generator" tool
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220 * **Maximal library size**\ : (integer, default: 32) Maximal number of constructs in the SBOL output.
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221 * **Get sequences**\ : (boolean, default: True) Grab the sequence for each part of the SBOL output.
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222 * **Back translate**\ : (boolean, default: True) Translate the protein sequence given by its Uniprot ID to a DNA sequence.
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223 * **Codon Table**\ : (text, default: Eecoli.cut) Codon Usage Table. See `codon_table <https://www.ebi.ac.uk/seqdb/confluence/display/JDSAT/EMBOSS+backtranseq+Help+and+Documentation#EMBOSSbacktranseqHelpandDocumentation-WebServices>`_ for more codons.
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224
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225 Output
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226 ------
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227
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228 * **Constructs**\ : Output SBOL file. It contains some combinations of constructs according to the algorithm described above.
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229
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230 Project Link
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231 ------------
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232
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233 * `Original Project <https://github.com/pablocarb/doebase>`_
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234
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235 License
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236 -------
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237
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238 `MIT <https://raw.githubusercontent.com/pablocarb/appoptdes/master/LICENSE>`_
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239
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240 Acknowledgments
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241 ---------------
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242
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243 * Joan Hérisson
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244 * Thomas Duigou
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245 ]]></help>
1
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246 <citations>
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247 <citation type="bibtex">
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248 @unpublished{pablocarb
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249 author = {Pablo Carbonell},
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250 title = {{doebase}},
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251 url = {https://github.com/pablocarb/doebase/},
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252 }
635ec9d1326f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit 381e8b82419e6002c74849cc37f924bc8296b0b1
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253 </citation>
635ec9d1326f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit 381e8b82419e6002c74849cc37f924bc8296b0b1
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254 </citations>
635ec9d1326f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe commit 381e8b82419e6002c74849cc37f924bc8296b0b1
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255 </tool>