Mercurial > repos > tduigou > doe_synbio_optdoe
annotate optdoe.xml @ 2:8376287c2c02 draft
planemo upload for repository ['https://github.com/brsynth/icfree-ml', 'https://github.com/pablocarb/doebase'] commit 1e01b679611d980f87089184e7d8a538b96d68c7
author | tduigou |
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date | Tue, 30 May 2023 21:02:09 +0000 |
parents | e56802e12fea |
children | 645d10db2819 |
rev | line source |
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planemo upload for repository ['https://github.com/brsynth/icfree-ml', 'https://github.com/pablocarb/doebase'] commit 6c01728900e4ebd1a833a7e7d697f61561d86dc6-dirty
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1 <tool id="doe_synbio_optdoe" name="Optimal Design of Experiment" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" license="@LICENCE@"> |
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2 <description>Combine selected genetic parts and enzyme variants for the desired pathways</description> |
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3 <macros> |
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4 <import>macros.xml</import> |
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5 <token name="@TOOL_VERSION@">v2.0.2</token> |
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6 </macros> |
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7 <requirements> |
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8 <requirement type="package" version="@TOOL_VERSION@">doebase</requirement> |
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9 </requirements> |
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10 <expand macro="stdio"/> |
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11 <command detect_errors="exit_code"><![CDATA[ |
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12 python -m doebase |
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13 --func doeGetSBOL |
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14 #if $adv.genes_sbol_file |
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15 --sbol_file '$adv.genes_sbol_file' |
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16 #end if |
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17 #if $adv.ref_parts_file |
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18 --ref_parts_file '$adv.ref_parts_file' |
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19 #end if |
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20 --libsize '$adv.libsize' |
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21 $adv.get_sequences |
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22 $adv.backtranslate |
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23 --codon_table '$adv.codon_table' |
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24 '$genes_file' |
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25 '$constructs' |
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26 ]]></command> |
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27 <inputs> |
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28 <param name="genes_file" type="data" format="csv" label="Genes" help="CSV file with header: Name,Type,Part,Step. Provided by the tool Selenzyme"/> |
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29 <section name="adv" title="Advanced Options" expanded="false"> |
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30 <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"/> |
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31 <param argument="--ref_parts_file" type="data" format="csv" value="None" optional="true" label="Ref Parts (default: E. coli compliant)" help="Provide fixed parts"/> |
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32 <param argument="--libsize" type="integer" value="32" min="32" label="Maximal library size" help="Maximal number of contructs in the output"/> |
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33 <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"/> |
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34 <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"/> |
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35 <param argument="--codon_table" type="select" label="Codon Table"> |
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36 <option value="Eecoli.cut">Escherichia coli K12</option> |
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37 <option value="Ehuman.cut">Homo sapiens</option> |
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38 <option value="Eacica.cut">Acinetobacter calcoaceticus</option> |
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39 <option value="Eagrtu.cut">Agrobacterium tumefaciens str C58</option> |
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40 <option value="Eanasp.cut">Anabaena sp</option> |
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41 <option value="Earath.cut">Arabidopsis thaliana</option> |
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42 <option value="Eazovi.cut">Azotobacter vinelandii</option> |
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43 <option value="Ebacme.cut">Bacillus megaterium</option> |
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44 <option value="Ebacst.cut">Geobacillus stearothermophilus</option> |
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45 <option value="Ebacsu.cut">Bacillus subtilis</option> |
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46 <option value="Ebacsu_high.cut">Bacillus subtilis (high)</option> |
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47 <option value="Ebommo.cut">Bombyx mori (silkmoth)</option> |
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48 <option value="Ebovin.cut">Bos taurus</option> |
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49 <option value="Ebpphx.cut">Bacteriophage phi-X174</option> |
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50 <option value="Ebraja.cut">Bradyrhizobium japonicum USDA 110</option> |
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51 <option value="Ebrana.cut">Brassica napus (rape)</option> |
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52 <option value="Ebrare.cut">Brachydanio rerio (zebrafish)</option> |
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53 <option value="Ecaeel.cut">Caenorhabditis elegans (nematode)</option> |
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54 <option value="Ecanal.cut">Candida albicans</option> |
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55 <option value="Ecanfa.cut">Canis familiaris (dog)</option> |
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56 <option value="Ecaucr.cut">Caulobacter crescentus CB15</option> |
