Mercurial > repos > tduigou > optdoe
diff optdoe.xml @ 3:34e11d0590fa draft default tip
planemo upload for repository ['https://github.com/brsynth/icfree-ml', 'https://github.com/pablocarb/doebase'] commit 2e8aa2e7c0581c7eed2074d15f7e4317ecde2ad6
| author | tduigou |
|---|---|
| date | Mon, 01 May 2023 01:29:51 +0000 |
| parents | 593e0f787172 |
| children |
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--- a/optdoe.xml Mon Oct 24 10:22:28 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,262 +0,0 @@ -<tool id="optdoe" name="Design of Experiment" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.09"> - <description>An optimal design of experiments (DoE) base package for synthetic biology</description> - <macros> - <token name="@VERSION_SUFFIX@">0</token> - <token name="@TOOL_VERSION@">2.0.2</token> - </macros> - <requirements> - <requirement type="package" version="@TOOL_VERSION@">doebase</requirement> - </requirements> - <command detect_errors="exit_code"><![CDATA[ - python -m doebase - --func doeGetSBOL - #if $adv.genes_sbol_file - --sbol_file '$adv.genes_sbol_file' - #end if - #if $adv.ref_parts_file - --ref_parts_file '$adv.ref_parts_file' - #end if - --libsize '$adv.libsize' - $adv.get_sequences - $adv.backtranslate - --codon_table '$adv.codon_table' - '$genes_file' - '$constructs' - ]]></command> - <inputs> - <param name="genes_file" type="data" format="csv" label="Genes" help="CSV file with header: Name,Type,Part,Step. Provided by the tool Selenzyme"/> - <section name="adv" title="Advanced Options" expanded="false"> - <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"/> - <param argument="--ref_parts_file" type="data" format="csv" value="None" optional="true" label="Ref Parts (default: E. coli compliant)" help="Provide fixed parts"/> - <param argument="--libsize" type="integer" value="32" min="32" label="Maximal library size" help="Maximal number of contructs in the output"/> - <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"/> - <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"/> - <param argument="--codon_table" type="select" label="Codon Table"> - <option value="Eecoli.cut">Escherichia coli K12</option> - <option value="Ehuman.cut">Homo sapiens</option> - <option value="Eacica.cut">Acinetobacter calcoaceticus</option> - <option value="Eagrtu.cut">Agrobacterium tumefaciens str C58</option> - <option value="Eanasp.cut">Anabaena sp</option> - <option value="Earath.cut">Arabidopsis thaliana</option> - <option value="Eazovi.cut">Azotobacter vinelandii</option> - <option value="Ebacme.cut">Bacillus megaterium</option> - <option value="Ebacst.cut">Geobacillus stearothermophilus</option> - <option value="Ebacsu.cut">Bacillus subtilis</option> - <option value="Ebacsu_high.cut">Bacillus subtilis (high)</option> - <option value="Ebommo.cut">Bombyx mori (silkmoth)</option> - <option value="Ebovin.cut">Bos taurus</option> - <option value="Ebpphx.cut">Bacteriophage phi-X174</option> - <option value="Ebraja.cut">Bradyrhizobium japonicum USDA 110</option> - <option value="Ebrana.cut">Brassica napus (rape)</option> - <option value="Ebrare.cut">Brachydanio rerio (zebrafish)</option> - <option value="Ecaeel.cut">Caenorhabditis elegans (nematode)</option> - <option value="Ecanal.cut">Candida albicans</option> - <option value="Ecanfa.cut">Canis familiaris (dog)</option> - <option value="Ecaucr.cut">Caulobacter crescentus CB15</option> - <option value="Echick.cut">Gallus gallus (chicken)</option> - <option value="Echlre.cut">Chlamydomonas reinhardtii</option> - <option value="Echltr.cut">Chlamydia trachomatis D UW-3 CX</option> - <option value="Ecloab.cut">Clostridium acetobutylicum ATCC 824</option> - <option value="Ecrigr.cut">Cricetulus greseus (hamster)</option> - <option value="Ecyapa.cut">Cyanophora paradoxa</option> - <option value="Ebraja.cut">Bradyrhizobium japonicum USDA 110</option> - <option value="Ebrana.cut">Brassica napus (rape)</option> - <option value="Ebrare.cut">Brachydanio rerio (zebrafish)</option> - <option value="Ecaeel.cut">Caenorhabditis elegans (nematode)</option> - <option value="Ecanal.cut">Candida albicans</option> - <option value="Ecanfa.cut">Canis familiaris (dog)</option> - <option value="Ecaucr.cut">Caulobacter crescentus CB15</option> - <option value="Echick.cut">Gallus gallus (chicken)</option> - <option value="Echlre.cut">Chlamydomonas reinhardtii</option> - <option value="Echltr.cut">Chlamydia trachomatis D UW-3 CX</option> - <option value="Ecloab.cut">Clostridium acetobutylicum ATCC 824</option> - <option value="Ecrigr.cut">Cricetulus greseus (hamster)</option> - <option value="Ecyapa.cut">Cyanophora paradoxa</option> - <option value="Edicdi.cut">Dictyostelium