[ { "id": "simul_coal", "name": "Coalescent Simulation", "article": "", "website": "", "git": "", "description": "", "version": "", "documentation": "", "multiqc": "custom", "commands": [ { "name": "simul_coal", "cname": "Coalescent Simulation", "command": "", "category": "genet_pop", "output_dir": "simul_coal", "inputs": [], "outputs": [ { "name": "msout", "type": "msout", "file": "msout", "description": "msout" } ], "options": [ { "name": "simul_coal_pop1", "prefix": "", "type": "text", "value": "", "label": "Population 1 name" }, { "name": "simul_coal_pop2", "prefix": "", "type": "text", "value": "", "label": "Population 2 name" }, { "name": "simul_coal_outgroup", "prefix": "", "type": "text", "value": "", "label": "Outgroup name" }, { "name": "simul_coal_samp1", "prefix": "", "type": "numeric", "value": 10, "min": "NA", "max": "NA", "step": 1, "label": "Sample size of population 1" }, { "name": "simul_coal_samp2", "prefix": "", "type": "numeric", "value": 8, "min": "NA", "max": "NA", "step": 1, "label": "Sample size of population 2" }, { "name": "simul_coal_nlocus", "prefix": "", "type": "numeric", "value": 1000, "min": 1, "max": "NA", "step": 1, "label": "Number of loci" }, { "name": "simul_coal_mlength", "prefix": "", "type": "numeric", "value": 1000, "min": 1, "max": "NA", "step": 1, "label": "Contig length: mean" }, { "name": "simul_coal_sdlength", "prefix": "", "type": "numeric", "value": 10, "min": 0, "max": "NA", "step": 1, "label": "Contig length: standard deviation" }, { "name": "simul_coal_Nref", "prefix": "", "type": "numeric", "value": 100000, "min": 0, "max": "NA", "step": 1, "label": "Size of the reference population" }, { "name": "simul_coal_mu", "prefix": "", "type": "text", "value": "0.00000002", "label": "Mutation rate per bp per generation" }, { "name": "simul_coal_seed", "prefix": "", "type": "numeric", "value": 0, "min": 0, "max": "NA", "step": 1, "label": "Seed for random number generation : ! to be changed between replicates !" }, { "name": "simul_coal_model", "type": "select", "choices": [ { "SC": "SC" }, { "SC2M": "SC2M" }, { "AM": "AM" }, { "AM2M": "AM2M" } ], "value": "SC", "label": "Model" }, { "name": "simul_coal_nreps", "prefix": "", "type": "numeric", "value": 1, "min": 0, "max": "NA", "step": 1, "label": "nreps: total number of multilocus sims" }, { "name": "simul_coal_spec_model", "type": "select", "choices": [ { "island": "island" }, { "allo": "allo" }, { "pallo": "pallo" }, { "sym": "sym" }, { "psym": "psym" }, { "iso": "iso" }, { "eqmig": "eqmig" } ], "value": "island", "label": "speciation model" }, { "name": "simul_coal_mig", "type": "select", "choices": [ { "homo": "homo" }, { "hetero": "hetero" } ], "value": "homo", "label": "homo for homogenous migration, hetero for heterogeneous migration" }, { "name": "simul_coal_dir", "type": "select", "choices": [ { "asym": "asym" }, { "sym": "sym" } ], "value": "asym", "label": "symetrical or asymetrical direction of migration" }, { "name": "simul_coal_n1", "prefix": "", "type": "numeric", "value": 1, "min": 0, "max": "NA", "step": "NA", "label": "ratio of N1\/N0" }, { "name": "simul_coal_n2", "prefix": "", "type": "numeric", "value": 2, "min": 0, "max": "NA", "step": "NA", "label": "ratio of N2\/N0" }, { "name": "simul_coal_na", "prefix": "", "type": "numeric", "value": 3, "min": 0, "max": "NA", "step": "NA", "label": "ratio of NA\/N0" }, { "name": "simul_coal_tau", "prefix": "", "type": "numeric", "value": 6, "min": 0, "max": "NA", "step": "NA", "label": "divergence time" }, { "name": "simul_coal_tausmall", "prefix": "", "type": "numeric", "value": 0, "min": 0, "max": "NA", "step": "NA", "label": "secondary contact or ancient migration