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57 <option value="Echick.cut">Gallus gallus (chicken)</option> |
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58 <option value="Echlre.cut">Chlamydomonas reinhardtii</option> |
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59 <option value="Echltr.cut">Chlamydia trachomatis D UW-3 CX</option> |
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60 <option value="Ecloab.cut">Clostridium acetobutylicum ATCC 824</option> |
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61 <option value="Ecrigr.cut">Cricetulus greseus (hamster)</option> |
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62 <option value="Ecyapa.cut">Cyanophora paradoxa</option> |
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63 <option value="Edicdi.cut">Dictyostelium discoideum</option> |
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64 <option value="Edicdi_high.cut">Dictyostelium discoideum (high)</option> |
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65 <option value="Edrome.cut">Drosophila melanogaster</option> |
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66 <option value="Edrome_high.cut">Drosophila melanogaster (high)</option> |
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67 <option value="Eecoli_high.cut">Escherichia coli K12 (high)</option> |
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68 <option value="Eemeni.cut">Emericella nidulans</option> |
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69 <option value="Eemeni_mit.cut">Emericella nidulans mitochondrion</option> |
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planemo upload for repository ['https://github.com/brsynth/icfree-ml', 'https://github.com/pablocarb/doebase'] commit 6c01728900e4ebd1a833a7e7d697f61561d86dc6-dirty
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70 <option value="Eemeni_high.cut">Emericella nidulans highly expressed</option> |
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planemo upload for repository ['https://github.com/brsynth/icfree-ml', 'https://github.com/pablocarb/doebase'] commit 6c01728900e4ebd1a833a7e7d697f61561d86dc6-dirty
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71 <option value="Eerwct.cut">Erwinia carotovora subsp atroseptica SCRI1043</option> |
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72 <option value="Ehaein.cut">Haemophilus influenzae Rd KW20</option> |
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planemo upload for repository ['https://github.com/brsynth/icfree-ml', 'https://github.com/pablocarb/doebase'] commit 6c01728900e4ebd1a833a7e7d697f61561d86dc6-dirty
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73 <option value="Ehalma.cut">Haloarcula marismortui ATCC 43049 (Halobacterium marismortui)</option> |
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74 <option value="Ehalsa.cut">Halobacterium salinarum NRC-1 (Halobacterium halobium)</option> |
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planemo upload for repository ['https://github.com/brsynth/icfree-ml', 'https://github.com/pablocarb/doebase'] commit 6c01728900e4ebd1a833a7e7d697f61561d86dc6-dirty
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75 <option value="Ehorvu.cut">Hordeum vulgare subsp vulgare (Barley)</option> |
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planemo upload for repository ['https://github.com/brsynth/icfree-ml', 'https://github.com/pablocarb/doebase'] commit 6c01728900e4ebd1a833a7e7d697f61561d86dc6-dirty
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76 <option value="Eklepn.cut">Klebsiella pneumoniae</option> |
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77 <option value="Eklula.cut">Kluyveromyces lactis NRRL Y-1140</option> |
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planemo upload for repository ['https://github.com/brsynth/icfree-ml', 'https://github.com/pablocarb/doebase'] commit 6c01728900e4ebd1a833a7e7d697f61561d86dc6-dirty
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78 <option value="Elacdl.cut">Lactococcus lactis subsp lactis Il1403 L. delbrueckii subsp lactis</option> |
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planemo upload for repository ['https://github.com/brsynth/icfree-ml', 'https://github.com/pablocarb/doebase'] commit 6c01728900e4ebd1a833a7e7d697f61561d86dc6-dirty
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79 <option value="Elyces.cut">Lycopersicon esculentum (tomato)</option> |
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80 <option value="Emacfa.cut">Macaca fascicularis</option> |
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81 <option value="Emaize.cut">Zea mays</option> |
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82 <option value="Emaize_chl.cut">Zea mays chloroplast</option> |
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planemo upload for repository ['https://github.com/brsynth/icfree-ml', 'https://github.com/pablocarb/doebase'] commit 6c01728900e4ebd1a833a7e7d697f61561d86dc6-dirty
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83 <option value="Emammal_high.cut">Mammalian species (high)</option> |
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84 <option value="Emanse.cut">Manduca sexta</option> |
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85 <option value="Emarpo_chl.cut">Marchantia polymorpha chloroplast (liverwort)</option> |
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86 <option value="Emedsa.cut">Medicago sativa</option> |
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87 <option value="Emetth.cut">Methanothermobacter thermautotrophicus str Delta H</option> |
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88 <option value="Emouse.cut">Mus musculus</option> |
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planemo upload for repository ['https://github.com/brsynth/icfree-ml', 'https://github.com/pablocarb/doebase'] commit 6c01728900e4ebd1a833a7e7d697f61561d86dc6-dirty
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89 <option value="Emyctu.cut">Mycobacterium tuberculosis H37Rv</option> |
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planemo upload for repository ['https://github.com/brsynth/icfree-ml', 'https://github.com/pablocarb/doebase'] commit 6c01728900e4ebd1a833a7e7d697f61561d86dc6-dirty
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90 <option value="Eneigo.cut">Neisseria gonorrhoeae</option> |
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planemo upload for repository ['https://github.com/brsynth/icfree-ml', 'https://github.com/pablocarb/doebase'] commit 6c01728900e4ebd1a833a7e7d697f61561d86dc6-dirty