discoideum</option> - <option value="Edicdi_high.cut">Dictyostelium discoideum (high)</option> - <option value="Edrome.cut">Drosophila melanogaster</option> - <option value="Edrome_high.cut">Drosophila melanogaster (high)</option> - <option value="Eecoli_high.cut">Escherichia coli K12 (high)</option> - <option value="Eemeni.cut">Emericella nidulans</option> - <option value="Eemeni_mit.cut">Emericella nidulans mitochondrion</option> - <option value="Eemeni_high.cut">Emericella nidulans highly expressed</option> - <option value="Eerwct.cut">Erwinia carotovora subsp atroseptica SCRI1043</option> - <option value="Ehaein.cut">Haemophilus influenzae Rd KW20</option> - <option value="Ehalma.cut">Haloarcula marismortui ATCC 43049 (Halobacterium marismortui)</option> - <option value="Ehalsa.cut">Halobacterium salinarum NRC-1 (Halobacterium halobium)</option> - <option value="Ehorvu.cut">Hordeum vulgare subsp vulgare (Barley)</option> - <option value="Eklepn.cut">Klebsiella pneumoniae</option> - <option value="Eklula.cut">Kluyveromyces lactis NRRL Y-1140</option> - <option value="Elacdl.cut">Lactococcus lactis subsp lactis Il1403 L. delbrueckii subsp lactis</option> - <option value="Elyces.cut">Lycopersicon esculentum (tomato)</option> - <option value="Emacfa.cut">Macaca fascicularis</option> - <option value="Emaize.cut">Zea mays</option> - <option value="Emaize_chl.cut">Zea mays chloroplast</option> - <option value="Emammal_high.cut">Mammalian species (high)</option> - <option value="Emanse.cut">Manduca sexta</option> - <option value="Emarpo_chl.cut">Marchantia polymorpha chloroplast (liverwort)</option> - <option value="Emedsa.cut">Medicago sativa</option> - <option value="Emetth.cut">Methanothermobacter thermautotrophicus str Delta H</option> - <option value="Emouse.cut">Mus musculus</option> - <option value="Emyctu.cut">Mycobacterium tuberculosis H37Rv</option> - <option value="Eneigo.cut">Neisseria gonorrhoeae</option> - <option value="Eneucr.cut">Neurospora crassa</option> - <option value="Eoncmy.cut">Oncorhynchus mykiss (rainbow trout)</option> - <option value="Eorysa.cut">Oryza sativa (rice)</option> - <option value="Eorysa_chl.cut">Oryza sativa chloroplast (rice)</option> - <option value="Epea.cut">Pisum sativum (pea)</option> - <option value="Epethy.cut">Petunia x hybrida</option> - <option value="Ephavu.cut">Phaseolus vulgaris</option> - <option value="Epig.cut">Sus scrofa (pig)</option> - <option value="Eplafa.cut">Plasmodium falciparum 3D7</option> - <option value="Eprovu.cut">Proteus vulgaris</option> - <option value="Epseae.cut">Pseudomonas aeruginosa PAO1</option> - <option value="Epsepu.cut">Pseudomonas putida KT2440</option> - <option value="Epsesm.cut">Pseudomonas syringae pv tomato str DC3000</option> - <option value="Erabit.cut">Oryctolagus cuniculus (rabbit)</option> - <option value="Erat.cut">Rattus norvegicus</option> - <option value="Erhile.cut">Rhizobium leguminosarum</option> - <option value="Erhime.cut">Sinorhizobium meliloti 1021</option> - <option value="Erhoca.cut">Rhodobacter capsulatus</option> - <option value="Erhosh.cut">Rhodobacter sphaeroides</option> - <option value="Esalsa.cut">Salmo salar (Atlantic salmon)</option> - <option value="Esalty.cut">Salmonella typhimurium LT2</option> - <option value="Eschma.cut">Schistosoma mansoni</option> - <option value="Eschpo.cut">Schizosaccharomyces pombe</option> - <option value="Eschpo_cai.cut">Schizosaccharomyces pombe (CAI equivalent)</option> - <option value="Eschpo_high.cut">Schizosaccharomyces pombe (high)</option> - <option value="Eserma.cut">Serratia marcescens</option> - <option value="Esheep.cut">Ovis aries (sheep)</option> - <option value="Esoltu.cut">Solanum tuberosum (potato)</option> - <option value="Esoybn.cut">Glycine max (soybean)</option> - <option value="Espiol.cut">Spinacia oleracea (spinach)</option> - <option value="Estaau.cut">Staphylococcus aureus</option> - <option value="Estrco.cut">Streptomyces coelicolor A3 2</option> - <option value="Estrmu.cut">Streptococcus mutans UA159</option> - <option value="Estrpn.cut">Streptococcus pneumoniae R6</option> - <option value="Estrpu.cut">Strongylocentrotus purpuratus (sea urchin)</option> - <option value="Esv40.cut">Simian Virus 40</option> - <option value="Esynco.cut">Synechococcus sp WH 8102</option> - <option value="Esyncy.cut">Synechocystis sp PCC 6803</option> - <option value="Etetth.cut">Tetrahymena thermophila</option> - <option value="Etheth.cut">Thermus thermophilus HB8</option> - <option value="Etobac.cut">Nicotiana tabacum (tobacco)</option> - <option value="Etobac_chl.cut">Nicotiana tabacum chloroplast (tobacco)</option> - <option value="Etrybr.cut">Trypanosoma brucei</option> - <option