time" }, { "name": "simul_coal_nm1", "prefix": "", "type": "numeric", "value": 2, "min": 0, "max": "NA", "step": "NA", "label": "4N1m1 migration into 1 from 2" }, { "name": "simul_coal_nm2", "prefix": "", "type": "numeric", "value": 0.2, "min": 0, "max": "NA", "step": "NA", "label": "4N2m2 migration into 2 from 1" }, { "name": "simul_coal_prop", "prefix": "", "type": "numeric", "value": 0, "min": 0, "max": "NA", "step": "NA", "label": "Proportion of loci crossing the species barriers" } ] } ], "install": [], "citations": { "priorgen": [ " Camille Roux, C Fra\u00efsse, Vincent Castric, Xavier Vekemans, G H Pogson, et al.. Can we continue to neglect genomic variation in introgression rates when inferring the history of speciation? A case study in a Mytilus hybrid zone. Journal of Evolutionary Biology, Wiley, 2014, 27, pp.1662-1675. (10.1111\/jeb.12425)." ], "msnsam": [ "Ross-Ibarra, J., Wright, S.I., Foxe, J.P., Kawabe, A., DeRose-Wilson, L., Gos, G. et al. 2008. Patterns of polymorphism and demographic history in natural populations of Arabidopsis lyrata. PLoS ONE 3: e2411." ], "numpy": [ "S. van der Walt, S. C. Colbert and G. Varoquaux, 'The NumPy Array: A Structure for Efficient Numerical Computation,' in Computing in Science & Engineering, vol. 13, no. 2, pp. 22-30, March-April 2011, doi: 10.1109\/MCSE.2011.37." ], "biopython": [ "Cock PA, Antao T, Chang JT, Chapman BA, Cox CJ, Dalke A, Friedberg I, Hamelryck T, Kauff F, Wilczynski B and de Hoon MJL (2009) Biopython: freely available Python tools for computational molecular biology and bioinformatics. Bioinformatics, 25, 1422-1423" ] }, "yaml": "{\n id: simul_coal,\n name: Coalescent Simulation,\n article: \"\",\n website: \"\",\n git: \"\",\n description: \"\",\n version: \"\",\n documentation: \"\",\n multiqc: \"custom\",\n commands:\n [\n {\n name: simul_coal,\n cname: \"Coalescent Simulation\",\n command: \"\",\n category: \"genet_pop\",\n output_dir: simul_coal,\n inputs: [\n # no input, simulate data from parameters\n ],\n outputs: [\n { name: msout, type: \"msout\", file: \"msout\", description: \"msout\" }\n ],\n options:\n [\n #{\n # name: simul_coal_argfile,\n # prefix: \"\",\n # type: text,\n # value: \"Description\",\n # label: \"Describes the speciation model\",\n #},\n {\n name: simul_coal_pop1,\n prefix: \"\",\n type: text,\n value: \"\",\n label: \"Population 1 name\"\n },\n {\n name: simul_coal_pop2,\n prefix: \"\",\n type: text,\n value: \"\",\n label: \"Population 2 name\",\n },\n {\n name: simul_coal_outgroup,\n prefix: \"\",\n type: text,\n value: \"\",\n label: \"Outgroup name\",\n },\n\n {\n name: simul_coal_samp1,\n prefix: \"\",\n type: numeric,\n value: 10,\n min: NA,\n max: NA,\n step: 1,\n label: \"Sample size of population 1\",\n },\n {\n name: simul_coal_samp2,\n prefix: \"\",\n type: numeric,\n value: 8,\n min: NA,\n max: NA,\n step: 1,\n label: \"Sample size of population 2\",\n },\n\n {\n name: simul_coal_nlocus,\n prefix: \"\",\n type: numeric,\n value: 1000,\n min: 1,\n max: NA,\n step: 1,\n label: \"Number of loci\",\n },\n\n {\n name: simul_coal_mlength,\n prefix: \"\",\n type: numeric,\n value: 1000,\n min: 1,\n max: NA,\n step: 1,\n label: \"Contig length: mean\",\n },\n\n {\n name: simul_coal_sdlength,\n prefix: \"\",\n type: numeric,\n value: 10,\n min: 0,\n max: NA,\n step: 1,\n label: \"Contig length: standard deviation\",\n },\n\n {\n name: simul_coal_Nref,\n prefix: \"\",\n type: numeric,\n value: 100000,\n min: 0,\n max: NA,\n step: 1,\n label: \"Size of the reference population\",\n },\n\n {\n name: simul_coal_mu,\n prefix: \"\",\n type: text,\n value: \"0.00000002\",\n label: \"Mutation rate per bp per generation\",\n },\n\n {\n name: simul_coal_seed,\n prefix: \"\",\n type: numeric,\n value: 0,\n min: 0,\n max: NA,\n step: 1,\n label: \"Seed for random number generation : ! to be changed between replicates !