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91 <option value="Eneucr.cut">Neurospora crassa</option> |
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planemo upload for repository ['https://github.com/brsynth/icfree-ml', 'https://github.com/pablocarb/doebase'] commit 6c01728900e4ebd1a833a7e7d697f61561d86dc6-dirty
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92 <option value="Eoncmy.cut">Oncorhynchus mykiss (rainbow trout)</option> |
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93 <option value="Eorysa.cut">Oryza sativa (rice)</option> |
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94 <option value="Eorysa_chl.cut">Oryza sativa chloroplast (rice)</option> |
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95 <option value="Epea.cut">Pisum sativum (pea)</option> |
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planemo upload for repository ['https://github.com/brsynth/icfree-ml', 'https://github.com/pablocarb/doebase'] commit 6c01728900e4ebd1a833a7e7d697f61561d86dc6-dirty
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96 <option value="Epethy.cut">Petunia x hybrida</option> |
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97 <option value="Ephavu.cut">Phaseolus vulgaris</option> |
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98 <option value="Epig.cut">Sus scrofa (pig)</option> |
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99 <option value="Eplafa.cut">Plasmodium falciparum 3D7</option> |
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planemo upload for repository ['https://github.com/brsynth/icfree-ml', 'https://github.com/pablocarb/doebase'] commit 6c01728900e4ebd1a833a7e7d697f61561d86dc6-dirty
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100 <option value="Eprovu.cut">Proteus vulgaris</option> |
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planemo upload for repository ['https://github.com/brsynth/icfree-ml', 'https://github.com/pablocarb/doebase'] commit 6c01728900e4ebd1a833a7e7d697f61561d86dc6-dirty
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101 <option value="Epseae.cut">Pseudomonas aeruginosa PAO1</option> |
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102 <option value="Epsepu.cut">Pseudomonas putida KT2440</option> |
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planemo upload for repository ['https://github.com/brsynth/icfree-ml', 'https://github.com/pablocarb/doebase'] commit 6c01728900e4ebd1a833a7e7d697f61561d86dc6-dirty
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103 <option value="Epsesm.cut">Pseudomonas syringae pv tomato str DC3000</option> |
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planemo upload for repository ['https://github.com/brsynth/icfree-ml', 'https://github.com/pablocarb/doebase'] commit 6c01728900e4ebd1a833a7e7d697f61561d86dc6-dirty
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104 <option value="Erabit.cut">Oryctolagus cuniculus (rabbit)</option> |
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planemo upload for repository ['https://github.com/brsynth/icfree-ml', 'https://github.com/pablocarb/doebase'] commit 6c01728900e4ebd1a833a7e7d697f61561d86dc6-dirty
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105 <option value="Erat.cut">Rattus norvegicus</option> |
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planemo upload for repository ['https://github.com/brsynth/icfree-ml', 'https://github.com/pablocarb/doebase'] commit 6c01728900e4ebd1a833a7e7d697f61561d86dc6-dirty
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106 <option value="Erhile.cut">Rhizobium leguminosarum</option> |
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planemo upload for repository ['https://github.com/brsynth/icfree-ml', 'https://github.com/pablocarb/doebase'] commit 6c01728900e4ebd1a833a7e7d697f61561d86dc6-dirty
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107 <option value="Erhime.cut">Sinorhizobium meliloti 1021</option> |
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planemo upload for repository ['https://github.com/brsynth/icfree-ml', 'https://github.com/pablocarb/doebase'] commit 6c01728900e4ebd1a833a7e7d697f61561d86dc6-dirty
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108 <option value="Erhoca.cut">Rhodobacter capsulatus</option> |
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planemo upload for repository ['https://github.com/brsynth/icfree-ml', 'https://github.com/pablocarb/doebase'] commit 6c01728900e4ebd1a833a7e7d697f61561d86dc6-dirty
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109 <option value="Erhosh.cut">Rhodobacter sphaeroides</option> |
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planemo upload for repository ['https://github.com/brsynth/icfree-ml', 'https://github.com/pablocarb/doebase'] commit 6c01728900e4ebd1a833a7e7d697f61561d86dc6-dirty
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110 <option value="Esalsa.cut">Salmo salar (Atlantic salmon)</option> |
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planemo upload for repository ['https://github.com/brsynth/icfree-ml', 'https://github.com/pablocarb/doebase'] commit 6c01728900e4ebd1a833a7e7d697f61561d86dc6-dirty
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111 <option value="Esalty.cut">Salmonella typhimurium LT2</option> |
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planemo upload for repository ['https://github.com/brsynth/icfree-ml', 'https://github.com/pablocarb/doebase'] commit 6c01728900e4ebd1a833a7e7d697f61561d86dc6-dirty
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112 <option value="Eschma.cut">Schistosoma mansoni</option> |
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planemo upload for repository ['https://github.com/brsynth/icfree-ml', 'https://github.com/pablocarb/doebase'] commit 6c01728900e4ebd1a833a7e7d697f61561d86dc6-dirty
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113 <option value="Eschpo.cut">Schizosaccharomyces pombe</option> |
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planemo upload for repository ['https://github.com/brsynth/icfree-ml', 'https://github.com/pablocarb/doebase'] commit 6c01728900e4ebd1a833a7e7d697f61561d86dc6-dirty
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114 <option value="Eschpo_cai.cut">Schizosaccharomyces pombe (CAI equivalent)</option> |
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115 <option value="Eschpo_high.cut">Schizosaccharomyces pombe (high)</option> |
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planemo upload for repository ['https://github.com/brsynth/icfree-ml', 'https://github.com/pablocarb/doebase'] commit 6c01728900e4ebd1a833a7e7d697f61561d86dc6-dirty
