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Changeset 1:c3f32929a4b7 (2022-02-02)

Previous changeset 0:7f13e58f1532 (2021-12-16) Next changeset 2:593e0f787172 (2022-10-24)

Commit message:
"planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"

modified:
optdoe.xml

removed:
test-data/constructs_lycopene.xml

diff -r 7f13e58f1532 -r c3f32929a4b7 optdoe.xml
--- a/optdoe.xml Thu Dec 16 13:23:29 2021 +0000
+++ b/optdoe.xml Wed Feb 02 18:11:50 2022 +0000

[

b'@@ -1,7 +1,10 @@\n-<tool id="OptDoE" name="Design of Experiment" version="2.0.1">\n+<tool id="optdoe" name="Design of Experiment" version="@TOOL_VERSION@" profile="19.09">\n <description>An optimal design of experiments (DoE) base package for synthetic biology</description>\n+ <macros>\n+ <token name="@TOOL_VERSION@">2.0.2</token>\n+ </macros>\n <requirements>\n- <requirement type="package" version="v2.0.1">doebase</requirement>\n+ <requirement type="package" version="@TOOL_VERSION@">doebase</requirement>\n </requirements>\n <command detect_errors="exit_code"><![CDATA[\n python -m doebase\n@@ -22,12 +25,133 @@\n <inputs>\n <param name="genes_file" type="data" format="csv" label="Genes" />\n <section name="adv" title="Advanced Options" expanded="false">\n- <param name="genes_sbol_file" type="data" format="xml" label="Optimised Genes" optional="true"/>\n- <param name="ref_parts_file" type="data" format="xml" value="None" label="Ref Parts" optional="true"/>\n- <param name="libsize" type="integer" value="32" label="Maximal library size" />\n- <param name="get_sequences" type="boolean" label="" checked="true" />\n- <param name="backtranslate" type="boolean" label="" checked="true" />\n- <param name="codon_table" type="text" value="Eecoli.cut" label="" />\n+ <param name="genes_sbol_file" type="data" format="xml" optional="true" label="Optimised Genes" />\n+ <param name="ref_parts_file" type="data" format="csv" value="None" optional="true" label="Ref Parts (default: E. coli compliant)"/>\n+ <param name="libsize" type="integer" value="32" min="32" label="Maximal library size" />\n+ <param name="get_sequences" type="boolean" checked="true" label="Get sequences" />\n+ <param name="backtranslate" type="boolean" checked="true" label="Back translate" />\n+ <param name="codon_table" type="select" label="Codon Table">\n+ <option value="Eecoli.cut">Escherichia coli K12</option>\n+ <option value="Ehuman.cut">Homo sapiens</option>\n+ <option value="Eacica.cut">Acinetobacter calcoaceticus</option>\n+ <option value="Eagrtu.cut">Agrobacterium tumefaciens str C58</option>\n+ <option value="Eanasp.cut">Anabaena sp</option>\n+ <option value="Earath.cut">Arabidopsis thaliana</option>\n+ <option value="Eazovi.cut">Azotobacter vinelandii</option>\n+ <option value="Ebacme.cut">Bacillus megaterium</option>\n+ <option value="Ebacst.cut">Geobacillus stearothermophilus</option>\n+ <option value="Ebacsu.cut">Bacillus subtilis</option>\n+ <option value="Ebacsu_high.cut">Bacillus subtilis (high)</option>\n+ <option value="Ebommo.cut">Bombyx mori (silkmoth)</option>\n+ <option value="Ebovin.cut">Bos taurus</option>\n+ <option value="Ebpphx.cut">Bacteriophage phi-X174</option>\n+ <option value="Ebraja.cut">Bradyrhizobium japonicum USDA 110</option>\n+ <option value="Ebrana.cut">Brassica napus (rape)</option>\n+ <option value="Ebrare.cut">Brachydanio rerio (zebrafish)</option>\n+ <option value="Ecaeel.cut">Caenorhabditis elegans (nematode)</option>\n+ <option