value="Etrycr.cut">Trypanosoma cruzi</option> - <option value="Evibch.cut">Vibrio cholerae O1 biovar eltor str N16961</option> - <option value="Ewheat.cut">Triticum aestivum (wheat)</option> - <option value="Exenla.cut">Xenopus laevis</option> - <option value="Eyeast.cut">Saccharomyces cerevisiae</option> - <option value="Eyeast_cai.cut">Saccharomyces cerevisiae original CAI set</option> - <option value="Eyeast_high.cut">Saccharomyces cerevisiae (high)</option> - <option value="Eyeast_mit.cut">Saccharomyces cerevisiae mitochondrion</option> - <option value="Eyeren.cut">Yersinia enterocolitica</option> - </param> - </section> - </inputs> - <outputs> - <data name="constructs" format="xml" label="Constructs" /> - </outputs> - <tests> - <test> - <!-- test 1: check if identical outputs are produced with default parameters --> - <param name="genes_file" value="genes_lycopene.csv" /> - <output name="constructs" > - <assert_contents> - <is_valid_xml /> - <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/"'/> - </assert_contents> - </output> - </test> - </tests> - <help><![CDATA[ -OptDoE -=========== - -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: - -.. math:: D_{eff} = \frac{1}{n}\abs{X^{T}X}^{\frac{1}{p}} - -| - -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. -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. -The resulting design is provided as an SBOL collection containing the definition of each DNA component and the combinatorial library of constructs. - -.. image:: https://raw.githubusercontent.com/brsynth/synbiocad-galaxy-wrappers/master/OptDoE/img/image3.png - :width: 80 % - :align: center - - -.. image:: https://raw.githubusercontent.com/brsynth/synbiocad-galaxy-wrappers/master/OptDoE/img/image46.png - :width: 80 % - :align: center - -| - -Above are examples of two constructs generated through optimal combinatorial design and represented using SBOL Visual in SynBioHub. -Note: if advanced parameter "input_parts" is left empty, the following parts are used: - - - +---------+------------+--------------------------------------------------+ - | Name | Type | SynBioHub | - +=========+============+==================================================+ - | PlacUV5 | Promoter | https://synbiohub.org/public/igem/BBa_K1847014/1 | - +---------+------------+--------------------------------------------------+ - | Ptrc | Promoter | https://synbiohub.org/public/igem/BBa_J56012/1 | - +---------+------------+--------------------------------------------------+ - | BBR1 | Origin | https://synbiohub.org/public/igem/BBa_I50041/1 | - +---------+------------+--------------------------------------------------+ - | p15A | Origin | https://synbiohub.org/public/igem/BBa_I50032/1 | - +---------+------------+--------------------------------------------------+ - | ColE1 | Origin | https://synbiohub.org/public/igem/BBa_J64101/1 | - +---------+------------+--------------------------------------------------+ - | res1 | Resistance | https://synbiohub.org/public/igem/BBa_I13800/1 | - +---------+------------+--------------------------------------------------+ - | Ter | Terminator | https://synbiohub.org/public/igem/BBa_B1006/1 | - +---------+------------+--------------------------------------------------+ - -The source of this file can be found here as a model: https://raw.githubusercontent.com/pablocarb/doebase/master/doebase/data/ref_parts.csv - -Input ------ - -Required: - -* **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. - -Advanced options: - -* **Optimised Genes**\ : SBOL file containing optimized versions of the genes associated with different RBS. Output of the PartsGenie tool. -* **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 -* **Maximal library size**\ : (integer, default: 32) Maximal number of constructs in the SBOL output. -* **Get sequences**\ : (boolean, default: True) Grab the sequence for each part of the SBOL output. -* **Back translate**\ : (boolean, default: True) Translate the protein sequence given by its Uniprot ID to a DNA sequence. -* **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. - -Output ------- - -* **Constructs**\ : Output SBOL file. It contains some combinations of constructs according to the algorithm described above. - -Project Link ------------- - -* `Original Project <https://github.com/pablocarb/doebase>`_ - -License -------- - -`MIT <https://raw.githubusercontent.com/pablocarb/appoptdes/master/LICENSE>`_ - -Acknowledgments ---------------- - -* Joan Hérisson -* Thomas Duigou - ]]></help> - <creator> - <person givenName="Pablo" familyName="Carbonell" email="pablo.carbonell@upv.es" identifier="https://orcid.org/0000-0002-0993-5625" /> - </creator> -</tool> \ No newline at end of file