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116 <option value="Eserma.cut">Serratia marcescens</option> |
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117 <option value="Esheep.cut">Ovis aries (sheep)</option> |
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118 <option value="Esoltu.cut">Solanum tuberosum (potato)</option> |
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119 <option value="Esoybn.cut">Glycine max (soybean)</option> |
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120 <option value="Espiol.cut">Spinacia oleracea (spinach)</option> |
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planemo upload for repository ['https://github.com/brsynth/icfree-ml', 'https://github.com/pablocarb/doebase'] commit 6c01728900e4ebd1a833a7e7d697f61561d86dc6-dirty
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121 <option value="Estaau.cut">Staphylococcus aureus</option> |
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122 <option value="Estrco.cut">Streptomyces coelicolor A3 2</option> |
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planemo upload for repository ['https://github.com/brsynth/icfree-ml', 'https://github.com/pablocarb/doebase'] commit 6c01728900e4ebd1a833a7e7d697f61561d86dc6-dirty
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123 <option value="Estrmu.cut">Streptococcus mutans UA159</option> |
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planemo upload for repository ['https://github.com/brsynth/icfree-ml', 'https://github.com/pablocarb/doebase'] commit 6c01728900e4ebd1a833a7e7d697f61561d86dc6-dirty
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124 <option value="Estrpn.cut">Streptococcus pneumoniae R6</option> |
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125 <option value="Estrpu.cut">Strongylocentrotus purpuratus (sea urchin)</option> |
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126 <option value="Esv40.cut">Simian Virus 40</option> |
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127 <option value="Esynco.cut">Synechococcus sp WH 8102</option> |
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planemo upload for repository ['https://github.com/brsynth/icfree-ml', 'https://github.com/pablocarb/doebase'] commit 6c01728900e4ebd1a833a7e7d697f61561d86dc6-dirty
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128 <option value="Esyncy.cut">Synechocystis sp PCC 6803</option> |
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129 <option value="Etetth.cut">Tetrahymena thermophila</option> |
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130 <option value="Etheth.cut">Thermus thermophilus HB8</option> |
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131 <option value="Etobac.cut">Nicotiana tabacum (tobacco)</option> |
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132 <option value="Etobac_chl.cut">Nicotiana tabacum chloroplast (tobacco)</option> |
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133 <option value="Etrybr.cut">Trypanosoma brucei</option> |
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134 <option value="Etrycr.cut">Trypanosoma cruzi</option> |
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135 <option value="Evibch.cut">Vibrio cholerae O1 biovar eltor str N16961</option> |
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136 <option value="Ewheat.cut">Triticum aestivum (wheat)</option> |
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137 <option value="Exenla.cut">Xenopus laevis</option> |
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138 <option value="Eyeast.cut">Saccharomyces cerevisiae</option> |
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139 <option value="Eyeast_cai.cut">Saccharomyces cerevisiae original CAI set</option> |
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140 <option value="Eyeast_high.cut">Saccharomyces cerevisiae (high)</option> |
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141 <option value="Eyeast_mit.cut">Saccharomyces cerevisiae mitochondrion</option> |
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142 <option value="Eyeren.cut">Yersinia enterocolitica</option> |
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143 </param> |
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144 </section> |
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145 </inputs> |
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146 <outputs> |
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147 <data name="constructs" format="xml" label="Constructs" /> |
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148 </outputs> |
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149 <tests> |
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150 <test> |
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151 <!-- test 1: check if identical outputs are produced with default parameters --> |
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152 <param name="genes_file" value="genes_lycopene.csv" /> |
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153 <output name="constructs" > |
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154 <assert_contents> |
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155 <is_valid_xml /> |
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156 <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/"'/> |
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157 </assert_contents> |
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158 </output> |
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159 </test> |
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160 </tests> |
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161 <help><![CDATA[ |
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162 OptDoE |
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163 =========== |
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164 |
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165 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 |
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167 .. 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 |
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171 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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172 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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173 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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174 |