value="Ecanal.cut">Candida albicans</option>\n+ <option value="Ecanfa.cut">Canis familiaris (dog)</option>\n+ <option value="Ecaucr.cut">Caulobacter crescentus CB15</option>\n+ <option value="Echick.cut">Gallus gallus (chicken)</option>\n+ <option value="Echlre.cut">Chlamydomonas reinhardtii</option>\n+ <option value="Echltr.cut">Chlamydia trachomatis D UW-3 CX</option>\n+ <option value="Ecloab.cut">Clostridium acetobutylicum ATCC 824</option>\n+ <option value="Ecrigr.cut">Cricet'..b't">Trypanosoma brucei</option>\n+ <option value="Etrycr.cut">Trypanosoma cruzi</option>\n+ <option value="Evibch.cut">Vibrio cholerae O1 biovar eltor str N16961</option>\n+ <option value="Ewheat.cut">Triticum aestivum (wheat)</option>\n+ <option value="Exenla.cut">Xenopus laevis</option>\n+ <option value="Eyeast.cut">Saccharomyces cerevisiae</option>\n+ <option value="Eyeast_cai.cut">Saccharomyces cerevisiae original CAI set</option>\n+ <option value="Eyeast_high.cut">Saccharomyces cerevisiae (high)</option>\n+ <option value="Eyeast_mit.cut">Saccharomyces cerevisiae mitochondrion</option>\n+ <option value="Eyeren.cut">Yersinia enterocolitica</option>\n+ </param>\n </section>\n </inputs>\n <outputs>\n@@ -37,13 +161,19 @@\n <test>\n \n <param name="genes_file" value="genes_lycopene.csv" />\n- <output name="constructs" file="constructs_lycopene.xml" ftype="xml" compare="sim_size"/>\n+ <output name="constructs" >\n+ <assert_contents>\n+ <is_valid_xml />\n+ <has_size value="451293" delta="100" />\n+ </assert_contents>\n+ </output>\n </test>\n </tests>\n <help><![CDATA[\n OptDoE\n ===========\n-This tool takes as input a rpSBML file, that contains for each heterologous reaction a ranked list of UniProt identifiers for the sequences, and the list of links to the DNA registry SynBioHub for the desired vector backbones, resistance cassette, and promoters (generated using the tool "OptDoE Parts Reference Generator"). 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:\n+\n+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:\n \n .. math:: D_{eff} = \\frac{1}{n}\\abs{X^{T}X}^{\\frac{1}{p}}\n \n@@ -86,26 +216,23 @@\n | Ter | Terminator | https://synbiohub.org/public/igem/BBa_B1006/1 |\n +---------+------------+--------------------------------------------------+\n \t \n-To generate another CSV\n+The source of this file can be found here as a model: https://raw.githubusercontent.com/pablocarb/doebase/master/doebase/data/ref_parts.csv\n \n Input\n -----\n \n Required:\n \n-* **genes_file**\\ : (string) Path to either tar.xz input collection of rpSBML files or a single rpSBML file.\n-* **-input_format**\\ : (string) Format of the input\n-* **-input_sbol**\\ : (string) Path to the SBOL input file\n-* **-input_parts**\\ : (string) 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\n+* **genes_file**\\ : (string) Genes File (csv).\n \n Advanced options:\n \n-* **genes_sbol_file**\\ : (string) Path to the optimised gens file (SBOL)\n+* **genes_sbol_file**\\ : (string) SBOL file containing optimised versions of the genes (RBS, etc)\n * **ref_parts_file**\\ : (string) 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\n * **libsize**\\ : (integer, default: 32) Maximal library size \n * **get_sequences**\\ : (boolean, default: True)\n * **backtranslate**\\ : (boolean, default: True)\n-* **codon_table**\\ : (text, default: Eecoli.cut)\n+* **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.\n \n Output\n ------\n'