\",\n },\n\n {\n name: simul_coal_model,\n type: select,\n choices: [\n SC: \"SC\",\n SC2M: \"SC2M\",\n AM: \"AM\",\n AM2M: \"AM2M\"\n ],\n value: \"SC\",\n label: \"Model\"\n },\n\n {\n name: simul_coal_nreps,\n prefix: \"\",\n type: numeric,\n value: 1,\n min: 0,\n max: NA,\n step: 1,\n label: \"nreps: total number of multilocus sims\",\n },\n\n {\n name: simul_coal_spec_model,\n type: select,\n choices: [\n island: \"island\",\n allo: \"allo\",\n pallo: \"pallo\",\n sym: \"sym\",\n psym: \"psym\",\n iso: \"iso\",\n eqmig: \"eqmig\"\n ],\n value: \"island\",\n label: \"speciation model\"\n },\n\n {\n name: simul_coal_mig,\n type: select,\n choices: [\n homo: \"homo\",\n hetero: \"hetero\"\n ],\n value: \"homo\",\n label: \"homo for homogenous migration, hetero for heterogeneous migration\"\n },\n\n {\n name: simul_coal_dir,\n type: select,\n choices: [\n asym: \"asym\",\n sym: \"sym\"\n ],\n value: \"asym\",\n label: \"symetrical or asymetrical direction of migration\"\n },\n\n {\n name: simul_coal_n1,\n prefix: \"\",\n type: numeric,\n value: 1,\n min: 0,\n max: NA,\n step: NA,\n label: \"ratio of N1\/N0\",\n },\n\n {\n name: simul_coal_n2,\n prefix: \"\",\n type: numeric,\n value: 2,\n min: 0,\n max: NA,\n step: NA,\n label: \"ratio of N2\/N0\",\n },\n\n {\n name: simul_coal_na,\n prefix: \"\",\n type: numeric,\n value: 3,\n min: 0,\n max: NA,\n step: NA,\n label: \"ratio of NA\/N0\",\n },\n\n {\n name: simul_coal_tau,\n prefix: \"\",\n type: numeric,\n value: 6,\n min: 0,\n max: NA,\n step: NA,\n label: \"divergence time\",\n },\n\n {\n name: simul_coal_tausmall,\n prefix: \"\",\n type: numeric,\n value: 0,\n min: 0,\n max: NA,\n step: NA,\n label: \"secondary contact or ancient migration time\",\n },\n\n {\n name: simul_coal_nm1,\n prefix: \"\",\n type: numeric,\n value: 2,\n min: 0,\n max: NA,\n step: NA,\n label: \"4N1m1 migration into 1 from 2\",\n },\n\n {\n name: simul_coal_nm2,\n prefix: \"\",\n type: numeric,\n value: 0.2,\n min: 0,\n max: NA,\n step: NA,\n label: \"4N2m2 migration into 2 from 1\",\n },\n\n {\n name: simul_coal_prop,\n prefix: \"\",\n type: numeric,\n value: 0,\n min: 0,\n max: NA,\n step: NA,\n label: \"Proportion of loci crossing the species barriers\",\n },\n \n ]\n },\n ],\n install: {\n # numpy: [\n # \"pip3 install numpy\"\n # ],\n # biopython: [\n # \"pip3 install biopython\"\n # ],\n },\n citations: {\n priorgen: [ \n \" Camille Roux, C Fra\u00efsse, Vincent Castric, Xavier Vekemans, G H Pogson, et al.. Can we continue to neglect genomic variation in introgression rates when inferring the history of speciation? A case study in a Mytilus hybrid zone. Journal of Evolutionary Biology, Wiley, 2014, 27, pp.1662-1675. (10.1111\/jeb.12425).\"\n ],\n msnsam: [\n \"Ross-Ibarra, J., Wright, S.I., Foxe, J.P., Kawabe, A., DeRose-Wilson, L., Gos, G. et al. 2008. Patterns of polymorphism and demographic history in natural populations of Arabidopsis lyrata. PLoS ONE 3: e2411.\"\n ],\n numpy: [\n \"S. van der Walt, S. C. Colbert and G. Varoquaux, 'The NumPy Array: A Structure for Efficient Numerical Computation,' in Computing in Science & Engineering, vol. 13, no. 2, pp. 22-30, March-April 2011, doi: 10.1109\/MCSE.2011.37.\"\n ],\n biopython: [\n \"Cock PA, Antao T, Chang JT, Chapman BA, Cox CJ, Dalke A, Friedberg I, Hamelryck T, Kauff F, Wilczynski B and de Hoon MJL (2009) Biopython: freely available Python tools for computational molecular biology and bioinformatics. Bioinformatics, 25, 1422-1423\"\n ]\n }\n}" } ]