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175 .. image:: https://raw.githubusercontent.com/brsynth/synbiocad-galaxy-wrappers/master/tools/doe_synbio/img/image3.png |
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176 :width: 80 % |
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177 :align: center |
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178 |
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179 |
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180 .. image:: https://raw.githubusercontent.com/brsynth/synbiocad-galaxy-wrappers/master/tools/doe_synbio/img/image46.png |
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181 :width: 80 % |
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182 :align: center |
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183 |
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184 | |
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185 |
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186 Above are examples of two constructs generated through optimal combinatorial design and represented using SBOL Visual in SynBioHub. |
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187 Note: if advanced parameter "input_parts" is left empty, the following parts are used: |
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188 |
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189 |
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190 +---------+------------+--------------------------------------------------+ |
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191 | Name | Type | SynBioHub | |
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192 +=========+============+==================================================+ |
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193 | PlacUV5 | Promoter | https://synbiohub.org/public/igem/BBa_K1847014/1 | |
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194 +---------+------------+--------------------------------------------------+ |
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195 | Ptrc | Promoter | https://synbiohub.org/public/igem/BBa_J56012/1 | |
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196 +---------+------------+--------------------------------------------------+ |
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197 | BBR1 | Origin | https://synbiohub.org/public/igem/BBa_I50041/1 | |
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198 +---------+------------+--------------------------------------------------+ |
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199 | p15A | Origin | https://synbiohub.org/public/igem/BBa_I50032/1 | |
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200 +---------+------------+--------------------------------------------------+ |
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201 | ColE1 | Origin | https://synbiohub.org/public/igem/BBa_J64101/1 | |
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202 +---------+------------+--------------------------------------------------+ |
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203 | res1 | Resistance | https://synbiohub.org/public/igem/BBa_I13800/1 | |
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204 +---------+------------+--------------------------------------------------+ |
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205 | Ter | Terminator | https://synbiohub.org/public/igem/BBa_B1006/1 | |
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206 +---------+------------+--------------------------------------------------+ |
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207 |
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208 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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209 |
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210 Input |
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211 ----- |
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212 |
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213 Required: |
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214 |
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215 * **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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216 |
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217 Advanced options: |
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218 |
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219 * **Optimised Genes**\ : SBOL file containing optimized versions of the genes associated with different RBS. Output of the PartsGenie tool. |
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220 * **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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221 * **Maximal library size**\ : (integer, default: 32) Maximal number of constructs in the SBOL output. |
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222 * **Get sequences**\ : (boolean, default: True) Grab the sequence for each part of the SBOL output. |
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223 * **Back translate**\ : (boolean, default: True) Translate the protein sequence given by its Uniprot ID to a DNA sequence. |
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224 * **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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225 |
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226 Output |
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227 ------ |
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228 |
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229 * **Constructs**\ : Output SBOL file. It contains some combinations of constructs according to the algorithm described above. |
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230 ]]></help> |
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231 <expand macro="creator"/> |
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232 <citations> |
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233 <citation type="bibtex"> |
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234 @unpublished{pablocarb |
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235 author = {Pablo Carbonell}, |
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236 title = {{doebase}}, |
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237 url = {https://github.com/pablocarb/doebase/}, |
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238 } |
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239 </citation> |
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240 </citations> |
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241 </tool> |