diff -r 7f13e58f1532 -r c3f32929a4b7 test-data/constructs_lycopene.xml
--- a/test-data/constructs_lycopene.xml Thu Dec 16 13:23:29 2021 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

b'@@ -1,5896 +0,0 @@\n-<?xml version="1.0" encoding="utf-8"?>\n-<rdf:RDF xmlns:dcterms="http://purl.org/dc/terms/"\n- xmlns:prov="http://www.w3.org/ns/prov#"\n- xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"\n- xmlns:sbol="http://sbols.org/v2#"\n- xmlns:sys-bio="http://sys-bio.org#">\n- <sbol:ComponentDefinition rdf:about="http://synbiochem.co.uk/ComponentDefinition/BBR1/1">\n- <dcterms:description>https://synbiohub.org/public/igem/BBa_I50041/1</dcterms:description>\n- <dcterms:title>BBR1</dcterms:title>\n- <sbol:displayId>BBR1</sbol:displayId>\n- <sbol:persistentIdentity rdf:resource="http://synbiochem.co.uk/ComponentDefinition/BBR1"/>\n- <sbol:role rdf:resource="http://identifiers.org/so/SO:0000296"/>\n- <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/>\n- <sbol:version>1</sbol:version>\n- </sbol:ComponentDefinition>\n- <sbol:ComponentDefinition rdf:about="http://synbiochem.co.uk/ComponentDefinition/ColE1/1">\n- <dcterms:description>https://synbiohub.org/public/igem/BBa_J64101/1</dcterms:description>\n- <dcterms:title>ColE1</dcterms:title>\n- <sbol:displayId>ColE1</sbol:displayId>\n- <sbol:persistentIdentity rdf:resource="http://synbiochem.co.uk/ComponentDefinition/ColE1"/>\n- <sbol:role rdf:resource="http://identifiers.org/so/SO:0000296"/>\n- <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/>\n- <sbol:version>1</sbol:version>\n- </sbol:ComponentDefinition>\n- <sbol:ComponentDefinition rdf:about="http://synbiochem.co.uk/ComponentDefinition/P21683/1">\n- <dcterms:description>P21683</dcterms:description>\n- <dcterms:title>P21683</dcterms:title>\n- <sbol:displayId>P21683</sbol:displayId>\n- <sbol:persistentIdentity rdf:resource="http://synbiochem.co.uk/ComponentDefinition/P21683"/>\n- <sbol:role rdf:resource="http://identifiers.org/so/SO:0000316"/>\n- <sbol:sequence rdf:resource="http://synbiochem.co.uk/Sequence/P21683/1"/>\n- <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/>\n- <sbol:version>1</sbol:version>\n- </sbol:ComponentDefinition>\n- <sbol:ComponentDefinition rdf:about="http://synbiochem.co.uk/ComponentDefinition/P21684/1">\n- <dcterms:description>P21684</dcterms:description>\n- <dcterms:title>P21684</dcterms:title>\n- <sbol:displayId>P21684</sbol:displayId>\n- <sbol:persistentIdentity rdf:resource="http://synbiochem.co.uk/ComponentDefinition/P21684"/>\n- <sbol:role rdf:resource="http://identifiers.org/so/SO:0000316"/>\n- <sbol:sequence rdf:resource="http://synbiochem.co.uk/Sequence/P21684/1"/>\n- <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/>\n- <sbol:version>1</sbol:version>\n- </sbol:ComponentDefinition>\n- <sbol:ComponentDefinition rdf:about="http://synbiochem.co.uk/ComponentDefinition/P21685/1">\n- <dcterms:description>P21685</dcterms:description>\n- <dcterms:title>P21685</dcterms:title>\n- <sbol:displayId>P21685</sbol:displayId>\n- <sbol:persistentIdentity rdf:resource="http://synbiochem.co.uk/ComponentDefinition/P21685"/>\n- <sbol:role rdf:resource="http://identifiers.org/so/SO:0000316"/>\n- <sbol:sequence rdf:resource="http://synbiochem.co.uk/Sequence/P21685/1"/>\n- <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/>\n- <sbol:version>1</sbol:version>\n- </sbol:ComponentDefinition>\n- <sbol:ComponentDefinition rdf:about="http://synbiochem.co.uk/ComponentDefinition/P21687/1">\n- <dcterms:description>P21687</dcterms:description>\n- <dcterms:title>P21687</dcterms:title>\n- <sbol:displayId>P21687</sbol:displayId>\n- <sbol:persistentIdentity rdf:resource="http://synbiochem.co.uk/ComponentDefinition/P21687"/>\n- <sbol:role rdf:resource="http://identifiers.org/so/SO:0000316"/>\n- <sbol:sequence rdf:resource="http://synbiochem.co.uk/Sequence/P21687/1"/>\n- <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/>\n- 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